Turning Points in Solid-State, Materials and Surface Science

A Book in Celebration of the Life and Work of Sir John Meurig Thomas

Photograph of John Meurig Thomas taken at the University of Wales,

Swansea, by John D Roberts, California Institute of Technology, in 1992
Sir John Meurig Thomas (right) with Sir Michael Atiyah, O.M. (left), 30th
April 2007
Turning Points in Solid-State,
Materials and Surface Science
A Book in Celebration of the Life and
Work of Sir John Meurig Thomas

Edited by

Kenneth D.M. Harris

School of Chemistry, Cardiff University, Cardiff, UK

Peter P. Edwards
Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
ISBN: 978-0-85404-114-5

A catalogue record for this book is available from the British Library

r The Royal Society of Chemistry 2008

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Introduction
CHAPTER 1

Voyages with the Master

AHMED H. ZEWAIL
Physical Biology Center for Ultrafast Science and Technology, Arthur Amos
Noyes Laboratory of Chemical Physics, California Institute of Technology,
Pasadena, CA 91125, USA

When I arrived in Philadelphia in August of 1969, I knew only of John Meurig

Thomas the scientist. For more than three decades since then I have had the
privilege of knowing John the scientist, the friend, and the communicator. In
each of these dimensions, John is a Master. And he has one more unparalleled
fourth dimension – a brilliant memory and a mental hard disk with unlimited
storage capacity! Very few scientists are as versatile as John in his cross-linking
of different science disciplines, and as cultured as he is in other facets of life –
even in sports he was, as a schoolboy, the walking-race champion of Wales, and
was also a member of the University of Wales cricket team in 1955.
My first encounter with John was in June of 1970 at the Molecular Crystal
Symposium organized by Robin Hochstrasser in Philadelphia at the Laboratory
for Research on the Structure of Matter (LRSM). Among the stars present were
Aleksander Davydov, Don McClure, Jan van der Waals, Hans Christoph Wolf,
Wilse Robinson, and others. What John presented was his studies of disloca-
tions in organic crystals and their vital role in determining optical and electrical
properties. As a beginner, I was unaware of the totality of his impact in the field,
but what impressed me most was his masterful presentation which he delivered
with clarity, eloquence, and scholarly intellect. This memorable experience at the
conference prompted me to squeeze myself in between the stars (Figure 1) in
order to have a picture in the proximity of the world-renowned Davydov and to
have a few words with John. Of course, at my level, the discussion was primarily
about his enchantment with Egypt which he explored later in 1973 as a Visiting
Professor at the American University in Cairo.
By the time of the eighth conference in the same series, organized in June of
1977 by Mostafa El Sayed (Figure 2), I was an invited speaker and went to
Santa Barbara from Caltech, where I had been appointed as an Assistant

3
4 Chapter 1

Figure 1 The conference photo taken in June of 1970 on the steps of the Laboratory
for Research on the Structure of Matter at the University of Pennsylvania,
Philadelphia. A.S. Davydov is in the first row, second from the left. John
Thomas and I are in the second row, seventh and third from the left,
respectively. The organizer of the conference, Robin Hochstrasser, is the
tallest in the back row, with a smile, next to Peter Rentzepis.

Professor. John was there, also as an invited speaker, and again he delivered a
powerful presentation. To this day I can recall the way John presented his work
and particularly the way he handled the Chair of his session. In a preemptive
strike designed to secure more time for himself he said, ‘‘Mr. Chairman, I am
about to finish,’’ meaning he needed another five minutes or more! At this
meeting I realized one of John’s most impressive traits – his expansive thirst for
knowledge and his resulting interest in broad areas of science in general and
scientists in particular. This was certainly true in my case. At the conference, I
spoke about the phenomena of ‘‘optical coherence’’ in molecular crystals and
the new techniques for direct probing, in a talk titled, ‘‘Optical dephasing and
radiationless transitions in molecular crystals.’’ Instantly, John became inter-
ested and asked me numerous questions with a display of genuine excitement
about the development, even though it was not his area of primary interest.
We did not cross paths again for some time, until a meeting at the Royal
Society in London in February of 1990. In this discussion meeting, during
which John presented his Bakerian lecture (on new crystalline catalysts), I gave
a lecture titled ‘‘Femtosecond reaction dynamics,’’ and John again was aware
Voyages with the Master 5

Figure 2 The conference photo taken in June of 1977 at a beachfront hotel in Santa
Barbara, California. John Thomas and I are in the third row from the back
(middle) and third row from the front to the right, respectively. The
organizer, Mostafa El Sayed, is in the front row fifth from the left.

of the research in this area. Following the lecture, he invited me for lunch where
he told me a story and made a prediction. The story relates to our 1987
publication with Marcos Dantus and Mark Rosker on the direct observation of
the transition state with femtosecond time resolution. John discussed the paper
with his students at the Royal Institution (RI) (in particular, Kenneth Harris)
and described it to them as a historic landmark paper. The prediction was that
the work was deserving of the Nobel Prize. John was serious and I trusted his
sincerity. But what was so unique was that he actually read the paper and
appreciated the value of a contribution that was far from his own field of
endeavor. In fact, he zoomed in on the central concept of coherence in
observing atomic motions; a difficult concept to grasp, even for some experts.
It was at this meeting that I earned an invitation from John, as Director of the
RI, to give the Faraday Discourse, enticing me – typical of John! – by
mentioning the names of previous speakers from Caltech such as Robert
Millikan, George Ellery Hale, Linus Pauling, and Murray Gell-Mann. John
and his beloved wife, Margaret, were truly gracious hosts at the RI. With John
as Director, the Faraday Discourse on March 22, 1991 was an experience
organized in the true tradition of the place and the history it had integrated over
time. Even though I knew the former Director, George Porter, for many years,
6 Chapter 1
this was my first time as an invited lecturer. In the Director’s flat, Margaret
arranged a lovely dinner in the company of David and Jill Buckingham,
Sir Brian and Lady Pippard, Sir Geoffrey and Lady Wilkinson, and Lord and
Lady Dainton (formerly Sir Fredrick Dainton). A few minutes before the lecture
I was locked in a small room, literally a ‘‘Faraday cage.’’ But just before caging
me, John handed me a postcard of Sir James Dewar of liquid hydrogen fame on
the back of which he had written the names of the three Nobelists from Caltech
who had been in a similar situation, with John again making his obvious
implication!
At exactly 9:00 p.m., John and I, in our tuxedos, walked together into the
theatre as its double doors opened, and I began the lecture. The Discourse was
held in the same place Michael Faraday lectured, and it surely radiated past
achievements and displayed a sense of history, and John fitted in well among
the previous Directors, Davy, Faraday, Bragg (Sir Lawrence), and Porter.
Eadweard Muybridge gave a discourse on ‘‘animals in motion’’, on March 13,
1882, at which T. H. Huxley and the poet Alfred, Lord Tennyson were present.
We found his discourse demonstration of a slotted drum which, upon rotation,
shows the animated horse in motion. I had thought of relating my discourse to
motion, but now to the motion of atoms, with the title, ‘‘Filming in a millionth
of a billionth of a second.’’ The theatre was packed and I thought of embar-
rassing John, but without success. I mentioned that the only way I could
explain the full attendance was that the Director must have promised them a
discourse by Omar Sharif. John led the audience with a big laugh!
Since that time, I have greatly enjoyed both my scientific and personal
interactions with John. I have become increasingly aware of his extraordinary
ability to look at the big picture of science and humanity and in his genuine
interest in popularizing science. His book on Faraday and his writings on
Humphry Davy, Lawrence Bragg, and Max Perutz are examples of his devo-
tion to the service of knowledge and his brilliant mastery of the English
language – with a strong, attractive Welsh accent! In fact, I have two bulky
files loaded with John’s outside-of-science writings. But, John is also a caring
fellow scientist. He has written many obituaries and given the eulogies of
distinguished scientists to salute their contributions to science and society. I
have repeatedly told John to write my obituary in advance as I know it will be
exceptional! He is also a cultured man in music, art, and history. John does all
of these activities while maintaining passionate interest in his own science with
pioneering contributions over six decades of research at the University of
Wales, in Bangor and Aberystwyth, University of Cambridge, and the RI.
John is distinguished for his innovative and diverse contributions, from solid
state chemistry to heterogeneous catalysis, including the study of nanostruct-
ures, long before they became popular! He and his co-workers have designed,
synthesized, and characterized hundreds of new heterogeneous catalysts. He
has also developed and applied a wide range of tools for the study of solids and
their surfaces, zeolites, clays, and other analogs. With these techniques, he has
elucidated the importance of the structure in the function. The methods
involved include high-resolution electron microscopy, electron diffraction,
Voyages with the Master 7
synchrotron radiation, solid-state NMR, photoelectron spectroscopy, and
computational techniques. At present, with Paul Midgley and others, he is
pioneering powerful ex situ techniques, such as nanotomography and nano-
holography, for studying solids. Moreover, he has established in situ methods
for investigating solid catalysts, the result of which, through his ‘‘single-site’’
solid catalysts, provide strategies that are applicable in the design of new
catalysts for a wide range of reactions. Earlier, John was a leader in elucidating
the manner in which the surface and bulk properties of crystals are influenced
by structural imperfections, notably dislocations. This work on dislocations
was critical to the understanding of physical, chemical, and spectral properties
of crystals such as graphite, layered minerals, and molecular solids.
His interest in diffraction and microscopy turned out to be the first scientific
bonding we had. In 1991, the same year I gave the Faraday Discourse, I
proposed ultrafast diffraction as a method for structural dynamics. Without
delay, in the same year, John wrote a ‘‘News and Views’’ piece in Nature1 titled
‘‘Femtosecond diffraction.’’ Towards the end of the piece, he concluded with
the following words: ‘‘If the experiment does indeed prove successful, it will
mark the dawn of an important new era . . .’’ It took one decade (2001), and
developments over several generations of instruments, to transform a dream
into reality, from the exploration of the potential of the approach to the
explosion of the applications in real experimental determination of isolated
transient molecular structures.
In retrospect, what is remarkable about John is his broader vision of the
significance of determining structures in the act of change irrespective of the
phase they are in. When we reached the condensed phase with ultrafast electron
crystallography in 2004, John published in Angewandte Chemie2 an overview
pointing out several potential applications including those in heterogeneous
catalysis. But, he reached the apex of excitement when it became possible to
image in real space with 4D ultrafast electron microscopy using single-electron
packets. Because John has followed the trajectory of developments since its
naissance, and is himself a pioneer in the applications of microscopy to
materials science, he decided to write a 2005 highlight in Angewandte Chemie3
describing the development and the prospects for numerous branching appli-
cations. In the same year, 2005, Kenneth Harris and John in a paper published
in Crystal Growth and Design4 explored some applications in domains of
biological macromolecules and solid-state chemistry. Once again his passion
for a new development was sincere and scholarly.
After Margaret passed away, John needed his friends as much as ever,
especially with the vacuum left behind by Margaret after decades of being
together and sharing wonderful events at the RI, Peterhouse, and places all
over the globe. And so I was delighted to see him in Cairo on the occasion of his
receiving an honorary degree from the American University in Cairo in 2002,
and we spent some time reflecting on life and science. To me, time spent with
John is never dull, and is always enriching to the intellect and spirit. This
tradition of intense and pleasurable discussion continues until today with visits
in Cambridge, Pasadena, and other places around the world. The last time
8 Chapter 1

Figure 3 A recent photo taken in June of 2006 at the University of Cambridge on the
occasion of an Honorary Degree celebration to the Archbishop of Canter-
bury, The Most Rev. and Rt. Hon. Dr. Rowan Williams (in Divinity) and
the author (in Science). John Thomas joined us in the celebration as a
member of the faculty dressed in his colorful Scarlet Festal Robe. The
Archbishop was born in Swansea into a Welsh-speaking family, making this
photo indeed special, as I am surrounded by Wales’ most distinguished men
of faith and of science.

I was in Cambridge in the summer of 2006 (Figure 3), we went on a walk and
John showed me the hospital where Margaret passed away and the walks that
they took together. And that is what life is about, especially when recognizing
our fate as noted by Shakespeare’s Prospero: ‘‘We are such stuff as dreams are
made on, and our little life is rounded with a sleep.’’ In Margaret’s eulogy in
October of 2002, John closed with the words, ‘‘She left the world a better
place.’’
In life one meets many people, interacts with some for the sake of mutual
benefits, dislikes some for their attitude or personality, but cherishes only a
special few for their integrity, professional achievement, and human decency.
John is just such a person. Despite his attributes of great value and character, I
dislike one thing about John. In his presence one feels a brain memory capacity
of kilobytes while his is gigabytes or more. He recalls with lucidity events,
names, and stories from long ago as if they happened yesterday, while the rest
of us struggle to remember. At a recent meeting of the American Philosophical
Society, I asked our mutual friend Jack Roberts, ‘‘Has John been consistent in
Voyages with the Master 9
his story telling over the years?’’ Jack answered, ‘‘The trouble is that I do not
know because I forget most of the stories!’’
John, you are truly a master of science and humanity. We all wish you a very
happy 75th birthday and we expect to celebrate your 100th remembering, John,
that Ramses II lived to be almost 100, and you do not yet have even close to his
110 children!

References
1. J.M. Thomas, Nature, 1991, 351, 694.
2. J.M. Thomas, Angew. Chem., Int. Ed., 2004, 43, 2606.
3. J.M. Thomas, Angew. Chem., Int. Ed., 2005, 44, 5563.
4. K.D.M. Harris and J.M. Thomas, Cryst. Growth Des., 2005, 5, 2124.
Foreword

John Meurig Thomas

One of John Thomas’s special qualities is his way of making instant, deep
connection with another person. I remember well our first meeting: I was
dispatched as a Chemical Society lecturer to the Coleg Prifysgol Cymru. By
train, of course. And, this being 1975 and the U.K., naturally there was a rail
strike the day after my lecture. And the day after that. But I did not mind the
enforced stay in Aberystwyth, for there I met John. At the time I was beginning
to work in inorganic and surface chemistry; I could not have wished for a better
initiation to amphiboles and zeolites than I got in those two days.
The contributors to this book celebrate the astounding diversity of John’s
work. Let me walk down another footpath, one that passes the leitmotifs I see
in John Thomas’s work, here all expressed in unvarnished English verbs:

seeing
loving complexity
trying to understand
getting things to go
reaching out

Seeing: From his earliest studies to this day, John has cared for structure and
found ways to probe it with evermore informative tools. Many of us remember
those Aberystwythian home-made – yet how sophisticated – stages for X-ray
induced photoelectron spectroscopy.
Chemistry (and science in general) progresses through experiment, cool logic
and wild ideas, with unwarranted yet fecund leaps of the imagination from a
hint of a shoulder in a spectrum to reliable knowledge. It is so often a kind of
knowing without seeing. But oh, what convinced certainty comes from super-
imposing a small drawing of a molecule on an in situ transmission electron
microscopy (TEM) image of a zeolitic catalyst!
Loving complexity: For John it always was more than fearlessness. It was
tough love. ‘‘Tough’’ because the polyphasic and intergrown materials whose
structure he and his able collaborators untangled did not yield up their rich
structures easily. And all those zeolites!

v
vi Foreword
Trying to understand: Yes, he loves the denumerable near-infinity of silicate
networks. But I have in mind something deeper, John Thomas’s proclivity ‘‘on
Newtonian wings to soar,’’ to use Humphry Davy’s phrase. It is that palpable
desire evident in every Thomas paper, the abiding passion to understand what
is behind chemical action.
Getting things to go: Now that sounds really Newtonian, but, of course, I
refer here to John’s love affair with catalysts. And his green (or shall we call it
‘‘oil-stained’’) thumb for designing catalysts. One of the few words to enter
common parlance, catalysis remains a wonder, a metaphor, a bridge twixt
science and magic. For thermodynamics just dryly delimits speculation, and by
and large chemistry is the science of transformations that refuse to go.
Catalysts are adventitious, catalysts are the heroines of serendipity tales. And
catalysts are designed. John Thomas is the reigning ringmaster of a catalytic
circus, in which various active particles jump, at his command, into tailored
nooks and crannies in lattice-works out of his imagination. And there do their
handsome, desired breaking and making of bonds. What fun!
Reaching out: So he sings. And John Thomas loves to talk. The Welsh gift,
the flourish, mixed with his love of science, and the strongest teaching impulse,
self-assemble for our good. Faraday wrote ‘‘. . . the generality of mankind
cannot accompany us one short hour unless the path is strewed with flowers.’’
Well, John Thomas has tossed bouquets upon bouquets to the world.
I think there never was, at least not since the founding spirits, a man so right
for the Royal Institution as John Thomas. Everything came together in the
discourses, in the Christmas Lectures of those five years. There was no need to
be locked up in Faraday’s lab; we could not wait to get to that lectern.
And the boy whose physics mistress roused him by talking of Faraday, could
stand at Faraday’s bench. . ..
The themes I have strolled by cannot capture the spirit of the great scientist
we celebrate. The 1795 Davy poem I cited (‘‘Sons of Genius’’) calls his heroes
‘‘Sons of Nature,’’ and has them delighting in ‘‘the train of mild philosophy’’ as
well as ‘‘the rough precipice’s broken steep.’’ That is an excellent characteri-
zation of John Thomas, for sure. Or shall we just call him the man with infinite
zest for catalysis?

Roald Hoffmann
Preface

Solid materials are ubiquitous in the world around us, and the wide array of
materials (ranging from ceramics to polymers, pharmaceuticals to pigments,
and catalysts to superconductors) that play a role in enhancing our everyday
lives have arisen, at least in part, through the work of solid-state and materials
scientists. An important pre-requisite for the development and exploitation of
materials for such applications is the elucidation of a fundamental understand-
ing of their properties, and in particular to establish the relationships between a
specific property or function of interest, and parameters such as the structure
and composition of the material. To advance our understanding of such
fundamental properties, and hence to pave the way for future generations of
applications, relies heavily on the ingenuity of those scientists who are dedi-
cated to advancing the fundamentals of this field, and their skills in deploying a
range of experimental and computational techniques to elucidate increasingly
detailed facets of information. Progress is also heavily reliant on the work of
those whose research is focused on advancing new aspects of such techniques
themselves, with the aim of increasing the power and scope of these techniques
to investigate systems in hitherto unexplored regimes of higher resolution,
shorter timescales or smaller quantities. There is no doubt that the exploration
of solid materials represents one of the most fascinating and rewarding areas of
scientific endeavour in the present day, and one of the intentions of this book is
to convey some of the excitement that is associated with research in this
particular area of science.
The aims of this book are two-fold: first, to provide a state-of-the-art survey
of some of the most important recent developments across the solid-state,
materials and surface sciences, and second (but intimately interwoven with the
first), to serve as a tribute to the life and work of Professor Sir John Meurig
Thomas, F.R.S., who has made monumental contributions to this field of
science throughout his distinguished 50-year career in research, during which he
has initiated, developed and exploited many important branches of this field.
The subject matter is sub-divided into four main sections: (i) inorganic solid
state chemistry, (ii) organic solid state chemistry, (iii) solid catalysts, surface
and materials chemistry, and (iv) electron microscopy and its contribution to
chemistry and materials science. The selection of these specific areas of the

vii
viii Preface
subject has been dictated in part by the fact that they span some of the most
important sub-disciplines of contemporary research in solid-state, materials
and surface sciences, but also in part because these areas represent the four
primary pillars of research achievement on which the career and reputation of
Sir John Meurig Thomas have been built. In addition to presenting a modern
survey of a specific area of the subject, each chapter is also intended to project
into the future development of the field. Each individual chapter is contributed
by an internationally leading expert in the relevant field, and we are particularly
delighted that two distinguished Nobel Laureates, Professor Roald Hoffmann
and Professor Ahmed Zewail, are among the authors who have contributed to
this book.
Sir John Meurig Thomas, who is currently Honorary Professor of Solid State
Chemistry at the University of Cambridge, is distinguished for his research
achievements across a very wide range of areas relating to solid-state, materials
and surface sciences. During the last 25 years in particular, his research has
been directed primarily towards the elucidation of fundamental principles of
heterogeneous catalysis, and the exploitation of these principles to design new
catalyst materials for effecting a wide range of chemically and industrially
important processes, under environmentally beneficial conditions. As a result
of his many pioneering and innovative contributions, he is widely regarded as
the pre-eminent scientist in this field in the world today. His seminal contribu-
tions in this field encompass: (i) the development of a broad range of new
techniques for characterization of heterogeneous catalytic systems, which have
led to an unprecedented level of understanding of the role of the active sites in
catalytic processes (with particular novelty in his use of techniques to probe
heterogeneous catalytic systems in situ, under real operating conditions, during
catalytic processes), (ii) the development of a fundamental physico-chemical
understanding of solid acid catalysts based on a wide range of structure types
(clays, zeolites, aluminophosphates, mesoporous materials and derivatives of
these materials), and (iii) the design of new generations of catalysts for carrying
out a range of chemically and industrially important transformations under
environmentally benign conditions (with particular recent interest in selective
hydrogenation reactions, including the introduction of enantioselectivity in
many of these reactions, and benign oxidation processes). His research in all of
these areas has been distinguished by its originality and creativity, and by
considerable productivity, and his contributions, encompassing both the elu-
cidation of fundamental principles and the application of this fundamental
knowledge to design and develop new and improved catalytic materials, have
represented a substantial contribution towards the advancement of the field of
heterogeneous catalysis. In addition to these fundamental achievements, his
work has also had a direct impact in underpinning a wide range of industrially
important chemical processes.
Throughout his recent research focusing on fundamentals and applications
of heterogeneous catalysis, and in his earlier, equally wide-ranging investiga-
tions of the properties of solid and their surfaces, Sir John Meurig Thomas has
held firmly to the belief that ‘‘tools and techniques play at least as important a
Preface ix
part in the evolution of scientific and technological progress as do ideas and
theories’’ (see Chapter 48 of this book). Illustrating this philosophy, and his
commitment not only to exploit the existing array of techniques but in addition
to initiate, to develop and to adapt new aspects of techniques to explore specific
issues, he has made many seminal contributions to the development of new
experimental techniques and strategies for the characterization of materials.
Some of the highlights from this aspect of his work include: (i) his multi-faceted
applications of electron microscopy and electron energy loss spectroscopy to
characterize structural and defect properties of materials, (ii) his ground-
breaking applications of high-resolution (magic angle spinning) solid state
NMR in the study of microporous solids, (iii) his development of the combined
use of X-ray diffraction and EXAFS spectroscopy for in situ characterization of
catalytic systems and processes, (iv) his development of electron tomography
(carried out using a scanning transmission electron microscope), with particular
interest in establishing this technique for characterization of the composition,
structure and morphology of nanoparticle catalysts on high-area supports, and
(v) his applications of computational techniques (often in tandem with exper-
imental studies) for elucidating detailed mechanistic insights into catalytic
processes.
In addition to his more recent focus on heterogeneous catalysis, it is relevant
to recall the many seminal contributions that he made to several other areas of
solid-state, materials and surface sciences at earlier stages of his career. For
example, at Bangor (1958 – 1969), he explored the chemical consequences of
dislocations and other structural imperfections in crystals, developed new
techniques of optical and electron microscopy, time-lapse microcinematogra-
phy, etch decoration, electrical resistance, space-charge limited current, and
conductivity-glow measurements to investigate the etching and reactivity of
minerals (graphite, molybdenite and calcite) and the excitonic behaviour of
molecular crystals such as anthracene, rotator-phase solids and protonic con-
ductors. He introduced the language of dislocation theory into chemistry,
which helped rationalize and explain many hitherto unexplained phenomena,
such as the rapid diffusionless phase-transitions of certain organic solids (in
terms of martensitic transformations), ‘‘anomalous’’ products in solid-state
organic photodimerizations (for example in substituted anthracenes) in terms
of stacking faults and partial dislocations, and the existence of singlet and
triplet exciton traps and charge carrier (electron and hole) traps in terms of
specific kinds of dislocations.
At Aberystwyth (1969 – 1978), he established the world’s leading group in
the solid-state chemistry and surface chemistry of solids, and he pioneered the
introduction and exploitation of electron microscopy within the chemical
sciences, both through fundamental developments of the technique, and
through his seminal demonstrations of the scope and potential for using
electron microscopy and related electron-beam techniques (particularly ana-
lytical X-ray photoelectron spectroscopy) to reveal details of structural, chem-
ical and electronic properties of solids (including an early report of carbon
nanotubes). In this regard, he introduced high-resolution electron microscopy
x Preface
as an indispensable tool for (real-space) structural elucidation of sub-picogram
quantities of a wide range of minerals and developed analytical electron
microscopy (using electron stimulated X-ray emission) to determine local
composition and non-stoichiometry with nanometre electron probes. He also
discovered many organic reactions that are catalyzed in the inter-lamellar
regions of clay minerals, as well as the existence of incommensurate structures
in intercalates, and he provided the first direct proof of the existence of staging
in the phenomenon of intercalation. Among the new techniques that he
developed were photoelectron diffraction, conversion-electron Mössbauer
spectroscopy, dynamic high-resolution electron microscopy, and photo- and
electroluminescence to elucidate a range of solid-state and surface phenomena.
Through his work on organic crystalline materials during this time (particularly
concerning photoreactivity of organic crystals, and the design of crystal struc-
tures for specific targeted photochemical reactions), he also laid the founda-
tions of the field of ‘‘crystal engineering’’, which is nowadays a burgeoning area
of activity.
Reading through the list of these highlights from his research career, it is
abundantly clear that many areas of contemporary importance within solid-
state, materials and surface sciences stemmed directly from early work that he
pioneered, and many of these contributions can be seen as genuine ‘‘turning
points’’ within their respective scientific disciplines.
During his distinguished career, Sir John Meurig Thomas has held some of
the most prestigious scientific appointments in the United Kingdom, includ-
ing Head of Department and Professor of Physical Chemistry at the Univer-
sity of Cambridge, and subsequently Director and Fullerian Professor of
Chemistry at the Royal Institution (an appointment held previously by several
other distinguished scientists, including Humphry Davy, Michael Faraday,
W.L. Bragg and W.H. Bragg). His achievements in research have been
recognized by many prestigious awards, including several of the premier
awards of the Royal Society (Bakerian Lectureship and Davy Medal), the
Royal Society of Chemistry (including the Faraday Medal, Longstaff Medal
and Sir George Stokes Medal), the Linus Pauling Gold Medal for contributions
to the advancement of science (the first non-American recipient of this award),
the Willard Gibbs Gold Medal of the American Chemical Society, the Semenov
Centenary Medal of the Russian Academy of Sciences, and the Giulio Natta
Gold Medal of the Italian Chemical Society. He was the first recipient (in 1999)
of the American Chemical Society Award for Creative Research in Homoge-
neous and Heterogeneous Catalysis; the citation for this award was ‘‘For laying
down the basic principles for catalytic active site engineering by designing and
synthesizing novel, exquisitely tailored solid catalysts and by pioneering the
development of techniques for determining active site structures under operating
conditions’’. And in recognition of his original contributions to analytical
mineralogy and geochemistry, the International Mineralogical Association, in
1995, named a new mineral (Meurigite) in his honour. A full list of his
achievements, awards and distinctions can be found in the brief curriculum
vitae included on pages xx–xxiv of this book, and a full list of his publications
Preface xi
(which number more than 1000) can be found at http://www-hrem.msm.
cam.ac.uk/people/thomas/
In addition to his immense contributions to scientific research, Sir John
Meurig Thomas has also taken a very active and innovative role in promoting
and advancing the public appreciation of science, particularly by inspiring the
scientific interests of young people. Following in the footsteps of Michael
Faraday (one of his predecessors at the Royal Institution, and undoubtedly one
of the greatest ever proponents of the popularization of science), Sir John has
taken a very active role through his many public lectures and television
broadcasts in promoting the awareness and popularization of science among
the general public (including the Royal Institution Christmas Lectures in 1987
and numerous lectures at the National Portrait Gallery in London on the lives
of famous people from the history of science). He is a uniquely gifted lecturer,
with a profound scientific knowledge spanning an exceptionally diverse range
of disciplines, and has a deep appreciation of the significance of contemporary
scientific progress and its historical context.
As an educator, teacher and research mentor, Sir John Meurig Thomas has
taught and inspired generations of young scientists, many of whom now hold
key academic and industrial positions throughout the world. His appointment
as Head of the Department of Physical Chemistry at the University of Cam-
bridge in 1978 led to a transformation of the teaching of the subject of Physical
Chemistry in Cambridge, and the research directions that he introduced to
Cambridge and the impact that he made at that time are still very much in
evidence in the Department of Chemistry in Cambridge today. As an interna-
tional statesman for science, Sir John Meurig Thomas has held a number of
important appointments, including Chairmanship of the CHEMRAWN
(Chemical Research Applied to World Needs) Committee of the International
Union of Pure and Applied Chemistry. He has also, through his scientific
endeavours and other work, been active in promoting the culture and language
of Wales both within the United Kingdom and beyond, and through his high
international scientific profile he has served in many ways as a cultural and
scientific ambassador for Wales.
We are particularly grateful to Sir John for contributing a chapter of his own
(entitled ‘‘Design and Chance in My Scientific Research’’) to this book. As
suggested by its title, this chapter provides a unique account of many of the key
‘‘turning points’’ that shaped his own scientific life, and conveys many fasci-
nating insights into the way in which the career of one of the most distinguished
scientists of the present day developed and blossomed. In addition to the
reminiscences written by his own hand in this chapter, many of the other
chapters of this book also contain personal reminiscences written by those
authors who have known and worked with Sir John (as students, colleagues
and collaborators) at different stages of his scientific career (including, in the
Appendices, some short articles that have been contributed solely for this
purpose). These reminiscences and anecdotes provide a fascinating account not
only of Sir John the scientist, the researcher and the educator, but also of the
personality, the unique character, and the human being. ‘‘An unforgettable
xii Preface
person’’, to quote the words of Professor John D. Roberts (former Provost and
Chairman of the Division of Chemistry and Chemical Engineering, California
Institute of Technology) in Appendix 3 of this book, seems to sum up perfectly
the impression that is gained by all those who have had the privilege of meeting
Sir John.
It seems somewhat anomalous that much of our discussion above seems to
have referred to Sir John’s career using the past tense, when we all know that,
as he approaches his 75th birthday, he is still as active, as energetic and as full
of enthusiasm for science as he has ever been. So, while taking this opportunity
to celebrate the many successes and achievements of his scientific career to date,
we also wish him continued good health and many more productive years at the
cutting edge of scientific research in the future.

Kenneth D.M. Harris

Peter P. Edwards
Contents

Curriculum Vitae, Awards and Honours of Sir John Meurig Thomas xx

Contributors xxv

Introduction

Chapter 1 Voyages with the Master 3

Ahmed H. Zewail

Section A: Inorganic Solid State Chemistry (Nanoporous Solids,

Complex Oxides, Zeolites, Minerals, Non-Stoichiometry,
Computation and Modelling)

Chapter 2 Multifaceted Studies of Zeolites and Other

Catalytic Materials 13
Anthony K. Cheetham

Chapter 3 The Deductive Approach to Chemistry,

a Paradigm Shift 22
Martin Jansen

Chapter 4 Future Energy Materials: Three Challenges

for Materials Chemistry 51
Peter P. Edwards and Vladimir L. Kuznetsov

Chapter 5 Structural Diversity and Potential Applications

of Metal–Organic Coordination Polymers 76
Jiesheng Chen and Ruren Xu

Chapter 6 Elucidating Crystal Growth in Nanoporous Materials:

The Importance of Microscopy 95
Michael W. Anderson, L. Itzel Meza, Jonathan R. Agger,
Martin P. Attfield, Maryam Shöâee`, Chin B. Chong,
Ayako Umemura and Colin S. Cundy

xiii
xiv Contents
Chapter 7 Exploration of New Porous Solids in the Search
for Adsorbents and Catalysts 123
Paul A. Wright and Wuzong Zhou

Chapter 8 Concerning the Solid State Packing of [(ButCO2)3M2]2

(l-9,10-anthracenedicarboxylate) Compounds
(M = Mo or W) and Other Matters 138
Malcolm H. Chisholm, Matthew J. Byrnes,
Ajatshatru Mehta and Patrick M. Woodward

Chapter 9 High Pressure and High Temperature Oxidation in the

IrSr2RECu2O8 Family of Cuprates: The Disordered
Multiple Perovskite (A1/3 A 0 2/3)(B1/3 B 0 2/3)O3-x Phases 151
A. J. Dos Santos-Garcı´a, G. Heymann, H. Huppertz
and M. Á. Alario-Franco

Chapter 10 Melting and Amorphisation 165

G. Neville Greaves

Chapter 11 Computer Modelling in Solid-State Chemistry 180

C. Richard A. Catlow, Said Hamad, Devis Di Tommaso,
Alexey A. Sokol and Scott M. Woodley

Chapter 12 Towards a Catalogue of Designer Zeolites 208

M. M. J. Treacy, M. D. Foster and I. Rivin

Chapter 13 Discovering New Crystal Architectures 221

Filipe A. Almeida Paz, Dorota Majda, Robert G. Bell
and Jacek Klinowski

Chapter 14 Chemical Modulations in Pb–Bi Sulfosalts: A Glimpse

at Minerals in Solid-State Chemistry 239
Allan Pring and Cristiana L. Ciobanu

Chapter 15 Complexity: In the Eye of the Beholder (This Beholder

is a Crystallographer) 250
Sven Lidin

Chapter 16 Synthesis and Characterization of Zn-T-Sites in Mazzite 258

David E. W. Vaughan, Ingrid J. Pickering,
Graham N. George and Jeffrey R. Shallenberger

Chapter 17 Anything Protons Do, Muons Do Better! 271

E. A. Davis
Contents xv
Section B: Organic Solid State Chemistry

Chapter 18 Molecular Cohesion and the Structure

of Organic Crystals 285
Jack D. Dunitz and A. Gavezzotti

Chapter 19 Aperiodicity in Organic Materials 302

Kenneth D. M. Harris

Chapter 20 From the Synthesis of Acetylenic Natural Products

to Seeing the Light with Polymers 334
Andrew B. Holmes, Paul L. Burn, Arno Kraft,
Jonathan M. White and Wallace W. H. Wong

Chapter 21 Molecular Recognition within One-Dimensional Channels 346

Mark D. Hollingsworth

Chapter 22 FTIR Study of Short Range Mobility in Some Crystalline

Peroxides: Solid-State Rotational Isomerism of CO2 362
J. Michael McBride and Kevin L. Pate

Section C: Solid Catalysts, Surface and Materials Science

Chapter 23 From ‘Nature’ to an Adventure in Single-Site

Epoxidation Catalysis 385
Hendrikus C. L. Abbenhuis and Rutger A. van Santen

Chapter 24 A Comparison between Enzymes and Solid State Catalysts 396

Robert J. P. Williams

Chapter 25 Zeolite Modelling: Active Sites in Different Framework

Structures and in Different Crystallographic Positions 441
Joachim Sauer

Chapter 26 Magnetic Resonance Imaging: A New Window on the

Catalyst Operating in the Reactor Environment 457
L. F. Gladden, B. S. Akpa, L. D. Anadon, C. P. Dunckley, M.
H. M. Lim, M. D. Mantle and A. J. Sederman

Chapter 27 Dissociative Chemisorption of Hydrogen Chloride

at Cu(110): Atom-Resolved Time-Dependent Evidence
for Transient States in the Formation of the ‘‘Final State’’
Stable Chloride Overlayer 479
A. F. Carley, P. R. Davies, K. R. Harikumar, R. V. Jones
and M. Wyn Roberts
xvi Contents
Chapter 28 Recent Advances in Single-Site Photocatalysts Constructed
within Microporous and Mesoporous Materials 492
Masakazu Anpo and Masaya Matsuoka

Chapter 29 Structural Organization of Catalytic Functions in Mo-Based

Selective Oxidation Catalysts 507
Masahiro Sadakane and Wataru Ueda

Chapter 30 Designing Active Sites for Surfaces: From Tightly Bound

to Loosely Anchored 519
Thomas Maschmeyer

Chapter 31 Polynuclear Transition Metal Cluster Complexes

Containing Tin Ligands: Precursors to New Heterogeneous
Nano-Catalysts 534
Richard D. Adams and Burjor Captain

Chapter 32 Selective Oxidation Using Gold and Gold–Palladium

Nanoparticles 550
Graham J. Hutchings

Chapter 33 Electronic Factors in Hydrocarbon Oxidation Catalysis 568

Jerzy Haber

Chapter 34 The Importance of Selectivity in Ammoxidation Catalysis 577

Robert K. Grasselli

Chapter 35 The Mysteries of Water in Catalyst Preparation:

Solvent or Much More? 588
Michel Che

Chapter 36 Solid Acid Microporous H-SAPO-34: From Early Studies

to Perspectives 604
Leonardo Marchese, Gloria Berlier
and Salvatore Coluccia

Chapter 37 Strategically Designed Single-Site Heterogeneous Catalysts

for Clean Technology, Green Chemistry and Sustainable
Development 623
Robert Raja

Chapter 38 Catalysis by Lewis Acids: Basic Principles

for Highly Stereoselective Heterogeneously
Catalyzed Cyclization Reactions 639
Mercedes Boronat, Avelino Corma and Michael Renz
Contents xvii
Chapter 39 Recent Advances in XPS of Non-Conductors 651
G. Michael Bancroft, H. W. Nesbitt, V. P. Zakaznova-Herzog
and J. S. Tse

Section D: Electron Microscopy and its Contribution to Chemistry

and Material Science

Chapter 40 Electron Microscopy Studies of Structural Modulation

in Micro- and Meso-Porous Crystals 667
Osamu Terasaki, Tetsu Ohsuna, Zheng Liu, Yasuhiro
Sakamoto, Keiichi Miyasaka, Nobuhisa Fujita,
Nozomu Togashi and Shunai Che

Chapter 41 Extrapolating from Fifty Years of Dislocation Imaging –

Reaching into the Core 687
Archie Howie

Chapter 42 Turning Points in Understanding the Emission of Brilliant

Light from Highly Defective GaN-Based Materials
and Devices 698
Colin J. Humphreys

Chapter 43 Electron Tomography: A 3D View of Catalysts

and Nanoscale Structures 711
Paul A. Midgley

Chapter 44 Nano and Mesoporous Materials: A Study by HREM 727

Jose´ M. González-Calbet, M. Luisa Ruiz-González
and Marı´a Vallet-Regı´

Chapter 45 In Situ Direct Observation at Atomic Scale Twinning

Transformations and the Formation of Carbon
Nanostructures in WC 745
Pratibha L. Gai, C. C. Torardi and E. D. Boyes

Chapter 46 A Survey of the Bi2O3–MoO3 Binary System 754

Douglas J. Buttrey

Chapter 47 An Investigation of the Surface Structure of Nanoparticulate

Systems Using Analytical Electron Microscopes Corrected
for Spherical Aberration 778
Rik Brydson and Andy Brown
xviii Contents

Closing Chapter

Chapter 48 Design and Chance in My Scientific Research 795

John Meurig Thomas

Appendices: Tributes to Sir John Meurig Thomas

Appendix 1 Tribute to John Meurig Thomas on the Occasion

of His 75th Birthday 853
David Buckingham

Appendix 2 John Meurig Thomas and the Royal Institution 855

John Waterlow

Appendix 3 Sir John Meurig Thomas: An Unforgettable Person 856

John D. Roberts

Appendix 4 John Meurig Thomas on His 75th Birthday 858

Ralph Kohn

Appendix 5 Remembering a Period of Work with

Sir John Meurig Thomas 861
Gilbert Sloan

Appendix 6 Reflections on John Meurig Thomas on the Occasion

of His 75th Birthday 863
Martin Pope

Appendix 7 Bangor 1966–1969; Aberystwyth 1969–1973;

Some Fond Reflections 866
Stan Moore

Appendix 8 Aberystwyth 1970–1973. Reflections and Lessons Learnt 868

Gari Owen

Appendix 9 Molecular Modelling Input to Organic Solid State and

Zeolite Chemistry: Reminiscences (1975-84) 872
S. Ramdas

Appendix 10 Reflections of a Cambridge Undergraduate 876

Angus Kirkland

Appendix 11 Sir John Meurig Thomas 879

Brian Johnson
Contents xix
Appendix 12 Getting the Details Correct 881
David Jefferson

Appendix 13 Tribute to Sir John Meurig Thomas on the Occasion of

His 75th Birthday 883
Gordon M. Parkinson

Appendix 14 Solid State Chemistry and the Edward Davies

Chemical Laboratories 885
Bill Jones

Subject Index 887

Curriculum Vitae, Awards and
Honours of Sir John Meurig
Thomas
PROFESSOR JOHN MEURIG THOMAS

Date of Birth: 15 December 1932, Llanelli, Wales, UK

Present Positions Held:

 Honorary Professor of Materials Science, University of Cambridge

(2002 – )
 Emeritus Professor of Chemistry, Davy Faraday Research Laboratory,
Royal Institution of Great Britain, London (since 2002)
 Honorary Distinguished Professor of Materials Chemistry, Cardiff Uni-
versity, Wales (2005 – )
 Distinguished Visiting Professor of Nanoscience, University of South
Carolina, USA (2005 – )
 Honorary Distinguished Professor of Materials Chemistry, University of
Southampton (2006 – )
 Honorary Professor, Graduate School of Engineering, Osaka Prefecture
University, Japan (2006 – )
 Honorary Professor, State Laboratory of Inorganic Chemistry and
Materials Science, Jilin University, China (2007 – )

Positions Formerly Held:

 Director, Royal Institution of Great Britain (1986–91)

 Director, Davy Faraday Research Laboratory (1986–91)
 Fullerian Professor of Chemistry, Royal Institution (1988–94)
 Head, Department of Physical Chemistry, University of Cambridge and
Professorial Fellow at Kings College, Cambridge (1978–86)

xx
Curriculum Vitae, Awards and Honours of Sir John Meurig Thomas xxi
 Master (Head) of Peterhouse (College), University of Cambridge (1993–
2002)
 Deputy Pro-Chancellor, Federal University of Wales (1991–94)
 Professor of Chemistry and Head of Department , University College,
Wales, Aberystwyth (1969–78)
 Assistant Lecturer, Lecturer, Reader in Chemistry, University of Wales,
Bangor (1958–69)

National and International Awards:

2007 The International Precious Metal Institute Distinguished Achieve-

ment Award ‘‘for pioneering contributions to the field of heteroge-
neous catalysis using precious metals’’
2005 Sir George Stokes Gold Medal, Royal Society of Chemistry ‘‘for
pioneering and innovative electron based nanochemical analysis’’
2004 Guilio Natta Gold Medal, Italian Chemical Society ‘‘for outstand-
ing work in catalysis’’
2003 Linus Pauling Gold Medal, Stanford University ‘‘for contributions
to the advancement of science’’
1999 First recipient of American Chemical Society Award ‘‘for Creative
Research in Heterogeneous and Homogeneous Catalysis’’
1997 Honorary Medal, Krakow Academy of Knowledge, Poland ‘‘for
Distinguished Public Service’’
1996 Semenov Centenary Medal, Russian Academy of Sciences
Honorary Medal, Polish Academy of Sciences, Warsaw
Longstaff Medal, Royal Society of Chemistry
1995 Willard Gibbs Gold Medal of the American Chemistry Society
(first British chemist to be honoured in 80 years): ‘‘for pioneering
work in solid-state chemistry and materials science ..... His original
work (on solids) has led to major advances in the science and
technology of absorbents and catalysts’’
New mineral, meurigite, named in his honour by International
Mineralogical Association to recognise his pioneering work in
geochemistry
1994 Davy Medal of the Royal Society (its premier medal in the Physical
Sciences)
1992 Messel Gold Medal, Society of Chemical Industry, awarded bien-
nially ‘‘for meritorious distinction in science, literature, industry or
public affairs’’
1989 Faraday Medal, Royal Society of Chemistry (its premier medal,
awarded every three years)
Sesquincentenary Medal of the Royal Microscopical Society
xxii Curriculum Vitae, Awards and Honours of Sir John Meurig Thomas
Other Medals:

 Hugo Müller Medal (1983), Solid-State Chemistry Medal (1978), Tilden

Medal (1973), Corday-Morgan Medal (1969) [all from the Royal Society
of Chemistry]
 The Pettinos Prize (first recipient), American Carbon Society (1969)
 Bruce-Preller Prize, Royal Society of Edinburgh (1989)
 Silver Medal ‘‘for services to science celebrating 750th Anniversary of the
University of Siena’’ (2005)

Honorary Doctorates from:

Wales (LL.D.); Council of National Academic Awards (D.Litt.); Heriot-Watt,

Edinburgh (D.Sc.); Birmingham (D.Sc.); Open University (D.Univ.); Lyon,
France (D.Sc.); Complutense, Madrid (D.Sc.); Glamorgan (D.Sc.); Western
Ontario, Canada (D.Sc.); Eindhoven, The Netherlands (D.Sc.);
Hull (D.Sc.); Surrey (D.Univ); Aberdeen (D.Sc.); American University in
Cairo (D.Sc.); Turin, Italy (D.Sc.); Clarkson, USA (D.Sc.); Sydney, Australia
(D.Sc.)

Honorary Foreign Fellowships or Memberships:

 2006, European Academy of  1994, Academy of Sciences of Ven-

Sciences
 2005, Mendeleev Chemical
Society, Moscow
 2004, Accademia Nazionale
dei Lincei, Rome
 2003, Göttingen Academy of
Sciences
 1999, Royal Spanish Acad-
emy of Sciences
 1998, Polish Academy of Sci-
ences
 1998, Hungarian Academy of
Sciences
 1995, Third World Academy
of Sciences, Trieste
ezuela
 1994, Russian Academy of Sci-
ences
 1993, Royal Society of Edinburgh
 1992, American Philosophical So-
ciety, Philadelphia
 1991, Engineering Academy of Ja-
pan
 1990, American Academy of Arts
and Sciences, Cambridge
 1989, Academia Europaea
 1985, Indian National Academy,
New Delhi
 1981, Indian Academy, Bangalore

John Meurig Thomas holds over forty honorary fellowships in universities

and colleges in the UK and elsewhere in the world. A Fellow of the Royal
Society since 1977, in 1999 he was elected Honorary Fellow of the Royal
Academy of Engineering for work that ‘‘has profoundly added to the science
Curriculum Vitae, Awards and Honours of Sir John Meurig Thomas xxiii
base of heterogeneous catalysis leading to the commercial exploitation of zeolites
through engineering processes’’. Also in 1999 he was made (honorary) Fellow of
the Institute of Physics.
Served as Government Advisor on the Council on Applied Research and
Development (1982-85) at the Cabinet Office, Whitehall, London.
Chairman of CHEMRAWN (Chemical Research Applied to World Needs)
of the International Union of Pure and Applied Chemistry (1988-92).
President of the Faraday Division of the R.S.C., and of the Chemistry
Division of the British Association for Advancement of Science; of the London
International Youth Science Festival; and a Trustee of the National Science
Museum (1990-95) and of the Natural History Museum (1989-91). He is the
vice-President of the Cambridge University Musical Society (1994 – ).
In 2000, the Electron Microscopy and Microanalysis Society of the Americas
held a three-day symposium in his honour at their annual convention in
Philadelphia.
He has broadcast extensively on radio and television in the UK and abroad,
and given numerous popular lectures to lay audiences world-wide and lunch-
time lectures at the National Portrait Gallery, London.

Named Lectureships Abroad and in the UK:

John Meurig Thomas has given over a hundred Named Lectures world wide,
including those named in honour of:
Rutherford (New Zealand); Van’t Hoff (Royal Academy Netherlands);
Helmholtz (Berlin); Darwin (Cambridge); Debye (Utrecht); Pauling (Caltech,
Stanford and Oregon); Larmor (Cambridge); Baker (Cornell); Woodward
(Harvard and Yale); Pitzer (Berkeley); Krishnan (New Delhi); Bernal
(London); Ziegler (Germany); Liversidge (Sydney); Polanyi (Toronto);
Sunner (Lund, Sweden); Willard Gibbs (ACS, Chicago); Faraday (RSC,
London); Birch (Canberra); Hund (Stuttgart); Watson (Caltech); Drickamer,
(Urbana); Taylor (Penn State); Guggenheim (Reading); Rogers (Michigan);
Shipley (Clarkson); Oersted (T.U. Denmark); Bakerian (Royal Society,
London).
In 1986 he was a plenary speaker, along with Professor Ken-ichi Fukui, at
the Japan Key Technology event, Tokyo, to honour the sixtieth year of the
reign of the Emperor of Japan.
In 2006 he was plenary speaker at the Tercentenary Celebrations of the birth
of Benjamin Franklin, American Philosophical Society, Philadelphia.

Short-term Visiting Professorships:

 Scuola Normale Superiore, Pisa  Texas A and M University

 University of Florence  Yale University
 Technical University, Eindhoven  Cornell University
xxiv Curriculum Vitae, Awards and Honours of Sir John Meurig Thomas
 Ecole Nationale Superieure,
Paris
 Jawaharlal Nehru Centre for
Advanced Studies, Bangalore
 Max Planck Institute, Mülheim
 Weizmann Institute of Science
 Universities of Western Ontario,
McMaster and Calgary
 University of California,
Berkeley
 Indiana University
 Northwestern University
 Pennsylvania State University
and Arizona State University
 California Institute of
Technology
 University of Sydney
 Ruprecht-Karls-Universität,
Heidelberg.

Membership of International Advisory Boards:

At various times, John Meurig Thomas has been a member of several

International Advisory Boards, including the following:

 Science Centre, University of Alexandria, Egypt

 Weizmann Institute, Israel
 Laboratory of Molecular Sciences, California Institute of Technology,
U.S.A.
 Beroskov Institute of Catalysis, Siberian Branch of the Russian Academy
of Sciences
 EXSELENT (Extremely Selective and Enantioselective Materials for
Controlled Sorption and Catalysis), Arrhenius Laboratory, University
of Stockholm, Sweden
 National Institute of Informatics, Tokyo, Japan

In 1991 he was knighted by Queen Elizabeth II for

‘‘services to chemistry and the popularisation of science’’

Awarded Medal of the Honourable Society of Cymmrodorion (London) for

services to Welsh culture and British public life (2003) – first scientist to be so
honoured since its inception 160 years ago.
John Meurig Thomas is the author of over 900 research papers on the
materials and surface chemistry of solids, and over 100 review articles on
science, education and cultural issues. He is the co-author of 25 patents, two
University texts on Heterogeneous Catalysis and a biographical–philosophical
study of Michael Faraday, 1991 (Japanese Translation, 1994; Italian Transla-
tion, 2007).
The full publication list of John Meurig Thomas is available at: http://www-
hrem.msm.cam.ac.uk/people/thomas/
Contributors

Hendrikus C. L. Abbenhuis Miguel A. Alario-Franco

Laboratory of Inorganic Chemistry Departamento de Quı́mica
and Catalysis Inorgánica
Eindhoven University of Technology Facultad de Ciencias Quı́micas
PO Box 513 Universidad Complutense de
NL-5600 MB Eindhoven Madrid
The Netherlands 28040 Madrid
Spain

Richard D. Adams
Department of Chemistry and Filipe A. Almeida Paz
Biochemistry Department of Chemistry
The University of South Carolina CICECO, University of Aveiro
631 Sumter Street Campus Universitario de Santiago
Columbia Aveiro 3810-193
SC 29208 Portugal
USA

L. D. Anadon
Jonathan R. Agger Department of Chemical
Centre for Nanoporous Materials Engineering
School of Chemistry University of Cambridge
The University of Manchester New Museums Site
Oxford Road Pembroke Street
Manchester, M13 9PL Cambridge, CB2 3RA
UK UK

B. S. Akpa Michael W. Anderson

Department of Chemical Engineering Centre for Nanoporous Materials
University of Cambridge School of Chemistry
New Museums Site University of Manchester
Pembroke Street Oxford Road
Cambridge, CB2 3RA Manchester M13 9PL
UK UK
xxv
xxvi Contributors
Masakazu Anpo Mercedes Boronat
Department of Applied Chemistry Instituto de Tecnologia Quimica
Graduate School of Engineering (UPV-CSIC)
Osaka Prefecture University Universidad Politécnica de Valencia
1-1 Gakuen-cho Avda. De los Naranjos s/n
Sakai, Nakaku 46022 Valencia
Osaka 599-8531 Spain
Japan

E. D. Boyes
Martin P. Attfield
Department of Physics
Centre for Nanoporous Materials
University of York
School of Chemistry
Heslington
The University of Manchester York, YO10 5DD
Oxford Road UK
Manchester, M13 9PL
UK
Andy Brown
Leeds Electron Microscopy and
G. Michael Bancroft Spectroscopy Centre
Department of Chemistry Institute for Materials Research
The University of Western Ontario SPEME
Chemistry Building 1151 Richmond University of Leeds
Street Leeds, LS2 9JT
London UK
Ontario N6A 5B7
Canada
Rik M. D. Brydson
Institute for Materials Research
Robert G. Bell School of Process, Environmental
Davy-Faraday Research Laboratory and Materials Engineering
The Royal Institution of Great Britain University of Leeds
21 Albemarle Street Clarendon Road
London, W1S 4BS Leeds
UK West Yorkshire LS2 9JT
UK

Gloria Berlier
Dipartimento de Chimica Inorganica, Paul L. Burn
Fisica e dei Materiali and NIS School of Molecular and Microbial
Centre of Excellence Sciences
Universitá de Torino University of Queensland
Via P. Giuria 7 St Lucia
10125 Torino Qld 4072
Italy Australia
Contributors xxvii
Douglas J. Buttrey Michel Che
Department of Chemical Laboratoire de Reactivité de Surface
Engineering et Structure
University of Delaware Université Pierre et Marie Curie
326 CLB 4 Place Jussieu
150 Academy Street Tour 54-55
Newark 75252 Paris Cedex 05
DE 19716 France
USA

Shunai Che
Matthew J. Byrnes School of Chemistry and Chemical
Department of Chemistry Technology
The Ohio State University Shanghai Jiao Tong University
Columbus Shanghai
Ohio, 43210 PR China
USA

Anthony K. Cheetham
Burjor Captain Materials Research Laboratory
Department of Chemistry and University of California
Biochemistry Santa Barbara
The University of South Carolina CA 93106
631 Sumter Street USA
Columbia
SC 29208
USA
Jiesheng Chen
State Key Laboratory of Inorganic
Synthesis and Preparative
A. F. Carley Chemistry, College of
School of Chemistry Chemistry
Cardiff University Jilin University
Park Place Changchun 130012
Cardiff, CF10 3AT People’s Republic of China
UK

Malcolm H. Chisholm
C. Richard A. Catlow Department of Chemistry
Department of Chemistry The Ohio State University
University College London 100 W. 18th Ave.
20 Gordon Street Columbus
London WC1H 0AJ Ohio 43210
UK USA
xxviii Contributors
Chin B. Chong E. A. Davis
Centre for Nanoporous Materials Department of Materials Science
School of Chemistry and Metallurgy
The University of Manchester University of Cambridge
Oxford Road New Museums Site
Manchester, M13 9PL Pembroke Street
UK Cambridge CB2 3QZ
UK

Cristiana L. Ciobanu
Department of Mineralogy
P. R. Davies
South Australian Museum
School of Chemistry
North Terrace
Cardiff University
Adelaide
Park Place
South Australia 5000
Cardiff, CF10 3AT
Australia
UK

Salvatore Coluccia
Dipartimento di Chimica Inorganica, C. P. Dunckley
Fisica e dei Materiali and NIS Department of Chemical
Centre of Excellence Engineering
Università di Torino, University of Cambridge
Via P. Giuria 7 New Museums Site
10125 Torino Pembroke Street
Italy Cambridge, CB2 3RA
UK

Avelino Corma
Instituto de Tecnologı́a Quı́mica
Jack D. Dunitz
(UPV-CSIC)
Chemistry Department OCL
Universidad Politécnica de Valencia
ETH-Hönggerberg HCI H333
Avda. de los Naranjos s/n
CH-8093 Zürich
46022 Valencia
Switzerland
Spain

Colin S. Cundy Peter P. Edwards

Centre for Nanoporous Materials Inorganic Chemistry
School of Chemistry Laboratory
The University of Manchester University of Oxford
Oxford Road South Parks Road
Manchester, M13 9PL Oxford OX1 3QR
UK UK
Contributors xxix
M. D. Foster Lynn F. Gladden
Department of Physics Department of Chemical
Arizona State University Engineering
PO Box 871504 University of Cambridge
Tempe New Museums Site
AZ 85287-1504 Pembroke Street
USA Cambridge CB2 3RA
UK

Nobuhisa Fujita
José M. González-Calbet
Department of Physical, Inorganic
Departamento de Quı́mica
and Structural Chemistry
Inorgánica
Arrhenius Laboratory
Facultad de Ciencias Quı́micas
Stockholm University
Universidad Complutense de
SE-106 91 Stockholm
Madrid
Sweden
28040 Madrid
Spain

Pratibha L. Gai
Department of Chemistry
Robert K. Grasselli
University of York
Department of Chemistry
Heslington
Technische Universität München
York, YO10 5DD
D-85748, Garching
Germany

A. Gavezzotti
Dipartimento di Chimica Strutturale G. Neville Greaves
e Stereochimica Inorganica Institute of Mathematical and
University of Milano Physical Sciences
Via Venezian 21 University of Wales Aberystwyth
I-20133 Milano Aberystwyth
Italy Ceredigion SY23 3BZ
UK

Graham N. George
Department of Geological Jerzy Haber
Sciences Institute of Catalysis and Surface
University of Saskatchewen Chemistry
114 Science Place Polish Academy of Sciences
Saskatoon ul. Niezapominajek 8
SK S7N 5E2 PL-30239 Krakow
Canada Poland
xxx Contributors
Said Hamad Andrew B. Holmes
Davy Faraday Research School of Chemistry
Laboratories and Department of The University of Melbourne
Chemistry Bio21 Institute
University College London Melbourne
20 Gordon Street Victoria 3010
London, WC1H OAJ Australia
UK

Mark D. Hollingsworth
K. R. Harikumar Chemistry Department
School of Chemistry 111 Willard Hall
Cardiff University Kansas State University
Park Place Manhattan
Cardiff, CF10 3AT KS 66506
UK USA

Archie Howie
Kenneth D. M. Harris
Department of Physics
School of Chemistry
University of Cambridge
Cardiff University
Cavendish Laboratory
Park Place
J.J. Thomson Avenue
Cardiff CF10 3AT
Cambridge CB3 0HE
UK
UK

G. Heymann
Department Chimie und Colin J. Humphreys
Biochemie Department of Materials Science and
Ludwig-Maximilians-Universität Metallurgy
München University of Cambridge
Butenandtsrasse 5-13 New Museums Site
81377 München Pembroke Street
Germany Cambridge CB2 3QZ
UK

Roald Hoffmann
Department of Chemistry and H. Huppertz
Chemical Biology Department Chimie und Biochemie
Cornell University Ludwig-Maximilians-Universität
Baker Laboratory München
Ithaca Butenandtsrasse 5-13
NY 14853-1301 81377 München
USA Germany
Contributors xxxi
Graham J. Hutchings Vladimir Kuznetsov
School of Chemistry Inorganic Chemistry Laboratory
Cardiff University University of Oxford
Park Place South Parks Road
Cardiff CF10 3AT Oxford, OX1 3QR
UK UK

Martin Jansen
Max Planck Institute for Solid State Sven Lidin
Research Department of Physical, Inorganic
Heisenbergstraße 1 and Structural Chemistry
D-70569 Stuttgart Arrhenius Laboratory
Germany Stockholm University, SE-106 91
Stockholm
Sweden
Brian F. G. Johnson
Department of Chemistry
University of Cambridge
Lensfield Road
M. H. M. Lim
Cambridge CB2 1EW
Department of Chemical
UK
Engineering
University of Cambridge
R. V. Jones New Museums Site
School of Chemistry Pembroke Street
Cardiff University Cambridge, CB2 3RA
Park Place UK
Cardiff, CF10 3AT
UK

Zheng Liu
Jacek Klinowski Department of Physical, Inorganic
Department of Chemistry and Structural Chemistry
University of Cambridge Arrhenius Laboratory
Lensfield Road Stockholm University
Cambridge, CB2 1EW SE-106 91 Stockholm
UK Sweden

Arno Kraft
Chemistry, School of Engineering Dorota Majda
and Physical Sciences Department of Chemistry
Perkin Building University of Cambridge
Heriot-Watt University Lensfield Road
Edinburgh, EH14 4AS Cambridge, CB2 1EW
UK UK
xxxii Contributors
M. D. Mantle L. Itzel Meza
Department of Chemical Centre for Nanoporous Materials
Engineering School of Chemistry
University of Cambridge The University of Manchester
New Museums Site Oxford Road
Pembroke Street Manchester, M13 9PL
Cambridge, CB2 3RA UK
UK

J. Michael McBride
Leonardo Marchese Department of Chemistry
Dipartimento di Scienze e Tecnologie Yale University
Avanzate Box 208107
Università del Piemonte Orientale New Haven
‘‘A. Avogadro’’ CT 06520–8107
C. so Borsalino 54 USA
I-15100 Alessandria
Italy
Paul A. Midgley
Department of Materials Science and
Thomas Maschmeyer Metallurgy
School of Chemistry University of Cambridge
University of Sydney New Museums Site
Building F11 Pembroke Street
Sydney Cambridge CB2 3QZ
NSW 2006 UK
Australia

Keiichi Miyasaka
Masaya Matsuoka
Department of Physical, Inorganic
Department of Applied Chemistry
and Structural Chemistry
Graduate School of Engineering
Arrhenius Laboratory
Osaka Prefecture University
Stockholm University
1-1 Gakuen-cho
SE-106 91 Stockholm
Sakai, Nakaku
Sweden
Osaka 599-8531
Japan

H. W. Nesbitt
Ajatshatru Mehta Department of Earth Sciences
Department of Chemistry The University of Western
The Ohio State University Ontario
Columbus London
Ohio, 43210 Ontario N6A 5B7
USA Canada
Contributors xxxiii
Tetsu Ohsuna Michael Renz
Department of Physical, Inorganic Instituto de Tecnologia Quimica
and Structural Chemistry (UPV-CSIC)
Arrhenius Laboratory Universidad Politécnica de Valencia
Stockholm University Avda. De los Naranjos s/n
SE-106 91 Stockholm 46022 Valencia
Sweden Spain

Kevin L. Pate I. Rivin

Department of Chemistry Department of Mathematics
Marietta College Temple University
Marietta 1805 North Broad Street
Ohio 45750 Philadelphia
USA PA 19122
USA

Ingrid J. Pickering
Department of Geological
M. Wyn Roberts
Sciences
School of Chemistry
University of Saskatchewen
Cardiff University
114 Science Place
Park Place
Saskatoon
Cardiff CF10 3AT
SK S7N 5E2
Wales
Canada

M. Luisa Ruiz-González
Allan Pring Departamento de Quı́mica
Department of Mineralogy Inorgánica
South Australian Museum Facultad de Ciencias Quı́micas
North Terrace Universidad Complutense de Madrid
Adelaide 28040 Madrid
South Australia 5000 Spain
Australia

Masahiro Sadakane
Robert Raja Catalysis Research Center
School of Chemistry Hokkaido University
University of Southampton North 21 West 10
Highfield Campus Kita-ku
Southampton SO17 1BJ Sapporo 001-0021
UK Japan
xxxiv Contributors
Yasuhiro Sakamoto Maryam Shoaee
Department of Physical, Inorganic Centre for Nanoporous Materials
and Structural Chemistry School of Chemistry
Arrhenius Laboratory The University of Manchester
Stockholm University Oxford Road
SE-106 91 Stockholm Manchester, M13 9PL
Sweden UK

A. J. Dos Santoa-Garcı́a Alexey A. Sokol

Laboratorio de Quı́mica del Estado Davy Faraday Research
Sólido Laboratories and Department of
Departamento de Quı́mica Inorgáni- Chemistry
ca and Laboratorio Complutense University College London
de Altas Presiones 20 Gordon Street
Facultad de Ciencias Quı́mica London, WC1H OAJ
Universidad Complutense de Madrid UK
28040 Madrid
Spain

Osamu Terasaki
Joachim Sauer Department of Physical,
Institut für Chemie Inorganic and Structural
Humboldt Universität zu Berlin Chemistry
Unter den Linden 6 Arrhenius Laboratory
D-10099 Berlin Stockholm University
Germany SE-106 91 Stockholm
Sweden

A. J. Sederman
Department of Chemical
Sir John Meurig Thomas
Engineering
Department of Materials Science
University of Cambridge
and Metallurgy
New Museums Site
University of Cambridge
Pembroke Street
New Museums Site
Cambridge, CB2 3RA
Pembroke Street
UK
Cambridge CB2 3QZ
UK
Jeffrey R. Shallenberger
Materials Research Institute
Pennsylvania State University Nozomu Togashi
University Park Namiki Precision Jewel Co. Ltd.
PA 16802 Tokyo
USA Japan
Contributors xxxv
Devis de Tommaso Ayako Umemura
Davy Faraday Research Centre for Nanoporous Materials
Laboratories and Department of School of Chemistry
Chemistry The University of Manchester
University College London Oxford Road
20 Gordon Street Manchester, M13 9PL
London, WC1H OAJ UK
UK

Marı́a Vallet-Regı́
Departamento de Quı́mica
C. C. Torardi Inorgánica y Bioinorgánica
DuPont Central Research and Facultad de Farmacia
development Universidad Complutense de Madrid
Wilmington Pza Ramon y Cajal
DE 19880-0356 28040 Madrid
USA Spain

Rutger A. van Santen

Michael M. J. Treacy Laboratory of Inorganic Chemistry
Department of Physics and Catalysis
Arizona State University Eindhoven University of Technology
P.O. Box 871504 P.O. Box 513
Tempe NL-5600 MB Eindhoven
AZ 85287-1504 The Netherlands
USA

David E. W. Vaughan
Materials Research Institute
J. S. Tse
Pennsylvania State University
Department of Physics
276 Materials Research Laboratory
University of Saskatchewan
Building
Saskatoon
University Park
SK S7N5E2
PA 16802
Canada
USA

Wataru Ueda Jonathan M. White

Catalysis Research Center School of Chemistry
Hokkaido University Bio21 Institute
North 21 West 10 The University of Melbourne
Kita-ku Melbourne
Sapporo 001-0021 Victoria 3010
Japan Australia
xxxvi Contributors
Robert J. P. Williams Ruren Xu
Inorganic Chemistry Laboratory State Key Laboratory of Inorganic
University of Oxford Synthesis and Preparative
South Parks Road Chemistry
Oxford OX1 3QR College of Chemistry
UK Jilin University
Changchun 130012
People’s Republic of China
Wallace W. H. Wong
School of Chemistry
Bio21 Institute V. P. Zakaznova-Herzog
The University of Melbourne Department of Earth Sciences
Melbourne The University of Western
Victoria 3010 Ontario
Australia London
Ontario N6A 5B7
Canada
Scott M. Woodley
Davy Faraday Research Laboratories
Ahmed H. Zewail
and Department of Chemistry
Physical Biology Centre for Ultrafast
University College London
Science and Technology
20 Gordon Street
Arthur Amos Noyes Laboratory of
London, WC1H OAJ
Chemical Physics
UK
California Institute of Technology
Mail Code 127-72
1200 East California Boulevard
Patrick M. Woodward
Pasadena
Department of Chemistry
CA 91125
The Ohio State University
USA
Columbus
Ohio, 43210
USA Wuzong Zhou
School of Chemistry
University of St. Andrews
Paul A. Wright Purdie Building
School of Chemistry St. Andrews
University of St. Andrews Fife KY16 9ST
St. Andrews UK
Fife KY16 9ST
UK
 Section A:
Inorganic Solid State Chemistry
(Nanoporous Solids, Complex Oxides,
Zeolites, Minerals, Non-Stoichiometry,
Computation and Modelling)
CHAPTER 2

Multifaceted Studies of Zeolites

and Other Catalytic Materials
ANTHONY K. CHEETHAM
Materials Research Laboratory, University of California, Santa Barbara, CA
93106, USA

1 Introduction
I believe that I was first introduced to John Thomas by Mike Goringe in the
mid-1970s. Mike and I lived in Woodstock at the time, just a few miles north of
Oxford, and we both played cricket regularly for the Blenheim Park club on the
south lawn of Blenheim Palace. John had come from Aberystwyth to visit the
Materials Department at Oxford and Mike invited him to make a guest
appearance at the club. Happily, none of us can remember our scores after
so many years, but I can remember being vividly struck by the keen intelligence
and quick-wittedness of our guest. This was the first of many meetings with
John in the 1970s: several in the Chemical Crystallography laboratory at
Oxford, where I had joined the faculty in 1974, once at a discourse by John
at the Royal Institution in London, and a number of times at Gordon
Conferences and other meetings.
It was not until about 1980 that we began our first collaboration. I had been
working extensively in the 1970s with the recently discovered Rietveld method
for analysing powder neutron diffraction data, and John, by then at Cambridge,
invited me over to talk about the possibility of applying this powerful tool to
some problems in the zeolite area. His enthusiasm and persuasiveness quickly
convinced me that this would be an exciting adventure, and thus began a
wonderful collaboration that lasted about 15 years and produced over 30
papers. The collaboration was further enhanced when John became the Director
of the Royal Institution (RI) in 1986 and persuaded the RI to appoint me to a
part-time chair in Solid State Chemistry. The collaboration also survived my
move from Oxford to the University of California at Santa Barbara in 1991, and
continued actively until about 1996 when our interests began to diverge, John’s

13
14 Chapter 2
focusing more on practical catalysis and mine on hybrid and magnetic materials.
The friendship remained, however, and it therefore gives me great pleasure to
dedicate this chapter to John on the occasion of his 75th birthday.

2 Zeolite Science
Our collaboration on zeolites, like much of our later work, involved the com-
plementary use of more than one technique. In order to probe the nature of
silicon–aluminium ordering in zeolite-A, we used a combination of the Rietveld
method with another recently developed tool: magic angle spinning nuclear
magnetic resonance (MAS NMR). The application of 29Si MASNMR to alu-
minosilicate zeolites was pivotal in establishing the credibility of this new tool for
addressing problems in the chemistry of materials. Following closely on the heels
of the pioneering work of Lippmaa and his colleagues in Tallin on aluminosil-
icates, we were quickly able to show that the widely studied structure of zeolite-A
had some unexpected features. Our first paper showed that it could be rho-
mbohedral rather than cubic, depending upon the Si/Al ratio,1 while a second
paper suggested that the Si/Al ordering might be more complex than had hitherto
been thought.2 It turned out that we were misled by the 29Si chemical shifts,
which spanned a larger range than had previously been thought, but the error
was quickly rectified in a joint paper with J.V. Smith,3 and John and I went on to
publish our first joint paper in Nature in which we demonstrated the power of the
combined neutron and NMR approach to zeolites for the elucidation of not only
the Si,Al ordering but also the precise locations of the exchangeable cations in
zeolite Tl-A.4 One of the features of the Nature paper that captured people’s
imagination was the sheer size of the unit cell of zeolite-A, which, at almost
15,000 Å3, was the largest structure ever refined by the Rietveld method to that
date. Slightly later, we also published similar work on zeolites ZK-4 and Na-Y.5
The success of our neutron work on Si,Al ordering and cation positions in
zeolites led us to explore other applications of the Rietveld method in this area.
Given the widespread use of zeolites as acid catalysts for hydrocarbon cracking
and isomerization reactions, we attempted to use neutrons to establish the
precise locations of the active sites in zeolite La-Y, an important commercial
catalyst. This was very successful and led to a detailed description of the cation
hydrolysis reaction that results in the formation of acid sites in La-Y.6 At about
the same time (ca. 1983), the success of molecular modelling in addressing host–
guest interactions in the field of pharmaceutical chemistry inspired us to examine
what this approach might offer in the context of adsorbed molecules in zeolite
cavities. With the able assistance of Ramdas, who later joined British Petroleum,
and Paul Betteridge and Keith Davies from Oxford, we were immediately
rewarded with some beautiful results on the behaviour of the simple hydrocar-
bons in a number of zeolites.7 Our early work took full advantage of the
powerful advances in computer graphics for representing the van der Waals
surfaces of the cavities and channels in zeolites (Figure 1) and utilized contour
maps to visualize the potential energy surfaces for adsorbed molecules.
Multifaceted Studies of Zeolites and Other Catalytic Materials 15

Figure 1 A net representation of the van der Waals surface of the sinusoidal and linear
channels in zeolite ZSM-5.

Having demonstrated that the computer modelling was able to predict the
location and heat of adsorption of a guest molecule in a zeolite cavity, we
proceeded to combine the simulations with neutron diffraction studies in order to
test the reliability of the calculations. This proved to be successful beyond our
wildest dreams, leading to the elucidation of the location of xenon in zeolite rho,8
and a subsequent study of the location of a hydrocarbon (pyridine) in the channel
of zeolite K-L.9 The latter result (Figure 2), which relied on the complementary
skills of Paul Wright and Andreas Novak, appeared on the front cover of Nature
in December 1985 and greatly added to the credibility of computer modelling in
the field of zeolites. Indeed, for the first time chemists were able to talk in terms of
the precise location of an adsorbed molecule in a zeolitic cavity. If scientific
research can ever be thought of in terms of a golfing analogy, then the recollec-
tion of this publication is cherished like the memory of one’s first birdie!
The work on pyridine in zeolite-L was published just as John was preparing
to move from Cambridge to the Royal Institution, and the pace of our
collaboration slowed down for a time while we established the infrastructure
for materials chemistry and catalysis at the RI. In addition to establishing a
powerful capability for doing more sophisticated computer simulations, we also
benefited from the arrival of people who knew exactly how to take full
advantage of them. One such person was Yashonath, who had done a post-
doc with Mike Klein at Penn and was a specialist in Monte Carlo methods. He
quickly adapted his codes to handle our complex zeolite problems, and our
initial work resulted in a paper in Nature on ‘‘The siting, energetics and
mobility of saturated hydrocarbons inside zeolite cages’’ (Figure 3).10
16 Chapter 2

Figure 2 The location of pyridine in the channel of potassium zeolite-L. Note the
manner in which the lone-pair on the nitrogen (shown in yellow) interacts
with the potassium (shown in blue), while the molecule itself lies close to the
wall of the cavity.9

Yashonath helped to train others, too, paving the way for a series of simulation
papers on adsorbed species in zeolites,11–14 including some of the first molecular
dynamics studies of hydrocarbons in zeolites, which were done in collaboration
with colleagues at Shell in Amsterdam.15,16
One last note on our aluminosilicate collaboration should not be forgotten.
In 1988 Richard Catlow took up a part-time chair at the Royal Institution,
bringing further capabilities to the RI’s computational programme. This led,
among other things, to a joint 1990 paper in Advanced Materials that involved
the three of us. Together with Julian Gale and Rob Jackson, we had under-
taken the daunting task of simulating, for the first time, the behaviour of an
organically pillared clay. We chose the analinium–vermiculite system because
there was a reasonable crystal structure of this high charge-density material,
and we obtained remarkably good agreement between the experimental struc-
ture and the energy-minimized model.17

3 Aluminium Phosphates
Our joint work on aluminosilicate zeolites during the 1980s took place against a
background of increasing interest in aluminium phosphate (AlPO4) molecular
sieves, which were first reported by Edith Flanigen and her colleagues at Union
Multifaceted Studies of Zeolites and Other Catalytic Materials 17
18
Carbide in 1982. As the potential of these new materials in catalysis began to
emerge, our imagination was captured by a report that SAPO4-34, which
adopts the chabazite structure, could catalyze the conversion of methanol to
light olefins. This provided us with an opportunity to carry out a beautiful in
situ NMR study of this interesting coupling reaction. My student Clare Grey
took the lead, and we published a very nice paper in a new journal that John
had helped to launch, Catalysis Letters.19
The high level of interest in AlPO4s also inspired us to start some synthetic
work in the area using hydrothermal and solvothermal methods. I had some
experience in the synthesis and characterization of mixed metal oxides and
metal phosphates by conventional solid state reactions, but these lower tem-
perature methods were new to both of us. We pursued our joint effort at both
the RI and Oxford with Richard Jones and Anne Chippindale, respectively.
This work led to a series of papers20–23 during the period when I was in the
process of moving from Oxford to Santa Barbara. I was frankly rather
disappointed because we failed to make any new 3-D AlPO4 architectures at
the time, but rather made a series of 1-D chains and 2-D layered structures.
Although this demonstrated that the aluminium phosphates could exist in a full
range of dimensionalities, just as Pauling had shown for the aluminosilicates
many decades earlier, the materials had no real utility in terms of catalysis. The
disappointment has been mitigated over the years, however, because these four
papers have garnered around 100 citations apiece, reminding me once more
that we are not always the best judges of our own work. Furthermore, we did
subsequently succeed in making 3-D AlPO4 frameworks, both jointly24 and
independently.
The joint work on AlPO4s had one other exciting outcome. In the mid-1990s,
by means of a trans-Atlantic collaboration that involved not only my group
and John’s, but also Leo Marchese in Turin and Paul Wright in St. Andrews,
we published an exciting paper in Science25 on the interaction between protons
and water in a solid acid catalyst (H-SAPO-34). My student Luis Smith did the
neutron diffraction work, while Leo made measurements by infrared (IR)
spectroscopy. The results gave us a fairly complete description of the formation
of hydronium-type ions in the cavities, a result that stimulated a great deal of
subsequent theoretical work. Shortly afterwards, we published a paper on the
nature of the acid sites in dehydrated H-SAPO-34, again using the same
combination of IR spectroscopy and neutron diffraction.26

4 In situ Studies of Metal Oxides and Supported

Metal Catalysts
John and I began to collaborate on natural gas conversion shortly before I
moved to UCSB in 1991. The RI was then nicely equipped with an X-ray
diffraction/mass spectrometry facility for studying catalysts in situ under real-
istic reaction conditions, and we chose to look at the fate of an oxide pyro-
chlore, Eu2Ir2O7, during the conversion of methane to synthesis gas by partial
18 Chapter 2
27
oxidation. The results elegantly confirmed what we had already suspected,
which was that reduction by the methane caused the oxide to disproportionate
into Eu2O3 and particles of iridium metal; in essence, we had generated a
supported metal catalyst in situ. This experiment was followed by a similar
in situ experiment at the Daresbury synchrotron, where we studied natural gas
conversion by CO2 reforming over Ln2M2O7 pyrochlores (M ¼ Ru, Ir) by
energy dispersive X-ray diffraction (XRD).28 The use of the synchrotron source
gave much better time resolution and enabled us to study the kinetics, though
the diffraction resolution with the energy dispersive XRD approach was not as
good as with the constant wavelength method. Complementary studies by
temperature programmed reduction under methane, hydrogen, and carbon
monoxide revealed that the mechanisms with the ruthenates were subtly
different from those with the iridates, with the former showing clear evidence
for the formation of an intermediate perovskite phase during the reduction of
the pyrochlore.
As a side product of the work on supported ruthenium and iridium catalysts
for natural gas conversion, we became curious about the relative strengths of
different methods by which the sizes of small particles could be estimated.
Working with metal particles of diameter 2–3 nm, we undertook a comparative
study by X-ray powder diffraction (line broadening), extended X-ray absorp-
tion spectroscopy (EXAFS), and transmission electron microscopy.29 Pub-
lished in 1994, this work was about a decade ahead of its time and was unable

Figure 3 Probability density distribution of methane in sodium zeolite-Y from Monte

Carlo calculations at 0 K, 100 K, 170 K, and 298 K.
Multifaceted Studies of Zeolites and Other Catalytic Materials 19
to benefit from the visibility that it might have received in the modern era of
nanotechnology and nanomaterials.
During one of my summer visits to the RI in the early 1990s, we also carried
out an interesting in situ study of gel crystallization during the synthesis of the
perovskite PZT, PbZr1
xTixO3, which is an important commercial ferroelec-
tric.30 In addition to discovering a previously unsuspected intermediate fluorite
phase and establishing the kinetics of the crystallization, we also found that it
was possible to control the particle size and we were able to study the evolution
of particle size as a function of processing temperature and time. The inter-
pretation of this data was greatly enhanced by discussions with Jim Speck, one
of my colleagues in the Materials Department at UCSB, while the experimental
work at the RI benefited greatly from the efforts of ‘‘Raj’’ Natarajan, who
subsequently became one of my post-docs in Santa Barbara and is now on the
faculty at the Indian Institute of Science in Bangalore.

5 Conclusions
Sitting at home in Santa Barbara writing this short chapter for the book in
honour of John’s 75th birthday, I am struck by many thoughts and reflections.
First, our 15 years of close collaboration between 1981 and 1996 produced a
very impressive body of work, with over 30 publications averaging more than
50 citations apiece. It gives me particular satisfaction, even now, to look back at
the way in which we brought a number of complementary tools to bear on our
problems in a multifaceted manner. We also benefited from the creativity and
hard work of some outstanding co-workers, many of whom have been men-
tioned in the paragraphs above. I have several reasons to be grateful to John.
By working closely with him, I learned for the first time the distinction between
interesting problems and important problems, for John has an extraordinary
knack of spotting the latter. He also influenced the scope of my research in a
number of ways. For example, in the years since our joint work on alumino-
silicate zeolites, which led to about 18 papers, I have published around 70
further papers on zeolites in my own right. And although my interest in
phosphates pre-dates my collaboration with John, in the area of phosphate
molecular sieves, where we had a handful of joint papers, I have since published
about 50 more.
Our collaboration took other forms, too, of course. We organized meetings
together, such as the UK–Russia workshop on Heterogeneous Catalysis at
Oxford in 1987. We travelled to Gordon Conferences in New Hampshire
together, on one occasion being diverted to Montreal where we hired a car to
drive down to Plymouth, NH. And in cooperation with Millie Dresselhaus, we
jointly launched Current Opinions in Solid State and Materials Science in 1996.
Looking back on my own career, I can see that my research went into a higher
gear in about 1980 when our collaboration began. There is no way of knowing
if it would have done so in the absence of John’s influence, but I can certainly be
confident that my career would have followed a quite different trajectory and
20 Chapter 2
that he has had an enormous influence on my scientific interests and ambitions.
Happy birthday, John, and thank you!

References
1. J.M. Thomas, L.A. Bursill, E.A. Lodge, A.K. Cheetham and C.A. Fyfe,
J. Chem. Soc., Chem. Commun., 1981, 276.
2. L.A. Bursill, E.A. Lodge, J.M. Thomas and A.K. Cheetham, J. Phys.
Chem., 1981, 85, 2409.
3. A.K. Cheetham, C.A. Fyfe, J.V. Smith and J.M. Thomas, J. Chem. Soc.,
Chem. Commun., 1982, 823.
4. A.K. Cheetham, M.M. Eddy, D.A. Jefferson and J.M. Thomas, Nature,
1982, 299, 24.
5. A.K. Cheetham, M.M. Eddy, J. Klinowski and J.M. Thomas, J. Chem.
Soc., Chem. Commun., 1983, 23.
6. A.K. Cheetham, M.M. Eddy and J.M. Thomas, J. Chem. Soc., Chem.
Commun., 1984, 1337.
7. S. Ramdas, J.M. Thomas, P.W. Betteridge, A.K. Cheetham and
E.K. Davies, Angew. Chem., Int. Ed. Engl., 1984, 23, 671.
8. P.A. Wright, J.M. Thomas, S. Ramdas and A.K. Cheetham, J. Chem. Soc.,
Chem. Commun., 1984, 1338.
9. P.A. Wright, J.M. Thomas, A.K. Cheetham and A.K. Nowak, Nature,
1985, 318, 611.
10. S. Yashonath, J.M. Thomas, A.K. Nowak and A.K. Cheetham, Nature,
1988, 331, 601.
11. D.E. Akporiaye, S.D. Pickett, A.K. Nowak, J.M. Thomas and
A.K. Cheetham, Catal. Lett., 1988, 1, 133.
12. S.D. Pickett, A.K. Nowak, A.K. Cheetham and J.M. Thomas, Mol. Simul.,
1989, 2, 353.
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1989, 9, 123.
14. A.K. Cheetham, J.D. Gale, A.K. Nowak, B.K. Peterson, S.D. Pickett and
J.M. Thomas, Faraday Discuss. Chem. Soc., 1989, 87, 79.
15. S.D. Pickett, A.K. Nowak, J.M. Thomas, B.K. Peterson, J.F.P. Swift,
A.K. Cheetham, C.J.J. den Ouden, B. Smit and M.F.M. Post, J. Phys.
Chem., 1990, 94, 1233.
16. A.K. Nowak, C.J.J. den Ouden, S.D. Pickett, B. Smit, A.K. Cheetham,
M.F.M. Post and J.M. Thomas, J. Phys. Chem., 1991, 95, 848.
17. J.D. Gale, A.K. Cheetham, R.A. Jackson, C.R.A. Catlow and
J.M. Thomas, Adv. Mater., 1990, 2, 487.
18. S.T. Wilson, B.M. Lok, C.A. Messina, T.R. Cannan and E.M. Flanigen, J.
Am. Chem. Soc., 1982, 104, 1146.
19. Y. Xu, C.P. Grey, J.M. Thomas and A.K. Cheetham, Catal. Lett., 1990, 4,
251.
Multifaceted Studies of Zeolites and Other Catalytic Materials 21
20. R.H. Jones, J.M. Thomas, R. Xu, Q. Huo, Y. Xu, A.K. Cheetham and
D. Bieber, J. Chem. Soc., Chem. Commun., 1990, 1170.
21. R.H. Jones, J.M. Thomas, R. Xu, Q. Huo, A.K. Cheetham and
A.V. Powell, J. Chem. Soc., Chem. Commun., 1991, 1266.
22. A.M. Chippindale, A.V. Powell, L.M. Bull, R.H. Jones, A.K. Cheetham,
J.M. Thomas and R. Xu, J. Solid State Chem., 1992, 96, 199.
23. J.M. Thomas, R.H. Jones, R. Xu, J. Chen, A.M. Chippindale, S. Natarajan
and A.K. Cheetham, J. Chem. Soc., Chem. Commun., 1992, 929.
24. A.M. Chippindale, A.V. Powell, R.H. Jones, J.M. Thomas, A.K. Cheetham,
Q. Huo and R. Xu, Acta Crystallogr. Sect. C, 1994, C50, 1537.
25. L. Smith, L. Marchese, A.K. Cheetham, J.M. Thomas, P.A. Wright and
J. Chen, Science, 1996, 271, 799.
26. L. Smith, A.K. Cheetham, L. Marchese, J.M. Thomas, P.A. Wright,
J. Chen and E. Gianotti, Catal. Lett., 1996, 41, 13.
27. R.H. Jones, A.T. Ashcroft, D. Waller, A.K. Cheetham and J.M. Thomas,
Catal. Lett., 1991, 8, 169.
28. A.T. Ashcroft, A.K. Cheetham, R.H. Jones, S. Natarajan, J.M. Thomas,
D. Waller and S.M. Clark, J. Phys. Chem., 1993, 97, 3355.
29. A.T. Ashcroft, A.K. Cheetham, P.J.F. Harris, R.H. Jones, S. Natarajan,
G. Sankar, N.J. Stedman and J.M. Thomas, Catal. Lett., 1994, 24, 47.
30. A.P. Wilkinson, J.S. Speck, A.K. Cheetham, S. Natarajan and J.M. Thomas,
Chem. Mater., 1994, 6, 750.
CHAPTER 3

The Deductive Approach to

Chemistry, a Paradigm Shift
MARTIN JANSEN
Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, Stuttgart
D-70569, Germany

1 Introduction
Even today the pillars called analysis and synthesis still constitute the founda-
tion of chemistry. Taken in its general sense, analysis goes far beyond deter-
mining chemical compositions, and includes investigating static structures,
dynamic behaviour as well as all chemical or physical properties of matter,
regardless of whether they might suggest applications or not. Synthesis, on the
other hand, comprises all actions that lead to defined chemical compounds.
Taken in their etymological senses, these terms appear to be in opposition to
each other. In chemistry, however, analysis and synthesis go hand in hand, even
in a synergetic manner, thus keeping chemistry on the track of steady and
fascinating progress. Two key factors are triggering innovation in chemistry:
new methods in analysis, e.g. providing ever better spatial or energetic resolu-
tion in determining atomic or electronic structures, respectively, and in syn-
thesis by providing new (classes of) chemical compounds.
There are very few scientists that have contributed in an equally innovative
manner to both fields. The extremely fruitful efforts by John Meurig Thomas in
providing new (single site) heterogeneous catalysts,1 superior with respect to the
relevant figures of merit, many even successful in various applications,2 and in
understanding how they function, provide such an example. Furthermore, he
has employed computational chemistry3 as another tool to create a harmonic
and prolific triad, together with the analytical and synthetic experimental
counterparts. Opting for such a strategy has been the logical consequence of
the self-imposed tasks of developing heterogeneous catalysts for specific reac-
tions in a directed manner and of understanding the catalytic mechanisms on
the microscopic level. In order to meet the latter requirement, one has to
22
The Deductive Approach to Chemistry, a Paradigm Shift 23
consider the local reaction sites, which at best exhibit short-range order, as well
as the impact of the long range ordered matrix. The resulting challenge to
monitor these two features simultaneously, i.e. in exactly identical conditions
and at the same spot of the sample, has been ingeniously met by John Thomas
in combining diffraction, addressing the long range structure, and spectroscopy
as a local probe, in one experiment.4,5
Synthesis and analysis often do not appear to be of equal weight for the
chemist. The analytical tools rather serve synthesis, which is at the core of
chemistry. Synthesis is in the focus for economic reasons, reflecting the huge
share of world market volume as contributed by materials and drugs, for
understanding and replicating our physical surroundings, be it biological or
inorganic matter, and in particular for knowledge driven basic research,
pleasing human curiosity and contributing to human culture. Therefore it is
well understandable that control of synthesis has continued to be on the top of
the chemical agenda.

2 Chemical Synthesis, Setting the Stage

Although, in the chemist’s daily work, synthesis is meant to transform certain
starting materials to the desired product compound, in an ultimately puristic
sense, it starts from the elements. Thus the number of different elements
available, and the multiplicity of bonding options they offer, stake out the
territory for synthetic chemistry. That part of the universe accessible to human
perception consists of one and the same set of chemical elements, out of which
about 86 are stable and can be employed in chemical synthesis. From this
number, one limiting factor results immediately, that is the maximal
P number of
possible combinations of element types, which amounts to 86 86 86
n¼0 n Þ ¼ 2 .
ð
From Figure 1, and the inset, it follows that the resulting number of different
chemical systems, even when considering only subsets, is beyond the power of
our imagination.6 It is interesting to note to what little extent these systems
have been investigated, not to speak of being fully explored, so far. The answer
to the more important question of how many different compounds can be made,
using 86 stable elements, is most probably ‘‘innumerably infinite.’’ It is easy to
give the reader a feeling for whether this statement comes close to the truth or
not. One might follow Pòlya who generated, and was able to count, the
compounds in the binary system of alkanes including all possible isomers,
employing graph theory.7 As one can see from Figure 2, using just 24 carbon
atoms 14 506 015 different alkanes can be made! A similar scenario develops for
extended solids, because of the variability of periodicity, which is in principle
unlimited. As a consequence, binary SiC can form an infinite number of
stacking variants (polytypes). We regard this as inconceivable, yet this breath-
taking plethora of possible chemical compounds represents the true face of
chemistry, virtually defining its identity.6 From the numbers and examples
given, it is obvious that only a minute portion of the compounds possible, much
less than the tip of an iceberg, has been realized, so far. Admittedly, it is
24 Chapter 3

Figure 1 ‘‘Mountain of materials,’’6 number of element combinations calculated for a

set of up to 86 different elements; the inset displays the number of possible
systems containing one to four components (red), and the number of those
investigated (green).

definitely hard to perceive these numbers as ‘‘limiting’’; they rather indicate

superabundant opportunities for chemistry.
Of course, one has to keep in mind the hypothetical character of the above
combinatorial considerations. In exploring the chemical world physically, one
will sooner or later run into practically insurmountable barriers. One quite
obvious limitation results from the total mass of matter available in the universe.
However, this aspect would only establish a restriction if one wanted to exper-
imentally investigate all possible chemical systems simultaneously. Further
arguments against accessibility of high component systems claim that it is
impossible to force more than about seven different elements into a solid
compound, via conventional all-solid-state reaction routes.8,9 The intricacies to
be managed at running such reactions, in particular in a reproducible fashion, are
well recognized.10 As another approach for estimating the highest practically
achievable number of constitutional components of a compound, it has been
assumed that the limit is set by those observed in nature, or thus far synthetically
realized.11–13 This number is said to converge towards a limit of seven. However,
by just looking into some pertinent databases we have already found compounds
with up to 11 elements: Cs2K4((W3Te(Te2)3(CN)6)2Cl)Cl(H2O)5,14 C30H34AuB-
CIF3N6O2P2PtW,15 ((C5H5)Re(NO)(PPh3)(ICH2Si(CH3)3)BF4*CH2Cl2.16 Also,
the observation that the free enthalpy of formation of a compound, e.g. from the
constituting binaries, converges towards zero with an increase in the number of
The Deductive Approach to Chemistry, a Paradigm Shift 25

Figure 2 Results of a graph theoretical enumeration of possible alkanes.

its components, has been used as an argument lending support to the opinion
that compounds consisting of a high number of different elements would not
exist. However, we regard all these considerations as speculative, defining our
present capabilities rather than the potential opportunities. Those former con-
clusions definitely depend on the procedures applied for synthesis, or conditions
prevailing during genesis, e.g. of minerals in the Earth’s mantle. It is our
conviction that removing the barriers in solid state synthesis – most commonly
impeding transport of matter – by using modern techniques like atom-by-atom
deposition17 will open the access to 20 (and higher) component systems. Finally,
we do not see any justification for excluding solid solutions,8,11 when discussing
limits on the number of elements in a compound. These are regular manifesta-
tions of matter, playing an important role in earth sciences and in optimizing
specific properties by extrinsic doping.
But regardless of what the maximum possible number of constituent ele-
ments in a chemical compound precisely happens to be, our rough combina-
torial estimates, even if ignoring practical restrictions, certainly give a proper
impression of the general magnitude of the problem to be coped with in
synthetic chemistry. From the numbers discussed, the overwhelming size of the
tasks required to run syntheses in a rational and purposeful manner is quite
obvious, and, at the same time they document what wide areas of chemistry
have still remained unexplored. Finally, the enterprise of systematically and
rationally investigating this treasure will be of a complexity18 challenging and
even overpowering the information technologies19 presently available.
26 Chapter 3

3 The Inductive Approach to Chemistry

At the beginning of chemistry as a scientific discipline, the observations were
naturally rather incoherent, and also imprecise. Thus they were difficult to place
into a consistent rationale, and virtually the only option left was just to document
them, and subsequently with growing factual knowledge, to extract some
systematics. Applying this inductive approach20 to chemistry has proved to be
extremely successful. The early stage of discovery of the elements and the
formulation of the periodic system of the elements (PSE) might serve as an
example corroborating this view.21 Firstly, all kind of matter was scrutinized for
characteristics typically attributed to elements, without knowing any underlying
principle or even the number of elements to be expected. In the next step,
attempts were made to classify the elements known, with all their greatly varying
appearances, by correlating chemical or physical properties, e.g. with their
atomic masses. This was a rather arbitrary approach; however, these efforts
eventually resulted in establishing the PSE by D. Mendelejew and L. Meyer
which has constituted a tremendous breakthrough in chemistry. In particular, the
way Mendelejew utilized this arrangement right from the beginning has pointed
the way to modern chemistry. Only some decades later, the underlying principles
of this ordering scheme were unveiled.
Taking a look at various classes of compounds, e.g. oxides, fluorides or
intermetallics, and how the knowledge of them has been developing, demonstrates
the continuous success of the inductive strategy. The progress in the chemistry of
binary and ternary fluorides as documented in a series of reviews22–25 may serve as
an example.
It is important to understand why chemists have stuck to the inductive and
descriptive procedures for so long. Firstly, because it was obviously a successful
way to cope with the intriguing fact that the observations were made on a
macroscopic level while the underlying mechanisms went on at the atomic scale
(which in the beginning was not accessible with the available tools). More
importantly, chemists have been correctly convinced that confirmed experi-
mental observations, added to the growing stock of knowledge, will survive for
all times, while the interpretations and the models conceived will be subject to
change. Following the guideline of inductionism, a wealth of knowledge has
been accumulated, providing systematics based on composition, structural
principles, and reactivities. However, this approach has left the various classes
of compounds in quite different states of maturity and completeness.

4 The Energy Landscape Concept

In an attempt to unify all classes of chemical compounds, one may look for a
feature shared by all of them. As one such common feature we identify the basic
precondition for a compound to exist for a given period of time in a given
(equilibrium) geometry. This property is the so-called ‘‘local ergodicity.’’6,26–29
Quite obviously, there must be some gain in binding energy, as compared to the
The Deductive Approach to Chemistry, a Paradigm Shift 27
same ensemble of unbonded atoms, and moreover, the equilibrium geometry is
typically associated with a minimum in binding energy. Since this holds true for
each stable chemical compound, and since one can move from one minimum to
another by modifying the structures (isomers), or exchanging, adding or remov-
ing atoms, one easily arrives at the concept of a landscape of (binding)
energy,6,26–30 with the minima associated with stable configurations, cf. Figure 3.
This way of projecting all known as well as not yet known chemical
compounds onto an energy landscape is providing a sound concept for any
attempt to analyze chemistry, in particular the issue of synthesis, on a universal
foundation.6,26–30 As a particular strength of our concept, all classes of matter
are included on an equal footing, thus artificial trenches are removed, e.g.
between chemistry of molecular compounds and extended solids, or between
natural and synthetic matter. Furthermore, valuable insights into many impli-
cations of chemical synthesis can be extracted without any effort. In the past,
the question of whether a target compound would be stable was almost
exclusively evaluated based on thermodynamic considerations.31,32 However,
kinetic stability alone is already sufficient for a certain chemical structure to be
experimentally accessible.30 Since composition and structure of a stable con-
figuration (associated with a locally ergodic region on the energy landscape) are
predetermined by natural laws, neither composition nor structure can be
subject to any kind of arbitrary tuning or shaping by the chemist, and using
the term ‘‘design’’ in the context of developing targets for chemical synthesis is
definitely inappropriate.26 As an even more substantial consequence of this
view, chemistry can be approached in a deductive way by deriving the structure

Figure 3 Visualization of a section of a multiminima energy landscape, e.g. of

chemical matter.
28 Chapter 3
of the respective energy landscape from ‘‘first principles.’’ Finally, a clear
definition of chemistry is provided with almost mathematical stringency: doing
chemistry corresponds to exploring the energy landscape associated with
chemical matter, thus accumulating the stockpile of all substances capable of
existence.

5 Exploration of Chemical Energy Landscapes

The first step to be done in synthesis planning is to identify a target compound
that is either thermodynamically or at least kinetically stable. Conventionally,
this can be achieved by relying on intuition or experience, frequently extra-
polating confirmed knowledge, e.g. by assembling structural increments known
to represent stable topologies. By now, as a rather common procedure, such
‘‘raw’’ configurations that had been derived through heuristic concepts, are
subjected to geometry optimizations on a quantum mechanical basis,33–35 and
are thus tested for stability before starting the respective experiments. However,
such local approaches suffer from a lack of generality, might be misled by
prejudice and thus fail to identify all compounds possible in the system under
investigation. In particular, such attempts to predict structures and stabilities of
extended solids that might be encountered when entering a yet unexplored
system would go astray, as a rule. Dealing with intermetallics in this respect is
awfully frustrating. Some of these pitfalls can be addressed appropriately by
globally exploring the relevant (part of the) energy landscape, most favourably
based on ab initio quantum mechanical energy calculations.

5.1 Computational Approaches

In principle, the configurations and energies corresponding to the ground and
excited states of a chemical system can be calculated by solving the respective
Schrödinger equation. However, it is quite obvious that the number of particles
to be considered in trying to cover the full compositional and structural diversity
exhibited by an ensemble of atoms of realistic size makes such a straightforward
approach intractable, at least by the currently available tools. Instead, for the
exploration of landscapes of high complexities, like the energy landscapes of
chemical matter under discussion, performing stochastic walks guided by phys-
ical (e.g. energy based) or nonphysical cost functions have proved to be an
efficient strategy. A variety of well-developed algorithms serving this purpose
have become available, the most important approaches being based on Monte
Carlo techniques, genetic algorithms or neural networks. Using appropriate cost
functions, virtually each of them would, in principle, be suited for global searches
of chemical landscapes. In our implementation we have chosen the ‘‘Metropolis
Monte Carlo’’ variant of ‘‘simulated annealing.’’27–29,36,37 In a similar way,
genetic algorithms have been employed at predicting inorganic crystal struct-
ures.38 The specific features of our implementation have been determined both by
the basic objective of our efforts, i.e. predicting targets for chemical synthesis,
The Deductive Approach to Chemistry, a Paradigm Shift 29
and by technical feasibility, considering the performance of algorithms
and computer hardware presently available. In marked contrast to the tech-
niques previously employed in computational determinations of crystal structures
of already synthesized solids,39 we allow the translational lattices as well as the
compositions to be freely varied. These are indispensable requirements to make
sure that the whole landscape under inspection is accessible and the full com-
positional and structural variability is explored. A flowchart of our implemen-
tation is displayed in Figure 4. Regrettably, we have to resort to rather general
two body potentials for the energy calculations, during the global Metropolis
runs.27 This was on one hand forced by the necessity to keep the computational
effort needed for full explorations of systems of realistic sizes within bounds, and
on the other to introduce as little bias as possible into the random walks. For
instance we do not use empirical potentials, optimized for a given compound,
because this would give an undesired preference to this, or a closely related,
structure. The price to be paid is a certain restriction of our approach to polar

Figure 4 Flowchart for the modular approach to predicting chemical compounds

capable of existence. Upper part refers to the global search and preliminary
ranking procedures, lower part to local ab initio optimization of particular
structure candidates.
30 Chapter 3
(ionic) compounds, and some preference to the more polar ones among the
configurations in the system under investigation. Furthermore, quantitative
details of the structures generated, such as lattice constants and total energies,
are not very precise, on this level. However, for many examples, we have been
able to demonstrate that our approach is rather robust, also with respect to the
parameters used in the potential functions: in all systems explored, those com-
pounds already known from experiment have been reproduced in our search
runs, and all additional local minima discovered have stayed stable during
subsequent local optimizations, using ab initio methods.
As the result of the global explorations, assuming T ¼ 0 K and suppressing
the zero-point vibrations, a continuous hypersurface of potential energy as a
function of the underlying configurations is obtained (see Figure 5, top). If one
excludes quantum mechanical effects such as tunneling, all minima identified
would correspond to stable configurations. For extended solids, these energy
landscapes already give a rather realistic idea of the most stable compounds to

Figure 5 Schematic presentation of the continuous landscape of potential energy, as a

function of configuration space (top). Locally ergodic regions, at finite
temperature and with vibrations allowed, based on the same configuration
space indicated by blue basins (bottom).
The Deductive Approach to Chemistry, a Paradigm Shift 31
be encountered when investigating that system experimentally, since for solid
matter temperature dependence of the enthalpies of formation as well as
entropic contributions commonly are too small to let low lying minima disap-
pear, when switching to nonzero and somewhat elevated temperatures. One
should however keep in mind that entropically stabilized and nonperiodic
configurations will be missed: the first due to focusing only on the minima of
potential energy, the second due to using finite simulation cells. Beyond
employing our implementation at identifying compounds capable of existence,
our approach also offers the opportunity to explore the barrier structure40 of
the landscape of potential energy by applying ‘‘lid’’ or ‘‘threshold’’ tech-
niques,41–44 or to spot entropically stabilized regions.45 Also an estimate for
the transition probabilities between the minimum regions can be provided. In
Figure 6 the results of such an investigation are displayed as a tree graph,
including the low lying minima, the heights of the barriers between them, and
the number of states associated with the respective minimum.
In order to validate the results of the global searches based on ‘‘cheap’’
empirical potentials, and to refine the structures and energies obtained, ab initio
local optimizations are subsequently performed for the most promising structure
candidates. Using public domain Hartree–Fock and DFT codes, e.g. CRYSTAL-,
WIEN-, or VASP-programs, the lattice parameters and the positional parameters
are optimized in an iterative process (cf. Figure 4),46 and in order to get insights
into the pressure dependence of the total energies of the candidate structures, these
iterations are repeated for various fixed volumes. In Figure 7, the results of such
an investigation are displayed for Li2CO3.47 The improvements in precision as
achieved by switching to ab initio tools are significant; however, the overall
structure of the energy landscape reflecting chemical configurations capable of
existence remains virtually unchanged. Comparing the results obtained for the
lattice constants to the experimental data reveals the well-known bias of the

Figure 6 Schematic illustration of a section of the energy landscape of chemical

compounds, including a tree graph representation. M1–M3 are local minima,
L(1)–L(4) energy lids applied and the grey areas indicate by their sizes the
number of states associated with the respective minima within an energy slice.
32 Chapter 3

Figure 7 E(V) curves for predicted polymorphs of Li2CO3; the modification stable at
ambient pressure, and a recently discovered high-pressure polymorph, are
marked by (a) and (b) respectively.

methods employed. HF is overestimating, and DFT is partly underestimating the

absolute values of the lattice vectors (cf. Figure 8). In numerous instances, and in
many aspects, the predictive power of our implementation has been demonstrated.
To give an example, among the E(V) curves for the low energy polymorphic
structures of Li2CO347 (see Figure 7), the one corresponding to the experimentally
known modification (at standard conditions) occurs at lowest energy, and, in
addition, a predicted high pressure modification has been found independently in
a DAC experiment.48
Although our general approach has proven to meet the objective of predicting
targets for (solid state) synthesis in systems of realistic size, it is still lacking the
desired generality with respect to the types of chemical bonding addressed. This is
due to the type of potentials used for the energy calculations during the simulated
annealing searches. The obvious, and in the final analysis only, way to overcome
the present limitations is to resort to ab initio methods. Problems of a size typically
encountered in inorganic solid state chemistry comprise 4–8 formula units and
2–16 atoms per formula unit, resulting in about 50–150 atoms per unit cell.
Bearing in mind that one ‘‘simulated annealing’’ run commonly takes 105–107
total energy calculations until convergence, and about 1000 such runs are required
at minimum to get close to a complete set of structure candidates for a given
system, the computational resources required increase dramatically, by a factor of
100 per total energy calculation. One way, of course, to cope with the situation is
to employ the highest possible computing power and to utilize the most efficient
codes, e.g. parallel operating ones. If, in addition, the configuration space to be
The Deductive Approach to Chemistry, a Paradigm Shift 33

Figure 8 Calculated and experimental lattice constants for the lithium halides em-
ploying different (HF, DFT) ab initio methods.

searched is restricted to a small part of respective interest, global searches using

high level ab initio energy calculations are tractable, as has been shown recently
for the polymorphism of SiO249 and the high pressure modifications of CaCO3.50
In order to extend the scope of our tools, we have decided to stick to a two step
approach, and to use fast ab initio codes allowing for an exhaustive global
exploration of systems of real size, as far as possible, at an acceptable expense of
precision, and to perform subsequent local optimizations of selected structure
candidates on a high level of precision.51
In pursuing our objective of computationally exploring energy landscapes of
chemical compounds, the combinatorial complexity, as pointed out above, has
caught up with us. Global runs on a given system can easily end up with some
tens of thousands of structure candidates,52 which have to be scrutinized for
identical ones and for those already known from experiment. Such a daunting
and tedious task can hardly be done by hand. Therefore, we have developed
tools for an automated processing of the results.46 In order to avoid arbitrar-
iness or prejudice, either with regard to translational or to rotational symmetry,
no symmetry constraints are applied during the global exploration, and the
thousands of candidates need to be analyzed regarding possible symmetries.
Thus, in a first step, within given tolerances, a conventional unit cell and all
symmetry elements present in the structures are elaborated,53 which is followed
by an automatic determination of the space group.54 Finally, using a pattern
recognition algorithm which allows isostructures to be matched,55 even if they
are on a grossly different scale, independently of the functions of the
34 Chapter 3
constituting atoms, e.g. anionic or cationic, the file of predicted configurations
is searched for equivalent ones and the resulting unique set is compared to
databases of already known structures. Besides serving this purpose, the
pattern recognition algorithm55 is an invaluable tool in screening data files like
ICSD56 for related structures, and the structural ‘‘distance’’ between them.57

5.2 Explorations Based on Non-physical Criteria

Although it is clear that energy is the pivotal factor determining the structure of
the energy landscape of chemical compounds, and thus their capability to exist,
rather efficient non-physical tools have become available for reliably predicting
not yet synthesized configurations, in distinct areas of chemistry. These latter
approaches of anticipating structures rely on topological features that are
known to be stable from experience, and in principle, all concepts in use for
classifying structures in chemistry also have some predictive potential, or are at
least suited for validating predicted structures.6 The classical crystal chemical
rules as formulated by V.M. Goldschmidt58 continue to provide a sound basis
for anticipating extended inorganic structures, which may be best demonstrated
by the example of the perovskite family. L. Pauling’s ideas on bond-length/
bond-strength relationships59 have been further developed60 and have been
used as cost functions in computationally generating structures for prescribed
compositions and lattice constants.61 In a similar way, plausible structures can
be derived by considering symmetry, space filling62 and types of packings63,64 as
well as the restrictions imposed by the intrinsic properties of 3D, e.g. reflected
by the space groups65 and Wyckhoff positions66 possible. In the area of
intermetallic phases, the well established tools like structure field analysis,67
electron counts,68 and electronegativity (work function) balances69 are provid-
ing more general than specific, or practically useful, structural information. All
these heuristic approaches suffer from lack of generality and of predictive
power because they inherently tend to extrapolate existing knowledge. They
most probably will also fail in achieving completeness.
In some domains of chemistry, the inductive approach has led to an admirable
ability in predicting unknown configurations. In these latter fields, the technique
applied to deriving structures is based on linking rigid structural fragments. Such
strategies are farthest developed in organic chemistry, where the local stereo-
chemistries of the atom types commonly involved are perfectly known. Among
the earliest systematic applications at exhaustively predicting (enumerating)
members of families of compounds is the work by Pòlya who, in the example
of alkanes, even tackled this task by formulating it mathematically.7 In this
context, one might also refer to that part of Leonhard Euler’s work dealing with
convex polyhedra which has enabled scientists to immediately enumerate all
possible topologies of fullerenes,70 when they were discovered about two centuries
later. Such general lines of action also apply to molecular inorganic chemistry of
main group elements, however, with significantly less dependable outcomes.
The virtually infinite size of extended solids makes it much more intricate to
deal with them, based on the concept of structural increments. Historically, the
The Deductive Approach to Chemistry, a Paradigm Shift 35
building block approach was first applied to solid state structures by deriving
the familiar and rather consistent systematics of silicates.71–73 Here again, the
criteria of classification have been successfully employed for the purpose of
prediction. For silicates, graph theoretical74 as well as graphical procedures75
have been used in enumerating (part of) the plethora of connectivities possible,
using the SiO4-tetrahedron as a building block. In the light of the considera-
tions presented here, one notices the limitations of these systematics, since the
nearly infinite ability to mix-and-match such building blocks in ever-increasing
unit cells is overwhelming. Applying such approaches to coordination polymers
has furnished an impressive breakthrough.76,77 Selecting directionally fixed
connectivities between bidentate or tridentate linkers, of defined lengths, and a
central metal, has allowed correct prediction of open framework structures,
including the accessible porosities and the correct translational symmetries. In
some instances, the configuration space accessible has been restricted success-
fully, hardly leaving any path to escape to nondesired configurations, during
the experimental realization.78,79
As another tool in the category of non-energy based approaches for system-
atically generating crystal structures, mathematical enumeration techniques, like
graph theory, are continuing to attract attention.74,80–82 Recently, a procedure
for enumerating crystalline networks, based on mathematical tiling theory,83 has
been suggested.84 As a particular strength of this approach, the complete set of
topologies possible is generated, at the boundary conditions given, and recently
this procedure has been discussed in the context of enumerating possible
zeolites.85 However, mathematical tilings of 3D do not necessarily correspond
to stable chemical configurations. Moreover, they do not even show all exper-
imentally possible configurations because the necessary definition of boundary
conditions does not contain information on the chemical elements, which would
be substantial because most of them show an appreciable variability with respect
to chemical bonding, and thus local topology, among others also depending on
the partner elements involved. Thus, they do not behave as uniformly as one
would have to assume for a mathematically defined object.
Nevertheless, (mathematical) enumeration of possible topologies is of sig-
nificant momentousness in exploring chemical landscapes. Its usefulness
strongly depends on the respective system under consideration. For the
alkanes, Pòlya’s approach exactly reproduces all possible configurations,7
including isomers, and each individual representative corresponds to a mini-
mum on the energy landscape, at least at 0 K. (At this point, we pass over the
otherwise interesting question of to what extent representatives of high molar
weight might be experimentally accessible.) However, with decreasing uniform-
ity and rigidity of the stereochemistry of the chemical elements involved, the
dependability and predictive power of purely mathematical enumerations will
also decrease. Of course, topologies generated by enumeration, as well as those
derived along other heuristic concepts (see earlier citations), may serve as
valuable starting configurations for (local) computational relaxation, thus
checking their kinetic stabilities, and determining their energies of formation,
lattice constants, and further relevant physical data. Where applicable, such a
36 Chapter 3
procedure might speed up searches for synthetic targets. Random walks based
on energy as a cost function, on the other hand, may save time because the new
configurations obtained are already preselected with respect to energy and
kinetic stability. When choosing the route most efficient for the particular
purpose, one has to carefully weigh up the advantages and disadvantages of the
competing approaches, often having to balance available computing time with
accuracy and completeness of the result. The outcome would be strongly
dependent on the chemical systems under investigation, and it is quite obvious
that one would rarely invest the efforts of computational global optimization
in, for example, planning syntheses in organic chemistry.

5.3 Experimental Exploration

The procedure traditionally followed in searching chemical systems for the
stable compounds they host has been the experimental one by ‘‘trial and error,’’
based on some more or less rational concepts, which also constitutes the basis
of the inductive approach to chemistry. Although such a way of discovering
new materials has been rather successful in uncovering new compounds
featuring exciting structures, bonding schemes or properties, scientists in this
situation have always felt uncomfortable for the obvious lack of control and
understanding. However, from a pragmatic point of view, it clearly might
appear attractive to let the chemical systems of interest find their stable
configurations on the energy landscape on their own. This is the basic idea
underlying the ‘‘multisample concept,’’86 or in modern terms the ‘‘high-
throughput techniques.’’ Basically, all these strategies have in common a
parallel processing of many samples of different compositions. Presently, this
field of experimental materials research is in full blossom, and numerous
pertinent reviews have become available.87–89 In the context of this essay, it
is interesting to examine whether, and under what conditions, high-throughput
syntheses really meet the challenging requirement of being suited to exhaus-
tively exploring chemical landscapes. Taking YBa2Cu3O7
x, as an example, a
rough estimate6 immediately demonstrates that an intractable number of
B1080 (parallel) experiments would be needed to ensure that one encounters
the target compound as one of the products, if the unrestricted configuration
space of 86 stable elements were to be searched. Irrespective of the precision of
this estimate, it is obvious that the discovery of new materials cannot rely upon
high-throughput techniques alone. However, the multisample concept of
processing many starting material mixtures in parallel has proved its particular
strength in optimizing known functional materials, like phosphors90 or heter-
ogeneous catalysts,91 by applying a fine meshed grid of compositions.
For the purpose of selecting new materials with desired properties straight-
forwardly, the single-sample concept has been suggested as a new tool for
combinatorial chemistry.8,9,12,13 Here, multicomponent mixtures of solids are
subjected to reactions at high temperature, and the products obtained are
directly screened, with respect to a predefined property like ferromagnetism or
superconductivity, utilizing the same property for the separation of the
The Deductive Approach to Chemistry, a Paradigm Shift 37
functional material from undesired by-products. However, there are some
doubts as to whether the full chemical variability can be explored along such
a route because the macroscopic grain sizes and the normally low diffusion
coefficients of cations in oxides, for example, will most probably impede all
compositions to be realized.

6 Relating ‘‘Configurational’’ and ‘‘Thermodynamic’’

Spaces
The energy landscape of chemical compounds as discussed thus far is based on
atomic configurations, defined by the types and numbers of atoms involved,
and their positional vectors.27–29 The behaviour of real chemical systems,
however, is controlled by the thermodynamic variables of state, i.e. by the
pressure (volume) and temperature conditions applied, and the concentrations
of the constituent elements. In the case of (global) thermodynamic equilibrium,
setting these variables to certain values uniquely fixes the state of the system
under consideration, i.e. its complete phase content. One should recall that
structural information is neither needed for, nor extractable from, such a
description. Furthermore, global equilibrium implies that we are considering
essentially infinitely long timescales. Since it is our declared goal to provide
generally applicable tools allowing for directed chemical syntheses, we can not
restrict our considerations to thermodynamically stable entities only, but have
to include kinetically stable states of matter that are thermodynamically
metastable on finite timescales as well. The equilibrium states are commonly
documented in phase diagrams that represent projections onto the space of the
thermodynamic variables of state of those parts of the (hyper)spaces of free
enthalpy attributed to locally ergodic minimum regions of a given system that
represent equilibrium states, at respective p, T, xi conditions (cf. Figure 9).
Including metastable states requires us to consider the full (hyper)spaces of free
enthalpy for all the phases in a chemical system that are kinetically stable. In
principle, the latter can be derived from the configuration space6 by determin-
ing all regions on the energy landscape that are locally ergodic on the timescale
tobs, for temperature T.28 In particular, this means that lattice vibrations
including zero point vibrations need to be taken into account. The lattice
vibrations will sample all configurations within the amplitudes of vibration,
thus generating an ensemble of configurations among which the system fluc-
tuates, depending on the conditions given. Raising the temperature would
enable transport and thus structural transformations to take place, and all
configurations that are not kinetically stable will decay. As a result, we
encounter discrete, locally ergodic minimum regions comprising a larger
number of configurations constituting states that are all populated at the
thermodynamic boundary conditions given (cf. Figure 5). Such regions can
encompass one or many local minima; they represent a macroscopic thermo-
dynamic ensemble, the state functions of which can be calculated according to
the prescriptions of statistical thermodynamics. If applied to crystalline solids,
38 Chapter 3

Figure 9 Three component phase diagram at constant temperature and pressure,

displaying surfaces of free enthalpies for three different locally ergodic
regions. In blue: solid solution A/B/C, red: melt A/B/C, green: surface of
free enthalpy for a metastable solid solution.

deriving the free enthalpy associated with a locally ergodic region, starting from
the potential energy (Epot), requires only a few, nevertheless intriguing, steps.
To the enthalpy, H ¼ Epot+pV, the entropy terms have to be added. In this
case, these are basically due to the phonon densities of states, and the config-
urational contributions, if many local minima contribute to the locally ergodic
regions. By evaluating these quantities for various temperatures and pressures,
the surface of free enthalpy can be scanned as a function of the thermodynamic
variables for a given locally ergodic region of the energy landscape that can be
associated with a prototype (ideal) structure.6
A given chemical system will exhibit many different locally ergodic regions, one
of them representing the global minimum of the free enthalpy. Two borderline
types of behaviour may be considered. For very long observation times, all locally
ergodic regions will merge into a globally ergodic region, and thermodynamic
equilibrium will be reached. At the opposite extreme, all configurations associated
with local minima are assumed to survive for the time of observation, thus
constituting metastable states. For the latter scenario, it is possible to determine
the free enthalpies associated with locally ergodic regions R as a function of
p, T, xi, and thus phase diagrams including metastable states of matter can
be constructed. Of course, now the full function GR(p,T,xi) (i ¼ 1
n) restricted
to such a region R needs to be considered, and the elegant way of densely
The Deductive Approach to Chemistry, a Paradigm Shift 39
displaying the information on equilibrium states by projecting G onto the
subspace of the variables p, T, xi (i ¼ 1
n) is no longer viable. It should be noted
that, as a highly welcome ‘‘spin-off’’, all relevant thermodynamic entities like
enthalpies, entropies, and specific heats are supplied.
The thermodynamic data generated along this procedure provide a sound
basis for predicting and assessing the (meta)stability of targets for chemical
synthesis. Moreover, they are suited to complement and validate the conven-
tional phase diagrams. Thus far, the various thermodynamic details known for
a given system are fitted together using the elegant CALPHAD approach,92,93
which, however, only affords interpolation and consistency checks of the
experimental data. A missing thermodynamically stable compound inevitably
leads to a seriously wrong phase diagram. Here, implementing data from
computational chemistry, accessible as described above, would improve the
reliability significantly.
In special cases, the construction of yet unexplored, or experimentally
inaccessible, regions of the phase diagrams has turned out to be rather
straightforward, employing our approach.97–99 For most of the ternary com-
binations of the alkali halides, AX/A 0 X, the high temperature regions of the
phase diagrams are well investigated while the low temperature parts have
proven to be experimentally inaccessible, due to slow kinetics. Here one might
encounter miscibility gaps or stable and metastable, respectively, ordered
crystalline compounds. Since the contributions from the phonon densities of
state to the entropy of reaction between two very much related alkali metal
halides, e.g. NaCl and LiCl, can be neglected to first order,97 the configura-
tional entropy constitutes the essential contribution that determines whether a
solid solution or an ordered compound is thermodynamically stable. The task
has been tackled by first exploring the landscape of the ternary systems AX/
A 0 X globally. The resulting configurations are then examined and attributed to
locally ergodic regions, according to their potential energies. Some of these
minimum regions represent thermodynamically stable or metastable individual
ternary structures, others constitute representative configurations of solid
solutions. For the latter, the enthalpies of formation have been calculated,
using various supercell descriptions. Finally, as the only contribution to the
entropy of reaction, the configurational entropy is computed, and the free
enthalpies of the various ordered compounds and solid solutions are obtained.
The approach and the results are illustrated in Figures 10 and 11, for two
exemplary cases. As one can see, quite reasonable results have been achieved,
without using any input from experiment. For NaCl/LiCl, the miscibility gap is
modeled properly, also meeting the two experimental points, while for CsI/LiI
as another realistic scenario, metastable and stable ternary structures prevail.

7 Exploring Routes of Synthesis

For the second of the two steps minimally required to enable directed chemical
synthesis, one has to provide synthetic procedures that would allow approaching
40 Chapter 3

Figure 10 Procedure followed in predicting phase diagrams. Global search for struct-
ure candidates (top), calculation of DHf based on the supercell approach
(middle), and free enthalpies calculated for three temperatures (bottom).
The Deductive Approach to Chemistry, a Paradigm Shift 41

Figure 11 Phase diagrams for quasi-binary systems NaCl–LiCl (top) and CsI–LiI
(bottom), solidus/liquidus parts from experimental data, treated by the
CALPHAD approach, low temperature parts predicted by the procedure
displayed in Figure 10.

the target of synthesis, as selected from the pool of configurations capable of

existence.6 Such processes are dynamic in nature, and time as well as temperature
play a crucial role. Therefore, one can no longer resort to virtual spaces and
hypothetical boundary conditions. Instead, appropriate paths of synthesis can only
42 Chapter 3
be identified on the landscape of free enthalpy associated with all starting material
phases, all possible intermediates and the reaction products, including the targeted
compound as well as the competing alternatives. In principle, such paths will
become available as a spin-off when establishing the landscapes of free enthalpy
through global exploration of the energy landscape of chemical systems. However,
it is quite obvious that such an enterprise would create a new dimension of
complexity, which will probably not be overcome in the near future.
Also, in this respect of identifying viable routes allowing for rationally
addressing a specific synthetic task, the various fields of chemistry differ
conspicuously in maturity. In particular, in organic chemistry, and some related
areas of molecular chemistry, one has arrived at almost full control. Typically,
the regio-, topo- or enantioselectivities are achieved by functionalizing the
starting material molecule, thus introducing reactive sites in an otherwise inert
backbone, and allowing one to run the reactions under kinetic control.
Although topotactic reactions can be regarded as conceptual counterparts in
solid state chemistry, those approaches of molecular chemistry do not apply to
the synthesis of extended solids. Here, only in some very limited circumstances
can one synthesize a targeted solid compound quite straightforwardly. If one
restricts the configuration space and the thermodynamic variables of state
accordingly, one might encounter a situation where the target compound is
thermodynamically stable, and, according to Gibbs’ phase rule, the only
condensed phase that would survive. In this instance, it is sufficient to provide
(thermal) activation in order to allow the reaction to proceed to the desired
(thermodynamically stable) product. In instances where also the reaction
proceeds in thermodynamic equilibrium, the underlying mechanisms, e.g.
interdiffusion, chemical transport or crystallization from a molten mixture of
starting materials, have been successfully modeled. However, such a strategy
would not apply to the synthesis of metastable compounds. The only way to
purposefully enter a particular locally ergodic region of the energy landscape is
to generate supercritical nuclei of the desired compound, and to let them grow.
As judged by its general validity and applicability, this latter stratagem con-
stitutes the counterpart of the control of molecular synthesis by deliberate
functionalization. The intriguing processes involved in nucleation100 across the
relevant time and length scales, however, will be extremely hard to master: from
gaseous, liquid or solid feedstocks of the starting materials, nuclei form while
passing through ill defined dynamic states of preorganization and subcritical
ensembles. In particular, coping with the population dynamics101 of all the
intermediate states involved constitutes a real challenge for computational
chemistry, and, in the next step, also for experiment. As another complication,
the supercritical nuclei may undergo structural phase transitions while growing.
It is quite obvious that gaining rational control of the structure directing steps
of nucleation and growth is a task ahead of us of herculean dimensions. What
can be done right now, is neither sufficient nor satisfying. One might follow the
ideas of W. Ostwald and M. Vollmer concerning the preferred nucleation of
metastable compounds from supersaturated feedstocks,17,102–104 or one could
vary the external boundary conditions (temperature, pressure or degree of
The Deductive Approach to Chemistry, a Paradigm Shift 43
supersaturation) during nucleation. Such measures would allow the outcomes
of the experiments to be influenced, but cannot be regarded as tools of control.
Approaches presently within reach are based on seeding, either homogeneously
or heterogeneously. In particular, heterogeneous seeding appears to be prom-
ising. For a target compound predicted to be metastable, one could inspect the
low indexed and most densely occupied lattice planes and look for known
crystalline compounds displaying a lattice plane that matches one of those of
the target compound, with respect to lattice spacings as well as polarities.6,105
If such a compound has been identified, the target compound could be
synthesized by epitaxial growth (heterogeneous nucleation), and the material
obtained could be harvested and used in further experiments for homogeneous
seeding.

8 The Deductive Approach to Discovery of Materials

Exhibiting Desired Properties
The impetus of chemical synthesis is nourished from two principally different
sources. On one hand, there is the academic world, striving for gain in
knowledge, on the other the industrial one, interested in creating competitive
products of high added value. Therefore, it is well understandable that, driven
by the prospects of potential industrial applications, there has always been a
strong demand for high efficiency in improving known and discovering new
materials. Being able to intentionally generate new materials with predefined
properties seems to be a particularly strong desire, as indicated by the wordings
‘‘tailoring’’ or ‘‘designing’’ materials or drugs, frequently used in this context.
However, as explained in the previous chapters, all chemical configurations
capable of existence are predetermined by natural laws, with respect to all
structural details and to their properties, as well. Thus, the only action that can
be taken by the chemist or materials scientist is to discover a material or to
search a chemical system for useful materials. This can be done experimentally
or computationally. Inevitably, the invention of any new material proceeds
through the discovery of at least a metastable compound, which can be
examined for certain properties in a subsequent step. Thus, what we call the
‘‘rational’’ or ‘‘deductive’’ approach to materials discovery proceeds in a one-
way fashion, from identifying a (meta)stable compound to its properties.106
Here, we restrict ourselves to addressing computationally assisted materials
discovery (see Figure 12). The first part is related to predicting structures and
stabilities of new solids by the procedures that have been extensively discussed
in Chapter 11. Next, based on the structures identified, all relevant properties
can in principle be calculated or at least estimated.107 It has to be admitted,
however, that the accuracy currently achievable varies for different properties,
and in certain cases, like superconductivity, the respective property cannot be
predicted at all, up to now. Of course, this fundamental scheme need not be
followed step by step. Instead, one might take short cuts, and, for instance,
44 Chapter 3

Figure 12 Rational approach to materials synthesis (flowchart).

directly use the raw configurations, as obtained from the global search, for
property screening. As another way of accelerating the process of realizing a
specific property, the desired score has been included next to energy as a second
rank cost-function during the random search of a selected configurational
space.108 However, we regard dropping stable compounds, just because they
lack the desired property, an unfortunate step. We rather prefer to collect all
stable configurations and to add them to the thesaurus of chemical compounds.
This would feature the advantage of having the configurations available at
screening for another property that might become relevant at a later time.
This approach as outlined above is rather fundamentalistic, and structured
for long term and general issues. In many instances there is some pressure on
developing a material with a certain property profile, within a time limit. The
directedness needed might be achieved by resorting to analogies, data mining or
optimizing known systems.

9 The Quintessence
Representing the multitude of all known and still unknown chemical compounds
on an energy landscape points the way to a deductive treatment of chemistry,
quite in contrast to the inductive approach thus far preferably followed in this
discipline. A rather simple scenario results if one resorts to the hypothetical
conditions of T ¼ 0 K, and the zero-point vibrations suppressed. Then for each
imaginable configuration the energy can be calculated. The resulting continuous
(hyper)surface of potential energy is directly related to the configuration space,
and each minimum of the landscape corresponds to a stable configuration at
T ¼ 0 K, and vice versa. Admitting finite temperature and pressure, i.e. under
The Deductive Approach to Chemistry, a Paradigm Shift 45
realistic conditions, for a given observation time all unstable configurations will
decay, while the (meta)stable ones constitute locally ergodic regions, correspond-
ing to a particular macroscopic thermodynamic state. Depending on the ther-
modynamic boundary conditions applied, one of these regions corresponds to
the thermodynamically stable state of the system under consideration, while the
(numerous) remaining minimum regions represent metastable ones, exhibiting a
wide spread of life times. Applying the procedures of statistical thermo-
dynamics, free enthalpies for each locally ergodic region can, in principle, be
derived, and phase diagrams including metastable states can be constructed.
Such physically realistic energy landscapes, exhibiting numerous locally
ergodic regions, offer a firm foundation for dealing with virtually all aspects
of chemistry, on a rational basis. Since the sufficient and necessary precondition
for any chemical compound to exist is that it belongs to a locally ergodic region,
without any exception all manifestations of chemical matter are covered, and
consequently the diverse fields of preparative chemistry are unified and can be
dealt with on a comparable footing. The versatility of the energy landscape
concept is becoming immediately obvious, when comparing the tools developed
for its exploration. Ranking them according to the degree of control they
provide, and the correctness of the underlying principles, one would mention,
in ascending order, (1) experimental exploration by trial-and-error, (2) exper-
imental exploration based on analogies and other heuristic concepts, (3)
structure prediction based on crystal chemical rules, (4) local computational
optimization of starting configurations as derived by analogy and other
empirical knowledge, (5) computational structure determination of already
synthesized compounds, utilizing experimental input (e.g. lattice constants or
composition), (6) global optimization using non-physical cost functions, (7)
structure prediction by mathematical enumeration and tiling, (8) global opti-
mization with empirical energy as the only cost function, and (9) global
optimization at the ab initio level. Each of these general approaches has its
own justification. To which one a scientist gives preference, he will decide
guided by pragmatism. To give two examples, an unexplored intermetallic
system would probably be approached experimentally by systematically scan-
ning a certain field of parameters, while for oxoborates one would prefer using
enumeration techniques relying on trigonal-planar or tetrahedral building
blocks. However, all concepts that do not rely on the correct physical descrip-
tion using energy as the only parameter of control, principally suffer from bias,
in various respects. On the other hand, the serious weak spot of a fully physical
description is also quite obvious; it is the giant complexity of the chemical
world that cannot be coped with satisfactorily, at least using the tools currently
available. However, the energy landscape of chemical matter inherently offers
two ways of reducing complexity. Firstly, the minima develop a hierarchy with
respect to stability. The low lying ones, if also surrounded by high barriers, will
be discovered first, experimentally as well as computationally, while the less
stable, shallow minima will be much more intricate to explore. This will
constitute a big challenge for future work in improving the respective theoret-
ical and experimental tools. Secondly, the configuration space can be easily
46 Chapter 3
divided into subspaces of interest. However, even for an elemental or binary
system, its full exploration with high accuracy would embody a tremendous
effort.
It is our conviction that the concept of the energy landscape of chemical
matter, based on a correct physical description and thus pointing the way
towards treating chemistry deductively, will be the most sustainable approach
to successfully address the issue of synthesis planning.

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The Deductive Approach to Chemistry, a Paradigm Shift 49
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CHAPTER 4

Future Energy Materials:

Three Challenges for Materials
Chemistry
PETER P. EDWARDS AND VLADIMIR L. KUZNETSOV
Inorganic Chemistry Laboratory, University of Oxford, South Parks Road,
Oxford, OX1 3QR, UK

1 Prologue: Personal Perspective by P.P. Edwards

I first met Professor John Meurig Thomas on Wednesday, 4th of July 1979,
shortly after I arrived at the University Chemical Laboratories at Cambridge.
I had recently been appointed to a University Demonstratorship in Inorganic
Chemistry by Professor Jack Lewis, whose support in offering me that position
enabled my first step towards an academic career. I still vividly remember that
first meeting. John instantly relayed to me his admiration for my research
activities at Cornell; indeed, such was the high level of glowing praise in the first
few minutes that the thought did cross my mind as to whether he had gotten
this Edwards mixed up with another Edwards – the highly distinguished
physicist, Professor Sam F. Edwards of the Cavendish Laboratory! But no,
John was indeed talking of ‘‘Edwards the Chemist’’ as he recounted my
research on metal–ammonia solutions and the metal–insulator transition.
I feel sure that this snapshot of my own first experiences with John will draw
resonances with all colleagues in this volume, for that episode reflects one of
his most endearing gifts; namely, his extraordinary, natural ability to make
one feel that one’s own research is unquestionably the most outstanding in the
field (even though he may be a participant himself in that field!). To simply
label this as a gift does not do justice to John’s munificence in that regard – this
is a gift honed by his prodigious memory, given credence by his vast command
of the scientific literature and, above all, it reflects his genuine desire to support
and encourage others. And such praise, delivered always with a command of

51
52 Chapter 4
the English language second-to-none, and this ‘‘despite English being his
second language’’! (Professor A.D. Buckingham, this volume).
So began our long friendship and fruitful association in many areas of
research. Our initial collaborations in the early 1980s centred on the study of
alkali metal clusters incarcerated within zeolite hosts.1–3 We were both united in
our zeal for what at the time we termed condensed matter chemistry, and we had
both been touched by the deep insights and enthusiasms of members of the Baker
Laboratory, Cornell University where we had, at different times, worked earlier.
In the early 1980s John and colleagues had achieved a series of break-
throughs in the real-space imaging of zeolites by high resolution electron
microscopy, coupled with their major advances in the structural elucidation
of this important class of solids.1
My own interests centred primarily on the nature of the metal–insulator
transition,4 divided metals and excess electrons in metal solutions. Coupled
with the arrival in Cambridge of an advanced Electron Spin Resonance (ESR)
spectrometer (another development which linked us to colleagues at Cornell)
we were ideally placed to examine the intriguing reports in the literature
concerning alkali metal ion clusters, e.g. Na431 effectively trapped within the
intrazeolite cavities. There collaborative studies led to the discovery of a large
family of ionic clusters – both paramagnetic and diamagnetic – and a model
which united the ‘‘dissolution’’ of alkali metals in both liquid polar solvents,
and dehydrated zeolites.1
In Figure 1 we show a schematic representation of the ionic Na431 and the
hypothetical Na8 neutral cluster, within zeolite Y, with the accompanying
colour changes (white - pink - blue) as more and more alkali metal is
‘‘dissolved’’ within the zeolite (in essence, a solid solvent).
John has also always been closely involved with the development of what we
now term materials chemistry and we take the opportunity here to offer some
personal reflections on the evolution of the subject and its importance and
impact in the field of energy materials.

2 Materials Chemistry: Awakening

During the past two decades, materials chemistry has attracted worldwide
interest as a new and important discipline,6 reflecting the confluence of the
streams of chemistry, materials science, physics and engineering. (The interface
between chemistry, biology and materials science has meant that much has now
been learnt from the principles of structure–function relation in mineralised
biological materials; for brevity this interfacial area is not covered here.)
The emergence of the subject has resulted from the gradual evolution of
chemistry in materials science,6c,7 most notably by the development of modern
high technologies. However, the discovery of totally new and unexpected
materials and physical phenomena have signalled a step-change in the develop-
ment of, and attitudes to, materials chemistry. No more so, in our view, than
the discovery of high-temperature superconductivity in ceramic cuprates.8
Future Energy Materials: Three Challenges for Materials Chemistry 53

Figure 1 Schematic representation of the formation of the alkali clusters Na431 and
Na8 located within the alpha and supercages of Na1-zeolite Y. Samples are
also shown of dehydrated zeolite Y, with increasing sodium (metal) con-
centration. Taken from Emsley and Edwards.5

So it was in 1986 with the breathtaking discovery8 by J.G. Bednorz and

K.A. Müller of high-temperature superconductivity in the La–Ba–Cu–O
system – surely one of the greatest ever scientific discoveries. It is interesting
to reflect here on the impact of this particular discovery on the development of
materials chemistry. From its genesis in 1911 up to 1987, superconductivity was
not a property of interest to the vast majority of solid-state chemists. Materials
exhibiting this remarkable natural phenomenon were deemed to be in the realm
of physicists, materials scientists and engineers. In addition the theory of
superconductivity was invariably couched in terms of wave vectors, phonons,
reciprocal space, etc.; chemists, of course, are much more at home in ‘‘real-
space’’ models, rather than those required in reciprocal or momentum space!9
Bednorz and Müller’s epoch-making advance changed all this; the phenom-
enon of superconductivity now truly entered the field of chemistry in a dramatic
and unexpected fashion. In our view this was a pivotal event in the true
dawning of the field of materials chemistry. For only through a detailed
knowledge of the science of preparative solid state chemistry could pure,
single-phase materials be synthesised and studied in a definitive fashion. Thus,
54 Chapter 4
the use (and development) of sol–gel routes, chimie douce chemistry, electro-
chemistry, microwave chemistry, combustion or self-propagating methods, have
been employed in the quest for pure, single-phase superconducting materials.
Here, chemists made substantial and often unique contributions to the develop-
ment of the subject. However, parenthetically, one must note that by far the vast
majority of new oxide superconductors were discovered by solid state physicists
(with a most notable exception being the mercurocuprate superconductors).10
One of the many quite unexpected and remarkable features to emerge from
the discovery of ‘‘High Tc’’ materials is the apparent degree of chemical
complexity at first presented by these compounds – for example the highest
Tc oxide11 HgBa2Ca2Cu3O71d is synthesized12 from four constituent oxides!
Equally unexpected was the unprecedented degree of ‘‘chemical control’’ of
High Tc now extant13 – as exemplified by the so-called septenary cuprates
(Tl1
yPby)Sr2(Ca1
xYx)Cu2O7. In Figure 2 we show the composition depend-
ence of Tc in the septenary cuprates, where small changes in chemical compo-
sition can transform an antiferromagnetic insulator to a high-temperature
superconductor (Tc Z 100 K), to a metallic, but non-superconducting oxide.
It is important to stress also that these complex septenary phases can be

Figure 2 The chemical control of high-temperature superconductivity. The tempera-

ture and composition dependence of the superconducting transition tem-
perature in the (Tl1
yPby)Sr2(Ca1
xYx)Cu2O7 septenary system. Original
data from Liu et al.13a redrawn by W.Y. Liang (Cavendish Laboratory).
Future Energy Materials: Three Challenges for Materials Chemistry 55
synthesised as phase pure materials across the entire 3-D compositional range
of chemical stoichiometry.13 And all of this against the backdrop of the absence
(even today) of a universally accepted theory of the phenomenon of high-
temperature superconductivity.8,14 One should perhaps draw an analogy here
with the great traditions of chemistry exploring the far reaches of the Periodic
Table – prior to the advent of any accepted atomic theory of the chemical
elements.
Another development, highlighted by J.M. Thomas,1 has been the possibility
of major advances catalysed by new (or improved) instrumentation, noting
‘‘the growth of chemistry depends at least as much on the availability of tools
and techniques as it does on concepts and theories’’. The High-Tc era surely
was pivotal in the realisation of the importance of determining structure in real
space – by electron microscopy – and not only in reciprocal space by electron
diffraction. Importantly, J.M. Thomas had earlier laid the foundations for
these advances by significant breakthroughs in the real-space imaging of
zeolites by high-resolution electron microscopy. An interesting example of this
approach in the field of superconductivity is given in Figure 3 which shows the
result of a high resolution electron microscopy (HREM) investigation and
model image simulation of the High-Tc superconductor Bi21xSr2Ca1
x
Cu2O81d; the recorded HREM image is the tip of a crystal just one lattice
vector wide, clearly showing in cross section the metal layers in the order (Bi–
Sr–Cu–Ca–Cu–Sr–Bi).15 These two examples drawn from our own contribu-
tions to the field of High-Tc hopefully reveal just how closely chemistry from

Figure 3 HREM image of the tip of one crystal a single c-lattice vector wide together
with a calculated image (left) and derived crystal structure inset. The image
clearly shows in cross section the metal layers in the order (Bi–Sr–Cu–Ca–
Cu–Sr–Bi); from W. Zhou et al.15
56 Chapter 4
1987 became woven into the science of materials – we would propose that this is
an object lesson in the development of materials chemistry.

3 Materials Chemistry: Intellectual Foundation

of the Field
Over the past 20 years the intellectual foundation of the field we now recognise
as materials chemistry has begun to take shape and the area has achieved
international recognition as a forefront area of modern science. C.N.R.
Rao6d,16 has defined the subject as follows:
‘‘materials chemistry deals with structure, response and function and has
the ultimate purpose of developing novel materials or understanding
structure/property relations and phenomena related to a wide range of
materials. Structure and synthesis are integral parts of the subject, and
they are fully utilised in the strategies for tailor-making materials with
desired and controlled properties. What distinguishes the subject from
pure solid state chemistry is the ultimate materials objective’’.
As noted in Section 2, the origin of materials chemistry results from the
evolution of chemistry in materials science, catalysed by the discoveries and
advances in High-Tc superconductors and other materials (e.g. C60 – Buckmins-
terfullerene) and the development of modern techniques and technologies.
The broad field of materials chemistry has been routinely defined around the
understanding and control of three basic elements:

1. The structure and composition of materials, encompassing the constituent

chemical elements and their atomic arrangements over a wide range of
length scales.
2. The synthesis of materials; the process by which the particular arrange-
ment of atoms in the material is achieved.
3. The properties of materials; be they electronic, magnetic, optical,
dielectric, thermal, adsorptive or catalytic.
In our view – the basic theme of this commentary – we now add to this list
another critically important element in the make up of the developing
field, namely;
4. The performance of materials.

These four elements hold close similarities with the now-established bench-
mark definition of materials science itself.7 This is a clear reflection of the fact
that chemists, materials scientists and physicists are beginning to be drawn
into a healthy mutual alliance centred around the science and technology of
materials. But what distinguishes materials chemistry from its sister multi-
disciplines is the fact that the basis of materials chemistry of course has its roots
in the chemistry of the elements – we label this here as The Periodic Table of
Materials.
Future Energy Materials: Three Challenges for Materials Chemistry 57

Figure 4 The four elements of materials science and engineering7 together with a
representation of the Periodic Table of the elements as backdrop: here the
height of the elemental columns is a measure of each element’s electro-
negativity (adapted from F.J. DiSalvo19). The aim here is to show the
confluence of materials chemistry and materials science.

Chemical periodicity and the Periodic Table find a natural interpretation in

the detailed electronic structure of the atom.17 Given that the chemical and
physical properties of a material derive from the constituent atoms’ electronic
configuration, and especially the configuration of its least highly bound elec-
trons, it follows that ultimately the properties of any material must necessarily
be interpreted in terms of the electronic structure of its constituent atoms.18–20
Thus, the concept of chemical periodicity, central to the study of inorganic
chemistry,17 may in future find a place in the systematisation and rationalisa-
tion of chemical and physical properties of materials – the materials chemistry
of the elements – as a natural focal point for the disciplines of chemistry,
physics, materials science and engineering.17–21 Figure 4 is an attempt to
illustrate the confluence of the various elements of the Periodic Table of
Materials. We now give a brief overview of three areas of energy materials in
which we attempt to illustrate how materials chemistry can impact upon the
intrinsic performance of these materials.

4 Energy Materials
Energy is now established as a global area of critical research where innovative
materials chemistry will play a pivotal role in meeting the needs of the
58 Chapter 4
22,23
future. Energy generation, consumption, storage and security of supply will
continue to be major drivers for the subject. There exists, in particular, the
urgent need for new materials for next generation energy-generating and
energy-storage devices. Many limitations on, for example, hydrogen storage,
fuel cells and photovoltaics are mainly materials and materials chemistry
limited. We highlight three areas of activity where materials chemistry is
already a significant element of world-wide activities.

4.1 Transparent Conducting Oxides

Electrical conduction in a transparent solid is the rarest form of conductivity.24
The seemingly contradictory properties of close-to ‘‘metallic’’ conductivity in a
material simultaneously exhibiting almost complete ‘‘nonmetallic’’ or insulat-
ing optical transparency, form the basis of numerous critical applications in
contemporary and emerging energy technologies.25–27
In many respects, the basic underpinning materials physics can be reasonably
well set out.28–31 Thus, the high conductivity of the prototypical transparent
conducting oxide (TCO) SnO2-doped In2O3 (ITO) derives from the presence of
shallow donor or impurity states located close to the host (In2O3) conduction
band, the donor states produced via chemical substitution of Sn41 for In31 or
by the presence of oxygen vacancy impurity states28 in In2O3
x (Figure 5). At
room temperature the proximity of such impurity states to the host conduction
band ensures facile thermal ionisation into the band, developing, ultimately, a
degenerate, itinerant electron gas of current-carrying electrons which also gives
rise to far-infrared (Drude-like) absorption and high electrical conductivity, but
at the same time the fundamental host band gap is left intact, i.e. the electrically
conductive material remains optically transparent in the visible region. For
doping levels above that set by the Mott criterion for metallisation32 (i.e. n4nc
B1018–1019 cm
3 for ITO), one can consider ITO to have a full valence band
and a host 5s conduction band partially filled by a degenerate free-electron gas.
Within the free-electron framework, the optical and transparent properties are
described quite well30 by a simple Drude model (the addition of a strongly
frequency-dependent electron scattering time t for Fermi surface electrons
provides a secondary level of sophistication; see below). Conduction electron
scattering in ITO thin films occurs from a number of different scattering centres
such as impurities, phonons, defects. However, the most dominant process
originates from the presence of the very impurity ions responsible for the
doping, and this sets the scope for any interpretation of the limiting perform-
ance of such materials.29
A calculation29 of electrical resistivity due to this ionised impurity scattering
provides an important lower limit to the attainable intrinsic resistivity (equiv-
alently an upper limit to the conductivity) of a TCO material; this is a key
performance indicator. The results of such calculations are shown as a function
of carrier concentration in Figure 6. The various data points are experimental
values taken from the literature for In2O3, ZnO and SnO2 doped systems and
Future Energy Materials: Three Challenges for Materials Chemistry 59

Figure 5 Schematic energy-band model for SnO2 doped In2O3 for small x (insulating)
and large x (metallic) materials. Taken from P.P. Edwards et al.30 as
modified from the work of Fan and Goodenough.28

the solid line represents a calculation29 of electrical conductivity due to ionised

impurity scattering. This sets the upper performance limit to the attainable
conductivity at any particular carrier concentration.
The similar behaviour observed in all three different systems strongly sup-
ports the idea that this impurity scattering mechanism dominates the electrical
resistivity (conductivity) in all three cases.
In an attempt to enhance the electrical performance by moving to higher
conductivities, the films need to be doped to increase the carrier concentration n
(Figure 6). However, increases in n will ultimately lead to a degeneration of the
optical performance of the material. Specifically, although low resistivity (high
conductivity) is highly desirable for the performance of the materials and
associated devices, the free-electron density in ITO cannot be increased beyond
2  1021 cm
3 without pulling the plasma frequency into the red end of the
visible spectrum – making it highly reflecting.30,31
Furthermore, any increase in the film thickness causes reduced transparency
due to a finite skin depth, d, emerging as the electrical conductivity increases
with doping.31 However, above the plasma frequency for nE1021 cm
3, we
find that increases in the electron mobility, me, cause increases in d, and
60 Chapter 4

Figure 6 Literature data for the three oxide systems In2O3, ZnO and SnO2 chosen as
displaying high electrical conductivity at any particular carrier concentra-
tion. The theory plot ( — ) is from the results of the calculation of
conductivity (resistivity) due to ionised impurity scattering. Adapted from
J.R. Bellingham et al.29

(approximately) d p me. This leads to the important conclusion that if me in

TCOs can be increased/maintained above the present state-of-the-art values of
around 50 cm2 V
1 s
1 to values of around 100 cm2 V
1 s
1, then very substan-
tial increases in transparency are possible whilst not sacrificing high electrical
conductivity. The clear message is that electron mobility increases will have
a significant impact on the key performance characteristics of the power
efficiency of light emitting diodes and related devices.
The materials physics of the problem can be captured in the following
way.30,31 For ITO in the limit of high electron density (i.e. n\1021 cm
3) and
high mobility (i.e. me ¼ etm*\20 cm2 V
1 s
1) then the plasma frequency,
op, can be written

1=2
ne2
op ffi
e1 e0 m

where eN is the high frequency dielectric pffiffiffi constant and e0 is the vacuum
permittivity. Hence in this limit op / n and thus is determined almost
exclusively by n and not t (i.e. the electron mobility, me, recalling that
me ¼ et0/m*). This means that for a film to be non-reflective to light of free
space l0 (i.e. opope/l0; where l0 is the dc wavelength of light) the electron
density n must satisfy
4p2 e0 m
no ;
m0 e2 l20
Future Energy Materials: Three Challenges for Materials Chemistry 61
which for ITO yields the criterion
nðcm
3 Þo1:6  1021 =l0

Therefore for efficient transmission of the whole visible spectrum (including

red light of free space wavelength up to 780 nm) the electron density should not
exceed 2.6  1021 cm
3.
To allow a suitable ‘‘safety margin’’ in our performance criteria, we consider
a plasma wavelength of just over 1 mm (i.e. in the near-infrared) in which case
the tolerable free electron density (nmax) is ca. 1.5  1021 cm
3. Clearly, values
of n>nmax are severely detrimental to the performance transparency of the
films owing to the plasma edge creeping into the red part of the visible
spectrum. The power reflection coefficient R at an interface between a thick
ITO layer and free space can be calculated from the expression;
pffiffiffiffiffiffiffiffiffiffi 
 eðoÞ
12
 
RðoÞ ¼ pffiffiffiffiffiffiffiffiffiffi 
 eðoÞ þ 1

An exact calculation30,31 of R using the full Drude formula for e(o) is

shown in Figure 7 as a function of n for various incident wavelengths in the
visible spectrum. For frequencies below the plasma frequency, R is close to 1
(i.e. it is very reflective) with a small amount of electromagnetic absorption
within the material (approximately equal to (1
R)). These results have impor-
tant consequence if high transparency films with very low sheet resistance are
required. This is therefore best achieved by increasing the electron mobility in

Figure 7 The power reflection coefficient at the interface between a thick TCO layer
and free space as a function of free electron density n for various incident
wavelengths in the visible spectrum. Taken from P.P. Edwards et al.30
62 Chapter 4
preference to n, since increasing n leads to increasing conductivity and a
proportionate reduction in the skin depth as the plasma frequency is increased.
This significant result illustrates the origin of me, so as to maximise this
quantity. Importantly, the intrinsic limit of me appears to be set around
90 cm2 V
1 s
1 as a result of ionised impurity scattering.29
In summary, therefore, the task before the materials chemists in an attempt
to enhance the intrinsic performance of TCOs is centred around the following
three performance criteria for new materials:

1. Maintain the condition of a wide band gap (43.5 eV) and low inter-gap
absorption.
2. Maintain the condition of moderate electron densities (n \1021 cm
3) –
but certainly not higher than this value.
3. Maintain the highest possible carrier mobility; ideally, close to, or above,
100 cm2 V
1 s
1.

Thus, the materials chemistry of such systems now has to be closely allied with
materials physics to understand how electron mobilities can be understood,
tuned and thereby enhanced.
It now appears that such performance limits are regularly being approached in
known materials and this fact29 sets the scene for major activities in materials
chemistry if new systems are to be discovered which optimise/enhance properties
of these important technological materials.

4.2 Thermoelectric Materials: Optimisation Challenges

Thermoelectric devices are unique heat engines, in which charge carriers serve as
the working fluid.33,34 They offer a reliable, fully solid-state means of cooling
and electrical power generation. One of the important aspects of thermoelectric
power generation technologies is the ability to provide electrical power from heat
gradients, which could be used in the recovery of large amounts of waste heat
and harvesting it into usable electrical energy. However, relatively low energy
conversion efficiency (typically around 5%) of thermoelectric materials limits
their performance and range of applications to niche areas in refrigeration and
power generation technologies. Although ingenious engineering approaches
could extend the scope of applications, the real economic impact of this
technology depends on the availability of more efficient thermoelectric materials.
For a given temperature range of operation the thermoelectric performance
of a material is determined by its thermoelectric figure-of-merit Z ¼ a2s/k,
where a is the Seebeck coefficient, s is the electrical conductivity and k is the
thermal conductivity (k ¼ ke+kL, where ke and kL are the electronic and lattice
contributions, respectively). Generally, the transport coefficients of a semicon-
ductor material are more complex than, for example, its optical or magnetic
properties, which are very closely related to the band structure. All established
thermoelectric materials possess a complex energy-band structure; their degree
of degeneracy is high and invariably several types of bonding are involved
Future Energy Materials: Three Challenges for Materials Chemistry 63
together with several co-existing carrier scattering mechanisms. All this,
together with often strong anisotropy of the charge and heat transport prop-
erties and the limitations of existing theoretical models, makes any theoretical
predictions regarding the thermoelectric figure-of-merit prohibitively difficult.
However, several useful conclusions on the directions in search for novel
improved materials can be drawn from the classical Fermi–Dirac statistics
and a simplified model of electron scattering. In this approximation the figure-
of-merit Z can be expressed in terms of the fundamental transport parameters
through the so-called materials parameter b:
3=2
Z / b¼mðm* Þ kL

where m is the carrier mobility and m* is the density of state effective mass.33,34
Therefore, to maximise the Z value, a material with large effective masses of
charge carriers, high carrier mobility and a low lattice thermal conductivity is
required.
Although significant improvements in the properties of state-of-the-art
thermoelectric materials have been achieved over the last 30 years, the maxi-
mum value of the dimensionless figure-of-merit ZT for the best thermoelectric
materials has remained around unity over the temperature range of 100–1200 K
(Figure 8), even though thermodynamics does not place any upper limit on ZT.
The major problem with increasing the performance of thermoelectric
materials is a close interrelation of all parameters that determine the figure-
of-merit, which makes it impossible to control these variables independently.
For example, both the Seebeck coefficient and electrical conductivity depend on

Figure 8 Temperature dependence of the dimensionless figure-of-merit ZT of some

n-type thermoelectric materials. The figure was compiled using various
literature sources.35–37
64 Chapter 4
the carrier density. However, while maximisation of the Seebeck coefficient
requires a reduction in carrier concentration, the electrical conductivity is, to
the first approximation, directly proportional to carrier concentration. While
the numerator a2s in the expression for Z can be maximised through optimal
doping (typically around 1019–1020 carriers/cm3), the reduction in the lattice
thermal conductivity is limited by the ability to reduce its lattice contribution to
a minimum value. The remaining contribution to the thermal conductivity is
electronic and proportional to the electrical conductivity (kepTs) according to
the Wiedemann–Franz law. An attempt to maximise the materials parameter
m(m*)3/2/kL also inevitably leads to a compromise concerning the value of
carrier mobility m and effective mass m* since these two transport parameters
tend to be inversely proportional to each other. The optimisation of these
contradictory requirements represents the major challenge for materials chem-
ists in the development of new thermoelectric materials with maximum dimen-
sionless figure-of-merit ZT.
The goal for a high-performance thermoelectric material is to maintain the
typical electronic properties of a conducting crystal while, at the same time,
having the thermal conductivity that is characteristic of an amorphous solid.
There are several ways to effectively reduce the lattice thermal conductivity and
simultaneously maintain and optimise the electronic structure of a material.
One of the traditional ways to reduce the lattice thermal conductivity of a
compound is to increase the point defect scattering of phonons by formation
of solid solutions. This method has been successfully employed over the last
40 years for the development of all state-of-the-art thermoelectric materials.
However, this approach has serious limitations since a high concentration of
atomic point defects also inevitably leads to a decrease in the electrical
conductivity and carrier mobility.34
One of the recently developed approaches to identify materials with high
thermoelectric performance is to search for solids that allow freedom to modify
and tailor their crystal structure. Among the most promising novel thermo-
electric materials are two classes of inclusion compounds with large voids in
their crystal structures, which are occupied by loosely bound atoms. The loose
bonds between the filling atoms and the oversized voids cause anharmonic
vibrations of the former, which greatly lowers the lattice thermal conductivity
value while weakly affecting the electronic transport. This results in a combi-
nation of high electrical conductivity typical of crystalline materials
and, at the same time, a very low lattice thermal conductivity typical of an
amorphous solid.38–40 The temperature dependence of ZT values of two
n-type materials that belong to skutterudite (Yb0.2Co4Sb12) and clathrate
(Ba8Ga16Ge30) families of inclusion compounds are presented in Figure 8.
Another promising class of novel materials with potentially large ZT values
is nanostructured materials such as quantum dot superlattices and quantum
wire arrays.35,41,42 In these materials the new variable of size becomes available
and it is possible to change dramatically the density of electronic states,
allowing new opportunities to vary a, s and k independently. In addition,
the introduction of many interfaces offers the opportunity to increase phonon
Future Energy Materials: Three Challenges for Materials Chemistry 65
scattering more than electron scattering so that the electrical conductivity is not
decreased much while the thermal conductivity is much reduced by interface
scattering processes. Significant improvement of the thermoelectric figure-of-
merit ZT in such materials is expected when the structural parameters are
carefully tuned to increase the carrier density of states while decreasing the
thermal conductivity due to phonon-boundary scattering or phonon spectrum
modification. This opens up new possibilities in designing novel materials with
enhanced thermoelectric performance.

4.3 Hydrogen Storage Materials

Reducing or eliminating our dependency on petroleum in transportation
system is a major objective worldwide. The combination of hydrogen and fuel
cells in particular represents a key enabling technology for a future sustainable
energy economy which has the potential to revolutionise our energy system
offering cleaner, more efficient alternatives to today’s energy technologies (fuel
cells are projected to have an energy efficiency twice that of internal combustion
engines).43
However, current hydrogen storage systems for vehicular transportation
are generally inadequate to meet the necessary driving range requirements of
some 300 miles (500 km) without significant intrusion into cargo or passenger
space. For this reason effective hydrogen storage is viewed as one of the most
critical barriers to the widespread use of hydrogen fuel cells as an energy
carrier.44,45 Typically 4–7 kg of hydrogen need to be stored on board a vehicle
to come close to the automotive requirements of a range of some 500 km as a
benchmark.
There are four major options for on board hydrogen storage systems,
variously: (1) compressed hydrogen (typically at pressures between 35–70 MPa
at room temperature); (2) cryogenic liquid hydrogen (operating at 20–30 K at
pressures of 0.5–1 MPa); (3) solid state absorbents, ranging from metal hydrides
and complex hydrides to high surface area porous materials; and (4) hybrid
solutions, incorporating at least two of the above technologies. These various
options are described in detail elsewhere;43,45 here we are concerned solely with
the issue of solid state hydrogen storage materials.
The objective44–49 is to tune a materials’ properties to obtain reversible
hydrogen storage materials with properties between those of the cryogenic
adsorbents (typically which have hydrogen binding enthalpies of between
4–20 kJ mol
1 H2) and the intermetallic and complex hydrides which have
bond enthalpies of between 30–55 kJ mol
1.
An ideal solid state hydrogen storage material should, for economic,
environmental and user-friendly reasons satisfy the following performance
criteria:44

(i) Hydrogen storage capacity; probably a minimum of 6.5 wt% of abun-

dance of hydrogen and at least 65 g L
1 of hydrogen available from the
material.
66 Chapter 4
(ii) Heat of formation (DH) must be reduced as low as thermodynamically
possible. An ideal hydrogen storage material releasing hydrogen via
thermal decomposition should be (possibly, only slightly) thermo-
dynamically stable at ambient conditions (1 atm, 25 1C). The desorption
should not be associated with a substantial heat release. For this reason,
and the necessity for incorporation into a PEM fuel cell for vehicular
applications, therefore, we would require;
(iii) Operating temperature of less than 70 1C; in essence, this would require
only a small amount of heat to evolve molecular hydrogen.
(iv) Reversibility of the thermal absorption/desorption cycle.

Of course, there are other key factors of cost, toxicity, confinement, etc., but we
focus here on the points above since they illustrate some of the major initial
materials chemistry challenges.
A summary of existing volumetric hydrogen densities and gravimetric
hydrogen contents for various hydrogen storage materials is illustrated in
Figure 9. We note that there is, as yet, no material known to meet simultane-
ously all of these, and other important criteria. Within Figure 9, we have also
attempted to highlight – in ‘‘broad-brush’’ terms – which of the three chemical
species H0, H– and H1 (in the extreme) is potentially the better source of
hydrogen; at least for the thermally activated process for hydrogen generation
from the storage material.
Simple atomic-number-based calculations reveal the obvious fact that only
the light chemical elements can be strictly entertained44 if criterion (i) is to
be met (this conclusion is clearly relaxed for stationary applications where
FeTiH1.7 and multiphase Ti–Zr–V–Fe–Ni systems are highly effective stores;
such a relaxation of wt% targets also forms the basis of current hybrid
solutions to onboard storage of hydrogen).
Accepting these multi-various performance requirements for the perfect
storage material now allows us to set objectives for the materials science
research as target values for a breakthrough storage compound. Currently,
four major approaches are being pursued to achieve those design/performance
parameters:

1. A combinatorial, high throughput approach designed to search for ma-

terials derived entirely from multinary combinations from ‘‘The Light
Periodic Table’’ not previously investigated (also, taking guidance from
the story of High-Tc (Figure 2)) where entirely new phases are observed
beyond binary and ternary systems.50
2. The destabilisation of existing materials through alloy formation or more
complex reaction schemes (see below): the aim here is to attempt to
modify the thermal characteristics of materials, while at the same time to
maintain a high weight percent for hydrogen storage.51
3. The cryo-adsorption of hydrogen on high-surface-area materials
(e.g. activated carbons, zeolites or metal–organic frameworks).52
Future Energy Materials: Three Challenges for Materials Chemistry 67

Figure 9 The gravimetric and volumetric densities and corresponding specific energy and
energy density of various hydrogen storage materials, compressed/liquid hydro-
gen and Li-ion batteries. The temperature data under the composition of some
materials indicate the equilibrium temperature for hydrogen pressure 1 bar.

4. A hybrid solution combining low DH hydride approaches with a (mod-

erately) high pressure compressed hydrogen design (e.g. operating at
30 MPa with a TiCrMn or related alloy).53

We use the second path, that is material destabilisation, to illustrate how

this key performance parameter, Tdec, representing the temperature of thermal
decomposition of a hydrogen storage material, can be modified; this is one
of the most important practical parameters connecting both the thermo-
dynamic and kinetic aspects of these materials. This leads us to a brief
discussion on how Tdec, the decomposition temperature, may be understood
and consequently tuned to optimise one performance parameter for a hydrogen
storage material.44,54
Grochala and Edwards44 have presented thermodynamic arguments for
understanding how the values of Tdec – certainly those for binary hydrides
68 Chapter 4

Figure 10 A correlation of the temperature, Tdec, at which thermal decomposition

of binary hydrides MH2 to the constituent elements proceeds, and the
corresponding standard redox potential of the Mn1/M0 redox pair in
acidic aqueous solutions, E0. The ranges of the working temperatures for
prototypical fuel cells are also shown. The E0 values for H2/2H
and
H0/H
redox pairs are indicated. Taken from Grochala and Edwards.44

(MHn) – might correlate with the E1 value for the corresponding Mn1/M1 pair
in aqueous solutions. Such a correlation is presented in Figure 10, where we
show a plot of the experimental Tdec versus E1 data for a wide variety of binary
hydrides. As one can discern from Figure 10, there is an excellent correlation
between Tdec and E1 for a wide range of (seemingly) chemically disparate metal
hydrides.
This simple empirical correlation, having its roots in the thermodynamics of
MHn formation, forms almost a ‘‘sorting map’’ of experimental systems. One
can clearly see also the importance of Tdec in matching the operating temper-
atures of different types of H2 fuel cells, ranging from alkaline, through
polymer electrolyte membrane, to solid oxide and molten carbonate cells.
The monotonic behaviour of the Tdec versus E1 relationship for the binary
Future Energy Materials: Three Challenges for Materials Chemistry 69
hydrides has been rationalised on the basis of thermodynamic and theoretical
arguments.44
Given the importance of Tdec, and its ‘‘matching’’ to the various operating
temperatures of fuel cells, the notion (2 above) arises of ‘‘destabilising’’ high
weight percent stores in an attempt to reduce decomposition temperatures of
hydrogen storage materials.51 Many hydrides of the light chemical elements
have DH values larger than the desired range of ca. 30–60 kJ mol
1 H2.
Experimental and theoretical work is currently underway on destabilised
systems by mixing chemical hydrides with other compounds.
Destabilisation enables one to precisely modify the thermodynamics of
dehydrogenation processes by substituting an energetically unfavourable reac-
tion with another reaction involving the formation of different compounds in
the dehydrogenated state. The formation of these compounds reduces the
enthalpy of the dehydrogenating reaction and lowers the dehydrogenation
temperature. An example55,56 of such an approach is illustrated in Figure 11 for
the LiBH4+MgH2 destabilised system exhibiting decreases in the enthalpy of
decomposition and the decomposition temperature by 23 kJ mol
1 H2 and
240 K, respectively, compared to pure LiBH4.56,57 In Figure 9 different colours
are used for different hydrides to distinguish the dominant charge of hydrogen
atoms. This general approach could facilitate the choice of pairs of hydrides for
development of novel destabilised systems.
Chemical reactions in the destabilised hydrogen storage systems often in-
volve the formation of intermediate compounds, for example Li4BH4(NH2)3 in
the LiBH4+LiNH2 system.58,59 Such intermediate compounds could signifi-
cantly improve the kinetics of the dehydrogenation process.
The number of possible destabilisation reactions significantly exceeds the
number of existing chemical hydrides which offers a promising avenue for
developing a viable hydrogen storage system. A number of destabilisation reac-
tions have already been studied; some of the results are presented in Figure 12.

Figure 11 Reduction in the decomposition temperature of destabilised

LiBH4+MgH2 system by 240 K compared to pure LiBH4.56
70 Chapter 4

Figure 12 Effect of destabilisation on gravimetric hydrogen density and hydrogen

decomposition temperature (1 bar).60–64

This suggests that the most promising candidate for a destabilised system
meeting the mobile storage requirements is ammonia–borane (Figure 12).
Another key performance challenge for many destabilised systems is to achieve
the reversibility of hydrogen storage, a particularly difficult challenge.
In summary, stabilising the dehydrogenated state of a hydrogen storage
material reduces the enthalpy of dehydrogenation, thereby increasing the
equilibrium hydrogen pressure. Using this approach, the key performance
parameter of Tdec can potentially be tuned to an extent finer than would be
possible with individual materials. The strategy of ‘‘chemically controlling’’ Tdec
by using alloying elements to form stable compounds or alloys upon dehydro-
genation opens up real possibilities for increasing the equilibrium pressures
of hydrogen-rich but strongly bound hydrides. We have focused on LiBH4
in combination with MgH2 in Figure 11, but as highlighted in Figure 12, a large
number of destabilised reactions have already been studied. Recent develop-
ments with ammonia borane, NH3BH3, also highlight the great potential of this
technique when applied to high weight percent, molecular compounds.
Maintaining high weight percent hydrogen storage, whilst reducing Tdec and
enhancing reversibility, will represent a major milestone in the area of materials
Future Energy Materials: Three Challenges for Materials Chemistry 71
chemistry; indeed this is widely recognised as a potential ‘‘show-stopper’’ for
the transition to a hydrogen economy.

5 Epilogue: Materials Chemistry, a New Interdiscipline

It is clear that materials chemistry is certainly now a multidiscipline in its own
right – rich in opportunities and challenges, and no more so than in the area of
energy materials research.
We have outlined how the tetrahedron of synthesis/structure/properties/
performance (Figure 4) outlines a good basis for a description of, and a basis
for, the continued development of the subject. We have attempted to illustrate
the importance of a basic understanding of the fundamental science in three
areas of energy materials, transparent conducting oxides, thermoelectric
materials and hydrogen storage materials, which provides deep insights into
the intrinsic performance limits of these systems.
To take one example, the optical and electronic properties of transparent
conducting oxides are crucial in limiting properties – and hence performance –
of these materials. This example, hopefully, also illustrates that relatively
simple models (here the free electron gas model of Drude) can be extremely
useful in establishing performance limits.
One should add that, despite the high sensitivity of a material’s properties on
processing issues and conditions (grain boundaries, etc.), a material’s electronic
structure is arguably the most important factor for understanding the unique
interplay between chemical, electronic, magnetic, thermodynamic and kinetic
properties of energy materials.
In our discussion we have concentrated on performance as a new dimension
for the emerging field, but of course implicit in this term are economic,
environmental and other key societal factors (public acceptability of a new
energy vector, e.g. hydrogen, etc.). The science-to-social need is a crucial part of
the subject’s development; the place of materials research in the ‘‘economy’’
and well-being of society will be analysed as never before.7 Nevertheless,
the core theoretical/experimental basis of the field is embedded in the tetra-
hedron shown in Figure 4, with the underlying parentage of the Periodic
Table, as a key distinguishing feature of materials chemistry. The search for
new materials must always be underpinned by such theoretical frameworks if
new materials with improved combinations of properties are to be discovered –
and utilised.
The (part) title of our volume is centred around the descriptor ‘‘Turning
points . . . ’’, the combination of words which is defined by the Oxford Dic-
tionary of Current English65 (admittedly, only John’s second language) as
‘‘Crisis : or prove the contrary of what was intended’’. This was clearly not
what was intended!
Indeed, the outcome of this marvellous collection of articles honouring John
Meurig Thomas is a vivid illustration of the corresponding definition of
‘‘crisis’’; defined from that same tome as ‘‘the decisive moment’’. We certainly
72 Chapter 4
do believe this is a decisive moment in the evolution and expansion of the
subject into major new fields.
John, in this same year as the 200th anniversary of Humphry Davy’s
discovery of K and Na, and also the 150th anniversary of Michael Faraday’s
pronouncement on gold in its metallic, divided state, we wish you a happy
75th birthday!

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CHAPTER 5

Structural Diversity and Potential

Applications of Metal–Organic
Coordination Polymers
JIESHENG CHEN AND RUREN XU
State Key Laboratory of Inorganic Synthesis and Preparative Chemistry,
College of Chemistry, Jilin University, Changchun 130012, People’s Republic
of China

Through his academic career, Sir John Meurig Thomas has realized great
achievements and contributions in a variety of areas. One of his main interests
has been in solid materials which find applications in catalysis. Zeolites, a class
of microporous crystalline compounds, are typical solid materials which have
been widely used in catalysis as well as in adsorption, ion-exchange and
separation. Sir John’s pioneering work1 in electron microscopic imaging of
zeolites shed an enormous amount of light on the structures of these intriguing
materials, and nowadays electron microscopies, especially transmission elec-
tron microscopy (TEM), have become important techniques for the elucidation
of microstructures of known and unknown zeolite materials. Sir John, in
association with C.R.A. Catlow and G. Sankar at the Royal Institution of
Great Britain (RIGB) and a few other co-workers, also extensively used
synchrotron radiation sources (mainly X-ray) to investigate the structures
and active catalytic sites of zeolitic materials.
Conventional zeolites are aluminosilicates with frameworks composed of Si,
Al and O, and in the 1980s microporous aluminophosphates (AlPOs) and their
derivatives were also synthesized. From the late 1980s, Sir John was involved in
studies on synthesis, structural characterization and catalytic properties of new
AlPOs and substituted AlPOs. His research work in this area carried out in
collaboration with one of us (Ruren Xu) resulted in a number of highly cited
publications.2,3 The other author of the current article (Jiesheng Chen) used to
work at RIGB as a postdoctoral research fellow under Sir John from 1990 to
1994, and his research work was mainly focused on the exploration of substituted
AlPO materials with new catalytic properties. At that time, not only J.S. Chen
76
Metal–Organic Coordination Polymers 77
but also a number of other colleagues such as Y. Xu, R. Bell, P.A. Wright, S.
Natarajan, G. Sankar, L. Marchese and R. Raja at RIGB were also involved in
this research area. It should be particularly mentioned that one of the colleagues
at that time, R.H. Jones, played an important role in the structural analysis of
new AlPO materials. In fact, aluminophosphate compounds show vast diversity
in structure as well. Not only three-dimensional (3D) frameworks but also 2D
sheet and 1D chain structures of aluminophosphates4,5 have been obtained in the
past, and the topologies and building-unit connections for 3D aluminophos-
phates vary enormously.
Apart from conventional zeolites and microporous AlPOs, many other open-
framework compounds composed of elements other than Si, Al and P have also
been synthesized, and their structural features are equally diverse. Notably,
from the late 1990s a new class of porous crystalline compounds whose
frameworks consist of metal centres and organic linkers have been discovered.
These compounds are usually designated metal–organic framework (MOF)
materials or metal–organic coordination polymers (MOCPs) in general.6,7
Three-dimensional framework MOCPs usually contain various channels, and
these channels differ from those of zeolites in shape, size and adsorption
properties. Many as-synthesized MOF materials accommodate guest molecules
in their channels or pores, and these guest molecules may be the solvent of the
synthetic system or templates used as for the synthesis of zeolites. The thermal
stability of MOFs is lower than that of inorganic framework porous materials,
and therefore their applications in conventional high-temperature catalysis are
limited. However, in non-conventional fields the applications of MOFs have
been showing great potential.

1 d-Block Metal Coordination Polymers

Multidentate ligands containing two or more carboxylate groups on a benzene
or a larger aromatic ring may easily connect metal ions into 3D coordination
polymers. In a mixed solvent system of water and ethanol, Williams and co-
workers synthesized a 3D framework porous compound [Cu3(TMA)2(H2O)3]n
using benzene-1,3,5-tricarboxylic acid (TMA or BTC) and copper ions as
reactants.8 This compound consists of [Cu2(O2CR)4] (R stands for aromatic
ring) structural units which are interconnected to form a 3D channel system.
The as-synthesized compound occludes guest water molecules in the channels,
but these molecules may be removed through thermal treatment, or may be
replaced by other guest molecules such as pyridine. This porous coordination
polymer is thermally stable up to about 240 1C.
1,3,5,7-Adamantane-tetracarboxylic acid (denoted ATC) has four carboxy-
late groups and is also an ideal multidentate ligand. The reaction of this ligand
with Cu21 under hydrothermal conditions (190 1C) results in a coordination
polymer Cu2(ATC)
6H2O. This compound possesses large channels, and the
guest molecules may be driven out without apparent change of the host
framework. The compound exhibits excellent microporous adsorption
78 Chapter 5
9 0 00
properties. The reaction of 4,4 ,4 -benzene-1,3,5-triyl-tribenzoic acid (denoted
BTB) and cupric nitrate in a mixed solvent of ethanol, dimethylformamide
(DMF) and water at 65 1C for 1 day gives rise to an interwoven coordination
polymer Cu3(BTB)2 (H2O)3
(DMF)9(H2O)2.10 This compound possesses chan-
nels with guest DMF and water molecules inside. Upon removal of the guest
molecules, the compound exhibits excellent adsorption properties.
The other common donor coordination atom besides O is N. Many aromatic
rings may contain one or more N heteroatoms. These aromatic rings may
interconnect one another to form larger ligands, and more than one N atom in
the compound may participate in coordination to metal ions. 4,4 0 -Bipyridine
(bpy) is an N-containing bidentate ligand widely used to form coordination
polymers. For example, bpy has been used as a ligand and a series of
framework compounds containing guest anions and water molecules have
been prepared in the reaction system of copper ions and AF6-type anions
(A ¼ Si, Ge and P). The framework structures of these compounds may be
controlled by varying the guest anions.11 The framework geometry of porous
3D framework compounds formed by some N-containing ligands and metals is
affected by the guest species in the channels to a great degree. Biradha and
Fujita used 1,4,6-tris(4-pyridyl)triazine (denoted TPT) as the ligand, and syn-
thesized the framework compounds [(ZnI2)3(TPT)2
5.5C6H5NO2] and
[(ZnI2)3(TPT)2
5.5C6H5CN] from the solution of ZnI2 and nitrobenzene or
cyanobenzene.12 It was discovered that in the presence of the guest nitroben-
zene or cyanobenzene molecules, the whole framework of the host is swollen,
whereas when the guest molecules are removed, the host framework apparently
shrinks. The guest species in this compound may also be replaced by other
molecules.
Lin et al. used an axially chiral bridging ligand (R)-6,6 0 -dichloro-2,2 0 -
dihydroxy-1,1 0 -binaphthyl-4,4 0 -bipyridine, L, to construct homochiral porous
MOFs.13 They obtained crystals of [Cd3Cl6L3]
4DMF
6MeOH
3H2O by
slow diffusion of diethyl ether into a mixture of the ligand and CdCl2 in
MeOH/DMF. The structure of this compound is a noninterpenetrating 3D
network with very large chiral channels of B1.6  1.8 nm cross-section. It was
revealed that the compound contains 54.4% void space that is accessible to
guest molecules, and X-ray powder diffraction demonstrated that the frame-
work structure was maintained upon removal of all the solvent molecules.
Interestingly, Ti-(OiPr)4 can react with the chiral dihydroxy groups in the
channels of the compound to afford a Lewis acidic material which is catalyt-
ically active for the addition of ZnEt2 to aromatic aldehydes to form chiral
secondary alcohols.
Some aromatic cyclic molecules not only contain N heteroatoms on the
aromatic ring but also are attached by carboxylate group(s) on one or more of
the carbon atoms. Therefore, these ligands can form coordination polymers
through coordination of not only their N but also their carboxylate groups. Zhao
et al. used pyridine-2,6-dicarboxylic acid (H2dipc) as ligand and synthesized a
coordination polymer with an empirical formula [Ln(dipc)3Mn1.5(H2O)
nH2O]
from Mn21 and rare-earth metal ions Ln31 (Ln ¼ Pr, Gd, Er) under
Metal–Organic Coordination Polymers 79
14
hydrothermal conditions. This polymeric compound possesses 1D channels
with a channel diameter of 0.6 nm, and the guest water molecules are distributed
in the channels. Structural analysis indicates that these guest water molecules
may be removed from the channels without collapse of the framework, and
therefore, this polymer may be used as a microporous crystal molecular sieve.
Because there are unpaired electrons on the framework metal ions, the com-
pound also exhibits magnetic properties.
Chiral porous coordination polymers have great application potential be-
cause they may be used as chiral catalysts, and it has been continually attempted
to introduce chirality into coordination polymers with various approaches. A
simple strategy is to use chiral ligands, and after the formation of coordination
polymers the chirality is automatically introduced into the polymer with the
ligand. Quitenine (6 0 -methoxyl-(8S,9R)-cinchonan-9-ol-3-carboxylic acid
(HQA)) is a chiral ligand molecule. If quitenine is reacted with Cd(OH)2 in a
hydrothermal system containing racemic 2-butanol, a host–guest coordination
polymer Cd(QA)2 with chiral channels crystallizes.15 In the chiral channels of
this compound there exist chiral 2-butanol guest molecules, suggesting that the
chiral channels are able to separate the guest enantiomers. 9,9-Diethyl-2,7-bis(4-
pyridylethynyl)fluorene, and chiral 9,9-bis[(S)-2-methylbutyl]-2,7-bis(4-
pyridylethynyl)fluorene were also used to react with copper nitrate to prepare
coordination polymers with grid channels. If the ligands are chiral, the coordi-
nation polymers obtained are also chiral.16 Another method of preparing chiral
coordination polymers is to use special guest molecules as templates which may
also induce the formation of chiral coordination polymers. Kepert
et al. used ethylene glycol and propylene glycol as templates to induce the
formation of metal benzene-tricarboxylate porous coordination polymers, the
framework of which exhibits chirality.17
Through mixing of N-containing and O-containing ligands in the same
reaction system, porous coordination polymers with two or more ligands
may be obtained. Under this circumstance, each ligand contains either N or
O, but the whole coordination polymer contains both N and O. Through
solvothermal reaction (150 1C) of a 1D chain coordination polymer [Co(bpdc)
(H2O)2]
H2O (bpdc ¼ bipyridine dicarboxylic acid) in a DMF solution, the
chain structure is converted to a porous 3D framework compound
[Co3(bpdc)3bpy]
4DMF
H2O.18 The solvent water and DMF molecules are
accommodated in the channels as guests. It is interesting that the conversion
from 1D to 3D is reversible. The channels of 3D framework compounds are
shape-selective, and they may act as ideal sites for shape-selective catalysis.
After reactions, the products may be isolated through reversible conversion of
the host framework to the 1D framework.

2 Adsorption and H2 Storage Properties of MOFs

The as-synthesized metal–organic framework compounds usually contain guest
species such as water and other solvent molecules in their pores and/or
80 Chapter 5
channels. Upon thermal treatment, these guest molecules may be driven out
of the framework structures of the MOFs, and in some cases the framework
structures of the thermally treated MOFs are maintained. The stable
MOFs after removal of guest species are porous and may adsorb a variety of
other molecules that are smaller than the pore size of the MOFs. H2 is a clean
energy source, and the use of H2 in fuel-cell operation is very promising.
However, the storage of H2 in high capacity (both in weight and in volume) is
still rather challenging. Recently, the use of MOFs as H2 storage media has
been extensively investigated, and it has been found that some MOFs exhibit
significant H2 storage capacities. So far as is known, most of the reported
MOFs with H2-storage capacities are composed of Zn(II) or Cu(II) and organic
linkers.19
Yaghi and co-workers investigated, in detail, the adsorption properties of
their MOF compounds composed of Zn(II) and multicarboxylate linkers. Type
I isotherms typical for zeolites and related microporous materials have been
observed for MOF-2, MOF-3 and MOF-5. After evacuation, MOF-5 possesses
a free pore volume of 55–60%. Metal coordinative unsaturation is present in
the channels of MOF-4, and as a result, a more complex sorption processes
may occur as observed for ethanol uptake in MOF-4. It was reported that
MOF-5 adsorbed hydrogen up to 4.5 wt% at 78 K and 1.0 wt% at room
temperature and a pressure of 20 bar.20 Inelastic neutron scattering spectro-
scopy indicates the presence of two binding sites associated with hydrogen
binding to zinc and the BDC linker, respectively. It was also found that the
topologically similar isoreticular IRMOF-6 and -8 with cyclobutylbenzene and
naphthalene linkers, respectively, exhibit approximately double and quadruple
the adsorption capacity of MOF-5 at room temperature and 10 bar. Following
the first report in H2 adsorption by MOFs, Yaghi et al. have also tested the H2
uptake properties of other MOF compounds, among which is MOF-505 with
an as-synthesized composition of [Cu2(bptc)(H2O)2(DMF)3(H2O)] where bptc
stands for 3,3 0 ,5,5 0 -biphenyltetracarboxylate and DMF for N,N-dimethylform-
amide. Upon removal of the guest molecules, this compound takes up 2.47 wt%
H2 at 77 K and 760 Torr.
A chiral zinc–organic framework compound [Zn2(L)]
4H2O has been syn-
thesized through hydrothermal reaction of ZnCl2 and 4,4 0 -bipyridine-2,6,2 0 ,6 0 -
tetracarboxylic acid (H4L).21 Structural analysis indicates that the framework
of the compound is a five-connected network with a 4466 topology comprising
Zn(II) bound to the L4 anion. The chirality is generated by the helical chains of
hydrogen-bonded guest water molecules in the channels of the compound, and
removal of these guest water molecules from the crystal leads to a porous
compound Zn2L which is thermally stable and chemically inert. The BET
surface area of the guest-removed Zn2L is 312.7 m2 g1 and the compound also
exhibits significant gas storage capacities for H2 (1.08 wt% at 4 bar and 77 K)
and for methane (3.14 wt% at 9 bar and 298 K). The adsorption behaviour of
Zn2L towards other organic solvent vapours such as benzene, chloroform and
toluene has also been investigated, and reveals that the adsorption is dominated
by adsorbate–adsorbate or adsorbate–adsorbent interactions.
Metal–Organic Coordination Polymers 81
Garberoglio et al. have modeled adsorption of light gases including H2 on a
number of MOF materials using molecular simulations.22 Good agreement
between simulations and experiments is observed for some cases but very poor
agreement also exists in other cases. Their calculations indicate that at room
temperature none of the tested materials is able to store significant amounts of
hydrogen for use in fuel-cell vehicles. Nevertheless, IRMOF-14 exhibits very
high H2 uptake at 77 K, and the total uptake of this material may reach
15 wt%. Yang and Zhong also performed Monte Carlo simulation and density
functional theory calculations on adsorption of hydrogen in MOF-505 to
provide insight into molecular-level details of the underlying mechanisms.23
Their calculation results show that metal–oxygen clusters are preferential
adsorption sites for hydrogen, and the strongest adsorption of hydrogen is
found in the directions of coordinatively unsaturated open metal sites. The H2
storage capacity of MOF-505 at room temperature and moderate pressures is
predicted to be low.
Cu3(TATB)2(H2O)3 (TATB stands for 4,4 0 ,400 -s-triazine-2,4,6-triyltribenzoate)
is an interesting interweaving MOF.24 Despite the interweaving feature of its
framework, the MOF compound exhibits N2 and H2 adsorption capacities after
removal of the guest water molecules in the channels. Although the surface area
(3800 m2 g1) of this MOF material is lower than those of IRMOF-20 and MOF-
177 (4346 and 4526 m2 g1, respectively), this compound has greater hydrogen
adsorption capacity (1.9 wt% versus 1.356 and 1.25 wt%, respectively for the
latter two at 77 K and 760 Torr). Hydrogen uptake has also been compared with
another two interpenetrating MOFs, IRMOF-9 and IRMOF-13. Cu3(TATB)2
possesses a higher hydrogen uptake than either (1.17 and 1.73 wt%, respectively).
The high H2 uptake has been attributed to the presence of accessible unsaturated
metal centres and the existence of pores and channels in a size range well suited to
the dihydrogen molecule. Long and coworkers reported the synthesis and hydro-
gen storage of a unique MOF compound [Mn(DMF)6]3[(Mn4Cl)3(BTT)8
(H2O)12]2
42DMF
11H2O
20CH3OH with exposed Mn21 sites.25 The 3D
MOF compound, which crystallizes from a methanol solution containing
MnCl2
4H2O and DMF at 70 1C, is composed of Mn21 cations and 1,3,5-
benzenetristetrazolate (BTT) with solvent molecules occluded in the pores of the
framework. After removal of the solvent molecules, the structure remains intact,
and shows a total H2 uptake of 6.9 wt% at 77 K and 90 bar. It has also been
revealed that the compound exhibits a very high isosteric heat of adsorption
(maximum 10.1 kJ mol1) which is related to H2 binding at coordinatively
unsaturated Mn21 centres in the framework.
Kitagawa et al.26 synthesized a yellow compound with the composition
[Zn(TCNQ)bpy]
6MeOH, where TCNQ stands for 7,7,8,8-tetracyano-p-qui-
nodimethane, by reacting Zn(NO3)2
6H2O with LiTCNQ and bpy in MeOH.
The Zn ions in this compound are octahedrally coordinated to the four cyanide
nitrogen atoms of TCNQ in the equatorial plane and the two nitrogen atoms of
the bpy at the axial sites. The Zn ions are linked by TCNQ molecules to give a
2D corrugated layer in the ab plane, whereas the bpy ligands bridge the Zn ions
in adjacent layers to form a 3D pillared layer structure. There exist 2D channels
82 Chapter 5
in the compound with a void space of about 50.7%. Charge balance of the
framework requires the charge number of the TCNQ in the compound to be
2, and therefore, the pore surface of the open framework is full of strong
donor sites (TCNQ2), which may interact with guest molecules. When the
compound is immersed in benzene, the guest MeOH can be exchanged with
benzene within 10 s leading to a new material which is red. The crystal structure
varies accordingly, but the coordination environment around the Zn ion
remains. Other guests such as toluene, ethylbenzene, anisole, benzonitrile,
and nitrobenzene may also be exchanged for MeOH in the compound. The
colour of the crystals is specific to the guest, and the guest exchange is reversible
upon removal/accommodation of the guests. However, it should be pointed out
that this compound does not possess the permanent porosity characterized by
sorption measurements.
MIL-100 and MIL-101 are two chromium carboxylate coordination poly-
mers built up from trimers of metal octahedra and di- or tricarboxylic acids.
These two compounds possess giant-pore systems and high surface areas, and
they adsorb large amounts of hydrogen at 77 K, with a capacity close to
6.1 wt% for MIL-101 as well as the highest heat of adsorption (10 kJ mol1) at
low pressure. Very large pores are not as effective for H2 storage as small pores,
and therefore it is believed that the relatively smaller pore system in MIL101
accounts for the high H2 uptake capacity of this MOF material.27
From a similar reaction system, Férey et al. synthesized a new 3D chrom-
ium(III) naphthalene tetracarboxylate, Cr3O(H2O)2F(C10H4(CO2)4)1.5
6H2O
(MIL-102), from an aqueous mixture of Cr(NO3)3
9H2O, naphthalene-
1,4,5,8-tetracarboxylic acid, and HF. The structure of MIL-102 is 3D and
consists of trimers of trivalent chromium octahedra and tetracarboxylate
moieties. In MIL-102 there are small 1D channels filled with water molecules,
which interact through hydrogen bonds with terminal water molecules and
oxygen atoms from the carboxylates. MIL-102 exhibits a hydrogen storage
capacity of about 1.0 wt% at 77 K, and it also adsorbs CO2, CH4 and N2.28 It
has also been reported that metal–organic framework compounds may be used
as host materials for drug delivery. The adsorption and delivery of a model
anti-inflammatory drug, ibuprofen, by MIL-100 and MIL-101 have been
demonstrated.29
The solvothermal reaction of zinc nitrate, sodium hydroxide and 1,3-benzene-
dicarboxylic (m-BDC) acid yielded a heterometallic MOF compound, [ZnNa(m-
BDC)2]
NH2(CH3)2 (MOF-CJ2),30 which contains zinc(II) and
sodium(I) as the metal centres and the dicarboxylate as the coordination linkers.
It is unusual that the alkali metal sodium cation, which normally functions as a
charge-balancing species in framework compounds, is incorporated into the
framework structure of MOF-CJ2. The framework of the compound consists of
M-O-C (M ¼ Na and Zn) rods formed by alternating six-coordinated Na(I)
centres and four-coordinated Zn(II) centres. These rods are further linked by the
m-BDC ligands to form primitive cubic (pcu) rod packing. This framework is
the first open-framework heterometallic MOF structure based on the assembly
of infinite rod building units.
Metal–Organic Coordination Polymers 83

3 Metal–Organic Coordination Polymers Involving

4f Metals
Although a series of 3d–4f heterometallic complexes with discrete structures
have been obtained through conventional self-assembly reactions in solution,
the synthesis of coordination polymer compounds, especially 3D framework
3d–4f heterometallic coordination polymers, has been less successful. Lantha-
nide ions behave as hard acids and they prefer oxygen to nitrogen donors in
coordination, while d-block metal ions are borderline acids, having a tendency
to coordinate to N-donors as well as O-donors. Therefore, a feasible approach
to construct 3d–4f heterometallic frameworks is self-assembly of mixed metal
ions and proper ligands containing mixed-donor atoms. In this regard, elab-
orately designed ligands with N-donor and O-donor atoms have been employed
to generate 3d–4f heterometallic coordination polymers. Using appropriate
ligands with mixed-donor atoms, we successfully synthesized three isostructural
3d–4f heterometallic compounds [Ln2(H2O)4M2(H2O)2(QA)5]
nH2O (H2QA¼
quinolinic acid; Ln ¼ Gd and Dy, M ¼ Ni and Co) from a hydrotherm-
ally pretreated reaction system. These compounds show an interesting 3D
open-framework topology with 1D chairlike channels which are occupied by
noncoordinating water molecules. It is obvious that the use of ligands with
mixed-donor atoms is a key strategy in the crystallization of 3d–4f frame-
works.31
If the reaction conditions are controlled properly, homometallic lanthanide
coordination polymer compounds can also be obtained. Under hydrothermal
conditions we synthesized four homochiral porous lanthanide phosphonates,
[Ln(H2L)3]
2H2O, (H3L represents (S)-HO3PCH2-NHC4H7CO2H, Ln ¼ Tb,
Dy, Eu and Gd) using chiral N-(phosphonomethyl)proline as the linking
ligand. These compounds are isostructural, and they possess a 3D supramo-
lecular framework (Figure 1) built up from 1D triple-strand helical chains.
Each of the helical chains consists of phosphonate groups bridging adjacent
Ln(III) ions. The helical chains are connected through hydrogen bonds to form
1D tubular channels in which helical water chains are located. Upon removal of
the water chains, the compounds exhibit adsorption capacities for N2, H2O,
and CH3OH molecules.32 The successful preparation of the four solid com-
pounds provides valuable information for further construction of other
homochiral porous lanthanide phosphonate frameworks. Such chiral porous
materials hold promise in applications such as enantioselective separation and
heterogeneous asymmetric catalysis.
The preheating and cooling-down synthetic approach not only reduces the
possibility of involvement of coordination water molecules in the compounds
but also improves the solubility of aromatic carboxylic acids and therefore
the formation of single crystals suitable for structural analysis. Through this
approach, four new rare-earth coordination compounds, [Eu(NDC)1.5
(DMF)2], [Nd2(NDC)3(DMF)4]
H2O, [La2(NDC)3(DMF)4]
0.5H2O, and
[Eu(BTC)(H2O)], where NDC stands for 1,4-naphthalenedicarboxylate and
84 Chapter 5

Figure 1 Space filling structure of [Ln(H2L)3]
2H2O viewed along the c axis.

BTC for 1,3,5-benzenetricarboxylate, have been prepared. The former three

compounds possess similar 2D structures, in which the NDC ligands link
M(III) (M ¼ La, Nd and Eu) ions of two adjacent double chains constructed by
NDC ligands and dinuclear M(III) building units, whereas in the fourth com-
pound, the Eu(III) ion is seven-coordinated by O atoms from six BTC ligands
and one terminal water molecule in a distorted pentagonal bipyramidal
coordination environment. The Eu-containing compounds exhibit strong red
luminescence upon 355 nm excitation. The Nd-containing material shows
interesting emissions in the near-IR region, and yellow (580 nm) pumping
of this compound results in UV and intense blue emissions through an
up-conversion process.33

4 Uranyl–Organic Coordination Polymers

The vast majority of MOCPs synthesized so far involve the d-block metals.
Whereas 4f metals were also reported to form such assemblies, the 5f metals
have been used less commonly as centres for the assembly of organic-bridged
coordination networks. Nevertheless, it has proved that 5f metals (at least
uranium) are able to form various coordination polymer compounds with
suitable ligands.34
A 3D metal–organic framework composed of uranyl and adipate
(UO2(C6H8O4)),35 is constructed via assembly of [(UO2)2O8] dimers through
flexible adipate linker species. This compound is unusual because other uranyl–
aliphatic dicarboxylates such as glutaric, pimelic, suberic, azelaic and sebacic
Metal–Organic Coordination Polymers 85
acids all result in 2D layered topologies consisting of either uranyl dimers, or
1D chains of edge shared hexagonal bipyramids.36,37 It is thought that the
rotation around C–C bonds within the adipate backbone allows for the 3D
arrangement of the compound.
Unlike in the case for d-block and 4f metal coordination polymers, pre-
paration of templated uranyl-containing MOFs has proven unsuccessful using
an aliphatic carboxylate as the linker and a N-containing organic molecule as
the template. Instead, what normally happens is that both the carboxylate
anion and the N-containing molecule directly coordinate to the uranyl centres.
For example, UO2(C6H8O4)(C10H8N2) (C6H8O4 stands for adipate and
C10H8N2 for 4,4 0 -bipyridine) is a uranyl compound with a structure consisting
of chains formed by the adipate groups and the uranyl units along the c axis.
These chains are linked together through 4,4 0 -bipyridine groups to form sheets
which are arranged in a three-way interpenetrating manner. Cahill et al. have
tried the construction of U(VI) compounds using multiple linker species, and a
number of new compounds with various topologies have been obtained. In
these compounds, the alipathic carboxylates are always linker species whereas
the aromatic pyridyl species act as either linkers or non-coordinating charge
balancing guests.
The hydrothermal reactions38 of UO2(NO3)2 with 1-oxo-4-cyanopyridine
(ocpy) and ethyl (S)-lactate lead to the formation of two chiral 2D uranyl
compounds, uranyl-bis(1-oxo-4-pyridylcarboxylate) UO2(opyca)2 and homo-
chiral uranyl-bis[(S)-lactate]. The structure of UO2(opyca)2 has a distorted
pentagonal bipyramid as the local coordination geometry around each U atom
centre, defined by seven oxygen atoms from two carboxylate groups, two
N-oxide and two oxo groups. The local coordination geometry around each
U(VI) centre in uranyl-bis[(S)-lactate] is similar to that found for UO2(opyca)2
but in this compound there are two crystallographically independent U(VI)
centres. At room temperature both compounds emit green light typical of uranyl
emission. Furthermore, the two compounds show nonlinear optical properties,
and the second harmonic generation coefficients of the powder samples are 0.4
and 0.1 times that of urea, respectively. The uranyl-bis[(S)-lactate] compound
also exhibits ferroelectric effects.
Through a hydrothermal technique, Thuery successfully synthesized two new
uranyl-organic polymeric compounds39 using citrate (cit) and tricarballylate
(tca) as structure linkers. The compounds are either 3D ([(UO2)2(Hcit)2]2) or
2D (uranyl-tca). O’Hare et al. reported40 the synthesis of several interesting
uranyl–organic framework compounds, in which the uranyl units are connected
by bidentate dicarboxylate anions such as succinate, glutarate and isophthalate.
Some of the as-prepared compounds contain cavities in which water and
organic species are accommodated. However, the thermal stability of the
compounds has not been demonstrated. The same research group also synthe-
sized and structurally characterized41 four new uranium isonicotinate frame-
work compounds which crystallize in the UO2(CH3CO2)
2H2O–HF–
isonicotinic acid system. The dimensionality of the hydrothermally obtained
uranyl isonicotinates varies from zero UO2(C5H5NCO2)(CH3CO2)2, to one
86 Chapter 5
[UO2F2][C5H5NCO2] and [UO2F3][C5H6NCO2]
0.5H2O, and two [UO2F2]2
[C5H5NCO2]
H2O. The material UO2(C5H5-NCO2)(CH3CO2)2 is composed of
UO8 hexagonal bipyramids in which the uranyl centre is coordinated by
two acetate and one isonicotinate ligands. The 1D compound [UO2F2][C5H5N-
CO2] consists of chains of edge-sharing [UO3F4] pentagonal bipyramids with
isonicotinate ligands, whereas the other 1D compound, [UO2F3][C5H6N-
CO2]
0.5H2O, is constructed from edge-sharing chains of [UO2F5] pentagonal
bipyramids and a hydrogen-bonding network of isonicotinic acid. The material
[UO2F2]2[C5H5NCO2]
H2O contains uranium oxyfluoride layers consisting of
edge-sharing dimers of UO3F4 and the corner-sharing UO3F4 chains. It seems
that the fluoride ions play an important role in the construction of these uranyl
isonicotinate compounds.
3,4-Pyridinedicarboxylic acid (3,4-pydaH2) and 2,4-pyridinedicarboxylic
acid (2,4-pydaH2) have also been used to react with uranyl cations under
hydrothermal conditions and two new uranium coordination polymers
(UO2)3(m3-O)(m3-OH)2-(3,4-pydaH)(3,4-pyda)0.5 and [(UO2)3(m3-O)(m3-OH)
(m2-OH)(2,4-pyda)(H2O)2]
H2O have been prepared.42 The former compound
features a wave-like 2D layer constructed by 1D UO(OH) ribbons and the
3,4-pyda ligands, whereas the latter compound consists of a planar ‘‘open-
layer’’, which is constructed by the UO(OH) polyhedra and the 2,4-pyda
ligands. The photoluminescent properties of the compounds depend on both
the ligands and the structural features of the inorganic building units.
UO2(pdc)(H2O) (pdc stands for pyridine-2,6-dicarboxylic acid) is a helical
chiral compound formed by coordination of uranyl units by pdc molecules.43
The material is thermally stable up to at least 350 1C and exhibits considerable
adsorption capacity for water and methanol upon removal of the guest species in
the microporous channels. Although the structure of this compound was previ-
ously described by Immirzi44 and its luminescence was discussed by Thuery and
co-workers,45 the existence of disordered water molecules in this compound was
not noticed. It is of interest that the helical arrangement (Figure 2) of the uranyl
ions and the pdc molecules generates a nano-channel with a diameter of about
6.36 Å. The void volume of the channels is estimated to be 20.4% of the total
volume of the compound. The compound does not adsorb ethanol after dehy-
dration, probably because the pore size is not large enough to allow the
penetration of ethanol molecules after dehydration, which leads to the shrinkage
of the crystal structure and consequently the puckering of the helical channels.
From a hydrothermal reaction system containing uranyl ions and carboxylic
acids, two new uranyl-organic compounds [(UO2)3O(OH)3(NA)2]
H3O1
(HNA ¼ nicotinic acid) and (UO2)2(phen)2(BTEC) (H4BTEC ¼ 1,2,4,5-
benzenetetracarboxylic acid, phen ¼ 1,10-phenanthroline) were crystallized.46
The former compound consists of infinite helical polyoxouranium ribbons built
up from trinuclear [(UO2)3O(OH)3]1 units and NA ligands, whereas the latter
is composed of 2D sheets joined together through p–p interactions. Both
compounds show intense emission under excitation of UV light.
Both homometallic and heterometallic uranyl-organic polymers can be pre-
pared by using pyridine-dicarboxylate (pdc) as a linker.47 A homonuclear
Metal–Organic Coordination Polymers 87

Figure 2 View of the 3D structure of UO2(pdc)(H2O) (a) along the c axis, (b) a single
channel formed by each single-stranded helix and (c) the single-stranded
helix along the a axis.

uranyl ‘‘end-member’’ UO2(C5H2N2O4)(H2O) with a layered structure has been

crystallized in the presence of pdc molecules and uranyl ions, and interestingly,
the uranyl cation is bound to both carboxylic groups and the N/O sites. If
Cu(II) centres are added into the reaction system, a heterometallic Cu(II)- and
U(VI)-containing compound (UO2)Cu(C5H2N2O4)2(H2O)2 in which the uranyl
centres remain coordinated to O-donor sites is formed. It is noted that the
luminescent property appears to be influenced by the Cu(II) centre as
UO2(C5H2N2O4)(H2O) is highly luminescent but (UO2)Cu(C5H2N2O4)2(H2O)2
is not. The presence of Cu(II) cations may quench the photoluminescence of the
uranyl units. A similar phenomenon has been observed in the uranyl-4,5-
imidazoledicarboxylic acid (4,5-idca) system. The uranyl ‘‘end-member’’,
(UO2)(C5H2N2O4), also shows N/O coordination and chelation. Addition of
Cu(II) to the reaction system leads to two higher-dimensional compounds
(UO2)2(C5N2O4H)2(C5N2O4H2)4Cu3(H2O)2
2H2O and (UO2)2 (C5H2N2O4)2
(OH)2Cu
2H2O. The former contains two distinct coordination geometries for
the Cu(II) sites (square planar and octahedral coordination), whereas the latter
contains sheets of [(UO2)2O8] dimers linked through dicarboxylate groups that
are also coordinated to Cu(II) centres in square planar geometry.
The uranyl cation can also form heterometallic polymeric compounds in
combination with Pb(II) centres through the use of 2,6-pyridinedicarboxylic
acid (H2pdc). In this case, two 3D structures [(UO2)(C7H3NO4)2Pb2(C2O4)
(H2O)2] and [(UO2)(C7H3NO4)2Pb
2H2O] have been prepared.48 Both com-
pounds contain edge-sharing uranyl and Pb(II) polyhedra. The first compound,
[(UO2)(C7H3NO4)2Pb2(C2O4)(H2O)2], consists of uranyl hexagonal bipyramids
edge-sharing with Pb(II)O6 octahedra to form trimers, which are linked by
88 Chapter 5
2,6-pydc into sheets. Interestingly, these sheets are connected through oxalate
ligands presumably formed from decarboxylation of the pydc linker.49
The second compound, [(UO2)(C7H3NO4)2Pb
2H2O], shows similar local
geometry about the metal centres.
Using Zn(II) acetate and uranyl acetate as reactants, we successfully prepared
a novel 3D coordination polymer comprising inorganic U–O–Zn-clustered
double sheets and organic ligands (ZnO)2(UO2)3(NA)4(OAc)2 (HNA stands
for nicotinic acid; HOAc for acetic acid) from a hydrothermal reaction system.50
X-Ray diffraction reveals that the structure of the compound is 3D (Figure 3)
with rich coordinations, including eight-coordinate hexagonal bipyramidal U(1)
cations, seven-coordinate pentagonal bipyramidal U(2) cations, six-coordinate
octahedral Zn(1) cations, and five-coordinate trigonal bipyramidal Zn(2) cati-
ons. Thermogravimetric analysis indicates that the coordination polymer is
rather thermally stable (up to 400 1C), due to the formation of U–O–Zn double
layers that solidifies the flexible organic ligands. It is interesting to note that the
compound shows semiconducting properties and it may be regarded as a 2D
semiconductor material. Under illumination without external electric field, the
surface photovoltage spectrum (SPS) of the compound shows two main re-
sponse bands at approximately 350 and 463 nm. Furthermore, photocurrent has
also been observed for the compound. The successful synthesis of (ZnO)2
(UO2)3(NA)4(OAc)2 and the discovery of its unusual physical properties suggest
that it is possible to prepare new semiconducting materials based on coordina-
tion polymer compounds containing actinides.

Figure 3 The 3D framework of (ZnO)2(UO2)3(NA)4(OAc)2 viewed along the [100]

direction.
Metal–Organic Coordination Polymers 89
A zinc(II)-containing uranyl–organic coordination polymer (UO2)2
(m2-OH)(pdc)2Zn(bpy)(OAc)2(H2O)9 (H2pdc ¼ pyridine-2,6-dicarboxylic acid,
bpy ¼ 4,4 0 -bipyridine, HOAc ¼ acetic acid)51 has also been synthesized. In this
compound, there exist voids generated by the stacking of the (UO2)2
(m2-OH)(pdc)2(OAc)Zn(bpy) chains, and these voids are occupied by water
chains each consisting of a cyclic water tetramer and a water pentamer. It is
believed that these infinite water chains play an important role in the stab-
ilization of the crystal structure.
It has also been demonstrated that uranyl and the d10 silver(I) ion are able to
form heterometal–organic coordination polymers.52 For example, we success-
fully obtained [Ag(bipy)(UO2)(bdc)1.5] (bipy ¼ 2,2 0 -bipyridyl, bdc ¼ 1,4-ben-
zenedicarboxylate) and [Ag2(phen)2UO2(btec)] (phen ¼ 1,10-phenanthroline,
btec ¼ 1,2,4,5-benzenetetracarboxylate) through hydrothermal assembly of
the metal sources with mixed ligands. Both compounds feature a 2D network
with p–p overlap interactions between the aromatic fragments in the neigh-
bouring layers. In the structure of [Ag(bipy)(UO2)(bdc)1.5], the uranyl units are
connected by bridging bdc ligands to produce chains. These chains are linked
by additional bdc groups to form a 2D network with [Ag(bipy)]1 subunits. The
structure of [Ag2(phen)2UO2(btec)] is composed of 2D layers with Ag–UO8–Ag
trinuclear cores linked by bridging btec ligands. These two compounds are
insoluble in water and they show photocatalytic degradation performance
superior to that of commercial TiO2 (Degussa P-25) when tested on nonbio-
degradable rhodamine B (RhB) as model pollutant. It is remarkable that
[Ag(bipy)(UO2)(bdc)1.5] also shows photocatalytic activity under visible-light
irradiation. On the basis of the monitored intermediate species and the final
mineralized products, the relationship between the structure of the photocat-
alysts and the photocatalytic activity has been elucidated, and it is believed that
the photodegradation of RhB in aqueous solution catalyzed by the two uranyl–
Ag compounds involves photoexcitation of the uranyl centres and molecular
oxygen.
In combination with divalent nickel cations, uranyl species may be assembled
to form microporous frameworks under the assistance of organic ligands. For
instance, a uranium–nickel–organic hybrid compound53 with micropores [Ni2
(H2O)2(QA)2(bpy)2U5O14(H2O)2(OAc)2]
2H2O (HOAc ¼ acetic acid; bpy ¼
4,4 0 -bipyridine; H2QA ¼ quinolinic acid) has been crystallized from a hydro-
thermal system, and this compound exhibits photocatalytic activity for the
degradation of methyl blue as a model pollutant. The structure of the com-
pound is a 3D network (Figure 4) constructed from the polyoxouranium
ribbons and Ni metal–organic layers through sharing QA ligands, in which
the polyoxouranium ribbons are composed of a UO8 hexagonal bipyramid and
two different UO7 pentagonal bipyramids. There are channels in the frame-
work structure, and these channels are occupied by disordered water molecules.
It has also been proved that the compound is thermally stable, and upon
dehydration, the material reabsorbs water molecules. Nevertheless, this metal–
organic-framework material shows no N2-adsorption capacity, probably be-
cause the pore size is not large enough to allow the penetration of N2 molecules.
90 Chapter 5

Figure 4 View of the structure of [Ni2(H2O)2(QA)2(bipy)2U5O14(H2O)2(OAc)2]

2H2O along the b (left) and a (right) axes.

5 p-Block Metal Coordination Polymers

p-Block metal coordination polymers are relatively rare. This class of coordi-
nation polymer compounds reported so far are mainly constructed from metal
centres of Pb and Al. [Pb(dimb)(DMF)(NO3)2] is a polymeric compound with a
1D zigzag chain structure, whereas [Pb(dimb)(SCN)2] (dimb ¼ 1,3-bis(imida-
zol-1-ylmethyl)-benzene) possesses a 2D corrugated network composed of
24-membered M2L2 metallocyclic rings. The structure of [Pb(bimb)1.5
(NO3)2](DMF) [bimb ¼ 4,4 0 -bis(imidazol-1-methyl)-biphenyl] contains a 1D
infinite noninterpenetrated molecular ladder with cavities, and DMF molecules
fill the channel formed by two adjacent ladders. All three complexes exhibit
third-order nonlinear optical (NLO) properties.54
The hydrothermal reaction of 5-hydroxyisophthalic acid (H3L) with lead and
nickel ions results in a heterometallic polymer Pb6Ni(m3-OH)8(La)2 containing
heptanuclear [Pb6Ni(m3-OH)8]61 units and a homometallic compound
[Pb(Lb)(H2O)]
(H2O)0.25 consisting of 1D lead oxide chains,55 where La and
Lb stand for 4,6-dinitro-5-hydroxyisophthalate and 2,4-dinitro-5-hydroxy-
benzoate, respectively. Obviously, the ligands are formed from in situ hydroxyl
directed dinitration of the L molecules during the hydrothermal reaction.
Assembly of 4,4 0 -bipyridine N,N 0 -dioxide (bpno) and lead(II) nitrate with or
without dicyanamido ions (dca) in aqueous solution leads to two coordination
polymer compounds Pb2(bpno)4(dca)2(NO3)2Pb2(bpno)4(NO3)4
5H2O and
Pb(bpno)(NO3)2
H2O.56 Both compounds consist of dinuclear Pb(II) units
bridged by bpno ligands, and the former material possesses a bilayered rhom-
bus grid whereas the latter has a monolayered rhombus grid. Upon excitation
by UV light at room temperature, the two compounds emit intense visible light
at wavelengths 616 and 617 nm, respectively.
Through use of different dicarboxylate linkers and nitrogen-containing
ligands (NCLs), a variety of lead(II) materials with rich architectures have
been synthesized hydrothermally or solvothermally.57 On the basis of synthesis
and structural characterization, we have elucidated the effects of ligands and
solvents on the construction of the coordination polymers. In addition, the
photoluminescence and nonlinear optical properties of these compounds have
Metal–Organic Coordination Polymers 91
been investigated in detail. It has been found that the NCLs, the organic acids,
and the solvents all affect the network structures of the coordination polymer
products. The geometry and size of the NCLs which provide potential supra-
molecular recognition sites for p–p stacking interactions, are essential in
determining the structures of the final metal assemblies. Through changing
solvents, the cis and trans conformations of H2CHDC are separated com-
pletely, and the large PbII wheels ([Pb8(cis-CHDC)8]) with bridging carboxylate
oxygen atoms are isolated successfully. The photoluminescence and nonlinear
optical properties of the compounds indicate that they may be good candidates
for luminescent materials.
Loiseau and co-workers described58 the hydrothermal synthesis and struc-
tural characterization of an interesting aluminium 1,4-benzenedicarboxylate
coordination polymer Al(OH)[O2CC6H4CO2]
[HO2CC6H4CO2H]0.70 (desig-
nated MIL-53 as (Al)). The 3D framework of this compound is built up of
infinite chains of corner-sharing AlO4(OH)2 octahedra, which are intercon-
nected by the 1,4-benzenedicarboxylate groups, creating 1D rhombic-shaped
tunnels. Disordered 1,4-benzenedicarboxylic acid molecules are trapped inside
these tunnels, but these guest molecules are removable through simple heating,
leading to a nanoporous open-framework (MIL-53 ht (Al)) with empty pores.
This solid shows a surface area of 1590 m2 g1 and is thermally stable up to
500 1C. It is interesting to note that after removal of the occluded 1,4-benzene-
dicarboxylic acid molecules, the compound reversibly adsorbs water molecules
which interact with the framework of the compound through H-bonds.
MIL-96, an aluminium trimesate Al12O(OH)18(H2O)3(Al2(OH)4)[btc]6

24H2O, was also prepared59 under hydrothermal conditions in the presence of
1,3,5-benzenetricarboxylic acid (trimesic acid or H3btc). The structure of MIL-96
features a 3D framework consisting of trinuclear oxo-bridged aluminum clusters
and infinite chains of AlO4(OH)2 and AlO2(OH)4 octahedra which form a
honeycomb lattice based on 18-membered rings. The 3D framework of MIL-
96 possesses three types of cages, two of which have pore volumes of 417 and
635 Å3, respectively. The third type has a smaller pore volume and contains
disordered octahedral aluminium Al(OH)6. This material is able to adsorb both
carbon dioxide and methane at room temperature and hydrogen at 77 K.

6 Perspectives
MOCPs show remarkable structural diversity, and in principle it is possible to
design the framework structures of these compounds and to synthesize them
rationally. It is also envisaged that through using ligands with functional
groups, MOCPs with various properties may be achieved. Although the ther-
mal stability of metal–organic compounds is generally lower than conventional
zeolite materials, the lower framework densities and higher surface areas, the
framework flexibility and the ease of topological adjustment for MOCPs render
this novel class of materials very attractive as efficient adsorbents, as gas
storage media, and as catalysts under mild conditions. The intrinsic properties
92 Chapter 5
(such as magnetism and luminescence) of the metal centres in a coordination
polymer may also lead to the appearance of new functions associated with the
polymeric compound. It is anticipated that MOCP materials will play increas-
ingly important roles in various application fields.

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CHAPTER 6

Elucidating Crystal Growth in

Nanoporous Materials:
The Importance of Microscopy
MICHAEL W. ANDERSON, L. ITZEL MEZA, JONATHAN
R. AGGER, MARTIN P. ATTFIELD, MARYAM SHÖÂEÈ,
CHIN B. CHONG, AYAKO UMEMURA AND
COLIN S. CUNDY
Centre for Nanoporous Materials, School of Chemistry, The University of
Manchester, Oxford Road, Manchester M13 9PL, UK

1 Introduction
A picture is worth a thousand words or a micrograph is worth a thousand pieces
of data. Microscopy has always had the distinct scientific advantage of the
power of persuasion, which, of course, is a double-edged sword. Nonetheless,
this is a significant advantage when deployed correctly and effectively. This is
illustrated eminently in the field of nanoporous materials where microscopy has
aided scientists to better understand the complexities of structure and crystal
growth. With the advent of high-resolution electron microscopy in the late 1970s
and early 1980s scientists were able to see for the first time, with their own eyes,
the pore structure of zeolites which is the seat of their incredible adsorption,
cation exchange and catalytic properties. Properties which were known by
scientists such as R.M. Barrer1 and D.W. Breck2 for decades previously and
yet to be able to see the pore architecture was, at the time, awe-inspiring.
I (MWA) remember an undergraduate lecture at the University of Edinburgh
delivered by the late Barrie Lowe, a zeolite chemist with a fascination for zeolite
synthesis. He was giving a final year lecture in 1980 on solid-state chemistry and

Many of the foundations of electron microscopy in nanoporous materials were laid down in the
early 1980s by the Cambridge group headed by J.M. Thomas. These principles have been carried
forward and in this paper we discuss some of the latest results from atomic force microscopy and
high-resolution electron microscopy and put these into a historical perspective.

95
96 Chapter 6
was relishing the opportunity to tell us about his personal fascination with
zeolites. But he was particularly excited that day because he had just read a
paper3 from the Cambridge group, headed by J.M. Thomas, which showed a
high-resolution electron micrograph of zeolite A revealing the pore structure
and cage units (see Figure 1). It brought to life the subject that Lowe had been
studying himself for much of his career.4 Indeed that early paper by Bursill
et al.3 is remarkable in that they had chosen a particularly difficult zeolite to
image, the high aluminium content rendering the zeolite particularly susceptible
to beam damage in the electron microscope. Indeed much of that paper
concerned the fragility of the structure in the electron microscope and tech-
niques to circumvent these problems. More recently with the development of
much higher accelerating voltages, HREM may be applied to highly beam
sensitive systems such as zeolite A with greater ease. Figure 2 shows an HREM
image of a complete nano-crystal of zeolite A recorded at 1 MeV accelerating
voltage. At such high energy, the cross-section for capture of the electron is
substantially diminished and consequently the sample is less susceptible to beam
damage. This image, recorded by the group of Osamu Terasaki (currently at the
University of Stockholm and a previous colleague of J.M. Thomas) shows
the remarkable clarity in the image, in particular at the surface of the crystal
which is beginning to reveal the important surface structure relevant to crystal
growth processes. The early paper on zeolite A also opened a window to the
study of defects and intergrowths in zeolites. This latter ability of microscopy
techniques to study non-periodic effects, such as defects, is crucial, as the crux of

Figure 1 Early transmission electron micrograph with simulation of the (001) zone
axis of zeolite Na-A by Bursill et al.,3 reproduced with permission from the
authors.
Elucidating Crystal Growth in Nanoporous Materials 97

Figure 2 Recent transmission electron micrograph of the (001) zone axis of nano-
crystalline zeolite Na-A recorded at 1 MeV accelarating voltage. Courtesy of
Osamu Terasaki.

real solid-state chemistry, stucture and function, is often governed by imperfec-

tions. This was to be the theme of many electron microscopy studies over the
next decades with much of the early work emanating from the Cambridge
group.5–15 But it was the enthusiasm of Barrie Lowe in his final year under-
graduate lecture which inspired MWA to pursue a PhD in zeolite chemistry and
indeed, perhaps to the annoyance of the group in Edinburgh, not to do a PhD in
Edinburgh but to move to Cambridge where he completed his PhD under the
guidance of J.M. Thomas. A quarter of a century later MWA finds his research
on the crystal growth of nanoporous materials relying heavily on microscopy
techniques. Still high-resolution transmission electron microscopy, but even
more key is the use of atomic force microscopy (AFM), a technique which had
not been invented in 1980.16,17 With AFM it is possible to measure with
precision the surface topography with sub-nanometre resolution. Figure 3
shows the surface topography of zeolite A recorded on an AFM integrated
with a high-power inverted optical microscope. This has the ability to position
the AFM tip on a desired crystal facet and also, as seen in Figure 3, to
superimpose the AFM image onto the optical micrograph. This technique has
been invented in particular for studying biological samples, however, it is also
particularly useful for crystal growth studies. Square terraces are immediately
apparent on the (100) crystal surface of zeolite A and the terrace height can be
measured accurately to be 1.2  0.1 nm. AFM also has the distinct advantage
98 Chapter 6

Figure 3 AFM of zeolite A showing surface topology superimposed on optical

micrograph of crystal. Terraces are 1.2 nm high and illustrate layer-by-layer
crystal growth.18

that it may be performed in solution under conditions suitable for crystal

growth. Such images, as discussed later, are therefore helping to reveal the
nature of fundamental crystal growth processes.

2 Crystal Growth: Learning from Defects

and Intergrowths
The most important aspect of a nanoporous crystal, with pore diameter of
dimensions from sub-nanometre up to about 1.4 nm, is the exceedingly high
surface area and confined geometry of the pore architecture. However, in
addtion to these geometrical constraints, the high electrical fields generated
within these nano-dimensioned cavities are responsible for many of their
important industrial applications. Consequently, understanding the details
of this crystal architecture is paramount. The crystals form this special
structure during nucleation and crystal growth from a solvo-thermal synthesis.
For zeolites, the solvent is normally water and the temperatures required range
from room temperature to 200 1C. Typical zeolite crystals are relatively
small with sizes ranging from ca. 100 nm to 200 mm. Similar to
all crystals, zeolites incorporate defects during growth. These defects are
extremely well defined and, because of the complex architecture of the zeolite
framework, the nature of these defects is often unique to a particular zeolite
structure. Furthermore, owing to the strong covalent bonding of the frame-
work, these defects will not readily migrate and anneal and as a conseqence
Elucidating Crystal Growth in Nanoporous Materials 99
they provide a signature of the crystal growth mechanism. In other words, any
growth mechanism postulated for a zeolite must be able to describe not only
the development of the regular crystalline framework but also the incorpora-
tion of specific aperiodic defect structures.19 Defects can be either local or
extended. In order to characterise the former, usually a short range spec-
troscopic approach such as infra-red or nuclear magnetic resonance spectro-
scopy is suitable. However, for extended defects, microscopy methods are
ideal. An illustration of the extreme complexity of extended defect structures
in zeolites was illustrated early on by the Thomas group (see Figure 4) in

Figure 4 HREM of zeolite L showing co-incidence boundary caused by a rotation of

the zeolite structure,12 adapted with permission from the authors.
100 Chapter 6
12
zeolite L. A curious coincidence boundary is formed by the rotation of one
layer of the zeolite L structure by 32.2 1. The resulting structure exhibits
coincidence of pores running in the (001) direction with a superlattice repeat
O13 times that of the original. As the new tunnel structure passes the full
length of the crystal, this can be seen easily in projection in the high-resolution
electron microscope. Other defects seem at first sight more conventional
in nature such as the screw dislocation observed in zeolite A. The dislocation
is most prominently revealed in the AFM images of the (100) surface, see
Figure 5, which show spiral terraces.20 Such spiral growth is a conventional
manner for crystal growth in dense phase materials, with the centre of the
spiral located at a screw dislocation running through the crystal. In zeolites the
phenomenon is harder to understand as a spiral around the screw dislocation
would require a diplacement Burger vector of tens of ångstroms in order for
the structure to reconnect without dangling bonds. The associated strain could
be accommodated by a mesoscopic void running through the crystal, around
which the screw dislocation is wound. Indeed there are indications from the
AFM images in Figure 5 that such a mesoscopic void exists. The size of this
void is difficult to judge as the hole observed by AFM is a convolution of the
AFM tip shape and the void. Interestingly, however, Slater et al.21 demon-
strated in a theoretical examination that a screw dislocation could be accom-
modated with little strain without any mesoscopic void. This is also shown in
Figure 5 whereby a twist in the structure allows reconnection and the strain is
relieved within a few unit cells.
Another good example whereby the defect and intergrowth structure in
a nanoporous material could be usefully controlled is the titanosilicate
ETS-10.22,23 Figure 6 shows a HREM image of ETS-10 which is a wide-pore
three-dimensional channel structure. It is a particularly interesting material for
a number of reasons. First, unlike an aluminosilicate zeolite where each
aluminium in the structure has a one minus charge, the octahedrally coordi-
nated titanium in ETS-10 has a two minus charge. As a consequence, ETS-10
has a very high affinity for divalent charge-balancing cations which makes it
particularly attractive for removal of heavy metal contaminants from aqueous
environments. Second, ETS-10 exists naturally as a random intergrowth be-
tween two end-member polymorphs. As can be seen from Figure 6, the stacking
of the main channels from the bottom of the micrograph to the top is randomly
to the left and right. One ordered polymorph, termed Polymorph A,22,23 has an
ordered arrangement left/right/left/right . . . (see Figure 6). If this polymorph
could be synthesised it would have a large spiral channel running through the
structure. Synthesis of such chiral structures in microporous oxides is elusive
and requires a much deeper understanding of the growth mechanism. How
ETS-10 grows is partly revealed by the presence of extended defects in ETS-10,
the double pores in Figure 6. These double pores must be incorporated as a
result of a layer-by-layer growth process. Therefore, in order to affect the
nature of a subsequent layer it will be necessary to prime the growing surface
which either encourages the desired next layer or prevents the unwanted layer
forming.
Elucidating Crystal Growth in Nanoporous Materials 101

Figure 5 AFM of (100) surface of zeolite A (lower four images showing spiral
growth.20 The upper structures illustrate possible screw dislocations deter-
mined theoretically.21
102 Chapter 6

Figure 6 Upper image structure of polymorph A of ETS-10 with the spiral channel cut
from the framework. The HREM image of ETS-10 below shows a random
intergrowth and defects.22,23

3 Faujasitic Structures
How crystals nucleate and grow is a problem that has challenged scientists
for many years: how order is created from disorder; the driving forces involved;
the quest for crystalline perfection.24–26 In many ways nucleation and crystal
growth should not be considered as separate phenomena, however, for
practical reasons it is useful to do so. The techniques at our disposal to follow
the nucleation and crystal growth stages are substantially different and
therefore there is often a visible seam between our perception of the two
processes. In terms of crystal growth, the advent of scanning probe micro-
scopies16 (SPM) and in particular AFM17 has permitted the detailed
Elucidating Crystal Growth in Nanoporous Materials 103
observation of nanometre-sized events at crystal surfaces. This is often possible
under in situ crystal-growth conditions as the technique can be operated to
observe surfaces under solution. Real-time images of growing crystals have
revealed terrace growth, spiral growth, the inclusion of defects and the occlu-
sion of foreign particles in a wide variety of growth studies.27,28 We have
recently recorded the first ever in situ images of the alteration of a zeolite
surface under a variety of supersaturation conditions.29 By measuring real-time
micrographs at a range of temperatures, the free-energy for individual growth
processes can be determined. To date most of these crystal growth studies have
been on dense phase ionic crystals, such as calcite, or molecular crystals, such as
proteins and viruses. There has been a modest amount of work performed on
nanoporous crystals such as zeolites and zeotypes of which we have been at the
forefront.30–39 The reason for this is two-fold: first, often the most interesting
open-framework structures can only be crystallised as micron-sized crystals,
making observation by AFM demanding; second, there has been a recent
emphasis within the community on making new materials rather than on
understanding formation. In our view, this is an oversight which is clear by
the vast amount of new information forthcoming on understanding crystal
growth in macromolecular systems which is helping to address problems such
as: overcoming crystal size limitations; improving crystal purity; controlling
intergrowth structures and controlling crystal habit. In open-framework
materials a better understanding of the crystal growth processes will lead to
new methodologies to control similarly important crystal features. But further-
more it could lead to both new structures and also more cost-effective routes to
existing but prohibitively expensive known structures.
Figure 7 illustrates an interesting example of how materials with similar
framework topologies grow via different crystal growth mechanisms. The
crystal system is the industrially important faujasite (FAU) topology. The
archetypal synthetic zeolite in this class is zeolite Y, used in the catalytic
cracking of petroleum fractions. Zeolite Y is an aluminosilicate cubic frame-
work structure typically synthesised from an alkaline aluminosilicate gel at
elevated temperature. However, the framework structure is amenable to rep-
lication with a variety of framework elements. One example discovered by Gier
and Stucky40 in 1991 was the zincophosphate analogue of the FAU structure.
The synthesis was carried out at very low temperature, ca. 4 1C, from an
initially clear solution. Similar to a zeolite, the zincophosphate has an anionic
framework which must be counterbalanced by extra-framework cations. This
synthesis was further tailored by the group of Prabhir Dutta34 who were
attempting to control the synthesis conditions in order to synthesise perfect
crystals. They adopted a method that relied on the preparation of micron sized
reaction vessels inside reverse micelle surfactant phases. The micro-water
droplets acted as micro-reactors. Using this method they were able to synthesise
crystals of very high quality. Figure 7 compares the surface topology of a
typical conventional aluminosilicate zeolite Y synthesis, which we reported,30
with that of a zincophosphate with FAU structure synthesised in a reverse-
micelle system.34 In both cases growth terraces are observed indicating a
104 Chapter 6

Figure 7 AFM images of the (111) surface of the FAU structure. Top image
aluminosilicate zeolite Y. Lower image ZnPO-X synthesised in a reverse-
micelle condition, reproduced by courtesy of the author.34
Elucidating Crystal Growth in Nanoporous Materials 105
layer-by-layer growth process. Also the terraces in both systems are approxi-
mately triangular, reflecting the three-fold symmetry along the (111) direction,
with terrace height ca. 1.5 nm. The height is indicative of an FAU sheet, a
fundamental structural unit of the FAU framework. However, the terraces
differ in one very important aspect, namely the orientation of the triangular
terraces with respect to the triangular (111) facet of the crystal. In the conven-
tional aluminosilicate zeolite Y, the terraces are rotated 60 1 with respect to the
crystal facet. In the zincophosphate system synthesised in reverse micelle the
terraces have coincident orientation with the crystal facet. The orientation of
these facets will be a direct result of the growth mechanism on this facet that
must be substantially different in order to effect the orientation change in the
terrace. In order to decipher the reason for this difference will require modelling
of the mechanism, similar to that shown later for zeolite A, but hitherto this
remains a matter for debate.

4 Zeolite A Transformations
Zeolite A is one of the most important commercial zeolites as it is used in
washing powders as a water softening agent and desiccant. AFM is beginning
to reveal some of the molecular events that occur during crystal growth.31,36
Figure 8 illustrates a typical AFM topography measured on the (100) surface of
zeolite A. This particular micrograph has been chosen because it exhibits many
different features on the one crystal, however, the occurence and abundance of
the different features is a function of the crystal growth conditions such as
temperature, supersaturation, pH, starting reagents, etc. First, the (100) surface
exhibits square terraces with the edges of the terraces aligned with the (100)
direction of the crystal. The principal step height of these terraces is
1.2  0.1 nm, equivalent to half a unit cell. The well-defined terrace topology,
both height and straight terrace edges, indicates that certain surface structures
have lower surface free-energy and are consequently more stable. It should be
pointed out that the AFM of crystals such as that shown in Figure 8 are
recorded on crystals that have been removed from the growing medium and
washed. Consequently the topologies observed will be the stable structures
which, although very important for the growth mechanism, will not give the full
picture of crystal growth. Also shown in Figure 8 are curved growth fronts.
These occur when two growing terraces merge creating a kink site at the point
of union. This kink site becomes the preferred growth point and a curved
growth front ensues until a new rectangular growth front is created. This has
been verified by modelling studies some of which are given in a later section of
this chapter. The morphology of the terraces, curved growth fronts and density
of separate growth nuclei yield the relative rates of surface nucleation, growth
at edge sites and growth at kink sites. Also shown in Figure 8 is a preponder-
ance of pyramid structures. This is a very common feature in zeolite A growth
and these can be easily seen in scanning electron micrographs as the height
of the pyramids can be tens of nanometres. Careful inspection of the
AFM micrographs shows that there is a defect at the centre of each pyramid
106 Chapter 6

Figure 8 AFM of (100) surface of zeolite A showing surface topology illustrating

square terraces, curved growth fronts, pyramids and defects.20

which causes the terraces all to nucleate at the same lateral position on the (100)
surface. These defects are removed preferentially during dissolution experi-
ments indicating that they are structurally less stable. This is an important part
of the growth mechanism in zeolite A, especially in crystals that are grown from
nutrient which has not been carefully filtered in order to remove fine impurities.
Indeed, when reaction mixtures are filtered, the resulting crystals do not exhibit
these pyramids and the surface topology does not indicate the presence of
defects. This suggests that the defects may well be associated with foreign
particles. Finally, Figure 8 shows substantial crack defects in zeolite A, another
feature which is typical when there are impurities in the starting nutrient.
Zeolite A does not only grow layer-by-layer but also, as pointed out previously,
via spiral growth as shown in Figure 5 although this is less common.
Figure 9 shows a series of atomic force micrographs which were recorded
under a solution of sodium hydroxide. Each image takes a few minutes to
record which is, consequently, the time-scale for measuring kinetic processes via
this method. Although there are some more modern methods to record atomic
force micrographs at much higher frequency, these are not very easy to adapt to
observing micron-sized crystals under solution. Initially in Figure 9 we observe
square terraces which are 1.2 nm in height.36 As the dissolution proceeds the
terrace withdraws across the zeolite surface. At short times the first parts of the
terrace to withdraw are at the holes in the terraces. These are essentially kink
sites, that were shown from the growth studies to be the preferred sites for
Elucidating Crystal Growth in Nanoporous Materials 107

Figure 9 4.3  4.3 mm2 deflection AFM images of (100) surface of zeolite A crystal
dissolving under 0.5 M NaOH.36

growth. Consequently, it is not surprising that these are the first sites to be
dissolved. As the terraces recede across the surface the terrace height is only
0.9 nm in height, in other words, not the full height of the half unit cell. Also
observed is a ‘‘shadow’’ of the withdrawing terrace which retains the original
shape of the terrace and this is only 0.3 nm in height. The terrace is therefore
being removed in a two-step process. First, by correlated removal by terrace
retreat of a 0.9 nm step followed by an uncorrelated removal of a 0.3 nm step.
The question then arises as to the nature of the units associated with these
different step heights. Zeolite framework materials are constructed from units
of well-defined structure, and it is therefore reasonable to expect that the
different heights observed in the atomic force micrographs correlate with
well-defined parts of the crystal structure. Zeolite A is composed of sodalite
cages, truncated octahedra, connected through double four-rings. The height of
one sodalite cage is approximately 0.9 nm. These sodalite cages are capped off
108 Chapter 6
with a single four-ring which is associated with another 0.3 nm step. It is
impossible to say whether these are indeed the terminations of the crystal,
however, there is strong evidence from theoretical calculations that indeed these
are the lowest energy structures at the surface of the zeolite. Therefore, we can
understand why the 0.3 nm step is removed in an uncorrelated fashion whereas
the 0.9 nm step is removed in a correlated fashion. Figure 10 shows

Figure 10 Schematic illustration of the dissolution process in zeolite A.36

Elucidating Crystal Growth in Nanoporous Materials 109
schematically the removal of different units. As can be seen, the single
four-rings are not connected to one another. Consequently, it is not surprising
that they are removed in an uncorrelated fashion. As the four-rings are not
connected to one another it is not necessary for one of the single four-rings to
be removed before its neighbour is removed. On the other hand, the sodalite
cages are connected to one another and consequently it is necessary for one
sodalite cage to be removed before the next sodalite cage can be removed. What
it is not possible to say from the atomic force micrographs is whether the
original surface is terminated with the single four-ring or with the sodalite cage.
Either explanation would fit with the experimental data. However, again from
theoretical calculations, it can be shown that the lowest energy structure is
based on the single four-ring. In order to address this question experimentally it
will be necessary to turn to high-resolution electron microscopy such as the
image shown in Figure 2. If the quality of the electron micrographs are
sufficient at the surface, and with the proviso that the images show the full
projected profile at the surface, then it should be possible to glean information
about the surface terminations. Indeed this has already been done for zeolite
L,41 zeolite Y42 and zeolite beta.43
Another very interesting feature that is observed upon the dissolution of
zeolite A can be seen in Figure 11. As the terrace withdraws it eventually breaks
up into small nano-squares which are very mono-disperse in size. They have
dimensions approximately 90  90  0.9 nm3. These nano-squares persist for
quite a long time before finally dissolving suggesting that they are in some ways
stabilised at this particular size. It is unclear why this should be the case and it
will be necessary to determine theoretically both the entropic and enthalpic
components of the process of dissolution to shed some light on this very curious
phenomenon. Further, in Figure 10 when the final nano-square is removed
from the top of the pyramid it is possible to see the underlying defect at the
centre of the pyramid as described previously.

5 Effect of Supersaturation: Silicalite System

Silicalite is another very important zeolite system. It is the purely siliceous end
member of the MFI system of which ZSM-5 is perhaps the most important
material. Figure 12 shows a scanning electron micrograph of two substantially
different types of crystals. The smaller crystals with round ends are synthesised
at relatively low temperatures and the synthesis is also stirred. The much larger
crystals that are boat-shaped are synthesised at high temperatures without
stirring. Despite belonging to the same crystal system, clearly these two crystal
habits are substantially different. The aspect ratio of the crystals is different and
the facets that are exposed, especially at the ends of the crystals, are also
different. Spectroscopic techniques also show that the smaller crystals exhibit
far fewer defects than the larger crystals. Consequently, if we can understand
something about the crystal growth mechanism in this system it should be
possible to say something about the different morphologies of these two
110 Chapter 6

Figure 11 1 mm  1 mm AFM images showing dissolution of zeolite A in mother liquor

diluted to 67%.
Elucidating Crystal Growth in Nanoporous Materials 111

Figure 12 SEM images of different morphologies of silicalite achieved by different

synthetic conditions. Scale bar 10 mm for the lower images synthesised at high
temperature and 5 mm for the upper images synthesised at low temperature.20

synthetic methods. The structure of silicalite is formed by connecting structural

chains composed principally of five-membered rings. These chains are chiral in
nature spiralling either in a left- or right-handed manner. As with any structural
enantiomorphic pair they can be connected to one another either through a
mirror plane or via a centre of inversion. The full structure for silicalite is
formed by connecting the chains in one direction via the mirror-plane and in the
orthogonal direction by an inversion centre. However, this leads to the possi-
bility of mistakes forming which are very common in this particular structure.
Indeed much of the work from the Cambridge group early on was involved
with research into intergrowths formed by such mistakes.
The surface topology of silicalite reveals a plethora of different
surface features which all give clues as to the nature of the growth mechanism.29
Figure 13 shows a variety of atomic force micrographs recorded on the larger
boat-shaped crystals. Figure 13a shows a large composite picture of a substan-
tial area of the (010) surface of silicalite. Different terrace structures can be seen
in different parts of the crystal. For instance, towards the left-hand side of the
figure and towards the centre of the figure, terraces are observed with more or
112 Chapter 6
less straight edges. The edges of these terraces run parallel to one of the
principal crystallographic directions. The height of the terraces is equivalent to
tens of unit cells, in other words they are not equivalent to a specific unit of the
structure of silicalite. Towards the right-hand side of Figure 13a the terraces are
circular in nature and the terrace height is now equivalent to one unit cell, that
is 1.0 nm. In Figure 13b some finer features are also observed emanating from
the large defect structure clearly apparent in the image. This seems to act as a
nucleation point for terrace growth in much the same way as the defect sites in
zeolite A which caused the pyramidal growth. Indeed this seems to be a
common feature in the growth of zeolites that defects and imperfections act

Figure 13 AFM micrographs showing the surface topography of silicalite. The insets
in each case show the crystal orientation and the area scanned.
(a) 27.0  7.2 mm2 amplitude image of the (010) face, (b) 3  3 mm2 ampli-
tude image of the (010) face, (c) 6 6 mm2 amplitude image of the (010) face,
(d) 7  7 mm2 amplitude image of the (100) face, (e) 7.5  7.5 mm2 amplitude
image of the (100) face.20
Elucidating Crystal Growth in Nanoporous Materials 113
as nucleation centres for growth. Of course this is not surprising as it is also a
common feature of crystal growth in dense phase systems. These large silicalite
crystals we know have a very large concentration of defects and this is likely as
a result of incorrect stacking of the growth units. We have shown that these
intergrowth structures caused by stacking sequence imperfections hinder the
growth but can be healed by an over-growth of the defect.35 This slowing down
of the growth process causes terraces to stack up resulting in these very high
features observed on the surface of the large crystals.
The atomic force micrographs shown in Figure 13 were recorded on crystals
that had been removed at the end of the synthesis from the nutrient. At this
point in the crystallisation all the silica nutrient has been exhausted and the
supersaturation is consequently very low. One way to address this issue of
supersaturation would be to record the AFM under in situ conditions. How-
ever, silicalite is grown normally at quite high temperatures well above 100 1C.
This is beyond the easily attainable temperature for AFM under solution.
Furthermore, the typical synthesis uses a gel which is opaque to the laser used
in the AFM in order to determine tip deflection. As a result it is not easy to
record measurements in situ for the silicalite system under these conditions. We
have used an alternative approach in these circumstances in order to achieve
meaningful information over a variety of supersaturation conditions. Syntheses
have been performed under continuous flow conditions whereby the supersat-
uration is maintained at a predefined level. The synthesis can then be stopped at
a particular point and the AFM recorded ex situ. This has been done for a
series of samples some of which are illustrated in Figure 14. The scanning

Figure 14 (a) and (b) show levels of supersaturation and crystal length during
crystallisation. Samples were extracted in the two highlighted regions.
(c) shows SEM images as the crystal grows.
114 Chapter 6
electron micrographs are all shown to the same absolute scale and illustrate
that the length of the crystals is increasing linearly with time. Also shown in
Figure 14 is a normal supersaturation profile as a function of time during the
crystal growth. At short times the supersaturation level is low as amorphous
nutrient is dissolved into solution. During this regime the crystal growth is very
slow. As the supersaturation increases it eventually reaches a constant and high
level at which time the crystals grow at a constant rate. At the end of the
synthesis all nutrient is consumed, the supersaturation level falls and the
crystals cease to grow. Using our ex situ method for growth we can prepare
crystals either in a regime of higher supersaturation or in a regime of low
supersaturation. The results of the AFM on a complete series of crystals
prepared in this manner are shown in Figure 15 and the results are quite
striking. The left side of Figure 15 shows the (010) face and the right side shows
the (100) face. At short times, Figures 15a–c, the atomic force micrographs are
recorded as the supersaturation level is increasing. From Figures 15d–h the
supersaturation level is high. Then the supersaturation level is allowed to drop
as the crystals equilibrate with the growing solution. Figure 15i is therefore
recorded at low supersaturation. Nutrient flow is then switched on again so that
from Figures 15j to 15m the supersaturation level is once again high. Finally the
nutrient is switched off once again such that the supersaturation level decreases.
The final atomic force micrograph, Figure 15n, is then recorded at low
supersaturation. There is a stark contrast between the atomic force micro-
graphs recorded at low and at high supersaturation. At high supersaturation
there are a plethora of nucleation sites observed covering both crystal facets. In
other words the nucleation density is very high. At low supersaturation the
nucleation density is very low, however, the terraces have continued to spread
across the surface of the facets resulting in well-defined terrace topography.
This indicates that the first process to be switched off as the supersaturation
drops is the surface nucleation. As the free-energy of a clean surface will be
lowest, the surface nucleation events will be the most energetically unfavour-
able, requiring the highest supersaturation. This issue is addressed again in the
section on modelling of crystal growth where we are able, in the computer, to
mimic these changes in supersaturation. However, this work illustrates how
fundamental growth processes can be individually switched on and off. This is
the beginning of the type of control that will be required in order to control
intergrowth structures.

6 MOFs
Metal–organic frameworks (MOFs) are a rapidly emerging class of hybrid
nanoporous materials. Their attraction derives from inclusion of both inor-
ganic and organic components within the framework. The latter may be
modified to allow for the design of materials with specific functionalities,
properties and structure.44 Certain MOFs are finding potential for commercial
application particularly in the field of selective gas adsorption. A particularly
Elucidating Crystal Growth in Nanoporous Materials 115

Figure 15 AFM images (a)–(n) on the left of (010) face and (a)–(n) on the right of
(100) face of silicalite. The images have different scales as the crystal grows.
116 Chapter 6
attractive prospect is the use of MOFs for hydrogen storage. However, indus-
trial usage will benefit from the ability to control defects and crystal habit. Such
control requires fundamental understanding of the crystal growth processes
involved. One MOF of particular interest is Cu3[(O2C)3C6H3]2(H2O)3,
HKUST-1,45 the structure of which is shown in Figure 16a.
Micrographs of (111) faces of HKUST-1 exhibit multi-nucleated growth, as
shown in Figures 16b and c. The nature of the spirals is complex – multiple,
interpenetrating spirals are often observed and these may grow in the same
direction or opposing directions. The latter phenomenon produces topography
similar to layer growth. Spirals adopt the trigonal symmetry of the growing
face. Detailed cross-sectional analyses reveal the predominant step height to be
1.5 nm, with additional step heights of 0.8, 2.2 and 3.0 nm (all 0.1 nm). These
step heights correspond to integer multiples of the 0.76 nm d222 spacing.
Whereas the separation between steps on the surface of zeolites decreases
towards the edge of the crystal, that of HKUST-1 remains constant. This is
indicative of non-diffusion limited growth, consistent with the low viscosity of
the synthesis medium.
Kink site growth does not predominate in this material. This is evidenced both
by the transition of the spiral shape from triangular to circular, Figure 16b, and
the persistence of terrace coalescence cusps, lower right portion of Figure 16c.
Faulting of the crystal surface is often observed, evidenced by streaking in the
micrographs (see Figure 17). The terrace structure is invariably commensurate
across these faults, indicative of faulting occurring after crystallisation is com-
plete. Such faulting highlights the fragility of this material and may be a
consideration for its usage in certain applications. This AFM study of
HKUST-1 is the first to be reported for a MOF material and provides insight
into its crystal growth process.

7 Modelling
The ultimate goal from this wealth of new information which has been derived
from AFM is to establish the growth mechanism and to determine activation
energies and rate constants for fundamental processes.31 Armed with this new
information it is hoped that it will be possible to control crystallisation with
precision hitherto impossible. This would allow, for instance, the preparation
of nanoporous materials in the absence, or with substantially reduced amounts,
of expensive templating agents. The question then arises how to extract the
maximum possible information from the atomic force micrographs. A process
of modelling is necessary. This can work from the bottom up or from the top
down. Working from the bottom up requires the calculation of fundamental
rate processes utilising either ab initio or molecular dynamics calculations to
determine reaction pathways. There has been considerable success recently
using such an approach for the molecular crystal system urea.46 Fundamental
rate constants were determined for particular attachment processes and these
rates used in turn to calculate crystal morphologies. The use of similar methods
Figure 16 (a) The structure of HKUST-1 viewed along (100) and AFM amplitude
images of (111) facets of HKUST-1 showing (b) a 6  6 mm2 image of a
double spiral and (c) an 8.5  8.5 mm2 image of a sextuple spiral.
118 Chapter 6

Figure 17 AFM image (8.0  8.0 mm2) of (111) face of the metal–organic framework
HKUST-1 showing spiral growth and linear defects.

for covalently bonded crystals such as framework nanoporous materials will be

substantially harder because of the complexity of the system.47 Nevertheless,
inroads have been made into the topic with the establishment of surface free
energies for realistic growth sites. The problem is compounded for zeolites by
the presence of both water and cations in the system and, consequently, most of
the initial work has been done on silica frameworks. If the rate constants can be
determined reasonably accurately then it should be possible to use that infor-
mation to calculate not only crystal morphologies but also surface topologies.
At present, in the absence of such information we are utilising a top-down
approach. In this method we start from the experimental information, that is,
crystal morphology from electron microscopy and surface topologies from
AFM. We then develop models based upon a simplified reaction mechanism to
which we assign fundamental growth rates. Using a three-dimensional model
we then compute crystal morphology and surface topology and compare this
with the experimental data. As the calculation is very rapid, at least for crystals
with a size of about half a micron, the process can be iterated until a unique set
of fundamental reaction rates gives a solution that matches the experimental
data.
Figure 18 shows an example of a three-dimensional calculation of both
crystal morphology and surface topography using this top-down approach.
The calculation in essence is suitable for a cubic system such as zeolite A or
sodalite. The structure of the zeolite is broken down into fundamental units
Elucidating Crystal Growth in Nanoporous Materials 119

Figure 18 Modelling of crystal growth in zeolite A. The three-dimensional model can

simulate both crystal morphology and surface topology in order to extract
fundamental growth rates by comparison with AFM and SEM data.48

such as cages or ring structures which are likely to be the lower energy
structures present at the surface of the crystal. A matrix is then developed
for the connectivity of these units and rates applied to those linkages depending
upon the structural neighbourhood. The accuracy of the calculation will
depend to some extent on how the local structure is differentiated. Considering
only first nearest neighbours means that only surface topography can be
calculated and not crystal morphology. Going to second nearest neighbours
120 Chapter 6
allows crystal morphology also to be determined. It is also possible to change
probabilities, or rates, as the calculation progresses and this will mimic chang-
ing supersaturation in the reaction mixture (similar to the situation that was
observed in silicalite).
Figure 18 shows three calculations with substantially different output both for
surface topology and crystal morphology. Depending upon the fundamental rate
processes either (100) facets are predominant or (110) facets become predomi-
nant. As all the rate processes become similar then the crystal morphology
becomes more or less spherical. Similarly, as kink site growth becomes predom-
inant over edge site growth then the surface terraces become more square in
nature. We are then able to compare these theoretical calculations with the
experimental data and iterate the process until a suitable match is found. In
principle it should be possible to marry the top-down and bottom-up approaches
with a unifying set of rate constants. At that point we should have a very good
model, from fundamental principles, of how these nanoporous materials grow.

Acknowledgement
We would like to acknowledge the assistance of R.J. Plaisted for help with the
continuous flow experiments. We also thank EPSRC and ExxonMobil for
funding.

References
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CHAPTER 7

Exploration of New Porous

Solids in the Search for
Adsorbents and Catalysts
PAUL A. WRIGHT AND WUZONG ZHOU
School of Chemistry, University of St Andrews, Purdie Building, North
Haugh, St. Andrews, Fife, KY16 9ST, UK

At the beginning of the 1980s, the field of ordered microporous solids, with its
well developed applications in adsorption and acid catalysis, was dominated by
aluminosilicate zeolites. These included materials prepared via fully inorganic
gel syntheses (such as zeolites A, L, Y and mordenite) as well as more siliceous
zeolites prepared with readily available organic bases that acted as structure
directing agents (SDAs). The most notable of these high silica zeolites were the
large pore zeolite Beta and the medium pore ZSM-5, both of which offered
improved properties over existing acid catalysts. The high silica materials are
stable structures with high acid strength. Furthermore, the medium pores of
ZSM-5 give excellent product selectivities, particularly in the conversions of
monoaromatics, and Beta, the first high silica zeolite with a three-dimensionally
connected pore system, finds increasing application in the conversions of larger
molecules, where it provides an alternative to zeolite Y.
Since the early 1980s, there has been a tremendous development of the
structural types of ordered porous solids. The novel structural chemistry
possessed by some of these offers improved properties in catalysis, particularly
in selective oxidation, and in adsorption, where very large pore volumes
have been observed. Furthermore, crystalline microporous solids (pore sizes
3–20 Å) were joined in the early 1990s by ordered mesoporous solids (pore
sizes 420 Å), described in the second part of this chapter. Throughout, we
will discuss recent developments in the synthesis of novel structure types
(micro- and mesoporous) and their impact (potential or actual) in adsorption
and catalysis.

123
124 Chapter 7

1 Developments in the Synthesis and Study

of Crystalline Microporous Solids
There has been tremendous activity in the synthesis of novel crystalline micro-
porous solids, which can be traced to key developments that include: expansion
of the range of inorganic composition of the frameworks, the rational design of
‘templating’ organics and the development of organic–inorganic hybrid solids
with permanent porosity. In parallel with all of these, structural methods have
been devised that are sufficiently powerful to determine the structures of
materials frequently synthesised as microcrystalline powders that are not
amenable to study by conventional laboratory single crystal X-ray diffraction.
The development of electron microscopy and synchrotron X-ray diffraction,
both single crystal and powder, have been invaluable here, frequently aug-
mented by neutron diffraction, solid state NMR and computer simulation to
establish structural details. Sir John Meurig Thomas has made major contri-
butions in all these areas, both at Cambridge and at the Royal Institution.
Early work on electron microscopy, for example, demonstrated the power of
high resolution transmission electron microscopy to identify structure and
microstructure in the important zeolite catalyst ZSM-5.1 Electron microscopy
has since developed into an indispensable tool, both in structure solution and in
the visualisation of structural intergrowths. A recent example from our own
laboratory is in the imaging of zeolite Beta,2 where the visualisation of ‘double
pore’ defects strongly supports a model of layer-by-layer growth for this
important large pore catalyst (in this case large pore refers to pores bounded
by 12 cations and 12 oxygen atoms, with a free diameter of ca. 8 Å). Pioneering
studies using the other methods to investigate the structure of zeolites with
adsorbed molecules and in situ under catalytic conditions have opened the way
to a much deeper understanding of microporous adsorbents and catalysts.

1.1 An Expanded Compositional Range

The widening of the compositional range from aluminosilicate zeolites and
their silica polymorphs to the much greater diversity we see now was prompted
by the discovery of the aluminophosphates by Flanigen and co-workers in the
early 1980s.3 They showed that tetrahedrally coordinated AlPO4 frameworks
are readily prepared with structures that are in some cases identical to those of
zeolites (A, X, Y and chabazite, for example) but also exhibit topologies not
observed as silicates, such as the very large pore VPI-5,4 which has channels ca.
1 nm in free diameter. Their chemistry can be expanded by framework substi-
tution during synthesis, for example (i) of metal cations such as magnesium,
cobalt or manganese for aluminium or (ii) of silicon for phosphorus or in a
coupled substitution for aluminium and phosphorus. These substitutions im-
part important catalytic functions to these solids, including those of selective
oxidation and acid catalysis, and it is in these areas that the group of Thomas
has made a major and sustained contribution.
Exploration of New Porous Solids 125
In most cases the acidity is not as strong as observed for zeolites of similar
structure. Indeed, this has been made use of in the application of the acidic
silicoaluminophosphate (SAPO) form of chabazite, SAPO-34, for which the
combination of acidity and pore shape gives an active and selective catalyst for
the methanol-to-olefins reaction that currently shows promise for the produc-
tion of ethylene and propylene precursors for polyolefins.5 Here the deactiva-
tion rate is slower than its aluminosilicate analogue because of its lower acidity.
By contrast, MgAPO-36, the structure of which was solved at the Royal
Institution by a combination of electron microscopy, powder diffraction and
computer modelling,6 possesses acidity comparable in strength with that of
zeolites. While some AlPO4-based solids do therefore possess combinations of
acidity and pore size giving catalysts of industrial promise they are unlikely to
supplant zeolites as industrial shape selective solid acid catalysts. However, as
Thomas and workers at Shell7 independently recognised, the chemical proper-
ties of their frameworks offer interesting possibilities for selective oxidation
catalysis. This catalytic behaviour results from the M21 " M31 redox couples,
as subsequently demonstrated and innovatively exploited by Thomas and
co-workers at the RI and Cambridge, and described elsewhere in this book.
In addition to aluminophosphates, other framework chemistries have been
expressed in microporous solids that have found catalytic application.
The titanosilicate analogues of zeolites, such as titanosilicalite-1 (TS-1),8 the
titanium-containing silica version of ZSM-5, and the large pore Ti-Beta, have been
found to have exceptional properties as selective oxidants, and stannosilicate
Beta has also been shown to be an excellent catalyst for fine chemical conver-
sions.9 The ability of the titanium and tin to coordinate peroxides and thereby
activate them for reaction with hydrocarbons is essential for their selective
activity. The inclusion of tetrahedral cations other than silicon or aluminium
can also have the effect of changing the structure that crystallises. Germanium,
for example, favours the formation of 3MRs and 4MRs, and as a result many
new germanosilicates have been prepared, including the recently discovered
extra-large pore germanosilicate, ITQ-33.10 In all these cases, framework
cations are tetrahedrally coordinated. There is a growing family of micropo-
rous solids, however, that include cations with different coordination into the
framework. In the titanosilicate ETS-10, for example, while the silicon is
tetrahedral the titanium is permanently octahedrally coordinated, within chains
of corner-sharing octahedra.11 Although in this material the titanium is not
active as a selective oxidation catalyst, it does possess interesting electronic and
optical properties. Other porous solids with mixed coordination include metal
phosphates, such as the nickel phosphate VSB-5.12

1.2 Designer Templates

For tetrahedrally coordinated silicates or aluminophosphates, the majority of
new structures are now prepared using organic amines or cations as SDAs, or
organic templates. They control the nucleation and growth of open frameworks
126 Chapter 7
and stabilise them with respect to denser phases. Whereas the early studies
concentrated on the use of relatively simple and readily available species, the
last 20 years have seen the use of increasingly complex molecules as templates.
In this approach, the final position of the organic species in the pore space is
governed by short range, non-bonding interactions that are well modelled
computationally by interatomic potentials. The close agreement between the
predicted location of templates (on the basis of combined Monte Carlo-Sim-
ulated Annealing routines) and that determined using diffraction supports the
accuracy of these simulations. Modelling can be used reliably to predict
template positions where they cannot be determined by experiment: conversely,
it means that templates can be designed for hypothetical structures that may be
energetically feasible but have not yet been prepared. The use of programs such
as ZEBEDDE (Zeolites By Evolutionary De-novo Design),13 in which poten-
tial templates are grown computationally within the pores of a hypothetical
structure, remains an attractive approach.
The empirical approach of the use of alkylammonium SDAs, rationally
designed on the basis of charge, stability, size and shape and synthesised via a
wide range of organic routes, has proved highly successful in the synthesis of
microporous silicates by the groups of Casci (at ICI), Zones (Chevron), Corma
(Valencia) and at Mobil and Mulhouse, leading in each case to a family of high
silica or pure silica zeolitic materials (named NU-n, SSZ-n, ITQ-n, ZSM/
MCM-n and IM-n, respectively). We have ourselves collaborated with the
group of Suk Bong Hong, in Korea, examining the structures of the TNU-n
series of silicates. Using the diquaternary template bis-N-methylpyrrolidinium-
butane, for example, several zeolites can be prepared by carefully adjusting the
synthetic conditions.14 The structure of one of these solids, TNU-9, was
recently solved in a multinational collaboration, including a state-of-the-art
combination of electron microscopy from the group of Terasaki in Stockholm
and X-ray powder diffraction analysis by researchers at ETH, Zurich.15 TNU-9
is the most complex zeolite known. The framework contains 24 symmetrically
distinct tetrahedral cation sites and two different medium pore 10MR channel
systems running down the b axis, linked perpendicularly and running between
identical but asymmetric silicate sheets that upon stacking give two distinct
intersheet regions. This pore structure is likely to give interesting shape select-
ivities in catalytic reactions. The role of the diquaternary cation as a structure
directing agent has been investigated by modelling, revealing four different sites
for a single type of SDA.16 It is likely that other, as yet unknown, structures will
have sets of sites of different geometry and size within their pore systems, and
these could be directed by mixtures of two or more template molecules. This
‘co-templating’ approach is therefore a promising route to new solids.
The use of more complex ‘designer’ templates has also been a profitable one
for the synthesis of novel aluminophosphate structures. The remarkable
metallo-aluminophosphate DAF-1, for example, was prepared at the Royal
Institution in 1992 using the decamethonium ion, ((H3C)3N1(CH2)10N1(CH3)3),
and was the first example of a structure with two parallel, distinct, large pore and
interconnected channel systems (Figure 1).17 Continued research into the
Exploration of New Porous Solids 127

Figure 1 Several novel aluminophosphate-based frameworks have been prepared by

the use of complex organic templates: (left) DAF-1; (right, above) STA-2,
showing also the position of the diquaternary template in the cages; (right,
below) STA-7, which possesses two cages of different sizes (key: green
spheres, aluminium; purple spheres, phosphorus; red, oxygen).

synthesis of novel aluminophosphate structures at St Andrews using diquater-

nary, triquaternary and also azamacrocyclic templates has given a rich variety of
structures. Figure 1 also shows STA-2 and STA-7, two novel small pore
structures with three-dimensionally connected pores prepared only as alumino-
phosphates.18 Suitable framework substitutions give catalysts active in methanol-
to-olefin or selective oxidation reactions mentioned previously. STA-7, for
example, is a small pore aluminophosphate related to SAPO-34 but with two
different cage sizes, rather than one. The structure is only synthesised as the
catalytically active and stable silicoaluminophosphate variety by choosing two
template molecules of different sizes, 1,4,7,11-tetraazacyclotetradecane (cyclam)
and tetraethylammonium, one to stabilise each of the cage types.

1.3 Microporous Organic–Inorganic Hybrids – MOFs

If there has been a steady increase in the chemical and geometrical range of
microporous inorganic solids, then this has been as nothing by comparison
with the number of porous hybrid framework solids that have recently been
prepared. Originally described as coordination polymers, they are more widely
128 Chapter 7
known as metal–organic frameworks (MOFs). Early examples include the
aluminium methyl phosphonates AlMePO-a and b, Al2(CH3PO3)3, similar to
AlPO4s but with their pores lined by fast-rotating methyl groups (Figure 2).19
As a consequence of their organic lining these solids have adsorption properties
quite different from purely inorganic AlPO4s, and adsorbed molecules have
much higher re-orientational mobilities within the pores, clearly shown by
deuterium NMR.20 Further microporous phosphonate solids have recently
been prepared, including a large pore nickel bisphosphonate (Figure 2)21
that consists of helical edge-sharing chains of octahedrally coordinated metal
cations, cross-linked by N,N 0 -piperazinebismethylenephosphonate groups.
While these phosphonates are of interest, by far the most well known and
varied family of MOFs is that of metal di- and tri-carboxylates. The best known
are those of Yaghi (MOF-n, especially MOF-522), those prepared at the

Figure 2 Selected microporous organic–inorganic hybrid solids, or MOFs: (a) the

b-polymorph of Al2(CH3PO3)3, with octahedral and tetrahedral alu-
minium in green and phosphonate tetrahedra in purple, (b) Ni2(H2O)2
O3PCH2NC4H8NCH2PO3 with NiO5N octahedra green and phosphonate
tetrahedra yellow, (c) MIL-53, in which corner-sharing chains of MO6 octa-
hedra (M ¼ Cr, Al, Fe, Ga), in yellow, are linked by terephthalate groups,
(d) HKUST-1, or copper benzene-tricarboxylate, in which dimers of CuO5
square pyramids (blue) are linked by benzene-1,3,5-tricarboxylate (trime-
sate) groups.
Exploration of New Porous Solids 129
Institute of Lavoisier in Versailles by the group of Férey (MIL-n, especially
MIL-53,23 -100, 10124), and the copper trimesate HKUST-1,25 all with stun-
ningly beautiful crystal architectures (MIL-53 and HKUST-1 are represented
in Figure 2). Many others continue to be prepared. Most work on these solids
has concentrated on their adsorption properties and in particular the very large
pore volumes they exhibit. Hydrogen storage properties have received the most
attention, but applications involving the adsorption of methane and carbon
dioxide are also possible. Relatively few catalytic studies using these solids have
appeared, but it seems likely that they could find use, suitably functionalised, in
low temperature solid/liquid phase reactions.

2 Mesoporous Solids: From Silica Supports to Porous

Single Crystal Metal Oxides
The discovery of ordered mesoporous silicates by Mobil scientists in 199226,27
opened a new research field in porous solids. These materials possess regular
pores in the 1.5–10 nm range and exhibit remarkable structural features that
heralded a new generation of adsorbents and catalysts. The Cambridge group
released its first report in the field in 1995 and has made an important contri-
bution to the synthesis and modification of mesoporous silicas. In particular,
Sir John Meurig Thomas focused on the development of the porous materials
into real catalysts and also published a number of important papers in HRTEM
(High Resolution Transmission Electron Microscopy), STEM (Scanning Trans-
mission Electron Microscopy) and electron tomography of catalytically active
nanoparticles inside the mesopores.28 In the last 15 years, the family of
mesoporous solids has been extended from silica into metal and metal oxide
compositions, and wide-ranging applications can be expected in the future.

2.1 Mesoporous Silicas

The first and simplest phase is MCM-41, which contains a hexagonal array of
cylindrical mesopores. Its pore structure can readily be observed by TEM along
the pore direction and perpendicular to the pores.29 However, the diverse forms
of liquid crystals of surfactants also lead to different pore dimensions and
geometries. The structure of SBA-15,30 for example, looks similar to that of
MCM-41, but the former also has smaller mesopores connecting the principal
pores, resulting in a 3-dimensional rather than a 1-dimensional pore system.
This feature is important in the later development of non-silicate porous
crystals.
Among the other mesoporous solids prepared by the group of Stucky in
Santa Barbara, SBA-2 contains spherical cages in a hexagonal close packed
(hcp) arrangement. In fact, our TEM studies revealed that irregular inter-
growths of hcp and cubic close packed (ccp) components commonly exist in
SBA-231 and we related this phenomenon to the intergrowths of the FAU (ccp)
and EMT (hcp) polytypic framework types observed in faujasite-type zeolites.
130 Chapter 7
(Three letter codes FAU and EMT refer to zeolite framework types seen, for
example, in faujasite and EMC-2.32) More cage-containing mesoporous sili-
cates have been developed. Their pore sizes can be easily tuned and their
thermal stability has been greatly improved. Two important phases are SBA-
1633 and FDU-12.34 SBA-16 has a body-centred cubic structure (space group
Im3m). FDU-12 is essentially face-centred cubic (space group Fm3m) with a ccp
arrangement of spherical cages, although, like SBA-2, an intergrowth of
domains with ccp and hcp is often seen.

2.2 Modified Mesoporous Silicates for Catalysis

Immediately after the first report of mesoporous silicas, it was realised that
these materials have high potential for application in catalysis and gas sepa-
ration due to their large uniform pores. However, two disadvantages must be
overcome. First, the composition of pure silica indicates that the materials lack
chemical activity. Second, almost all the mesoporous silicas templated by
organic surfactants have amorphous walls, which are normally less stable than
crystalline materials. As a result, modifications of the mesoporous silicas have
been investigated extensively over the last 15 years.
The classic method of increasing chemical activity of silica-based materials is
by doping with elements of oxidation state lower than 4+. For example, a
reasonably large amount of aluminium can be added into the silica wall of
MCM-41.35,36 However, the stability of the materials is greatly reduced. In fact,
many other elements can be used to substitute Si in these mesoporous materials
and almost all of the processes inevitably reduce the stability.37
Another way to turn mesoporous silicas into catalysts is by loading catalytic
nanoparticles into the pores. An early example is introducing bimetallic nano-
particles of Ru and Ag3Ru10 into mesoporous MCM-41 with a pore diameter
of 3 nm, in a project led by Johnson and Thomas.38,39 The materials were tested
as catalysts in a reaction of the hydrogenation of hex-1-ene to hexane. A high
selectivity (in excess of 99%) and a high turnover frequency of at least 6300 mol
hexane per mol [Ag3Ru10] per hour were observed. Although the nanopar-
ticles were not strictly ordered in the pores, they are all in contact with the inner
surface of the pores which are themselves ordered in a hexagonal array.
Therefore, the nanoparticles can be imaged with different image contrast
from the silica background in the HRTEM images and more significant
contrast in annular dark-field high-resolution electron microscopic images.
Extended X-ray absorption fine structure (EXAFS) confirmed the bimetallic
composition of the nanoparticles, which were firmly anchored inside the
siliceous mesopores.
When the metallic nanoparticles (Ru10 or Ru6) were partially ordered in the
mesopores of MCM-41, as we demonstrated in 1998,40 one may observe the
corresponding SAED patterns and therefore estimate the average inter-particle
distance (Figure 3). The ruthenium clusters, which possess high activity as
hydrogenation catalysts, were well separated inside the pores with an average
Exploration of New Porous Solids 131

Figure 3 Left: STEM bright-field image of MCM-41 loaded with [H2Ru10

(CO)25][PPN]2 showing highly regular features along the pore axis, with
its Fourier transform (inset). Right: Van der Waals surface interactions of
two [H2Ru10(CO)25]2– and two PPN1 molecules packing along a single
mesopore.

distance (2.95 nm) determined by the dimensions of the precursor complex

salts, e.g. [Ag3Ru10C2(CO)28Cl][PPN]2 and [Ru12C2Cu4(CO)32Cl2][PPN]2.
Accordingly, the HRTEM images show a ‘rosary’ pattern along the mesopores.
Furthermore, our subsequent STEM dark-field Z-contrast images revealed
nanoparticles in the mesoporous silicas much more clearly.41
When larger nanoparticles are loaded into mesopores, atomic images can be
directly observed, even when a mesoporous silicate without long range order is
used as a support. This was demonstrated in our report of Co and NiPd
nanoparticles used as highly effective, cheap, recyclable and industrially-viable
catalysts for the hydrogenation of a range of nitro-substituted aromatics under
mild conditions.42 The group of Thomas developed single site catalysts based
on the mesoporous silicas, which are discussed elsewhere in this book.
The above examples concern the post-synthesis introduction of metal nano-
particles. Recently, a new method, the so-called true liquid crystal templating
method, was developed. The addition of metal-containing precursors to the
synthetic system for mesoporous silicas prior to sol–gel condensation results in
the successful incorporation of nanoparticles of RuO2 in MCM-41. The
resulting materials are effective catalysts for alkene hydrogenation43 and water
oxidation.44,45 Similarly, many transition metals nanometres in size (e.g. Pd,
Au, Ir, Pt, Fe, Co, Cr)46 as well as bimetallic nanoparticles, such as PtCo,
PdAu,47 have been introduced into mesoporous silicas by this route.
Finally, the extra-large pore SBA-15, suitably functionalised, has been found
to be an excellent support for immobilising enzymes,48 a possibility foreseen by
132 Chapter 7
Sir John Meurig Thomas in his far-sighted commentary on the possibilities of
mesoporous silicas written soon after they had first been reported.49

2.3 Non-Silicate Mesoporous Oxides

All these ordered mesoporous silicates were fabricated by using liquid crystal-
line arrangements involving micelles of organic surfactants as templates, in the
so-called soft templating method. This method can also be used to prepare non-
silicate mesoporous transition metal oxides. In fact, almost all transition metal
oxides can be made in this porous form if a suitable precursor is used and the
materials may give different properties to meet the requirement for a particular
application. However, the walls of these materials are amorphous, since the
organic surfactants cannot be maintained at the high temperature needed for
crystallisation of the oxides. On the other hand, if mesoporous silicas are used
as templates, in the so-called hard templating method, we can make porous
crystals of oxides. The first demonstration of the hard-templating methodology
was given by Korean scientists in 1996,50 when they tried to image the channels
of mesoporous silica by filling it with platinum. This method has now been
developed to make nanowires and many porous crystals of transition metal
oxides. Our first specimen of porous single crystals of metal oxide, Cr2O3
templated by SBA-15, was synthesised and characterised in 2003 in collabora-
tion between Zhou and He’s group in Fudan University, Shanghai.51 These
materials are of great interest because they can be regarded as self-supported
nanoscale catalysts and have a high potential for catalytic application.
The general route for producing porous crystals of oxides using mesoporous
silicas as templates is by introduction of a metal-containing precursor into the
silica pores, followed by its thermal decomposition and the subsequent crystal
growth of the metal oxide inside the pores upon continued heating. A crucial
step in the above process is the impregnation of the precursor. Several methods
have been developed, the so-called surface modification ‘‘two solvents’’ meth-
od, the evaporation method and the solid–liquid method.
In the surface modification method, the inner surface of the mesoporous
silica template is functionalised via aminosilylation of the surface silanols and
then a selected heteropolyacidic precursor (e.g. H2Cr2O7 for Cr2O3 and
H3PW12O40 for WO3) is anchored.51,52 The functionalised surface is positively
charged and the metal-containing ions are negatively charged (heteropolyacidic
anions). Therefore, the driving force for migration of the precursor is mainly
ionic attraction. In the ‘‘two solvents’’ method, a suspension of mesoporous
silica in dry hexane is mixed with an aqueous solution of metal nitrate,
e.g. Cr(NO3)3
9H2O. The precursor molecules will then move into the pores
during overnight stirring.53 In the evaporation method, the mesoporous silica
template is mixed with a metal nitrate in ethanol. It was thought that the nitrate
precursor entered the pores during the evaporation of ethanol by capillary
action. Very recently, we found the nitrate precursor did not enter the pores
during the evaporation of ethanol and the migration actually took place during
Exploration of New Porous Solids 133
the thermal treatment when the nitrate melted. We then used a solvent-free
solid–liquid method to introduce nitrates and high quality porous crystals of
metal oxides were obtained.54,55
After the nitrate precursor was loaded, it decomposed during stepwise thermal
treatment. The sequence of decomposition inside the mesopores was different
from that without the mesoporous silicate. A confinement effect of pores, as a
nanoreactor, is obvious. For example, when Cr(NO3)3
9H2O was used as the
precursor, the formation temperature of Cr2O3 crystals inside the pores was
350 1C, while the corresponding temperature without mesoporous template was
400 1C. At 350 1C in the latter case, formation of Cr2O5 was observed. By way of
comparison, Co(NO3)2
6H2O decomposed inside the pore to form intermediate
crystalline phases of Co(NO3)2
2H2O and CoNO3(OH)
H2O, and finally
Co3O4 crystals at 150 1C. Without using the mesoporous template, only

Figure 4 TEM examination of a porous single crystal of Cr2O3 viewed down two
principal zone axes. (a) TEM image showing mesopore structure along the
[1 1 1] direction of the KIT-6 related cubic unit cell and (b) the correspond-
ing SAED pattern indexed onto the rhombohedral unit cell of Cr2O3.
(c) TEM image showing the mesopore structure along the [1 0 0] zone axis
of the KIT-6 related unit cell and (d) corresponding HRTEM image on the
[2 2 -1] zone axis of the Cr2O3 unit cell.
134 Chapter 7
Co(NO3)2
4H2O crystallised and heating Co(NO3)2
6H2O gave different inter-
mediate phases of a mixture of Co(NO3)2
4H2O and Co(NO3)2.56
TEM examinations of the porous crystals of these oxides (Cr2O3, Co3O4, NiO,
WO3, etc.) indicate that the original pore systems of the mesoporous silicates can
be replicated perfectly. Consequently, the morphology of the porous oxides
templated by SBA-15 is an array of nanorods connected by some small bridges51
and that templated by KIT-6 is wave-shaped nanowires.53 If SBA-16 and
FDU-12 were used as templates, we can expect the structures of the porous
oxides to be three-dimensional arrangements of solid nanospheres connected to
each other by some very short nanorods.54 The beauty of these porous crystals
of transition metal oxides is that the whole particles are single crystals with a
three-dimensional regular mesopore network as shown in Figure 4.
The novel structures of the porous crystals of transition metal oxides imply
that the new materials can be developed into self-supported nanoscale catalysts
with activities comparable to those of nanoparticle catalysts but can also give
shape selectivity due to the regular mesopores. It is also expected that the
materials may have interesting physical properties in magnetism and gas
adsorption.

3 Conclusion
The nanoporous solids we have described offer a range of properties far beyond
those of the zeolites known at the beginning of the 1980s. It seems to us that the
inspiration for this remarkable expression of form and function lies in their
exquisite nanoscale structure, the ‘architecture of the invisible’, so memorably
elaborated by JMT in a 1993 commentary of the role of 80 years of diffraction
in chemistry.57 Diffraction is one of many techniques he has championed in his
studies of catalysts at Cambridge and the Royal Institution, in an endeavour
we, like many others, are grateful to have shared with him.

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CHAPTER 8

Concerning the Solid State

Packing of [(ButCO2)3M2]2
(l-9,10-anthracenedicarboxylate)
Compounds (M = Mo or W)
and Other Matters
MALCOLM H. CHISHOLM, MATTHEW J. BYRNES,
AJATSHATRU MEHTA AND PATRICK M. WOODWARD
Department of Chemistry, The Ohio State University, Columbus, Ohio
43210, USA

1 Introduction
Upon completion of my PhD with Professor D. C. Bradley, FRS, at Queen
Mary College (QMC), London University I (M.H.C.) took up an appointment
as a postdoctoral fellow with Professor H. C. Clark at the University of
London Ontario. The move from London to London, Ontario in 1969 was
very interesting for its contrasts. Ontario then had some very strange provincial
rules, no doubt as a result of a Scottish Presbyterian influence. For example a
group trip to a local pub on a Friday evening was a segregating affair. There
was just one woman in the Clark group of 10 or 12 and the pub had two types
of bars: one for ladies and escorts and the other for men only. A lady could only
have three male escorts! Nor could one in those days stand to drink a beer or
move from one table to another table with a drink in one’s hand. The barman
was required to move the drink. These limitations aside the group’s comrade-
ship and the chemistry were great and several of my immediate lab mates went
on to have distinguished careers in academe (Professors Richard J. Puddephatt,
Hideo Kurosawa and Kenji Itoh) or industry (Dr Leo E. Manzer) to name just
those with whom I have maintained steady contact. The world seemed larger in
those days and Canada more remote. When visiting speakers came to lecture at
138
Concerning the Solid State Packing 139
the newly established Chemistry Department at the University of Western
Ontario (UWO) they often gave two or three lectures and stayed for several
days. This, of course, allowed for more socializing with the visitors, and
the students and postdoctoral fellows in addition to the academic members
of staff got to participate in discussions of chemistry and other matters. This
was a very thrilling and stimulating experience and one that was rather different
from that at London University where I had rarely spoken with visiting
speakers – though I do recall one day at QMC meeting the late Henry Gillman
and being totally amazed as he recounted his discussions with Grignard. This
had seemed to me as a 21 year old like listening to someone who had known
Moses. To the great credit of the chemistry department at UWO they main-
tained a very distinguished visiting lecture series and thinking about this now I
realize how greatly I benefited and was influenced by this and how much it must
have cost them financially. But it was surely worth every penny for the seminar
series in any department is the window of engagement with the outside world
and in many ways just as influential as the written words that appear in the
literature. It was during this time that I got to meet Henry Taube, Harry Gray,
Daryle Busche, Jay Kochi, Malcolm Green and the man we honour in this
volume, Professor Sir John Meurig Thomas. A truly great lecture requires that
its form be every bit as good as its content. Indeed without a good delivery the
information is most often lost on the audience due to inattention, boredom,
and sleep. Circa 1970, John’s star had already risen and he was publishing both
prolifically and profoundly and seemed to continually command the attention
of the reviewers and editors of Nature. As I recall, his lecture at UWO was on
the imperfections and dislocations within crystals and their significance in
determining reactivity. Though this subject matter was far removed from my
own research interests at that time, which dealt largely with the organometallic
chemistry of cationic complexes of platinum(II), I do well recall his engaging
and inspirational delivery. This has, of course, become a trademark of all
John’s lectures. His selection of a word and crafting of a phrase together with
impeccable pace and timing provide for a near theatrical experience of the
highest order.
The second time I met John was at a meeting I organized in Bloomington,
Indiana in 1982 shortly after I had moved to Indiana University from Princeton
University. This conference was jointly sponsored by the inorganic divisions of
the American Chemical Society, the Royal Society of Chemistry (UK), and the
Canadian Institute of Chemists, as it was then called, with additional funding
from numerous agencies and industries. The conference theme and its pub-
lished volume and proceedings was titled ‘‘Inorganic Chemistry: Toward the
21st Century.’’ The emphasis was forward looking and I must say that the turn
of the millennium in 1982 seemed just as far away as Orwell’s ‘‘1984’’ had when
read at school ca. 1960. To this symposium were sent 20 speakers from the
USA, and 10 from each of the UK and Canada and John was amongst the 10
from the UK contingent. Aside from the representatives from the USA,
the other speakers were selected by their countries and I had no hand in the
selection process. John was by this time Professor of Physical Chemistry in the
140 Chapter 8
University of Cambridge and when I saw his name on the UK list I wondered
how this interloper had been selected. Surely this was a sign of weakness in the
folds of UK inorganic chemistry. John’s lecture was, however, perfectly
appropriate and highlighted the power of high resolution electron microscopy
to the study of the surfaces of inorganic materials. This has been one of his
continuing interests along with pioneering the applications of numerous ana-
lytical techniques to problems of solid state inorganic materials and catalysis so
this talk was truly well placed and influential. The Department of Chemistry
prevailed upon John to stay a little longer in order to give another lecture. This
he did with great effect and he returned to an earlier theme relating organic
reactions within the solid state to their intermolecular ordering.
Since that time I have often had the opportunity to host John for a lecture and,
indeed, to enjoy his company in more social settings. There can hardly be a more
entertaining raconteur or dinner companion whether the subject be related to
science, politics or trivia. For my part as a synthetic chemist, my area of expertise
lies completely far afield from John’s though we share many common interests in
reactivity and catalysis. Synthetic chemists have to rely on applying physical and
analytical methods to know what they have made and in this regard the physical,
analytical and theoretical chemists are much more clever. However, the value of
synthesis in chemistry cannot be denied. To paraphrase the late Sir Geoffrey
Wilkinson: ‘‘If you can’t make it, you can’t measure it.’’ It is also probably true
that while the study of reaction mechanisms has led to our understanding of
catalysis, the most significant discoveries in catalysis were made by serendipitous
synthesis. Similarly new modes of chemical bonding, as in the discovery of
sandwich metal complexes, dinitrogen and dihydrogen complexes and MM
multiple bonding, were recognized only after synthesis.
Probably the most powerful method of determining what you have made
these days is single crystal X-ray crystallography. For relatively small molecules
this can all be done in one day, from data collection to full refinement and with
good data there can be no question concerning the arrangement of the atoms
with respect to each other. All other spectroscopic techniques cannot compete
in this regard and as stated by the late Professor Cotton may be viewed merely
as ‘‘sporting techniques’’. However, single crystal X-ray crystallography does
still require the preparation of single crystals and sometimes this proves too
difficult for even a talented synthetic chemist. Sometimes the crystals are too
small, too thin, or whisker-like for even modern instrumentation or synchro-
tron sources. Sometimes a chemist may know the overall molecular structure of
the subunits, as for example with an aromatic ring, a porphyrin or a paddle-
wheel carboxylate, M2(O2CR)4, having a virtual D4h M2(O2C)4 core of the type
shown in I below, but not how these units are connected or arranged in space in
the solid state. Yet it is often the molecular connectivity that is important in
determining the physical properties of the material in the solid state – the
magnetism, conductivity, optical properties, etc. Fortunately recent develop-
ments in the applications of powder X-ray diffraction (PXRD), as pioneered by
one of the editors in this volume along with others, can greatly assist in
clarifying these matters and this forms the scientific portion of this article.1
Concerning the Solid State Packing 141

C
C
O O O
O

M M I

O O O
O
C C

2 Dicarboxylate Linked M2 Quadruply Bonded Complexes

When two MM quadruply bonded complexes are linked by a dicarboxylate
group, the M2 centres may be electronically coupled as a result of the M2 d
orbital combinations mixing with the ligand bridge p-system. The two CO2
units act as alligator clips: they link the M2 units together covalently and
electronically couple them via the p-system. The key orbital interactions are
shown in II and III below for the oxalate bridge.2

II (b3u in D2h symmetry) III (b1g in D2h symmetry)

Of the two orbital interactions shown, II is the most important because of

orbital energy and overlap considerations. [The filled CO2 p orbitals lie roughly
6 eV lower in energy than the M2 d orbitals]. Consequently metal d to bridge p*
bonding occurs, splitting the energy of the two M2 d combinations and leading
to the preference of a planar oxalate bridge. The free oxalate dianion, however,
has a twisted D2d structure which minimizes electrostatic repulsion between the
oxygen atoms. As a consequence, of those two opposing forces the planar
structure is favoured by only a modest amount, B4–9 kcal mol–1, based on
electronic structure calculations on model compounds in the gas phase. Thus in
solution, there exists a Boltzmann distribution of rotamers with respect to the
dihedral angle between the two CO2 units of the oxalate bridge. The electronic
coupling of the two M2 centres is a maximum for the planar D2h structure and
is completely lost in the D2d structure. The oxalate bridge thus acts as a
molecular rheostat with Y ¼ 0 (D2h) being fully on and Y ¼ 901 (D2d) being off.
As a consequence, the oxalate-bridged complexes show thermochromism in
solution but not in the crystalline state. The colour arises from the metal d to
bridge oxalate p* transition.
142 Chapter 8

Figure 1 Electronic absorption spectra of [(ButCO2)3W2]2(m-O2CCO2) at 2, 50, 100,

150, 200, 250 and 300 K in 2-methyltetrahydrofuran solution. Reproduced
from Ref. 2 with permission.

The electronic absorption spectrum of the complex [(ButCO2)3W2]2

(m-O2CCO2) in 2-methyltetrahydrofuran is shown in Figure 1. The room tem-
perature absorption maximum, lE700 nm with eE36 000 M
1 cm
1 shifts
smartly to the red on cooling and sharpens in intensity to eE150 000 M
1 cm
1
at 2 K. The prominent vibrational features seen to shorter wavelength (higher
energy) arise from the coupling of the electronic wave function with the totally
symmetric vibrations of the oxalate ligand in the photoexcited state. As can be
anticipated from the description of the LUMO, placing an electron in a CO
antibonding orbital and a C–C bonding orbital produces a significant change in
C–C and C–O distances.
In contrast to the spectral features described above, the electronic absorption
spectra of the molybdenum and tungsten oxalate-bridged complexes are quite
different when recorded either as a Nujol mull or in the solvents toluene or
water. The latter spectra are remarkably similar and are shown in Figure 2.
This puzzling observation was shown to arise because in toluene and in water
the compounds do not truly dissolve: they form colloidal suspensions or nano-
particles due to the association of units in solution via intermolecular M2  O
bonds (vide infra).3
Despite repeated attempts, crystals of these complexes suitable for single
crystal diffraction studies could not be obtained because they formed fibrous
Concerning the Solid State Packing 143

Figure 2 Electronic absorption spectra of [{(tBuCO2)3W2}2(m-O2C2O2)] measured in

water, Nujol mull, and toluene. Reproduced from Ref. 3 with permission.

needle-like crystals. Therefore, we turned to X-ray powder diffraction (XRPD)

methods in hopes of elucidating the solid state packing schemes of these
molecules. Data were collected by using a Bruker D8 diffractometer equipped
with an incident beam Ge monochromator, a spinning capillary stage and a
position sensitive detector. The air-sensitive samples were ground in a mortar
and pestle and were sealed in 0.7 mm diameter capillaries inside a glove box.
Patterns were indexed using the CRYSFIRE4 suite of indexing programs.
Direct space structure solution was performed based on prior knowledge of
molecular connectivity and geometry using the simulated annealing minimiza-
tion algorithms incorporated in the program DASH.5,6
The solution reveals the molecular packing of molecules and the dihedral
angle between the two CO2 planes of the bridging oxalate. With these limita-
tions in mind, the drawing shown in Figure 3 indicates the salient features of
the structure of the [(tBuCO2)3Mo2]2(m-O2CCO2) molecule in the solid state.
Each unit contains a near planar central oxalate bridge where the O2C–CO2
dihedral angle is 15  31. Each molecule is connected to its nearest neighbours
via weak intermolecular dative oxygen to metal bonds. These intermolecular
Mo  O interactions involve both certain pivalate oxygen atoms and the
oxygen atoms of the oxalate bridge. The axial ligation shown in Figure 3 leads
to infinite chains of Mo4 containing molecules in the solid state and is a more
complex variation of the packing of Mo(O2CR)4 compounds in the solid
state that form laddered structures based on the coordination packing shown
in IV below.
144 Chapter 8

Figure 3 Intermolecular Mo–O interactions in [(ButCO2)3Mo2]2(m-O2CCO2), which

run parallel to the b-axis. All intermolecular Mo–O distances are 2.9(1) Å.
The tert-butyl groups have been omitted for clarity, and the colour scheme is
Mo ¼ green, O ¼ red and C ¼ grey. Reproduced from Ref. 2 with permission.

It should be noted that the molecular geometry of the gas phase calculated
structure for the model compound [(HCO2)3Mo2]2(m-O2CCO2) remains present
in this solution, where tert-butyl groups have replaced the H atoms in the C–H
bond. Only the dihedral angle between the two CO2 planes of the oxalate ligand
were allowed to vary in the solid state structure determination.

Based on a knowledge of this solid state structure for the oxalate-bridged

Mo4-containing compound, we can reasonably understand why the electronic
absorption spectra in the solid state (recorded in a Nujol mull or as a colloid)
are so very different from the spectrum collected in tetrahydrofuran solution
where each molecule is isolated. The change in the electronic absorption spectra
Concerning the Solid State Packing 145
upon association of one molecule with its nearest neighbours is reminiscent of
that seen for aromatic molecules that show concentration dependent p–p
stacking in solution.7 Subsequent to this work we found very similar spec-
troscopic properties for p-terephthalate-bridged MM quadruply bonded dimers
of dimers. The complexes also associated in the solid state by way of intermo-
lecular M2 to carboxylate oxygen bonds to form laddered structures.8

3 The 9,10-Anthracenedicarboxylate-Bridged
Compounds
In contrast to the oxalate- and terephthalate-bridged compounds, which main-
tain the same colour to the eye in the solid state and in solution, the related 9,10-
anthracenedicarboxylate complexes [(ButCO2)3M2(C14H8-9,10-(CO2)2) where
M ¼ Mo or W] appear very different.9 As shown in Figure 4, the molybdenum
compound is yellow as a powder and intensely red in THF (tetrahydrofuran)
solution while the tungsten complex is a pink-red powder that forms a green-blue
solution. As expected from the obvious differences in appearance as judged by
the eye, the electronic absorption spectra recorded as Nujol mulls and in solution
are vastly different. For example, the tungsten complex which has an absorption
centered at 550 nm in the Nujol mull shows a band maximum B750 nm in THF
solution, which is responsible for its blue-green colour. We were naturally
curious concerning the origins of this effect and being unable to grow single
crystals, we once again looked to gain insight concerning the molecular packing
through the aid of PXRD.
Direct space structure solution of molecular solids from powder data is
particularly well suited to structures that contain only one crystallographically
unique molecule per unit cell and to molecules where a large part of the electron

Figure 4 The solids and their solutions as they appear to the eye. The tungsten
complexes are shown on the left and the molybdenum on the right.
146 Chapter 8

Figure 5 View of the minimum energy twisted D2 (y ¼ B541) formate structure

[{M2(O2CH)3}2(m-9,10-C14H8(CO2)2)] (where M ¼ Mo, W).

density originates from a well-defined structural unit such as a planar ring, a

rigid rod, and/or a heavy atom.1 The molecules under consideration are thus
ideal; they have a well-defined M2(O2C)4 unit for which there are now numer-
ous well refined structures10 as well as the planar anthracene unit. Electronic
structure calculations on the model compound [(HCO2)3Mo2]2(m-9,10-(CO2)2-
C14H8) indicated a minimum energy structure having D2 symmetry.9 The gas
phase structure of the model compound is shown in Figure 5. The nonplanar
structure of the bridge represents a compromise of steric and electronic factors.
Even though M2 d bridge p* interactions favour a planar-bridged structure,
which maximizes electronic coupling across the bridge, the peri CH  O inter-
actions of the 9,10-anthracenedicarboxylate prevent this from being realized.
Indeed, for the model compounds, the planar D2h structure is calculated to be
B12 kcal mol–1 higher in energy than the D2 structure where the dihedral angle
between the CO2 and the anthracene planes is 541. This geometry for the central
portion of the molecule is essentially the same as that seen in the solid state
structures of 9,10-anthracendicarboxylate esters. The model compound shown
in Figure 5 thus represented the unit employed in the structural refinement
where the C–H moieties were replaced by an idealized C–CMe3 unit.
The PXRD data for the molybdenum and tungsten complexes showed these
two compounds to be isomorphous. The molybdenum diffraction data were
superior and are shown in Figure 6.
Based on the positions of the first 13 peaks in the diffraction pattern the unit
cell was determined to be monoclinic with cell dimensions: a ¼ 21.3662 Å,
b ¼ 5.6757 Å, c ¼ 12.6829 Å, and b ¼ 106.981. The systematic absences were
consistent with a primitive cell, leading to possible space group symmetries of
P121, P1m1, and P12/m1. Peak intensities were extracted (w2 ¼ 2.332) using the
whole pattern fitting routine in DASH, which is based on the Pawley method.
Concerning the Solid State Packing 147
Intensity

3 8 13 18 23 28 33 38 43 48 53 58
2 theta

Figure 6 Powder diffraction data for [(tBuCO2)3Mo2]2(m-9,10-C14H8(CO2)2).

As with the oxalate-bridged molecules, the structural determination was

carried out using the global optimization approach within DASH. In this case
there are three variables to describe the position of the molecule within the unit
cell, three variables to define the orientation of the molecule, six torsional
degrees of freedom associated with the Me3C groups and one torsional degree
of freedom associated with the twist about each C–CO2 bond of the anthracene
ring. This reduces the number of variables from 194 to 14. In the light of the
relatively small number of observed reflections, this reduction in the number of
variables is essential to extract a meaningful structure from the data. The
profile w2 was found to be 6.4 when the space group symmetry was assumed to
be P2, which is a very good fit for the data. When the space group symmetry
was taken to be P2/m or Pm, the profile w2 value increased dramatically, to 29
and 57, respectively. Hence P2 was confirmed as the correct space group. As a
final step in the structure determination, rigid-body Rietveld refinement was
carried out on the molecule. The orientation and location of the molecule and
anthracene torsion angles were refined. The torsion angles of tert-butyl groups
were kept fixed during refinement. Figure 7 shows the molecular packing of the
structure.
In contrast to the structures of the oxalate and p-terephthalate-bridged
complexes which form laddered structures due to intermolecular M2  O
interactions, the present structure contains ‘‘isolated’’ molecules. The shortest
intermolecular Mo–O distance in a neighbouring molecule is B3.6 Å which is
far too long to invoke even the weakest of interactions. Indeed, the packing of
the molecules is more influenced by hydrocarbon interactions than by Mo2  O
148 Chapter 8

Figure 7 Space filling representation of the crystal packing of [(tBuCO2)3Mo2]2(m-

9,10-C14H8(CO2)2) showing the layer of molecules viewed down b-axis.
Atomic colour scheme: Mo ¼ purple, O ¼ red, C ¼ grey, H ¼ white.

intermolecular attractive forces. The dihedral angle between the Mo2O2C and
the anthracene C14 planes is 551, as expected from both the calculations on the
model compound and the known structures of 9,10-diethers of anthracene.

4 Concluding Remarks
Powder X-ray diffraction can be used to reliably establish the gross features of
the packing of these oxalate and 9,10-anthracenedicarboxylate linked MM
quadruply bonded compounds in the solid state. The structures presented here
do not represent a full structural determination as all the M–M, M–O, O–C and
C–C distances were estimated from electronic structure calculations rather than
Concerning the Solid State Packing 149
directly determined using crystallographic methods. Nevertheless, the distances
and angles are all quite reasonable, based on related single crystal structural
studies. The lack of significant M2  O intermolecular interactions in the solid-
state structure is in marked contrast to what will exist in THF solutions where
metal–oxygen THF bonds along the M–M axis will be present. Given that the
colour of these compounds arises from metal to bridge charge transfer it is not
surprising that a ‘‘gas phase’’ colour should differ from that in solution. As has
been shown for the oxalate-bridged complexes, these complexes show marked
solvatochromism.11 The stabilization of the positive charge on the metal by the
donor THF molecules which arises on photoexcitation into the MLCT pro-
duces a marked bathochromic shift. This we propose is principally responsible
for effects described herein for the anthracenedicarboxylate-bridged com-
pounds and shown in Figure 4. Furthermore, it is becoming more and more
apparent that the application of direct space methods to the determination of
the ordering of molecules in the solid state will become a common practice for
chemistry in years to come.
Finally, I should like to state that it is a great pleasure to contribute to this
volume which celebrates the occasion of the 75th birthday of Sir John Meurig
Thomas. We have surely all learned a great deal from John. In his research he
has been both prolific and profound. In his teaching and promotion of science
to the public he has been a true evangelist. In his company we have enjoyed his
generosity, his humanity, and his humor.

Acknowledgments
We thank the National Science Foundation for support of this work.

References
1. K.D.M. Harris and E.Y. Cheung, Chem. Soc. Rev., 2004, 33, 526.
2. B.E. Bursten, M.H. Chisholm, R.J.H. Clark, C.M. Hadad, S. Firth, A.M.
Macintosh, P.M. Woodward, P.J. Wilson and J.M. Zaleski, J. Am. Chem.
Soc., 2002, 124, 3050.
3. M.H. Chisholm and N.J. Patmore, Inorg. Chim. Acta, 2004, 357, 3877.
4. CRYSFIRE was written by Robin Shirley and can be obtained free of
charge from http://www.ccp14.ac.uk/tutorial.htm
5. DASH was written by W.I.F. David and K. Shankland and can be
purchased from the Cambridge Crystallographic Data Centre. See
www.ccdc.cam.ac.uk for more details.
6. W.I.F. David, K. Shankland and N. Shankland, Chem. Commun., 1998, 931.
7. J.N. Murrell, in The Theory of the Electronic Spectra of Organic Molecules,
Methuen and Co. Ltd., London, 1963.
8. B.E. Bursten, M.H. Chisholm, R.J.H. Clark, S. Firth, C.M. Hadad, P.J.
Wilson, P.M. Woodward and J.M. Zaleski, J. Am. Chem. Soc., 2002, 124,
12244.
150 Chapter 8
9. M.J. Byrnes, M.H. Chisholm, D.F. Dye, C.M. Hadad, B.D. Pate, P.J.
Wilson and J.M. Zaleski, Dalton Trans., 2004, 523.
10. Multiple Bonds between Metal Atoms, ed. F.A. Cotton, C.A. Murillo and
R.A. Walton, 3rd edn, Interscience, New York, 2005.
11. M.H. Chisholm and N.J. Patmore, Inorg. Chim. Acta, 2004, 357, 3877.
CHAPTER 9

High Pressure and High

Temperature Oxidation in the
IrSr2RECu2O8 Family of
Cuprates: The Disordered
Multiple Perovskite (A1/3 A 02/3)
(B1/3 B 02/3)O3
x Phases
A. J. DOS SANTOS-GARCÍA,1 G. HEYMANN,2
H. HUPPERTZ2 AND M. Á. ALARIO-FRANCO1
1
Laboratorio de Quı́mica del Estado Sólido, Departamento de Quı́mica
Inorgánica, and Laboratorio Complutense de Altas Presiones, Facultad de
Ciencias Quı́mica, Universidad Complutense de Madrid, 28040 Madrid,
Spain; 2 Department Chemie und Biochemie, Ludwig-Maximilians-
Universität München, Butenandtstrabe 5-13, 81377 München, Germany

1 Introduction
In previous studies we have performed a wide investigation of the structure,
microstructure and magnetic properties of a new family of cuprates, IrSr2RE-
Cu2O8 (Ir-1212)1,2 where RE is a rare earth cation, prepared at high pressure
(HP) and high temperature (HT). This is an interesting family of materials since
in many of its members there coexist magnetic and superconducting properties.
Structurally, these compounds show the well known M-1212 type structure,3 a
perovskite triple superstructure characteristic among many others of YBCO,
and the well known ruthenocuprates, of general formula RuSr2RECu2O8
(Ru-1212).4,5
When the synthesis conditions are far from optimal and, in particular, under
oxidizing conditions, another perovskite phase is usually obtained as an

151
152 Chapter 9
impurity. In this way, SrRuO3 is often quoted to appear in the synthesis of the
Ru-1212 materials.6,7 In the case of the Ir-1212 materials, by controlling the
synthesis, we have been able to isolate a new perovskite phase as a single one.
This is a disordered version of the usual M-1212 structure in which both the big
(Sr and RE) and the small (Cu and Ir) cations are randomized in their
respective sites. A certain oxygen substoichiometry has also been observed.
We have determined that the average symmetry of this novel phase changes
with the rare earth, being cubic for RE ¼ Sm and orthorhombic for the
remaining ones (Nd, Eu, Gd and Tb).
As this type of ‘‘simple’’ perovskite is not that common, and in view of the
importance of the M-1212 type structure, we have made a detailed structural,
microstructural and magnetic study of these disordered multiple perovskites.
This has also allowed us to ascertain the true unit cell and symmetry of the
different novel phases as well as to analyze the influence of the disordering on
the magnetic properties.

2 Experimental
Samples were prepared at HPs (r80 kbar) and HTs in a Belt type press, located
in the Laboratorio Complutense de Altas Presiones–UCM Madrid,8 while those
requiring higher pressures (480 kbar) were made in a Walker-type multianvil
pressure module9,10 installed at the Ludwig-Maximilians-Universität München.11
Adequate amounts of a mixed oxide precursor SrCuO2, prepared beforehand
by solid state reaction, together with IrO2, CuO, RE2O3 (or Tb4O7) and SrO2
(AR, Sigma Aldrich) were thoroughly mixed inside a glove box. Then, the
mixture was pressed on a platinum capsule (for RE ¼ Sm, Eu and Gd) or a BN
crucible (for RE ¼ Nd and Tb) and treated at HPs and HTs according to:

SrCuO2 þ 1=2RE2 O3 þ IrO2 þ CuO þ SrO2 ! IrSr2 RECu2 O9
d ð1Þ

The presence of SrO2 makes a more oxidizing reaction atmosphere so the

oxygen content is higher than the expected value of 8 for Ir-1212 (see below).
Samples were characterized by X-ray powder diffraction (XRD) on a Philips
X’Celerator diffractometer (CuKa1-radiation, l ¼ 1.54056 Å). The XRD patterns
were refined with the Rietveld procedure using the Fullprof_Suite program.12
High-resolution TEM images and selected area electron diffraction (SAED)
were performed on Jeol JEM 3000EX and 200KV and Philips CM 200 FEG
microscopes. Cationic compositions were checked by EDS (Link Pentafet 5947
Model, Oxford Microanalysis Group) by in situ observations in the electron
microscope.
The oxygen content was determined by thermogravimetric analysis
performed on a homemade system based on a Cahn D-200 electrobalance.
Magnetic susceptibility measurements were performed over the temperature
range 1.9–300 K, using a Squid Quantum Design XL-MPMS magnetometer.
High Pressure and High Temperature Oxidation 153

3 Results and Discussion

3.1 Synthesis
Table 1 shows the optimal conditions (pressure, temperature and time) required
for the synthesis of both type of materials: ordered Ir-1212, i.e. IrSr2RECu2O8 and
the novel disordered perovskite materials, of general formula (Sr2RE)
(Cu2Ir)O9
d. It can be seen that keeping constant the optimum pressure used to
obtain the IrSr2RECu2O8 compounds, at higher temperatures one is able to obtain
the corresponding disordered (Sr2RE)(Cu2Ir)O9
d new phases. It is clear that the
temperature and the oxidizing conditions are crucial in the disordering process.

3.2 The Chemical Composition

Cationic ratios were determined by EDS spectra on several crystals. The
normalized average value obtained from all the samples corresponds to the
1212 nominal composition, i.e. IrSr2RECu2Ox. Furthermore, the thermal
decomposition of the pure Gd sample, made in air at temperatures up to
950 1C, gives as final products CuO and the corresponding double perovskite,
i.e. Sr2GdIrO6.
On the other hand, the oxygen content was obtained by thermogravimetric
analysis from the direct reduction of the gadolinium single phase,
(Sr2Gd)(Cu2Ir)O9
d. The total reduction of this material to Cu, Ir, Gd2O3
and SrO, under a reducing atmosphere (0.2 atm He–0.3 atm H2) and heating up
to 625 1C, at a rate of 6 1C min
1, allows one to determine a weight loss
corresponding to 9 – d ¼ 8.82.

Table 1 Optimal pressure, temperature and time conditions required for the
synthesis of both types of materials: ordered and the novel, disor-
dered multiple perovskite.
ABO3
(Sr2RE)(IrCu2)O9
d
RE Nd Sm Eu Gd Tb
VIII 31 1
rRE /Å 1.109 1.099 1.066 1.053 1.040
P/kbar 115 60 30 60 92
T/K 1373–1473 1673 1575 1673 1673
t/min 20 90 60 90 30
Ir-1212
IrSr2RECu2O8
VIII
rRE31/Å1 1.109 1.099 1.066 1.053 1.040
P/kbar – 60 30 60 92
T/K – 1373 1173 1393 1373–1473
t/min – 30 35 30 20
1
Shannon and Prewitt data from Ref. 29.
154 Chapter 9
Therefore, the chemical composition of these samples can then be written as
(Sr2RE)(Cu2Ir)O8.82, for the Gd material. This is an important oxygen excess
with respect of the original IrSr2RECu2O8 sample, and rather close to the
oxygen content of a triple perovskite: A3B3O9.

3.3 The Average Structure

X-ray diffraction patterns can be indexed as a cubic perovskite for the Sm
sample, Figure 1a, and as an orthorhombic perovskite for the remaining ones,
corresponding to Nd, Eu, Tb and Gd (Figure 1b shows the pattern corre-
sponding to Gd). In order to refine them, by the Rietveld procedure, we used
the SrTiO313 cubic perovskite structure for the Sm sample while orthorhombic
SrRuO314 was used for the Gd sample as starting models. The A site of these
single perovskites was fully occupied at random by 2 Sr and 1 RE, while 2 Cu
and 1 Ir were placed in the B sites. In this structural model, such a situation was
treated by assigning to the different atoms the same x,y,z site and the same
displacement parameters Uij. One of the atoms (Sm/Ir) was then given a site
occupancy of k (1/3) and the other one (Sr/Cu) a site occupancy of 1
k (2/3).

Figure 1a Rietveld refinement fit of the X-ray diffraction pattern for (Sr2Sm)

(Cu2Ir)O9
d. The ‘‘impurity’’ observed corresponds to the ordered
IrSr2SmCu2O8.
High Pressure and High Temperature Oxidation 155
As there was a strong correlation between the site occupancy and the displace-
ment factor, it was better to refine them in alternating cycles of refinement until
they converged. Since there also existed a number of oxygen vacancies, the
corresponding oxygen site occupancy was varied freely until the final value was
reached.15
The results of the refinement can be seen on Figures 1a and b; Table 2 gives
the refined cell and atomic parameters as well as the fit agreement factors
obtained for (Sr2RE)(Cu2Ir)O9-d with RE ¼ Gd and Sm. Taking together the
analytical data and the crystal structure refinement, it appears that the oxida-
tion of the ordered IrSr2RECu2O8 1212-type structure to the disordered
(Sr2RE)(Cu2Ir)O9
d one leads to the conversion of the vast majority of the
copper pyramids [Cu–O5] to octahedra [Cu–O6]; at the same time, Ir and
copper are randomly distributed in the octahedra. Concomitantly, Sr and RE
ions randomize in the resulting cubo-octahedral positions. In both of these
polyhedra there are some oxygen vacancies; for the oxygen content of the
Gd case these amount to B3.7% while B1.7% was found in the Sm case. This
may be related to the differences in the average structures; the Sm one, the
closer to stoichiometric, is cubic while the Gd one is orthorhombic. However,

Figure 1b Rietveld refinement fit of the X-ray diffraction pattern for

(Sr2Gd)(Cu2Ir)O9
d.
156 Chapter 9
Table 2 Unit cell parameters and crystallographic sites, as well as fit agree-
ment factors, obtained from the Rietveld refinement of (Sr2RE)
(Cu2Ir)O9-d with RE ¼ Gd and Sm.
(Sr2Gd)(Cu2Ir)O9
d (S.G. Pbnm)
a/Å b/Å c/Å V/Å3 Rwp Rp w2
5.542(1) 5.540(1) 7.8472(7) 240.95(9) 0.0915 0.0693 1.20
Atom Wyckoff Position x Y z Uiso/Å2 Occ
Sr 4c
0.015 (1) 0.011 (2) 0.25 0.9 (1) 0.658
Gd 4c
0.015 (1) 0.011 (2) 0.25 0.9 (1) 0.342
Cu 4b 0.5 0.0 0 0.843 0.671
Ir 4b 0.5 0 0 0.843 0.329
O1 8d 0.889 (8) 0.371 (9) 0.176 (4) 0.05 1.89
O2 4c
0.008 (1) 0.53 (1) 0.25 0.05 1
(Sr2Sm)(Cu2Ir)O9
d (S.G. Pm3m)
a/Å b/Å c/Å V/Å3 Rwp Rp w2
3.923(1) 3.923(1) 3.923(1) 60.389(1) 0.125 0.0713 4.82
Atom Wyckoff Position x Y z Uiso/Å2 Occ
Sr 1a 0 0 0 0.374 0.583
Sm 1a 0 0 0 0.374 0.292
Cu 1b 0.5 0.5 0.5 0.377(2) 0.694
Ir 1b 0.5 0.5 0.5 0.377(2) 0.347
O 3c 0.5 0.5 0 0.05 2.946

we have not seen any evidence of oxygen vacancy ordering and, as discussed
below, the cell observed by ED and TEM is always orthorhombic. Presumably
this oxygen deficiency could be eliminated/increased if somewhat stronger/
softer oxidizing conditions were to be used. It is especially relevant that both
the ordered and disordered phases have exactly the same cation stoichiometry
although different oxygen content. We are then not really dealing with a simple
order–disorder change,16 like in a phase transition; it is in fact a chemical
oxidation process accompanied by a disordering of both metal sublattices of
the triple perovskite cell.
Figure 2 shows the relation between both structures. This is indeed reminiscent
of several oxygen intercalation–deintercalation processes, such as Ca2Mn2O5 to
CaMnO317,18 or indeed YBa2Cu3O6 through Y2Ba4Cu3O13 to YBa2Cu3O7.19
However, the present case has the added interest of the disordering of the cations
present in both the A and B perovskite positions, which take place with the
oxidation. Disordering of the big cations (i.e. A-cations) is present in, for
example, (LaSr)CuGaO520,21 or (LaSr)CuAlO5.22,23 Yet, in these cases the
B- and B 0 -cations are distinctly ordered, unlike the cases reported here. A
somewhat related case is that of synthetic isolueshite (Na0.75La0.25)(Nb0.5Ti0.5)O3
where the cations are also disordered, although in that case there are two
different A sites in the space group Cmcm.24 The closest cases are, however,
those of the disordered double perovskites BaLaFeMoO625 and CaBaZrGeO625
which are cubic. On the other hand, SrLaCaRuO626 and SrLaFeCuO627 are
High Pressure and High Temperature Oxidation 157
orthorhombic due to the tilt octahedra in the absence of cation ordering and
show the CaTiO3 structure (space group Pnma).
Table 3 gives the principal interatomic distances and angles for the Sm and
Gd compounds. The observed bond lengths are of course the average of the
Cu–O and Ir–O distances in the disordered material; we assume that the Ir–O
environment is constant, [Ir–O6], and that changes in the average are due to
changes in the Cu–O environment, from [Cu–O5] to [Cu–O6].
It is also interesting to make a comparison between the distances in the
ordered and disordered Gd phases. The equatorial octahedron/pyramid

A) B)

Ir

Sr A (Sr/ TR)

Cu

RE
+ O2

Cu

Ir B (Cu/Ir)

Figure 2 Schematic structural representation of the oxidation of ordered IrSr2RE-

Cu2O8 to disordered (Sr2Sm)(Cu2Ir)O9
d.

Table 3 Principal interatomic distances and angles obtained from the refine-
ment of the Gd and Sm disordered compounds.
Distances/Å Angles/degrees
(Sr2Gd)(Cu2Ir)O9
d

Cu/Ir–O(1)  4 1.97 (1) O(1)–Cu/Ir–O(2) 95.6

Cu/Ir–O(2)  2 1.96 (1) O(2)–Cu/Ir–O(2) 180
Gd/Sr–O(1)  8 2.78 (1) O(1)–Cu/Ir–O(1) 180
Gd/Sr–O(2)  4 2.77 (1)

(Sr2Sm)(Cu2Ir)O9
d
Cu/Ir–O 1.96 O–Cu/Ir–O 90
Gd/Sr–O 2.77 O–Cu/Ir–O 180
158 Chapter 9
distances in the ordered material (Ir–O ¼ 1.98 Å and Cu–O ¼ 1.92 Å, average
1.95 Å) and pseudo-octahedron equatorial distances in the disordered one
(Ir/Cu–O ¼ 1.97 Å) are rather close. However, the conversion from the vast
majority of square planar pyramids in the ordered phase to pseudo-octahedral
groups in the oxidized disordered one makes the axial distances (i.e.
Cu–O ¼ 2.30 Å and Ir–O ¼ 1.82 Å, average 1.96 Å) in ordered Ir-1212 become
equal in the disordered phase, (i.e. Ir/Cu–O ¼ 1.96 Å). When Cu12 occupies a
site with tetragonal symmetry, the eg band will be split into two sub-bands due
to the strong Jahn–Teller effect in these orbitals. If, as we explained above, the
conversion of the square copper pyramids is to copper octahedra, the number
of Cu12 ions that occupy a site with tetragonal symmetry are considerably
diminished, and therefore the Jahn–Teller effect is not so important. In fact, the
pseudo-octahedron is almost regular, ra/e ¼ 1.96/1.97 E1, in the disordered
phases.
It is also interesting to consider the octahedron tilt angle in these disordered
perovskites. This can easily be done with the program SPUDS.28 However, one
needs the oxidation state of the cations. As we have two different transition
metals Ir and Cu in the B position, one has to guess their respective oxidation
states. Two main possibilities appear to be Ir15 and Cu12 or Ir14 and Cu13,
and indeed any intermediate situation. The corresponding tilt angles are for the
Gd case F ¼ 14.71 and 13.01, respectively, and in the Sm case F ¼ 14.51 and
12.71, respectively. One can see that the charge distribution does not affect too
much the tilt angle (o12%).
Once we have characterized this new family of orthorhombic disordered
perovskites, it is worth trying to see their respective tolerance factors (t-factors).
For that we need the ionic radii of the corresponding RE cations in 12-fold
coordination. It so happens that there are only available data29 for La, Ce, Nd
and Sm(III ) and, as we have prepared the compounds corresponding to Nd,
Sm, Eu, Gd and Tb rare earth ions, a simple linear extrapolation of the
Shannon and Prewitt data for the experimentally known coordination was
performed, giving an interesting plot of the lanthanide contraction for the
XII
rRE13 ions (Figure 3). Notice that the experimental Shannon–Prewitt data
known in 12-fold coordination follow a higher contraction than those obtained
by extrapolation. . .!
In any event, though, the t-factors of all the compounds established on the
basis of either set are rather similar, e.g. tNd exp ¼ 0.954 vs. tNd extrapolated ¼
0.963, tSm exp ¼ 0.95 vs. tSm extrapolated ¼ 0.96. On the basis of these values, it is
not surprising that these disordered multiple perovskites are not cubic but
orthorhombic.
Interestingly, it was common to obtain in the same sample – and even in the
same crystal! (see below) – both ordered (1212) and disordered
((Sr2RE)(Cu2Ir)O9
d) phases. This is a clear indication that the synthesis
conditions are close to the ‘‘ideal equilibrium’’: IrSr2RECu2O8+(1
d)/2O2
- (Sr2RE)(Cu2Ir)O9
d. However, we have not yet succeeded in making the
back reaction, i.e. to reduce the disordered phase to the ordered one. Another
interesting point worth mentioning is that the XRD patterns corresponding to
High Pressure and High Temperature Oxidation 159
1.42
Shannon & Prewitt
1.40
Extrapolated
1.38 La

1.36 Nd
1.34
1.32 Sm
XIIrRE+3

1.30
Tb
1.28
1.26
Er
1.24
1.22
1.20
Lu
1.18
0 2 4 6 8 10 12 14
f electrons

Figure 3 A plot of the XII coordinated radii of the trivalent lanthanide cations (see
text for details).

h/2 k/2 0

100p

010p

[001]p

Figure 4a Electron diffraction pattern of (Sr2Gd)(Cu2Ir)O9
d along the perovskite

[001]p zone axis. Two twofold superstructures are present. Also there are
spots at h/2 k/2 0 (h and k odd). See text for details.

the other RE (data not shown, i.e. Nd, Eu and Tb) show as the main impurity
iridium metal. This phenomenon is indicative of an excess temperature that
decomposes the samples. In spite of the presence of the impurities, these
disordered phases can be obtained as main phases, although the poor quality
160 Chapter 9

100p

2ap 010p

[001]p
√2ap

√2ap
100 p
010p
2ap

ap
[001]p

Figure 4b A high resolution electron micrograph showing a three-dimensional mi-

crodomain texture. The long c axis of the supercell (cl ¼ l2ap E 7.8 Å 0 ) is
randomly distributed in the three space orientations. The Fourier trans-
form, shown as inset, corresponds to the pattern in Figure 4a.

of the corresponding XRD patterns makes it difficult to refine them from

powder diffraction data.

3.4 The Microstructure

Although the ideal, or Pm3m aristotype, perovskite structure is cubic, it has
been shown that the majority of synthetic simple ABX3 perovskite group
compounds are distorted derivatives resulting from: (1) rotation or tilting
of distortion-free BX6 polyhedra (more common situation); (2) first order
Jahn–Teller distortion of BX6 octahedra; (3) second order Jahn–Teller effects
on A- and B-cation polyhedra, reflecting mixing of molecular orbitals and/or
lone pair effects. Although these distortion phenomena are frequent enough,
their observation is somewhat complicated, especially from X-ray powder
diffraction. In view of past experience concerning the true symmetry of these
perovskites,30–34 we have performed a microstructural study by means of
SAED and high resolution electron microscopy (HREM).
The electron diffraction patterns corresponding to the whole series – including
the Sm case – show clear evidence of the presence of the so-called diagonal
cell BO2ap  O2ap  2ap. This superstructure arises as a consequence of the
octahedral tilt around the unit cell axes in order to achieve the lowest energy for
the crystal to accommodate a small A-cation for the 12-fold site within a BX6
polyhedral framework.
In the electron diffraction pattern corresponding to the Gd sample in Figure 4a,
the strong spots can be indexed on the basis of a [001]p perovskite zone axis.
High Pressure and High Temperature Oxidation 161

c) b)

7.8 Å

11.6 Å

2ap

3ap
B A

10 nm a)

Figure 5 (a) Electron micrograph of a crystal showing an intergrowth of the ordered

IrSr2TbCu2O8 (c E 3ap) and disordered (Sr2Tb)(Cu2Ir)O9
d (c E 2ap). (b)
Fourier transform of same showing the presence of the two cells. (c) Higher
resolution image showing the regularity of the intergrowth boundary.

Besides, the weak spots at h/2 k/2 0, where h and k are integers, suggest the
presence of the indicated diagonal cell. Also the spots present at h/2 0 0 and 0 k/2 0,
together with the corresponding HREM shown in Figure 4b indicates a micro-
domain texture, in which the c ¼ 2ap axis of the diagonal cell is distributed at
random in the three space directions.
It is worth mentioning that a low tilt angle, such as observed here – see above
– favours the presence of a microdomain texture (see the discussion of this part
in Ref. 30).
A very interesting microstructural situation can be seen in Figure 5a, corre-
sponding to a crystal of the Tb-iridocuprate, by no means exceptional, in which
both the ordered IrSr2TbCu2O8 and the disordered (Sr2Tb)(Cu2Ir)O9
d phases
coexist and are joined along a rather regular boundary. The Fourier transform
for the whole image, Figure 5b, shows the cord ¼ 3a periodicity of the ordered
phase (region A), together with the cdisord ¼ 2a periodicity from the disordered
phase (region B). In Figure 5c, at higher resolution, it can be seen that
both phases join at the boundary in a rather smooth way. This is certainly
due to the fact that both have the topology of a perovskite and very close metric
as indicated by their lattice parameters (Table 2). Yet, this seems to have
162 Chapter 9
important implications concerning the oxygen stoichiometry of the system. The
fact that both end members of a hypothetical ‘‘solid solution’’, IrSr2RECu2O8
and (Sr2RE)(Cu2Ir)O9
d, coexist in the same crystal seems to indicate that we
have an intergrowth phase mixture rather than a non-stoichiometric continu-
ous solid solution. Changes in oxygen content appear to modify the relative
proportions of the end members.

3.5 Magnetic Properties

As expected, the random distribution of the Ir/Cu and Sr/RE cations in their
respective crystallographic sites makes less likely the presence of long range
magnetic interactions. In fact, paramagnetic behaviour is to be expected for
these phases.
In this sense, Figure 6 shows the AC susceptibility measurement of both
ordered and disordered Gd phases. The shoulder observed at B15 K in the
ordered phase, reported elsewhere,2 does indicate an overall ferrimagnetic
order between Gd and Ir sublattices below 15 K. On the other hand, all the
disordered phases that we have prepared show a not unexpected paramagnetic
behaviour. This is somewhat deceptive compared to the rich magnetic behav-
iour shown by the ordered 1212 phases.

IrSr2GdCu2O8
0.12 0.10 (Sr2Gd)(Cu2Ir)O9-δ
χ (emu mol-1)

0.10
0.05
χ (emu mol-1)

0.08

0.06 0.00
0 50 100
0.04 T (K)

0.02

0.00

0 50 100 150 200 250 300

T (K)

Figure 6 Magnetic susceptibility (AC mode) as a function of temperature of the

ordered and disordered phases. Inset shows an enlarged section of the
magnetic phase transition region in the ordered phase.
High Pressure and High Temperature Oxidation 163

4 Conclusions
Searching for the optimal synthesis conditions for the iridates IrSr2RECu2O8,
we have been able to isolate a new disordered perovskite in which both the
A and B positions are multiply occupied, (Sr2RE)(Cu2Ir)O9
d. Although the
average structure seems to change with cation size, the true structure is
common for all of these materials and has orthorhombic symmetry (space
group Pbnm, cell BO2ap  O2ap  2ap). This structure is, on the other hand,
distributed at random in microdomains.
This order–disordering HP and HT chemical oxidation reaction is a remark-
able one which exhibits interesting aspects concerning the differences between a
solid solution and a phase mixture.
A final point worthy of note is that, usually under pressure one gets a more
ordered phase and a lower symmetry. Here, however, the oxidation reaction –
as opposed to a phase transition – leads to an increase in the symmetry and a
cubic disordered phase.

Acknowledgements
We would like to thank financial support from CICYT, programa MAT2004-
01641, Comunidad Autónoma de Madrid, programa MATERYENER,
PRICYT S-0505/PPQ-0093 (2006), Fundación Areces, Programa Fı́sica de
Bajas Temperaturas (2003) and the European Science Foundation within the
COST D30 network (D30/003/03). We also thank Dr J. Romero de Paz,
Dr J. M. Gallardo-Amores and A. Gómez-Herrero for technical assistance.

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CHAPTER 10

Melting and Amorphisation

G. NEVILLE GREAVES
Centre for Advanced Functional Materials and Devices, Institute of
Mathematical and Physical Sciences, University of Wales Aberystwyth,
Aberystwyth, Ceredigion SY23 3BZ, UK

While John Meurig Thomas was not the first person to interest me in
microporous crystals, he was certainly the most insistent that these were ideal
candidates for the new combinations of X-ray techniques I was developing in
the late 1980s with non-crystalline materials in mind. Shortly before he moved
from Cambridge to the Royal Institution (RI) he visited my office at the
Synchrotron Radiation Source and simply enthused over what X-ray spectro-
scopy, diffraction and scattering could bring to feed his passion for watching
zeolites form and catalysis happen. It needed the new X-ray detectors and
geometries that were being commissioned by my Materials Science Group at
Daresbury Laboratory. A most fruitful collaboration resulted between our-
selves and the groups at the RI that John and also Richard Catlow were
establishing, and a sizeable body of novel in situ materials chemistry was born,
both in catalysis1 and in other areas.2 The starting point was the first
experiment coupling in situ X-ray spectroscopy with X-ray diffraction, which
Nature highlighted as the ‘‘Daresbury Double’’.3
Melting, however, is the subject of this birthday contribution. The connec-
tion with microporous catalysts is the inherent instability of zeolites and their
tendency at high temperatures and pressures to amorphise into new and
exciting glasses. The same combined X-ray techniques that proved so essential
in the early 1990s for charting the synthesis of zeolites have proved just as
useful in following their destruction. Amorphisation of minerals4 turns out to
be a rather special case of melting, while melting per se remains one of the
major unsolved problems in physics.5 For instance, melting and freezing are
traditionally envisaged as opposite sides of the same first order phase transi-
tion, defined by a critical point in temperature and pressure. Yet there is
increasing evidence that melting is preceded by progressive internal disordering
within the period lattice.6 Freezing, on the other hand, is a non-equilibrium

165
166 Chapter 10
kinetic phenomenon leading to the fascinating supercooled state out of which
glasses can emerge if the liquid is sufficiently viscous7 or crystals if it is not.
Indeed the extent to which a liquid supercools before it crystallises is dependent
on how it is contained. If it is not, which is possible using levitation furnaces,8,9
glasses can be formed that would be precluded if cooled from a crucible.
Melting and also amorphisation therefore reside at the cross roads of the liquid,
glassy and crystalline states – a burgeoning area in the physical sciences.10

1 Melting
1.1 Clausius–Clapeyron Relation
The physics and chemistry of melting started in the mid-19th century with the
Clausius–Clapeyron relation that defines first order phase transitions, viz:
dT DV
¼ ð1Þ
dP DS

Where melting is concerned, Equation (1) defines the boundary between liquid
(L) and crystalline (C) phases, where DV ¼ VL–VC and DS ¼ SL–SC are the
respective differences in molar volume and entropy. Simple close-packed
materials like metals and alkali halides expand on melting at ambient pressure
and become disordered, so DV and DS are both positive as is the slope of the
melting curve, dT
dP .
m

1.2 Melting Curve of Alumina

Alumina provides a striking example of melting and of the versatility of new
experimental methods. The impressive experiments of Shen and Lazor,11 which
are included in Figure 1a, follow the rise in the melting point from 2323 K at
ambient pressure up to 3675 K at 25 GPa. They are bounded in Figure 1a by two
schemes for melting adopted in the molecular dynamics (MD) simulations of
Ahuja et al.12 No less impressive is the huge increase in the molar volume, DV,
measured at the melting point (Figure 1b), results obtained with an aerodynamic
levitation furnace, where the density of the crystalline state has been determined
from in situ X-ray diffraction as the melting point, Tm, is approached.13 The
densities of the supercooled and molten states are derived from high speed
camera images of the changing diameter of levitating drops.14 Given that the
increase in entropy on melting DS ¼ LF/Tm, where LF is the latent heat of fusion,
the melting curve predicted by the Clausius–Clapeyron relation (Equation (1))
at ambient pressure is plotted in Figure 1a. The agreement is surprisingly good
considering the inevitable inaccuracies in these difficult experiments, but also the
fact that the local structure of alumina changes on melting.
Structure factors, S(Q), for liquid alumina were first measured using X-rays
in 1997 by Ansell and co-workers who reported a sharp drop in coordination
number compared to corundum.15 These groundbreaking experiments using an
Melting and Amorphisation 167
40
4500 (a) (b) Al2O3
Al2O3 38
4000
36
Melting Temperature / K

dTm /dP=∆V/∆S

Molar Volume / cm3

3500 34

3000 32 ∆V

2500 30

28
2000 MD Ahuja et al 1998
Expt. Shen & Lazor 1995
26 Tm
1500
24
−5 0 5 10 15 20 25 30 0 1000 2000 3000
Pressure / GPa T/K

Figure 1 Melting corundum. (a) Melting curve combining the experimental measure-
ments of Shen and Lazor11 with the results of MD calculations published by
Ahuja et al. for one and two phase systems.12 (b) Stepwise increase in molar
volume on melting obtained from in situ X-ray diffraction13 and the imaging
of molten drops.14 The prediction of the Clausius–Clapeyron relation
(Equation (1)) using LF ¼ 110 kJ/mol and Tm ¼ 2323 K and the increase in
molar volume, DV, at ambient pressure shown by the red line in (a). Insert in
(b): the network-like structure of molten alumina obtained from empirical
potential structure refinement analysis of the experimental neutron structure
factor.9

aerodynamic levitation furnace were followed by neutron S(Q) experiments9

where the three-dimensional structure was modelled using the empirical
potential structure refinement method of Alan Soper16 incorporating the
density measurements of Glorieux.14 The coordination numbers of AlO6 and
OAl4 in corundum fall to almost AlO4 and OAl2.7 on melting, resulting in the
quasi-network structure illustrated by the inset in Figure 1b. The Al–O distance
reduces at Tm from 1.93 Å in corundum at 2170 K17 to 1.76 Å in molten
alumina.9 At the same time the average separation between atoms, r, which
parameterises the Debye Model – vide infra – increases from 2.04 to 2.23 Å.
Accordingly liquid alumina is more similar to the network structure of silica
than the more closely packed structure of a-Al2O3. Nevertheless at the melting
point of alumina both the free energy of the crystal and the liquid should be
identical if the Clausius–Clapeyron relation (Equation (1)) is to apply.

1.3 Lindemann’s Melting Rule

Virtually all accounts of melting over the last century come back to Lindemann’s
melting rule18 which had its origins in Einstein’s vibrational model of specific
168 Chapter 10
heat. Lindemann originally proposed that melting occurs when atoms oscillating
about their mean positions begin to collide with one another – a kinetic rather
than a thermodynamic description. In the form later developed by Gilvarry,19
melting is predicted to occur when the incoherent root
mean
1=2square displacement
of the average atoms about their mean positions u2 exceeds a certain
r. In terms of the Debye model20
fraction of their average separation, 
    

2 YD 1 YD
u ¼ 9 h2 T=mk
 B Y2D F þ ð2Þ
T 4 T
where m  is the mean atomic mass, YD is the Debye temperature, kB is
Boltzmann’s
R YD =T zdz constant and h is Planck’s constant divided by 2p. F YTD ¼
T
YD 0 ez
1 approaches unity when T4YD and the zero point motion
h2
9  1=3 
4mkB YD becomes a minor correction. Therefore taking rm ¼ VA , where VA is

the average atomic volume, the melting temperature Tm is given by
Tm ¼ om2m 4kB mY  2D =9h2 ¼ L2 kB mY
 2D r2m2 =9h2 ð3Þ


where L2 ¼ u2m = r2m . For many simple crystalline materials L E 0.1 at
the melting temperature, Tm,21 in which case inserting L ¼ 0.1 in Equation (3)
provides an empirical law for predicting Tm. The prerequisite, though, is that the
crystalline systems are ‘‘Debye-like’’, which is generally meant to mean that
the Debye frequency, oD ¼ kB YD = h, approximately aligns with the top of the
measured vibrational density of states (VDOS).22 For a-Al2O3, for instance,
n D ¼ oD =2p equals 22 THz, which is in the vicinity of the optic modes measured
by inelastic neutron scattering23 and from Equation (3), L ¼ 0.1. For quartz, on
the other hand, despite the stronger chemical bond, nD equals 10 THz, falling in
the bottom half of the VDOS, and L ¼ 0.2 at the melting temperature. For
zeolites, where Si–O and Al–O bond strengths are similar, these discrepancies
become even more exaggerated. Nevertheless for crystalline systems, like metals
and alkali halides and oxides that are reasonably close packed, the harmonic
Debye model offers a global structure-independent description of the dynamics
and Lindemann’s rule (Equation (3)) is surprisingly predictive.21,24
Of course, as melting is approached the vibrational energy rises through the
asymmetric interatomic potential leading to anharmonic vibrations. Never-
theless, if the expansion coefficient a remains linear with temperature, thermo-
dynamic properties can still be successfully described by assuming that
vibrations remain harmonic as interatomic separations increase with tempera-
ture – the quasi-harmonic approximation. In this approximation, at tempera-
tures above YD, quantities like the specific heat at constant volume, the
Grünheisen parameter and also aK, the product of the expansion coefficient
and the bulk modulus K, should all be temperature independent.22 Alumina
conforms well to the quasi-harmonic approximation as Tm is approached.
1=3
In the Debye model oD / v=VA ,20 where v is the Debye speed of sound.
Accordingly, frequencies of the harmonic (acoustic) modes are directly related
to the bulk and shear moduli, K and G, of the crystal. Gilvarry appealed to this
connection between kinetics and thermodynamics19 in order to develop
Melting and Amorphisation 169
Equation (3) into an expression for the melting curve that complements the
Clausius–Clapeyron relation (Equation (1)):
 
dTm Tm dK
¼
1 ð4Þ
dP K dP
dK=dP can be obtained in the quasi-harmonic approximation relation from the
slope of lnK versus ln r, if the temperature dependences of the density r and of
the bulk modulus K are known as Tm is approached. Virtually the same melting
curve expression (Equation (4)) is obtained from Poirier’s dislocation melting
model.21 Indeed Equation (4) also emerges from Lennard-Jones and Devon-
shire’s atomic disordering theory of melting.25 Both these models overcome a
common criticism of Lindemann’s melting rule that, unlike the Clausius–
Clapeyron law which is based on the coexistence of liquid and crystal each
with the same free energy along the phase transition boundary, Equation (3) is
only tied to the properties of the crystalline state. For both the dislocation
model21 and the atomic disordering model25 however, disordered as well as
periodic components are present at the melting point and Lindemann’s rule is
returned. Accordingly at the melting point Equation (4) indicates

dKL dKC
KC
KL ¼ KC
KL ¼ DK ð5Þ
dP dP
As the high frequency bulk modulus of a solid KN, which can be obtained
from Brillouin scattering or inelastic X-ray scattering, approximately equals the
static bulk modulus K, KL for the liquid can be approximated from measure-
ments of the respective transverse and longitudinal sound velocities, vT and vL ,
viz: K ¼ C11
4C44/3, where C11 ¼ rv2L and C44 ¼ rv2T . In particular KC 4 KL so
the step change in specific volume DV at the melting point (Figure 1b) is also
accompanied by a step change in bulk modulus DK in the opposite sense.

Returning to Equation (3), the total mean square displacement u2 is

h m2 i Q 2 = 3
contained in the Debye–Waller factor familiar in crystallography
2 e ,
where Q is the scattering wave vector. At modest temperatures u is readily
measured from the decrease in intensity of
the
 Bragg peaks compared to the
background of thermal diffuse scattering. u2 is also contained in for crystals
and glasses the intermediate scattering function, F(Q, t), in the limit as Q-0
and t -N. F(Q, t) can be obtained by inelastic X-ray scattering experiments26
and also from MD simulations from the transform of the van Hove space–time
correlation function. As a result, excellent opportunities are now emerging to
explore Lindemann’s rule not just by extrapolating Equation (2) to Tm using
room temperature densities and elastic constants – the harmonic approxima-
tion – but also by looking for departures from Equation (2) as elastic constants
soften in the vicinity of the melting
temperature.

At temperatures close to melting, u2 becomes more difficult to extract from
24
diffraction experiments because
2 of anharmonic factors. However, when these
are correctly accounted for, u is found to rise above the value predicted by
the harmonic Lindemann rule (Equation (3)).24 Our preliminary results for
170 Chapter 10
corundum are reproduced in Figure 2a where synchrotron radiation powder
diffraction patterns from levitated spheres have
been analysed by the Rietveld
1=2
method to obtain the Lindemann ratio L ¼ u2 =r.13 Some softening of the
elastic constants K and G as melting is approached is accompanied by a
significant increase in thermal diffuse scattering. Analogous disordering of
the periodic structure as T-Tm has been reported recently in fascinating
studies of colloidal crystals.27 These beautifully imaged premelting phenomena
have been specifically correlated with extended defects in the close-packed
periodic colloidal structures – notably grain boundaries but also dislocations.
It is interesting to note that the softening of elastic constants as Tm is
approached is also inherent in the supercooled state. Mode coupling theory, for
example, predicts that above the glass transition the speed of the slow a
processes of the glassy state accelerate towards the speed of the fast vibrational
b processes, the two becoming indistinguishable once the classical liquid state is
reached.10,28 This effect is accompanied by an increase in translational diffu-
sion,29 particularly for fragile liquids, of which molten alumina appears to be
an extreme example.10,30 This is the same temperature range where the
harmonic and quasi-harmonic approximations
divide (Figure 2a).
1=2
Also included in Figure 2 are values for m2 r which we have estimated
=
from the remarkable X-ray inelastic scattering data of liquid alumina, recently
published by Sinn et al.31 The downward discontinuity in the bulk modulus at
the melting point DK (Equation (5)) is matched by an upward discontinuity in

0.6
α-Al2O3 Lindemann Law (a) (b)
0.22
α-Al2O2 XRD Debye-Waller Factors
Liquid Al2O3
0.20 0.5
0.18
Crystal
0.16 0.4 Liquid
Al2O3
<µ2>1/2/<r>

0.14 MD
<µ2>1/2

0.3
0.12

0.10
0.2
0.08

0.06 Tm
0.1
0.04 Tm

0.02 0.0
1000 1500 2000 2500 3000 −1 0 1 2 3 4 5 6 7
T/K Temperature

Figure 2 Mean square displacement

1=2above and below the melting point, Tm. (a)
Preliminary results of m2 r for crystalline alumina up to Tm.13 Data for
=
liquid alumina13 estimated from inelastic X-ray scattering
data. 1=2
31
(b)
LaViolette and Stillinger’s Lennard-Jones MD simulations of m2 versus
temperature across the melting point.32
Melting and Amorphisation 171

2 1=2
m (Figure 2a). A similar picture appeared in early MD simulations by
LaViolette and Stillinger.32,33 Using an interatomic

potential derived from the
1=2
Lennard-Jones potential, they calculated L ¼ m2 =r ¼ 0:5 in the liquid
state, rather larger than what is observed when alumina melts. More recent
Lennard-Jones MD calculations by Luo and co-workers account for anhar-
monicity at the melting point34 and yield a Lindemann ratio L of 0.116
increasing to 0.143, virtually matching the behaviour in alumina shown in
Figure 2a. These authors also follow the T–P melting curve for a Lennard-
Jones system, and confirm that L remains virtually constant with increasing
pressure, therefore establishing that the Lindemann rule (Equation (3)) applies,
not just at ambient pressure, but at high pressures too.

2 Amorphisation
2.1 Negative Melting Curves
Melting curves are not always positive, ice being the familiar example. DVo0
and DS40 and so from Equation (1), dT dP ¼ DS o0. Predicting the depression in
DV

the melting point of ice with pressure by the Thomsons was one of the first
successful applications of thermodynamics. Now 150 years on it is the riches of
the physics of crystalline, supercooled and glassy water that are attracting
attention.35,36 Critical in this renaissance of the thermodynamics of water have
been the groundbreaking experiments of Mishima and colleagues who showed
how the low temperature hexagonal phase of ice could be amorphised to a glass
at 77 K under 1 GPa of compression – the critical T–P point intersecting the
extrapolated negative melting curve.37 Moreover, by reducing the pressure, a
second glassy phase was discovered together with a reversible first order phase
transition between the two viz: from a high density amorphous (HDA) phase to
a low density amorphous (LDA) phase.38 In addition to the difference in molar
volume between these two glassy states or polyamorphs, DV ¼ VHDA
VLDA, a
difference in entropy, DS ¼ SHDA
SLDA, is also expected, the LDA phase being
the more ordered. Accordingly, a decompressive HDA–LDA liquid–liquid
phase transition should be exothermic, with a stepwise decrease in density
and entropy. If DV ¼ VHDA
VLDAo0 and DS ¼ SHDA
SLDA40, Equation (1)
predicts that the characteristic temperature of this transition will fall with
increasing pressure, like the melting curve of ice, but now originating below Tm
from a critical point in the supercooled region.35
The existence of more than one supercooled amorphous phase – now
generally referred to as polyamorphism39 – has been advanced as the destabilis-
ing factor that might trigger the amorphisation of other crystalline systems
under thermobaric stress – not just ice.40 Indeed, after the amorphisation of
ice was first discovered37 an analogous transformation in quartz was soon
reported, a-SiO2 amorphising to a glass under the rather larger pressures of
30 GPa.41 Amorphisation, or low temperature vitrification, now embraces many
minerals, destabilisation being promoted not just through pressure but also for
172 Chapter 10
4
high density phases through decompressive stress. In either case, the route to
an alternative stable crystalline phase is kinetically hindered by an amorphous
intermediate phase.

2.2 Zeolite Amorphisation

It was this background of crystalline destabilisation under thermobaric stress
that led to our own studies of the collapse of zeolites.42,43 These experiments
benefited from the combined synchrotron radiation techniques originally
exploited in studying the synthesis of catalytic microporous materials.1 Crystal-
line microporous materials like Na zeolite A and Na zeolite Y are extremely
resilient, considering their low density structures. Nevertheless once calcined
they eventually succumb to thermobaric stress, their filigree periodic low
density structures amorphising with an abrupt reduction in volume, DVA, as
illustrated in Figure 3a. The Debye–Scherrer pattern disappears abruptly over a
narrow range of pressure and/or temperature, the process being irreversible –
certainly over periods of months. For instance, at ambient temperature zeolite
collapse occurs around 3–4 GPa (PA) and at ambient pressure at around 1100 K
(TA) which defines the ‘‘negative amorphisation curve’’ shown in Figure 4a for
zeolite A.
However, the low temperature melting of zeolites is more subtle. The
negative amorphisation curve defines a liquid–liquid transition between LDA
and HDA phases, but zeolite collapse in practice involves excursions into a
region of negative pressure,44 as Figure 4 illustrates. The decrease in molar
volume DVA on amorphisation in Figure 3a is defined by P1 and T1, where
collapse commences, and by P2 and T2, where collapse is completed. Adding
these to the T–P diagram in Figure 4a establishes experimental boundaries for a
zone of instability either side of the negative amorphisation line defined by
TA,PRP
TRT,PA, with T1,PRP
TRT,P1 defining the thermobaric limits for
zeolite stability and T2,PRP
TRT,P2 the limits beyond which vitrification
appears irreversible. In the Ponyatovsky–Barkolov model for amorphisation,40
the LDA–HDA liquid–liquid phase transition across the TA,PRP
TRT,PA
negative amorphisation curves between the low and high density phases that
are believed to destabilise the periodic lattice is defined by dT DV
dPA ¼ DS , where
A

DS ¼ SLDA
SHDAo0 and DV ¼ VLDA
VHDA40. This is bounded by the

respective spinodal limits defined by d2G/dc2 ¼ 0, where c, for example, is the
concentration of the LDA phase.10,45 These limits for the LDA and HDA
phases are shown by the dashed lines in Figure 4a and are in reasonable
alignment with the experimental T1,PRP
TRT,P1 and T2,PRP
TRT,P2 bound-
aries determined from Figure 3a.42
Figure 4 includes important new ab initio 0 K computer simulations which
model the amorphisation processes in zeolites induced by compression but also
by decompression.46 With increasing pressure these calculations reveal a
displacive order–disorder transition (marked II–III). This is identified by an
abrupt decrease in volume close to 3 GPa and is associated with a narrowing of
Melting and Amorphisation 173
T/K
950 1000 1050 1100
zeolite A 120
110 (a) HDA (b) 0.04
25 kJ/mol
16 kJ/mol 110
100
LDA 0.03

100 0.02
90 CP
Molar Volume / cm3

0.01

β / GPA21
P1 T1
90
80
0 0.00
80
70 ∆VA PA
TA −1 −0.01

Pint / GPa
70
60 −2 −0.02
P2 T2
60 −3 −0.03
50
50 −4 −0.04
40
0 2 4
40 P / GPa
0 5 10
P / GPa

Figure 3 Amorphisation of zeolite A. (a) Stepwise decrease in volume DVA under

pressure at 1 mPa s
1 (left) and temperature at 30 mdeg s
1(right). T1 and P1
define the start and T2 and P2 the end of zeolite collapse while TA and PA
define the turning points. These are used to identify the boundaries between
zeolite, LDA and HDA phases in Figure 4. A DTA scan is shown together
with the enthalpy changes DH taken from Ref. 53 for zeolite A, nepheline
(LDA) and high density glass (HDA). (b) Dependence of macroscopic
compressibility b (right) and the internal pressure Pint (left) on applied
hydrostatic pressure during compressive amorphisation, measured from
changes in the zeolite diffraction pattern. Taken from Refs. 42 and 44.

the Si–O–Al bridging angle. In all other respects the crystalline phase II and the
amorphous phase III are toplogically equivalent and the phase transition is
found to be reversible but with hysteresis (Figure 4b). Interestingly, this first
order transition lies close to our experimental T1,PRP
TRT,P1 line extrapolated
to 0 K. We therefore associate zeolite A at ambient pressure with Peral and
Íñiguez’s phase II and our LDA phase with their amorphous phase III.
At higher pressures of around 5 GPa the simulations reveal a subsequent first
order topologically disordering transition, now between two amorphous phases
labelled III and IV. At this point the double four-fold rings – the smallest of the
secondary building units of the zeolite A structure – collapse with a further
reduction in the bridging oxygen bond angle.46 The III–IV transition is
reversible but the hysteresis bypasses the amorphous phase III eventually
recovering the reference zeolite close to
4 GPa. Our experimental nega-
tive amorphisation curve TA,PRP
TRT,PA extrapolated to 0 K falls close to
the III–IV transition from which we can associate our HDA phase with Peral
and Íñiguez’s topologically disordered phase IV. This phase is maintained to
174 Chapter 10
PRP
1200
T2
(a) P internal(TA ) C TA
1000 P internal(T1) T1 Z:A
II -> III
800

III -> IV
600
T/K

P internal(PA )
400 P internal(P1 )
P1 PA P2
TRT

200 Z:A Z:A Z:A LDA HDA

I I/IV * II III IV
0

-4 -2 0 2 4 6 8 10
P / GPa

(b)

Figure 4 Comparison between the various thresholds in the collapse of zeolite A.

Upper frame: experiment.10,42,44 The limits T1, P1, T2, P2, TA and PA
for thermal and pressure-induced amorphisation are taken from Figure 3a.
The dashed lines are the spinodal limits calculated from the model of
Ponyatovsky and Barkolov.40 The dashed lines at negative pressures
refer to the decompression at the start of collapse (blue) and the turning
point (green) illustrated in Figure 3a. Lower frame: ab initio 0 K computer
simulations of volume vs. pressure.46 First order discontinuous transitions
II–III and III–IV are reversible via IV* and IV** to the reference zeolite I.
The vertical arrows in (b) follow extrapolations of the experimental data to
0 K in (a), and associate the zeolite at positive pressure and the amorphous
LDA and HDA phases with II, III and IV, respectively.

pressures of 10 GPa at the point TRT,P2 where experimentally we find all of the
zeolite has amorphised.42
An exciting outcome of these simulations46 is that, not only are the zeolite–
LDA and LDA–HDA transitions analysed from experiment (Figure 4a)42
Melting and Amorphisation 175
replicated (Figure 4b), but also these are abrupt in the 0 K calculations and
well-separated thermodynamically. In particular the LDA or phase III shares
the topology of the zeolite. We have already drawn attention to the fact that
the LDA phase should be an ordered or perfect glass,10,42,43,47 equivalent to the
ideal melt-quenched glass predicted by Kauzmann48 with entropy equal to the
equivalent crystal at some finite glass transition temperature, TK. Synthesising
a perfect glass from a crystalline precursor rather than from a supercooled
liquid avoids the interruption of recrystallisation that has so far precluded
reaching this low entropy LDA glass by conventional cooling from the
melt.10,49,50 The alumino-silicate melts equivalent to a conventional HDA
alumino-silicate melt are the feldspars. The entropy difference between molten
and crystalline states is the configurational entropy, Sc, acquired when a crystal
melts and for which the extra configurations are mainly responsible for the
increase in specific volume, DV at Tm (Figure 1b). If DCP(T) is the difference in
specific heat between R T the supercooled liquid and the crystal at a given
temperature, Sc ¼ TmK DCP d ln T. So, if LDA is a perfect glass
Sc ¼ DS ¼ SHDA
SLDA, the difference in volume between the HDA and LDA
phases, DV ¼ VHDA
VLDA, should be given by Equation (1)
dT
DV ¼ DS
dP
Taking the measured value of Sc ¼ DS for nepheline (15 J mol K
1)51 and
the slope of the negative amorphisation curve from Figure 4(a) dT=dP ¼

210
7 K Pa
1 gives VLDA
VHDA ¼ 3 cm3 or 12% of DVA ¼ Vzeolite
VHDA
from Figure 3a. This is in reasonable agreement with Peral and Íñiguez’s MD
calculations (Figure 4b), where VIII
VIV is 14% of the total volume change
between the ambient zeolite phase II and the topologically disordered phase IV.
The increase in entropy between the LDA and HDA phases is reflected in the
endothermic step in CP (Figure 3a).
Finally we turn to the unusual T–P behaviour in zeolite collapse that occurs
at negative pressures (Figure 4a) where the MD calculations indicate the
reversibility of the amorphisation processes (Figure 4b).46 Experimentally we
find that thermal collapse is accompanied by a sharp rise in the expansion
coefficient of the residual crystalline fraction while pressure-induced collapse is
accompanied by a lowering in the compressibility42 – in either case the
remaining zeolite is stretched signifying negative internal pressures, as shown
in Figure 3b. Dramatic evidence for decompression can be seen in micrographs
of recovered material (see the inserts in Figure 3b). In the model of Cohen
et al.52 for displacive amorphisation, long range order is destroyed because
domain nucleation overwhelms growth. If nucleation is of higher density than
the precursor crystal and randomly distributed, then intervening periodic zones
should suffer decompression on average. The internal pressure is estimated in
Figure 3b from the difference in compressibility b with the ambient value and
registers approximately
2 GPa at P1, the point at which collapse starts to
accelerate, and around
4 GPa at P2 by the time the ruby calibrant in the
diamond anvil cell has reached 4 GPa and collapse is complete.44 In the same
176 Chapter 10
way, for temperature-induced collapse, the increase in thermal expansion
coefficient and the ambient compressibility enable the internal pressure in the
crystalline fraction to be estimated. These negative internal pressures at the
start of collapse TRT,P1 and T1,PRP and at the turning point TRT,PA and
TA,PRP are shown connected by the dashed blue and green lines respectively in
Figure 4a. Extrapolated to 0 K these extend over reference I in the computer
simulations at negative pressures in Figure 4b.46 Because experimentally
thermobaric stress is applied sequentially, we conclude that the zeolite–LDA
transition is progressively achieved through a process of compression and
decompression followed by recompression, until full transformation to the
LDA phase (III) is achieved. The dynamics of zeolite collapse should
therefore be controlled by the viscosity of the LDA phase, as it is gradually
accumulated.10,42
Thermally-induced zeolite collapse to the LDA phase is accompanied by a
sharp exotherm in CP which anticipates the endothermic step associated with
the LDA–HDA transition (Figure 3a).42 This exotherm confirms that the
zeolite has a higher enthalpy than the amorphous phase it transforms into.
The enthalpies of anhydrous zeolites, glasses and feldspar crystals have been
meticulously catalogued by Navrotsky and Tian in a comprehensive study and
decrease in that order.53 Setting the enthalpy of the LDA phase equal to that of
nepheline, the different enthalpies for zeolite A, LDA and HDA are sketched in
Figure 3a, signifying a drop of 25 kJ mol
1 for the zeolite-LDA transition.
Taking the average decompression, DP, between the applied temperatures T1
and TA of 0.3 GPa (Figure 3a) and the mean molar volume, V, for the zeolite–
LDA system of 78 cm3 (Figure 4a), V DP experiences a similar drop of 23 kJ
mol
1. Given that DH ¼ TDS + VDP, this suggests that DS E 0. Little entropy
change between the zeolite and LDA phases is consistent with the displacive
nature of the II–III transition46 (Figure 4b) and the ‘‘perfect glass’’ label we
have used for the LDA phase.10

3 Amorphisation and Double Well Potentials

Displacive phase transitions in silicates – like a to b quartz – can be modelled
on the dynamics of low frequency rigid unit modes between adjacent tetra-
hedra.54 Equilibrium positions are paired through double well potentials
associated with very soft modes. We have recently detected strong non-
dispersed features by inelastic neutron scattering at very low frequencies
(4  1011 Hz) in zeolites and also in glasses including silica,43 which we have
attributed to the librational modes responsible for the destabilisation of
microporous crystals as well as the unusual low temperature thermal properties
of glasses.55 In amorphised material these modes should promote the transfor-
mation of LDA into HDA phases and now, considering Figure 4, the
reversibility of these first order phase transitions. The recent observation of
similar sub-terahertz (THz) features in quartz and corundum13 encourages us in
the view that they may also lie at the heart of normal melting and freezing. This
Melting and Amorphisation 177
would put the emphasis of melting on twisting rather than on the stretching
criterion that forms the basis of the Lindemann rule.19 At lower temperatures,
librational modes in standing wave configurations can promote network
distortion at metal sites in zeolites, which has been advanced as an explanation
of their catalytic activity56 – as observed in Ni exchanged zeolite Y,57 one of the
first discoveries to be made by John, myself and our colleagues at Daresbury
Laboratory and the Royal Institution from combining X-ray spectroscopy and
X-ray diffraction.

Acknowledgements
Steve Fearn, Louis Hennet, Jorge Íñiguez, David Keen, Chris Martin, Florian
Meneau, Alexandra Navrotsky, Irina Pozdnyakova, Sabyasachi Sen and
Martin Wilding are thanked for stimulating discussions. The support of the
Higher Education Funding Council of Wales is acknowledged through the
Centre for Advanced Functional Materials and Devices, as is Science and
Technology Facilities Council for providing access to the Synchrotron Radia-
tion Source.

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CHAPTER 11

Computer Modelling in Solid-

State Chemistry
C. RICHARD A. CATLOW, SAID HAMAD, DEVIS DI
TOMMASO, ALEXEY A. SOKOL AND
SCOTT M. WOODLEY
Davy Faraday Research Laboratories and Department of Chemistry,
University College London, 20 Gordon Street, London WC1H 0AJ, UK

1 Introduction
Model building goes back to the beginning of scientific thought; and com-
puter modelling is simply the application of contemporary technology to this
core scientific activity. Modelling now pervades all scientific disciplines and is
applied on almost all the length and time scales used in present-day science.
Applications in chemistry and materials sciences have been particularly
successful and this article will focus on the role of modelling techniques in
solid-state chemistry, where the range and applicability for the techniques
has developed enormously in the last 30 years and whose importance was
realised in the early days of the field by Sir John Meurig Thomas.1 We
cannot in an article of this length survey adequately what has become a
major field of contemporary chemical and materials sciences; but we hope to
show how the field has developed, to outline some of its major achievements,
and to indicate the range and excitement of recent applications. We will
concentrate on modelling at the atomic and molecular level while acknowl-
edging the growing importance of modelling at larger length and longer
timescales.

2 Motivation and Background

We have noted that modelling is an indispensable scientific tool, but why do
we need models? In contemporary physical, including solid-state, sciences,
180
Computer Modelling in Solid-State Chemistry 181
modelling is used for four main reasons:

To gain insight and understanding of complex systems, for example,

catalytic processes and the mechanisms of crystal growth and nucleation.

To derive numerical data, for example, the formation energies of defects
in solids and the binding energies of molecules to surfaces.

To obtain information on systems that may be very difficult or inacces-
sible to experimental study, for example, materials under extreme condi-
tions of temperature and pressure in planetary interiors.

To predict new systems and phenomena, for example, new, as yet
un-synthesised crystal structures.

These categories are neither comprehensive nor mutually exclusive, but they
are useful and we may find many examples in solid-state chemistry of all
four categories, with an increasing emphasis in recent work on predictive
applications.
The earliest applications in solid-state chemistry in the 1960s and 1970s
concerned calculations of lattice and defect energies and a still useful review of
this earlier work is available in Ref. 2. The importance of this work is that it
showed that for ionic and semi-ionic solids, using carefully parameterised Born
model potentials, it was possible to achieve quantitative agreement with
experiment. The impact in the field of the physics and chemistry of defective
solids was particularly marked, and in the early 1980s modelling methods
rapidly became a routine adjunct to experimental studies. An important
landmark was the development by Norgett of the HADES code (see Ref. 3),
which was based on the approach originally proposed by Mott and Littleton4
and which allowed calculations on defect formation and migration energies to
be undertaken in a straightforward and automated manner. By the late 1980s
the field had become mature and well established, but the importance of
calculations on defects and impurities in solids remains strong in the contem-
porary field although such calculations now often make use of quantum
mechanical (QM) methods as discussed later in this article.
From these early foundations the field rapidly developed in a number of
different directions. Modelling of defects rapidly engaged with the structural
problems posed by non-stoichiometric solids and by fast ion conduction.
Lattice energy calculations moved from simple ionic solids to far more complex
systems, where a particularly fruitful field developed in the modelling of silicate
minerals.1,5 Modelling studies embraced amorphous as well as crystalline solids
and surface in addition to bulk properties. These and other achievements will
be discussed in greater detail below.
The vitality of the field has relied on three main factors: first the contin-
uing development in methods and algorithms; second, the continuing expo-
nential growth in computer power; and third and most importantly, the
engagement with experiment; and it is in this latter respect that John Meurig
Thomas has made such significant contributions to computational solid-
state chemistry.
182 Chapter 11

3 Methods
Our account here is brief as the field has been very extensively reviewed in
recent years (see, for example, Refs. 6 and 7). Earlier work was largely based on
interatomic potential (IP) based methods, which do not attempt to solve the
Schrödinger equation for the system studied, but rather use parameterised
functions representing the interaction energy between pairs or larger numbers
of atoms or ions. Such potentials may be implemented in static lattice or energy
minimisation methods (as in the defect and lattice energy calculations referred
to above), Monte Carlo methods or molecular dynamics techniques. Potentials
may be parameterised by empirical fitting procedures or by direct calculation of
the interaction energy using theoretical methods. Good quality potentials are
now available for many inorganic and molecular materials and there is a wide
range of excellent general-purpose software. Applications using these tech-
niques continue to make an important contribution to the field.
Despite their versatility, potential based methods are, however, limited in
their scope. They cannot model problems and properties that depend directly
on electronic structure, for example, reactivity and spectroscopy; and there may
sometimes be uncertainties about the extent of transferability of potential
parameters. The last 10 years have, however, seen an explosion in the appli-
cation of electronic structure methods. The vanguard of these developments
has been in density functional theory (DFT), which rests ultimately on the
pioneering work of Hohenberg, Kohn and Sham,8,9 and which allows calcu-
lations of ground-state energies and electron densities for molecules and solids
with a reasonable level of accuracy using affordable computer resources.
Particularly attractive aspects of DFT are the relatively low scaling, that is,
the calculation time increases less dramatically with system size than with the
more traditional Hartree–Fock (HF) methods. The methods are, therefore,
applicable to increasingly large and complex systems and the range of appli-
cations is set to expand with the growth in ‘‘Order N’’ techniques, that is,
methods for which the computational requirements scale linearly with system
size. The majority of recently published electronic structure calculations on
solids have therefore employed DFT, but HF methods continue to have a
significant role in the field; moreover, there has been a considerable growth in
hybrid approaches which blend ‘‘exact’’ HF exchange with the DFT approach.
We refer the reader to the reviews cited above for details.
Electronic structure methods can be implemented in a number of ways.
The most popular in recent applications in solid-state science is to use
three-dimensional periodic boundary conditions (PBC), with defects, impurities
and sorbed species, as well as surfaces and interfaces, being treated using a
super-cell. Such methods have many technical advantages and the plane wave
pseudopotential approach has been particularly effective; moreover, the method
may be employed in dynamical simulations either in straightforward (if expen-
sive) adiabatic procedures or using the more ingenious fictional electron
dynamics of the celebrated Car–Parrinello approach.10 The use of PBC does,
however, become more problematic when studying, for example, large sorbed
Computer Modelling in Solid-State Chemistry 183
molecules and complex defects, where a better approach is based on an old idea
in computational chemistry and physics in which the system is partitioned into
the region of interest, for example, the defect or sorbed molecule, and the
surrounding (embedding) matrix: the former is treated at a high QM level; the
latter is described using more approximate level, typically IP based methods, as
it is usually only necessary to describe the electrostatic and steric constraints of
this region. A number of technical developments have given this method much
greater reliability and applicability in recent years and we may anticipate that
embedded cluster methods will make a major contribution to the field in the
future.
We conclude this section with the following reflections and comments on the
present status of computational methodologies in solid-state science:

(i) There will be a continuing role for IP based methods: even in the era of
O(N) DFT and petaflop computing, such methods will be the only way
to tackle many of the complex problems and systems posed by con-
densed matter science. Moreover, there are many problems, for example
the modelling of bulk structures and defects where, given good quality
potential models, these methods are probably the most appropriate and
accurate.
(ii) DFT is an approximate method. There is no exact exchange-correlation
functional and the common use of the term ‘‘first principles’’ in
describing DFT calculations, although not incorrect, has had a ten-
dency to be misleading and to imply that they are exact. DFT has
made a huge contribution to the field, but its role must be kept in
perspective.
(iii) A multi-technique approach is generally needed for the problems
addressed by the solid-state chemist; in particular, it is often necessary
to combine potential based and QM methodologies. This feature will
become apparent in the later sections of this article.

4 Achievements
Earlier, we attempted to describe the early development of the field; here we
shall try to summarise some of the main achievements of computational solid-
state chemistry since its genesis in the 1970s. We highlight the following main
areas.

4.1 Crystal Structure Modelling and Prediction

One of the most fundamental challenges in theoretical solid-state science is the
prediction of crystal structures. And indeed in a notorious ‘‘News and Views’’
article in Nature in 1988, John Maddox11 commented that ‘‘One of the
continuing scandals in the physical sciences is that it remains in general
184 Chapter 11
impossible to predict the structure of even the simplest crystalline solids from a
knowledge of their chemical composition’’. Maddox’s provocative remarks
were not true when they were first made 20 years ago; and indeed structure
prediction is one of the great success stories of the field. Early developments
were based on lattice energy calculations, which in the 1980s were then coupled
with energy minimisation methods. Considerable success was enjoyed in mod-
elling oxides and silicate structures,1,5,12 and some of the greatest successes were
achieved in the field of microporous aluminosilicates (zeolites).13 Of particular
note was the successful modelling of the polymorphs of zeolite beta14 and the
monoclinic distortion of the pure silica pentasil zeolite, silicalite – a subtle
structural feature that was accurately reproduced by the lattice energy calcu-
lations of Bell et al.15 These calculations are, however, ‘‘modelling’’ and not
‘‘prediction’’. They take (possibly approximate) structures, which are refined by
minimisation. Their success, however, validates the methods and potentials,
and such calculations are a necessary precursor to further modelling studies.
The methods may also be of real value in refining approximate or inaccurate
structures as shown by the elegant work of Shannon et al.16 on zeolite nu, which
was essentially solved using minimisation methods.
The major challenge is, of course, prediction and here there have been
substantial developments in the last 10 years. The problem is essentially one of
devising procedures to explore the energy landscape quickly and effectively so
that the low energy regions, in which the stable structure(s) lie, can be located.
A number of procedures are available of which the following are the most
widely used.
Simulated annealing (SA), which explores energy landscapes by undertaking
a molecular dynamics or Monte Carlo simulation, initially at high tempera-
tures; subsequent cooling (or annealing) allows the system to freeze into low
energy regions. The approach has been used to great effect in structure solution
(see, for example, Ref. 17) and in a number of elegant, predictive studies of
inorganic solids by Schön and Jansen.18,19 It is a straightforward and robust
procedure. If it has a weakness, it is that the exploration of the energy
landscape necessarily starts from a single point and it is possible that not all
low energy regions may be accessed. To minimise this danger, multiple runs
with different initial parameters must be undertaken, as in the recent work of
Hamad et al.20 on nanoparticle structure prediction.
Genetic algorithm (GA) methods, or more generally evolutionary algorithm
(EA) methods, avoid the difficulty of the single starting point by setting up a
population of structures, where typically different random arrangements of
atoms make up each candidate structure in the initial population. A cost
function is specified, which must be a rapidly computable ‘‘figure of merit’’ for
the structure: it may be a simple function depending on bond lengths and
coordination numbers or a crude estimate of the lattice energy. The algorithm
works by mimicking Darwinian (or in some cases Lamarckian) evolution. The
system passes through many (typically, several hundred) generations. The
better structures, as measured by the cost function, pass directly to the next
generation (elitism); while a proportion of these structures are chosen for
Computer Modelling in Solid-State Chemistry 185
‘‘breeding’’ (with selection biased towards better structures) in which each pair
of structures generates offspring by a process in which they can exchange
information and undergo mutations. The latter procedure ensures that the
population retains its diversity while it evolves towards structures with opti-
mum cost functions. At the end of the GA, the better structures are subjected to
standard full lattice energy minimisation. The viability of this approach in
structure prediction has been shown in a series of studies of Woodley and co-
workers who have applied the techniques successfully to both dense21 and
microporous22 oxide structures; in the latter case, it is necessary to specify
‘‘exclusion regions’’ in order to model the microporosity of the system. We also
note that GA methods have been successfully used in structure solution23 where
the cost function is now the crystallographic ‘‘R-factor’’, and that EA methods
are widely and generally applicable to problems in structure prediction and
solution in chemistry.
Application of topological methods, for which there is a long history in
crystallography. The approach is most appropriate and successful for the case
of microporous structures of which there have been several studies, most
notably of Smith,24 Treacy et al.25 and recently, Bell, Foster and Klinowski.26,27
The latter studies use combinatorial tiling theory to enumerate networks
systematically; the resulting topologies are then used to generate pure silica
structures whose energies are then calculated using lattice energy minimisation.
This feature is important: as well as generating new structures, it is essential to
test their thermodynamic feasibility. Bell et al. have predicted a number of new,
stable, but at present hypothetical structures; an example is shown in Figure 1.
The challenge is now to synthesise these new materials.
Molecular packing methods, which have been widely used in structure
prediction of molecular crystals; the different modes of molecular packing
are explored in a systematic manner and candidate structures are then subjected
to energy minimisation. The method has been very widely used and automated
in recent years by Price.28 A very nice example of their recent work is the
prediction of a new crystalline polymorph of the pharmaceutical compound,
5-fluorouracil, which was subsequently crystallised from an anhydrous solvent.
A detailed account of structure prediction for inorganic materials is given in
Ref. 29. Here, it will suffice to say that the field has responded well to Maddox’s
challenge of 20 years ago.

4.2 Structures of Amorphous Solids

The need for modelling tools in the structural chemistry of amorphous mate-
rials is probably even greater than with crystalline solids owing to the greater
difficulty in obtaining unambiguous models from experiment. The most widely
used procedure is the ‘‘melt–quench’’ approach in which the melting of an
appropriate crystalline solid is simulated using molecular dynamics; the melt is
then rapidly cooled so as to freeze into an amorphous structure. This proce-
dure, of course, mimics the real way in which glasses are prepared, although the
186 Chapter 11

Figure 1 Framework structures of some of the uninodal hypothetical zeolites derived

from tiling theory: (a) structure 1_11, derived from one of the simple tilings,
has a very low framework density. The cages are shown more schematically
in (b), illustrating the openness of the structure; (c) large-pore structure 1_71
has unidirectional 12-ring channels; and (d) tetragonal structure 1_14 has
elongated 12-ring channels, which run in orthogonal directions, intersecting
to form a 3-D pore system.

speed of the simulated quench (which will, at most, be a few nanoseconds) is

many orders of magnitude greater than that of a real quench. Nevertheless, the
method has proved to be of great value. There have been many studies of
amorphous silica (see, for example, Ref. 30), which have generated models that
agree well with experimental scattering data. The field has been extended to
include silicates31 and most recently bioglasses.32 Modelling methods are now
established tools in the science of amorphous solids.

4.3 Surface Structures and Properties

As with amorphous systems, there is a strong need in surface structural studies
to have complementary information from modelling; and indeed simulation
tools have become quite standard and routine in contemporary surface science.
Pioneering work was undertaken in the late 1970s by Tasker, who established
Computer Modelling in Solid-State Chemistry 187
the effectiveness of surface structure and energy calculations based on 2D
PBC.33 Tasker also made a substantial contribution to the field by his classi-
fication of ionic surfaces in terms of the electrical dipole moment in the repeat
unit perpendicular to the surface and his demonstration that systems in which
such dipoles are non-zero are intrinsically unstable. The field of oxide surface
modelling progressed rapidly in the 1980s with the widespread demonstrations
of surface rumpling and relaxation effects. A particularly notable study con-
cerned the 0001 surface of alpha-Al2O3,34 which predicted very large inward
relaxation of the top layer of Al31 ions. These predictions used IP based
calculations and were subsequently supported by DFT calculations; they were
verified by impressive grazing angle incidence, X-ray diffraction studies.35
The field developed in two directions in the 1990s: IP methods were applied
to systems of growing complexity, for example, carbonates and silicates; and
DFT techniques were increasingly (and successfully) applied to both oxide and
metallic surfaces. There was also growing interest in the adsorption of water on
a range of systems including calcite and TiO2. The (110) surface of TiO2 has
proved to be a particularly fertile field for joint computational/experimental
studies; Ref. 36 provides a good review.
The contemporary field is interacting increasingly strongly with the complex
issues posed by reactivity (see below), growth and dissolution (see, for example,
the collection of articles in Ref. 37), where modelling has acquired a truly
predictive capacity both qualitatively and quantitatively.

4.4 Defect Structures and Energies

As discussed above, many of the earlier successes of the field concerned the
chemistry of defective solids, where modelling was shown to be able to make
quantitative predictions and to provide valuable qualitative guidance and
insight. The following features deserve particular note:

(i) IP based calculations using the Mott–Littleton method4 on ionic and

semi-ionic solids with closed-shell ions are able to give accurate values of
the formation and migration energies of point defects, impurities and
defect clusters.2 Indeed, for these systems there is no convincing evidence
that superior results can be obtained using QM (including DFT) methods.
(ii) Mott–Littleton methods have proved very powerful in unravelling the
complex defect structures of non-stoichiometric compounds, such as
TiO2x,38 UO21x39 and Fe1xO40 and have proved highly complemen-
tary to experimental investigations using diffraction and microscopy
techniques.
(iii) Molecular dynamics techniques have been of great value for modelling
systems showing high ionic conductivity (fast-ion or superionic conduc-
tors), as shown by earlier work on fluorite-structured halides and Li1
conducting solids (see Ref. 41 for a review) and more recent studies of
oxygen ion conducting materials.42 Such simulations have achieved
188 Chapter 11
good agreement with measured transport coefficients and have provided
valuable insights into ion transport mechanisms.

DFT methods will make a growing contribution to the field, with calculations
commonly performed on three dimensional periodic defect supercells, although
we note the caveat on ionic systems in (i) above. Embedded cluster methods in
which a quantum mechanically described cluster containing the defect is
embedded in an IP description of the surrounding lattice are perhaps the more
appropriate technique and have been used effectively in, for example, recent
studies of hydrogen containing defects in silicate minerals.43
The majority of calculations on defect structures have concerned point
defects; but very useful studies have been reported on grain boundaries, shear
planes and dislocations. Studies of both point and extended defects will remain
an important and active area of the field.

4.5 Sorption
This wide-ranging field has been reviewed extensively in recent years (see, for
example, the chapters of Smit and of Auerbach in Ref. 44). Broadly speaking,
the field can be divided into the following kind of studies.

(i) Qualitative investigations of sorption sites, where straightforward energy

minimisation methods proved useful, as in the early studies of Wright
and co-workers using combined minimisation/neutron scattering tech-
niques to locate sorbed molecules in zeolites.45 Somewhat more sophis-
ticated techniques were developed by Freeman et al.46 based on a crude
Monte Carlo method, which was combined with minimisation methods
to locate low energy sites in microporous materials, a good illustration
of which was their early study of butane in the zeolite ZSM-5. These
methods are now routine and very widely applicable.
(ii) Detailed, quantitative modelling of sorption isotherms and thermo-
dynamics, which are usually based on the application of Grand Canonical
Monte Carlo (GCMC) techniques. Such calculations are critically depend-
ent on the availability of high quality IPs for the host–sorbate interactions;
but when such parameters are available, good quantitative agreement with
experiment can be achieved, as discussed by Smit in Ref. 44.
(iii) Applications of MD techniques to modelling the diffusion of sorbed
species. Such studies have enjoyed considerable success. They have
revealed valuable insight regarding migration mechanisms and in some
cases quantitative agreement with experiment. The article of Auerbach,
referred to above in Ref. 44, provides a good account of the state of the
art in this field.

The work referred to above has concerned physisorption and has employed IP
based techniques, which are most appropriate for such studies. Indeed it should
Computer Modelling in Solid-State Chemistry 189
be noted that physisorption is often dominated by dispersive interactions,
which can, in general, not be adequately modelled with DFT. Modelling of
chemisorption will be addressed in the next section.

4.6 Reactivity
We again address a very extensive field, which has been particularly active in
recent years, and where DFT methods have proved effective and robust. We
confine our attention to applications in heterogeneous catalysis, and focus on
recent work on microporous and oxide catalysts, while noting the very exten-
sive and successful application to the field of metallic catalysts. Good illustra-
tions of the current status of the field are found in our recent article,47 which
highlighted work in two areas:

(i) Metal substituted microporous oxidation catalysts, in particular the

widely studied TS-1 catalyst, which is a titanium substituted silicalite
material, widely used in industrial partial oxidation catalysis. A combi-
nation of computer modelling studies and X-ray absorption spectros-
copy48 has successfully elucidated detailed models for the active sites in
these catalysts and has provided valuable insights into reaction mecha-
nisms. Indeed this work nicely illustrates the complementary nature of
computation and synchrotron based experiment in this field.
(ii) Methanol synthesis catalysis, in particular the conversion of syngas
(CO–CO2–H2) to methanol using the ZnO–Cu catalyst, where modelling
has been able to identify active sites on the ZnO surface and to propose a
plausible catalytic cycle (see Figure 2); see Ref. 49.

Such calculations necessarily require QM techniques. The work on the Cu–ZnO

catalyst employed the embedded cluster techniques referred to above. Such
methods should have a wide range of applications in catalytic science as
discussed in more detail in Ref. 47.

4.7 Synthesis, Nucleation and Growth

Among the most challenging fields of application of modelling tools are those
relating to the understanding of solid-state synthesis and to the guidance of
synthetic strategies. Good examples of both categories of application are found
in the field of zeolite science. Zeolites are synthesised hydrothermally with
organic templates being commonly added to the synthesis gel in order to direct
the synthesis towards specific microporous architectures. A number of model-
ling studies have sought to elucidate the fundamental condensation processes
occurring in the synthesis gel. The most recent is the work of Mora-Fonz et al.50
who applied DFT methods to study the condensation reactions of small silica
clusters. Their work highlighted the role of pH, as condensation was shown
to require anionic clusters which are only stable under conditions of high pH.
190 Chapter 11

Figure 2 Proposed catalytic cycle for conversion of CO–H2 to methanol.

Figure 3 DAF-5 structure containing de novo designed template.

The study also showed that formation of rings – particularly those containing
four Si atoms – is highly favoured – a finding that is again very relevant to
zeolite synthesis.
The challenge of guiding zeolite synthesis was met by Lewis and Willock who
developed methods for computational design of templates for the synthesis of
specific microporous architectures. The ZEBEDDE code51 uses de novo design
techniques to ‘‘grow’’ template molecules computationally within the target
microporous host. The most successful application of this technique is illus-
trated in Figure 3, which shows the computationally designed template for
synthesis of the DAF-5 host.52 This template succeeded in synthesising the
target material, phase pure and in a few hours, in contrast to earlier syntheses,
Computer Modelling in Solid-State Chemistry 191
which required lengthy periods and produced a multi-phase sample. This work
remains one of the nicest examples of computational materials design.

5 Recent Case Studies

The previous sections of this article have, we hope, given a general indication of
the range and scope of computational solid-state chemistry. Here we attempt to
give an indication of its current status with four brief descriptions of recent
topical applications.

5.1 Nanocluster Structures and Energies

As discussed earlier, global optimisation techniques have commonly been
employed to generate approximate, or ‘‘sensible’’, structures, which may be
subject to further refinement, and the achievements of this approach in crystal
structure prediction were briefly summarised in the previous section. Here, we
concentrate on the challenges posed by the prediction of the structures of
nanoparticles – a topic of growing importance in solid-state science and one
that poses many challenges.
For particles whose size is greater than tens or hundreds of nanometres, the
structure is likely to resemble relaxed fragments cut straight from the bulk
phase. But for smaller clusters the structure may be remarkably different, as
illustrated in Figure 4. If we are to determine the structures adopted by these
small inorganic particles, we clearly require different experimental techniques
from those used to determine the structure of the bulk or large particles.
Calculation of the properties of model clusters (infrared spectra, for example,

Figure 4 GM structure, found for MgO53 (left) and ZnO54 (right).

192 Chapter 11
1000

800
Intensity (km/mole)

600

400

200

0
0 300 600 900 1200
Frequency (cm-1) (ZrO2)7

Figure 5 Calculated infrared spectra for two zirconia clusters.

-30 9 10
8 9
-30.2 10
8
7 11 -32 11
1
Binding energy (eV/n)

-30.6 2 7 1 2
3
-31 6 -34
3 12
5 6 4 12
-31.4 4 5
-36
-31.8 13
13
-38
-32.2 14 14
15 15
-32.6 -40
3 4 5 6 7 8 9 10 11 12 13 14 15 1 3 5 7 9 11 13 15

56 57
Figure 6 GM structures and formation energies of ZnS and TiO2.

see Figure 5) may assist the structure solution; but before the properties of any
model cluster can be computed, we first need to predict its structure.
Clusters are postulated to adopt the configuration with the lowest energy of
formation, that is, the global minimum (GM) structure. Relaxing fragments cut
from the bulk phase with the correct number of ions and stoichiometry will not
necessarily generate the GM structure. Hence, global optimisation methods,
particularly EAs (see Hartke54 for a more detailed review) are used to search
the potential energy landscape for low energy isomers for each cluster size.
Two examples of GM structures found by the application of this approach55,56
are shown in Figure 6. Ideally, the model used to define the formation energy
for inorganic particles should include electronic effects; however, as many
isomers need to be considered, QM calculation of energies and forces is
often too computationally expensive. QM approaches also require a good
starting configuration; otherwise the calculation is problematic (for example,
the self-consistent field cycle may fail to converge). Although global optimi-
sation searches on the QM energy landscape have been applied to some specific
small cluster sizes,57 atomistic models (employing IPs) have been traditionally
used to select the key structures to be refined using a QM approach. As
the order of stability may change upon switching models, EAs are employed
Computer Modelling in Solid-State Chemistry 193
to generate a set of low energy configurations, rather than just the GM defined
by IPs.
The focus now is on the structure of small-sized particles formed by laser
ablation of II–VI compounds. Clusters with a complete range of sizes and with
no one particular size dominant can be produced from ZnO.58 However, ZnS
clusters, in contrast, are dominated by an abundance of (ZnS)131, and possibly
(ZnS)341. The ‘‘magic number’’, n ¼ 13, is also found for clusters produced by
laser ablation of CdS and CdSe.59 It is widely held that magic numbers indicate
particularly stable clusters. In particular, it has been established that for alkali
halides, a cuboid fragment, particularly if it has square faces, carved from the
bulk, is more stable than the same structure with two ions added or removed;
examples are shown in Figure 4. The relative stability of the clusters therefore
accords with ‘‘magic number’’ behaviour. However, for ZnS this simple
approach fails: the relative stabilities of GM structures, shown in Figure 6,
would suggest incorrectly that n ¼ 12 is more likely to be a magic number
for ZnS.
A comparison of structures adopted for (ZnS)13 and (ZnO)13 may shed light
on why n ¼ 13 is a magic number for ZnS and not ZnO. There have been many
structures proposed for (ZnS)13, as shown in Figure 7, which also reports
calculated energies obtained using IP techniques. Three can be obtained by
relaxing an appropriate fragment cut from the rock salt structure (which was
shown for (MgO)13 to have the lowest energy60) and the two bulk phases of
ZnS, respectively. During the geometry relaxation of the wurtzite fragment, the
double layer structure inflates, which results in the creation of a bubble-
structured cluster. As might be expected, for larger sized clusters, the wurtzite
fragment has a lower formation energy than zinc blende, which is the more
stable polymorph for ZnS. By simulating the process of annealing with MD,
two lower energy isomers were generated;58 one taking the form of an ‘‘ash-
tray’’ (containing one octagon and reported as the GM structure for
(Mg21O2)1360) and another, ‘‘basket 1’’. To date, the lowest energy structure

Bubble 1 Ashtray Wurtzite Bubble 2 Bomb 1

-32.45 -32.43 -32.40 -32.35 -32.17

Basket 1 Basket 2 Rock-salt Zinc-Blende Bomb 2

-32.38 -32.40 -32.06 -31.97 -32.05

Figure 7 Key low energy structures for (ZnS)13, with energies per formula unit in
electron volts.56
194 Chapter 11
for (ZnS)13 is a bubble composed of hexagons and squares, and labelled
‘‘bubble 1’’ in Figure 7, which was found61 by an approach popularised by
Wales, called Monte Carlo Basin Hopping,62 and also using a GA within a
multi-stage approach.55 During the GA search, the possible location of each
ion is constrained to a predefined grid, after which the better candidates are
relaxed in the second stage in continuous space. This approach readily gener-
ated the GM and the next five lowest energy metastable structures, including
another basket and another bubble. However, before modifications were
made to the search algorithm, the dense-like structures, ‘‘bombs 1 and 2’’,
were not found.
The formation of a dense cluster (as opposed to a bubble or basket as its
interior contains a cation), shown in Figure 7, has been considered59 as a key
reason for the abundance of n ¼ 13 sized clusters. The central cation is
4-coordinated to 4-coordinated anions on the surface of the cluster. In order
to encourage the GA to find such structures, a Zn ion or a [ZnS4]6 tetrahedron
was fixed within a shell of grid points. Applied to clusters of size n ¼ 13, the four
dense structures (two pairs of enantiomeric configurations) were then found,
but just as importantly no dense structures were found for clusters of sizes 11,
12, 14 and 15. If (ZnS)13 does adopt a dense structure, whereas clusters of other
sizes are hollow, then this could account for the first magic number of ZnS. If
the nucleation of (ZnS)n can be envisaged as a process of growing bubbles, then
further growth from (ZnS)13 will be kinetically and thermodynamically hin-
dered, as there are no stable, next sized, dense clusters. Note, however, that the
dense clusters are not the GM structure for n ¼ 13.
The models shown in Figure 7 were used to investigate the (MX)13 structures
for a range of II–VI compounds, M ¼ Zn, Cd and X ¼ O, S, Se, Te, using high
quality QM calculations. Bubble 1 is found to be the GM configuration for
(MX)13, except for (ZnO)13 and (CdO)13, where basket 2 and the rock salt
clusters, respectively, are favoured. The latter is not too surprising, as larger
ring-like GM structures were reported for (ZnO)n63 than for (ZnX)n, where
X ¼ S, Se and Te. Remarkably, (CdS)13 has four configurations within the
range of typical thermal excitations. All four can be expected therefore to
dominate the population of (CdS)13 and 13 is a magic number for this
compound. Although with fewer configurations, a similar uncertainty in the
GM configuration is found for (ZnS)13. In contrast, for the other materials the
GM configuration is unique. Both enantiomeric configurations for bomb 2
were found to be unstable for (ZnO)13, for which the configurations relaxed to
the enantiomeric configurations for the bomb 1 structure. Thus, there is a
smaller number of low energy stable structures for (ZnO)13, which does not
have 13 as a magic number (and likewise for (CdO)13).
To summarise, there is a diversity of low energy stable (MX)13 configurations
for certain compounds, which could prove to be the major factor behind the
appearance of islands of stability of the cluster sizes that have been
observed.58,59 Although the formation energy of the GM for cluster n ¼ 13 is
not lower than that found for the GM of similar sized clusters, the kinetic
barrier for cluster nucleation could be an alternative explanation.
Computer Modelling in Solid-State Chemistry 195

5.2 Pre-Nucleation Phenomena and Polymorphism

Polymorphism, that is, the ability of a molecule to pack in different crystal
structures, is an issue of great importance for the pharmaceutical industry.
Since the physical and chemical properties of a molecular crystal depend
strongly on the crystal packing, drugs can only be patented for a particular
polymorph. The emergence of a more stable polymorph during the process of
drug manufacturing can have dramatic consequences, as happened in the case
of the anti-HIV pharmaceutical ritonavir,64 which had to be withdrawn from
the market, causing enormous financial losses.
Here, we show how molecular dynamics (MD) simulations have shed light on
the polymorphism of the important molecular crystal, 5-fluorouracil, which has
been used in anti-tumour treatments since 1957. For many years, the only
polymorph known was ‘‘form I’’, shown in Figure 8, in which the main
characteristic is the presence of regions with close F  F interactions. But a
recent computational study65 predicted the existence of a very stable polymorph,
‘‘form II’’, which comprises chains of doubly hydrogen bonded molecules. This
study was followed by an extensive polymorph screening, and the predicted
polymorph was crystallised from only one of the solvents used, pure nitrometh-
ane. All other solvents (including nitromethane that had been exposed to the
atmosphere) induce the growth of form I. There was no direct explanation of this
behaviour, but solvation effects are clearly crucial, so we proceeded to study the
relationship between solvation and polymorphism using MD.66
All the MD simulations were performed on the HPCx terascale facilities at
Daresbury Laboratory, using the code DL_POLY2.67 The unit cell consisted of
1550 water molecules, modelled with the SPC potential, and 16 5-fluorouracil
molecules, modelled with the DREIDING force field.68 The system was kept at
ambient pressure and temperature using the Nosé-Hoover thermostat and
barostat, with parameters between 0.1 and 0.4 ps. The timestep was 0.75 fs,
and the cell size was around 37 Å. After an initial equilibration period of 50 ps,
we simulated the system for 4 ns. We found that 5-fluorouracil molecules have
hydrophobic (F atom) and hydrophilic (O atoms) regions. The simulations show

Figure 8 Form I (left) and form II (right) of 5-fluorouracil. Hydrogen bonds are
represented by dotted lines.
196 Chapter 11

Figure 9 Left: snapshot showing a single hydrogen-bond formed between 5-fluorouracil

molecules in aqueous solution. Right: snapshot of a chain of three doubly
hydrogen bonded 5-fluorouracil molecules, formed in pure nitromethane
solution.

frequent F  F interactions in aqueous solution, as a consequence of the weak

hydration of this hydrophobic end of the molecule. There are also C–O  H–N
hydrogen bonds between the molecules, but doubly hydrogen bonded chains of
the type appearing in form II are rarely observed. A closer examination of the
dynamics of the system shows that doubly hydrogen bonded dimers are not
observed because the interaction between water molecules and 5-fluorouracil is
very strong, which favours solute–solvent, rather than solute–solute interactions
(see Figure 9). The formation of the nuclei which could lead to the growth of
form II is therefore very unlikely, since the clusters formed will mostly contain
singly hydrogen bonded molecules, as well as close F  F interactions. It is thus
clear that our simulations suggest that crystallisation from aqueous solution will
yield form I, in which such close interactions and H-bonds are observed.
We also performed simulations of 5-fluorouracil in pure nitromethane solu-
tion, using 480 nitromethane and 16 5-fluorouracil molecules, with a unit cell
size and simulation parameters similar to those of the previous simulation. Our
simulations showed that the interaction between 5-fluorouracil and nitrometh-
ane is relatively weak, which in turn induces the formation of doubly hydrogen
bonded chains. It is therefore clear that nitromethane will favour the crystal-
lisation of form II, which has these chains as building units.
Our last set of simulations was aimed at providing an understanding of the
reasons why form II can only be grown from pure nitromethane solutions. We
modelled the presence of water impurities by introducing 64 water molecules in a
unit cell with 496 nitromethane molecules and 16 5-fluorouracil molecules. The
number of water molecules is of the order of magnitude expected in un-purified
solutions, due to the hygroscopic nature of nitromethane. The simulations show
that water molecules interact strongly with 5-fluorouracil molecules, forming
clusters around them, and that even this small number of water molecules is
enough to inhibit the formation of doubly hydrogen bonded chains. Conse-
quently form I will be the polymorph that is most likely to be grown from
contaminated nitromethane solutions, in agreement with the experiment.
Computer Modelling in Solid-State Chemistry 197
Our three sets of MD simulations provide a rationalisation at the atomic
level of the experimental observations relating to the polymorphism of
5-fluorouracil. They have given very valuable insights into the pre-nucleation
processes that take place in its crystallisation from solution, and into the
important role that solvation plays in controlling the polymorphic outcome.

5.3 Defects in Semiconducting Oxides: ZnO

ZnO is widely used in catalysis, electrical devices, optoelectronics and phar-
maceuticals, which often depend crucially on the defect properties of this
versatile material. The nature of the intrinsic defects in ZnO, however, remains
elusive, and, so far, there is no unambiguous assignment of experimental data
to particular defect species (with the possible exception of the positron anni-
hilation spectroscopic evidence for Zn vacancies – see Refs. 69–71 and refer-
ences therein). Theoretical work is therefore essential to complement the
extensive body of experimental data.
We have investigated first the intrinsic point defects in ZnO and second, H,
N, P, Li, Fe, Cu, Al and In impurity centres.72 Atomic and electronic structures
as well as defect formation energies have been obtained for the main oxidation
states of all the defects using our embedded cluster, hybrid QM–molecular
mechanical approach to the treatment of localised states in ionic solids.73,74 In
contrast to a large number of recent periodic density functional calculations, we
are able to employ in these studies significantly more accurate QM methods, for
example, those based on hybrid exchange-correlation density functionals,
which allows us to approach the limit of chemical accuracy in the energetics
of defect formation, which are given in Table 1, where we also report energies
calculated using the classical Mott–Littleton approach.4
The results show that oxygen Frenkel pairs have low energies of formation;
moreover, we note that O interstitials have the lowest energies of formation
among all intrinsic defects, which suggests their dominance under oxidising
conditions. However, both Zn interstitials (2.2 eV) and O interstitials (1.7 eV)
have similar, relatively low energies of formation. Moreover, the Schottky
pairs are slightly more favourable than oxygen Frenkel pairs. Hence, the
dominant defect species should be determined by the sample history and
working conditions.
Next, based on the calculated values of the vertical ionisation potential and
electron affinity, we have determined defect levels in the band gap of ZnO; the
results are illustrated in Figure 10. With these calculations we have been able to
explain the following experimentally observed phenomena:

We propose that the neutral and singly positively charged Zn interstitial

defect is responsible for E1 and E3 (majority) donor bands from electrical
measurements.

Zn vacancies are proposed as the majority acceptor in agreement with
experimental assignment based on positron annihilation spectroscopic
and other studies. This defect is found to be stable in five charge states.
198 Chapter 11
Table 1 Calculated energies (eV) for the defect pair formation in ZnO. Pure MM
energies obtained using the Mott–Littleton approach and interatomic
potentials are shown for comparison for relevant charged defects.
Defect Reactions QM/MM Energy MM Energy
Frenkel pair in O sublattice

OXO + VXi - VXO + OXi 6.948

OXO + VXi - VdO + O 0 i 7.964
OXO + VXi - VddO + O00 i 8.868 8.797

Frenkel pair in Zn sublattice

ZnXZn + VXi - VXZn + ZnXi 12.002

ZnXZn + VXi - V0Zn + Zndi 9.637
ZnXZn + VXi - V00 Zn + Znddi 7.380 7.501
ZnXZn + VXi - VXZn + Znddi + 2e 0 9.463

Schottky pair

ZnXZn + OXO - VXZn + VXO + ZnO (s) 8.872

ZnXZn + OXO - V0Zn + VdO + ZnO (s) 7.645
ZnXZn + OXO - V00 Zn + VddO + ZnO (s) 6.896 6.749

Exciton recombination at this defect species is proposed as a source for

the main photoluminescence bands: ultraviolet (an acceptor level at
3.2 eV in a donor to acceptor photoluminescence (DAP) transition);
green (a triplet level at 2.5 eV), and red (at 1.9–2.0 eV).

The neutral O interstitial in a split-interstitial peroxy configuration (at
2.8 eV) should also contribute to blue and green luminescence by an
exciton recombination and DAP transition from donor Zn interstitials.

O vacancies could not be a source of green luminescence, but could
contribute to near-gap (UV) and red-orange luminescence bands (at
2.1 eV and below) via the exciton recombination mechanism. The corre-
sponding surface species, however, may contribute to the luminescence of
freshly prepared samples.

Our calculations confirm that Cu, which is stable in ZnO in two charge
states, is an efficient electron scavenger. The singly negatively charged Cu
impurity is proposed as an E4 donor. Calculated defect levels (at 2.7 and
0.55 eV) are in good agreement with experiment, which established Cu as
a distinct source of green luminescence from ZnO.

Our calculations on impurities show their donor and acceptor properties in

agreement with experiment where available. Curiously, our calculations suggest
that a number of such extrinsic defects, for example Li and N, can also
contribute to the green luminescence band, the origins of which caused much
controversy in the literature.
Computer Modelling in Solid-State Chemistry 199

Figure 10 Calculated energy levels (eV) of intrinsic and extrinsic defects in ZnO.

These studies are currently continuing on other extrinsic defects and defect
complexes.

5.4 Enantioselectivity in Ruthenium(II) Hydrogenation Catalysts

This section highlights the role of computational methods in catalytic science
and concerns one of the most significant developments in the synthesis of
200 Chapter 11
enantiomerically pure alcohols, namely the discovery by Noyori and co-workers
of highly efficient Ru(II)-amine-based complexes for the hydrogenation of
prochiral ketones.75 Among the best catalysts for carbonyl hydrogenation
developed by Noyori are ternary ruthenium complexes made up of (phos-
phane)n and diamine, and a Ru(II) centre.75 The experimental evidence shows
how subtle modifications of these organic ligands, especially the substituents of
the phosphorus, produce very significant changes in the enantioselectivity. One
example is reported in Scheme 1: the acetophenone is reduced to (R)-phenyl-
ethanol with an enantiomeric excess (ee) of 99% if the reaction is catalysed by
trans-Ru(H)2(S,S-dpen)(S-xylbinap) (1), and the ee is drastically reduced to
80% when the reaction is promoted by trans-Ru(H)2(S,S-dpen)(S-tolbinap) (2).
The position of the methyl groups in the aryl substituents at the phosphorus
atom is the only structural difference between 1 and 2.
Here, we report a computational study on the reduction of acetophenone
catalysed by trans-Ru(H)2(S,S-dpen)(S-xylbinap). The aim is to provide a
theoretical characterisation of the factors controlling the enantioselectivity in
the Ru(diphosphine)(diamine) class of catalysts.
To model the approach of the ketone to the catalyst, we have applied a
geometry optimisation technique where, starting from separate non-interacting
reactants, at each stage the geometry of the system is optimised with respect to
the constraint, namely the (Ru–)H  C(¼O) distance.76 In fact, a computa-
tional study on a model Ru(diphosphine)(diamine) catalyst77 has shown that
(Ru–)H  C(¼O) is the ‘‘pseudo’’ reaction coordinate for the metal–ligand

O OH

+ H2 Ru(II) complex
CH3 CH3

Ar2 H H2
P N H
Ru

P N
Ar2 H H2
H

(S)-xylbinap: Ar = 3,5-(CH3)2C6H3 (1)

(S)-tolbinap: Ar = 4-CH3C6H4 (2)

Scheme 1 Hydrogenation of acetophenone to phenylethanol catalysed by Ru

(diphosphine) (diamine) complexes.
Computer Modelling in Solid-State Chemistry 201

Relative Energy - 9 Ang [kJ/mol] 40,0

30,0 P P P P P P P P

Ru Ru Ru Ru
20,0 O ON O O
N N N N N N N

10,0 Q1 Q2 Q3 Q4

0,0

-10,0 Q1
Q2
-20,0 Q3
Q4
-30,0
1,0 2,0 3,0 4,0 5,0 6,0 7,0 8,0 9,0
d (O=)C---H(-Ru) [Ang]

Figure 11 Electronic energy variation of the system [trans-Ru(H)2(S,S-dpen)(S-xylbi-

nap)+acetophenone] along the [(Ru-)H  C(¼O)] internuclear distance for
each possible approach (Q1, Q2, Q3, Q4). Values computed at the DFT–
PBE level of theory.

bifunctional catalysis, the mechanism involved when the reduction of a ketone

is promoted by Noyori-type complexes.78 Figure 11 shows the energy variation
of the system [1+acetophenone] as a function of (Ru–)H  C(¼O) for each
possible approach of the acetophenone on the active sites (Ru–H, N–H) of the
catalyst [Q1 and Q4 give (R)-phenylethanol; Q2 and Q3 give (S)-phenyl-
ethanol]. All four pathways show a maximum energy centred at approximately
2 Å, which corresponds to the transition state structure for the H-transfer
acetophenone–phenylethanol reaction (Hydrog. TS). The relative energies of
the Hydrog. TS structures are: 7.61 kJ mol1 for Q1, 9.58 kJ mol1 for Q2,
25.70 kJ mol1 for Q3 and 35.36 kJ mol1 for Q4. Since the reaction will
proceed mostly through the lowest energy saddle point, the Q1 approach is
by far the most favourable kinetically.
The four alternative pathways display very different energetic trends. In
particular, Q1 displays a double-well energy profile and two distinct minima at
3.75 Å (INT-I) and 2.5 Å (INT-II), while along Q2, a single minimum is located
at 3.75 Å (INT-I). The structure of the transition state (TS) and of the freely
optimised minima along Q1 and Q2 are reported in Figure 12 and described in
Table 2.
For Q1, the intermediate INT-I corresponds to the situation where the
acetophenone is outside the ‘‘pocket’’ made by the bulky aryl groups of the
catalyst 1 and where the phenyl group of the acetophenone is approximately on
the plane defined by the C–CQO atoms (in Table 2, g ¼ 4.51). In the
intermediate INT-II, the phenyl group of the acetophenone rotates (in Table 2,
g changes from 4.51 in INT-I to 19.81 in INT-II) in order to enter into the
202 Chapter 11

Figure 12 Minima (INT-I, INT-II for Q1 and INT-I for Q2) and transition state (TS)
structures for acetophenone entry in the active sites of the trans-
Ru(H)2(S,S-dpen) (S-xylbinap) catalyst as computed by the DFT-PBE
method.

‘‘pocket’’ of the catalyst 1. Table 2 shows that the torsional angle of the phenyl
group g is the only structural parameter that changes significantly on going
from INT-I to INT-II. In particular, the out-of-plane angle t in INT-I
and INT-II indicates that the carbonyl carbon is still sp2 in character.
In Table 2, the relative energies of the intermediates INT-I and INT-II indi-
cate an extra stabilisation of 9.78 kJ mol1 when the acetophenone enters into
the ‘‘pocket’’ (INT-II). We explain the larger stabilisation of INT-II in terms
of electronic effects (formation of stronger XH–p hydrogen bonds, where
X ¼ N and C, when the acetophenone enters into the ‘‘pocket’’) and steric
effects (the minimum CH3  H3C distance decreases from 2.36 Å in INT-I to
2.48 Å in INT-II). In the Hydrog. TS structure, the torsional angle of the
phenyl group (g ¼ 20.41) is the same as in the intermediate INT-II (g ¼ 19.81).
This result indicates that along Q1 the formation of a stable interme-
diate (INT-II) is induced by the rearrangement of the phenyl group [rota-
tion along C–C(¼O)] in order to have a conformation closer to that of
Hydrog. TS.
For the Q2 approach, the minimum INT-I in Figure 12 is analogous to the
intermediate INT-I along Q1 and corresponds to the situation where the
acetophenone is outside the ‘‘pocket’’. No other intermediates have been
located along Q2 and in Hydrog. TS the conformational structure of the
acetophenone is very different from the conformation in INT-I. In particular,
the torsional angle g changes drastically from 4.01 in INT-I to 41.31 in
Hydrog. TS (see Table 2). Therefore, when the reaction proceeds along the Q2
pathway, there is an extra energy cost to go from the reactant-complex INT-I to
Hydrog. TS associated with the torsion of the phenyl group. In fact, at
Table 2 Energetic and structural characterisation of the minima (INT-I, INT-II for Q1 and INT-I for Q2) and transition state
(TS) structures for the trans-Ru(H)2(S,S-dpen)(S-xylbinap)-catalysed acetophenone reduction as computed by the
DFT–PBE method. Energies in kJ mol1, distances in Å and angles in degrees. DE: electronic energy difference with
respect to energy at 9 Å separation; t: out-of-plane bending of the carbonyl carbon; g: torsional angle of the phenyl
group along the C–C(¼O) bond.
Computer Modelling in Solid-State Chemistry

trans-Ru(H)2(S,S-dpen)(S-xylbinap) Acetophenone
DE r(CH1) r(RuH1) r(RuH2) r(RuN) r(RuP) r(N–H) r(CO) r(OH) t g
Q1 INT-I 13.23 3.76 1.72 1.71 2.20 2.25 1.02 1.23 3.42 1.0 4.5
INT-II 23.01 3.65 1.72 1.70 2.21 2.25 1.02 1.23 3.79 1.1 19.8
TS 7.61 2.00 1.78 1.67 2.18 2.27 1.04 1.26 1.95 16.2 20.4
Q2 INT-I 17.50 3.77 1.72 1.70 2.20 2.25 1.02 1.24 3.52 1.5 4.0
TS 9.58 1.90 1.82 1.66 2.19 2.27 1.04 1.26 1.93 20.4 41.3
203
204 Chapter 11
the DFT-PBE level, the energy difference between the conformation of
the acetophenone with g ¼ 4.01 and the conformation with g ¼ 401 is approx-
imately 9 kJ mol1. Since the difference between the activation energy for
the H-transfer process along Q1 (DEaQ1 ¼ 15.40 kJ mol1) and along Q2
(DEQ2a
¼ 27.08 kJ mol1) is close to 9 kJ mol1, we argue that in the trans-
Ru(H)2(S,S-dpen)(S-xylbinap)-catalysed acetophenone hydrogenation the high
enantioselectivity for the R-alcohol is associated with the existence of a stable
intermediate (INT-II) along the Q1 reaction pathway, where the acetophenone
has the same conformation as in the Hydrog. TS structure. The formation of
this intermediate is hindered for the competitive pathways.
Further details of this work are given in reference 79.

6 Conclusions
Computational methods now provide us with some of the most powerful tools
for studying matter at the atomic and molecular level. The techniques are at
their most powerful when used in conjunction with experiment and their
growing predictive power will allow them to lead and not to follow experimen-
tal studies. The continuing growth in computer power, with the advent of the
‘‘petaflop’’ era, together with developments and innovations in techniques,
offer an exciting future for the field.

Acknowledgements
We are grateful to Sir John Meurig Thomas and many other colleagues for
their contributions to the work summarised in this article. The work has been
supported by several grants from EPSRC, EU, ICI and Johnson Matthey.

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CHAPTER 12

Towards a Catalogue of
Designer Zeolites
M. M. J. TREACY,a M. D. FOSTERa AND I. RIVINb
a
Department of Physics, Arizona State University, P.O. Box 871504, Tempe,
AZ 85287-1504, USA; b Department of Mathematics, Temple University,
1805 North Broad Street, Philadelphia, PA 19122, USA

1 Introduction
John Thomas has made many important contributions to the field of zeolites.
His research interests have spanned the field, from synthesis and applications,
to structure characterisation. His passionate interest in transmission electron
microscopy as a characterisation tool in solid state chemistry, and his early
realisation of its importance for the study of defects in materials,1–3 led to a
number of influential discoveries and at least one well-known aphorism.4 His
influence has been far-reaching. The study of defects in zeolites by transmission
electron microscopy (TEM) was an area of research of one of us (MMJT) when
employed at the Exxon Corporate Research Laboratory in the 1980s, and
John’s visits were always enjoyed and his wisdom valuable. The present work,
although apparently unrelated to TEM, can be traced back directly to those
days. The study of periodic defects and their permutations to produce new
topologies is central to this work, and it is a pleasure to dedicate this article to
John.
At present, each new zeolite framework discovery is essentially a
serendipitous event. Although skilful synthesis chemists know how to choose
productive areas within the synthesis phase space, the final product is seldom
known in advance. The material structure, if new, is determined usually by a
herculean structure refinement involving a combination of X-ray, neutron and
electron scattering, and sometimes using connectivity data gleaned from
nuclear magnetic resonance. The Structure Commission analyses the data
supporting the newly proposed topology, and if approved, the framework
joins the ‘‘Zeolite Hall of Fame’’ i.e. the Atlas of Zeolite Framework Types.

208
Towards a Catalogue of Designer Zeolites 209
Occasionally, the new framework will exhibit potentially useful sorption or
catalytic properties, and will be scrutinised for commercial usefulness. It is fair
to say that, at present, the rate of discovery of zeolite frameworks that are
uniquely useful to society is distressingly low.
Given the huge economic benefits that are potentially available, a more
rational approach to zeolite synthesis is needed. We need to know the frame-
works in advance of synthesis, so that we can model their properties. The
potentially useful frameworks then become synthetic targets and serendipity
plays less of a role. This scenario involves two crucial assumptions; the first is
that we can predict and model new zeolite frameworks; the second is that
synthesis chemists can make framework materials on demand. Much progress
has been made over the past 50 years on the first step, with much being owed to
the early pioneers, A.F. Wells and J.V. Smith.5–8 For a more detailed review of
the earlier work see the introduction to Ref. 9. The targeted synthesis step is
known to be a hard one, but there are no a priori reasons that it should be
impossible. However, before we reach this stage, we need a database of
potential frameworks whose physical and chemical properties are estimated.
This database, or catalogue, would be the vade mecum for the synthesis chemist.
It would contain details of the topology, the likely unit cell dimensions and the
pore sizes. It would be an interactive resource, allowing one to explore frame-
work composition, visualise molecules passing in and out, and ideally would
suggest template molecules for synthesis.
We have begun to create such a catalogue.9–11 It can be viewed and searched
at http://www.hypotheticalzeolites.net. It is presently just one step towards a
future turning point in zeolite chemistry where useful zeolites can be identified
and then synthesised. In this article, we explain how the frameworks are
generated at present, and outline the mathematical challenges that lie ahead
before the promise can be fulfilled.

2 Zeolites as Graphs
Zeolites are crystals, which means that their idealised structures are invariant
with respect to one of the 230 crystallographic space groups. It is usual to think
of the unit cell as the basic crystallographic tile that fills space. However, each
space group has a fundamental domain that is usually smaller in volume than
the unit cell. The unit cell itself can be constructed by translating, rotating and
mirroring copies of the fundamental domain, and tiling those copies. These
copying operations are the space group symmetry elements, and are distinct
from the translation operations that are common to all space groups. The
fundamental domain cannot be further subdivided without altering the space
group symmetry.
All the information necessary to understand a zeolite framework can be
expressed in terms of the atoms contained in this fixed fundamental domain.
Although actual zeolites can have complicated and varied compositions, we
here concern ourselves only with the framework, ignoring guest atoms in the
210 Chapter 12
channels and cages, and assuming a pure tetrahedral TO2 composition. In
zeolites, the tetrahedral ‘‘T-atoms’’ tend to be typically silicon, aluminium and
phosphorus. In our treatment, we simplify further by omitting oxygen atoms
and treat T-atoms generically to produce a four-connected framework.
The next step is to examine the network fragment inside the fundamental
domain, and to specify how it connects to the neighbouring images of the
fundamental domain.
Figure 1 depicts the fundamental region and the unit cell for the FER
framework, which has four unique basis T-atoms. The figure shows how the
four basis atoms connect to the adjoining environment, which comprises
images of the basis atoms, to build the framework.
Each T-atom in a fundamental domain D is a unique basis atom, and is
connected to four other atoms, either in D itself or in some image gD of one of
the basis T-atoms, where g is an element of the crystallographic group. This
information can be thought of as a degree four graph with ‘‘coloured’’ edges
(connections) – the colours being the group elements g. The number of colours,
when described this way, is infinite, but it is not an unreasonable assumption
that only side-pairing transformations g are of interest where we concern

2
1
c a

Figure 1 The FER framework (space group Immm, No. 71) contains four unique
(basis) T-atoms, which are shown here as blue tetrahedra with labels 1–4.
These basis atoms lie within the fundamental region, which is outlined. The
T-atoms all lie on sites. T1 lies on the edge (x, 0,0), Wyckoff site e. T2 lies on
the face (x, 0, z), Wyckoff site m. T3 resides inside the fundamental region
on the general site (x, y, z), Wyckoff site o. T4 lies on the face (x, y, 0),
Wyckoff site n.
Towards a Catalogue of Designer Zeolites 211
ourselves only with connections between adjacent images of the fundamental
domain. For the p unique T-atoms, we perform a combinatorial symmetry-
constrained inter-site bonding search (SCIBS) over all permutations of sites
and all combinations of bond colours that generate degree four graphs. The
graphs that are missed because of the adjacency assumption will be recovered
when we examine subgroups of the space group, but not necessarily with the
same count of basis T-atoms.
The ‘‘coloured’’ graph for FER is represented diagrammatically in Figure 2.
In this representation, each of the four basis T-atoms has four outward
connections to images of the basis atoms. A connection made through the
identity operator (x,y,z) represents a direct connection to another basis T-atom.
The number of inbound connections is determined by the symmetry of the
T-atom’s resident site, and can contain redundant information. For example, the
connection 1 (x,y,z) 2 automatically implies the reverse connection 2 (x,y,z) 1.
An efficient representation of the coloured graph is listed to the right of the
figure. The coloured graph contains no information about the unit cell dimen-
sions, the location of the T-atoms or about the T–T bond distances. It contains
topological information only. Thus, not all degree four graphs can necessarily
be realised as zeolites.
Lists of all degree four graphs are generated. Simple labelling permutations
are redundant. However, some space groups, particularly those with mirror
symmetry elements, can create degenerate graphs that are not simple permu-
tations of labels. These isomorphic graphs can be computationally costly to
detect, and are not filtered at this stage.

Figure 2 A diagrammatic representation of the coloured graph for FER in space

group Immm. The operator generating the bond is the ‘‘colour’’ of that edge,
or connection, and is applied to the bonded basis T-atom (the atom that is
being pointed at by the arrow) to generate the connected image. Each of the
four basis T-atoms has four outward connections, including connections to
themselves. However, the number of inbound connections can vary since all
connections are to images of these sites. The operator (x, y, z) is the identity
operator and so represents a direct bond between basis atoms. A more
compact description is presented on the right, with redundant connection
data removed.
212 Chapter 12
Since we are interested in identifying the chemically viable subset of these
graphs, we need to embed them into Cartesian space – that is, to try to turn them
into tetrahedral silicates. As a goodness of fit, we examine the energy of
formation of these graphs with respect to perfect SiO4 tetrahedra. To do this
with reasonable computational speed, we use an empirical potential created by
Boisen, Gibbs and Bukowinski (BGB)12,13 that works well for regular tetrahedral
siliceous materials. Oxygen atoms are initially placed at the midpoints of the T–T
linkages, with appropriate crystallographic constraints applied (such as when an
oxygen sits on a mirror plane). We use a modified form of their potential, mBGB,
that inhibits the breaking of T–O–T linkages since these are fixed for each graph.
Although the energy for the mBGB modification deviates significantly from the
normal BGB energy for large distortions from regular tetrahedral SiO4 geometry,
it agrees exactly for small distortions. Since we are interested mainly in structures
that are close to being regular tetrahedral, this mBGB modification is well suited
to our problem. The graphs are embedded using a variety of Monte Carlo
methods, mostly simulated annealing. The procedures used have been described
in more detail elsewhere,9,10,14 but are also evolving with time.

3 Present Status
In principle, the SCIBS method is bounded, generating a complete set of
graphs. Given a space group and the number of basis T-atoms, then the number
of adjacent degree four graphs is finite and enumerable. In practice, the
subsequent embedding step may inadvertently discard a viable graph. Tests
performed on example data sets reassure us that the methods used do not
discard many viable frameworks, if any.
The price paid for this completeness is that there is a combinatorial explosion
of graphs as the number p of basis T-atoms increases. Figure 3 presents log–
linear plots of the number of graphs as a function of p for five space groups.
The growth in number of graphs is clearly exponential in p. For space group
Pnma (No. 62) there are already 107 graphs for p ¼ 3 basis atoms. It is a
sobering fact that the well-known zeolite framework MFI occurs in this space
group with p ¼ 12 basis T-atoms. Extrapolating the line, we find that there will
be a staggering B1025 graphs to examine in order to identify the MFI frame-
work. Clearly, an efficient method for further filtering (or simply not generat-
ing) the unfeasible graphs is needed.
It is also found that the fraction of viable frameworks decreases rapidly with
p. Consequently, the rate of discovery of new frameworks decreases dramat-
ically as p increases. Nevertheless, to date, we have refined over 3.5 million low
energy graphs. A large fraction of these are duplicates since the same topology
can recur in different space groups, or even within the same space group with
reoriented and enlarged cell volumes. For example, the LTL topology occurs in
P6/mmm (No. 191) for all p Z 2.
We have not yet identified unambiguously the unique topologies in our
database. For example, we know that quartz recurs about 100 times, and
Towards a Catalogue of Designer Zeolites 213

108

number of graphs, N
106

104
230
227
102 191
63
62
100
0 1 2 3 4 5 6
number of basis T-atoms, p

Figure 3 Plot showing the combinatorial explosion of degree four graphs as the
number p of basis T-atoms increases, for five space groups. At present, the
practical upper limit for the annealing step is about 108 graphs. Thus, we
have been able to explore up to p ¼ 6 for some high-symmetry space groups,
but only p ¼ 2 for others. Not all space groups support uninodal (p ¼ 1)
graphs, such as P6/mmm, No. 191 for which p Z 2.

cristobalite is also a commonly occurring topology. By examining coordination

sequences out to the 16th shell, we conservatively estimate that there are at least
100 000 unique topologies present.
In parallel with our studies, other groups have made important progress in
zeolite database generation using different strategies. Each method, of course,
has its pros and cons. Earl and Deem15 have constructed a similar database of
zeolite frameworks by using an adaptive simulated annealing approach. At
present, it is hosted on our web site in parallel with our database. They start by
selecting a space group and a number of basis T-atoms, which are all placed in
the general site at random starting configurations. During the anneal, basis
T-atoms can merge if the energy is lowered by the merger according to a cost
function that is optimised for tetrahedral frameworks. After many such runs, a
collection of low energy frameworks is found, some being found many times.
An attractive feature of this approach is the analogy to thermodynamic
equilibrium, in that a cost of formation and the entropy of the system are
allowed to determine the resulting frameworks. This has the advantage over
our approach in that the graph formation and the embedding are occurring in
the same step, with the annealer rapidly rejecting implausible (i.e. high energy)
graphs early in the process. However, a possible disadvantage is that some of
the narrower local minima could be missed, preferring to seek out the global
minimum – i.e. quartz and cristobalite dense phases are probably found
frequently. Nevertheless, the Earl and Deem database has a comparable
number of entries to ours. At the time of writing, the two databases, both
being new, have not yet been compared or merged.
Friedrichs et al.16 have used an alternative approach that takes advantage of
the fact that zeolites are built from polyhedral units. By tiling combinations of
214 Chapter 12
pre-assembled polyhedra, they identify the space-filling forms. In their
approach, the space group and basis T-atoms must be identified after the fact.
Friedrichs has developed a powerful computational tool, SYSTRE,17,18 that
uniquely identifies each topology by making use of a partial embedding of each
graph in order to identify the maximum topological symmetry.
Many of the frameworks discovered are mesmerising. We show one of them in
Figure 4, chosen for its large pore size. It is labelled as framework number
229_5_8058871 (i.e. space group 229, or Im3m, five basis T-atoms, graph number
8058871). It has enormous cavities capable of holding a sphere 24.7 Å in diam-
eter. Spheres up to 10.8 Å diameter can diffuse freely through the framework.

4 The Turning Points: Past, Present and Future

The graph in Figure 5 reveals clearly the rapid growth in the number of
hypothetical zeolites in recent years. The number of zeolite frameworks that

Figure 4 The final embedding of graph number 229_5_8058871. It occurs in space group
Im3m (No. 229) with five basis T-atoms. It contains large cavities, capable of
supporting spheres 24.7 Å in diameter, which are shown here in yellow.
Spheres up to 10.8 Å diameter can diffuse freely through the framework.
Towards a Catalogue of Designer Zeolites 215

200
Known zeolites
3.0

Hypothetical (millions)
Hypothetical zeolites
150 2.5
Known 2.0
100
1.5
1.0
50
0.5
0 0.0
1980 1990 2000 2010
Date

Figure 5 Graph showing the increase with time of the number of known zeolites
(circles) and the number of hypothetical zeolites (squares). The hypothetical
count is restricted to those entries in our database. The database of Deem
and co-workers has a comparable number. Prior to 2003, the number of
hypothetical frameworks known was undoubtedly fewer than 10 000, and
probably closer to 1000.

have been assigned three-letter framework codes by the Structure Commission

of the International Zeolite Association is growing exponentially, but appears
sedate compared to the rapid explosion in hypothetical zeolites. The present
growth in number of hypothetical structures is traceable to a number of
developments, which are enumerated here.

1. The demonstration that systematic permutations and combinations of

linkages between building units (sheets and cages) leads to new zeolite
topologies. These discoveries were driven most notably by Wells5,6 and
Smith,7,8 although others had remarked that recurrent twinning and the
systematic introduction of defects produced new topologies.1,19 Later,
Friedrichs et al.16 formalised the mathematics underpinning the three-
dimensional space-filling tilings of polyhedra. Independently, Treacy et al.
and Joachim-Klein (for uninodal graphs) developed the SCIBS method
for enumerating connections between tetrahedral units.9,10,20,21
2. The early transmission electron microscopy work of John Thomas and his
colleagues provided important proof of the existence of crystallographic
defects in zeolites, most notably in MFI, LTL and FAU materials. This
affirmed that the elusive hypothetical framework topologies could exist,
at least locally within another related structure.1 Importantly, they dem-
onstrated that the hitherto hypothetical ‘‘Breck’s Structure 6’’,19 or
‘‘hexagonal faujasite’’, exists at the local level in the neighbourhood of
planar defects within some synthetic cubic faujasites. The elusive hexa-
gonal synthetic target was later synthesised in pure form by Delprato
et al.,22 and is now known as the EMT framework.
3. The development of computerised structure embedding methods has been
vital. The original distance least squares program DLS76 of Baerlocher
216 Chapter 12
23
et al. is still a standard tool in zeolite structural studies. Advances in
computerised embedding methods, such as simulated annealing, have also
been crucial. Naturally, the constant growth in computer performance
has been highly enabling, in this, and in all areas of science. The devel-
opment of efficient and accurate empirical potentials24 has proven
important for the final embedding stage. Ab initio methods, although
accurate, are computationally costly. The empirical potential of Boisen
et al.12,13 has been valuable to the authors’ SCIBS method. The general
utility lattice program (GULP)25 has proven useful in this research.
4. The solution to the graph uniqueness problem by Friedrichs and O’Keeffe
has eliminated a tricky graph-theoretic barrier for the growth of zeolite
framework databases.17
5. The development of the internet allowing access to important research
results and to vast databases has been important. Given the frequent
updates, a physical paper catalogue, or even a periodically distributed
disk of hypothetical zeolites, would be unmanageable.

It is clear that these databases are still in their infancy, and future efforts will
be to render them as complete as is practically possible. Technically, the
number of zeolitic graphs is infinite. However, in practice the list of chemically
realisable frameworks will be finite.
Future advances will undoubtedly be enabled by developments in the math-
ematics relating to crystallographic graphs, as well as developments in com-
putational algorithms. Some of the outstanding computational, combinatorial
and probabilistic questions can be summarised as follows:
Question 1. How does the number of isomorphism classes of coloured graphs
depend on their size and the group? In other words, how many different zeolite
frameworks are there with a fixed symmetry group and with a given number of
crystallographically unique T-atoms?
Question 2. How does one generate all coloured graphs up to a certain size,
taking care to generate each isomorphism class exactly once? Questions 1 and 2
are closely related, since enumeration and generation methods are often closely
related. One quite promising, and insufficiently explored, approach is to
develop a complete ‘‘transformation grammar’’ on degree four graphs, whereby
existing graphs (preferably realisable frameworks) form the starting point for
new families of graphs. This is related to the setup used by Sleator et al.,26 who
demonstrated a way to compactly encode all the graphs described by words of
length m in a graph grammar. This gives both tight upper bounds on the
number of such graphs, and furthermore, an efficient method of constructing
them.
A completely different (and independent) approach, which has recently been
found very useful in robotics (but is, in some sense, closely related to the
approach of Ref. 26.) is the use of CAT(0) complexes to find short paths in
combinatorial configuration space.27
Question 3. Is there a way to determine whether a framework is a suitable
candidate for a physically occurring structure based strictly on its topology?
Towards a Catalogue of Designer Zeolites 217
A structure is considered suitable if it admits a low energy embedding in three-
dimensional space. In turn, the energy is determined by the various Coulomb
forces and the constraints of quantum mechanics, and is quite expensive to
compute. Finding an embedding of minimal energy is more difficult yet.
Finding a simple combinatorial action that is well correlated with the physical
properties is of considerable interest to both mathematics and chemistry. There
are some simple filters we already use, such as constraints on the topological
density.10 An idea that we are starting to explore is to use the spectral properties
of the graph.28 Since the framework is infinite, computing them is tricky,
especially since the obvious idea of looking at bigger and bigger pieces of the
framework quickly becomes prohibitively expensive since the complexity of
computing eigenvalues and determinants grows cubically with the number of
vertices. Luckily, there are ‘‘closed form’’ ways of defining graph determinants
and spectral zeta functions, which were recently worked out in the context of
geometric group theory and von Neumann algebras.29,30 This should allow us
to investigate the relationship between the regularised logarithm of the deter-
minant of the graph Laplacian and the energy. It is known, due to the work of
Kenyon,31 that in the planar case this is related to the Gibbs free energy of the
framework, and so there is at least a philosophical reason to expect some level
of success. There is also the possibility of exploring the connection of these
questions to hyperbolic geometry, in the spirit of Refs. 32 and 33.
Question 4. How do we find an optimal (or quasi-optimal) embedding of a
framework rapidly? This has two aspects: first, how to quickly compute the
energy and (if possible) its derivatives, and secondly how to optimise the energy
over the space of the configurations of T-sites. In order to evaluate the energy
function, the first observation is that the potential is the sum over pairs of sites
that are near each other, and so there is a natural way to evaluate this –
Greengard’s algorithm34 for fast evaluation of Coulomb-type potentials. A
completely different (and somewhat faster, though somewhat less accurate
idea) is to use dynamic Voronoi diagrams.35 We can quickly compute and keep
updated a Voronoi diagram of our sites, and computing interactions with only
the nearby sites gives a simple linear time algorithm to compute a good
approximation to the energy. Which of these algorithms is preferred depends
in part on the optimisation scheme used. For local optimisation (for example,
the conjugate gradient method), it is useful to be able to compute very good
approximations to the gradient of the energy with respect to the positions of the
sites, and the best method for that appears to be automatic differentiation.36
Our experiments indicate that finite differencing is unstable in these applica-
tions, and symbolic differentiation is prohibitively expensive. However, it is
important that the underlying algorithm be amenable to automatic differenti-
ation, and we will be investigating this. For global optimisation, there are
(at least) two possibilities – a version of the simulated annealing algorithm
(which has been our workhorse to date) and also a tree optimiser.
Question 5. What will be the physical properties of a hypothetical zeolite
framework? In particular, what are the pore shapes and sizes? This question
comes down to some quite subtle questions in computational geometry. To
218 Chapter 12
determine the size of the largest sphere that can fit into the pores of the
structures, it seems that Delaunay tessellations provide the most convenient
tools,35,37 although the correct object – the Apollonian tessellation – is quite
hard to compute, even though algorithms are known.38 In any event, the
important question is whether a zeolite framework can ‘‘accommodate’’ a given
organic molecule, or a piece thereof. This requires much more sophisticated
technology, and is related to the work of Edelsbrunner on a-shapes,39 and of
Ghrist on sensor networks and homology.40 John Thomas and his colleagues41
have made important inroads in this problem with the ZEBEDDE program,
which can assemble potential template molecules within the confines of the
zeolite pores.
At present, the authors are exploring methods to estimate the absorption
capacity of zeolites by packing spheres of known radii into the voids. Figure 6
shows graphically the outcome when spheres with the nominal diameters of He,
Ne, Ar, Kr and Xe are packed into the MFI framework. However, the ultimate
computational goal is to pack non-spherical molecules efficiently and thermo-
dynamically realistically, into the frameworks. The recent discovery that real
zeolite frameworks are flexible (i.e. the tetrahedral linkages within the frame-
work can flex cooperatively to expand or shrink the unit cell within a certain
range, or ‘‘window’’) is potentially important, and may provide the key to
rapidly identifying viable frameworks.42

Figure 6 Sphere packing results for the MFI framework. From left to right, the
packed spheres and their nominal van der Waals radii are: He (1.40 Å), Ne
(1.54 Å), Ar (1.88 Å), Kr (2.02 Å) and Xe (2.16 Å). Assuming an oxygen
radius of 1.32 Å and a silicon radius of 0.9 Å, we find that we can pack 64.4,
39.5, 24.8, 20.6 and 17.2 atoms per unit cell, respectively.
Towards a Catalogue of Designer Zeolites 219
At present, about 50% of all new structures presented to the Structure
Commission of the International Zeolite Association were already present in
our database. This is already a strong indicator that the database is a zeolitic
gold mine. However, the tools needed to reliably predict the useful frameworks
are still primitive. At the time of writing, these newly emerging databases are
more ‘‘postdictive’’ than they are predictive. Future developments in the
mathematics of computational geometry and algorithm design will surely turn
these databases into tempting wish lists of possibly useful zeolites. However, it
will take additional developments in the techniques of targeted synthesis before
the promise of a designer catalogue can become reality.

References
1. M. Audier, J.M. Thomas, J. Klinowski, D.A. Jefferson and L. Bursill, J.
Phys. Chem., 1982, 86, 581.
2. G.R. Millward, S. Ramdas, J.M. Thomas and M.T. Barlow, J. Chem. Soc.,
Faraday Trans., 1983, 79, 1075.
3. O. Terasaki, J.M. Thomas and G.R. Millward, Proc. R. Soc. London, Ser.
A, 1984, 395, 153.
4. J.M. Thomas, Chem. Br., 1970, 6, 60.
5. A.F. Wells, Three-Dimensional Nets and Polyhedra, Wiley, New York,
1977.
6. A.F. Wells, Further Studies of Three-Dimensional Nets, American Crystallo-
graphic Association, Monograph No. 8, Polycrystal Book Service,
Pittsburgh, 1979.
7. J.V. Smith, Chem. Rev., 1988, 88, 149.
8. J.V. Smith, in Zeolites: Facts, Figures, Future, vol 49A, ed. P.A. Jacobs
and R.A. van Santen, Elsevier Science Publishers, Amsterdam, 1989, 29.
9. M.M.J. Treacy, K.H. Randall, S. Rao, J.A. Perry and D.J. Chadi,
Z. Kristallogr., 1997, 212, 768.
10. M.M.J. Treacy, I. Rivin, E. Balkovsky, K.H. Randall and M.D. Foster,
Microporous Mesoporous Mater., 2004, 74, 121.
11. M.D. Foster and M.M.J. Treacy, 2005, http://www.hypotheticalzeolites.net/
12. M.B. Boisen Jr. and G.V. Gibbs, Phys. Chem. Miner., 1993, 20, 123.
13. M.B. Boisen Jr., G.V. Gibbs and M.S.T. Bukowinski, Phys. Chem. Miner.,
1994, 21, 269.
14. S.A. Wells, M.D. Foster and M.M.J. Treacy, Microporous Mesoporous
Mater., 2006, 93, 151.
15. D.J. Earl and M.W. Deem, Ind. Eng. Chem. Res., 2006, 45, 5449.
16. O.D. Friedrichs, A.W.M. Dress, D.H. Huson, J. Klinowski and
A.L. Mackay, Nature, 1999, 400, 644.
17. O.D. Friedrichs and M. O’Keeffe, Acta Crystallogr., Sect. A, 2003, A59,
351.
18. M.D. Foster and M.M.J. Treacy, http://www.gavrog.org//, 2006.
220 Chapter 12
19. D.W. Breck, Zeolite Molecular Sieves. Structure, Chemistry and Use,
Wiley, New York, 1974.
20. M.M.J. Treacy, S. Rao and I. Rivin, in Proceedings of the 9th International
Zeolite Conference, Montreal 1992, vol 1, ed. R. von Ballmoos, J.B. Higgins
and M.M.J. Treacy, Butterworth-Heinemann, Stoneham, MA, 1993, 381.
21. H.-J. Klein, in 10th International Conference on Mathematical Modelling
and Scientific Computing, July 1995, Boston, vol 6, ed. X.J. Avula and
A. Nerodi, Principia Scientia, St. Louis, 1996, 940.
22. F. Delprato, L. Delmotte, J.L. Guth and L. Huve, Zeolites, 1990, 10, 546.
23. C. Baerlocher, A. Hepp and W.M. Meier, DLS-76 – A Program for
Simulation of Crystal Structures by Geometric Refinement, ETH Report,
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Commun., 1984, 1271.
25. J.D. Gale, J. Chem. Soc., Faraday Trans., 1997, 93, 629.
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1992, 5, 428.
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29. R.I. Grigorchuk and A. Zuk, The Ihara zeta function of infinite graphs,
the KNS spectral measure and integrable maps, in Random Walks and
Geometry, Walter de Gruyter GmbH & Co. KG, Berlin, 2004.
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0608229, 2006.
31. R. Kenyon, Invent. Math., 2002, 150, 409.
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Concepts and Applications of Voronoi Diagrams, 2nd edn, Wiley Series in
Probability and Statistics, Wiley, Chichester, 2000.
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Mathematics. Principles and Techniques of Algorithmic Differentiation, vol
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2006, 5, 962.
CHAPTER 13

Discovering New Crystal

Architectures
FILIPE A. ALMEIDA PAZ,1 DOROTA MAJDA,2,3 ROBERT
G. BELL4,5 AND JACEK KLINOWSKI3
1
Department of Chemistry, CICECO, University of Aveiro, Campus
Universitário de Santiago, Aveiro, 3810-193, Portugal; 2 Department of
Chemistry, Jagiellonian University, ul. Ingardena 3, 30–060 Kraków, Poland;
3
Department of Chemistry, University of Cambridge, Lensfield Road,
Cambridge, CB2 1EW, UK; 4 Davy-Faraday Research Laboratory, The
Royal Institution of Great Britain, 21 Albemarle Street, London W1S 4BS,
UK; 5 Department of Chemistry, University College London, 20 Gordon
Street, London WC1H 0AJ, UK

1 Introduction
The contrast between the small number of physical laws and the enormous
number of structures to which these laws give rise is an intriguing aspect of the
natural world. The handful of rules of chemical bonding results in many
thousands of crystalline inorganic compounds with a bewildering number of
different structures, even when only a few chemical elements are involved. For
example, over a half of all known minerals are silicates and aluminosilicates
with distinct structures, although their frameworks are built only of silicon,
oxygen and aluminium.
Enumeration of networks of atoms in inorganic structures is a matter of
considerable interest, but a formidable task for a scientist. Apart from the pure
academic interest in the problem, there are two reasons why such enumeration
is important. First, a ‘‘library’’ of well-characterised, chemically feasible,
hypothetical structures would facilitate design strategies that would ultimately
lead to their syntheses. Second, X-ray, neutron and electron diffraction pat-
terns calculated for such structures would be a great boon in determining the
atomic coordinates of newly prepared open-structured materials: it would
simply entail a straightforward comparison of the experimentally obtained
pattern with the database.
221
222 Chapter 13

2 Crystalline Molecular Sieves

Derivation of chemically viable hypothetical networks is particularly desirable
for crystalline microporous molecular sieves, of which there are now 176
recognised structure types, with several new ones being added to the list
every year (Table 1).1 Crystalline molecular sieves are a class of porous
crystalline open-framework solids which includes aluminosilicates (zeolites),
aluminophosphates and related materials.2 Zeolites are built from corner-
sharing SiO4 and AlO4 tetrahedra linked by the apical oxygen atoms to form
frameworks of high internal surface area with regular channel systems and
cavities of molecular size (Figure 1). Other elements, such as Ga, Ge, B and Fe
can substitute for Si and Al. The net negative charge of the framework, equal to
the number of the constituent aluminium atoms, is balanced by exchangeable
cations located in the channels which normally also contain water. The name
‘‘zeolite’’ (from the Greek zeo ¼ to boil and liyos ¼ stone) was coined to
describe the behaviour of the mineral stilbite which loses water on heating
and thus seems to boil. There are ca. 40 identified zeolite minerals and more
than 130 purely synthetic species.1
All known zeolites, both natural and synthetic, contain channels circum-
scribed by tetrahedrally coordinated Si or Al atoms. Microporous silicates with
windows of insufficient size to sorb water molecules reversibly are known as
clathrasils.3 The AlPO4 molecular sieves, the porous crystalline equivalents of
aluminium phosphate, are built from alternating AlO4 and PO4 tetrahedra.4
Incorporation of an Si source into AlPO4 gives silicoaluminophosphates
(SAPO) and the incorporation of a metal (Me) into AlPO4 and SAPO gives
the MeAPO and MeAPSO sieves, respectively. Other zeolite-related structures
with novel compositions such as zincosilicates, gallophosphates, aluminoarse-
nates, galloarsenates and beryllophosphates have also been reported. Of the 44
recognised AlPO4 and related structures, 19 have the framework topologies of
known zeolites, and the rest are novel structures (Table 1). Some microporous
aluminophosphates contain wider channels (410 Å) than any known zeolite.
Open-structure aluminosilicates are centrally involved in the catalytic conver-
sions of the petrochemical industry5 (in cracking, hydrocracking, alkylation,
isomerisation and de-hydroisomerisation). Framework-substituted, open-
structure AlPO catalysts are also important.6 For example, a SAPO-347 cat-
alyst has been commercialised for the acid-catalysed dehydration of methanol
to yield ethene and propene for the polymer industry. Transition-metal,
framework-substituted AlPOs exhibit a wide variety of catalytic action in
selective oxidations8 (such as the aerial oxidation of cyclohexane to adipic
acid), the in situ production of hazardous reagents (such as hydroxyl-
amine from NH3 and air), the conversion of cyclohexanone, NH3 and air
to e-caprolactam and nylon-6,9 and the generation of organic chemicals
of value as pharmaceuticals. The annual industrial consumption of zeolites is
ca. 550,000 tonnes, of which 135,000 tonnes are used in catalysis, 375,000 as ion
exchangers in detergent powders and 40,000 as sorbents. The topology of
zeolitic, AlPO4 and related structures has been reviewed.10
Discovering New Crystal Architectures 223
Table 1 Microporous zeolitic and related molecular sieves.
Silicates and
Silicates phosphates Phosphates Germanates Others
AFG GIU MFI RUT ABW ACO NPO ASV CZP
BEA GME MFS RWR AFI AEI OSI BEC DFT
BCT GON MON SFE ANA AEL PON IWR OSO
BIK GOO MOR SFF AST AEN SAO IWW RWY
BOG HEU MOZ SFG BPH AET SAS SOS WEI
BRE IFR MSE SFH CAN AFN SAT UOZ
CAS IHW MTF SFN CGS AFO SAV UTL
CDO IMF MTN SGT CHA AFR SBE
CFI ISV MTT SSY ERI AFS SBS
–CHI ITE MTW STF FAU AFT SBT
CON ITH MWW STI GIS AFX SFO
DAC ITW NAB STT LAU AFY SIV
DDR IWV NAT SZR LEV AHT UEI
DOH JBW NES TER LOS APC USI
DON KFI NON THO LTA APD VFI
EAB LIO NSI TOL MSO ATN ZON
EDI –LIT OBW TON OWE ATO
EMT LOV OFF TSC RHO ATS
EON LTL –PAR TUN SOD ATT
EPI LTN PAU UFI ATV
ESV MAR PHI VET AWO
ETR MAZ –RON VNI AWW
EUO MEI RRO VSV CGF
FAR MEL RSN –WEN –CLO
FER MEP RTE YUG DFO
FRA MER RTH EZT

3 Structural Description of Molecular Sieves

Si, Al and P atoms (known as T-atoms) in molecular sieves occupy four-
connected vertices of a three-dimensional net, and the oxygen atoms occupy
two-connected positions between the four-connected vertices. Given that each
oxygen lies between two T-atoms, the topology of the framework may be
considered simply in terms of the connectivity of the T-atoms. Thus each
T-atom is treated as a vertex of a three-dimensional net, and each vertex lies at
the intersection of four T–T edges. Such a net is said to be four-connected. If all
vertices in a net are topologically identical, the net is described as uninodal.
Binodal, trinodal, etc. nets are those with two, three, etc. topologically distinct
types of vertices.
The diversity of known structures is such that topological classification of
structures is necessarily based on subunits of linked tetrahedra, known as
secondary building units (SBU) (Figure 2).11 The SBU’s are the smallest
number of simple units from which all known structures can be built. Poly-
hedral cages, the larger building blocks, are each composed of a handful of SBU’s
and can in turn be combined to form an infinite framework. For example, the
224 Chapter 13

Figure 1 Framework structures of zeolites of structure types SOD (sodalite), LTA

(zeolite A), FAU (faujasite), CAN (cancrinite), KFI (zeolite ZK-5) and
RHO (zeolite Rho). The positions of tetrahedral atoms are at the crossings
of the straight lines which symbolise T–T linkages. Oxygen atoms (not
shown) lie approximately halfway between the T-atoms. The types of cages
involved in each structure are represented by polyhedra which have been
shrunk towards their centres. Sodalite (structure type SOD) is formed by
direct face sharing of four-membered rings in the neighbouring truncated
octahedra, more correctly described as tetrakaidodecahedra (also known as
‘‘sodalite cages’’ or ‘‘b-cages’’). Zeolite A (structure type LTA) is formed by
linking the sodalite cages through double four-membered rings. Faujasite
(structure type FAU) is formed by linking the sodalite cages through double
six-membered rings. Cancrinite is formed by direct linking of 11-hedra
(‘‘e-cages’’ or ‘‘cancrinite cages’’). Other polyhedra are the ‘‘a-cage’’
(26-hedron of type I); double eight-membered ring; double six-membered
ring (hexagonal prism) and the 18-hedron (‘‘g-cage’’). Exchangeable non-
framework cations are not shown for clarity.

truncated octahedron (or b-cage), may be linked directly to other b-cages to

form the SOD structure type, via double four-membered rings to form zeolite A
(LTA structure type), or via double six-membered rings to form the zeolitic
mineral faujasite (FAU) (Figure 1).
A periodic network of tetrahedral atoms can be described in terms of the
‘‘circuit symbol’’ of each T vertex. Each T vertex participates in six Ti–T–Tj
angles, and for each angle there is a shortest circuit of edges T–Ti


Tj–T. The
set of six numbers forms the circuit symbol of the vertex,12 which reflects the
degree of compactness of a net. A simplified form of the circuit symbol is a
‘‘loop coordination’’: a graph showing only the number of three- or four-
membered rings in which a given T-atom participates (Figure 3).
Discovering New Crystal Architectures 225

Figure 2 Secondary building units (SBU’s) found in molecular sieve structures.

Numbers show in how many structure types a given SBU appears.

A powerful description of a net involves the concept of ‘‘coordination

sequence’’ (Figure 4).13 Thus, in a four-connected network each T-atom is
connected to N1 ¼ four neighbouring T-atoms through oxygen bridges. These
are then linked to N2 T-atoms in the next shell, in turn connected to N3
T-atoms, etc., including each T-atom only once. For example, the coordination
sequence for FAU is 4, 9, 16, 25, 37, 53, 73, 96, 120, 145. Although the
coordination sequence for each kind of T-atom is not completely unique to a
given structure, and occasionally distinct structures (such as LTA and RHO)
have the same coordination sequence, it is a very useful guide since structures
with different coordination sequences are guaranteed to be different. Frame-
work density (FD) is defined as the number of T-atoms per 1000 Å3, while
topological density, r10, defined so that 1000r10 is the number of T-atoms in the
first 10 coordination shells of a given T-atom,14–16 also reflects the degree of
compactness of a net.
Recent structural descriptions of molecular sieves use the concept of nodal
surfaces,17 equipotential surfaces and triply periodic minimal surfaces (TPMS),
226 Chapter 13

Figure 3 Loop configurations:1 solid lines represent T–O–T linkages, dotted lines
represent non-connected T–O bonds found in interrupted frameworks.

surfaces with zero mean curvature at all points.18 These concepts are funda-
mentally different from the ‘‘conventional’’ approaches described above in that
they do not consider chemical bonds and bond angles but treat structures as an
assembly of atoms ‘‘decorating’’ an infinite surface.

4 Non-Systematic Structural Enumeration

Enumeration of zeolitic structures originates in the work of Wells.12,19 Early
enumerations were derived by empirical methods, and new structures predicted
by linking together structural subunits in new ways, either by building models
or by computer simulation. As the T–O distances in all known zeolites are in
the 1.58–1.78 Å range (so that all T–T edges are close to 3.1 Å) and the T–O–T
angles are in the 130–1601 range, models can be built using identical sections of
plastic tubing attached at each end to tetrahedral nodes.
Discovering New Crystal Architectures 227

Figure 4 Graphical representation of the calculation of the coordination sequence for

the site marked with an arrow in a two-dimensional five-connected plane net.

However, of the many structures which are generated, only some will be
‘‘chemically reasonable’’.20 Topology takes no account of chemistry and the
basic requirement for chemically realistic structures is that bond lengths and
angles are within a certain acceptable range. O’Keeffe16 described as ‘‘realisa-
ble’’ nets which can be realised geometrically with each vertex having only four
equidistant nearest neighbours and with the T–T linkages corresponding to the
edges of the net, and suggested that the number of such uninodal nets is finite
and amounts to ‘‘some hundreds’’.
For the known zeolites and zeolite-type materials, the values of framework
density, FD, range from 12.5–25.1. The magnitude of FD depends on the
type and relative number of the smallest rings.21 The frameworks of lowest
density have a maximum number of four-membered rings, and the minimum
framework density increases with the size of the smallest rings. Brunner22
considered the likelihood of preparing highly siliceous frameworks of a
given topology in terms of the loop configuration. By examining tetrahedral
structures with respect to the smallest rings, bond angles, symmetry, loop
configuration and framework density,23 he concluded that the lowest density is
obtained for structures of high symmetry.
Aware of the practical importance of nets with very open frameworks
(FDo12) and wide channel openings (containing a maximum of three- and
four-rings), Barrer and Villiger24 were the first to find a chemically realistic net
with wide unidimensional channels. Meier25 and Hansen26 derived a series of
low-density nets, while Smith and co-workers described a large number of
hypothetical stereochemically realisable structures.27,28 One of their interesting
results was the prediction28 of the net with 18-rings (net 81(1) in the original
paper) which was subsequently identified in the aluminophosphate VPI-5 (VFI
structure type).29
228 Chapter 13
O’Keeffe and co-workers derived many new structures using empirical com-
puter search algorithms.14,16 A point was moved in small increments through-
out the asymmetric unit of the unit cell of all the cubic, hexagonal, tetragonal
and orthorhombic space groups in turn. All the equivalent points in the cell
generated by the group-symmetry operations were then identified. The topo-
logy of the net defined by the four nearest neighbours of the initial point was
then characterized by its coordination sequence. Most of these nets were new.
Treacy et al.30 described a computer method for generating periodic four-
connected frameworks. Given the number of unique tetrahedral atoms and the
crystallographic space group type, the algorithm explored all combinations of
connected atoms and crystallographic sites, seeking the four-connected graphs.
This database, which lists hypothetical structures enumerated by exploring all
combinations of connected atoms and crystallographic sites, contains no fewer
than 933,672 structures,31 including the results of an elegant topological search
for the framework of ZSM-10.32
Hyde and co-workers34 have shown that many low-density frameworks are
related to periodic minimal surfaces. The results were considered in the light of
framework densities of highly siliceous zeolites, clathrasils and dense silicates in
order to separate the roles of geometry and chemistry in determining frame-
work topology. Using an analogy with three-connected networks of hyperbol-
ically curved single sheets, Fogden and Jacob33 described a method for
construction of frameworks corresponding to their interconnected, double-
sheet relatives, and gave models of hypothetical frameworks fitting the triply
periodic minimal surfaces P,35 D36 and G.36 The channels and cavities in these
structures are significantly larger than those in known zeolites.

5 Systematic Enumeration Using Tiling Theory

The work on enumeration described above has been very useful, but suffers
from the drawback of being non-systematic: it is never quite certain that all the
structural possibilities have been considered. Our approach,37 which takes care
of this problem, is based on advances in combinatorial tiling theory.38–41 All
periodic tilings of the Euclidean plane, the sphere and the hyperbolic plane have
been classified earlier,40,42 and algorithms, which enumerate and permit the
visualisation of all possible topological types of tilings for each two-dimen-
sional symmetry group with 1, 2, 3, etc. kinds of inequivalent vertices, devel-
oped.42 We could therefore address the three-dimensional case, which has
direct applications to structural chemistry. We define a tiling as a periodic
subdivision of space into bounded, connected regions without holes, which we
call tiles. If two tiles meet along a surface, we call the surface a face. If three or
more faces meet along a curve, we call the curve an edge. Finally, if at least
three edges meet at a point, we call that point a vertex. A network is thus
formed by the vertices and edges. The configuration of edges, faces and tiles
around a given vertex can be described by what is known as the ‘‘vertex figure’’,
obtained by placing the centre of a small notional sphere at the vertex and
Discovering New Crystal Architectures 229
considering the tiling of that sphere formed by the intersections with the
different tiles touching that vertex.
The starting point is to associate with each type of periodic tiling a unique
‘‘Delaney symbol’’.39,40 This is arrived at by breaking the tiling down into
simplices using a barycentric subdivision. Any (n+1) points in n-space which
do not lie in an (n – 1)-dimensional space are the vertices of an n-dimensional
simplex. A simplex in two dimensions is thus a triangle, and in three dimen-
sions, a tetrahedron. A tiling is uniquely described by a Delaney symbol, and a
unique Delaney symbol describes one, and only one, tiling.
As it would be difficult to visualise how tilings are generated in 3-D Euclidian
space, we shall use a two-dimensional example. Consider a two-dimensional
tiling composed of squares and octagons (Figure 5). The central point of each
of the tiles is connected with dashed lines to the centres of the edges, and with
dotted lines to the vertices, producing six different kinds of triangles, labelled
A–F. The Delaney symbol for the tiling is constructed by specifying from which
kind of original tile the different kinds of triangles originate, and how they are
linked together (Figure 6).39,40 For example, triangle A comes from the octag-
onal tile (with eight edges), is adjacent to triangles B, D and B in that tile, and
the original vertex belongs to three surrounding tiles. The Delaney symbol for
the whole tiling is thus
BDB83 ACA83 DBF83 CAE83 FFD43 EEC43
where each group of characters contains information about one class of
triangles in the barycentric subdivision: group 1 for class A, group 2 for class
B, etc. The letters refer to the neighbours across dashed, dotted and solid lines,
respectively, of this class of triangles, while the numbers are the same as those
inside the rectangles in Figure 5.
The classification of all periodic tilings of a given kind then reduces to the
enumeration of the corresponding Delaney symbols, which is equivalent to
‘‘mutating’’ the inorganic gene. This approach can be used in any number of
dimensions by dividing polytopal tiles into simplices. We have so far described
all possible Euclidean uni-, bi- and trinodal tilings based on ‘‘simple’’ vertex
figures (tilings with vertex figures which are tetrahedra) and all ‘‘simple’’ and
‘‘quasi-simple’’ uninodal tilings with vertex figures containing up to six extra
edges38 (in ‘‘quasi-simple’’ tilings the vertex figures are derived from tetrahedra,
but contain double edges). There are exactly 9 and 117 topological types of
four-connected uninodal43 and binodal44 nets, respectively, which are based on
‘‘simple’’ tilings. In addition, there are at least 157 additional uninodal nets
derived from ‘‘quasi-simple’’ tilings.43,45 For example, zeolitic structure types
SOD, LTA, RHO, FAU, KFI and CHA are all based on ‘‘quasi-simple’’ tilings
(Figure 1). Although we originally claimed that there are exactly 926 trinodal
structures based on simple tilings,44 it turns out that we had mistakenly
dismissed a further 412 structures.
Known zeolitic structure types involve n-nodal structures with n up to 12,
found in zeolite ZSM-5 (MFI structure type), one of the most complex
inorganic structures known. Given the vast number of possible combinations
230 Chapter 13

Figure 5 Barycentric subdivision of a two-dimensional tiling composed of squares and

octagons.

Figure 6 Graphical representation of the Delaney symbol for the tiling shown in
Figure 5.

of various vertex figures, MFI is not expected to be found among the first few
billion structures enumerated. All the same, the method is systematic and
exhaustive, and will eventually deliver the ZSM-5 structure. Further, only a
small fraction of the many structures will be chemically feasible (with bond
lengths and angles within an acceptable range).20 Given a realisable hypothet-
ical structure, a least-squares fit leading to optimal atomic positions can then be
performed by computer.

6 Chemically Feasible Zeolitic Structures

We have used computational chemistry methods to identify the most chemi-
cally plausible hypothetical frameworks. Aware of the fact that zeolites are
Discovering New Crystal Architectures 231
formally derived from silica, we have treated the structures as silica polymorphs
with the chemical formula SiO2. Silicon atoms were inserted at each vertex of
the enumerated networks, and a bridging oxygen was placed between each pair
of neighbouring Si atoms, separated by a typical Si


Si distance. An energy
minimisation program46 then calculated the framework energy relative to
a-quartz, the most stable form of the mineral, and the framework density
(the number of tetrahedral atoms per 1000 Å3) for each structure. These were
then compared with the corresponding values for known zeolite frameworks,
also treated as silica polymorphs.
Figure 7 gives the plot of framework energy relative to a-quartz, EF, vs. the
framework density, FD, for all known zeolites treated as silica polymorphs. We
excluded the four non-silicate structure types which substantially deviate from
the rest: WEI (calcium beryllophosphate), CZP (sodium zincophosphate), OSO
(potassium beryllosilicate) and RWY (gallium germanium sulphide). The line
of best fit has the formula y ¼ –1.436x+40.094, where x is framework density
(FD) and y is DEquartz. The important conclusion from the figure is that for all
silicate zeolites, the framework energy relative to a-quartz is below 30 kJ mol1.
The Cerius2 software suite47 was used for visualising and manipulating the
structures and for calculating free volumes, space group symmetry and other

Figure 7 Framework energy, EF (kJ mol1), with respect to a-quartz, vs. framework
density (Si atoms per 1000 Å3) for (a) all known zeolitic structure types. The
equation of the straight line (in blue) is EF ¼ –1.436 FD+40.094 and was
calculated from a total of 154 points (labelled structures were left out); (b)
hypothetical uninodal structures and (c) hypothetical binodal structures.
232 Chapter 13
parameters. In addition to calculating the energetics of the hypothetical struc-
tures, it is important to compare the calculated values with the values for all
known zeolite frameworks. Thus all relevant properties were also calculated for
the purely siliceous forms of all known zeolite topologies. Lattice energies were
calculated relative to a-quartz, the most stable form of the mineral at ambient
temperature.
The ‘‘accessible volume’’ was determined by tracing out the volume by the
centre of the probe molecule as it follows the structure contours, but with the
extra requirement that the probe must enter the unit cell from the outside via
sufficiently wide pores or channels. The accessible volume gives an indication of
the space available within each structure for applications in molecular sieving
and catalysis. The calculations of the accessible volume were performed using
the Free Volume module of the Cerius2 package, which applies the Connolly
method48 consisting of ‘‘rolling’’ a probe molecule with a given radius over the
van der Waals surface of the framework atoms. We have used a probe molecule
with a radius of 1.4 Å (such as water) and 1.32 and 0.9 Å for the radii of O and
Si atoms, respectively.
Enumeration of chemically realisable frameworks containing large amounts
of internal space (i.e., those containing channels and/or voids) is of particular
interest, because such materials can act as ‘‘microreactors’’ containing
implanted catalytically active groups or encapsulated transition-metal

Figure 8 Structures enumerated and subsequently synthesised. (a) RWY50 (our

structure 1_1);51 (b) NPO52 (our structure 1_88);51 (c) BCT53 (our structure
1_211)51 and (d) UFI54 (our structure 3_835).
Discovering New Crystal Architectures 233
49
complexes. The crucial structural parameters here are the amount of void
volume and its accessibility (whether or not a molecule can enter the structure
from the outside), which we have calculated for all the hypothetical structures.
The accessible volume for known zeolites is in the range of 0–28 Å3 per Si atom.
Our search for more of these continues.
When our original paper37 was published, the database maintained by the
International Zeolite Association contained 121 recognised structure types, and
the current number is 176. The 55 new structures can, in principle, all be

Figure 9 Hypothetical uninodal zeolites with 12-membered rings. Our structures:

(a) 1_71; (b) 1_73; (c) 1_89.

Figure 10 Hypothetical binodal zeolites with 12-membered rings. Our structures:

(a) 2_51; (b) 2_53.
234 Chapter 13
obtained using our method. Among the structures synthesised since 1999 we
have specifically described structure types RWY50 (our structure 1_1)51, NPO52
(our structure 1_88)51, BCT53 (our structure 1_211)51 and UFI54 (our structure
3_835) (Figure 8).
As mentioned above, we are particularly interested in ‘‘low energy’’ and
‘‘open framework’’ materials. In a series of papers37,43–45,55 we have described
many such materials. Here, we concentrate on new results concerning zeolites
with wide channels (i.e., 12-membered or larger). In Figures 9–12 we illustrate
such new hypothetical structures. All are chemically feasible according to our

Figure 11 Hypothetical trinodal zeolites with 12-membered rings. Our structures:

(a) 3_660; (b) 3_818; (c) 3_681; (d) 3_772; (e) 3_757 and (f) 3_934.
Discovering New Crystal Architectures 235

Figure 12 A hypothetical trinodal zeolite with 16-membered rings (our structure

3_971).

criteria, and we believe that most of them will be synthesised very soon. Note in
particular the astonishing 16-membered channel structure shown in Figure 12.
This material has very low framework density (FD ¼ 11.32 Si atoms per 1000 Å3)
and framework energy of 28.26 kJ mol1 with respect to a-quartz.

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CHAPTER 14

Chemical Modulations in Pb–Bi

Sulfosalts: A Glimpse at
Minerals in Solid-State
Chemistry
ALLAN PRING AND CRISTIANA L. CIOBANU
Department of Mineralogy, South Australian Museum, North Terrace,
Adelaide, South Australia 5000, Australia

1 Introduction
Mineralogy and chemistry share a common history and in many ways it can be
rightly said that chemistry, particularly inorganic and solid-state chemistry,
developed from mineralogy. Minerals are, after all, inorganic products formed
by geological processes. Indeed most of the chemical elements, apart from the
gases, were discovered during the analysis of minerals. Great chemists such as
Karl Scheele (1742–1786), Joseph Louis Gay-Lussac (1778–1850), Jöns Jacob
Berzelius (1779–1848) and Humphrey Davy (1778–1829) are all equally famous
for their mineralogical contributions. The minerals, scheelite (CaWO4), gaylussite
(Na2Ca(CO3)2
5H2O), berzelianite (Cu2Se), berzeliite (Ca,Na)3(Mg,Mn)2(AsO4)3
and davyne (Na,Ca,K)8Al6Si6O24(Cl,SO4,CO3)23 are testament to the promi-
nence of these chemists in mineralogy. There is also avogadrite (K,Cs)BF4 named
for Amadeo Avogadro (1776–1856), vauquelinite (Pb2Cu(CrO4)(PO4)(OH) for
Louis Vauquelin (1763–1829) and meurigite [K(H2O)2.5][Fe3+8(PO4)6(OH)7
(H2O)4] named for Sir John Meurig Thomas.
The modern concept of a mineral as a naturally occurring inorganic com-
pound was formulated late in the eighteenth century, when mineral descriptions
approaching today’s standards began to appear.1 There was rapid growth in
the number of known mineral species throughout the nineteenth century,
driven in part by a growing need to develop methods to systematically identify

239
240 Chapter 14
minerals and describe their properties for industrial purposes. The rapid
discovery of new elements was largely a result of improved mineral analysis.
Important developments in mineralogy paralleled those in chemistry and
also drove new research directions in crystallography, leading to understanding
of the structure of matter. By the time of the discovery of X-rays by Röntgen
in 1895, the number of recognised minerals had reached almost 800.2 The work
of Max von Laue and W.H. Bragg and W.L. Bragg launched the field of
crystal structure analysis in 1912, and the knowledge of the precise positions of
atoms in crystal structures and the distances between them gave structural
meaning to the chemical formula of many minerals and a new basis for
their classification. Hence, the concept of minerals being the salts of hypo-
thetical acids was banished. It is an interesting footnote in the history of
science that the great English amateur crystallographer, William Barlow, and
the chemist, William Pope, had correctly deduced the crystal structures of
NaCl, KCl, CsCl, ZnS and several other simple compounds. This work was
based solely on ideas of close-packing and symmetry that were developed some
years before the discovery of X-ray diffraction.3 It was, however, W.L. Bragg
and his group in Manchester, Goldschmidt in Oslo and Pauling in Pasadena
who made significant contributions to crystal chemistry during the period after
World War I, and laid the foundations for modern crystal chemistry in broad
terms.
It can rightly be said that the advances in X-ray crystallography in the first
half of the twentieth century and the development of microanalytical tech-
niques such as the electron microprobe around 1960 revolutionised mineralogy
and solid-state chemistry. The widespread use of such techniques greatly
enlarged the understanding of the chemical variation between and within
minerals. The electron microprobe for the first time brought a high level of
spatial resolution to chemical analysis and showed the inhomogeneous nature,
at the microscopic scale, of many minerals. This made possible the development
of many new applications for petrology and ore geology.
Analytical limitations are steadily decreasing and modern technology is able
to detect internal crystalline order at better than nanoscale resolution. The
development of high resolution transmission electron microscopy (HRTEM) in
the 1970s revealed that the ultra-microstructure of minerals can be quite
complex and that chemical substitutions via solid solution and non-stoichiome-
try via point-defect mechanisms were not the only means of chemical adapt-
ability revealed by minerals.w

w
The first HRTEM papers on minerals started to appear while one of us (AP) was an undergrad-
uate at Monash University in the mid-1970s. It was the work on the rock-forming silicates that
John Thomas was conducting with David Jefferson and others that prompted AP to join the
Thomas group in Cambridge as a Ph.D. student in 1980. At the time the Thomas group had
around 40 members, who pursued active research in zeolites, chain and layer silicates, as well as a
variety of catalysts, and solid-state organics. AP’s Ph.D. project investigated natural and synthetic
Ba and Cs compounds to assess their potential for nuclear waste immobilisation using HRTEM.
Chemical Modulations in Pb–Bi Sulfosalts 241

2 Modular Crystallography
Running parallel with increasing progress in transmission electron microscopy
in the 1970s were major developments in mineralogy that recognised the
modularity of crystal structures of complex minerals, such as the lead bismuth
sulfides.4,5 The ideas behind modular crystal chemistry have their roots in the
work of Baumhauer.6 He introduced the concept of polytypism in order to
explain the many structural modifications of SiC, formed by different stacking
sequences of layers that are identical both structurally and chemically. Magnéli7
introduced the concept of a homologous series to describe groups of compounds
that have variable chemistry but can be characterised by a general formula using
a structural operator to derive one member from another. This concept is now
applied to many groups of minerals and in particular sulfosalts such as the
lillianite series5,8 that will be discussed here. The somewhat parallel idea of
polysomatism was introduced by Thompson9,10 in order to explain the rela-
tionship between structures that are based on ordered intergrowths of two or
more structurally and chemically distinct types of units or modules. This is
different to the polytypical approach that requires identical crystal–structural
units or to the homology concept that uses a common structural operator for all
minerals in a group. One of the best-known examples of polysomatism is the
biopyribole mineral group.11
In modular crystallography, families of structures are generated by stacking
structural units in different ways with the central requirement being that the
energy of the interface between such component units is relatively low. The
most extensive modular structural families are those whose individual modules
have a very low residual electrostatic charge and consequently low surface
energies. Structural disorder due to errors in the stacking sequence have been
observed in nearly all modular series, particularly in synthetic compounds that
are obtained in experiments where conditions can be far from equilibrium. Can
structural disorder also be observed in minerals formed in geologic environ-
ments where cooling rates are orders of magnitude longer than in experimental
runs? Can minerals, in particular sulfides, preserve disorder, when we know
that atomic diffusion rates can be significant even at temperatures as low as
o200 1C?z
Several HRTEM studies on synthetic compounds formed in the Pb–Ag–Bi
sulfide system – analogues to minerals from the lillianite series – have shown
extensive disorder in samples prepared either by quenching or annealing.13,14 In
the following sections we will discuss the same type of compounds, but those
formed instead as minerals in a natural occurrence. The idea behind this
approach is to see in what ways the natural specimens compare to the synthetic
ones. In particular, could disordered intergrowths of different block sizes in
z
AP started to research these complex sulfosalt minerals when he returned to Australia in 1983 and
for a number of years concentrated on the Pb-As-S minerals, which occur in well-formed crystals.
In this system, however, disorder proved to be rather rare, although stacking disorder in the
polytypes of baumhauerite (named appropriately for Baumhauer) is not uncommon.12 CC came to
Adelaide in 2005 on a research fellowship to undertake HRTEM studies on sulfosalt minerals.
242 Chapter 14
these minerals provide an alternative mechanism to solid solution to explain
their chemical flexibility, and is this possibly linked to long-range compositional
modulations?

3 The Lillianites
The lillianite homologous series is a group of Pb–Bi(Ag) sulfosalts that have
structures based on the ordered intergrowth of a ‘galena-like’ motif cut parallel
to (110)PbS. The different blocks correspond to individual homologues having
a ‘chemically twinned’ arrangement consisting of chains of MS6 octahedra
that are linked by bi-capped trigonal prisms of PbS612 along mirror planes
(Figure 1).15–18 Distinct lillianite homologues in the series differ in the width of
the galena-like slabs. This can be expressed by N, the number of metal
octahedra in the chains that run diagonally across individual galena-like slabs
and parallel to (110)PbS. Homologues are denoted N1,N2L, where N1 and N2
are the number of metal sites in the two alternating slabs. The general formula
for the lillianite series is PbN12xBi21xAgxSN12, where N ¼ (N1 + N2)/2
and x is the Ag + Bi ¼ 2Pb substitution coefficient, with xmax ¼ (N2)/2. The
lillianite group contains both orthorhombic (N1 ¼ N2) and monoclinic
(N1 a N2) members, including lillianite (4,4L) (Pb3Bi2S6) and vikingite (4,7L)
(Pb8Ag5Bi13S30) (see Table 1 for full list of natural members of the series). The

Figure 1 Structural diagram of lillianite showing the atomic arrangement. The

chemically twinned PbS(110) like units are arranged about the twinned
plane. The metal sites on the mirror plane are in bi-capped trigonal
prismatic co-ordination. The different homologues in the series are gener-
ated by variation in the length of the octahedral chains between twin planes.
In this case N ¼ 4.
Table 1 Summary of compositional and structural data for the members of the lillianite homologous series. (After Makovicky.5)
Diagnostic
Mineral Formula Structure Cell Repeats (Å) Angle (1) Space Group Reflection
4,4
Lillianite Pb3Bi2S6 L a ¼ 13.54 b ¼ 20.45 c ¼ 4.10 Bbmm 0 12 0
Chemical Modulations in Pb–Bi Sulfosalts

4,4
Gustavite PbAgBi3S6 L a ¼ 7.08 b ¼ 19.57 c ¼ 8.27 b ¼ 107.2 P21/c 0 12 0
4,7
Vikingite Pb8Ag5Bi13S30 L a ¼ 13.60 c ¼ 25.25 b ¼ 8.22 b ¼ 95.6 P2/a 0 0 15
4,8
Treasurite Pb6Ag7Bi15S32 L a ¼ 13.35 c ¼ 26.54 b ¼ 4.09 b ¼ 92.8 C2/m 0 0 16
7,7
Heyrovskyite Pb6Bi2S9 L a ¼ 13.71 b ¼ 31.21 c ¼ 4.13 Bbmm 0 18 0
5,9
Eskimoite Pb10Ag7Bi15S36 L a ¼ 13.46 c ¼ 30.18 b ¼ 4.10 b ¼ 93.4 C2/m 0 0 18
11,11
Ourayite Pb15Ag12.5Bi20.5S52 L a ¼ 13.46 b ¼ 44.04 c ¼ 4.09 Bbmm 0 0 26
Schirmerite PbAgBi3S6 to Pb3Ag1.5Bi3.5S9 Disordered
243
244 Chapter 14
substitution Ag + Bi ¼ 2Pb results in additional members when over half of the
available Pb sites are occupied by Ag and Bi. Thus gustavite, even though it has
the same homologue notation as lillianite, i.e. (4,4L), is different in composition,
i.e., PbAgBi3S6. Chemical analyses of many lillianite homologues give non-
integral values for N and this suggests that the differences might be due to
variation in the frequency of the ‘chemical twinning’ (that is block-width
disorder).
In their extensive HRTEM study on synthetic compounds from the lillianite
series, Skowron and Tilley14 examined both quenched and annealed material and
found several new homologues that are not yet described from natural speci-
mens, including 4,5L, 7,8L and 8,8L. They also found that the temperature of
annealing was important in stabilising each homologue. At their higher anneal-
ing temperature (700 1C) the phases were dominated by homologues with N ¼ 4
or 7 blocks, either ordered or disordered, whereas a wider variety of homologues
was stable at the lowest temperature they considered for the experiments
(500 1C). They also found disordered intergrowths involving different N-sized
blocks inserted in an otherwise perfectly ordered matrix; for example, pairs of 8,8
blocks in 7,7L. Skowron and Tilley14 did not find synthetic phases corresponding
to the minerals eskimoite (5,9L) or ourayite (11,11L), thus again highlighting those
differences that exist between the behaviour of this system experimentally and in
nature. Pring et al.8 confirmed the existence of disordered intergrowths of
lillianite/gustavite-like blocks (N ¼ 4) and heyrovskyite-like (N ¼ 7) structural
blocks. One disordered sequence, examined in detail, gave an average homologue
number N ¼ 4.92 corresponding to a composition of Pb1.52Bi3.2Ag1.2S6.92. An
axial next-nearest neighbour Ising model was used to follow the fluctuations in
the average homologue number N across the crystal. This yielded compositional
fluctuations of the order of 70–170 Å over an 1800 Å region of the crystal, with a
220 Å lamella of ordered vikingite (Figure 2). This extensive disorder suggested
that it might be linked to some form of compositional modulation. Vikingite
(4,7L) occurs in macroscopically well-ordered states, so it is clear that the
sequence 4,7 is more stable than a random intergrowth of four and seven
ribbons having the same bulk composition.
Detailed examination of the sequence of slabs in Figure 2 reveals some
evidence of partial ordering.8 There are 163 slabs in the image; 113 slabs have
N ¼ 4 ribbons and 50 slabs have N ¼ 7 ribbons. The sequence 7,4,4,4 or 4,4,4,7
occurs 20 times in the image, including a section where the sequence is repeated
four times. The 7,7 units generally only occur in single strips although there is a
sequence of three such units on the left-hand side of Figure 2. The sequence
4,4,7,7 occurs eight times in the image while the alternative 7,4,7,7 occurs only
twice. The sequence 4,4,7,7 is compositionally equivalent to vikingite, whereas
the 7,4,7,7 sequence represents a composition richer in Pb. Trends in the
randomness of the gustavite-vikingite intergrowth were evaluated and the
dominant slab sequence was found to be 4,4,4,7 and 4,4,7,7, suggesting that
some longer-period homologues may be stable.
One can argue that the ordered long sequences 7,4,4,4, are also more stable
than a random intergrowth of four and seven ribbons having the same bulk
Chemical Modulations in Pb–Bi Sulfosalts 245

77 44 44 77 44 44 44 47 47 47 44 47 44 44 47 44 44 44 44 47 47 44

50 Å

200 Å

Figure 2 Image showing the disordered intergrowth of 4,4L, 4,7L and 7,7L blocks
(denoted as N1 + N2 sums) projected down the [001] direction. From the
weighted average of homologue numbers for the images it is possible to
calculate the composition of the disordered area, Pb1.52Bi3.2Ag1.2S6.92 where
Naver = 4.92.

composition, but probably less stable than those formed by exsolutions of

vikingite (7,4) in gustavite (4,4). Thus, the long-period ordered intergrowths
probably represent an intermediate stage in a diffusion-controlled exsolution
process from a not quite homogeneous unknown precursor with Naver E 5. This
concept is in agreement with the observed structural faults.
Figure 3 shows a HRTEM image of one of the more complex defects found
by Pring et al.8 In this defect, the unit sequence 4,7,4,7,7,7,4,4,4,4,7,4 is
transformed by the ‘jogging’ of three twin planes to give the sequence,
4,7,4,4,7,4,7,4,7,4,7,4. In this defect, the number of twin planes is conserved
across the defect and thus the average value of N (and hence the composition)
does not change. This was a common feature found in all defects reported by
Pring et al.8 and also by Skowron and Tilley.14 These defects do not operate as
a mechanism for compositional variation, but rather locally change block
width.
A long-range compositional modulation in a mineral could provide interest-
ing clues into the nature of its formation. Is this related to periodic variations in
the composition of the mineralising fluid that in turn can be linked to self-
organising phenomena that arise due to fluctuations, instability and chaotic
behaviour of one or the other parameters controlling that system?19 Or are they
related to fluctuations in supersaturation associated with fluid flow and volume
that have also been shown to lead to compositional zoning in minerals grown
under hydrothermal conditions?20 Are these mineral systems useful models for
the production of crystals that process gradients in physical properties?
To test these ideas of long-range compositional variation via block-width
modulation in these Pb–Ag–Bi sulfide minerals, we needed to examine a much
longer structural sequence than the one presented above. In order to do this it
is necessary to prepare an ion-thinned foil in the correct crystallographic
246 Chapter 14

47 47 77 44 44 47 47

44 47 47 47

50 Å

Figure 3 HRTEM image of crystal defects in which the chemical twin planes are
altered (or jogged) to accommodate change in block width. The sequence
4,7,7,7 4,4,4,4 is transformed by the ‘jogging’ of three twin planes to give the
sequence, 4,4,7,4 7,4,7,4.

orientation, with the stacking sequence running parallel to the edge of the holes.
This proved to be not a trivial task for an opaque mineral that is impossible to
orient before ion-beam thinning, but we finally obtained a suitable sample; this
was a crystal of the mineral eskimoite, the 5,9L homologue (Pb10Ag7Bi15S36)
and an Ag-substituted polymorph of the more widespread 7,7L homologue
heyrovskyite (Pb24Bi4S36). The eskimoite as well as the disordered lillianite/
gustavite crystal above, both came from the same hand specimen, which
originated at the Ivigtut cryolite deposit in southern Greenland.
A number of overlapping HRTEM images were obtained to give a lattice image
mosaic of over 80,000 Å of the eskimoite crystal edge. This was then analysed to
establish the stacking sequence of the various homologue blocks. A portion of the
crystal is shown in Figure 4, and the disorder is clearly visible, however many of
the defects represent antiphase boundaries, in which the stacking sequence simply
reverses 9,5,9,5,9,5|5,9,5,9,5,9,5 or 5,9,5,9,5,9|9,5,9,5,9,5,9. There is, however,
some genuine block-width disorder, such as extra pairs of N ¼ 9 blocks and
extra pairs of N ¼ 5 blocks. These often occur in groups where the defect pairs
are separated only by short sequences of ordered material (1–5 unit cells).
These block-width errors appear to be largely self-correcting, as a 5,5 block
inserted in an ordered eskimoite sequence (5,9,5,5,5,9) is often followed at a short
distance away by the insertion of a 9,9 block in the same matrix (5,9,5,9,9,9,5,9).
Over the length of the edge measured that contains some 2698 unit cells there
are 94 additional nine units giving an average N value of 7.07 corresponding
to a composition of approximately Pb2.57Bi3.75Ag1.75S9.07; this is close to
the composition of stoichiometric eskimoite (Table 1). There are three regions
Chemical Modulations in Pb–Bi Sulfosalts 247

1000 Å

300 Å

Figure 4 HRTEM images of eskimoite crystal edge projected down the [010] direc-
tion. Above is a small segment of the 80,000 Å long crystal edge at low
magnification. Note the distribution of defects in the image. Below is a
higher resolution image of the same region of the crystal with a 5,5,9,9 defect
marked (arrow) and other defects clearly visible in the crystal.

N=9

0 300 600 900 1200 1500 1800 2100 2400 2700

N=5

Figure 5 Schematic diagram showing the distribution of extra N ¼ 5 and N ¼ 9 blocks

in the eskimoite crystal. The horizontal axis represents the number of unit
cells in the sequence from one end. Note that there are more N ¼ 9 defects
than N ¼ 5 defects and also that the N ¼ 5 defects tend to be always closely
associated with N ¼ 9 defects. Note also that the distribution of extra N ¼ 9
defects is uneven through the crystal resulting in compositional zoning.

of the crystal with over 200 unit cell repeats that have no extra 9,9 or 5,5 blocks,
indicating some modulation in the density of block-width defects with variable
distance in the crystal (Figure 5). A detailed statistical analysis of the sequence is
currently in progress.
Based on the above, the compositional modulation in the eskimoite crystal is
minor. This is because, even though the 5,5 and 9,9 ‘defects’ are commonly
present as extra units, inserted at intervals of variable length in the ordered 5,9
parent matrix of the crystal, their combination from one interval to another
generally preserves the composition along the sequence. There is, nonetheless, a
248 Chapter 14
certain periodicity in the insertion and relative abundance from one region to
another of such ‘defect’ blocks, with inverse chemical effects in the eskimoite
crystal and this can be considered to map a rhythmic zonation at the lattice scale
(Figure 5). The alternation of (5,5) and (9,9) pairs over sequences of 100–150 Å
show a compositional loop between Ag-poor (5,5) and Ag-rich (9,9) modules
with amplitude that is relevant only at this scale. Such compositional repeats can
be interpreted as the expression of medium-range chemical oscillations that are
encoded within the the longer range structural modulation.
The crystal-structural modularity of sulfosalts, such as the example presented
here, is well-suited to lock in subtle chemical variations if there is a coupling
between such oscillations and the rate of atom ordering within coherent struc-
tural units at the lattice scale. Based on experiments that produced oscillatory
zoning in crystals, the conditions required for the appearance of this self-
patterning phenomenon in hydrothermal systems is a non-stirred solution, as
occurs in closed cavities in mineralising systems.21 So, although the inlet solution
remains unchanged during the crystal formation, the crystallisation process itself
may induce chemical oscillations in the same solution by a feedback effect,
coupling the rate of diffusion to the induced changes in the respective fluid.
It is interesting to contrast the difference in the states of order in the crystals
with N ¼ 4 and 7 blocks, both synthetic and natural, with the N ¼ 5 and 9
blocks in eskimoite. The eskimoite homologue (5,9L) was not one of those noted
by Skowron and Tilley,14 although they did find a number of other homologues
with N ¼ 5 blocks. This suggests that the stability of the 5,9L homologue is
linked to its high Ag and Bi contents, especially when compared to its poly-
morph heyrovskyite (7,7L); the latter is known to have limited compositional
field with respect to Ag in nature.22 It is also worth noting, when considering
the relative stabilities of the various block sizes, that eskimoite (5,9L), vikingite
(4,7L) and gustavite (4,4L) are all intergrown in specimens from Ivigtut. Exam-
ination of the distribution of the lillianite minerals in nature and in synthetic
studies indicate that N ¼ 4 and N ¼ 7 are more stable over a larger range of
temperature and composition than other homologues. There is also a ‘mineral’
in nature, ‘schirmerite’, which is believed to be a disordered intergrowth of
N ¼ 4 and N ¼ 7 blocks.
The mechanisms for compositional zoning on a range of scales from the
atomic to the macro can be subtle in minerals, as nature is able to anneal and
transform on timescales unimaginable to the laboratory. It is clear that there is
so much that solid-state chemists and materials scientists can still learn about
the subtleties of crystal chemistry by looking at minerals. J.S. Anderson once
mused that solid-state chemists should set up long-term annealing experiments
and will them to their grandchildren!

Acknowledgements
AP wishes to thank Professor John Meurig Thomas for introducing him to
HRTEM. For the current work, thanks are due to Dr D.A. Jefferson of the
Chemical Modulations in Pb–Bi Sulfosalts 249
Department of Chemistry, University of Cambridge, for access to HRTEM
facilities, Dr Ole Petersen of the Geological Museum, Copenhagen, for the
sample of the gustavite-cosalite-galena-bearing mineral suite from Ivigtut, and
Mr D. Ware for assistance in preparation of the ion-thinned specimens. The
experimental work for this study was undertaken while one of us (AP) was a
visiting fellow commoner at Trinity College, Cambridge and, thanks are
extended to the master and fellows of that college for their hospitality and
financial support. The financial support of the Australian Research Council is
also gratefully acknowledged.

References
1. A.G. Bulakh, A.A. Zolotarev and S.N. Britvin, Neues Jb. Miner. Monat.,
2003, 446.
2. B.J. Skinner and H.C.W. Skinner, Mineral. Rec., 1980, 11, 333.
3. L. Pauling, in: Structure and Bonding in Crystals, M.A. O’Keefe and
A. Navrotsky (ed), Academic Press, New York, 1981, Vol. 1, 1.
4. Y. Takéuchi, in: Volcanism and Ore Genesis, T. Tatsumi (ed), University of
Tokyo Press, Tokyo, 1970, 395.
5. E. Makovicky, Fortschr. Mineral., 1981, 59, 137.
6. H. Baumhauer, Z. Kristallogr., 1915, 55, 249.
7. A. Magnéli, Acta Crystallogr., 1953, 6, 495.
8. A. Pring, M. Jercher and E. Makovicky, Mineral. Mag., 1999, 63, 917.
9. J.B. Thompson Jr., Am. Mineral., 1970, 55, 292.
10. J.B. Thompson Jr., Am. Mineral., 1978, 63, 239.
11. D.R. Veblen, Am. Mineral., 1991, 76, 801.
12. A. Pring, Schweiz. Miner. Petrogr., 2001, 81, 69.
13. A. Skowron and R.J.D. Tilley, Chem. Scripta, 1986, 26, 353.
14. A. Skowron and R.J.D. Tilley, J. Solid State Chem., 1990, 85, 235.
15. E. Makovicky and S. Karup-Møller, Neues. Jb. Miner. Abh., 1977, 130,
264.
16. E. Makovicky, Neues. Jb. Miner. Abh., 1977, 131, 187.
17. E. Makovicky and S. Karup-Møller, Neues. Jb. Miner. Abh., 1977, 131,
56.
18. E. Makovicky, in Modular Aspects of Minerals, S. Merlino (ed), Eötvös
University Press, Budapest, 1977, 237.
19. F. Di Benedetto, G.P. Bernardini, P. Costagliola, D. Plant and
D.J. Vaughan, Am. Mineral., 2005, 90, 1384.
20. A. Putnis, M. Prieto and L. Fernandez-Diaz, Geol. Mag., 1995, 132, 1.
21. A.J. Reeder, R.O. Fagioli and W.J. Meyers, Earth Sci. Rev., 1990, 29,
39.
22. E. Makovicky, W.G. Mumme and B.F. Hoskins, 1992, Can. Mineral.,
1992, 29, 553.
CHAPTER 15

Complexity: In the Eye of the

Beholder (This Beholder is a
Crystallographer)
SVEN LIDIN
Department of Physical, Inorganic and Structural Chemistry, Arrhenius
Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden

1 Complexity
Complexity is something of a buzzword in structural science, and we all love to
present our findings as complex since this not only puts the findings in a
glorified light, but the glory also rubs off on the finder who must have been
devilishly clever to solve the complex problem, hence our part of our fascina-
tion with complexity, real or imagined. But what is structural complexity really?
A common definition deals with the number of parameters needed to describe a
solution, but an equally valid interpretation is to consider complexity to be a
measure of the difficulty of a structural problem.

1.1 Complexity in Structural Solution

Looking back on the history of structural solution by X-ray diffraction, we find
that this complexity is a function of time. The very first structural solutions
were found using symmetry considerations and trial-and-error methods, and
complexity would emerge as soon as the number of possible solutions went
beyond what was testable with the computational capabilities of the time. The
notion of complexity changed with the introduction of the Patterson function
in the 1930s that allowed the solution of structures with a small number of
independent atoms, alternatively, with a small number of relatively heavy
atoms to start phasing. The introduction of the Patterson function was clearly a
turning point in structural science. The next important step in materials
250
Complexity: In the Eye of the Beholder 251
crystallography and small molecule crystallography was the advent of direct
methods developed by Hauptman and Karle in a series of papers starting in the
early 1950s. This method allows for the solution of rather large structures,
provided certain conditions are met. This time complexity changed meaning in
a more subtle way. Perhaps the most common reason direct methods fail
(barring bad samples and errors in the analysis) is problems with pseudo-
symmetry. Particularly difficult cases include low symmetry superstructures in
high symmetry systems where automated procedures are poor at picking up
subtle symmetry imbalances, and the choice of origin becomes crucial. Quite
often, the only recourse is to work in P1 to solve the problem, and then revert to
the proper space group, and this method is by no means foolproof.

2 Incommensurability
An interesting turning point in inorganic chemistry was the introduction of the
concept of incommensurability. Although this phenomenon was recognized
very early in crystallography, it did not attract a lot of attention until the work
of deWolff on NaCO3.1 This seminal work marked the starting point of a
sequence of papers, mainly from the Netherlands and Japan, dealing with
various aspects of aperiodic crystallography. While progress was rapid, accept-
ance was still slow in a rather conservative crystallographic community.
Readily affordable area detectors, and the increased use of electron diffraction
provided an ever-increasing number of examples of incommensurability, but
the real breakthrough in the larger community came with the software system
JANA2 developed by Vaclav Petricek and his co-workers in Prague. With this
splendid tool, suddenly the world of aperiodic analysis became available to the
non-experts.
At about this time I had the good fortune to be called for an interview for a
position, where one of the referees was Sir John Meurig Thomas. One of the
research projects I presented was on super-structure ordering in intermetallics. I
had successfully completed some work, while other parts eluded me due to my
limited knowledge of aperiodicity. When pressed by Sir John on how to
proceed with these issues, I produced a somewhat lame ‘‘that would require
aperiodic analysis, of which I have no command.’’ I got the expected reply
‘‘perhaps it’s time to take that command.’’ The thought had certainly crossed
my mind before, but this contact provided the spark I needed to start the
ignition.

2.1 Charge Flipping

I have been lucky to be involved in this branch of structural science that has
enjoyed a tremendous growth over the last few years, and very recently I have
had the privilege to watch a new turning point being reached – the introduction
of charge flipping.3 While refinement of small amplitude modulations has long
been an easy task, large scale modulations have provided a real challenge. The
252 Chapter 15
correct initial phasing of the modulation functions has been a non-trivial task,
and for complicated structures it has been outright difficult, and very time-
consuming, since the correctness has sometimes been difficult to ascertain
without proceeding quite far in the refinement work. Many blind alleys may
have to be negotiated before the proper solution is found. Certainly there has
been work on multidimensional direct methods and the Patterson function
still applies, but for the more demanding cases it has been down to some trial-
and-error work or lucky guessing.
So what is charge flipping? This remarkable, and very robust method works
in a way that is reminiscent of several earlier methods, but the application of the
procedure to ab initio structural solution had not been tried previously. The
recipe is extremely simple: assign random starting phases to a data set, compute
the Fourier transform, identify any part of the electron density map that has a
charge below a certain positive threshold value, and change the sign of that
charge. Calculate the phases associated with this charge-flipped electron density
map, and use them together with the experimental amplitudes to generate a
second iteration of the electron density map, etc. The most remarkable feature
of this procedure is that it works. Sometimes it works quickly, but quite
frequently it takes several hundred cycles to obtain convergence. An important
feature of the procedure is that it operates in P1. For the method to work, it
appears that it must be allowed to sample a large part of the configurational
phase space.

2.2 A Practical Example

What then are the advantages of this method compared to direct methods? It is
model independent, symmetry independent and dimensionally independent,
meaning it can be used to phase an incommensurately modulated structure in
its entirety. Because of the symmetry independence, it is also impervious to
pseudo-symmetry. The main remaining problems are incomplete data (com-
pleteness to a good resolution is a prerequisite) and bad data (twinning is still an
issue). To illustrate the power of the method, I will review an incommensurate
case that we solved a few years ago using trial-and-error phasing and a great
deal of huffing and puffing, and where the strength and ease of charge flipping
becomes apparent. The case in question is the high temperature polymorph of
Zn3 xSb2.4 The published structure of this incommensurately modulated phase
contains six independent Sb positions and 18 Zn positions. Five of the Sb
positions are weakly modulated, while the sixth shows a large, sawtooth-like
displacement along the modulation direction. Only one of the Zn atoms shows
full occupancy, while the others exhibit more or less erratic occupational
behaviour. Solution and refinement of this structure was difficult because
although a correct initial phasing was soon found, there was little progress in
terms of refinement R-values, the obvious reason for this being the non-
harmonic behaviour of the strongly modulated atomic positions. A reasonable
fit was first achieved only when all pertinent positions were treated with
Complexity: In the Eye of the Beholder 253
non-harmonic modulation functions, i.e. step functions and sawtooth-like dis-
placements. The cause for all this anharmonicity is the peculiar nature of the
compound: the Sb atoms form a rather rigid sub-lattice of icosahedra interpen-
etrating along the a-axis (Figure 1). This leads to three distinct Sb–Sb distances,
vertex-to-vertex, vertex-to-centre and centre-to-centre. While the vertex-to-cen-
tre distances are not too different from the vertex-to-vertex distances, the centre-
to-centre distances are significantly different. In fact, while vertex-to-vertex
distances are typical for Sb3 –Sb3 contacts, the centre-to-centre distances are
closer to, albeit a little longer than, those expected for Sb42 . This inherent
frustration in the structure is resolved by alternating short Sb42 units and lone
Sb3 , the proportion being given by the ratio between their ideal distances and
the geometrical constraints of the icosahedral arrangement. This is the cause of
the non-stoichiometry of the compound. It is also the cause of the modulation.
What complicates matters is that the positions of the Zn atoms are at the centres
of the tetrahedral interstices of the Sb sub-lattice. The occupancy follows the

Figure 1 Part of the Sb network in ht-Sb2Zn3 x. Note how Sb positions in the centre
of the column of pentagonal antiprisms (grey spheres) alternate between
exhibiting long distances corresponding to Sb3 and short distances corre-
sponding to Sb42 units.

70

60

50
Residua

40

30

20

10

0
1 11 21 31 41 51 61 71 81 91 101
Iterations

Figure 2 Convergence of charge flipping for the structural solution of Sb2Zn3 x.

254 Chapter 15
(a)
2.0
x3=0.543,
x2=0.747
x4

1.6

1.2

0.8

0.4

0.0
-0.40
-0.20
0.00
(b) 0.20 x1
2.0 0.40
x3=0.042, x2
=0.748
x4

1.6

1.2

0.8

0.4

0.0
-0.40
-0.20
0.00
0.20 x1
0.40

Figure 3 Electron density map of the strongly modulated Sb position. (a) Density
from published model (sawtooth modulation indicated in red). (b) Density
obtained from charge flipping.
Complexity: In the Eye of the Beholder 255
(a)
2.0
x3=0.847,x
2=0.503
x4

1.6

1.2

0.8

0.4

0.0
-0.20
0.00
(b) 0.20
0.40 x1
2.0
x3=0.651, x2=0
.494
x4

1.6

1.2

0.8

0.4

0.0
-0.20
0.00
0.20
0.40 x1
2
Figure 4 Electron density map of the position Zn . (a) Density from published model
(sawtooth modulation indicated in red). (b) Density from charge flipping.
256 Chapter 15
(a)
2.0
x3=0.308, x2=0
.903
x4

1.6

1.2

0.8

0.4

0.0
-0.20
0.00
(b) 0.20
2.0 0.40 x1
x3=0.193,x2=
0.097
x4

1.6

1.2

0.8

0.4

0.0
-0.20
0.00
0.20
0.40 x1

Figure 5 Electron density map of the position Zn3. (a) Density from published model
(sawtooth modulation indicated in red). (b) Density from charge flipping.
Complexity: In the Eye of the Beholder 257
normal rule that face-sharing tetrahedral interstices cannot be occupied simul-
taneously, and further, Sb-tetrahedra that contain the short Sb–Sb contact from
the Sb42 unit as an edge are too small to host an interstitial Zn. The result is a
Zn occupancy that is erratically jumping from one interstitial position to
another in a fashion that is rather difficult to model. Incomplete models lead
to high residual electron densities, high R-values, and doubts in the mind of the
crystallographer that the solution is correct.
I recently attempted a de novo solution of the structure from charge flipping
using the software ‘‘Superflip’’ developed by Lukas Palatinus.5 Convergence of
the procedure was reached after about 80 cycles (Figure 2) and the solution
from charge flipping is quite complete: the six Sb atoms are clearly distin-
guished from the Zn positions, and one of the Sb atoms shows the expected,
strongly modulated behaviour (Figure 3). For Zn, 13 positions are found in the
initial search of the electron density map. More importantly, the occupational
modulations are clearly evident for all Zn positions. Examples are given in
Figures 4 and 5. This is very valuable information since the solution is model
independent. No prejudice concerning the occupational modulation will affect
the electron density. A comparison between the electron density for a few of the
atomic positions in the two models clearly shows that they are very similar, not
only in general, but in detail, and thus that, charge flipping can yield not only
qualitatively correct solutions, but quantitative agreement, even for complex
cases.

3 Conclusion
I hope I have been able to convey the advantages of charge flipping for
incommensurate structure analysis. It should however be pointed out that
the method is very generally applicable, and that my experience is that it may be
successfully applied to many cases where other methods fail. The simplicity of
the method and the ease of use of software available in the public domain will
certainly make this new tool widespread and appreciated. My only concern is
that the frontiers of complexity are bound to move again, leaving most of my
work in the despised area of simplicity.

References
1. P.M. De Wolff, Acta Crystallogr., 1972, A28, S101.
2. V. Petricek, M. Dusek and L. Palatinus, Jana2000 Institute of Physics,
Academy of Sciences of the Czech Republic, Praha, 2005.
3. G. Oszlanyi and A. Suto, Acta Crystallogr., 2004, A60, 134.
4. M. Bostrom and S. Lidin, J. Alloys Compd., 2004, 376, 49.
5. L. Palatinus and G. Chapuis, Superflip – computer program for solution of
crystal structures by charge flipping in arbitrary dimensions, 2006, http:/
superspace.epfl.ch/superflip.
CHAPTER 16

Synthesis and Characterization

of Zn-T-Sites in Mazzite
DAVID E. W. VAUGHAN,a INGRID J. PICKERING,b
GRAHAM N. GEORGEb AND
JEFFREY R. SHALLENBERGERa
a
Materials Research Institute, Pennsylvania State University, University
Park, PA 16802, USA; b Department of Geological Sciences, University of
Saskatchewen, 114 Science Place, Saskatoon, SK, Canada, S7N 5E2

1 Introduction
The substitution of divalent metal ions into zeolite framework tetrahedral
positions (T-sites) is well established in ALPO zeolites,1 and several zincosilicate
zeolites2–4 are known, including Zn-‘‘silicalite’’ (MFI).5 Reports of zinc substi-
tutions into aluminosilicate zeolites are relatively rare and are mainly reported in
the patent literature. Vaughan and Strohmaier prepared Zn-aluminosilicate
mazzite (MAZ)6 and Linde-L (LTL)7 and Araya and Creeth8 made faujasite
(FAU-X,Y), offretite (OFF) and gismondine (GIS). The latter authors also
substituted zinc into these frameworks by secondary synthesis. Zn-divalent
cation substitution increases the charge density of the framework, and hence
the cation exchange capacity of the zeolite, and provides for a more reactive
T-site. The former property can be used to improve the sorption or catalytic
selectivity of the zeolite, as demonstrated for improved O2/N2 separation using
Zn substituted low ratio FAU.9 The latter property facilitates the creation of
reactive framework metal sites, the extraction of which by mild acid treatments
can create lattice vacancies. These lattice ‘‘hydroxyl nests’’ can be filled with Si to
produce higher stability, moderate acidity, higher Si/Al ratio zeolites. When Fe,
Ni or Zn are the substituents, the zeolite will scavenge sulfur containing
molecules (H2S, COS, mercaptans, etc.) providing useful materials for pollution
abatement and gas purifications.
In addition to expanding the compositional range, interest in such Zn-
T-atom substitutions in the MAZ structure10 was stimulated by the possibility

258
Synthesis and Characterization of Zn-T-Sites in Mazzite 259

Figure 1 Comparison of the MAZ and the theoretical ‘‘omega’’ structure.

that they may initiate the crystallization of the closely related theoretical
structure ‘‘omega’’ proposed by Barrer and Villiger,11 shown in Figure 1. Both
structures are built from identical columns of gmelinite cages linked through
common 6-rings, but in MAZ the columns are related by a 63 rotation rather
than the normal 6 rotation in ‘‘omega.’’ The two structures have similar
theoretical powder X-ray diffraction patterns (PXRD), ‘‘omega’’ being differ-
entiated by additional weak peaks at 11.651 (001) and 22.801 (221) 2y. These
peaks were not observed in PXRD patterns of our samples. MAZ is one of
several stable 12-ring channel zeolites of interest in catalysis,12–14 an interest
strengthened by the commercialization of the LTL zeolite for the conversion of
paraffins to aromatics.15,16
A major problem in studies of this kind is the issue of differentiating between
cations in the framework and interstitial cations in exchange sites. Ion exchange
with other cations may remove some exchangeable Zn21 but the possibility of
cations located in ‘‘locked-in’’ sites (small cages or prisms) complicates the
differentiation. More than one T-site and three T-atoms further complicate the
MAZ characterization, particularly for NMR analyses. Ristic et al.17 charac-
terized Zn-APO-50 (AFY) using Rietveld analysis of PXRD, 31P-NMR data,
and extended X-ray absorption fine structure (EXAFS)18 but failed to locate
extra-framework ions. Hunsicker et al.19 used X-ray photoelectron spectro-
scopy (XPS) to characterize Zn-aluminosilicate FAU with Si/(Al+Zn) frame-
work ratios near unity, indicating that zinc is distributed between cation and
framework sites.

2 Experimental
2.1 Sample Preparation
Two Zn-aluminosilicate MAZ samples and a non-Zn conventional alumino-
silicate MAZ were synthesized using the general methods described for the
synthesis of transition metal containing MAZ (ECR-22D)5,20, using the tetra-
methylammonium (TMA) cation as the template. Attempts to make Zn-MAZ
with other templates known to promote the crystallization of MAZ in the
260 Chapter 16
absence of Zn (choline, bis-dihydroxydiethyl-dimethylammonium22) also
21

co-crystallized FAU, SOD and GIS.

Maz-1 was made from a gel having a Si/(Al+Zn) ratio of 4.44 and a
composition: 0.95 TMA2O: 4.9 Na2O: Al2O3: 1.6 ZnO: 16 SiO2: 238 H2O:
(3.2 NaNO3: 0.5 Na2SO4). (This is similar to Example 2 of Ref. 5, but replacing
NiCl2 with the same moles of Zn(NO3)2.) The gel was made by mixing 25 g of
25% TMAOH (SACHEM) with 130.6 g of N-Sil sodium silicate (PQ Corp.),
followed by 10.4 g of ‘‘seed solution,’’23 24.6 g of Na-aluminate solution (15.5%
Al2O3, 14% Na2O), 17.84 g of Zn(NO3)2
6H2O dissolved in 15.5 g H2O, and 4 g
of aluminum sulfate (17H2O ) dissolved in 6 g H2O. After thorough mixing in a
blender, a 30 g sample was placed in a 45 ml Parr Teflon lined ‘‘acid-digestion
bomb’’ and reacted for 15 h at 140 1C. The MAZ product was filtered, washed
on a vacuum filter and dried at 110 1C. The product comprised very thin lath-
like crystals (Figure 2) and chemical analysis gave an oxide composition: 0.182
TMA2O: 1.33 Na2O: Al2O3: 0.546 ZnO: 6.43 SiO2. (The TMA value was
derived from the TGA weight loss between 500 1C and 600 1C.) The Si/
(Al + Zn) ratio was 2.53; assuming that all the Zn21 is in the framework, this
represents a T-site occupancy of 6%. Additional samples run in 125 ml Teflon
bottles at 100 1C yielded MAZ samples after 3 and 5 days. Maz-2 was made
from a gel having a Si/(Al + Zn) ratio of 6.14 and a composition: 0.45 TMA2O:
5.75 Na2O: Al2O3: 0.16 ZnO: 13.27 SiO2: 314 H2O. The gel was made by mixing
79.2 g of N-Sil with 4 g of TMABr dissolved in 10 g of H2O, 1 g of seeds, 20 g of
sodium aluminate solution (14.5% Al2O3, 14.2% Na2O), and 1.32 g of
ZnSO4
7H2O dissolved in 15 g of H2O. Fifteen grams of this gel were
reacted in a 23 ml Parr ‘‘bomb’’ for 90 h at 140 1C, followed by vacuum filtration

Figure 2 SEM images of Maz-1 (left); Maz-2 (right). Bar ¼ 1 mm.

Synthesis and Characterization of Zn-T-Sites in Mazzite 261
and washing with H2O. The MAZ product comprised thin lath-like crystals
(Figure 2) with a composition: (0.185 TMA2O): 0.97 Na2O: Al2O3: 0.175 ZnO:
6.63 SiO2. (The TMA value was derived from the TGA weight loss between
450 1C and 600 1C.) The Si/(Al + Zn) ratio was 3.05, representing a Zn-T-site
occupancy of 2%. An identical 87 h experiment gave a similar high purity MAZ
product. Experiments run at 100 1C were contaminated with GIS.
Maz-3 is a nano-crystal aluminosilicate Na,TMA-MAZ made using the
method described in detail elsewhere.24 The analyzed Si/Al ratio was 2.68.
Zn-montmorillonite was made by first forming a gel by diluting 15 g of HS-40
colloidal silica with 5 g of de-ionized water, mixing in a solution of 0.68 g
NaOH dissolved in 8 g de-ionized water, followed by 5.64 g of NaNO3 and
9.94 g of Zn(NO3)2
6H2O dissolved in 20 g de-ionized water, giving a compo-
sition: SiO2: 0.36 ZnO: 0.34 Na2O: 20H2O. Ten grams of this gel were reacted in
a 23 ml Parr ‘‘bomb’’ at 175 1C for 23 days, at which time PXRD and scanning
electron microscopy (SEM) showed the product to be excellent montmorillo-
nite but of very small crystal size (very similar to the commercial synthetic
Laporte Laponiter montmorillonite). This was used as a standard for octahe-
dral Zn21 in the XPS experiments. When the zinc nitrate was replaced with the
corresponding sulfate, willemite (Zn2SiO4)25 was the main product together
with minor montmorillonite.

2.2 Analytical Procedures

All samples were evaluated by PXRD using a Siemens D500 diffractometer
(y/y, CuKa radiation, Bragg–Brentano geometry, MDI Jade 7 software).
Elemental analysis was by ICP-AES after fusing the zeolites at 1050 1C in a
solid mixture of 90% lithium tetraborate and 10% lithium carbonate, followed
by dissolution in dilute nitric acid. SEM images were obtained on a Hitachi
S3500-N SEM after coating the samples with gold. Thermogravimetric analyses
(TGA) were carried out in air from 25 1C to 1000 1C at 10 1C min-1 on a
Thermo-Electron 2050 instrument.
X-ray absorption spectroscopy was carried out on Beamline 7-3 at the
Stanford Synchrotron Radiation Laboratory with the SPEAR storage ring at
3 GeV and 70–100 mA. The beamline configuration consisted of a double
crystal monochromator with Si(220) crystals, an upstream vertical aperture
of 1 mm, and no focusing optics. Harmonic rejection was achieved by detuning
one monochromator crystal to 50% off peak. Mazzite samples were packed
neat into a 1 mm path length plate with Mylar tape for windows. Measurements
were made in transmission with N2-filled ion chambers and the sample was held
at approximately 15 K in a liquid helium flow cryostat. The spectrum of a zinc
foil was collected simultaneously with that of each sample; the first energy
inflection of the foil was assumed to be 9660.7 eV. Data collection was carried
out using the program XAS_COLLECT.26
Data analysis used the program suite EXAFSPAK (http://ssrl.slac.stanford.
edu/exafspak.html). The EXAFS spectra were analyzed using full multiple
262 Chapter 16
scattering phase and amplitude functions calculated using the program
FEFF7.27,28 Coordinates were taken from the crystal structure for MAZ10 with
the coordinates of the first shell oxygens adjusted radially to give the ZnO
distance of 1.94 Å observed in preliminary fits. The scale factor was refined
according to coordination numbers of 6 for aqueous zinc sulfate,29 and fixed at
1.32. The nominal threshold value, E0, was fixed at 9680 eV and then a correction
to the threshold value DE0 was initially refined to be 10.4 eV and fixed thereafter.
Paths were examined for significance and three single scattering paths (ZnO,
Zn


Si (next nearest neighbour) and Zn


Si4R (across the 4-ring) were kept
together with the triangular path ZnOSi


Zn. The 4-leg ZnOSiOZn
path was considerably lower in amplitude and was not significant. In all of the
refinements the degeneracy of the 3-leg path was constrained to be twice that of
the 3.2 Å Zn


Si path and their Debye–Waller factors (measures of static and
thermal disorder) were constrained to be the same. In order for the best compar-
ison, the Debye–Waller factors of the outer shells were refined for sample Maz-1
and then these values were copied and fixed for the other sample. In both cases the
coordination numbers and interatomic distances were refined.
XPS was performed on a Kratos Analytical Axis Ultra instrument utilizing
monochromatic Al Ka X-rays (hn ¼ 1486.6 eV). The binding energy was cali-
brated using sputter cleaned copper (932.7 eV) and gold (84.0 eV) foils. The
samples were dusted onto 3Mt double sided adhesive tape. Sample charging
was controlled through the use of a low energy electron flood gun.
Choosing a reference peak to charge reference to is difficult in these speci-
mens. The carbon peak is the typical choice, although some specimens dis-
played evidence of two hydrocarbon peaks being present at different potentials.
Most likely these are due to hydrocarbons from the tape and TMA trapped
within the gmelinite cages of the MAZ. (It is also possible, but rare, for TMA to
occupy both channel and cage sites.) Charge correction was done by shifting
the silicate peak to 103.38 eV.19 The presence of Na and Zn are expected to
lower the Si 2p binding energy, so attention was paid to absolute differences in
peak positions which are unaffected by the choice of charge reference.
The elemental compositions were determined by applying relative sensitivity
factors to the integrated peak areas after subtracting linear backgrounds. All
measurements were performed at a takeoff angle of 901 with respect to the
sample surface plane.

3 Results and Discussion

For all the Zn21 to be in framework T-sites, Na1 and TMA1 cations must
balance the MAZ framework charge deficiency. As (Na + TMA) ¼ (Al + 2Zn)
(approximately) in both Zn-MAZ samples, Zn must be located almost com-
pletely in framework sites. The morphologies of both Zn-MAZ samples (Figure
2) were unusual in that they formed very thin (o20 nm) and narrow (100–
200 nm) lath-like crystals. We cannot ascribe this to the presence of zinc as the
zinc-free Maz-3 sample had identical morphology to Maz-2. Sulfate is an
Synthesis and Characterization of Zn-T-Sites in Mazzite 263

Figure 3 Powder X-ray diffraction patterns of Zn-aluminosilicate Maz-1 and Maz-2

compared to the nano-crystal aluminosilicate Maz-3 sample.

unlikely cause as previous numerous aluminosilicate MAZ syntheses in the

presence of sulfate24 produced agglomerates of bundled larger needles or rods,
similar to those observed by others.30 Similarly, nitrate, used in the Maz-1
synthesis but not the Maz-2 and -3 preparations, cannot be the cause. The small
crystal dimensions are reflected in the X-ray diffraction pattern peak broadening
shown in Figure 3. Indexing of the PXRD patterns gave unit cell values
(hexagonal, P63/mmc (#194)) for Maz-1, a ¼ 18.240 Å, c ¼ 7.672 Å,
V ¼ 2210.7 Å3; Maz-2, a ¼ 18.253 Å, c ¼ 7.661 Å, V ¼ 2210.4 Å3; Maz-3,
a ¼ 18.233 Å, c ¼ 7.664 Å, V ¼ 2206.7 Å3. The unit cell similarities, despite the
inclusion of Zn in T-sites in samples Maz-1 and -2, reflects the flexibility of the
framework; the longer Zn–O bond length being compensated by changes in bond
angles, confirmed by the EXAFS results.
The Maz-1 and -2 TGA analyses are similar (Figure 4) and show a peak at
B120 1C indicative of water loss from surfaces of these thin crystals, a second
peak at B200 1C representing water loss from the 12-ring channel, and a third
peak at B600 1C indicative of burn-off of the TMA template trapped in the
gmelinite cages. The lack of a peak between 350 1C and 500 1C, characteristic of
de-hydroxylation of T-site species, suggests the absence of octahedral or
pentahedral hydroxylated Zn in T-sites. The total weight loss is 16% wt.
Zinc K near-edge spectra of the two preparations of Zn-MAZ (Maz-1 and -2)
are shown in Figure 5 compared with dilute zinc sulfate. The Zn-MAZ spectra
are shown to closely resemble each other, and to differ substantially from that
of the Zn21 solution, which is hex-aqua. The Zn K-edge EXAFS spectra,
264 Chapter 16

0.1 100
0.09
Deriv. Weight (%/°C)

0.08
0.07 Deriv. Weight

Weight (%)
0.06
0.05 TGA 90
0.04
0.03
0.02
0.01
0 80
0 100 200 300 400 500 600 700 800 900 1000
Temperature (°C)

Figure 4 Thermogravimetric analysis of the Maz-2 sample.

Figure 5 Zinc K X-ray absorption near-edge spectra of aqueous zinc sulfate solution
and zinc MAZ samples.

together with the corresponding Fourier transforms, are shown in Figure 6 for
the Zn-MAZ samples. The Fourier transforms are dominated by first shell
interactions at around 2.0 Å but also show some backscattering at 3–3.5 Å and
a smaller peak just above 4 Å.
The results of multiple scattering fit analyses of the EXAFS are shown in
Table 1 and Figure 6. There are no significant differences between the EXAFS
fits of the two different Zn-MAZ samples (Table 1); in all cases the values
obtained for a given parameter are within 3 e.s.d.s of each other. The first shell
fits well in all cases to 4 ZnO at 1.94–1.95 Å, in exact agreement with the
EXAFS data of Araya and Creeth8, who also made Zn-aluminosilicate FAU,
and the average Zn–O bond length found by Rietveld analysis of PXRD data
Synthesis and Characterization of Zn-T-Sites in Mazzite 265

Figure 6 Zn K-edge EXAFS (a) and corresponding Fourier transforms (b) for zinc in
Maz-1 and Maz-2 samples. The Fourier transforms have been phase-
corrected for first shell Zn–O. Data are shown as solid lines and the best
fit as a dashed line. The parameters determined by the best fit are shown in
Table 1.

Table 1 Results of EXAFS curve-fitting of Zn-MAZ samples.a

Maz-1 Maz-2
ZnO N 3.9(2) 4.1(3)
R 1.944(2) 1.935(3)
s2 0.0052(3) 0.0055(5)
Zn


Si N 3.5(1.2) 5.3(1.0)
R 3.175(8) 3.182(8)
s2 0.011(2) 0.011d
ZnOSi


Znb R 3.40(2) 3.37(2)
Zn


Si4Rc N 1.4(9) 1.6(8)
R 4.41(2) 4.40(3)
s2 0.006(4) 0.006d
a
Coordination numbers, N, interatomic distances, R (Å) and Debye–Waller factors, s2 (Å2). Three
times the estimated standard deviation in the last digit(s) is shown in parentheses after the value,
and is equivalent to the 99% confidence limit. This value is a measure of the precision of the fit.
The value of the accuracy is in general somewhat higher than the precision and is typically 20%
for N and 0.02 Å for R.
b
For this shell, N, which in this case is the path degeneracy, is twice that of Zn


Si and s2 is
constrained to an identical value to that of Zn


Si.
c
Interaction across the four-ring.
d
For Maz-2 these values were held constant at the values obtained for Maz-1.

for Zn-phosphate-FAU.31 A search of the Cambridge Crystallographic data-

base for zinc coordinated by 4, 5 and 6 oxygens yielded mean interatomic
distances of 1.96  0.03, 2.04  0.02 and 2.10  0.02 Å, respectively, further
confirming the assignment of 4-coordinate zinc. The second shell at 3–3.5 Å was
modeled as a combination of a 2-leg Zn


Si path and the 3-leg ZnOSi


Zn
path (having twice the degeneracy of the 2-leg path). The distances of these two
paths were allowed to independently float in the fits. Combining the ZnO and
266 Chapter 16
Zn


Si observed distances, together with an idealized value of 1.60 Å for the
SiO distance, a 3-leg path length of 3.36 Å is obtained, in very good agree-
ment with the refined values of 3.40 and 3.37 Å (Table 1). The same 2-leg
distances yield a mean ZnOSi angle of 1271, much more acute than the
average angle of 1501 obtained from the MAZ crystal structure of Galli10 using
a similar approach. Presumably this is due to the substitution of the substan-
tially bigger Zn21 cation for the Al31 (typical Al–O bond length of 1.74 Å), a
relative expansion of 11.5%, while the Zn


Si distance only expands 1.4% over
the crystal structure mean distance of 3.13 Å. The third shell fits to a Zn


Si4R
interaction at 4.40–4.43 Å and is essentially identical to the mean distance
across a 4-ring in the MAZ structure.
The core level photoemission spectra are shown in Figure 7 and the data are
summarized in Tables 2 and 3 along with the comparable FAU data from
Hunsicker et al.,19 who compared Zn21 in a zinc exchanged aluminosilicate
FAU (cationic, Table 2) with a directly synthesized Zn-aluminosilicate FAU
(tet) together with a sample of the latter post-treated with an alkali zinc oxide
solution (mix). The octahedrally coordinated Zn montmorillonite reference
material has lower Zn 2p3/2 and Zn 3d binding energies compared with the
MAZ samples and the Hunsicker cationic, tetrahedral and mixed coordination
samples. The Maz-1 Zn peak positions are consistent with the tetrahedral FAU
(tet) sample previously reported by Hunsicker. Maz-2 has a broader Zn 2p3/2
peak and is centred at a lower binding energy, between that for Maz-1 and the

6×104

Zn-montomorillonite
BE⫽1022.03 eV
5×104 FWHM⫽1.65 eV
Counts per sec

4×104
MAZ-2
BE⫽1022.23 eV
FWHM⫽2.04 eV
MAZ-1
3×104 BE⫽1022.58 eV
FWHM⫽1.88 eV

2×104

1028 1026 1024 1022 1020 1018

Binding energy (eV)

Figure 7 Zn core level photoemission spectra.

Synthesis and Characterization of Zn-T-Sites in Mazzite 267
Table 2 Core level photoemission data for Maz-1 and Maz-2 compared to
published work.
Maz-2 Maz-1 Zn-montmorillonite Cationic Tet Mix
From Ref. 19

Zn 2p3/2 1022.23 1022.58 1022.03 1023.68 1022.62 1022.93

Zn 3d – 11.5 11.04 12.56 11.47 11.67
Zn 2p3/2 1011.08 1010.99 1011.12 1011.15 1011.26
–Zn 3d
Si 2p 103.38 103.38 103.38 103.38 103.38
Al 2p 74.98 75.08 73.78 74.99 75.11 75.32
Zn 2p3/2 FWHM (eV)
2.04 1.88 1.65 1.85 1.8 1.84

Table 3 XPS chemical analyses for Zn-MAZ samples (in atom%).

Maz-2 Maz-1 Cationic Tet Mix
From Ref. 19

Na 6.1 7.5 4.6 9.4 10.6

Zn 0.4 1.9 1.2 1.4 3.7
O 55.9 54.3 54.2 54.8 51.6
C 14.4 14.7 11.3 7.3 10.3
Si 17.6 17.1 21 19.7 16.3
Al 5.7 4.6 7.7 7.4 7.5
Si/(Al + Zn) 2.89 2.63 2.34 2.24 1.47

Zn-montmorillonite, possibly indicating some Zn21 hydroxylated framework

or cation component. The XPS compositional data are quite different to the
compositions obtained by bulk chemical analysis (ICP-AES); for Maz-1 Na, Zn
and Si values are all high compared to Al, and for Maz-2 Na is high and Zn and
Si values are low. The inconsistencies are reflected in the XPS Si/(Al+Zn)
ratios; for Maz-1 it is 4% high and for Maz-2 it is 5% low.

4 Conclusions
The combined analyses are in broad agreement that zinc is incorporated into
framework tetrahedral sites but are somewhat in conflict for the low zinc
containing sample as to the extent of incorporation. This may be due to the
surface sensitivity of XPS, in contrast to the bulk sensitivity of EXAFS and
chemical analysis. The bulk chemical analysis and EXAFS confirm that the zinc
in these samples is in the framework tetrahedral sites, although the T-site zinc
occupancies, assuming all the zinc is tetrahedral, are low (6% and 2%), as were
those reported by others.8,19 The Na1 and TMA1 balance the net negative
charge on the framework derived from replacement of Si41 by Al31 and Zn21.
268 Chapter 16
The EXAFS data show that the longer Zn–O bond length is compensated by a
more acute Zn–O–Si bond angle (1271 compared to 1501 for the aluminosilicate
Si–O–Al bond angle) and this is reflected in the similar unit cell values for the
zinc-aluminosilicates (Maz-1 and -2) and aluminosilicate (Maz-3) samples. The
XPS data for Zn are comparable to those obtained by Hunsicker et al.19 for Zn-
FAU, who noted that, depending on sample treatments, the Zn21 may be
distributed between framework and cation (or hydroxylated framework) sites.
These XPS data establish a mutual confirmation for tetrahedral Zn21 in the
two structures. Although these results demonstrate Zn in the T-sites, one notes
that in the case of lower Zn input (Maz-2) in the gel, all the Zn is incorporated
into the product, but in the higher Zn loading (Maz-1) only about 75% of the
Zn21 in the starting gel is incorporated into the product. This may indicate that
for aluminosilicate zeolites, toleration for Zn in T-sites is limited to low values,
B6% in the case of MAZ.

Acknowledgments
Two co-authors (DEWV and IJP) have had a long, stimulating and enjoyable
association with Sir John Meurig Thomas. DEWV first met him in 1963 in the
University Club (Penn State) ‘‘pool hall,’’ where he and another South Walian
regularly won free beers from the local pool cognoscente. John was also a
founding member of the Penn State Cricket Club. (That summer he also made a
classic film of the reactivity of transition metal particles and defects on graphite
oxidation.) Our friendship continued after we both returned to the UK, and
our common interest in what are now called nano-materials, and catalysis, was
strengthened by scientific collaborations, consulting and family friendships.
IJP, now a Canada Research Chair, earned her Ph.D. as his first graduate
student at the Royal Institution and expresses her heartfelt gratitude to him for
his guidance and tutelage during her formative years.
DEWV is supported in part by the Penn State Materials Research Institute
(PSMRI) and the Penn State MRSEC under NSF grant DMR 0213623. GNG
and IJP are supported by the Canada Research Chairs program, the Province
of Saskatchewan and NSERC Canada. Portions of this research were carried
out at the Stanford Synchrotron Radiation Laboratory, a national user facility
operated by Stanford University on behalf of the U.S. Department of Energy,
Office of Basic Energy Sciences. The SSRL Structural Molecular Biology
Program is supported by the Department of Energy, Office of Biological and
Environmental Research, and by the National Institutes of Health, National
Centre for Research Resources, Biomedical Technology Program. We thank
Dr Maria Klimkiewicz (PSMRI) for the SEM images.

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CHAPTER 17

Anything Protons Do, Muons

Do Better!
E. A. DAVIS
Department of Materials Science and Metallurgy, University of Cambridge,
Pembroke Street, Cambridge, CB2 3QZ, UK

1 Introduction
The simulation of hydrogen by positive muons has proved to be extremely
valuable in the identification of potential sites for hydrogen in semiconductors
and insulators. Although the muon has a mass one-ninth that of the proton, its
interaction with the host lattice, both electronically and chemically, is virtually
identical to that of a proton. During its 2.2 ms lifetime (experiments are
frequently undertaken over a timescale of up to 10 lifetimes), the muon can
diffuse, interact with, and adopt positions in the lattice that protons themselves
would occupy. If the temperature is sufficiently low, muons can capture
electrons to form muonium (Mu ¼ m1+e
) – effectively a light isotope of
hydrogen.
The reduced mass of muonium is within 5% of that of hydrogen and so its
Bohr radius and ionization energy are essentially the same as those of hydro-
gen. Just as for donors or acceptors in doped semiconductors, the ionization
energies of hydrogen or muonium incorporated into materials with a high
relative permittivity are reduced from their vacuum-state value of 13.6 eV –
sometimes by several orders of magnitude, leading to extended ground-state
wave functions or orbitals. Confirmation of shallow states associated with
muonium in several II–VI semiconductors, in at least one III–V, and in several
large-bandgap oxides, has recently been obtained from muon spin rotation
experiments. Prior to these discoveries, it had been assumed that the electronic
states associated with muonium implanted into semiconductors always lay deep
in the energy gap of the host material. The breakthrough came after judicious
recognition of a beating in the spin precession signal corresponding to transi-
tions between muonium levels whose degeneracy is split in a magnetic field. A

271
272 Chapter 17
Fourier transform of the raw data revealed line spectra from which a hyperfine
constant could be extracted.
The relevance of this work to the semiconductor community – including
those interested in commercial development of devices – is the need to under-
stand the behaviour of hydrogen in semiconductors. Whether added inten-
tionally (for example, to activate or passivate dopants) or incorporated
unavoidably perhaps during processing, the role played by hydrogen is always
significant but not easy to predict or determine. This applies not only to its
atomic position in the host lattice but also to the location of its associated
electronic states in the energy gap. Muonium spectroscopy has been particu-
larly successful in answering both these questions for many semiconductors.
Another field to which such studies contribute is that of the choice of new
materials for gate dielectrics. Silicon dioxide, the traditional insulator used for
this purpose, is facing limitations in new applications, for example, those
involving ‘flexible electronics’. Insulators with large band gaps and high
relative permittivities are being sought from new families of oxides. If hydrogen
forms shallow donor centres in any of these, this fact alone makes them
unsuitable candidates. Already it has been demonstrated that muonium (and
by implication hydrogen) forms a shallow donor level in ZnO and many other
oxides.
There are several reasons for the success of the muon experiments over
similar attempts using hydrogen itself. One of these is the extraordinary
sensitivity of the techniques available, by which one can essentially ‘see’
individual muons implanted one at a time. In contrast, in order to be visible,
hydrogen has to be incorporated in relatively large concentrations, leading to
problems associated with solubility, interactions, chemical reactions, etc. An-
other and more fundamental aspect is that hydrogen frequently forms what is
known as ‘a negative-U system’, which means in essence that neutral states of
hydrogen dissociate into positively and negatively charged states, making the
neutral state inaccessible under thermal equilibrium conditions. Such condi-
tions do not apply in the muon experiments, a situation that permits observa-
tion of both the ionized (charged) and unionized (neutral) states.

2 Experimental Techniques
The majority of experiments have been undertaken using the ISIS pulsed muon
source at the Rutherford Appleton Laboratory, UK (see Figure 1), or the
TRIUMF continuous source in Vancouver, Canada. Muons are produced from
the decay of pions, these being generated when a target of graphite or other
light element is bombarded with high-energy protons from an accelerator. The
muons have an initial energy B4 MeV and are 100% spin polarized. This
polarization is retained during their thermalization within a sample and it is the
subsequent evolution of this with time that forms the basis of muon spin
relaxation or muon spin rotation experiments. The technique of transverse-field
spin rotation involves applying a magnetic field perpendicular to the direction
Anything Protons Do, Muons Do Better! 273

Figure 1 Muon beam lines at the Rutherford Appleton Laboratory (courtesy of the
Rutherford Appleton Laboratory).

of the incoming beam of muons (transverse to their spin) and monitoring the
resulting precession signal via the emission of positrons that are emitted
preferentially in the direction of the spin at the moment of the muon’s
radioactive decay. For bare muons this is simply the Larmor frequency but
for muonium several frequencies are observed. The resulting spectra can be
analysed to determine the components of the hyperfine coupling constant
between electron and muon, and to infer the nature of the trapping sites for
muonium in the lattice.
In order to illustrate the kind of information that can be obtained using the
techniques of muon spectroscopy as applied to semiconductors, two examples
will be described in some detail. The first is silicon, a material in which the
electronic levels associated with muonium (and by inference, hydrogen) lie deep
in the gap but for which there are two distinct sites. The second is zinc oxide in
which the levels are shallow.
274 Chapter 17

3 Deep Centres: Silicon

Early transverse-field muon spin rotation experiments on crystalline silicon at
low temperatures1 revealed evidence for the existence of two paramagnetic
sites for the neutral state of muonium Mu0 (see Figure 2). The first is identified
by a pair of lines whose splitting yields a hyperfine coupling constant (between
the muon and its bound electron) that is approximately half the value for
vacuum-state muonium or muonium in SiO2. These lines, labelled MuT0 in
Figure 2, are associated with muonium in a site (T) that has tetrahedral
symmetry, namely the open cages in the silicon structure. The reduced hyper-
fine constant results from the electron spending some of its time on the
surrounding atoms. Rapid diffusion of this centre between equivalent sites is
inferred from the linewidths. The second site, characterized by a pair of lines at
lower frequencies (see Figure 2), has axial symmetry along the o1114 direc-
tions and has been identified2–4 as a bond-centred (BC) site, Mu0BC. For this
centre the isotropic component of the hyperfine tensor (the contact term) is
small, the electron wave function having a node at the muon and maximum
amplitude on the silicon antibonding orbitals.5 The silicon atoms relax out-
wards by more than 20% of the bond length to accommodate the muon.
Finally, we see in Figure 2 a signal labelled m1 associated with bare muons that
have not formed muonium.

Figure 2 (a) Muon spin rotation spectra from Si at 77 K compared with that of fused
quartz (SiO2) at room temperature in a magnetic field of 100 gauss. The pairs
of lines at high frequency arise from muonium in a tetrahedral cage site. The
splitting of these lines reflects (inversely) the magnitude of the hyperfine
coupling constant, which has a value close to that of vacuum-state muonium
or muonium in quartz, but is approximately half as large in silicon. The pair
of lines at 40–50 MHz (for Si only) is associated with bond-centred muonium.
The very-low-frequency lines correspond to diamagnetic muonium. (b) Sites
associated with muonium in the silicon lattice (from Refs. 1 and 26).
Anything Protons Do, Muons Do Better! 275

Figure 3 (a) Configurational-coordinate diagram for muonium states in Si. (b)

Electronic energy levels associated with muonium in the T and BC sites
(from Ref. 6).

As the temperature is raised, both Mu0T and Mu0BC ionize above about 230 K
and 130 K respectively with activation energies of a few tenths of an electron-
volt. Such measurements and related studies yield the depths of the levels
associated with these centres within the energy gap of silicon. An estimate of the
depth of the donor level associated with Mu0BC is 0.21 eV below the conduction
band edge6,7 – considerably deeper than those of typical shallow dopant levels.
This energy is denoted by E0/+ BC in Figure 3b. The energy to place a second
electron on the bond-centre site is likely to be high and the level associated with
Mu
BC is predicted to be in the conduction band. In contrast MuT can accom-
modate a second electron, yielding an acceptor level in the gap at a depth below
the conduction band edge denoted by E
/0 T in Figure 2b. Note that if, as shown,
the acceptor level lies below the donor level, the levels comprise a negative-U
system.
The schematic configurational-coordinate diagram illustrated in Figure 3a
has been proposed6 to account for experimental findings on the various charge
states and sites of muonium in silicon. It should be equally applicable to
hydrogen in silicon, apart from slight differences related to the higher zero-
point energy of muon. The solid curves represent states that are active in
intrinsic and p-type material – namely the neutral and positively charged states
of MuBC and the neutral state of MuT. The negatively charged state of Mu0T
(dotted curve) is observed in n-type silicon. The various possible charge and site
conversions that occur can be followed on this diagram. Note that e
c refers to
an electron at the bottom of the conduction band; addition to the curves of the
energy of one or two of these electrons permits easier comparison of ionization/
barrier energies.
276 Chapter 17
The ground state of the system is neutral muonium in the bond-centre site,
Mu0BC. Conversion to Mu0BC from the neutral tetrahedral (T) site, Mu0T,
involves surmounting a barrier of height B0.39 eV but with a net gain in
energy of B0.2–0.3 eV. The reverse process is therefore unfavourable. Mu0BC
can ionize to Mu+ BC by electron emission or hole capture, or it can capture an
electron (in n-type silicon) by surmounting a barrier of height B0.34 eV, in
which case a site change to Mu
T occurs and some of this energy is recovered.
Theoretical predictions8 concerning the location of isolated hydrogen in
semiconductors involve calculations of the total energy when it is located at
various high-symmetry sites. Most studies find the bond-centre location to be
the most stable. With regard to the charged states, H1 in the BC site is found to
be even more stable than H0, which is perhaps not surprising as the non-
bonding state in the gap is then empty. The positively charged BC state lies
more than 1 eV below that of the T site, the latter having a local maximum on
the total energy surface for H1. The situation for H
is the reverse of that for
H1: the T site is favoured over the BC site by about 0.5 eV. These predictions
are borne out by the muonium results.
The relative proportions of H in the various charge states under equilibrium
conditions can be determined by calculations of their formation energies with
respect to the Fermi level. It is found that H0 is not stable for any position of
the Fermi level. The variation in energy of H in the three charge states with
their position in the silicon lattice9 is shown in Figure 4. From these theoretical
results, one can see that H0 has a minimum at the BC site, H
at the T site, and
H1 at a site about half-way between the BC and P sites. The average of the H1
and H
minima lies below the minimum of H0, meaning that the reaction

Figure 4 Calculated variation of the energies of the three charge states with position
between the BC and T sites for optimally relaxed Si atom positions. For H0
and H1 the energies include those of one or two electrons, respectively, at
the bottom of the conduction band (from Ref. 9).
Anything Protons Do, Muons Do Better! 277
2H - H +H is exothermic. A consequence of this negative-U situation for
0 1

H in Si is that the neutral state cannot be observed experimentally without

departure from equilibrium conditions, requiring, for example, illumination of
the sample. Muon studies do not have this limitation, the various sites being
populated in accordance with the kinetics of the implantation process.

4 Shallow Centre: ZnO

ZnO is a semiconductor that is invariably found to have n-type conductivity. The
theoretical prediction10 that this could arise from hydrogen impurity acting as a
shallow donor state was quickly confirmed by muon implantation studies11,12.
Below 40 K, a distinctive beating of the muon precession signal provides the
required signature (Figure 5a). In the case of a small hyperfine constant, one
can easily reach the so-called Paschen–Back regime in moderate field. Then a
triplet of lines is seen in a Fourier transform of the raw data, the central one of
which corresponds to the bare muon (Figure 5b). The separation of the two
satellite lines provides a direct measure of the hyperfine coupling constant
between the muon and the electron. For ZnO this is 500  20 kHz, which is
0.011% of the free-muonium value of 4463 MHz, immediately indicating a
small electron spin density at the site of the muon and an extended wave

Figure 5 Muonium spin precession signal for a ZnO powder sample at 5 K. The upper
plot (a) is the raw time-domain spectrum (corrected for the muon decay)
while the lower plot (b) is the corresponding frequency spectrum. The central
line corresponds to the Larmor frequency of the bare muon (ionized
muonium) and the two symmetrically disposed satellites are associated with
muonium. The dotted curve is a theoretical fit using a powder-pattern
lineshape. (From Refs. 11 and 27.)
278 Chapter 17
function associated with a shallow donor state. Additional measurements13 in
longitudinal magnetic fields have provided further evidence for these findings.
Studies of the temperature dependence of the lines reveal that, as the
temperature is raised, the central line increases in amplitude at the expense of
the satellites. This is to be expected for ionization of the donor state. Arrhenius
plots produce activation energies for the central (diamagnetic) line of B26 meV
and of the satellite (paramagnetic) lines of B33 meV. The results imply that
muonium in ZnO ionizes above B40 K with an activation energy of about
30  3 meV.
Investigations by others have yielded a variety of possible values for the
depth of hydrogen donors in ZnO. Hall effect studies14 have been analysed in
terms of the ionization of two donors having energies of 31 meV and 61 meV,
with the authors preferring to associate the lower of these two values with
hydrogen donors. Hofmann et al.15, as part of their ENDOR investigations,
also made Hall effect measurements and found two activation energies with
values 35 and 66 meV. Early photoluminescence data16 gave 52 meV as the
depth of a hydrogen donor. More recent photoluminescence studies17 suggest a
lower value of 40 meV.
Assuming for the sake of simplicity an isotropic centre, the effective Bohr
radius a* can be obtained directly from the hyperfine constant A*, since this
scales as the third power of the radius:

a ¼ a0 ðA0 =A Þ1=3

where A0 is the free-muonium hyperfine constant and a0 is the Bohr radius.
Taking A0 ¼ 4463 MHz and a0 ¼ 0.053 nm, we find a* ¼ 1.1 nm. This can be
compared with the value estimated from a ‘hydrogenic’ model:
a ¼ a0 eðme =m Þ
where e is the relative permittivity and m* the effective mass for electrons in
ZnO. Using the values e ¼ 8 and m*/me ¼ 0.24, gives a* ¼ 1.7 nm, in fair
agreement with the value deduced from the data.
In a similar vein we can estimate the ionization energy from the hyperfine
constant:

I  ¼ I0 ðA =A0 Þ1=3 =e

where I0 is the Rydberg ¼ 13.6 eV. This yields I* ¼ 51 meV, which can be
compared with the ‘hydrogenic’ value, given by
I  ¼ I0 ðm =me Þ=e2
of 50 meV.
The agreement is good, bearing in mind the assumptions in the hydrogenic
model – no central-cell corrections for example.
The experiments described above were made on powder samples of 99.999%
purity from Alfa Aesar. Single-crystal studies have also been undertaken.13
Spectra taken at different orientations, y, of the crystallographic c-axis with
Anything Protons Do, Muons Do Better! 279
respect to the muon beam reveal a shift of the central peak that is consistent
with the centre being anisotropic. The frequency dependence is given by
D
Dn ¼ A þ b ð3 cos2 y
1Þ
2
where A* is the isotropic part of the hyperfine tensor and D is a dipolar term.
These data yield a very similar value of A* (namely 490  10 kHz) to the
powder sample studies but confirm an anisotropy of the centre with
D ¼ 260  20 kHz. From the angular dependence one can deduce that the
symmetry axis of the centre is parallel to the c-axis. Of the possible sites that
hydrogen (muonium) can occupy in the wurtzite lattice, a BC site has been
shown theoretically to have the lowest energy18. Experimentally, it is difficult to
distinguish between this site and the site antibonding to oxygen along the
c-axis. Shimomura et al.19 have also made muonium studies on single crystals
of ZnO and claim to have identified two distinct shallow centres, one associated
with each of the above sites.

5 Shallow versus Deep

The reason why muonium (and by implication hydrogen) acts as a shallow
centre in some materials and as a deep centre in others is intriguing20. It appears
that the electron affinity of the host is a crucial parameter, as revealed by the
plot shown in Figure 6. Here the muonium hyperfine constant, relative to the
vacuum-state value, is plotted versus electron affinity for a variety of materials,
from insulators such as SiO2 and diamond on the left (for which A*/A0 is close
to unity) to semiconductors in the middle of the plot. The five semiconductors
with an effectively zero (on this scale) hyperfine constant are those in which
muonium forms shallow centres. It is evident that the ‘dilation of the wave-
function’ from atomic-like to extended occurs rather suddenly on this plot,
corresponding to an electron affinity of about 3.7 eV.
The concept of the electron affinity of the host being the all important factor
influencing the deep to shallow transition is implicit in the band-offset diagrams
proposed by Van de Walle21. An example is shown in Figure 7 for a few
materials. In this diagram, Ec represents the energy of the bottom of the
conduction band and Ev the top of the valence band, both plotted on an
absolute energy scale, i.e. with respect to the vacuum level. The dashed line
marked +/
gives the energy at which the formation energies of the positively
and negatively charged states of hydrogen are equal. This represents the position
at which the Fermi level would be pinned in a negative U system. If this level lies
in the conduction band (as in ZnO and InN22) hydrogen forms a shallow donor
level. If the level lies in the band gap (as for the other three materials) then
hydrogen forms a deep centre. The predictive nature of this model is currently
being tested for other semiconductors, in particular oxides other than ZnO.23,24
Peacock and Robertson25 have questioned whether the hydrogen level really
does lie at a constant depth below the vacuum level. A subtle point relevant to
280 Chapter 17

Figure 6 Plot of the normalised muonium hyperfine constant versus electron affinity
(from Ref. 20).

Figure 7 Band-offset diagram embracing several semiconductors (from Ref. 22).

this question is that the donor state actually lies at the level +/0, i.e. the energy
through which the Fermi level would pass when the centre ionizes, changing
from the neutral to the positively charged state. This level differs by U/2 from
the +/
level and so, even if the +/
level is invariant, the +/0 level is not
Anything Protons Do, Muons Do Better! 281
expected to be so. Under thermal equilibrium conditions the Fermi level is
pinned at +/
(for a negative U system). Such conditions do not apply in the
muonium experiments and so we are able to explore the higher +/0 level
directly, without the need to illuminate the sample to reveal the neutral state, as
required for, say, ENDOR experiments using hydrogen itself.15

Acknowledgements
The author wishes to acknowledge fruitful and enjoyable collaboration with
several colleagues, namely S F J Cox (Rutherford Appleton Laboratory and
University College London), P J C King, J S Lord and S P Cottrell (Rutherford
Appleton Laboratory), J M Gil, H Alberto, R Vilão, J Piroto Duarte and N
Ayres de Campos (Coimbra University, Portugal) and R Lichti (Texas Tech
University, USA).
As a physicist it is a pleasure to have been invited to contribute this chapter
to a book in honour of a distinguished chemist. Sir John Meurig Thomas’
interests are of course much wider than this label might imply – a fact that has
been made very evident to me over the past few years in the Department of
Materials Science and Metallurgy in Cambridge where fate brought us together
and where we have had many coffee-time discussions on topics beyond the
boundaries of our respective disciplines. Many thanks for your friendship John,
and, of course, ‘happy returns’.

References
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D.G. Fleming and A. Schenck, Phys. Rev. Lett., 1973, 31, 143.
2. R.F. Kiefl and T.L. Estle, in: Hydrogen in Semiconductors, J.I. Pankove
and N.M. Johnson (eds), Academic Press, New York, 1991, 547.
3. S.F.J. Cox, Philos. Trans., 1995, 350, 171.
4. R.F. Kiefl, M. Celio. T.L. Estle, S.R. Kreitzman, G.M. Luke, T.M. Riseman
and E.J. Ansaldo, Phys. Rev. Lett., 1988, 60, 224.
5. S.F.J. Cox and M.C.R. Symons, Chem. Phys. Lett., 1986, 126, 516.
6. S.R. Kreitzman, B. Hitti, R.L. Lichti, T.L. Estle and K.H. Chow, Phys.
Rev, 1995, B51, 13117.
7. R.L. Lichti, K.H. Chow, S.F.J. Cox, J.M. Gil, D.L. Stripe and R.C. Vilão,
Physica B., 2006, 376–377, 587.
8. J.I. Pankove, Appl. Phys. Lett., 1978, 32, 812.
9. N.M. Johnson, C. Henry and C.G. Van de Walle, Phys. Rev. Lett., 1994,
73, 130.
10. C.G. Van de Walle, Phys. Rev. Lett., 2000, 85, 1012.
11. S.F.J. Cox, E.A. Davis, S.P. Cottrell, P.J.C. King, J.S. Lord, J.M. Gil,
H.V. Alberto, R.C. Vilão, J. Piroto Duarte, N. Ayres de Campos,
A. Weidinger, R.L. Lichti and S.F.C. Irvine, Phys. Rev. Lett., 2001, 86,
2604.
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12. J.M. Gil, H.V. Alberto, R.C. Vilão, J. Piroto Duarte, P.J. Mendes,
L.P. Ferreira, N. Ayres de Campos, A. Weidinger, J. Krause, E.A. Davis,
S.P. Cottrell and S.F.J. Cox, Phys. Rev., 2001, B64, 075205.
13. H.V. Alberto, R.C. Vilão, J. Piroto Duarte, N. Ayres de Campos,
R.L. Lichti, E.A. Davis, S.P. Cottrell and S.F.J. Cox, Hyperfine Interact.,
2001, 136/137, 471.
14. D.C. Look, D.C. Reynolds, J.R. Sizelove, R.L. Jones, C.W. Litton,
G. Cantwell and W.C. Harsch, Solid State Commun., 1998, 105, 399.
15. D.M. Hofmann, A. Hofstaetter, F. Leiter, H. Zhou, F. Henecker,
B.K. Meyer, S.B. Orlinskii, J. Schmidt and P.G. Baranov, Phys. Rev.
Lett., 2002, 88, 045504.
16. D.C. Reynolds and T.C. Collins, Phys. Rev., 1969, 185, 1099.
17. D.C. Look, C. Coskun, B. Clafin and G.C. Farlow, Physica, 2003,
B340–342, 32.
18. E.V. Lavrov, J. Weber, F. Börrnert, C.G. Van de Walle and R. Helbig,
Phys. Rev., 2002, B66, 165205.
19. K. Shimomura, K. Nishiyama and R. Kadono, Phys. Rev. Lett., 2002, 89,
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20. S.F.J. Cox, J. Phys.: Condens. Matter., 2003, 15, R1727.
21. C.G. Van de Walle and J. Neugebauer, Nature, 2003, 423, 626.
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Lett., 2003, 82, 592.
23. S.F.J. Cox, J.S. Lord, S.P. Cottrell, J.M. Gil, H.V. Alberto, A. Keren,
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Matter, 2006, 18, 1061.
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 Section B:
Organic Solid State Chemistry
CHAPTER 18

Molecular Cohesion and the

Structure of Organic Crystals
JACK D. DUNITZa AND A. GAVEZZOTTIb
a
Chemistry Department OCL, ETH-Hönggerberg HCI H333, ETH-Zurich,
CH-8093 Zurich, Switzerland; b Dipartimento di Chimica Strutturale e
Stereochimica Inorganica, University of Milano, Via Venezian 21, I-20133
Milano, Italy

1 Some History
Among John Meurig Thomas’s scientific interests, too many and too multifar-
ious to be listed here, a major preoccupation is with the forces that guide and
preserve atomic and molecular architectures in the solid state. The analysis of
known solid-state structures in terms of ‘‘non-bonded’’ forces, the design of
solids with desired properties and reactivities, the prediction and preparation of
new phases – these are all areas that have attracted Sir John’s attention and
where he has made far-reaching contributions. In deference to Sir John’s
enduring concern for the history of science, for how its past has influenced
its present and its foreseeable future, we shall attempt here to outline the
development of theoretical models of intermolecular forces with special refer-
ence to the organic solid state and point to possible new directions.
The notion that macroscopic bodies are made of atoms and molecules that
attract one another is as old as antiquity, even if it was expressed in very
different terminologies to those in our modern vocabulary. In his Opticks, Isaac
Newton wrote: ‘‘There are therefore Agents in Nature able to make the Particles
of Bodies stick together by very strong Attractions. And it is the Business of
experimental Philosophy to find them out.’’1 Newton was probably thinking of
solids when he wrote those memorable lines; and the notion that solid matter is
made of small particles sticking together so as to produce a compact arrange-
ment came to the mind of natural philosophers very early on, long before the
quantitative assessment of molecular properties in terms of chemical bonding,
shape and structure became possible: ‘‘As for solids . . . in order that among their
285
286 Chapter 18
molecules or particles be made such a tight binding as is cause of their compact-
ness, it is necessary that they may be located in certain given ways, which are
appropriate for cohesion to exert its energy’’;2 ‘‘The attractive forces acting
between the atoms will cause the portions of space which they respectively
appropriate . . . to be in contact with one another, at the maximum number of
points; as a result . . . the molecules themselves will also pack closely together’’.3
An early recognition that molecules exert attractive forces on one another
also in the gaseous state arose in the latter part of the 19th century and has
come down to us mainly from van der Waals’s interpretation of experimental
deviations of real gases from ideal gases. In the van der Waals equation:
RT a
P¼
2 ð1Þ
Vm
b Vm
relating the volume of a real gas to the applied pressure, the quantity b is related
to the finite volume of the molecules (assumed to be zero in the ideal gas
equation), and a is a factor arising from the virial of intermolecular attractive
forces, that leads to reduction in pressure. This quantitative relationship came
out of accurate experimental observations and modern chemical thinking,
although the nature of the molecular entities and of the forces acting among
them was only approximately known; still today we talk about van der Waals
molecular volumes and van der Waals radii, and also about van der Waals
forces without defining too closely what they mean.
As a young man, even before his astonishing series of papers in 1905, Albert
Einstein was occupied with the problem of intermolecular interactions – in
addition to his other interests. His first published paper,4 written when he was
21 years old, is concerned with intermolecular forces in liquids. Although many
eminent physicists and chemists at the time were still reluctant to accept that
molecules really exist, Einstein seems to have had no doubts about this. He
assumed that the potential between two molecules is of the form
P ¼ P1
c1 c2 fðrÞ ð2Þ

where f(r) is a universal function of the intermolecular distance and the

constants c1 and c2 depend on the molecular species, being sums of ci values
for the constituent atoms. Without going into detail, we note that by fitting to
experimental values of measurable properties, such as surface tension (cap-
illarity) and compressibility of common organic liquids, Einstein estimated
atomic c values in arbitrary units for several elements, for example:
cH ¼ 1:6; cC ¼ 55; cO ¼ 46:8; cCl ¼ 60; cBr ¼ 152; cI ¼ 198
Although the paper is today of no more than historical interest, the molecular
c’s may be seen to be somewhat analogous to molecular polarizabilities in the
much later London expression for the dispersion force between two molecules
and the atomic c’s to atom polarizabilities. From a modern compilation,5
atomic polarizabilities a in Å3 units are:
aH ¼ 0:36; aC ¼ 1:44; aO ¼ 0:92; aCl ¼ 1:62; aBr ¼ 2:02; aI ¼ 2:65
Molecular Cohesion and the Structure of Organic Crystals 287
Indeed, apart from the values for hydrogen, there is even a rough proportion-
ality.
In 1912, following Max von Laue’s intuition, came the discovery of X-ray
diffraction by crystals. In the course of a discussion with Peter Paul Ewald, it
seems to have become clear that the distances between atoms in crystals should
be of the same order of magnitude as the wavelength of X-rays and hence that
interference phenomena might be expected to occur. Soon after the experimen-
tal verification by Walther Friedrich and Paul Knipping, the news traveled to
Cambridge where the Braggs, William Henry and William Lawrence, father
and son, used the X-ray diffraction patterns produced by simple ionic crystals
to determine their internal atomic arrangements. The first analyses were of
alkali halide crystals, which were shown to be built from alternating patterns of
cations and anions. Today we take this so much for granted that it may be hard
to imagine how difficult it was for contemporary chemists to accept such ideas.
Even as late as 1927, Henry E. Armstrong wrote in Nature:6 ‘‘Prof. W. L. Bragg
asserts that in sodium chloride there appear to be no molecules represented by
NaCl. The equality in number of sodium and chlorine atoms is arrived at by a
chess-board pattern of these atoms: it is a result of geometry and not of a pairing-
off of these atoms. . . . Chemistry is neither chess nor geometry, whatever X-ray
physics may be. . . . It were time that chemists took charge of chemistry once more
and protected neophytes against the worship of false gods; at least taught them to
ask for something more than chess-board evidence’’.
As the systematic determination of crystal structures progressed, the atomic
arrangements in simple ionic compounds were found to be understandable in
terms of a few simple rules associated with the names of Ewald himself, Max
Born, Fritz Haber, Erwin Madelung, and Kasimir Fajans; and, of course, the
Braggs themselves, who led the way in the systematic determination of crystal
structures. While simple ionic crystals, such as the alkali halides, are somewhat
limited in the types of crystal structure they can adopt, this is certainly not the
case for more complex minerals, such as mica KAl3Si3O10(OH)2 or zunyite,
Al13Si5O20(OH)18Cl, for example. In 1929, Linus Pauling7 formulated a set of
rules that was successful not only in testing the correctness of known structures
but also in predicting unknown ones. As Pauling himself remarked, these rules
are neither rigorous in their derivations nor universal in their application but
they have proved remarkably successful. Pauling’s second rule states essentially
that electrostatic lines of force stretch only between nearest neighbours. In his
1937 book on the structure of minerals,8 W. L. Bragg wrote: ‘‘The rule appears
simple. But it is surprising what rigorous conditions it imposes on the geometrical
configuration of a silicate. . .To sum up, these rules are the basis for the stereo-
chemistry of minerals.’’ As far as the metallic state is concerned, the arrival of
X-ray diffraction soon showed that the arrangements of atomic nuclei in
metallic crystals led to a simple model in terms of close-packed structures of
atomic spheres with high coordination numbers: cubic and hexagonal close
packing with coordination number 12 and body-centered packing with coor-
dination number 14. Of course, a more refined quantum-mechanical descrip-
tion reveals that the electron density is smeared out into an electronic sea where
288 Chapter 18
atoms are no longer spherical, but the simple model of close-packed spheres
preserves its fascination and its didactic value besides its predictive power.
Questions about how organic molecules attract or repel one another took
longer to be asked and even longer to be answered in a proper scientific,
quantitative manner. There are several reasons for this. In the first place, most
simple organic compounds are liquids at normal temperature and pressure, so
that they are more difficult to obtain and to study in the crystalline state. The
low vaporization temperatures of the liquids and the low melting points of most
organic crystals indicate that cohesive forces among organic molecules are only
a small fraction of those operative in typical inorganic salts and metals. Then
again, the exact shapes and sizes of organic molecules were still unknown in
those early days or at best matters for informed speculation.
Most of the early X-ray crystallographic studies of organic compounds were
concerned with the determination and systematization of molecular shapes and
sizes, with an emphasis on interatomic distances and angles; crystal packing
matters were largely ignored. In contrast to simple inorganic compounds,
which tend to form high-symmetry crystals, organic crystals typically crystallize
in systems of lower symmetry: orthorhombic, monoclinic or triclinic. While
sodium chloride forms cubic crystals and its structure could be derived by
applying symmetry rules, crystals of anthracene, examined in 1920,9 were
monoclinic and thus intractable by the methods then in use. There were
exceptions, of course, and it is interesting and perhaps not merely coincidence
that two of the earliest examples of successful molecular structure determina-
tion involved high-symmetry crystals and correspondingly high-symmetry
molecules. One was the 1923 analysis of hexamethylenetetramine,10 C6H12N4.
The crystals are cubic, space group I
4m3 with two molecules per unit cell.
Symmetry considerations require that the four nitrogen atoms occupy vertices
of a regular tetrahedron and the six carbon atoms vertices of a regular
octahedron, enough to establish the cage structure of the molecule. The other
example is the 1928 analysis of hexachloro- and hexabromocyclohexane;11 the
crystals are cubic, space group Pa3, with four molecules in the unit cell. Here,
application of symmetry arguments led to the establishment of the chair form
of the cyclohexane ring with the substituents in equatorial positions.
In those early days, and indeed until much later, the main information to be
derived from the crystal structure analysis of an organic compound was about
the molecular constitution and conformation, with approximate values of
interatomic distances and angles from which often far-reaching conclusions
about the bonding details were drawn. One intermolecular linkage that was
early recognized in organic crystals as well as in inorganic ones was the
hydrogen bond. Because of their low electron density, hydrogen atoms are
difficult to locate with X-rays. Thus, hydrogen atoms were generally located by
stereochemical model considerations, that is, by informed guessing. Often they
were just left out of the structural description altogether so that in many
early pictorial representations of the crystal structures there appeared to be
empty regions of space between the molecules. However, even if the locations of
hydrogen atoms in crystal structures needed to be guessed rather than located
Molecular Cohesion and the Structure of Organic Crystals 289
experimentally, by the late-1930s, hydrogen bonds had been recognized as an
important kind of structural glue, not only in ice and solid hydrogen fluoride
but also in simple carboxylic acids and amides, where O–H. . .O and N–H. . .O
hydrogen bonds were assigned a dominant role in controlling the molecular
arrangements found in crystals. Otherwise, little attention was given to ques-
tions of what holds the molecules together in a given crystal structure. Often it
seemed to be mere empty space.
However, molecular wave functions extend to infinity, so that space is never
quite empty. As far as the physics of intermolecular interactions is concerned,
what matters is the nature and strength of the electromagnetic fields produced
by the electrons and nuclei. The strong Coulombic field exerted by the highly
polar cations and anions in minerals was comparatively easy to study, and
atomic cohesion in such crystals seemed to present no fundamental problems.
Similarly, as an obvious extension, it was soon shown that the average inter-
action energy between molecules with a permanent dipole moment, e.g. water,
is attractive. The nature of the cohesive forces among neutral unpolar mole-
cules remained elusive. As an extreme example consider solid argon, for which
no theory based on classical mechanics and electrostatics could possibly
reproduce the lattice energy. The mysterious missing term, the dispersion
energy, could only be understood after the advent of quantum mechanics.
No one better than London himself has expressed the underlying source of
dispersion forces:12 ‘‘These very quickly varying dipoles, represented by the zero-
point motion of a molecule, produce an electric field and act upon the polaris-
ability of the other molecule and produce there induced dipoles, which are in phase
and in interaction with the instantaneous dipoles producing them . . . we may
imagine a molecule in a state k as represented by an orchestra of periodic dipoles
mkl which correspond with the frequencies nkl ¼ (El
Ek)/h of (not forbidden)
transitions to the states l. These ‘oscillator strengths’, mkl, are the same quantities
which appear in the ‘dispersion formula’ which gives the polarisability of the
molecule in the state k when acted on by an alternating field of the frequency n.’’
The theoretical treatment shows that the leading term in these forces decays as
the inverse sixth power of intermolecular distance. It is thus obvious that in
order for these weak, short-range forces to exert their action as efficiently as
possible, molecules must be in close contact, bumps into hollows, with as little
empty space as possible. It was A. I. Kitaigorodski’s great achievement, starting
from a critical survey of organic crystal structures coming to be known in
sizeable numbers by the early 1960’s, to put these concepts on a systematic
quantitative footing.13

2 More Recent Times

2.1 The Atom–Atom Method
The simplest approach for estimating the potential energy of a pair of mole-
cules or of an assembly of molecules, as in a crystal, goes under the name of
290 Chapter 18
atom–atom potentials; the basic assumption here is that the centres for the
evaluation of the potential coincide with the nuclear positions. Such an
approach is an extension of the methods that were being developed around
mid-century for conformational analysis of organic molecules by West-
heimer,14 Hill,15 Dunitz and Schomaker,16 Hendrickson,17 Wiberg,18 Bartell
et al.,19 Lifson and Warshel,20 Allinger et al.,21 Scott and Scheraga22 and others
(for a critical review see Ref. 23). The emphasis there was on the role of non-
bonded interactions or ‘‘steric effects,’’ as they were often called, in dictating the
variation in interatomic distances and angles and conformations of organic
molecules. While ‘‘packing effects’’ could be invoked to explain almost any
unusual observation in the solid state, this was clearly not the case for
observations on isolated molecules. The need for ‘‘non-bonded’’ terms arose
when it was realized that the gas-phase conformations of organic molecules
could not always be explained on the basis of standard bond lengths and angles,
using only bond-stretch, bond-angle-bending and torsional force-field terms,
parameterized from vibrational spectroscopic data. For example, the stretched
C–C bonds in cyclobutane could only be explained by postulating that there is a
strong repulsion between the atoms across the diagonals of the four-membered
ring.16 This and other evidence revealed that interactions between formally
non-bonded atoms need to be included in any attempt to calculate the equi-
librium geometry and energy of a molecule.
The idea behind molecular mechanics, namely that the atoms of a given
molecule interact by some sort of attractive–repulsive potential found an
obvious extension in the evaluation of potentials and forces between atoms
in different molecules, and thus opened the way to the study of condensed
phases. By the mid-1960s, such non-bonded interactions were being used by the
Kitaigorodski school,24 especially by Kira Mirsky, as a basis for calculating
lattice energies of molecular crystals. In a series of papers that quickly became
citation classics, D. E. Williams25 was able to parameterize a consistent set of
intermolecular potentials for crystals of organic molecules containing C, H, N,
O, F and Cl atoms. The basic assumption, both in the intra- and in the
intermolecular approach, is that the interaction potential Vij between a pair of
atoms i and j which are not bound through a proper chemical bond, or more
appropriately, which do not in any way share an interaction mediated by the
intervening electrons (as, for example, in pairs of atoms chemically bound to
the same atom), depends only on the interatomic distance Rij, and can be
expressed in the form of a sum of repulsive and attractive terms, for example:

Vij ¼ A expð
BRij Þ
CR
6
n
1

ij þ D Rij þ qi qj Rij þ    ð3Þ

with A, B, C, D, . . . empirical parameters and q’s formal atomic charges. For a

crystal, the lattice energy is obtained by an appropriate summation over all
such terms. The main reason for the almost instantaneous popularity and
success of this model is that it was readily applicable even with the modest
computer resources of those times. Since then it has been continuously devel-
oped and used in countless applications for estimates of lattice energy, for
Molecular Cohesion and the Structure of Organic Crystals 291
example in assessing the relative energies of crystal polymorphs and in crystal
structure prediction exercises. The widely used OPEC (organic potential energy
calculations)26 allows one to estimate the potential energy increase resulting
from molecular rotations or translations in a crystal and has been much used in
studies of solid-state chemical reactions. The continuing success of this simple
model rests upon the very high results/parameters ratio and on its ease of
application, even to extensive molecular dynamics simulations. The atom–atom
potential method is still a vital tool in modern molecular simulation and will
remain so for a long time.
All atom–atom pair potential curves share some characteristic common
features (Figure 1). The deeper the minimum, the sharper the curvature at
the turning point; the anharmonicity of the curve is such that when an
interatomic distance is decreased below its equilibrium value, the energy rises
more steeply than when the distance is increased. For distances slightly smaller
than the turning point (Req) the interaction term may be stabilizing, i.e. the
potential energy is still negative, but the interatomic force is repulsive, not
attractive. In descriptions of molecular packing in crystal structures, the
emphasis is usually on short intermolecular distances or ‘‘contacts.’’ Insofar
as these typically correspond to local repulsive forces between the atoms
concerned, and the system is in equilibrium (no net force), the repulsive forces
must be balanced by attractive forces arising from interactions between more
distant atom pairs in the different molecules. Thus, in attempts to describe and
systematize intermolecular interactions in crystals, the usual, natural preoccu-
pation with short interatomic contacts as the main structural glue may be
misleading. Since hydrogen atoms are usually the ones on the peripheries of
organic molecules, they are the ones that are typically invoked in intermolecu-
lar contacts. Indeed, C–H. . .X contacts in organic crystals are almost unavoid-
able. Uncritical interpretations of the significance of such C–H. . .X contacts

Figure 1 A typical interatomic model potential as a function of interatomic distance

(Å). For the usual atoms of organic chemistry, one energy unit in the graph
may be of the order of 0.5
1 kJ mol
1.
292 Chapter 18
can lead to questionable conclusions, for example, that they necessarily corre-
spond to structurally significant although weak intermolecular hydrogen
bonds. Undoubtedly, O–H. . .O and N–H. . .O interactions can correspond to
very strong hydrogen bonds and play an important if not decisive role in
stabilizing structures in which they occur. However, the extrapolation to
weaker and weaker types of interaction needs to be done with much more care
than is often allotted to the task. If you search almost any organic crystal
structure for C–H. . .X contacts (where X naturally depends on which other
elements are present on the molecular periphery), then you are likely to find
them.
Experimental support for specific bonding atom–atom interactions between
neighboring molecules has been inferred on the basis of intermolecular bond-
paths (in the Bader sense) observed in electron-density distributions in crystals.
The matter has been carefully analyzed by Gatti.27 The question is whether
such bond paths arise as the result of intermolecular bonding interactions or
merely from residual overlapping of charge clouds of atoms in neighboring
molecules. For strong intermolecular O–H. . .O and N–H. . .O hydrogen bonds
the former may well be the case. But even in the case of such hydrogen bonds,
Spackman28 has shown that to a good approximation experimental bond paths
are close to those produced by simple addition of non-interacting overlapping
spherical atom electron densities. Experimental bond paths have reportedly
been observed for intermolecular H. . .H interactions between phenyl groups in
crystalline salts of tetraphenylborates.29 We do not believe that such observa-
tions should be regarded as evidence for specific atom–atom interactions in
crystals. More likely, they arise as a result of the inevitable H. . .H contacts that
arise between phenyl groups of different molecules in crystals of tetraphenyl
compounds.
Notwithstanding these more philosophical issues, the atom–atom potential
method has been and is still one of the pillars of computational molecular
simulation. Its power was appreciated by John Meurig Thomas quite early in
his career during the period when he was interested in solid–solid phase
transformations and photochemical reactions in organic crystals. In particular,
this approach was used by Thomas and his collaborators to derive molecular
packings and lattice energies of organic crystals from incomplete and some-
times fragmentary experimental data. We take here two examples out of many.
On cooling crystals of pyrene to below 120 K they often shatter. From electron
diffraction patterns of small regions of cooled crystals the unit cell dimensions
of the low-temperature phase (pyrene II) could be measured and, in the
absence of reliable diffraction intensities, its structure was derived through
the use of atom–atom potential calculations.30 Many years later, the essential
correctness of the proposed structure was confirmed from neutron powder
diffraction data from a deuterated sample at 4.2 K.31 Then there was the
question of the structure and dynamics of a new, triclinic phase of anthracene
(II), produced by shearing stress at ambient temperature. As in the pyrene
example, the existence of the new phase was detected from the electron
diffraction pattern of a tiny crystallite containing both transformed and
Molecular Cohesion and the Structure of Organic Crystals 293
untransformed regions. In the absence of diffraction intensities, the crystal
structure of the new form (triclinic, P1, Z ¼ 2) was derived by the atom–atom
potential method.32 In this case, as a notable extension of the method, lattice
dynamical calculations were used to compute the infrared and Raman active
vibrations of both crystal modifications. The atom–atom calculations sug-
gested that other anthracene structures, comparable in energy with the stable
anthracene I, can be generated from the stable structure by motion along slip
planes. Indeed, evidence for another metastable anthracene phase formed by
vapour growth has been adduced from X-ray diffraction measurements33 but it
is not the same as the phase generated by shear. In any case, the evidence for
the new polymorph is questionable.34
In spite of the popularity and strengths of the atom–atom approach there
are obvious weaknesses. The constants A, B, C, . . ., as well as the ‘‘atomic
charges’’ qi, need to be assigned individually for each kind of atom pair, and
this cannot be done by theoretical considerations. The adherence of the
mathematical model to physical reality is intrinsically weak, and the required
parameters must be obtained by the ad hoc expedient of fitting to a large
amount of experimental data, mainly statistical data on atom–atom distances
of closest contact between molecules in available crystal structures and on
heats of sublimation.35 There are no constraints on the values of these
constants as long as they properly carry out their job. This manner of fitting
a model to experimental data has its dangers, especially that of encouraging
belief in the physical reality of the model, even when it is has no underlying
theoretical basis. Thus, although there have been attempts to recover the
physics of the interaction a posteriori by identifying the various terms in the
analytical power expansion with real effects in terms of basic phenomena, this
can only be misleading. For example, although the exponential term behaves
as a repulsion energy, it has no counterpart in terms of fundamental theories.
Similarly, the R
6 term behaves like the leading term of dispersion energy,
but the proportionality constant is just a black-box number. Even the R
1
term, formally representing the Coulombic interaction between atoms is far
from giving a faithful reproduction of the actual Coulombic interaction
between molecular charge distributions. Very wisely, Kitaigorodski himself
expressed the opinion that ‘‘. . . the atom–atom potential method represents a
variational treatment using . . . A’s, B’s and C’s as variational parameters.
Clearly, there is no reason to attach any physical meaning to the parameters . . .
there is no reason to regard the sum of the
AR
6 terms as the dispersion
energy . . . and the sum of qq 0 r
1 terms as the electrostatic energy’’.36 The
atom–atom potential method is an expert system but it has no basis in
fundamental physics.

2.2 Distributed Charge Methods

The assumptions embedded in the atom–atom approach to intermolecular
energies are indeed far from physical reality; for example, negative charges
294 Chapter 18
may be placed at the positions of atomic nuclei! In more elaborate descriptions,
the charge distribution is modeled by a set of distributed multipoles, designed to
fit the electrostatic field of the molecule as computed by some quantum-
mechanical procedure. The Coulombic contributions to the intermolecular
potential energy can then be calculated as sums of multipole–multipole inter-
action terms; the missing dispersion, polarization and repulsion terms must be
evaluated by some additional procedures. This approach, originally developed
by Anthony Stone,37 has been extensively exploited for molecular crystals by
Sally Price and co-workers.38
Molecular charge distributions from good quality wave functions can of
course be obtained from ab initio molecular orbital calculations, or even from
electron density studies in accurate X-ray diffraction analyses at very low
temperature. These charge distributions can then be expanded using a linear
combination of terms including radial functions and spherical harmonics.
Intermolecular Coulombic energies between two approaching charge distribu-
tions can then be calculated by direct integration.39,40 These energies are as
accurate as the wave function is.

2.3 Penetration Energy

An important limitation of models involving localized point charges or dis-
tributed multipoles to represent the charge density distribution around the
atomic nuclei in a molecule is the neglect of penetration energy. When electron
densities of neighbouring molecules overlap there is a destabilizing Coulombic
energy contribution from electron–electron repulsion but there is also a stabi-
lizing contribution from the interaction between the electron density of each
molecule with the positive nuclear charges of the other. The balance between
these two opposite Coulombic energy contributions depends on fine details of
the overlap. For the overlap between charge distributions of neighbouring
molecules at normal intermolecular separations, the energy balance usually
corresponds to a small overall stabilization.
A simple example may demonstrate the dramatic difference between energies
derived from a point-charge model and from interactions between delocalized
electron densities. Figure 2a shows the Coulombic energy for the approach of
two pseudoatoms each with nuclear charge +7.0 and electron charge –7.2. In
the point-charge model, the electron charges are assumed to be localized at the
nuclei, to yield two localized net charges of
0.2. The result is, as expected,
repulsion at all distances; negative charges repel one another. In the delocalized
model, each electron charge of
7.2 is spread over 1782 points in accordance
with an exponential decrease with distance out to 2.6 Å from each nucleus. The
interaction energy is identical to that of the point-charge model at large
internuclear separation. However, in contrast to the point-charge model, the
interaction energy goes through a turning point and at shorter internuclear
separation it becomes strongly stabilizing. Figure 2b shows the corresponding
energies when one of the atoms has net charge
0.2 (+7.0,
7.2), as before,
Molecular Cohesion and the Structure of Organic Crystals 295
a) b)
30
10
25

20
Coulombic energy, kJ/mol

Coulombic energy, kJ/mol

0
15

10
-10
5

0 -20
point-charge
-5
integration point-charge
-10 -30
integration
-15

-20 -40
2 3 4 5 6 2 3 4 5 6
distance distance
Figure 2 (a) Coulombic energy (kJ mol
1) of two pseudoatoms each with nuclear
charge +7 and electron charge
7.2, approaching at a variable distance.
Squares: point-charge energy for a net charge of
0.2 at the nuclear
location; triangles: negative charge distributed over 1782 points around
the nucleus. (b) As before, but one atom with electron charge
7.2, the other
with electron charge
6.8, ie opposite net charges.

and the other has opposite net charge +0.2 (+7.0,
6.8). Here the point-
charge model gives, as expected, stabilization at all distances, while the delo-
calized model produces a more complex behaviour. Here the interaction energy
is stabilizing at about 6 Å internuclear distance, but the force becomes slightly
repulsive at internuclear separation between about 5 and 3 Å, then strongly
attractive in the region 3 to 2 Å. Although this is only a computational
experiment on pseudoatoms, what a difference! It is clear that inferences based
on localized charge models may be right or wrong, depending on features of the
outer regions of the molecular electron densities, which play no part in point-
charge or distributed multipole models.
We should then not be entirely surprised that theories of molecular packing
based on point-charge models have led to pictures of attractive chlorine–
chlorine interactions (the so-called ‘‘chloro effect’’) and also of repulsive
halogen–halogen interactions. In another extreme example, the Coulombic
energy of the hexachlorobenzene crystal is calculated by the point-charge
model with a charge of +0.1 on carbon to be destabilizing (+18 kJ mol
1),
but it is correctly calculated to be stabilizing (
40 kJ mol
1) by the delocalized
Pixel model described below. The reason why the atom–atom method has been
so successful is that such gross deficiencies of the point-charge Coulombic
model are damped if not entirely corrected by the parameterization of the other
terms in the potential; two errors may cancel, but the real physics of the
situation becomes obscure.
296 Chapter 18

2.4 The Pixel Method

Nowadays, with computers that are able to carry out calculations at the
teraflop per second level, the time has come to move to fully delocalized models
of the electron density even in semi-empirical methods.
The SCDS (semi-classical density sums) or Pixel approach41 uses an accurate
electron density for the individual molecules and then estimates the interaction
energy due to reorganization of the electron density in the extended system by
introducing separate polarization, dispersion, charge transfer and repulsion
terms. The electron density of the molecule is obtained by some standard
quantum-mechanical calculation and sampled on a grid containing about 106
pixels, and is then contracted into super-pixels each containing n  n  n
original steps, where n is typically 3, 4 or 5. Pixels containing less than some
minimum charge of about 10
6 electrons are discarded as insignificant, and the
pixel contents are renormalized to balance the sum of the nuclear charges. In
this way, the molecular density ends up being described by some 10,000 pixels.
Clusters of molecules or crystals are then built by simple juxtaposition of the
Pixel electron densities of individual molecules.
The Coulombic energy of the system (ECOUL) is calculated by direct summation
over pixel–pixel, pixel–nucleus, and nucleus–nucleus Coulomb interactions: this is
the change in Coulomb energy that occurs on forming the molecular cluster from
the molecules at infinite separation. If there were no reorganization of the
molecular charge distribution on going from the isolated molecules to a molecular
cluster, the Coulomb energy calculated in this way would be entirely correct.
However, on passing from the isolated molecule to a cluster of molecules, the
molecular charge distributions of the individual isolated molecules are slightly
changed by their interactions with the charge distributions of other molecules.
This charge reorganization requires the introduction of correction terms in the
model, terms which cannot be calculated in a rigorous manner but can be
estimated with good accuracy with the help of a few reasonable assumptions
based on physical principles. They are the polarization energy (EPOL), the
dispersion energy (EDISP) and the repulsion energy (EREP). This partitioning of
the intermolecular energy is semi-empirical and hence to some extent arbitrary.
However, the separate terms can be calibrated for some representative systems by
comparison with more accurate but more time-consuming methods, such as
Stone’s IMPT (Inter-Molecular Perturbation Theory).42 Although this way of
partitioning the interaction energy is not rigorous, it corresponds to well esta-
blished concepts in structural chemistry and the results turn out to agree largely
with chemical expectations. For example, polarization terms (EPOL) turn out to be
important in hydrogen-bonded systems where they compensate, so to speak, for
neglect of the large reorganization of the molecular density distributions in such
systems. Dispersion energies (EDISP) are large in contacts among hydrocarbon
molecules, especially aromatic ones, and are relatively less important in chemical
environments where contacts between atoms of different electronegativity occur.
Obviously there is no possibility for allowing antisymmetrization of the wave
function in this simple repetition of molecular charge densities. One effect of
Molecular Cohesion and the Structure of Organic Crystals 297
antisymmetrization would be to remove charge density from overlapping
regions, thus increasing the nucleus–nucleus repulsion. The Pixel repulsion
term is calibrated as roughly proportional to the overlap integral between
individual molecular densities, as a partial replacement for the missing effects
of Pauli exclusion.
In spite of its many approximations and assumptions, Pixel is able to
reproduce the sublimation enthalpies of organic crystals43 and mimics the ab
initio results for molecular clusters with considerable accuracy44 at a small
fraction of the computational cost. For example, one can run the lattice energy
of a molecule such as anthraquinone in about 10 min on an ordinary PC, and
parallelization even makes it possible to optimize lattice energies with respect to
lattice parameters and molecular orientation.

2.5 The Ab initio Approach

In principle, if we had a powerful enough computer, we could calculate the
lattice energy of any given crystal structure from quantum mechanics. In
principle! Take benzene as an example. First we would calculate the energy
of a benzene molecule at some suitable ab initio level (say MP2/6**g(d,p) – it is
not necessary for the non-specialist to know exactly what these symbols mean),
making sure that we had reached the energy minimum in the multiparameter
space defining the nuclear coordinates. This calculation would yield a numer-
ical value of the energy, around
231.518 a.u. (atomic units), equivalent to

607836.6 kJ mol
1. This is not the energy of formation of a benzene molecule
from six carbon and six hydrogen atoms in their ground states; it is the energy
of formation of a benzene molecule from six nuclei of charge +6, six nuclei of
charge +1, and 42 electrons at infinite separation. The energy of a benzene
dimer, calculated in the same way, with minor modifications to take care of
technical problems, would come out at around
463.041 a.u., very nearly twice
the above value. The small difference:
463.041
2(
231.518) ¼ –0.005 a.u. or

13 kJ mol
1 would be the calculated energy of the benzene dimer with respect
to two separated benzene molecules, i.e., the cohesive energy of the benzene
dimer (at 0 K without zero-point-energy, inclusion of which would only com-
plicate the argument without adding anything of importance). The calculation
yields this number and this number alone, so there is no point in arguing about
to what extent the small stabilization of the dimer with respect to two mon-
omers arises from Coulombic interactions between the separate charge distri-
butions or from polarization or from dispersion or from anything else. At the
fundamental ab initio level these would be meaningless questions. What applies
to the dimer would apply equally to an assembly of benzene molecules, and in
particular to the particular assembly that corresponds to the benzene crystal.
As far as ab initio methods are concerned, the benzene crystal is just about
the limit of what is practicable today.45 For assemblies of much larger mole-
cules, ab initio methods are still on the horizon: some attempts at simulating the
dispersion energy terms have appeared.46
298 Chapter 18
In terms of the basic physics, the only energy terms that appear in the ab
initio calculation are Coulombic: the Coulombic repulsion between the nuclei
and between the electrons, and the Coulombic attraction between the nuclei
and the electrons. According to the Hellman–Feynman theorem, the force on a
nucleus can be calculated from the charge distribution as if it were classical, i.e.
by using Coulomb’s law. If the exact wave function were known for any
molecule or assembly of molecules in its equilibrium configuration, the bonding
could then be analyzed in purely Coulombic terms. Thus, in principle, if the
correct electron density were available, a purely Coulombic calculation would
suffice to yield the correct energy. In practice, such a calculation is not
practicable today for an extended system such as a crystal of moderate
complexity. The difficulty is not that Coulomb’s law breaks down; it is that
we do not have the correct electron density. Allowance for the reorganization
of the electron density on going from the isolated molecule to the dimer and to
larger molecular assemblies would require very large basis sets and extensive
optimization of the many variables needed to describe the systems. At present
we cannot do this for molecular crystals of even modest complexity. Here the
newly developed Pixel method provides a compromise that offers sufficient
accuracy for most purposes with the additional bonus of (or at the price of,
depending on one’s outlook) introducing separate polarization, dispersion,
charge transfer and repulsion terms.

3 A Future Challenge
Prediction is a risky business, especially when it concerns events whose outcome
is still uncertain. Crystal structure prediction (CSP) is an exercise in which
unknown crystal structures of organic molecules are deduced (or guessed) from
the information expressed by molecular connectivity alone. We have at our
disposal a vast library of known crystal structures of organic and organome-
tallic compounds in the Cambridge structural database (CSD, with almost
400,000 entries as of January 2007).47 Information from this source, together
with all too scarce thermodynamic data48 has been utilized in the construction
and parameterization of atom–atom force fields34 that have been supple-
mented, more recently and to a limited extent, by the use of first principles
quantum-chemical calculations. All these have provided a consistent and
robust body of knowledge for the understanding of known crystal structures
and for the computer simulation of organic condensed phases.49 The next
development must involve the transition from reassuring post-diction towards
reliable prediction of organic crystal structures and energies. The accomplish-
ment of this task is, however, confronted with numerous practical and con-
ceptual obstacles, as has been demonstrated by the results of recent objective
tests.50 The problem is not that of generating a sufficiently large library of
possible periodic arrangements; typically, for any given molecule, a large
collection of computational crystal structures can be produced without diffi-
culty, often in a matter of minutes with modern computers. Usually, the
Molecular Cohesion and the Structure of Organic Crystals 299
experimental structures are to be found among the computational ones, but not
necessarily among those with the most stabilizing lattice energy. There are
several possible reasons for this. Energy differences between crystal poly-
morphs are extremely small, a matter of a few kilojoules per mole. The same
holds for different possible crystal structures of a given molecule. Typically, a
computational search produces many different periodic arrangements within a
narrow window of lattice energies, with unknown energy barriers between
them. Besides, since entropic factors are difficult to estimate accurately in
computations, the ordering of free energies at normal temperature and pressure
becomes even more uncertain. To complicate matters further, the crystalliza-
tion process is under kinetic rather than thermodynamic control. Relative rates
of nucleation and growth of different crystal phases determine which crystal
phase will be produced under the conditions of crystallization. At present, it is
virtually impossible to properly account for the dynamics of crystallization
processes involving solvent–solute interactions. Once formed, a thermodynam-
ically unstable crystal form can indeed, in principle, transform to a thermo-
dynamically more stable form, but solid–solid phase transitions tend to be slow.
A metastable crystal form can persist for a long time, indeed practically forever.
Thus, the experimentally found crystal structures of a given compound need
not be those of minimal free energy. Besides these problems, the force fields
employed in the computations may not be sufficiently accurate, and the search
for possible periodic molecular arrangements may not be sufficiently exhaus-
tive. How successful can one expect computational methods to be that essen-
tially neglect temperature and time? At present, success in crystal structure
prediction is very limited, even for rigid molecules, and it is virtually zero for
flexible molecules, where conformational adjustment is coupled to inter-
molecular aggregation requirements. However, as is usual in science, work is
in progress and new developments can be expected.51–53

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25. D.E. Williams and T.L. Starr, Comput. Chem., 1977, 1, 173; L.-Y. Hsu and
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26. A. Gavezzotti, OPEC, Organic Packing Energy Calculations, University of
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38. D.J. Willock, S.L. Price, M. Leslie and C.R.A. Catlow, J. Comput. Chem.,
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Della Valle, E. Venuti, A. Dzyabchenko, J.D. Dunitz, B. Schweizer, B.P.
van Eijck, P. Erk, J.C. Facelli, V.E. Bazterra, M.B. Ferraro, D.W.M
Hofmann, F.J.J. Leusen, C. Liang, C.C. Pantelides, P.G. Karamertzanis,
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CHAPTER 19

Aperiodicity in Organic
Materials
KENNETH D. M. HARRIS
School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT,
UK

1 Introduction
The most significant turning point in my scientific career was without a doubt
being given the opportunity (in 1985) to join the research group of Sir John
Meurig Thomas at the University of Cambridge to study under his supervision
for a PhD degree. Not only did this opportunity provide a springboard to
transform childhood scientific dreams into reality, but one could not have
wished for a more erudite, enthusiastic, encouraging and supportive supervisor
at this formative stage of one’s entry into scientific research. During this time,
every meeting with ‘‘JMT’’ (whether in his office, on a train between Cambridge
and London, at lunch in the graduate centre, or joining him on a 2-minute walk
while he posted a letter) was a source of new ideas and inspiration, and one was
always left feeling scientifically enriched by the experience. His unbounded
enthusiasm for science was inspirational, and his ability to provide wise
guidance and perpetual encouragement were such that those working in his
research group were continuously instilled with a tremendous feeling of opti-
mism and excitement for their research. Furthermore, research discussions with
him were not only occasions to learn from his seemingly colossal intellect and
to progress with one’s research through deep contemplation and uninhibited
debate, but they were also interesting (and often entertaining) occasions,
punctuated as they typically were by relevant anecdotes (which, whenever the
opportunity arose, reflected a passionately Celtic perspective), historical asides
and his characteristic ability to blend seriousness and good humour. And just
as impressive as the depth of his knowledge in his own field of specialization
was the breadth of his knowledge across the full spectrum of scientific disci-
plines – thus, in the course of our discussions on the topics of my own research

302
Aperiodicity in Organic Materials 303
work, he succeeded in introducing me to fields as diverse as fractal geometry,
molecular electronics, the structural biology of proteins and viruses, and the
pioneering work of Ahmed Zewail in the development of femtosecond spec-
troscopy, to list just a few. In addition to the profound interest that he showed
in our research work and the great motivational drive that he exerted in
encouraging us to generate new knowledge and deeper understanding in our
research, it was very clear that he also cared deeply about each person in his
research group as an individual, and he took great interest in, and responsibility
for, their education and scientific development. In every meeting with JMT, he
was a continual source of new ideas, but he was also fully supportive in
encouraging us to develop our own scientific thoughts and opinions. In this
way, he cultivated in his research group a fertile breeding ground for new
scientific ideas to germinate, and he provided the support, encouragement and
resources to enable these ideas to be brought to full fruition. Certainly, I had
the over-riding impression during my time in his research group that we were
members of a team that was leading the way at the cutting edge of research in
the field, and that we were being led in this important quest by the pre-eminent
scientist in the field. It really was a privilege to have been given the opportunity
to spend a period of time within this environment and it has been a continued
privilege to maintain my scientific collaboration with him to the present day,
and hopefully long into the future.
A few months after beginning my PhD research, JMT suggested during one
of our regular meetings that I should start some research on structural prop-
erties of urea inclusion compounds, in addition to the project (on solid state
photodimerization reactions) that I was currently undertaking at that time.
Mark Hollingsworth, who had just joined the research group as a postdoc
studying photochemical reactions of organic molecules (diacyl peroxides)
within zeolites, had been given similar encouragement to study the same
reactions in urea inclusion compounds, and the aim was for Mark and myself
to work in tandem on studies of photochemical and structural properties of
these materials, respectively. In this way, a very fruitful collaboration and
friendship was started, and I learned greatly from my interaction with Mark
during this time. Such is the rich and diverse array of properties that has been
found to be exhibited by urea inclusion compounds, and the seemingly endless
opportunity to exploit these materials to gain new facets of fundamental
understanding of the nature of the organic solid state, that we have both
continued to carry out research on urea inclusion compounds ever since. Soon
after recording our first X-ray diffraction photograph of a urea inclusion
compound, it was clear that these materials exhibit some very interesting
diffraction properties, which we could understand on the basis that they are
incommensurate materials. Early thoughts on general aspects of the structural
properties of these materials, which evolved through many discussions on this
subject with JMT, are summarized in Ref. 1, while specific details relating to the
diacyl peroxide/urea inclusion compounds were published subsequently.2
Another important collaboration during this time was with Andrew Rennie,
a mathematics undergraduate in Cambridge who had written to JMT (in his
304 Chapter 19
position as Director of the Royal Institution) to enquire if he could carry out a
summer research project there. I felt greatly honoured that JMT asked me to
supervise Andrew in this project, which led to the development of our math-
ematical model of incommensurate versus commensurate behaviour in one-
dimensional inclusion compounds,3–5 which is described in more detail in
Section 2.4.
From these early beginnings started a long fascination with aperiodic crys-
talline materials (of which incommensurate solids are a subset) that has
continued to the present day. Aperiodic crystals may be defined, in general
terms, as materials that lack three-dimensional translational periodicity (and
are thus distinct from conventional crystals), but yet have aspects of long-range
order that give rise to sharp Bragg reflections in their X-ray diffraction
patterns. This article is devoted to surveying two aspects of aperiodicity in
organic materials. The first part of the article is focused on the concept of
incommensurateness in one-dimensional inclusion compounds, and is illus-
trated mainly by examples from our research on urea inclusion compounds
(covering work that ranges in time from my PhD studies with JMT to the
present day). The second part of the article is focused on the concept of
quasicrystalline materials, and particularly concerns the development of a
strategy for the design of a quasicrystal based on discrete organic molecular
building units. The aim of both parts is to raise and discuss key concepts within
these themes, rather than to provide a comprehensive overview of the field.

2 Incommensurate Materials
2.1 Introduction to the Structural Classification of
Commensurate/Incommensurate Inclusion Compounds
From the chemical viewpoint, solid inclusion compounds are composed of two
chemically distinguishable substructures: the host and guest substructures. In
many cases, the guest molecules are disordered within the host structure, but
when the guest molecules are ordered (at least sufficiently well ordered that an
average lattice periodicity can be defined), an important concept is the degree of
structural registry between the two periodic (host and guest) substructures.
Here we focus only on the simplest case in which the host substructure is a
periodic one-dimensional tunnel, within which the guest molecules are ordered
with a well-defined periodicity along the tunnel axis (c-axis) (see Figure 1). The
periodic repeat distance of the guest molecules along the tunnel is denoted cg
and the periodic repeat distance of the host substructure along the tunnel is
denoted ch.
From the structural viewpoint, the degree of registry between these two
periodic substructures is assessed by considering the relationship between cg
and ch (we shall discuss later some physical properties of inclusion compounds
that depend on the degree of structural registry between the host and guest
substructures). Conventionally, the ratio cg/ch is used to subdivide these
Aperiodicity in Organic Materials 305

ch ch ch ch ch ch ch ch ch ch

cg cg cg cg cg cg cg

Figure 1 Schematic representation of a tunnel inclusion compound viewed perpendicular

to the tunnel axis. The definitions of cg and ch are shown.

materials into two categories: commensurate and incommensurate. In the clas-

sical definition, the inclusion compound is assigned as commensurate if cg/ch is
a rational number and incommensurate if cg/ch is an irrational number.
However, since experimental measurements of cg and ch can never be made
with infinitely high precision, a more practical definition is to assign an
inclusion compound as commensurate if the ratio cg/ch is sufficiently close to
a rational number with low denominator. Thus, for a commensurate system,
sufficiently small integers p and q can be found such that pch E qcg, whereas if
no sufficiently small integers p and q can be found to satisfy this relationship,
the inclusion compound is incommensurate.
The values of cg and ch can be determined from appropriate diffraction
studies. For example (Figure 2), in the case of an incommensurate system, a
single crystal X-ray diffraction rotation photograph recorded for the crystal
rotating about the tunnel axis shows separate sets of layer lines from the host
and guest substructures, and the values of cg and ch can be determined from the
spacing of the layer lines in each set. As evident from Figure 2, the zero layer
line is common to both substructures, but there is no coincidence of any other
higher-order layer lines from the host and guest substructures. For a commen-
surate inclusion compound on the other hand, separate layer lines due to the
host and guest substructures cannot be distinguished, and all layer lines are
described by a single common periodicity along the c-axis.
We now consider in more detail some consequences of the incommensurate/
commensurate nature of a tunnel inclusion compound in terms of diffraction
and structural properties, focusing in particular on the case of urea inclusion
compounds. Subsequently, we discuss the implications in terms of energetic and
vibrational properties.

2.2 Introduction to Urea Inclusion Compounds

As all the examples discussed in this part of the article concern urea inclusion
compounds,6–10 it is relevant to give a brief introduction to these materials here.
In ‘‘conventional’’ urea inclusion compounds, the host structure1,11 is constructed
from a hydrogen-bonded arrangement of urea molecules, within which there are
linear, parallel tunnels (Figure 3). The diameter of the urea tunnel varies between
ca. 5.5 Å and 5.8 Å as a function of position along the tunnel,12 and is suitable for
306 Chapter 19

(H, K, 3, 0)
(H, K, 0, 4)
(H, K, 0, 3)
(H, K, 2, 0)
(H, K, 0, 2)
(H, K, 1, 0)
(H, K, 0, 1)
(H, K, 0, 0)

Figure 2 Single crystal X-ray diffraction rotation photograph for an incommensurate

tunnel inclusion compound (the 1,9-diiodononane/urea inclusion com-
pound), recorded with the single crystal rotating about its tunnel axis. The
layer lines (horizontal) from the host component are indicated by red arrows
and the layer lines from the guest component are indicated by yellow arrows.
In this case, the guest layer lines contain both discrete scattering (sharp
spots) and diffuse scattering. The fact that separate sets of layer lines are
observed for the host and guest components is a consequence of the
incommensurate relationship between ch and cg. Indexing of the layer lines
is shown on the right hand side (see Section 2.3 for a definition of the Miller
indices (H, K, L, M)).

accommodating guest molecules based on a sufficiently long n-alkane chain, with

only limited substitution of the n-alkane chain permitted. The urea tunnel
structure is stable only when the tunnels are filled with a dense packing of guest
molecules (removal of guest molecules from urea inclusion compounds leads to
the instantaneous collapse of the ‘‘empty’’ tunnel structure to form a structure of
higher density – the well-known crystal structure of ‘‘pure’’ urea, which does not
contain empty tunnels). A wide range of different types of guest molecules have
been shown to form urea inclusion compounds, and the vast majority of these
inclusion compounds have the same urea host structure at ambient temperature.
Such cases are called ‘‘conventional’’ urea inclusion compounds and are charac-
terized by: (i) a hexagonal host tunnel structure (space group P6122 or P6522),
(ii) an incommensurate relationship between the periodicities of the host and guest
substructures along the tunnel axis (Figure 2), and (iii) substantial dynamic
disorder (reorientation about the tunnel axis) of the guest molecules at ambient
temperature. In most cases, order–disorder phase transitions occur at sufficiently
low temperature, and are associated with a distortion of the host tunnel (to a
lower symmetry than hexagonal) and a concomitant decrease in the reorienta-
tional motion of the guest molecules. A wide range of fundamental physico-
chemical properties are found to be exhibited by urea inclusion compounds, and
Aperiodicity in Organic Materials 307

Figure 3 Structure of the hexadecane/urea inclusion compound at ambient tempera-

ture, showing nine complete tunnels (with van der Waals radii) viewed along
the tunnel axis. The guest molecules have been inserted into the tunnels
illustrating orientational disorder (which is known, from X-ray diffraction
data and spectroscopic investigations, to exist at ambient temperature).

there has been much interest (by several research groups) in understanding the
incommensurate structural properties,1–3,13–15 the order–disorder phase transi-
tions,16–19 dynamic properties (particularly concerning molecular motion of the
guest molecules),20–25 properties relating to one-dimensional confinement,26–29
host–guest chiral recognition,30–33 chemical reactions,34 the control of crystal
morphology,35,36 and ferroelastic properties.37,38

2.3 Diffraction Properties and Structural Aspects

The diffraction properties and structural properties of a commensurate inclu-
sion compound are similar to those of a conventional crystal. The periodicities
of both the host and guest molecules are described by a common three-
dimensionally periodic lattice and the symmetry of the structure is described
by a conventional three-dimensional space group. All diffraction maxima in the
diffraction pattern are described by a single three-dimensionally periodic
reciprocal lattice, and are indexed by three integer Miller indices (H, K, L).
Failure to be able to account for the positions of all maxima in the diffraction
pattern of an inclusion compound by a single three-dimensionally periodic
reciprocal lattice (or the need to employ non-integer Miller indices) often
provides the first indication that the structure may be incommensurate.
308 Chapter 19
For a tunnel inclusion compound in which the host and guest substructures
are incommensurate along the tunnel (c-axis), the two substructures are usually
commensurate in other directions by virtue of the fact that the guest molecules
are constrained to occupy the host tunnels. Thus, when the structure is
projected on to a plane perpendicular to the tunnel axis, there is a commen-
surate relationship between the host and guest substructures, and they thus
have a common a*b* reciprocal lattice plane.
Each substructure in the inclusion compound can be considered in terms of an
incommensurately modulated ‘‘basic structure’’. The basic structure has three-
dimensional lattice periodicity and has crystallographic symmetry described by
a three-dimensional space group. The incommensurate modulation to a given
basic structure represents the structural perturbations that arise from its inter-
action with the other substructure. Thus, the basic structure itself is a hypo-
thetical entity, and represents the structure to which the real substructure would
relax if there were no interaction with the other substructure (i.e. in the absence
of host–guest interaction). Clearly, the incommensurate modulations in one
subsystem have the same periodicity as the basic structure of the other sub-
system, and the incommensurate inclusion compound can be considered as an
intergrowth of two incommensurately modulated substructures.
To illustrate the concept of an incommensurate modulation, Figure 4 shows
a schematic case of a displacive modulation in a one-dimensional array of
atoms (which could, for example, represent the guest substructure in a tunnel
inclusion compound). The period of the basic structure is denoted cb and the
period of the modulation is denoted cm. Clearly the modulation is incommen-
surate if the ratio cb/cm is irrational.

(a)
z
cb
(b)
d(z)

cm z

(c)

Figure 4 Schematic illustration of a one-dimensional structure (an array of atoms)

containing an incommensurate displacive modulation: (a) the one-dimen-
sional basic structure with periodicity cb, (b) the modulation function, which
in this example is a sinusoidal wave with wavelengh cm (the value of d(z)
indicates the displacement along z of an atom located at position z in the
basic structure), and (c) the actual modulated structure (the modulation is
incommensurate if cm/cb is irrational).
Aperiodicity in Organic Materials 309
1,7,13,14
Returning to urea inclusion compounds, the lattice describing the
periodicity of the basic host structure is {ah, bh, ch} and the corresponding
reciprocal lattice is {ah*, bh*, ch*}. The lattice describing the periodicity of the
basic guest structure is {ag, bg, cg} and the corresponding reciprocal lattice is {ag*,
bg*, cg*}. The vectors ch and cg are parallel to each other and are directed along
the tunnel axis. As a consequence of the incommensurate relationship between ch
and cg, the complete diffraction pattern from the inclusion compound cannot be
rationalized on the basis of a single three-dimensionally periodic reciprocal
lattice. Thus, it is not possible to express the positions (S*) of all diffraction
maxima within the diffraction pattern in terms of a linear combination
S
¼ Ha
1 þ Ka
2 þ La
3
of three reciprocal lattice vectors {a1*, a2*, a3*} with integer coefficients H, K
and L. For an incommensurate tunnel inclusion compound, one additional
reciprocal lattice vector (a4*) is required in order to have integer indexing of all
maxima in the diffraction pattern. Thus,
S
¼ Ha
1 þ Ka
2 þ La
3 þ Ma
4
with integer coefficients H, K, L and M.
In practice, one possible choice for the set of reciprocal lattice vectors {a1*,
a2 , a3*, a4*} for a urea inclusion compound is {ah*, bh*, ch*, cg*}, recalling that
*

the host and guest substructures have a common a*b* reciprocal lattice plane,
and hence ah* ¼ ag* and bh* ¼ bg*. The diffraction maxima, which are indexed
by the four integer Miller indices (H, K, L, M), can be subdivided as follows:

(i) M ¼ 0: ‘‘main reflections’’ from the host substructure, which primarily

contain information on the basic host structure, but also contain
information on the incommensurate modulations within the guest sub-
structure (note that these modulations have the same periodicity as the
basic host structure).
(ii) L ¼ 0: ‘‘main reflections’’ from the guest substructure, which primarily
contain information on the basic guest structure, but also contain
information on the incommensurate modulations within the host sub-
structure (note that these modulations have the same periodicity as the
basic guest structure).
(iii) L a 0 and M a 0: ‘‘satellite reflections’’ that arise due to the inter-
modulations of the two substructures.

Clearly the (H, K, 0, 0) reflections are a superposition of main reflections from

both substructures, representing the common a*b* reciprocal lattice plane
discussed above.
We note that the satellite reflections with L a 0 and M a 0 are typically very
weak in comparison with the other types of reflections in the diffraction
pattern. A normal powder X-ray diffraction pattern of a urea inclusion com-
pound (Figure 5) shows no discernible evidence for these satellite reflections
(note that reflections of the type (H, K, 0, M) are also significantly weaker than
310 Chapter 19

Intensity (a.u.)

h
h
g m h gg h
h h
h
2θ
10 20 30 40

Figure 5 Powder X-ray diffraction pattern of the 1,8-dibromooctane/urea inclusion

compound. Peaks labelled ‘‘m’’ are of the type (H, K, 0, 0), peaks labelled ‘‘h’’
are of the type (H, K, L, 0), and peaks labelled ‘‘g’’ are of the type (H, K, 0, M).

those of the type (H, K, L, 0), in part as a consequence of the dynamics20–25 of

the guest molecules). To observe the reflections with L a 0 and M a 0, and thus
to provide direct evidence for the incommensurate inter-modulation of the host
and guest substructures, one-dimensional scans through reciprocal space have
been recorded for a single crystal of the 1,10-dibromodecane/urea inclusion
compound using synchrotron X-ray radiation (on Station 16.3 at Daresbury
Laboratory). A typical scan of this type is shown in Figure 6, and was carried
out as a function of L for fixed H and K, with the specific H and K chosen such
that the scan passed through main reflections (H, K, 0, M) of the guest
substructure but did not pass through main reflections (H, K, L, 0) of
the host substructure (note that although the host and guest substructures
are commensurate in projection onto the plane perpendicular to the tunnel axis,
the guest substructure in the 1,10-dibromodecane/urea inclusion compound39 is
a superstructure of the host substructure in this plane). This scan reveals direct
evidence for the existence of satellite reflections with L a 0 and M a 0, which,
as expected, are substantially weaker than the other types of reflections in the
diffraction pattern.
Given that four reciprocal lattice vectors are required to describe the positions
of all maxima in the diffraction pattern, we now consider how this situation
transforms to describe the real structure in direct space. For urea inclusion
compounds, the structural periodicity in direct space requires four lattice vectors
and the symmetry of the composite inclusion compound can be described using a
four-dimensional space group.1,13 Thus, in general, for a material that is incom-
mensurate in d dimensions, the symmetry can be described in a (3+d)-dimensional
space group.40–44 Here we focus only on the case, exemplified by urea inclusion
compounds, in which d ¼ 1. We note that only a subset of all (3+d)-dimensional
Aperiodicity in Organic Materials 311
20

(H, K, 0, 1)
15
Satellite
(H, K, 1, –1)
Satellite
10
Intensity
(H, K, 1, 1)

5 c∗ c ∗h
g

0
0 1 2 3 L
1 2 3 4 5 M

Figure 6 One-dimensional scan through reciprocal space for the 1,10-dibromodecane/

urea inclusion compound parallel to the cg* direction (or ch* direction,
which is parallel to cg*), for fixed values of H and K. The horizontal axis is
labelled both according to the guest reciprocal lattice vector cg* (Miller index
M) and the host reciprocal lattice vector ch* (Miller index L). Note:
ch* ¼ 1.65 cg* for 1,10-dibromodecane/urea. Two satellite reflections
(H, K, 1, 1) and (H, K, 1, 1) are observed in this scan. Note that, because
of the particular H and K values chosen for this scan, there is no main
reflection from the host substructure at (H, K, 1, 0).

space groups are actually suitable for describing the symmetry properties of a
material that is incommensurate in d dimensions, as some stringent conditions
exist for a higher-dimensional space group to be suitable in this regard. Thus, not
all symmetry operators in (3+d)-dimensional space are allowed for incommen-
surate crystals, and in particular, symmetry operators that mix the coordinates
corresponding to three-dimensional space with the additional coordinates
arising because of the incommensurateness are forbidden. As a consequence, for
materials (such as urea inclusion compounds) that are incommensurate in one
dimension, only 775 of the 4895 four-dimensional space groups satisfy these
stringent conditions.
It is important to recall that, while the symmetry of an incommensurate one-
dimensional inclusion compound can be completely described using an appro-
priate four-dimensional superspace group, the real material is a three-dimensional
entity that exists in the same three-dimensional world that we live in. Thus, the
real incommensurate material can be regarded as an appropriate three-dimen-
sional section through the four-dimensional space that is required to define the
symmetry of the system. The Fourier transform of the four-dimensional direct
space is a four-dimensional reciprocal space, in which each diffraction maximum
is described by four integer Miller indices (H, K, L, M) as discussed above. Again,
the actual experimental diffraction pattern is measured in three-dimensional
space, and corresponds to an appropriate projection of the four-dimensional
reciprocal space onto three-dimensional space. It is relevant to note that, upon
Fourier transformation, a three-dimensional section through four-dimensional
312 Chapter 19
direct space transforms as a three-dimensional projection of the corresponding
four-dimensional reciprocal space.
The methods of superspace symmetry have been used to derive the four-
dimensional superspace groups that are applicable in the case of incommensu-
rate urea inclusion compounds,13 and superspace descriptions for the specific
cases of the heptadecane/urea,15 octane/urea,45 octanedioic acid/urea46 and
suberic acid/urea47 inclusion compounds have been reported.
It is important to emphasize the benefits of understanding the symmetry
properties (and structural properties) of the composite inclusion compound in a
four-dimensional superspace group, rather than restricting the structural
description of such materials at the level of the separate basic host and basic
guest structures. Knowledge of the structural properties of the separate basic
structures contains no information on the modulations within each subsystem
in the real inclusion compound. Even though the modulations may in some
cases represent rather small structural perturbations, they may nevertheless
have an important bearing on properties of the inclusion compound.

2.4 Energetic Aspects

As discussed in several other chapters of this book, the structure of any
crystalline material arises as a consequence of the drive to attain an energetically
favourable arrangement of the constituent molecules, and thus the observed
structure arises as a consequence of the underlying energetic properties of the
system. Similarly, to obtain a fundamental understanding of the incommensurate
versus commensurate nature of a one-dimensional inclusion compound, it is
necessary to understand the energetic properties of the system. Thus, the struc-
tural definition of incommensurate versus commensurate systems, based on the
rationality of the ratio cg/ch, is merely a consequence of the underlying energetic
properties, and it is essential to understand the energetic factors that lead to
incommensurate or commensurate behaviour in these materials.
To obtain a more fundamental understanding of this issue, a commensurate/
incommensurate classification that reflects a division in the energetic ‘‘behav-
iour’’ of one-dimensional inclusion compounds has been developed.3 We begin
by considering the key definition of commensurate/incommensurate behaviour
within this theoretical approach. For a given value of guest periodicity cg, we
consider the fluctuation in the average host–guest interaction energy per guest
molecule as the guest substructure is moved along the tunnel, keeping cg fixed.
If the fluctuation is sufficiently small (i.e. less than e, where e is a physically
relevant energy quantity for the system of interest), the inclusion compound is
considered to exhibit incommensurate behaviour (Figure 7a). In principle, for
an incommensurate system in which the tunnel has infinite length, the fluctu-
ation is exactly zero. On the other hand, if the fluctuation is sufficiently large
(i.e. larger than e), the inclusion compound is considered to exhibit commen-
surate behaviour (Figure 7b). In the commensurate case, energetic ‘‘lock-in’’
between the host and guest substructures will occur for a specific position of the
Aperiodicity in Organic Materials 313
<Ehg> (a)

+ε
λ
−ε

<Ehg> (b)

+ε
λ
−ε

Figure 7 Schematic illustration of the fluctuation in the average host–guest interaction

energy (oEhg4) as a function of the position (l) of the guest substructure
relative to the host substructure in a one-dimensional inclusion compound
for (a) incommensurate behaviour and (b) commensurate behaviour.

guest substructure relative to the host substructure. For the incommensurate

case, the energy of the inclusion compound is essentially independent of the
position of the guest substructure relative to the host substructure. It is
important to note that, even for an inclusion compound for which the optimal
value of cg corresponds to incommensurate behaviour, the fluctuation in host–
guest interaction energy for a single guest molecule translated along the host
tunnel can be large – the important issue underlying the definition of an
incommensurate material is not the fluctuation in the host–guest interaction
energy for a single guest molecule but rather the fluctuation in the host–guest
interaction energy averaged over the complete set of guest molecules along the
tunnel.
With this basic definition of the energetic distinction between incommensu-
rate and commensurate systems, methodology has been developed5 for applying
these concepts to predict structural properties of one-dimensional inclusion
compounds from knowledge of potential energy functions for the inclusion
compound (assuming that the host structure is known and ch is fixed). Funda-
mental to this approach is the definition of an appropriate energy expression –
the ‘‘characteristic energy’’ of the inclusion compound – that directly indicates
the relative energetic favourability of inclusion compounds with different guest
periodicities. The ‘‘characteristic energy’’ defined as:
! !
1 1 Xn1
^ nÞ ¼
Eða; inf Eh ðka þ lÞ þ E^guest ðaÞ þ E^intra
a l n k¼0
314 Chapter 19
In this expression, n is the number of guest molecules in the host tunnel, a is the
ratio cg/ch (representing a scaled guest periodicity), the first guest molecule is
located at position t ¼ l along the tunnel, Eh(t) is the host–guest interaction
energy for an individual guest molecule at position t along the tunnel, E^guest (a)
is the guest–guest interaction energy per guest molecule when the scaled guest
periodicity is a, and E^intra is the intramolecular potential energy of the guest
molecule (it is assumed that all guest molecules adopt the same conformation
inside the tunnel, as required for a strictly periodic system). As elaborated fully
elsewhere,3,5 a critical feature of the definition of characteristic energy is the
factor 1/a, which ensures that the characteristic energy refers to energy per unit
length of tunnel, rather than energy per guest molecule. The potential energy
functions Eh(t), E^guest (a) and E^intra may be readily computed using appropriate
potential energy parameterizations for the inclusion compound of interest. The
optimum guest structure for the inclusion compound corresponds to minimum
characteristic energy, and methodology has been developed3,5 to allow the
following structural properties to be predicted for the inclusion compound of
interest: (i) the optimum value of the guest periodicity cg, (ii) whether the
optimum value of cg corresponds to commensurate or incommensurate behav-
iour, and (iii) the optimum conformation of the guest molecules within the host
structure. The method has been applied successfully to predict structural prop-
erties of alkane/urea inclusion compounds48 in good agreement with experi-
mental results. The method has also been used to rationalize unusual
conformational behaviour in a commesurate inclusion compound.49
In Section 2.1, our structural classification of a commensurate material was
based on the ability to find sufficiently small integers p and q such that
pch E qcg, with the material otherwise classified as incommensurate. Relevant
questions in this regard are how small is ‘‘sufficiently small’’ and what do we
mean by ‘‘approximately equal to’’? The mathematical analysis in Ref. 3
approaches the definition of commensurate/incommensurate systems purely
from the viewpoint of the energetic behaviour of the material, but this
approach is found to lead to excellent agreement with the commonly applied
practical criterion that a one-dimensional inclusion compound is commensu-
rate if and only if sufficiently small integers p and q can be found such that cg/ch
is approximately equal to p/q. However, the energetic definition is successful in
giving mathematical rigour to the somewhat vague terms ‘‘sufficiently small’’
and ‘‘approximately equal to’’, and provides a more fundamental approach for
understanding the basis of incommensurateness in such materials.

2.5 Some Physical Properties Relating to Incommensurateness

Incommensurateness in a solid inclusion compound can have important con-
sequences for some physical properties of the material, including: (i) the
distribution of guest molecule environments (with implications for issues such
as host–guest chiral recognition, chemical reactions and inhomogeneous broad-
ening of spectral lines), (ii) vibrational properties, and (iii) the possibility of
Aperiodicity in Organic Materials 315
activationless transport of guest molecules through the tunnels. This section
discusses some issues relating to each of these aspects.

2.5.1 Distribution of Guest Molecule Environments

An important consequence of an incommensurate relationship between the
host and guest substructures in an incommensurate inclusion compound is that,
in principle, each guest molecule within a given tunnel samples a slightly
different local environment with respect to the host structure. For a commen-
surate material, on the other hand, the guest molecules in the tunnel sample
only one or a small number of different local environments within the host
structure. Clearly several chemical and spectroscopic properties of the guest
molecules may reflect these differences in the distribution of local environments
for commensurate and incommensurate systems.
For example, if a chemical reaction of the guest molecules occurs for which
the mechanism is highly sensitive to the local environment, the product
obtained from the reaction may be critically dependent on the exact location
of the guest molecule within the host structure. Such a reaction occurring in an
incommensurate inclusion compound would be expected to lead to a product
distribution that reflects the distribution of local environments of the reactant
guest molecules. Another scenario would be for the reaction of each guest
molecule to lead to the same product, but for the rate of reaction to depend on
the exact location of the guest molecule within the host structure. In this
situation, the incommensurate nature of the material would lead to a distribu-
tion of rate constants for the reaction, and so-called ‘‘dispersive kinetics’’.50
Another physical manifestation of incommensurateness arises if the spec-
troscopic properties of the guest molecules are influenced strongly by their local
environment. In this situation, the spectroscopic properties of the guest molecules
would be expected to depend critically on the exact location of the guest molecule
with respect to the host structure, and a distribution of spectroscopic responses
would be observed for an incommensurate inclusion compound. For such ma-
terials, inhomogeneous broadening of spectral lines would be expected, leading
inter alia to the opportunity to carry out ‘‘hole-burning’’ types of experiments.
Another aspect for which the distribution of guest molecule environments
can have important implications concerns the question of host–guest chiral
recognition, which is relevant for cases in which the host tunnel and guest
molecules are both chiral. In addition to the prospects for exploiting the
chirality of the host structure through chemical reactions of the guest species,
applications based on separation of the two enantiomers of a chiral guest may
also be envisaged. Clearly, the extent of host–guest chiral recognition depends
on the extent to which the host–guest interaction energies are different for the
two enantiomers (R and S) of a chiral guest molecule within a given enantio-
morph of the chiral host tunnel. However, it is important to recall that host–
guest interaction depends on the position (z) of the guest molecules along the
tunnel, and the relative energetic preferences for the two enantiomers of the
guest may vary as a function of z. This issue becomes particularly pertinent for
316 Chapter 19
incommensurate systems, recalling that each guest molecule within the tunnel
experiences a different local environment with respect to the host structure (and
hence samples a different part of the host–guest interaction potential). For this
reason, investigations of host–guest chiral recognition in incommensurate
inclusion compounds must give due consideration to the way in which the
host-guest interaction energy varies as a function of z.
As discussed in Section 2.2, the urea tunnel structure is chiral, with the tunnel
constructed from a spiral hydrogen-bonded arrangement of urea molecules. A
given single crystal of a urea inclusion compound either contains only right-
handed spirals (space group P6122) or only left-handed spirals (space group
P6522). There is clearly considerable potential to exploit this chirality in the
properties and applications of these materials, although an important factor is
the extent to which the interaction between a host tunnel of a given chirality
(e.g. P6122) differs for the two enantiomers (R and S) of a chiral guest
molecule. In spite of the potential for exploiting the chirality of urea inclusion
compounds, virtually all reported studies of urea inclusion compounds have
focused on achiral guest molecules (an important exception is the work of
Schlenk30,31 which demonstrated experimentally that urea inclusion com-
pounds are indeed able to exhibit some degree of chiral recognition). To
investigate fundamental aspects of host–guest chiral recognition in urea inclu-
sion compounds, we have carried out computational studies of host–guest
interaction for chiral 2-bromoalkane32 and 2-hydroxyalkane33 guest molecules.
For each guest molecule considered, both R and S enantiomers were studied,
and for each enantiomer the following conformations of the end-group con-
taining the Br atom or OH group were considered: (i) Br/OH trans and CH3
group gauche (denoted by subscript t); (ii) Br/OH gauche and CH3 group trans
(denoted by subscript g). Thus, for each guest molecule, the following four
different conformation/enantiomer combinations were considered: Sg, St, Rg
and Rt. In each case, the host–guest interaction energy was determined as a
function of the position (z) of the guest molecule along the host tunnel (within
the unique range 0 r z r ch/6). Representative results for the 2-bromotetrade-
cane/urea and 2-hydroxytridecane/urea inclusion compounds are shown in
Figure 8. The results of these studies32,33 show that for all 2-bromoalkane guest
molecules considered, the Br trans conformation is preferred over the Br gauche
conformation at all positions along the tunnel for both enantiomers (in con-
trast, the Br gauche conformation is preferred for isolated 2-bromoalkane
molecules). Furthermore, in this conformation, the R enantiomer is preferred
over the S enantiomer at all positions along the tunnel of the P6122 host
structure (with the exception of 2-bromoundecane, for which some regions of
the tunnel have a slight preference for the S enantiomer). On taking into
account the incommensurate nature of the 2-bromoalkane/urea inclusion
compounds (i.e. on carrying out an appropriate averaging of the host–guest
interaction energy as a function of z), an overall excess of the R enantiomer
within the P6122 host structure is predicted in all cases. For 2-hydroxyalkane/
urea inclusion compounds, on the other hand, a substantially different picture
emerges. In general, the OH gauche conformation is preferred over the OH
Aperiodicity in Organic Materials 317

z/Å
(a) 0.0 0.5 1.0 1.5 2.0
-165

-175 Sg
E hg (z) / kJ mol-1
-185 Rg

-195 St
min

-205
Rt
-215
z/Å
0.0 0.5 1.0 1.5 2.0
-204
(b)
-208 St
E hg (z) / kJ mol-1

-212
Rt
-216
Sg
min

-220

-224
Rg
-228

Figure 8 Computed host–guest interaction energies to probe host–guest chiral recog-

nition in urea inclusion compounds. The computed host–guest interaction
energy is shown as a function of position (z) along the tunnel for a single
guest molecule of (a) 2-bromotetradecane and (b) 2-hydroxytridecane in the
P6122 urea host structure. In each case, the results are shown for both the R
and S enantiomers of the guest molecule in both the Br/OH trans and Br/OH
gauche conformations.

trans conformation. For some alkane chain lengths, there is a marked prefer-
ence for the R enantiomer over the S enantiomer, whereas for other chain
lengths, the host–guest interaction energy is lower for the R enantiomer in some
regions of the tunnel and lower for the S enantiomer in other regions (see the
results for 2-hydroxytridecane/urea in Figure 8b). In these cases, when the
results are considered over all positions of the guest molecules within the host
tunnel, it is predicted that no substantial enantiomeric excess would be
observed in the inclusion compound.

2.5.2 Vibrational Properties

As discussed in Section 2.3, the observation of satellite reflections with L a 0
and M a 0 in the X-ray diffraction pattern of a one-dimensional inclusion
compound provides direct experimental evidence for the incommensurate
nature of the material. Another opportunity to obtain direct experimental
318 Chapter 19
evidence of incommensurateness arises from consideration of vibrational prop-
erties. In particular, as now discussed, the energetic reasons that underlie
incommensurate behaviour in a solid inclusion compound have a direct man-
ifestation in terms of the acoustic vibrational modes of the material. First, we
recall that conventional crystals (including commensurate inclusion com-
pounds) have three translation invariances (i.e. a translation of the crystal with
no change of energy), corresponding to translation along the x, y and z axes in
three-dimensional space. An incommensurate one-dimensional inclusion com-
pound, on the other hand, has four translation invariances. The extra trans-
lation invariance is an internal translation invariance, and corresponds to the
shift of the guest substructure relative to the host substructure along the
incommensurate direction (as discussed above, the energy of an incommensu-
rate inclusion compound is, in principle, independent of the shift of the guest
substructure relative to the host substructure along this direction). There is an
acoustic phonon corresponding to each translation invariance in a crystal, and
therefore an incommensurate one-dimensional inclusion compound should
have four acoustic phonons and a commensurate inclusion compound should
have three acoustic phonons. The additional acoustic mode in the incommen-
surate system is called the ‘‘sliding mode’’, and observation of the sliding mode
can be taken as direct experimental evidence for incommensurate behaviour of
the inclusion compound. Unfortunately, the converse is not true, as there are
experimental reasons that the sliding mode may be difficult to detect, even if the
material is incommensurate. With this motivation, Brillouin scattering inves-
tigations51 of the heptadecane/urea inclusion compound have provided
evidence for a fourth acoustic mode, assigned as the sliding mode, thus
substantiating the incommensurate nature of this inclusion compound. How-
ever, we note that Brillouin scattering investigations for other urea inclusion
compounds have not been able to observe the sliding mode.52–54

2.5.3 Molecular Transport Processes

Many different types of solid inclusion compounds (e.g. zeolites) have found
important applications in molecular separation processes, based on the fact
that the host structure displays selectivity with regard to the incorporation of
guest molecules of differing size and shape. In the case of urea inclusion
compounds, however, the fact that the ‘‘empty’’ urea tunnel structure is
unstable limits the opportunity to develop analogous types of applications
based on molecular adsorption and/or molecular separation. Nevertheless, a
process for achieving guest exchange in urea inclusion compounds, by a
mechanism that does not proceed via the empty host tunnel structure, has been
identified and demonstrated27 to occur successfully. This process involves net
transport of guest molecules in one direction along the tunnel in the urea host
structure by inserting ‘‘new’’ (thermodynamically more favourable) guest
molecules at one end of a crystal of a urea inclusion compound (e.g. by dipping
the crystal into the liquid phase of the new guest), with the ‘‘original’’ guest
molecules expelled from the other end of the crystal (Figure 9). This mechanism
Aperiodicity in Organic Materials 319

Figure 9 Schematic illustration of guest exchange in a single crystal of a urea inclusion

compound. The original guest molecules (green) are replaced by new (ener-
getically more favourable) guest molecules (blue) by dipping one end of the
original crystal into the liquid phase of the new guest molecules.

for guest exchange satisfies the requirement that the tunnels remain fully
occupied at all stages throughout the guest exchange process, but with the
actual identity of the guest molecules changing as a function of time during the
process. Single crystal X-ray diffraction studies for a crystal that has undergone
partial guest exchange demonstrate incontrovertibly that the transport of guest
molecules occurs inside the tunnels (Figure 10). An important feature under-
lying the idea of carrying out such guest transport processes within an incom-
mensurate inclusion compound was the fact that the energy of an
incommensurate inclusion compound is essentially independent of the position
of the guest substructure relative to the host substructure (see Section 2.4),
suggesting the possibility of activationless translation of the guest substructure
along the host tunnel. However, the effects at the ends of the tunnel must also
be considered, as there may be a significant activation associated with the entry
of a new guest molecule at one end of the tunnel and/or the expulsion of an
original guest molecule from the other end of the tunnel.
To obtain deeper insights into such guest exchange processes in urea inclusion
compounds, we have used confocal Raman microspectrometry as an in situ probe
(Figure 11), demonstrating55 that this technique can yield information on the
spatial distribution of the original and new guest molecules within the crystal, and
details of how the spatial distribution of the original and new guest molecules
varies as a function of time during the process. Our work in this area has focused
primarily on the system comprising the 1,8-dibromooctane/urea inclusion com-
pound as the original crystal, and pentadecane as the new type of guest molecule.
Analysis of the Raman microspectrometry data has focused55 on studying the
variation of the intensity of the C–Br stretching band of the original 1,8-dibromo-
octane guest molecules (for the predominant trans end-group conformation), as a
function of position in the crystal and as a function of time (Figure 12). Clearly,
320 Chapter 19

Figure 10 Single crystal X-ray diffraction rotation photographs for (a) the 1,8-
dibromooctane/urea inclusion compound, and (b) the same single crystal
after partial exchange with pentadecane guest molecules (ex situ measure-
ment). The X-ray diffraction photograph shown in (b) provides clear
evidence for the presence of both 1,8-dibromooctane and pentadecane
guest molecules inside the single crystal (characteristic guest layer lines are
labelled with red and green arrows respectively).

Raman laser scanned

along the crystal
Reservoir
containing Y
liquid X
pentadecane
Z

Sealing Original single crystal of

system 1,8-dibromooctane/urea

Figure 11 Schematic illustration of the experimental assembly for in situ Raman

microspectrometry to probe guest exchange in a urea inclusion compound,
comprising the single crystal of the urea inclusion compound (green),
initially containing 1,8-dibromooctane guest molecules, attached to a
reservoir containing liquid pentadecane (blue).
Aperiodicity in Organic Materials 321
18 hours

29 hours

40 hours
Y (µm)

600 1
0
0 1000 2000 3000 0
4000 5000
RN

Figure 12 In situ time-resolved and spatially resolved monitoring of guest exchange in

a single crystal of a urea inclusion compound, using Raman microspect-
rometry. The Raman micrographs were recorded during transport of
pentadecane molecules into and along the tunnels, displacing the guest
molecules (1,8-dibromooctane) originally present. The probed region
shown represents only part of the crystal, and the transport of guest
molecules occurs from left to right (the tunnels run horizontally in the
micrographs shown). Regions coloured blue are rich in pentadecane, and
regions coloured green are rich in 1,8-dibromooctane. The time taken to
record each micrograph was ca. 28 minutes; the three micrographs shown
were recorded (a) 18 h, (b) 29 h, and (c) 40 h after commencement of the
guest exchange process.

such data provide access to quantitative information on kinetic and mechanistic

aspects of the transport of guest molecules through the host tunnel structure
during the guest exchange process. For example, at ambient temperature, the
progress of the transport process shows a linear variation with time, and occurs at
a rate in the range ca. 70–100 nm s1 (the rate of movement of the centroid of the
sigmoidal distribution shown in Figure 13a), which corresponds to between about
30–50 new guest molecules entering the tunnel per second. Furthermore, our in
situ studies employing confocal Raman microspectrometry56 have revealed that
the guest exchange process is associated with significant changes in the confor-
mational properties of the original (1,8-dibromooctane) guest molecules, corre-
sponding to a significant increase in the proportion of 1,8-dibromooctane guest
molecules with the gauche end-group conformation within the ‘‘boundary region’’
between the original and new guest molecules (Figure 13b).
We now consider the physical basis for the observation that the guest
transport process occurs at constant rate. Displacement of the complete set
of guest molecules along the tunnel relies upon insertion of new guest molecules
at one end of the tunnel and expulsion of the original guest molecules at the
other end of the tunnel. As translation of the complete guest substructure along
the tunnel in an incommensurate inclusion compound should approximate to
activationless transport, the rate limiting step of the guest exchange process
must correspond either to the entry of new guest molecules or the expulsion of
the original guest molecules at the two ends of the tunnel. Both of these
interfacial processes are expected to exhibit zeroth order kinetics, from which
the rate of the overall guest exchange process is expected to be independent of
322 Chapter 19

(a) 1.2 (b) 3

1 2.5
0.8 2

RN,G(Xo)
RN,T(Xo)

0.6 1.5
0.4 1
0.2 0.5
0 0
0 5000 10000 15000 20000 0 5000 10000 15000 20000
Xo /µm Xo /µm

Figure 13 Variation in the intensity of the C–Br stretching vibration as a function of

position along the crystal for (a) C–Br bonds in the trans conformation and
(b) C–Br bonds in the gauche conformation during exchange of 1,8-
dibromooctane guest molecules by pentadecane guest molecules. The
sigmoidal distribution in (a) reflects the replacement of 1,8-dibromooctane
guest molecules (right side) by pentadecane guest molecules (left side), with
the guest transport process occurring from left to right. The data in (b)
provides clear evidence for a local increase in the proportion of 1,8-
dibromooctane guest molecules in the gauche conformation within the
‘‘boundary region’’ (shown by blue vertical lines).

time, as observed experimentally. These qualitative concepts are currently being

embodied within the development of a rigorous kinetic model to describe the
guest transport process in these materials.
At this stage, several fundamental aspects relating to such guest exchange
processes remain to be understood, and a variety of techniques are currently
being employed for this purpose. Clearly, the development of an understanding
of the fundamentals of the guest exchange process in such materials is a pre-
requisite for developing and optimizing a range of potential applications in
molecular separation, based for example on discrimination of molecular size,
shape and chirality.

2.6 Concluding Remarks

In spite of the apparent structural simplicity of inclusion compounds based on
one-dimensional tunnel structures, it is clear that these materials display several
properties of fundamental physico-chemical significance that will continue to
challenge researchers in this field for years to come. Conceptually, the diffrac-
tion properties of incommensurate materials and the corresponding structural
descriptions in direct space extend beyond the normal crystallographic princi-
ples encountered for conventional crystals; clearly an important aspect for
future endeavour is to obtain a deeper understanding of the ways in which the
physical properties of these materials are influenced by their incommensurate-
ness, and ultimately to find strategies to exploit these properties.
Aperiodicity in Organic Materials 323

3 Quasicrystalline Materials
3.1 Introduction to Quasicrystals
At the time that I joined JMT’s research group in Cambridge in the mid-
1980s, it seemed that many of the most important developments in the
physical sciences were happening in the solid state, and it really felt like an
exciting time to be entering this field of science. Of course, JMT himself was
responsible for many of these developments and several seminal advances
were being made within his research group. Elsewhere, two particularly
revolutionary discoveries were made around this time – high-temperature
superconductivity57 (for which there was much interest locally, with Peter
Edwards, then in Cambridge, spearheading the U.K. effort in this new
field)58,59 and quasicrystals.60
The discovery of quasicrystals was made in 1984, with the observation by
Schechtman and co-workers60 that certain metal alloy materials (typified by
AlxMny) can exhibit diffraction patterns with 10-fold symmetry. This obser-
vation was apparently contradictory, as the diffraction patterns of these
materials comprise sharp Bragg-like reflections, characteristic of ordered crys-
talline materials, but yet it had long been known61 that 10-fold or 5-fold
symmetry is impossible in a crystalline material with long-range periodic order.
This issue was resolved62–64 by recognizing that certain quasiperiodic tilings
(e.g. the Penrose tiling)65 have diffraction patterns that contain sharp Bragg-
like reflections based on a 10-fold symmetric reciprocal space,66 resembling
those observed for the metal alloy materials. Such tilings67–69 are constructed
from a set of geometrically well-defined tiles, assembled according to well-
defined rules, but do not have translational periodicity. Subsequently, a wide
range of other materials have been discovered to exhibit diffraction patterns
with 10-fold symmetry, and their properties have been investigated experimen-
tally and theoretically.70–74 The term ‘‘quasicrystal’’ is now widely used for such
materials. To a large extent, structural rationalization of quasicrystals has
focused on pursuing analogies to the Penrose tiling,71–73,75 although other
quasiperiodic models have also been proposed (such as the cluster model73,76–78
based on a quasiperiodic ‘‘coverage’’, rather than quasiperiodic ‘‘tiling’’), and
symmetry properties have been rationalized in higher-dimensional super-
spaces70,79–83 employing similar principles to those used to describe incommen-
surate materials (see Section 2.3).
In spite of the huge interest in quasicrystalline materials during the last 20
years or so, the examples reported during this time were dominated by metal
alloy materials, and there was no report of a molecular quasicrystal. Recently,
however, we reported the first proposal of a quasicrystalline material in which
the building units are organic molecules, based on similar design principles to
those that are employed in the design of crystalline molecular materials – an
endeavour called ‘‘crystal engineering’’. We now give a brief description of
crystal engineering (Section 3.2), before describing some key elements of our
strategy for the design of a molecular quasicrystal (Section 3.3).
324 Chapter 19

3.2 Concepts of ‘‘Crystal Engineering’’

There is currently much interest in understanding the fundamental factors that
control the observed structural properties of crystalline organic materials as
such knowledge is an essential pre-requisite for the design of molecular crystals
for specific applications. The name crystal engineering84–89 is used to describe
this area of activity (although the term is just as frequently misused in contexts
that do not actually involve any real element of crystal design). Proper ration-
alization of the factors that control the structural properties of such materials is
often far from straightforward, as an experimentally observed crystal structure
arises from the subtle inter-play of several different types of intermolecular
interactions of comparable strengths. Nevertheless, when one specific interac-
tion (or a small number of interactions) has a dominant role in directing the
structure, it may be possible to reach a reliable rationalization of the observed
arrangement of molecules in the crystal, and hence to exploit such understand-
ing as the basis for the reliable a priori prediction of the structural properties of
other (related) materials. Most successful crystal engineering strategies have
exploited this approach, particularly by focusing on hydrogen bonding as the
basic constructional element.90,91 The success of this approach is based on the
fact that the hydrogen bond is generally more geometrically discriminating
than the other types of intermolecular interaction that arise in organic molec-
ular crystals. As discussed in Section 3.3, our work to design a quasicrystalline
molecular material has applied such crystal engineering principles.
It is relevant to note the pioneering contributions made by JMT, particularly
during the 1970s and early 1980s, towards the birth of the field of crystal
engineering through his work on photoreactivity of organic crystals,85 and
specifically on the design of crystal structures for specific targeted photochem-
ical reactions. Indeed, some of his earliest papers in this field are the first to use
the term ‘‘crystal engineering’’,86,87 and the great Russian physical chemist A.I.
Kitaigorodsky, who himself made major contributions towards deriving a
fundamental understanding of the structures of organic molecular crystals,
describes JMT in one of his seminal review articles92 as ‘‘one of the pioneers of
this particular field’’.

3.3 The Design of a Molecular Quasicrystal

Our strategy for the design of a molecular quasicrystal93 has used the Penrose
tiling (Figure 14) as the basic structural template, with the aim of positioning a
molecule at each node (vertex) of the tiling, and with each molecule forming a
robust intermolecular linkage to each neighbouring molecule (along the lines
between adjacent nodes on the tiling). It is important to emphasize that, within
this design strategy, the molecules represent the nodes of the Penrose tiling and
do not represent the tiles themselves. The two types of tile (thick rhombus and
thin rhombus) within the Penrose tiling are instead represented by the regions
of space between molecules (see below). Clearly, the intermolecular linkages
Aperiodicity in Organic Materials 325

Figure 14 A Penrose tiling, with one example of each of the seven different types of
node indicated by a red circle.

should be strong and directional (linear), such that aggregation of the mole-
cules in the proposed tiling arrangement is energetically favourable.
As highlighted in Figure 14, a Penrose tiling contains seven different types of
node, and our aim was to design a set of molecules with the same geometric
properties as each of these nodes. The angles between the lines at each node are
integer multiples of 36 1, and we therefore require a molecular core that has
10-fold symmetry (or at least approximate 10-fold symmetry), together with
linear intermolecular linkages that are oriented in the same way as the lines that
emanate from each node in the tiling. In designing an appropriate molecular
core, it is important to emphasize that molecules with 10-fold symmetry are
exceptionally rare, if not unprecedented, but the molecule shown in Figure 15a
(C30H10; 10,5-coronene) has been shown to be an appropriate candidate. To
date, however, there has been no reported synthesis of this molecule.
In our design strategy, the intermolecular linkages (representing the lines
between nodes on the tiling) are formed by substituents on the 10,5-coronene
ring of the type (Figure 15b) –(CRC)n–CO2H (n ¼ 0, 1, 2, . . .), based on the
following design elements: (i) the substituents are linear, (ii) the intermolecular
linkage formed between two such substituents is the well-known carboxylic
acid dimer motif (Figure 15c) comprising two strong O–H  O hydrogen bonds
and is such that the two substituents are collinear with each other, and (iii)
there is scope to vary, and hence to optimize, the length of the substituent by
changing n (in practice, we have found that n ¼ 1 is optimal; see below). For
n ¼ 1, the distance between the centres of two molecules linked through the
hydrogen bonding arrangement shown in Figure 15c is ca. 21.37 Å.
326 Chapter 19

Figure 15 (a) 10,5-coronene (C30H10), (b) an example of a molecule from the

C30H10m(CCCO2H)m family (m ¼ 5), and (c) the linear interaction
between two –CRC–CO2H substituents via the carboxylic acid dimer
motif, which involves two O–H  O hydrogen bonds.

Figure 16 The seven types of node in a Penrose tiling, and the corresponding molecule
from the C30H10m(CCCO2H)m family. The red ‘‘star’’ indicates the part of
the tiling that is actually ‘‘occupied’’ by the molecule shown. The relative
frequencies of occurrence of each of the seven types of node in a Penrose
tiling are indicated, where t is the ‘‘golden ratio’’ [(1+O5)/2 E 1.618].

There are seven different types of node in the Penrose tiling,67–69,94 each
characterized by a different local geometry. Figure 16 shows each type of node
together with the molecular representation based on the 10,5-coronene core and
the relevant arrangement of –CRC–CO2H substituents. All of these molecules
are members of the general family C30H10m(CCCO2H)m, with m ¼ 3–7. The
linear hydrogen-bonded linkages between neighbouring molecules represent the
lines between adjacent nodes in the tiling, and create the two types of tile (thick
and thin rhombuses) as the region between groups of four molecules (Figure 17).
We note that the optimal length (n ¼ 1) of the substituents is dictated by
properties of the thin rhombus (Figure 17). Thus, for n ¼ 0, the molecular cores
across the short diagonal of the thin rhombus would give rise to severely
unfavourable repulsive interactions. For n ¼ 1 (Figure 17a), the shortest H  H
Aperiodicity in Organic Materials 327

Figure 17 (a) The thick rhombus and thin rhombus in the molecular representation of
a Penrose tiling, generated from groups of four molecules from the
C30H10m(CCCO2H)m family interacting through hydrogen bonding in
the carboxylic acid dimer motif. (b) The molecular quasicrystal constructed
from the Penrose tiling shown in Figure 14 (showing exactly the same
region of the tiling as Figure 14). Examples of the thick rhombus and thin
rhombus are shaded blue and green respectively.

distance across the short diagonal of the thin rhombus is ca. 2.3 Å, which is close
to the optimal van der Waals contact distance for a non-bonded H  H inter-
action. Values of n Z 2 would lead to an unfavourably low density of molecular
packing in the plane. As our proposed molecular quasicrystal is composed of
seven different molecules, it is thus analogous to a multi-component co-crystal
material. For an infinite Penrose tiling, the seven different types of node occur in
well-defined frequency ratios, as shown in Figure 16, and the relative frequency
of occurrence of each of the seven types of molecule in the quasicrystal should
match these ratios.
Starting from the Penrose tiling shown in Figure 14, the corresponding
molecular quasicrystal constructed using the strategy discussed above (after
minimization of the intermolecular potential energy) is shown in Figure 17b,
and the X-ray diffraction pattern calculated for this molecular quasicrystal is
shown in Figure 18. Clearly, the diffraction pattern has sharp Bragg-like
maxima, and the positions and intensities of these diffraction maxima define
a 10-fold symmetric reciprocal space, as found for established classes of
quasicrystals based on metal alloys. In the course of our work, we have
generated a large number of finite sections of Penrose tilings and constructed
the corresponding molecular quasicrystals. The diffraction patterns obtained in
each case are essentially indistinguishable from each other, provided the
sampled section of tiling used to calculate the diffraction pattern is sufficiently
large. Patterson maps corresponding to these molecular quasicrystals are also
essentially indistinguishable, provided again that a sufficiently large section of
the tiling is sampled. These observations follow directly from well-established
328 Chapter 19

Figure 18 X-ray diffraction pattern calculated for the molecular quasicrystal shown in
Figure 17b. Note: a denotes the distance between the centres of adjacent
molecules (after relaxation) and has the value a ¼ 21.37 Å.

properties of Penrose tilings,65,67–69 in particular the fact that any region of a

given Penrose tiling can be found to exist in any other (infinite) Penrose tiling.
Future extensions of the design strategy to generate a structurally more diverse
range of molecular quasicrystals based on generalized Penrose tilings94 will lead
to well-defined differences between the diffraction patterns and Patterson maps
of different molecular quasicrystals (generalized Penrose tilings involve other
types of node, all of which are represented by molecules within the
C30H10m(CCCO2H)m family, in addition to the seven types of node of the
standard Penrose tiling).
The primary challenge for preparation of the quasicrystal from the seven
molecular components, for example in a crystallization experiment, will be to
direct the crystallization towards the desired quasicrystal instead of other
competing processes, such as the formation of crystalline phases comprising
a single type of molecule, or co-crystals comprising two or more types of
molecule. At present, none of the individual molecules shown in Figure 16 have
been synthesized and their crystal structures are unknown, and we are therefore
unable at this stage to assess the relative energetic properties of the molecular
quasicrystal versus such crystalline phases.
Finally, we note that the design shown in Figure 17b is a two-dimensional
quasicrystalline molecular array, and to extend this concept to construct a
three-dimensional quasicrystal implies appropriate stacking of these two-dimen-
sional sheets. In addition to the aim of achieving the experimental realization of
a three-dimensional molecular quasicrystal, the study of two-dimensional
quasiperiodic molecular arrays (such as that shown in Figure 17b) adsorbed
Aperiodicity in Organic Materials 329
on appropriate substrates would also be interesting, particularly from the
viewpoint of controlling and understanding surface structural properties.

3.4 Future Directions

The successful strategy to design an energetically stable quasicrystal constructed
using organic molecules as the building units represents the first proposed
example of a molecular quasicrystalline material. The proposed molecular
quasicrystal has arisen through rational design principles, based on the central
idea of identifying discrete molecular building units that promote strong inter-
molecular interactions in well-defined local geometric arrangements that corre-
spond to the local geometries of nodes in the Penrose tiling. Our strategy
provides a basis not only for the realization of quasicrystalline molecular
materials based on the standard Penrose tiling, but can also be extended directly,
by appropriate selection of other well-defined sets of molecular building units
within the C30H10m(CCCO2H)m family, to design molecular quasicrystals based

Figure 19 Proposal of a new macromolecular quasicrystal, based on the 10,5-

coronene core (a) representing the nodes in a Penrose tiling and linear
tetraethynyl linkages representing the lines between adjacent nodes (b).
330 Chapter 19
on generalized Penrose tilings. Further generalizations of our strategy to design
other types of quasiperiodic molecular material, including those based on other
‘‘forbidden’’ symmetries such as 7-fold or 8-fold, may also be readily envisaged.
Another future direction95 concerns the design of a macromolecular quasi-
crystalline array, in which the hydrogen bonded linkages between nodes are
replaced by covalent linkages. In this regard, our present focus is directed
towards the material shown in Figure 19 containing linear covalent tetraethynyl
linkages, for which computational investigations are currently underway to
explore the electronic properties. At least at a superficial level, the resemblance
to graphene sheets96 may be noted.

Acknowledgements
As discussed in Section 1, I am grateful to Professor Sir John Meurig Thomas
for introducing me to the fascinating subject of urea inclusion compounds (as
well as to many other areas of research in solid state science) and for the many
aspects of help and guidance that he has given to me over the years. I am also
grateful to the members of my research group and research collaborators who
have made substantial contributions to our research in the specific areas
covered by this article (particularly Mao-Hsun Chao, Arnaud Desmedt,
François Guillaume, Mark Hollingsworth, Benson Kariuki, Andrew Rennie,
Javier Martı́-Rujas, Lily Yeo, Zhongfu Zhou and others mentioned in the
references cited). Fang Guo is thanked for help in the preparation of figures for
this article.

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CHAPTER 20

From the Synthesis of Acetylenic

Natural Products to Seeing the
Light with Polymers
ANDREW B. HOLMES,a,b PAUL L. BURN,c
ARNO KRAFT,d JONATHAN M. WHITEa AND
WALLACE W. H. WONGa
a
School of Chemistry, Bio21 Institute, The University of Melbourne,
Melbourne, Victoria 3010, Australia; b Department of Chemistry, Imperial
College, South Kensington, London, SW7 2AZ, UK; c School of Molecular
and Microbial Sciences, University of Queensland, St Lucia, Qld. 4072,
Australia; d Chemistry, School of Engineering and Physical Sciences, Perkin
Building, Heriot-Watt University, Edinburgh EH14 4AS, UK

1 Introduction
In 1972 Andrew Holmes was appointed as a University Demonstrator (Univer-
sity Assistant Lecturer) in the Department of Organic, Inorganic and Theoretical
Chemistry at the Cambridge University Chemical Laboratory in Lensfield Road.
Working with Professor Ralph Raphael, he and Nick Wellard developed the
synthesis of conjugated cis-enynes; application of this method to marine natural
products unexpectedly produced a polymer that led to a stimulating interaction
with Professor John Meurig Thomas and ultimately Richard Friend in the
Cavendish Laboratory. This chapter is a personal historical account of the work
in Cambridge which led to the serendipitous discovery of light emitting polymers
and the formation of Cambridge Display Technology.

2 Conjugated cis-Enynes and Polydiacetylenes

In 1971 Witkop and Daly reported the structure of the spirocyclic piperidine
alkaloid histrionicotoxin 1.1 (Scheme 1), which had been isolated from skin
extracts of the Colombian poison arrow frog Dendrobates histrionicus.1
334
Synthesis of Acetylenic Natural Products 335
Cl
O

O
NH OH SiMe3
Br

Histrionicotoxin 1.1 cis-Maneonene-A 1.2

Scheme 1 The frog venom alkaloid histrionicotoxin 1.1 and the Hawaiian marine
natural product cis-maneonene A 1.2.

OH SiMe3 H , Lindlar catalyst

2 OH Bu4NF OH
methanol
2.1 2.2 2.3
65%

SiMe3

Scheme 2 The synthesis of a model cis-enyne 2.3 for histrionicotoxin.

In addition to its intriguing structure (including the presence of two pendant

cis-enyne side chains) this alkaloid exhibited fascinating properties as a selective
inhibitor of the nicotinic acetyl choline receptor, and there was a real demand
for its synthesis, especially as a ban had been placed on the export of frog skins
from Colombia. In addition, frogs reared in captivity did not secrete this
particular compound, suggesting that its origin was dietary. We commenced
work on the synthesis of histrionicotoxin. In the intervening years, the molecule
has been synthesised by a number of research groups2–4 including, ultimately,
our own.5,6 Our approach, developed in collaboration with Professor Ralph
Raphael, to a model compound 2.3 containing a cis-enyne side chain is shown
in Scheme 2.7
Partial catalytic hydrogenation of the less hindered (internal) triple bond
afforded selectively the silylated enyne that was deprotected with fluoride ion to
afford the required model compound 2.3. Having developed a suitable method
for the introduction of the cis-enyne grouping we searched the literature for
other natural products containing this side chain. Our attention was drawn to
the family of maneonenes isolated from the Hawaiian red alga Laurencia
nidifica by Erickson and colleagues.8 The attraction of cis-maneonene A 1.2
(Scheme 1) was that it had not been previously synthesised and, there being no
further supplies of the natural material in existence, that a trip to Oahu would
ultimately be necessary to collect further samples of the natural material to
compare with our synthetic material.
336 Chapter 20
OH OH SiMe3
O O O
CHO
SiMe3 H2, Lindlar catalyst
Li
hexane-MeOH-EtOAc
MgBr2, ether -78 °C O O
O OMe SiMe OMe
OMe
Br 51% H H
Br Br

3.1 3.2 (major diasteroisomer) 3.3

OH SiMe3 Cl SiMe3
O O
200 °C Me2NC(Cl)=CMe2 Bu4 N+ F - cis-maneonene A
0.1 mm Hg CH2 Cl2, 0 °C THF, 25 °C
30 min 59% O
30 min, 40%
O
20% Br Br
3.4 3.5

Scheme 3 End stages of the synthesis of cis-maneonene A 1.2.

OH
O

Recrystallise
from aq. MeOH Blue-black metallic like material
O
OMe SiMe3
H
Br 3.2

1. Bu4N+F- in THF, 25 °C
2. Recrystallise from EtOAc-petroleum

OH
O
on standing in light
(or heat, or γ-rays)
O
OMe
H
Br 4.1

Scheme 4 Desilylation of the silylated diacetylene to produce the diyne 4.1.

The last stages of our synthesis of cis-maneonene A 1.2 are summarised in

Scheme 3. The partial catalytic hydrogenation sequence worked perfectly to
introduce the cis-enyne functionality (3.3), and the remaining steps were com-
pleted in short order through the intermediates 3.4 and 3.5. In order to know the
relative stereochemistry of the hydroxy-substituent in the intermediate diacety-
lene 3.2 we attempted to grow crystals suitable for X-ray analysis by recrystal-
lisation from aqueous methanol. Surprisingly, we obtained blue-black crystals
with a shiny metallic appearance on the surface (Scheme 4 and Figure 1).
We subsequently discovered through the collaboration about to be described
that if the silylated diyne was desilylated with fluoride in the absence of light, a
colourless crystalline product was obtained that was the free diacetylene 4.1.
Synthesis of Acetylenic Natural Products 337

Figure 1 Optical microscope images of (a) the colourless crystals of the diyne 4.1 and
(b) the blue-black crystals described in Scheme 4 (the latter using plane
polarised light).

Exposure of this material to light or heat or gamma irradiation afforded the

coloured crystals which eventually turned a jet black colour. The colourless
crystals are illustrated in Figure 1 together with a view of the coloured crystals
through an optical microscope using polarised light.
The usual reaction of a synthetic organic chemist at this stage would have
been to discard the unwanted material and to proceed to completion of the
synthesis in hand. However, we were blessed by having Professor John Meurig
Thomas as Head of the Department of Physical Chemistry. Not only was he a
world leader in the properties of solid-state materials, but also he engaged in
lively outreach to all his colleagues, including the synthetic organic chemists. So
we approached him and explained what we had done, showed him the crystals
and asked his advice. We remember him taking us aside and explaining that
we had probably inadvertently prepared an ordered poly(diacetylene), which
exhibited interesting non-linear optical properties and the phenomenon of
pleochroism or anisotropy in the behaviour of the crystals to the transmission
of polarised light. He pointed us to William Jones (presently Head of the
Department of Chemistry in Cambridge) and Gordon Parkinson, who kindly
helped us acquire the image shown in Figure 1b. This clearly shows the rosy
purple appearance of the crystals through transmitted polarised light and the
essential transparency of the same crystals when turned through an angle of
about 901 through the long axis. At that time we were also strongly influenced
by two sabbatical visitors in Cambridge, Craig Eckhardt from the University of
Nebraska-Lincoln and J. Michael McBride from Yale. Through many discus-
sions and suggestions from all the above-mentioned people, we were encour-
aged to follow up this observation through investigation of the properties of the
diyne 4.1. The original sample had been prepared by Clive Jennings-White as
part of his PhD project. He was succeeded by David Kendrick who completed
the synthesis of the maneonenes (Scheme 3) and showed that crystals of the
freshly prepared diyne 4.1 were colourless.9 The original crystals were analysed
338 Chapter 20

Figure 2 Chem-3D representation of (a) X-ray crystal structure of diyne 4.1 and (b)
crystal packing.

by Dr (now Professor) Paul Raithby, but the samples and full X-ray data have
not survived the passage of time. Samples of the silylated diyne were also
prepared by Guy Pooley during his PhD project and these have recently
been reconverted into the diyne in collaboration with Dr Wallace Wong in
Melbourne; the X-ray analysis of these freshly prepared crystals was carried out
by Jonathan White in Melbourne.10 The X-ray structure is illustrated in Figure
2a and the unit cell (originally analysed by Professor McBride) is shown in
Figure 2b. Analysis of the unit cell (Figure 2b) of the crystals of the diyne 4.1
clearly shows the orientation of the diacetylene units in the ‘‘ladder-like’’
arrangement proposed by G. Wegner to explain the phenomenon of polymer-
isation of ordered diacetylenes in the solid state.11 The mechanism of this free
radical-induced process has subsequently been exhaustively analysed by Sixl
and is thought to involve alkynyl carbene intermediates.12 We therefore
followed up the original observation by monitoring the solid-state polymeri-
sation of the diyne 4.1 under gamma irradiation. Working with a PhD student,
Joan Pennington, and with Bill Jones and Gordon Parkinson, we analysed
Weissenberg photographs of the behaviour of the diyne as a function of time to
try and correlate the original order in the monomeric crystal with that in the
developing polymer. We received financial support from the British Technology
Group whose programme manager Dr Ken Hills suggested that we engage with
other collaborators to follow up the non-linear optical properties of the
polydiacetylenes. Dr Hills also drew our attention to the physics group led
by Richard Friend in the Cavendish Laboratory, and their use of polyacety-
lenes in field effect transistors.

3 Light Emitting Polymers – a Shift in Direction

Following the recommendation from Dr Hills we eventually made contact with
Richard Friend and were able, in 1988, to write a joint grant proposal for a new
UK Science and Engineering Research Council (now Engineering and Physical
Sciences Research Council) call for research under the ‘‘Molecular Electronics
Initiative’’. The proposal called for the study of polydiacetylenes and
Synthesis of Acetylenic Natural Products 339
poly(arylene vinylene)s in applications for optoelectronics. Paul Burn was
appointed to a postdoctoral position in chemistry and joined the Cavendish
team of Jeremy Burroughes and Donal Bradley. Adam Brown (physics) and
Arno Kraft (chemistry) joined the team in the following year. The project called
for the synthesis of diacetylenes and poly(p-phenylene vinylene) (PPV, 5.6) the
synthesis of which was developed and improved in Lensfield Road (Scheme 5).
In investigating the properties of this PPV as an insulating material for field
effect transistors, Jeremy Burroughes observed that it emitted green-yellow
light when sandwiched between charged electrodes. This caused much excite-
ment as, although the electroluminescence (EL) of thin films of conjugated
organic molecules had by then been well established by Tang and Van Slyke,13
no-one had expected this phenomenon in conjugated polymers. The team
rapidly turned its attention to the field of polymer EL and for about a year
had opportunities to exploit a field of research without competition from other
groups. The first results were communicated in 1990 after much effort to
protect them in patent applications.14

Cl
S S
ClCH2 CH2Cl

Cl S
5.2
5.1
Base

Cl
Quinomethide
intermediate
(detectable by UV/VIS)
S
5.3

OMe

MeOH
5.5 n
S
Cl
Heat,
H+
Heat n
5.4

n
5.6

Scheme 5 Wessling sulfonium route to PPV 5.6.

340 Chapter 20
The phenomenon of organic and polymer EL is best understood by consid-
eration of the simplified Jablonski diagrams in Figure 3.15 Photoexcitation can
excite an electron from the highest occupied molecular orbital (HOMO, the
valence band) to the lowest unoccupied molecular orbital (LUMO, the con-
duction band). Radiative decay from the first excited singlet state leads to
fluorescence. The HOMO–LUMO energy gap determines the wavelength of
light emitted and the fraction of photons emitted as a function of those
absorbed is a measure of the photoluminescence (PL) efficiency. This figure
can reach about 60% for the most efficient solid-state materials. PL in solid
organic films is generally a much less efficient process than in dilute solution
where the excited entities are kept well separate and have no efficient non-
radiative pathway by which to decay. Singlet lifetimes are generally of the order
of nanoseconds. In the EL experiment (Figure 3b) charge injection at the anode
leads to negatively charged species (radical anions or negative polarons) at the
interface of the polymer with the cathode and to radical cations (positive
polarons) at the interface with the anode. When the organic material is a thin
film of the order of 100 nm, the strong electric field created by the applied bias
voltage across the electrodes draws the charged species to the oppositely
charged electrode by a hopping mechanism from chain to chain. Charge
annihilation on the same conjugated segment results in the formation of an
exciton, which as a singlet can produce fluorescence, as in the PL experiment.
EL is therefore the consequence of fluorescence induced by double charge
injection and charge annihilation. The typical Cambridge device configuration
illustrated in Figure 4 is representative of all polymer light emitting devices
(LEDs) fabricated up to the present day.

(a)
LUMO

hν photon

HOMO

Singlet state

(b)
Cathode (Ca, Li, Al etc)
Electron injection

Conduction band
(LUMO)

Hole injection
Valence band
(HOMO) Radical anion Singlet state photon Radical cation
(positive polaron) Anode (ITO)
(negative polaron)

Figure 3 Excitation of and emission from a conjugated species by (a) photolumines-

cence and (b) electroluminescence.
Synthesis of Acetylenic Natural Products 341

* Al, Mg or Ca
*
n cathode
PPV
Indium tin oxide (ITO) External circuit
anode

glass substrate

Figure 4 A typical device configuration for a polymer LED.

OC6H13
MeO OC6H13
* CN
* *
*
n * C6H13O NC *
n
m C6H13O n R R
OMe
6.1 6.2 6.3

Scheme 6 Tunable copolymers 6.1, cyano-PPV 6.2 and polyfluorene 6.3.

The early Cambridge work showed that the wavelength of light emitted was
essentially determined by the HOMO–LUMO gap of the luminescent polymer.
The first PPV polymers 5.6 were prepared by the Wessling route (Scheme 5).16
Variation of substituents and the use of the Gilch dehydrohalogenation proce-
dure17 on derivatives of the bis-chloromethyl benzene 5.1 carrying solubilising
side chains led to solution-processible conjugated polymers that essentially
emitted over much of the visible spectrum. An important contribution was the
recognition that statistical copolymers (e.g. 6.1, Scheme 6) could be used to tune
this emission; this observation lies at the heart of all commercial light emitting
polymer technology.18,19 Many factors determine the efficiency of polymer
LEDs. These include the efficiency of charge injection, the mobility of charges
in the device (and the balance of mobility of charges), the percentage of electron-
hole recombinations that leads to fluorescence and the efficiency of out-coupling
of emitted light.15,20 In respect of the barrier to charge injection, it was discovered
that the solution-processible cyano-substituted PPV derivative 6.2 (Scheme 6)
exhibited a significantly higher electron affinity than the earlier generations of
PPV derivatives and enabled efficient negative charge injection using aluminium
electrodes, resulting in a 10-fold enhancement in device efficiency.21 This material
formed one of the very early polymers used in a bulk polymer heterojunction
photovoltaic device to reverse the LED function of the active polymer layer and
harness light and turn the energy into electricity.22

4 Polyfluorenes and Analogues

The poly(arylene vinylene)s have a HOMO–LUMO gap that is not large
enough to generate blue luminescence. This problem has been solved by the
342 Chapter 20

* *

* *
Si Si
n n
C8H17 C8H17 C6H13 C6H13

7.1 7.2

Scheme 7 Poly(2,7-dibenzosiloles) 7.1 and poly(3,6-dibenzosiloles) 7.2.

use of polyfluorenes (e.g. 6.3, Scheme 6) that have become the mainstay of most
commercial light emitting polymers.23,24 However, it has emerged that poly-
fluorene can develop a long wavelength emission (around 530 nm) that has been
attributed to the presence of fluorenone defects.25
These can be minimised by purification techniques26 or, as we have shown,
by simply replacing the carbon atom at C-9 in fluorene by a silicon atom as in
the 2,7-polydibenzosiloles 7.1 (Scheme 7).27

5 Triplet Emitters and Phosphorescence

Reference to Figure 3b indicates that the spin state of the recombining charged
species is statistical and it can be argued that this should generate three times as
many triplet excited states as singlets. The triplet states are much longer-lived
than singlets and are not efficiently emissive because they have a greater chance
of non-radiative decay than fluorescence. This problem was first addressed in
small molecule EL by Forrest and Thompson and their colleagues who showed
that incorporating phosphorescent organometallic complexes could result in
efficient energy transfer (Dexter transfer) from the organic host to the phospho-
rescent guest, leading to very large improvements in device efficiency.28 The
energy transfer must take place from a higher energy triplet host to a lower
energy phosphorescent guest, and this technology is likely to have applications in
all red organic LEDs. The opportunity exists to apply these principles to polymer
LEDs as well. The phosphorescent guest could be simply blended with the
polymer host, although there may be problems with solution processibility of the
phosphorescent small molecule, or covalently attached to the polymer host. We
and others have addressed these opportunities. We have covalently linked the
polymer host conjugatively to the phosphorescent ligand complex as in the
fluorene derivative 8.1 and also tethered the iridium(III) complex non-conjuga-
tively to the 9-position of the fluorene as in the complex 8.2 (Scheme 8).29,30
Both materials produce devices that are more efficient than the correspond-
ing blended material, but the more efficient material was the non-conjugated
tethered complex 8.1 with a long (eight carbon atoms) tether. Such approaches
require the preparation of high triplet energy polymer hosts, and the poly(3,6-
dibenzosilole) 7.2 illustrates one such opportunity.31 However, even higher
Synthesis of Acetylenic Natural Products 343

S
C8H17
C8H17 N
S
Ir
O
N

C8H17
C8H17

8.1

S N
Ir
N O
O

H17C8
8

H17C8 C8H17 H17C8 C8H17

m n m
8.2

Scheme 8 Solution-processible polymeric phosphorescent materials 8.1 and 8.2.

triplet energy host materials will be required for blue electrophosphorescent

guests.

6 Future Prospects
Cambridge Display Technology was founded by the inventors of light emitting
polymers in partnership with the University of Cambridge and Cambridge
Research and Innovation Limited. The company has developed three research
centres and a joint venture with Sumitomo.32 These efforts have produced light
emitting polymers that emit over the full range of the visible spectrum and that
have device lifetimes suitable for commercialisation in full colour flat panel
displays such as are seen in mobile telephones, hand held personal organizers
and laptop computers. Extrapolated lifetimes (in hours) for polymer devices
344 Chapter 20
under constant current driving conditions from an initial brightness of
100 cd m 2 are: Red – 400,000 h (10 cd A 1); Green – 600,000 h (14 cd A 1);
Blue – 330,000 h (9 cd A 1).33 When added to the potential of fabricating these
devices by inkjet printing techniques, prospects for commercialisation are
indeed very good. While some early products are already in the marketplace,
the growing success and improvements in liquid crystal displays will continue to
provide a focus for improvement and optimisation. However, it is already very
clear that organic luminescent materials will have applications in displays, in
solid-state lighting and in the reverse process of organic based solar cells that
are expected to contribute to the problem of sustainable power generation from
low cost large area devices.

Acknowledgement
We acknowledge with grateful thanks the personal inspiration and encourage-
ment provided by Professor Sir John Meurig Thomas throughout this project,
and it is a pleasure to dedicate this article to him. None of this work would have
been possible without the long-term collaboration with Professor Sir Richard
Friend and colleagues in the Cavendish Laboratory, and we appreciate their
inspiration, patient teaching and warm friendship over many years. We
acknowledge with thanks the contributions of our many co-workers on this
project and the generous financial support provided by the EPSRC, the
European Commission, the Australian Research Council, CSIRO, the Univer-
sity of Melbourne and the Victorian Endowment for Science Knowledge and
Innovation, and Cambridge Display Technology Limited.

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B. Witkop, Proc. Natl. Acad. Sci. U.S.A., 1971, 68, 1870.
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Williams, J.E. Davies, P.R. Raithby, J.P. Adams, I.T. Forbes, N.J. Press
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Chem. Commun., 1983, 415.
Synthesis of Acetylenic Natural Products 345
10. The crystallographic data has been deposited with the Cambridge Cry-
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R.H. Friend, P.L. Burn and A.B. Holmes, Nature (London), 1990, 347, 539.
15. A. Kraft, A.C. Grimsdale and A.B. Holmes, Angew. Chem., Int. Ed., 1998,
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Friend and R.W. Gymer, Nature (London), 1992, 356, 47.
19. P.L. Burn, A.B. Holmes, A. Kraft, D.R. Baigent, D.D.C. Bradley, A.R.
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J. Am. Chem. Soc., 1993, 115, 10117.
20. R.H. Friend, R.W. Gymer, A.B. Holmes, J.H. Burroughes, R.N. Marks,
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and W.R. Salaneck, Nature (London), 1999, 397, 121.
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Bull., 2002, 451.
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33. D. Fyfe, All Plastic OLED Displays – Hype Revived?, Plenary lecture
presented at Plastic Electronics Conference, Frankfurt, Germany, October
24–25, 2006.
CHAPTER 21

Molecular Recognition within

One-Dimensional Channels
MARK D. HOLLINGSWORTH
Department of Chemistry, 111 Willard Hall, Kansas State University,
Manhattan KS 66506, USA

1 Introduction
Just as it was a great privilege to work as a postdoctoral research associate with
John Meurig Thomas (JMT throughout this chapter), it is now a great honour
to contribute to this book that celebrates his tremendous enthusiasm for science
and his many years of leadership in the field of solid-state chemistry and
materials science. JMT has influenced my career and outlook on science in too
many ways to enumerate here, so this chapter will restrict itself to tracing some
of the origins of a long-standing research program in molecular recognition to
my postdoctoral work with him.
I had started my graduate research with Mike McBride in solid-state organic
photochemistry in 1980, the year that Mike had spent a sabbatical semester
with JMT in Cambridge. In 1983, when I wandered into Mike’s office to ask
what he thought I should do after I finished my PhD, his answer went
something like, ‘‘Why not do a post-doc with John Thomas in Cambridge?
He is one of the brightest lights in British science, and it would broaden your
horizons.’’ This was great advice. Mike was well aware of JMT’s elegant work
in both solid-state organic and inorganic chemistry, and the more I read about
this unfamiliar side of my field of research, the more intrigued I became. During
my PhD work, we had been so wrapped up with ‘‘seeing’’ the fragments
rearrange in organic crystals during solid-state reactions1–4 that the prospect of
‘‘seeing’’ atoms with electron microscopy 5–8 was tantalizing, to say the least.
By 1983, JMT’s reach in the field was already quite long. As I was digging
into his work, I found that JMT had already published articles in over 100
journals, including 25 in Nature, half of which had been published in the
previous five years. His work in solid-state organic chemistry and crystal

346
Molecular Recognition within One-Dimensional Channels 347
9–16
engineering, especially with Bill Jones, was much more familiar to me than
his work on zeolites, but throughout there were many common threads17–21
with the work that I was doing in the McBride group on the role of local stress
in solid-state reactions.
It is appropriate here to thank JMT for his tremendous patience with me as I
tried to finish my dissertation and begin my work in his group. The grant from
the Science and Engineering Research Council that was to fund my research
had started early in 1984, but the best I could do was to show up for a month in
September of 1984 to overlap with Charis Theocharis, who was wrapping up
his work in the group. The plan was to return to Yale to finalize my dissertation
and be back in Cambridge by January. Unfortunately, I learned the hard
way that it is essential to ‘‘dock’’ before you ‘‘postdoc.’’ When I returned to
Yale in October of 1984, the threads that held my dissertation together began to
fray, and I found that much of what I had written was wrong! Two months
turned into thirteen, and I finally made it to Cambridge for good in November
1985. Luckily, by then I had my own funding, so the fact that JMT’s grant
was almost finished was not as much of an obstacle. Upon reviewing our
correspondence from 1983 to 1985, I am simply amazed at how gracious
and understanding JMT was about my struggle with my dissertation as well as
my ever-unrealistic projections of when I might eventually finish it. My loss
was that JMT moved from Cambridge to the Royal Institution in the sum-
mer of 1986, so I was not able to work with him as much as I would have
otherwise.
Soon after my arrival, I set about trying to use electron paramagnetic
resonance (EPR) to observe radical pairs by photolysing long-chain peroxides
in channel-type zeolites such as silicalite (Scheme 1). From work in the McBride
group, we knew that the zero-field splitting in EPR spectra of triplet radical
pairs could provide exquisitely accurate distances between the radical centres
and that hyperfine splittings (hfs) could provide information on dynamics,1–4 so
we were optimistic that this work would complement the other research in
JMT’s group on intercalation and reactions of organic guests in zeolites and
clay minerals.
When, in the first EPR experiments, we found only isolated radicals upon
photolysis of diundecanoyl peroxide (UP) in silicalite, our attention turned
immediately to urea inclusion compounds (UICs), which we thought would be
more controllable analogs of the channel-type zeolites. My PhD research had
focused on the local stress that is generated in solid-state photofragmentation
reactions of peroxides. By using the asymmetric stretching mode of CO2 as a
probe, we had shown that reaction-generated stresses could be as large as

Scheme 1
348 Chapter 21
20 kbar (B20,000 atmospheres) in certain single crystals of peroxides.1–4
Because the rigid framework of the urea channels and the loose packing of
guests within them constrained the reaction-induced stress to be transmitted
more or less along the channel axis, this seemed like an ideal way of turning this
terribly complicated three-dimensional (3-D) problem of anisotropic stress into
a 1-D one.
The 1-D channel systems were complicated enough, however. At liquid
nitrogen temperatures, light UV photolysis of UP/urea gave a clear signal
from a triplet radical pair that had a maximum zero-field splitting when the
needle axis of the crystal (the channel axis) was aligned along the magnetic field.
However, the hfs from eight nearby protons made these spectra horribly
complex and not amenable to any simple analysis.22 Furthermore, the temper-
ature dependence of the zero-field splitting was anomalous, since it appeared
that the distance between radicals was changing as a gradual function of
temperature from 20 to 190 K instead of in discrete steps, as one might have
expected from related studies on molecular crystals.
The confusion over these deceptively simple spectra of unlabeled radicals was
resolved by employing diundecanoyl peroxide that had been labeled with
deuterium in the a and b positions (from B. E. Segmuller1). With their collapsed
hfs, the much simpler spectra from these crystals showed that between 35 and
190 K, there were at least three discrete radical pairs that existed in equilibrium
with each other.23 The symmetry averaged projections of the inter-radical
vector along the channel axis increased from 6.8 Å (Pair 1) to 8.5 Å (Pair 2) to
9.5 Å (Pair 3) as the temperature was raised. Pair 2, in which the inter-radical
separation approximated the sum of the van der Waals radii of the fragments,
was enthalpically the most stable, but Pair 3 predominated at the highest
temperatures. Although the radicals in this pair appeared to be beyond van der
Waals contact, Pair 3 was favoured by entropy at the highest temperatures
because of the increased rotational freedom that occurs in that species.
The rates of collapse of radical pairs, which were highly dispersive, were
influenced appreciably by substituents.22 Both 5-bromopentyl radicals (from
6-bromohexanoyl peroxide/urea or 6-BrHP/urea)) and 3-methyloctyl radicals
(from 4-methylnonanoyl peroxide/urea) decayed more slowly than the decyl
radicals generated in UP/urea, suggesting either that the mid-chain methyl or
the terminal bromine could act as ‘‘anchors’’ or that these provided steric
barriers to the escape of CO2 from the radical pair cage.
One question that arose, however, was whether the rates of collapse could be
influenced by terminal substituents in neighboring guest molecules. There was
ample precedent for remote substituent effects in the photoreactions of single
crystals of peroxides,1,4,24,25 so intermolecular substituent effects seemed likely.
Because of the tremendous sensitivity of EPR, it also seemed likely that mixed
UICs containing terminally substituted peroxides as dilute impurities (say 2%)
in the presence of a,o-disubstituted alkanes (98%) could be used to study the
influence of intermolecular environment on the structure and kinetics of radical
pairs (Scheme 2). Such ‘‘solvent effects’’ would be very specific since the guest
molecules were constrained to lie in the same urea tunnel and within van der
Molecular Recognition within One-Dimensional Channels 349

Scheme 2

Waals contact. The 1-D urea tunnels seemed ideal for isolating interactions
between terminal functional groups, and EPR of radical pairs seemed parti-
cularly well suited to studying their influence on solid-state reactions.
Although I made preliminary attempts to detect radical pairs in mixed UIC
crystals of 6-BrHP and 1,10-dicyanodecane during the summer of 1986, it soon
became apparent that I had no idea of whether the incorporation of the minor
guest would be random or not. As I was starting my independent academic
career in 1987, it dawned on me that the 1-D channels of urea were an especially
good way of understanding molecular recognition and that cross polarization
magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR) might be
ideal for probing these functional group interactions. This research program
appeared to have much broader implications for the field of crystal engineering
and solid-state chemistry than the original study of substituent effects on the
collapse of radical pairs.
After Kurt Zilm had joined the faculty at Yale, I had become familiar with
some aspects of solid-state NMR,26,27 but I had gained a much more detailed
knowledge of this technique while in Cambridge. In the early 1980s, JMT and
his colleagues had been pioneers in the use of solid-state NMR to study
aluminosilicates,28–34 and Kenneth Harris, who was JMT’s graduate student
and my closest colleague in Cambridge, had been studying guest dynamics of
perdeuterated hexadecane in urea with 2H NMR.35
Just as with the zeolites, where the large chemical shift dispersion of 29Si and
27
Al could be used to distinguish different sites, 13C, 15N and 19F MAS NMR
seemed well suited to ascertain and quantify the local environments of terminal
functional groups. Because the UICs were typically incommensurate solids,
the guest molecules should reside in a multitude of roughly equivalent host
environments.36–38 Extensive spectroscopic work had shown that linear hydro-
carbons and many of their terminally substituted analogs exhibited high ampli-
tude librations and/or rapid rotations about the channel axes of these inclusion
compounds.39–46 Such rapid motions suggested only modest interactions between
the hosts and guests, so the guests were expected to give rise to sharp lines in the
CP-MAS spectra. This was certainly the case for a,o-disubstituted alkanes,
whose terminal carbons typically gave sharp singlets and whose chemical shifts
were relatively insensitive to chain length in the UICs that were thought to be
incommensurate.
Although the original idea had been to study the interactions between guests
in mixed UICs, the NMR study was better suited to channel inclusion com-
pounds containing unsymmetrically substituted guests. In such systems, where
H and T are the head and tail of the guest, respectively, the end-group parity
350 Chapter 21
could be ‘‘head-to-head’’ (HH), ‘‘tail-to-tail’’ (TT) or ‘‘head-to-tail’’ (HT).
Unlike other studies of molecular recognition in the solid state, this 1-D
channel system isolated the functional groups of interest as pairs in a system
that gave essentially the same crystal packing for a wide variety of chain lengths
and functional group identities.
Because of the orientational averaging in these crystals, it seemed reasonable
that the resonances for terminal functional groups in HH and HT pairs could
be resolved and that it would therefore be possible to measure the populations
of these species. With a statistical distribution of guest orientations, the ratio of
(HH+TT) and 2(HT) would be unity, and the peak ratio for a given resonance
would be 1:1. To the extent that guest–guest and/or host–guest interactions
biased the orientation of guests in the growing crystal, however, the guests
should pack in a non-random fashion, and this would be reflected in the peak
intensities.
For the UICs, this became a study of molecular recognition during crystal
growth. Because the UICs containing guests with very short chains are un-
stable, it was necessary to use guests with a minimum of six or so carbons in
their chains. However, once these guest molecules were incarcerated within the
urea tunnel, the rigid, hydrogen-bonded host framework effectively prevented
them from undergoing either end-for-end reorientation or ‘‘reptation’’ past
each other to a new location (and recognition site) in the channel. In many
cases, such as methyl 10-undecenoate/urea (Figure 1), the chemical shift
dispersion of terminal functional groups was adequate to resolve the HH and
HT pairs, but the bias (2(HT)/(HH+TT) ¼ 1.3) was fairly small. The similarity
in molecular recognition for this unsaturated ester and its saturated analog
(methyl undecanoate, where 2(HT)/(HH+TT) ¼ 1.27)47 suggested the prefer-
ential adsorption of the ester (a hydrogen bond acceptor) onto the {0001}
growth faces of this crystal.
In other cases, such as cyanoalkanes, both the site splitting and the bias
were much larger.23 With the nitrile carbons and other nitrogen-containing
systems, however, it was necessary to distinguish site splittings (i.e. HH
versus HT) from residual dipolar interactions between 13C and 14N that were
not completely averaged by the MAS.48 Such residual dipolar interactions
are typically manifested as 2:1 doublets, which was exactly the ratio observed
for 1-cyanodecane/urea! With the incommensurate UICs in which guest–
guest interactions were relatively weak, large amplitude guest motions are
sufficient to average these interactions and give narrow singlets for each type
of site. Initially, however, this was the source of great confusion, particularly
because other authors had erroneously interpreted band doubling in related
spectra in terms of residual dipolar interactions49,50 but also because our first
dinitrile/urea ‘‘standard’’ (sebaconitrile/urea) was a commensurate structure in
which the host and guest were hydrogen bonded to each other.51 Such
hydrogen bonding effectively quenches the guest motions and gives rise to
significant residual dipolar interactions, which can be distinguished from site
splittings by their inverse dependence on magnetic field (or by labeling
with 15N).
Molecular Recognition within One-Dimensional Channels 351

13
Figure 1 C CP-MAS NMR spectrum (50.3 MHz) of methyl 10-undecenoate/urea,
showing band doubling for the methoxy carbon and the two alkenyl
carbons, but not for the carbonyl. Chemical shifts for HH and TT pairs
were established with spectra of dimethyl sebacate/urea and with 1,8-non-
adiene/urea, which gave sharp singlets for the resonances from terminal
functional groups. In this crystal, grown from methanol, there is a small bias
towards HT alignment of guests.

2 A Scale of Functional Group Interaction Energies?

Although the original goal of this work had been to study the kinetic control of
guest orientations and occupancies during crystal growth, it soon became appar-
ent that by achieving thermodynamic control of guest orientations, this method
could provide an empirically determined set of rules that could guide researchers
in their attempts to design new systems such as polar crystals and supramolecular
assemblies. In most molecular crystals, each molecule is surrounded by six nearest
neighbours, so the lattice sums that determine the overall crystal packing typically
contained several hundred terms, only a fraction of which were known accurately,
if at all. When designing new materials (or other supramolecular systems),
however, chemists needed the answers to simple questions: Which contacts are
reliable? When there is a choice between two or more interactions, which way will
it go? What is the energetic bias? By isolating functional groups as pairs in a 1-D
channel that approaches the spatial constraints of a molecular crystal, while
exhibiting the equilibrium control of partitioning that is characteristic of liquids
and gases, the goal of this research program was to answer the simple question
of ‘‘What sticks to what, and by how much?’’ Equilibrium control of the guest
352 Chapter 21
orientations in 1-D channels seemed to be a powerful way of developing a self-
consistent scale of interaction energies for a variety of functional group pairs, and
the hope was that it would complement the work of Peggy Etter and others on
hydrogen bond preferences.52–54
But how to achieve equilibrium and transferability of interactions? Because
of the chain length and stability problems mentioned above, thermodynamic
control was not possible for the UICs, so we soon turned our attention to
channel inclusion compounds of perhydrotriphenylene (PHTP; Scheme 3).
Since the mid-1960s, Mario Farina and his co-workers had studied the inclu-
sion properties of this host and had shown that PHTP, like urea, typically
formed incommensurate inclusion compounds in which the guests were packed
within van der Waals contact of each other.55–59 The crystal packing in PHTP
inclusion compounds containing linear guests was essentially isomorphous, and
the channels were separated by 14.3 Å, so interchannel ordering of guests,
which we had observed in certain UICs,60–62 was insignificant. Combined with
the relative stability of PHTP inclusion compounds containing short chain
guests, the wider (B5.7–6.7 Å) and more flexible channels of PHTP gave us a
fighting chance to observe end for end exchange of the guest molecules within
the tunnels. The channel walls of PHTP were also quite ‘‘smooth,’’ and were
composed of simple hydrocarbons, so this system minimized specific host–guest
interactions (Figure 2).
Just as with urea, the 13C CP-MAS NMR spectra of dozens of unsymmet-
rically substituted alkanes (X(CH2)nY) included in PHTP showed asymmetric
band doubling for terminal functional groups and adjacent carbons, but none
for internal carbons.63 And, once again, aliphatic nitriles exhibited a significant
bias towards head-to-head alignment (Figure 3a–c), this time with a 4:1 ratio of
(HH+TT)/(2HT). Although we had long sought equilibrium control of guest
partitioning, we were still surprised (and obviously delighted) by the spectrum of
1-cyanopentane/PHTP (Figure 3d), whose nitrile carbon region exhibited a
single, broad Lorentzian line between the peaks we had observed for HH and
HT pairs in higher homologs. As temperature dependence studies of numerous
guests have now demonstrated, 1-cyanopentane undergoes end-for-end ex-
change that is rapid enough to average the HH and HT resonances to a single
line at room temperature (Scheme 4). With the higher homolog, 1-cyanohexane,
coalescence occurs near 320 K; analysis of the spectra for this exchanging system
showed that for a two-state system (with energies EHT and (EHH+ETT)/2),
enthalpy favours the ‘‘symmetric’’ state by 5.2(3) kcal mol
1. Entropy disfavours

Scheme 3
Molecular Recognition within One-Dimensional Channels 353

Figure 2 Channel axis view of the van der Waals surface of an inclusion compound of
PHTP containing an arbitrarily oriented linear hydrocarbon. Coordinates
are from Ref. 56.

the same state by 14(3) cal mol
1 K
1, presumably because of restricted motional
freedom for the CN    NC pairs, which are thought to be overlapped signif-
icantly and tethered by dipole–dipole interactions.64
As outlined in Table 1, the use of guests with short chain lengths in PHTP
provides a general strategy for studying many other functional group pairs. The
principal criteria are isomorphous packing in a minimally interacting system
that allows equilibrium control of partitioning between functional group pairs.
This work is not without its difficulties, however. The rates of end-for-end
exchange of guests are dramatically dependent on chain length and substitu-
ents, as are the residual dipolar interactions that complicate interpretation of
these spectra. Unpublished NMR studies in our laboratory by Ulrike Werner-
Zwanziger show that the nitrile peaks in 1-cyanoheptane/PHTP show no sign
of broadening and coalescence even at 358 K, so this constrains the chain length
of the guest quite significantly.65 In those systems with longer chain guests, site
exchange can occur, however, most likely through a reptation mechanism that
does not achieve true equilibrium.
354 Chapter 21

13
Figure 3 C CP-MAS NMR spectra (50.3 MHz) of the nitrile region of nitrile/PHTP
inclusion compounds. The spectrum of the symmetric dinitrile (f) establishes
the chemical shift of the CN    NC pair, whereas that of 7-bromoheptane-
nitrile (e) helps demonstrate that the upfield resonances in a–c arise from
CN  Me pairs. Rapid end-for-end exchange in 1-cyanopentane/PHTP
produces a single Lorentzian line (d). At higher temperatures, the bands
for 1-cyanohexane/PHTP collapse to a broad singlet whose position shifts
with increasing temperature. Adapted from Ref. 63 with permission from the
American Chemical Society.

In systems with the potential for strong guest–guest interactions, such as

6-aminohexanenitrile/PHTP, band doubling again occurs in the nitrile region
(Figure 4). However, the doubling arises not from site differences between HH
and HT pairs, but from residual dipolar interactions that are not averaged by
guest motion. In this system, the guests appear to exist almost exclusively as HT
Molecular Recognition within One-Dimensional Channels 355

Scheme 4

Table 1 Rationale for using PHTP and analogs to measure functional group
interactions.
Requirements
1. Isomorphous replacement of
substituents
2. Isolation of functional group pairs
within van der Waals contact
3. Minimal bias for specific guest
positions in channel by host
4. Quantitative evaluation of partitioning
5. Transferability of interaction strengths
a. Equilibrium, not kinetic control of
guest orientations
b. DH (not DG) differences required
6. Adequate sensitivity, dynamic range
and spectral windows
7. Accurate structural characterization of
functional group pairs
8. Independent probes of interaction
strengths
Approach
Use host–guest system in which host
structure controls the packing
Use channel inclusion compounds
Use incommensurate channel inclusion
compounds in which the host is less
stable without the guest
MAS NMR of 13C, 15N, 29Si and 19F
shows site differences and occupancies
Use short chain length guests in PHTP to
allow end-for-end exchange of guests
Measure partitioning at different
temperatures
Use labeled guests (typically 15–90%)
Use a range of spectroscopic and
diffraction methods to assess pairwise
geometries in PHTP and more
tractable UICs
Use other spectroscopic probes such as IR
and Raman

pairs, so the guest molecules behave as a hydrogen bonded polymer whose

motions are relatively frozen (Scheme 5).
Although equilibrium control of guest partitioning in 1-D inclusion
compounds is necessary for measuring the energetic bias for certain pairwise
interactions, the kinetic control of guest orientations that normally occurs
with larger guests has important implications for materials design. Under
kinetic control, guest incorporation may be treated with a Markov chain
formalism,66–68 and the same sort of molecular recognition processes described
above can give rise to polar arrangements of guests. For unsymmetric guests,
the relative energetics of these three types of contacts (and in particular, the
356 Chapter 21

13
Figure 4 C CP-MAS NMR spectrum of 6-aminohexanenitrile/PHTP at 75.3 MHz.
The 2:1 doublet near 120 ppm arises from unaveraged residual dipolar
interactions between 13C and 14N in this extensively hydrogen-bonded
system, not from site differences btween H–H and H–T sites.

Scheme 5

difference between HH and TT pairs) dictate the orientation of guests emerging

from opposite ends of these crystals. For 1-(4-nitrophenyl)piperazine in PHTP,
for example, strong –NO2    H–N– interactions, weaker –N–H/H–N– inter-
actions and unfavorable –NO2/O2N– interactions give rise to a self-correcting
crystal growth mechanism in which opposite ends of the crystal are decorated
with nitro groups. As shown by the extensive work by Hulliger and colleagues
on these systems,69–77 this appears to be a general phenomenon, and it is
directly related to the broader problem of sector-dependent generation of
polarity formation in both solid solutions and pure crystals.78–82 Structure
solution of 1-(4-nitrophenyl)piperazine/PHTP required a heroic effort by some
of the world’s top crystallographers, who used diffuse X-ray scattering and
models of disorder to create an exquisitely detailed picture of the disorder in
this system.83,84
Molecular Recognition within One-Dimensional Channels 357

3 Prospects and Conclusions

Coupled with the generality of the Markov chain model, the empirical method
for assessing pairwise functional group interactions described here should
facilitate a rational approach for forming polar inclusion compounds.
Although 13C and 15N NMR studies will always require a significant synthetic
effort to prepare isotopically labeled compounds, the much higher sensitivity of
1
H NMR and especially 19F NMR make them especially well suited to efficient
measurement of interactions within functional group pairs. Alternative strat-
egies, developed by Kenneth Harris and colleagues, utilize the differential
incorporation of symmetrically disubstituted guests with different chain lengths
as a way of separating the contributions of host–guest and guest–guest inter-
actions in 1-D channel systems.85–87
The most significant challenge with this research is the determination of the
local structures of functional group pairs. Although comparisons can be made
with certain commensurate structures,23,51,62,88–90 which are often interesting in
their own right,91,92 obtaining such structures is difficult, at best, in the incom-
mensurate systems containing dynamically averaging guests.93 Nevertheless, we
are inspired by the great courage that John Meurig Thomas has shown through
his career as he has pushed the limits of diffraction and spectroscopy to sort out
the structural details of so many disordered solids.94–99 Thank you, John, for
showing us what is possible and for inspiring so many others to follow your lead.

Acknowledgments
I would like to thank A. R. Palmer, N. Cyr, K. D. M. Harris, U. Werner-
Zwanziger, M. E. Brown, J. Huang and J. W. Zwanziger for their help with this
work, which was supported by the Natural Sciences and Engineering Research
Council of Canada, the National Science Foundation (CHE-9423726,
CHE-0096157), and the donors of the Petroleum Research Fund of the
American Chemical Society (Nos. 24396-AC4 and 43708-AC10).

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J.C. Huffman, K.D.M. Harris and S.P. Smart, J. Am. Chem. Soc., 1999,
121, 9732.
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CHAPTER 22

FTIR Study of Short Range

Mobility in Some Crystalline
Peroxides: Solid-State
Rotational Isomerism of CO2
J. MICHAEL McBRIDEa AND KEVIN L. PATEb
a
Department of Chemistry, Yale University, Box 208107, New Haven,
CT 06520-8107, USA; b Department of Chemistry, Marietta College,
Marietta, Ohio, 45750, USA

1 Introduction1
I owe a great deal to organic peroxides – they helped me earn my PhD, find and
keep my academic position, and conduct a long series of research projects on
solid-state organic chemistry with outstanding collaborators.2 They were also
responsible for my meeting a loyal and inspiring friend in John Meurig
Thomas.
Azoalkanes and desperation had introduced me to solid-state chemistry.
After beginning my PhD work with Paul D. Bartlett at Harvard with a
preliminary, solution-phase peroxide project,3 I was hoping to study the
coupling of triplet-state radical pairs within a solvent cage. I planned to show
that a pair of radicals generated from a precursor with chiral carbons would
undergo more randomization by rotation when their coupling was slowed
because their azoalkane precursor had decomposed from the triplet, rather
than the singlet, photoexcited state, and I hoped that quantitative evaluation of
the phenomenon would allow estimating the rate of interconversion between
triplet and singlet states.
To my chagrin, the radicals from the azoalkane I had painstakingly synthe-
sized for this study, whatever their electronic state, were so hindered and slow
to couple that they failed to react within the lifetime of the fluid solvent cage. In
the spring of 1966, desperate to complete a respectable thesis and begin
362
FTIR Study of Short Range Mobility in Some Crystalline Peroxides 363
teaching at Yale in the fall, I decided to force cage collapse by conducting the
photolysis in frozen solutions, where mobility would be minimized.4 Even if the
result would be irrelevant to the question of electron spin correlation, it would
say something about reactions in rigid media. Most of my subsequent research
over more than 40 years has focused on how a rigid environment can control
the mobility of molecular fragments.
At first I had naively assumed that the primary effect of freezing a solution
was to make it more viscous, but reading the seminal publications of Schmidt
and Cohen on solid-state photodimerization5 soon convinced me that there
were more subtle effects to study in crystal chemistry.
Our early work at Yale focused on pure azoalkane crystals. We learned
X-ray diffraction in order to determine the initial atomic coordinates for the
reacting molecules and their neighbours, and we studied the nature and
stereochemistry of products to infer how the intermediate radical pairs had
come together, but we were particularly intrigued by the possibility of studying
the reaction intermediates directly by low-temperature electron paramagnetic
resonance spectroscopy (EPR).
During my PhD research I had used powder EPR to observe radical pairs in
my azoalkane,6 but hearing Clyde Hutchison describe his comprehensive
single-crystal work with Gerhard Closs on details of a photochemical carbene
mechanism convinced me that this technique deserved much wider applica-
tion.7 I met Hutchison, as well as Gerhardt Schmidt and Mendel Cohen, at the
Second International Symposium on Organic Solid-State Chemistry in Re-
hovot during ‘‘Black’’ September of 1970. This was surely the most influential
meeting I ever attended, in part because it convinced me that there was an
international community interested in the type of research I wanted to do.
It seemed to me that within my research lifetime simple organic reactions
were likely to become as easy to study by quantum mechanics as by experiment,
but that comparable understanding of the influence of medium on reaction
mechanism was much further in the future. Thus there would be continuing
need for reliable experimental results on medium effects. Where better to study
such effects than in single crystals, where the reaction cavity is uniform and
precisely defined? As in the case of structural studies by X-ray diffraction,
crystals would be useful for detailed mechanistic studies by EPR not only
because they enable the necessary spectroscopies, but also because they provide
well-defined structures for investigation.
Preliminary EPR studies had shown that, contrary to my intuition, molecular
fragments within a pure crystal do not fly every which way upon photolysis, but
rather that they lodge in a series of intermediate structures, each as well defined
geometrically as those determined by X-ray diffraction for the starting material.
The underlying goal of all our subsequent research on solid-state chemistry has
been not only to develop qualitative ideas about what makes solid reactions
special, but even more to determine enough geometric and energetic detail about
these reaction sequences to undergird, and provide critical tests of, a new level
of detailed theoretical simulation of reactions in condensed media. In favourable
cases, the zerofield splitting from electron–electron magnetic interaction in
364 Chapter 22
single-crystal EPR allowed determination of the length of radical–radical
vectors within a few thousandths of an Ångstrom, and their orientation in the
crystal frame within a degree or two. Anisotropy of the g- and nuclear hyperfine
splitting tensors supplied analogous information about the orientation of indi-
vidual radicals.8 Such items of information would not, by themselves, suffice to
establish atomic trajectories for the reacting molecules, but they should be more
than sufficient to identify reliable computer simulations of such trajectories.
The solid-state photochemistry of azoalkanes had proven relatively simple,
because the radical pairs formed by loss of a single nitrogen molecule between
two radicals ultimately collapsed in the crystal cage by coupling or H-atom
transfer, so we decided to study diacyl peroxides, where either one or two CO2
molecules could be lost between two radicals, and greater mechanistic diversity
was possible. Previous reports of observing methyl–phenyl (MP) or phenyl–
phenyl radical pair intermediates in diacyl peroxides were encouraging,9 and
our own work prospered, but most radical pairs were stable only below liquid
nitrogen temperature.
Might it be possible to prepare radical pairs that survive at much higher
temperature? We reasoned that although it would be difficult to immobilize
radicals as small as methyl or phenyl, bulky radicals separated by two CO2
molecules might survive at much higher temperatures. So we studied pairs of
2,2,2-triphenylethyl and triptycyl radicals, but discovered that they also found
ways to react at low temperature.10
It then occurred to us that solid-state immobility might relate not so much to
the size of radicals as to the efficiency with which they pack in the crystal lattice.
For example, a long-chain alkyl radical, despite its small cross section, might be
relatively immobile if it were efficiently packed. Studying such simple systems
was also attractive because, lacking charge, polarity, and complex functional-
ity, they seemed well suited for ultimate study by computational simulation.
Thus we embarked on a 20-year study of long-chain diacyl peroxides that kept
10 collaborators busy and generated some 3700 dissertation pages.11

2 Meeting John Meurig Thomas

In 1980, as we were beginning to study long-chain peroxides, John Meurig
Thomas, whom I will presume to refer to below as John, hosted me for a
formative sabbatical term in Cambridge. Several years earlier Mendel Cohen
had focused my attention on J.M. Thomas of Aberystwyth, who was building
on impressive accomplishments with inorganic solids to become a powerful
force in solid-state organic chemistry. Cohen and I were particularly impressed
by Thomas’s work using optical and transmission electron microscopy (TEM)
to suggest a crucial role for defects in several solid-state organic reactions.12 In
a 1975 paper with S.E. Morsi and J.O. Williams, he had described studies of
dibenzoyl peroxide, one of our favourite materials at that time.13 John and I
established a correspondence, and we met first in New York, then at the 1978
Brandeis ICCOSS conference, just as he was preparing to move to Cambridge.
FTIR Study of Short Range Mobility in Some Crystalline Peroxides 365
He graciously invited me to consider spending a sabbatical leave in Cambridge.
Within a year and a half I appeared on his laboratory doorstep.
We had planned to collaborate on studying organic peroxide crystals by
cryogenic TEM. Many hours of peering through the dark over the expert
shoulders of Gordon Parkinson convinced me that our particular samples
would be difficult for anyone to study by TEM, and impossible for me at Yale.
But the hospitality and intellectual stimulation from John and his collaborators
set me on a fruitful new research track.
I clearly remember the fascinating subjects we discussed while John led me to
luncheon at Kings College on a January day early in my sabbatical. Walking
from Lensfield Road up Tennis Court Road we discussed the possibility of
using IR spectroscopy to monitor reaction-generated local stress in crystalline
diacyl peroxides.
Turning into Pembroke Street he offered to loan me a translation of the 14th
century Welsh bard Dafydd ap Gwilym – and a pamphlet suggesting that
Prince Madoc ap Owain Gwynedd had established a Welsh Indian tribe in
America in the late 12th century.
In Free School Lane we paused at the entrance to the Old Cavendish
Laboratory to pay homage to James Clerk Maxwell, J.J. Thomson, William
Lawrence Bragg, and the others who had made it a well-spring for physics,
chemistry, and biology over more than a century.
Thus I first learned of John’s scholarly interest in the origins of our science
and of his respect for the accomplishments and humanity of our scientific
forbearers, a respect that subsequently became so clear in numerous eloquent
lectures and publications on Michael Faraday and John’s many other friends
and heroes.
We then exercised his prerogative by marching straight across the lawn at
Kings.
This was heady stuff and a suitable introduction to diverse life in John’s
intellectual and cultural fast lane. I subsequently followed up on each of the
topics we had discussed, but the one most relevant here is using Fourier
Transform Infrared Spectroscopy (FTIR) to study peroxide decomposition.

3 FTIR of CO2
Single-crystal EPR spectroscopy is a reliable workhorse for studying the motion
and reaction of radical pairs in exquisite geometric detail, as studies of long-chain
diacyl peroxides culminating in Michael Biewer’s comprehensive dissertation
have subsequently underlined.11g But insensitivity to diamagnetic intermediates,
the great strength of EPR for studying radical intermediates at very low
concentration, is also a potential liability. EPR gives only indirect information
about diamagnetic intermediates and products, and it seemed possible that it was
revealing only minor side reactions in the overall photolytic decomposition
scheme. Using isotope dilution and low conversion to prove that the dominant
products arose from the intermediates studied by EPR was very laborious.14
366 Chapter 22
Bonnie Whitsel’s EPR studies of acetyl benzoyl peroxide (ABP) suggested
that the local pressure generated by fragmenting a molecule within an otherwise
pure crystal could have dramatic influence on subsequent reactions. Despite the
possibility that such phenomena should be pervasive in solid-state reactions,
this stress was necessarily very local and difficult to measure in a lightly
damaged crystal.15 But in 1968, Riepe and Wang at Yale had used IR frequency
shifts to study the possibility that CO2 was stressed in the active site of carbonic
anhydrase.16
The high oscillator strength and unusual frequency of CO2 asymmetric
stretching made the sensitivity of FTIR comparable to that of EPR for studying
intermediates at low concentration. In the IR spectra of CO2 might chance have
provided both an ideal probe of local stress within reacted sites in diacyl
peroxides and a means to supplement EPR spectroscopy by revealing diamag-
netic reaction intermediates?
John Meurig Thomas played two key roles in helping us to realize the potential
of this technique. First, he encouraged the project begun in preliminary trials during
my term in Cambridge; second, he made substantial sacrifices to allow Mark
Hollingsworth the time to complete a remarkable thousand-page Yale dissertation
on this subject.11b Mark is one of very few individuals I know who work as hard
and effectively as John Meurig Thomas. In early 1983, as he was starting to wrap
up his experimental work on applying FTIR spectroscopy of CO2 as a probe of
stress and mechanism in crystalline diacyl peroxides, Mark determined to spend his
postdoctoral years in Cambridge. John promptly accepted Mark’s application and
arranged funding to begin in early 1984. Mark decided that it was critical to do a
few more experiments, and by early 1984 he had only begun analyzing his FTIR
spectra and writing his dissertation full time. At the same time Simon Kearsley
came to Yale from Cambridge and began to apply molecular mechanics to analyze
the peroxide EPR data we had been accumulating.17
The more Mark analyzed and wrote, the more treasure he discovered.
Despite my repeated, if half-hearted, threats to cut off his support and force
him to Cambridge, he kept analyzing and writing diligently for a year and a
half, arriving in Cambridge only in late 1985. The extraordinary sympathy and
patience of John Meurig Thomas during this productive but trying period
became as legendary at Yale as Mark’s dissertation itself, which won the ACS
prize for the best of the year.
As a tribute to John and to acknowledge his patience, the balance of this
chapter will describe a project that could never have occurred but for the time
he made available to Mark in 1984–1985.
If the reader is less patient than John and chokes on the mass of seemingly
trivial quantitative detail in the following account, let him turn to the Summary
and Apologia at the conclusion of this chapter.

4 Isotopic CO2 as a Probe of Mechanism

As his analysis progressed, Mark became increasingly confident about tiny
spectral blips that I suspected were simply residual noise in his after–before
FTIR Study of Short Range Mobility in Some Crystalline Peroxides 367
difference spectra. The fraction of peroxide molecules that had been photo-
lyzed in his experiments was very small, typically less than 1 in 2000, so
only CO2’s unique asymmetric stretching frequency allowed the discernment of
any product peaks at all among the forest of strong absorptions from
undamaged matrix molecules. In the fourth and final appendix to his thesis,
Mark interpreted apparently negligible blips as signals from natural abun-
dance 18OQCQO, which would represent less than one molecule in 100,000.
In a few cases there was a tiny blip at the 18O-mass-corrected position
corresponding to a normal CO2 peak, but in most cases there appeared instead
a pair of peaks, hardly larger than the noise, flanking that position and split by
as much as 2 cm
1. Mark attributed this splitting to two antiparallel orientat-
ions of 18OQCQO in unsymmetrical lattice sites. Although the intermolecular
forces on the two ends of such a molecule necessarily balance at the equilib-
rium structure, the intermolecular force constants could differ, creating a
difference in the asymmetric stretching frequency between OQCQ18O and
18
OQCQO.18
Nearly a decade later Kevin Pate decided to test Mark’s suggestion that this
difference would allow studying end-for-end rotation of 18OQCQO in a
suitably labeled crystalline sample.1 Kevin studied three peroxides with which
our group had long experience: ABP, di-11-bromoundecanoyl peroxide
(BrUP), and 11-bromoundecanoyl decanoyl peroxide (BrUDP).

O
ABP O
H3C O
O
O
O Br
Br O
BrUP O
O
O CH3
Br O
BrUDP O

5 ABP: End-for-End Rotation and CO2 Interchange

In previous EPR investigations Whitsel and Merrill had studied two kinds of
radical pairs in photolyzed single crystals of ABP: the methyl-benzoyloxyl
radical pair (MB) from loss of one CO2 molecule, which decays with a half-life
of 1 min at about 76 K (Ea ¼ 5.7 kcal mol
1); and the MP radical pair from loss
of two CO2 molecules, which decays at this rate at about 79 K
(Ea ¼ 7.7 kcal mol
1).15,19 Both MP and MB structures are structurally well-
defined, but selective 17O labeling showed that the benzoyloxyl radical of MB
undergoes exchange of oxygens, presumably by rotation of its
CO2 group,
with a half-life of 1 min at about 72 K (Ea ¼ 4.7 kcal mol
1).20
368 Chapter 22
O O C O
C 76K
CH3 O O
O H3C
O O
MB
O
O
H3C O MP O C O
O
O O O C O
79K
C C
H3C
CH3 O O

Hollingsworth had studied three isotopic variants of ABP using FTIR to

show that photolysis of a single crystal at 90 K, at which temperature all radical
pairs collapse, generates a single CO2 geometry in sites that have lost only the
acetoxyl CO2 and formed methyl benzoate (MB), but it generates two different
pairs of CO2 molecules corresponding to differently structured sites that
include toluene product.11b,18
In the present work we attempted to study ABP by FTIR at lower temper-
atures, where the radical pairs would be stable, and end-for-end rotation of
CO2 might be frozen. This work proved challenging, because in many exper-
iments the growth of a broad, unidentified peak21 obscured the sharp CO2
peaks of interest.
One particular crystal provided much of the information we sought. It was
grown using ABP that had been prepared by reacting acetyl chloride with
peroxybenzoic acid, which itself had been prepared by reacting 90% H2O2
with a commercial sample of 99% carbonyl 13C labeled benzoic acid. This
ABP crystal contained 1% (natural abundance) 13C in its acetyl CO2, 99%
13
C in its benzoyl CO2, and 4–7% 18O in its benzoyl carbonyl group.22 Thus,
in Figure 1, OQCQO FTIR signals (in the region 2335–2350 cm
1) originate
from the acetyl group of ABP, OQ13CQO FTIR signals (2270–2285 cm
1)
originate from the benzoyl group, and 18OQ13CQO FTIR signals
(near 2260 cm
1) originate from benzoyl groups with 18O in the carbonyl
position.
The blue curve of Figure 1, which was measured at 17 K after 15 min of
photolysis at that temperature, shows five principal CO2 peaks. (Asymmetric
stretching frequencies for the CO2 pairs in various isotopic permutations are
assigned in the Appendix.)
Some of these five peaks shift when the crystal is warmed successively to a
specified temperature (45 K, green; 70 K, orange; 90 K, red) for about 30 s
before cooling again to 17 K for measurement. Comparison of these spectra
with those from an unlabeled crystal of ABP showed that the five peaks
represent two isotopically mixed 13CO2–12CO2 pairs, whose MP radical
pairs decay to toluene, and an isolated 12CO2, whose MB radical pair decays
to MB.
The isolated peak for the CO2 molecule with the MB radical pair shows no
change whatever after warming to 90 K. This hints that in most cases this
FTIR Study of Short Range Mobility in Some Crystalline Peroxides 369

Figure 1 Asymmetric stretching FTIR spectrum (cm
1) for CO2 pairs in a crystal of
ABP that is 99% labeled with 13C in the carbonyl position of its benzoyl
group and B5% labeled with 18O in the carbonyl oxygen of the
same group. The crystal was photolyzed at 17 K and then measured at
17 K with brief annealing at the indicated temperatures. The top frame
shows peaks of unlabeled CO2 from the acetyl group. The bottom
frame shows peaks of 13CO2 from the benzoyl group. The inset shows
peaks of 18OQ13CQO from the benzoyl group. The spectra are offset in
frequency according to the differences among the corresponding is-
otopomers in the gas phase. There is a persistent peak for a single CO2
in the presence of methyl benzoate (MB). Two pairs of CO2 molecules in
the presence of methyl/phenyl radical pairs (MP and MP 0 ) decay at
different temperatures to a single pair of CO2 molecules in the presence
of toluene (T). Subscripts a and b distinguish peaks that derive from acetyl
and benzoyl groups, respectively. See Figure 2 for more detailed spectra of
18
OQ13CQO.

radical pair has already decayed at 17 K, so that the trapped MB radical

pair, whose decay at 76 K was studied by EPR, may represent a minor
pathway. EPR experiments down to 4.2 K failed to find the hypothetical
rapidly decaying MB pair.14b It is possible, but unlikely, that collapse of the
MB radical pair would fail to shift the frequency of the adjacent CO2 by at
least 0.2 cm–1.
370 Chapter 22
The CO2 pairs formed with the MP radical pairs are more interesting,
because one of the molecules is isotopically labeled. At 17 K (blue) the major
pair has a low-frequency peak for the acetyl-derived CO2 (MPa) and a high-
frequency peak for benzoyl-derived 13CO2 (MPb). The minor pair has the
opposite, a high-frequency peak from the acetyl-derived CO2 (MP 0 a) with a
low-frequency peak from benzoyl-derived 13CO2 (MP 0 b).
Upon brief warming to 45 K (green), the minor MP 0 peaks disappear,
presumably because the adjacent radical pair collapses to form toluene. The
resulting new CO2 pair has a high-frequency peak from acetyl-derived CO2 (Ta)
together with a low-frequency peak from benzoyl-derived 13CO2 (Tb). Note
that the subtle 0.2 cm–1 shift of the low-frequency peak from MP 0 b to Tb is
clearly evident. The minor radical pair associated with MP 0 and its decay below
45 K have not been observed by EPR.
Subsequent brief warming to 70 K (orange) decreases the MPa peak slightly
and increases Ta, showing that the major MP pair is beginning to convert to the
same T species formed below 45 K from the minor MP 0 pair, although most of
the major MP survives briefly at this temperature. In this case the frequency
shifts are much more dramatic: acetyl-derived CO2 shifts by 8.2 cm
1 (MPa to
Ta), benzoyl-derived 13CO2 by 5.2 cm
1 (MPb to Tb). This transition is surely
the same one observed by EPR at 79 K.23
Warming to 90 K causes the major MP species to complete its conversion to
the toluene product. More interestingly, two new peaks appear which differ
from those of the previous T pair solely in respect to which site contains 13CO2.
The new ‘‘exchanged’’ pair, TE, has a low-frequency peak from acetyl-derived
CO2 (TaE) with a high-frequency peak from benzoyl-derived 13CO2 (TbE). The
small TbE peak in the orange 70 K spectrum suggests that a small amount of
CO2 site-exchange may arise during conversion of the major MP species to
toluene.
It is remarkable that when Hollingsworth photolyzed ABP at 90 K he
observed a second CO2 pair in addition to the one seen in the present work,
in which photolysis at 17 K was followed by warming to 90 K. However it may
not be surprising that lattice control over product structure becomes less
stringent at higher photolysis temperature.
The 18OQ13CQO region of the spectrum shows end-for-end rotation of the
MPb molecule. In the 17 K spectrum there is a single peak at 2260.2 cm
1,
slightly lower than the 2260.45 cm
1 expected for the change in reduced mass
from OQ13CQO. The corresponding spectra after warming to 45 and 70 K
show this peak at about half its initial intensity together with a new peak of the
same intensity (rot MPb) on the other side of the expected frequency. Both
peaks disappear when MP converts to T at 90 K.
In a separate experiment the rate of end-for-end rotation at 23 K was
measured by monitoring these two peaks at 17 K after successive periods of
warming to 23 K (Figure 2).
Together with the previous EPR results, these observations establish the
following kinetic scheme for the decomposition mechanism of photolyzed ABP.
FTIR Study of Short Range Mobility in Some Crystalline Peroxides 371

O
O
H3C O
O

O
O O hν 17K
C
C C
CH3 O
CH3 O O O
O
MP MP' MB
partial
25K radical-pair
rotation of CO 2 collapse?

T 45K
radical-pair
collapse

72K
73K
radical-pair -CO 2 rotation
O
collapse
O
76K
90K radical-pair
CO 2 -pair collapse
exchange

Figure 2 End-for-end rotational equilibration at 23 K of the benzoyl-derived CO2 in

the MP pair of ABP. The peak at 2260.8 cm
1, due to 18O in the peroxyl-
derived end of the molecule, grows at the expense of the peak at 2260.1 cm
1,
due to 18O in the carbonyl-derived end of the molecule. The inset, a plot of
the logarithm of the difference in peak height against time, shows good first-
order kinetics over more than 90% decay towards equilibrium with a half-
life of 2.2 min.
372 Chapter 22

6 BrUDP: Rotation, Site Exchange, and Preservation

of Asymmetry
EPR studies have shown that in long-chain diacyl peroxides there is no
analogue of the singly decarboxylated MB radical pair of ABP. Both acyloxyl
radicals decarboxylate upon photolysis to generate pairs of alkyl radicals
separated by a pair of CO2 molecules. Peroxides with a wide variety of chain
lengths and terminal substituents occur in two local crystal packing motifs,24
each of which has its own characteristic kinetic scheme.25
For quantitative study of lattice influence on reaction mechanism it is
particularly valuable to compare crystals with the same local packing motif
in the vicinity of the reacting group, so that any dramatic structural differences
are remote ones. Such cases should provide good tests for the ability of a
computer simulation to predict the direction of a structural or kinetic change in
response to a subtle packing change, analogous to the study of substituent
effects in solution chemistry.
For example one can compare the photolytic mechanism in BrUP with that in
BrUDP. Figure 3 compares the packing of these two crystals. On the left are five
molecules from a central layer of BrUP, which is shown in Br  Br contact with
three molecules in each of the two adjacent layers. On the right are the analogous
five molecules in a central layer of BrUDP, which is shown in Br  Br contact
with three molecules in the layer below and in CH3  CH3 contact with three
molecules in the layer above. The packing similarity is obvious.

Figure 3 Crystal packing comparison of BrUP (left) with BrUDP (right) with
hydrogen atoms omitted. Portions of three successive layers are shown.
The surroundings of reaction centres in the middle layer (red line) are
isostructural for the two crystals within the blue lines (to 10 Å in the
direction of the decanoyl chain, to 30 Å in the direction of the bromounde-
canoyl chain). Coordinates from Refs. 11g and 24.
FTIR Study of Short Range Mobility in Some Crystalline Peroxides 373
The red line in Figure 3 shows the centre of the layer, where CO2 pairs and
radical pairs will be generated. The blue lines delimit the region of close
structural analogy between BrUP and BrUDP. Up to 9.8 Å in one direction
from the reaction centre, and 29.5 Å in the other direction, the packing is
virtually identical. The RMS difference in distance to corresponding non-
hydrogen atoms within 4 Å of the oxygens in BrUP and BrUDP is 0.09 Å. The
RMS difference for such atoms between the two chains of BrUDP is 0.04 Å.
The isostructural range is even longer, 11 and 40 Å, when measured along the
slanted alkane chains, which transmit the strongest mechanical influence.
Comparing the structure and kinetics of corresponding intermediates
between BrUP and BrUDP reveals the influence of subtle lattice differences.
Reaction sites in BrUP have twofold symmetry, which is only approximate in
BrUDP. This means that when the two members of a pair of molecular
fragments within a reaction site undergo different motion, as they almost
invariably do, two symmetry-related structures will be generated in BrUP, but
in BrUDP there is the possibility for two different structures related by only
approximate symmetry. Thus one can study subtle lattice influence not only by
comparing separate experiments on BrUP and BrUDP, but also by comparing
the pseudosymmetric pairs of intermediates within a single experiment on
BrUDP. The spectra of Figure 4 provide the basis for the latter kind of
comparison.
The two 18O-labeled BrUDP samples for Figure 4 were prepared by reacting
an unlabeled peroxyacid with the complementary 18O-labeled acid chloride.
Since the acid chlorides were prepared from carboxylic acid that had been
labeled by treating acid chloride with H218O, only half of their molecules
contained 18O label. Thus each sample contained 50% of unlabeled
BrUDP and 50% of BrUDP that was 18O-labeled in the carbonyl group of
either the 11-bromoundecanoyl chain (Figure 4a) or the decanoyl chain
(Figure 4b). Obviously peaks deriving from unlabeled BrUDP are identical
between 4a and 4b.
Consider the three low-temperature spectra in Figure 4 (18, 25 and 46 K in
4a; 17, 25 and 44 K in 4b). A few minor peaks (see below) disappear before
46 K, but five significant peaks persist in each sample and are denoted by
vertical lines. All five correspond to the lowest-temperature CO2 pair observed
by Hollingsworth in unlabeled BrUP, which showed a very strong peak at
2346.6 cm
1, and a very weak peak at 2327.9 cm
1.26 These BrUP peaks result
from strong (9.0 cm
1) coupling between a CO2 with a high intrinsic frequency
(2339.4 cm
1) and an adjacent CO2 with a low intrinsic frequency
(2335.1 cm
1). The strong peak corresponds to in-phase vibration of the pair
of parallel molecules, and the very weak peak to their out-of-phase vibration.
In BrUDP there are two pseudosymmetric CO2 pairs of this type, which we call
1a and 1b. Pair 1a has intrinsic frequencies of 2339.3 and 2335.3 cm
1 (coupling
8.3 cm
1); Pair 1b has intrinsic frequencies of 2338.3 and 2336.4 cm
1 (coupling
8.5 cm
1). They give the same strong in-phase peak at high frequency (black
line in Figure 4, 2345.8 cm
1), but their out-of-phase peaks are too weak to
discern in Figure 4.
374 Chapter 22

Figure 4 FTIR spectra for CO2 asymmetric stretching (2310–2350 cm
1) in photo-
lyzed BrUDP measured at 17 K after photolysis at that temperature and
brief annealing at the colour-coded temperature. In each frame, the carbonyl
oxygen atom indicated in red was 50% 18O labeled. Vertical lines are drawn
at the frequencies for pseudosymmetrically related signals of the initial CO2
pairs P1a (blue) and P1b (pink). Note that P1a peaks disappear at slightly
lower temperature than P1b peaks. Note also that while the low-frequency
(18OQCQO) peaks for P1a and P1b are single, those for R1 and R2 are
doubled because of end-for-end rotational equilibration.
FTIR Study of Short Range Mobility in Some Crystalline Peroxides 375
Isotopically mixed Pair 1a gives the peaks marked by blue vertical lines in
Figure 4, while isotopically mixed Pair 2b gives the peaks marked by pink lines.
Since the high-intrinsic-frequency unlabeled CO2 of isotopically mixed Pair 1a
(blue, 2342.2 cm
1) appears in Figure 4b, and not in Figure 4a, it is clear that
this molecule comes from the bromoundecanoyl carbonyl group, which is
unlabeled in Figure 4b but labeled in Figure 4a. By the same reasoning the
high-intrinsic-frequency unlabeled CO2 of isotopically mixed Pair 1a (pink,
2341.4 cm
1) appears in Figure 4a and originates from the decanoyl carbonyl
group. That is, Pair 1a and Pair 1b are related by pseudosymmetry in the
BrUDP lattice, and correspond to Pair 1 in BrUP. As expected these three pairs
are similar in their intrinsic frequencies and in their coupling constants. The
differences in these parameters demonstrate the influence of structural dissim-
ilarity due to differences in packing 10 Å or more from the reaction site.
There are other similarities between Pair 1a and Pair 1b of BrUDP. The
18
OQCQO peaks of the isotopically mixed pairs are offset from the expected
average positions, because the orientation of the carbonyl oxygen in the
starting carbonyl group persists in these molecular pairs. Only one of the
end-for-end rotational isomers appears for the low-frequency 18OQCQO
(2315.9 cm
1 for Pair 1b in Figure 4a, 2314.8 cm
1 for Pair 1a in Figure 4b).
In each case the rotamer formed is the one that gives the lower frequency.
The high-frequency 18OQCQO signals (2318.4 cm
1 for Pair 1b in Figure
4b, 2318.8 cm
1 for Pair 1a in Figure 4a) are even more interesting. For both
peaks there is a partner about 1/4 as large at lower frequency that corresponds
precisely to expectation if 20% of the molecules rotate end-for-end during
formation of the high-frequency member of each pair. Note that this partial
rotation must have occurred during formation of the pairs, since no further
rotation occurs as long as the pairs survive.
Precisely the same behaviour is observed for Pair 1 in BrUP. With carbonyl
labeling, the low-intrinsic-frequency 18OQCQO appears exclusively as the
low-frequency rotamer, and the high-intrinsic-frequency 18OQCQO appears
four times more often as the high-frequency rotamer than as the low-frequency
rotamer. In the case of BrUP, this observation was confirmed by independent
analysis of a peroxy-labeled crystal, which revealed the high-frequency to low-
frequency rotamers in a 20:80 ratio, exactly the opposite of what was observed
in the carbonyl-labeled crystal.
To summarize, in all of these three versions, Pair 1 of BrUP and Pairs 1a and
1b of BrUDP, one CO2 is formed at 17 K without end-for-end rotation, and the
other is formed with 20% end-for-end rotation, but there is no subsequent
rotation up to about 48 K.
Despite these mechanistic similarities, there is a kinetic difference between
pseudosymmetry-related Pairs 1a and 1b of BrUDP. In both Figures 4a and 4b
it is clear from the bands due to the unlabeled CO2 in isotopically mixed pairs
(the strong doublet between 2339 cm
1 and 2345 cm
1) that Pair 1a (blue)
decays at a lower temperature that Pair 1b (pink). This difference is very subtle
(481 versus 501), but the 21 difference is completely reliable since the processes
being compared are observed simultaneously in the same crystal. One could not
376 Chapter 22
be confident of so subtle a difference measured for processes in two different
crystals.
The difference in decay temperatures shows clearly, if not surprisingly, that
the pseudosymmetry-related Pairs 1a and 1b of BrUDP do not equilibrate with
one another even at the temperature at which they acquire sufficient mobility to
decay irreversibly to a new structure.
EPR studies of BrUDP by Biewer showed that the decay of Pair 1, the initial
radical pair, at these temperatures generates a radical pair in which the radical
carbons have been displaced by rotation about the next-adjacent carbon–
carbon bonds of otherwise immobile alkyl chains.11g Rotation in the radical
from the bromoundecanoyl chain is by about 421; rotation in the radical from
the decanoyl chain is by about 1601.
The spectra of Figure 4 show that both Pair 1a and Pair 1b decay in this
process to the same product mixture, not to pseudosymmetry-related mixtures.
That is, the product structure is determined by the lattice, not by the arrange-
ment of the starting fragments. Isotopically mixed pairs from the dominant
species in this mixture, Pair R1, show a strong doublet centred at 2327.3 cm
1
in Figure 4a and a strong barely-resolved doublet centred at 2318.4 cm
1 in
Figure 4b.
That both of these signals are symmetrical doublets shows that 18OQCQO
molecules in both sites have undergone complete end-for-end rotational equi-
libration. But the paired CO2s have not undergone complete equilibration by
exchanging positions with one another, which would have made the spectra of
4a and 4b identical. Instead, about 75% of the 18OQCQO molecules in the
high-frequency position of this pair derive from the original bromoundecanoyl
chain, and only about 25% from the original decanoyl chain.
There are similar but weaker doublet signals at slightly higher frequency,
which we attribute to a Pair R2, probably related by pseudosymmetry to
Pair R1.
The minor peaks observed below 30 K (and referred to above) represent two
intermediates on a secondary pathway that also leads to species R1 at 25 K,
whereas normal formation of R1 from Pairs 1a and 1b requires warming to
nearly 50 K. A remarkable feature of this low-temperature conversion to R1 is
that it occurs with only slight end-for-end rotation of 18OQCQO. Rotational
equilibration for this R1 was found to begin at 42 K, so it is not surprising that
equilibration has occurred in R1 pairs that are formed from Pairs 1a and 1b
at 50 K.

7 Summary and Apologia

The current results increase our knowledge about the scope of motion available
to intermediates during reactions within molecular crystals. At the very least
they validate Hollingsworth’s conjecture that FTIR can measure end-for-end
rotation of 18OQCQO in an unsymmetrical lattice site. They show that such
rotation sometimes occurs, at least to a limited extent, upon initial CO2
FTIR Study of Short Range Mobility in Some Crystalline Peroxides 377
formation. More often the initial CO2 molecules retain specific orientation with
respect to the starting material, and end-for-end rotation occurs upon subse-
quent warming, at 23 K for the MPb molecule in ABP, and at 42 K for the R1B
molecule in BrUDP.
These results also support other qualitative conclusions: that it is possible,
but not easy, for a pair of adjacent CO2 molecules to exchange positions, that
such exchange can occur during a structural transformation, even when it does
not occur at the same temperature after the transformation, that a structural
relaxation that carries a starting material into two pseudosymmetrically related
product structures is sufficiently irreversible that the two product structures
cannot equilibrate with one another.
Reaching these qualitative conclusions required a great deal of synthetic,
experimental, and analytical effort. The data referred to in this chapter is the tip
of the iceberg of detailed quantitative spectroscopic and kinetic information on
diacyl peroxides recorded in the dissertations cited. Publishing all these num-
bers would be like publishing diffraction intensities for X-ray structural deter-
mination of the ribosome.
Our goal has been to develop a comprehensive understanding, in structural
and kinetic detail, of how a matrix controls all the atomic trajectories involved
in a solid-state reaction sequence. Our experimental results provide very
suggestive, but only partial, glimpses of these trajectories. Our conclusions
thus far, while they demonstrate clearly that there are detailed reaction mech-
anisms worth knowing, probably do not by themselves justify the enormous
amount of effort devoted to the project by such talented students.
We hope to be vindicated in the future, when our data may anchor and
validate a computational simulation of the atomic trajectories for these reac-
tions. We chose these systems with an eye to making them as easy as possible to
simulate. If a reliable simulation cannot be developed for such simple systems,
it is difficult to see how one could believe simulations of more complex
processes like enzyme catalysis. Simon Kearsley’s preliminary simulation for
ABP showed that achieving this goal should be possible.17
Thus we have chosen to honour the 75th birthday of the pioneer John
Meurig Thomas not by presenting a completed project, but rather by inviting a
new generation of experimental and computational chemists to use these and
other data to develop a comprehensive picture of what controls reactivity in
organic solids.

Acknowledgments
In addition to thanking John Meurig Thomas for his patient encouragement of
this work and for the long personal friendship between his family and that of
JMM, we would like to acknowledge the collaborators cited in the references,
in particular Mark Hollingsworth and Michael Biewer. We are grateful for
financial support from the Mechanics Division of the Office of Naval Research
and from the National Science Foundation.
378 Chapter 22

Appendix
Tables 1 and 2 show the asymmetric stretching frequencies (cm
1) for CO2
pairs in crystalline ABP and BrUDP/BrUP, respectively. Frequencies in bold
face were observed experimentally. Frequencies in italics were not observed
directly, because of inappropriate labeling or interference by stronger peaks, so
they were calculated from the ‘‘intrinsic’’ frequencies for the two unlabeled
CO2s and the coupling (cm
1) between them, with appropriate correction for
the effect of isotopic substitution on reduced masses. Observed frequencies
agree with calculated frequencies to within 0.1 cm
1 for Table 1 and to within
0.2 cm
1 for Table 2. Hi and Lo denote the higher and lower frequencies for a
particular pair whose isotopic composition is given in parentheses with the
occupant of the high-intrinsic-frequency site cited first. For example, ‘‘Lo (13/
18-12)’’ denotes the average position of the lower-frequency peak for a pair in
which OQ13CQ18O occupies the higher-intrinsic-frequency site, and the other
site is occupied by normal CO2. Since in this case 18O end-for-end isomerism is
involved, the separation of the doublet that flanks this average peak position is
reported as ‘‘Hi 18 split.’’

Table 1 FTIR frequencies for CO2 pairs in ABP.

Species MP MP 0 T
Decay Temperature (K) 40 80 490

Hi (intrinsic) 2343.4 2345.7 2347.2

Lo (intrinsic) 2339.1 2338.3 2338.2
Coupling 1.2 4.6 5.0
Hi source Benzoyl Acetyl Acetyl

Hi (12-12) 2343.7 2347.8 2349.4

Lo (12-12) 2338.8 2336.0 2335.8

Hi (12-13) 2343.5 2346.1 2347.6

Lo (12-13) 2273.6 2272.7 2272.5

Hi (13-12) 2339.3 2338.6 2338.6

Lo (13-12) 2277.9 2279.8 2281.1

Hi (12-13/18) 2343.4 2345.9 2347.5

Lo (12-13/18) 2256.3 2255.4 2255.2
Lo 18 split 0.3 1.0

Hi (13/18-12) 2339.1 2338.6 2338.5

Lo (13/18-12) 2260.5 2262.4 2263.9
Hi 18 split 0.6 1.8

Hi (18/18) 2326.7 2330.9 2332.4

Lo (18/18) 2321.9 2319.2 2319.0
Hi 18 split 1.5
Lo 18 split 0.8
FTIR Study of Short Range Mobility in Some Crystalline Peroxides 379
Table 2 FTIR frequencies for CO2 pairs in BrUDP and BrUP.
BrUDP BrUDP BrUP BrUDP BrUP BrUDP BrUP
Species 1a 1b 1 R1 R1 R2 R2
Hi (intrinsic) 2339.3 2338.3 2339.4 2344.2 2345.5 2345.4 2342.1
Lo (intrinsic) 2335.3 2336.4 2335.1 2335.2 2336.4 2336.6 2335.6
Coupling 8.3 8.5 9.0 0.0 1.5 1.0 1.2
Hi source BrU D — B80% D — Mostly BrU —

Hi (12-12) 2345.8 2345.8 2346.5 2344.2 2345.6 2345.6 2342.4

Lo (12-12) 2329.0 2328.6 2327.9 2335.1 2336.2 2336.6 2335.4

Hi (12-13) 2340.3 2339.3 2340.6 2344.2 2345.5 2345.5 2342.2

Lo (12-13) 2268.9 2270.0 2268.7 2269.9 2271.1 2271.3 2270.2

Hi (13-12) 2336.4 2337.5 2336.4 2335.2 2336.4 2336.7 2335.6

Lo (13-12) 2272.8 2272.0 2272.8 2278.7 2280.0 2279.8 2276.6

Hi (12-18) 2342.2 2341.4 2342.8 2344.2 2345.7 2345.4 2342.2

Lo (12-18) 2315.5 2316.2 2314.9 2318.4 2319.5 2319.8 2318.6
Lo 18 split 1.4 0.6 1.0 0.4 0.8 0.7 0.6

Hi (18-12) 2339.4 2340.3 2339.8 2335.2 2336.7 2336.6 2335.7

Lo (18-12) 2318.2 2317.7 2317.8 2327.3 2328.3 2328.2 2325.3
Hi 18 split 1.3 1.3 1.1 1.3 1.1 1.1 2.1

References
1. Sections 1–4 are by JMM, Sections 5–7 are taken in part from K.L. Pate,
Probing Molecular Mobility of Reaction-Generated CO2 in Photolyzed
Acyl Peroxide Single Crystals: An FT-IR Investigation, Dissertation, Yale
University, 2000.
2. M.D. Hollingsworth, J.A. Swift and B. Kahr, Cryst. Growth Des., 2005, 5,
2022.
3. P.D. Bartlett and J.M. McBride, J. Am. Chem. Soc., 1965, 87, 1727.
4. P.D. Bartlett and J.M. McBride, Pure Appl. Chem., 1967, 15, 89. The
inspiration for trying a viscous medium came from supervising the senior
research project of Harvard undergraduate Alan Dafforn, who, as a junior,
had worked with John Lombardi on a project involving phosphorescence
depolarization with A.C. Albrecht of Cornell. J.R. Lombardi, J.M.
Raymonda and A.C. Albrecht, J. Chem. Phys., 1964, 40, 1148.
5. M.D. Cohen and G.M.J. Schmidt, J. Chem. Soc., 1964, 1996.
6. My interest in EPR had begun in graduate school, in part because Jim
Vincent, my roommate, and his advisor August Maki were among the first
to observe photoexcited triplet states by EPR. J.S. Vincent and A.H. Maki,
J. Chem. Phys., 1963, 39, 3088.
7. C.A. Jr. Hutchison, Pure Appl. Chem., 1971, 27, 327.
8. J.M. McBride, M.W. Vary and B.L. Whitsel, ACS Symp. Ser. (Org. Free
Radicals), 1978, 69, 208. In principle electron-nuclear double resonance
380 Chapter 22
spectroscopy (ENDOR) would provide additional information about
radical positions with respect to surrounding molecules,7 but exploiting
ENDOR in these systems proved to be beyond our experimental grasp.
9. A.V. Zubkov, A.T. Koritsky and Ya.S. Lebedev, Dokl. Akad. Nauk USSR,
1968, 180, 1150; H.C. Box, E.E. Budzinski and H.C. Freund, J. Am. Chem.
Soc., 1970, 92, 5305; V.I. Barchuk, A.A. Dubinsky, O. Ya. Grinberg and
Ya.S. Lebedev, Chem. Phys. Lett., 1975, 34, 476.
10. D.W. Walter and J.M. McBride, J. Am. Chem. Soc., 1981, 103, 7069, 7074.
Triptycyl radical pairs collapsed by reacting with a common chloroform
molecule in the solvated crystal, unpublished work by C. Reichel and
B. Kahr.
11. In addition to Ref. 1, these dissertations include: (a) B.E. Segmuller,
Diundecanoyl peroxide: EPR study and product analysis, Dissertation,
Yale University, 1982; (b) M.D. Hollingsworth, IR studies of CO2 dimers
as a probe of local stress in solid state reactions, Dissertation, Yale
University, 1986; (c) D.E. Mills, Bis(11-bromoundecanoyl) peroxide:
remote substituent effects on a solid-state reaction, Dissertation, Yale
University, 1986; (d) X.W. Feng, Mechanistic ESR study in the solid-state
radical reactions in crystal of bis(11-bromoundecanoyl) peroxide and its
analogues, Dissertation, Yale University, 1989; (e) S.B. Bertman, Solid
substituent effects: systematic investigation of the influence of molecular
interaction on bulk properties of organic solids, Dissertation, Yale Uni-
versity, 1990; (f) R.L. Carter, Solid state chemistry Part I: mechanistic
studies on the decomposition of didecanoyl peroxide, Dissertation, Yale
University, 1993; (g) M.C. Biewer, Investigation of radical motion in the
single crystal photolytic decomposition mechanism of (11-bromoundeca-
noyl) (decanoyl) peroxide, Dissertation, Yale University, 1995.
12. M.D. Cohen, Z. Ludmer, J.M. Thomas and J.O. Williams, Proc. Roy. Soc.
A, 1971, 324, 459.
13. S.E. Morsi, J.M. Thomas and J.O. Williams, J. Chem Soc., Faraday Trans.
1, 1975, 71, 1857.
14. (a) A.B. Jaffe and J.M. McBride, Solid Org. State, 1974, 4, 16; (b) B.L.
Whitsel, The kinetics and structure of radical pairs: acetyl benzoyl peroxide,
Dissertation, Yale University, 1977.
15. N.J. Karch, E.T. Koh, B.L. Whitsel and J.M. McBride, J. Am. Chem. Soc.,
1975, 97, 6729; cf. Ref. 14b.
16. M.E. Riepe and J.H. Wang, J. Biol. Chem., 1968, 243, 1779.
17. S.K. Kearsley, and J.M. McBride, Mol. Cryst. Liq. Cryst. Inc. Nonlinear
Opt., 1988, 156, 109. Despite the preliminary success of Kearsley, thus far
only he and Gavezzotti have used any of our experimental data for their
intended purpose of formulating and testing theories for solid-state reac-
tion mechanism. A. Gavezzotti and R. Bianchi, Chem. Phys. Lett., 1986,
128, 295.
18. M.D. Hollingsworth and J.M. McBride, in Advances in Photochemistry,
vol 15, D. Volman, G.S. Hammond and K. Gollnick (eds), 1999, 279–379,
345.
FTIR Study of Short Range Mobility in Some Crystalline Peroxides 381
19. Temperatures are noted as ‘‘about’’ because it is difficult to measure the
temperature of a small crystal cooled by a stream of cold gas or by
mounting on a cooled salt plate. Absolute values of temperature are
probably accurate to within a few degrees, and relative temperatures for
either EPR or FTIR within about one degree.
20. R.A. Merrill, The benzoyloxyl radical, a 2B2 ground state, Dissertation,
Yale University, 1986. cf. J.M. McBride and R.A. Merrill, J. Am. Chem.
Soc., 1980, 102, 1723.
21. As noted by Hollingsworth, the broad peak was particularly troublesome
when using older ABP crystals, even those stored in a darkened cold room.
He suggested that prior decomposition may be sufficient to generate line-
broadening stress fields in older crystals.
22. The commercial benzoic acid was prepared from 13C-enriched CO2, which
is fortuitously enriched in 18O.
23. The 91 temperature difference is attributable to systematic differences in
temperature measurements and to the time required to warm and cool the
FTIR sample holder.
24. J.M. McBride, S.B. Bertman and T.C. Semple, Proc. Natl. Acad. Sci.
U.S.A., 1987, 84, 4743; J.M. McBride, S.B. Bertman, D.Z. Cioffi, B.E.
Segmuller and B.A. Weber, Mol. Cryst. Liq. Cryst. Inc. Nonlinear Opt.,
1988, 161, 1. cf. Ref. 11e.
25. J.M. McBride, B.E. Segmuller, M.D. Hollingsworth, D.E. Mills and
B.A. Weber, Science, 1986, 234, 830; X.W. Feng and J.M. McBride,
J. Am. Chem. Soc., 1990, 112, 6151. cf. Refs. 11c,d,f.
26. M.D. Hollingsworth and J.M. McBride, Chem. Phys. Lett., 1986, 130, 259.
 Section C:
Solid Catalysts, Surface and Materials
Science
CHAPTER 23

From ‘Nature’ to an Adventure

in Single-Site Epoxidation
Catalysis
HENDRIKUS C. L. ABBENHUIS AND RUTGER A. VAN
SANTEN
Laboratory of Inorganic Chemistry and Catalysis, Schuit Institute of Catalysis,
Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven,
The Netherlands

1 Introduction: ‘Provoked by Nature’

Sir John Meurig Thomas’s research over the past 20 years has focused on the
design, preparation and testing of new solid catalysts. He has been conspicuously
successful in modifying nanoporous materials so as to place isolated, single-site
active centres on their large internal areas. As such, it should be no surprise that
our research, aimed at detailed molecular understanding of catalytic events
created synergy, adding to our relationship.
Especially so in the summer of 1994 when we started an experimental work
with the aim of using organometallic building blocks to construct heterogene-
ous catalysts, through lego-like chemistry, that would render catalytic materials
with controlled pore size and molecularly defined, isolated active sites. Soon,
we became deeply involved in the topic of titanium-mediated catalytic epoxi-
dation and consequently titanium-grafted silicas (Figure 1).1 So was Sir John
Meurig Thomas.2
In the fall of 1995, Sir John published in Nature on the direct grafting of
organometallic synthons onto the inner walls of mesoporous silica MCM-41.3
This generated a shape-selective catalyst with a large concentration of acces-
sible, well-spaced and structurally well-defined active sites. Specifically, attach-
ment of a titanocene-derived catalyst precursor to the pore walls of MCM-41
produced a catalyst for the epoxidation of cyclohexene and more bulky cyclic
alkenes.

385
386 Chapter 23

Si
OH OH O
T Ti Ti
SiO OH OSi OSi
SiO SiO
O O O
Si Si Si
a)
a b c

Figure 1 Environment of the terdentate chelated titanium sites (type b) in surface-

grafted TiTMCM4l catalysts (blue ¼ Ti, yellow ¼ Si, red ¼ O, white ¼ H) and
relation with possible framework titanium sites in titanosilicates: (a) bipodal
site, (b) tripodal (open lattice) site and (c) tetrapodal (closed lattice) site.

In doing so, Sir John took a shortcut compared to our approach that
provoked ample discussion. For instance, were these catalysts really stable?
Why did they only work with anhydrous organic peroxides? Was there a
difference with just titanium on silica as employed industrially in Shell’s SMPO
(Styrene Monomer Propylene Oxide) process for propylene oxide? How to
make molecularly defined catalytic materials? What was the relationship with
microporous titanium silicalite (TS-1) that performed so beautifully with
aqueous hydrogen peroxide?
Indeed, Nature publications like Sir John’s should provoke and inspire
and this was certainly so for us. In fact, it stimulated experimental work that
brought excitement and which is still not finished to date. In this account, we
will discuss our work following the original questions.

2 Are Silica-Grafted Titanate Catalysts Really Stable?

When we started our search in 1994 for non-leaching heterogeneous liquid-
phase oxidation catalysts, detailed studies of how the catalytically active metal
species are bonded to the support were rare. As today, usually more attention
was paid to the performance of the catalyst, rather than to the fundamental
question of whether the catalyst is truly heterogeneous or not. In fact, many
catalysts consisting of a metal oxide on an inert carrier owe their catalytic
From ‘Nature’ to an Adventure in Single-Site Epoxidation Catalysis 387
activity to rapid leaching of the metal from the surface to form active homo-
geneous catalysts, a fact that the designers of the original catalysts clearly did
not have in mind.
In order to approach this problem at a molecular level, we first reported in
1997 on epoxidations catalyzed by model systems, titanium silsesquioxanes.
Soon, Sir John and co-worker Thomas Maschmeyer followed with their own
findings, as did leading industrial researchers from Shell!1
In these silsesquioxanes, the titanium site is incorporated via spatially
oriented siloxy bonds (Ti–O–Si) which structurally resemble surface sites that
have been purportedly identified on silica surfaces (Figure 2). Heterogeneous
titanium catalysts are very important in oxidation processes but at the same
time have been reported to undergo some leaching in liquid-phase applications.
For instance, the highly active Shell titanium/silica epoxidation catalyst used is
the SMPO process for propylene oxide, becomes only truly heterogeneous after
a certain time on stream.4 Similar materials, that were reported as the result of
grafting silica or MCM-41 mesoporous silica with titanium derivatives, or even
novel titanosilicates, might therefore be only partially heterogeneous when
applied in liquid-phase oxidation reactions.
With silsesquioxane model systems, we proved that liquid-phase, silica-
supported titanium epoxidation catalysts are predicted to be accessible and
active in many cases but will be truly heterogeneous only when stringent
conditions are met.5 Particularly, the titanium site should be incorporated in
a silanol nest rendering at least terdentate silanolate coordination. These
findings are consistent with a mechanism for alkene epoxidation in which

Figure 2 Incompletely condensed silsesquioxanes (POSS) suitable for modeling ter-

dentate (a), bidentate (b) and monodentate (c) silanolate chelation and
examples of titanium derivatives.
388 Chapter 23

Figure 3 Part of the epoxidation pathway proposed by Clerici and Sheldon in which
the peroxide reacts with the titanium site to form an active species for
epoxidation.

reversible hydrolysis of a titanium siloxy function occurs. This supports

the now firmly established mechanism of heterogeneous alkene epoxidation
by titanium silicalites proposed by Clerici, Ingallina, Sheldon and co-workers
(Figure 3).6
Still, the debate on catalyst stability has not ended. Clearly, denticity of
siloxy chelation is the factor that determines whether a titanium silsesquioxane
catalyst is stable in anhydrous media. For silica-supported titanium sites, this
statement is further collaborated by computational work, for instance, of
Hillier et al.7 However, when a wet medium for the epoxidation reaction is
used, the denticity is not the only factor that determines the stability of the
catalyst. In addition, the intramolecular surrounding of the titanium site should
then be hydrophobic enough to assist in further protecting this site against
irreversible hydrolysis.

3 Modeling Shell’s SMPO Process

for Propylene Oxide
As Sir John’s titanium-grafted MCM-41 material contains mainly robust
tripodally anchored titanium sites, it should follow that the catalyst should
not leach titanium in aprotic liquid-phase epoxidation catalysis. After synthe-
sis, the coordination sphere of titanium was completed by a cyclopentadienide
ligand.
At the start of epoxidation with organic peroxide, this Cp ligand is gradually
displaced by alkoxide, for instance t-butoxide if TBHP (tert-butylhydrogen
peroxide) is employed as the oxidant. As a result, the catalysis kinetics exhibit
an induction period before second order kinetics are observed. Replacing Cp
with hydroxyl renders very active catalysts that display truly second order
kinetics from the start of the epoxidation (Figure 4).8

4 How to Make Molecularly Defined

Catalytic Materials?
In the mid-1990s, the major hurdle in the use of silsesquioxanes, not even to
mention the impossibility to turn them into heterogeneous catalysts, was the
From ‘Nature’ to an Adventure in Single-Site Epoxidation Catalysis 389

Figure 4 Epoxidation kinetics of TiCp (left) and TiOH (right) POSS catalysts
revealing displacement of Cp.

long preparation time (ranging from a few weeks to 36 months) and the limited
scope of the organic side groups on the silicon atoms (non-reactive groups
unsuitable for ligand immobilization). Since then, new developments and ideas
have shortened the preparation times and broadened the scope considerably.
Starting with Thomas Maschmeyer, the use of high-throughput experimenta-
tion and synthesis robots have accelerated the optimization of synthesis con-
ditions.9 Recently, base-catalyzed polycondensation reactions have proven to
be an excellent way to prepare large quantities of silsesquioxanes. Parallel and
in synergy with Joe Lichtenhan we have applied for patents on the preparation
of completely condensed and incompletely condensed silsesquioxanes with iso-
butyl and iso-octyl side groups that can be prepared on large scales in a short
time. Until recently, functionalization of silsesquioxane silanols has been limi-
ted to either corner-capping of trisilanols with a trihaloorganosilane moiety,
leaving no further reactive silanol groups, or reaction of the trisilanol with
mono- or di-haloorganosilane reactants, leaving two or one silanol groups,
respectively. In the first case, a large number of possible side groups can be
introduced, ranging from simple alkyl groups to reactive alcohols, amines
and alkenyl groups. These groups allow the silsesquioxane cores to be included
in polymeric materials. Furthermore, there was substantial interest in octa-
functional silsesquioxanes where all the side groups on the silicon atoms are
identical and reactive. In these cases the functionality ranges from alkyls,
alcohols, amides and carboxylates to halides, nitrates and phosphanes.10 These
can even be used as building blocks for dendrimers, as shown by Cole-
Hamilton et al. for use in catalytic hydroformylation reactions.11 The latest
development involves the synthesis of functionalized silsesquioxane trisilanols.
With these, homogeneous catalysts like our titanium-based epoxidation cata-
lysts can be straightforwardly converted into molecularly defined catalytic
materials.
Clearly, silsesquioxane-derived metal catalysts should no longer be regarded
as chemical curiosities. They provide new catalysts with both homogeneous and
heterogeneous applicability. Most interestingly, it is now firmly established that
390 Chapter 23

Figure 5 Graphical representation of the adsorption of a silsesquioxane titanium

complex in the 30 Å pores of all-silica MCM-41.

the steric and electronic properties of silsesquioxane silanolate ligands

render metal centres more Lewis acidic than conventional alkoxide or siloxide
ligands do. This concept has been exploited in newly developed catalysts
beyond epoxidation as for example alkene metathesis, polymerization and
Diels–Alder reactions of enones. Other applications are envisioned in the near
future. In fact, we believe so strongly in the inherent nanotech innovation that
we recently founded the company ‘Hybrid Catalysis’ to further commercialize
silsesquioxane derived catalytic materials.
With homogeneous, active epoxidation catalysts in hand, we started to work
on their immobilization. An exciting first finding was that this could be achieved
by exploiting the strong adsorption of complex 1 in all-silica MCM-41 channels
(Figure 5).12 The resulting self-assembled materials are active, truly hetero-
geneous and recyclable catalysts for alkene epoxidation in the liquid phase.
Essential for an irreversible adsorption of the silsesquioxane complex proved
the use of somewhat hydrophobic, aluminium-free MCM-41.
Somewhat disappointing was the finding that none of the epoxidation
catalysts developed so far were active in applications with aqueous hydrogen
peroxide, as was the case for the Shell SMPO catalyst. Clearly, just having a
robust, accessible titanium site was not enough, nor was every combination of
just such a site with any support.

5 Why Water Kills the Cat

For us, this was a puzzle that needed to be solved soon! Solvay was by then
funding our research and as a major producer of hydrogen peroxide they were
not too pleased with catalysts that refused to work with their oxidant.
Little help came from the observation that few catalysts have been truly
efficient in alkene epoxidation with aqueous hydrogen peroxide. Development
of such catalysts was, and still is, so important since with regard to desirability,
this oxidant comes second only to oxygen itself.13 Still rather unbeatable,
the best catalyst in this field is the synthetic titanium containing zeolite,
titanium silicalite-1 (TS-1),14 which is active for a wide range of oxidation
From ‘Nature’ to an Adventure in Single-Site Epoxidation Catalysis 391

Figure 6 Synthesis of three-dimensionally netted polymeric catalysts, these bio-

inspired catalytic ensembles are indeed active with aqueous hydrogen
peroxide.

reactions, including epoxidation.15 For TS-1, activity seems to originate from a

combination of a robust active Ti(OSi)n site (n ¼ 3, 4),16 and its location in a
hydrophobic channel or cavity in the MFI (ZSM-5) structure.17 The resulting
catalytic ensemble prevents poisoning of the active site by water as well as
unproductive decomposition of the oxidant.
Through our previous work on homogeneous epoxidation catalysis, we knew
that we had robust silsesquioxane titanium derivatives in hand. The next
challenge was to convert these compounds into materials that would add a
hydrophobic environment, if not to dream of defined pores and cavities, to the
active site (Figure 6).
Profiting from advances in silsesquioxane ligand synthesis, we were able to
make titanium derivatives with a function suitable for ligand tethering. Such a
function was provided by a vinyl containing silsesquioxane ligand that could be
grafted on a commercially available silicone system through hydrosilylation.
Subsequently, we were very excited when we found that these catalytic mate-
rials could indeed be used in heterogeneous epoxidation with aqueous hydro-
gen peroxide.18
These first results demonstrated that grafting of functionalized titanium
silsesquioxanes on polysiloxanes provided a way to realize the formation of a
catalytic ensemble that was capable of performing epoxidation with aqueous
hydrogen peroxide. Clearly, the entire system was capable of outperforming the
sum of its parts; it was the synergy between active site and its environment that
allowed our hybrid catalysts, and likewise TS-1, or even metalloenzymes to
achieve their desirable performance.
Having said so much, our hybrid catalysts were relatively simple, amorphous
materials that did not compete in activity with TS-1. The next challenge was
how to control the porosity of our materials.
392 Chapter 23

6 The Quest for Hybrid Catalysis

Catalyst immobilization as shown above, either involving inorganic solids or
polymer supports are the two most commonly used heterogenization pro-
cedures. They each have some advantages over the other, and provide routes to
catalytic materials that can meet special demands in chemical reaction engi-
neering.19 Inorganic supports often possess rigid porous structures and high
specific surface areas and are easy to separate, while organic polymers often
make the catalyst behave more homogeneously because of the better compati-
bility with organic reaction media. Considering this fact and our previous
results for the immobilization of titanium silsesquioxanes, we proposed com-
bining these two methods to synthesize porous inorganic solid-supported
polymeric silsesquioxane films. The resulting hybrid catalyst should have
several merits: facilitated diffusion of reactant molecules, better accessibility
of the active sites due to the rigid porous structure of the inorganic support, and
improved compatibility between host and guest species and organic solvents
arising from the specific properties of the organic polymer films.
Of course there is a catch in any project aimed at making complex materials.
First, it is necessary to avoid pore blockage by the polymer since an open
porous structure is important for the accessibility of the active sites, so
appropriate choices of inorganic support and the polymerization method
should be made. The second challenge is to increase the stability of the polymer
on the inorganic support. Ordered mesoporous silica provides an ideal support
as the ordered open mesopore systems with uniform pore diameters are
beneficial for diffusion and dispersion of guest species and hence will reduce
the possibility of pore blockage. There have been several previous investiga-
tions of the synthesis of organic polymers inside mesoporous silica. The
resulting hybrid composites showed some interesting physical properties due
to the confinement of the nanopores.20 However, in most cases, the entire pore
volume of the mesoporous silica was filled by the incorporated polymer.21
Therefore, for retaining a porous structure after the polymer incorporation, an
efficient immobilization method needs to be developed. Here, we got inspira-
tion from Ryoo et al. who reported recently that functional polymer–silica
composites with well-defined mesoporosity could be obtained by in situ po-
lymerization of monomers adsorbed on the pore walls of mesoporous silica
SBA-15.22 A key step to avoid pore blockage was to form a uniform monomer
film on the pore wall surface of SBA-15 before polymerization by selectively
removing the solvent used for the impregnation of monomers. SBA-15 is
probably one of the best supports for the synthesis of porous organic poly-
mer–silica composites.23 In addition to the ordered two-dimensional hexagonal
mesoporous structure similar to MCM-41, SBA-15 presents the advantage of
larger pore diameters (47 nm) than the MCM-41 used previously for the
immobilization of our catalysts. This is important for efficient diffusion and
dispersion of POSS-containing monomers inside the nanopores and for reduc-
ing the risk of pore blockage. (The titanium silsesquioxanes have an approx-
imate diameter of 1.5 nm, roughly half the pore diameter of MCM-41.)
From ‘Nature’ to an Adventure in Single-Site Epoxidation Catalysis 393

Figure 7 Schematic presentation of the procedure for the synthesis of SBA-15-

supported hybrid catalysts.

Moreover, for most SBA-15 materials, there are complementary mesopores/

micropores inside the mesopore walls connecting the mesopores in a three-
dimensional porous structure, which can help the polymer film interconnect
into a three-dimensional network, interpenetrate with the silica framework, and
thus increase the stability of the polymer on the silica support. Not to forget the
context with TS1 and hydrophobic pores, Ryoo et al. reported the synthesis of
ferrocene-functionalized mesoporous polymer–silica nanocomposite materials
that exhibited high activity and selectivity towards catalytic hydroxylation of
phenol, which was once more attributed to the hydrophobic nature of the
supported polymer surface (Figure 7).24
Using the lessons learned in previous studies, we demonstrated the successful
combination of two commonly used immobilization methods by integrating
titanium silsesquioxanes into an SBA-15-supported polystyrene film by in situ
copolymerization. The resulting hybrid materials have highly ordered meso-
porous structures and proved to be very active heterogeneous catalysts for
394 Chapter 23
25
alkene epoxidation with TBHP or aqueous hydrogen peroxide. Fusion of the
silica support (highly porous structure, hydrophilic surface) and of the poly-
styrene and POSS (Polyhedral Oligomeric Silsesquioxanes) (hydrophobic net-
work) into one entity makes the hybrid materials behave as interfacial catalysts
in epoxidation with aqueous peroxides and leads to much higher activity than
their homogeneous counterparts due to the hydrophobic environments around
the active centres.

7 A Word in Retrospect
In the summer of 1995, we were obviously provoked, triggered and inspired by
one of Sir John’s publications in Nature. For us, this marked the start of an
adventure in epoxidation catalysis that has still not ended today. We have come
a long way starting with modeling the active sites of proposed heterogeneous
catalysts using silsesquioxane chemistry. From that, Lego-like chemistry and
methodology were developed for hybrid precision catalysts. At present, the
toolbox for modifying nanoporous materials so as to place isolated, single-site
active centres on their large internal areas has become available. As such, the
start of new adventures is marked with a technology push for the application of
advanced catalysts aimed at sustainability, cascade reactions, rapid lead finding
and industrial implementation.

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Dalton Trans., 1999, 21, 3791.
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Snelgrove, K.U. Ingold and D.D.M. Wayner, Angew. Chem., Int. Ed.
Engl., 1996, 35, 2787.
3. T. Maschmeyer, F. Rey, G. Sankar and J.M. Thomas, Nature (London),
1995, 378, 159.
4. H.P. Wulff, US Pat., 3 923 843, 1975 (Chem. Abstr., 84, 89977d); H.P.
Wulff and F. Wattimena, US Pat., 4 021 454, 1977 (Chem. Abstr., 87,
22393d).
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1997, 331.
6. U. Romano, F. Esposito, F. Maspero, C. Neri and M.G. Clerici, La
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H.-J. Hamann, J. Prakt. Chem., 1996, 388, 1; H.X. Gao, G.X. Lu, J.S. Suo
and S.B. Li, Appl. Catal., 1996, 138, 27; P. Ingallina, M.G. Clerici, L. Rossi
and G. Bellussi, Stud. Surf. Sci. Catal., 1994, 92, 31; R.A. Sheldon, J. Mol.
Catal., 1980, 7, 107 and unpublished results from Schram and Van
Broekhoven cited therein.
7. D. Tantanak, M.A. Vincent and I.H. Hillier, Chem. Commun., 1998, 1031.
8. H.C.L. Abbenhuis et al., Dalton Trans., accepted for publication.
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9. P.P. Pescarmona, J.C. Van der Waal, I.E. Maxwell and T. Maschmeyer,
Angew. Chem., Int. Ed., 2001, 40, 740.
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D.J. Cole-Hamilton, J. Chem. Soc., Dalton Trans., 2002, 4323.
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R.A. van Santen, Angew. Chem., Int. Ed., 1998, 37, 356.
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Kluwer, Dordrecht, 1992.
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886812, 1981 (Chem. Abstr., 1981, 95, 206272k).
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Boscherini, F. Buffa, F. Genoni, G. Leofanti, G. Petrini and G. Vlaic,
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and H.C.L. Abbenhuis, Angew. Chem., Int. Ed., 2002, 41, 637.
19. For recent reviews on immobilization of homogeneous catalysts, please see:
N.E. Leadbeater, M. Marco, Chem. Rev., 2002, 102, 3217; C.A. McNa-
mara, M.J. Dixon and M. Bradley, Chem. Rev., 2002, 102, 3275; Q.H. Fan,
Y.M. Li and A.S.C. Chan, Chem. Rev., 2002, 102, 3385; C.E. Song and S.
Lee, Chem. Rev., 2002, 102, 3495; D.E. De Vos, M. Dams, B. F. Sels and
P.A. Jacobs, Chem. Rev., 2002, 102, 3615; P. Mastrorilli and C.F. Nobile,
Coord. Chem. Rev., 2004, 248, 377.
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Chem. Soc., 2005, 127, 1924.
23. D. Zhao, J. Feng, Q. Huo, N. Melosh, G.H. Fredrickson, B.F. Chmelka
and G.D. Stucky, Science, 1998, 279, 548.
24. A. Dubey, M. Choi and R. Ryoo, Green Chem., 2006, 8, 144.
25. L. Zhang, H.C.L. Abbenhuis, G. Gerritsen, N. NiBhriain, P.C.M.M.
Magusin, B. Mezari, W. Han, R.A. van Santen, Q. Yang and C. Li,
Chem.–Eur. J., 2007, 13, 1210.
CHAPTER 24

A Comparison between Enzymes

and Solid State Catalysts
ROBERT J. P. WILLIAMS
Inorganic Chemistry Laboratory, University of Oxford, South Parks Road,
Oxford OX1 3QR, UK

1 Introduction
The major interests of John Meurig Thomas have been, and still are, in solid
state materials, especially in their structural features, and in the synthesis of
catalysts from solid state porous oxides containing metal ions, see Figure 1.1
Now a feature of these catalysts is that they are rarely selective and considerable
rate enhancement often requires high pressures or high temperatures. They do
not have the power of metallo-enzymes.2 Enzymes have to be very active and
selective in their reactions since they are taken from biological cells in ambient
conditions. In cells a multitude of sensitive reagents are present, many very
aggressive, e.g. O2 and H2O2. By way of further contrast a solid state catalyst is
employed in a reaction of individually selected reactants and their product
control needs only to be modest. This raises the question as to why there is this
big difference in the ability to catalyse. Comparison is made difficult however by
the way rate enhancement and selectivity have been examined and the theoretical
treatments employed to explain them. When we have tackled these two points we
can see what common factors there are and what are the major advantageous
features of enzyme action. Similar difficulties are apparent when we compare
molecular catalysts3 with enzymes. I shall deliberately select examples from
John’s research to illustrate the comparison. (From the outset I stress that there
has been much input to its contents from John himself.)

1.1 The Use of Rate Expressions

Two approaches will be described here in very simplified conceptual equations.4
In the earliest analyses of rates of reaction the expression used was

rate ¼ k½reactants
n ð1Þ

396
A Comparison between Enzymes and Solid State Catalysts 397

Figure 1 Three-dimensional representation of the pore structure of AlPO-18,

AlPO-36 and AlPO-5 (pore apertures are, respectively, 3.8 Å, 6.57.5 Å;
and 7.3 Å). The size of the atoms in the structures corresponds to their van
der Waals radii. A metal ion can be substituted for an Al31 ion or a metal
ion complex can be attached to or included in the framework. From
Thomas et al.25 with permission.

where k is a rate constant and [reactants]n can be expressed by product functions

for any number of reactants. The temperature dependence of k was given by
k ¼ CPeDG/RT where the constants related to collision rate, C, and orientation
factors, P, in the collision. For a catalyst reaction in solution an extra concen-
tration term is that of the catalyst. In a catalysed unimolecular reaction, (now
bimolecular) only the value of DG is reduced. For a catalysed bimolecular
reaction in solution an improbable three molecule collision must occur, making
it extremely unlikely. The rate of reaction on collision is increased again by
reduction of DG. Solid catalysts can be described in a similar way replacing the
concentration dependence of the catalyst by sites on the surface.
An alternative approach stresses the prior binding of reactants to the catalyst
such that in the bound state the reaction is unimolecular. The simplest rate
constant expression becomes
0
rate ¼ Kk ¼ KeDG =RT ð2Þ

where K is an equilibrium constant (equilibrium holds provided on/off binding

rates are faster than reaction rates (see ‘‘Note’’ at the end of the article)). There are
398 Chapter 24
also two separate considerations of orientation and of exponential temperature
dependent factors in K and k. A clear advantage of binding is that it increases the
probability of reaction and DG values can also be reduced. The difficulties for any
comparison we meet are in the ability, even the wish, to follow reactions in
sufficient detail to obtain the parameters in either equation in all cases.
Experimental approaches using the different catalysts, Table 1, have had
different objectives too so that the rate enhancements achieved are again
difficult to compare in terms of factors in Equations (1) or (2). Often exam-
ination of a molecular or a solid state catalyst activity stops with knowledge of
the yield of a product in a given time. Selectivity study is not necessary since the
reaction and catalysts are chosen so as to yield a definite product and, unless
enantioselectivity is required, even a degree of mixture of products can be
satisfactory. Enzymes have been subjected to much more detailed experimental
kinetic appraisal as their products and their purity are almost taken for granted
as 100%. Another problem for comparison is that while enzymes operate in
aqueous solution at pH ¼ 7 and ambient temperature/pressure, other catalysts
do not have any such limitations to their use.
In an earlier paper5 we have recognised these difficulties and proposed that
there were three kinds of safe topics for comparisons between the catalyst
classes.

(a) The metal ions chosen in man-made catalysts as opposed to those

selected by nature in enzymes for a given reaction.
(b) Given the selected metal ion, the choice of donor atoms of ligands as
binding groups.

Table 1 Principal types of catalysts.

Name or classification Properties
Homogeneous

1. Molecular systems Single atom/ion site (not constrained)

(a) Soluble small molecule active in solution
(Heterogenized (b) Small molecule attached by flexible-linker to a surface
variants)
2. Enzymes Soluble large proteins active usually in water including
proteins such as antibodies modified for catalytic
purposes
(Heterogenized Membrane catalysts including enzymes
variants)
3. Heterogeneous Continuous solids such as oxides and sulphides
solid systems
Nanoporous solids Open frameworks including immobilised atoms, complexes
or nanoparticles of metals
Dendrimers
Metallic and Metals, alloys, metal conductors
conducting

Note: The active site atoms in all the cases except the first may be constrained, see text.
A Comparison between Enzymes and Solid State Catalysts 399
(c) The manner in which the complexes of (a) and (b) were held in a
framework, that is the overall structure especially that of the catalytic
region.

The comparison of catalysts had to be restricted more or less to single sites

containing one metal ion in order to remove participation of the frameworks in
the catalytic acts. We left to one side catalysts with adjacent sites or distant
non-adjacent sites as their properties could depend so much on the nature of
the very different frameworks. Here we shall explore these cases further. As an
entry into the topic we shall take a step backward at first and look at some
common ground associated with the above three points of comparison, sum-
marizing them in Sections 2 and 3 so as to introduce the energetics as used
particularly in studying enzymes following elaboration of Equation (2). While
we look at the specific nature of enzyme frameworks we shall refer to the
frameworks of other types of catalyst, especially solids (Table 1).

2 The Concepts of the ‘‘Active Site’’

and the ‘‘Active Region’’
It is commonly assumed that catalysts have active ‘‘sites’’. Somewhat curiously
the concept of the catalytically active site first entered the field in the description
of heterogeneous metal catalysis in the 1920s when H.S. Taylor proposed that
topographical irregularities, such as steps and kinks at otherwise flat metal
surfaces, were likely to exhibit enhanced reactivity compared with sites at flat
surfaces. We shall see later that, as applied to metals, it is a difficult definition
to analyse in structural detail. The concept of an active site in small molecule
catalysts generally and in the field of biological (chiefly enzymatic) catalysts was
discussed in the early 1930s and is much easier to appreciate. It referred to a
small centre of possible binding to and of attack by the catalyst, e.g. a metal
ion. The small molecules were usually of known outline structure even at that
time and often the sources of activity were clear. The binding and the attacking
site were seen as one and the same, see Figure 2. As a result, and with increased
sophistication in the development of the small molecular metal-containing
catalysts, Figure 2,6 together with more detailed knowledge of their structures
and the energetics of their mechanism, much of the application of the active site
principle has been limited to action of the metal elements as will be familiar to
any scientist interested in the theory of these catalysts.3,4 When molecular
catalysts have considerable molecular weight they can be compared directly
with enzymes, while when these small molecular catalysts are embedded in or
attached to surfaces they can be compared with heterogeneous solid catalysts.
We turn next to the idea of an active ‘‘site’’ in an enzyme.
A dramatic advance in our understanding of the nature of active regions (not
just attacking sites as we shall see) in enzymes occurred in the 1950s–1960s
period, when the atomically resolved structures, first of a protein, myoglobin,
Figure 3,7 and then of lysozyme, an enzyme, were determined by X-ray
400 Chapter 24

[Ru(OAc)2((R)-binap)] [Ru(OAc)2((S)-binap)]

R3 COOH H2 R3 COOH

R2 R1 R2 R1

COOR1 COOR1

NHCOR2 NHCOR2

Figure 2 Stick models depicting the R and S BINAP enantioselective hydrogenation

catalysts (see text) devised by Noyori et al.6 Note the steric hindrance in the
binaphthalene ligand contributing to constraint and enantioselectivity. The
metal ion at the centre binds and activates reaction.

crystallography.8 Immediately the three-dimensional details of the oxygen

binding site of myoglobin revealed a possible first step of catalysed oxygen
reactions, haem iron binding, but the site was complicated by the further
interaction of O2 with other protein groups. A similar situation arose with the
well-defined substrate-binding cleft (active region) of lysozyme, that exists in
the folded structure of its 128 amino acids, which apparently allowed the
visualisation of a defined active ‘‘site’’ of two attacking carboxylates. The
function of these, lysozyme’s, non-metal attacking groups, was aided however
by the sterically restricting and binding side chains located nearby. Only when
consideration was given to them (together with the attacking groups) was it
made possible to formulate a plausible catalytic mechanism for lysozyme’s
mode of action and to demonstrate its selectivity in terms of complex kinetics.
Somewhat distantly, these were related to Equation (2). These structures
brought into focus the fact that the ‘‘active site’’ of an enzyme could be a
much more complicated structure (region) than had been conceived from small
complex molecule or metal (solid state) structures since it involved not just
active attacking sites but considerable areas of the matrix surface at least in
binding. The substrates of lysozyme are in fact large polysaccharides. The
surface and the matrix of the protein were proved later to be far from static so
that the catalytic act involves in addition a dynamic cycling of not just local
groups near the site but of more remote regions and indeed of the whole
matrix.9 This makes the energetics of the lysozyme action difficult to describe.
A Comparison between Enzymes and Solid State Catalysts 401
The allosteric switch in haemoglobin, a tetramer of myoglobin-like units, also
shows this mobility during O2 binding. In many of the immediately following
sections we shall avoid discussion of mobility in enzymes as there is little here in
common with other catalysts.
Now lysozyme’s attacking groups are not metal ions, so that any comparison
with small metal complexes and solid state metal ion lattice catalysts (the major
number of catalysts) is not easily made. We shall therefore use metal enzymes,
Table 2, as the basis of discussion and for any comparison with solid state and
molecular catalysts. We shall take the structure of myoglobin, Figure 3, a haem
iron containing protein, as one example which, though not catalytically active,
can be made into an enzyme by mutation.10 We shall also reduce the complexity
of the discussion by referring most frequently to small molecular substrates,
such as H2, O2, N2, CH4, H2O, which we note are almost invariably activated
by metal-containing catalysts.
Now, on the basis of the early studies, mostly those of enzymes, different
ideas as to the way in which active regions catalyse reactions were developed
(Table 3). Our concern will be to illustrate these general ideas and to introduce
others while we examine enzymes in some detail. Note that Figures 1–3
illustrate the very different nature of frameworks in three different classes of
catalyst. We restrain from discussing the fourth, conducting frameworks, until
Section 9.

Figure 3 A protein like myoglobin, shown here, contains a haem group, which is the
open-sided active site for the binding of oxygen (after Kendrew). (Strictly
speaking, myoglobin is not an enzyme, but, by genetic mutation,10 it can be
converted into one). The key point here is that this well-defined structure
illustrates well the manner in which a spatially small active centre is
embedded within a large a-helical proteinaceous matrix.
402 Chapter 24
Table 2 Examples of metallo-enzymes.
Class of Catalysis Example of active site Mn1
Acid/base hydrolysis Zn (Mg, Co, Ni, Ca)
Electron transfer Fe, haema (Fe), Cu
Oxidation (O2) Fe, haema (Fe), Cu
Oxidation (H2O) Moa, Wa, Mn
Oxidation (H2O2, RO2H) Se, Fe, haema (Fe)
Hydrogenation Ni, Fe
Group transfer (–CH3) Co (B12)a
Group transfer ðOPO23 Þ Mg
Group transfer (CO) Ni (F-430)a

Note: Organic side-chains and metal ions can be substituted. The organic side chain substitution is
usually done by gene mutation but metal ion substitution is done by direct exchange and in fact this
can be done for S and Se.
a
In these cases the metal ion is in a metal complex.

Table 3 Active site concepts.

1. Basic idea of a catalytic ion or complex (19th century)
2. Taylor’s concept of local regions of heightened activity on metal surfaces. Parallel
views of special points in molecules and on enzyme surfaces (1920–1940)
3. Haldane’s suggestion of steric strain on binding of a substrate (1935)
4. Pauling’s proposal that the binding of a substrate by the catalyst changed its structure
to one close to that of the transition state for reaction, see Figure 6 (1945)
5. Koshland’s idea of induced fit whereby the enzyme (catalyst) enclosed itself around
the substrate (1958)
6. The proposal of Gray, Malmström and Williams that the matrix or framework of
a catalyst induced constraints on the catalyst activating its attacking active site
(1960–2002)
7. The discovery that many catalytic acts required mobility through NMR and other
methods (1970 to today)

3 Survey of Single Sites of Metal Ions in Catalysts

Elsewhere we have provided a comparative description of single site metal
catalysis.5 Rather than repeating our earlier analysis here we summarise those
properties which show similarities and differences between the three groups of
catalyst, leaving to one side conductor and cluster catalysts and any discussion
of mobility until later.

3.1 The Choice of Metal Atom or Ion

In the case of enzymes, choice is restricted to the environmentally available
elements mainly Mg, V, Mn, Fe, Co, Ni, Cu, Zn in oxidation states I, II or III
and Mo and W in oxidation states IV or VI.5 For all other classes of catalyst the
choice is more open, that is from all elements of the Periodic Table. The states
A Comparison between Enzymes and Solid State Catalysts 403
H(O)CC2H4R H
CO CO CH2 CHR
Co
H2 CO CO
CO

R
CH2
O CH2
CH2 CHR
CO CO H CO
Co Co
CO CO CO CO

R CO
CH2
CH2
CO CO
Co
CO
CO CO

Figure 4 The hydroformylation reaction, which converts an alkene CH2QCHR into

an aldehyde in the presence of H2 and CO, is catalysed by the homogeneous,
molecular entity HCo(CO)4 as outlined here (After Leeuwen, Ref. 20a,
p. 127). Note the movements of the substrate on the metal.

of the metal ions of the first transition series when the oxidation state is II or III
are usually high-spin. In special cases low-spin Fe, Co and Ni are made
by insertion in synthesised chelates, haem, vitamin B12 and F-430, i.e. in
coenzymes. In the second and third row transition metal series of molecular
and solid state catalysts, the states of the metal atoms or ions are virtually all
low-spin with definite kinetic advantages. In molecular catalysts, the oxidation
state zero is also common, for example in carbonyls, Figure 4. This state is
not available to enzymes. Thus enzymes must have very refined metal ion
complexes to match the catalytic powers of the other groups of catalyst.

3.2 The Choice of Ligand Atoms

The ligand atoms for binding metal ions are restricted in enzymes to the
biological protein donors O, N and S with a very rare C-ligand, but they can be
in unsaturated rings in coenzymes, see Figure 7 later. Solid state catalysts have
binding atoms, which are largely restricted to the O of framework oxides, see
Figure 1, or those of synthesised bound molecular complexes. However, there is
also the possibility of using C and S in carbides and sulfides and a greater
variety has been introduced with the synthesis of soft solid matrices. Finally it is
possible to synthesise solids with other donors by replacement of the atoms of
the framework. Molecular complexes can have a great variety of O, N, S and C
donors, of different saturated or unsaturated ligands, note CO and cyclopen-
tadiene, see Figures 2 and 4. They can also have P- or even As-donors,
especially phosphines. Note that molecular units can be attached to surfaces
404 Chapter 24
of, or put inside, certain solid frameworks. Variety is again most limited in
enzymes.

3.3 The Nature of Metal Ions Plus Ligands

The structure of the unit formed from (1) and (2) is frequently an open-sided
cavity, see Figures 1, 2 and 3. It can then select by exclusion so that
enantiomorphic substrates can be separated. Selection by binding, see also
frameworks, is not great except in enzymes where there is greater need for
it. The symmetry of the metal ion site can also be selected opposite function in
enzymes, (see below), but less so in molecular catalysts and is considerably
limited in solid state, catalysts. We stress the advantage of the nature and the
properties of the folding of proteins below.

3.4 The Solvent and the Thermal Stability

The solvent for enzymes is usually water at pH ¼ 7. Solvents for molecular and
solid state catalysts can be chosen at will and solids can be used with gaseous
reactants. The separation of products is simple when using solids but not in the
other two cases. Moreover while enzymes give but one product other catalysts
give mixtures requiring separation. Thermal stability is only good for solid state
catalysts.

3.5 The Substrates

There are limitations to enzyme substrates as they must be soluble in water.
No such restriction applies to the other catalysts.

4 The Frameworks Holding Active Sites

In this article I shall assume that the reader is familiar with the basic features of
the frameworks of all the four classes of catalysts, molecular and enzymic
(homogeneous) and non-conducting and conducting solids (heterogeneous),
Table 4, see earlier figures. As pointed out above, it was conventional to
consider catalysis in all classes as involving an active metal ‘‘site’’ without much
reference to these frameworks. We have seen already however how the attack
can be refined by the way in which the framework holds the metal ion. It can be
made to be open-sided or with an easily displaced simple ligand in all kinds of
catalyst. The most conventional sites are of incomplete octahedral or tetrahe-
dral symmetry. Elsewhere5,11 we have explained that a very stable ground state
is not likely to be the most advantageous for catalysis. It should be noted then
that the framework can force upon a metal an unlikely coordination structure
and energy. Such constrained (entatic) states are seen in many enzymes and
have been shown to match catalytic needs, Figure 5,11 and they are not
A Comparison between Enzymes and Solid State Catalysts 405
Table 4 Some commonly used solid heterogeneous catalysts.
Catalyst Reaction Catalysed
Finely divided nickel Hydrogenation of fats/unsaturated naturally occurring
molecules
Iron (with potassium Synthesis of ammonia (from N2 and H2)
promoter)
Cobalt-based alloys Fischer-Tropsch synthesis of alkanes, alkanols or alkenes
supported on oxides from ‘‘synthesis gas’’ (CO+H2 mixture)
Pt/Al2O3 Reforming of hydrocarbons, i.e. production of alkanes
from linear ones
La31-exchanged zeolite-Y Catalytic cracking of hydrocarbons
Pt on H1-zeolite-Y Hydroisomerisations
H1-ZSM-5 (i) Isomerisations, e.g. of but-1-ene to 2-methyl
propene
(ii) Catalytic dewaxing (conversion of linear alkanes to
branched ones)
(iii) Alkylation of aromatics, e.g. production of ethyl
benzene from benzene and ether

TS-1 (Ti silicalite) (i) Ammoximation of cyclohexanone (in the produc-

tion of e-caprolactam)
(ii) Oxidation of benzene to phenol with H2O2
Ti(IV) in SiO2 Epoxidation of alkenes with ROOH
Zirconocene alkyls (on (i) Stereoregular polymerisation of alkenes
oxide supports) (ii) Selective hydrogenation of aromatics
SAPO-11 and SAPO-34 Dehydration of methanol (selectively) to light olefins
Acidic clays (i) Alkylation of aromatics and other unsaturates
(ii) Synthesis of ethyl acetate from glacial acetic acid
and ethane

unknown in the other classes of catalysts. It is a particular feature of enzymes in

that their protein folds readily give rise to such sites.
There are some common features of the frameworks as they all can be
designed to be of enantiomorphic selectivity or to have cavities excluding
ligands of certain sizes and shapes while allowing others to the active site. It is
within the cavity where we see further the advantages of enzymes since a folded
protein with some twenty different side chains of its amino acids and a hundred
or so folds can create binding cavities of a very great variety. (Each unit in the
protein is an optically active amino acid.) Moreover, these cavities differ from
those in other classes of catalyst in two respects. The side-chains in combination
give almost specific binding properties and they have a limited but potentially
useful mobility, see later. Returning to the case of lysozyme, we saw that the
binding site extended over a considerable distance so that we could well
consider an active region where binding itself can enhance catalysis. Two
substrates can then be aligned for selected and specific reaction. In order to see
the advantages of enzymes so produced in greater detail we need to increase
406 Chapter 24

Figure 5 The structure of the copper protein, plastocyanin. It is a catalyst for electron
transfer. Note that the protein is a relatively rigid b-sheet (see arrows) and
that this helps to constrain the structure and electronic state of the copper
enabling electron transfer (see insert). The metal ion here is enclosed. The
figure is reproduced from Ref. 11c.

somewhat the sophistication of our approach using transition state theory.

Although this theory is commonly used in the literature of enzyme action, it is
somewhat less employed in that of molecular catalysts and unfortunately even
less so in the analysis of solid state catalyst action. So as to have a comparative
outline of the catalysis we have compiled Table 5 for reference.

5 Free-Energy Diagrams and Their Value

in Interpreting Catalytic Phenomena
As indicated in the introduction there are two different approaches to catalysis
represented in outline by Equations (1) and (2).4 In the case of Equation (1) we
can only ask about collision frequency, orientation and energetics of the
collisional state between catalyst and reactant. Equation (2) considers the
alternative that there is equilibrated binding between them. Now as stated in
the bound condition there can be a series of steps in which the substrate
(reactant) passes through intermediates all in energised steps, Figure 6. Using
Eyring transition state theory4 we can treat each bound intermediate as being in
A Comparison between Enzymes and Solid State Catalysts 407
Table 5 Features of individual active sites.
Molecular Enzyme Solid State
Selection of metal All possible Environmentally All possible
available
Structure (a) Open-sided Open-sided Open-sided
(b) Sterically hindered Constrained Often constrained
Spin state Usually low-spin Frequently high-spina Usually high-spina
Flexibility Modest Considerable Low
Selectivity High Very high Modest
Cooperativity Not common Frequent Not common
between sites
Solvents Usually organic Usually water Versatile
Substrates Very versatile Water soluble Very versatile
Chemical Different ligands Mutation metal Metal substitution
modification substitution (see Limited matrices
lattice)
Stability 0–100 1C 0–100 1C Very wide temperature
range
a
(1) Low-spin complexes can be incorporated with Co, Ni and Fe in porphyrins. (2) Clusters and metal catalysts
are excluded due to the ill-defined nature of their active sites, Section 10.

a given free energy state. As mentioned earlier, to calculate the rate of a step the
transition between any bound (intermediate) state is treated as an equilibrium
between it and the top of a barrier, the transition state, when the actual rate
step is reduced to a (simple) vibronic change from one side of the barrier to the
other. We outline the simple approach we shall use here while later we give
reasons for believing the real situation is more complicated. Notice that one of
the steps will be overall rate-limiting and that we assume that on- or off-rates
are not rate-limiting.
As stated in the Introduction, catalysts are agents that accelerate specific
reactions and, by definition, under ideal conditions, their state at the termina-
tion of a conversion is the same as that at their commencement. There can be no
overall change in the free energy of the catalyst but it can cycle during reaction.
In a real situation, depicted as in Figure 7, there is a series of states, each rate
being given by Equation (2). The reactants and the catalyst are intimately
combined in binding region(s) in the series of states. Both experience changes of
internal free energy in the processes that can lead to the formation of transition
states (T) and of intermediates (I). A catalyst may be seen to undergo a cycle of
energy and conformational changes as it goes through a series of states, an
example is given in Figure 7,12 which we have dissected into parts in Figure 6.
Whereas the intermediates In have readily measurable lifetimes, ranging from
minutes to as short as 106 to 1010 s, the transition states Tn are so short (of
the magnitude of the time of a bond vibration (1013 s)) that their lifetimes are,
in general, not usually experimentally accessible, but see Ref. 13. The separa-
tion of the catalytic site from the reactants allows us to focus on the structure
and free energy of the states of the attacking groups alone as well as on those of
the possible intermediates, I, and of the transition states, T, of the substrates
408 Chapter 24

T
T T T
∆G
I

I
I

Reactants Enters Product leaves

Reaction Coordinate

∆G T
T

I
Reactants Enters Product leaves

Reaction Coordinate

Figure 6 (A) Free-energy profile as a function of reaction coordinate depicting

changes associated with the formation of bound intermediates (I) and
transition states (T) that are involved in the course of the overall reaction.
The steeply rising (dashed) curve indicates the situation that prevails when
the reactants cannot even form a bound intermediate, because of the
inability of reactants to enter the framework of the catalyst. The fourth
step is the activation of substrate leaving. (B) The free-energy profile of the
catalyst only but which contributes to the profile of (A). The selectivity of a
catalyst for a particular product is governed mainly by the relative heights
of transition-state maxima, and the ability of the catalyst to prevent leaving
of intermediates. Note that, the maxima and minima coincide closely with
those for the overall reaction, but this is not a necessity. The catalyst may
have atoms in its active site with specially constrained geometric or elec-
tronic states even in its substrate-free condition, see (—) on ordinate in
figure B due to the mode of binding in its framework. Passage over barriers
(T) can therefore be strongly facilitated thus contributing to the lowering of
those in (A) during catalytic action.

with their chemical consequences. (Note that the framework can be intimately
involved in the initial and intermediate states of the attacking groups in all the
intermediates as seen in the case of lysozyme.) While structures of I are often
determinable by experiment, especially in enzyme reactions, as are their free
A Comparison between Enzymes and Solid State Catalysts 409
N2O + CO N2 + CO2

Ts

CO
CO 47.2
N2O
6D Fe+ 0.9
TS CO N2
14.9

61.8 0.9
CO
22.9 30.6 TS 86.7
CO
47.8
61.4
N N2
O Fe+ + N2O FeO+ + N2
6D Fe+
C
N2 N2
Fe CO2

FeO+ + CO Fe+ + CO2

Figure 7 The computed profile of the overall reaction: N2O+CO-N2+CO2, when

divided into two discrete steps (Fe1+N2O-FeO1+N2 and FeO1+CO-
Fe1+CO2) at a gas-phase single-site catalyst such as Fe1 (from Ref. 12).

energies, it is theoretical calculation that is most valuable in deriving probable

structures and energies of intermediates in many cases and in all cases of
transition states, T.14 We also observe that the diagram allows for mobility of
the catalyst structure so that we are considering a series of structures as well as
energies of intermediates in the cycle.
A major feature of the active region, other than the activation of the
substrate(s) by reducing the energies required to reach the transition state, is
that when there is more than one substrate the site can concentrate the
substrate species so that they are in close proximity and align them correctly
for reaction. In effect, this is an entropy reduction in the bound states relative
to the free substrates. It is for this reason, and in consideration of other entropy
factors, that we plot the free energy, DG, on the ordinate rather than energy DE.
Binding of any substrate in itself has other features in that, if there are two
points of attachment, the substrate may be strained although these points may
be remote from the bond to be attacked, see Table 5. Increasing the number
of points of attachment or of repulsion (no binding, i.e. in a collisional process,
see Equation (1)) to a relatively rigid surface of any substrate will increase
selectivity and strain, but it also gives rise to enantioselectivity, as pointed out
by Ogston.15 When there are two substrates the active region may have two
adjacent attacking sites. These considerations make it clear that the framework
410 Chapter 24
of a molecular catalyst and the matrix of solid state catalysts and that of
enzymes especially can play a very decisive role in the catalytic act. While we
have conceptually separated the active site attacking groups from the binding
sites, they are obviously linked. The idea of an active region is, therefore, a
composite cooperative one and this conclusion will be developed in subsequent
sections of this article. It is here that the subtle nature of enzyme catalysis rests.
We need to make it clear that as much as a catalyst activates a reaction, it is
not usually the case that the product is a thermodynamic end point. Most
usually, a catalyst is required to selectively produce a simple ‘‘intermediate’’
product so that catalysis has to stop in a chosen way. Almost invariably, an
enzymatic catalyst is also required to be capable of selecting (with high
precision) its actual substrate (reactant) from among a wide range of com-
pounds. Overall, selectivity is in accepting as well as processing. Homogeneous
(small molecule) as well as heterogeneous catalysts (in laboratory or industrial
contexts) have difficulty in stopping reactions at given stages of conversion. Of
course enantiomorphic selection is sometimes required of all catalyst classes.
Only occasionally, as in shape-selective conversions involving nanoporous
catalysts (a special interest of John Meurig Thomas, see below), does it exercise
selectivity of substrate in a similar manner to that of an enzyme, and the degree
of selectivity is normally not great in the activity of a molecular catalyst.
The fidelity attainable in enzymatic catalysts often exceeds 1 in 105, whereas in
non-enzymatic catalysis (homogeneous or heterogeneous) selectives seldom
exceed 1 in 102 except in enantioselective processes. It is the enzyme framework
which is so important here.

5.1 Complications in Transition State Theory

The basis of Figure 6 is transition state theory of reactions as outlined by
Eyring and Evans. This theory is often illustrated by the uncatalysed reaction

H2 þ D , DH þ H

in which reactants proceed up a three-dimensional energy hill towards a pass

which is the single transition state T. The T-state pass is crossed by a single
vibrational disruption of the energised H2 in the presence of D, giving
D  H  H, and then allowing DH to form on leaving the pass and to run
down the opposite side of the energy hill to DH and H. This simplistic account
will not describe a real passage of reactants of a complicated structure to
products, since the reactants and products have many degrees of freedom and
can reach transition states of somewhat varying energy, limited by Boltzmann
factors, see Equations (1) and (2). Moreover, as they approach the transition
state, there can be internal redistribution of energy within the participating
molecules so that a multitude of equilibrated energy valleys and approaches to
the T-states (now plural) can be envisaged. Lastly there is no guarantee that
equilibrium of states is approached in a given flow of reaction via intermediates.
Undoubtedly, there should be a more elaborate picture but it lends itself only to
A Comparison between Enzymes and Solid State Catalysts 411
a more complex mathematical analysis and no pictorial representation. We shall
therefore use the simple diagram, Figure 6, trusting the reader to set aside all the
aforementioned complications, at least initially, for this allows us to compare
the energetics of the different classes of catalyst at a first level of approximation.

5.2 Computational Approaches to Active Sites

Whereas considerable advances have recently been made in the experimental
(in situ) determination of the structures of all types of catalysts, there has also
been a burgeoning in the deployment of density functional theory (DFT),
giving quantitative insights into the energetics of individual steps that take
place at such catalysts (see Figure 7). These calculations14 include not just the
transformation of the substrate but also the cyclic changes of the catalysts. The
number of atoms in such calculations can now be well over a hundred. It has
become fashionable of late to invoke the results of DFT calculations in
examples of molecular and enzymic (homogeneous) catalysts. Whilst this is a
reflection of the power of computational approaches, there are dangers in
giving them too much weight, especially when the errors involved in such
calculations (10 kJ mol1) or the assumptions made in order to make the
calculations manageable, are not emphasised.
Now while we can see that the real situation may be very complicated and
computerised searches may be helpful, we draw attention to the work of
Marcus16 and others, since their basic algebraic descriptions of the steps of
electron and atom, especially hydrogen, transfer have proved remarkably
successful. We shall devote three sections, one to the theories of electron
transfer, Section 11.3, the second on proton flow (Section 11.4) and the third on
ion or atom transfer (Section 11.5) as these steps are of considerable impor-
tance in many catalysed processes. Note that the substrates considered here are
extremely simple in themselves but their movements are not.
Turning to practical examples, we shall assume familiarity with the simplest
catalysts with a single metal ion ‘‘site’’1,3,5 and consider the cases of more
complex catalytic ‘‘regions’’ where clearly the framework is essential. Under
each major heading, we describe molecular catalysts very briefly as their ligand
framework is much less important than in enzyme and solid state catalyses.

6 Catalysts Using Adjacent Sites

6.1 Molecular Catalysts
It is not easy to synthesise small molecular catalysts with adjacent sites and it
becomes even more difficult to synthesise them with non-adjacent sites, see
Section 7. One example of adjacent site catalyses with a single metal ion is that
of a metal ion complex bound in a unit with cyclodextrins for use in both
hydrolytic and oxidative chemistry. Here one site is a metal and the second is an
organic centre for binding substrates (see Ref. 32). Recently the investigation of
412 Chapter 24
such possibilities has been intensified. An example of two metal ion adjacent
sites is the insertion catalyst composed of a pair of Cr metal centres linked
together by a flexible chain,17 and Cowie and co-workers have initiated a series
of studies using heavy metal complexes.18 It is also possible to use maquettes to
bind two adjacent sites as in the peptides which bind iron porphyrins.19 These
are unusual examples as can be seen by consulting a text on molecular catalysts,
which is overwhelmingly devoted to single metal element sites.20

6.2 Enzymes
By way of contrast most metal enzymes use adjacent site catalysis2,5 amongst
which we note especially those with one metal and one or more organic side-
chains. We have in mind as clear examples many zinc and other cationic
hydrolytic enzymes such as proteases, nucleases and saccharases. There is also a
huge variety of oxidases and peroxidases, Table 6, where the organic protein
framework binds and helps to activate the substrate while the metal activates
oxygen, see Figure 2, or hydrogen peroxide. In the peroxidases, peroxide
activation is at the Fe31 haem while the substrate binds some 5–7 Å away in
the matrix.21 Electron transfer generates the substrate radical which is then
attacked by water to give a hydroxylated species. The catalyst is cycled first via
oxidation of the iron and the porphyrin ligand and to the MO state sometimes
then by reduction on oxidation of the substrate.
There is a huge variety of enzymes which may insert O2, O or OH into a
multitude of selected organic molecules or generate energy by remote oxidation
of substrates while giving 2H2O, Table 6. Substrate selection is based on
preferential binding of some, and exclusion of other, molecules from the active
site cavity, and the substrate is bound in an exact regio- and enantio-selective
specific manner by the organic side-chains of the protein at a nearby site. The
sophistication of these catalysts based on protein matrices is far beyond that of
any man-made inorganic catalyst. The activation of oxygen is by special
constrained metal ion sites involving almost invariably Fe21, as a simple ion
or as haem, or Cu1, or both at adjacent sites. Examples are, cytochrome P-450,
given in Figure 8 (top) and cytochrome oxidase. We shall not describe in detail
the iron or haem iron sites involved in direct bound oxygen attack on substrates
here as they are expertly described by Poulos et al.,22 who show the series of
intermediates also seen in peroxidases. The mechanisms are very well docu-
mented and often have a preferred order of addition such that only the
substrate bound enzyme allows the iron to be reduced, then oxygen to bind
while the enzyme side-chains are protected by the substrate, before O2 is
partially reduced. The partial reduction of the metal and oxygen to MO+H2O
is achieved by long-range electron transfer from non-adjacent sites,
Section 11.3. The overall process seen in products is always apparently due
to two one-electron oxygen or hydroxyl transfer steps where for example the
bound substrate and oxygen are retained until product release. Transient
radicals often include porphyrin or amino-acid side chains in the matrix but
A Comparison between Enzymes and Solid State Catalysts 413
Table 6 Some oxidative enzymes employing two adjacent sites.
Enzyme Metal Reaction
(a) Using O2
Cytochrome P-450 Fe(haem)21 Hydroxylation. Epoxidation of
saturated carbon compounds
Methane oxidase Fe2O Hydroxylation of methane
Lipoxygenase Fe21 Regio-specific oxidation of lipids
Stearyl desaturase Fe2O Introduction of C(9) unsaturation
Galactose oxidase Cu1 Galactose to a hexadialose
Naphthalene 1-2 Fe21 Oxidation to
dioxygenase dihydroxynaphthalene
Cephalosporin synthetase Fe21 5-membered ring expansion
(b) Using H2O2
Peroxidase Fe(haem)31 Oxidation of phenols
Chitinase Fe(haem)31, Oxidation of chitin
Mn31
Hydroperoxidase Fe(haem)31 Oxidation of CN, Cl
Vanadyl 51 Oxidation of Cl

Note: One site is the organic matrix adjacent to the bound metal ion site.

radicals are rarely released. These enzymes, Figure 8 (top), often utilise mobility
at and around the active site to control ordered addition of O2 and substrate – a
very different mechanism to that in solid state catalysis. This type of mecha-
nism using MO species derived from O2 is also seen on metal surface catalysts.
(The reader may come across the term co-enzyme in the context of these and
other biochemical catalysts. The co-enzyme is a small molecular unit or
complex which may be immobile in the enzyme, as iron porphyrins are,
or can be a mobile small unit which carries groups such as –H, –CH3 or
–NH2 or just electrons. Compare the use of molecular complexes bound to or in
solid state frameworks. In the case of cytochrome P-450 a pyridine derivative is
the small coenzyme, NADH, which carries reducing equivalents to the enzyme
from a non-adjacent distant site to the haem iron. We refer to this part of the
activity of the enzyme in Section 7.1.)
In the examples of the use of oxygen reduction to water in energy trans-
duction employing enzymes such as cytochrome oxidase there is a long chain of
electron- and proton-transfer centres making wiring circuits of both particles
Section 11. The long-range electron transfer is also managed in all kinds of
catalysis using electrodes to supply electrons. Enzymes attached to electrodes
are used as sensors.

6.2.1 A Rearrangement Catalyst Related to Oxidative Enzymes

A strange case of radical intermediates in a rearrangement reaction is that
catalysed by coenzyme vitamin B12. Here radical Hd atom transfer occurs
between a cobalt–adenosyl complex and the substrate via an adenosyl free
radical intermediate where the adenosyl anion is initially bound to the cobalt,
Figure 9. On substrate binding to the matrix, not the cobalt, the anion is
414 Chapter 24

Figure 8 The enzyme cytochrome P-450 (top) which acts as a hydroxylating agent
using molecular oxygen. To do so it must cycle through intermediates,
different constrained states of the iron. The substrate binds before the
oxygen in a protective manner. The bound oxygen is reduced first to water
and an iron oxene which is the hydroxylating agent. The reaction scheme
(bottom) illustrates some of the conformational changes as seen in oxygen-
binding proteins such as haemoglobin. Note there is a non-adjacent site for
electron supply. The cycling of the catalyst can be considered separately
from the processes of the substrate reaction; see Figure 6. The figure is
adapted from Ref. 3.
A Comparison between Enzymes and Solid State Catalysts 415

Figure 9 Coenzyme B12. For the reaction pathway of rearrangement of methyl-

malonyl CoA, see Ref. 48a. Note that there is bond-breaking of R, the
adenosyl ligand, at the cobalt with redox-state change, but the metal ion
remains in a low-spin state. The cobalt–carbon bond is held in a constrained
manner so as to facilitate ‘‘break’’.23

released homolytically as a R – CHd2 radical and a Co21 ion.22 (We could call
this conjoint metal/ligand catalyst as in the subsequent steps it is the CHd2
which acts in H atom transfer23). The cobalt is always in a low-spin state. We
include this case here as an illustration for it is clearly an example of adjacent
site catalysis with a ligand bound metal ion where the ligand becomes a second
adjacent site attacking agent.
Before proceeding we stress the remarkable sophistication of these enzymes.
Substrates are held in alignments suitable for reaction, small mobility is allowed
so that relaxation energies necessary for the passage through intermediates are
kept small, and attacking groups, metal ions and others, are in usual states
reducing DG of the catalyst itself (Figure 6). We cannot find similar features in
molecular or solid state catalysts.

6.2.2 Hydrolytic Enzymes

One further illustration of the value of the framework in enzyme catalysis is
provided by the zinc enzyme carbonic anhydrase. The framework provides:

(1) A constrained (entatic) zinc ion site, slightly adjustable,24 suitable for
catalysis (Figure 10a).
(2) A deep cavity for the entry of substrates, restricted to CO2 and H2O
appropriately positioned, for details see Ref. 48b.
416 Chapter 24

Figure 10 The enzyme carbonic anhydrase which holds zinc at the active site in a
constrained state (top), but such that it can move through different states
by small conformational changes (bottom). The two substrates enter the
site via a narrow selective channel. The probable scheme of reaction at the
zinc is shown as a cycling through coordination number changes.24

(3) An adjacent base, an imidazole, to assist attack.

(4) A catalysed pathway for proton movement to the active region,
see Section 11.4.
(5) Very limited but useful mobility to allow adjustments as the reaction
passes through intermediates. Compare the even more limited movement
allowed in the copper enzyme, Figure 4, both are b-barrel structures, and
the greater mobility in the helical enzymes, see Figures 3 and 8b.
A Comparison between Enzymes and Solid State Catalysts 417
The extremely effective design features allow highly heightened activity and
great selectivity where the structure has arisen through repeated mutation of
amino acids to attain an optimal catalyst. This is probably the simplest example
of the result of ‘‘design’’ in enzymes. It has been very difficult to find a good
molecular catalyst for this cyclic reaction.24

6.3 Solid State Catalysts

An example of an adjacent-site effect in heterogeneous catalysis (as already
mentioned) occurs in the oxyfunctionalisation of n-hexane within the chabazitic
cage of a MIIIALPO-18 (or MIII ALPO-34) nanoporous catalyst where MIII is
FeIII,25 see Figure 1. The known regioselective attack of terminal methyl groups
of a linear alkane (in the presence of O2 and a MIIIALPO catalysts), can occur
sequentially at each end of n-hexane when the catalyst has two active sites
separated spatially by 5.4 Å, the same distance that separates the two terminal
CH3 groups of n-hexane, Figure 11. Adipic acid is therefore produced as the
favoured product of this aerial oxidation.25 This catalyst is quite rigid and one
or other of the iron ions can attack any available substrate so that it has only a
small degree of selectivity. While ALPO-31 retains the substrate as it passes
through intermediates only releasing the desired product, Fe-ALPO-5 with a

Figure 11 The nanoporous solid AlPO-5 becomes a powerful oxidation catalyst when
a few of the Al31 ions in the framework are substituted by transition metal
ions in high oxidation states (such as Fe31, Co31 and Mn31) and tetra-
hedral coordination. Free radicals, such as C6H11 d
are readily formed when
cyclohexane enters the pores (diameter 7.3 Å) of this open-framework
catalyst. A series of reactions of cyclohexane lead to the formation of a
number of partially oxidised products. If FeAlPO-31 is used as a catalyst in
place of FeAlPO-5, a much larger yield of adipic acid is obtained. Note the
rigidity of the lattice may constrain the geometry and electronic states of
the cation site but allows little mobility (after Thomas et al.25).
418 Chapter 24

Figure 12 The catalytic pathways of sequential hydrogenation of benzene and ster-

eoregular polymerisation of alkenes at the zirconocene-type cation,
CpZr(CH3)21 bound to an alumina surface pre-treated with sulfuric acid
Cp is cyclopentadienyl (after Marks et al.26).

larger cavity of 7.3 Å releases the first product of oxidation of cyclohexanol

(Figure 11). Much of the difference in selectivity is based upon restrictions on
entry and leaving. The basic framework has little sophistication in its structure
when compared with an enzyme. Finally a sophisticated solid state catalyst of a
molecular complex on a zirconium oxide surface is shown in Figure 12 where
the surface oxide (converted to –OH) undoubtedly act as adjacent sites to the
complex.26

7 Catalysts with Non-Adjacent Sites

7.1 General Considerations: Molecular and Enzyme Catalysts
There are two major classes of non-adjacent sites amongst molecular, enzymic
and solid state catalysts, while we still exclude discussion of conductors. The
two are catalysis by (a) two immobile sites separated by at least several
Ångstroms and (b) two mobile sites separated initially by several Ångstroms
but which come together so as to be together during catalysis. The second
group will be described in Section 8.2. The case of two fixed remote sites is
readily appreciated by giving an example from enzymes which is an extension
of the discussion of the P-450 cytochromes where we have already seen how
oxygen and substrate are handled. Electrons are supplied in this enzyme from a
remote, non-adjacent site to reduce bound O2 to FeO. Under these conditions
introduction of electrons stops at a particular state, for otherwise, many
unwanted oxidations could occur. In an alternative to reaction to an oxene
and H2O, as in the P-450, the oxygen can be taken down to 2H2O using four-
electron reduction in one-electron steps, the electrons coming from a remote
site. This is the function of laccase,27 a copper enzyme (Figure 13, see also
Figure 4). Here the second substrate, indicated by ‘‘electrons’’ in Figure 13, is
A Comparison between Enzymes and Solid State Catalysts 419

Figure 13 The enzyme Laccase, non-adjacent site catalyst of oxidation. One electron
oxidation occurs at the single copper ion by electron transfer, see Figure 4,
from polymerisable monomers. The electrons pass through the protein to the
multi-copper site which binds oxygen but does not release it until it is
reduced to 2H2O. This requires not only electrons but protons to travel in the
matrix, see Section 11. The figure is modified from Messerschmidt et al.48b

bound close to a single copper which acts so as to abstract one electron at a

time from a substrate and then passes electrons to a two (or three) copper ion
centre. It is this centre which holds the various intermediates from O2 down to
2H2O. Many enzymes work via these chains of electron transfer, some of which
allow the capture of the energy difference between the redox potentials of a
reductant and an oxidant. Now this is the general function of the fuel cell
reaction 2H2+O2 - 2H2O, giving electric power. Here in man-made devices
doped metal electrodes act as H2 and O2 catalysts separated by a metal wire.
This remarkable parallel with biological energy conversion will lead us to a
discussion of electron (and proton) transfer in matrices which in the limits of
conduction can be semi-conductors or even metals, see Section 11. It is clear
that catalytic enzymes could also be connected to electrodes and this is also the
basis of many man-made sensors using catalysts while in organisms the
embedding of enzymes in membranes gives rise to parallel properties of sensing
by electron transfer. Another way of utilising oxygen is to bring about remote
420 Chapter 24

Figure 14 The molybdenum coenzyme used in the transfer of oxygen atoms from H2O
(oxidised) to aldehydes giving ketones. Molybdenum is peculiarly suited to
atom transfer catalysis.2

two-electron oxidation of a substrate by it

O2 þ 2RCHO ! 2RCOOH
where O2 is bound at a non-adjacent site.
Molybdenum enzymes for this purpose use a complex, Moco (Figure 14),
embedded in a protein.28 Here the oxidation by O2 is not direct but occurs as
follows:
O2 ðremote siteÞ þ MoIV ðsecond siteÞ gives by electron transfer

O2 VI
2 ðremote siteÞ þ Mo ðsecond siteÞ

MoVI þ H2 O ! MoO þ 2Hþ

MoO þ RCHO ! RCOOH þ MoIV

þ
O2
2 þ 2H ! H2 O2 at the remote site

Electrons pass from MoIV to O2 via the protein. Many molybdenum enzymes
use this mechanism of oxidation in which the solvent for the reaction, H2O, acts
much like the solvent of the solid state matrix of the Mn/Ca/O oxidative
catalyst for dehydrogenation of propane and butane to benzene and p-xylene,
respectively.
As mentioned already it is possible to attach molecular or solid state catalysts
to electrodes. The reverse reaction of H2O - O2 through the action of light
can be connected to the production of H1 and OH– by enzymes in different
parts of space,29
oxidation (O2)

H2O hv e + +
recombination + usable energy

reduction (H2)

where " is a positive hole, which is formed away from e.

This use of spatially separated catalysts is the essence of photo-energy
capture devices. There are many attempts by man to discover parallel devices
for clean conversion of light to useful energy.
A Comparison between Enzymes and Solid State Catalysts 421
Molecular catalysts of this kind are little studied, though molecular wires
connecting donors and acceptors have been intensely studied in an effort to
understand electron transfer in organic matrices.

7.2 Solid State Catalysts

One example of the involvement of two non-adjacent sites in nanoporous
(solid) catalysts is exhibited in the one-step conversion of cyclohexanone to
e-caprolactam in the presence of NH3 and O2 (or air). Here the catalyst is a
microporous ALPO in which some of the AlIII ions have been replaced by a
redox ion (typically MnIII or CoIII) and some by a Lewis acid divalent cation30
such as Mg21, Zn21 or CoII. At the redox centre, the ammonia is converted into
hydroxylamine, in situ:
MnIII
NH3 þ 12O2 ! NH2 OH

This then converts the cycohexanone within the pore of the solid catalyst
to the oxine, which is then converted, by the Brønsted catalytic activity of
the loosely attached proton associated with the framework divalent ion, to the
caprolactam (the precursor of nylon-6). This is an example of what the
heterogeneous catalysis community refers to as a bi-functional catalyst.

8 Mobility at Active Sites

We have mentioned mobility of catalysts several times. Here we give a more
detailed description of minor local mobility and of gross conformational
change.

8.1 Minor Mobility of Active Sites

We have assumed until now that the catalyst atoms are largely immobilised: a
common view of an active site. In fact, in almost every example, the atoms of
the catalyst experience changes of bond length and bond angle to some degree.
It is recognition of this fact which allows us to see the way in which catalyst
atoms can pass over their transition states in Figure 6, especially where there
are many steps in the overall process. Examples of some mobility of the
coordination sphere have been described in homogeneous catalysis and en-
zymes, e.g. coenzymes B12 and cytochrome P-450 reactions. Elsewhere, we have
stressed that the zinc ion is an excellent acid catalyst in an initially tetrahedral
site in enzymes. Like Co21 (high-spin) Zn21 has no strongly preferred coordi-
nation number and in its catalytic cycle change of coordination adjusts all bond
lengths and angles (Figure 10). By constraining Ti41 in a tetrahedral site in
nanoporous solids, a similar possibility for coordination number change is
induced with bond distance changes, see Figure 15 and Figure 12. Mobility on
the smaller scale is recognised in other instances, e.g. by the Debye–Waller
422 Chapter 24

Figure 15 On the basis of XAFS analysis and computations using density functional
theory, this scheme is proposed for the epoxidation of alkene by alkyl
hydroperoxides (HOOR 0 ). Experimental evidence shows that both the Z1
and Z2 intermediates may be formed; and the original (constrained) four-
coordinated Ti active site passes through a six-coordinated state (e.g. the Z2
intermediate) in the course of the epoxidation. The Ti41 state remains
as such during the ‘‘acid–base’’ process, wherein the oxygen of the hydro-
peroxide serves as the base (after Thomas et al.25).

factors in X-ray spectroscopy studies of transition metal ions incorporated into

nanoporous silicas and enzymes. The movement of atoms on heterogeneous
metal catalyst surfaces is often much more considerable,3 and it has also been
seen with nanoparticles of metals, see Section 10.
Minor motions such as rotations of groups and vibrations within bonds
are included in the approach to the transition state (Figure 6). In Marcus’
theory of hydrogen transfer, that is of a hydrogen atom or ion, the rate of
transfer is a product of a temperature dependent vibrational/rotational term
and a tunnelling term between neighbouring groups.16 The hydrogen cannot
tunnel more than about 0.5 Å and the distance between the two potential
energy minima involved in the transfer process must then be at, or less than,
this distance. The implication is that H-bonding between the centres will assist
transfer where the distance between minima is small. However although this
H-bonding is often strong in acid–base proton changes it can be very small for
C–H bonds. Hence in the second case compression or vibronically induced
compression of the separation will aid transfer rate by increasing the tunnelling
contribution. The best solution involves perfect alignment of the two substrates
for H-transfer as seems to be the case in many enzymic reactions. Here then the
mobility of a framework, the solvent of molecular catalysts or the mobility of
the matrix of proteins, can aid catalysis much more effectively at low temper-
ature than the rigid matrix of solid catalysts both in terms of compression on
binding (binding energy assisting conformational progression to the transition
A Comparison between Enzymes and Solid State Catalysts 423
state) and in low energy vibrations locally of the matrix. The effects have been
demonstrated in enzyme studies of hydrogen isotope effects especially in
lipoxygenases.31 In solid catalysts such vibrations may be important only at
high temperature.

8.2 Mobile Segments and Arms: Allosteric Systems

The design of catalysts which can bring together two sites of binding by
mechanical adjustments or by surface diffusion is to be seen in the development
of some molecular catalysts and of some surface attached molecular catalysts
but it is best observed in a number of enzymes. A simple molecular example has
been designed by Breslow and has cyclodextrin movable arms attached to a
framework including a porphyrin metal ion catalytic centre.32 As described
already, the arms carry the organic substrate to be attached and the porphyrin
has either zinc, as an acid–base centre to resemble the enzymes peptidases or
esterases, or iron, as an oxidation centre for activating oxygen or hydrogen
peroxide to resemble P-450 cytochromes.
Guided chemical segment movement of enzymes is common. Even the first
enzyme crystallised, lysozyme, closes its groove around the substrate on
substrate binding. More extensive movements are seen in group-transfer
enzymes and we illustrate these cases with the enzyme phosphoglycerate kinase
(Figure 16). The enzyme consists of a hinged pair of domains.33 The two
domains bind magnesium adenosine triphosphate, MgATP, and glycerate at a
considerable distance apart but binding of both causes the phosphate of ATP to
move close to the glycerate and be aligned for transfer. Reaction follows to
equilibrium in which this third phosphate of ATP is transferred giving adeno-
sine diphosphate (ADP), and phosphoglycerate. Considerable segmental mo-
tions are also observed in the series of enzymes of bioenergetic processes. A
general description of such mobility in enzymes is given in Ref. 9. We add a
note here to the effect that the unit ATP, a carrier of phosphate, is open to free
diffusion from enzyme to enzyme as are many other coenzymes carrying –H, –
NH2, –COCH3, etc. so connecting two or more free enzymes which are remote
in space. Whether carrier assisted sequential catalysis is a useful possibility in
organic chemistry is open to test. It is readily seen however that molecular
catalysts, free or bound to surfaces, could be designed to mimic the mobile
enzymes. Solid state catalysts as designed at present do not use such massive
changes of structure. We stress again the remarkable functionality of enzyme
matrices in a variety of mobilities.

9 Summarising Survey of Active Regions

in Non-Conductor Catalysts
Reverting to our introduction, we note that, in Figure 6, the over-riding
concern is to lower the overall activation energy of the reactions, retaining
424 Chapter 24

Figure 16 The open structure of phosphoglycerate kinase, an enzyme which catalyses

transfer of phosphate from adenosine triphosphate to glycerate, but it only
does so on closing. There are two largely b-domains linked by a hinge of
helices. Molecular machines are made by using such motions.33

intermediates as far as possible, while obtaining selectivity of attack. Various

ideas using the binding energy of the substrate to lower the activation energy
of the intermediates have been described, see Table 3. These ideas initially
applied to enzymes are now becoming useful in the description of solid
state catalysis where the inorganic matrix plays a role somewhat parallel to
that of a protein. There is often inadequate kinetic and structural analysis of
binding to allow comparison of enzymes with the other classes of catalyst as
fully as we would wish. The more general qualitative similarity between
all the three different types of catalyst can be seen in their roles in moving
electrons or atoms in the active sites. Some further similarities and differ-
ences are:

(1) Hydrolytic reactions are catalysed by metal ions, which cannot

undergo one-electron steps, in all three classes of catalyst, e.g. Zn21,
Zr(IV), Ti(IV). The metal ions are selected by cells for enzymes from a
very limited number of elements but the choice in other catalysts is not
restricted.
(2) The geometry of the cavity and its size are controlled extremely well in
enzymes, but nowadays improvingly so in solid state catalysts. Molec-
ular catalysts have less matrix control over selection.
A Comparison between Enzymes and Solid State Catalysts 425
(3) Oxidation is often by one electron steps of the catalytic metal ion
implying organic radicals and the series of some or all the intermediates
O 
2 , O2H and H2O. In the best cases only the final products are freed,
d

contrast cobalt as a simple ionic homogeneous catalysis with Fe

oxidations in pores and in catalysis by enzymes such as cytochromes
P-450. Enzymes control the reactivity of intermediates extremely well.
Two electron reactions require control of oxidation states such as MO.
(4) The metal ion, by its mode of binding, is often activated in a constrained
structural site, open-sided but limited in access, and often in a special
electronic state as well as of limited coordination number by matrices of
all kinds, including the framework of complex molecular catalysts. In
effect the ground state of the metal ion may be close to its transition state
in free energy, see Figure 6, so smoothing out its part in the reaction
energy profile. Sometimes on reaction, with change in oxidation state, the
metal ion undergoes coordination number change (contrast electron
transfer in Section 11.3). During some reactions the metal ion cycles
through several transition states and here the matrix, especially proteins,
can guide the sequence of changes.
(5) The matrix binds and retains intermediates as well as controlling
reactivity until the required products are produced.
While the similarities are qualitative, this must not hide the fact that
enzymes are quantitatively superior in almost all the above respects.
The differences are:
(6) The nanoporous matrix itself cannot be attacked by reagents such as
oxygen but the molecular and enzyme matrix can be. To avoid such
attack, the enzyme requires a fixed order addition of reactants so that
the protein is protected by the first bound substrate often not at the
metal, e.g. see P-450 cytochromes. Oxygen is a major menace for
molecular catalysts and is often excluded from the reaction vessel.
(7) The matrix, especially the protein of enzymes, can align two reactants
accurately as to ease the energetics of reaction.
(8) In oxidation catalysis the abstraction of H from the substrate is often
directly by the metal ion in the nanoporous solid (see Figure 11), but it
is by the metal-oxene (MO) in the enzyme (Figure 8, but see co-enzyme
B12 rearrangement reactions, Figure 9).
(9) The protein matrix may have considerable local flexibility while the
nanoporous solid has comparatively little. Protein surfaces adapt to
their substrates and the small conformation changes assist binding and
reaction by induced fit.
(10) The reactants and products of enzyme reactions can be optically active
enantioselective in all reaction classes and so can certain molecular
catalyst reactions but this selection is not easily gained in solids unless
molecular catalytic units are attached.
(11) The nanoporous solid can be used at high temperatures and pressures
and with gaseous substrates while enzymes and molecular catalysts are
of limited temperature stability.
426 Chapter 24

10 Ill-defined Active Sites

So far we have been concerned with well-defined metal ion active sites but we
must now turn to the less clearly describable catalysis by metal or metal-like
‘‘sites’’ such as atoms in clusters. These clusters may contain more or less
strongly linked metal ions or metal atoms. In fact there are many materials
where this distinction between metallic and ionic systems is not easily made
because the strength of interaction between the partners in the matrix (or with
atoms in the support) allows distribution of electrons over all the atoms in it.
For example, Re2O7 is metallic but it looks, by formula, as if it should be a
typical oxide written with a rhenium charge of +7. RuO2 is an example of a
good electron conductor which is not a metal. As the non-metal is made larger
in many series of metal ion compounds going, for example, from O to Se and
Te the properties change: bulk NiTe is as an alloy, as opposed to NiO, a salt,
and even in a small cluster valence electrons need not be localised. Now this
difficulty of separating more generalised even bulk properties from localised
sites is very clear in doped semi-conductors. There is a gradual change in
electrical conductivity as dopants interact more strongly with the matrix. In
fact there is a continuum from insulators to metals where electron transfer
proteins (metal ions doped in protein matrices) and doped salts (metal atoms
doped in oxide lattices, e.g. Li atoms in NiO) and even ‘‘doped’’ materials such
as the tungsten bronzes, lie in between. In previous sections we have maintained
a description of ‘‘active sites’’ which have strong local charge separation and
so their structural limits were closely defined. In this section, this is no longer
true, even in enzyme clusters such as Fe4S4 individual atoms have no simple
oxidation state.

10.1 Molecular ‘‘Ionic’’ Cluster Catalysts

We know of many examples of molecular clusters such as Au55(PPh3)12Cl634
where it is difficult to describe charge distribution. Charge in some is to a degree
localised but in others localisation is not observed. Behaviour in the cluster is
either that of a good semi-conductor or of metal-like behaviour. The transition
from a non-metal to a metal can be mapped sometimes with the size of the
cluster but is often temperature- and composition-dependent. Such a cluster
complex may be attached to a soft or hard matrix surface. Many model clusters
have been synthesised to resemble enzyme clusters but few are catalytically
active.

10.2 Clusters in Enzymes

In enzymes, there are many examples of small clusters of ‘‘ions’’ bound together
by sulfide and a few bound by oxide (Table 7).2 A simple one is the hydrogen-
ases, where the active site is multinuclear in an Fe4 or an Fe3Ni centre bound by
simple sulfide ligands. The problem with the description of catalytic activity
A Comparison between Enzymes and Solid State Catalysts 427
Table 7 Some classes of multiple atom non-adjacent active sites in enzymes.
Site Reaction
MoFe7S8/Fe8S7 N2+6H1+6e-2NH3
FenSm/FenSm General electron transfer
Ni/Fe/S/FenSm Hydrogenase H2-2H1
Cu.haem(Fe)/Cu O2-H2O
Mn4Ca/chlorophyll H2O-O2
Ni/Fe/S/FenSn CO+CH3-CH3CO–

Note: For many more details see Ref. 2.

here is that it is not known to which metal ions the protons, hydrogen atoms (or
molecules) and electrons are bound, all of which may be involved in activity.
There are many examples of active FenSm related clusters of n up to 8. Another
mixed cluster is that of the nitrogen fixation enzyme, Fe7MoS8(X), where X is
isocitrate. It is not known where N2, H2 or any of the many intermediates bind.
(The situation is rather akin to the behaviour of bimetallic catalysts like Pd/Ru,
which freely hydrogenate alkenes; but we are uncertain, as yet, as to where
precisely the H2 and the alkene are bound.) The reactions to form acetate from
CO and CH4 by the enzyme, acetyl CoA synthetase, also carbon monoxide
dehydrogenase, present a similar problem involving an Ni/Fe/S cluster. These
clusters resemble small pieces of known minerals leading to ideas concerning
the origin of life. A different type of cluster occurs in the manganese enzyme for
the photo-oxidation of water to oxygen. Here the binding of the H2O and the
intermediates on the way to O2 are all unknown and may not be describable by
simple formulae.

10.3 Solid State Cluster Catalysts

In assessing our degree of understanding of this branch of catalysis it is
convenient to work progressively from very small clusters, through to nano-
particle clusters (containing from a dozen to several thousand atoms) and then
to the bulk (solid) metals.

10.3.1 Nanoparticles of Various Diameters

When such nanoparticles are supported on a variety of oxides it is clear,35
certainly in the case of Au, that a maximum is exhibited in the catalytic activity
as a function of particle size. What is not clear is the precise cause of this effect.
One suggestion is that only those Au atoms situated at the edges of the interface
between the particle and the underlying support are the active sites. Another
suggestion is that particle thickness is a relevant determinant of catalytic
activity. As against the last view Freund et al.36 have shown exclusively that
monolayer Au islands with a thickness of one or two monolayers on an
FeO(111) substratum are found to exhibit identical CO adsorption behaviour
428 Chapter 24
as large Au particles. This demonstrates that particle thickness here plays no
significant role in CO adsorption and that, therefore, size effects for the low-
temperature oxidation of CO are not related to quantum size effects.
Particle size effects on Pd catalysts for alkene hydrogenation, on the other
hand, are real. Thus adsorption of trans-2-pentene on well-defined Pd/Al2O3
model catalysts was shown36 to exhibit site-specific behaviour, which results in
a strong increase in hydrogenation activity within the 1–5 nm particle size
ranges, in contrast to ethene hydrogenation (see Figure 17). The size effects are
explained by the hydrogenation reactions proceeding via di-s-bonded pentene,
which is favoured on the (flat) terrace sites of large particles, but p-bonding of
ethene. The underlying facts here are that all the exposed atoms in these small
particles, as in some instances with bulk metal catalysts (e.g. Cu atoms in
methanol synthesis from CO and H2), are catalytically active.
Another interesting fact pertaining to the far greater catalytic activity of Pd
nanoparticles compared with single crystal (extended) surfaces of the same
metal36 – in the hydrogenation of 2-pentene and ethene – is that, in the former,
the adsorbed organic reactants have access to weakly bound subsurface hydrogen
(not present in the single crystals).
It has long been known that minute (nano) particles consisting of two distinct
metals do exhibit catalytic performance – activity and selectivity – very different
from the performance, under identical experimental conditions, of nanoparti-
cles of the separate constituents. Sinfelt37 was the first to fully investigate
this phenomenon on nanoparticles of Pt–Ir and Pt–Re of diameters in the
range 10–100 nm in processes such as the isomerisation of alkanes and their
hydrogenolysis (rupture of C–C bonds) in the presence of hydrogen.
More recent studies38,39 on even smaller nanoparticles (diameter ca. 1 nm)
consisting of such noble metal pairs, in the form of naked clusters of, for
example, Ru5PtC, Ru10Pt2C2, Pd6Ru6 and Ru12Cu4C2, have demonstrated
beyond doubt that much superior catalytic performance results with these
catalysts, especially in the hydrogenation of ethylenic bonds. A good example is
the hydrogenation of muconic acid to yield adipic acid which occurs very

Figure 17 Particle size effects for alkene hydrogenation catalysed by nanoparticles of

Pd (after Dayle et al.36).
A Comparison between Enzymes and Solid State Catalysts 429
rapidly in the presence of such small Ru10Pt2C2 nanoparticle catalysts, in which
the individual atom sites are adjacent to one another in a precisely known form.
Much more needs to be done, theoretically, to understand the precise origin of
this synergy. But in qualitative terms such behaviour is understandable. Thus,
Pd6Ru6 (or Pt5RuC) are expected to be very good catalysts for the hydrogen-
ation of alkenes because Pd atoms are known to activate H2 and Ru atoms
activate ethylenic bonds.
This section illustrates that man has synthesised catalysts of great power,
mostly using elements not available to enzymes in large clusters of metal atoms,
again not available in enzymes. They are frequently in reactions for which
enzymes have not been devised since enzymes catalyse mainly water-soluble
substrates. It remains difficult to define precisely active ‘‘sites’’. The next section
explores another set of catalysts which cannot be synthesised by cells.

11 Catalytic Functions of Bulk Matrices

As stated earlier, generalisations that are valid as interpretations of the catalytic
performance of bulk metals and many semi-conductors are elusive. Examples
are given in Table 8. One can legitimately argue that the reason why both Pt
and Pd are such good and versatile catalysts is because they each exhibit a
surface reactivity with an aptitude to form bonds (that are not too strong) with
a large variety of the elements that figure in organic molecules: C, O, N, H, S.
It is also true that dissociative adsorption of H2 and O2 are facile on these
metals, so that, compared to a homogeneous gas-phase reaction involving these
reactants, the crucial elements (atomic hydrogen or atomic oxygen) are readily
available as mobile entities on the catalyst surface. The potential energy
diagram that resembles this dissociation of a diatomic molecule applies equally
to other species such as N2 or Cl2. And in the case of iron catalysts, dissociative
chemisorption of N2 occurs readily, as proven by numerous experimental
studies. Indeed for the synthesis of ammonia from N2 and H2, a good under-
standing exists of the series of reactions in quantitative terms, see Figure 18,

Table 8 Some examples of metallic catalysts.

Catalyst
Finely divided nickel
Iron (with potassium
promoter)
Cobalt-based alloys
supported on oxides
Pt/Al2O3
Reaction Catalysed
Hydrogenation of fats/unsaturated naturally occurring
molecules
Synthesis of ammonia (from N2 and H2)
Fischer–Tropsch synthesis of alkanes, alkanols or alkenes
from ‘‘synthesis gas’’ (CO+H2 mixture)
Reforming of hydrocarbons, i.e. production of alkanes
from linear ones

Note: If placed in Table 6 these catalysts are of low molecular selectivity, not very flexible, of quite
high thermal stability and have high electrical conductivity.
430 Chapter 24
N + 3h

75
NH + 2H

93
270
NH2 + H
335 –230
(-100 + 2.55)
-130 110
(-65 + 65)
E*

1- N 1- N 12
NH3
2 2 2 2,ad 62 -8
+ 23- H2 -28
NH2,ad NH3,ad
Nad+3Had NHad
+Had
+2had

Figure 18 Potential-energy diagram illustrating the progress of the catalytic synthesis

of NH3 on iron (after G. Ertl40).

thanks largely to the work of Ertl40a,40b and others:40c,41

H2 ðgÞ ! 2HðadÞ

N2 ! N2 ðadÞ ! 2NðadÞ

NðadÞ þ HðadÞ ! NHðadÞ

NHðadÞ þ HðadÞ ! NH2 ðadÞ

NH2 ðadÞ þ HðadÞ ! NH3 ðadÞ

NH3 ðadÞ ! NH3 ðgÞ

Under steady-state conditions, the general situation at the surface of the Fe

catalyst is understood in terms of the underlying view that all the Fe atoms are
catalytically active. (The comparison with the enzyme for the synthesis of NH3,
Figure 19, is difficult but the formation of H and N atoms may occur.) Facile
dissociation of species, such as N2, O2, and even ethane, also occurs at steps on
a metal surface. Even at room temperature it has been found that ethane
decomposes exclusively at step edges.42 The step edges are poisoned by the
reaction products which grow as carbidic islands. Quite remarkably a metal
surface giving an MO species from O2 can be likened to the MO of P-450 and
both metals (Cu, Ag) can be used to introduce atomic oxygen into organic
molecules – a difficult reaction in homogeneous catalysis.
A Comparison between Enzymes and Solid State Catalysts 431
14
Much theoretical work, involving both extended Hückel and, more re-
cently, DFT calculations have rationalised much of the behaviour of molecules
at metal catalyst surfaces. Only relatively rarely, however, is there a sufficient
depth of understanding to be able to indicate which metals or alloys will exhibit
superior catalytic behaviour. A further great difficulty with exploration of
active ‘‘sites’’ is that at the temperatures used in catalysis the atoms of the metal
become mobile, flowing and so rearrange the surface.

11.1 Bulk Semi-Conductor Solids

Many of the semiconductor solid state catalysts used in industry are made from
such materials as combinations of Co, Mo and S or other non-metals from
boron to oxygen. They are of unknown or uncertain structures and are not just
used as pure substances but often as films on surface supports such as alumino
silicates or silica. Today there is no simple way of describing their activity. We
note that a large percentage of the industrial catalysts of this kind are made
empirically so that composition in the active region(s) is uncertain. Deposition
on an inert substratum matrix could generate unusual crystal phases. Despite
these caveats the work of Ertl et al.40 has shown that a great deal can be
understood concerning the activity of well-defined surfaces such as that of RuO2.

11.2 Flow between Sites through Matrices

Two of the most important considerations in catalysis are the movements of
electrons and protons. When electron movement is very local as in bond
changes then we address the theoretical problems as described in Section 5
while Section 8.1 covers the treatment of hydrogen atom bond changes. An
extension of the movement of hydrogen over very short distances was treated in
part by Marcus’ theory of vibronically assisted tunneling.16,31 These treatments
leave to one side long-range movements of electrons and protons between
catalyst centres which are far apart as described below. We have therefore
added a section on the long-range flow of these charged species. It is also
known that many small or even larger molecular units can flow in matrices.
Much of the description of that flow was discussed under channels to active
sites which could be rigid or mobile. In the case of mobile channels, it is possible
to use energy to control flow through conformational switches as seen in
proteins especially. Deliberately in this article we have not stressed earlier
long-range access to sites of higher specificity although they can dominate
overall rates of reaction.

11.3 Electron Flow

Now the rate of electron transfer from a donor, D, to an acceptor, A,
conductor has two terms.
log kDA ¼ tunnelling rate þ thermal rate
432 Chapter 24
The relative importance of the two terms depends on the nature of
the medium between D and A which provides a conduction orbital or band
and the temperature. If the highest occupied orbital of D (HOMO) lies near the
conduction band then the electron transfer is readily achieved and similarly
electron (hole) transfer is possible if the acceptor takes electrons from the
highest occupied orbitals of the matrix. In these cases we expect thermal
excitation to be important at room temperature as is well known in doped
semi-conductors:
logðrateÞ varies as DH=RT

where DH is the energy gap between the donor and the conduction band.
Tunnelling only becomes important at very low temperatures. If the donor
and/or acceptor states lie at a considerable energy from those of the matrix
then, at low to modest temperatures, temperature independent tunnelling will
become important. It is the relative energies of energy states of the matrix and
those of D and A which are important in all cases. We noted in Section 7 that in
oxidations electron transfer can be from a remote site where there are two non-
adjacent catalytic sites and where the second site is the site of substrate binding.
This mechanism is much used by enzymes and in bio-energetics where the
reaction is of O2 with reducing agents to give water and they keep control over
reaction at the two separate but linked sites, see Figures 8, 13 and 19. We wish
now to elaborate upon this long-range tunnelling electron transfer through a
matrix as it can be used outside biological systems.
For any poor conductor, electron flow tunnelling between two sites, a donor
D and an acceptor, A, is described by the Marcus equation.16 In the equation

Figure 19 A schematic diagram of the enzyme nitrogenase, for the reaction N2+3H2-
2NH3. The enzyme has many electron transfer centres and a FeMoCo active
site, above. It requires energy from ATP and undergoes cyclic conformat-
ional changes. The site of binding of substrates is ill-defined.
A Comparison between Enzymes and Solid State Catalysts 433
in the absence of temperature dependent terms the electron transfer rate is
given by:
 log kDA varies as CbðrÞ
where C and b are constants and r is the distance between sites. b is a property
of the matrix and can be found by plotting log kDA against r. We now wish to
compare proteins43 with other catalysts which have semi-conductor frame-
works. Figure 20 shows that b varies from zero for a metal or extended cluster
to about 3.5 for a vacuum.44 A very modest conducting matrix close to
an insulator with low-lying D and A states will have a large b. What are the
implications for useful transfer between two catalyst sites now represented by
D and A in industry? From Figure 20 it is clear that electron transfer is
sufficiently fast for catalysis if D and A are separated by 10–15 Å where b is
close to 1.0. This is the value found for proteins with conventional donors and
acceptors such as Cu1/Cu21 and Fe21/Fe31, and we have observed that many
enzymes are dependent upon such electron transfer rates. For bc1.0 the matrix
inhibits electron transfer but for b{1.0 a large separation of sites up to 4100
Å allows fast transfer. For example any doped oxide such as an oxide MO or a

Ge:Sb/Ga
14
Si:P

NH3:Li
10
MeNH2:Li

EtNH2:Li
Log kDA

5 NiO:Li

Unsaturated
molecular chains and
Vacuum Water Proteins metal complexes
0
0 10 20 30 40
D to A Distance (Å)

Figure 20 A plot of logkAD (where kAD is the rate of electron transfer across different
doped matrices) against donor (D) to acceptor (A) distance. The slope,
b, characterizes the energetics of these electron transfer ‘‘semi-conductors’’
from almost b ¼ 0 (the value for a metal) to b ¼ 3.5 for a vacuum. Soft
protein materials lie around b ¼ 1.0, while doped metal ion oxides can have
b values around unity to zero. The b value for a donor/acceptor is related
to the conduction energy of the connection relative to the donor, DE, by the
pffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
the expression b ¼ C DE; m where m* is the effective mass of the
electron (after P.P. Edwards et al.44).
434 Chapter 24
silicate can carry electrons by tunnelling when the donors are not too low in
energy, e.g. Lix Ni3þ 2þ
x Ni1x O, (b ¼ 0.5) while they can also transfer thermally
excited electrons at higher temperatures.44 As stated, separating oxidising and
reducing catalytic centres across a distance is the basis of fuel cells. Presently a
great effort is being made to devise the corresponding photo-activated electron
transfer to improve the use of sunlight. The H2 and O2 from H2O will be allowed
to react again across a membrane or at separate electrodes to give non-polluting
energy. Much of the theory here has been aided by studies of molecular wires.43

11.4 Proton Transfer

Proton transfer is of equal importance as electron transfer in catalysis. The
proton can generate hydrolytic attack locally itself or by leaving from water to
give hydroxide as an attacking group. Again it can compensate by long range
migration for charge changes in substrates, such as oxygen, either in oxidation
or reduction reactions. Local proton transfer can occur by tunnelling but only
in 0.3 Å steps and is generally less interesting than thermally activated transfer
but Marcus’ work shows how the two can be combined.16 In long-range proton
transfer there is a required rotatory movement of the carrier atoms, O or N, so
as to allow protons to move in from one donor and out to an acceptor (as in
the phenomenon of Grotthus conduction). Here the importance of –OH (H2O)
or – NH2 (QNH) groups is dominant. The picture is of a Grotthus type flow of
protons illustrated by a water channel in Figure 21.45 Here the channel is in a
protein but the water can be replaced by other H1 carriers. There is exactly the
same possibility in solid state pores. In metals the dissociation of H2 to
2H1+2e allows the possibility of proton migration with an electron in metals
such as palladium. The value of such proton flow arises in certain types of
man-made and biological fuel cells where proton flow is separated from
electron flow. Proton flow separated from that of electrons can be controlled
in proteins or other matrices as it does not flow in the same part of a material as
the electron. The remarkable versatility of the membrane matrix must not be
missed in this respect.46 Enzymes, where proton transfer is important, are
very numerous and include many oxidases, hydrogenases and some hydrolases,
e.g. carbonic anhydrase. A highly instructive study of an enzyme is that of
carbonic anhydrase where catalysed H1 migration is a rate limiting state in the
reaction. Minor mutational changes of the channel for CO2 and H2O greatly
change the catalysed H1 migration.

11.5 Molecular Flow

Another feature often seen in enzymes and porous solids is the flow of solvent
and other molecules in channels.47 Particularly important is the flow of water as
its fluctuations and those of H-bond structures of the protein can provide a path
for H2O itself but also of H1. The movement of water molecules is exceedingly
important in reactions of O2 where H2O is a leaving product often connected to
A Comparison between Enzymes and Solid State Catalysts 435

Figure 21 A schematic representation of a water channel for protons supported by

membrane protein helices. Some parts of cross-membrane channels are
known to have this type of structure.45

a chain of other H2O molecules and in osmotic control. The movement of water
in porous solid catalysts has also been shown to be important. Note again that
fluctuations may give rise to many transition states while the only points on
Figure 6 open to study are intermediates, unless the kind of femtosecond studies
of Zewail13 can be made generally possible. Flow through matrices of larger
molecules is well-known in protein pumps and channels leading substrates to
compartments. Some use of such channels in other matrices has been found
employing man-made resins, zeolites and sephadex.

12 Summary
For convenience we have repeatedly divided the review into separate descrip-
tions of active sites and matrices or frameworks and their properties. The fact
that the two are interwoven is however clear especially as we chart the degree of
complexity of the catalysts. The distinct active site concept, (Table 3) is most
readily of value in catalysts which are dependent on a single attacking metal ion
although its properties are often energetically set by the matrix. As we have
stated, it is convenient to consider active sites simply as catalytic units retained
by a matrix so as to bring out properties of the metal ions, and their differences,
that interact directly with substrates. This being the case we summarised the
major points we have made concerning active sites in the three classes of
catalyst: molecular, enzymic, and solid state, in Section 3.
436 Chapter 24
When we have discussed activity more widely, we have stressed that the
framework will often bind substrates but also assists attack more than by just
increasing bimolecular reaction probability and more than the catalysis that
would result from the collision activity with the isolated metal element at the
centre of an active region. We have shown that the attacking groups, metal
elements, are often of enhanced catalytic strength due to the way they are
bound in the matrices. We have termed these ‘‘sites’’ constrained (entatic)
towards the transition state of their particular action as discussed in the free
energy diagram (Figure 6). We have stressed that in this diagram, and else-
where, the description of active region energies is pictorial and unsophisticated
as it takes no account of the possibility of many routes over barriers. We
extended this discussion to catalysts in which the active region is composed of
two or more adjacent centres.
The involvement of the matrix clearly increases as we proceed to examine
adjacent ‘‘site’’ catalysts, which are fixed in structures or relatively flexibly
disposed. Here active ‘‘sites’’ become properties of the matrix either directly
through the properties of near-neighbour centres both in binding and attack-
ing, or by the conformational mobility of the matrix. The metal ion site and the
matrix come more and more to be one catalytic region in local parts of the
structure. This stress on the functional value of the matrix is a novel feature of
this review.
In the examination of combinations of remote non-adjacent regions, which
can communicate through the matrix (Section 11) two special cases were
considered where transport of electrons and/or protons through matrices were
analysed. There are possibilities too for the channelled diffusion of many small
molecules, e.g. CO, O2 and H2O, and of even larger substrates. Again diffusion
can be on surfaces rather than through matrices. Here the matrix plays an
integral part in the catalysis and Figure 20 illustrates, for electron transfer
tunnelling, that different matrices of catalysts can be compared. Remote
binding sites can be brought to interact by mechanical flow of the two remote
centres in a metal bringing them to one site for reaction.
By drawing attention to differences between the different catalysts as well as
similarities, we stress that such knowledge can help in the design of novel
catalysts. The advantages of the protein matrix, for example, are the ease of
synthesis using sequential addition of monomers (amino-acids), as happens in
cells, allowing small (mutational) adjustment in the final protein by experi-
menters. Parallel synthesis of soft solid state supports can be achieved in
principle with any set of monomers using condensation polymerisation, while
control over radical polymerisation is possible but more difficult. Now an easier
substitution, by exchange, is of the metal ions at active sites and here while
biological synthesis is limited by availability this does not apply to chemical
manipulation of enzymes, catalytic solids or to the synthesis of molecular
catalysts. There are some ten catalytic metal ions used in living cells and
taken from their environment but some sixty possible ones in the Periodic
Table. The choice of metal ions is not often applied to enzymes. Thus, lessons
derived from the molecular and solid state catalysis can indicate a way to
A Comparison between Enzymes and Solid State Catalysts 437
enhance enzymes; on the other hand, the degree of finesse of enzymes and their
versatility is an objective for the design of all other classes of catalyst.
At present the control over all kinds of dynamics in protein structures is much
more sophisticated than in other matrices and the use of the protein matrix for
linking remote catalytic sites to a common purpose is also markedly more
advanced. While many enzyme properties are of little value in the synthesis of
bulk materials from simple substrates, they indicate possibilities in the synthesis
of high added-value products. Can chemists synthesise catalysts as sophisti-
cated as enzymes? Reading the literature has made the author realise how
research effort in one area of catalysis is often unaware of advances in others.
We hope the novelty of the comparative approach to catalysis used here
will draw the attention of others to some useful knowledge from somewhat
disparate areas of catalytic activity.

Acknowledgement
This article is dedicated to Sir John Meurig Thomas but I must make it clear
that it could not have been written without his input. All judgements are my
own however. I have also benefited from a long exchange with Dr G.F. Sweigers
of the CSIRO Molecular and Health Technology Institute, Melbourne,
Australia, who has circulated a monograph on his view of catalytic action.
The figures of proteins have been modified slightly and are from Ref. 48, which
provides a comprehensive list of metallo-enzyme structures with commentary. The
figures of solid state catalysts have been supplied by Prof. J.M. Thomas, see Ref. 2.

Note
The simplest approach to enzyme, E, and general kinetics is to write the
Michaelis–Menton equation:
k1 k2
E + S ES P + E
k−1

where S is the substrate, ES is the enzyme/substrate complex, and P is the

product. The forward rate constant is k1, substrate off-rate is k1 and product
formation or off-rate is k2. The equation for the rate is:
Vmax jSj
Rate ¼
jSj þ KM

where Vmax is the maximum velocity, and KM is a Michaelis constant

KM ¼ k1/k1. KM can be replaced by a simple binding constant if k1 and
k14k2. Modification of the equation may be necessary for reasons associated
with reaction steps which we shall not discuss. Again the enzyme may not
return immediately to the initial state E in which case there is a relaxation term
of the enzyme. For a detailed study see Ref. 49. In principle the equation is
438 Chapter 24
applicable to other catalysts and the energy states of ES can be described by
transition state theory.

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CHAPTER 25

Zeolite Modelling: Active Sites

in Different Framework
Structures and in Different
Crystallographic Positions
JOACHIM SAUER
Institut für Chemie, Humboldt Universität zu Berlin, Unter den Linden 6,
D-10099, Berlin, Germany

1 Introduction
Zeolites are not only an important class of industrially used catalysts, they are
also a perfect example of the active site concept (‘‘The tortuous tale of the
catalytically active site’’).1 The large variety of zeolite structures2 for which
three-letter codes (e.g. FAU, MFI) are used can be described as microporous
aluminosilicate polymorphs, (M1)m[SiO2]n
m[AlO2
]m, made of corner-sharing
TO4 tetrahedra (T ¼ Si, Al–). The negative framework charge, defined by the Al
content, is compensated by protons or metal cations. These cations are the
origin of the catalytic activity of zeolites and the position of Al in the lattice
defines the position of the active site. The proton forms of zeolites, H-zeolites,
are solid acids.3 Their Brønsted sites have the proton attached to one of the O
atoms of the AlO4 tetrahedron thus forming bridging hydroxyl groups,
Si–O(H)–Al at corner-sharing O atoms connecting the AlO4 tetrahedron with
a neighbouring SiO4 tetrahedron (Figure 1).
Transition metal cations as charge compensating cations are also catalyti-
cally active. They are either coordinated to two O atoms of one AlO4 tetra-
hedron, or to two to four O atoms of several TO4 units, typically within an
aluminosilicate ring (Figure 2).
The activity and selectivity of zeolite catalysts featuring the same active sites
can vary substantially. Active sites in different frameworks (Figure 1) or at
different framework positions (Figure 2) may be differently accessible for
441
442 Chapter 25

Figure 1 Zeolitic Brønsted sites – bridging hydroxyl groups in different framework

structures.

SIII

I2
SII

Z6
MFI FAU
Type I (Z6 in MFI, SII in FAU): coord. to 3-4 O atoms
Type II (I2 in MFI, SIII in FAU): coord. to 2 O atoms

Figure 2 Cu1 sites in MFI and FAU frameworks.33,45

reactant molecules or may accommodate transition structures of the catalytic

step differently. Beyond this latter concept of shape selectivity,4,5 also the
intrinsic activity of the sites may be different in different frameworks or in
different crystallographic positions of a given framework, due to different
structural boundaries, different ability of adjusting to structural changes in the
course of elementary catalytic processes or different long-range interactions
with the surrounding crystal.
Hence, knowing the crystallographic position of the active sites is key to
understanding the structure activity relation for zeolite catalysts. Since the
position of the active site within the zeolite lattice is intimately connected with
the crystallographic position of Al in the aluminosilicate framework, under-
standing the Al siting in zeolite structures is a priority, but remained a challenge
till today. X-ray and neutron diffraction methods are of limited use in this
Zeolite Modelling 443
respect, because of the very similar scattering properties of Si and Al. The
problem is particularly severe for catalysts with a low Al content (high-silica
samples) which usually are the most active ones. Further complications arise
from the fact that it is not clear if Al is preferentially occupying certain
crystallographic sites or if it is statistically distributed. Substantial progress in
differentiating between crystallographic positions and in determining the Al
distribution has been made with high-resolution solid state NMR due to magic
angle spinning (MAS). In 1979 Günter Engelhardt and Endel Lippmaa dem-
onstrated that 29Si-MAS-NMR can be used to distinguish SiO4 tetrahedra with
one, two, three or four Al neighbours in zeolites.6–8 John Thomas together with
his colleagues Jacek Klinowski and Colin Fyfe immediately recognized the high
potential of that method for structure determination,9 in particular when used in
addition to diffraction techniques and high-resolution electron microscopy. For
high-silica zeolites, ‘‘resolving crystallographic distinct tetrahedral sites’’ became
possible even for structures with low symmetry such as ‘‘silicalite and ZSM-5’’.10
The activities of the early years (‘‘Every spectrum told us something new,
because nothing had been done before . . . ’’)11 are described in the book of
Engelhardt and Michel.12 The exceptional resolution of the 29Si-NMR spectra
showing more than 10 separated resonances in a 10 ppm range could not be
reached by MAS for the quadrupolar 17O and 27Al nuclei. Distinguishing
between different positions of 17O13,14 and of 27Al15–17 in the zeolite framework
is an achievement of the last decade only, thanks to the development of double
rotation (DOR) and multi-quantum (MQ) techniques, respectively.
Atomistic modelling, in particular by quantum methods, is indispensable in
assigning spectroscopic signals to structural features and, in addition, can
provide information about structure and reactivity of active sites that cannot
easily be obtained by experiments. By lattice energy minimization we can
compare structures of the same framework with the active site in different
positions. We can then calculate spectroscopic signatures and see which struct-
ures fit best the observations. Moreover, we can calculate adsorption energies,
energy barriers and reaction rates for catalytic reactions at the different sites
and monitor differences.
Discussions with John M. Thomas at the Royal Institution about the details
of zeolite structures, in particular the Al distribution and the framework and site
specifics of catalytic properties, helped to encourage C. Richard A. Catlow and
the author in developing force fields for the atomistic simulation of zeolite
frameworks with Al and bridging hydroxyl groups in different positions.18,19
The functional form chosen was that of the ion-pair shell-model potentials20 and
parameters for the bridging hydroxyl group have been chosen such that agree-
ment of the average of the predicted active site structures with quantum
mechanical results of small cluster models was achieved. Later, refined param-
eters have been obtained by fitting to quantum chemical data exclusively, first at
the Hartree–Fock level,21 later at the density functional theory (DFT) level.22
Further progress was made with the development of hybrid quantum mechanics/
molecular mechanics (QM/MM) methods, which treat a portion of the zeolite
including the active site by quantum methods, but the periodic environment by
444 Chapter 25
23
force fields. Today, DFT calculations of the complete periodic structure are
feasible, in particular for zeolites with small unit cells and at least for benchmark
purposes,24,25 and hybrid QM/QM methods are applied to overcome some
limitations of DFT by combining them with wavefunction-based electron cor-
relation calculations for the active site.26,27

2 The FAU and MFI Structures

The first lattice energy simulations with the ion-pair shell-model potential for
zeolites were made for the faujasite (FAU)18 and silicalite/ZSM-5 (MFI)19
framework structures which represent extreme cases. The former has high
symmetry (space group Fd  3m) and only one crystallographic distinct tetra-
hedral site (T site), whereas the latter has 24 distinct T sites in its monoclinic low-
temperature structure (P21/n) and 12 in the orthorhombic high-temperature
structure (Pnma). The two examples also differ in their typical Al content. In
MFI (Figure 3) the Si/Al ratio is typically high (15–100), and interactions
between Al sites are minor. The question is: are there energetically preferred
crystallographic positions for Al insertion and is the resolution of 27Al-MAS-
NMR high enough to distinguish between Al(4Si) sites with different local
structures.
In the FAU lattice (Figure 4), there is only one crystallographically distinct T
site, which means that there is only one possibility to create an isolated Al site,
but the Si/Al ratio of FAUs is much lower, around 2.7 in Y-zeolites and as low
as 1.3 in X-zeolites. The limiting Si/Al ratio is 1 because corner-sharing AlO4
tetrahedra are unstable (Loewenstein or Al avoidance rule). For realistic Si/Al
ratios (between 1.2 and 3) there are different possible substitution patterns with
the same relative populations of the Si(0Al), Si(1Al), Si(2Al), Si(3Al), Si(4Al)
structural units. They can be calculated from the Si/Al ratio provided that
Loewenstein’s rule is obeyed. 29Si-NMR can distinguish between the Si(nAl)
sites and the intensities of the respective signals are given by the Si/Al ratio, but
the specific Al substitution pattern cannot be deduced. The fundamental
question is: is the Al distribution for a given Si/Al ratio random or are there
energetic preferences.
Before we discuss energetic preferences for crystallographic sites in MFI or
for substitution patterns in FAU, we should remember that zeolites are
metastable crystalline solids and, therefore, it is doubtful that during the zeolite
synthesis the lowest energy structure will form. Many zeolite catalysts are also
heavily modified after the initial synthesis process, e.g. by cation exchange and/
or calcination. Do these procedures result in energy minimum structures for the
final cation content or is the Al distribution given by the original form?
Computational chemistry can be helpful in both situations. It can predict the
crystallographic Al site or the Al distribution with the lowest energy, but it can
also help to identify non-random, non-equilibrium Al siting and distributions
by assigning NMR signals to Al in specific crystallographic sites or to a specific
Al distribution.
Zeolite Modelling 445

Figure 3 MFI structure details.

3 Crystallographically Distinct Sites in the MFI

Structure
In 1982 a 29Si-MAS-NMR spectrum of a highly crystalline sample of silicalite
(all-silica form of MFI) was reported showing nine resolved signals (Figure 5,
top left).10 Their intensities pointed to 24 crystallographic distinct T sites in
agreement with a monoclinic structure. Over the years, even better resolved
spectra became available (Figure 5, bottom left).28 The observed chemical shifts
are determined by the local structure around the nucleus, but bond distances
and bond angles cannot directly be deduced from the shift data. A semiempir-
ical correlation29 between the 29Si chemical shift and the average of the four
Si–O–Si angles can be used for calculating chemical shifts from XRD-data
(Figure 5 shows an example). This proved useful for removing ambiguities from
structure refinements, in particular when only powder diffraction data are
446 Chapter 25

Figure 4 FAU structure. Tetrahedral arrangement of sodalite cages connected by

D6R. Top: Primitive cell with Al distribution for Si/Al ¼ 3. Bottom: Two of
the four inequivalent O sites with bridging hydroxyl groups (O1 and O3).

available. The correlation can also help to assign 29Si-NMR signals to cry-
stallographic positions, but since the connectivity of T sites is available
from two-dimensional NMR,30 this has become the main tool for assigning
29
Si-NMR spectra.
Instead of diffraction data, bond angles from lattice energy minimizations
employing force fields (or DFT calculations) can be used as input for the
correlation, and the agreement with observed chemical shifts can serve as a
‘‘quality check’’ for the structure prediction. It is possible to go a step further,
replacing the semiempirical correlation between average bond angle and chem-
ical shift by a quantum mechanical calculation of the chemical shift using either
finite cluster models defined around the magnetic nucleus31 or periodic plane
wave methods.32 Using the former approach for zeolites MFI, MEI, MTW,
TON, FAU the structures predicted by the non-empirical shell-model potential
prove as accurate as the diffraction structures when judged on the quality of
the 29Si-NMR shifts.31 Figure 5 shows on the right the predicted and observed
Zeolite Modelling 447

29
Figure 5 Si-NMR spectra of ZSM-5/silicalite (MFI). Left: Early (top)10 and highly
resolved spectrum (bottom)28 of the monoclinic structure (24 T sites). The
chemical shifts calculated from the bond angles of the XRD refinement are
also shown. Right: Quantum chemically calculated shifts for the simulated
orthorhombic structure (12 T sites)31 compared to the observed spectrum.

29
Si-NMR spectra of the orthorhombic MFI structure.31 The quantum
mechanical shift calculation for simulated structures yields the right sequence
of lines for the different T sites. The observed spectrum is reproduced with an
offset of
0.4 ppm and a standard deviation of 1.5 ppm, better than the one
obtained with the conventional approach (shift-bond angle correlation, XRD
structure) with a standard deviation of 1.9 ppm.
Already, the early study of silicalite/ZSM-5 reported two peaks for Al in T
sites, at 54.5 and 56.7 ppm.10 A later MQ study found two peaks at 54.5 and
57.1 ppm (H-ZSM-5) and a third one at 59.4 ppm (Na-ZSM-5).15 The question
was whether these peaks belong to Al in two (or three) specific crystallographic
sites or whether they are composed of contributions from several sites. Our
early lattice energy simulations for Al in MFI (using the empirical shell-model
ion-pair potential)19 already showed that the energy differences between Al in
different sites are small (a few kilocalories per mole) and that thermodynamics
would predict little deviation from a random distribution. Table 1 shows the
relative energies for the orthorhombic and monoclinic MFI structures obtained
with the DFT-parametrized shell-model potential.16,33 The conclusion remains
the same, although the details of the stability sequence have changed.
448 Chapter 25

1
Table 1 Relative energies (kcal mol ) of MFI structures with Al in different
T sites.
Orthorhombica Monoclinicb
T site Energy T site Energy T site Energy
T1 0.0 T1 6.2 T13 0.0
T2 4.1 T2 5.2 T14 4.0
T3 4.7 T3 4.5 T15 4.5
T4 3.0 T4 2.1 T16 2.7
T5 5.7 T5 0.2 T17 6.8
T6 8.7 T6 2.5 T18 9.8
T7 1.3 T7 1.1 T19 2.0
T8 2.2 T8 3.0 T20 2.7
T9 2.2 T9 4.9 T21 2.5
T10 3.1 T10 2.6 T22 3.4
T11 2.8 T11 2.5 T23 3.3
T12 3.9 T12 4.0 T24 4.1
a
Ref. 33.
b
Ref. 16.

18,3 7

24 1 17 12 6 4,8 20

Figure 6 Calculated 27Al-NMR chemical shifts for Al in 24 different T sites of the

monoclinic MFI structure (lines) compared to observed (MQ-NMR) shifts
for differently synthesized MFI samples.16 Open triangles indicate less safely
identified shifts.

If the energetic differences are small, it is possible that different synthesis

procedures for ZSM-5 zeolites with different (but low) Al content and different
cations may lead to different Al substitution patterns, thus increasing the total
number of resolved 27Al signals in the MQ-27Al-NMR spectra of the whole set
of samples. This strategy indeed resulted in the identification of ten distinct
resonances, each found for at least two samples, which extend over a range of
13.6 ppm.16 For a given sample, the number of resonances varied between one
and three. It was also shown that the cation (H, Li, Na) had a negligible effect
on the 27Al shift.
The conclusion that the observed resonances belong to Al in different
crystallographic sites is supported by quantum mechanical shift calculations
(Figure 6).16 The shifts calculated for Al in the 24 different T sites of the
Zeolite Modelling 449
monoclinic structure extent over an even wider range of 14.1 ppm. The
observed shifts fall into this range and comparison of the predicted and observed
shift patterns even suggests a partial assignment (Figure 6): the resonance at
53.7 ppm belongs to Al in T8 or T4, the resonance at 54.7 to Al in T6 and
the resonance at 62.8 belongs to T17. Of the additional resonances those at 50.0
and 63.6 ppm could be tentatively assigned to T20 and T1 respectively.
These results tell us that the Al distribution is not controlled by thermo-
dynamic stability, but depends on the synthesis procedure. It would be very
interesting to examine the properties of H-zeolites generated from a series of
samples with resonances that extend over the full range. If the ion exchange and
calcination procedure would not change the Al positions, we may expect a
larger variability of acidic sites than we see now for H-ZSM-5 catalysts.34

4 Brønsted Sites and the Al Distribution in FAU

As there is only one crystallographically distinct T site in the FAU lattice, there
is only one possibility to create an isolated Al site. However, there are four
possible O sites to which the proton can be attached creating four different
bridging hydroxyl groups.
For more than one Al in the lattice, electrostatic arguments predict that Al
atoms assume the largest possible distance for a given Si/Al ratio35 which is
known as Dempsey’s rule. This rule makes no mention of the cations that
compensate the framework charge due to Al. There is a difference between
protons that attach directly to one framework oxygen, thus causing a local
deviation from the tetrahedral AlO4
structure, and other cations. For two Al
substitutions in the primitive FAU cell (24 T atoms), lattice energy minimiza-
tions have been made for all possible substitution patterns.36 The expected
decrease of the lattice energy with the Al–Al distance has been found only for
global charge compensation (the Al charge of 2  (
1) was compensated by
increasing all T site charges by 2/24), but not for local charge compensation
when one proton is added to an oxygen atom of each AlO4 tetrahedron. In the
latter case, there was a strong preference for Al–O–Si–O–Al pairs in four-
membered rings. This observation has been confirmed by quantum mechanical
calculations on double six-membered ring (D6R) models. Al–Si–Al pairs within
a four-membered ring were always more stable than isomers with the largest
possible Al–Al separation. This is not a peculiarity of the FAU lattice, but was
also found for other frameworks featuring D6R secondary building units
(offretite, zeolite L, erionite, chabasite, gmelinite).36
For FAUs with low Si/Al ratios (zeolites Y and X) two types of methods
have been used to determine substitution patterns that are compatible with the
measured NMR intensities for a given Si/Al ratio and obey Loewenstein’s rule.
One is a statistical approach, relying on electrostatic energy calculations for
achieving non-random distributions. The other uses electrostatic arguments for
Si/Al orderings in small building units (largest Al–Al distance) and combines
them with crystal symmetry arguments. Studies of the latter category have been
450 Chapter 25
published in 1981–1982, again in parallel by the Cambridge/Ontario37,38
and Berlin/Tallin39,40 teams. For the Si/Al ratios of 3.0 and 2.43, typical of
Y-zeolites, just one substitution pattern survived for each Si/Al ratio (see
Figure 4, top).
To rationalize the dependence of the Brønsted acidity of H-FAUs on the
Si/Al ratio two extreme models have been invoked, a local one assuming that
the acid strength decreases with increasing number of Al in T sites that are in
next-nearest neighbour position with respect to the AlO4 tetrahedron with the
Brønsted proton, and a global one assuming that the acid strength depends on
the mean (Sanderson) electronegativity of the zeolite.
The heterogeneity of Brønsted acidity resulting from the Al distribution has
been examined by hybrid QM/MM techniques for two types of materials: high-
silica FAU with isolated or paired Al sites (1 or 2 Al per 48 T sites) and
Y-type materials with Si/Al ratios of 3 and 2.43 for which we adopt the
distribution pattern of Refs. 38 and 40 (see Figure 4). The Brønsted acid
strength has been characterized by calculated energies of deprotonation and, as
a spectroscopic signature of the different bridging hydroxyl groups, their
infrared OH stretching frequencies have been calculated. Even for an isolated
Brønsted site with only one crystallographically distinct Al site in the FAU
lattice, there are four possible O sites to which the proton can be attached
creating four different bridging hydroxyl groups. The preference for O1 and O3
occupation and the assignment of the respective OH groups to high frequency
(HF) and low frequency (LF) infrared bands is well-established and reproduced
by both force field18 and hybrid QM/force field calculations.41,42 For the 2.43
and 3.0 Si/Al ratios O1:O2:O3:O4 proton occupation patterns of 8:2:4:0 and
7:2:3:0, respectively, have been adopted which are close to the ratios inferred
from powder neutron diffraction experiments. Figure 7 shows the calculated
OH stretching frequencies as a function of the calculated deprotonation ener-
gies.42 The most important observation is that the former are primarily deter-
mined by the local structure (O1 or O3) while the latter primarily depend on the
number of Al atoms in next-nearest neighbour positions. The overall Si/Al ratio
seems to affect the acid strength of a particular site only indirectly, the lower the
Si/Al ratio the higher the probability that next-nearest Al neighbours exist.

5 Cu(I) Sites in MFI and FAU Frameworks

Cu(I) exchanged zeolites, specifically Cu(I)-ZSM-5 are highly active catalysts
for the decomposition and selective reduction of NO in exhaust gas.43 The
preferred Cu1 sites in the lattice and the coordination of Cu1 ions in these sites
could not be determined by experiments. Simulations for MFI,33 FER44 and
FAU45 frameworks succeeded in identifying two different types of sites with
different coordination and different reactivity. A three-step computational
strategy proved very useful.33 The first step is lattice energy minimizations
with Al in all possible T sites (Table 1). In a second step lattice energy
minimizations are made with at least 10 different Cu1 extra-framework
Zeolite Modelling 451

Figure 7 OH stretching frequencies and energies of deprotonation of bridging

hydroxyl groups in H-FAUs as a function of the Al content.42 ‘‘2Al/3’’
denotes that there is a second Al in next nearest neighbour position and that
the Si/Al ratio in the framework is 3. The bars ‘‘O1’’ and ‘‘O3’’ on the right
side indicate the range of data for the two types of O positions.

positions for each Al position. This allows for a fast determination of the most
favoured sites. Third, for selected structures QM-Pot energy minimizations are
made using DFT for embedded clusters large enough to capture the most
important interactions between the Cu1 ion and the zeolite framework. In both
MFI and FER zeolites sites were found with two-, three-, or fourfold coordi-
nated Cu1 ions. The sites were classified depending on the number of O atoms
coordinating the Cu1 ion and its position in the framework, as shown in
Figure 8. Type II site copper ions (Figure 2) are coordinated to two O atoms of
one AlO4
tetrahedron, either at the channel intersection (I2 site in MFI and
FER) or on the walls of the main or perpendicular channels (M2 and P2 sites,
respectively in FER). Higher coordinated sites, summarized as type I sites, have
one or two additional coordinations to other oxygen atoms within a five- or six-
membered (TO)n ring (Figure 2). Large energetic preferences for one or the
other Cu1 site or for Al in special T sites are not found. The occurrence of Cu1
with different coordination numbers is supported by an average coordination
number of 2–3 found in EXAFS experiments. The coexistence of the two types
of sites also emerged from experimental photoluminescence spectra. While the
observed 3d10(1S0)–3d94s1(1D2) excitation spectra show two well-separated
452 Chapter 25

Figure 8 Different Cu1 sites in the MFI framework located in rings of different size
on the walls of the main channel (M), the zig-zag channel (Z), or at the
channel intersection (I).33

bands, the band splitting almost disappears in the emission spectra. The
QM-Pot calculations not only confirmed this observation but also provided
an explanation.46 In the ground state, different types of Cu1 coordination
cause large variations in the excitation energies. In contrast, in the excited state
the coordination differences between type I and type II sites disappear. The
type I sites give up their additional coordination and retain only the twofold
coordination to the AlO4 tetrahedron, whereas type II sites remain unchanged.
The reason is that on excitation the 4s orbital becomes occupied, which is much
larger than the 3d orbital, and so the Cu1 ion moves away from the zeolite wall.
Thus, because the excited structures are alike for all Cu1 sites considered, the
emission energies are also very similar.
For Y- and X-zeolites (FAU framework), Cu1 ions may be found in the
general cation sites SI (inside the double six-ring), site II (in the plane of a six-
membered aluminosilicate ring), and SIII (above the three annealed four-
membered aluminosilicate rings). Sites II and III are on the wall of the large
cage in the FAU structure (Figures 2 and 4). Simulations have shown that Cu1
binds significantly less strongly in sites III than in sites I and II.45 Hence, SIII
sites will be only occupied in CuX zeolites with a larger Cu/Al content because
not all of the larger number of Cu1 ions can be accommodated in SI/SII sites.
Cu1 in SIII sites belongs to type II sites (low-coordination), while Cu1 in
SII-FAU sites belongs to type I sites (3–4 coordination in six-membered rings).
Whereas in high-silica zeolites (MFI, FER) isolated Al sites will prevail, in
Cu(I)-Y zeolites we may find six-membered aluminosilicate rings with one or
two Al atoms. They can be distinguished by the stretch frequency of adsorbed
CO. Hybrid QM/MM simulations show that the HF (2160 cm
1) and LF CO
Zeolite Modelling 453

1 47 1
bands (2145 cm ) observed for Cu(I)-Y zeolites can be assigned to Cu in
SII sites with one and two Al in the six-membered ring, respectively.45 In Cu(I)-
X zeolites the LF band (2130 cm
1)47 is tentatively assigned to SII sites with the
maximum number of Al (three) in the six-membered ring, whereas the HF
band47 at 2155 cm
1 is assigned to low-coordinated SIII sites (type I), which are
occupied in Cu(I)-X only.45
In high-silica zeolites (MFI, FER) it is hardly possible to distinguish between
type I and type II sites by monitoring the CO stretching frequency. After CO
adsorption, the structure of the adsorption complexes for type I and type II
sites is very similar, Cu1 is coordinated to CO and to two O atoms of the AlO4

tetrahedron. This means that on CO adsorption its coordination to the zeolite
framework remains unchanged for type II sites, whereas it loses one or two
coordinations to framework oxygen atoms for type I sites.48
Crucial is the question whether the two different types of Cu1 sites in MFI
and FER exhibit different catalytic activity. Hybrid DFT/MM calculations
have been performed to investigate the influence of the Cu1 ion coordination
on adsorption of not only probe molecules such as CO,48 but also substrate
molecules such as NO49 and NO2.50 On interaction with the ad-molecule the
coordination of the Cu1 ion to the zeolite framework remains unchanged for
type II sites. For type I sites, the Cu1 ion prepares for optimum bonding of the
ad-molecule by giving up its coordination to one or two framework oxygen
atoms and moving away from the channel wall. For this reason the interaction
energies with the higher coordinated type I sites in MFI are 6–8 kcal mol
1
smaller (in FER are 11–13 kcal mol
1) than with the two-coordinated type II
sites (Table 2). Cu1 in type II sites binds NO (and NO2) even stronger than
gas phase Cu1 ions which points to an unusual ‘‘activation’’ of Cu1 by
the ‘‘zeolite’’ ligand which involves 3d10 - 3d94s1 promotion.49,50 The main

Table 2 NO and CO heats of adsorption on different Cu1 sites in zeolites.a

Site Type DH0 DH300 Observed b
Cu1NO 26.5 26.1  1.2 (0 K)c
ON-CuMFI II(I2) 28.6 26.5 B24d
I(Z6) 21.4 19.3
Cu1CO 35.4 35.5  1.6 (0 K)e
OC-CuMFI II(I2) 33.2 31.1 28.7f; B31g
I(Z6) 26.3 24.2 23.9f
OC-CuFER I(P6) 18.1g 20.5g
OC-CuY I(SII,1-2Al) 17.9
13.9h 19.1–15.5i
a
Calculated results from Ref. 49 if not otherwise noted.
b
Heat of adsorption at 300 K if not otherwise noted.
c
Ref. 51.
d
Ref. 52.
e
Ref. 53.
f
Ref. 54.
g
Ref. 55.
h
Ref. 45.
i
Ref. 56.
454 Chapter 25
difference between the two types of sites is how much heat is released on
binding the NO substrate. Adsorption can affect the overall kinetics of the
catalytic process by making the apparent barrier much lower than the intrinsic
barrier. While the intrinsic barrier may be similar on both types of sites, the
apparent barrier will be significantly lower for type II sites and catalytic
conversion at these sites will be much faster.
The more reactive type II sites are located at the intersection of the straight
(main) channel and the zig-zag channel in the MFI lattice. This puts some limits
on the location of Al in the MFI framework. Type II sites will occur for Al in
T1, T2, T6 or T12, but not for T11, T4 or T10.33

6 Outlook
Zeolites are unique in offering distinct crystallographic positions for Al as the
central constituent of the catalytically active site. In spite of substantial
progress with high-resolution NMR for quadrupolar nuclei, identifying the
Al positions in high-silica materials remains a challenge. Atomistic simulations
tell us that there is little energetic preference between Al in different sites, and
experiments point to different populations for different synthesis procedures.
For the example of Cu1 sites in high-silica (MFI, FER) zeolites, using quantum
calculations we have shown that the catalytic properties of active sites in
different locations can vary substantially. This sets the future agenda: under-
stand the synthesis process at the atomic scale and control the Al distribution.

Acknowledgements
I thank all colleagues with whom I had the pleasure to work on the original
publications cited in this chapter, many of whom have been also helpful in
preparing the figures. I thank the German Research Foundation (DFG) and
the Funds of the Chemical Industry (FCI) for support.

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CHAPTER 26

Magnetic Resonance Imaging:

A New Window on the Catalyst
Operating in the Reactor
Environment
L. F. GLADDEN, B. S. AKPA, L. D. ANADON,
C. P. DUNCKLEY, M. H. M. LIM, M. D. MANTLE
AND A. J. SEDERMAN
Department of Chemical Engineering, University of Cambridge, Pembroke
Street, Cambridge CB2 3RA, UK

1 Introduction
Magnetic resonance imaging (MRI) is an emerging measurement technique for
the study of chemical reactions in situ within reactor environments,1 and a
subject closely related to, and derived from, the work and vision of John
Meurig Thomas. The real opportunities in developing MRI for application to
the study of heterogeneous catalytic processes occurring in the working reactor
derive from the ability of magnetic resonance (MR) techniques to probe both
physical and chemical phenomena – this means that, in principle, we can image
flow fields inside reactors, measure molecular diffusion coefficients inside
catalyst pellets, and spatially map chemical conversion within a reactor. In
this chapter, we will focus on fixed-bed reactors. These process units are the
workhorse of the chemical industry and typically comprise a cylindrical column
packed with millimetre-scale catalyst pellets. Somewhat fortunately, fixed-bed
reactors can be studied by MRI at a size-scale from which the results can be
scaled up for real process application.
This chapter addresses recent developments in MRI that enable us to
measure intra-pellet diffusion, chemical reaction and single- and two-phase
flow in fixed-bed reactors. Before doing this it is worth putting these different

457
458 Chapter 26

103
intra-pellet inter-phase
ideal
mass transfer limitation mass transfer limitation

1
Effectiveness factor

10−3

10−6

10−9
10−3 1 103 106 109 1012 1015
Thiele modulus

Figure 1 A plot of catalyst effectiveness factor against Thiele modulus. Increasing

Thiele modulus identifies the increasing dominance of mass transfer
limitation.

types of MR measurements into context; that is, why do we need this array of
measurements to study the in situ behaviour of a heterogeneous catalyst? The
answer to this is found in Figure 1. This is the type of diagram much more
associated with the world of chemical engineering than chemistry. However, it
provides a clear explanation of what we need to consider if we are attempting to
perform a truly in situ experiment. With reference to Figure 1, let us first define
what we are plotting. Effectiveness factor is a dimensionless quantity which is
defined as the ratio of the observed rate of reaction to the ‘ideal’ rate that would
occur in the absence of mass or heat transfer limitations. The ideal rate is that
which characterises the reaction when all reactants have unhindered access to
the catalytically active site, and all products can pass unhindered back into the
inter-pellet space, and hence the output stream, of the reactor; under these
circumstances the effectiveness factor takes the value unity. The horizontal axisffi
pffiffiffiffiffiffiffiffiffiffi
of Figure 1 is identified as the Thiele modulus which is defined as L k=De ,
where L is the characteristic dimension of the catalyst pellet (typically its
radius), k is the intrinsic rate constant of the reaction and De is the diffusion
coefficient of the molecular species moving within the pore space of the catalyst.
Thus, for a given chemical reaction and size of catalyst pellet, k and L take
constant values, and increasing values of Thiele modulus reflect decreasing
access to the catalytically active site. Any concentration gradients that develop
within the catalyst during operation (which may then be associated with
temperature gradients as a result of spatially varying reaction rates), will
normally act to reduce catalytic activity below its ‘ideal’ value. If molecular
mobility within the catalyst is hindered, thereby giving rise to loss of
Magnetic Resonance Imaging 459
conversion, the catalytic process is said to be suffering from the effects of mass
transfer limitation. As seen from Figure 1, conversion can be decreased by
orders of magnitude as a result of intra-pellet mass transfer limitation. Even
greater loss of catalytic activity is caused by inter-phase mass transfer limita-
tions, associated with delivering reactants to, and products from, the external
surface of the catalyst. As chemists we might naturally assume that each
catalyst pellet within the reactor ‘sees’ exactly the same environment (i.e.,
reactant composition) at its external surface. What MRI clearly shows is that
this is not the case – these limitations in getting reactants to, and products
away, from the catalyst surface can destroy the performance of an otherwise
good catalyst. Thus, we see that while the chemist primarily concerns himself
with designing the active site for optimal conversion and selectivity, the
observed performance of the working catalyst within a reactor can be modified
significantly by intra- and inter-pellet mass transfer processes. Now that we are
beginning to develop the toolkit to look at the relevant physical and chemical
processes occurring within a reactor, we have the opportunity to design the
catalyst and reactor as an integrated unit.
MRI is unique in its ability to address chemistry, molecular diffusion and
flow, and to achieve these measurements non-invasively and without need for
chemical or radioactive tracers. The value of using an imaging technique is that
we see how the local chemical and physical processes differ from the associated
global characteristics. This is very important because until now, most process
models will, of necessity, take single value descriptors of a process and assume
that these global values provide an adequate description of the overall process
performance. An example of this would be using overall (superficial) gas and
liquid velocities through the reactor and assuming that such values are ade-
quate for the characterisation of the flow fields contacting each catalyst pellet
within the reactor. Later in this chapter we will show just how wrong that
assumption can be (Section 4).
The images provided by MRI provide invaluable insight into real catalyst
and reactor operation, and these data can be used directly in process design.
Moreover, if sufficient care is taken to ensure that quantitative data are
acquired with respect to both the chemistry and hydrodynamics within the
reactor, this developing field of research provides a wealth of new data which
can be used in the validation and development of numerical and theoretical
models of the relevant transport and reaction processes. The process models
which can then be developed will be based on the true physical and chemical
phenomena that exist within the reactor, and will therefore be far more reliable
when used in designing catalytic reactors and identifying their optimum mode
of operation.
In the remainder of this chapter we will summarise the recent developments in
MRI applied to heterogeneous fixed-bed catalytic reactors. There have been
three main areas of development: (i) chemical mapping, (ii) ultra-fast imaging of
flow fields and (iii) solids imaging. The last of these – solids imaging – will not be
considered here since its primary area of application in reaction engineering is in
understanding the operation of fluidised-bed2,3 as opposed to fixed-bed reactors.
460 Chapter 26

2 Chemical Mapping
Chemical mapping inside catalytic reactors is still in its early stages of develop-
ment. Initial studies have employed 1H observation because of the high signal-
to-noise associated with 1H measurements. However, as will be discussed, if
chemical mapping techniques are going to be used widely in measuring catalyst
performance within reactor environments, then 13C observation is the more
likely way forward. In the following sections we discuss the reasons for this, and
illustrate some of the work in this area.

1
2.1 H Observation
Yuen et al.4 first demonstrated the nature of the information that can be
obtained regarding chemical mapping within a fixed-bed reactor, using the
liquid phase esterification of methanol and acetic acid catalysed within a fixed
bed of H1-ion exchange resin catalyst (Amberlyst 15, pellet size 600–850 mm) as
the model reaction system. Experiments were performed in a fixed-bed reactor
of internal diameter 10 mm. A two-dimensional (2-D) slice image through the
bed is shown in Figure 2a; the full dataset was recorded as a 3-D image with an
isotropic resolution 97.7 mm
97.7 mm
97.7 mm. The reactions were
performed at an ambient temperature of 295 K.

(a) (b) (c)

10% X 54%

Figure 2 (a) 2-D slice through a 3-D RARE image of a fixed bed of ion exchange
resin. The image has an isotropic resolution of 97.7 mm
97.7 mm
97.7 mm.
The image slice in which the local volumes are located for the volume-
selective spectroscopy study is identified. The image was acquired by satu-
rating the bed with pure methanol. The acquisition parameters were set to
exploit T2-contrast such that signal was acquired only from the methanol in
the inter-pellet space. Visualisation of mean conversion, X, within selected
volumes located within the slice section identified in (a) are shown in (b) and
(c) for feed flow rates of 0.025 and 0.05 mL min1, respectively. The local
volumes have in-plane dimensions of 1.5 mm
1.5 mm and a depth (image
slice thickness) of 500 mm.
Magnetic Resonance Imaging 461
In these studies, chemical conversion was determined in situ by measuring the
1
H resonance associated with OH groups present. In practice two such reso-
nances exist associated with chemical species inside and outside the catalyst
pellets, respectively. The difference in chemical shift between these intra- and
inter-pellet species arises because of the different electronic environment of the
molecules inside the catalyst pellets compared to their environment in the bulk
fluid in the inter-pellet space. In this work, chemical conversion was determined
from the MR signal acquired from species in the inter-pellet space of the bed
because the signal from inside the catalyst pellets is also going to be influenced,
to an unknown extent, by relaxation time contrast. In addition to possible
relaxation contrast effects, there will also be modifications to the chemical shifts
of individual species resulting from adsorption onto the catalyst; this may cause
peak broadening and reduces the accuracy with which we can determine the
chemical shift of the species of interest. As follows from Equation (1) which
describes the esterification reaction of methanol and acetic acid to form methyl
acetate and water:
CH3 OH þ CH3 COOH Ð CH3 COOCH3 þ H2 O ð1Þ

we see that the chemical shift of the OH resonances in the reaction mixture,
dobserved, will be given by:
dobserved ¼ xAcOH dAcOH þ xMeOH dMeOH þ nxH2 O dH2 O ; Sxi ¼ 1 ð2Þ

where di is the chemical shift associated with the pure compound i, and xi is the
mole fraction of species i in the mixture; all chemical shifts are referenced to
tetramethylsilane (TMS). n is the ‘‘number’’ of 1H species associated with OH
groups within the water molecule; the physical interpretation of this parameter
has been discussed in detail elsewhere.4 The form of Equation (2) arises because
of the phenomenon of 1H fast-exchange5 (i.e., occurring on a timescale o106 s)
between OH groups associated with the acetic acid (AcOH), methanol (MeOH)
and water (H2O) molecules present within the reaction mixture. In the esterifi-
cation reaction considered here, as conversion increases so the 1H resonance
associated with the OH groups moves to lower chemical shift, referenced to
TMS; i.e., towards the 1H chemical shift of pure water. Thus, the value of
dobserved provides an accurate measurement of the chemical composition of a
given reaction mixture. From this value of the mole fraction of acetic acid within
the reaction mixture, the extent of conversion within the system is determined.
An upper limit on the error in conversion determined using this approach is
B2% for a given set of experimental conditions. Clearly, in this particular
example, chemical shift provides an elegant measure of conversion and avoids
errors in determining concentrations based on analysis of spectral intensities
that may be influenced by line broadening and relaxation time effects. However,
this approach can only be used when the spectrum is sufficiently simple that all
the spectral resonances can be assigned unambiguously.
Figures 2b and c show the results of a volume selective spectroscopy
experiment in which spectra were recorded from local volumes of dimension
462 Chapter 26
1.5 mm
1.5 mm
0.5 mm within the fixed bed; the data acquisition time for
each spectrum was 3 min. Each selected volume has been colour-coded accord-
ing to the conversion within that volume as determined from the localised
spectroscopy experiment. These images highlight two generic and important
features of local catalyst performance in a fixed-bed reactor. First, within a
given transverse slice section through the reactor, there exists a range of
conversions; in this case a fractional variation in conversion (DX=X)
of
B20% is observed, where X
is the mean conversion calculated from the 10
local volume measurements of conversion. Second, increasing the flow rate
through the bed results in a decrease in conversion. This is expected since the
faster the reactants flow through the bed, the smaller the contact (or residence)
time of the reactants with the catalyst pellets. However, it follows from this
observation that if local velocities adjacent to individual catalyst pellets vary
then this will cause local variation in catalytic conversion. This heterogeneity in
local flow field is indeed observed in fixed-bed reactors and will be illustrated in
Section 4.1. Of course, it is not sufficient to simply correlate spatially resolved
conversion and flow velocities at a single axial location along the bed. The
conversion observed at a given position along the length of the reactor will be
the resultant of the interplay of hydrodynamics, intra-pellet diffusion and
chemical kinetics for all the reactant species that have moved through the
reactor to reach that location. The long-term objective of the work described in
this chapter is that by applying these various MR techniques we can obtain a
sufficiently good understanding of hydrodynamics, diffusion and reaction in
reactors, that we can predict the spatial distribution of conversion within real
reactors, and use the numerical tools derived from this knowledge to design
new, cleaner and more efficient catalytic processes.
Studies of this reaction have recently been extended to acquisition of a 4-D
CSI dataset, shown in Figure 3; the grey scale indicates the extent of conversion.
In such a 4-D dataset, we have three spatial dimensions of imaging and a fourth
spectral dimension. As expected from the volume selective spectroscopy studies
discussed earlier, conversion is seen to be heterogeneous within transverse
sections through the bed at any position along the direction of superficial flow.
Although 1H MRI has been used to map the progress of chemical reactions
as described above and in application to the catalytic hydrogenation of
a-methylstyrene, as reported by Koptyug et al.,6 1H MRI observation is
unlikely to become a generic tool for chemical mapping in catalytic reactors.
This is because the 1H nucleus is associated with a narrow chemical shift range
and, further, most of the species participating in the reaction will have a large
number of 1H resonances associated with them. These characteristics of 1H
observation mean that it is often impossible to deconvolve unambiguously the
resonances of specific reactant and product species in the resulting 1H spectra.
Hence, quantitative conversion and selectivities cannot be determined. The
situation is made even worse by the decrease in nuclear spin–spin relaxation
times of molecules when they interact with the catalyst surface, which causes
broadening, and hence increased overlap, of the 1H resonances. Therefore, it
follows that, as used in solid state NMR spectroscopy,7,8 13C observation may
Magnetic Resonance Imaging 463

Figure 3 3-D cutaway image showing the extent of conversion of an esterification

reaction occurring within a fixed-bed reactor. The conversion was calculated
from the chemical shift of the OH peak in a 4-D chemical shift image. The
chemical shift image was acquired with an isotropic spatial resolution of
625 mm. The RARE image of the structure of the bed was acquired at an
isotropic spatial resolution of 78 mm. Both datasets have been re-inter-
polated on to a common array giving an effective isotropic spatial resolution
of 156 mm. The direction of flow is in the negative z direction. The grey scale
indicates the fractional conversion within the bed.

have potential advantages in studying catalytic systems because the 13C nucleus
has a wider chemical shift range than 1H, making the spectral resonances of
individual molecular species more easily resolved. Further, there will be fewer
carbon environments, and hence spectral resonances, in a 13C spectrum when
compared to a 1H spectrum of the same system. However, the disadvantage of
using 13C is that its natural abundance is only 1.07% and its NMR sensitivity is
lower than that of 1H by a factor of 5870, therefore there is considerable loss of
signal-to-noise when employing 13C as opposed to 1H observation. In solid
state NMR, which typically uses small, closed, sample volumes (B1 cm3), this
decrease in sensitivity and natural abundance is overcome by isotopically
enriching the species of interest with 13C. However, this approach is too costly
for the larger sample volumes required for flow-through reactor studies. It is for
this reason that interest in exploiting polarisation transfer techniques has
developed.
464 Chapter 26
13
2.2 C Observation
As far back as the late 1980s it was demonstrated that it is possible to combine
polarisation transfer techniques used in NMR spectroscopy with imaging pulse
sequences9 thereby enabling the natural abundance 13C signal to be spatially
resolved. In theory, a signal enhancement of up to a factor of 4 (i.e., gH/gC,
where gi is the gyromagnetic ratio of nucleus i) can be achieved with 13C
DEPT.10 In this dual resonance experiment, initial excitation is on the 1H
channel. Consequently, the repetition time for the DEPT experiment is con-
strained by T1H (oT1C); where T1i is the T1 relaxation time of nucleus i. This
favourable condition allows increased signal averaging, thereby further improv-
ing the signal-to-noise ratio, for a given acquisition time. The 13C DEPT-MRI
pulse sequence is a direct combination of the 13C DEPT pulse sequence used in
MR spectroscopy with the double phase encoding, orthogonal pair of gradi-
ents applied during the third evolution period to introduce spatial resolution
into the measurement. As the polarisation transfer from 1H to 13C is non-linear,
the final 1H y pulse affects the magnitude of the signal depending on which CHn
(n ¼ 1, 2, 3) groups are present. The value of y is therefore chosen to select either
all or combinations of CHn groups.10 The resulting spectra are analysed to
recover quantitative data characterising the amount of the different chemical
species present.
To date, 13C DEPT-MRI has been used in two case studies of catalytic
processes. Akpa et al.11 employed 13C DEPT-MRI to follow a reaction in
which competing etherification and hydration reactions of 2-methyl-2-butene
(2M2B) were followed within a fixed bed of H1 ion exchange resin; the resin
was the same as that used in the esterification reaction described earlier. The
reactants used were 2M2B, methanol and water, and the products of the
etherification and hydration reactions are tert-amyl methyl ether (TAME, or
2-methoxy-2-methylbutane) and tert-amyl alcohol (TAOH, or 2-methyl-butan-
2-ol), respectively. All experiments were performed using a Bruker DMX 300
spectrometer with a 7.0 T vertical magnet equipped with shielded gradient coils
providing a maximum gradient strength of 100 G cm1. A birdcage r.f. coil of
diameter 20 mm – dual tuned to 300 and 75.5 MHz for the 1H and 13C
resonances, respectively – was used. The data were recorded as a 5
7 (x
z)
2-D array of spectra, with the data being averaged in the third, y, direction; the
centre of the image volumes were separated by a distance of 2.5 mm in the axial
(z) direction. The reaction temperature was 313 K. In Figure 4, spectra from the
central column of the array are shown, at each of six axial positions. It is seen
that the chemical shift range of 13C gives sufficient spectral resolution that we
can follow the loss of reactants and the formation of products without need for
spectral deconvolution. In calculating concentration and selectivity from these
spectra the spectral resonances of the same carbon group must be compared
between species, since the degree of polarisation transfer and hence signal
enhancement is dependent on the chemical environment of each specific carbon
atom. In the calculation of conversion the CH3 resonances of TAME and
TAOH occurring at 7.8 and 8.7 ppm respectively were used, and compared with
Magnetic Resonance Imaging 465

12.5 mm
2M2B TAME &
Signal intensity (arbitrary units) TAME TAOH
10.0 mm TAME

TAOH
7.5 mm

5.0 mm

2.5 mm

0.0 mm

40 35 30 25 20 15 10 5 0
Chemical shift (ppm relative to TMS)

Figure 4 Spatially resolved 13C DEPT-MRI spectra recorded for the competitive
etherification and hydration reactions of 2M2B to TAME and TAOH
respectively. Spectra recorded at six positions along the length of the bed
are shown, at 2.5 mm intervals. The entrance to the bed is at 0 mm.

any of the CH3 resonances of 2M2B (these appear at 13.4, 17.3 and 25.7 ppm);
all chemical shifts are quoted with respect to the 13C resonance of TMS.
Selectivity to TAME was quantified by comparing the intensity of well-resolved
CH3 resonances of TAME and TAOH, which occur at 25 and 28 ppm,
respectively. Analysis of the data shown in Figure 4 showed that over the
15 mm height of the bed for which spectra are shown, conversion increased
by approximately 25% while selectivity remained approximately constant at
75–80%.
This MR method has now also been successfully applied to investigate
alkene hydrogenation in a trickle-bed reactor.12 Trickle-bed reactors are well-
established in industries with large throughputs such as the petrochemical
industry where they are used primarily for hydro-cracking, hydro-desulfurisa-
tion, and hydro-denitrogenation. They consist of a fixed bed of catalyst pellets,
contacted by a gas–liquid two-phase flow, with co-current downflow as the
most common mode of operation. Figures 5 and 6 show 13C DEPT-MRI data
recorded for the hydrogenation of 1-octene occurring over a 1 wt.% Pd/Al2O3
catalyst. The reactor was of inner diameter 2.5 cm and the catalyst was loaded
to a bed height of 3 cm. By employing 13C observation it was possible to
spatially map not only 1-octene and octane species but also the formation of 2-,
3- and 4-octene isomers; this would not have been possible using 1H MR.
Figure 5 shows 2-D maps of the 13C DEPT MR datasets recorded along the
length of the trickle bed; 13C DEPT spectra are acquired separately for (a) the
466 Chapter 26
(a) (b)

160 140 120 100 60 40 20 0

ppm ppm

160 140 120 100 60 40 20 0

13
Figure 5 2-D map of C DEPT-MRI spectra recorded along the length of a trickle
bed. Separate acquisitions were made for each of the (a) olefinic and (b)
aliphatic regions of the spectrum. The data were acquired with the bed
operating at steady state for gas and 1-octene flow rates of 32 and
1.0 mL min1, respectively. The white, horizontal lines indicate the limits
of the catalyst packing. Below each 2-D map, the 1-D 13C DEPT NMR
spectrum recorded at an axial location just before the reactants reach the
catalyst (just above the upper white line) is shown. The peaks at 114 and
139 ppm indicate that only unreacted 1-octene exists within the bed at this
location, as expected.

olefinic and (b) the aliphatic regions of the 13C spectrum. In this experiment
the gas and 1-octene (liquid) flow rates were 32 and 1 mL min1, respectively.
The intensities shown in the 2-D map are those of the spectral peaks in the 13C
DEPT spectrum. Any horizontal cut through the 2-D map recovers an indi-
vidual 13C DEPT spectrum. The spectra shown below each 2-D map were
acquired just above the upper white line; this line identifies the interface
between the pure catalyst support and the catalyst. Therefore in the olefinic
spectrum only two peaks occurring at 114 and 139 ppm with respect to TMS are
seen. These peaks are associated with 1-octene. No other peaks are seen at this
position in the bed because no reaction has occurred at this point. As the
reactants move down the bed (below the upper white line) additional peaks are
seen at 124 and 131 ppm indicating the formation of 2-octene. More detailed
analysis of the relative intensities of peaks within the olefinic region provide
evidence that small amounts of 3- and 4-octene isomers are also formed.
Figure 6 shows data recorded for a higher gas flow rate of 64 mL min1 at the
same 1-octene flow rate of 1 mL min1. Comparing Figures 5a and 6a it is clear
Magnetic Resonance Imaging 467
(c)
(a) (b)

160 140 120 100 60 40 20 0

ppm ppm

Figure 6 2-D map of 13C DEPT-MRI spectra recorded along the length of a trickle
bed. Separate acquisitions were made for each of the (a) olefinic and (b)
aliphatic regions of the spectrum. The data were acquired with the bed
operating at steady state for gas and 1-octene flow rates of 64 and 1.0 mL
min1, respectively. (c) 2-D 1H MR image of the spatial distribution of
liquid within the bed. At this higher gas flow rate greater reaction occurs as
the reactants contact the catalyst resulting in local vaporisation within the
bed identified by the region of zero signal intensity.

that increasing the gas flow rate has significantly influenced the product
distribution. In Figure 6a, as reaction progresses along the length of the reactor
there is loss of spectral intensity at B114 and B139 ppm indicating the
disappearance of 1-octene. As 1-octene is used up, so the intensity of a
resonance at B131 ppm increases. This feature is predominantly associated
with cis- and trans- 3- and 4-octene, since the resonance at B124 ppm, which is
associated with 2-octene isomers, is of significantly lower intensity than that at
B131 ppm. It is also seen that the integrated intensity of the olefinic region
decreases down the reactor while that of the aliphatic region increases, con-
sistent with octane formation. The absence of any peak appearing at a chemical
shift of B35 ppm shows that significant amounts of trans 4-octene are not
being produced suggesting that most of the further isomerisation from 2-octene
is to 3-octene and not 4-octene. Detailed analysis of the spectra yields quan-
titative conversion and selectivity data. Figure 6c shows a 2-D 1H image of the
spatial distribution of liquid within the bed. The loss of 1H signal intensity
immediately the feed encounters the catalyst shows that under these operating
conditions significant vaporisation occurs upon reaction; gas phase species are
not imaged using the acquisition parameters employed in this experiment. The
vaporisation event is also seen as a loss of signal intensity in the 13C data shown
in Figures 6a and b.
468 Chapter 26
Figure 7 shows recent work in which it was demonstrated that data can be
acquired sufficiently fast using 13C DEPT-MRI that reactor start-up and the
approach to steady-state operation can be followed. Again 1-octene hydrogen-
ation was the reaction of interest. For the data shown in Figure 7, the gas and
liquid flow rates are 30 and 2 mL min1, respectively; corresponding to a mole
ratio of 1-octene to hydrogen of 2. The data acquisition time was 15 min. Mole
fractions of 1-octene, 2-octene and n-octane along the length of the reactor are
shown at three time points; namely, when the reactant (in the absence of
hydrogen) is first introduced to the bed (t ¼ 0 min) and then at 22.5 and 82.5
min after introduction of hydrogen. The time associated with a given dataset is
the time at the halfway point through the total data acquisition time. From
these data the conversion and selectivity to 2-octene and n-octane, as a function
of both time and axial position along the bed, are obtained.13
Where are the future developments in this field? The major driver is
undoubtedly to increase signal-to-noise in the MR measurement, while at the
same time maintaining the quantitative nature of the data, and retaining
adequate spatial and spectral resolution. Ideally we wish to acquire 3-D
datasets such that chemical conversion and selectivity are mapped within the
reactor with the same level of detail as is currently possible for the imaging of
hydrodynamics (to be described in Section 4).

(a) (b)
Mole fraction, y (-)

Mole fraction, y (-)

1 1
0.8 0.8
0.6 0.6
0.4 0.4
0.2 0.2
0 0
0 5 10 15 20 25 0 5 10 15 20 25
Axial position, z (mm) Axial position, z (mm)

(c)
Mole fraction, y (-)

1
0.8
0.6
0.4
0.2
0
0 5 10 15 20 25
Axial position, z (mm)

Figure 7 Time resolved axial composition profiles obtained from 13C DEPT MRI
measurements during start-up of the hydrogenation of 1-octene over a fixed
bed of 1 wt.% Pd/Al2O3 catalyst, for a 1-octene:hydrogen mole ratio of 2.0.
Concentrations of 1-octene (J), 2-octene (&) and n-octane (E) along the
length of the bed are shown (a) before start-up and then at (b) 22.5 min and
(c) 82.5 min after start-up.
Magnetic Resonance Imaging 469

3 Intra-Pellet Molecular Diffusion

Earlier, we identified intra-pellet and inter-phase mass transfer limitations as
the major contributing factors to loss in catalyst performance when moving
from the ‘ideal’ catalyst to the catalyst pellet functioning within the working
reactor. The majority of the work in our laboratory has focussed on the fluid
contacting patterns within the reactor, with the longer-term objective of quan-
tifying mass transfer between the inter-pellet space and the catalyst pellets
comprising the bed. However, we have recently begun to develop and imple-
ment MR pulse sequences to obtain spatially resolved, chemically specific
measurements of molecular diffusion within individual catalyst pellets. Figure
8 shows the results of our initial study.14 In this example, equal volumes of
methyl ethyl ketone and 2-butanol were mixed and then imbibed within 5 wt.%
Ru/SiO2 catalyst pellets; the pellets were approximately spherical and of
diameter B4 mm. Data were recorded at 293 K. In Figure 8a, images of the
liquid phase within two pellets positioned one above the other in a 5 mm test
tube are shown. Figure 8b shows spatially resolved measurements of the
molecular diffusion coefficients, acquired simultaneously for the two chemical
species. The dotted and solid lines refer to 2-butanol and methyl ethyl ketone,
respectively. The values of chemically specific, spatially unresolved molecular
diffusion coefficients within the catalyst pellet are shown by the horizontal
lines. The chemically resolved molecular diffusion data are acquired from an
image slice, of rectangular cross-section, taken through one of the pellets at the
position shown by the dashed line in Figure 8a; spatial resolution of the

(a) (b)
2

1.5
Diffusivity (10-9m2/s)

0.5

0
-3 -2 -1 0 1 2 3
Radial distance (mm)

Figure 8 (a) Spin-echo image of liquid distribution within two catalyst pellets. The
image has in-plane spatial resolution of 20 mm
78 mm. (b) Molecular
diffusion coefficients of methyl ethyl ketone and 2-butanol as a function
of radial position across the dashed line identified in (a). The data for methyl
ethyl ketone and 2-butanol are shown by the solid and dotted lines, respec-
tively. MRI data were acquired with a spatial resolution of 156 mm. The
horizontal lines identify the spatially unresolved measurement of the re-
spective diffusion coefficient within the catalyst.
470 Chapter 26
diffusion measurement is 156 mm. These values compare with the free diffusion
values of 2-butanol and methyl ethyl ketone of 1.18
109 m2 s1 and
1.90
109 m2 s1, respectively. The steep rise in measured diffusion coefficient
towards the edge of the profiles shown in Figure 8b corresponds to liquid
outside the pellet towards the wall of the test tube. A sharp edge to the pellet is
not seen because, in this experiment, the distance over which data were acquired
extends over a vertical distance of 625 mm. The profile shown in Figure 8b is
therefore influenced by the changing radius of the pellet over this height.

4 Imaging Flow Fields in Reactors

Thus far we have considered chemical mapping and chemically resolved
transport processes occurring within individual catalyst pellets. The last piece
of the jigsaw in understanding how catalyst pellets perform in the reactor
environment comes from understanding the way the reactant streams contact
the pellet surface, and how this influences transport of molecules into and out
of the catalyst pore space.

4.1 Single-Phase Flows in Fixed-Bed Reactors

High resolution MRI studies of fluid flow within packed beds of column-
to-pellet diameter ratio typical of narrow fixed-bed reactors were first reported
in the mid-1990s. These first studies were performed on beds of column-to-pellet
diameter ratio 10–20, and used non-porous packing (i.e., glass spheres). Figure
9 shows 2-D sections through a 3-D volume image of the z component of flow
velocity within a fixed bed of non-porous spherical pellets; the +z direction is
the direction of superficial flow in the reactor. In this particular example, the
superficial flow velocity was 0.56 mm s1 corresponding to a Reynolds number
of 2.8, hence flow in much of the bed is dominated by viscous forces, associated
with flow velocities less than, or of the order of, the superficial velocity. The
most striking characteristic of these images is the extent of heterogeneity in the
flow field; a relatively small fraction of the inter-pellet space carries a high
percentage of the liquid flow.15,16 Such regions of the bed are associated with
high fluid velocities and inertial effects increasingly influence the flow profile.17
On the basis of these images, it is clear that any theoretical analysis of the flow
within such a reactor must account for distinct populations of fast and slow
moving liquid – channelling (i.e., fast flow regions) is not just occurring at the
walls of the bed. As a result of this heterogeneity in flow within the bed, the
contact time between feed and catalyst will differ very significantly across the
bed; i.e., by up to at least an order of magnitude in regions of the bed
characterised by the highest and lowest flow velocities, and this will introduce
spatially varying mass transfer characteristics within the bed. This is an
excellent illustration of how a single value characterising the flow velocity
through the reactor must be a gross approximation to reality; that is, local
behaviour is significantly different from global behaviour.
Magnetic Resonance Imaging 471
yz

xy

xz z

-2.7 mm s-1 vz 9.0 mm s-1

Figure 9 MR visualisation of water flowing within a fixed bed of spherical glass beads;
the beads have no MR signal intensity associated with them and are
identified as black voxels. Flow velocities in the z-direction are shown with
slices taken in the xy, yz and xz planes. In the xy-image the positions at
which the slices in the other two directions have been taken are identified.
Voxel resolution is 195 mm
195 mm
195 mm. The glass beads are of diam-
eter 5 mm and are packed within a column of internal diameter 46 mm. Local
flow velocities vary by up to an order of magnitude within the bed.

4.2 Two-Phase Flow in Fixed-Bed Reactors: The Trickle Bed

The ability to image the distribution of gas and liquid within a reactor has
provided strong motivation for developing MRI techniques to study trickle-bed
reactors. Figure 10 shows the steady-state distribution of liquid during ‘trickle
flow’ within a fixed bed. The trickle-flow regime occurs at relatively low gas and
liquid flow rates, and is characterised by a constant spatial distribution of gas
and liquid within the reactor. In this experiment, only the liquid is imaged, and
therefore both the gas phase and catalyst pellets are associated with zero signal
intensity (black on the grey scale). Subsequent image analysis of these data
enable us to identify all image pixels associated with a liquid–solid interface,
and hence we have what, to date, is the only direct measure of catalyst wetting
within such systems.18 These experiments have been used to confirm that
depending on the way the feed streams to the reactor are introduced, the
spatial distribution of reactant–catalyst contacting may be quite different.
Our more recent research has focussed on the development and implemen-
tation of ultra-fast MRI techniques to study unsteady-state phenomena. In the
context of trickle-bed reactors, this has enabled us to image the hydrodynamic
phenomena that occur within the reactor as the liquid flow rate is increased and
the bed moves from the trickle flow to the pulsing flow regime. The pulsing
regime takes the form of alternate gas- and liquid-rich bands moving along the
472 Chapter 26

Figure 10 Imaging of liquid holdup within a fixed bed of 5 mm diameter glass spheres
contained within a column of 40 mm. The data were acquired in a 3-D
array with an isotropic voxel resolution of 328 mm
328 mm
328 mm. (a)
The original image of trickle flow is first binary gated, so that only the
liquid distribution within the image is seen (white); gas-filled pixels and
pixels containing glass spheres show up as zero intensity (black). (b) Pixels
containing any liquid–solid interface are then identified using image anal-
ysis techniques and ‘images’ of surface wetting are produced. Data are
shown for liquid and gas superficial flow velocities of 3 mm s1 and
66 mm s1, respectively.

reactor such that at any given location within the catalyst bed, there is a time-
varying liquid content. Many industrial reactors operate close to the transition
between the trickle- and pulsing-regimes, and relatively little is known with
regard to the nature of the transition itself. Thus, previously it has not been
possible to validate theoretical and numerical models of the transition upon
which reliable reactor designs can be based.
To study this hydrodynamic transition we have used ultra-fast 3-D MRI
which allows us to investigate the spatial distribution of liquid within the bed as
a function of time, and clearly reveals when regions of the bed are associated
with a constant gas–liquid distribution (i.e., trickle flow) or if a given region has
moved into an unstable flow regime characterised by a rapidly changing gas–
liquid distribution.19 MRI has provided the first direct experimental evidence
that the transition to the pulsing regime is initiated by the formation of local
pulses (or instabilities) within the bed, and that the number of these local pulses
increases until reaching a maximum number at which point they grow and
merge until a single large pulse is formed which covers the full dimensions of
the bed. Further, MR data provide evidence of fluctuations in the liquid films
on the catalyst pellets; such fluctuations may be the precursor to the formation
of liquid bridges which then lead to the formation of the local pulsatile events
within the bed.20
Magnetic Resonance Imaging 473
A typical experiment proceeds by acquiring successive 3-D images of liquid
distribution within the bed which takes the form of a column of diameter
B45 mm, packed with catalyst or support pellets of dimension 1–3 mm. In this
work, a 3-D image with a field of view of 60 mm (x)
60 mm (y)
60 mm (z)
was acquired as a data array of size 16
16
32, thereby giving a spatial
resolution of 3.75 mm
3.75 mm
1.87 mm. Each 3-D image was acquired in
280 ms, i.e., 3-D images were acquired at rates of 3.6 f.p.s. Six series of eight
consecutive 3-D images were acquired for each set of flow rates. The stability of
the liquid distribution within the reactor is quantified by calculating the
standard deviation in the signal intensity associated with each individual voxel
throughout the time series of images acquired, thereby producing a 3-D image
or map of standard deviation values. Voxels associated with a constant gas–
liquid distribution (i.e., typical of trickle flow) are associated with values of
standard deviation B0. In contrast when the gas–liquid distribution in the
voxel is unsteady (i.e., a local pulse is occurring), that voxel will be associated
with a standard deviation value of Z 1. Typical standard deviation maps are
shown in Figure 11. Inspection of Figure 11 shows the location of isolated
hydrodynamic instabilities within the bed, identified by red voxels. From such
data it is possible to determine the spatial extent of the local pulsing regions as
the bed moves from the trickle to the pulsing regime. Figure 12 shows how the
number of isolated pulses (i.e., in the maps shown in Figure 11, a pulse is
defined as a group of connected voxels characterised by a standard deviation
Z 1) changes as liquid velocity through the bed is increased, at a constant gas
velocity of 300 mm s1. The exact form of this plot varies depending on the

Figure 11 3-D standard deviation maps, combined with a RARE image of the bed,
calculated from data acquired at a constant gas velocity of 75 mm s1 for
liquid velocities of (a) 7.0 and (b) 10.0 mm s1. The height of the bed shown
is 28 mm. Data are shown for half of the bed volume imaged. The standard
deviation maps (3.75 mm
3.75 mm
1.87 mm) have been linearly inter-
polated to the same resolution as a high resolution 3-D RARE image
(175 mm
175 mm
175 mm) of the bed to provide insight as to how local
pulsing relates to the structure of the bed.
474 Chapter 26
30

25

Number of pulses
20

15

10

uLT
0
0 2 4 6 8 10 12 14
uL[mm s-1]

Figure 12 Analysis of 3-D standard deviation maps calculated from data acquired
with the bed operating at a constant gas velocity of 300 mm s1. The plot
shows the average number of independent liquid pulses identified at each
liquid velocity. Liquid ‘pulses’ are only visually observed and detected
by conductance measurements at liquid velocities greater than B9 mm s1,
when the bed is characterised by 1–2 large liquid instabilities; i.e., when all
the small isolated pulses have merged such that distribution of all liquid
within the bed is temporally unstable.

nature of the packing elements used. We have defined the liquid velocity at
which the maximum number of isolated liquid pulses exists as the transition
point, uLT. Thus, in addition to identifying the physical mechanism by which
the hydrodynamic transition occurs, MRI has also shown that there is no
specific transition point; that is, the transition actually occurs over a range of
liquid velocities. Moreover, the nature of the transition can be controlled by
selection of the shape and size of the catalyst pellets; so we now identify further
factors that influence catalyst effectiveness!
The same ultra-fast MRI techniques are now being applied to the study of
periodic operation of trickle-bed reactors, in which the reactor is forced to
operate under transient conditions in order to exploit the non-linearities
associated with sudden changes in one or more variables when compared to
operating at the corresponding steady-state condition.21 Given that reactions
taking place in trickle beds are often controlled by mass transfer processes,
periodic operation offers the possibility of optimising and intensifying reactions
in trickle beds by modulating or interrupting the flow of gas or liquid reactants,
thereby periodically reducing mass transfer resistances. A typical periodic
operation strategy is to cycle the liquid feed rate to the reactor from a constant,
high liquid velocity to a constant, low liquid velocity; this is the periodic
Magnetic Resonance Imaging 475

signal
intensity

5 × noise

noise = gas

pellets

Figure 13 2-D MR image of spatially resolved liquid holdup during periodic oper-
ation. The image frame shown is recorded during the high liquid velocity
phase of the cycle. A single image frame was acquired in 200 ms. The 2-D
image of the structure of the bed was acquired as a data array of 256
256
pixels giving an in-plane resolution of 175 mm
175 mm; it was acquired in
B34 min.

strategy we have investigated.22 Although our studies are only in their very
early stages, they clearly show the power of MRI to reveal how local liquid–
catalyst contact may differ very significantly from the global characteristic of
the bed. The fact that MRI can reveal the locally varying reactant–catalyst
contacting behaviour suggests that we may now be able to understand far more
about the science that underpins the apparent advantages of operating peri-
odically. This knowledge will lead to greater confidence in exploiting these new
methods industrially and also in designing more effective periodic operation
strategies.
Initial results from MRI are shown in Figures 13 and 14. Data were recorded
for the reactor operating with a period (i.e., full cycle) of 8 s, with equal times of
4 s spent operating at high and low liquid velocities of 15 and 1 mm s1,
respectively. The gas velocity was constant at 75 mm s1. 2-D FLASH images
were acquired in 200 ms, in-plane spatial resolution was 351 mm
700 mm, with
a 2 mm slice thickness. In Figure 13, the pellets are identified as black pixels,
and pixels associated with signal intensity greater than five times that of the
noise level are deemed to be associated with the liquid phase. Pixels with signal
intensity at or below this critical value are assigned as gas-filled. Figure 14a
shows the integrated signal intensity from a time series of images such as that
shown in Figure 13; each point in Figure 14 represents the integrated signal
intensity from a single 2-D image; i.e., it is proportional to the total liquid
holdup in the 2-D cross section, analogous to a conductance measurement of
liquid holdup. A smooth drainage profile is observed – this is the global
476 Chapter 26
(a) 10

signal intensity [a.u.]

8

0
0 2 4 6 8 10 12 14 16
Time [s]

(b) (c)
signal intensity [a.u.]

1.8
signal intensity [a.u.]
1.6
1.6
1.2
1.2
0.8 0.8

0.4 0.4
0 0
0 2 4 6 8 10 12 14 16 0 2 4 6 8 10 12 14 16
Time [s] Time [s]

Figure 14 (a) Integrated liquid holdup during the same periodic operation strategy as
used in Figure 13. The continuous line shows the integrated signal intensity
(associated with the liquid phase) calculated from a time series of images
such as that shown in Figure 13. The dashed line shows the timing
associated with the cycling of the liquid feed. Local holdup profiles during
periodic operation can vary markedly from the global characteristic as
shown in (b) and (c).

drainage characteristic of the bed. To investigate how the local liquid–catalyst

contacting characteristics vary within the bed, image analysis algorithms are
used to segment the inter-pellet space of the bed into individual ‘flow channels’
or ‘pores’. Typically an image of the type shown in Figure 13 would be
segmented into B700 flow channels, which are of dimension comparable to
that of the packing elements comprising the bed. These channels are then
identified in the 2-D images and the temporal evolution of the local liquid
holdup throughout the cycle is calculated. The MRI analysis clearly shows that
only some of the channels within the bed are associated with a local liquid–
catalyst contacting profile of the form shown in Figure 14a. Other common
contacting profiles are shown in Figures 14b and c, which differ markedly from
the global characteristic. In ongoing work we are incorporating these data into
numerical modelling schemes to investigate the importance of including the
correct local liquid–catalyst contacting profile into numerical simulations pre-
dicting activity and selectivity during periodic operation.
Magnetic Resonance Imaging 477

5 Summary
This has been a whirlwind tour through the world of MRI applied to the study
of heterogeneous fixed-bed catalysis. It is an area in which many developments
are being made, and in which, in the near future, we can expect to explore the
interaction of physical and chemical phenomena occurring within catalysts and
reactors using a new generation of in situ techniques.
Recent developments in ultra-fast MRI and MR chemical mapping tech-
niques now make MRI a robust tool for studying both hydrodynamics and
chemical conversion within reactors. The versatility of the MR technique, to
some extent, remains a barrier to its use, in that for quantitative measurement
very careful development and implementation of the relevant MR methods are
required. However, if such care is taken, the ability of MR to study 3-D
optically opaque reactors and give quantitative information on both the
chemistry and hydrodynamics within the reactor provides significant opportu-
nity for the reaction engineer to design more effective catalyst–reactor systems
as well as to use the MR data to validate and develop numerical and theoretical
models of the relevant transport and reaction processes, which can then be
used, with confidence, in subsequent process design.

References
1. L.F. Gladden, M.D. Mantle and A.J. Sederman, Adv. Catal., 2006, 50, 1.
2. C.R. Muller, J.F. Davidson, J.S. Dennis, P.S. Fennell, L.F. Gladden, A.N.
Hayhurst, M.D. Mantle. A.C. Rees and A.J. Sedreman, Phys. Rev. Lett.,
2006, Art. No. 154504.
3. C.R. Muller, D.J. Holland, J.F. Davidson, J.S. Dennis, L.F. Gladden,
A.N. Hayhurst, M.D. Mantle and A.J. Sederman, Phys. Rev. E, 2007, Art.
No. 020302.
4. E.H.L. Yuen, A.J. Sederman and L.F. Gladden, Appl. Catal., 2002, A232,
29.
5. R.K. Harris, Nuclear Magnetic Resonance Spectroscopy, Longman,
Harlow, 1986.
6. I. Koptyug, A.A. Lysova, A.V. Kulikov, V.A. Kirilov, V.N. Parmon and
R.Z. Sagdeev, Appl. Catal., 2004, A267, 143.
7. A.G. Stepanov, K.I. Zamaraev and J.M. Thomas, Catal. Lett., 1992, 13,
407.
8. M.W. Anderson and J. Klinowski, Chem. Commun., 1990, 918.
9. H.N. Yeung and S.D. Swanson, J. Magn. Reson., 1989, 83, 183.
10. E.D. Becker, High Resolution NMR: Theory and Applications, Academic
Press, New York, 3rd edn, 2000.
11. B.S. Akpa, M.D. Mantle, A.J. Sederman and L.F. Gladden, Chem.
Commun., 2005, 2741.
12. A.J. Sederman, M.D. Mantle, C.P. Dunckley, Z. Huang and L.F. Gladden,
Catal. Lett., 2005, 103, 1.
478 Chapter 26
13. C.P. Dunckley, Z. Huang, M.D. Mantle, A.J. Sederman and L.F. Gladden,
J. Catal., 2007, submitted.
14. M.H.M. Lim, A.J. Sederman, M.D. Mantle and L.F. Gladden, Appl.
Catal., submitted.
15. A.J. Sederman, M.L. Johns, A.S. Bramley, P. Alexander and L.F. Gladden,
Chem. Eng. Sci., 1997, 52, 2239.
16. A.J. Sederman, M.L. Johns, P. Alexander and L.F. Gladden, Chem. Eng.
Sci., 1998, 53, 2117.
17. M.L. Johns, A.J. Sederman, A.S. Bramley, P. Alexander and L.F. Gladden,
AIChE J., 2000, 46, 2151.
18. A.J. Sederman and L.F. Gladden, Chem. Eng. Sci., 2001, 56, 2615.
19. L.D. Anadon, A.J. Sederman and L.F. Gladden, AIChE J., 2006, 52, 1522.
20. L.F. Gladden, L.D. Anadon, M.H.M. Lim, A.J. Sederman and E.H. Stitt,
Ind. Eng. Chem. Res., 2005, 44, 6320.
21. P.L. Silveston and J. Hanika, Chem. Eng. Sci., 2002, 57, 3373.
22. L.F. Gladden, L.D. Anadon, C.P. Dunckley, M.D. Mantle and A.J.
Sederman, Chem. Eng. Sci., 2007, in press.
CHAPTER 27

Dissociative Chemisorption of
Hydrogen Chloride at Cu(110):
Atom-Resolved Time-Dependent
Evidence for Transient States in
the Formation of the ‘‘Final
State’’ Stable Chloride
Overlayer
A. F. CARLEY, P. R. DAVIES, K. R. HARIKUMAR,
R. V. JONES AND M. WYN ROBERTS
School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK

The dissociative chemisorption of hydrogen chloride at Cu(110) has been

studied by scanning tunnelling microscopy (STM) with emphasis given to the
isolation of transient states in the formation of the chloride overlayer. There is
atom-resolved evidence at 295 K for a transition from disorder to an ordered
overlayer involving chlorine adatom surface diffusion, nucleation, domain
(soliton) formation, surface buckling, step-movement and time-dependent
relaxation. It can also be considered as a model system revealing possible
structural states present in the dissociative chemisorption of diatomic molecules
which can influence reactivity in catalytic reactions.

Some Personal Reminiscenses by Wyn Roberts

I have known John for nearly 60 years having been brought up in the Amman
Valley just a few miles from John in the Gwendraeth Valley in Carmarthenshire.
479
480 Chapter 27
We went to different schools but with close connections, the schools sharing
some staff including the sports/physical education teacher. It was as a conse-
quence of us both being members of the Carmarthenshire County Athletics
Team that we first became acquainted but it was as students at University
College Swansea that the friendship developed and crystallised. It is well docu-
mented that it was through my persuasion that John after graduation, chose to
change his research direction from pursuing postgraduate work in steroid
chemistry to surface chemistry, initially studying the oxidation of carbon mon-
oxide at carbon surfaces. I had suggested that he surely did not aspire to be a co-
author of ‘‘Part 55 Walden Inversion’’, Professor Shoppee, a very eminent
steroid chemist, and his intended supervisor, being already on Part 54! I had
the task of talking to Charles Shoppee, explaining that John had second
thoughts. But chemistry at Swansea was a very civilised department and Shop-
pee, a gentleman, agreed that John should transfer his registration for a PhD to
physical chemistry under the supervision of Keble Sykes, also my supervisor.
However, if the change had not occurred I am certain that John would have
become as distinguished in steroid chemistry as he is in solid state and surface
chemistry.
John focussed initially on the surface structure of carbon and its relevance to
chemical reactivity and I took up the challenge of the chemistry of metal
surfaces, initially the role of sulfur as a catalyst in the formation of nickel
carbonyl. Both our research groups became involved in the application and
development of experimental methods in the areas of solid state and surface
catalysis. John was ‘‘best man’’ at my wedding in 1957, I was his some 2 years
later.
In this chapter we illustrate the role that STM has had in revealing the
complexities that can be associated with the dissociative chemisorption of
diatomic molecules at metal surfaces where both the metal substrate and the
molecular fragments are mobile and how these may impact on the observed
catalytic chemistry.

1 Introduction
The classical approach in the development of models for surface reactions and
chemical reactivity have relied heavily on the Langmuir–Hinshelwood (L–H)
and Eley–Rideal (E–R) mechanisms.1,2 These have been central to the develop-
ment and current views in heterogeneous catalysis.
L
H : AðgÞ þ BðgÞ ! AðaÞ þ BðaÞ ! ABðaÞ ! ABðgÞ

E
R : AðgÞ þ BðgÞ ! AðaÞ þ BðgÞ ! ABðaÞ ! ABðgÞ

Assumptions are then made regarding the applicability of one of the accepted
adsorption isotherms (e.g. Langmuir) and the reaction rate expressed in terms
of the gas phase pressures PA and PB. For the above reactions the rates would
Dissociative Chemisorption of Hydrogen Chloride at Cu(110) 481
be given by the following rate expressions:
kbA PA bB PB
RL
H ¼
ð 1 þ bA P A þ bB P B Þ 2
and
kbA PA PB
RE
R ¼
1 þ bA PA
Various assumptions can also be made regarding the strength of the surface
bonding in the chemisorbed states A(a) and B(a), and whether, for example,
they are dissociatively chemisorbed, enabling kinetic expressions to be derived
providing evidence for kinetic reaction orders to be anticipated. In the case of
the E–R mechanism, molecule A is thermally accommodated and chemisorbed
while B is an incoming gas phase molecule which forms a complex AB which
desorbs as the product.
With the advent of surface spectroscopies (X-ray photoelectron spectroscopy
(XPS) and Auger electron spectroscopy (AES)) surface concentrations could be
determined directly and models developed based on structures observed by low
energy electron diffraction (LEED). This is a static surface science approach.
But what is more relevant to extracting meaningful kinetic information on
reaction mechanisms at single crystal metal surface is the applications of
surface sensitive spectroscopies under dynamic conditions in real time – an
approach rarely used.3
The problem we face in heterogeneous catalysis is to be able to pinpoint the
active sites under dynamic conditions and well illustrated by our studies of
catalytic oxidation at single crystal metal surfaces – ammonia oxidation at
Cu(110) and Zn(0001) and propene oxidation at Mg(0001).4,5 With both
reactants (NH3 and O2) present simultaneously in the gas phase it became
clear that transient precursor states could provide low energy pathways to
products (NH(a)). There was no spectroscopic (XPS) evidence for adsorption
of the reactants ammonia and oxygen, with transient O
states implicated in
the rate-determining step in what was a radical-type mechanism (shown below)
analogous to a two dimensional gas reaction.6

O2 ðgÞ ! O2 ðsÞ
NH3 ðgÞ ! NH3 ðsÞ
1=2O2 ðgÞ ! O
ðsÞ
O
ðsÞ þ NH3 ðsÞ ! NHðaÞ þ H2 OðgÞ
O
ðsÞ ! O2
ðaÞ

Both O
(s) and NH3(s) are present at 295 K at immeasurably low concentra-
tions, the reactions conforming neither to L–H nor E–R mechanisms, with the
formation of the final O2
state shutting down (poisoning) the reaction.7 The
mechanism also has implications for theoretical studies where assumptions are
482 Chapter 27
made on the energy parameters to be assumed for the reacting
surface species. What should be assumed for the surface transients O
(s) and
NH3(s)?
It was against this background of the ‘‘final state’’ not being catalytically
active that prompted us to search, in the dynamics of dissociative chemisorpt-
ion, for atom-resolved STM evidence for transient states.8 In this chapter we
consider the dissociative chemisorption of hydrogen chloride at Cu(110) at
room temperature. There was also further interest in chlorine (as HCl) being
used as an additive in industrial catalysis for redispensing and activating
catalysts. Was this a consequence of chlorine induced mobility of the catalyst
substrate and could it be monitored in real time by STM?

2 Experimental Details
An STM developed by Omicrom Vacuum Physik with in situ facilities for XPS
and mass spectrometry was used to study the dissociative chemisorption of
hydrogen chloride at a Cu(110) surface at 295 K. A tungsten tip was used for
STM and AlKa (1486.6 eV) radiation for obtaining XP spectra. The base
pressure of the spectrometer was B1  1010 mbar. The Cu(110) crystal was
obtained from Metal Crystals and Oxides Ltd. and cleaned by Ar1 bombard-
ment (0.6 keV, B15 mA) followed by annealing in vacuum at 800 K for 30 min.
The cleanliness of the sample was checked by both STM and XPS.
Surface coverages of chlorine adatoms were determined by analysis of
the intensities of the Cl(2s) and Cu(2p3/2) spectra. Hydrogen chloride
(99%) was obtained from Argo International and checked for purity mass
spectrometrically.

3 Results and Discussion

The atomically clean Cu(110) surface (Figure 1) was exposed to hydrogen
chloride at a pressure of 1  10
8 mbar at 295 K and the sequential develop-
ment of the structural features observed by STM. A number of distinct stages
have been isolated.

3.1 Disorder and Nucleation

During the initial exposure the surface is mainly disordered but with streaks –
black dashes – present (Figure 1). These are attributed to mobile chlorine
adatoms undergoing surface diffusion (hopping) during the time the STM tip
has moved across it but with the chlorine adatom having moved away when the
tip returns to its original position. Very similar images were observed by
Wintterlin et al.9 for oxygen adatom diffusion at Ru(0001) at room tempera-
ture. Analysis of the Cl(2s) intensity in the XP spectrum (Figure 1) at 268.4 eV
binding energy indicates a chlorine adatom concentration of 4.5  1014 cm
2 at
Dissociative Chemisorption of Hydrogen Chloride at Cu(110) 483

Figure 1 Images of the Cu(110) clean surface (a) and after exposure to hydrogen
chloride (10 L) at 295 K (b); note the streaks associated with chlorine
adatoms undergoing surface diffusion 1 L  10
6 Torr). Also shown is the
XP spectrum (c) with a peak at 268.4 eV binding energy assigned to Cl(a),
the concentration of which is estimated to be 4.5  1014 cm
2. The adatoms
are disordered.
484 Chapter 27

Figure 2 Nucleation of a single chloride domain structure at a defect site at Cu(110)

following exposure (11 L) to hydrogen chloride. The majority of the chlorine
adatoms are disordered.

this stage but with no obvious structure present. Wintterlin et al.9 have,
however, developed a fast STM with an imaging rate of 20 frames per second
and have therefore been able to monitor directly the surface hopping (diffusion)
of individual oxygen adatoms. The hopping rate is estimated to be 14  3 s
1
with an activation energy of 0.7 eV.
Nucleation is seen to be initiated at a defect (Figure 2) with the surface
gradually being dominated by domains running in the o00014 direction
separated by islands of a c(2  2) structure with also evidence for copper sites
present. The Cl(2s) intensity indicates that the chlorine adatom concentration is
4.9  1014 cm
2 and the binding energy at 268.4 eV (Figure 3).
With time the domains become well defined, approximately 2.5 Å in height
and separated from each other by c(22) structures, the domains being 18 Å
apart (Figure 4). The domain walls (or solitons) are a consequence of compe-
tition between the elasticity of the surface adlayer and the underlying substrate
copper lattice potential. When the adlayer structure, in this case the c(22) Cl
lattice, differs from the Cu(110) surface periodicity the misfit is accommodated
by restructuring and the formation of domain walls or ‘‘surface strings’’
running in the o0014 direction. With the highly electronegative chlorine
adatoms removing charge from the copper substrate atoms the surface buckles.
The zig-zag structure associated with domains (Figures 4 and 7) is a secondary
reconstruction within the domains and reminiscent of the herringbone recon-
struction of the Au(111) surface, where partial dislocations are present at the
‘‘turns’’ in the herringbone structure.
The ordered c(22) structure separating the domains has unit cell dimen-
sions of 5.1 Å in the o1104 direction and 7.2 Å in the o0014 direction.
Similar c(22) structures have been observed10 for chlorine – (from Cl2
dissociation) at Cu(100).
Dissociative Chemisorption of Hydrogen Chloride at Cu(110) 485

Figure 3 Islands of c(22) Cl with domain structures running in the o0014 direction
and clean copper sites.

Figure 4 Cu(110) surface with the completely formed domain structures running in
the o0014 direction; the domains are 18 Å apart and approximately 2.5 Å
in height.
486 Chapter 27

3.2 Surface Relaxation and the ‘‘Final State’’ Structure

When the chlorine induced surface-reconstructed surface (Figure 4) was left in
vacuum for 2 h at 295 K it relaxes to the c(2  2) structure (Figure 5). However,
further exposure (4400 L) to hydrogen chloride results in an increase in the
chlorine atom concentration to 6.8  1014 cm
2, i.e. well beyond the c(22)
monolayer concentration (B5  1014 cm
2), and the development of well
defined domain walls of the reconstructed surface (Figure 6). This is a very
stable chloride structure, unchanged after heating to 550 K.

3.3 Chlorine Induced Step Movement

In Figure 7 are shown a sequence of images taken every 40 s over a period of
15 min when the Cu(110) surface was exposed to hydrogen chloride at a
pressure of 1.5  10
8 mbar at 295 K. At the completion of the exposure
analysis, the Cl(2s) intensity indicated a chlorine atom concentration of
B6  1014 cm
2. The domain structures covered the entire surface but what
is also evident is that there is considerable movement of copper atoms resulting
in the coalescing of two surface steps during reconstruction. This is also evident
by comparing the line profiles taken across the surface at the beginning and the
end of the 15 min exposure (Figure 8). We estimate that between the fourth
image and the sixth image the two steps have coalesced involving a movement
of copper atoms of 100 Å in 80 s, i.e. a rate of about 1 Å per second. It is this
high mobility of copper substrate atoms induced by chlorine that is the likely
driving force in reactivation of heterogeneous catalysts by chlorine on the
industrial scale.

4 Surface Reactivity, Transient and Disordered States

The dissociative chemisorption of hydrogen chloride at Cu(110) involves the
participation of transient states, with finite lifetimes, and precursors of the
stable chloride overlayer. It also illustrates, a general principle, of how transient
states may well have a role in controlling reaction pathways in catalysis, with
significant experimental evidence emerging for well ordered surface structures
at metal surfaces being inactive. This was first gleaned from classical surface
spectroscopic studies3–7 with the transient O
-state active in catalytic oxidation
reactions (e.g. of ammonia, propene, water, etc.) and Iwasawa’s study11 of the
oxidation of carbon monoxide at Cu(110) where activity ceased with the
formation of the well ordered reconstructed (21) O phase (observed by
LEED). Likewise in ‘‘applied catalysis’’ Panov’s group12 concluded that the
radical O
species was the oxidant of benzene to phenol and also the active
oxygen in the oxidation of butane reported by Wang and Barteau,13 the
O2
-state being by comparison inactive.
STM has taken us much further, in that it has provided atomically resolved
images where catalytic activity can be correlated with surface disordered
Dissociative Chemisorption of Hydrogen Chloride at Cu(110) 487

Figure 5 Relaxation of a domain dominated surface structure when left for 2 h at

295 K with the development of a well ordered c(22) structure (a). The XP
spectrum (b) indicates that the chlorine adatom concentration is
4.9  1014 cm
2.
488 Chapter 27

Figure 6 The reconstructed surface after high exposure (400 L) to hydrogen chloride
with domain structures running in the o0014 direction (a). The XP
spectrum (b) shows the characteristic binding energy of chlorine adatoms
at 268.4 eV indicating a concentration of 6.8  1014 cm
2 i.e. well beyond the
monolayer (B5  1014 cm
2).
Dissociative Chemisorption of Hydrogen Chloride at Cu(110) 489

Figure 7 Sequence of images taken during the exposure of Cu(110) to hydrogen

chloride at 295 K and a pressure of 1  10
8 mbar. Images are taken every
40 s over a total exposure time of about 15 min.

states and inactivity correlated with their transformation to well ordered

structures. Examples so far available are the oxidation of ammonia and
propene at Cu(110) and Mg(0001),14 the cyclotrimerisation of acetylene to
benzene15 at Pd(111), H2–D2 exchange reaction and ethane hydrogenation at
Pt(111), both poisoned when CO was introduced into the gas phase and
resulting in a well ordered but inactive surface.16 The previous active state
was disordered. To progress further the many questions unanswered in the
molecular understanding of surface catalysis requires expertise in a wide range
of experimental methods that can operate under dynamic conditions and with
appropriate theoretical inputs – not easily achieved in a single university
laboratory!
490 Chapter 27

Figure 8 Line profiles (a) and (b) taken from two images (1) and (8) (Figure 7); two
surface steps have merged resulting in two terraces rather than the original
three.

Acknowledgement
We are grateful for the support of EPSRC.

References
1. J.M. Thomas and W.J. Thomas, Principles and Practice of Heterogeneous
Catalysis, VCH Publishers Inc., Weinheim, 1997.
2. M.W. Roberts and C.S. McKee, Chemistry of the Metal–Gas Interface,
Clarendon Press, Oxford, 1997.
3. M.W. Roberts, Chem. Soc. Rev., 1989, 18, 451; Appl. Surf. Sci., 1991, 52,
133; A.F. Carley, P.R. Davies and M.W. Roberts, Catal. Lett., 2002, 80,
25; Philos. Trans. R. Soc. A, 2005, 363, 829; P.R. Davies and M.W.
Roberts, Atom Resolved Surface Reactions: Nanocatalysis, RSC Publish-
ing, Cambridge, 2007.
4. C.T. Au and M.W. Roberts, Nature, 1986, 319, 206; J. Chem. Soc.,
Faraday. Trans. 1, 1987, 83, 2047; General Discussion, p. 2085; A.F.
Carley, S. Yan and M.W. Roberts, J. Chem. Soc., Faraday Trans, 1990,
86, 2701.
5. C.T. Au, L. Xing-Chang, T. Ji-An and M.W. Roberts, J. Catal., 1987, 106,
538.
Dissociative Chemisorption of Hydrogen Chloride at Cu(110) 491
6. A. Boronin, A. Pashusky and M.W. Roberts, Catal. Lett., 1992, 16, 345.
7. C.T. Au, A.F. Carley, A. Pashusky, S. Read, M.W. Roberts and
A. Zeini-Isfahan, in Adsorption on Ordered Surfaces of Ionic Solids and
Thin Films, ed. E. Umbach and H.-J. Freund, Springer Series in Surface
Science Springer, Berlin, Heidelberg, 1993.
8. A.F. Carley, P.R. Davies and M.W. Roberts, J. Chem. Soc., Chem.
Commun., 1998, 538.
9. J. Wintterlin, J. Trost, S. Renisch, R. Schuster, T. Zambelli and G. Ertl,
Surf. Sci., 1997, 394, 159.
10. C.Y. Nakakura, G. Zheng and E.I. Altman, Surf. Sci., 1998, 401, 173.
11. T. Sueyoshi, T. Sasaki and Y. Iwasawa, Chem. Phys. Lett., 1995, 241, 189.
12. V.S. Chernyavsky, L. Pirutko, A.K. Uriarte, A.S. Kharitonov and G.I.
Panov, J. Catal., 2007, 245, 466.
13. D.X. Wang and M.A. Barteau, Catal. Lett., 2003, 90, 7.
14. A.F. Carley, P.R. Davies and M.W. Roberts, Philos. Trans. R. Soc. A,
2005, 363, 829.
15. T.V.W. Janssens, S. Volkening, T. Zambelli and J. Wintterlin, J. Phys.
Chem. B, 1998, 102, 6521.
16. M. Montano, K. Bratile, M. Salmeron and G.A. Somorjai, J. Am. Chem.
Soc., 2006, 128, 13229; G.A. Somorjai and A.L. Marsh, Philos. Trans. R.
Soc. A, 2005, 363, 879.
CHAPTER 28

Recent Advances in Single-Site

Photocatalysts Constructed
within Microporous and
Mesoporous Materials
MASAKAZU ANPO AND MASAYA MATSUOKA
Department of Applied Chemistry, Graduate School of Engineering, Osaka
Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai Osaka 599-8531,
Japan

1 Introduction
The design of highly efficient and selective photocatalytic systems that work
with no loss of energy for applications in reducing global environmental
problems or energy issues is one of the most urgent and vital goals in environ-
mentally friendly catalytic research. Recently, investigations to address such
concerns using semiconducting TiO2 powdered catalysts have been extensively
carried out for such significant applications as the decomposition of atmos-
pheric NOx,1,2 the degradation of organic impurities diluted in water,2,3 and the
decomposition of water into H2 and O2.4 Studies elucidating the dynamics and
mechanisms behind the photocatalytic reactions have shown that the electrons
and holes produced in the conduction and valence bands, respectively, of the
semiconducting TiO2 powdered catalysts under UV light irradiation play a
major role in these reactions. It has also been shown that with a decrease in the
particle size of the TiO2 catalyst to less than 100 Å, a higher efficiency in the
reactions can be observed.5 As the size of the TiO2 particles is reduced below a
certain critical dimension, the gap between its highest occupied molecular
orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) starts to
increase, leading to an enhancement of the reduction ability of the photo-
formed electrons in the LUMO as well as the oxidation ability of the photo-
formed holes in the HOMO. This ‘‘size quantization effect’’ leads to high and
492
Recent Advances in Single-Site Photocatalysts 493
selective photocatalytic reactivity quite different from photoelectrochemical
reactions occurring on bulk TiO2 powder5,6 due not only to an electronic
modification of the TiO2 catalysts but also to the close existence of the photo-
formed electron and hole pairs and their balanced contribution to the reactions.
Of special interest is the design of ion and/or cluster size catalysts within
zeolites or mesoporous materials since these fascinating supports offer unique
nano- or meso-scaled pore systems, an unusual internal surface topology, and
ion-exchange capacities.2 The transition-metal oxide species within these
supports are considered to be highly dispersed at the atomic level and also
well-defined catalysts which exist in the specific structure of the support
framework. These highly dispersed transition metal oxide species can act as
efficient photocatalysts having strong oxidation and reduction abilities as
expected from the size quantization effect. In fact, highly dispersed transi-
tion metal oxide species, such as Ti, V, Cr, Mo, etc., can induce unique
photocatalytic reactions due to the following ligand to metal charge-transfer
process:1,2
hν
n+
O2− (n−1) O−

These charge transfer excited states, in which the electron-hole pair states are
localized in close proximity, were found to play a significant role in various
photocatalytic reactions such as the decomposition of NO into N2 and O2,7
the degradation of organic impurities in water,8 the photo-oxidation reaction
of hydrocarbons9 and the photoinduced metathesis reaction of alkanes.10 In
fact, except for highly dispersed transition metal oxides, isolated transition
metal ions such as Cu1 or Ag1 ions within zeolites can induce unique
photocatalytic reactions such as the decomposition of NOx (NO or N2O)
into N2 and O211,12 due to the following inner shell type transitions:
hν
Cu+ ([Ar]3d10) Cu+ *([Ar]3d94s1)

hν
Ag+([Kr]4d10) Ag+ *([Kr]4d95s1)

These highly dispersed transition metal oxides or ions can be regarded as

‘‘single-site photocatalysts’’ since their local structures are atomically and
uniformly regulated due to the framework structure of the zeolite or meso-
porous materials.7 This chapter deals with the photocatalytic activities of such
single site photocatalysts incorporated within the framework structures or
cavities of zeolites or mesoporous materials. Their local structures are also
discussed based on the results obtained by various in situ spectroscopic tech-
niques such as photoluminescence, electron spin resonance (ESR), X-ray
absorption fine structure (XAFS), ultraviolet-visible spectroscopy (UV-Vis),
and Fourier transform infrared spectroscopy (FT-IR) analyses. Special atten-
tion is focused on the relationship between the local structures of these single
site catalysts and their photocatalytic properties.
494 Chapter 28

2 Photocatalysis on Ti-oxide Single-Site Catalysts

Anchored in Zeolite Cavities; The Direct
Photocatalytic Decomposition of NO and Reduction
of CO2 with H2O
The development of efficient photocatalytic systems which can decompose
NOx directly into N2 and O2 is strongly desired in order to establish clean and
environmentally friendly deNOx systems for atmospheric purification. It has
been reported that the decomposition reaction of NO can proceed photocataly-
tically on powdered TiO2 at room temperature (rt) and N2O is produced as the
major product.13 To decompose NO directly into N2 and O2, single site
Ti-oxide photocatalysts were prepared and their photocatalytic activities were
investigated. UV light irradiation of powdered TiO2 and Ti-oxide/Y-zeolite
catalysts prepared by ion-exchange (ex-Ti-oxide/Y-zeolite) or impregnation
(imp-Ti-oxide/Y-zeolite) methods in the presence of NO led to the evolution of
N2, O2 and N2O in the gas phase at 275 K with different yields and product
selectivity.2,14 As shown in Figure 1, the yields of the photo-formed products
increased linearly against the UV irradiation time and the reaction immediately

O2-

Ti4+ Ti-oxide Single Site Photocatalysts

O2- O2-
O2-
50 100
60
Selectivity for CH3OH Formation/%

Light Light Light

Yields /µmol g-Ti-1

On Off
Selectivity for N2 Formation / %

Off
N2
40
40 80
Light
On
20
N2O
30 60
0
0 200 400
UV irradiation time /min

20 40

10 20

0 0
3.5 4 4.5 5 5.5 6 6.5
O2-
Coordination Number O2- O2-
4+
hν Ti
CO2 + H2O CH3OH + CH4 (QE = 0.3 %) O2-
O2-
hν O2-
2NO N2 + O2 (QE = 17.5 %)
(QE : quantum yield )

Figure 1 Relationship between the coordination numbers and photocatalytic reactiv-

ities of titanium oxides.
Recent Advances in Single-Site Photocatalysts 495
Table 1 The yields of the photoformed products, N2 and N2O in the photo-
catalytic decomposition of NO at 275 K and their distribution on
various Ti-based photocatalysts.
Yields
Ti content (mmol/g of TiO2 h) Selectivity (%)
Catalysts (wt% as TiO2) N2 N2O Total N2 N2O
ex-Ti-oxide/Y-zeolite 1.1 14 1 15 91 9
imp-Ti-oxide/Y-zeolite 1.0 7 10 17 41 59
TiO2 powder 2 6 8 25 75

ceased when irradiation was discontinued. A comparison of the photocatalytic

activity of the Ti-oxide/Y-zeolite catalysts and the widely used bulk TiO2
powdered catalyst was of special interest. And as shown in Table 1, the specific
photocatalytic reactivity of the Ti-oxide/Y-zeolite catalysts, which have been
normalized for the unit amount of TiO2 in the catalysts, are much higher than
that for the bulk TiO2.2,14 Moreover, the selectivity for the formation of
N2 strongly depends on the type of catalyst. The ex-Ti-oxide/Y-zeolite exhib-
ited the highest selectivity for the formation of N2 while N2O was the major
reaction product for both the bulk TiO2 catalyst and imp-Ti-oxide/Y-zeolite.
Ti K-edge XAFS (X-ray absorption near-edge fine structure (XANES)
and extended X-ray absorption fine structure (EXAFS)) investigations of
ex-Ti-oxide/Y-zeolite show that the Ti-oxide species exist in an isolated state
with a tetrahedral coordination (Ti–O coordination number: 3.7, Ti–O atomic
distance: 1.78 Å) as a ‘‘single site photocatalyst’’. On the other hand, XAFS
investigation revealed that the Ti-oxide species has an octahedral coordination
as a small TiO2 cluster catalyst within the imp-Ti-oxide/Y-zeolite. The rela-
tionship between the coordination number of the Ti-oxide species and the
selectivity for N2 formation in the photocatalytic decomposition of NO on
various type of Ti-oxide based photocatalysts are also shown in Figure 1.7
There is a clear dependence of the N2 selectivity on the coordination number of
the Ti-oxide species. From these results, it was shown that a highly efficient and
selective photocatalytic reduction of NO into N2 and O2 could be achieved with
the ex-Ti-oxide/Y-zeolite which includes the highly dispersed isolated tetrahe-
dral Ti-oxide as the active species. The formation of N2O as the major product
was also observed for the bulk TiO2 and imp-Ti-oxide/Y-zeolite catalysts,
which include the octahedrally coordinated aggregated Ti-oxide species.
As shown in Figure 2, the ex-Ti-oxide/Y-zeolite exhibited a photolumines-
cence spectrum centered at ca. 490 nm by excitation at ca. 290 nm at 77 K. The
photoluminescence spectrum is attributed to the radiative decay process from
the charge-transfer excited state to ground state of the highly dispersed Ti-oxide
species in tetrahedral coordination, as follows:
hν
( Ti4+ − O2−) (Ti3+ − O−)*
hv'
496 Chapter 28

Figure 2 Photoluminescence spectrum of (a) the ex-Ti-oxide/Y-zeolite catalyst; its

excitation spectrum (EX); and (b–e) the effect of the addition of NO on the
photoluminescence spectrum. Measured at 77 K, excitation beam: 290 nm,
emission monitored at 490 nm; amounts of added NO: (a) 0.0, (b) 0.2,
(c) 0.8, (d) 7.6, (e) 21.3 mmol/g.

On the other hand, the imp-Ti-oxide/Y-zeolite did not exhibit any photolu-
minescence. These results show that the ex-Ti-oxide/Y-zeolite involves a highly
dispersed isolated tetrahedral Ti-oxide species as the ‘‘single site photocatalyst’’
while the imp-Ti-oxide/Y-zeolite consists of an aggregated octahedral Ti-oxide
species which does not exhibit any photoluminescence. The addition of NO
onto the ex-Ti-oxide/Y-zeolite led to an efficient quenching of the photolumine-
scence spectrum and the lifetime of the charge-transfer excited state was also
found to be shortened, its extent depending on the amount of NO added.14
These results show not only that the tetrahedrally coordinated titanium oxide
species may be located at positions accessible to the added NO but also that the
added NO easily interacts with the charge-transfer excited state of the spe-
cies.7,14 Based on these results, the reaction mechanism for the photocatalytic
decomposition of NO on the isolated tetrahedral Ti-oxide species could be
proposed, as shown in Scheme 1. The NO molecule could adsorb onto the oxide
species as weak ligands to form the reaction precursors. Under UV light
irradiation, the charge-transfer excited complexes of the oxides, (Ti31–O
)*,
were formed. Within their lifetimes, the electron transfer from the trapped
electron centre, Ti31, into the p-antibonding orbital of NO takes place and,
simultaneously, the electron transfer from the p-bonding orbital of another NO
into the trapped hole centre, O
, occurs. These electron transfers led to the
direct decomposition of two sets of NO on (Ti31–O
)* into N2 and O2 under
UV irradiation in the presence of NO even at 275 K. With the aggregated or
bulk TiO2 catalysts, the photo-formed holes and electrons rapidly separate
Recent Advances in Single-Site Photocatalysts 497

O2-

Ti4+

O2- O2- O2-

2NO N2, O2
ground state

h+
O2- (N O) (N O) O- (N O)
(N O)
hv
Ti4+ Ti3+ e-
(excitation)
O2- O2- O2- O2- O2- O2-

excited state

Scheme 1 Reaction scheme of the photocatalytic decomposition of NO into N2 and

O2 on the Ti-oxide/Y-zeolite catalyst at 275 K.

spatially from each other (with large distances between the holes and electrons),
thus, preventing the simultaneous activation of two NO on the same active sites
and resulting in the formation of N2O and NO2 in place of N2 and O2.
Moreover, the decomposed N and O species react with NO on different sites to
form N2O and NO2, respectively. These results clearly demonstrate that the use
of zeolites as supports could enable the anchoring of a Ti-oxide species in a
highly dispersed state as ‘‘a single site photocatalyst’’ within the zeolite cavities
and such tetrahedrally coordinated Ti-oxide photocatalysts are promising
candidates for systems to remove toxic NOx compounds from the atmosphere.
It was also found that Ti-oxide/Y-zeolite catalysts (ex-Ti-oxide/Y-zeolite and
imp-Ti-oxide/Y-zeolite) can act as efficient photocatalysts for CO2 reduction
with H2O.15 The photocatalytic reduction of CO2 with H2O into chemically
valuable compounds such as CH4 or CH3OH is one of the most desired yet
challenging goals in the research of environmentally friendly catalysts, which
can simulate artificial photosynthesis. UV irradiation of powdered TiO2 and
Ti-oxide/Y-zeolite catalysts in the presence of a mixture of CO2 and H2O led to
the evolution of CH4 and CH3OH in the gas phase at 328 K with a good
linearity against the UV irradiation time, accompanied by trace amounts of CO,
C2H4, C2H6 and O2. The ex-Ti-oxide/Y-zeolite exhibits a high reactivity and
selectivity for the formation of CH3OH, while the formation of CH4 was found
to be the major reaction on bulk TiO2 as well as the imp-Ti-oxide/Y-zeolite.
A clear relationship between the coordination number of the Ti-oxide species
and the selectivity for CH3OH formation can be observed (Figure 1), showing
the highly efficient photocatalytic reduction of CO2 with H2O into CH3OH
using the ex-Ti-oxide/Y-zeolite, which includes the highly dispersed isolated
tetrahedral Ti-oxide as the active species.
498 Chapter 28
The reaction mechanism for the photocatalytic reduction of CO2 with H2O
was investigated by photoluminescence and ESR analyses.2,15 The addition of
H2O or CO2 molecules to the ex-Ti-oxide/Y-zeolite led to an efficient quench-
ing of the photoluminescence as well as shortening of the photoluminescence
lifetime, suggesting that the added CO2 or H2O interacts or reacts with the
Ti-oxide species in both its ground and excited states. UV irradiation of the
anchored Ti-oxide catalyst in the presence of CO2 and H2O at 77 K was also
found to lead to the appearance of ESR signals due to the Ti31 ions, H atoms,
and carbon radicals.2,15 From these results, the following reaction could be
proposed: the CO2 and H2O molecules interact with the excited state of the
photoinduced (Ti31–O
)* species and the reduction of CO2 and the decom-
position of H2O proceed competitively. Moreover, H atoms and OHd radicals
are formed from H2O and react with the carbon species formed from CO2 to
produce CH4 and CH3OH. These results clearly demonstrate that single site
Ti-oxide photocatalysts incorporated within zeolite cavities can enable such
artificial photosynthetic reactions as a CO2 fixation reaction with H2O to
produce CH3OH with a high selectivity.2,15

3 Design of Visible Light-Responsive Ti-oxide

Single-Site Catalysts
Ti-oxide single-site photocatalysts anchored within various zeolites exhibited
unique and high photocatalytic activity for various reactions such as the direct
decomposition of NO into N2 and O2 or the reduction of CO2 with H2O.
However, the isolated tetrahedral Ti41 oxide species, the active site of the
Ti-oxide single-site photocatalyst, absorbs UV light of wavelengths below
300 nm since the HOMO–LUMO energy gap of this isolated tetrahedral Ti41
oxide species becomes significantly larger than that of bulk TiO2 due to the size
quantization effect. In other words, Ti-oxide single-site photocatalysts cannot
utilize the abundant solar energy that reaches the earth, necessitating a
UV light source for its use as a photocatalyst. From this viewpoint, photo-
catalysts that can operate efficiently under both UV and visible light irradiation
are the most desired for practical and widespread use. The metal-ion-implan-
tation method has recently been applied to modify the electronic properties of
Ti-oxide single-site photocatalysts by bombarding them with high-energy metal
ions, leading to the discovery that metal-ion implantation with various tran-
sition-metal ions such as V, Cr, accelerated by high electric fields can, in fact,
produce a large shift in the absorption band of Ti-oxide single-site photocat-
alysts towards visible light regions.16 Figure 3 shows the effect of V-ion
implantation on the diffuse reflectance UV-Vis absorption spectra of
Ti-containing mesoporous materials, Ti/HMS and Ti/MCM-41. Their absorp-
tion spectra at around 200–260 nm can be attributed to the charge-transfer
absorption process, involving an electron transfer from the O2– to the Ti41 ion
of the highly dispersed tetrahedrally coordinated TiO4 unit of these catalysts.16
These spectra shift smoothly towards visible light regions, the extent strongly
Recent Advances in Single-Site Photocatalysts 499

(a) Ti / HMS

Absorbance / a.u

(4)
(3)
(2)
(1)

200 250 300 350 400 450 500

Wavelength / nm

(b) Ti / MCM-41
Absorbance / a.u

(4)
(3)
(2)
(1)

200 250 300 350 400 450 500

Wavelength / nm

Figure 3 Diffuse reflectance UV-Vis absorption spectra of (a) V-ion-implanted Ti/

HMS and (b) Ti/MCM-41. Amount of implanted V ions: (1) 0, (2) 0.66,
(3) 1.3, (4) 2.0 (mmol g-cat
1).

depending on the amount of V ions implanted. These results indicate that the
interaction of the implanted V ions with the TiO4 units leads to the modifica-
tion of the electronic properties of the titanium oxide species within the zeolite
frameworks.16 The V K-edge FT-EXAFS spectra of the Ti/HMS catalyst
implanted with V ions show that the next neighbours of the V environment
are not the same as vanadium-oxide based catalysts (e.g., V2O5) and suggest the
formation of tetrahedral titanium oxides having V–O–Ti bonding instead of
V–O–V linkages.16 These findings show that the formation of the V–O–Ti
bridge structures between the isolated tetrahedral TiO4 unit and implanted
V ions affect the electronic structure of the isolated tetrahedral TiO4, leading to
a red shift in the absorption spectra of these catalysts.
500 Chapter 28
25
Light Light
off on N2
20

Yields/
mol g-TiO2-1
15
λ > 390 nm
10
N2O
N2
5
λ > 420 nm
N2O
0
-1 0 1 2 3
Time/h

Figure 4 Reaction time profiles of the photocatalytic decomposition of NO on

Ti/HMS and V ion-implanted Ti/HMS under visible light irradiation
(l>390 nm, 420 nm). Amount of implanted V ions: 2.0 mmol/g-cat. The
yield of N2(K) and N2O(’) formation on V ion-implanted Ti/HMS; the
yield of N2 ( ) and N2O( ) formation on Ti/HMS.

The photocatalytic activity of the V-ion-implanted Ti/HMS and Ti/MCM-41

was investigated for the decomposition of NO into N2 and O2 under visible
light irradiation (l>420 nm). As shown in Figure 4, visible light irradiation of
the V-ion-implanted Ti/HMS led to the efficient decomposition of NO into N2
and O2, while the unimplanted original Ti/HMS exhibited no activity for the
reaction under the same reaction conditions. Moreover, no NO decomposition
could be confirmed under UV (l 4 300 nm) or visible light irradiation
(l 4 420 nm) on the V-ion-implanted HMS. These results show that ion-
implantation is an effective technique for the modification of the electronic
properties of Ti-oxide single-site photocatalysts, enabling them to absorb and
operate under visible light (l 4 420 nm) as highly efficient photocatalysts.

4 Photocatalysis on Cr-Oxide Single-Site Catalysts

Anchored in Zeolite Cavities under Visible Light
Irradiation; The Preferential Photocatalytic
Oxidation of CO with O2 in the Presence of Excess
Amounts of H2
Highly dispersed Mo or Cr oxide catalysts have been shown to exhibit high
activity for various photocatalytic reactions such as the photo-oxidation of
hydrocarbons17,18 or the photo-induced metathesis of alkanes.6 Recently, Mo
or Cr oxide catalysts highly dispersed on mesoporous silica (Mo-MCM-41,
Cr-MCM-41) have been reported to exhibit photocatalytic activity for the
Recent Advances in Single-Site Photocatalysts 501
preferential oxidation of CO (PROX reaction) with O2 in the presence of excess
amounts of H2.19,20 The PROX reaction has been applied for the removal of
CO impurities from H2-rich gas in the development of efficient fuel cell systems
with Pt or Rh-loaded catalysts at relatively high temperature. This section deals
with the photocatalytic PROX reaction on Cr-MCM-41 under visible or solar
light irradiation and the mechanism behind the reaction.
The UV-Vis spectrum of Cr-MCM-41 exhibits three distinct absorption
bands at around 240, 350 and 460 nm due to the ligand to metal charge transfer
transition (LMCT: from O2
to Cr61) of the tetrahedrally coordinated Cr61-
oxide species.17,20 The local structure of the Cr61-oxide species was also
investigated by Cr K-edge XAFS (XANES and EXAFS) measurements.
Fourier transform of EXAFS showed only a single peak due to the presence
of the neighbouring oxygen atoms (Cr–O) at ca. 0.8–1.5 Å without any
additional peaks due to the Cr–O–Cr bonds. These results indicate that the
Cr61-oxide species exist in a highly dispersed state. Curve-fitting analysis of the
Cr–O peaks revealed that the Cr61-oxide species exists in a highly distorted
tetrahedral coordination with two shorter Cr¼O double bonds (bond length:
1.59 Å, coordination number: 2.0) and two longer Cr–O single bonds (bond
length: 1.85 Å, coordination number: 2.1).20
Cr-MCM-41 exhibited a photoluminescence spectrum at 550–800 nm upon
excitation at around 500 nm at 293 K. The absorption and emission spectra are
attributed to the following charge transfer processes on the Cr¼O moieties of
the tetrahedral monochromate species (CrO2
4 ) involving an electron transfer
from the O2
to Cr61 ions and a reverse radiative decay from the charge
transfer excited triplet state:17,20

hν
[Cr6+ =O2−] [Cr5+ −O−]*
hv'

The photoluminescence of Cr-MCM-41 was found to be quenched in its

intensity by the addition of CO, O2 and H2, indicating that the Cr61-oxide
species, in its charge transfer excited triplet state, easily interacts with CO, O2
and H2. The photophysical processes on Cr-MCM-41 in the presence of the
quencher molecules can be depicted as follows:20
photoluminescence (kp)

[Cr 5+−O−]* radiationless deactivation (kd)

deactivation by quencher (kq)

The Stern–Volmer equation can be obtained for the quenching of the

photoluminescence by the quencher molecules by applying a steady-state
treatment to the above reaction mechanism, as follows:
F0 =F ¼ 1 þ t0 kq ½Q

where F0 and F show the yields of the photoluminescence in the absence and
presence of the quencher molecules, respectively, and where t0, kq and [Q] are
502 Chapter 28
61
the lifetimes of the charge transfer excited triplet state of the Cr -oxide species
in the absence of quencher molecules, the absolute quenching rate constant and
the concentration of the quencher molecules, respectively. The F0/F values
exhibited a good linear relationship with the concentrations of the quencher
molecules. The kq value (l/mol s) for each gas was determined by the slope
of the Stern-Volmer plots and were found to increase in the following order:
H2 (8.63  105) { CO (5.91  109) o O2 (1.12  1010).20
The photocatalytic preferential oxidation of CO with O2 in the presence of
H2 was investigated on Cr-MCM-41 at 293 K. Visible light irradiation
(l>420 nm) of the catalyst led to the efficient oxidation of CO into CO2,
accompanied by the stoichiometric formation and consumption of CO2 and O2,
respectively, as shown in Figure 5. The concentration of the CO gas reached
below 8 ppm after light irradiation of 150 min, while the amount of H2
remained almost constant. CO conversion and selectivity reached B100%
and 97%, respectively, after visible light irradiation of 150 min. The reaction
was also found to proceed efficiently even under solar light irradiation.20
In order to elucidate the reaction mechanism, FT-IR investigations were
carried out. Visible light irradiation of Cr-MCM-41 in the presence of CO led
to the appearance of a typical FT-IR band at 2201 cm
1 due to the mono-
carbonyl Cr41 species [Cr41(CO)], accompanied by the formation of CO2.20
The addition of O2 to these systems under dark conditions led to the complete

25

H2
23 Dark Light on

~
~
Amounts of gasses /µmol

O2
6

CO2
4

CO
0
0 30 60 90 120 150 180
Reaction Time / min

Figure 5 Reaction time profiles of the photocatalytic oxidation of CO with O2 in the

presence of H2 on Cr61-MCM-41 under visible light irradiation
(l 4 420 nm). (Initial amount of gases: CO: 3.8 mmol; O2: 7.5 mmol; and
H2: 24.6 mmol.)
Recent Advances in Single-Site Photocatalysts 503
Tetrahedrally coordinated
Cr6+oxide species in Cr-MCM-41

O2- O2-
CO
Cr6+
Reoxidation of Cr 4+ O O hv
reduced-species by O2 Charge transfer
excited triplet state
1/2 O2 *
O2- O-

O2- CO Cr5+

Cr4+ O O
H2
O O
H2O

2 CO

Reduction of Cr-oxide
CO2
species by CO

Scheme 2 Complete reaction cycle for the photocatalytic oxidation of CO with O2 in

the presence of H2 on Cr61-MCM-41.

disappearance of these FT-IR bands. These results clearly suggest that the
Cr61-oxide species reacts with CO in its photo-excited state and is reduced into
the Cr41 carbonyl species, while these species are easily oxidized by O2 into the
original Cr61-oxide species. From these results, the catalytic reaction cycles on
Cr-MCM-41 can be proposed as in Scheme 2. Initially, the tetrahedral Cr61-
oxide species is photo-excited to its charge transfer excited triplet state and
reacts with CO to form CO2 and a photo-reduced Cr41 carbonyl species. The
Cr41 oxide species is then efficiently oxidized by O2 and the original Cr61-oxide
species is generated. The high CO selectivity can be attributed to the high and
selective reactivity of the photo-excited Cr61-oxide species with CO, as indi-
cated by the high quenching efficiency of CO as compared to H2.

5 Photocatalytic Reactivity of the Cu1/ZSM-5

Catalyst for the Decomposition of NO
into N2 and O2
This section focuses on investigations on the characteristics of the Cu1 species
anchored onto the nano-pores of the ZSM-5 zeolite by in situ photolumines-
cence, ESR, XAFS and UV-Vis analyses and their reaction with NO under UV
light irradiation.
Cu1/ZSM-5 and Cu1/Y-zeolite catalysts were prepared by evacuation of the
Cu21/ZSM-5 and Cu21/Y-zeolite samples prepared by an ion-exchange
504 Chapter 28
11,12 1
method at 973 K. UV irradiation of the Cu ion catalysts in the presence of
NO even at 275 K was found to lead to the formation of N2 and O2, with a good
linear relationship between the irradiation time and NO conversion. The
formation of by-products such as N2O and NO2 was negligible. Cu1/ZSM-5
exhibited photoluminescence at around 440 nm due to the isolated Cu1 ions
under UV irradiation at around 300 nm. The yields of the photocatalytic
decomposition reaction of NO greatly depend on the pretreatment degassing
temperature of the Cu21/ZSM-5 samples, showing a good parallel relationship
with the dependency of the intensity of the photoluminescence due to the Cu1
ions. These results indicate that the photo-excited states of the isolated Cu1 ion
as a single site photocatalyst play a significant role in the photocatalytic
decomposition of NO.11,12 Moreover, the Cu1/ZSM-5 catalyst exhibits higher
photocatalytic activity as compared to the Cu1/Y-zeolite catalyst. Considering
that Cu1/Y-zeolite exhibits a typical photoluminescence (ca. 520 nm) due to the
Cu1 dimer species, it could be concluded that the photocatalytic reactivity of
the Cu1 monomer species is higher than that of the Cu1 dimer species. In fact,
the photoluminescence spectrum of the Cu1/ZSM-5 catalyst was quenched
more efficiently by the addition of NO than for the Cu1/Y-zeolite, indicating
that the photo-excited state of the Cu1 monomer species interacts with NO
more efficiently than with the Cu1 dimer species.11,12
The addition of NO onto Cu1/ZSM-5 led to the appearance of FT-IR
and ESR signals due to the Cu1–NOd
adduct species. UV irradiation of the
Cu1/ZSM-5 catalyst having a Cu1–NOd
adduct species led to a decrease in
the intensity of the ESR signal assigned to the Cu1–NOd
species with

Cu+ (3d10) Cu2+

evac.
O O O O
reduction

NO Monomer
adsorption (N O)ad

electron transfer
NOδ-
into copper
Cu+ δ+ N2+O2
nitrosyl O O
adduct NO
+*(3d9
Cu )

h (N O)ad

Cu+ *(3d94s1) electron transfer into

excited state -anti-bonding orbital of NO

Scheme 3 Reaction scheme of the photocatalytic decomposition of NO into N2 and

O2 on the Cu1/ZSM-5 catalyst at 298 K (& denotes an electron vacancy).
Recent Advances in Single-Site Photocatalysts 505
irradiation time, without the appearance of any new signal. After UV irradi-
ation was discontinued, the intensity of the signal returned to its original level.
These reversible changes in the ESR signal assigned to the Cu1–NOd
adduct
species indicate not only that the Cu1–NOd
species acts as a reaction precur-
sor but also that the photo-induced decomposition of NO proceeds catalyti-
cally.
Together with the results obtained by in situ photoluminescence, ESR, and
FT-IR measurements, the mechanism for the photocatalytic decomposition of
NO into N2 and O2 on the Cu1/ZSM-5 catalyst at 275 K under UV irradiation
could be proposed, as follows (Scheme 3): electron transfer from the excited
state of the Cu1 (3d94s1 state) to a p-anti-bonding orbital of NO and simul-
taneous electron transfer from the p-bonding orbital of another NO to the
vacant electronic state of the Cu1 ion (3d94s0 state) occurs, causing local charge
separation and a weakening of the N–O bond of the two NO molecules, thus
initiating the decomposition of NO into N2 and O2.11,12

6 Conclusions
The activity of various transition metal oxides (Ti, Cr) incorporated within the
zeolite framework structures as well as transition metal ions (Cu1) exchanged
into zeolite cavities as single-site heterogeneous photocatalysts have been
outlined here. These single-site heterogeneous photocatalysts with a coordina-
tively unsaturated coordination sphere could induce unique photocatalyst
reactions such as the direct decomposition of NO into N2 and O2 or reduction
of CO2 with H2O. Moreover, an ion-implantation method was shown to be an
effective method to prepare visible light-responsive Ti-oxide loaded zeolite
photocatalysts. And in the case of Cr-MCM-41, the preferential selective
oxidation of CO impurities in H2 by visible light irradiation was demonstrated.
It should be emphasized that the use of zeolites as a support made it possible
to control the local structure of the highly dispersed transition metal oxides or
ions at the atomic level, leading to a precise control of the photocatalytic
activity as well as selectivity of a reaction. It can, thus, be seen that zeolitic
frameworks offer one of the most promising approaches in designing single-site
photocatalysts for the development of effective new systems to reduce and
eliminate global air and water pollution by harvesting visible or solar light.

References
1. M. Anpo, Bull. Chem. Soc. Jpn., 2004, 77, 1427.
2. M. Anpo, S. Dohshi, M. Kitano, Y. Hu, M. Takeuchi and M. Matsuoka,
Annu. Rev. Mater. Res., 2005, 35, 1.
3. M. Kitano, K. Funatsu, M. Matsuoka, M. Ueshima and M. Anpo, J. Phys.
Chem. B, 2006, 110, 25266.
4. M. Kitano, M. Takeuchi, M. Matsuoka, J.M. Thomas and M. Anpo,
Catal. Today, 2007, 120, 133.
506 Chapter 28
5. M. Anpo and M. Che, Adv. Catal., 2000, 44, 119.
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91, 4305.
7. M. Anpo and J.M. Thomas, Chem. Commun., 2006, 3273.
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451.
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H.H. Patterson, Coord. Chem. Rev., 1998, 171, 175.
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3175.
14. H. Yamashita, Y. Ichihashi, M. Anpo, M. Hashimoto, C. Louis and
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Chem., 1997, 101, 2632.
16. M. Anpo and M. Takeuchi, J. Catal., 2003, 216, 505.
17. H. Yamashita, K. Yoshizawa, M. Ariyuki, S. Higashimoto, M. Che and
M. Anpo, Chem. Commun., 2001, 435.
18. S. Higashimoto, R. Tsumura, S.G. Zhang, M. Matsuoka, H. Yamashita,
C. Louis, M. Che and M. Anpo, Chem. Lett., 2000, 408.
19. T. Kamegawa, R. Takeuchi, M. Matsuoka and M. Anpo, Catal. Today,
2006, 111, 248.
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J. Phys. Chem. C, 2007, 111, 1076.
CHAPTER 29

Structural Organization of
Catalytic Functions in Mo-Based
Selective Oxidation Catalysts
MASAHIRO SADAKANE AND WATARU UEDA
Catalysis Research Center, Hokkaido University, North 21, West 10,
Kita-ku, Sapporo, 001-0021, Japan

1 Background and Introduction

About one-third of industrial organic products are synthesized via catalytic
selective oxidation processes, and continuous efforts have been devoted to the
development of high performance catalysts because of the high demand for the
effective utilization of chemical resources in response to environmental con-
cerns.1 Solid-state catalysts like mixed metal oxides used for industrial oxida-
tion processes have, generally speaking, been composed of complicated
compositions and phase-mixtures so far, but the next generation of catalysts
will have to be composed of much more advanced and well-organized materials
possessing multi-catalytic functions. In this context, it seems highly important
to develop new rationale synthetic methods for solid-state catalysts in order to
replace the conventional catalyst preparation method, the so-called mixed-and-
baked, which still, however, has various merits in aspects of industrial produc-
tion, such as cost, easy to obtain starting metal materials, large-scale produc-
tion, and so forth.
On stepping forward to the next generation of catalyst preparation and
putting the current preparation systems aside, an example of crystalline Mo-
and V-based complex metal oxide catalyst development recently initiated by
Mitsubishi Chemicals is highly informative in terms of structural organization
of catalytic functions. The catalyst is a crystalline MoVTe(Sb)NbO mixed oxide
which shows high catalytic performance in the propane oxidation to acrylic
acid and the ammoxidation of propane to acrylonitrile (AN).2 Although
the crystal structure of the catalyst has not yet been fully confirmed, it is
507
508 Chapter 29
ascertained that the oxide is a layered (orthorhombic) structure with a slab
consisting of six- and seven-membered ring units with MO6 octahedra and
pentagonal {(M)M5O27} units with an MO7 pentagonal bipyramid and five
edge-sharing MO6 octahedra (Figures 1a and b). There are four pentagonal
units, six-membered rings, and seven-membered rings in one unit cell which is
isotypic with Cu–Nb–O–x (x ¼ Cl, Br, I) and Cs–Nb–W–O systems (Figures 1c
and d).3 The main components are Mo and V, and Nb and Te (or Sb) can exist
in the structure as minor elements. The Te and Sb are believed to be located in
the hexagonal rings.4 Our recent works on this catalyst system evidently show
that each element arranged individually in the structure and the elemental
network constructed by the structural units (Figure 1) can cooperatively work
in the course of the propane oxidation at the same time and accomplish the
catalytic cycle effectively. This is a prominent example demonstrating that
multi-step reactions such as propane oxidation cannot proceed by the admix-
ture of several active sites working separately, but can proceed over the zone of
active site network formed structurally and spatially. There is no doubt that
this happened because the structural materials were discovered, and this
obviously marks a turning point in solid-state oxidation catalysts. Our basic
research revealed at the same time that the evolution of the structural materials
is sustained by a new-type formation process of solid-state materials which is
completely different from the conventional ‘‘mixed-and-baked’’ method.

Figure 1 Ball and stick (a) and polyhedral (b) presentation of the pentagonal unit and
orthorhombic Mo3VOx, a–b plane (c) and b–c plane (d).
Structural Organization of Catalytic Functions 509
We describe here our recent achievements including (1) the formation
mechanism of orthorhombic and trigonal Mo–V oxides, both of which contain
the same building units (six- and seven-membered rings and pentagonal unit)
with different ratios, (2) an outstanding catalytic performance of the ortho-
rhombic Mo3VOx and the trigonal Mo3VOx in the selective oxidation of
acrolein to acrylic acid, and (3) propane ammoxidation catalyzed by the pure
orthorhombic Mo–V based mixed metal oxide with and without additional
metals (Nb, Te or Sb), which allows us to discuss the roles of each element and
structural unit.

2 Synthesis, Structural Characterization,

and Formation Mechanism of Orthorhombic
and Trigonal Mo3VOx5a
Both the orthorhombic and trigonal Mo3VOx mixed metal oxides were syn-
thesized by hydrothermal treatment of a mixture of ammonium heptamoly-
bdate (NH4)6Mo7O24
4H2O and vanadyl sulfate VOSO4
nH2O (Mo 50 mmol
and 12.5 mmol) in H2O (240 mL) (Figure 2). By controlling the pH of the
precursor solution with sulfuric acid, two types of crystalline Mo3VOx with
orthorhombic structure and trigonal structure were synthesized at pH ¼ 3.2 and
pH ¼ 2.2, respectively. Since the crude materials contained an amorphous
phase as a by-product in each case, the materials were washed with an aqueous
solution of oxalic acid for removal. Metal composition was determined by ICP-
AES and Mo/V was found to be ca. 3 for both materials.

Figure 2 Synthesis of orthorhombic and trigonal Mo3VOx.

510 Chapter 29

Figure 3 HRTEM images and selected-area electron diffraction (SAED) patterns

(insets) of orthorhombic Mo3VOx viewed along the [001] direction (a) as
well as the corresponding simulated contrast calculated for a crystal thick-
ness close to 24 nm and a defocus value Df ¼ 130 nm (b). L and S indicate
large and small spots, respectively.

Fundamental structures of the orthorhombic and trigonal Mo3VOx were

constructed on the basis of the HRTEM images of each sample. Figure 3
represents HRTEM images along the [001] zone axis of the orthorhombic
Mo3VOx. An ordered arrangement of two kinds of white spots (large one and
small one indicated as L and S in Figure 3, respectively) was observed in
accordance with the structure shown in Figure 1c. The large spot and small spot
clearly correspond to the seven-membered and six-membered rings of the
octahedra, respectively. The pentagonal rings were surrounded by three
seven-membered rings and two six-membered rings.
A crystal structure of the trigonal Mo3VOx was constructed under the same
assumption. Three large white spots corresponding to the seven-membered ring
and two small spots corresponding to the six-membered ring were found in one
unit cell (Figure 4c). The pentagonal unit was placed in a position surrounded
by three seven-membered rings and two six-membered rings, then producing
the structure presented in Figure 4a. The trigonal structure produced was
confirmed by analyzing the powder XRD pattern using the Rietveld method.
The XRD pattern was well-simulated using the structure (with lattice param-
eters a ¼ 21.433(3) Å, c ¼ 4.0045(18) Å, space group P3 (No.143)) and reason-
ably converged (Rwp ¼ 12.23%).
From the above structural analysis, two Mo3VOx solids are regarded as
structure variants with the same structural units as the pentagonal ring, the six-
membered ring, and the seven-membered ring but with different arrangements
of them. Then one can easily assume that these kinds of solid materials are
constructed by stacking of the pentagonal ring units. This interesting crystal
formation scheme could be justified by the following facts.
As described above, the orthorhombic or trigonal Mo3VOx were synthesized
from the precursor solution with a colour of dark violet, which was instantly
obtained by mixing the solutions of ammonium heptamolybdate and
vanadyl sulfate. We found that the coloured solution gave characteristic
Structural Organization of Catalytic Functions 511

Figure 4 Polyhedral presentation of trigonal Mo3VOx: a–b plane (a) and b–c plane
(b). HRTEM images and SAED patterns (insets) of trigonal Mo3VOx
viewed along the [001] direction (c) as well as the corresponding simulated
contrast calculated for a crystal thickness close to 20 nm and a defocus value
Df ¼ 155 m (d). L and S indicate large and small spots, respectively.

Figure 5 Raman spectra (left) of Mo–V solution (Mo/V ¼ 4, Mo ¼ 0.21 M, pH 3.3)

(a), Mo–V solution (Mo/V ¼ 4, Mo ¼ 0.21 M, pH 2.2) (b), aqueous Mo72V30
solution (1 g, 30 mL1) (c), aqueous Mo132 solution (1 g, 30 mL1) (d), and
aqueous Mo57V6 solution (1 g, 30 mL1) (e). UV–Vis spectra (right) of
Mo–V solution (Mo/V ¼ 4, Mo ¼ 0.42 M, pH 3.3) (linear line) and aqueous
Mo72V30 solution (dotted line).

Raman bands at 1000–700 cm1 which were completely different from those
of each solution before mixing. Then, the Raman spectrum of the precursor
solution before the hydrothermal reaction (Figures 5a and b) was com-
pared with that of the solution of three different polyoxomolybdates,
512 Chapter 29

Figure 6 Polyhedral presentation of Mo72V30{[K10Mo72V30O282(H2O)56(SO4)12]26}

(a), Mo132{[Mo132O372(H2O)72(CH3CO2)30]42} (b), and Mo57V6{[H3Mo57
V6(NO)6O183(H2O)18]21} (c). Grey polyhedra represent the pentagonal unit
and black balls represent vanadium metal.

Mo72V30{[K10Mo72V30O282(H2O)56(SO4)12]26}, Mo132{[Mo132O372(H2O)72-
(CH3CO2)30]42}, and Mo57V6{[H3Mo57V6(NO)6O183(H2O)18]21}, all of which
exhibit the pentagonal {(Mo)Mo5} unit in the discrete structure. Very similar
characteristic Raman peaks were observed at 1000–700 cm1 for the poly-
oxomolybdates (Mo72V30 (Figure 6a),6 Mo132 (Figure 6b),7 and Mo57V6
(Figure 6c)8), shown in Figures 5c–e, respectively. The UV–Vis spectrum of
the solution was also similar to that of Mo72V30 (Figure 5, right), where the
IVCT (Inter Valence Charge Transfer) (VIV - MoVI) peak was observed at ca.
510 nm.6 The Mo72V30 polyoxomolybdate has 12 pentagonal {(MoVI)MoVI5}
units connected by 30 vanadium (IV).6
From these results, we conclude that the pentagonal {(Mo)Mo5} unit is
present in the precursor solution before the hydrothermal reaction and inter-
acts with VO21 cations to form a polyoxo-type species in the solution. In fact,
discrete polyoxomolybdates have been prepared from room temperature to
363 K by a reaction of the pentagonal units with molybdenum and other
elements.9 The pH in this case is known to be one of the most important factors
for this formation. Similarly, the formation of the orthorhombic or trigonal
Mo3VOx depended on the pH, so that selection of the solid-state phase is
controlled by the pH dependent polyoxo-type species with the pentagonal unit.
Hence, assembly of the polyoxo-type species consisting of the pentagonal unit
could occur under hydrothermal conditions to form three-dimensional metal
oxide solids as illustrated in Figure 7. We believe that the unit assembly under
hydrothermal conditions will be employed in many cases, and creates new-type
crystal solid materials having high-dimensional networks of catalytic elements,
and ultimately brings about extremely high performance catalysts.

3 Crystalline Mo3VOx as a True Catalytic Phase for

Acrolein Oxidation
As summarized in Table 1, the trigonal Mo3VOx catalyst has an outstanding
catalytic performance for oxidation of acrolein to acrylic acid; the conversion
Structural Organization of Catalytic Functions 513

Figure 7 Image of formation of orthorhombic Mo3VOx from the pentagonal unit

under hydrothermal conditions.

Table 1 Acrolein oxidation over the orthorhombic and trigonal Mo3VOx

catalysts.a

Surface area Conversion Selectivity (%)

Catalyst (m2 g1) (%) AA b
AcAc COx
Trigonal Mo3VOx 15.6 99.7 90.5 3.2 6.3
Orthorhombic Mo3VOx 14.9 99.4 93.6 1.5 4.9
a
Reaction condition: amount of catalyst, 0.45 g diluted by 0.05 g of SiC; gas composition, acrolein/
O2/H2O/N2 ¼ 4.8/7.6/26.9/60.6; total flow, 103.3 mL min1; reaction temperature, 463 K. Both
catalysts were calcined at 673 K under nitrogen flow before the reaction test.
b
AA, acrylic acid.
c
AcA, acetic acid.

of acrolein was achieved to almost 100% at 463 K and the selectivity to acrylic
acid was 90%. The orthorhombic Mo3VOx catalyst shows similar high catalytic
performance. The catalytic activities attained over the catalysts are significantly
superior to those of Mo–V based oxide catalysts reported in patents and
papers; the patent catalysts need much higher reaction temperature (usually
more than 500 K)10 in order to obtain similar activity to that of the present
Mo3VOx catalysts. The main differences between the patent catalysts and the
present Mo3VOx catalysts are the preparation method, the former conventional
and the latter hydrothermal, and structure, the former being XRD-disordered
materials and the latter crystalline solids. Since the XRD-disordered materials
514 Chapter 29
have the same elemental composition as the crystalline Mo3VOx, the less active
XRD-disordered materials might be constructed with the structural units in a
disordered fashion, while the highly active crystalline Mo3VOx is constructed in
an ordered fashion, thereby allowing for more active sites on the surface. The
seven-membered ring site is likely responsible for the oxidation. As a conse-
quence, the trigonal and/or orthorhombic Mo3VOx are potentially true cata-
lytic active phases in the industrial Mo–V based oxide catalysts for acrolein
oxidation to acrylic acid.

4 Catalytic Role of Constituents in Orthorhombic

Mo3VOx Based Catalyst for Propane
Ammoxidation5b
Nb, Te, and Sb are common additional elements for the orthorhombic Mo–V
based catalyst in order to enhance catalytic performance. However, the cata-
lysts prepared by the conventional method contain impurities (the most com-
mon of which has pseudohexagonal structure), and the true roles of each
element have been unclear.11 We have recently achieved the preparation of five
single-phase Mo–V based mixed metal oxides having the same orthorhombic
structure (Figure 1c), Mo-V-O, Mo-V-Te-O, Mo-V-Sb-O, Mo-V-Te-Nb-O and
Mo-V-Sb-Nb-O, by modifying the hydrothermal conditions (Table 2). It has
been confirmed that Te and Sb sit in the six-membered rings and Nb substitutes
for the Mo and/or V site.3
We tested these single-phase catalysts for the propane ammoxidation to
acrylonitrile (AN) and elucidated the roles of the constituent elements in the reac-
tion. Propane conversions and product distributions are compared at ca. 680 K,
the temperature at which the least stable Mo-V-O can exist without decompo-
sition (Table 3). All the catalysts were found to be active to the same extent for

Table 2 Elemental compositions and surface areas of orthorhombic Mo–V

based oxide catalysts.
Composition (Mo/V/Te or Sb/Nb) Surface area
Catalysts Bulka Surfaceb Calcination (m2 g1)
Mo-V-O 1.00/0.34 1.00/0.23/–/– N2, 773 K 6.5
Mo-V-Te-O 1.00/0.36/0.06 1.00/0.23/ Air, 553 K + 12.2
0.08/– N2, 873 K
Mo-V-Te-Nb-O 1.00/0.25/0.13/ 1.00/0.11/0.25/ N2, 873 K 19.8
0.11 0.16
Mo-V-Sb-O 1.00/0.33/0.06 1.00/0.16/ Air, 593 K + 13.8
0.08/– N2, 873 K
Mo-V-Sb-Nb-O 1.00/0.33/0.11/ 1.00/0.15/0.19/ N2, 873 K 11.2
0.11 0.20
a
Determined by ICP-AES.
b
Determined by XPS.
Structural Organization of Catalytic Functions 515
Table 3 Product distribution in the ammoxidation of propane over Mo–V
based catalysts.
Reaction Conversion (%)a Selectivity (%)b
temperature
Catalyst (K) C3H8 NH3 O2 AN PEN AcN COx
Mo-V-O 682 24.2 25.2 51.9 25.2 28.4 5.3 40.0
Mo-V-Te-O 683 47.7 23.0 59.9 38.8 22.1 3.5 35.4
Mo-V-Te-Nb-O 682 52.7 33.2 57.7 61.0 15.8 4.1 18.2
Mo-V-Sb-O 683 42.5 28.7 58.4 48.9 18.4 4.0 28.3
Mo-V-Sb-Nb-O 682 33.8 19.0 39.6 46.6 26.3 4.1 22.4
a
Reaction condition: amount of all catalysts, 0.5 g; total flow rate, 52.5 mL min1; gas composition,
C3H8/NH3/O2/He ¼ 5.7/8.6/17.1/68.6 (%).
b
AN, acrylonitrile; PEN, propene; AcN, acetonitrile. The selectivities to hydrogen cyanide, acetic
acid, and acrylic acid were less than 1%.

Figure 8 Proposed propane ammoxidation pathways used for calculation of rate

constants.

propane ammoxidation. The propane conversions of the Te-containing catalysts,

however, tended to be slightly higher than those of the Sb-containing catalysts.
Despite the fundamental differences in the catalyst compositions (for data see
Ref. 5b), the rates of propane oxidation per unit surface area of the catalysts were
close in the entire reaction temperature range of 633–713 K. It is, therefore,
rational to assume that Mo and V as common constituent elements largely
contribute to the creation of active sites for the activation of propane. On the
other hand, product selectivity is strongly dependent on the catalyst composi-
tions. Over the Mo-V-Te-O, Mo-V-Sb-O, Mo-V-Te-Nb-O and Mo-V-Sb-Nb-O
catalysts, AN was the major product, whereas overoxidation products such as
COx were mainly produced over the Mo-V-O catalyst.
In order to quantitatively clarify the role of each element in the course of the
propane ammoxidation, we compared five catalysts in terms of kinetics on the
basis of the proposed ammoxidation network (Figure 8), where propane is first
oxidized to propene, then propene is further converted to AN, and at the same
time the direct route from propane to AN and COx was also considered. We
calculated the initial reaction rate of propane at 683 K and the activation energy
for propane oxidation by fitting product (AN, propene and COx) distribution
 516

Table 4 Initial reaction rates, activation energy for C3H8 conversion, and simulated rate constants of Mo–V based oxide
catalysts.

Initial rate Acitivation energy Relative rate constanta

Catalyst (mmol m2 min1)a (kJ mol1)b k1 k2 k3 k4 k5 k6
Mo-V-O 9.6 131 0.84 5.77 2.46 13.17 0.02 0.14
Mo-V-Te-O 13.8 105 0.82 8.89 1.68 3.79 0.06 0.12
Mo-V-Te-Nb-O 12.6 131 0.81 10.37 0.46 4.20 0.02 0.17
Mo-V-Sb-O 12.6 122 0.84 9.82 1.23 5.06 0.02 0.14
Mo-V-Sb-Nb-O 9.6 107 0.86 7.20 1.99 2.34 0.03 0.11
a
Reaction conditions: reaction temperature, 683 K; W/F, 0.0012–0.019 gcat min mL1; C3H8/NH3/O2/He ¼ 5.7/8.6/17.1/68.6 (%).
b
Reaction conditions: reaction temperature, 653–683 K; W/F, 0.0012 gcat min mL1; C3H8/NH3/O2/He ¼ 5.7/8.6/17.1/68.6 (%).
Chapter 29
Structural Organization of Catalytic Functions 517
versus propane conversion obtained under various contact times (for details see
Ref. 5b). The results are summarized in Table 4. From these data, it is clear
again that Mo and V in the octahedral network in the orthorhombic structure
are responsible for the activation of propane. Te or Sb as a third constituting
element plays an important role in the allylic oxidation of the formed propene,
yielding a dramatic improvement in the AN selectivity. Moreover, the oxidative
decomposition of ammonia is also suppressed by Te or Sb. Nb, which seems to
have a dilution effect on V located in the network, bringing about a further
improvement of the AN selectivity, resulting in the Mo-V-Te-Nb-O catalyst
exhibiting the highest AN yield. The cooperative actions of each catalytic
element in the course of the ammoxidation of propane are very remarkable
and undoubtedly are sustained by the high-dimensional structure.

5 Turning Point in the Synthesis of Selective

Oxidation Catalysts
The selective oxidation catalysts based on metal oxides have become more and
more complicated due to the needs of achieving higher yield and extreme
selectivity. While it is inevitable that this trend will continue, at the same time
the creation of new types of effective catalysts is becoming more difficult. With
conventional preparation methods, it has been very hard to prepare crystalline
complex multi-elemental oxide catalysts in pure form, yet they will be very
important catalytic materials for the next generation of oxidation catalytic
systems. For instance, only the hydrothermal method could produce the
crystalline form of Mo3VOx phase materials, as described. As far as the
conventional preparation method has to be used in synthesizing complex metal
oxide catalysts, precise controls on many preparative factors are absolutely
necessary. But they are not always possible. We now need a clear design
methodology for catalytically active sites and spatial zones. The unit organi-
zation process to produce high-dimensional solid materials as demonstrated
here seems promising and is likely to become more important in the evolution
of metal oxide catalysts such as zeolite catalysts.

References
1. (a) G. Centi, F. Cavani and R. Trifiro, in Selective Oxidation by Hetero-
geneous Catalysis, ed. M.T. Twigg and M.S. Spencer, Kluwer Academic/
Plenum Publishers, New York, 2001; (b) B.K. Hodnett, Heterogeneous
Catalytic Oxidation, Wiley, New York, 2000.
2. (a) T. Uchikubo, K. Oshima, A. Kayou, T. Umezawa, K. Kiyono and
I. Sawaki, Mitsubishi Chem. Corp., Patent EP 529853, 1993; (b)
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EP 608838, 1994; (c) T. Uchikubo, K. Oshima, A. Kayou, M. Vaarkamp
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J. Am. Chem. Soc., 2002, 124, 5608.
518 Chapter 29
3. (a) H. Tsuji, K. Oshima and Y. Koyasu, Chem. Mater., 2003, 15, 2112; (b)
P. DeSanto Jr., D.J. Buttrey, R.K. Grasselli, C.G. Lugmair, A.F. Volpe Jr.,
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D.J. Buttrey, R.K. Grasselli, C.G. Lugmair, A.F. Volpe, B.H. Toby and
T. Vogt, Top. Catal., 2003, 23, 23; (d) R. Ross, B. Kratzheller and
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P. Koegerler and A.W.M. Dress, Coord. Chem. Rev., 2001, 222, 193; (c)
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CHAPTER 30

Designing Active Sites for

Surfaces: From Tightly Bound
to Loosely Anchored
THOMAS MASCHMEYER
Laboratory of Advanced Catalysis for Sustainability, School of Chemistry,
Building F11, The University of Sydney, NSW 2006, Australia

Our understanding of catalytic sites has increased exponentially over the last
two to three decades. It is now possible to speak of ‘designing’ a catalytic site
without exaggeration. Advances in experimental and theoretical techniques, for
example synchrotron-based in situ investigations or the sheer calculational
power now available, already in the humble desktop computer, have made this
possible.
There were many ‘turning points in catalysis’ along this path, not a few of
which were directly or indirectly associated with Prof. Sir John Meurig Thomas.
I have had the great fortune and pleasure to be ‘in his orbit’ one way or another
since 1995 – a circumstance which influenced me greatly scientifically as well as
personally. In the following pages it is my aim to re-visit,w as well as highlight
new, exciting developments in the fascinating area that is single site hetero-
geneous catalysis.
Homogeneous catalysts are more easily studied than their heterogeneous
counterparts, for the obvious reason that they are single site catalysts dissolved
in a well-defined reaction medium. Spectroscopic responses of active sites in
heterogeneous catalysts are often masked by the response of the bulk material
and it is very difficult to tease out structural information of the active site, even

w
The work involving metallocene grafting as well as cobalt acetate and diphenyl-
phosphinoferrocenyl (dppf ) tethering was my first contribution during my stay with Sir John as
Australian Bicentennial Research Fellow at the Royal Institution (RI); the second contribution
was the carbonyl cluster work discussed here, when EU Marie Curie joint fellow at the RI and
Cambridge with Sir John and Prof. Johnson.

519
520 Chapter 30
before catalysis, let alone during catalysis – particularly if the support is
amorphous and/or if the active sites are not crystallographically distinct.
One way of slightly mitigating this difficulty is to start with a well-defined
homogeneous species that can be immobilised in some way on a support
surface. With such an approach it is possible to select/design the active site
precursor with great confidence regarding its structural features and then to
match these to the expected surface reactivity. Approaching the design of
heterogeneous catalysts in this way, one is in a much more comfortable position
than when starting from, for example, a mixed-oxide species where the struc-
tural defects might be expected to be the catalytically active sites.
In the mid-1990s the preparation of isolated titanium species supported
by silica was a topic of great interest, in part due to the development of zeolite
TS-1 (an MFI structure with framework-substituted isolated titanium atoms).
Ti ions incorporated into the framework sites of silicalite I and II (i.e. TS-1 and
TS-2 respectively, introduced by the Enichem Company)1 as well as into the
framework sites of ZSM-12,2 ZSM-48,3,4 zeolite b5 and analogous microporous
alumino- (and silico-) phosphates such as ALPO-5, ALPO-11 and SAPO-5 all
show remarkable catalytic properties.6,7
However, one disadvantage of these titano-microporous catalysts was, and
is, that their pore dimensions are too small to allow access to bulky reactants of
the kind that dominate most of the chemical transformations which are of
central importance in the fine-chemical and pharmaceutical industries. A
significant step forward was reported8,9 with the preparation and use of
Ti-MCM-41 in which the Ti is incorporated (during synthesis) in the frame-
work of mesoporous SiO2 having a pore diameter of ca. 30 Å (see Figure 1).
It appeared that either titanol or titanyl species were the active sites, but it
was difficult to prepare them with confidence. By extending the concepts of
what has come to be known as interfacial co-ordination chemistry11 and of
surface organometallic chemistry,12,13 we grafted titanocene dichloride onto the
totally accessible inner surfaces of siliceous MCM-41 in the presence of a base,
as schematised in Figure 2.
The resulting material, with well-separated, well-defined, high surface concen-
trations of Ti-containing active sites, exhibited very high catalytic performance.
By using such a well-defined organometallic precursor it was possible (a) to
predict what would happen chemically during the grafting process and (b) to
design the system in such a way that one was confident of having isolated sites
which could then be interrogated with the synchrotron radiation technique
EXAFS (extended X-ray absorption fine structure) to determine the nature of
the site unequivocally.
Titanocene dichloride is superior to both TiCl4 and Ti(OR)4 as a grafting
reagent since, with both of the latter there is a marked tendency for oligomeric
titano-oxo species and/or some anatase by-products to be formed during the
grafting. This is circumvented by the titanocene dichloride method as the
relatively stable cyclopentadienyl ligands protect the titanium centre and,
hence, prevent either dimerisation and/or oligomerisation. Moreover, with
TiCl4, the evolved HCl is potentially damaging to the siliceous MCM-41,
Designing Active Sites for Surfaces 521

Figure 1 Illustration of titanocene dichloride diffusing into a channel of MCM-41.10

whereas using our methodology the evolved HCl is scavenged by an amine

rendering it harmless.
Furthermore, by then looking at this system under in situ reaction condi-
tions, it is possible to study the active site during reaction, thereby following the
course of action of the whole reaction (given that the products of the reaction
were analysed as well).
By following the pre-edge peak in the XANES (X-ray absorption near edge
structure) region, it was possible to detect when the co-ordination environment
changed from four- to six-fold co-ordination. Together with the EXAFS
analysis we could categorically state that the titanium centres were atomically
dispersed (as expected since the cyclopentadienyl ligands were to prevent dimer-
or oligomerisation of the titanium species) and that they were surrounded by
four equidistant oxygen atoms before catalysis and by the same four oxygens as
well as two additional oxygens at a longer distance during catalysis. The four-
co-ordinated state was entirely reversible. There was no evidence of the much
shorter titanyl oxygen, neither in terms of an average distance that would be
less than the one expected for a Ti–O bond in an oxide (based on crystal
structure data), nor in terms of atomic density (i.e. we did find four not three
oxygens). The two oxygens at a larger distance during catalysis are clearly due
522 Chapter 30

Figure 2 Illustration of the surface reactions associated with the grafting of titanocene
dichloride.10

to the substrates (cf. Figure 2b). Also, inspect Figure 3 to assess the quality of
the fit between the model and raw data.
Following on from this line of thinking the next step then is not only to use
well-defined molecular precursors to generate well-defined sites after calci-
nation, but also to use these as functional elements in their own right. Here,
the tethering approach comes into play, where for example a well-defined
Designing Active Sites for Surfaces 523

Figure 3 (a) XANES and (b) EXAFS fits corresponding to isolated titanol surface
groups.10

trimeric cobalt acetate species is anchored onto a silica surface derivatised with
carboxylate groups (cf. Figure 4).14
This catalyst is very active for the conversion of cyclohexane to cyclohexanol
and cyclohexanone, using an organic peroxide. Again, investigation by in situ
EXAFS, using the first reported flow cell that allowed for measurement of
X-ray diffraction as well as EXAFS during catalysis, simulating a fixed bed
reactor, was able to illuminate an unsuspected mode of action of the catalyst
(cf. Figure 5).
The in situ EXAFS data clearly illustrated that the co-ordination environ-
ment of the cobalt centres had changed and the trimer underwent a contraction,
due to the loss of acetates which were replaced by bridging oxygen groups
524 Chapter 30

(a) (b)

CH3 py
C O
O CH3
CH3 O Co C
C O O
O O O C
py Co O N
O Co Si
py
O O
C O
CH3 C

CH3

Figure 4 (a) A space-filling model of the trimeric cobalt acetate species, clearly
showing the central active site and (b) an illustration of the tethered
catalysts inside an MCM-41 mesopore.

Figure 5 Structure of the tethered cobalt trimer after immobilisation and during
catalysis, as derived from in situ EXAFS, using a flow cell.

(most likely derived from the various oxygenated species associated with the
conversion of cyclohexane to the corresponding alcohol and ketone).
The next step was not only to use the grafted or tethered species on its own,
but also to make use of its surroundings, i.e. to use the fact that the pore in which
it sat presented a confinement of the active site, thereby reducing the degrees of
freedom available to the system, much like the case in an enzyme (cf. Figure 6).
The catalyst of choice here was a chiral amino-derivative of the diphenyl-
ferrocenyl palladium dichloride complex (cf. Figure 7). Here it was possible to
influence the chemistry to a very significant degree. The reaction of cinnamic
acid methyl ester with benzylamine produces two regio-isomers, one of which is
Designing Active Sites for Surfaces 525

Auxilliary Directing
41
Group M-
MC

Chiral Directing
Group Reactant

Through-Space
Interactions
Catalytic Centre

“Chiral Space”

Figure 6 A schematic illustrating a generic model of the confined chiral amino-

derivative of the diphenylferrocenyl palladium dichloride complex catalyst.15

Figure 7 (a) The chiral amino-dppf ligand and (b) complexed and anchored inside
MCM-41.

chiral. Therefore, a total of three isomers are obtained and it is possible to

probe in just one reaction, both regio- and enantio-selectivity.
When tethering the complex onto a silica surface of a solid silica particle the
enantioselectivity increased significantly compared to that of the homogeneous
counterpart, however, when it was anchored inside a mesoporous channel the
increase in selectivity became remarkable, i.e. increasing the branched product
from 2 to 60% and the enantiomeric excess (ee) from 65 to 95%! Computa-
tional modelling showed that the catalyst effectively ‘curls up’ inside the pore,
leading to the reduced degrees of freedom (see Figure 8).16
526 Chapter 30

O H2N
+
O

40° C, cat.
THF

P P
Pd

NH

HN

R&S

Figure 8 The isomers generated during the allylic amination reaction.

So far, we had looked at complexes of one metal centre; what about those of
many centres, such as mono- and bi-metallic carbonyl clusters? Such clusters,
especially if charged, would be easily persuaded to stay on a silica, or other
oxide, surface. However, by themselves as fully saturated clusters they are not
known to exhibit remarkable catalytic properties. This might be a different
situation if one were to ‘denude’ them of the carbonyl ligands and create mono-
disperse nanoparticles, supported on oxide surfaces, using vacuum thermo-
lysis.17 Indeed, it is possible to follow such removal of the carbonyls with in situ
infrared spectroscopy (cf. Figure 9).
Starting from such well-defined precursors is a much more precise route
compared to the more commonly employed deposition of metal salts, followed
by their high-temperature reduction with hydrogen. Here, we were able to
design in a pre-determined way the size, dispersion and composition of the alloy
nanoparticles. Furthermore, we could engineer stability into the particles as the
copper was to act as a ‘glue’ (being oxophilic) for the surface anchoring of the
Designing Active Sites for Surfaces 527

Figure 9 FTIR-spectra of a copper–ruthenium cluster being exposed to increasing

temperatures under high vacuum, showing clearly the disappearance of the
carbonyl groups in the region of 2100–1700 cm
1.

Figure 10 (i) Crystal structure of the bimetallic carbonyl cluster used for (ii) depo-
sition into mesoporous MCM-41 employing vacuum thermolysis and (iii)
after silica vitrification. The labels a–d show clearly that even after sinte-
ring the particles remain in their original positions.

nobler ruthenium – translating into unmatched stability, even after support

vitrification (cf. Figure 10).
Again, in situ EXAFS allowed us to follow the transformation of the species
from carbonyl cluster to alloy particle with great precision (cf. Figure 10),
Figure 11.
Finally, we were able to correlate successfully the Ru–Ru distances from our
EXAFS analysis with those from computational modeling. The initial
528 Chapter 30

Figure 11 Plot of the atomic density for the (a) Ru and (b) Cu K-edges as a function
of temperature, (c)–(f ) the corresponding simultaneous EXAFS refinement
after heating to 180 1C, using one common bimetallic model structure,
reducing the degrees of freedom to a minimum – and well in excess of what
renders the analysis statistically meaningful.18,19

approach based on molecular mechanics did yield good agreement for the
distances associated with Cu, but the Ru–Ru distances were too long. When
employing ab initio density functional theory (DFT) level calculations, we were
able to replicate the main characteristics of the EXAFS, including the ruthe-
nium bond distances – due to the surprising result that the carbide carbon
moves out of the cluster to the surface of the particle, illustrating beautifully the
power in the combination of experiment and computation (cf. Figure 12).20
Although successful, these methods all rely on either the destruction by
oxidation (titanocene dichloride) or vacuum thermolysis (carbonyl clusters) of
our catalyst precursors, or need a complex chemical modification (dppf ligand)
of a homogeneous complex which we know works well already – such modi-
fications can enhance, but also reduce the enantioselective prowess of a chirally
selective catalyst. Hence, the next step in the exploration of the design of active
sites for heterogeneous catalysts was to immobilise well-defined homogeneous
catalysts without any chemical modification. This was possible by using
Designing Active Sites for Surfaces 529

Figure 12 Modelling unexpected EXAFS results successfully with DFT calculations.

electrostatic interactions which served to anchor the catalyst to a charged

surface (aluminosilicate). Now the effort was directed along two main paths:
(1) fine-tuning of the support surface in terms of charge and surface area and
(2) tuning the solvent to the catalyst and support interaction. It turns out that
the energetic differences that control enantioselectivity (B4 kJ mol
1)21 are of a
very similar dimension to those responsible for the complex remaining on the
surface,22 rather than leaching from it back into solution. As a consequence,
solvent effects seem to have a great influence on the enantioselectivity of any
such electrostatically immobilised system.
Our most successful result in this area so far involves the electrostatic
immobilization of a rhodium catalyst, comprised of two monophos ligands
and (initially) a cyclooctadiene (COD) group (cf. Figure 13).
We found that as the polarity of a solvent increased, the leaching of the
complex also increased; furthermore, in low polarity solvents the enantio-
selectivity was often very poor for the systems we studied (e.g. enantioselective
hydrogenation of dimethyl itaconate). Surprisingly, water acts as an excellent
solvent for these systems as it is too polar and the catalyst remains happily
on the surface of the support, while the catalysis proceeds with very high
enantioselectivities, rendering the system as selective and reactive as the homo-
geneous equivalent, with the added bonus of ease of separation and recyclability.
This then paves the way for reactions in which these immobilised catalysts
can be used in combination with a second catalyst (e.g. an enzyme) in
water as solvent, i.e. an aqueous cascade reaction, thereby using a benign
solvent as well as reducing the number of separation steps during synthesis
(cf. Figure 14).
530 Chapter 30
20
18
MeOH
16
14
Rh loss (%)

12
10
8 2-PrOH

6 EtOAc
4 CH2Cl2
2
MTBE Water
0
0.0 0.2 0.4 0.6 0.8 1.0 1.2
ETN

Figure 13 Leaching behaviour of [(monophos)2Rh(COD)]1 immobilised on the meso-

porous sponge Al-TUD-1 in various solvents plotted as a function of their
polarity.

O N
P
O
Rh+
O
P
N
O
HO O O O OH
Al Si Al Si

1-AlTUD-1 Acylase I
Acylase I AM
Phosphate buffer

O
O 5 bar H2, S/C = 200 H OH
N N
H O 1-AlTUD-1 H O
0.05 M

Intermediate Conv. = 100% ee= 95%

Overall Conv. = 98% ee > 98%

Figure 14 A compartmentalised cascade reaction: [(monophos)2Rh(COD)]1 immo-

bilised on the mesoporous sponge Al-TUD-1, working together with the
enzyme acylase I to achieve outstanding conversions and selectivity.

This approach relies on one main condition, i.e. the two catalysts do not
interfere with one another – however, this condition may not always be
satisfied. Therefore, it would be useful to devise a generic method by which
one could encapsulate any catalyst to keep it separate from any other catalyst
and thereby circumvent any limitations on cascade reactions imposed by
catalyst incompatibility (see Figure 15).
Designing Active Sites for Surfaces 531

Figure 15 Formation of hollow nanocapsules (f ) through successive adsorption of

positively (orange) and negatively (blue) charged polyelectrolytes onto
colloidal templates (a–d), followed by their dissolution (e–f ).23

OH OAc

CALB, vinyl acetate

fast
(R )-enantiomer

"100%"

Coated
Zeolite H-Beta
Nanoreactors

OH OAc

CALB, vinyl acetate

slow (S )-enantiomer

Figure 16 DKR of 2-phenyl ethanol, as catalysed by zeolite b and CALB.

One such example, where catalyst incompatibility exists, is that of the

dynamic kinetic resolution (DKR) of secondary alcohols. Here, the racemi-
sation catalyst of choice (zeolite b) interacts destructively with the enzymatic
catalyst (Candida Antarctica lipase B, CALB) (Figure 16).
532 Chapter 30

Figure 17 Fluorescence micrograph (lex ¼ 450–490 nm) of fluorescence-tagged zeolite

(orange) surrounded by a polyelectrolyte capsule (blue).

We encapsulated the zeolite with a polyelectrolyte membrane as described

above and were able to record a much improved enantioselective performance
(up by 25 percentage points), while maintaining largely undiminished racemi-
sation activity. In order to visualise the zeolite particles inside the polyelectro-
lyte capsule, we ion-exchanged the zeolites with a fluorescent orange dye,
[Ru(bipy)3]21, that is distinct from the inherent fluorescence of the poly-
electrolyte capsule (which is blue) (cf. Figure 17).24
This contribution has explored how it is possible to design and prepare
reliably various single site heterogeneous catalysts by a number of methods,
ranging from calcination to vacuum thermolysis and from tethering via elec-
trostatic immobilisation to encapsulation. In every case a well-defined mole-
cular precursor was used to design the eventual heterogeneous catalytic single
site, showcasing the incredible variety of possibilities, challenges and opportu-
nities that lie within this branch of catalysis.

Acknowledgements
Clearly the work presented here is the work of many, as indicated by the
references – however, above all it has been due in no small measure to the
Designing Active Sites for Surfaces 533
inspirational presence and the direct as well as indirect contributions of Prof.
Sir John Meurig Thomas over the years.

References
1. M. Tamarasso, G. Parego and B. Notari, 1983, U.S. Patent 4410501.
2. A. Tuel, Zeolites, 1995, 15, 236.
3. D.P. Serrano, H.X. Li and M.E. Davis, J. Chem. Soc., Chem. Commun.,
1992, 745.
4. K.M. Reddy, S. Kaliaguine, A. Sayari, A.V. Ramaswamy, V.S. Reddy and
L. Bonneviot, Catal. Lett., 1994, 23, 175.
5. M.A. Camblor, A. Corma and J. Perez-Pariente, Zeolites, 1993, 13, 82.
6. N. Ulagappan and U. Krishnasamy, J. Chem. Soc., Chem. Commun., 1995,
373.
7. A. Tuel and Y. Ben-Taarit, J. Chem. Soc., Chem. Commun., 1994, 1667.
8. P.T. Tanev, M. Chibwe and T.J. Pinnavaia, Nature, 1994, 368, 321.
9. G. Sankar, F. Rey, J.M. Thomas, G.N. Greaves, A. Corma, B.R. Dobson
and A.J. Dent, J. Chem. Soc. Chem. Commun., 1994, 2279.
10. T. Maschmeyer, F. Rey, G. Sankar and J. M. Thomas, Nature, 1995, 378,
159.
11. S. Scott and J. M. Basset, J. Mol. Catal., 1994, 86, 5.
12. A. Zecchina and C. Otero-Arean, Catal. Rev. Sci. Eng., 1993, 35, 261.
13. Comprehensive Organometallic Chemistry, ed. G. Wilkinson, F.G.A. Stone
and E.W. Abel, Pergamon, Oxford, 1982.
14. T. Maschmeyer, R.D. Oldroyd, G. Sankar, J.M. Thomas, I.J. Shannon,
J.A. Klepetko, A.F. Masters, J.K. Beattie and C.R.A. Catlow, Angew.
Chem., Int. Ed. Engl., 1997, 36, 1639.
15. B.F.G. Johnson, S.A. Raynor, D.S. Shephard, T. Maschmeyer,
J.M. Thomas, G. Sankar, S. Bromley, R. Oldroyd, L. Gladden and
M.D. Mantle, Chem. Commun., 1999, 1167.
16. S. Bromley and C.R.A. Catlow (unpublished results).
17. D.S. Shephard, T. Maschmeyer, G. Sankar, J.M. Thomas, D. Ozkaya,
B.F.G. Johnson, R. Raja, R.D. Oldroyd and R.G. Bell, Chem. – Eur. J.,
1998, 4, 1214.
18. R.W. Joyner, K.J. Martin and P. Meehan, J. Phys. C – Solid State Phys.,
1987 20, 4005.
19. P.J. Ellis and H.C. Freeman, J. Synchrotron Rad., 1995, 2, 190.
20. S.T. Bromley, G. Sankar, C.R.A. Catlow, T. Maschmeyer, B.F.G. Johnson
and J.M. Thomas, Chem. Phys. Lett., 2001, 340, 524.
21. C.R. Landis and J. Halpern, J. Am. Chem. Soc., 1987, 109, 1746.
22. S. Feldgus and C.R. Landis, J. Am. Chem. Soc., 2000, 122, 12714.
23. E. Donath, G.B. Sukhorukov, F. Caruso, S.A. Davis and H. Mohwald,
Angew. Chem., Int. Ed., 1998, 37, 2201.
24. A. Fois, A.F. Masters and Th. Maschmeyer, Catalysis Today, (submitted).
CHAPTER 31

Polynuclear Transition Metal

Cluster Complexes Containing
Tin Ligands: Precursors to New
Heterogeneous Nano-Catalysts
RICHARD D. ADAMS AND BURJOR CAPTAIN
Department of Chemistry and Biochemistry, University of South Carolina,
631 Sumter Street, Columbia, SC 29208, USA

1 Introduction
Tin has been shown to be a useful modifier of platinum group metals for
heterogeneous catalysts used for petroleum reforming,1 catalytic hydrogena-
tions2 and dehydrogenations.3 It is believed that the tin helps to anchor metallic
nanoparticles onto nanoporous supports in a highly dispersed and uniform
manner resulting in catalysts with higher activities.2 Tin ligands have been
shown to improve the product selectivities of homogeneous transition metal
catalysts.4
Triphenylstannane is known to undergo facile oxidative addition reactions at
the metal atoms of unsaturated metal complexes to yield products containing
triphenyltin and hydride ligands (Equation (1)).5 Palladium complexes will
dehydrogenate stannanes catalytically to yield polystannanes.6

P(C6H11)3

Pt[P(C6H11)3]2 + HSnPh3 H Pt SnPh3 ð1Þ

P(C6H11)3

534
Polynuclear Transition Metal Cluster Complexes 535

2 Reactions of Carbido–Pentarutheniumcarbonyl
Clusters with Triphenylstannane
We have shown that triphenylstannane Ph3SnH is an excellent reagent for
introducing phenyltin ligands into polynuclear metal carbonyl complexes.
Our studies began with our investigation of the reaction of Ru5(CO)15(m5-C),
1 with Ph3SnH.7 In the presence of ultraviolet (UV) irradiation 1 reacts with
Ph3SnH by reaction of the SnH and cleavage of one of the apical-basal Ru–Ru
bonds in the cluster of 1 to yield the adduct Ru5(CO)15(SnPh3)(m5-C)(m-H), 2
(Equation (2)).
H
Ru Ru
Ru
Ru Ph3SnH
C Ru C Ru
Ru Ru ð2Þ
hν
Ru

Ru
1 2
SnPh3

The benzene derivative of 1, Ru5(CO)12(C6H6)(m5-C), 3 reacts with Ph3SnH at

68 1C to yield two products: Ru5(CO)11(SnPh3)(C6H6)(m5-C)(m-H), 4 and
Ru5(CO)11(SnPh3)2(C6H6)(m5-C)(m-H)2, 5 formed by the addition of one and
two equivalents of Ph3SnH which is accompanied by the loss of one and two
CO ligands, respectively.7 Both contain square pyramidal Ru5 clusters with one
and two SnPh3 groups, respectively (Equation (3)). There was no evidence of
the formation of stable open cluster complexes in this reaction, as was found in
the reaction of 1 with Ph3SnH.
SnPh3
Ru Ru H H Ru H

Ru Ru Ph3SnH Ru Ru Ru Ru
C C + C
Ru Ru 68 °C Ru Ru Ru Ru
C6H6 Ph3Sn C6H6 Ph3Sn C6H6

3 4 5
ð3Þ

At 68 1C, compound 4 is slowly converted to the new compound Ru5(CO)11

(C6H6)(m4-SnPh)(m3-CPh), 6 by loss of benzene and a shift of one of the phenyl
groups from the tin ligand to the carbido carbon atom to form a triply bridging
benzylidyne ligand. The tin ligand is transformed into a novel quadruply
bridging stannylyne ligand (see Figure 1).
The reactions of 1 and 3 with Ph3SnH at 127 1C yielded multiple tin addi-
tion products. Ru5(CO)10(SnPh3)(m-SnPh2)4(m5-C)(m-H), 7 was the principal
536 Chapter 31

Figure 1 Diagram of the structure of 6.

Figure 2 Diagram of the structure of 7.

product obtained from the reaction of 1 with Ph3SnH at 127 1C.7 Compound 7
contains five tin ligands. Four of these are SnPh2 groups bridging each edge of
the base of the Ru5 square pyramidal cluster (see Figure 2). The fifth tin ligand
was a SnPh3 group that was terminally coordinated to one of the ruthenium
atoms in the base of the square pyramidal cluster. The SnPh2 groups were
formed by the cleavage of one phenyl ring from the Ph3SnH. This phenyl ring
was combined with the tin hydrogen atom and was eliminated as benzene. The
Polynuclear Transition Metal Cluster Complexes 537
cleavage of a phenyl ring to yield a bridging SnPh2 ligand was subsequently
found to be a preferred pathway at high temperatures and would be the source
of a wide variety of high nuclearity transition metal–tin cluster complexes.
Dialkyl- and diaryltin groups are known to be effective bridging ligands in
polynuclear metal carbonyl complexes.8
The reaction of 3 with an excess of Ph3SnH at 127 1C led to formation of two
new high-nuclearity cluster complexes: Ru5(CO)8(m-SnPh2)4(C6H6)(m5-C), 8,
and Ru5(CO)7(m-SnPh2)4(SnPh3)(C6H6)(m5-C)(m-H), 9. Both compounds con-
tain square pyramidal Ru5 clusters with four SnPh2 groups bridging the edges
of the square base. Like 7, compound 9 contains one terminal SnPh3 ligand.
When treated with CO at 45 atm, compound 9 was converted to 7 by replace-
ment of the benzene ligand with three CO ligands.

3 Reaction of H4Ru4(CO)12 with Ph3SnH

The tetrahedral tetrahydridotetraruthenium cluster complex H4Ru4(CO)12, 10
reacts with Ph3SnH to give tin containing tetraruthenium cluster complexes in
which the Ru4 cluster has been converted into a square planar form.9 Two of
these new ruthenium–tin cluster complexes are Ru4(CO)12(m4-SnPh)2, 11 and
Ru4(CO)8(m4-SnPh)2(m-SnPh2)4, 12 (see Equation (4)). Both complexes contain
two quadruply bridging SnPh stannylyne ligands which produce an octahedral
shaped Ru4Sn2 cluster. All of the hydrido ligands were lost in the formation of
10 and 11 mostly by combining with some of the phenyl groups that were
eliminated from Ph3SnH to from the SnPh ligands. To form 12, four CO
ligands were also replaced by SnPh2 ligands that bridge each of the four Ru–Ru
edges of the Ru4 square (see Figure 3).

Figure 3 Structural diagram of compound 12.

538 Chapter 31

Ph Ph
Ru Sn Sn
Ph3SnH Ph2Sn
H H H Ru SnPh2
Ru
125 °C Ru Ru
+ Ru Ru
Ru Ru Ru
Ru Ru Ph2Sn
SnPh2
H Sn Sn
Ph Ph
H4Ru4(CO)12
11 12
ð4Þ

4 Reactions of Rhodium and Iridium Carbonyl Cluster

Complexes with Triphenylstannane
The reactions of Rh4(CO)12 and Ir4(CO)12 with Ph3SnH have yielded the first
rhodium–tin and iridium–tin cluster complexes: M3(CO)6(m-SnPh2)3(SnPh3)3, 13
(M=Rh) and 14 (M=Ir).10 These complexes contain triangular M3 clusters with
three bridging SnPh2 ligands and three terminal SnPh3 ligands (see Figure 4).
The Rh–Rh bond distances are unusually long. Molecular orbital calculations of
13 have shown that the cluster is stabilized by strong Rh–Sn bonding. The direct
Rh–Rh interactions are delocalized and weak, as shown by the contour diagram
of the highest occupied molecular orbital (HOMO) of 13 shown in Figure 5.
Interestingly, the reaction of 13 with Ph3SnH yielded the complex
Rh3(CO)3(SnPh3)3(m-SnPh2)3(m3-SnPh)2, 15 that contains an unprecedented
eight phenyltin ligands including the first examples of triply bridging SnPh
ligands (see Figure 6).

Figure 4 Diagram of the structure of 13.

Polynuclear Transition Metal Cluster Complexes 539

Figure 5 Diagram of the HOMO in 13.

Figure 6 Diagram of the structure of 15.

5 Dirhenium Cluster Complexes Containing

Diphenyltin Ligands that add Platinum and
Palladium to the Re–Sn Bonds
Reaction of Re2(CO)8[m-Z4-C(H)¼C(H)Bun](m-H) with Ph3SnH yielded the new
compound Re2(CO)8(m-SnPh2)2, 16 that contains two SnPh2 ligands bridging two
Re(CO)4 groups (see Figure 7).11 The reaction of 16 with Pd(PBut3)2 yielded the
bis-Pd(PBut3) adduct Re2(CO)8(m-SnPh2)2[Pd(PBut3)]2, 17 that contains the first
examples of Pd(PBut3) groups bridging transition metal–tin bonds, in this first case
they are Re
Sn bonds (see Figure 8). Fenske–Hall molecular orbital calculations
show that the Pd(PBut3) groups form three-centre two-electron bonds with the
540 Chapter 31

Figure 7 A diagram of the structure of 16.

Figure 8 A diagram of the structure of 17.

neighbouring rhenium and tin atoms (see Figure 9). The decrease in electron
density in the vicinity of the unbridged Re–Sn bond explains why these two bonds
increase in length when the Pd(PBut3) groups are added to their neighbouring Re–
Sn bonds. The mono- and bis-Pt(PBut3) adducts, Re2(CO)8(m-SnPh2)2[Pt(PBut3)],
18 and Re2(CO)8(m-SnPh2)2[Pt(PBut3)]2, 19 were formed when 16 was treated with
Pt(PBut3)2.

6 Reactions of Triosmium Carbonyl Cluster

Complexes with Triphenylstannane
It was shown many years ago that triphenylstannane reacts with Os3(CO)11
(NCMe) to yield the triphenyltin complex Os3(CO)11(SnPh3)(m-H), 20.12 Com-
pound 20 is also obtained from the reaction of Os3(CO)12 with Ph3SnH
in refluxing xylene (140 1C), but in addition a new triosmium complex
Os3(CO)9(m-SnPh2)3, 21 is also obtained. Compound 21 consists of a central
Os3 triangle with three bridging SnPh2 groups, one on each of the three Os–Os
bonds (Figure 10).13
Polynuclear Transition Metal Cluster Complexes 541

PH3
Pd
Re

H2Sn SnH2

Re
Pd
H3P

Figure 9 The 3ag HOMO of the Re2(CO)8(m-SnH2)2[Pd(PH3)]2 model complex of 17.

Figure 10 A diagram of the structure of 21.

Two new cluster complexes Os3(CO)12(Ph)(m3-SnPh), 22 and Os4(CO)16

(m4-Sn), 23 were formed when the complex 20 was heated to reflux in toluene
solvent in the presence of an atmosphere of CO.14 Compound 22 contains three
osmium atoms with a triply bridging SnPh group (see Figure 11). Benzene was
eliminated in the formation of 22 and the cluster was opened by cleaving two of
the Os–Os bonds. One of the phenyl groups was shifted from the tin atom to
one of the osmium atoms.
Compound 22 was transformed to 23 when a solution in octane solvent was
heated to reflux under a CO atmosphere. Biphenyl is a coproduct in this
542 Chapter 31

Figure 11 A diagram of the structure of 22.

Figure 12 A diagram of the structure of 23.

reaction. Compound 23 contains two Os2(CO)8 groups held together by a

naked quadruply bridging tin atom having a spiro-type structure for the five
metal atoms (see Figure 12). Two other new compounds Os2(CO)6
(m-SnPh2)2(SnPh3)2, 24 and the monoosmium complex HOs(CO)4(SnPh3), 25
were formed from the reaction of 22 with an additional quantity of HSnPh3.
Compound 24 contains only two osmium atoms linked by an Os–Os bond and
two bridging SnPh2 ligands. Each osmium atom in 24 also contains one
terminal SnPh3 ligand. Compound 25 contains only one osmium atom, one
SnPh3 ligand and a terminal hydrido ligand cis to the SnPh3 ligand in the six-
coordinate pseudo-octahedral complex (see Figure 13).
As observed with 19, the reaction of 21 with Pt(PBut3)2 provided a Pt(PBut3)
adduct Os3(CO)9[Pt(PBut3)](m-SnPh2)3, 26 by adding a Pt(PBut3) group across
one of the metal–tin bonds (see Scheme 1).13 The osmium and tin atoms lie in a
Polynuclear Transition Metal Cluster Complexes 543

Figure 13 A diagram of the structure of 25.

Ph2
Ph2 But3P
Sn
40 °C Sn 68 °C Pt SnPh2
+ Pt(PPh3)4 + Pt(PBut3)2
Os Os
Os Os Os Os
Ph
Ph2Sn Os Sn – "Pt(PPh3)2" – PBut3
PPh3 120 °C Ph2Sn Os SnPh2 Ph2Sn Os SnPh2
Pt
27 Ph PPh3 21 26

Scheme 1

plane while the Pt(PBut3) group is displaced slightly out of that plane. By contrast
the reaction of Pt(PPh3)4 with 21 yielded the complex Os3(CO)9[Pt(Ph)(PPh3)2]
(m-SnPh2)2(m3-SnPh), 27 in which a Pt(PPh3)2 was inserted into one of
the Sn–C bonds to one of the phenyl groups. The resultant Pt(Ph)(PPh3)2
group is terminally bonded to one of the tin atoms. The platinum atom of the
Pt(Ph)(PPh3)2 group has a square planar geometry with the two PPh3 ligands in
cis coordination sites. Interestingly, when heated, compound 27 reverts to 21 by
expelling the Pt(PPh3)2 fragment.

7 The Activation of the Hydride Complex

HOs(CO)4(SnPh3) by Pt(PBut3)2
Because of our successful studies of the interactions of Pt(PBut3) groups with
M–M15 and M–Sn bonds,11,13 it was decided to investigate the reaction of
compound 25 with Pt(PBut3)2. This reaction resulted in the formation of the
compound PtOs(CO)4(SnPh3)(PBut3)(m-H), 28 that can be viewed as a Pt(PBut3)
adduct of 25 (see Figure 14).16 There is no significant bonding inter-
action between the platinum atom and the tin atom in 28, but there is a
544 Chapter 31

Figure 14 A diagram of the molecular structure of 28.

Figure 15 A diagram of the molecular structure of 29.

substantial interaction with the hydrido ligand and a bond was formed be-
tween the platinum atom and the osmium atom, Pt–Os ¼ 2.7628(3) Å. The
hydrido ligand is bonded both to the Pt and Os atoms as a bridging ligand,
Pt(1)–H(1) ¼ 1.92(6) Å and Os(1)–H(1) ¼ 1.95(6) Å. Interestingly, it was found
that 28 readily reacts with phenylacetylene PhC2H to yield the alkenyl com-
plex PtOs(CO)4(SnPh3)(PBut3)[m-HCC(H)Ph], 29 formed by the insertion of
the PhC2H into the Pt–H and Os–H bonds to the bridging hydrido ligand with
transfer of the hydrido ligand to the phenyl-substituted carbon atom (see
Figure 15). The alkenyl ligand is p-bonded to the osmium atom and s-bonded
to the platinum atom. Interestingly, compound 25 does not react with PhC2H
even at 110 1C. Molecular orbital calculations have shown that there is a low
lying orbital on the platinum atom (see Figure 16) that most likely assists in the
addition of the PhC2H molecule to the complex and then facilitates its com-
bination with the hydrido ligand.
Polynuclear Transition Metal Cluster Complexes 545

O
t C
Bu 3P
Pt Os
H
SnPh3

Figure 16 Lowest unoccupied molecular orbital (LUMO) of 28 shows large empty

atomic orbital on the platinum atom.

8 Synthesis of Platinum Ruthenium Tin Cluster

Complexes from the Reaction of Triphenylstannane
with Platinum–Ruthenium Complexes
The reaction of the closed PtRu cluster complex PtRu5(CO)14(PBut3)(m-H)2
(m6-C), 30 with HSnPh3 yielded two trimetallic PtSnRu cluster complexes,
PtRu5(CO)13(PBut3)(m-H)3(SnPh3)(m5-C), 31 and PtRu5(CO)13(PBut3)(m-H)2
(m-SnPh2)(m6-C), 32.17 Complex 31 formed by a simple oxidative addition of
the SnH bond of the HSnPh3, but unlike its precursor 30, it has an open
structure in which the Pt(PBut3) group bridges an edge of the square base of the
square pyramidal Ru5 cluster. It contains a single SnPh3 ligand and three
bridging hydrido ligands. When heated to 97 1C, compound 31 is converted to
32 by cleavage of a phenyl group from the SnPh3 ligand and elimination of
benzene by its combination with one of the hydrido ligands (see Scheme 2). The
PtRu5 cluster then closes and the SnPh2 ligand adopts a bridging coordination
across one of the Ru–Ru bonds (see Figure 17).

9 Formation of a Highly Active and Selective

Hydrogenation Nano-Catalyst from a Platinum
Ruthenium Tin Precursor Complex
Thomas et al. have shown that platinum–ruthenium carbonyl cluster complexes
can be precursors to high quality bimetallic nanoparticles for catalytic hydro-
genations when activated in mesoporous silica.18 Recent studies have shown
that tin can have an important modifying effect on the catalytic activity of
ruthenium nanoparticles. It is thought that the oxophilic character of the tin
assists in the anchoring of the bimetallic tin containing particles to siliceous
supports.2 This anchoring effect helps to prevent aggregation/sintering proc-
esses that are common on silica and lead to catalyst deactivation.
In collaboration with Thomas and Raja, we have recently obtained evidence
that a combination of the three metals, platinum, ruthenium and tin, provides
as yet the best catalyst for the hydrogenation of dimethylterephthalate (DMT)
546 Chapter 31

PBut3

H Pt H
Ru Ru 97 °C
C Ru
Pt Ru C Ru
But3P Ru Ru
−C6H6 Ru
H H
Ru H SnPh2
Ru
SnPh3

31 32

Scheme 2

Figure 17 Diagram of the structure of 32.

O O H2 O O H2
MeO C C OMe MeO C C OMe HOH2C CH2OH

dimethyl terephthalate (DMT) dimethyl hexahydroterephthalate (DHMT) 1,4−cyclohexanedimethanol (CHDM)

Scheme 3

to 1,4-cyclohexanedimethanol (CHDM), a valuable reagent for the synthesis of

copolymers (see Scheme 3).19,20
The trimetallic PtSnRu5 cluster complex PtRu5(CO)15(m-SnPh2)(m6-C), 33
(see Figure 18) was deposited on mesoporous Davison 38 Å silica. All of the
ligands including the phenyl groups on the tin ligand are easily removed by
heating to 200 1C.19 HAADF TEM (high angle annular dark field trans-
mission electron microscopy) images of the silica revealed the presence of
Polynuclear Transition Metal Cluster Complexes 547

Figure 18 The structure of the molecular cluster PtRu5(CO)15(m-SnPh2)(m6-C), 33.

Figure 19 HAADF images of Ru5PtSn nanoclusters on Davison 38 Å silica (a) before

and (b) after catalysis.

nanoparticles 1–2 nm in size. XEDS (X-ray energy dispersive spectroscopy)

analysis of individual particles showed that their composition was precisely the
same as that of the precursor complex Ru5PtSn within experimental error. The
particles remain small during the catalysis. See the HAADF TEM images of
catalyst particles before and after use for the catalytic hydrogenation of DMT
to CHDM in Figure 19.
Figure 20 shows a comparison of the activity of some different combinations
of metals with ruthenium for the hydrogenation of DMT to CHDM. The
trimetallic Ru5PtSn clearly exhibits the best conversion and best selectivity of
all. This is a reaction of major commercial importance. Eastman prepares over
200 million pounds of CHDM per year for use in the synthesis of copolyesters
by a two-step reduction process of DMT.20
548 Chapter 31

Figure 20 A bar chart comparing the activity and selectivity of the Ru5PtSn catalyst
with other bi- and trimetallic catalysts for the hydrogenation of dime-
thylterephthalate.

Acknowledgments
We wish to acknowledge the many contributions of Erin M. Boswell, Wei Fu,
Robert Raja, Jack L. Smith, Jr., and Lei Zhu to this work. Special thanks to Sir
John Meurig Thomas for his valuable contributions to the catalysis work and
for his support, encouragement and friendship. With every best wish on his
75th birthday.

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Ruhl, Can. J. Chem., 1988, 66, 3120.
6. P. Braunstein and X. Morise, Chem. Rev., 2000, 100, 3541.
7. R.D. Adams, B. Captain, W. Fu and M.D. Smith, Inorg. Chem., 2002, 41,
5593.
8. D.J. Cardin, in Metal Clusters in Chemistry, vol 1, P. Braunstein, A. Oro,
P.R. Raithby (eds), Wiley-VCH, Weinheim, 1999, 48.
9. R.D. Adams, E. Boswell, B. Captain, Faraday Trans., 2007 (in press).
10. R.D. Adams, B. Captain, J.L. Smith Jr., M.B. Hall, C.L. Beddie and
C.E. Webster, Inorg. Chem., 2004, 43, 7576.
11. R.D. Adams, B. Captain, R.H. Herber, M. Johansson, I. Nowik,
J.L. Smith Jr. and M.D. Smith, Inorg. Chem., 2005, 44, 6346.
12. K. Burgess, C. Guerin, B.F.G. Johnson and J. Lewis, J. Organomet. Chem.,
1985, 295, C3.
13. R.D. Adams, B. Captain and L. Zhu, Organometallics, 2006, 25, 2049.
14. R.D. Adams, B. Captain and L. Zhu, Organometallics, 2006, 25, 4183.
15. (a) R.D. Adams, B. Captain, W. Fu, M.B. Hall, J. Manson, M.D. Smith
and C.E. Webster, J. Am. Chem. Soc., 2004, 126, 5253; (b) R.D. Adams, B.
Captain, W. Fu and M.D. Smith, J. Am. Chem. Soc., 2002, 124, 5628; (c)
R.D. Adams, B. Captain and L. Zhu, Organometallics, 2006, 45, 430; (d)
R.D. Adams, B. Captain, W. Fu, P.J. Pellechia and M.D. Smith, Angew.
Chem. Int. Ed., 2002, 41, 1951; (e) R.D. Adams, B. Captain, W. Fu, P.J.
Pellechia and M.D. Smith, Inorg. Chem., 2003, 42, 2094; (f) R.D. Adams,
B. Captain, W. Fu, P.J. Pellechia and L. Zhu, Inorg. Chem., 2004, 43, 7243;
(g) R.D. Adams, B. Captain, M.B. Hall, J.L. Smith Jr. and C.E. Webster,
J. Am. Chem. Soc., 2005, 127, 1007; (h) R.D. Adams, B. Captain, P.J.
Pellechia and J.L. Smith Jr., Inorg. Chem., 2004, 43, 2695.
16. R.D. Adams, B. Captain and L. Zhu, J. Am. Chem. Soc., 2006, 128, 13672.
17. R.D. Adams, B. Captain and L. Zhu, Inorg. Chem., 2005, 44, 6623.
18. J.M. Thomas, B.F.G. Johnson, R. Raja, G. Sankar and P.A. Midgley, Acc.
Chem. Res., 2003, 36, 20.
19. A.B. Hungria, R. Raja, R.D. Adams, B. Captain, J.M. Thomas,
P.A. Midgley, V. Golvenko and B.F.G. Johnson, Angew. Chem. Int. Ed.,
2006, 45, 4782.
20. S.R. Turner, Polym. Sci., 2004, 42, 5847.
CHAPTER 32

Selective Oxidation Using Gold

and Gold–Palladium
Nanoparticles
GRAHAM J. HUTCHINGS
School of Chemistry, Cardiff University, Main College, Park Place, Cardiff
CF10 3AT, UK

1 Introduction
The new field of oxidation catalysis based on gold nanoparticles is the focus of
this article. Until recently gold has been overlooked as a key component of both
homogeneous and heterogeneous catalysts. However, the observation that
nanocrystalline gold supported on oxides is an effective catalyst for low
temperature carbon monoxide oxidation has provided the impetus for research-
ers to open up new directions in oxidation catalysis, namely selective oxidation
of alkenes and alcohols. In this paper, the use of gold and gold–palladium
nanoparticles as catalysts for both the direct formation of hydrogen peroxide
and the selective oxidation of alcohols will be described. The key features of the
catalysts will be discussed and the future prospects for gold-based nanoparticles
in oxidation catalysis will be discussed.
It is a pleasure to provide an article for this publication in honour of the 75th
birthday of Sir John Meurig Thomas. The paper is based on a François Gault
lecture given by the author on behalf of EFCATS during 2007; this is
considered appropriate as Sir John was elected as the first EFCATS François
Gault Lecturer in 1996 in recognition of his outstanding achievements in
catalysis.
The subject of this paper relates to catalysis by gold. Such a topic seems
counter-intuitive to many scientists and the concept of gold being involved in
550
Selective Oxidation Using Gold and Gold–Palladium Nanoparticles 551
some way in rapid chemical processes is at odds with the view of gold held by
the public at large. Gold, after all, is used in jewellery to fashion items of great
beauty and durability. Gold has been the element of commerce for millennia
due to its chemical immutability and ability to withstand oxidation, particu-
larly during fires. Gold is also used in dentistry due to its malleability and
inertness. Hence, for many chemists gold is the least interesting element in the
Periodic Table, after all the chapters in inorganic textbooks dealing with gold
usually have the least pages; while for most non-scientists it is the object of
desire. Perhaps the position of gold in the Periodic Table should have alerted
researchers to an apparent anomoly, since it is surrounded by elements that are
used in a broad range of catalytic processes including oxidation. Hence, there
should not have been too much surprise when it was found that gold was active,
but this was not the case and, indeed, some argued that it was the impurities
present in gold that led to the observed activity. It was the chemical inertness of
gold on the macroscopic scale that limited investigations into its use as a
catalyst, since it is only when gold is present as nanocrystals or cations that the
activity is perceived. This new discovery opens up the possibility of gold acting
as an effective oxidation catalyst and recent studies are confirming this to be the
case.
It was the discovery in the 1980s that finely divided supported nanoparticles
of gold could act as catalysts for reactions at low temperatures that changed
this perception of gold as the inert element; indeed the observation that gold,
and gold containing alloys, can be the best catalyst for a wide range of reactions
has to be considered as one of the most fascinating current topics in chemistry.
This has heralded an explosion of interest in gold catalysis (Figure 1) and
consequently, a large number of experimental and theoretical studies are being
undertaken to try to elucidate the nature of this interesting catalytic activity.
This recent research has been reviewed by Haruta,1–5 Bond and Thompson,6,7

Figure 1 Percentage of publications on gold catalysis normalised against all chemical

publications.12
552 Chapter 32
Bond et al., Thompson, Freund and co-workers, Cortie, Hashmi,12 Hutch-
8 9 10 11

ings,13–15 Hutchings and Scurrell16 and Hashmi and Hutchings.17

In this article, there is no need to go over the major ground covered in these
extensive reviews, but rather the use of supported gold and gold–palladium
catalysts for selective oxidation will be explored. In particular, the use of Au/C
for the selective oxidation of glycerol, a feedstock that is receiving great current
interest as a biorenewable material, will be used as a starting point, and
subsequently the use of supported gold–palladium alloys for the direct synthe-
sis of hydrogen peroxide and the rationale for the discovery that these catalysts
are exceptionally efficient for the oxidation of alcohols will be used as the
background for consideration of where future developments in gold catalysis
can be expected.

2 Targets for Oxidation Reactions

Oxidation reactions using gas or liquid phase reagents to produce valuable
intermediates or products for the chemicals industry remains a major area of
research interest.17 At present, major interest in oxidation catalysis remains
focused on the products of the bulk chemical industry, e.g. the oxidative
dehydrogenation of alkanes to alkenes and the epoxidation of alkenes are
intensely researched fields. However, there are major challenges that remain,
and personally these are classified as dream reactions. In this category one would
place the direct oxidation of methane to methanol, a reaction that has fascinated
catalysis researchers for decades.17 The reason for this fascination is three-fold,
(a) if this reaction could be achieved at realistic conversions with high selectivity,
the discovery would revolutionise the chemical industry, (b) the reaction looks
deceptively simple since all four C–H bonds in methane are equivalent and
(c) we know it is possible as nature has already figured it out and methane mono-
oxygenase readily carries out this reaction at ambient conditions. The much
more demanding direct oxidation of long chain alkanes to primary alcohols, a
reaction made more demanding as now regioselectivity as well as chemoselec-
tivity are crucially important, and the direct hydrogenation of oxygen to form
hydrogen peroxide exclusively would also be placed in the category of dream
reactions. However, there is immense scope to identify new catalytic uses for
oxidation catalysis. This opportunity exists as there are many oxidation proc-
esses operated in the fine chemicals industry, but unfortunately many reactions
are still carried out using stoichiometric oxygen donors often with particularly
non-green components. We can anticipate new developments in the future and
this is an area of research which promises great opportunities for anyone
entering the field of oxidation catalysis. Perhaps one of these areas will be the
expansion of oxidation into everyday life and bring it into closer contact with
society as a whole. This is the challenge presented by catalytic washing. Initially,
this concept was suggested for the washing of fabrics using di-manganese
complexes that activated molecular oxygen,18 and although this was far from
a commercial success it still represents a fascinating opportunity for research.
Selective Oxidation Using Gold and Gold–Palladium Nanoparticles 553

3 Au/Carbon as a Selective Catalyst for Glycerol

Oxidation
Amongst the potential new uses of catalytic oxidation technology, the oxida-
tion of alcohols and polyols to chemical intermediates represents a demanding
target. Supported platinum and palladium nanoparticles are generally
acknowledged as effective catalysts for the oxidation of polyols, for example,
in carbohydrate chemistry for the oxidation of glucose to glucinic acid. Glycerol
is a highly functionalised molecule that is readily available from biosustainable
sources, for example, it can be obtained as a by-product of the utilisation of
rape seed and sunflower crops. This makes glycerol a particularly attractive
starting point for the synthesis of intermediates, and a large number of products
can be obtained from glycerol oxidation (Figure 2). One of the key problems is
the potential complexity of the products that can be formed and so control of
the reaction selectivity by careful design of the catalyst is required. Glycerol
oxidation, in aqueous solution, has been extensively studied and in general,
palladium catalysts were found to be more selective than platinum, but in all
these previous studies using Pt and Pd, mixtures of most of the potential
products were formed in addition to non-selective products such as formic acid
and carbon dioxide. Hence, glycerol has remained a challenging starting point
for the synthesis of chemical intermediates.
The field of selective alcohol oxidation was opened up by the seminal studies
of Rossi, Prati and co-workers19–22 demonstrating that supported gold nano-
particles can be very effective catalysts for the oxidation of alcohols, including
diols. Recently, we extended these studies to show that Au supported on
graphite (1 wt% Au/C) can oxidise glycerol to glycerate with 100% selectivity
using dioxygen as the oxidant under relatively mild conditions (Table 1).23,24
NaOH was added as a base since, in the absence of NaOH, no glycerol

HO
OH

O
OH OH

HO OH HO OH
TARAC
OH
GLYA O O O
HO OH
O
O O
GLY HO OH
HO OH
HO OH
O O
DHA O
HYPAC MESAC

CO2

Figure 2 Reaction scheme for the oxidation of glycerol.

 554

Table 1 Oxidation of glycerol using 1 wt% Au/C catalysts.a,24

Glycerol Selectivity
Glycerol Po2 Glycerol/metal NaOH conversion (%) Glyceric Tartronic
Catalyst (mmol) (bar) (mol ratio) (mmol) (%) acid Glyceraldehyde acid
1 wt% Au/activated carbon 12 3 538b 12 56 100 0 0
1 wt% Au/graphite 12 3 538b 12 54 100 0 0
1 wt% Au/graphite 12 6 538b 12 72 86 2 12
1 wt% Au/graphite 12 6 538b 24 58 97 0 3
1 wt% Au/graphite 6 3 540c 12 56 93 0 7
1 wt% Au/graphite 6 3 540c 6 43 80 0 20
1 wt% Au/graphite 6 3 214d 6 59 63 0 12
1 wt% Au/graphite 6 3 214d 12 69 82 0 18
1 wt% Au/graphite 6 6 214d 6 58 67 0 33
1 wt% Au/graphite 6 6 214d 12 91 92 0 6
1 wt% Au/graphite 6 6 214d 0 0
a
60 1C, 3 h, H2O (and 20 ml), stirring speed 1500 rpm.
b
220 mg catalyst.
c
217 mg catalyst.
d
450 mg catalyst.
Chapter 32
Selective Oxidation Using Gold and Gold–Palladium Nanoparticles 555
conversion was observed. In addition, the carbon supports were also inactive
for glycerol oxidation under these conditions, even when NaOH was present,
which is an essential feature for an effective catalyst support. For all the data
presented in Table 1, the carbon mass balance was 100% indicating that, under
these conditions, supported Au/C catalysts are extremely selective for this
reaction and no C1 or C2 by-products were detected, which was not the case
with Pt or Pd catalysts.23–27 In addition, it is apparent that the selectivity to
glyceric acid and the glycerol conversion are very dependent upon the glycerol/
NaOH ratio. In general, with high concentrations of NaOH, exceptionally high
selectivities to glyceric acid can be observed. However, decreasing the concen-
tration of glycerol, and increasing the mass of the catalyst and the concentra-
tion of oxygen, leads to the formation of tartronic acid via consecutive
oxidation of glyceric acid. Interestingly, this product is stable with these
catalysts. It is apparent that, with careful control of the reaction conditions,
100% selectivity to glyceric acid can be obtained with 1 wt% Au/C. For
comparison, the supported Pd/C and Pt/C always gave other C3 and C2
products in addition to glyceric acid and, in particular, also gave some C1
by-products. In a final set of experiments, catalysts with lower Au concentra-
tions were investigated. For catalysts containing 0.25 or 0.5 wt% Au supported
on graphite, lower glycerol conversions were observed (18% and 26% respec-
tively as compared to 54% for 1 wt% Au/graphite under the same conditions)
and lower selectivities to glyceric acid were also observed. The previous studies
for diol oxidation by Rossi, Prati and co-workers19–22 also showed that the
conversion is dependent on the Au loading upon the support. This is considered
to be due to a particle size effect of the Au nanoparticles on the support. Gold is
known to be a highly effective catalyst for the oxidation of CO,1–17 and it has
been shown that the activity is highly dependent on the particle size, and the
optimum size is ca. 2–4 nm. However, most interestingly, the Au supported
catalysts that were selective for glycerol oxidation comprised Au particles as
small as 5 nm and as large as 50 nm in diameter. The majority, however, were
about 25 nm in size and were multiply twinned in character. Decreasing
the loading to 0.5 wt% or 0.25 wt% did not appreciably change the particle
size distribution; the particle number density per unit area was observed to
decrease proportionately however, which may be correlated to the decrease in
glycerol conversion and selectivity to glyceric acid. The catalysts that were
active and selective for glycerol oxidation were not found to be active for the
CO oxidation reaction. Consequently, we concluded that different active sites
are involved in these two contrasting reactions.
Recently, we have used cyclic voltammetry to study the Au catalysts sup-
ported on graphite,27 since in this case the support is conducting and this very
incisive technique can be used. A set of CV experiments were carried out with
the Au/graphite catalysts in the presence of glycerol, air and NaOH, thereby
studying the behaviour in situ under reaction conditions (Figure 3). In the
forward potential sweep, all catalysts showed a broad signal associated with the
electrooxidation of glycerol at ca. 0.9–1.3V (labelled C) and a narrower feature
on the reverse sweep (labelled D). Peak D corresponds to the situation in which
556 Chapter 32
0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6
5000 5000

4500 D 4500
a
4000 4000

3500 3500
Current Density (µA cm-1)

3000 3000
C
2500 2500

2000 2000

1500 1500
F
1000 1000

500 500
E
0 0

-500 -500
0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6
E (Pd/H Reference) / Volts
0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6
4000 4000
D
3500 3500
b
3000 3000
Current Density (µA cm-1)

2500 2500
C
2000 2000

1500 1500
F
1000 1000

500 500
E
0 0

-500 -500
0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6
E (Pd/H Reference) / Volts

Figure 3 Cyclic voltammetry of Au/graphite catalysts in aqueous NaOH ð0:5 mol=lÞ

and glycerol ð0:5 mol=lÞ. (a) 0.25 wt% Au/graphite; (b) 0.5 wt% Au/
graphite.15

the gold surface is being stripped of bulk oxide leaving behind only the Au–OH
species (peak A) with a minimal amount of molecular fragments adsorbed
(since these have been oxidised during the previous positive potential sweep).
This situation leads to peak D being the most intense and the catalyst being in
its most active state. Peak C corresponds to the same situation although the
relative amounts of strongly adsorbed molecular fragments is increased (since
these have not yet been oxidised) and hence a smaller concentration of Au–OH
Selective Oxidation Using Gold and Gold–Palladium Nanoparticles 557
species due to site-blocking via glycerol decomposition. Both of these factors
lead to peak C being smaller than peak D. This behaviour also emphasises the
poisoning effect on the reaction of bulk gold oxides which quench reaction at
potentials >1.3 V on the forward sweep and also down to 1.1 V on the negative
sweep due to hysteresis in the ‘‘irreversible’’ formation/desorption of the bulk
oxide phase.28 This suggests that there should be a strong correlation between
activity and the relative intensities of peaks C and D. This proposition is
explored below. In addition, it should be noted that the 0.25% and 0.5% Au/C
catalysts gave rise to two less intense peaks labelled E (0.38 V) and F (1.0 V).
For the active catalyst displaying total specificity to glycerate (1 wt% Au/
graphite) peaks E and F are both absent and we also considered this to be a key
finding. Furthermore, current density positive of 1.3 V associated with the
electrooxidation of strongly adsorbed glycerol fragments increases in the order:

1% Au/C o 0.5% Au/C o 0.25% Au/C o 1% Au/C (inactive)

In this way, the CV study, however, revealed differences between all the four
catalyst samples we investigated. In particular, two features were identified that
appeared to correlate with catalyst activity: (a) the relative intensities of specific
peaks observed in the CV and (b) the amplitude of the current density at
>1.3 V. Therefore, in Figure 4, these two parameters are plotted versus catalyst
activity, namely (i) the ratio of current densities (j) of peak C/peak D and (ii)
the ratio of current density at 1.6 V to the current density at 1.15 V (peak C).
Both these parameters express the rates of surface blocking (poisoning) relative
to oxidation by adsorbed Au-OH species. Inspection of Figure 4 demonstrates
a smooth correlation between activity and both of these parameters, and we
considered that this observation may have significance in the design of

Figure 4 Plot of current density at 1.6 V ( j1.6)/current density at 1.15 V ( j1.15) and
ratio of peak C/peak D versus percentage conversion for various supported
Au/C catalysts used for glycerol oxidation.15
558 Chapter 32
improved oxidation catalysts and that the use of CV as a diagnostic method
should be encouraged.

4 Selective Oxidation Using Gold–Palladium Alloy

Catalysts
4.1 Direct Synthesis of Hydrogen Peroxide
The direct synthesis of hydrogen peroxide from the oxidation of molecular
hydrogen by molecular oxygen is considered to be of immense current interest.
Hydrogen peroxide is a noted green oxidant that is useful in many large-scale
processes such as bleaching and as a disinfectant. Its use in the fine chemical
industry accounts for a much lower consumption but since it is viewed as a
green oxidant with water being the only by-product, it is recognised to have
significant potential in chemical synthesis, particularly in the production of
propene oxide using the microporous redox catalyst titanium silicalite
TS-1.29,30 In addition, it is considered possible that hydrogen peroxide can
replace stoichiometric, i.e. non-catalytic, oxygen donors in a number of
processes. At present, hydrogen peroxide is produced by the sequential hydro-
genation and oxidation of an alkyl anthraquinone,31 a process that is only
economic at a large scale. In contrast most uses of hydrogen peroxide require
relatively small amounts. Hence there is a significant mismatch between the
current scales of production and usage. The direct small-scale production of
hydrogen peroxide at the site where it is used would offer many advantages, not
least that this will negate the need to transport concentrated solutions of
hydrogen peroxide. At present, no commercial process exists for the direct
formation of H2O2, but there has been significant interest in this reaction in
industrial laboratories for over 90 years.32 Indeed, Degussa-Headwaters have
announced recently that they will commercialize a direct route to produce
hydrogen peroxide that can be used in the production of propene oxide.33 Until
very recently the catalysts used in these investigations have been based on Pd,
and since many researchers have concluded that it is important to try to achieve
the highest rate of product formation most of these earlier studies used H2/O2
mixtures in the explosive region; solutions of over 35 wt% hydrogen peroxide
have been made by reacting H2/O2 over Pd catalysts at elevated pressures.34
However, operating in the explosive region with H2/O2 mixtures can be
considered extremely dangerous, and more recently, studies have concentrated
on carrying out the reaction with dilute H2/O2 mixtures well away from the
explosive region.35,36
In our initial papers concerning the direct synthesis of H2O2 we showed that
catalysts based on Au–Pd alloys supported on alumina can give significant
improvements in the rate of hydrogen peroxide formation when compared with
the Pd only catalyst.37,38 A detailed study of Au–Pd catalysts supported on
alumina showed that only a relatively small amount of palladium is required to
achieve a significant enhancement in the rate of hydrogen peroxide synthesis
Selective Oxidation Using Gold and Gold–Palladium Nanoparticles 559

Figure 5 Au(4d) and Pd(3d) spectra for a 2.5 wt% Au–2.5 wt% Pd/TiO2 catalyst after
different heat treatments (a) uncalcined, (b) calcined at 200 1C in air, (c)
calcined at 400 1C in air and 500 1C in hydrogen.40

(Figure 5). Addition of Pd to Au significantly enhances the catalytic perform-

ance for the synthesis of H2O2, and moreover, it is interesting to note that there
is an optimum Pd–Au composition (Pd/AuE1:5) where the rate of H2O2
production is much higher than for the pure Pd catalyst, which in itself is
significantly more active than pure gold. It is apparent that the addition of Pd
to Au also enhances the selectivity to H2O2, and the enhanced rate of H2O2
synthesis is achieved at lower H2 conversion.
We decided to study the effect of storage on catalyst activity as, typically,
catalyst performance declines with storage for many catalysts. This is well
known for catalysts that are used for CO oxidation. We stored a sample of the
most active 2.5 wt% Au–2.5 wt% Pd/Al2O3 catalyst, which had been previously
calcined at 400 1C, in a sealed container in the dark for 12 months at ambient
conditions. Re-evaluation of the catalytic performance of this catalyst showed
that under the standard reaction conditions, the activity of the sample had
increased from 15 mol of H2O2/h/kgcat to 52 mol of H2O2/h/kgcat,39 represent-
ing a dramatic increase in productivity. A detailed scanning transmission
electron microscopy-X-ray energy dispersive spectroscopy (STEM-XEDS)
analysis of the fresh and the aged Au–Pd catalysts showed that the particle
size of the gold–palladium alloy particles increased on storage, through sinte-
ring, and these larger particles are associated with the enhanced activity
observed. This confirms that for the direct synthesis of hydrogen peroxide,
small gold–palladium alloy nanocrystals are not preferred. This study was also
a remarkable demonstration of the wide variation in active sites that can be
observed with gold catalysts, since the catalysts that are active for CO oxidation
560 Chapter 32
decrease in activity with storage whereas those active for the synthesis of H2O2
increase in activity.
To date the highest activities we have reported39–41 have been with TiO2-
supported catalysts. In general, Au–Pd/TiO2 catalysts give rates of hydrogen
peroxide synthesis that are three times higher than the fresh Au–Pd/Al2O3
catalysts. The reaction time and amount of catalyst used are important vari-
ables in the direct synthesis reaction since there are a number of competing
processes that lead to the decomposition of hydrogen peroxide, even at 2 1C.
The effect of increasing reaction time in the autoclave is shown in Table 2 for
the 2.5% Au/2.5% Pd/TiO2 catalyst calcined at 400 1C. Separate experiments
were conducted for each reaction time and so the data present the amount of
H2O2 formed as an average over the reaction period. It is apparent that the
yield of H2O2 increases steadily with reaction time and consequently the rate of
formation decreases with increased reaction time, and under these reaction
conditions it was concluded that 30 min gives a reasonable compromise be-
tween rate and overall yield of H2O2 for the purposes of comparing the catalytic
performance of these catalysts. Of course the optimal conditions will vary with
other conditions such as temperature and pressure, and so it can be reasonably
anticipated that at higher temperatures and reaction pressures much shorter
reaction times will be preferred. This means that the direct synthesis method
using diluted reactants, that avoids the potential for explosion hazards, will
only produce relatively dilute solutions and hence the methodology may be
better suited to in situ utilisation in chemical syntheses in which the H2O2 is
used as soon as it is formed. In this scenario, optimum use can be made of the
very high initial rates of H2O2 formation displayed by the catalysts (Table 2).
For the 2.5% Au/2.5% Pd/TiO2 calcined at 400 1C, the initial rate after 5 min
reaction time is >100 mol kgcat
1 h
1 with a hydrogen selectivity of >90%;
consequently if the hydrogen peroxide can be selectively transferred to a
substrate then this process would be exceptionally efficient.
One of the key factors that must be considered for heterogeneous catalysts
operating in three phase systems is the possibility that active components can
leach into the reaction mixture, thereby leading to catalyst deactivation or, in
the worst case, leading to the formation of an active homogeneous catalyst. To
demonstrate that the TiO2 supported catalysts function as wholly heterogene-
ous catalysts, an experiment was carried out using a supported gold catalyst

Table 2 The influence of reaction time on the conversion of H2 and selectivity

to hydrogen peroxide synthesis.a,40
Productivity
Reaction time (mol-H2O2/h/ H2 conversion H2O2 selectivity H2O2 yield
(min) kgcat) (%) (%) (%)
5 114 8 93 7.6
30 66 44 60 26.4
120 17 93 29 27.6
a
2.5% Au–2.5%Pd/TiO2 catalyst (20 mg) calcined at 400 1C.
Selective Oxidation Using Gold and Gold–Palladium Nanoparticles 561
(calcined at 400 1C) at 2 1C and the yield of H2O2 was determined. Following
this reaction, the gold catalyst was removed by careful filtration and the
solution was used for a second experiment using O2/H2. No further H2O2
was formed and this confirms that the formation of hydrogen peroxide involves
the gold–palladium alloy acting as a wholly heterogeneous catalyst.
Detailed structural characterisation has been carried out using X-ray photo-
electron spectroscopy (XPS) (Figure 5)40 and transmission electron microscopy
(Figure 6).41 Figure 5 shows the combined Au(4d) and Pd(3d) spectra for a
2.5 wt% Au/2.5 wt% Pd/TiO2 catalyst after different heat treatments. For the
uncalcined sample, which exhibits the highest rate of H2O2 production that we
have observed to date for a titania-supported catalyst, there are clear spectral
contributions from both Au and Pd leading to severe overlap of peaks. After
heat treatment at 200 1C there is a dramatic decrease in the intensity of the
Au(4d) peaks, and after calcination in air at 400 1C followed by reduction in H2
at 500 1C, the intensity of the Au(4d3/2) feature is below detection limits. The
uncalcined samples, although more active, were very unstable and leach Au and
Pd into solution during reaction, and these cannot be reused. However,
catalysts calcined at 400 1C were stable and active. Bulk analysis of the calcined
catalysts confirmed an overall Au:Pd ratio of 1:1, and hence we concluded that
the XPS results were revealing a core–shell structure for the Au–Pd nanopar-
ticles with a gold rich core. Subsequent detailed transmission electron micros-
copy confirmed this to be the case.41
We have subsequently found that Au–Pd catalysts supported on Al2O3,
Fe2O3 and TiO2 all give this core–shell structure for the gold–palladium alloy
particles and high activity and selectivity can be achieved for the direct
synthesis of hydrogen peroxide with these catalysts.39–42

4.2 Oxidation of Alcohols

It is well known that metals supported on oxides can be effective catalysts for
the oxidation of alcohols to oxides. In the earlier studies in which supported
gold nanocrystals were used as catalysts for the oxidation of alcohols, the
addition of base was essential for the observation of activity.19–24 Recent
studies have shown that the addition of base is not required for the oxidation
under mild solvent-free conditions, and this is a major advantage. In particular,
two recent studies have shown that supported metal nanoparticles can be very
effective catalysts for the oxidation of alcohols to aldehydes using O2 under
relatively mild conditions. Kaneda and co-workers43 have shown that hydro-
xyapatite-supported Pd nanoclusters (Pd/HAP) give very high turnover fre-
quencies for the oxidation of phenylethanol and benzyl alcohol but show very
limited activity in octan-1-ol oxidation. Corma and co-workers44 have shown
that the addition of Au nanocrystals to CeO2 converts the oxide from a
stoichiometric oxidant to a catalytic system with turnover frequencies similar
to those of Kaneda and co-workers.43 As we have shown in the previous
section, supported Au–Pd alloys are very efficient catalysts for the direct
562 Chapter 32

Pd-Lα O-Kα

Ti-Kα Au-Pd-Ti

Figure 6 Montage showing the annular dark field (ADF)-STEM image of a bimetallic
particle and the corresponding multivariate statistical analysis (MSA) proc-
essed STEM-XEDS maps of the gold M2, palladium La, oxygen Ka, and
titanium Ka signals. Also shown is a reconstructed MSA filtered Au–Pd–Ti
composition map (Ti ¼ red, Au ¼ blue, and Pd ¼ green).41
Selective Oxidation Using Gold and Gold–Palladium Nanoparticles 563
synthesis of hydrogen peroxide from the oxidation of H2 by O2 at low
temperatures. Hydroperoxy species are considered to be involved in H2O2
formation and since hydroperoxy species are known to be key reagents/inter-
mediates in the oxidation of alcohols,44 we reasoned that the catalysts active for
hydrogen peroxide synthesis would also be effective for the oxidation of
alcohols, and subsequently41 we demonstrated that TiO2-supported Au–Pd
alloy nanocrystals gave significantly enhanced activity for alcohol oxidation
under solvent free conditions with O2. When compared with mono-metallic
supported Au44 and Pd43 the Au–Pd catalyst nanocrystals give turnover
frequencies enhanced by a factor of ca. 25.
The TiO2 supported Au–Pd catalysts were investigated for the oxidation of
benzyl alcohol at 100 1C using O2 as oxidant in the absence of solvent (Figure 7).
It is clear that the Au–Pd/TiO2 catalysts are very active for this reaction and
the selectivity to benzaldehyde was Z 96% and only benzyl benzoate was
observed as a by-product. Carbon mass balances were 100% and no carbon
oxides were formed. The effect of adding Au to a Pd/TiO2 catalyst is clearly
apparent in these studies. Although the Pd/TiO2 catalyst exhibited high initial
activity, and the addition of Au decreases the activity, the Au–Pd/TiO2 catalyst
retains high selectivity to benzaldehyde at high conversion, a feature that is not
observed with the supported Au and Pd catalysts. One of the key factors that
must be considered for heterogeneous catalysts operating in three phase sys-
tems is the possibility that active components can leach into the reaction
mixture, thereby leading to catalyst deactivation or, in the worst case, to the
formation of an active homogeneous catalyst.
Kaneda and co-workers43 and Corma and co-workers44 had previously
demonstrated that supported Pd and Au monometallic catalysts were highly

100 100
90 90
Benzy alcohol conversion/%

Benzaldehyde selectivity/%

80 80
70 70
60 60
50 50
40 40
30 30
20 20
10 10
0 0
0 2 4 6 8 10 12 14 16 18 20 22 24
Time/h

Figure 7 Benzyl alcohol conversion and selectivity in benzaldehyde with the reaction
time at 373 K, 0.1 MPa O2 pressure: (’) Au/TiO2, (K)Pd/TiO2, (m) Au-Pd/
TiO2; solid symbols – conversion, open symbols – selectivity.41
564 Chapter 32
effective for the oxidation of 1-phenylethanol under solvent free conditions at
160 1C with 1 atm oxygen pressure. Under these conditions the Pd/HAP and
Au/CeO2 catalysts gave TOFs of 9800 and 12500 h
1 for 1-phenylethanol as
substrate. With the Au–Pd/TiO2 alloy catalyst a TOF of 269000 h
1 was
obtained. This is a significantly higher activity than that reported to date for
selective alcohol oxidation. Hence these studies showed that supported Au–Pd
catalysts, prepared by a relatively simple impregnation procedure, are very
effective catalysts for the selective oxidation of a range of straight chain,
benzilic and unsaturated alcohols, in particular primary alcohols, in addition to
being effective for the direct synthesis of hydrogen peroxide.

5 Future Prospects for Catalysis by Gold

In a recent review17 the extensive literature on both heterogeneous and homo-
geneous catalysis by gold has been discussed. Gold is therefore finding numer-
ous applications in all facets of catalysis. Once gold was considered as the last
element one would select as a component of a catalyst, whereas now, to many it
appears to be the first choice; this is indeed a remarkable reversal in fortunes.
However, this has yet to be translated into commercial technology and this has
to be the goal for the future, since then the lasting legacy of this early work on
catalysis by gold will have been secured. Recently, Thompson and co-workers45
have reviewed the commercial prospects for gold catalysis and they have
identified many targets.
There are a number of areas in which catalysis by gold can be expected to
advance. First, at present there is very limited mechanistic understanding of
how supported gold nanocrystals or cations achieve the remarkable activities
and selectivities. This, therefore, represents an area where a number of key
studies are now required, particularly using in situ spectroscopies together with
key experiments aimed at unraveling the kinetics of the reactions. At present,
the emphasis has been on reaction discovery since this has provided such rich
rewards. This is a challenge that has been recognised in the latest commentary
on catalysis by gold by Thomas and Edwards.46
As demonstrated by the work discussed on the direct synthesis of oxygen to
form hydrogen peroxide, supported gold catalysts are highly effective for selec-
tive hydrogenation after early work by Bond and co-workers47 showed that
small gold nanocrystals were effective for the selective hydrogenation of dienes,
and subsequent studies by Baillie et al.48 showed that ZnO-supported gold
crystallites were highly selective for the challenging selective hydrogenation of
a,b-unsaturated aldehydes to yield the unsaturated alcohol. Hydrogenation using
gold catalysis has recently been reviewed by Claus.49 Interestingly, selective
hydrogenation is much less well studied and hence major opportunities to
discover new uses for gold in this field exist. Very recently, Corma and Serna50
have demonstrated the regioselective reduction of a nitro group when other
reducible functions are present using gold nanoparticles supported on TiO2 or
Fe2O3. The chemoselective hydrogenation of functionalized nitroarenes with
Selective Oxidation Using Gold and Gold–Palladium Nanoparticles 565
H2 under mild reaction conditions was demonstrated providing a previously
unknown route for the synthesis of the industrially important cyclohexanone
oxime from 1-nitro-1-cyclohexene. This demonstrates the clear potential that is
offered by gold for innovation in selective hydrogenation.
It is clear that new reactions involving gold for selective hydrogenation will
be discovered in the near future. However, the clear advantage offered by gold–
palladium alloys for oxidation reactions also needs to be exploited. With
respect to the direct synthesis of hydrogen peroxide, there are two facets where
we can expect advances. First the major problem in the direct synthesis reaction
is that any catalyst that is effective for the selective hydrogenation of dioxygen
to hydrogen peroxide is also an effective catalyst for the over-hydrogenation to
form water. This is a particular problem with mono-metallic Pd catalysts.
Hence we can expect innovations in this area to try to control the over-
hydrogenation to give improved hydrogen peroxide selectivity. This can be
expected to result from an understanding of the reaction mechanism coupled
with improved preparation methodology. Secondly, the current gold–palla-
dium catalysts have been shown to give very high rates for the formation of
hydrogen peroxide in the absence of acid stabilisers and promoters. This can be
exploited to develop reaction methodologies in which the hydrogen peroxide is
captured in situ to generate selective oxidation products without the need to
isolate the hydrogen peroxide as an intermediate.
In summary, it is clear that supported gold catalysts can give exceptional
performance for a wide range of redox reactions. This outstanding catalytic
activity had remained undiscovered for many years, but now it is widely
recognized.1–17 One wonders what new discoveries we now await.

References
1. M. Haruta, Catal. Today, 1997, 36, 153.
2. M. Haruta and M. Date, Appl. Catal. A, 2001, 222, 427.
3. M. Haruta, CATTECH, 2002, 6, 102.
4. M. Haruta, Chem. Record, 2003, 3, 75.
5. M. Haruta, Gold Bull., 2004, 37, 27.
6. G.C. Bond and D.T. Thompson, Catal. Rev. Sci. Eng., 1999, 41, 319.
7. G.C. Bond and D.T. Thompson, Gold Bull., 2000, 33, 41.
8. G.C. Bond, C. Louis and D.T. Thompson, Catalysis by Gold, Imperial
College Press, 2006.
9. D.T. Thompson, Appl. Catal. A, 2003, 243, 201.
10. R. Meyer, C. Lemaire, S.h.K. Shaikutdinov and H.-J. Freund, Gold Bull.,
2004, 37, 72.
11. M.B. Cortie, Gold Bull., 2004, 37, 12.
12. A.S.K. Hashmi, Gold Bull., 2004, 37, 51.
13. G.J. Hutchings, Gold Bull., 1996, 29, 123.
14. G.J. Hutchings, Gold Bull., 2004, 37, 37.
15. G.J. Hutchings, Catal. Today, 2005, 100, 55.
566 Chapter 32
16. G.J. Hutchings and M.S. Scurrell, CATTECH, 2003, 7, 90.
17. A.K.S. Hashmi and G.J. Hutchings, Angew. Chem., Int. Ed., 2006, 45,
7896.
18. R. Hage, J.E. Iberg, J. Kerschner, J.H. Koek, E.L.M. Lempers, R.J.
Martins, U.S. Racherla, S.W. Russell, T. Swarthoff, M.R.P. van Vliet,
J.B. Warnaar, L. van der Wolf and B. Krijnen, Nature, 1994, 369, 637.
19. L. Prati and M. Rossi, J. Catal., 1998, 176, 552.
20. F. Porta, L. Prati, M. Rossi, S. Colluccia and G. Martra, Catal. Today,
2000, 61, 165.
21. C. Bianchi, F. Porta, L. Prati and M. Rossi, Top. Catal., 2000, 13, 231.
22. L. Prati, Gold Bull., 1999, 32, 96.
23. S. Carrettin, P. McMorn, P. Johnston, K. Griffin and G.J. Hutchings,
Chem. Commun., 2002, 696.
24. S. Carretin, P. McMorn, P. Johnston, K. Griffin, C.J. Kiely and G.J.
Hutchings, Phys. Chem. Chem. Phys., 2003, 5, 1329.
25. H. Kimura, A. Kimura, I. Kubo, T. Wakisaka and Y. Mitsuda, Appl.
Catal. A, 1993, 95, 143.
26. P. Gallezot, Catal. Today, 1997, 37, 405.
27. S. Carretin, P. McMorn, P. Jenkins, G.A. Attard, P. Johnston, K. Griffin,
C.J. Kiely and G.J. Hutchings, ACS Symp. Ser. (Feedstocks for the
Future), 2006, 921, 82.
28. M.A. Schneeweiss, D.M. Kolb, D. Liu and D. Mandler, Can. J. Chem.,
1987, 75, 1703.
29. L.Y. Chen, G.K. Chauh and J. Jaenicke, J. Mol. Catal. A, 1999, 132, 281.
30. W. Lin and H. Frei, J. Am. Chem. Soc., 2002, 124, 9292.
31. H.T. Hess, in Kirk-Othmer Encyclopaedia of Chemical Engineering, vol. 13,
I. Kroschwitz and M. Howe-Grant (eds), Wiley, New York, 1995, p. 961.
32. H. Henkel and W. Weber, US Pat., 1108752, 1914.
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35. J. van Weynbergh, J.-P. Schoebrechts and J.-C. Colery, US Pat., 5447706,
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36. B. Zhou and L.-K. Lee, US Pat., 6168775, 2001.
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Kiely and G.J. Hutchings, Phys. Chem. Chem. Phys., 2003, 5, 1917.
39. J.K. Edwards, B.E. Solsona, P. Landon, A.F. Carley, A. Herzing, M.
Watanabe, C.J. Kiely and G.J. Hutchings, J. Mat. Chem., 2005, 15, 4595.
40. J.K. Edwards, B.E. Solsona, P. Landon, A.F. Carley, A. Herzing, C.J.
Kiely and G.J. Hutchings, J. Catal., 2005, 236, 69.
41. D.I. Enache, J.K. Edwards, P. Landon, B. Solsona-Espriu, A. F. Carley,
A.A. Herzing, M. Watanabe, C.J. Kiely, D.W. Knight and G.J. Hutchings,
Science, 2006, 311, 362.
Selective Oxidation Using Gold and Gold–Palladium Nanoparticles 567
42. B.E. Solsona, J.K. Edwards, P. Landon, A.F. Carley, A. Herzing, C.J.
Kiely and G.J. Hutchings, Chem. Mater., 2006, 18, 2689.
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Soc., 2004, 26, 10657.
44. A. Abad, P. Concepción, A. Corma and H. Garcia, Angew. Chem. Int. Ed.,
2005, 44, 1596.
45. C.W. Corti, R. Holliday and D. Thompson, Top. Catal., 2007, 44, 331.
46. J.M. Thomas and P.P. Edwards, Angew. Chem., Int. Ed., 2007, 46, 5480.
47. P.A. Sermon, G.C. Bond and P.B. Wells, J. Chem. Soc., Faraday Trans. 1,
1979, 75, 385.
48. J.J. Bailie and G.J. Hutchings, Catal. Commun., 2001, 291.
49. P. Claus, Appl. Catal., A, 2005, 291, 222.
50. A. Corma and P. Serna, Science, 2006, 313, 332.
CHAPTER 33

Electronic Factors in
Hydrocarbon Oxidation
Catalysis
JERZY HABER
Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences,
Krakow, Poland

Oxygen is one of the most interesting elements playing a fundamental role in

catalysis, because on the one hand it is a component of the most widely used
type of catalysts – oxides, and on the other hand it is the reactant in one of the
most important types of chemical processes – oxidation.1–3 The attack of
oxygen on the hydrocarbon molecule is the easiest route to functionalize this
molecule, and selective oxidation processes, in which hydrocarbon molecules
are oxygenated to form alcohols, aldehydes or acids, are the basis of the
modern petrochemical industry. They may be divided into vapour or liquid-
phase reactions, which are catalyzed by solid oxide catalysts and are carried out
as heterogeneous catalytic processes, and reactions in the liquid phase, cataly-
zed by transition metal organometallic complexes or by enzymes, which are
commonly realized as homogeneous catalytic processes, but efforts are under-
taken to immobilize the catalysts and turn the processes heterogeneous.
The process of oxidation of a hydrocarbon molecule must begin with the
activation of the C–H bond. Realization of this first elementary step is parti-
cularly challenging, because it must be achieved in the presence of many
constraints.4 The C–H bonds in the initial reactant are usually stronger than
those in the intermediates, which are the required products. This makes these
intermediates prone to rapid further oxidation to thermodynamically stable
CO2 and renders the C–H bond activation rate determining and the selectivity
kinetically controlled.
In homogeneous liquid-phase catalytic processes the initiation consists of the
transfer of one electron between the hydrocarbon and the metal complex

568
Electronic Factors in Hydrocarbon Oxidation Catalysis 569
followed by abstraction of a proton and formation of a radical:

P:Mþn þ RH ! P:Mþðn
1Þ :RHþ

P:Mþðn
1Þ RHþ ! P:Mþðn
1Þ þ R þ Hþ

where P denotes an organic complex, e.g. the porphyrin ligand, and R the
hydrocarbon radical, starting the chain reaction. Facility of the radical formation
along this pathway will depend on the redox potential of the metalloporphyrin,
and the strength of the C–H bond of the reactant. The redox potential of the
metalloporphyrin may be modified by the choice of the metal, selection of the
axial ligand and introduction of substituents into the porphyrin ligand. As an
example Figure 1 shows the dependence of the yield of cyclooctanone in the
reaction of cyclooctane with dioxygen in the presence of manganese porphyrin
catalysts as a function of their half-way reduction potential.5
The second possibility involves generation of alkyl radicals as a result of the
abstraction of a hydrogen atom from the hydrocarbon molecule by a coordi-
nated dioxygen, i.e. a superoxo or peroxo metal complex, which has electro-
philic properties:

P:Mþðn
1Þ þ O2 ! P:Mþn
O
O

P:Mþn
O
O þ RH ! P:Mþn
O
OH þ R

30

25 C-one+C-ol, %

20
C-one, %
Yield, %

15

10

5 C-ol, %

0
-0.25 -0.15 -0.05 0.05 0.15 0.25
E1/2 [V]

Figure 1 Yields of cyclooctanone and cyclooctanol in the presence of manganese

porphyrin as catalyst as a function of its half-way potential modified by
introduction of substituents.5
570 Chapter 33
or direct oxidation by a reactive high valent oxometal species

P:Mþðnþ1Þ ¼ O þ RH ! P:Mþðnþ1Þ
OH:R ! P:Mþn þ ROH

In the case of heterogeneous catalytic oxidation, in the liquid or gas phase, the
hydrocarbon molecule is activated by the cleavage of the C–H bond on adsorp-
tion at the surface of the solid. The transfer of electrons from an adsorbed
hydrocarbon molecule, which behaves as a redox pair, into an oxide with
semiconducting properties can take place spontaneously only if the redox
potential of this pair is situated above the Fermi level of the solid and above
the bottom of the conductivity band, and the extraction of electrons from the
solid can take place when the redox potential is located below the Fermi level and
below the top of the valence band. This is illustrated in Figure 2.6 The probability
of these processes is a function of the density of states in the conductivity and
valence band respectively at the potentials corresponding to the redox potential
of the adsorbed species. The relative positions of the energy levels in the solid and
the redox potential of the reacting molecules may be adjusted by (a) formation of
one or more oxide/oxide interfaces with such values of the contact potential that
the energy levels in the solid will shift to the optimum position, (b) doping of the
oxide with altervalent ions, which will shift the Fermi level, (c) generation of
surface defects, which will create a broad distribution of surface electronic

Hydrocarbon Hydrocarbon

Eredo Eredo
Hydrocarbon
E E E
Eredo

Eredo Eredo

Oxygen Oxygen
Eredo

Oxygen

Catalytic oxidation of Catalytic oxidation of Catalytic oxidation of

hydrocarbon molecule hydrocarbon molecule hydrocarbon molecule
can proceed cannot proceed, because cannot proceed, because
the molecule is not the catalyst is not
activated reoxidized

Figure 2 Energy diagram of the electron transfer from a hydrocarbon molecule to

oxygen in the heterogeneous catalytic oxidation mediated by an oxide of
semiconducting properties.6
Electronic Factors in Hydrocarbon Oxidation Catalysis 571
states mediating the exchange of electrons between the reacting adsorbed
molecule and the oxide catalyst, or (d) application of an external potential.
The distribution of electrons in the reacting molecule may also play an important
role and the possibility that different orbitals participate in the interaction with
the solid surface depending on the way the molecule becomes adsorbed.
Experimental evidence from different surface sensitive techniques reveals the
presence at oxide surfaces of alkoxy and OH groups indicating that both parts
of the cleaved C–H bond become bonded to the surface oxide ions.7
The quantum-chemical calculations with the DFT (density functional
theory) method for a methane molecule interacting with a vanadium oxide
cluster V3O12H9 as a model mimicking a fragment of the oxide surface showed
indeed that the most probable is such reaction pathway, in which both frag-
ments of the dissociating C–H bond become attached to the surface oxide ions.8
The proton forms an OH group, the hydrocarbon fragment forms an alkoxy
group and two electrons become injected into the conductivity band of
the oxide:

The reaction proceeds usually by the Mars–van Krevelen mechanism, in

which the molecule is oxidized by the catalyst, which is then reoxidized by gas
phase dioxygen. The catalyst must thus be able to undergo easily the change of
oxidation state of its cations. Since transition metal cations in oxides are able to
change the electronic state in a wide spectrum, these oxides are components of
all active and selective catalysts. The oxidation of a hydro-
carbon molecule at the surface of an oxide catalyst involves thus the operation
of two redox couples:
R
CH3 þ 2O
2 ! R
CHO þ H2 O þ 2VO þ 4e

O2 þ 2VO þ 4e
! 2O
2

(where VO denotes an oxygen vacancy) of which the first injects electrons into
the oxide catalyst, whereas the second one extracts them from the oxide.
In the first redox couple the hydrocarbon molecule is activated by the
cleavage of the C–H bond, which is usually the rate determining step in the
hydrocarbon oxidation processes, followed by addition of nucleophilic oxygen.
As an example, the exchange of electrons with catalysts composed of vanadia
supported on titania in liquid phase heterogeneous oxidation will be discussed.
Scanning tunneling microscopy shows that heating in vacuum generates surface
oxygen vacancies on the surface of the rutile monocrystal.9 By using cyclic
voltammetric experiments it has been possible to show that these vacancies are
active sites mediating the transfer of electrons in the oxidation of water and
evolution of oxygen, the rate being proportional to the surface concentration of
572 Chapter 33
0.15
A1
A2
0.10
A3
0.05
j [mA . cm-2]
0.00
0.2 0.6 1.0 1.4 1.8 2.2
-0.05 E [V]
C3

?
-0.10
C2
-0.15 C1
V4+ / V3+

V5+ / V4+

Figure 3 Stationary cyclic voltammetry curves for the rutile electrode reduced in
hydrogen and then heated with V2O5 in argon atmosphere at 730 K.10

these vacancies. Vanadium ions deposited at the surface of rutile generate local
energy levels (Figure 3) below the conductivity band edge (Figure 4) and
mediate the electrocatalytic oxidation of many organic molecules, catechol
being an example, pure rutile surface being inactive.10 The rate of the oxidation
reaction to quinone (Figure 5) is proportional to the number of vanadium ions
present at the surface11 indicating that these ions play the role of active centres
in the catalytic oxidation. V14 ions diffuse into the subsurface layer and can be
reduced to V13 oxidation state due to charge compensation by protons incor-
porated into the surface layer, but only the outermost vanadium ions can be
oxidized to V15 oxidation state as a result of chemisorption of oxygen. Thus, the
position in the energy spectrum of the solid and the ability to change the valence
state makes it possible for vanadium ions to mediate the electron transfer
between the reacting organic molecules and the catalyst and the oxidation of
these molecules takes place, the catalyst mediating the flow of electrons from the
organic molecule to dioxygen, which cannot take place directly.
A second example is the oxidation of lower alkanes with dioxygen over the
vanadium phosphate catalyst to form acids and anhydrides. The rate of
oxidation depends on the position of the Fermi level determining the nu-
cleophilicity of the surface as expressed by the binding energy of O1s electrons
determined by XPS (X-ray photoelectron spectroscopy) (Figure 6).12
Transition metal oxides are nonstoichiometric compounds (Bertholides) with
composition depending on the equilibrium between the lattice and its constit-
uents in the gas phase. This is a dynamic equilibrium, in which the rate of
dissociation of the oxide lattice and evolution of oxygen in the form of O2
molecules is equal to the rate of its incorporation from the gas phase into the
surface layer of the solid. In the process of dissociation the lattice oxide ions
must be extracted from the surface, electrons must be injected into the solid,
Electronic Factors in Hydrocarbon Oxidation Catalysis 573

0.5 mol dm-3 H2SO4

E E [V]
-0.5 -0.5

EC 0.0 0.0
Eox
V4+/V3+ EC e-
0.5 0.5 λ
EF E0 redox
EF λ
V5+/V4+
1.0 1.0 e- Ered

1.5 1.5

2.0 2.0

2.5 2.5

EV
3.0 3.0

EV

OH O
OH O
+ 2H+ + 2e-

Figure 4 Energy diagram of TiO2 doped with vanadium ions as catalyst in electro-
catalytic oxidation of catechol.

0.6

0.5 ja

0.4
j [mA . cm-2]

jc

0.3

0.2

0.1

0.0
0.0 0.5 1.0 1.5 2.0 2.5
Q [mC . cm-2]

Figure 5 Anodic ( ja) and catodic ( jc) current density due to oxidation of catechol to
quinone as a function of the surface concentration of vanadium ions.

and oxygen atoms must recombine to form molecules and desorb as dioxygen.
The reverse series of elementary steps takes place upon incorporation. These
elementary steps result in surface equilibria:
O2
$O


ðchemÞ þ VO $O2ðchemÞ $O2ðchemÞ $O2ðadsÞ $O2ðgasÞ
2

574 Chapter 33
3

C4H10
2
W.104, mol/h.m2

VPO

C5H12

VPO
C3H8
VPO

0
531.0 531.5 532.0
B.E. O 1s, eV

Figure 6 Rate of the oxidation of propane, butane and pentane as a function of the
binding energy of O1s electrons in the (VO)2P2O7 catalyst modified by
doping.12

so that the surface of an oxide is always populated with different oxygen

species. The surface coverage by these species depends on oxygen pressure in
the gas phase, the rate constants of adsorption and chemisorption (transfer of
electrons between adsorbed oxygen molecules and the solid), the rate constant
of recombination of oxygen ions with surface oxygen vacancies and the
dissociation pressure of the oxide.13 The different oxygen species present at
the oxide surface have different reactivities and may react with other reactants,
adsorbed at the surface, along different pathways. Thus, the selectivity of the
reaction will strongly depend on the relative coverages of the surface by these
species. Lattice O2
ions exposed at the surface are nucleophiles and are usually
responsible for selective oxidation, whereas O


2(chem) and O(chem) are elect-
rophiles and lead to the formation of radicals, starting the chain reaction,
which in the gas phase eventually results in total oxidation.14 They are equiv-
alent to ‘‘hot oxygen atoms’’ described by Roberts et al.15 and their presence
may be detected by the same procedure, using probe molecules, which undergo
combustion, but are known not to react with lattice oxide ions.
Thus, different oxygen species present at the oxide surface compete for
hydrocarbon molecules. Moreover, a competition also exists between hydro-
carbon molecules and surface oxide vacancies for the electrophilic O
(chem)
species, which can either be captured by hydrocarbon molecules to form
Electronic Factors in Hydrocarbon Oxidation Catalysis 575
products of electrophilic oxidation or be incorporated into the surface by
reaction with oxygen vacancies VO. Two parallel reaction pathways followed
by a hydrocarbon molecule when adsorbed at the surface of an oxide catalyst,
its selective oxidation (allylic oxidation in the case of olefins) by surface lattice
oxide ions (nucleophilic oxidation) or its destructive oxidation by reactive
oxygen species O


(chem), O2(chem) (electrophilic oxidation), are described by
different rate equations, but are coupled together by the equation describing
the generation and annihilation of surface oxygen vacancies: O
2 O #
V
O +O

(chem) . 13
The contributions from these two pathways depend on the
relative values of kn, ke, kinc, kdiss, kchem and kads. The first two rate constants
depend on the nature of the hydrocarbon molecule, whereas the rate constants
describing the transformation of surface oxygen species kinc, kdiss, kchem and
kads are characteristic of the oxide. Measurements of the rate of homomolecular
isotopic exchange of oxygen permits comparison of the population of the
surface of different oxides by electrophilic oxygen.16
The consequence of the dynamic interaction of the catalyst with the gas
phase is the adaptability of the oxide to changes in external conditions. The
surface of an oxide catalyst may respond to changes in composition of the
reacting catalytic mixture resulting in changes of the redox potential of the gas
phase in three ways:

 the steady-state degree of reduction of the catalyst surface may change,

the surface defect equilibria at the oxide surface and in the bulk may be
shifted, and changes of concentration of a given type of site involved in
the catalytic transformation may cause changes in catalytic properties;
 when the concentration of defects at the oxide surface surpasses a certain
critical value, ordering of defects or formation of a new bidimensional
surface phase may occur resulting often in a dramatic change of catalytic
properties;
 when a redox mechanism operates in the catalytic reaction, the ratio of
the rate of catalyst reduction and its reoxidation may be different for
various phases and hysteresis in the dependence of catalytic properties on
the composition of the gas phase may appear, these properties being then
strongly influenced by the type of pretreatment.

References
1. A. Bielañski and J. Haber, Oxygen in Catalysis, Marcel Dekker, New
York, 1991.
2. G. Centi, F. Cavani and F. Trifiro, Selective Oxidation by Heterogeneous
Catalysis, Kluwer Academic/Plenum Press, New York, 2001.
3. R.A. Sheldon and R.A. van Santen (eds), Catalytic Oxidation, World
Scientific, Singapore, 1995.
4. J.A. Labinger, J. Mol. Catal.: A Chem., 2004, 220, 27.
576 Chapter 33
5. J. Poltowicz and J. Haber, J. Mol. Catal.: A Chem., 2004, 220, 43.
6. J. Haber, Stud. Surf. Sci. Catal., 1997, 110, 1.
7. F. Finocchio, G. Busca, V. Lorenzelli and R.J. Viley, J.Catal., 1995, 151,
204.
8. E. Broczawik, J. Haber and W. Piskorz, Chem. Phys. Lett., 2001, 333, 332.
9. N. Spiridis, J. Haber and J. Korecki, Vacuum, 2001, 63, 99.
10. J. Haber and P. Nowak, Top. Catal., 2002, 20, 75.
11. J. Haber, P. Nowak and P. Zurek, unpublished results.
12. V.A. Zazhigalov, J. Haber, J. Stoch and E.V. Cheburakova, unpublished
results.
13. J. Haber and W. Turek, J. Catal., 2000, 190, 320.
14. J. Haber, ACS Symp. Ser., 1996, 638, 20.
15. A.F. Carley, P.R. Davies and M.W. Roberts, Phil. Trans. Roy. Soc. A,
2005, 363, 829.
16. J. Haber and B. Grzybowska, J. Catal., 1973, 28, 489.
CHAPTER 34

The Importance of Selectivity in

Ammoxidation Catalysis

ROBERT K. GRASSELLIa,b
a
Center for Catalytic Science and Technology, University of Delaware,
Newark, DE19716, USA; b Department of Chemistry, Technische
Universität München, D-85748, Garching, Germany

1 Background
I have had the pleasure to meet Sir John about 30 years ago when I was at
SOHIO (Cleveland, OH, USA), and where he was invited to give a series of
lectures. A few years later, at the Discussions of the Faraday Society in
Nottingham, England (1981), he came to my rescue when I proposed in my
lecture surface shear structures as being responsible for the superior perform-
ance of our new multiphase-multicomponent ammoxidation catalysts. On our
mutual train ride from Nottingham, destinations Oxford and Cambridge, Sir
John’s persuasive account of his instrumental facilities convinced me to switch
my plan of having the catalyst samples, brought with me for Sir Peter Hirsch of
Oxford to examine in his HREM, that we lacked in Cleveland at that time, to
Cambridge for analysis. I delivered my lecture at Oxford, never mentioning my
samples and headed for Cambridge. From there on, our scientific cooperation
and my esteem for Sir John both as a scientist and a person has flourished
unabated.
Selectivity is of utmost importance in heterogeneous oxidation catalysis as
the cost of feed materials continues to escalate. In commercial processes,
selectivity at acceptably high conversions is imperative. Heeding this premise
we proposed, some forty years ago, the concept of site isolation, defining one of
the key requirements needed to achieve selectivity in oxidation catalysis. This
concept retains its usefulness in the conceptual design of new selective oxidation
catalysts and successfully describes the selectivity behaviour of the currently
leading contender, MoV(Nb,Ta)(TeSb)O system, for the ammoxidation of

577
578 Chapter 34
propane to acrylonitrile. The system is comprised of at least two crystalline
phases, orthorhombic Mo7.8V1.2NbTe0.94O28.9 (M1) and pseudo-hexagonal
(Mo4.67V1.33Te1.82O19.82) (M2), wherein the M1 phase is the key paraffin
activating and ammoxidation catalyst, its active centres containing all key
catalytic elements V51, Te41, Mo61, properly arranged to transform propane
directly to acrylonitrile. Four Nb51 centres, each surrounded by five moly-
bdenum–oxygen octahedra, isolate the active centres from each other, prevent-
ing overoxidation to COx. Symbiosis between the M1 and M2 phases is
observed at commercially interesting high propane conversions, provided the
two phases are finally divided, thoroughly mixed and in nano-scale contact with
each other. The M2 phase serves as a cocatalyst to the M1 paraffin activating
phase, converting desorbed propylene intermediate effectively to acrylonitrile
in a phase cooperation mode.

2 Introduction
Selectivity is of utmost importance in industrial catalytic processes with the feed
hydrocarbons becoming less abundant and thereby more expensive. In suc-
cessfully devising catalysts of commercial importance, selectivity of the desir-
able product must be achieved at reasonably high conversions. Industrial
researchers recognized this requirement already in the forming years of hetero-
geneous selective oxidation catalysis. Thus, as early as 1963 Callahan and
Grasselli1 put forward their hypothesis of site isolation. This hypothesis states
that oxidation catalysts become selective when the number of reacting surface
oxygens at the active centres is limited and these centres are spatially isolated
from each other. This hypothesis has been verified on many catalytic systems
since its inception and served their originators well in the discovery of an array
of catalytic solids for the oxidation and ammoxidation of light olefins that have
successfully been commercialized (seven generations of propylene to acrylonit-
rile ammoxidation catalysts and five oxidation of propylene to acrolein and
acrylic acid catalysts).2
The site isolation hypothesis can now be extended to include also paraffin
conversion catalysts such as MoV(Nb,Ta)(Te,Sb)O and is the subject of this
contribution. Although the well known SOHIO/BP process2,3 for the direct
ammoxidation of propylene to acrylonitrile is very efficient giving 80+%
acrylonitrile yield on commercial scale,4 there is currently a substantial incen-
tive, because of the large price differential between propane and propylene, to
discover an effective propane catalyst so that future ammoxidation processes
would be paraffin based. Promising catalyst candidates are promoted VSbO
and MoVNb(Te,Sb)O systems, with the latter holding a substantial edge over
the former.5–7
Site isolation is also central for achieving good selectivity in the epoxidation
of propylene to propylene oxide using TS-1 and hydrogen peroxide,8 the
hydroxylation of phenol to p-dihydroxybenzene using also TS-1 and hydrogen
peroxide,9 and the hydroxylation of benzene to phenol using Fe-ZSM-5 and
The Importance of Selectivity in Ammoxidation Catalysis 579
10,11
N2O. The desired selectivity is attained only after the respective active sites
are sufficiently isolated from each other in the framework structure to prevent
undesirable side reactions. Similarly, site isolation also plays a central role in
achieving superior selectivity levels in reactions studied by J.M. Thomas and his
group. Exemplary are the oxidation of cyclohexane/cyclohexanone using
FeAlPO-5 or FeAlPO-31 as catalysts to produce adipic acid,12 n-hexane
oxidation using CoAlPO-18 to produce adipic acid,13 and the ammoximation
of cyclohexane with ammonia and dioxygen to produce e-caprolactam using
MgMnAlPO-5 as catalyst.14,15 All of these catalysts are bi-functional in nature,
and it is imperative in the design of the catalysts that the two respective,
differing catalytic functions be spatially separated from each other (site isola-
tion) to achieve the desired product selectivity.

3 Experimental
The methods employed for the preparation, evaluation and optimization of
MoV(Nb,Ta)(Te,Sb)O catalysts and for their structure determinations
have been described earlier.16 Further details pertaining to the solutions of the
M1 and M2 structures are found in references.17–19 The preparation, compound-
ing and catalytic testing of M1/M2 physical mixtures is described in Ref. 20.

4 Results and Discussion

Over the past forty years, the site isolation hypothesis1 has been extended
from the original CuO catalyst to include V2O5/KVO4, Bi9PMo12O52,
(K,Cs)(Ni,Co,Mg)(Fe,Ce)(Sb,P)BiMoO, USb3O10, FeSbO, VSbO, (VO)2P2O7,
and now also the MoV(Nb,Ta)(Te,Sb)O systems and has recently been
reviewed.6,21 In these systems, high product selectivity can be explained on
the basis that the reactive oxygens at the respective active centres are limited in
number and that the active centres are spatially separated from each other. The
desired site isolation on the surface of the respective solid catalyst can be
achieved either by partial reduction (CuO), by breaking up interconnecting
M–O–M–O–M chains (V2O5/KVO4), by phosphate ‘‘fences’’ ((VO)2P2O7) or
by the structural makeup of the solid (remaining examples above).
While selectivity is of utmost importance in oxidation catalysis, driving
innovation by itself, it is not sufficient if searching for a commercially viable
catalyst. Selectivity by itself cannot be bottled or put into drums and sold!
Selectivity must be coupled with sufficient activity in a catalyst so that reason-
able product yields are achieved. It is much easier to obtain high catalyst
selectivity at low conversions than at high conversions; but that is commercially
an impractical result. Therefore, it is important to discover catalysts having
high selectivity also at high conversions. All of the above listed catalysts,
obeying the site isolation concept, fall into this category.
It is well known by now that most heterogeneous catalysts effective for
paraffin activation and subsequent selective oxidation or ammoxidation
580 Chapter 34
contain vanadium as the key paraffin activating element, be it VSbO,
MoVNb(Te,Sb)O or AlVON.5–7 In order to achieve selectivity at reasonable
paraffin conversions, it is necessary to structurally isolate the paraffin activat-
ing vanadium centers from each other. Only V51 sites activate paraffins, V41
sites are ineffective for paraffin activation.5–7,16,21
At present, the MoVNbTeO system gives the highest acrylonitrile
yields (B62%);5–7 MoVNbSbO is a close second (B55+%).6,22 The two
systems are structurally very similar. Catalytically both systems employ
(V51¼O 2 41Vd–Od) moieties as their paraffin activating sites, located in
their respective active centres. In the first system Te41–O sites, also located in
the active centre, are the a-H abstracting moieties activating the chemisorbed
propylene intermediate once formed, while in the second Sb31–O sites perform
this function.5–7
The MoVNbTeO system originally discovered by the Mitsubishi Company23
is comprised of three crystalline phases: orthorhombic Mo7.8V1.2NbTe0.94O28.9
(M1), pseudo-hexagonal Mo4.67V1.33Te1.82O19.82 (M2) and a trace of mono-
clinic TeMo5O16.5–7 The key paraffin conversion phase is M1 (Figure 1). This
phase contains active centres comprised of an assembly of five metal oxide
octahedra (2V510.32/Mo610.68, 1V410.62/Mo510.38, 2Mo610.5/Mo510.5) and two
tellurium-oxygen sites (2Te410.94), which are stabilized and structurally isolated
from each other (site isolation) by four Nb51 sites, each surrounded by five
molybdenum-oxygen octahedra. These centres contain all necessary key ele-
ments within bonding distance of each other to effectively convert propane to
acrylonitrile without need of desorption of reaction intermediates. The V51¼O
sites activate the propane by abstracting a methylene hydrogen, the Te41–O
sites abstract the a-H of the chemisorbed propylene once formed and the
adjacent O¼Mo61¼NH sites insert NH into the chemisorbed p-allylic inter-
mediate forming the acrylonitrile precursor as shown in Figure 1. Based on
these proposed catalytic steps, derived on the basis of sound classical organic
chemistry and in depth knowledge of the M1 structure, a complete reaction
mechanism can be written which is recorded in the literature16 but will not be
further elucidated here because of space limitations.
To attain selectivity, the catalytically active centres of M1 are spatially
isolated from each other by Nb51–5Mo51/41 pentagonal bipyramids as illus-
trated in Figure 2. This arrangement of active centres on the surface favours
acrylonitrile selectivity and minimizes unwanted overoxidation to COx. A
statistical analysis of the various elemental distribution probabilities at the
active centres of M15 predicts that a maximum acrylonitrile selectivity of 81%
is attainable using M1 as the catalyst. Thus far the maximum experimentally
obtained acrylonitrile selectivity is 72%.5,6 A possible explanation for the
difference is that some propylene desorbs from the M1 active centres before
it is fully converted to acrylonitrile, begins to migrate, encounters other
unoccupied V51 sites and combusts to COx. Experimentally, some unconverted
propylene is observed at high throughputs24,25 whereas symbiosis between M1
and M2 phases leading to improved acrylonitrile yields is observed at high
propane conversions.5–7,16 The optimum acrylonitrile yield is obtained
The Importance of Selectivity in Ammoxidation Catalysis 581

6 8
11
10 3
5 10
9 8 5 9
6
12 11 1

7 4
2
4 7

1 12
11 5 8 6
10
9 3 9 5
6 10
8
11

M1: V4+0.26 / Mo5+0.74 M4: Mo6+0.5 / Mo5+0.5 M9: Nb5+1.0

M2: V4+0.62 / Mo5+0.38 M5, 6, 8,10: Mo6+1.0 M11: Mo5+1.0
M3: V5+0.42 / Mo6+0.58 M7: V5+0.32 / Mo6+0.68 M12: Te4+0.94

O O

V5+ O O V4+ O O
O NH O NH
O M7 O Mo 6+
Te 4+ O M7 O Mo 6+
Te4+
O O M4 O M1 O O O M4 O
M1 O

O 6+ O 6+
Mo Mo
O O O
Nb5+ O
M5 O Nb5+ O M5
O O
O M9 O M9

Figure 1 Catalytically active centre of Mo7.8V1.2NbTe0.94O28.9 (M1) phase in [001]

projection and ChemDraw illustration of the active centre.5

with catalysts comprised of about 60% M1 and 40% M2 (Figure 3). This
experimental result suggests a cooperative effect (symbiosis) between the
phases.
Symbiosis between M1 and M2 phases, cooperating with each other, is
observed when the two phases are prepared together in one container (optima
of Figure 3). Separately prepared phases, co-mingled after preparation as
physical mixtures exhibit also symbiosis, however, only if the precursor phases
are in the size range of 5 mm, or lower.6,20 The observed catalytic results of a
50 wt% M1/50 wt% M2 physical mixture (4:1 on surface area basis) are shown
in Figure 4. The symbiotic effect is clearly observed, particularly at the higher
conversions, as expected.5,6 At conversions below 5% there is no enhancement
in acrylonitrile selectivity or yield of the physical mixture over that of the M1
phase alone. However, at higher conversions the enhancement is substantial as
582 Chapter 34

Figure 2 Site isolation: four catalytically active centres on M1 surface in [001]

projection.16

80

70

60
N
AN Yield (mole%)

50
Ta
40

30

20

10

0
0 20 40 60 80 100
% orthorhombic phase

Figure 3 MoV(Nb,Ta)TeO system. Acrylonitrile yield versus % orthorhombic phase

(M1).7
The Importance of Selectivity in Ammoxidation Catalysis 583
50

45

40
Selectivity to Acrylonitrile (%)

symbiosis
35

30

25

20

15
Legend: M1: 5 µm 250-425 µm
10

5 = M1 M1
= M1 M2
M1 M1
+M +M + +M , , = +M
0
0 10 20 30 40 50 60
Conversion (%)

Figure 4 Symbiosis of M1/M2 physical mixtures in propane ammoxidation.7,20 Leg-

end: }, Pure M1 phase; ’, M1 and M2 mixed as particles (250–425 mm);
,
M1 and M2 mixed as powders (B5 mm) and pressed; ~, M1 and M2 mixed
as powders, pressed and reheated at 550 1C for 1 h; m, M1 and M2 mixed as
powders, pressed and reheated at 600 1C for 1 h. The physical mixtures
consisted of 50 wt% M1/50 wt% M2, corresponding to a surface area
ratio of 4:1. Reaction temperature ¼ 380 1C; propane/ammonia/oxygen/
argon ¼ 6.1/7.0/18.0/70.2; space velocity ¼ 3.3–26.3 N cm3/(min g).

revealed in Figure 4. One can reason that at the lower conversion the classical
site isolation for M1 dictates the selectivity,5,6,16 while at higher conversions a
substantial amount of propylene that forms on the M1 phase desorbs before it
can be directly converted to acrylonitrile at the first encountered active centre,
and leaves the centre without encountering and adsorbing on a new unoccupied
V51 site which would lead to combustion. Instead, the ultimate proximity of
the M2 phase allows the desorbed propylene to interact with its surface rather
than the M1 surface from where it originated. Since the M2 phase does not
possess any V51 centres (only benign V41 centres), but ample Te41 centres
(more than on the M1 surface) it activates the olefin effectively and converts it
to acrylonitrile. It is also known that the M2 phase is more efficient for the
conversion of propylene to acrylonitrile than is M1.20,24,25
Based on the above studies, a reaction network involving the M1 and M2
phases can be proposed as illustrated in Figure 5. A schematic of M1 and M2
surface active centre distributions, as derived from the statistics of the respec-
tive phase structures, 5,6 is shown in Figure 6. The schematic illustrates that at
low throughput (mild reaction conditions) the M1 phase suffices to convert
propane to propylene. At high conversions (demanding reaction conditions)
584 Chapter 34
M1
k3

M1
k5

M1
H2 M1 H H
M1 M1 H k6
C C C C
H 3C CH 3 H 3C CH3 H 3C CH 2 H 2C CN COx
k1 k2 k4 M2
a a k7

k8
k1 = rate determining
k 2 > k1 k7 <<< k4
k3 << 1/5 k2 k8 ~ k4 > k1
k4 > k1< k2 k9 < k8
k5 << 1/5 k2 k10 < 1/5 k2 M1 M1
k6 <<< k4 k11 > k8 > k9 H k9 k
C 10
k12 < k10 H3C CH 2 M2 M2
k11 k12

Figure 5 Proposed propane ammoxidation reaction network using M1 and M2

catalysts.5,6

Mild Operating Conditions (Low Throughput and Low Conversion)

AN AN AN
C3=
C30

NH3

O2

COx C3=
AN AN
M1 M2
Demanding Operating Conditions (High Throughput and High Conversion)
AN AN AN AN AN AN
C3= C3=
C30
NH3
For C30 For C3=
Active Active
O2 Inactive Active
Waste Waste

C3=
COx AN AN C3=
M1 M2

Figure 6 Schematic of propane ammoxidation over MoV(Nb,Ta)(Te,Sb)O catalysts.5,6

The Importance of Selectivity in Ammoxidation Catalysis 585
cooperation of the phases (symbiosis) sets in, with the M2 phase becoming a
cooperative (mop-up) phase to the M1 phase.
Since symbiosis was demonstrated not only for M1/M2 mixtures prepared
together in one container but also when prepared separately and post com-
mingled as a physical mixture, provided the particle size of the phases was small
enough (r5 mm), it opens up the opportunity to alter the compositions inde-
pendently in an effort to improve the catalytic performance of either and/or
both of the phases. This is the subject of current studies.

5 Conclusions
Selectivity in heterogeneous oxidation catalysis is paramount with feed mate-
rials for commercial petrochemical processes becoming less abundant and ever
more expensive.
The desired selectivity behaviour of many heterogeneous oxidation and
ammoxidation catalysts can be explained on the basis of the site isolation
hypothesis originally proposed some forty years ago by Callahan and Grass-
elli.1 This includes many model (e.g., CuO; V2O5/KVO4), as well as well known
commercial catalysts (e.g., Bi9PMo12O52, USb3O10, FexSbyOz, (VO)2P2O7,
(K,Cs)(Ni,Co,Mg)(Fe,Ce)(Sb,P)BiMoO, and now the leading commercial
candidate for propane ammoxidation MoV(Nb,Ta)(Te,Sb)O to acrylonitrile).
The concept is a useful tool in catalyst design.
The optimized MoVNbTeO catalyst system discussed here is comprised of
three crystalline phases: Mo7.8V1.2NbTe0.94O28.9 (M1), pseudo-hexagonal
Mo4.67V1.33Te1.82O19.82 (M2) and a trace of TeMo5O16, wherein the M1 phase
is the key paraffin activating and acrylonitrile forming phase. The active centres
of M1 as proposed16 contain all key elements V51, Te41 and Mo61 properly
spaced and within bonding distance of each other, to effectively transform
propane directly to acrylonitrile under ammoxidation conditions. The active
centres are spatially separated from each other by four Nb51 pentagonal
bipyramids (each surrounded by five Mo–O octahedra), which provides for
the necessary site isolation, consistent with our isolation concept.1,2
At high propane conversions, symbiosis between the M1 and M2 phases is
observed provided the two phases are finely divided (B5 mm),20 thoroughly
mixed and in intimate contact with each other (nano-scale). Under these
conditions enhanced selectivity and yields of acrylonitrile are obtained as a
result of phase cooperation, a concept also well known in oxidation cataly-
sis.2,21 With the demonstration that symbiosis can be obtained when the two
phases are prepared separately and mixed later, the two phases can be doped
independently in an effort to improve the overall catalytic performance of the
system.
While selectivity is a key requirement for successful selective oxidation and
ammoxidation catalysis, it is not sufficient by itself and must be coupled with
acceptable activity, particularly when designing and formulating commercially
feasible catalysts. Selectivity and activity must be optimized and balanced
586 Chapter 34
simultaneously in a catalytic composition. The mutual attainment of optimal
selectivity and activity might be helped by employing the described concepts of
site isolation1 and phase cooperation21 in the design of new catalysts.

Acknowledgement
The author thanks the Alexander von Humboldt Foundation for partial
financial support of the work reported here.

References
1. J.L. Callahan and R.K. Grasselli, AIChE J., 1963, 9, 755.
2. R.K. Grasselli, Top. Catal., 2002, 21, 79.
3. R.K. Grasselli, Handbook of Heterogeneous Catalysis, vol 5, G. Ertl,
H. Knözinger and J. Weitkamp (eds), 1997, 2303; ibid., Proceedings of
DGMK Conference, Hamburg, Germany, 2001, 147; ibid., La Chimica e
l’Industria, 2001, 83, 25.
4. R.K. Grasselli, Catal. Today, 1999, 49, 141.
5. R.K. Grasselli, D.J. Buttrey, P. DeSanto Jr., J.D. Burrington, C.G.
Lugmair, A.F. Volpe Jr. and T. Weingand, Catal. Today, 2004, 91–92, 251.
6. R.K. Grasselli, Catal. Today, 2005, 99, 23.
7. R.K. Grasselli, D.J. Buttrey, J.D. Burrington, A. Andersson, J. Holmberg,
W. Ueda, J. Kubo, C.G. Lugmair and A.F. Volpe Jr., 2006, 38, 7.
8. G. Belussi and M.S. Rigutto, in: Advanced Zeolite Science and Applications,
Stud. Surf. Sci. Catal., vol 85, J.C. Jansen, M. Stoecker, H.G. Karge and
J. Weitkamp (eds), Elsevier, Amsterdam, 1991, 177.
9. G. Belussi and C. Perego, Handbook of Heterogeneous Catalysis, vol 5,
G. Ertl, H. Knözinger and J. Weitkamp (eds), 1997, 2329.
10. G.I. Panov, A.S. Kharitonov and V.I. Sobolev, Appl. Catal., 1993, 98, 1.
11. E.V. Starkov, K.A. Dubkov, L.V. Pirutko and G.I. Panov, Top. Catal.,
2003, 23, 137.
12. J.M. Thomas, R. Raja, G. Sankar and R.G. Bell, in Proceedings of 12th Int.
Congr. On Catalysis, Granada, Stud. Surf. Sci. Catal., vol 130, A. Corma,
F.V. Melo, S. Mendioroz and J.L.G. Fierro (eds), Elsevier, Amsterdam,
2000, 887.
13. R. Raja, G. Sankar and J.M. Thomas, Angew. Chem. Ind. Ed., 2000, 39,
2313.
14. J.M. Thomas and R. Raja, Proc. Nat. Acad. Sci., 2005, 102, 13732.
15. J.M. Thomas, Top. Catal., 2006, 38, 3.
16. R.K. Grasselli, J.D. Burrington, D.J. Buttrey, P. DeSanto Jr., C.G.
Lugmair, A.F. Volpe Jr. and T. Weingand, Top. Catal., 2003, 23, 5.
17. P. DeSanto Jr., D.J. Buttrey, R.K. Grasselli, C.G. Lugmair, A.F. Volpe Jr.,
B.H. Togy and T. Vogt, Top. Catal., 2003, 23, 23.
18. P. DeSanto Jr., D.J. Buttrey, R.K. Grasselli, C.G. Lugmair, A.F. Volpe Jr.,
B.H. Togy and T. Vogt, Z. Krist., 2004, 219, 152.
The Importance of Selectivity in Ammoxidation Catalysis 587
19. E. Garcia-Gonzalez, J.M. Lopez Nieto, P. Botella and J.M. Gonzalez-
Calbet, Chem. Mater., 2002, 14, 4416.
20. J. Holmberg, R.K. Grasselli and A. Andersson, Appl. Catal. A: Gen., 2004,
270, 121.
21. R.K. Grasselli, Top. Catal., 2001, 15, 93.
22. C.G. Lugmair, J. Zysk and R.K. Grasselli, U.S. Patent Appl. 2005/0054869
A1.
23. M. Hatano and A. Kayo, European Patent 318,295, 1988; T. Ushikubo,
K. Oshima, A. Kayou, T. Umezawa, K. Kiyono and I. Sawaki, European
Patent 529,853, 1992; T. Ushikubo, K.Oshima, A. Kayou, T. Umezawa,
K. Kiyono, I. Sawaki and H. Nakamura, US Patent 5,472,925, 1995;
H. Hinago, S. Komada and A.K. Kogyo, US Patent 6,063,728, 2000.
24. J. Holmberg, R.K. Grasselli and A. Andersson, Top. Catal., 2003, 23, 55.
25. W. Ueda, D. Vitry and T. Katou, Catal. Today, 2005, 99, 43.
CHAPTER 35

The Mysteries of Water in

Catalyst Preparation: Solvent or
Much More?
MICHEL CHE
Institut Universitaire de France, Laboratoire de Réactivité de Surface,
Université Pierre et Marie Curie - Paris 6, 4 Place Jussieu, 75252 Paris Cedex 05,
France

1 Introduction
A hundred years ago, in the single and miraculous year 1905, Einstein wrote
five papers1–5 that shook the world and changed the face of physics. They were
at the origin of the World Year of Physics 2005 (Einstein in the 21st century),
which led the French CNRS (National Centre for Scientific Research) to
publish a special issue,6 in which the 10 great enigmas of physics were identified.
It is striking that the first one, expressed as ‘‘the mysteries of water’’, could have
been ranked also as N1 1 for biology and chemistry, so overwhelming is the role
of water in life processes and in the genesis of intelligent materials, among
which catalytic systems can be included.7
In view of the importance of catalysis and catalysts in the production of
chemicals, it is not surprising that the American Chemical Society decided to
establish an award in 1999 for ‘‘creative research in homogeneous and hetero-
geneous catalysis’’. In selecting Sir John Meurig Thomas as first recipient ‘‘for
having laid down the basic principles for catalytic site-engineering by designing
and synthesising novel, exquisitely tailored solid catalysts’’, the American
Chemical Society beautifully underlined three features of Sir John’s research:
its conceptual nature, its innovating character and its elegance. It is important
to underline that Sir John largely contributed to the development of physical
techniques especially designed for determining active site structures under
operating conditions.

588
The Mysteries of Water in Catalyst Preparation 589
The present contribution deals with two topics, catalyst preparation and
water,8 which always have been dear to Sir John (see for instance Refs. 9 and 7,
respectively).
Supported catalysts constitute the most important class of catalytic systems,
because of the variety of reactions they are able to promote.10 Several strategies
exist to design and synthesize such catalysts and Sir John has reviewed one of
them, the integrated strategy, for active site-engineering in micro- and meso-
porous solids.11 When large quantities of catalysts are required, some strategies
however become difficult or impossible to apply.
The present lecture concerns such types of catalysts, particularly oxide-
supported ones, produced at the industrial scale from conventional oxides
(alumina, silica, zeolites) using water-soluble transition metal complexes as
precursors of the catalytically active phase.
It is noteworthy that the second and third enigmas of physics identified by
the CNRS6 are the untractable turbulence and the obscure nature of glass,
both involved when catalysts are to be prepared in aqueous solution at the
laboratory scale.

2 Molecular Approach to Supported Catalyst

Preparation
In recent years, major advances have been made in physical techniques12
particularly for the in situ characterization of catalysts, either during prepara-
tion or in working conditions.13–15 A molecular approach based on the use of
such techniques and of transition metal elements has been developed in our
laboratory and applied to the study of oxide-supported catalysts.16 The role of
transition metal complexes is threefold16: (i) transition elements generally have
remarkable catalytic properties, (ii) their partly filled d orbitals provide them
also with unique optical and magnetic properties, and (iii) such properties
followed by suitable spectroscopies strongly depend upon the immediate envi-
ronment of the transition metal elements which can thus function as probes of
their own interactions with the oxide support in the course of preparation, thus
providing very valuable information on the role played by water.
The preparation of catalysts10 involves several stages called unit operations
in industry17 or preparation steps in the laboratory, such as impregnation,
elimination of the solvent, drying, calcination, sulfidation and reduction. In-
dustry and laboratory procedures are the same and only differ by the quantities
of catalysts prepared, typically of the order of the ton and gram respectively.
Therefore, we shall use either unit operation or preparation step in what follows.
This contribution will consider the deposition methods most frequently used
in the industry, i.e., impregnation and equilibrium adsorption. The catalysts
obtained are characterized both at the molecular level by spectroscopies such as
diffuse reflectance UV–Visible, NMR and EXAFS, and at the macroscopic
level by techniques such as TEM, TPR and XRD.
590 Chapter 35

3 The Versatile Role of Water

3.1 Water as Ionizing and Dissociating Solvent
Despite numerous studies, it is still a challenge for theoretical chemists to
explain the three anomalies of water simultaneously6: (i) its strong cohesion
(high fusion and high boiling temperatures), (ii) its large expansion below 4 1C
and upon solidification, and (iii) its high dielectric constant (e ¼ 80). The last
property makes water an ionizing and dissociating solvent. It is the most
widespread and safest solvent used for the preparation of industrial catalysts,
all the more as it is largely available, cheap and environment-friendly.

3.2 Water as r Donor–p Donor Ligand and/or Acid–Base

Entity
The early stages of reforming catalyst preparation start by the deposition of
platinum on g-alumina from a hexachloroplatinic acid precursor solution.18
The diluted commercial aqueous solutions of hexachloroplatinic acid (say
5
103–7
102 M in Pt), possibly containing added HCl but not modified
otherwise, can be conveniently investigated by 195Pt NMR.19,20 From the NMR
spectra and the chemical shifts of the various peaks ([PtCl6]2 is taken as
reference), the speciation21 of platinum can be easily followed.19 Two types of
reaction can be evidenced depending on pH and the concentrations of HCl and
hexachloroplatinic acid:
(i) substitution of chlorides

½PtCl6 2 þ H2 O ! ½PtCl5 ðH2 OÞ þ Cl ð1Þ

0 ppm 504 ppm

½PtCl5 ðH2 OÞ þ H2 O ! ½PtCl4 ðH2 OÞ2  þ Cl ð2Þ

1016 ppm

and (ii) acido–basic reactions

½PtCl5 ðH2 OÞ ! ½PtCl5 ðOHÞ2 þ Hþ ð3Þ
640 ppm

½PtCl4 ðH2 OÞ2  ! ½PtCl4 ðOHÞðH2 OÞ þ Hþ ð4Þ

½PtCl4 ðOHÞðH2 OÞ ! ½PtCl4 ðOHÞ2 2 þ Hþ ð5Þ

1167 ppm

In these reactions, because of the two electron doublets on oxygen, water acts
as s donor and p donor ligand22 in the platinum(IV) complexes (Reactions (1)
and (2)), and/or as acid–base entity (Reactions (3)–(5)).
The Mysteries of Water in Catalyst Preparation 591

3.3 Water as Viscous Solvent Able to Favour Ion Pairs

in the Presence of a Charged Surface23
When solid oxides are put in aqueous solutions, surface hydroxyl groups are
formed which behave as amphoteric species: they may be protonated (reverse of
Reaction (6)) or deprotonated (Reaction (7)), according to the solution pH:
SOHþ
2
! SOH þ Hþ Ka1 ð6Þ

SOH ! SO þ Hþ Ka2 ð7Þ

Therefore, a pH-dependent surface charge will develop. In particular, there

will be a value of pH ¼ (pKa1 + pKa2)/2 for which the total electric charge of
the surface is zero: the point of zero charge (PZC). At lower pH values, the
surface bears a global positive charge, able to attract negatively charged
complexes such as [PtCl6]2– and at higher pH, a global negative charge, able
to attract positively charged complexes such as [Ni(NH3)6]21 by mere electro-
static adsorption. Typical PZCs are 2–2.5 for silica, 8–8.5 for alumina and
4.5–6.5 for titania. Figure 1 illustrates the various adsorption models (I–IV) of
a transition metal complex in an aqueous solution in contact with an oxide
surface together with the corresponding pertinent types of chemistry.24 It
corresponds to the case of a positively charged complex in contact with a
negatively charged surface at a pH 4 PZC of the corresponding oxide. In
aqueous solution and in the absence of any oxide, a transition metal complex

A-
A-
A- A-
L L OH OH
L L
M
L L S M
L L
OH OH
A-
L L
A-
L L
A-
M
L L L L
M L L
L L M
I
O- O-
II
OH OH
III
O- O-
IV Mixed phase

Electrochemistry
Supramolecular Chemistry
Support
Coordination Chemistry
Geochemistry

Figure 1 Various adsorption models (I–IV) of a transition metal complex initially in

aqueous solution upon contact with an oxide surface and depending on
experimental conditions.24 The figure corresponds to the case of a positively
charged complex in contact with a negatively charged surface at a
pH 4 PZC of the corresponding oxide. Typical examples are aqueous
solutions of octahedral [Ni(NH3)6]21 or square planar [Pd(NH3)4]21 pre-
cursor complexes put in contact with silica at pH 4 PZC of SiO2. The
corresponding pertinent types of chemistry are also given.
592 Chapter 35
enjoys rotational and translational freedom which becomes much more
restricted upon electrostatic adsorption on a charged surface (model I) because
of the viscosity of water.
Even in dilute electrolyte solutions, many properties of water are strongly
modified in the immediate vicinity of a charged interface, especially its density.
This effect has chiefly been studied by electrochemists interested in charged
metallic surfaces: water close to a silver electrode bearing a surface charge of
0.25 C/m2 reaches a density of 2.0,25,26 i.e., close to that of ice VII which is
formed at a pressure of 2.2 GPa (22,000 atmospheres). This phenomenon is
called electrostriction.
In the first layer of water molecules, the interaction of water dipoles with the
surface electric field can be an order of magnitude stronger than hydrogen bonds
(which are themselves an order of magnitude higher than kT at room temper-
ature). Thus, the electric dipoles of the water molecules are strongly oriented, in
the direction of the surface or away from it depending on the sign of the surface
charge. As a consequence, the electric permittivity e falls down from ebulk ¼ 78,
to values as low as 2.5.27 It is expected that ion pairing should be favoured in the
interface region with respect to the bulk solution. Furthermore, transition metal
ions located in this region will have a strongly decreased mobility as though they
were imbedded in a glassy matrix.28 Thus, water close to charged surfaces
becomes a viscous solvent favouring the formation of ion pairs.

3.4 Water as Ligand and/or H-Bond Intermediate

An intermediate situation between electrostatic adsorption (Figure 1, model I)
and inner sphere complex formation (model III) is the formation of an outer
sphere complex (model II) where the original ligands remain coordinated to the
metal ion but form weak specific bonds with the surface, for instance hydrogen
bonds. This is closely related to the field of supramolecular chemistry.29
Unless the precursor complex bears no charge (molecular complex) and/or
the surface is neutral (pH ¼ PZC), this supramolecular interaction is accom-
panied by an electrostatic interaction as described earlier.
Outer sphere complex formation can be followed in the [PtCl6]2–/silica
system.30 195Pt NMR spectra indicate that the main species, at the liquid–solid
interface, are [PtCl5(H2O)]– and [PtCl4(H2O)2]. By comparison with the
[PtCl5(H2O)]–/crown ether 18-C-6 model system, which has been studied by
several techniques (particularly X-ray diffraction) and shows a very similar
195
Pt NMR shift,31 it has been proposed that the [PtCl5(H2O)]– complex is
bonded to the surface of silica by means of a solvent molecule and hydrogen
bonds (Figure 2). The three oxygens involved belong either to three of the six
oxygens of the crown ether in the model system or to three oxygens of (Si–O)6
cycles, denoted S6R, at the silica surface.
It seems that there is a molecular recognition phenomenon between the outer
sphere Pt complex and the oxide support, and that the solvent has an important
role in this three-partner (precursor complex–solvent–oxide support) system.30
The Mysteries of Water in Catalyst Preparation 593

Cl Cl
Cl Cl Cl Cl
494 ppm PtIV 493 ppm Pt IV

Cl Cl Cl Cl
O O
H H H H

O O O O
Si
Si Si
O O
18-C-6 O S6R O
H H
O H H O
Si

O O O Si
O
Si

Figure 2 Outer sphere complex formed between [PtCl5(H2O)]– and the crown ether
18-C-6 surface model after Ref. 31 and extrapolation to the cycle S6R of the
silica surface, both characterized by 195Pt NMR with chemical shifts of 49431
and 493 ppm30 respectively.

While the complex is the guest, the oxide support acts as the receptor, the basic
phenomenon being here self-assembly, based on hydrogen bonding and van der
Waals interactions. This type of specific interaction falls into the so-called
heterosupramolecular chemistry;32 in this context, the [PtCl5(H2O)]–/silica
system can be seen as a non-covalent heterosupramolecular assembly while
water behaves as ligand and/or H-bond intermediate.

3.5 Water as Labile and Weak r Donor–p Donor Ligand

Catalytically active transition metal ions are generally held to the oxide support
by sufficiently strong iono-covalent bonds (model III) (Figure 1) to withstand
catalytic reaction conditions (usually flow of reactants, high temperature and high
pressure). The bonding of the transition metal precursor complex to the oxide
surface corresponds to the so-called grafting process,33 i.e., the substitution of the
ligands by surface oxygens leading to the formation of an inner sphere complex.
The grafting process would correspond to the following reaction:

f2  SiO ; ½NiðNH3 Þ4 ðH2 OÞ2 2þ g ! ½NiðNH3 Þ4 ð SiOÞ2  þ 2 H2 O ð8Þ

Reaction (8) shows that the two water molecules are the targets for grafting
to occur by ligand substitution. In practice, this however may not happen
because both water and ammonia are kinetically labile. To make sure that
substitution indeed occurs via Reaction (8), the following conditions should be
met by the precursor Ni(II) complex in aqueous solution:34,35

(i) The complexation equilibria in the aqueous phase should be such as to

start with almost 100% of nickel as one complex of well-defined
594 Chapter 35
21
Table 1 Formation constants of complexes [Ni(H2O)62x(en)x] in water
solution at 25 1C (horizontal lines of data correspond to different
references given in Ref. 34).
log b1 log b2 log b3
5.47 11.69 16.76
7.45 13.68 18.02
7.54 13.94 18.39
7.60 14.08 19.13

17
Table 2 Water exchange rates k1 at 25 1C, measured by O NMR.34
Complex k1 (s1)
[Ni(H2O)6]21, pH 5.5 3.6
104
[Ni(H2O)5(NH3)]21 2.5
105
[Ni(H2O)4(NH3)2]21 6.1
105
[Ni(H2O)3(NH3)3]21 2.5
106
[Ni(H2O)6]21, pH 6 4.4
104
[Ni(H2O)4(en)]21 4.4
105
[Ni(H2O)2(en)2]21 5.4
106

stoichiometry rather than with a mixture of different complexes. This is a

thermodynamic condition. Table 1 illustrates that the formation con-
stants of Ni(II) complexes involving water and ethylenediamine
(en ¼ NH2–CH2–CH2–NH2) are well separated and respond to this
criterion.
(ii) The ligands that are to be substituted in the grafting process should be
sufficiently labile while ‘‘spectator ligands’’ should be inert. This condi-
tion has thermodynamic as well as kinetic aspects.

From a kinetic point of view, it is well known that substitution of some aqua
ligands for polydentate ligands, such as ethylenediamine, in octahedral com-
plexes increases the lability of the remaining aqua ligands34 as evidenced by
Table 2. It is seen that replacement of two water molecules by the bidentate en
ligand increases the exchange rate of water k1, each time, by an order of
magnitude.
This lability has some practical consequences. It allows in particular to graft
Ni(II) ions by 1, 2 or 3 bonds to the silica surface when the precursor com-
plexes contain 1, 2 or 3 labile water ligands, i.e., [Ni(en)(dien)(H2O)]21,
[Ni(en)2(H2O)2]21 and [Ni(dien)(H2O)3]21 respectively, (dien ¼ NH2–CH2–
CH2–NH–CH2–CH2–NH2 is the tridentate ligand diethylenetriamine). Figure
3 gives the structures of the supported complexes, deduced from EXAFS and
UV–Visible data, after grafting of these precursor complexes to the surface of
silica.36
The previous results surprisingly observed with amorphous silica, which is
formed of randomly distributed –[Si–O]n– cycles, with n Z 337 (Figure 4),
The Mysteries of Water in Catalyst Preparation 595

[Ni(en)(dien)(H2O)1]2+ [Ni(dien)(H2O)3]2+

[Ni(en)2(H2O)2]2+

A A A
A

A A
O
O
A = Si or Si Si (strained)

Silica

Figure 3 Models for molecular recognition with interactional complementarity

(V. Marchi-Artzner, F. Artzner, O. Karthaus, M. Shimomura, K. Ariga,
M. Kunitake, J.-M. Lehn, Langmuir, 1998, 14, 5164) between Ni(II)
amine complexes ([Ni(en)(dien)(H2O)]21, [Ni(en)2(H2O)2]21 and [Ni(dien)
(H2O)3]21) and surface sites of silica after Ref. 36. The complementarity is
assumed to result from cooperative formation of covalent bonds between
Ni and Si–OH ligands, and hydrogen bonds joining H of amine ligands and
acceptor groups on the silica surface.

OH
O Si
O O OH Si Si O O
OH O OH
Si
Si OH Si O O Si
3 O OH
Si SiOH 7
O O
O 5 OH Si O
Si O 3
6 Si O OH O O O
8 O Si
Si Si O
Si
O O OH OH Si OH
Si OH O Si Si
O
O O 5 6 O
O Si Si O O Si
6 Si O
O OH Si O O O Si
O O O OH Si 5 Si
SiOH 8 O
O O OH
Si 4 OHSi 5 O O Si O OH
O OH Si
O Si Si
O Si O O 4 7 O
Si O
OH O
OH 3 O
O O O Si
OH Si Si
Si O Si OH
O OH O O
Si

Figure 4 A model of the amorphous surface of silica after Ref. 37.

suggest that transition metal complexes can act as probes towards specific
adsorption sites of silica, hence leading to a similar phenomenon encountered
in bio- and supramolecular chemistry, referred to as molecular recognition,36
already mentioned for outer sphere complexes (Section 3.4).
596 Chapter 35
Because of its two electron doublets on oxygen, we have seen that water
behaves as a s donor–p donor ligand (Section 3.2). The question now arises as
to what type of ligand belongs the surface groups able to graft transition metal
complexes to oxides?
Pure cases of inner sphere complex formation are scarce since other
phenomena such as dissolution–reprecipitation (see Section 3.6) may occur
in parallel. The clearest instances are observed when ‘‘spectator’’ ligands
are inert to substitution, either because of the chelate effect (cis-[Ni(en)2(-
H2O)2]21 on various supports34) or because of high crystal field activation
energy ([Co(NH3)5(RO)]x1 on Z-Al2O338, RO ¼ OH, H2O or alcohol).
After deposition from the liquid phase and drying at room temperature, the
cis-[Ni(en)2(H2O)2]21 complex with its two labile H2O ligands binds to SiO2,
g-Al2O3 or Y zeolite to lead to cis-[Ni(en)2(SO)2]x1. On the basis of their crystal
field parameter D, oxide supports (in bold) form a spectrochemical series which
can be introduced into the ligand spectrochemical series, showing that surface
groups of oxides are weak ligands:22,34

DCl oDAlO oDZO oDSiO oDH2 O oDNH3 oDen

In summary, the results presented above show that water is a labile and weak
s donor–p donor ligand, which can be used to target the grafting process of
transition metal complexes to oxide surfaces, by one, two or three iono-
covalent bonds to the surface of oxides whose surface groups appear to be
ligands weaker than water.

3.6 Water as Reactant or Reaction Product

Many reports have been published on the formation, during the deposition step
itself, of mixed phases or molecular species, containing both the transition
metal of the precursor complex and an element from the support. Typical
examples are the formation of the mixed phase nepouite, Si2Ni3O5(OH)4, for
the Ni(II)/SiO2 system39 (Figure 1, model IV) or the molecular heteropolyan-
ion, Al(OH)6Mo6O183–, for the Mo7O246–/g–Al2O3 system.40 The phenomenon
is quite general, since it occurs upon contact of conventional oxides (silica,
alumina) with aqueous solutions of precursor complexes, be they cationic, e.g.
[Ni(NH3)6]21, or anionic, e.g. Mo7O246–, and for different methods of deposi-
tion (impregnation, equilibrium adsorption, deposition–precipitation).
Although there has been no systematic study on this aspect, the contact time
between the solution and the support seems to play an important role. The
formation of such mixed phases and/or molecular entities is all the more
important as the contact time increases. For instance, after an exchange process
of 500 h, nickel is found to be essentially as a nickel silicate deposited on
silica.41
It turned out that this came as no surprise to the scientific community of
geochemists. They have been studying for years the alteration of primary
The Mysteries of Water in Catalyst Preparation 597
minerals on weathering, i.e., those changes brought about by climatic factors,
including exposure to the soil solution. Dissolution followed by neoformation
of secondary phases usually results.
Of course geochemistry is most often concerned with ‘‘geological’’ time-
scales, but this is not necessarily so. Many relevant data are to be found in Ref.
42. To give orders of magnitude for support oxides, the half-life of a surface Al
is 669 days (5.8
107 s) for a-Al2O3, but only 44 days (3.8
106 s) for
d-Al2O3.43 As discussed below, the presence of transition metal complexes
may speed up dissolution phenomena. In the case of the [MgII(H2O)6]/SiO2
system, the timescale for dissolution–reprecipitation was typically a few tens of
hours, or 105 s,44 i.e., an order comparable to the duration of unit operations in
catalyst preparation.17 Furthermore, catalyst preparation often includes a
drying step generally performed at temperatures between 90 and 120 1C. In
this temperature range, some water solution may remain in the porosity for a
significant lapse of time before drying is completed, and of course dissolution
reactions will be speeded up with respect to room temperature.45
In all those geochemistry processes, water plays a dominant role, first as
reactant and second as transport agent (see Section 3.7).
Let us now consider the case of g-alumina, the oxide support most frequently
used in the industry to prepare supported catalysts. Hydration of this oxide has
often been reported to occur via the transformation of the surface into
aluminium hydroxide-like layers, but there was little evidence to support this
hypothesis. It has now been shown46 by XRD, TEM, electron diffraction and
solubility studies that a second process of hydration takes place that involves
the dissolution of alumina and subsequent precipitation of well-shaped
Al(OH)3 particles from supersaturated alumina aqueous solution. This process
can be observed at a macroscopic scale (XRD, TEM) at pH 5 (Figure 5) and

200 nm

002
112

110

JCPDS # 76-1782

Figure 5 TEM image of g-alumina after suspension in distilled water for 880 h at pH
5. The insert shows the electron diffraction pattern obtained for the large
particle circled in the centre of the picture. The gibbsite structure is in
agreement with the XRD results at this pH.46
598 Chapter 35
above, provided that the contact time between alumina and water exceeds
10 h.46 In the reaction:

g-Al2 O3 þ 3 H2 O ! 2AlðOHÞ3 ðbayerite; gibbsiteÞ ð9Þ

and in geochemistry terms, alumina is the primary mineral while bayerite and
gibbsite are the secondary minerals, while water is a chemical reactant.
Let us now consider the same system but in the presence of a molybdenum
salt, say ammonium heptamolybdate, often used to prepare hydrodesulfurizat-
ion catalysts. The deposition of Mo on g-Al2O3 by the equilibrium adsorption
method has been studied by 95Mo NMR, Raman and IR.40 Spectroscopic data
converge to indicate that a previously unrecognized species, the Anderson-type
heteropolymolybdate, Al(OH)6Mo6O183–,47 plays a major role in this type of
synthesis as it is quantitatively formed in the solution within a few hours, by
reaction of the heptamolybdate with dissolved aluminic species. This results in
a considerable increase of alumina solubility in conditions generally thought to
be non-aggressive. Furthermore, this species is also evidenced by proton cross
polarization (CP) 27Al NMR on the surface of the supported catalysts after
deposition of molybdenum, although it is harder to observe than in the liquid
phase, because of the presence of the Al atoms of the support. A parallel is
drawn with a well-known concept from geochemistry, i.e., ligand-promoted
oxide dissolution. Figure 6 gives a schematic representation of the ligand-
promoted dissolution of alumina together with the corresponding 27Al NMR
spectra.40
In more general terms, those phenomena, i.e., the dissolution of the oxide
support followed by reprecipitation of a mixed species, containing elements of
both the support (Al) and the precursor (Mo) require the formation of bonds
such as Al–O–Mo which can be accounted for by the following types of
reaction:48
SOH þ H2 OM ! SOHM þ H2 O ð10Þ

SOHþHOM ! SOM þ H2 O ð11Þ

where no attempt is made to indicate the complete coordination sphere;

only the pertinent ligands around S (Al, Si, etc.) representing the support
element and M (Ni, Mo, Pd, Pt, etc.) representing the metal of the precursor are
given.
The dissolution of the oxide support leads to support monomers which can
react with the precursor complex to form mixed entities.
Olation (Reaction (10)) and oxolation (Reaction (11)) are heterocondensa-
tion processes in which a hydroxy or an oxo bridge between S and M are
formed respectively with water as reaction product. Because it has two lone
pairs, water has been known for long to be a bridging ligand, as are OH groups
and oxide ions which can form bonds with both S and M. In Reaction (10) and
for some specific cases, it has been observed that upon bonding to the hydroxyl
The Mysteries of Water in Catalyst Preparation 599

Figure 6 Schematic representation of the ligand-promoted dissolution of alumina in

an aqueous solution containing heptamolybdate following equilibrium
adsorption.40 The 27Al NMR liquid-state spectra of the filtrates obtained
after 168 h at various pH are presented on the left top, while the 27Al
CP-MAS NMR spectra of g-Al2O3 alone and with 6 and 8 wt.% Mo
prepared at pH 4 after 168 h are shown on the right top.

group water forms a m-(H3O2) bridging ligand, from which water can be
eliminated as reaction product.49 When ligands such as NH3 or en, with only
one lone pair per N are found in the coordination of the metal centre, then
heterocondensation Reactions (10) and (11) are no longer possible.16,50

3.7 Water as Transport Agent

One of the important aims of geochemists is to understand how minerals are
formed and to study the circulation of the elements in nature, on the basis of
the properties of their atoms and ions.51 As emphasized earlier, water plays a
dominant role particularly to transport matter as molecular entities after
dissolution of minerals by processes described above. If proper conditions
are met, reprecipitation can then occur with the formation of neophases. There
are many examples which can be found in nature and this has been reviewed by
Stumm.42
As far as catalyst preparation is concerned, the role and the importance of
water as transport agent have been elegantly demonstrated by Clause and
co-workers in the formation of hydrotalcites on leaving alumina for 2 weeks at
333 K in contact with 10–2 M aqueous solutions of Co(II), Ni(II) or Zn(II) at
600 Chapter 35

Figure 7 Experiment evidencing the process of dissolution–reprecipitation occurring

in the preparation of oxide-supported catalysts: it illustrates the role of water
as transport agent (see text).

pH ¼ 9.52 Figure 7 gives a schematic representation of the experiment, whose

key element is a dialysis membrane. At the beginning, the membrane containing
only the alumina support in the form of spheres was introduced into water in
the beaker. The solution containing the Co(II), Ni(II) or Zn(II) aqua complexes
was then introduced drop-wise into the beaker. After 2 weeks at 333 K, the
precipitates formed both inside and outside the membrane were recovered
separately and analyzed. They were found to be the same: a hydrotalcite
containing the two elements originally separated by the dialysis membrane.
This evidences that alumina has dissolved to produce [Al(OH2)6]31 able to
cross the membrane to form hydrotalcite outside the membrane. The aqua
complexes were able to cross the membrane in the opposite direction to form
hydrotalcite inside the membrane. Examples of water as transport agent are
now frequently found in the literature on supported catalyst preparation.

4 Conclusions: Still on Water, and its Surface

I remember reading Sir John’s comments on the book Faraday: The Life by
James Hamilton, Harper Collins, pp. 465+XXI, 2002 with great attention.
They demonstrated that he loved accuracy, science and comprehensiveness. He
entitled his comments: ‘‘Mozart – but only a little of his music’’. I do hope that
Sir John will read my contribution with the same critical eyes and tell me its
weaknesses. I am sure he will come up with some most valuable comments,
leading to future collaboration. I am looking forward to it.
The Mysteries of Water in Catalyst Preparation 601

Figure 8 A physico–chemical promenade on the Seine river: water as a moving

surface.

After this little physico–chemical promenade between water and oxide

surfaces, I cannot refrain from remembering the moments of pure pleasure
we all had ‘‘on’’ the Seine river with Lady Margaret and Daniele on 22 May
1993 (Figure 8). This perhaps was the motivation to organize the banquet of the
13ICC in Paris in 2004 on the Seine river.
I am also delighted with the title of the book in honour of Sir John. I
remember inviting him to deliver the opening lecture at the very First
EuropaCat Congress on Catalysis in Montpellier (France) in 1993, and pro-
posing the title ‘‘Turning Points of Catalysis’’! His lecture led to two reviews
published in Angew. Chem., Int. Ed. Engl., 1994, 33, 913 (Turning Points of
Catalysis) and Bull. Soc. Chim., 1994, 131, 463 (Landmarks in the evolution of
heterogeneous catalysts).

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19. B. Shelimov, J.F. Lambert, M. Che and B. Didillon, J. Am. Chem. Soc.,
1999, 121, 545.
20. B. Shelimov, J.F. Lambert, M. Che and B. Didillon, J. Mol. Catal. A, 2000,
158, 91.
21. For the definition of speciation see D.M. Templeton, F. Ariese, R. Cornelis,
L.-G. Danielsson, H. Mantau, H.P. Van Leeuwen and R. Lobinski, Pure
Appl. Chem., 2000, 72, 1453.
22. C. Lepetit and M. Che, J. Mol. Catal., 1995, 100, 147.
23. J.F. Lambert and M. Che, Stud. Surf. Sci. Catal., 1997, 109, 91.
24. K. Dyrek and M. Che, Chem. Rev., 1997, 97, 305.
25. M.F. Toney, J.N. Howard, J. Richer, G.L. Borges, J.G. Gordon, O.R.
Melroy, D.G. Wiesler, D. Yee and L.B. Sorensen, Surf. Sci., 1995, 335, 326.
26. I. Danielewicz-Ferchmin and A.R. Ferchmin, J. Phys. Chem., 1996, 100,
17281.
27. I. Danielewicz-Ferchmin, J. Phys. Chem., 1995, 99, 5658.
28. V. Bassetti, L. Burlamacchi and G. Martini, J. Am. Chem. Soc., 1979, 101,
5471.
29. J.M. Lehn, Supramolecular Chemistry, VCH, Weinheim, 1995.
30. S. Boujday, J. Lehman, J.F. Lambert and M. Che, Catal. Lett., 2003, 88, 23.
31. D. Steinborn, O. Gravenhorst, H. Hartung and U. Baumeister, Inorg.
Chem., 1997, 36, 2195.
32. X. Marguerettaz, A. Merrins and D. Fitzmaurice, J. Mater. Chem., 1998, 8,
2157.
The Mysteries of Water in Catalyst Preparation 603
33. For the definition of grafting, see F. Averseng, M. Vennat and M. Che,
Handbook of Heterogeneous Catalysis, G. Ertl, H. Knözinger, F. Schüth
and J. Weitkamp (eds), VCH-Verlag, Weinheim, 2007.
34. J.F. Lambert, M. Hoogland and M. Che, J. Phys. Chem. B, 1997, 101,
10347.
35. E. Marceau, X. Carrier, M. Che, O. Clause and C. Marcilly, Handbook of
Heterogeneous Catalysis, G. Ertl, H. Knözinger, F. Schüth and J. Weitkamp
(eds), VCH-Verlag, Weinheim, 2007.
36. S. Boujday, J.F. Lambert and M. Che, Chem. Phys. Chem., 2004, 5, 1003.
37. S.H. Garofalini, J. Non-Cryst. Solids, 1990, 120, 1.
38. Y. Chen, J. Hyldtoft, C.J.H. Jacobsen, D.H. Christensen and O.F. Nielsen,
Spectrochim. Acta, 1994, 50A, 1879.
39. P. Burattin, M. Che and C. Louis, J. Phys. Chem. B, 1997, 101, 7060.
40. X. Carrier, J.F. Lambert and M. Che, J. Am. Chem. Soc., 1997, 119, 10137.
41. M. Houalla, F. Delannay, I. Matsuura and B. Delmon, J. Chem. Soc.,
Faraday Trans. I, 1980, 76, 2128.
42. W. Stumm, Chemistry at the Solid-Water Interface: Processes at the
Mineral-Water and Particle–Water Interface in Natural Systems, Wiley,
New York, 1992.
43. B. Wehrli, E. Wieland and G. Furrer, Aquatic Sci., 1990, 52, 52, quoted in
Ref. 42.
44. J.B. d’Espinose de la Caillerie, M. Kermarec and O. Clause, J. Phys.
Chem., 1995, 99, 17273.
45. C. Louis, Z.X. Cheng and M. Che, J. Phys. Chem., 1993, 97, 5703.
46. X. Carrier, E. Marceau, J.F. Lambert and M. Che, J. Colloid Interface Sci.,
2007, 308, 429.
47. For a description of the structure and properties of polyoxometalates, see
the review: P. Gouzerh and M. Che, L’Actualite´ Chimique, 2006, 298, 9.
48. C.J. Brinker and G.W. Scherer, Sol-Gel Science, Academic Press, New
York, 1990, 26.
49. M. Ardon, A. Bino and K. Michelsen, J. Am. Chem. Soc., 1987, 109, 1986.
50. J.Y. Carriat, M. Che, M. Kermarec, M. Verdaguer and A. Michalowicz,
J. Am. Chem. Soc., 1998, 120, 2059.
51. V.M. Goldschmidt, Geochemistry, Clarendon Press, Oxford, 1954.
52. J.B. d’Espinose de la Caillerie, M. Kermarec and O. Clause, J. Am. Chem.
Soc., 1995, 117, 11471.
CHAPTER 36

Solid Acid Microporous

H-SAPO-34: From Early
Studies to Perspectives
LEONARDO MARCHESE,a,* GLORIA BERLIERb
AND SALVATORE COLUCCIAb
a
Dipartimento di Scienze e Tecnologie Avanzate and Centro Inter-
disciplinare, Nano-SISTEMI, Universitá del Piemonte Orientale, Via Bellini
25G, 15100 I-Alessandria, Italy; b Dipartimento di Chimica, Inorganica,
Fisica e dei Materiali and NIS Centre of Excellence, Università di Torino,
Via P. Giuria 7, 10125 Torino, Italy

1 Introduction
In the early 1990s, a group of researchersw working at the Royal Institution
of Great Britain, London, grouped around the leading figure of Sir John
Meurig Thomas, was enthusiastically involved in the study of H-SAPO-34, a
silico–aluminophosphate (SAPO) with the same structure as natural chabazite
(Figure 1). Sir Thomas was kindly named within the group with the acronym
JMT, as he used to sign messages or the front page of relevant papers that he
passed to the co-workers. Different approaches and techniques, both experi-
mental and theoretical (thanks to the strong connection with the research group
of Prof. Catlow,z who was also working at the Royal Institution), were
employed to study the nature of the Brønsted acidity of H-SAPO-34 and other
structure-related materials, SAPO-18 and MeAPO-18, which were found to be
highly selective in the conversion of methanol to light olefins.
The strength of the experimental studies developed at the Royal Institution
was that the expertise of the researchers who joined at that time the JMT group

w
In the period 1992–1994 the group was formed by P. Wright, J. Chen, G. Sankar, S. Natarajan,
L. Marchese and S.M. Bradley.
z
Among others, J.D. Gale, D.W. Lewis and G. Sastre were working with Prof. Catlow in the title
topic.

604
Solid Acid Microporous H-SAPO-34 605

Figure 1 Schematic representation of: (A) the methanol conversion to C2 and C3

olefins inside the chabazite cage of H-SAPO-34 and (B) four possible
configurations for Brønsted sites. In (A) yellow and red sticks represent
Al/P and O atoms, respectively. The presence of Brønsted sites pointing in
the large cage (small grey spheres) is related to the isomorphous substitution
of Si atoms (green spheres). In (B) atoms are designated by the following
colours: yellow spheres represent Al, blue ones Si and P, red and white O
and H respectively. O1 belongs to two 4-T and one 8-T rings, connecting the
two 6-T rings of the double 6-T ring layers; O2 belongs to one 4-T, one 6-T
and one 8-T ring; O3 belongs to two 4-T and one 6-T ring; O4 belongs to
one 4-T and two 8-T rings, forming the bridge between two double 6-T
rings. The orientation of the proton with respect to the framework has only
a pictorial meaning. Reprinted with permission from Ref. 25. Copyright
2007, American Chemical Society.
606 Chapter 36
ranged in several fields of solid-state chemistry. Synthesis of microporous
molecular sieves and their characterization using a large variety of techniques
(X-ray diffraction, solid-state NMR, EXAFS/XANES, thermogravimetric
analysis, Fourier transform infrared) were well developed within the group
along with catalytic tests. The investigations were thus devoted to understand-
ing the catalytic performance of the materials, trying to pin down the influence
of structure and chemical composition on the catalytic performances.
One fundamental hint towards the understanding of the acidity of SAPOs
and zeolites came from the elegant work of the group of Prof. Barthomeuf, who
rationalized the mechanism of silicon insertion in ALPO frameworks, and the
trends governing the number and strength of Brønsted acid sites produced in
this way.1 These studies, along with the emerging interest for H-SAPO-34 as a
commercial catalyst, drove the work of the JMT group in the search for new
acid molecular sieves.2–4
The use of zeolites and zeotypes as catalysts for hydrocarbon conversion
represents an important tool of the modern chemical and petrochemical industry.
The introduction of microporous solid acids for gasoline conversion5 and other
processes such as methanol transformation to light olefins (methanol-to-olefin
(MTO))6 or gasoline (methanol-to-gasoline (MTG)) resulted in great advantages
in terms of safety and waste reduction. The methanol-to-hydrocarbon
technology was primarily regarded as a powerful method to convert coal into
high-octane gasoline, and was then expanded to the formation of other fuels and
chemicals in general.
Depending upon the employed conditions and, more importantly, upon the
catalyst used, the process can be modulated in order to have a high selectivity to
light olefins, resulting in the MTO process.6 Among others, H-SAPO-342,7–9 has
shown peculiar selectivity towards ethylene and propylene formation (mixture
of C2 and C3 products higher than 80%) with the flexibility of altering the ratio
between the two olefins by varying the reactor conditions.6 This catalyst is thus
central to the industrial application of MTO processes, being used in the UOP/
Norsk Hydro MTO technology, which is currently under commercialization.7,10
The different selectivity of small-pore H-SAPO-34 with respect to medium-pore
zeolite H-ZSM-5, successfully employed for MTG processes, has been explained
in terms of shape selectivity and of acid strength. In fact, H-ZSM-5 catalysts
oligomerize light olefins giving higher molecular weight olefins or aromatics, while
the reaction stops at low olefins on H-SAPO-34. Even if one could explain this
trend in terms of product diffusion (H-SAPO-34 has a cage structure rather than a
channel structure as in ZSM-5), it is likely that the high selectivity of H-SAPO-34
to C2–C4 hydrocarbons is also related to the medium acid strength of the
catalyst.9 When the activity in MTO of H-SAPO-34 and its zeolitic homologue
H-chabazite is compared, in fact, the faster deactivation on H-chabazite is
acknowledged,11 this process being related to coke formation as a consequence
of consecutive reactions between light olefins and strong Brønsted sites.
Sir J.M. Thomas in one of the early papers devoted to this subject elegantly
commented that: ‘‘There is a class of heterogeneous catalysts in which essen-
tially all the atoms of the bulk of the solid participate directly or are implicated
Solid Acid Microporous H-SAPO-34 607
indirectly in the key catalytic processes of the overall reaction. Well known
examples are zeolites, the silicoaluminophosphates (SAPOs) etc.12 There is little
doubt that one of the keys of the methanol conversion is the loosely bound
extraframework proton, which facilitates the formation of intermediate carbo-
cations and other transitory species’’.13
It may be easily recognized that the local structure of Brønsted acid sites in
zeolites and SAPOs is similar, being constituted by Si–O(H)–Al units, however
the acidity of these materials may be largely different, even in the case of
structurally similar systems. The acidity depends on several factors, such as
bond angles and bond lengths, the electrostatic potential around the acid
centres and within the zeolite cages, etc. Among these factors, the atomic
environment around the acid centres plays a relevant role. The first coordina-
tion sphere of T atoms around the aluminium is formed exclusively of Si atoms
in zeolites, whereas Si and P can be present in SAPOs.1,14–16 In addition, the
formation of Si islands in SAPOs (Figure 2A) leads to an even larger number of
acid site environments;17 this makes the acidity of SAPOs more tunable than
that of zeolites, providing that the Si insertion can be controlled.16,18
This chapter deals with the issues related to understanding the Brønsted
acidity of H-SAPO-34 and to the possible strategies to improve the catalyst
lifetime. The early studies related to this topic will be reviewed, with particular
attention to the results obtained by Sir J.M. Thomas and his collaborators.
Even if many years have passed since the early studies, these topics are still hot
in catalysis, due to the importance of natural gas conversion for green chem-
istry, but also for the scientific debate on the mechanisms of acid-catalysed
reactions in solid microporous materials.
Recent results concerning a new methodology for a quantitative determi-
nation of acid sites with slightly different acidity will be resumed. On the basis
of these new results, future perspectives of the title subject will be discussed,
focussing on the potentiality of novel synthesis approaches, combined with
feedback from careful characterization and theoretical predictions.

2 The Early Stages: Understanding the Brønsted

Acidity of H-SAPO-34 and its Catalytic
Performance for MTOs
Among the first studies devoted to the investigation of H-SAPO-34 perform-
ance in MTO reactions, we mention the elegant paper by Xu et al. where magic-
angle-spinning NMR, gas chromatography and FTIR studies were combined
to get some insight into the reaction mechanism of acid-catalysed methanol
transformations.9 It was proposed that the reaction proceeds through a se-
quence of consecutive steps passing from dimethyl ether, alkenes, alkanes and
finally aromatics. The reaction could be stopped at olefins by optimizing flow
rates. The authors concluded that high selectivity to olefins is related to its
medium acidity, more than to the small size of the pores, which can only play
608 Chapter 36

Figure 2 (A) Planar scheme for the Si, Al and P distribution in a SAPO network: (a)
isolated Si, (b) 5Si island, (c) 11Si island and (d) Si–Al phase with 1 Al in the
siliceous island. Reprinted with permission from Ref. 16. Copyright 2005
Annual Reviews. 29Si-MAS-NMR of SAPO-34 prepared in the presence of
morpholine (B) and TEAOH (C) at increasing Si concentration (wSi). (B) wSi:
0.10 (a), 0.14 (b), 0.16 (c), 0.18 (d), 0.23 (e) and 0.33 (f). (C) wSi: 0.10 (a), 0.10
(b), 0.11 (c), and a chabazite with Si/Al ¼ 2.34 (d) is also reported for
comparison. Adapted from Ref. 17.
Solid Acid Microporous H-SAPO-34 609
an important role in controlling the product distribution (in relation to the
limiting product diffusion rate). In that period, small-pore zeolites such as
chabazite, erionite, ZSM-34 were tested as catalysts for MTO, since the pore
openings consisting of eight T-membered rings were regarded as just fitting the
size of small olefin molecules (Figure 1). Indeed those catalysts gave consider-
ably high selectivity to ethylene and propylene but also rapid deactivation of
the catalyst performance, as a result of coke formation inside the cavities.
Different methods were thus employed to limit the deactivation, by trying to
reduce acid strength or density.
One of the ways followed to this aim was to synthesize SAPO and ALPO
catalysts with small amounts of transition metal ions, like nickel,13 Zn, Mg2 or
cobalt,2,19 and this led to the formation of loosely bound extraframework
protons related to the presence of Me21(OH)P51 groups.2,20–23 The impressive
selectivity to ethylene (nearly 100%) of Ni-SAPO-3424 was related to the
modification of the acidity of the zeolite by nickel introduction.13 Structural
effects were also investigated by comparing the catalytic performance of differ-
ent SAPO structures.4 The authors rationalized the activity and selectivity of the
diverse catalysts in terms of the strength of Brønsted sites and cavity dimensions.
The understanding of the catalytic performances of H-SAPO-34 and related
materials in MTO was not only related to direct measurements of the catalytic
activity. In the early 1990s, the group of Sir J.M. Thomas at the Royal
Institution was studying the nature of Brønsted sites in solid microporous
materials. In those days, one fundamental step towards the understanding of
the acidity of SAPOs and zeolites came from a massive, independent work of
D. Barthomeuf and her group, who rationalized the mechanism of silicon
insertion in ALPO frameworks. A topological approach, which took into
account both the structure topology and the Al content, was first developed
for several zeolites12 and subsequently applied to SAPOs.1
With the aid of planar schemes for representing the distribution of Si and Al
in zeolites and Si, Al and P in SAPO networks (Figure 2A), Barthomeuf
proposed that the occupation by Al, Si and P atoms of the first and second shell
of T atoms around a central Si governs the acid strength through the electro-
negativity of atoms and the connectivity of tetrahedral units. The acid strength
increases as the first shell contains more Si and as the second shell contains
more P. The presence of Si islands leads to the formation of stronger acid sites
by forming Si(nAl) species (no4) at the border of the islands. The number of
these acid sites and of the n value depends on the dimension of the islands,
which is related to the Si concentration and to the structure topology. A
correlation between acid strength and 29Si MAS NMR chemical shift as the
environment of Si in the first and second shell of the tetrahedral unit becomes
richer in silicon was finally proposed. These results were lately supported by a
theoretical study of Sastre et al. (vide infra).
The role of the structure directing agent (SDA) in governing the Si distribu-
tion in SAPOs was also investigated. Again the work of Barthomeuf and her
group is exemplary; they described, using 29Si-MAS-NMR spectroscopy, the Si
distribution in SAPO-34 prepared in the presence of morpholine or
610 Chapter 36
tetraethylammonium hydroxide (TEAOH) as SDAs (Figures 2B and C). The
model proposed for SAPO-34, subsequently generalized to other SAPOs,
suggests that the Si distribution depends on the number of framework charges
which is influenced both by the number of SDA molecules embedded within the
cages and by the Si atoms introduced within the framework.17
Keeping in mind the models proposed by Barthomeuf, the effect of Si
incorporation in different ALPO structures was investigated at the Royal
Institution by combining different techniques, namely 29Si-MAS-NMR (Figure
3A) and FTIR spectroscopy (Figures 3B and C).3 The authors confirmed
that at low Si content (xSi E 0.10, in agreement with Barthomeuf previsions),
H-SAPO-34 presents essentially isolated Si centres. However, it has been

Figure 3 Results from combined 29Si-MAS-NMR (A) and FTIR (B,C) study showing
that SAPO-34 (wSi ¼ 0.10) displays essentially isolated Si centres (with 29Si
chemical shift at
92 ppm), and bridged Si–(OH)–Al hydroxyls at 3626 and
3600 cm–1 (B). In SAPO-18 materials with lower silicon fraction (wSi ¼ 0.047,
curve b and 0.087, curve c) Si islands are instead formed, as testified by the
NMR signals at d ¼
111 ppm for Si(OSi)4 ,
96,
100 and
105 ppm for
Si(OSi)n(OAl)4–n species. Accordingly, the concentration of Brønsted acid
sites in SAPO-18 is much lower than SAPO-34 (C). Panel (B) shows the
spectra of (a) ALPO-18, (b–e) SAPO-18 with different silicon concentration
and (f ) SAPO-34. Reprinted with permission from Ref. 16. Copyright 2005,
Annual Reviews.
Solid Acid Microporous H-SAPO-34 611
recently reported, thanks to the improved performance of cross polarization
(CP) techniques, that small Si islands are present also in H-SAPO-34 samples
where these species represent less than 10% of the total Si.25 The work by Chen
et al. showed that Si islands are formed in H-SAPO-18 catalysts at very low Si
content (Figure 3A). This implies a smaller concentration of Brønsted sites in
SAPO-18, e.g. larger amount of silicon islands, as testified by the normalized
intensity of the infrared (IR) bands related to bridged Si(OH)Al hydroxyls,
adsorbing at 3626 and 3600 cm–1 (Figures 3B and C).
FTIR spectroscopy has often been used for the characterization of Brønsted
acidity, either by the analysis of the vibrational modes of the Si(OH)Al bridged
hydroxyls (see for instance Figure 3B) or by use of probe molecules, as detailed
in the next paragraph.26–31 In the early 1990s, this technique was applied to get
more insight into the nature of Brønsted sites of H-SAPO-34, by studying the
spectroscopic features of adsorbed water.32 Being a relatively weak base, H2O
can be used for assessing the Brønsted acidity of zeolites, even if the shape of
the bands is modified by the presence of strong Fermi resonance effects.27,29
The FTIR spectra obtained at increasing H2O coverage (Figure 4A) were
first interpreted as due to H3O1 oxonium ions H-bonded to oxygen atoms of
the framework because all the six IR vibrations predicted for such species were
identified.32 However, Pelmenschikov and van Santen33 proposed that the
bands attributed to H-bonded H3O1 could also be interpreted in terms of
Brønsted hydroxyl groups H-bonded to H2O whose band shape is strongly
modified by Fermi resonance effects.
The nature of the species formed when water interacts with Brønsted acid
sites in H-SAPO-34 was further investigated by structural14 and computa-
tional34 approaches. A combination of an FTIR and neutron diffraction study
showed that H2O adsorption on H-SAPO-34 led to the formation of both 1:1
H-bonded complexes and H3O1 species (Figure 4B), the latter being the result
of a proton transfer reaction from the most acidic protons to the H2O
molecules.14 However, ab initio simulations of large clusters, which included
fragments of the H-SAPO-34 framework and water molecules, suggested that
only a protonated water cluster H3O1 . 2H2O is stabilized by a proper arrange-
ment of proton sites within the micropores of the solid (Figure 4C).34 The
discrepancy of the results could be interpreted by limitations of both tech-
niques: the possible formation of clusters of adsorbates within the zeolites even
at low coverages should be avoided from the experimental point of view, while
proper zeolitic structures and their possible ‘solvent’ effects on the adsorbed
molecule should be accounted for from the computational point of view.
Finally, a quantitative description of the Brønsted acidity in H-SAPO-34
came from the contribution of Smith et al.35 On the basis of FTIR and neutron
diffraction experiments, the authors assigned the two IR bands of H-SAPO-34
at 3630 and 3600 cm–1 (see Figure 3B, and following paragraph) to Si(OH)Al
bridged hydroxyls with different acid strength related to two well-defined
crystallographic positions. The high frequency band at 3630 cm–1 (named A
species, OHA) and the low frequency component at 3600 cm–1 (OHC) were
assigned to loosely bonded protons on O4 and O2 structural configurations,
612 Chapter 36

(H 2O) n·(H 3O) +

[γOH···O ]
795 765
Absorbance [a.u.]

1
1353
[2γOH···O ]

0
3600 2700 [2δOH···O]
3625 [νOH] νOH···O 1353 [δOH···O]
3500 3000 250 0 200 0 150 0 75 0
(A) Wavenumbers [cm-1]

(B) (C)

Figure 4 (A) FTIR spectra of increasing doses of H2O adsorbed on H-SAPO-34.

Dotted lines correspond to high H2O dosages, H1/H2O 4 1, which lead to
the formation of (H2O)n(H3O)1 clusters. (B) Ball and stick representation of
the structure of hydrated H-SAPO-34, showing both the hydronium ion and
H-bonded water molecules, proposed on the basis of powder neutron
diffraction and IR spectroscopy. (C) Alternative model proposed on the
basis of ab initio simulations: two water molecules hydrogen-bonded to
H3O1 in the 8-T ring of H-SAPO-34. (A) and (C) reprinted with permission
from Ref. 29, copyright 1999, Elsevier; (B) reprinted with permission from
Ref. 14, copyright 1996, Science.

respectively (Figure 1B).35 The acidity of these sites was estimated by measuring
the shift of the corresponding vibration upon CO adsorption (see below for
further details), indicating the different strength of the sites. A third family of
acid sites absorbing at 3625 cm–1 (OHB) was also found, but its nature was not
discussed in terms of crystallographic positions. When monitored by CO
adsorption, the acidity of this site (present as a minor fraction) was found to
be very high. Recent work on chabazite-related SAPO materials has thrown
some light on the nature of this site, as detailed in the following.25
Solid Acid Microporous H-SAPO-34 613

3 Insight into the Nature of Brønsted Sites by

Computational Techniques
It has often been recommended, for monitoring the acidity of catalysts, to use
small and weakly interacting probe molecules, such as CO, H2, N2, etc., which
induce only a mild perturbation of the catalytic sites.28–30 Nowadays, notwith-
standing the above guidelines for experimental determination of relative acid-
ity, the use of computational methods for the determination of acidity
differences is becoming increasingly present. The modelling of Brønsted acidity
in SAPOs by computational tools is, in fact, becoming more and more
relevant.15,36–42 Many studies have been reported, trying to pin down the
relations between acid strength and short- and long-range structural factors,
such as SiOAl angles or Si–O, Al–O distances,43,44 flexibility of the frame-
work45 and electrostatic potential generated inside the cavities.46–48
Many energy contributions, such as the electrostatic potential, electric field,
etc., can now be taken into account in the calculations for determining the
vibrational frequency of Brønsted sites and the energy required to elongate
the OH bond.49 An example of the level of reliability of the computational tools
are the results which describe the correlation between O–H stretching frequency
of Brønsted acid centres in zeolites and SAPOs and the gradient norm of the
electrostatic potential, that allowed the vibrational properties of microporous
solids with a large variety of structure and composition to be described.48
Theoretical studies were also performed to verify the results reported by the
group of Barthomeuf on the basis of the topological approach.1,12 Sastre et al.
investigated the Si island formation and confirmed that siliceous patches within
both SAPO-5 and SAPO-34 are energetically stable, and are more favourable in
SAPO-5 where they form at lower silicon concentration.50 These authors
reviewed carefully the literature concerning both experimental and theoretical
results on the mechanisms of Si substitutions in SAPOs.
One of the main results of the theoretical work by Sastre et al. is the
estimation of the deprotonation energies of different acid sites, which fully
supported the model that indicated that the acidity is greater at the edges of Si
islands.15 A correlation between acidity and island dimension was established
by considering 5Si and 8Si islands in SAPO-5 and SAPO-34. In addition, a
structure-dependence on the formation energy of 8Si islands was found, and
this showed that larger islands were more favourable in SAPO-5 because of its
more flexible framework structure. Subsequently, these studies were extended
to SAPO-11, SAPO-18 and SAPO-31.51

4 Recent Results: Revisiting the Nature of the Acidity

in Chabazite-Related SAPOs
Concerning the experimental techniques, acid strength of Brønsted sites can be
monitored by using probe molecules with basic character, such as ammonia or
614 Chapter 36
31
pyridine, by the analysis of their spectroscopic features or by measuring the
temperature at which these molecules are desorbed (TPD measurements).3
However, these techniques are not able to discern among families of Brønsted
sites with small differences in acid strength, that could have serious conse-
quences on activity, selectivity and lifetime of the catalysts. In this case the use
of probe molecules with weaker basicity is compulsory.
One of the most sensitive experimental techniques for this purpose is FTIR
spectroscopy.14,16,26,29,35,52,53 This technique is based on the analysis of the IR
spectra in the OH stretching (nOH) region and on their perturbation upon
adsorption of small molecules (N2, CO, C2H4, etc.), which act as weak bases (B)
forming H-bonded adducts (OH  B) with the Brønsted sites. The measure of
the DnOH shift upon formation of the OH  B adducts represents a classical
method to estimate the acidity of Brønsted sites.28,54
In a recent work, FTIR spectroscopy of adsorbed CO and C2H4 was used to
compare the strength and distribution of Brønsted sites in H-SAPO-34 samples
with similar chemical composition but prepared with different SDAs.25 A
chabazite-related SAPO, CAL-1, recently synthesized adopting an original
procedure using a lamellar ALPO as precursor,55,56 and having a high Si
loading, was also studied. A detailed analysis of the FTIR spectra in the OH
stretching region, and of the downward shift of the OH bands upon CO and
C2H4 adsorption (Figures 5A and 6B, respectively), evidenced the presence of
three distinct acid sites (named as OHA, OHB and OHC) absorbing at 3631,
3617 and 3600 cm–1 respectively as average values.
A relation between width of the OH bands and Si content of the chabazite-
related samples was observed, as exemplified in Figure 5A, where the spectra
obtained on a sample prepared with triethylamine – H-SAPO-34 (E), wSi ¼ 0.14
– are compared with those of CAL-1 (wSi ¼ 0.23). While OHA and OHC are
clearly resolved in H-SAPO-34 (E), where the contribution of OHB is small,
CAL-1 shows broader features, and a larger concentration of the OHB com-
ponent. The 29Si-CP-MAS-NMR spectra of the two samples (Figure 5B) shows
that CAL-1 is characterized by a large amount of Si islands, while only a very
small amount of Si patches, likely formed by ca. 10 Si atoms,57 is present in H-
SAPO-34 (E). Notice that 29Si-MAS-NMR, e.g. without CP, was not able to
detect the presence of a minor fraction of small Si patches in similar H-SAPO-
34 (see above and Figure 3A).
The estimation of the acid strength of the three distinct sites was made by
performing careful multi-curve fitting also of the broad and intense absorption
(Figure 5A) related to the formation of H-bonded OH  CO adducts. The
following scale of acidity was found: OHB 4 OHA 4 OHC, each component
being downward shifted upon CO adsorption by 331 cm–1 (OHB), 276 cm–1
(OHA) and 150 cm–1 (OHC) (average values). The shift measured for OHB is
very large when compared to the usual values measured for isolated sites in
SAPO structures,25 which are normally less acidic than those of aluminosili-
cates with analogous structure.15,39,41 This value resembles that measured upon
CO adsorption on protons of the synthetic aluminosilicate with chabazite
structure, H-SSZ-13 (316 cm–1).58
Solid Acid Microporous H-SAPO-34 615

Figure 5 (A) FTIR and (B) 29Si-CP-MAS-NMR spectra of as prepared H-SAPO-34-

related samples with different Si content. Top: CAL-1 (synthesized adopting
an original procedure with a lamellar ALPO as precursor and hexamethyl-
eneimine (HMI) as SDA), wSi ¼ 0.23, bottom: H-SAPO-34 (E) prepared with
triethylamine, wSi ¼ 0.14 (bottom spectra). (A) FTIR spectra outgassed at
773 K before CO dosage (short-dotted curve) and at the highest CO
coverage (PCO D 20 torr, dashed-dotted line). Bands obtained by three-
peaks best fitting procedure are reported in full line with the corresponding
assignment (OHA is transformed to OHA 0 upon CO adsorption and so on).
The position of nOH for free OH and OH  CO adducts of H-SSZ-13, with
the corresponding DnOH, is reported for comparison, from Ref. 60. Re-
printed with permission from Ref. 25. Copyright 2007, American Chemical
Society.
616 Chapter 36
The consistency of the curve fitting procedure was checked following the work
by Makarova et al.54 who found a linear correlation between the intensity growth
(and band broadening) of the Brønsted OH bands of H-ZSM-5 and the DnOH
shift for OH  B adducts, in agreement with hydrogen-bonding theory. The linear
correlation DA/A0 ¼ 0.018DnOH/cm
1 was reproduced and a good agreement was
observed for the OHA and OHB data measured on the chabazite-related samples
(Figure 6A).25 The data related to OHC species could be corrected by assuming
that they are tilted towards the centre of the six rings of the hexagonal prism
where they H-bond to framework oxygens (O2 in Figure 1B).25,35
The acidity of the three families of Brønsted sites in chabazite-related SAPO
samples was also monitored by probe molecules with different basicity. As a
case study we report the results obtained on a H-SAPO-34 (T) sample prepared
with TEAOH upon ethylene adsorption (Figure 6B). In agreement with the
higher basicity of the probe with respect to CO, a larger shift of the OHA, OHB
and OHC bands is observed. As a consequence, the low frequency component
of the broad band due to OHB  C2H4 adducts (indicated by an arrow in
Figure 6B) can be better appreciated. Also these data show a good agreement
with the DA/A0 versus DnOH plot (Figure 6A, light grey hexagons).
As far as the nature of OHB sites is concerned, it was suggested that they are
located at the borders of Si islands, where they feel a chemical environment
similar to that present in zeolites. This hypothesis is in agreement with both the
large downward shift upon CO adsorption, and 29Si-CP-MAS-NMR results
(Figure 5B). To our knowledge, this is the first report of the presence of such
strong acid sites in SAPO materials, confirming the results coming from
theoretical calculations,15 that foresaw an acidity comparable to zeolites for
sites formed at the borders of silicon-rich regions, in agreement with the
topological models proposed by Barthomeuf.

5 Future Perspectives: Catalysts with Modified

Morphology and Designed Distribution
of Brønsted Acid Sites
One of the main drawbacks of the MTO process is related to the fast deacti-
vation of the catalyst, due to coke formation as a consequence of consecutive
reactions between light olefins and strong Brønsted sites. This process is due to
the presence of strong acid sites and to the limited diffusion of reactants/
products within the chabazite cages. As a consequence, new approaches are
needed to prepare catalysts with finely tuned distributions of Brønsted sites and
properly designed morphology.
ALPO and SAPO molecular sieves are generally prepared by sol-gel pro-
cesses and hydrothermal synthesis. H-SAPO-34 samples prepared by conven-
tional routes very often present rhombohedral particles with size of the order of
microns (Figure 7a), that do not facilitate the mass transfer during catalytic
reactions.
Solid Acid Microporous H-SAPO-34 617

Figure 6 (A) Plot of the increase of the intensity DA/A0, (A and A0: intensity of the
perturbed and unperturbed OH bands, respectively) versus the DnOH shift, as
a consequence of the formation of OH  B adducts in H-ZSM-5 ( ): (1) O2,
(2) N2, (3) CO, (4) C2H4. ,, J and &: data obtained upon CO adsorption
on H-SAPO-34 prepared with different SDA;B on CAL-1. Full symbols .,
K, ’ andE: OHC data corrected by assuming an increase of the extinction
coefficient caused by hydrogen bonding with framework oxygen atoms.
Circled ,, J, & and B: OHC values before correction of the extinction
coefficient. Light grey hexagons: corrected data obtained upon C2H4
adsorption on sample H-SAPO-34 (T), prepared with TEAOH. (B) FTIR
spectra of sample H-SAPO-34 (T) outgassed at 773 K before C2H4 dosage
(short-dotted curve) and at the highest C2H4 coverage (PC2H4 D 20 Torr,
dashed-dotted line). Bands obtained by three-peaks best fitting procedure
are reported in full line. Reprinted with permission from Ref. 25. Copyright
2007, American Chemical Society.
618 Chapter 36

Figure 7 Scanning electron micrographs of (a) SAPO-34 prepared form conventional

gel procedures, (b) ALPO-kan, (c) CAL-1 and (d) detail at high magnifica-
tion of CAL-4 prepared using layered ALPO-kan precursor.

Recently, a new synthetic approach was proposed, based on the use of

lamellar aluminophosphate ALPO-ntu, with the structure of the siliceous
kanemite, also referred to as ALPO-kan (Scheme 1y).55,56 It was shown recently
that ALPO-kan with intercalated butylamine can be transformed into CAL-1
and CAL-2 (CAL ¼ CAmpinas-ALessandria) with structure analogous to
SAPO-34, and into CAL-4 with structure analogous to SAPO-44, depending
on the SDA used and the synthesis conditions (Scheme 1). This synthetic
strategy has been discussed in a recent review.56
The synthesis procedure based on ALPO-kan, which is composed of dis-
ordered thin blades of various shapes and dimensions (Figure 7b), has a strong
influence on the particle morphology. CAL-1 is, in fact, formed of randomly
distributed lamellae and some small rhombohedral particles formed by the
pilling and condensation of lamellae (Figure 7c). This morphology can be
observed on other samples prepared from the same precursor (see for instance
the high magnification image of CAL-4, Figure 7d).
The resulting crystallites are also characterized by lower density with respect
to H-SAPO-34 prepared in the classical way.56 The layered-type morphology
should affect diffusion and mass transport properties since acid sites are more
accessible than in larger, compact particles. Thus, reactions are expected to be
y
H.O. Pastore, personal communication.
Solid Acid Microporous H-SAPO-34 619

Scheme 1

facilitated and possibly lead to higher conversions when using materials pre-
pared in the proposed way.
In relation to the acidity, the synthesis of SAPOs from lamellar ALPO-kan
allows the production of materials with a wide range of Si content. The
different Si distribution obtained by this way has been explained by a reaction
mechanism involving the attack of the silicate anions to different Al sites in
ALPO-kan, so that the resulting chabazite structure is characterized by a more
heterogeneous (that is, disorganized) configuration of the hydroxyl groups in
CAL-1 in comparison with the ones in SAPO-34.25,56 This new approach can be
used to prepare catalysts with the desired distribution of Brønsted sites in terms
of strength and density, that is to minimize the strongest Brønsted sites
probably responsible for the fast deactivation of the catalyst.

6 Personal Remarks
A unique feeling captures us when Sir John speaks about Science: we are all
contemporaries. We live with Galileo, Newton, Faraday, Lavoisier, Volta and
the others, the excitement of their everyday work, success and disillusion. This
is an ingredient of the everlasting ability of Sir John to guide generations of
scientists to the frontiers of the most demanding and demanded research goals.
And indeed we belong to three different generations enriched by the contact
620 Chapter 36
with the knowledge, creativity and humanity of Sir John. The first time we met
in Torino is vivid in our memory, having a light lunch on the river bank and
enjoying the view of the Valentino Park and the Mole Antonelliana in the
company of unforgettable sweet Margaret.
We wish to remember the enthusiasm of Sir John for science and the
wonderful and stimulating periods that some of us spent at the Royal Institution
working with him. His passion for the history of science, which he popularizes
enthusiastically both in public conferences and by innumerable anecdotes, is
admirable.
Our first joint paper was written in the period when Sir John jumped from
one cab or train to another, for he was deputy pro-chancellor of the Federal
University of Wales, lived in Cambridge and spent a few days per week at the
Royal Institution in London as professor of chemistry. The correction of the
manuscript of FTIR of water adsorbed on H-SAPO-34 and the related
discussions were made on both cabs and metro lines, for lack of time and for
the urgency of the divulgation of the results.
There are several anecdotes and facts which characterize our scientific
collaboration with Sir John, and exemplify his attitude towards science. Some
of them remain vivid in our mind. ‘‘The best paper is always the next one’’, in
replying to a comment of one of us, or ‘‘All is marvellous in science, not all is
useful’’, in replying to a proposal of work, are just two examples of his way of
thinking.

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CHAPTER 37

Strategically Designed Single-

Site Heterogeneous Catalysts
for Clean Technology, Green
Chemistry and Sustainable
Development
ROBERT RAJA
School of Chemistry, University of Southampton, Highfield Campus,
Southampton, SO17 1BJ, UK

1 Introduction
Eleven years ago, on July 1, 1996, I had the rather unexpected and pleasant
opportunity of meeting Sir John Meurig Thomas (JMT) at the 11th Inter-
national Congress on Catalysis in Baltimore, USA. I was a PhD student at the
National Chemical Laboratory (India) and due to the unforeseen illness of my
PhD supervisor, I was asked (coerced!) to deliver the lecture in his place. Sir
John (whom I did not know at that time) was the first to ask me some revealing
questions about zeolite mimics of enzyme catalysts (ZEOZYMES) after my
lecture, but, when he asked me a penetrating question about the nature of the
active site, I did not have a clue and answered that ‘‘this was not on the list of
questions that my PhD supervisor had given me!’’. This response clearly
amused him, but this was the beginning of a long-lasting and fruitful collab-
oration in our fascinating journey into the realms of single-site heterogeneous
catalysis.
After completing my PhD I was awarded an 1851 Exhibition to work with
JMT at the Davy Faraday Research Laboratory (DFRL) of the Royal Insti-
tution of Great Britain (1997–1999) in London. It was here, in the basement of
the DFRL (adjacent to Michael Faraday’s laboratory and workshop) that we
designed and built our unique, state-of-the-art, robotic high-pressure catalytic
623
624 Chapter 37
reactor with online analytical capabilities. By the summer of 1999, JMT was
keen that I move to Cambridge (he was the Master of Peterhouse at that time)
and introduced me, on one eventful train journey from London King’s Cross,
to Brian Johnson, who was the Head of Inorganic Chemistry. Sir John and
Lady Margaret Thomas made us feel welcome in Cambridge and our relation-
ship, both scientific and personal, began to blossom. There were times when we
were working on many parallel research topics and needed to be in touch
continuously (Lady Thomas, who was always a charming and welcoming host,
would often joke that it would be better for me to move in with them) – JMT
would pick the most exquisite of places (the Deer Park and Fellows Garden at
Peterhouse, The Orchard at Grantchester, Wandlebury and the Perse Cricket
grounds, just to name a few) to stimulate these scientific discussions.
The focal theme of our research in the past 10 years of our collaboration, has
been the discovery, design and synthesis of novel nanoporous and mesoporous
solid materials for application as single-site heterogeneous catalysts in chemi-
cal, pharmaceutical, fine-chemical and environmental technologies, for selec-
tive oxidations, selective hydrogenation and asymmetric syntheses, using
environmentally benign reagents, energy-renewable feedstocks and sustainable
processes. The approach that we have adopted1–3 embraces the principles and
practices of solid-state chemistry, augmented by lessons derived from enzymo-
logy, as well as computational chemistry.
The dominant issue in our pursuit of green chemistry and clean technology
was the need to have a widely applicable strategic principle that offers adequate
scope for the rational de novo design of single-site heterogeneous catalysts. This
was derived from a better understanding of the atomic and molecular basis of
catalytic action by porous inorganic solids, based on the structural under-
standing of the nature of the active sites, the mode of activation of catalyst
precursors and the secrets of their selectivity and durability. This entailed the
design and synthesis of novel inorganic solids, especially those with open
structures where the active sites are atomically engineered and fully character-
ized, the microporosity and mesoporosity of which confer attractive and
adaptable adsorptive and catalytic properties.
In this way we have succeeded in designing a range of new catalysts to effect,
inter alia, shape-selective, regioselective, bifunctional and enantioselective cat-
alytic conversions. In particular, large fractions of these catalysts are ideally
suited for the era of clean technology in which single-step and/or solvent-free
processes abound, and in which benign oxidants such as air or oxygen and
inexpensive nanoporous materials are employed.4–8
We have had many successes, both academically and in the indus-
trial context, and I would like to share a few experiences that gave us
both immense satisfaction. A range of nanoporous and nanoparticle cata-
lysts, designed, synthesized, characterized and tested, that meet most of the
stringent demands of sustainable development and responsible (clean) technol-
ogy will be described in this chapter. Some specific examples which highlight
the industrial and commercial significance of our joint successes in the areas of
bulk, fine and pharmaceutical chemistry that are illustrated here include: (a) the
Strategically Designed Single-Site Heterogeneous Catalysts 625
production of adipic acid (the precursor for Nylon-6,6, polyamides and poly-
urethanes) from cyclic alkanes, avoiding the use of concentrated nitric acid and
the production of greenhouse gases such as nitrous oxide (N2O); (b) the single-
step production of e-caprolactam (precursor of Nylon-6) using a mixture of air,
ammonia and a bifunctional microporous solid, without the use of oleum and
hydroxylamine sulfate; (c) the bromine-free synthesis of p-xylene from ter-
ephthalic acid; (d) conversion of muconic acid to adipic acid using atomically
engineered, anchored bimetallic nanoparticle catalysts and (e) the asymmetric
synthesis of high-value pharmaceutical intermediates (such as methyl mand-
elate) using constrained chiral catalysts.

2 Conventional Industrial Methods of Manufacturing

Nylon-6, Nylon-6,6 and Terephthalic Acid
Most commercial processes for the production of Nylon-6 from cyclohexane as
a feedstock involve multiple steps using a homogeneous cobalt naphthenate
catalyst and entail the nitric acid oxidation of K–A (mixture of cyclohexanol
and cyclohexanone) oil to adipic acid (see Figure 1). The environmentally
undesirable features of this multi-step mode of manufacture are the generation
of voluminous (5 % of total global N2O emissions in 2000) quantities of N2O (a
greenhouse gas that also depletes the ozone layer), massive consumption of
concentrated nitric acid (which is used as a stoichiometric oxidant) and several
downstream processing disadvantages associated with many of the multiple
steps (use of CrIII salts and their problematic disposal).9 The industrial pro-
duction of adipic acid accounted for emissions of 13.2 million metric tons of
CO2 in 2005.
In 1999, the worldwide annual production of adipic acid was 2.5 million
metric tons and since that time it has increased further. The main use of adipic
acid is in the preparation of Nylon-6,6 fibres and resins. Large amounts are also
converted to esters for use in plasticizers, lubricants and in a variety of
polyurethane resins. Adipic acid is also added to gelatines and jams as an
acidulant, and to other foods as a buffering or neutralizing agent. Other uses
include adhesives, insecticides, tanning and drying agents, paper manufacture
and in the textile industry.
Nylon-6, on the other hand, is the polymerized product of e-caprolactam,
which is currently manufactured in two distinct ways, each being a two-step
process, and one of them (a) involving extremely aggressive reagents (Scheme 1)
such as hydroxylamine sulfate, oleum and sulfuric acid.10 Moreover the former
method of manufacture generates four times the mass of e-caprolactam as
ammonium sulfate, a costly waste product to render neutral or useful. Nylon-6
is currently used for a wide variety of purposes: in the textile industry (lingerie,
hosiery, sportswear, leisurewear, fashion wear, linings, parachutes, umbrellas,
tents and sleeping bags), floor coverings (carpets and rugs), industrial yarns
(tyres, conveyor belts, ropes, nets, fishing lines and tarpaulins), engineering
626 Chapter 37

Figure 1 Conventional methods of producing K–A oil and adipic acid.

plastics (automotive air-inlets, engine covers and aircraft windows) and in films
(food and industrial packaging).11
Notwithstanding the fact that ammonium sulfate is a low-value fertilizer, it is
a major disadvantage in the conventional processes employed to date as it
is produced in large volumes (nearly 4 kg for every kg of e-caprolactam
produced); disposal therefore is a problem. Also, it affects the purity of
e-caprolactam requiring expensive vacuum distillation and vacuum crystalliza-
tion followed by treatments with ion-exchange resins. Even as a fertilizer, it has
a lower output of nitrogen (21–22%) (hence requiring larger volumes for
efficiency) and has a high acidity (requiring more lime to keep the soil
neutralized). In the end, profitability for caprolactam is dependent upon the
amount of ammonium sulfate produced as a by-product.11–13
Nylon-6,6 begins as a polymer whereas Nylon-6 is made from caprolactam, a
monomer, where the internal (hydrogen) bonding is weak. Carpets made from
Nylon-6 can be depolymerized into its precursor, caprolactam, which, in turn,
Strategically Designed Single-Site Heterogeneous Catalysts 627

Scheme 1 Two industrial methods of producing e-caprolactam.

can be repolymerized and made into Nylon-6. The entire process recovers more
than 99% of the energy and materials used to make Nylon-6 carpet yarn
(closed-loop recycling). In contrast, Nylon-6,6 is a condensation polymer
formed by combining hexamethylene diamine (HMD, the first ‘‘6’’) with adipic
acid (the second ‘‘6’’), which make separation and recycling difficult, due to a
greater degree of hydrogen bonding and maximum alignment between mole-
cular chains. Best efforts result in down-cycling Nylon-6,6 carpet fibre into low-
performance applications, such as carpet backing. All Nylon-6,6 products
eventually end up in landfill sites or incinerators. In Europe, recycling of fibres
and plastics is of increasing importance, therefore Nylon-6 manufacture, on
this score, is preferred over that of Nylon-6,6 or other (equally recalcitrant)
variants.
Terephthalic acid is industrially produced14 by a multi-step, liquid-phase air
oxidation of p-xylene in the presence of soluble manganese and cobalt acetate
catalysts to form p-toluic acid, which is subsequently converted, under quite
demanding reaction conditions (at least 175–225 1C; 1500–3000 kPa) in the
presence of a bromide and/or bromine salts (Brd and dCH2CO2H radicals in
acetic acid) to form crude terephthalic acid (Figure 2). The highly corrosive
bromine–acetic acid environment coupled with the high exothermicity of the
reaction necessitates the use of expensive titanium-lined equipment.15 Crystal-
line crude terephthalic acid is collected as wet cake and dried. It is purified by
dissolving in hot water/solvents under pressure and selectively hydrogenating
the contaminants catalytically. Downstream processing and purification are
quite intense and expensive, as the homogeneous catalyst needs to be recovered
628 Chapter 37
CH3
Multi Step Process
p-xylene

CH3 Homogeneous
catalysts

Co/Mn acetate
175-225°C
acetic acid solvent
1500-3000 KPa
Highly corrosive
H O bromine-acetic acid
CH3 environment;
.
O2, Br highly exothermic
p-toluic acid reaction
H2O, HBr

HO O O
HO
4-formylbenzoic acid Titanium-lined
equipment

HO O

Solvent evaporation
terephthalic Disposal of bromine salts
by-products +
acid High solvent loss
Catalyst recovery and recycle
HO O Purification step

Figure 2 Current industrial method for the oxidation of p-xylene.

and the bromide salts need to be disposed.16 Terephthalic acid is primarily used
in the manufacture and production of polyester fibres, films, polyethylene
terephthalate solid-state resins and polyethylene terephthalate engineering
resins. In 1993, the worldwide production was estimated to be 17–21 billion kg.

3 Environmentally Benign Production of Nylon-6,

Nylon-6,6 and Terephthalic Acid
The design strategy for synthesizing a single-site heterogeneous catalyst for the
‘‘N2O-free’’, aerobic oxidation of cyclohexane to adipic acid involved assem-
bling a transition metal in high oxidation state (such as FeIII) within a MAlPO
(metal-substituted aluminophosphate) structure in which the pore aperture is
significantly smaller than that of FeAlPO-5 (7.3 Å diameter)17 so as to create a
constrained environment for the cyclohexane oxidation and thus modify the
selectivity of the reaction. The framework structure of the microporous catalyst
that we targeted here was the one-dimensional channel system, AlPO-31.18
Because of the more puckered inner walls, compared with AlPO-5, there is a
Strategically Designed Single-Site Heterogeneous Catalysts 629
smaller diameter of pore, 5.4 Å, which introduces the very kind of constrained
environment that is required to enhance the product selectivity of the reaction.
What we capitalized on was shape selective catalysis (i.e. ‘‘product shape
selectivity’’ – only those products with appropriate molecular dimensions may
diffuse easily out of the pores, whereas larger ones formed in the course of the
reaction are trapped inside) using a carefully designed microporous solid.
The free-radical oxidation that ensues, proceeds in a highly localized manner,
in the restricted environment of the catalytically active sites where the FeIII ions
are located. We may envisage18 the free radical and molecular intermediates
(cyclohexanol, cyclohexanone formed from cyclohexyl hydroperoxide or 2-
hydroxycylohexanone and 1,2-cyclohexanedione) to be held in the vicinity of
the active site, until oxidation proceeds further to yield the more mobile (and
desired) linear product (adipic acid; see Figure 3).
Our aim,19 when we embarked on the task of devising a low-temperature,
solvent-free benign method of synthesizing e-caprolactam, was to identify a
family of single-site catalysts that could be controllably tuned to yield maximal
efficiencies with regard to the production of (i) hydroxylamine (NH2OH) under
in situ conditions and (ii) e-caprolactam. It is a method that utilizes the notion
of a bifunctional, open-structure catalyst, and one of its supreme practical
advantages is that, unlike the conventional method described in Section 2
which generates massive quantities of a low-grade waste product, ammonium
sulfate, it yields no waste.
The single-site bifunctional nanocatalysts that we have designed20 (see Figure 4)
perform well in consecutively converting cyclohexanone to its oxime and

Figure 3 N2O-free route for the one-step production of adipic acid from cyclohexane.
630 Chapter 37

Figure 4 Single-step, solvent-free route to e-caprolactam using molecular oxygen.

e-caprolactam because hydroxylamine (NH2OH) is readily formed in situ inside

the pores from NH3 and O2 at the MIII redox active site. The NH2OH converts
cyclohexanone to its oxime both inside and outside the pores, and, likewise, at
the Brønsted (MII) active sites, cyclohexanone–oxime is isomerized to e-cap-
rolactam inside the nanopores of the catalyst. We found that increasing
the concentration of Brønsted (MII) active sites enhances the selectivity for
e-caprolactam and these catalysts exhibit excellent shape and substrate specifi-
city (see Figure 4). The ‘‘imine’’ mechanism postulated for TS-1 (see Scheme 1b)
can be categorically ruled out as there was no evidence for the formation of the
C6H10¼NH intermediate or peroxy dicyclohexylamine (PDCA) by-products.
Our approach1 to the design of suitable catalysts for the ‘‘bromine-free’’
oxidation of p-xylene to terephthalic acid relies on the use of single-site
catalysts where the active sites are CoIII or FeIII ions in framework sites
substituting for AlIII ions. These catalysts operate under solvent-free conditions
without the need for corrosive activators and initiators such as bromine or
bromide salts. Their mode of operation21 relies on shape-selective free-radical
processes of a spatially constrained kind, where we found that assembling up to
10 atom percent of transition metal ions in the framework of the molecular
sieve suppresses the formation of 4-formylbenzoic acid and increases the
selectivity for terephthalic acid.
As in the case of CoIIIAlPO-18, containing ca. 10 atom percent of CoIII ions
in the framework,22 one might envisage the oxyfunctionalization occurring
Strategically Designed Single-Site Heterogeneous Catalysts 631

Figure 5 Bromine-free route for the aerobic oxidation of p-xylene to terephthalic acid.

simultaneously at both methyl ends of p-xylene, which could well be the reason
for the higher selectivity of the MnIIIAlPO-36 (0.10) catalyst for terephthalic
acid (see Figure 5), compared to MnIIIAlPO-36 (0.04). Contrary to earlier
observations,14,15 where it was shown that this reaction proceeds in a sequential
manner via the formation of p-tolualdehyde and p-toluic acid, thereby requiring
the use of the corrosive bromide activators (for activating the second methyl
group), our detailed kinetic experiments have revealed the simultaneous oxi-
dation of both methyl groups in p-xylene to produce terephthalaldehyde and
terephthalic acid (Figure 5).

4 Adipic Acid from Sustainable Resources Using

Atomically Engineered Nanoparticle Catalysts
Industrially desirable chemical products such as adipic acid (synthesized from
fossil-fuel-based starting materials such as benzene) may be produced in good
yields and selectivities from renewable plant-based feedstocks, which can be
derived biocatalytically from D-glucose. Because of the need23–25 to expedite the
greater utilization of chemical feedstocks derivable from plant or other replen-
ishable sources, research efforts are gradually being focussed on developing
high-performance catalysts that yield desirable industrial products in an envi-
ronmentally benign fashion. It has been shown by Draths and Frost26 that
632 Chapter 37
microbe-catalyzed conversions of simple, plentiful and renewable carbo-
hydrates, such as D-glucose, offer potentially attractive new routes to desirable
materials such as adipic acid. In particular, new biosynthetic pathways, involv-
ing appropriate genetic manipulation, so as to convert D-glucose into cis,cis-
muconic acid, have already been worked out.
This feedstock is currently synthesized from D-glucose under controlled
fermentation conditions using a microbial catalyst under aerobic conditions.
A large-scale manufacturing process of this feedstock would be somewhat
similar to the microbial synthesis of L-lysine from D-glucose under fermentation
conditions. Given the current purchase price of resin-grade adipic acid, it is
quite obvious that the estimated cost of synthesizing adipic acid from carbo-
hydrates requires significant cost reduction.26 However, it should be noted that
this current price of resin-grade adipic acid does not reflect the problems (and
recently introduced legislation) associated with the generation of N2O as a
by-product and the use of benzene as a starting feedstock.
We have found that bimetallic nanoparticles anchored within silica nano-
pores display high activities and selectivities in a number of single-step (and
often solvent-free) hydrogenations at low temperatures due to the synergy of the
two monometallic constituents. Good selective performance is observed27 in
the hydrogenation of a wide range of aromatics, olefins, cyclic polyenes and of
benzoic acid to cyclohexane carboxylic acid (again, relevant in the production
of Nylon-6). By capitalizing on the synergistic aspects of our designed bime-
tallic nanoparticle catalysts, we were able to convert muconic acid, derived
from glucose, to adipic acid (Figure 6). This novel route28 also avoids the use of
concentrated nitric acid as the oxidant and the generation of large volumes of
‘‘greenhouse gases’’ such as N2O.
It can be seen from Figure 6 that one of our atomically engineered nano-
particle catalysts, Ru10Pt2, is exceptional in its selectivity to other bimetallic
nanocatalysts, but more interestingly, it is also superior to industrially used
monometallic supported catalysts such as Pt and Rh. This augurs well for the
future use29 of high-area, thermally stable, nanoparticle catalysts in a wide
range of hydrogenations that may be effected to yield desirable chemical
products from plant-crop sources. It is of relevance to point out that D-glucose
may also serve as a source of hydrogen as recently demonstrated.26

5 High Performance Non-Phosphine-Based

Constrained Chiral Catalysts for the Production
of Methyl Mandelate
Enantiomerically enriched a- and b-hydroxy carboxylic esters are valuable
reagents for optical resolution and are important intermediates in the prepa-
ration of pharmaceuticals and agrochemicals.30,31 Esters of mandelic acid, for
example, are used as precursors in the synthesis of pemoline, a CNS stimulant
and in the production of artificial flavours and perfumes. Methyl mandelates
Strategically Designed Single-Site Heterogeneous Catalysts 633

Figure 6 A catalyst to convert sugar to nylon: bimetallic nanoparticle catalysts for the
production of adipic acid from sustainable resources.

are prepared by direct esterification of mandelic acid with alcohols in the

presence of sulfuric acid.32 This method of direct esterification with strong acids
not only has the disadvantages associated with the corrosive nature of the acid,
but is usually accompanied by side-reactions such as carbonization, oxidation
and etherification, which decrease the overall selectivity and enantiopurity.32,33
In addition, expensive downstream processing and post-treatment pollution
problems make the process commercially and environmentally unattractive.
Even though enzymes are currently more extensively used industrially than
asymmetric transition-metal complexes for enantioselective catalytic conver-
sions involving pharmaceuticals and agrochemicals, the latter are of growing
importance. Biological processes using microorganisms for asymmetric reduc-
tion have inherent problems of stability of the enzyme and the need to maintain
an expensive NADH reconstitution system.31 The use of organometallic chiral
complexes has, however, overwhelmingly been utilized homogeneously and
their heterogeneous asymmetric counterparts have hitherto performed disap-
pointingly so far as their enantioselectivity is concerned, largely because they
contained a range of different kinds of active centres, each with its own
catalytic selectivity. Moreover, one of the major disadvantages of using chiral
phosphines is their high cost (the cost of the ligand, in most applications, far
outweighs the cost of the final product) and sensitivity to oxidation, which
limits their industrial applicability.
634 Chapter 37
34
Maschmeyer et al. showed that by constraining tethered organo-
metallic chiral phosphines within the nanopores of MCM-41, a significant
enhancement in enantioselectivity can be achieved for the allylic amination of
cinnamyl acetate with benzyl amine. The synthetic strategy here involved the
reaction between (S)-1-[(R)-1,2A-bis(diphenylphosphino)ferrocenyl]ethyl
acetate and 3-(methylamino)propyltrimethoxysilane to form a silane function-
alized ferrocenyl ligand. The incorporation of palladium dichloride forms the
target ferrocenyl precursor. The ferrocenyl precursor was then reacted with the
mesoporous silica, MCM-41, to yield the anchored catalyst (see Figure 7B). A
striking illustration of the power of the confinement effect in favouring chiral
conversions was demonstrated in the case of chiral allylic aminations35 and in
the one-step hydrogenation of ethyl nicotinate to ethyl nipecotinate,36 for
which the performance of the same active site can be compared in a homoge-
neous and confined heterogeneous form. Whereas the homogeneous chiral
phosphine-based catalyst yields a racemic mixture with no enantioselectivity
(ee), the spatially constrained form produces substantial amounts of the desired
products and a high value of ee.35,36
The validity of the above strategic principle, boosted by support from the
German Chemical Industry,37–39 led us to evaluate the reality of tethering
rather inexpensive, diamine asymmetric ligands (Scheme 2) onto the inner walls
of non-ordered mesoporous silicas. The argument behind using such an

Figure 7 Enantioselectivity can be induced by tethering chiral phosphine-based

catalysts to the inner walls of mesoporous silica (B) or by anchoring
diamine asymmetric ligands (see Scheme 2) onto concave surfaces (A). In
the case of the former, it is the constraints imposed by the space surround-
ing the metal centre that facilitates the enantioselectivity, whereas in the
case of the latter, it is the restricted access generated by the concavity of the
pore that is the principal determinant for the ensuing enantioselectivity.
Strategically Designed Single-Site Heterogeneous Catalysts 635
NH2
Ph Ph
O
Ph
N
NH2 O
H2N NH2
Et N
(S)-(-)-2-aminomethyl- (1R,2R)-(+)-1,2- H
1-ethylpyrrolidine diphenylethylenediamine L-tryptophanbenzyl ester

PhH2C CH2Ph
N N

N N
O O
2,2’-Bis[(4S)-4-benzyl-2-oxazoline H
(S)-(+)-1-(2-Pyrrolidinylmethyl)-Pyrrolidine

Scheme 2 Some non-phosphine-based chiral ligands that can be anchored to concave

silica surfaces via the covalent or non-covalent tethering approaches.

approach was to substantiate the concept that the diamine ligands tethered at
concave silica surfaces would boost the enantioselectivity to a far greater
degree, in contrast to having them attached to convex surfaces. The idea is
that the confining dimensions of the interior of a pore should be able to restrict
the possible orientations that a bulky reactant can assume as it approaches a
chiral catalytic centre that is attached to a concave pore wall (see Figure 7A). If
a reactant is nudged by its surroundings into the right orientation for a
stereospecific reaction, then the reaction should proceed enantioselectively.
The ligands shown in Scheme 2 can be anchored either covalently40 to the
inner walls of the mesoporous silica using a BF4– anion which is hydrogen-
bonded to the nitrogen of the amino group in the ligand, or via a non-covalent
immobilization method41 that uses a surface-bound triflate (such as CF3SO3–)
counter-ion to secure the cationic organometallic catalyst in place. Catalysts
prepared via the latter method do not require a brominated trichlorosilane
tether for anchoring the ligand and hence are an order of magnitude (about
one-eighth the cost) cheaper than the covalently tethered analogues. The
methodology is also quick, convenient and results in robust effective catalysts,
which make them industrially attractive.
The comparative performance of one such catalyst [Rh(COD)-(S)-(+)-1-(2-
pyrrolidinylmethyl)pyrrolidine]CF3SO3 (ligand shown in Scheme 2), tethered
to the inner walls of non-ordered mesoporous silica samples with pore dimen-
sions ranging from 38 to 250 Å, is shown in Figure 8A. The catalyst’s ability to
steer the asymmetric hydrogenation of methyl benzoylformate to methyl
mandelate diminished systematically with increasing pore size, with the homo-
geneous counterpart yielding little or no enantioselectivity. As the size of the
636 Chapter 37

Figure 8 The effect of surface curvature (B) and concavity of the support in facili-
tating the asymmetric hydrogenation of methyl benzoylformate to methyl
mandelate (A), using mesoporous silica-tethered [Rh(COD)-(S)-(+)-1-(2-
pyrrolidinylmethyl)pyrrolidine]CF3SO3 catalysts.

pore in the mesoporous silica is progressively increased, the support becomes

less effective in constraining the reactant’s orientation (Figure 8B). This con-
finement effect has been independently verified and multiply demonstrated by
German, Chinese and Korean chemists.42–44

6 Summary and Future Outlook

In summary, the range of new single-site heterogeneous catalysts that we have
been instrumental in designing opens up fresh approaches in our pursuit of
‘‘clean chemistry’’ and ‘‘green technology’’ by enabling processes that minimize
(i) the consumption of energy and production of waste; (ii) the use of ‘‘unac-
ceptable’’ homogeneous catalysts and the problems associated with product
separation and purification, requiring expensive downstream processing; (iii)
the use of corrosive, explosive, volatile or non-biodegradable solvents; (iv) the
use of aggressive, ecologically harmful caustic oxidants such as peracids, oleum,
concentrated nitric acid and other such reagents; and (v) the use of aggressive
activators such as molecular bromine and other initiators that result in the
liberation of noxious by-products and greenhouse gases, such as N2O, that
result in ozone depletion and global warming.
Strategically Designed Single-Site Heterogeneous Catalysts 637
In particular, large fractions of the versatile catalysts described in this
chapter are ideally suited for the era of green chemistry and clean technology,
where it will be necessary to develop renewable sources of energy, to minimize
(or recover) waste, to use atom-efficient processes and more importantly, to
design novel catalysts that are highly selective as well as being benign to meet
the demands of sustainable development.

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13. L. Vargas, Material change in nylon manufacture, Business Weekly, Sep-
tember 23, 2005, vol. 426, p. 5.
14. R.J. Sheeman, Ullmann’s encyclopedia of industrial chemistry, in: Ter-
ephthalic Acid, Dimethyl Terephthalate and Isophthalic Acid, online edn,
Wiley-VCH, Weinheim, 2005, 1.
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Marcel-Dekker, New York, 1990, 321–346.
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Chicago, IL, 1993.
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21. R. Raja, J.M. Thomas and V. Dreyer, Catal. Lett., 2006, 110, 179.
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CHAPTER 38

Catalysis by Lewis Acids:

Basic Principles for Highly
Stereoselective Heterogeneously
Catalyzed Cyclization Reactions
MERCEDES BORONAT, AVELINO CORMA
AND MICHAEL RENZ
Instituto de Tecnologia Quimica (UPV-CSIC), Universidad Politécnica de
Valencia, Avda. de los Naranjos s/n, 46022 Valencia, Spain

1 Introduction
Menthol is an important fragance compound used in many consumer products
such as cigarettes, chewing gums, toothpastes, pharmaceutical and personal
care products. It is produced on a large scale in the fine chemical industry, and
has an estimated worldwide consumption of 6000 tons/year.1–3 Of the eight
stereoisomers of menthol, only (
)-menthol possesses the refreshing pepper-
mint odour and physiological cooling effect that makes it valuable. Therefore,
an asymmetric synthesis has been designed for the industrial process of menthol
production (Scheme 1). In the first step, an allylic amine, 1a or 1b, is isomerized

NEt2 I
1a
NEt2
III IV V
O OH OH

II (R )-2 (R )-3 (R)-4 (R)-5

1b NEt2

Scheme 1 Takasago process for (–)-menthol production (for details see Ref. 1).

639
640 Chapter 38
asymmetrically into an enamine of citronellal (R)-2 in the presence of a
Rh/BINAP catalyst with 97% ee. Then, citronellal ((R)-3) is produced by
hydrolysis of (R)-2 in aqueous acidic conditions. The cyclization of citronellal
((R)-3) into isopulegol ((R)-4) in the presence of a Lewis acid produces two
other stereogenic centres in the adequate configuration and then, a final hydro-
genation of the remaining double bond gives the desired stereoisomer of the
final product menthol ((R)-5).
For several years, the cyclization step has been carried out in the presence
of ZnBr2, since the stereoselectivity achieved is higher than that obtained with
other Lewis acids like FeCl3, AlCl3, SnCl4 or TiCl4,4 or also NbCl5, TaCl5,
InCl35 and Bi(OTf)3.6 However, the stoichiometric amounts of ZnBr2
required may cause waste disposal problems, since it acts as a marine toxin.7
Another critical factor in this process is the hygroscopic character of anhy-
drous ZnBr2 and the fact that wet ZnBr2 is much less active and selec-
tive than the anhydrous form. To eliminate these drawbacks from the indu-
strial process, Takasago has introduced an alternative metal complex, namely
aluminium tri-(2,6)-diphenylphenoxide,8 that provides very high stereo-
selectivities in the cyclization (up to 499.3%). Unfortunately, the catalyst
has to be destroyed with NaOH after the reaction and therefore cannot be
recovered and re-used.
Solid materials like zeolites and molecular sieves,9–12 sulfated zirconia,13
hydrous zirconia or Al2O3–SiO2 mixed oxides14 have been applied as catalysts
for the cyclization step. Zn15,16 and heteropoly acid (H3PW12O40)17 have been
supported onto silicas, and Zr has been introduced into montmorillonite by
cation exchange.18 However, none of these catalysts fulfil the demands for an
economically reasonable industrial process. In general, the diastereoselectivity
obtained is not high enough and turnover numbers are low. Some of these
materials suffer from metal leaching, and some others, especially strong
Brønsted acidic materials, lack product selectivity.
In a more promising concept, zeolites containing isolated and well-defined
Lewis acid centres, such as Sn19 or Zr20 atoms occupying framework positions
in Beta zeolite, have been employed in the cyclization step. Using Sn–Beta in a
fixed bed continuous reactor, more than 104 reaction cycles for each catalytic
site were achieved.19
The catalyst provided a 99% conversion during 48 h, and the diastereo-
selectivity was 83% in favour of the desired isomer when acetonitrile was
employed as solvent, although it dropped to 72% in the absence of any
solvent.21 In the case of Zr–Beta catalyst, the diastereoselectivity was as high
as 93%, and the presence of a certain amount of water was found to be
advantageous both for activity and selectivity. To convert Sn–Beta or Zr–Beta
into real heterogeneous substitutes of the homogeneous ZnBr2 or Al(OR)3, the
diastereoselectivity has to be improved. In this work, the nature of the catalyti-
cally active sites has been determined and the mechanism of the cyclization
reaction has been studied by means of density functional theory (DFT) calcu-
lations. On these bases, leads are given for designing better catalysts and
processes.
Catalysis by Lewis Acids 641

2 Characterisation of the Catalytic Active Sites

in Sn–Beta
When Sn–Beta was introduced as a solid catalyst, its Lewis acidity was
attributed to tetrahedrally coordinated tin atoms incorporated into the zeolite
framework.21,22 Recently, theoretical23,24 and in situ IR spectroscopic studies25
have shown that the catalytic activity of Sn–Beta zeolite for the Baeyer–Villiger
(BV) oxidation and the Meerwein-Ponndorf-Verley (MPV) reduction is related
to the presence of partially hydrolyzed tetrahedrally coordinated framework
(SiO)3SnOH sites (Site A), fully coordinated Sn(OSi)4 sites (Site B) being much
less active for these two reactions. Sites A are formed from sites B by hydrolysis
of a Sn–O–Si bridge during the calcination process, so that it is possible to
obtain catalysts with different concentrations of sites A and B by changing the
calcination procedure.
To test the activity of both sites for the cyclization reaction, several Sn–Beta
samples subjected to different post-synthesis treatments, and therefore con-
taining different number of partially hydrolyzed (SiO)3SnOH sites, were used to
catalyze the BV oxidation of adamantanone with H2O2 and the cyclization of
citronellal ((R)-3) into isopulegol ((R)-4). The initial rates for the two reactions
were measured and they are compared in Figure 1. There is a linear correlation
between both series of data, indicating that the activity for the cyclization also
increases with the number of hydrolyzed (SiO)3SnOH sites as was seen for BV
oxidations. However, the straight line does not meet the origin, which means
that there is a contribution other than that of the hydrolyzed (SiO)3SnOH sites
to the catalytic activity of Sn–Beta for the cyclization reaction. Since the parent

25
initial rate BV oxidation in mmol/h/g cat.

20

15

10

0
0 100 200 300 400 500 600
Initial rate cyclization in mmol/h/g cat.

Figure 1 Correlation of the initial rates of Baeyer–Villiger oxidation of adamantanone

with hydrogen peroxide and citronellal cyclization, both reactions catalyzed
by a series of samples of Sn-Beta zeolite subjected to different post-synthesis
treatments.
642 Chapter 38
system, i.e. all-silica Beta zeolite, has been found to be completely inactive,19
this catalytic activity cannot be related to silanol groups or other defect sites,
but we have to associate it to fully coordinated tetrahedral Sn(OSi)4 centres i.e.
sites B. Thus, in contrast to the BV oxidation and the MPV reduction, the
cyclization of citronellal ((R)-3) into isopulegol ((R)-4) is catalyzed by the two
types of Lewis acid centres (A and B) existing in Sn–Beta zeolite.

3 Theoretical Study of the Reaction Mechanism

The mechanism of cyclization of citronellal (R)-3 into the desired (
)-isopul-
egol and the most abundant undesired (+)-neo-isopulegol catalyzed by Sn–,
Zr– and Ti–Beta zeolites has been theoretically investigated using DFT
methods. Since the activity of partially hydrolized Sites A is higher than that
of fully coordinated Sites B, the M(O–SiH3)3OH (with M ¼ Sn, Zr, Ti) cluster
models described in the previous work24 were used to simulate the Lewis acid
active sites. All calculations were performed using the density functional
B3PW91 method,26,27 a LANL2DZ effective core potential basis set for Zr,28
Sn29 and Ti,26 and the standard 6-31G(d,p) basis set30 for C, O, Si and H atoms.
The reaction involves a nucleophilic attack of the C¼C double bond to the
carbonyl carbon atom, resulting in formation of a new C–C bond and a proton
transfer from one methyl group to the carbonyl oxygen atom yielding a
hydroxyl group. Both reactions (nucleophilic attack and proton transfer) occur
at the same time in a concerted way, i.e. in a cyclic carbonyl–ene reaction
involving six atoms and six electrons. The optimized structures of citronellal
(R)-3 adsorbed on the Lewis acid site, of the transition state for the reaction,
and of the adsorbed isopulegol (R)-4 product are depicted in Figure 2, and the
most relevant calculated bond lengths are summarized in Table 1.
On all three catalysts, the first step in the mechanism is coordination of the
oxygen atom of the carbonyl group in citronellal to the Lewis acid metal centre.
As discussed in previous work,31 this interaction consists of an electron density

Figure 2 Optimized structures of (a) citronellal ((R)-3) adsorbed on the Lewis acid
site, (b) transition state for the cyclization, and (c) (
)-isopulegol ((R)-4)
adsorbed on the Lewis acid site.
Catalysis by Lewis Acids 643
Table 1 B3PW91 optimized values of the most important bond distances (Å)
in the structures involved in the cyclization of citronellal ((R)-3) into
isopulegol ((R)-4) catalyzed by Sn–, Zr– and Ti–Beta. The atom
labelling is shown in Figure 2.
Sn Zr Ti
(R)-3 TS (R)-4 (R)-3 TS (R)-4 (R)-3 TS (R)-4
r(OM) 2.284 2.113 2.262 2.341 2.178 2.318 2.287 2.062 2.251
r(CaO) 1.228 1.330 1.443 1.228 1.333 1.441 1.222 1.324 1.435
r(CaCb) 3.079 1.766 1.539 2.999 1.743 1.539 3.090 1.766 1.540
r(CbCc) 1.344 1.423 1.517 1.345 1.427 1.516 1.344 1.423 1.516
r(CcCd) 1.504 1.441 1.340 1.504 1.436 1.340 1.504 1.435 1.340
r(CdH) 1.097 1.153 2.482 1.098 1.165 2.478 1.097 1.168 2.524
r(HO) 3.416 1.727 0.977 3.126 1.673 0.977 3.294 1.662 0.975

Figure 3 Calculated energy profiles for the cyclization of citronellal ((R)-3) into
isopulegol ((R)-4) catalyzed by Sn-, Zr- and Ti-Beta zeolites.

transfer from the carbonyl oxygen atom to the metal empty orbitals, and a
back-donation from the catalyst to the carbonyl p*CO. This back-donation
activates the C¼O double bond and an increase in the positive charge on the
carbon atom occurs, making it more susceptible to the nucleophilic attack from
the C¼C double bond. In the transition state, the CO bond length increases to
1.32–1.33 Å, the Ca–Cb distance is about 1.75 Å, indicating that a C–C bond is
being formed, and the H atom, although still bonded to the methyl carbon
atom, begins to be transferred to the carbonyl oxygen. The final product is in all
three cases a (–)-isopulegol molecule bonded to the Lewis acid metal centre
through the oxygen atom of the newly formed hydroxyl group. Although not
shown, the mechanism of cyclization of citronellal into (+)-neo-isopulegol is
equivalent, and occurs in one step involving similar structures and interactions.
The calculated energy profiles for the Sn–, Zr– and Ti–Beta catalyzed cycliza-
tion of citronellal into (
)-isopulegol are depicted in Figure 3, and the
644 Chapter 38
Table 2 Calculated adsorption (Eads), activation (Eact) and reaction (DE)
energies (kcal/mol) for the cyclization of citronellal into (–)-isopul-
egol and (+)-neo-isopulegol.
citronellal - (
)-isopulegol citronellal - (+)-neo-isopulegol
Sn Zr Ti Sn Zr Ti
Eads
14.3
16.1
8.6
15.4
17.3
9.8
Eact 13.0 12.6 15.7 14.3 14.1 17.2
DE
10.5
10.7
10.3
2.3
2.1
2.0

Table 3 Measured stereoselectivity towards (
)-isopulegol (in %) and (N2/N1)

values calculated for Sn–, Zr– and Ti–Beta zeolites.
Sn Zr Ti
Stereoselectivity (%) 72 80 59
(N2/N1)exp 0.39 0.25 0.69
(N2/N1)products 0.33 0.29 0.31
(N2/N1)TS 0.75 0.71 0.60

calculated adsorption, activation and reaction energies for this process and
for the cyclization of citronellal into (+)-neo-isopulegol are summarized in
Table 2. In all cases, adsorption of citronellal on the metal Lewis acid centre is
exothermic, but this interaction is more stabilizing in Sn– and Zr– than in
Ti–Beta. The activation barriers, calculated as energy differences between the
transition state and adsorbed citronellal are quite similar for Sn– and Zr–, and
slightly higher for Ti–Beta, while the reaction energy, calculated as energy
difference between adsorbed product and adsorbed reactant, is similar in
the three catalysts. It is important to note, in relation to the stereoselectivity
of the cyclization step, that the adsorption and activation energies involved in
the formation of (
)-isopulegol and (+)-neo-isopulegol are quite similar,
and the main difference between them is the considerably lower stability of
the (+)-neo-isopulegol isomer.
The stereoselectivity, or relative abundance of both isomers, can be estimated
using a Boltzmann distribution:
 
N2
ðE2
E1 Þ
/ exp
N1 RT

where N2 and N1 are the number of molecules of (+)-neo-isopulegol and

(
)-isopulegol, respectively, E2 and E1 are their calculated energies, and T the
reaction temperature. Table 3 summarizes the stereoselectivity towards
(
)-isopulegol experimentally measured for Sn–, Zr– and Ti–Beta zeolites (data
from Table 4), the relative abundance of both isomers (N2/N1) obtained from
these experimental data, and the values given by the Boltzmann distribution.
Experiment indicates that Zr–Beta is the most selective catalyst followed by
Catalysis by Lewis Acids 645
Table 4 Conversions and diastereoselectivity for the cyclization of citronellal
((R)-3) into isopulegol ((R)-4) by different Beta zeolite catalysts. The
experimental conditions of Ref. 19 are used in all Tables if no other
information is stated.
Ratio Conversion Diastereoselectivity From
Entry Catalyst Si/M Solvent (%) (%) Ref.
1 Sn–Beta 123 – 67 72 19
2 Sn–Betaa 123 MeCN 99 83 19
3 Sn–Betab 250 MeCN 97 85 19
4 Sn–Betac 123 MeCN 73 85
5 Ti–Beta 65 – 40 59
6 Ti–Beta 65 MeCN 35 57 19
7 Zr–Beta 100 tert-BuOH 94 93 20
8 Zr–Betad 100 tert-BuOH 61 90 20
9 Zr–Betae 100 tert-BuOH 36 86 20
10 Zr–Beta 100 MeCN 96 91 20
11 Zr–Beta 116 – 67 80 –
12 Zr–Beta 116 MeCN 89 87 –
a
Sn–Beta sample with initial rates of 602 and 21.9 mmol/h/g cal for cyclization and BV oxidation,
respectively.
b
Sn–Beta sample with initial rates of 453 and 12.1 mmol/h/g cal for cyclization and BV oxidation,
respectively.
c
Sn–Beta sample with initial rates of 281 and 3.3 mmol/h/g cal for cyclization and BV oxidation,
respectively.
d
Pretreatment of the catalyst: drying at 100 1C for 4 h.
e
Pretreatment of the catalyst: drying at 300 1C for 4 h.

Sn–Beta, and that the selectivity of Ti–Beta towards (
)-isopulegol is consid-

erably lower. If we use the calculated energies of adsorbed (
)-isopulegol and
adsorbed (+)-neo-isopulegol as E1 and E2 in the Boltzmann equation, the
relative distribution of both isomers is in agreement with experiment for Zr– and
Sn–Beta catalysts. However, the value obtained for Ti–Beta, 0.31, is far from the
experimental value of 0.69. Another possibility is to relate the product distribu-
tion not with the stability of the products, but with the activation energy
necessary to form them. In this case, the E1 and E2 values are the calculated
energies of the transition states leading to formation of (
)-isopulegol and (+)-
neo-isopulegol, respectively. In this case, the product distributions obtained for
Zr– and Sn–Beta are completely different from the experimental values, but the
calculated value for Ti–Beta, 0.60, is close to the experimental value of 0.69.
The reason for the different behaviour of the three catalysts can be found in the
energy profiles depicted in Figure 3. The energy released by adsorption of
citronellal on Sn– and Zr–Beta is larger than the activation energy necessary to
convert it into any of the two isomers of isopulegol considered. This means that
both competitive reactions (cyclization to (
)-isopulegol and to (+)-neo-iso-
pulegol) will occur, and the relative abundance of both isomers will be deter-
mined only by their relative stability (thermodynamic control). On the contrary,
the adsorption energy of citronellal on Ti–Beta is not as large as the activation
energy necessary for the cyclization reaction to occur. Therefore, the relative
646 Chapter 38
abundance of both isopulegol isomers will not be determined by their stability,
but by the activation energy necessary to obtain them (kinetic control).
An additional beneficial effect might be due to the size of the metal atom
incorporated into the zeolite framework. It has been reported earlier31 that the
Sn–O bond is shorter than the Zr–O bond in an M–O–Si bridge with 1.881 and
1.963 Å, respectively. Consequently, it can be assumed that the zirconium atom
is slightly displaced from the original silicon framework position towards the
zeolite channel, invading the latter. This restricts the available space around the
active centre. In the case of the cyclization it has been shown that a reduced
space favours the formation of the desired diastereomer.8 Indeed, when one
compares the measured and the calculated N2/N1 values for Sn– and Zr–Beta it
seems that there is also a positive steric effect in the Zr case.

4 Influence of Solvents and Water

on the Diastereoselectivity
For the cyclization of citronellal (3) into isopulegol (4), it has been reported that
lower conversions and also lower diastereoselectivities are achieved with Zr–Beta
or Sn–Beta samples that have been dried accurately (Table 4). We have found in
this work (see Table 5) that when a freshly calcined Sn–Beta catalyst is employed
in the cyclization reaction the diastereoselectivity is only 75%, and it improves
just by increasing the time period between calcination and reaction. During this
period no special treatment is applied to the catalyst, it is just stored at ambient
conditions. If the diastereoselectivity of fully coordinated Sn(OSi)4 sites (Sites B)
and (SiO)3SnOH centres (Sites A) was quite different, the observed behaviour
could be related to the hydrolysis of sites B into A by ambient water. However, it
can be seen in Table 4 (entries 4 and 2) that samples with almost exclusively
Sn(OSi)4 sites gave selectivities of 85% whereas samples with a significant
amount of (SiO)3SnOH centres provided selectivities of 83%. Although it could
be demonstrated that water itself has a beneficial effect on the diastereoselectiv-
ity, the way of action could not be ascertained. It can be seen in Table 6 that

Table 5 Cyclization of citronellal (3) to isopulegol (4) catalyzed by Sn–Beta

zeolite samples. The samples have been exposed to ambient condi-
tions during different time periods. Conversions and diastereoselec-
tivity towards the desired isopulegol diastereomer are given for 60
min reaction times.
Aging Conversion Selectivity
Entry (Days) (%) (%)
1 1 99 76
2 2 99 78
3 5 98 81
4 11 99 82
5 26 99 83
6 126 99 84
Catalysis by Lewis Acids 647
Table 6 Cyclization of citronellal (3) to isopulegol (4) catalyzed by Sn-Beta
zeolite (aged for 29 days) in the presence of different amounts of
water. Conversions and diastereoselectivity towards the desired
isopulegol diastereomer are given for 30 min reaction times.
Water amount Conversion Selectivity
Entry (mg) (%) (%)
1 0 97 82
2 40 96 84
3 60 96 84
4 100 86 84
5 200 67

Table 7 Cyclization of citronellal (3) to isopulegol (4) catalyzed by Sn-Beta

zeolite (aged for 2 days) in different amounts of acetonitrile solvent.
Conversions and diastereoselectivity towards the desired isopulegol
diastereomer are given for 30 min reaction times. Reaction condi-
tions: 600 mg of citronellal and the solvent were mixed and a 50 mg
sample of the catalyst was added.
MeCN Conversion Selectivity
Entry (g) (%) (%)
1 0 63 73.1
2 0.25 79 77.7
3 0.75 90 77.7
4 1.40 89 77.7
5 3.00 93 77.7

small amounts of water, i.e. 40–60 mg, improve the diastereoselectivity towards
the desired product from 82 to 84% (cf. entries 1–3), but higher amounts of
water were not of interest since the activity of the catalyst declined.
A special influence on conversion and diastereoselectivity has also been
reported for the solvent.19 In the absence of any solvent the reaction reached a
plateau of below 70% conversion and the diastereoselectivity did not surpass
75% (cf. Table 4, entry 1). The addition of acetonitrile solvent in any amount
(Table 7) improved the diastereoselectivity significantly, and increasing amounts
of acetonitrile accomplished higher conversions after 30 min reaction time. This
effect should be partly due to the better diffusion of substrate and product
molecules in the presence of a small solvent molecule. However, as a working
hypothesis, competitive coordination of the acetonitrile to the active centre could
explain both phenomena. The alcohol product is rather bulky, and the approach
of the aldehyde substrate to the active centre to which the alcohol product is still
coordinated is difficult. However, a small solvent molecule like acetonitrile could
compete favourably with isopulegol, which would leave the reaction centre and
diffuse into the zeolite channels. The approach of a new molecule of citronellal
would be much easier, and the catalytic cycle could start again. Furthermore, the
presence of a small molecule coordinated to the Lewis centre would partially
648 Chapter 38
Table 8 Cyclization of citronellal (3) to isopulegol (4) catalyzed by Sn-Beta
zeolite (aged for 126 days) in different nitrile solvents at 80 1C.
Conversion and diastereoselectivity towards the desired isopulegol
diastereomer are given for 60 min reaction times.
Conversion Selectivity
Entry Solvent (%) (%)
1 MeCN 99 84.2
2 EtCN 80a 84.6
3 n-PrCN 99 85.4
4 iso-PrCN 7 89.8
5 iso-BuCN 27 82.7b
a
Conversions of 93% and 96% have been observed at 90 and 95 1C; the selectivity remained
essentially the same.
b
Selectivity towards the cyclization was only 76%.

restrict the space around the reaction centre, not as much as to impede the
approach of a substrate molecule, but enough to improve the diastereoselectivity.
If this working hypothesis were true, diastereoselectivity would improve with
increasing size of the nitrile solvent, and when the solvent was bulky enough to
impede the approach of citronellal to the active centre, conversion would
decrease. And this is exactly what occurs. Whereas linear propionitrile and
butyronitrile guaranteed a smooth reaction (Table 8, entries 2 and 3), branched
2-methylpropanenitrile and 3-methylbutanenitrile as solvents accomplished only
low conversion levels after 60 min (Table 8, entries 4 and 5). At the same time the
diastereoselectivity was improved in the solvent series acetonitrile, propionitrile,
butyronitrile, and 2-methylpropanenitrile in parallel with their molecule size (cf.
Table 8, entries 1–4). Therefore, we can conclude that the nitrile solvent coor-
dinates to the catalytic centre, helps to replace the product molecule and restricts
the space sufficiently to improve the diastereoselectivity.
However, in the case of an alcohol solvent, it is not clear whether the same
way of action can be claimed or a different type of interaction has to be
expected. The first hint for this doubt is that tert-butanol is quite bulky,
comparable to 2-methylpropanenitrile, and the reaction proceeds smoothly.
Furthermore, the actions of both solvents could be synergetic. As shown in
Table 9, the diastereoselectivity achieved in a mixture of both solvents is higher
than the diastereoselectivities obtained in each solvent alone. When the
cyclization was carried out in the presence of Zr–Beta and 3.00 g of tert-
butanol, a diastereoselectivity of 89.4% was obtained (Table 9, entry 2) whereas
3.00 g of acetonitrile as solvent gave only 88.5% selectivity (Table 9, entry 4).
However, any mixture of both solvents resulted in a higher selectivity.
It can be concluded that the cyclization of citronellal to isopulegol is very
sensitive to small changes in the environment. Water molecules, nitriles and
tertiary alcohols can contribute to achieve higher diastereoselectivity. It is very
likely, and in one case (nitrile) it has been shown, that the improvement of the dia-
stereoselectivity should be due to steric restriction around the catalytic centre.
Catalysis by Lewis Acids 649
Table 9 Cyclization of citronellal (3) to isopulegol (4) catalyzed by Zr-Beta
zeolite (aged for 35 days) in different solvents or solvent mixtures.
Conversions and diastereoselectivity towards the desired isopulegol
diastereomer are given for a 30 min reaction time. Reaction condi-
tions: 600 mg of citronellal and the solvent were mixed and a 50 mg
sample of the catalyst was added.
MeCN t-BuOH Conversion Selectivity
Entry (g) (g) (%) (%)
1 0 0 67a 80.0
2 0 3.0 93 89.4
3 0 5.0 83 90.3
4 3.0 0 85 88.5
5 2.3 0.8 84 90.0
6 1.5 1.5 81 91.3
7 0.7 2.3 86 91.3
8 0.8b 2.3 81 91.3
a
Catalyst aged for only 2 days.
b
Propionitrile was employed instead of acetonitrile.

5 Beneficial Factors for the Diastereoselectivity

The cyclization of citronellal to isopulegol is a Lewis acid catalyzed process and
there is no doubt that the main factor governing diastereoselectivity is the
nature of the Lewis acid centre. It has been shown, experimentally and
theoretically, that zirconium and tin are the most suitable elements for the
production of a heterogeneous catalyst. The second important factor is the
space available around the catalytically active Lewis-acid centre. This space is
mainly determined by the zeolite morphology, but a fine tuning can be obtained
by using a combination of small solvent molecules. In the case of Beta zeolite
the presence of water, nitriles and tertiary alcohols in adequate concentrations
further improve the diastereoselectivity of the reaction.
It will be interesting in the future to incorporate zirconium and tin into
zeolites with other morphologies and different channel sizes. With subsequent
solvent fine-tuning, a cyclization process could be designed to replace the actual
industrial production process.

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CHAPTER 39

Recent Advances in XPS of

Non-Conductors
G. MICHAEL BANCROFT,a H. W. NESBITT,b
V. P. ZAKAZNOVA-HERZOGb,c AND J. S. TSEd
a
Department of Chemistry, The University of Western Ontario, Chemistry
Building, 1151 Richmond Street, London, Ontario, N6A 5B7 Canada;
b
Department of Earth Sciences, The University of Western Ontario,
London, Ontario, N6A 5B7 Canada; c Institute of Isotope Geochemistry and
Mineral Resources, ETH Zurich, 8092 Zurich, Switzerland; d Department of
Physics, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E2
Canada

1 Introduction
It is a great pleasure to be able to present a research paper in honour of John
Thomas’s 75th birthday. John had an incredibly important influence on GMB’s
early career 35 years ago. It is remarkable that the research reported here is so
closely related to the research begun with John in 1971; and it is probably
interesting (at least to John) of the circuitous path that GMB and HWN’s
research has taken since 1971 to improve the quality of the XPS spectra of
silicates 35 years after the initial study.
GMB arrived at the chemistry department of the University of Western
Ontario (UWO) in 1970, after a very rewarding 6 years at the University of
Cambridge using the recently discovered Mössbauer spectroscopy (or nuclear
gamma ray resonance1) to study bonding and structure in inorganic chemistry
and geochemistry.2–4 The chemistry department at UWO, with Howard Clark
as Head, had a very active visiting professor program. John Thomas came as a
visiting professor to the UWO Physical Chemistry group in 1971, mainly
because of his strong previous contacts with the senior physical chemistry
professor Pat Jacobs. During his 2 week stay at UWO, GMB was fortunate
to have several enthusiastic research discussions with John concerning the use
of Mössbauer spectroscopy, and the recently developed XPS (or electron

651
652 Chapter 39
5
spectroscopy for chemical analysis (ESCA) ) and UV photoelectron spectro-
scopy.6 John had a rather new AEI ES100 photoelectron spectrometer with
achromatic Mg Ka and Al Ka sources in Aberystwyth, and was planning to
begin solid state Mössbauer studies; whereas GMB had a working Mössbauer
spectrometer for Fe and Sn studies, and was planning to order a photoelectron
spectrometer to begin ultraviolet (UV) and X-ray photoelectron studies. They
immediately planned a joint photoelectron project (with his graduate student
Ian Adams) using the Aberystwyth spectrometer to perform one of the first
photoelectron studies of silicate minerals, using the excellent silicate separates
that had been provided by Roger Burns7 for the earlier productive collabora-
tive Mössbauer studies in Cambridge from 1965 to 1969.2,3
But in addition, John approached Pat Jacobs and Howard Clark with the
suggestion that they nominate GMB for the British chemistry awards for
chemists under 30 years of age – the Meldola Medal from the Royal Institute of
Chemistry, and the Harrison Prize from the British Chemical Society. GMB
was fortunate enough to win both prizes in late 1971. These awards had a huge
impact on a young scientist’s career!
The 1971/1972 collaboration with John and Ian resulted in one short survey
paper on silicate minerals8 (and another on studies on a correlation of
Mössbauer and ESCA results on Fe organometallic compounds9). Neither
paper was groundbreaking. Indeed, apart from a small difference in Al 2p
binding energies for Al in 6 and 4 coordination in the silicate study, ‘‘all other
binding energies and linewidths appear to be insensitive to chemical and
structural changes’’.8 But these studies showed immediately that XPS of non-
conductor compounds and minerals (especially powders) had fundamental
problems (mentioned briefly by Siegbahn et al.10), primarily due to the charging
(and especially differential charging) of the photoelectron peaks that results in
peak shifting, with much broadening and asymmetry.11,12 This led GMB on a
career quest to improve XPS resolution on all types of samples, so that bonding
and structural information could be readily obtained.
Compared to the XPS studies of gases, metals and semiconductors, resolu-
tion on non-conductors has shown surprisingly little progress in the last 35
years! (Of course the intensities have increased greatly on modern instruments.)
The introduction of monochromatized Al Ka sources13 and electron flood
guns12,14 only made a substantial linewidth and lineshape difference on ‘‘perfect
surfaces’’ such as smooth polymers15 cleaved alkali halide surfaces,14 and very
thin films of non-conductors deposited on metals from solution or vapour
deposition.16,17 In these ‘‘ideal cases’’, linewidths under 1 eV could be obtained
(e.g., a C ls linewidth of 0.85 eV for the –O–C¼O C ls peak of poly(ethylene
teraphthalate)15 (PET)). However, for silicate XPS studies, there has been little
improvement. For the early XPS silicate studies with achromatic Mg Ka X-ray
sources, the O 1s linewidths were well over 2 eV. Even with this resolution, Yin
et al.18 suggested that the even broader O 1s peak from a pyroxene was due to
two contributions: one from the structural Si–O–Si oxygens (the so-called
bonding oxygens (BO)), and another from the Si–O–M (M ¼ a metal cation)
oxygens (the so-called non-bonding oxygens (NBO)) in the pyroxene structure.
Recent Advances in XPS of Non-Conductors 653
19–22
In more recent monochromatic XPS studies, the O 1s and Si 2p linewidths
of silicate minerals and glasses remained at about 2 eV, making it difficult to
resolve the strongly overlapping O 1s BO and NBO peaks. As a result of this
poor resolution, most researchers have used only XPS broadscan intensities to
quantify the differential release of cations from the surface of silicates23,24 –
very useful for determining the initial mechanisms of mineral dissolution.
In contrast, advances in the XPS studies of metals, semiconductors and
molecular gas phase compounds has been spectacular, primarily because of the
use of monochromatized synchrotron radiation.25,26 Eastman and co-workers,
along with several other solid state physicists working at the Aladdin synchro-
tron, pioneered the use of low-energy, high-resolution photoemission studies to
obtain the band structure of metals and semiconductors.27 Using vapour
evaporation to deposit thin films of non-conductors on metals, GMB collab-
orated with Eastman to obtain core linewidths of 0.7 eV with instrumental
resolutions of 0.3 eV.28 These studies were the first attempt to resolve and
characterize a novel splitting of core level XPS peaks which has been called the
electric field gradient splitting (or ligand field splitting), which is proportional
to the nuclear quadrupole splitting observed by Mössbauer spectroscopy.29
Much better resolution was required to resolve this splitting of o0.4 eV, which
led GMB to use high resolution He I (21.2 eV) and He II (40.8 eV) photoelec-
tron sources to initially resolve this splitting on low binding Zn 3d and Cd 4d
levels in Zn and Cd compounds, respectively,30 with total linewidths of
o0.1 eV. The chemical sensitivity of the ligand field splitting to bonding and
structure was demonstrated experimentally and theoretically;29,30 and high
resolution synchrotron XPS studies extended these studies to higher binding
energy BE core levels such as I 4d, Xe 4d and Br 3d in I, Xe and Br compounds
respectively31 with total linewidths of o0.15 eV.
More importantly for this publication, the core level vibrational splittings
(first observed on the C 1s level of CH413) on the Si 2p levels of simple silanes were
resolved and characterized.32 These studies showed that a major cause of line-
broadening in the Si 2p spectra from solid state non-conductor silicates was due to
vibrational splitting in the ion state. Recent gas phase Si 2p and C 1s XPS studies
of silanes and hydrocarbons, using the third generation ALS Berkeley synchro-
tron,33,34 gave total linewidths that are very close to the natural linewidths –
e.g. 38 meV for SiH4. Thus, the Si 2p linewidths in gas phase silanes have
decreased from over 1 eV to o0.1 eV in the last 35 years, while the Si 2p linewidths
in the silicate spectra have remained close to 2 eV!
Meanwhile, HWN had begun XPS studies (using laboratory monochroma-
tized Al Ka sources) of semiconductor mineral sulfides and arsenosulfides in
the early 1990s.35 Because of the increase in both spectral resolution and surface
sensitivity with synchrotron sources, GMB and HWN began a productive
collaboration (along with Rudiger Szargan from Leipzig) at the Aladdin
synchrotron to determine the surface chemistry of sulfides and arsenosulfides,
and the initial mechanisms of oxidation of these minerals.36–38 Total linewidths
of B0.4 eV were obtained on these semiconductors using room temperature;
and linewidths of o0.3 eV have been obtained on other semiconductor sulfides
654 Chapter 39
39
such as PbS and MoS2 using high resolution synchrotron XPS. On semicon-
ductor Si samples, Si 2p3/2 linewidths of B0.2 eV have been obtained.40
The development of the Kratos Axis Ultra XPS, with a novel magnetic
confinement charge neutralizer, offered the prospect of much better resolution
for non-conductors.41 For example, the C 1s linewidth on the –O–C¼O peak of
PET of 0.69 eV was substantially less than the 0.85 eV quoted earlier15 on an
‘‘ideal’’ polymer sample. HWN headed up a UWO effort (while GMB was the
Director of the Canadian Light Source in Saskatoon) to obtain this new Kratos
instrument, and with the collaboration of Stewart McIntyre in Surface Science
Western (SSW), the Kratos instrument began running at SSW in 2003. The rest
of this paper provides a few of the results obtained with this instrument,
showing that optimal results for XPS of non-conductors can be obtained (with
linewidths equivalent to those collected for analogous semiconductors and
metals), making the XPS technique much more useful for surface and structural
studies on all silicates.

2 Results and Discussion

Nearly all the spectra reported in this chapter were obtained with monochro-
matized Al Ka radiation from the Kratos Axis Ultra spectrometer on fractured
non-conductor mineral surfaces. The optimized overall instrumental width with
10 eV pass energy (photon+electron width) was 0.35 eV. Charge compensation
from the novel magnetic charge compensation system was adjusted for every
sample to obtain the minimum linewidth. The spectra were fit with between
50% Gaussian–50% Lorentzian to 70% Gaussian–30% Lorentzian lineshapes
and Shirley backgrounds, as described in the recent publications from this
Kratos instrument in SSW.42–48
Our first study42 focussed on the question: can one obtain the same linewidth
on a non-conductor as on an analogous semiconductor? Previous high resolu-
tion studies on Si, Ge, Sn, P and As gas phase molecules revealed: first, that the
As 3d line had a rather narrow inherent lifetime linewidth (r0.2 eV) with little
or no vibrational broadening in the ion state;49 and second, that the total As 3d
linewidth for the semiconductor FeAsS was o0.4 eV using high resolution
synchrotron radiation.38 We chose to study the As 3d level on fractured
surfaces in two analogous minerals: the non-conductor orpiment, As2S3, along
with the well-studied semiconductor arsenopyrite, FeAsS.38 The charge com-
pensation system is required only for the non-conductor; and this mineral gave
a severe test of the charge compensation system because fracturing yielded an
irregular surface. The resulting room temperature As 3d spectra in Figures 1a
and b are very satisfying: the As 3d linewidths for both minerals are identical at
0.52 eV, and the lineshapes are identical and well-behaved. In an independent
study of the As 3d line in As metal on the same instrument, Mark Biesinger at
SSW (personal communication) also obtained an As 3d linewidth of 0.51 eV.
These results show that the charge compensation system works extremely well,
and gives no observable differential charge broadening. The effect of such
Recent Advances in XPS of Non-Conductors 655

Figure 1 As 3d XPS spectra of (a) FeAsS, (b) As2S3 taken with the Kratos XPS, and
(c) the As 3d spectrum taken with an SSX-100-XPS.41

broadening is shown in Figure 1c, which shows an As 3d spectrum of the non-

conductor with a modern SSX-100 XPS instrument using a monochromatic Al
Ka source and a traditional directional flood gun. This spectrum is much
broader (linewidth of 0.8 eV) and gives unexplainable charge broadening in the
peak tails.
The small peaks in the spectra in Figure 1 are due to surface species,
identified more clearly on FeAsS in previous surface sensitive synchrotron
XPS studies.38 The major contributions to this width are the instrumental width
of 0.35 eV, a ground state phonon broadening of r0.1 eV,39 and the As 3d
inherent width of r0.2 eV.49 Using a high resolution synchrotron source with
an instrumental width of o0.1 eV at low temperature to remove the phonon
broadening, it is expected that the total As 3d linewidth for the non-conductor
will be r0.3 eV.
But what about the much broader O 1s and Si 2p linewidths for silicates?
Figure 2 shows the optimized Si 2p and O 1s spectra for fractured SiO2.42 These
spectra show very well-behaved peak shapes and much narrower linewidths
than seen previously, but both the total Si 2p and O 1s linewidths of 1.3 and
1.2 eV, respectively, are much broader than the As 3d widths in Figure 1. This
Si 2p width is consistent with the broad Si 2p width (1.4 eV) on a thin uniform
uncharged SiO2 film on Si metal taken at similar resolution on a synchrotron
source.50 The previous high resolution gas phase Si 2p spectra of SiF432a,33 and
the close analogue Si(OCH3)432b strongly pointed to unresolved ion state
vibrational splitting as the cause of the broadening in the Si 2p spectrum. In
Figure 3, we compare the Si 2p spectra of the two tetrahedral SiO4 analogues,
Si(OCH3)4 and an orthosilicate olivine. The Si–O bond lengths and Si–O
656 Chapter 39

Si 2p, Qz, vac. frac. (a) O 1s, Qz, vac. frac. (b)
FWHM3/2,1/2=1.05eV FWHM=1.20eV
FWHMtotal=1.30eV

3/2
Intensity

1/2

106 104 102 100 98 536 534 532 530

40 40
20
Diff. %

20
0
-20 0
-40 -20
106 104 102 100 98 536 534 532 530
Binding energy (eV)

Figure 2 Core level XPS spectra of quartz, SiO2: (a) Si 2p and (b) O 1s.42

symmetric stretch are very similar in the two compounds, as shown at the top
of the figure. Figure 3 illustrates the effect of just broadening each Si 2p peak
in the vibrational envelope from 0.17 eV in the gas phase Si(OCH3)4 spectrum
(Figure 3a) to 0.4 eV for olivine (Figure 3b). The overall Si 2p width with these
vibrational fits increases from 1.1 to 1.26 eV – in rather good agreement with
the Si 2p width in the mineral olivine and in all other silicates that have been
studied.42–44,47,48 The fit to the Si 2p olivine spectrum is rather good: the width
is underestimated in the fit by only about 0.05 eV. This is again a strong
indication that the Si–O vibrational envelope from the Si–O symmetric stretch
causes the broad Si 2p linewidths.
The O 1s linewidth is probably also due to unresolved vibrational broaden-
ing. The O 1s linewidth (1.20 eV in Figure 3) is always slightly broader than the
Recent Advances in XPS of Non-Conductors 657
Si(OCH3)4 Mg2SiO4
Tetramethoxysilane (gas) Olivine (solid)
C Si-O Bond length: Mg
O 0.161Å vs 0.163Å O
C O Si O C Vibrational Splitting Mg O Si O Mg
O O
842 vs 863cm-1
C Mg

Vibrational Contributions a Vibrational Contributions b

FWHM = 0.170 eV FWHM = 0.40 eV
Splittings = 0.125 eV Splittings =0.125 eV

1.10 eV 1.26 eV
Counts

111 110 109 108 107 106 104 103 102 101 100
Binding Energy(eV) Binding Energy (eV)

Figure 3 Comparison of: (a) the Si 2p XPS spectra of: the gas phase Si(OCH3)4
analogue taken with an instrumental resolution of B0.15 eV32b and (b) the
solid state spectrum of a fractured non-conductor olivine, Mg2SiO4,42 taken
with the Kratos XPS with an instrumental resolution of B0.35 eV. The dots
give the experimental spectra, and the overall solid line from the fit with 10
vibrational peaks and the Si 2p spin-orbit splitting fits the experimental
spectrum rather well in both cases.

component Si 2p3/2 line (1.05 eV), indicating that the number of component
vibrational peaks is probably larger for O 1s than for the Si 2p spectra.
However, Figure 3 indicates that the O 1s spectra should be more sensitive
than the Si 2p spectra to the individual peak linewidths (see below, final
paragraph of conclusions). Thus, in Figure 3a, the overall Si 2p width is 1.1 eV,
whereas the Si 2p3/2 width is 0.8 eV. Other papers using the Kratos from
SSW,44,45 and a recent O 1s study of TiO2,51 give somewhat similar O 1s
linewidths.
The enhanced resolution is critical to resolve and characterize the O 1s
spectra of silicates such as orthopyroxenes (Figure 4) that have both structural
BO and NBO.44 In diopside, [Ca(Mg0.8Fe0.2)Si2O6], two resolved peaks are seen
658 Chapter 39

O 1s, Diopside (a) O 1s, Diopside (b) O 1s, Bronzite (c)

FWHM1,2,3=1.11eV FWHM1=1.11eV FWHM1=1.16eV
FWHM2=1.41eV FWHM2=1.51eV
FWHM3=1.14eV FWHM3=1.40eV
Intensity

1
1
2
3
3 2

3 2 1

40 40 40
20
Diff. %

20 20
0 0 0
-20 -20 -20
-40 -40 -40
538 536 534 532 530 528 538 536 534 532 530 528 538 536 534 532 530 528

Binding energy (eV)

Figure 4 The O 1s XPS spectra fitted with three equal area contributions of: (a)
diopside with the additional constraint that the three widths are equal, (b)
diopside with no additional constraint, and (c) bronzite with no additional
constraint.

clearly in a silicate mineral for the first time, and these two peaks can be
immediately assigned based on previous results: the high energy O peak to the
O atoms in the bridging Si–O moiety (Si–O–Si) (BO), and the low energy O
peak to the O atoms in the M–O–Si moieties (M ¼ Mg, Ca, Fe) (NBO). The BE
for these two peaks are very similar to the BO in quartz, and the NBO in
olivine, respectively. The ratio of areas of these two peaks NBO:BO should be
2:1 (there are 4 NBO and 2 BO in the Si2O6 moiety), but a two peak fit with
identical linewidths44 gives a ratio of 1.6:1. Examination of the diopside crystal
structure52 shows that there are three crystallographically distinct O atoms in
the Si2O6 unit with proportions of 2:2:2 for SiOSi, (Mg,Fe)OSi and CaOSi.
Two three peak fits are given in Figures 4a and b. In Figure 4a, the linewidths
for all peaks were constrained to be equal, and the areas and peak positions
were allowed to vary. This fit is satisfactory, and the spectrum can be readily
assigned based on the order of electronegativities SicMg>Ca: peak 3 to the O
in the SiOSi moiety, peak 2 to (Mg,Fe)OSi and peak 1 to CaOSi. A better fit
(Figure 4b) can be obtained when the three areas are constrained to be equal,
but the linewidths are allowed to vary. The broader width of peak 2 is expected
because the Fe resides with the Mg in the so-called M1 site, and the FeOSi
moiety would give a larger O 1s BE than MgOSi because the electronegativity
of Fe21 is larger than that of Mg21. A similar three peak fit is given for the
O 1s spectrum of a bronzite [(Fe0.2Mg0.8)2Si2O6]44 in Figure 4c. The separation
between peaks 1 and 3 is only 1.4 eV, and so the BO (peak 3)
and NBO peaks (peaks 1 and 2) are not resolved as for diopside. The Fe21
and Mg21 are known to order on the M2 and M1 sites respectively;52,53 and
Recent Advances in XPS of Non-Conductors 659

O 2s

Quartz

5
4 3 2 1

Diopside
Ca 3p
Intensity

1
2

30 26 22 18
4 3
5

2? 1

Bronzite

4 3
5

2?
1

Mg-rich 4 3
olivine

2 1
O 2s

35 30 25 20 15 10 5 0
Binding energy (eV)

Figure 5 The inner valence ‘‘O 2s’’ and outer valence band XPS spectra (VBXPS) of
quartz, diopside, bronzite and Mg-rich olivine (from top to bottom).
660 Chapter 39

CaMgSi2O6
4 3
5

6
Intensity

2
Diopside 1

3
5 4
Mg2Si2O6
6

2?
1
Bronzite

20 18 16 14 12 10 8 6 4 2 0
Binding energy (eV)

Figure 6 The VBXPS spectra of diopside (top) and bronzite (bottom), background
subtracted. The calculated XPS spectra (solid lines) for the diopside (top)
and enstatite end members (no iron) are given above the experimental
spectra. The intensity of each state was corrected for cross-section and each
band broadened by 0.37 eV to match the instrumental resolution. The
calculated spectra were aligned to the experimental energies of peak 6.

together with the electronegativities, we can readily assign peaks 2 and 1 to

(Mg,Fe)OSi (Mg,Fe are in M2) and MgOSi (Mg is in M1) respectively.
Finally, it is important to note: first, that excellent valence band spectra of
these minerals can be obtained; second, that these spectra are very sensitive to
the nature of the tetrahedral linkages in the silicate; and third, that theoretical
calculations reproduce the experimental spectra very well. It was a pleasure to
have a former PhD student (JST) collaborate once again on the theoretical
calculations. These spectra are much weaker than the core level spectra, and
great stability of the surface charge neutralization is required to obtain the
spectra of these minerals shown in Figure 5. The inner valence band consists of
relatively intense O 2s peaks that chemically shift with the O 1s peaks. The
outer valence band peaks 1 and 2 in the lower three spectra can be assigned to
the Fe 3d orbitals split by ligand field splitting. The other peaks 3, 4 and 5 can
be assigned qualitatively based on MO considerations for a tetrahedral SiO4
moiety.43
Recent Advances in XPS of Non-Conductors 661
It is worth noting the chemical sensitivity of these spectra. For example, peak
5 is shifted by about 4 eV from olivine to quartz. High quality calculations of
the band structure were performed using pseudopotential density functional
theory54,55 and compared with the spectra of these minerals. Using the Gelius
approximation,56 and atomic cross-sections,57 the calculated valence band
spectra have been obtained for all of these minerals. The agreement with the
experimental spectra is excellent as shown for the two pyroxenes of idealized
composition (without any Fe21) in Figure 6.44 Six peaks are more apparent in
these expanded spectra, and subtle differences between the spectra are repro-
duced by the calculations. For example, peaks 3 and 4 are shifted to higher
energy in bronzite than in diopside; and there is a larger splitting between peaks
3 and 4 in bronzite than in diopside.

3 Conclusions
Excellent XPS spectra of non-conductor silicates have been obtained for several
different types of fractured silicate minerals using the Kratos Axis Ultra
spectrometer. The linewidths and lineshapes are well-characterized, and the
linewidths are substantially less than obtainable with other charge compensa-
tion systems. The valence band spectra are very sensitive to the structure and
chemistry of the silicate mineral, and high quality theoretical calculations
reproduce these valence band spectra very well. The O 1s spectra are immedi-
ately useful for characterizing the different types of O atoms in silicates, and
both the O 1s and valence band spectra should be very useful for characterizing
the silicate species in more complex silicate materials such as glasses and
zeolites. Already, the O 1s spectra have been extremely useful for determining
the silicate species in Pb silicate glasses.47 In addition, it is now possible to use
these spectra for detailed surface dissolution studies. For example, our study of
the dissolution of olivine shows the first direct evidence for a surface monolayer
of Si–O–H species from both the O 1s and valence band spectra combined with
theoretical valence band calculations.48
In the future, it will be important to have the Kratos XPS on a high
resolution synchrotron beamline to increase the O 1s resolution, and especially
to increase the surface sensitivity for surface dissolution studies as has been
done on sulfides.37,38 The overall Si 2p linewidths will probably not decrease by
more than 0.2 eV because of the large vibrational envelopes and the Si 2p spin-
orbit splitting of 0.61 eV. For example, for Si 2p, even assuming that an
individual peak linewidth is close to the Si semiconductor width of 0.2 eV40
at low temperature, the minimum overall Si 2p linewidth will not be substan-
tially less than the 1.1 eV (shown in Figure 3). But for O 1s, it is expected that
the overall O 1s linewidth should decrease to close to the Si 2p3/2 linewidth of
0.8 eV shown in Figure 3a. This better resolution would obviously make
another big improvement to the O 1s spectra, and a concomitant increase in
the amount of structural and chemical information.
662 Chapter 39

Acknowledgements
This research was funded by the Natural Science and Engineering Research
Council (NSERC) of Canada. We would like to thank the SSW staff at the
UWO (especially R. Davidson, M. Biesinger and N.S. McIntyre) for all their
help and advice with the Kratos XPS.

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37. A.G. Schaufuss, H.W. Nesbitt, I. Kartio, K. Laajalehto, G.M. Bancroft
and R. Szargan, Surf. Sci. Lett., 1998, 411, 321.
38. A.G. Schaufuss, H.W. Nesbitt, I. Kartio, K. Laajalehto, G.M. Bancroft
and R. Szargan, Am. Miner., 2000, 85, 1754.
39. J.A. Leiro, K. Laajalehto, I. Kartio and M. Heimonen, Surf. Sci., 1998,
412/413, L918; S. Mattila, J.A. Leiro, M. Heinomen and T. Laiho, Surf.
Sci., 2006, 600, 5168.
664 Chapter 39
40. C.J. Karlsson, F. Owman, E. Landmark, Y.-C. Chao, P. Partensson and
R.I.G. Uhrberg, Phys. Rev. Lett., 1994, 72, 4145; S.M. Scholz and
K. Jacobi, Phys. Rev. B, 1995, 52, 5795.
41. Kratos web page: http://www.kratos.com.
42. H.W. Nesbitt, G.M. Bancroft, R. Davidson, N.S. McIntyre and
A.R. Pratt, Am. Miner., 2004, 89, 878.
43. V.P. Zakaznova-Herzog, H.W. Nesbitt, G.M. Bancroft, J.S. Tse, X. Gao
and W. Skinner, Phys. Rev. B, 2005, 2, 205113.
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45. M.C. Biesinger, C. Brown, J.R. Mycroft, R.D. Davidson and N.S. McIntyre,
Surf. Interface Anal., 2004, 36, 1550.
46. A.P. Grosvenor, M.C. Biesinger, R.S. Smart and N.S. McIntyre, Surf. Sci.,
2006, 600, 1771.
47. K.N. Dalby, H.W. Nesbitt, V.P. Zakaznova-Herzog and P.A. King,
Geochim. Cosmochim. Acta (accepted).
48. A.P. Zakaznova-Herzog, H.W. Nesbitt, G.M. Bancroft and J.S. Tse,
Geochim. Cosmochim. Acta (submitted).
49. Z.F. Liu, G.M. Bancroft, J.N. Cutler, D.G. Sutherland and K.H. Tan,
Phys. Rev. A, 1992, 46, 1688.
50. F.J. Himpsel, F.R. McFeely, A. Taleb-Ibrahimi, J.A. Yarmoff and
G. Hollinger, Phys. Rev. B, 1988, 38, 6084.
51. H. Perron, J. Vandenborre, C. Domain, R. Drot, J. Roques, E. Simoni,
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57. J.J. Yeh and I. Lindau, Atomic Data and Nuclear Data Tables, 1985, 32, 1.
 Section D:
Electron Microscopy and its Contribution
to Chemistry and Material Science
CHAPTER 40

Electron Microscopy Studies

of Structural Modulation in
Micro- and Meso-Porous Crystals
OSAMU TERASAKI,a TETSU OHSUNA,a,b ZHENG LIU,a,c
YASUHIRO SAKAMOTO,a KEIICHI MIYASAKA,a
NOBUHISA FUJITA,a,d NOZOMU TOGASHIe AND
SHUNAI CHEf
a
Department of Physical, Inorganic and Structural Chemistry, Arrhenius
Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden;
b
CREST, Japan Science and Technology Agency, Kawaguchi, Japan;
c
National Institute of Advanced Industrial Science & Technology, Tsukuba,
Japan; d Institute of Multidisciplinary Research for Advanced Materials,
Tohoku University, Sendai, Japan; e Namiki Precision Jewel Co. LTD.,
Tokyo, Japan; f School of Chemistry and Chemical Technology, Shanghai
Jiao Tong University, Shanghai, PR China

1 Introduction
1982 Marked a turning point for one of us, Osamu Terasaki (OT), to work with
Sir John as a Guest Research Fellow of the Royal Society. OT was fascinated
with zeolites as containers for making novel arrayed clusters, which would have
new properties quite different from bulk crystals, within their cages or channels
by self-assembly,1,2 and was attracted by the works of Sir John, especially on
high resolution transmission electron microscopy (HRTEM) imaging of LTAw
zeolite.3 Up until then, OT had concentrated on transmission electron micro-
scopy (TEM) study of modulated structures in Au-based closed-packed alloys
such as Au–Mn and Au–Zn alloys. The application of HRTEM to the study of
open-structures itself constitutes a major turning point in solid-state and

w
Structure Commission of the International Zeolite Association gives a structural code for each
framework type of zeolite by three capital letters, e.g. LTA, LTL, MOR etc.

667
668 Chapter 40
materials science. As will become evident below, no other technique can cope
with the structural problems posed by mesoporous silicas in which the silica
walls themselves are amorphous but the arrangement of the cages, channels and
pores is crystallographic, as a ‘‘cavity crystal’’. In 2001, Sir John and OT,
together with his other colleagues, wrote a brief review of the power of
HRTEM and STEM in elucidating the nature of microporous and mesoporous
solids.4
‘‘Space filling and partition’’ is a very important concept in understanding
and explaining the self-assembly mechanism. We are impressed that living
creatures are intelligent enough to live peacefully by partitioning spaces like
Voronoi cells as shown in Figure 1 (a colour picture of coral from Gotland,
Sweden). Soap bubbles fill three dimensional (3d) space freely and will arrange
themselves to minimise the total area of the interfaces between the bubbles.
When three bubbles meet, a line is formed as the common edge of the bubbles
by deforming their spherical shapes. A maximum of four soap bubbles can
meet at a point, where four lines are connected with the tetrahedral angle,
cos
1(
1/3). This is similar to a zeolite framework structures, where Si atoms
take the tetrahedral positions and the lines correspond to the Si–O bondings.
For a long time Kelvin’s partition, which is known as the zeolite SOD
framework type, was believed to be a solution for the arrangement for which

Figure 1 Coral from Gotland, Sweden, taken from a collection of Prof. Mori, Tohoku
University, Sendai, Japan.
Electron Microscopy Studies of Structural Modulation 669
the total area of the interfaces between the cells of a uniform volume is a
minimum. More than 10 years ago, it was shown that another zeolite frame-
work-type called MEP (melanophlogite, SG: Pm3n), which has two kinds of
cells, dodecahedron (12-hedron) and tetrakaidecahedron (14-hedron) of equal
volume, surpassed Kelvin’s partition by 0.3% in area.5 This MEP is a gas
clathrate type I (type II has Fd 
3m structure) and is also classified as one of the
tetrahedrally close packed (tcp) structures, whose bondings are exclusively
tetrahedral like zeolites.
In this review, we outline the advances with specific examples, that begin by
recalling relevant facts about the Au–Mn alloy system, which then lead on to
structural modulations in mesoporous crystals.

2 Modulations in Structure and Composition

of Micro- and Meso-Porous Crystals: Lessons
from Long-Period Ordered Structures
of the Au-Rich Au–Mn Alloys
It is instructive for understanding structural modulations to briefly address an
example of the structure A1. Before we go through case studies of porous
materials, A1 face centred cubic (fcc) and is known as one of the closest
packings of a uniform sphere. In Au–Mn systems at high temperature, the
Au-rich alloys form disordered A1 structures across a wide composition range
up to about 28 at. % Mn. At low temperature, Mn atoms arrange in ordered
fashion on an fcc lattice. Various ordered structures with increasing Mn
content such as Au4Mn, Au22Mn6, Au31Mn9, Au3Mn and Au5Mn2 were
studied by HRTEM experiments. At 20 at. %, Mn atoms occupy every fifth
(420)c and ( 240)c planes, where subscript c refers to the fundamental fcc
structure. Therefore the Au4Mn (D1a type) structure is described by the
stacking sequence of the (420)c plane, Au-plane and Mn-plane, as . . . Mn
Au Au Au Au Mn. . . .
Excess Mn atoms from 20 at. % can be accommodated by creating a planar
defect as shown by large white arrows in Figure 2a, and at 21.4 at. % Mn,
excess Mn atoms from 20 at. % can be accommodated by introducing the
planar defects every three Mn atom planes parallel to (420)c. The stacking
sequence then becomes . . . Mn Au Au Au Au Mn Au Au Au Mn Au Au Au
Au Mn . . . and the Au22Mn6 structure results. The Au22Mn6 structure is
regarded as a 1d-modulated structure of Au4Mn. A further increase in Mn
content causes another planar defect system parallel to (240)c planes in
Au22Mn6, and Au31Mn9 and results in the composition of 22.5 at. % Mn.
The Au31Mn9 structure is regarded as a 1d-modulated structure of Au22Mn6,
and therefore as a 2d-modulated structure of Au4Mn. Changes in the structures
with an increase of Mn content from A1 to Au4Mn (D1a type), from Au4Mn to
Au22Mn6 and from Au22Mn6 to Au31Mn9 are simply described in terms of a
structural/density modulation.6–8 These structural changes are schematically
670 Chapter 40

Figure 2 Structures of Au4Mn (a), Au22Mn6 (b) and Au31Mn9 (c) projected along the
[0 0 1] direction and thick squares show their unit cells. Large and small
circles lie in the planes z ¼ 0 and z ¼ 1/2 of the A1(fcc) structure, and open
and solid circles represent Au and Mn atoms, respectively.

summarised in Figure 2, which was confirmed by both HRTEM images and

their corresponding electron diffraction (ED) patterns. Their structural stabil-
ities were discussed based on a pairwise interaction model developed for the
Ising spin system on an fcc lattice.9 Whereas, in the foregoing, all compositional
changes are described by the stacking sequences of Au- and Mn-planes on a fcc
lattice, we now turn to a different situation.

2.1 Case 1. Structural Modulation of Mesoporous Crystals

Since the discovery of silica mesoporous crystals,10,11 different structures have
been synthesised using both ionic and non-ionic surfactants. An assembly of
oligomeric silica under the influence of surfactant molecules forms mesoporous
structures. Two basic formation mechanisms have been proposed: (i) the
assembly starts from a pre-formed liquid crystal mesophase12 and (ii)
the surfactant and silica assemble cooperatively to produce liquid crystalline
arrangements.13 In most cases, a cooperative mechanism seems to be in
operation. It is important to understand the inter-relationship between the
intermicellar interaction, the silica-condensation rate and rigidity of the mice-
lles, water activity,14 surfactant mobility and the final structure of the meso-
porous crystals. Other important concepts that should be considered are: (i)
charge matching between surfactant and silica and (ii) surfactant packing
parameters.
The closest packing of uniform hard spheres is fcc (SG: Fm3m) or hexagonal
close packing (hcp, SG: P63/mmc), while the foam with MEP type (SG: Pm3n)
is known to be the area-minimised structure. The ‘‘minimal surface-area
principle’’ is incompatible with closest packing and favours the MEP type over
Electron Microscopy Studies of Structural Modulation 671
fcc/hcp. These structures may be considered to be stabilised by a soft-intermi-
cellar potential and hard-core potential, respectively.15 The competition of two
different types of potentials may also produce many different structures with
space-groups Fm 3m, P63/mmc, Fd  3m, Pm 3n, P42/mnm and so on, covering the
range from dispersed spherical micelle structures to the 2d-hexagonal struc-
tures. It is interesting that the fcc structure can be stabilised with a hard-core
intermicellar potential even without an attractive potential part10 or with a
hard-core intermicellar potential plus soft repulsive tail.16 However, we have
also found mesoporous crystals with a ‘‘five-fold symmetry’’ morphology
resulting from a multiply twinned particle (MTP) as will be discussed below.17
All the external surfaces of the particles are covered by only {1 1 1} planes,
which suggests that the surface-boundary energy for {1 1 1} is substantially
smaller than that for other planes. This is explained by speculating that the
intermicellar pair potential has an attractive potential term, which has a
minimum at the intermicellar distance (similar to a Lenard–Jones potential)
in addition to a strong repulsive potential (hard-core). It is then natural to
conjecture that the uniform spherical micelles, surfactant and silica are co-
assembled in this way. A close packing of spheres with radius R forms extra
octahedral and tetrahedral pores (corresponding inscribed spheres have radii of
0.414 R and 0.225 R, respectively), which are widely used for producing
negative opal structures. It is important for a future discussion of the two
formation mechanisms of mesoporous crystals to know what kind of TEM
image contrast can be observed due to the existence of the extra pores in the
case that silica does not fill these pores formed by the close packing of hard
spherical shells. Using software written by one of the authors (TO), TEM
images are simulated for three different cases of fcc packing: (A) spherical shells
of silica, (B) spherical empty cavities embedded in silica with inter-cavity
distance 2 nm (silica wall), and (C) the same as case (B) except that neigh-
bouring cavities contact each other directly. The case (C) closely corresponds to
mesoporous silica with Fm 3m that we observed using TEM. It is clear from the
simulated images along [1 1 0] that we can clearly distinguish between the three
cases, especially between the spherical shell of silica (A) and spherical empty
cavities (B and C) as shown in Figure 3.

2.1.1 Not a Quasicrystal but a Multiply Twinned Crystal

Using a gemini cationic surfactant, crystals with fcc structure (Fm3m) were
synthesised. We have observed unusual morphologies inconsistent with the
point-group symmetry m 3m expected for the Fm3m space-group symmetry.
Figures 4a–d show SEM images and corresponding schematic drawings of the
crystals with pentagonal dipyramid and icosahedral shapes, respectively. Both
regular dodecahedron and rhombic triacontahedron have been observed in
bulk quasicrystals.18 However, from HRTEM analyses it was concluded in this
case that these crystals are not a quasicrystal but multiply twinned particles
with Fm 3m structure.17 The closest packing may be explained by a naı̈ve
672 Chapter 40
Case A Case B Case C
shell thickness = 1nm cavity distance = 2nm cavity distance = 0nm

a b e f i j

c d g h k l

FCC crystal of silica shell, FCC crystal of spherical cavity FCC crystal of spherical cavity
radius; (a)5nm, (b)10nm, (c)20nm, radius; (e)4nm, (f)9nm, (g)19nm, radius;(i)5nm, (j)10nm, (k)20nm,
(d)40nm, thickness; 1nm (h)39nm (l)40nm
boundary roughness; 0.2nm boundary roughness; 0.2nm boundary roughness; 0.2nm
TEM simulation, defocus; 200nm, thickness; 20nm, acceleration Voltage; 300kV

Figure 3 TEM simulated images of three different fcc packings of spherical shells
(Case A), and spherical cavities embedded in amorphous silica (Case B) and
(Case C). The images are simulated for the [1 1 0] incidence at the following
conditions; defocus value: 200 nm, crystal thickness: 20 nm, acceleration
voltage: 300 kV.

Figure 4 SEM images of silica mesoporous crystals with Fm

3m and their schematic
representations. Pentagonal dipyramidal (a, b) and icosahedral (c, d)
morphologies.
Electron Microscopy Studies of Structural Modulation 673
speculation that surfactant and silica assembled to form spherical micelles
cooperatively.
It is worth noting that the structure of the product is so sensitive to synthesis
conditions that a crystal with Pm 3n symmetry, where a ‘‘minimal surface-area
principle’’ is operating, was synthesised by changing the amount of H2SO4 or
synthesis temperature within the same synthesis system.19

2.1.2 Modulation in Anionic-Surfactant-Templated Mesoporous

Silica (AMS)
Recently, using anionic surfactants and co-structure directing agents (CSDA),
one of us (SC) has developed a novel synthesis route for mesoporous silica
crystals termed AMS-n.20–24 All the structures synthesised with ‘‘conventional’’
cationic or polymeric surfactants have been reproduced as highly crystalline
materials. This was achieved through small variations in the synthesis condi-
tions and in all cases using an anionic surfactant with a CSDA. Interestingly,
silica mesoporous crystals with fcc and with MEP type structures were suc-
cessfully synthesised in the same synthesis system as the AMS series.
By careful choice in the synthesis systems of anionic surfactants, such as
lauric acid and amino acid derived amphiphiles, together with a CSDA, it is
possible to scan ‘‘the phase (synthesis space) diagram’’ for new mesostructures
which offers new insights into structural relationships between template and
inorganic counterpart.23 Within this system, it has also been possible to
synthesise for the first time a new bicontinuous silica mesoporous crystal with
D-minimal surface, SG Pn 3m, termed AMS-10.24
Figure 5a shows an HRTEM image of an AMS-2 crystal with SG Pm3n
recorded with [0 0 1] incidence. The structure of AMS-2 is the same as the MEP
type consisting of two different polyhedra, a 12-hedron with 12 pentagons and
a 14-hedron composed of two opposite hexagons and 12 pentagons. A planar
fault is observed in the image as marked by a black arrow. For clarity, the unit
cells of the MEP type are shown by white squares and those across the fault are
shown by three white triangles. The arrangement of the polyhedra and the main
pore connectivity through hexagonal windows across the fault plane are shown
in Figure 5d. At the fault, a new 15-hedron with 3m (C3v) symmetry, with the
three-fold axis parallel to [0 0 1], composed of 3 hexagons and 12 pentagons is
introduced. Periodical planar faults are also observed as a structural modula-
tion indicated by black arrows and result in a new 1d–modulated structure
based on Pm 3n (Figure 5b). This is similar to the case of Au22Mn6 from Au4Mn
(Figure 2) except that the lattice is not fixed in the mesoporous system and that
there is a small contraction to form a regular triangular-column as shown in
Figure 5d. Extra spots due to the periodic modulation along bc* perpendicular
to the (0 1 0)c plane appear to divide the distance to the 002 reflection into 4.
At the left side of Figure 5b, another modulation indicated by white arrows
can also be observed. At the intersection of the two modulations, we can see
the same Pm 3n structure (marked by white square and rhombi, top left in
674 Chapter 40

Figure 5 HRTEM images and corresponding ED patterns from AMS-system with

SG Pm3n (a) to 1d-modulated structure (b) and 2d-modulated structure
(AMS-9) with P42/mnm (c). A schematic drawing of the micellar arrange-
ment (z coordinates are referred to the unit cell of Pm
3n) and the main
pore connectivity through hexagonal windows across the planar defect is
shown (d).

Figure 5c) as in the original, but rotated by 601. When the second type of
modulation is also introduced periodically, the AMS-9 structure with P42/mnm
results (Figure 5c). These observations may suggest that if a synthesis system is
well controlled and silica condensed slowly relative to surfactant mobilisation,
then structural changes in the liquid-crystal is well preserved as silica mesopo-
rous crystals. These structural variations are hardly observed by diffraction
measurements alone and are explained well by the simulated images inserted in
Figure 5 [TO’s software]. Intergrowth of Fm 3m and Fd 3m structures will be
discussed separately (Y. Sakamoto et al.).

2.1.3 Chiral Mesoporous Crystal Based on 2d-Hexagonal p6mm

We now turn to a novel type of modulation, chiral structures, for which the
chiral pitch and handedness are experimentally controllable. Recently, a chiral
ordered mesoporous crystal was synthesised by SC using the chiral surfactant
N-myristoyl-L-alanine sodium salt (C14-L-AlaS) as a template, 3-amino-
propyltriethoxysilane (APES) and N-trimethoxysilylpropyl-N,N,N-
trimethylammonium chloride (TMAPs) as CSDAs and tetraethoxylsilane
(TEOS) as an inorganic source.20 An SEM image of the crystal and a schematic
chiral channel system are shown in Figure 6. The crystal has a characteristic
structure, i.e. a twisted hexagonal rod like morphology which possesses hexa-
gonally ordered channels that run along the long axis of the rods at the same
Electron Microscopy Studies of Structural Modulation 675
c tube diameter
a

D
a t

3 2 1

d10 =a/ 3
d11 =a/2

321

d
b

Pitch

tube
direction

Projection
10

Figure 6 SEM image of chiral silica mesoporous crystal (a) and schematic drawing of
its morphology along the {1 0} direction (b). The channel system is shown in
cross section (c) and perpendicular to the tube (d). {1 0} planes are parallel to
o1 04 and therefore {10} fringes are observed only at the positions marked
by the arrowheads in (b).

time as winding around the central axis of the rods. The positions where {1 0}
fringes appear are marked by arrowheads in Figure 6b.
TEM combined with image simulations confirmed the above structural
model as shown in Figure 7.20 The chiral pitch of the channels inside hexagonal
chiral mesoporous crystals was measured from the intermittent period. Between
two sets of {1 0} fringes marked by black arrows (Figure 7a and b), the rod has
twisted by 601, which means that the distance between two sets of {1 0} fringes is
one-sixth of one pitch. {1 1} Fringes are also observed in Figures 7a and b
as marked by white arrows. The chirality (possessing the quality of being
right or left-handed) was determined from the tilt direction of a channel
compared with the direction of incident electrons and the curvature direction
of the curved intermitted fringes as viewed in the TEM images.25 The chirality
and the morphology of the mesoporous silica are controlled by the stirring
rate during the chiral surfactant self-assembly.26 Several interesting points were
676 Chapter 40

Figure 7 HRTEM images of the chiral silica mesoporous crystal (a) and tube (c), and
the corresponding simulated images (b) and (d), respectively. The positions
where {10} and {11} fringes appear are maked by black and white arrows in
(a) and (b).

observed: (i) there is a linear relationship between pitch length and rod
diameter, (ii) the left/right handedness ratio was ca. 3/1 for the total sample
regardless of differences in stirring rate or direction, as long as the rate is faster
than 400 rpm. Furthermore, a racemic chiral mesoporous silica with twisted
2d-hexagonal structure has been synthesised by using achiral surfactant SDS.27
Recently, right- and left-handed excess chiral mesoporous silica nanotubes with
helical channel walls have been formed by self-assembly of SDS in the presence
of (R)-(+)- and (S)-(
)- 2-amino-3-phenyl-1-propanol ((R)-(+)- and (S)-(
)-
APP) chiral molecules. TEM combined with computer simulations confirmed
the presence of ordered chiral channels winding around the central axis of the
tubes of B100 nm inner diameter (Figures 7c and d).28

2.2 Case 2. Structural Modulation in Microporous Crystals

2.2.1 Si/Al Concentration Modulation in the Framework
of Zeolite MOR
Zeolite MOR has SG Cmcm with unit cell parameters a ¼ 18.1 Å, b ¼ 20.5 Å,
c ¼ 7.5 Å, and has 1d-channels with elongated 12-membered rings (12MR) of
Electron Microscopy Studies of Structural Modulation 677
6.5  7.0 Å size along [0 0 1] (Figure 8a). Selenium has an electron configuration
[Ar]3d104s24p4. Various allotropes have two nearest neighbours at approxi-
mately 901 from each other, and a Se-chain spiral around the [1 1 1] direction of
a primitive cubic lattice is expected. However, in the real structure of trigonal-
Se, the chains are stretched along the axis so that the angles become larger
(1051) and the distance between the nearest neighbouring chains (3.6 Å) is much
larger than that within the chain (2.32 Å). It is interesting to notice that the 1d-
channels of MOR seem to ideally accommodate the isolated spiral chains of Se.
Photos of Se containing MOR single crystals (Se@MORs) under optical
microscopes with polarized light (above: with electric vector E1 parallel to
the c-axis of the crystal 1, below: with electric vector E2 parallel to the c-axis of
the crystal 2) are shown in Figure 8b. From the above polarized optical
microscope images, we expect that isolated Se-chains were formed in the 1d-
channels of MOR. It is easy to see a structural change of Se by the naked eye

c-axis Capillary
100
m

Se@MOR
Å
6.5 x 7.0 Å MOR Se-chain
(a) (c)

c1
18.07 Å

Se

E1

100
m
20.04 Å

Na

c2

b
E2
a c
(b) (d)

Figure 8 MOR single crystals containing Se-chains (Se@MOR). Schematic drawing

of MOR single crystal and its channel system (a), polarised microscope
images of Se@MOR under two different polarised light conditions (b).
Se@MOR sealed in glass capillary for resonant X-ray scattering (c) and the
projected atomic arrangement obtained from the resonance X-ray scattering
along the channel [0 0 1] (d).
678 Chapter 40
through the change in colour from brown for trigonal-Se to orange for the new
Se-chain. Using a Se@MOR single crystal sealed in a SiO2 glass capillary under
a He atmosphere (Figure 8c) and synchrotron X-ray radiation, the structure of
the Se-chain within a channel was studied by resonant X-ray scattering of Se,
and the observed structure was a little more complex than the above and the
projection of the structural solution along [0 0 1] is shown in Figure 8d. The
detailed results will be published separately.30
During the preparation of these isolated Se-chains in the channels of
powdered MOR, we observed an unusual black and white wavy contrast
with wave fronts parallel to the (0 1 0) plane as shown in Figure 9.
This peculiar contrast was determined as an amplitude contrast due to
Se-concentration modulation along the b axis.31,32 From the optical absorp-
tion spectra of Se confined in the channels, it was concluded that a finite
number, ca, 10–20, of atoms of Se are physisorbed at each electric dipole
induced by an AlO4
and associated non-framework cation.33 Consequently,
Se atoms can be used to probe the compositional variation of Al in the
framework of large pore structures at the unit cell scale by producing contrast
in the HRTEM images.34

Figure 9 Unusual black and white contrast in the HREM image of MOR (Si/Al ¼ 10)
containing Se at [0 0 1] incidence. Se-chains in the channels are imaged as
dark dots and the contrast variation is due to the modulation of the Se
content along the channel.
Electron Microscopy Studies of Structural Modulation 679

2.2.2 Modulation in LTL

Zeolite LTL has SG P6/mmm with a ¼ 18.4 Å and c ¼ 7.5 Å and has a
1d-undulating channel with 12-MR. The framework structure contains two
important secondary building units, the cancrinite (CAN) cage and the double
hexagonal ring (D6R) alternating to form a column. The structure can be
described by a two-dimensional hexagonal arrangement of the columns form-
ing both 8-rings and 12-rings. The crystal morphology is a hexagonal cylinder
or plates with various aspect ratios. Three different structural modulations
were observed. The first one is a coincidence boundary, which was studied at
Cambridge,35 and others are a rotational defect and pffiffiffiffiffia columnar
pffiffiffiffiffi hole.36 The
coincidence boundary is a super-mesh structure 13  13 which entails a
rotation of one part of the crystal on the (0 0 1) plane through 32.21. An
illustration of the coincidence boundary was used in a school textbook of
inorganic chemistry in Greece (Figure 10). An HRTEM image of the rotational
defect is shown in Figure 11a. A group of six CAN columns surrounded one
main 12-ring channel rotated 301 as a unit around the c-axis and the schematic
drawing of the defect and simulated images are shown in Figure 11b–c,
respectively.

2.2.3 Incommensurate Modulation in SSZ-24 via Collective

Framework Distortion
The XRD powder pattern and 29Si MAS NMR of the silica zeolite SSZ-24
suggest the presence of an extra feature to the previously proposed AFI type
framework structure (SG P6cc or the highest symmetry P6/mcc). We have
found by TEM that this feature is a result of incommensurate structural
modulation. Any structural modulations are barely observed either in ED
patterns or HRTEM images taken with [hkl] incidence, where l is not equal to 0.
Figure 12a shows an HRTEM image taken with [0 0 1] incidence and the
corresponding ED pattern, where we cannot see the effect of structural mod-
ulations. However, extra spots produced from a structural modulation are
observed along the c* axis.37 Figure 12b shows an ED pattern taken at room
temperature with [0 1 0] incidence. The incommensurate extra spots are
observed and can be explained by a modulation with wave vector q(0, 0, a)
along the reciprocal lattice vector c* and a B 0.38. We observed the corre-
sponding super-period structure in the HRTEM image.
In the case of Au-based alloys, we observed various incommensurate modu-
lations of atomic arrangements on the fcc lattice where the modulation wave
vectors were governed by the electron atom ratio or size/shape of the Fermi
surface. On the other hand, the modulation in SSZ-24 is associated with the
‘‘soft-mode’’ instability of the silica framework. More precisely, each of the
SiO4 tetrahedral units in the framework is very rigid against deformation, while
neighbouring units can change their relative configurations easily through
bending/rotating around the corner shared O atom. Thus the framework
structure may be thought of as a network of multiple hinges, and a displacive
680 Chapter 40

Figure 10 The cover of an inorganic chemistry textbook in Greece.

lattice distortion may occur if the framework topology allows a collective move
of the hinges. In the harmonic approximation, such a distortion corresponds
to a soft mode in the phonon spectra. By the use of the rigid-unit mode
approach,38,39 we have analysed the distribution of such soft modes in
Electron Microscopy Studies of Structural Modulation 681

Figure 11 HRTEM images of a rotational defect observed in LTL taken with [0 0 1]

incidence (a) and corresponding schematic drawings of the framework (b)
and a simulated image for the specimen thickness of 10 nm, defocus value
of
68 nm (c).

reciprocal space. In particular, we found a high-symmetric soft mode at the

wave vector q ¼ (0, 0, a) with a ¼ 0.392, which was very close to the observed
value of a B 0.38 for the modulation.
The modulated structure transforms into a disordered one through electron
irradiation or heat treatment. In Figure 13a, an ED pattern taken at 100 1C is
shown, where incommensurate extra spots are no longer observed. Instead,
there are diffuse streaks stretched along the D-line: k ¼ (0, 0, a), slightly curved
lines in the vertical direction to the D-line and also weak but rather sharp lines
along the 001 direction through the fundamental 00l (l ¼ even) spots. Both of
the first two diffuse streaks seem to coincide with the distribution of low-
symmetric soft modes, as shown in Figure 13b. The third ones, rather sharp
streaks passing through 00l (l ¼ even) spots, also have counterparts in the
phonon spectra. However, this may result either from the narrow width
of the crystal along [100] or from the diffraction effect from the crystal edge
because no lines through 00l (l ¼ odd) spots were observed.

2.2.4 Zeolite BEC Overgrown on BEA*

Zeolite Beta is the first large pore zeolite with a 3d-channel system and a high
Si/Al ratio. Beta contains disorder in the stacking sequence, which does not
significantly affect the accessible pore volume but influences the tortuosity of the
pore connectivity. Two different ordered polymorphs A (SG: P4122 or P4322)
682 Chapter 40

Figure 12 An HRTEM image of SSZ-24 taken with [0 0 1] incidence (a), and ED

pattern taken with [0 1 0] incidence at room temperature with a schematic
drawing to show an incommensurate modulation with q(0, 0, a), a B 0.38
(b).

and B (SG: C2/c) were proposed on the basis of HRTEM images and their
corresponding ED patterns. A hypothetical polymorph C (SG: P42/mmc) was
also suggested.40 The structure of zeolite Beta polymorph C (BEC) was recently
solved and confirmed by a Fourier reconstruction of HRTEM images. Low and
high magnification TEM images and a corresponding ED pattern taken
with JEM-4000EX (400 kV) from the as-synthesised ITQ-14 are shown in
Figures 14a–c, respectively. Figure 14a shows that a new crystal with pillar-
shape morphology overgrows onto ordinary Beta (BEA*). From Figure 14c, it
can be seen that besides the many streaks coming from the mixtures of
polmorphs A and B (matrix), there are also new spots just lying on the streaks
with a nearly square mesh. It should be noticed that the tips of the crystals vary
from crystal to crystal and that some growth steps are observed. From the
HRTEM image (Figure 14b) the steps can be seen and are shown by arrows.
We can determine the stacking sequence, either polymorph A or B, from the
Electron Microscopy Studies of Structural Modulation 683

Figure 13 An ED pattern of SSZ-24 taken with [0 1 0] incidence at 100 1C (a) and the
distibution of the soft phonon modes in the relevant section of the reci-
procal space calculated within the rigid-unit-mode model (b).

arrangement of white dots (pores) and they are marked on the HRTEM image.
In addition to these polymorphs A and B, a new stacking is clearly observed
at the region marked by ‘‘New’’. This is the first experimental demonstration of
the real existence of polymorph C in the SiO2 system, which was solved and
identified by electron crystallography developed for this study. A beautiful
single-crystal pillar overgrown on an ordinary Beta* was used for the structural
analysis. The electrostatic potential map was reconstructed from a set of
HRTEM images, however the map was too blurred to locate the atoms. The
atomic positions were enhanced in the blurred potential map with the support of
a Patterson map derived from selected area ED patterns.41,42 Simulated
HRTEM images of the polymorphs are inserted in the top left of Figure 14b.
Projected framework types of polymophs A, B and C are also shown in Figure
14d. The surface structure, growth mechanism and rate, and the morphology
were also discussed in separate papers.43,44

3 Conclusion
Here we described TEM studies of various structural modulations in
micro- and meso-porous crystals, which started at Cambridge in 1982 and
continues to the present. These demonstrate the strength of electron micro-
scopy (EM) in this field of materials science, as well as the necessity of
continuing the development of electron crystallography from traditional
methods in order to solve specific problems inherent to nanostructures.
684 Chapter 40

Figure 14 Low- and high-magnification TEM images of BEC, ITQ-14 (a and b), and
ED pattern (c). Schematic drawings of three different polymorphs A, B and
C are also shown (d).

Acknowledgements
The authors would like to thank the Japanese Science and Technology Agency,
IST and the Swedish Research Council, VR for their financial support.
Electron Microscopy Studies of Structural Modulation 685

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CHAPTER 41

Extrapolating from Fifty Years

of Dislocation Imaging –
Reaching into the Core
ARCHIE HOWIE
Department of Physics, Cavendish Laboratory, University of Cambridge,
J. J. Thomson Avenue, Cambridge CB3 0HE, UK

1 The Age of Inspired Conjecture

In near coincidence with the event whose 75th anniversary is celebrated in this
volume, the bold concept of crystal dislocations was put forward independently
by Taylor,1 Orowan2 and Polanyi.3 This ultimate turning point in crystal
plasticity spun the subject on its head by transforming the central mystery of
the amazing weakness of crystals into the continuing problem of explaining
their strength. Direct and incontrovertible experimental evidence for the exist-
ence of dislocations and their properties did not emerge for another 25 years
but this intervening period did allow free rein to brilliant geometrical thinkers
like F.C. Frank with his concept of the emergent screw dislocation4 as an
inexhaustible supply of surface steps to explain crystal growth under near
equilibrium conditions. Peierls5 pinpointed the problem of moving the dislo-
cation core over the periodic barriers generated by the crystal structure. The
sideways motion of kinks on a dislocation line at the point where it crossed
these barriers was thus identified by Mott and Nabarro6 as the basic atomic
process in plastic flow indicated in Figure 1. More detailed considerations of
dislocation core structure in close packed crystals led Heidenreich and Shock-
ley7 to propose the dissociation of dislocations into partial dislocations sepa-
rated by ribbons of stacking fault. With the development of dislocation
imaging, many, though not all, of these ideas have been beautifully confirmed.
Despite great advances in instrumentation, atomic or molecular detail in the
dislocation core region nevertheless remains elusive, particularly for the con-
figuration and motion of kinks or the trapping and decay of excitations in

687
688 Chapter 41
(a)

(b)

Figure 1 A dislocation line lying in the valleys between Peierls barriers progressively
surmounts the barriers by sideways propagation of the kinks as shown by
arrows in (a). Eventually a fresh loop of dislocation, shown as a broken line
in (b) has to be thrown forward by stress-assisted thermal activation.

photolysis as first proposed in the case of cyanoanthracene by John Thomas

and his colleagues.8

2 Electron Microscopy Developments for Dislocation

Imaging
2.1 Diffraction Contrast Microscopy and Transmission
Channelling
The initial transmission electron microscope observations of dislocations es-
tablished with remarkable accuracy a twin track road map for subsequent
developments. Menter’s crystal plane imaging approach9 offered an apparently
more direct image of the atomic arrangements but could not be applied to most
structures of interest because of an inability to resolve the atomic planes with
the instrumentation then available. The diffraction contrast method, pioneered
independently by Bollmann10 and by Hirsch et al.,11 did not depend on
resolving the crystal planes and could address complex dislocation arrange-
ments. It was therefore much more productive in the immediately following
years although it lacked the spatial resolution to resolve detail below about
5 nm in the dislocation core region. Even this modest resolution was adequate
to uncover a connection between dislocation ribbon width, stacking fault
energy and electronic structure.12 For the study of dislocations and other
defects in crystals of thickness exceeding ca. 100 nm, the usefulness of the
diffraction contrast method was found to be enormously extended by channel-
ling effects whereby the fast electron waves can be concentrated between the
Extrapolating from Fifty Years of Dislocation Imaging 689
(a) (b)

Figure 2 Schematic depiction of channelling effects. When the incident direction is

tilted away from the crystal axis by slightly more than a Bragg angle, the
electrons channel between the atomic planes with high transmission (a). For
incidence along the crystal axis, the electrons channel on the planes with
high probability for inelastic and thermal diffuse scattering (b).

atomic planes of the crystal and thus avoid the strong scattering conditions
near the atomic core regions.13,14 These high transmission channelling condi-
tions typically involve using incident beam directions deviated from the crystal
axis by just over a Bragg angle and are thus in contrast to the generally
preferred axial orientation for structure imaging where the fast electrons are
concentrated on the atomic columns (see Figure 2).

2.2 Weak Beam Imaging

A major advance in the spatial resolution achievable in diffraction contrast
imaging came with the development of the weak beam technique by Cockayne,
Ray and Whelan15 making it possible to resolve dislocation dissociation and
stacking fault ribbon widths at the 1.5 nm levels which occur in many metals
and semiconductors. Although the weak beam method has been displaced by
the more recent high resolution structure imaging methods described below, it
is still extensively used, particularly for the study of dislocation arrangements
and dislocation core dissociation in more complex crystals. Any study of
dislocation arrangements and structures in for example meurigite would almost
certainly start with diffraction contrast and weak beam imaging!

2.3 Development of Coherent Structure Imaging

The immediate visual link between the image and the crystal structure which
Menter’s method seemed to offer has always been irresistibly attractive even if
the original work exposed the difficulty of interpreting two-dimensional
690 Chapter 41
projected images of the three-dimensional structure. In the case of dislocations
it was already clear that it would be essential to work with dislocation lines
accurately lying along a crystal axis and which was itself oriented to the
incident electron beam direction. Instrumental restrictions, including electrical
and mechanical stabilities as well as lens aberrations, precluded such observa-
tions in most crystals of interest until about twenty years ago. By using tilted
illumination conditions in a symmetrical two-beam imaging condition (see
Figure 3), the effects of chromatic aberration could be sufficiently reduced to
yield lattice images with the characteristic extra half plane signature of edge
dislocations but the consequences of projection failure and spherical aberration
in this non-axial configuration complicated the interpretation too much. Fol-
lowing a striking demonstration of the power of axial imaging at a grain
boundary in Ge,16 electron microscopists were encouraged to tackle the imag-
ing of dislocations lying along prominent crystal axes aligned with the incident
beam direction. Although this symmetrical configuration is disadvantageous
for transmission channelling, since the electron trajectories are concentrated on
the atomic planes or columns, the sacrifice is not too serious in the rather thin
crystals generally used. More problematic for these highly coherent images has
been the sensitivity to instrumental misalignments and the need to get high
phase contrast by balancing the positive spherical aberration constant of
the objective lens with a substantial negative defocus leading to appreciable
delocalisation effects. Systematic analysis of through-focal-series has been
developed to overcome these difficulties eventually yielding reliable separation
of the amplitude and phase contributions to the image. Atomic-scale structural
imaging of dislocation core regions by high resolution transmission electron
microscopy has thus been almost routinely available over the past decade.15 By

(a) (b) (c)

diffraction

image
Tilted illumination Axial illumination Axial illumination
Crystal on axis Crystal on axis Crystal off-axis

Figure 3 Schematic arrangements for structure imaging in transmission electron

microscopy. (a) Tilted two-beam illumination. (b) Generally used axial
illumination with on-plane channelling. (c) Axial illumination but with the
crystal tilted for between-plane channelling.
Extrapolating from Fifty Years of Dislocation Imaging 691
operating at positive defocus with very small negative values of spherical
aberration using the new generation of aberration-corrected electron lenses,16
high resolution electron microscopy (HREM) imaging is now providing even
higher contrast and unprecedented spatial resolution.17

2.4 Incoherent Structure Imaging

Successful development of the high-brightness, cold field-emission source by
Crewe and his colleagues18 opened the door for high resolution scanning
transmission microscopy (STEM). They also pioneered the use of an annular
dark field detector for high resolution imaging leaving a central (low-angle
scattering) region to provide electron energy loss spectra with microanalysis
capability via the characteristic atomic core loss edge features. With progressive
improvements in instrumentation, most notably the use of a high angle annular
dark field (HAADF) detector, Pennycook and Nellist have played the
leading role in developing the STEM HAADF approach illustrated in Figure
4 to image atomic columns in crystals with simultaneous column by column
chemical analysis being provided by the energy loss spectrum.19 Although the
focused electron probe which is scanned over the crystal surface to collect these
images has to be highly coherent, the HAADF signal is essentially incoherent,
i.e. a simple sum of intensities from the atoms in each column. Interference

HAADF Detector

Energy Loss Spectrum

E – ∆E

Figure 4 Schematic arrangement for HAADF STEM operation. As the incident

probe is scanned across the surface, the annular dark field signal shows the
atomic column positions and the energy loss spectrum can be collected
simultaneously.
692 Chapter 41
between contributions from different atoms is largely suppressed because the
total signal is integrated over the whole azimuthal and radial range of the
detector. Furthermore, at the typical scattering angles in excess of 100 mrad,
thermal diffuse scattering makes a dominant contribution to the HAADF
image. These incoherent images are much less sensitive to defocus effects than
the highly coherent HREM images. Although spatially resolved electron energy
loss spectroscopy can now also be carried out in HREM using imaging
spectrometers, the STEM configuration is generally more powerful. The impact
of aberration-corrected lenses for STEM may be even greater than in HREM.
Not only can they be operated at zero spherical aberration but the current in the
probe can be greatly increased. Figure 5 illustrates an example of atomic

Figure 5 HAADF STEM image of dislocation core configurations in GaN (a) with
a diagram of the atomic column positions (b). Courtesy Philosophical
Magazine.20
Extrapolating from Fifty Years of Dislocation Imaging 693
20
column imaging of dislocation core configurations in GaN. This material can
also exhibit hollow core, nanopipe dislocations and the loss spectra reveal an
associated increase of O impurity substituting for the N concentration near the
core.20

3 Shortcomings of Current Imaging Methods

3.1 Projection Failures
Since HREM and STEM HAADF images are both essentially two-dimen-
sional projections of the atomic structures studied, they are ideally suited to
situations where the atoms are all arranged in cleanly separated atomic
columns aligned in the viewing direction. The zig-zag structure of some
atomic columns in the diamond structure, giving rise to dumbbell features
in the image, is well recognised and recent work has indicated that partial
occupancy of atomic columns can be quantitatively assessed from intensity
measurements in the HAADF signal. In semiconductors, individual heavy
atom dopants and their positions in the column may even be identified by
the depth of focus effect.21 High resolution electron tomography may also be
able to address situations with chemical variations along the column (see
Chapter 43).
Without detailed and, in each instance quite elaborate computations, it is
much harder to assess the effects of transverse atomic displacements varying
irregularly along the column such as could occur for example in a heavily
kinked dislocation core. A striking example was published several years ago of
such a dislocation imaged by bright field HREM in plan view incorporating
weak reflections from the first-order Laue zone.22 When such a dislocation is
imaged end-on, it seems probable14 that the electron waves, channelling on the
mean position of the atomic column, will simply plough straight through
the kinks with some change in the high angle scattering but no obvious effect
in the HREM image beyond a slight reduction in contrast. Reduced contrast in
the core regions of aligned dislocations is indeed often observed but has not
been analysed quantitatively. For displacements which vary more smoothly
along the atomic column, it seems likely14 that the electrons will simply
adiabatically follow the displacement by channelling with even less visible
effect in the image.
Other deviations from the ideal projection geometry can also be seen to be
inevitable on the grounds of elasticity theory. Surface relaxation for end-on
screw dislocations in a thin film results in additional displacements known as the
Eshelby twist. This twist was easily noticed in early diffraction contrast work14
but is harder to detect in the much thinner crystals used in HREM. For a
dissociated dislocation threading a thin film, elasticity analysis revealed that in
the minimum energy configuration the component partial dislocations will not in
most cases run parallel to each other.23 Although this effect may not be relevant
in ceramics or semiconductors where the dislocations are insufficiently mobile to
694 Chapter 41
reorient during the thinning process, for dissociated dislocations in metals it has
been observed both in weak beam images and in computer simulations.24

3.2 Background Contributions

If the inevitably very weak signals generated by kinks or other small or highly
localised atomic displacements in dislocation cores are to be detected, it is
obviously crucial to reduce the image background level as much as possible.
Inelastic scattering, previously identified25 as the dominant background con-
tribution in weak beam imaging, can now routinely be removed by energy
filtering opening the way to the use of still weaker beams for imaging at higher
resolution. The removal of thermal diffuse scattering is more difficult but can
be achieved in sideband holography.26 Elastic scattering from disordered or
contaminated surface layers is perhaps more problematical still and will require
that electron microscopists devote even more attention than hitherto to thin
sample preparation combined with surface characterisation.

4 New Imaging Methods

4.1 Reversion to Plan View Imaging and Transmission
Channelling Conditions
The power of new forms of plan view imaging of dislocation core structure was
already mentioned in Section 3.1. At some sacrifice in spatial resolution, the
background intensity from the perfect crystal regions above and below the
dislocation was substantially reduced in that case since the main zero-order
Laue zone reflections were eliminated from the image.22 Ideally one would wish
to use larger objective apertures combined with aberration correction to
achieve the highest possible spatial resolution for plan view imaging of dislo-
cation cores and other small three-dimensional defect regions. A reversion to
transmission channelling conditions as shown in Figure 3c may then offer the
best means of reducing the perfect crystal background contribution. Thanks to
aberration correction it should be possible to maintain axial illumination with
an off-axis orientation of the crystal and thus avoid the problems previously
experienced with tilted illumination imaging.

4.2 Improved Mapping of Valence States

Core loss spectroscopy provides information not only about local chemical
composition but also about empty electron states in the conduction band through
the analysis of near edge structure. More direct information about valence states
is in principle available from the low loss part of the spectrum but not generally at
the very high spatial resolution most useful for dislocation core studies because of
the dominance of small momentum transfers in such low-energy Coulomb
excitations. As shown by off-axis ALCHEMI spectroscopy with lightly bound
Extrapolating from Fifty Years of Dislocation Imaging 695
specimen
HAADF Annular
detector illumination
aperture

∆E = EBethe

= E [1+( E/2m0c2 )]4 sin2(θ/2)

Figure 6 Possible hollow cone illumination in STEM for simultaneous Bethe ridge
mapping and HAADF STEM imaging.

core excitations, better spatial resolution can be achieved at the expense of signal
strength by selecting larger momentum transfers.27 With increasing momentum
transfer in the valence loss region, plasmons and other collective excitations are
replaced by the Compton scattering regime which was investigated many years
ago by Thomas and colleagues.28 A possible high resolution extension of their
approach involving large angle hollow cone illumination in aberration-corrected
STEM is shown schematically in Figure 6. The scattered electrons are then
collected in a spectrometer working near axis with an energy loss window set to
the Bethe ridge energy corresponding to the momentum transfer defined by the
hollow cone illumination. For a hollow cone semi-angle of 30 mrad at 100 keV
the Bethe ridge energy is about 90 eV. The combination of momentum and
energy selection employed in this Bethe ridge mapping procedure would eliminate
many contributions from core losses as well as from double scattering events such
as plasmon excitation followed by thermal diffuse scattering. At the same time
the HAADF image could be acquired to provide registry between the Bethe
ridge, valence density map and the atomic columns.

4.3 Scanned Probe Microscopy Imaging

Spatial resolution in both imaging and spectroscopy superior to that available
in HREM or STEM has for many years been demonstrated in various modes of
scanned probe microscopy, particularly scanning tunnelling microscopy
(STM). The exponential dependence with distance of the vacuum barrier
tunnelling probability responsible for this performance also ensures that the
images are almost always very surface sensitive and thus potentially most useful
for studying the influence of dislocation cores on surface structure and
696 Chapter 41
reactivity. Nevertheless it is now possible to link STM studies of dislocation
structures at surfaces to their structure in the bulk by first principles compu-
tations.24 We should also note that the imaging of sub-surface dislocations in Si
by ballistic electron microscopy methods was strikingly demonstrated over a
decade ago29 but not apparently followed up.

5 Conclusions
A brief summary has been given of the impressive progress that has been made
in determining static dislocation core structure by applying HREM and STEM
HAADF high resolution imaging methods to dislocations aligned with the
incident beam direction. It may however be necessary to employ plan view
imaging with appropriate steps to reduce the image background level if fine
details of kinks and non-periodic structural features of the core are to be
resolved. If to some extent this seems a reversion to older methods, we may
console ourselves that the path is not likely to be a purely circular one but more
akin to a spiral which after all is quite appropriate for any circuit of a
dislocation. The study of dislocation dynamics at the atomic, or even near-
atomic level, is an even more formidable problem than those addressed within
the short space available here. For such work an alliance between the high
spatial resolution afforded by electrons and the greater precision in timing or in
energy resolution provided by photons seems the most promising way forward.

References
1. G.I. Taylor, Proc. R. Soc. London, Ser. A, 1934, 145, 362.
2. E. Orowan, Zeit. Phys., 1934, 89, 605, 614, 634.
3. M. Polanyi, Zeit. Phys., 1934, 89, 660.
4. F.C. Frank, Adv. Phys., 1952, 1, 91.
5. R.E. Peierls, Proc. Phys. Soc., 1940, 52, 34.
6. N.F. Mott and F.R.N. Nabarro, Report on Strength of Solids, Physical
Society, London, 1948, 1.
7. R.D. Heidenreich and W. Shockley, Report on Strength of Solids, Physical
Society, London, 1948, 57.
8. M.D. Cohen, Z. Ludmer, J.M. Thomas and J.O. Williams, Proc. R. Soc.
London, Ser. A, 1971, 324, 459.
9. J.W. Menter, Proc. R. Soc. London, Ser. A, 1956, 236, 119.
10. W. Bollmann, Phys. Rev., 1956, 103, 1588.
11. P.B. Hirsch, R.W. Horne and M.J. Whelan, Phil. Mag., 1956, 1, 677.
12. A. Howie and P.R. Swann, Philos. Mag., 1961, 6, 1215.
13. H. Hashimoto, A. Howie and M.J. Whelan, Philos. Mag., 1960, 5, 967.
14. P.B. Hirsch, A. Howie, R.B. Nicholson, D.W. Pashley and M.J. Whelan,
Electron Microscopy of Thin Crystals, Butterworths, London, 1965.
15. D.J.H. Cockayne, I.L.F. Ray and M.J. Whelan, Philos. Mag., 1969, 20, 1265.
16. O.L. Krivanek, S. Isoda and K. Kobayashi, Philos. Mag., 1977, 36, 931.
Extrapolating from Fifty Years of Dislocation Imaging 697
17. K. Tillmann, L. Houben and A. Thust, Philos. Mag., 2006, 86, 4589.
18. A.V. Crewe, J.P. Langmore and M.S. Isaacson, in Physical Aspects of
Electron Microscopy and Microbeam Analysis, ed. B. Siegel and D. Bea-
man, Wiley, New York, 1975, 47.
19. P.D. Nellist and S.J. Pennycook, in Adv. Imaging and Electron Phys.,
ed. B. Kazan, T. Mulvey and P. Hawkes, vol. 113. Elsevier, New York,
2000, 147.
20. I. Arslan, A. Bleloch, E.A. Stach, S. Ogut and N.D. Browning, Philos.
Mag., 2006, 86, 4727.
21. M. Varela, S.O. Findlay, A.R. Lupini, H.M. Christen, A.Y. Bosevich,
N. Delby, O.L. Krivanek, P.D. Nellist, M.P. Oxley, L.J. Allen and
S.J. Pennycook, Phys. Rev. Lett., 2004, 92, 095502.
22. H.R. Kolar, J.C.H. Spence and H. Alexander, Phys. Rev. Lett., 1996, 77,
4031.
23. P.M. Hazzeldine, H.P. Karnthaler and E. Wintner, Philos. Mag., 1975, 32,
81.
24. J. Christiansen, K. Morgenstern, J. Schiøtz, K.W. Jacobsen, K.-F. Braun,
K.-H. Rieder, E. Laegsgaard and F. Besenbacher, Phys. Rev. Lett., 2002,
86, 206106.
25. P.L. Gai and A. Howie, Philos. Mag., 1975, 31, 519.
26. C.B. Boothroyd and R.E. Dunin-Borkowski, Ultramicroscopy, 2004, 98,
115.
27. J. Taftø and O.L. Krivanek, Phys. Rev. Lett., 1982, 48, 560.
28. B.G. Williams, J.M. Thomas and T.G. Sparrow, J. Chem. Soc., Chem.
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29. H. Sirringhaus, E.Y. Lee and H. Vonkanel, Phys. Rev. Lett., 1995, 74,
3999.
CHAPTER 42

Turning Points in Understanding

the Emission of Brilliant Light
from Highly Defective GaN-
Based Materials and Devices
COLIN J. HUMPHREYS
Department of Materials Science and Metallurgy, University of Cambridge,
New Museums Site, Pembroke Street, Cambridge CB2 3QZ, UK

1 Introduction
Professor Sir John Meurig Thomas has been responsible for many turning
points in science: points where his insights have profoundly changed our
understanding. I would like personally to acknowledge not only the inspiration
but also the pleasure I have received from listening to many of his beautifully
tailored talks as well as reading his carefully crafted papers. John Meurig
Thomas is a great wordsmith as well as a great scientist.
One of the key points I have learnt from his publications is the importance of
using a variety of techniques for solving a given problem, particularly a difficult
problem. A difficult problem often has many facets, and a given technique
usually reveals information on only one of these. To build up a complete multi-
faceted solution, a range of techniques is therefore necessary, each of which
illuminates a different aspect of the problem.
In this chapter I will discuss the fascinating problem of how InGaN quantum
wells emit brilliant light, even though they have a very high dislocation density.
Scientists worldwide thought they knew the answer to this problem: it was
believed that In-rich clusters form in the quantum wells, these clusters localise
the carriers (electrons and holes) and hence prevent them from diffusing to
dislocations, which would quench the light emission since dislocations are non-
radiative recombination centres. However, the evidence for these indium-rich
clusters was based on only one technique, electron microscopy. When other
698
Turning Points in Understanding the Emission of Brilliant Light 699
techniques are used, and also when the electron microscopy is performed
with great care, it is found that indium-rich clusters do not exist in the InGaN
and a different mechanism must therefore be responsible for localising the
carriers.
Our work on whether In forms In-rich clusters in InGaN echoes the seminal
study by John Thomas and his colleagues of ruthenium clustering in mesopo-
rous silica using high-resolution transmission electron microscopy,1 and the
study of Si, Al ordering in zeolites2 using a combination of techniques. In our
work, as well as using high resolution electron microscopy, we also used a range
of other techniques, including electron energy loss spectroscopy, in which John
Thomas has made pioneering contributions.3

2 Background
A remarkable feature of InGaN/GaN quantum well LEDs is that they emit
intense light, even though the dislocation density is typically 109 cm
2. In all
other light-emitting semiconductors the light emission is quenched if the
dislocation density exceeds about 103 cm
2. Yet InGaN quantum wells emit
strong blue and green light (depending on the In concentration) when the
dislocation density is one million times higher than that in other light-emitting
semiconductors, even though it is known that dislocations in InGaN are non-
radiative recombination centres.
The widely believed solution to the above problem, up to a few years ago,
was that InGaN was an unstable alloy and the In in the InGaN quantum wells
formed In-rich clusters. Since the band-gap of InN is less than that of GaN, the
bandgap of these In-rich clusters is reduced, and hence the electrons and holes
are spatially localised in these clusters. At room temperature (and below) in
InGaN, an electron and hole form a bound exciton, hence the In-rich clusters
localise the excitons. The clusters were believed to be small, on a nanometre
scale. Statistically, most threading dislocations would not pass through these
nanometre-scale In-rich clusters, even for a dislocation density of 109 cm
2 at
which the average dislocation spacing is about 300 nm. Hence it was almost
universally believed that the In-rich clusters localised the excitons away from
most of the dislocations so that they did not quench the light emission. Thus it
was believed that the intense light emission observed from InGaN quantum
wells with a high dislocation density was due to In-rich clusters.
In this chapter we first present evidence to support this argument. We then
show that In-rich clusters are produced in InGaN in the electron microscope
due to electron-beam damage. However, careful low-dose electron microscopy
reveals no gross In clustering, but it cannot rule out small In fluctuations. We
then report that three-dimensional (3D) atom probe analysis of InGaN quan-
tum wells yields that InGaN is a random alloy, with no In fluctuations other
than would be expected of any random alloy. This is consistent with our
electron microscopy results. Finally, we return to the question of why InGaN
emits intense light despite having a high dislocation density.
700 Chapter 42

3 The Evidence for Exciton Localisation in InGaN

There is clear evidence that, at low temperature, the dominant emission from
InGaN/GaN quantum-well structures involves the recombination of strongly
localised excitons (see for example Refs. 4–6). Graham et al.6 studied the low
temperature (T ¼ 6 K) optical properties of a series of InxGa1
xN/GaN single-
quantum-well (SQW) structures where the indium fraction x varied from
sample to sample over the range 0.05–0.25. The structures were grown by
metal organic vapour phase epitaxy (MOVPE), and the InGaN quantum well
was 2.5 nm thick. By comparing the strengths of the phonon-accompanied
recombination with those obtained from a theoretical model, the spatial extent
of the carrier wavefunctions in the plane of the quantum well was estimated.
This localisation length was found to range from 1 nm for the InGaN quantum
well containing 25% indium, to 3 nm for the 5% indium alloy. Thus the exciton
localisation length in the plane of the quantum well is typically about 2 nm. The
key question is what causes this localisation.

4 The Case for Gross In-rich Clusters in InGaN

4.1 Thermodynamics
It has long been recognised that InGaN epilayers could separate into indium-
rich and indium-poor phases during prolonged annealing.7 Thermodynamic
calculations then showed that there is a miscibility gap in the InxGa1
xN
system and that for typical compositions (x B 0.1 for blue emission, x B 0.2 for
green) and typical InGaN growth temperatures (600–800 1C) the unstrained
homogeneous alloy is unstable, leading to decomposition into In-rich and In-
poor regions.8 It is not clear how applicable these equilibrium thermodynamic
calculations are to the InGaN layers grown by MOVPE or molecular beam
epitaxy (MBE) (see later), but Ponce et al.9 have reported phase separation in
MOVPE grown thick (200 nm) epilayers of InGaN with In fractions of 0.1 and
above.

4.2 The Evidence from Electron Microscopy for Indium-Rich

Clusters
Bright-field transmission electron microscopy (TEM) images of InGaN/GaN
quantum well structures were reported to show dark dot-like features with a
size of about 3 nm in the InGaN quantum wells.10,11 Since an indium atom is
much larger than a gallium atom, fluctuations in InGaN compositions will
cause variations in lattice strain and hence strain contrast in TEM images. The
dot-like features were therefore attributed to strain contrast. Energy-dispersive
X-ray analysis in the TEM suggested a correlation between the dark spots and
higher indium content.11 This was confirmed by Cho et al.12 who used energy-
filtered transmission electron microscopy (EFTEM) to analyse the regions of
Turning Points in Understanding the Emission of Brilliant Light 701
strain contrast observed in InGaN quantum wells. EFTEM images clearly
revealed these strained regions to be indium-rich clusters with a size of 2–3 nm.
A popular method for studying these indium-rich clusters has been lattice
parameter mapping. In this technique, high-resolution TEM lattice images are
taken of InGaN/GaN quantum well structures. The indium-rich clusters give
rise to localised strain, and by measuring the local lattice fringe spacings a 2D
lattice parameter map can be plotted, which shows the size of the indium-rich
clusters to be typically a few nm. Strains of the order of 10% are found in these
clusters. By using Vegard’s law, the lattice parameter map can be converted to a
composition map. For InGaN quantum wells grown with 10–20% indium, the
indium-rich clusters are typically found to contain at least 80% indium,13–16
although the projection problem in TEM makes it difficult to quantify the
indium content. We will call such clusters ‘‘gross indium-rich clusters’’. It was
reported that such gross indium-rich clusters may, in fact, be pure InN,14 and
pure InN regions with a 1–3 nm size were reported in InGaN quantum wells
grown by both MOVPE and MBE, as measured using high resolution TEM
lattice parameter mapping of samples with mean composition of 16% In in the
InGaN quantum wells.17

4.3 The Argument for Gross In-Rich Clusters

The argument for gross indium clustering in InGaN quantum wells appears to
be strong. We know from optical measurements that the excitons in InGaN are
localised on a 1–3 nm scale. Thermodynamic calculations show that InGaN is
unstable and should decompose into In-rich and In-poor regions. TEM shows
gross In-rich clusters in InGaN quantum wells on a nanometre scale, similar to
the scale on which the excitons are localised.
Because of the apparently strong and convincing arguments given above,
many hundreds of papers have been published stating that InGaN quantum
wells contain gross In-rich clusters, and that these clusters are responsible for
the exciton localisation. The Cambridge GaN research group has observed
such clusters in the TEM many times, and indeed they are among the authors of
a paper demonstrating that those clusters are indium-rich.12 However, this
work necessarily used high electron doses for the EFTEM images which
revealed the In-rich clusters. We will now demonstrate that in the wide range
of InGaN materials we have examined, such gross indium-rich clusters do not
exist, and they are produced by electron beam damage in the TEM.

5 The Effect of Electron Beam Damage on InGaN in

the TEM
5.1 Growth and Sample Preparation
InGaN/GaN quantum well structures were grown by MOVPE in a Thomas
Swan 6  2 in. close coupled showerhead reactor. Trimethyl gallium, trimethyl
702 Chapter 42

Figure 1 A pair of HRTEM lattice fringe images demonstrating the electron-beam

induced damage to an In0.22Ga0.78N quantum well. The (0 0 0 2) lattice
fringe images were obtained using a JEOL 4000 EX operating at 400 kV. (a)
Shows the image after minimal exposure to the beam, and (b) the same
region after only a few minutes of exposure. (c) Is a lattice parameter map of
(a), and (d) is a lattice parameter map of (b).

indium and ammonia were used as precursors, and hydrogen and nitrogen as
carrier gases. Thin GaN nucleation layers were established at 530 1C on c-plane
sapphire substrates prior to growth of GaN epilayers at 1030 1C with nominal
thickness of 2 mm. InxGa1
xN wells and GaN barriers, all having the hexagonal
crystal structure, were grown on these epilayers without growth interrupts and
at a single temperature. The SQW with a composition of In0.22Ga0.78N in
Figures 1 and 2 was grown at a nominal temperature of 710 1C and had a well
thickness of 3.0 nm. The SQW with a composition of In0.18Ga0.82N in Figure 2
was grown at a nominal temperature of 730 1C. The quantum well thicknesses
were measured using high resolution TEM, and the compositions measured
using X-ray reflectivity and high resolution X-ray diffraction as described
elsewhere.18,19
Wedge-shaped cross-sectional TEM specimens were prepared by tripod
polishing on diamond lapping mats. Using a wedge angle of B31, the In-
GaN/GaN at the thin end was reduced to electron transparency. To remove
surface damage associated with mechanical polishing, the samples were ion
milled for a few minutes (Gatan PIPS; Ar+ ions) at 3.2 keV with ion guns at
angles of 41 relative to each of the wedge surfaces. This ion polishing was
performed under ‘‘single modulation’’ (each ion gun active for about 3 out of
every 10 s) to minimise any heating of the sample.
Turning Points in Understanding the Emission of Brilliant Light 703

Figure 2 Lattice parameter maps of two different InxGa1
xN quantum wells, with
x ¼ 0.18 and 0.22, taken from HRTEM (0 0 0 2) lattice fringe images using a
low electron dose. Note that the colour scale is different here from that used
in Figure 1. Any possible In fluctuations are of a similar magnitude to the
noise in the lattice parameter maps and significantly smaller than those
usually reported in the literature for InGaN quantum wells.

5.2 Transmission Electron Microscopy

We have found that InGaN quantum wells damage extremely rapidly in the
electron beam of a TEM at the beam currents normally used for imaging. The
damage causes indium-rich clusters to form. Figure 1 shows (0 0 0 2) lattice
fringe images of an In0.22Ga0.78N quantum well using high-resolution TEM
(HRTEM). The lattice fringe images were obtained with the specimen tilted
about 6–71 away from a o1 1  2 04 axis towards the adjacent o1 0 1 04 pole.
At this orientation, a systematic row of reflections are excited with (0 0 0 2) and
(0 0 0 
2) under equal excitation. The images in Figures 1 and 2 were recorded
using 400 keV incident electrons in a JEOL 4000EX. Figure 1a was recorded
within 20 s of first exposing this part of the quantum well to the electron beam,
Figure 1b is the same area after a few minutes of exposure. We have analysed
these images to produce lattice parameter maps19,20 using a process similar to
the DALI (digital analysis of lattice images) technique.14 After only a few
minutes exposure to the electron beam we found nanometre-size indium
clusters formed which caused local strains of up to 10%, corresponding to
an indium fraction x of 60%. These cluster sizes, strains and compositions are
typical of those found by others using TEM (for example).13,14 However, we
have found no evidence at all of gross indium clustering if low electron beam
currents are used. At low electron dose, the lattice fringe image of the quantum
well and the lattice parameter map are both reasonably uniform (Figures 1a
704 Chapter 42
19,20
and c). We have studied the effect of 200, 300 and 400 keV incident
electrons. For the 200 keV electrons we used a FEI Tecnai F20-G2. We reduced
the electron beam current substantially below the maximum available, so that
the current density incident on the sample was 35 A cm
2. Electron beam
damage of the InGaN QWs was already strong after less than 30 s of exposure
to 200 keV electrons at this current density.
Since publishing the Smeeton et al.19,20 papers, it has been suggested to us
that our results may apply only to InGaN grown on MOVPE equipment at
Cambridge, or may be related to our TEM specimen preparation procedures,
rather than being a general effect. We have therefore purchased a very bright
blue commercial LED and examined the InGaN quantum wells it contains by
TEM. Again, we found no evidence of gross indium clustering at low electron
beam currents and short exposure times in the TEM. However, as the electron
dose increased, indium-rich clusters formed, just as in the Cambridge grown
samples.21 O’Neill et al.22 also reported that In-rich clusters formed as a result
of electron beam damage in their specimens. We also prepared TEM speci-
mens using only mechanical polishing instead of using a combination of
mechanical polishing followed by ion beam thinning. We observed no differ-
ences in the behaviour of both specimens in the TEM, suggesting that the
susceptibility of InGaN to electron beam damage is intrinsic to the InGaN/
GaN system and not a consequence of our ion milling procedures.21 We have
also studied MBE grown InGaN/GaN structures. In all the samples we have
studied, we observe no gross indium clustering in the TEM at low beam
currents and short exposure times. Indium-rich clusters only appear at higher
electron doses.

6 Does TEM Give Any Evidence for Genuine in

Clustering?
Slight fluctuations in the TEM image contrast of InGaN quantum wells can be
observed in low-dose images. This could be due to genuine low-level compos-
itional fluctuations or to the noise which is inherently present in low-dose
images. In addition, the initial stages of damage may already have occurred in
low-dose images, since significant radiation damage can occur in orienting the
specimen in the electron microscope before recording the image. Hence even
the lowest dose images should not be treated as a faithful representation of the
original specimen.
We have analysed the fluctuation in lattice parameter in lattice parameter
maps of low-dose high-resolution TEM images of InGaN quantum wells of
various compositions. A typical result is that for an InxG1
xN quantum well
with x ¼ 0.18, as measured by X-ray reflectivity and high-resolution X-ray
diffraction. In our low-dose lattice parameter maps (Figure 2), the maximum
measured fluctuation in the strain (defined as d(InGaN)/d(GaN) for the (0002)
Turning Points in Understanding the Emission of Brilliant Light 705
lattice fringes) is 0.01. This could be due to noise or it could correspond to a
maximum fluctuation in indium content x of 0.06, using Vegard’s law. Hence,
an InxGa1
xN alloy with x ¼ 0.18 has possible indium fluctuations in the range
0.12–0.24, averaged through the specimen because of the projection problem.
The noise in our low-dose lattice parameter maps is at a similar level to the
fluctuations observed above. We therefore conclude that small-scale indium
fluctuations may genuinely exist in InGaN quantum wells, but be masked by
the noise in our TEM images. We note that these compositional fluctuations, if
they do exist, are significantly smaller than the gross fluctuations reported in
the literature.
In the light of the Smeeton et al.19,20 papers, which suggested that the
gross indium-rich clusters in InGaN quantum wells reported by many re-
searchers might be due to electron beam damage, the Gerthsen group revised
their earlier conclusions.14,15 They observed that the indium concentration in
the clusters increased with increasing irradiation time in the electron micro-
scope. However, because they found In-rich clusters already in their first
HRTEM images taken after only 20 s of exposure to the electron beam they
concluded that In-rich clusters genuinely existed in their InGaN quantum
wells, but that the In concentration was significantly lower than they had
previously stated.23
The Kisielowski group has recently made detailed studies of indium cluster-
ing in InGaN, following their earlier work.13 They claim that InGaN quantum
wells can be imaged in HRTEM with negligible electron beam damage and that
indium-rich clusters genuinely exist.24 They have found25 that no measurable
alteration of the initial element distribution occurs for electron irradiation
times of up to 2 min and current densities of 20–40 A cm
2. They report that
green InxGa1
xN quantum wells (with average indium fraction x about 0.2)
have genuine indium-rich clusters, 1–3 nm wide with In content up to 0.40.26
This disagrees with our findings reported above (see Figure 2).
A key question is whether the electron micrographs carefully recorded and
reported in the above papers23–26 are, in fact, damage free. Electron-
beam damage of inorganic materials in an electron microscope can be a
complex process and the damage mechanism for strained thin layers of
InGaN is not yet known. In some inorganic materials, there appears to be
a threshold electron beam current density for damage to occur, below which
there appears to be little or no damage.27,28 If InGaN behaves in this way
then Gerthsen and Kisielowski may be correct that damage-free electron
micrographs of this material can be recorded. However, for other inorganic
materials there appears to be no lower threshold electron beam current
density for damage, which can also occur for incident electron energies
as low as 40 keV.29 If InGaN behaves in this way then damage-free micros-
copy is impossible. Until more is known about the mechanism(s) by
which strained thin layers of InGaN damage, we cannot be sure that it is
possible to record high resolution electron micrographs in which the damage
is negligible.
706 Chapter 42

7 3-D Atom Probe Studies of Indium Clustering

Our low-dose TEM studies have revealed that gross indium clustering does not
exist in the many InGaN quantum wells we have studied. However, we cannot
rule out lower level indium clustering for the reasons given above, namely the
fact that such genuine clustering, if it exists, may be masked by the noise in low-
dose images, and genuine clusters cannot be distinguished from indium-rich
clusters already created by the electron beam in even low-dose images. In
addition, since the electron-beam damage mechanism in strained layers of
InGaN is not yet known, we do not know if it is possible to record damage-free
electron micrographs of this material. In order to assess whether low-level
indium clustering genuinely exists, we therefore need a different technique from
electron microscopy. The method should not involve exposure to high-energy
electrons, and it should preferably provide direct information, at the atomic
level, of the distribution of indium in InGaN quantum wells. In addition, the
technique should preferably avoid the projection problem in TEM.
It is well known that the 3D atom probe (3DAP) can provide nanometre-
scale information about composition variations in a variety of materials.30 We
have recently applied this technique to InGaN quantum wells. The InGaN/
GaN multiple quantum well (MQW) sample used was grown by MOVPE
under similar conditions to the samples used for TEM described above, except
that approximately 6 mm of GaN was grown on c-plane sapphire at 1020 1C,
following deposition of a 30 nm GaN buffer at 540 1C. The QWs and barriers
were grown at a single temperature of 740 1C. High resolution X-ray diffraction
gave the thickness of the InxGa1
xN layers as 2.38  0.10 nm, and the indium
fraction x ¼ 0.18. Room temperature photoluminescence (PL) showed bright
blue emission at 454 nm.
Needle-shaped 3DAP specimens were prepared in a FEI Dualbeam Quanta
FIB/SEM. All SEM imaging was performed at 5 kV and exposure times and
currents were minimised in order to limit the risk of damage to the InGaN
quantum wells. The 3DAP images were obtained using an Oxford NanoScience
instrument fitted with a prototype laser module.
Figure 3 shows reconstructions of the InGaN/GaN structure with the indium
and gallium atoms displayed. Four indium-containing quantum wells are
clearly visible, and we have analysed in detail the indium distribution in the
bottom three of these since the top well may have been damaged by sample
preparation. We have compared the indium distribution with the expected
distribution from a random alloy. No significant deviations were found from
that expected in a random alloy for all three of the quantum wells (for further
details see Ref. 31). We therefore conclude that there is no evidence of indium
clustering in this sample.
Two independent direct imaging techniques, TEM and 3DAP, have therefore
found no evidence for indium clustering in InGaN quantum wells. The 3DAP
results indicate that the distribution of In in the InGaN sample studied is that
of a random alloy. Local compositional fluctuations statistically exist of course
in a random alloy, but there is no atomic clustering.
Turning Points in Understanding the Emission of Brilliant Light 707

Figure 3 Three-dimensional atom probe field ion microscope image of InGaN/GaN

multi-quantum wells. Each dot represents a single atom: light blue is gallium
and orange is indium. Statistical analysis shows that the indium distribution
is as expected in a random alloy.

8 Localisation Mechanisms
The evidence for exciton localisation on a nanometre scale in InGaN quantum
wells is strong (see Section 2). This is consistent with InGaN quantum well
structures emitting intense light with high quantum efficiency, despite having a
high dislocation density. In this section we discuss possible mechanisms for the
carrier localisation, having ruled out gross indium clustering.

8.1 Quantum Well Thickness Fluctuations

At low temperature, excitons are known to be localised in GaAs/AlGaAs
quantum wells by well-width fluctuations. The localisation energy is typically
only a few meV, and so localisation by this mechanism only occurs at low
temperature in GaAs/AlGaAs.32 However, the localising effects of well-width
fluctuations are much greater in the InGaN/GaN quantum-well system, both
because the InGaN is more highly strained and because the piezoelectric effect
is much stronger than in GaAs/AlGaAs.
High-resolution electron micrographs show that in the InGaN/GaN quan-
tum well system, the lower quantum well interface appears to be atomically
abrupt, whereas the upper interface is atomically rough6. The in-plane extent of
these well-width fluctuations is small, typically 1–2 nm. The thickness variation
is typically one monolayer (¼0.259 nm). Calculations show that for an InGaN/
GaN quantum well system with an indium fraction of 0.25, and well widths of
3.3 nm and 3.3 nm+1 monolayer, the quantum well bandgap for the n ¼ 1
electron and hole confined states decreases by 58 meV. Since kT at room
temperature is 25 meV, a monolayer change in quantum well thickness, con-
sistent with electron micrographs, is sufficient to localise the carriers.6

8.2 In-localised Hole Wave Functions

Bellaiche et al.33 have suggested from theoretical calculations of cubic InGaN
that even for a perfectly homogeneous InGaN material the carriers could be
708 Chapter 42
localised. The calculations predict localisation of the hole wave functions
around In in InGaN along randomly formed In–N–In chains. Hole localisation
leads to exciton localisation because of the small effective Bohr radius of
excitons in GaN (¼3.4 nm). Chichibu et al.34 have recently explained their
positron annihilation results in InGaN in terms of such In–N–In chains.
Unfortunately there is no theoretical calculation of the carrier localisation
energy due to In–N–In chains in a random hexagonal InGaN alloy.

9 Thermodynamics of Strained InGaN

The thermodynamic calculations reported earlier8 which predicted the decom-
position of InGaN were for bulk material. However Karpov35 has calculated
the phase diagram for an InGaN layer epitaxially matched to a GaN layer,
which puts the InGaN into biaxial compression. The effect of the strain is to
stabilise the InGaN, and no decomposition is predicted for normal growth
conditions.
Electron microscopy of the InGaN quantum wells we have studied in this
paper reveals no misfit dislocations. We are aware that the measured critical
thickness for the introduction of misfit dislocations depends on the resolution
of the experimental technique used to detect the dislocations36 and that electron
microscopy, because of the limited volume of specimen sampled, may over-
estimate the critical thickness. However, electron microscopy indicates that, at
least locally, our InGaN quantum wells are fully strained, and this is confirmed
by our X-ray diffraction measurements.
Hence we would not expect indium-rich clusters to form in our strained
InGaN quantum wells, and this is precisely what our TEM and 3DAP results
reveal.

10 Conclusions
1. Low-dose TEM shows no evidence of gross indium clusters in InGaN
quantum wells.
2. 3DAP shows that InGaN is a homogeneous random alloy, consistent
with TEM results and with thermodynamic calculations that take strain
into account.
3. Indium-rich clusters in InGaN are not necessary to localise the excitons.
Excitons can be localised by atomic scale well-width fluctuations and by
In atoms in In–N–In chains forming statistically in a homogeneous
InGaN alloy.
4. Calculated localisation energies at In atoms in In–N–In chains in hexag-
onal InGaN are not yet available. However, the localisation energy
provided by a monolayer well-width fluctuation of an InGaN quantum
well is about 60 meV, sufficient to localise excitons at room temperature.
5. We therefore have a consistent story that in the InGaN/GaN quantum-
well system, the InGaN is a random alloy. Localisation of the excitons
Turning Points in Understanding the Emission of Brilliant Light 709
may be due to monolayer thickness variations of the quantum wells,
which TEM shows occur on a 1–2 nm in-plane length scale, consistent
with the PL evidence of the in-plane localisation length of the excitons of
1–2 nm. The 60 meV localisation energy strongly localises the excitons at
room temperature. Additionally, excitons may be localised around In
atoms in InGaN, but the localisation energy for this in hexagonal InGaN
is not yet known.

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CHAPTER 43

Electron Tomography: A 3D
View of Catalysts and Nanoscale
Structures
PAUL A. MIDGLEY
Department of Materials Science and Metallurgy, University of Cambridge,
New Museums Site, Pembroke Street, Cambridge, CB2 3QZ, UK

1 Scanning Transmission Electron Microscopy

Since moving from Bristol to Cambridge 10 years ago, I have had the great
pleasure of working closely with Professor Sir John Meurig Thomas (known by
most simply as ‘JMT’) and the opportunity to interact with some of his
colleagues and collaborators on understanding the structure–property relation-
ships of a variety of nanoscale materials. Much of our early work together was
in using scanning transmission electron microscopy (STEM) to investigate the
fine-scale structure of mesoporous materials and especially those used for
heterogeneous catalysis.1 In fact JMT had been using STEM for many years
and had recognised its potential for studying the structure and composition of
catalysts and other nanostructures at very high resolution.2
A schematic diagram of the STEM technique is shown in Figure 1. Unlike
conventional transmission electron microscopy (TEM), STEM uses a highly
focussed beam (often sub-nanometre in size) to interrogate the specimen and
this is rastered over the sample to build up an image pixel-by-pixel, just as is
the case for scanning electron microscopy (SEM). However, unlike SEM, in
STEM the specimen is electron transparent (beam energies used are typically
200–300 keV) and thus, in general, the electron detectors are placed ‘down
stream’ of the specimen to intercept electrons scattered as they pass through the
specimen. In particular, the high angle annular dark-field (HAADF) detector,
proposed by Archie Howie,3 plays a key role in STEM as it detects only those
electrons that have been scattered to high angles, typically 50 mrad and above.
For single atoms or disordered clusters, such scattering can be thought of as

711
712 Chapter 43

Incident
convergent
beam
X-rays

X-Y raster

Specimen

Post-specimen
lenses

HAADF ADF BF ADF HAADF

Figure 1 Schematic diagram showing the detector arrangement for STEM imaging.
The far-field detectors are for BF imaging, ADF imaging and HAADF
imaging.

Rutherford-type scattering, in which the electrons interact predominantly with

the atom core. For Rutherford scattering there is a strong atomic number (Z)
dependence (in the unscreened limit this is Z2) and this is highly advantageous
when visualising nanoparticles in heterogeneous catalysts.
One of the great advantages of STEM is that simultaneous signals can be
acquired with the focussed beam. As shown in Figure 1, a bright-field (BF)
detector can record a BF image at the same time as the HAADF, or indeed an
annular dark-field (ADF), image. In addition, as with SEM, X-rays generated
by the beam–sample interaction can be collected and compositional inform-
ation can be married directly with structural information. Together with Vicki
Keast, then a Royal Society Hodgkin Fellow at Cambridge and now a lecturer
at the University of Newcastle in Australia, we showed how STEM could be
used to map structural and compositional information from heterogeneous
catalysts with very high spatial resolution.w Importantly, using X-ray micro-
analysis, it was also possible to investigate the composition of single nanopar-
ticles (see Figure 2), with each particle having a mass of only a few zeptograms
(a case of zepto-analysis!).4
Compared to conventional TEM, STEM is also very sensitive to the presence
of ultra-small particles especially when buried in another medium. Conven-
tional BF images of catalyst particles often show weak contrast and are difficult
w
Later, similar work was performed with Dr Lydia Laffont, now at Universite de Picardie in
Amiens, France and Dr Ana Hungria currently in Cambridge.
Electron Tomography: A 3D View of Catalysts and Nanoscale Structures 713

HAADF Pd Ru

15 nm
(a) (b) (c)

Figure 2 (a) STEM HAADF image, (b) Pd X-ray elemental map and (c) Ru X-ray
elemental map recorded on a VG HB603 STEM. There is a good correlation
between the Ru and Pd signals and the position of the particles in the
HAADF image.

to detect when in the 1–2 nm size range. A short paper5 written with JMT
showed how, for heterogeneous catalysts composed of MCM-41 mesoporous
silica with 3 nm pores and nanometre-sized active particles, BF TEM images, if
acquired out of focus (with optimum phase contrast) can reveal ordered silica
mesopores but do not show any evidence for particles inside the pores (see
Figure 3a). However, when the same region is imaged using HAADF STEM,
the particles are clearly revealed. The difference between the two techniques lies
in the coherence of the scattering process. By defocussing the BF image, phase
changes brought about by the beam passing through the material are ‘con-
verted’ to amplitude, and hence intensity, variation. If the BF image is acquired
in focus, there is almost no contrast at all. However, the phase change brought
about by individual nanoparticles is small and any phase contrast seen in the
image is ‘disguised’ by that of the silica pores. On the other hand, STEM
HAADF images are acquired in focus, and the image contrast generated by the
high sensitivity of the (incoherent) Rutherford-like scattering process to the
atomic number (BZ2). This Z-contrast is easily seen in the image (Figure 3b)
and highlights the need to use STEM HAADF imaging in conjunction with
conventional BF imaging for imaging at this length scale.
For crystalline specimens, the advantages of STEM HAADF imaging are
also striking.6 Figure 3 also compares a BF image with an STEM HAADF
image recorded from a Si/Si–Ge quantum well. In the BF image of Figure 3c,
the contrast is dominated by strain contrast (bend contours) brought about by
the buckling of the thin sample. Very little compositional contrast is evident. In
the STEM HAADF image of Figure 3d, the contrast is very different. The
slowly varying intensity changes are because the sample is thicker on the left of
the figure. The fine bright stripes delineate the quantum wells, which contain
B15% Ge, and the higher atomic number of the germanium leads to this clear
compositional signal.
Many of the early catalysts examined by STEM were grown in the Cam-
bridge Inorganic Chemistry Department in Prof. Brian Johnson’s group by Dr
Robert Raja, now a Reader at Southampton University – see elsewhere in this
714 Chapter 43

BF-TEM HAADF

(a) 20 nm (b)

BF-TEM HAADF

(c) 300 nm (d)

Figure 3 (a,b) Images of mesoporous MCM-41 silica. (a) An underfocus BF image

showing ordered silica mesopores. The lower inset is a magnified part of the
main image. The upper inset is the same magnified region but recorded in
focus showing minimal amplitude contrast. (b) The same area of specimen
as the image on the left but recorded as an STEM HAADF image; the pores
can now be seen to be filled with Ru–Pt nanoparticles, invisible in the BF
image. (c,d) A comparison between (c) a BF TEM image and (d) a HAADF
STEM image of a Si/Si–Ge quantum well structure. The TEM image is
dominated by diffraction contrast, the STEM HAADF image reveals very
clearly the quantum well structure.

book for their contributions. These were heterogeneous catalysts composed of

bimetallic (and occasionally trimetallic) nanoparticles deposited on and within
mesoporous silica. Many of the catalysts were based on MCM-41 mesoporous
silica which has a very high specific surface area and is composed of ordered
hexagonal arrays of mesopores with each pore about 3 nm in diameter. Energy-
dispersive X-ray (EDX) microanalysis spectra acquired in STEM mode were
used to determine two-dimensional (2D) chemical composition and ‘maps’ of
nanoparticle composition could be correlated directly with the catalyst struc-
ture from the HAADF image. It was this success in visualising catalyst
structures in two dimensions that prompted JMT to think about whether we
might do something similar in three dimensions, using electron tomography.
Electron Tomography: A 3D View of Catalysts and Nanoscale Structures 715

2 Moving to Three Dimensions

Three-dimensional (3D) imaging, using tomographic methods, is not a new
idea; the principles go back 90 years to the work of the German mathematician
Johannes Radon and the Radon transform is the basis for all tomography
reconstructions.7 Although the first practical use of tomography was in 1956
when Bracewell8 proposed using tomography to map solar emissions measured
by a radio telescope, the key advance was in 1963, when Cormack and
Hounsfield, later awarded jointly the Nobel Prize for Medicine in 1979,
developed the X-ray computerised tomography (CT) scanner.9 Electron tomo-
graphy began in 1968 with three seminal publications by de Rosier and Klug,10
Hoppe et al.11 and Hart.12 Following this tomographic annus mirabilis, a flurry
of papers quickly followed that discussed the theoretical limits of Fourier
techniques,13 approaches to real space reconstruction14 and the use of iterative
reconstruction routines.15
In the majority of cases, electron and X-ray tomographic reconstruction
relies on real space methods and particularly the idea of back-projection to yield
high quality 3D reconstructions. Normally a tilt series of images is acquired,
and each image is smeared, or ‘back-projected’, into a 3D object space at the
angle of the original projection. Using a sufficient number of back-projections
from different angles, the superposition of all the back-projected ‘rays’ will
return the original object (see Figure 4). In the resulting ensemble of data the
high frequencies are relatively under-sampled (see Figure 5), and this must be
corrected, using either a simple weighting filter or by using iterative methods to
constrain re-projections of the reconstruction to best match the original images;
iterative routines are more robust to the presence of noise and retain more
information at high resolution. If the specimen cannot be viewed from every
direction, as is often the case for electron tomography, then a missing ‘wedge’
of information, as shown in Figure 5, will degrade the reconstruction further
and lead primarily to an elongation in one direction of the reconstruction. This
can be improved if a second tilt series is recorded about a tilt axis perpendicular
to the first and iterative routines applied to both series simultaneously.16

3 Electron Tomography in the Physical Sciences

In general terms, the intensity of an image to be used for tomographic
reconstruction should be a monotonic function of some projected physical
quantity – the so-called ‘projection requirement’.17 This is often the case in
conventional X-ray absorption tomography in which image contrast is gener-
ated by changes in the X-ray absorption coefficient and sample thickness. In
electron microscopy, however, there is a number of competing contrast mecha-
nisms some of which, to varying extents, obey the projection requirement.
One of the very first demonstrations of electron tomography in the physical
sciences used a series of BF TEM images to study the 3D structure of block co-
polymer systems.18 Here the BF image contrast arises from mass-thickness
716 Chapter 43

(a)

(b)

Figure 4 A schematic diagram of tomographic reconstruction using back-projection

methods. (a) An object is sampled by projection from a range of angles. (b)
A reconstruction is achieved by summing 2D projections at the original
sampling angles into the 3D object space.

contrast brought about by staining certain components of the polymer system.

Then, in 2000, Bram Koster, working with Krijn de Jong and colleagues, in
Utrecht published a paper showing how internal porosity in a zeolite could be
imaged using BF electron tomography.19 Koster had been working for some
years developing electron tomography to differentiate cellular organelles using
either stained specimens, or with the cell in its more natural state using cryo-
microscopy techniques.
For amorphous or weakly scattering materials, the contrast in conventional BF
TEM images arises primarily from changes in specimen density or thickness and is
therefore suitable for tomography. However, many samples in the physical sciences
are strongly scattering crystalline objects, in general the interaction of the electron
beam with the specimen is dynamical and the exit wave function is not a simple
monotonic function of the projected thickness or mass-density. This complex
relationship between image intensity and the specimen rules out the use of BF
images for electron tomography in a large number of cases. BF TEM micrographs
can be used to examine crystalline specimens in a tomographic fashion but great
care must be exercised to make sure artefacts are identified as such.
Electron Tomography: A 3D View of Catalysts and Nanoscale Structures 717
data points

missing
θ
wedge

missing
wedge
α

Figure 5 A representation in Fourier space of the sampling of an object by a single tilt

series of images. The radial lines in the figure represent Fourier planes.
Although each plane has an even sampling of data points (solid circles), the
ensemble of images leads to an under-sampling of high frequency inform-
ation and a consequent blurring of the reconstructed object. y is the angular
sampling and a is the maximum tilt angle. The limited tilt range leads to a
missing wedge of information which in turn leads to elongation artefacts in
the final reconstruction.

While the BF mode gave satisfactory results for the Utrecht zeolite, JMT and
I realised that for finer-scale structures, STEM HAADF tomography should
provide superior results, as shown by the images of Figure 3. Heterogeneous
catalysts composed of small (1 nm) particles of high atomic number supported
on low Z silica provided ideal test beds to develop the idea of STEM HAADF
tomography.
Matthew Weyland, at that time one of my PhD students in Cambridge, now
at Monash University, had been studying how to optimise STEM HAADF
imaging and X-ray microanalysis and comparing the performance of the
dedicated vacuum generators (VG) STEM equipped with a cold field emission
gun (FEG) with our newly commissioned Philips (later FEI Company)
Schottky FEG CM300 (S)TEM. JMT proposed that we should try to develop
electron tomography using STEM HAADF imaging and Matthew took up the
challenge with relish and, as it turned out, with some success!
Our first tomographic acquisition was on the Philips instrument using a
standard single tilt holder with rather limited tilt range (
401). We found a
relatively large metal aggregate and a series of images was acquired every 51 tilt,
re-centred and re-focussed by hand (unlike modern acquisition schemes!) – the
tilt series is shown in Figure 6a.z Tomographic reconstruction of the series,

z
When viewed as a series, the ensemble of images looks a little like snapshots of pirouetting dancers
(albeit nano-dancers!); however at the time the reconstruction was known by the rather more
prosaic name of ‘the lump’!
718 Chapter 43

Figure 6 (a) A tilt series of STEM HAADF images of a palladium/ruthenium metal

agglomerate and (b) a surface render of the first STEM tomogram
(bar ¼ 250 nm).

shown in Figure 6b, was accomplished using code written in the Interactive
Data Language (IDL) programming language using a back-projection algo-
rithm. The reconstruction is far from ideal, there is severe elongation in one
direction (brought about by the limited tilt range) and the resolution degraded
by the limited number of images in the series. Nevertheless this proved that in
principle the ideas of STEM tomography were valid and applicable to the study
of heterogeneous catalysts.

4 Development of the Tomography Technique and Our

First Catalyst Tomogram
Buoyed by initial success, STEM tomography was developed further, with
improvements to the rather limited tilt range made top priority. The design of
modern electron microscopes is such that the space between the pole pieces of
the objective lens is minimised to reduce the aberration of the lens (especially
the spherical aberration) and so improve the image resolution. Conventional
holders allowed only 401 of tilt in most ‘analytical’ microscopes. In the Philips/
FEI instrument the lens pole-piece gap was 5.4 mm but the specimen itself is
typically in the form of a 3 mm grid and so there was certainly plenty of scope
to maintain the specimen size but reduce the holder width and profile to enable
a larger tilt range. In the Department of Materials Science at Cambridge there
are a number of distinguished research fellows, of whom JMT is one, and Ron
Broom another. As a pastime Ron builds clocks and watches and as such he has
both the watchmaker’s tools and expertise (and indeed steady hands!) to make
fine-scale changes to delicate instruments, and in this case to the TEM holder.
Judicious use of a fine metal file enabled a standard holder to be reduced in
width by approximately 1 mm without significant degradation of the holder’s
strength. This allowed a maximum tilt of 601 and enabled tomographic recon-
structions to be made with greatly reduced artefact. These days modern
commercial ultra-high tilt holders have now become commonplace and de
rigeur for electron tomography.
Electron Tomography: A 3D View of Catalysts and Nanoscale Structures 719
JMT’s interest in the microstructure of heterogeneous catalysts was the
driving force behind many of the first examples of electron tomography
undertaken in Cambridge. While the first proof-of-principle had been achieved
on an aggregated metal particle, if STEM-based electron tomography was to be
of widespread use in the characterisation of catalysts, and indeed other nano-
scale materials, then the technique had to be able to visualise in three dimen-
sions the internal distribution of nanometre-sized particles within porous
media. It is perhaps worth noting that while scanning probe techniques, e.g.
atomic force microscopy (AFM) and scanning tunneling microscopy (STM),
give remarkably clear pictures at high spatial resolution of the specimen
surface, in general very little information is gleaned about the internal struc-
ture, beneath the surface.
The first detailed STEM-based electron tomographic reconstruction of a
catalyst showed how this form of tomography could be used to reveal new
information about the 3D distribution of nanoparticles and the structure of the
underlying porous support. A brief description of the new STEM tomography
technique together with the reconstructed catalyst tomogram (Pd6Ru6 clusters
in MCM-41 mesoporous silica) was published in 2001 in Chemical Communi-
cations20 with a longer paper in Journal of Physical Chemistry published later.21
The work was highlighted as a breakthrough in Chemical and Engineering News
(the magazine of the American Chemical Society). This first STEM catalyst
tomogram is shown in Figure 7a. Although somewhat imperfect, it achieved
close to nanometre resolution in all three dimensions. A similar but more recent
catalyst reconstruction of nanometre-sized Ru10Pt2 particles on a disordered
mesoporous silica support is shown in Figure 7b for comparison – the
improvement in fidelity and resolution from that of the first tomogram is clear.

Figure 7 (a) The first STEM catalyst tomogram composed of Pd–Ru nanoparticles
(red) on and within an MCM-41 silica support (white). The inset shows a
voxel projection of the tomogram viewed parallel to the pore axis and
indicates the position of a single particle within an individual pore. (b) A
surface render of a recent (2006) reconstruction of Ru10Pt2 particles on a
disordered mesoporous silica support. The magnified inset emphasises how
the quality of the reconstruction has improved.
720 Chapter 43

5 Further Development of Electron Tomography

The technique has been improved and refined over the last few years. With the
help of Jose-Jesus Fernandez, of the University of Almeria in Spain, at the time
working with Tony Crowther at the Laboratory for Molecular Biology in
Cambridge, noise reduction algorithms, based on ‘anisotropic non-linear diffu-
sion’, or AND for short, were adapted to improve the fidelity of our 3D
reconstructions and allowed accurate quantitative details to be gleaned from
reconstructions. MCM-48, an ordered 3D variant of MCM-41, was investi-
gated in 200622 in collaboration with Osamu Terasaki, of Stockholm Univer-
sity, who writes elsewhere in this volume. One of the problems we tackled was
whether electron tomography could be used to determine 3D crystallography,
in other words by recording a tilt series of STEM HAADF images about a
single, but crystallographically unknown, axis could one reconstruct the full 3D
lattice of the ordered silica? Although at a different length scale, this is in many
ways similar to the efforts being made by the TEAM project,23 funded by the
Department of Energy in the USA to enable 3D reconstructions of crystal
lattices at atomic resolution.
Figure 8a shows a montage of voxel (volume pixel ) projections computed
from a 3D tomographic reconstruction of MCM-48 mesoporous silica. Each
projection in the figure is at a major zone axis encountered when rotating about
a o1124 axis through a symmetry-independent sector of reciprocal space. A
{112} plane, whose normal is vertical in the plane of the paper, is common to all
projections. On the right of each image is a simulation of the MCM-48 structure
based on an approximate gyroid surface. Power spectra for both experiment and
simulation are shown as insets. The agreement between experiment and simu-
lation is remarkably consistent for each projection. The o1354 axes contain

Figure 8 (a) A montage of tomographic voxel projections of MCM-48 shown at

successive major zone axes as the 3D tomographic reconstruction is rotated
about a o1124 zone axis. (b) A reconstructed slice through the MCM-48
reconstruction perpendicular to the o1104 zone axis. A Bragg-filtered
inset enhanced the periodic detail. The pairs of spots in the power spectrum
correspond to {332} and {224} reflections. Adapted from ref. 22.
Electron Tomography: A 3D View of Catalysts and Nanoscale Structures 721
two dominant sets of {112} planes, the strongest scattering planes in the MCM-
48 lattice. Although such projections could in principle be acquired through
successive images recorded at zone axes found by tilting the specimen in the
microscope, in practice for MCM-48, which can be prone to beam damage, or
for example for interfacial phases or small embedded crystallites, it can be a very
difficult and time-consuming task to identify major zone axes in situ. Electron
tomography therefore offers a way of recording images about a ‘random’ tilt
axis, performing a 3D reconstruction and then, post facto, aligning the whole
crystal in the computer – a far less demanding task than in the electron
microscope! In addition, by collecting over a large angular range, access is
made possible to almost all major zone axes of interest, which may not be
possible, or may be missed, with conventional microscopy.
Figure 8b shows a reconstructed slice perpendicular to a o1104 direction.
A Bragg-filtered version, used to reduce non-periodic artefacts, has been
superimposed for clarity. The inset shows a power spectrum of the slice
indicating strong pairs of Fourier components, which if indexed according to
a o1104 diffraction pattern, correspond to {332} and {224} reflections, the
latter set demonstrating 4.7 nm periodic resolution within the slice. The ability
to slice through different planes of the crystal can be of great advantage when
visualising complex 3D geometry. All projections and slices from the recon-
struction are consistent with the proposed space group of Ia3d.
Success in visualising nanoparticles in catalysts led to the use of STEM
tomography in the investigation of nanoscale structures found in bacteria and
cells. Although many life science specimens will damage very quickly, others
are more resistant to the electron beam and can be examined using STEM
HAADF imaging. One example is that of magneto-tactic bacteria, composed of
a ‘backbone’ of iron oxide or iron sulfide crystals which the bacteria can use to
sense the earth’s geo-magnetic field. A series of STEM HAADF images of such
bacteria were recorded and a reconstruction of the crystallites was made with
sufficient clarity that measurements of the facet size could be used to elucidate
crystal growth trends. Figure 9a shows a surface render of a reconstruction with
the external surface of the bacterial membrane and a chain of magnetite
crystals, together with examples of slices through an individual crystal to reveal
clear crystallographic faceting.24 The second example, in Figure 9b, shows
plan-view and cross-sectional slices from a reconstruction of part of a liver cell
from a patient suffering from haemochromatosis, a disease which leads to excess
iron storage in the body, and especially the liver. The reconstruction reveals a
remarkable 3D array of the iron-rich cores of individual ferritin molecules – the
origin of this ordering has yet to be fully explained.
Although STEM HAADF tomography, through its atomic number depend-
ence, can reveal changes in composition, there are situations where alternative
image modes are needed to see 3D chemical variation. For many years JMT
and colleagues have been using electron energy loss spectroscopy (EELS) to
investigate the chemistry of nanoscale materials – see for example the chapter
of Rik Brydson in this book. EELS, and especially energy loss imaging, or
energy-filtered TEM (EFTEM), has been combined with electron tomography
722 Chapter 43

Figure 9 (a) A tomographic reconstruction of magneto-tactic bacteria strain MV-1.

The ‘backbone’ of magnetite crystals is evident. Slices, taken through a
single magnetite crystal in the ‘backbone’, reveal the perfect crystal faceting
of the cubic crystals. Adapted from Ref. 24. (b) Side view (top) and plan
view (bottom) of a 3D ordered array of ferritin molecules in a diseased liver
cell from a patient suffering from haemochromatosis. Power spectra and
Bragg-filtered images are also shown.

to enable changes in composition to be mapped in three dimensions. 3D maps

can be reconstructed using core-loss electrons but images formed using low-loss
electrons, and especially those close to the plasmon maximum, can also reveal
chemical variations in nanoscale samples. Figure 10 shows one example, of
multi-walled carbon nanotubes (MWNTs)y covered in a nylon sheath, where
conventional 3D EFTEM using core-loss data is not appropriate because both
components of the ‘composite’ structure are carbon-based, and a more uncon-
ventional approach had to be used. By forming an image from the ratio of two
low-loss images, ‘tuned’ to emphasise the difference in chemical bonding, the
3D structure of the MWNT–nylon composite can be readily seen. Further, by
recording an energy series of EFTEM images at every tilt, it has been possible
to reconstruct the 3D structure at every energy increment and therefore
interrogate the energy loss spectrum at every voxel, thus enabling a form of
‘volume-spectroscopy’.25 This method now allows energy loss spectra to be

y
JMT’s work in carbon nanotubes stretches back a quarter of a century – see for example Figure 13
in Ref. 2.
Electron Tomography: A 3D View of Catalysts and Nanoscale Structures 723

Figure 10 A montage of images from an MWNT–nylon composite. Left: energy-

filtered images: zero-loss image, and images formed from the ratios of two
low-loss energies 21 eV/27 eV and 27 eV/21 eV, corresponding to the
plasmon excitations of the nylon and the nanotube. Right: surface renders
of the nanotube (purple) and nylon (grey) from the tomographic recon-
struction of the plasmon ratio 27 eV/21 eV. Nylon that has filled the top
end of the nanotube is shaded a lighter purple. A hole that occurs in the
nylon can be seen running just under the top end of the nanotube and voids
within the nanotube are represented by pale green volume. Adapted from
ref. 25.

extracted from isolated sub-volumes of interest, improving the interpretation of

each spectrum and minimising the possibility of being misled because of the
superposition of two signals in projection.

6 Aberration-Corrected Instruments and the

Cluster-to-Crystal Transition
In electron microscopy there has been something of a technological revolution
in the past few years. It had long been known that the lenses of electron
microscopes were, comparatively speaking, of very poor quality. They suffer
from large aberrations, spherical aberration being the most well-known and
important, which could not be corrected in conventional designs. Recently
724 Chapter 43

Figure 11 (a) STEM HAADF image taken on the SuperSTEM showing nanoparticles
embedded within MCM-41 mesopores. (b) A high magnification STEM
HAADF image showing crystallinity in the larger particles. The arrows
indicate two particles with the one on the right showing evidence for close
packed planes, the one on the left looking more disordered and giving the
appearance of a large cluster rather than a crystal. Analysis of similar
images revealed little difference in the size distribution of particles (c)
before and (d) after catalysis. The pink curve is a best-fit Poisson distribu-
tion and the relatively poor agreement hints at the possibility of preferred
cluster sizes. Adapted from ref. 26.

however, non-round lenses have been built composed of multi-pole elements

which can introduce ‘negative’ aberrations to compensate the ‘positive’ aber-
rations of the conventional imaging lenses. It is now possible to acquire TEM
images with sub-Ångstrom resolution, and form sub-Ångstrom probes for
ultra-high resolution STEM images with atomic-scale microanalysis.
One such aberration-corrected STEM instrument has been installed at the
SuperSTEM Laboratory in Daresbury and using that instrument we investi-
gated the detailed structure of catalyst nanoparticles. Figures 11a and b show
an image acquired at the SuperSTEM revealing quite clearly the alignment of
particles within mesopores and, at higher magnification, the crystallinity of the
larger particles. Analyses of such data led to a paper, published in Chemical
Communications,26 in which we showed how the distribution of particle size
changed very little from before to after catalysis (see Figures 11c and d). As
Electron Tomography: A 3D View of Catalysts and Nanoscale Structures 725
seen in the figure, the fit to a Poisson distribution was not especially good,
perhaps indicative of preferred cluster sizes and with what seems to be a clear
enhancement of particle number at the low size range. Further, we analysed the
structure of individual particles and found that below B200 atoms the particles
showed no signs of crystallinity and were best described as an atomic cluster.
Above B200 atoms, the particles were distinctly crystalline. This transition
from cluster-to-crystal agreed very well with theoretical work published a few
years previously.27
There is no doubt that such aberration-corrected instruments, coupled with
the advent of monochromators to provide 300 keV electron beams with 0.1 eV
energy resolution, will give rise to new techniques, new results and an improved
understanding of complex nanoscale systems, such as heterogeneous catalysts.
Combined with tomographic techniques, this may yet lead to the exciting
prospect of full 3D analytical capabilities with atomic resolution.

7 Conclusions
This chapter is about scientific turning points and JMT’s ideas and determi-
nation to visualise catalysts with high spatial resolution and in three dimensions
was certainly a key turning point in the development of electron tomography
for the physical sciences in Cambridge. Indeed without JMT’s drive and
enthusiasm the development of materials-based electron tomography in Cam-
bridge would perhaps have never come to fruition. The development of STEM
tomography has spawned a number of other tomographic techniques in Cam-
bridge, not only EFTEM tomography, as described earlier, but also weak-beam
dark-field (WBDF) tomography to elucidate the 3D structure of dislocation
networks28 and holographic tomography, used to map 3D electrostatic poten-
tials in semiconductor devices.29 It has been enormously rewarding working
with JMT over these past 10 years or so and I look forward to encountering
many more scientific turning points with JMT in years to come.

Acknowledgements
The author would like to thank Matthew Weyland, Tim Yates, Vicki Keast,
Jonathan Barnard, Mhairi Gass and Edmund Ward for their contributions to
this chapter.

References
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2. J.M. Thomas and P.A. Midgley, Chem. Commun., 2004, 11, 1253.
3. A. Howie, J. Microsc., 1979, 117, 11.
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4. P.A. Midgley, J.M. Thomas, L. Laffont, M. Weyland, R. Raja, B.F.G.
Johnson and T. Khimyak, J. Phys. Chem. B, 2004, 108, 4590.
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6. P.A. Midgley, M. Weyland, T.J.V. Yates, I. Arslan, R.E. Dunin-Bokowski
and J.M. Thomas, J. Microsc., 2006, 223, 185.
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P.A. Midgley, Scr. Mater., 2006, 55, 29.
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P.W. Stephens and R. L. Whetten, Phys. Rev. Lett., 1997, 70, 1873.
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CHAPTER 44

Nano and Mesoporous

Materials: A Study by HREM
JOSÉ M. GONZÁLEZ-CALBET,a
M. LUISA RUIZ-GONZÁLEZa AND
MARÍA VALLET-REGÍb
a
Departamento de Quı́mica Inorgánica, Facultad de Ciencias Quı́micas,
Universidad Complutense de Madrid, 28040 Madrid, Spain; b Departamento
de Quı́mica Inorgánica y Bioinorgánica, Facultad de Farmacia, Universidad
Complutense de Madrid, Pza Ramon y Cajal, 28040 Madrid, Spain

1 Introduction
Host–guest materials comprise a wide group of great interest due to their
intrinsic properties that allow the development of classic and new applications.
Among them, silica ordered porous materials constitute a very interesting
example. There are materials with different pore sizes that can be used as hosts
and consequently different compounds that can be inserted. This variety of size
and composition gives rise to an enormous range of applications.
Zeolites, represented by the general formula Mx/m[Si1
xAlxO2]  nH2O, have
been the most extensively studied type. They are built up from corner-sharing
SiO4 and AlO4 tetrahedra which form large cavities and channels in the 0.1–
10 nm range, which are responsible for their role as catalysts, ion exchangers,
gas purifiers, etc. Crystallographic studies and their implications for practical
applications have been extensively reviewed. Moreover, there are many possi-
bilities for the occurrence of short-range order and extended defects. To solve
these structural imperfections, high resolution electron microscopy is a very
powerful tool as demonstrated in the pioneering works on micro- and meso-
porous materials by J.M. Thomas and co-workers.1,2 Larger pore sizes and
enhanced performances occur in the related silica mesoporous materials which
were first synthesized by the Mobil Oil Company in 1991.3 They have been
devoted mainly to uses in catalysis, polymerization, absorption and nano-
particle preparation.4–6 In addition, intense research has been aimed at the

727
728 Chapter 44
7–9
development of this system to act in controlled delivery of drugs and, more
recently, at their role as bioactive materials.10
The above host materials are built up from ordered arrangements of channels
or cavities, but we can also think about isolated units or cylindrical structures,
resembling the above channels in mesoporous materials, able to accommodate
different substances or guests. This is the case for nanotubes, which can be of
different nature although the most studied are, undoubtedly, the carbon
nanotubes (CNTs).11 This research started and quickly grew up in 1985 after
the C60 discovery by Kroto et al.12 In 1991, Ijima13 discovered, in an arc
experiment, another carbon form corresponding to MWCNTs (multiwall car-
bon nanotubes). A few years later, SWCNTs (single wall carbon nanotubes)14
were synthesized. MWCNTs are made up of two or more cylindrical shells of
sp2 graphene layers concentrically arranged around a central hollow. The
distance between layers is constant and around 0.34 nm, i.e., nearly equal to
graphite d-spacing. SWCNTs exhibit a more simple structure comprising only
one sp2 graphene layer. Both types of compounds form cavities with different
diameter; in the 1–2 nm range for SWCNTs and between 2 and 25 nm for
MWCNTs. The CNT lengths usually extend up to several microns. The
discovery of CNT and especially of SWCNT gave rise to new insights in
materials research because of their properties associated to the nanometre
dimension in one direction. They show unique mechanical, chemical and
electronic properties15 which have prompted the development of potential
applications such as, for instance, reinforcements in composite materials16
and cathodes for electron field emitters.17 Moreover, similarly to mesoporous
materials, they are suitable to incorporate substances. Materials can then be
confined along one dimension to the nanometre scale which, usually, involves
surprising changes in their structural and physical properties.18 However, the
development of these and other applications show limitations as a consequence
of the difficulty in obtaining large quantities of pure and uniformly sized
nanotubes. In this sense, a lot of research has been devoted to the synthesis
procedures, the most important being carbon arc evaporation, laser ablation
and chemical vapour deposition.
The discovery of fullerenes12 and, later on, of CNTs13,14 promoted extensive
research in an unexplored area leading to the discovery of new polyhedral
fullerene-like nanostructures not only limited to carbon but also made of
different inorganic compounds,19–25 able to accommodate substances inside.
These inorganic compounds are commonly called IFs (inorganic fullerenes).
For instance, well known layered compounds such as MX2 (M: W, Mo; X: S,
Se)19,20 can give rise to close hollow structures. Nanoparticles of these layered
compounds are unstable in the platelet form and spontaneously form close cage
structures similar to carbon fullerenes and CNTs.25 They are derived from
hexagonal 2H-type stacking of units that comprise one sixfold-bonded tungsten
layer sandwiched between two threefold-bonded tungsten layers, held together
by van der Waals forces.19 Such materials can incorporate non-hexagonal
defects into their structures resulting in the formation of closed spheroidal or
nanotubular like structures. IF-WS2 and MoS2 exhibit good properties as solid
Nano and Mesoporous Materials: A Study by HREM 729
lubricants. Other proposed applications include tips for scanning probe micro-
scopy and electrochemical hydrogen storage.
The concept of accommodating substances inside ‘‘boxes’’ is not a new one
or at least not so different to that referring to compositional accommodation in
solids. Indeed, one of the most explored areas in solid state chemistry during
the last century has been devoted to non-stoichiometry in mixed oxides, for a
better understanding of their properties. Among these, perovskite-related oxi-
des arouse enormous interest especially after the HTSC discovery in copper
mixed oxides.26 Moreover, there are many properties which are sensitive to
small changes in composition and this can give rise to short order phenomena
involving few unit cells.
The aim of this chapter is to show several representative examples of different
matrices such as mesoporous, CNT, IFs which can accommodate substances
inside but also to discuss the general case of solid compositional variations.

2 Mesoporous Materials
The importance of mesoporous materials in different areas of materials science
has already been underlined. Considering the field of biomaterials, they are
promising candidates for scaffold fabrication useful in tissue regeneration as a
consequence of their proven ability as drug delivery systems7–9 and their
bioactive properties.27–28 These facts can be positive when combined with the
drug release and/or biological active specimens. In fact, the mesoporous
cavities of these ceramic matrices can incorporate different substances such
as drugs, peptides, proteins and growth factors.7–9,29–31 Figure 1, schematically,
represents a mesoporous material whose pores are occupied by ibuprofen,
nitrofurazone, amoxycilin, cis-platinum, docarbacin, gentamicin and alendron-
ate, respectively. This release comprises, usually, two steps: (i) fast, during the
first hours and (ii) a more continuous one, in the following days.32,33 In these
mesoporous matrices it would be possible to combine tissue regeneration and
drug delivery in order to adjust both kinetics in such a way that the release of
antibiotics, antiinflammatories, anticarcinogens or antitumorals is favoured
during the first hours after implantation in the living body. This would confer
an added value to the implant, since together with the matrix action of bone
regeneration, the infection and/or inflammation is treated, or the antitumoral
action initiated in a local and continuous way as necessary.34,35 In this sense,
the introduction of biologically active molecules in mesoporous materials is of
particular interest because they can accelerate the bone formation reinforcing
the bioactive behaviour of these matrices.
Bioactivity is a property that encompasses the ability of a given material to
form interfacial bonds with tissues when in contact with physiological fluid
involving, always, the formation of a layer of hydroxycarbonoapatite.
Although the mechanisms of apatite nucleation and crystallization are not fully
understood, the features of both substrates and fluids seem to have important
influence. Concerning the solution, parameters such as pH, temperature and
730 Chapter 44

Figure 1 Schematic representation of different drugs incorporated in a mesoporous

material.

ionic concentration determine the type of calcium phosphate formed as well as

its precipitation rate. On the other hand, the presence of silanol groups and
porosity seem to be crucial in the apatite layer formation. In this sense,
mesoporous silica materials, having pore sizes in the range 2–50 nm and surface
silanol and siloxane reactive groups, are promising candidates as bioactive
materials.
We have studied the bioactivity properties of three mesoporous materials,
SBA-15, MCM-48 and MCM-41, by means of in vitro assays in simulated body
fluid (SBF),36 which has the composition and ionic concentration similar to
human plasma, at 37 1C during different immersion periods. Mesoporous
materials with different structural and textural properties were chosen in order
to evaluate their influence on the corresponding in vitro response. Different
characterization techniques (FTIR, SEM-EDS, TEM-ED-EDX) show that,
after the in vitro tests, SBA-15 and MCM-48 surfaces are modified, as a
consequence of the reaction of the materials with the fluid, giving rise to the
growth of a hydroxycarbonoapatite layer.37 The kinetics for each material are
quite different; SBA-15 develops the apatite layer after 30 days while 60 days
are required in the case of MCM-48. Nevertheless, after 60 days of immersion
the apatite layer did not appear in MCM-41. SEM and EDS studies of samples
SBA-15 and MCM-48 before and after 15, 30 and 60 days in SBF show that the
surface has been covered with needle-type crystal aggregates forming spherical
Nano and Mesoporous Materials: A Study by HREM 731
particles. The EDS analysis confirms the presence of Ca and P on the surface.
In the case of MCM-41, the surface is not modified and Ca and P have not been
detected. HREM images before the treatment show the pore size characteristic
of the raw material. After the indicated periods of time the apatite formation is
confirmed at SBA-15 and MCM-48 surfaces.37
Figure 2 corresponds to TEM images of SBA-15 before and after the
immersion in SBF (60 days). The characteristic hexagonal pore distribution
is observed in the image corresponding to SBA-15 before the treatment while
after 60 days acicular particles appear over the mesoporous surface, which is
simultaneously degraded. Moreover, HREM studies indicate the crystalline
nature of the above particles, as observed in Figure 3, which are imbibed in an
amorphous matrix. There are compositional differences between crystalline and
amorphous areas; the crystalline region comprises Ca and P while the amor-
phous region contains Si. Since only Si is present in the amorphous matrix, it
seems logical to relate it with the original mesoporous material that is trans-
formed. Minor areas where the mesoporous material has not yet been com-
pletely decomposed are also found, as reflected in Figure 4. In fact, fringes of

Figure 2 TEM images of SBA-15 before and after 60 days immersion in SBF. The left
hand side image, at the bottom, corresponds to the raw material and shows
the hexagonal pore distribution, as schematically represented in the top. The
right hand side image, at the bottom, shows an acicular particle which
appears over the mesoporous surface after the treatment. At the top the
potential implant of mesoporous material covered with hydroxyapatite is
schematically shown.
732 Chapter 44

Figure 3 Top: Enhanced image of SBA-15 after 60 days in SBF. Two areas, A and B,
are clearly observed. Bottom: HREM image of each area; Area A shows the
crystalline nature of the particles showing periodicities characteristic of the
hydroxyapatite cell. Area B indicates the amorphous nature of the meso-
porous material after treatment. FTs are displayed for each image.

Figure 4 TEM images of a minor area in SBA-15 after 60 days. The left hand side
image is a low magnification one that shows a mesoporous area which is not
yet decomposed as well as an acicular particle not here imbibed. On the right
hand side, a higher magnification image of the particle is depicted, showing,
again, its crystalline nature. Notice that the particle is over an amorphous
matrix in contrast to the above one, not yet decomposed and without
formation of apatite.

8.8 nm periodicity, in agreement with SBA-15, in a clear process of modifica-

tion, are observed. Notice that in this case the needle-like particles are not
placed over the mesoporous walls as happens in the majority areas, described
above, also evident on the right hand side of this image. Higher magnification
reveals, again, the crystalline nature of the particle, with periodicities in
Nano and Mesoporous Materials: A Study by HREM 733
agreement with the apatite cell, imbibed in a completely amorphous area, as
reflected in the corresponding Fourier transform (FT). It is then clear that the
mesoporous surface is modified when apatite is formed. This process cannot be
studied on bioactive glasses due to their total structural disorder.
The different behaviour shown for SBA-15, MCM-48 and MCM-41
can be understood on the basis of the compositional, textural and structural
properties of the mesoporous material. As already mentioned, the silanol
groups (Si–OH) can act as nucleation sites of the apatite layer.38–40 In this
sense, the silanol group concentration seems to be an important factor to be
considered. MCM-41 shows a rather lower concentration of silanol groups
(B2 mmol SiOH  m
2) than SBA-15 and MCM-48 (B13 mmol SiOH  m
2).
This could be one reason to explain the absence of bioactivity in MCM-41.
Moreover, the textural and structural properties must also be taken into
account in order to justify this negative behaviour. Both factors are related
to the possible ion diffusion inside the mesoporous material. Bigger and more
accessible pores will favour the ion diffusion, i.e. the apatite nucleation will be
faster.41–43 Contrary to this, the ion diffusion becomes slower and more
difficult if the pore size decreases, diminishing the nucleation rate. In this
sense, SBA-15 shows the largest pore size (8.8 nm) being considerably lower
(3.6 nm) in the cases of MCM-48 and MCM-41. This fact could explain the
better kinetics observed in SBA-15 compared to MCM-48 and MCM-41.
Furthermore, the dimension and shape of the pores is also a very important
factor to be considered. In this sense, MCM-41 has pure one dimensional
character while MCM-48 and SBA-15 are connected through complementary
pores favouring the diffusion paths. However, the identical pore size of
MCM-48 and MCM-41 does not justify the great difference on their bioactive
behaviour, but can be understood taking into account the silanol concentra-
tion as well as the structure. Silanol concentration in MCM-41 walls is lower
than in MCM-48 and the 2D-hexagonal lattice without channel connections is
less accessible to the ions if compared with the 3D-cubic one exhibited by
MCM-48. Moreover, local curvatures for MCM-41 comparing to SBA-15
and MCM-48, being both quite similar, are different and may also have an
influence.
The above discussion allows understanding, on the basis of compositional,
textural and structural properties, of why apatite formation happens in SBA-15
and MCM-48 in 30 and 60 days, respectively, while MCM-41 does not suffer
any alteration after 2 months of assay. It does not mean, in principle, that it is
impossible to develop the apatite layer, but it is clear that the rate is too slow.
All the discussed factors are put together in Figure 5, which summarizes the fact
that mesoporous silica matrices are good candidates for bone regeneration in a
period longer than a month, as a consequence of their bioactive quality, being
able, at the same time, to act as hosts for different drugs (antibiotics, anti-
inflammatories, anticarcinogens) but also for other biologically active sub-
stances to accelerate the process of formation of new bone (peptides or growth
factors) achieving a controlled release of both types of molecules in the first few
days following the implantation.
734 Chapter 44

Figure 5 Schematic representation of the mesoporous potentialities as bioactive

materials and as host for drugs desirable for the developing of new
implants. Active substances to accelerate the bone formation have also
been included. HREM images of the mesoporous material (MCM-48) and
surface covering (hydroxyapatite) are also included.

3 Carbon Nanotubes and Inorganic Fullerenes

Visualizing substances inside mesoporous materials is not always easy due to
the thickness of the material. Only a few examples have been reported44 and the
filling is always with metallic wires, which provide stronger contrast than
the silica mesoporous walls. This problem can be overcome in CNTs due to the
lower thickness of the tubes. As previously mentioned, CNTs resemble meso-
porous materials from the point of view that they comprise channels or cavities
in the nanometre scale. Nevertheless these cavities are isolated in the case of
CNTs, being ideal candidates for substance incorporation and further identi-
fication. For comparison, longitudinal and transverse view images of both
SWCNT and MCM-41 are shown in Figure 6. Filling CNTs is not easy and
many factors must be taken into account involving a great synthetic effort.
Besides, confirmation of the substance incorporation requires also the help
of TEM, HREM being an indispensable tool. The group of Malcolm Green
has pioneered filling CNTs with inorganic substances, studying and devel-
oping different procedures45–49 either at low temperature from a solution
or at high temperature from the melt of the precursor guests. They have also
studied the filling, by means of TEM, and investigated the structure of the
Nano and Mesoporous Materials: A Study by HREM 735

Figure 6 Top and side view of MCM-41(a,c) and SWCNT(b,d) for comparison
purposes. The channel diameters are comparable.

incorporated substance by the exit wave reconstruction using a through

focus series.50 In this chapter we report some examples of how TEM evidences
the encapsulation inside the tubes, and is indispensable for their structural
characterization.
A representative example of substance incorporation is shown in Figure 7
which corresponds to MWCNT filled with Co particles. An image of an
SWCNT filled with PdI2 is depicted in Figure 8. The monoclinic cell of PdI2
along the [010] zone axis is better observed in the filtered image shown in the
inset. Notice that almost the whole tube is filled. In spite of the synthetic efforts,
the homogeneity of the filling is not always as good as desirable and it is
possible to find less favourable situations as shown in Figure 9, which corre-
sponds to SWCNTs filled with Bi2O3. The starting material was bismuth citrate
which is converted into oxide after heating in the presence of tubes.
On the other hand, CNT samples are not always pure and homogenous
due to the high temperatures and use of catalysts involved in the synthesis
736 Chapter 44

Figure 7 Low magnification image of an MWCNT filled with cobalt.

Figure 8 HREM image of an SWCNT filled with PdI2. The inset shows the filtered
image where the cell along [001] is better observed.

procedures. In fact, different carbon structures are frequently observed as for

example, ‘‘onminum type’’, and/or close hollow structures (Figure 10) with
periodicities in agreement with graphite interlayer spacing. These shapes are
similar to that exhibited by IFs as WS2,18 NiCl251 or CsO2.52 For instance,
Figure 11 shows a concentrically arranged structure characteristic of WS2,
exhibiting periodicities of 0.65 nm between the tubular walls, and 0.27 nm
along layers. In this case, WS2 IF has been formed by heating KxWO3 with
Nano and Mesoporous Materials: A Study by HREM 737

Figure 9 HREM image of a bundle of SWCNTs treated with bismuth citrate. Filling
of the tubes is evident on the outside part of the bundle, as better observed in
the enlarged image shown at the right hand side inset. The left hand side
inset shows the FT and iFT which are in agreement with the Bi2O3 mono-
clinic unit cell along [0
21].

Figure 10 Close hollow structure coexisting with bundles of SWCNT’s. Distances

between layers agree with graphite periodicity.

H2S.53 This not only gives rise to the IF formation, but also to the encapsu-
lation of the corresponding bronze inside the WS2 tubular structure. Sloan et al.
have previously reported the encapsulation of WC in WS254 and also the related
WO3
x system.55 KxWO3 belongs to a group of interesting compounds,
738 Chapter 44

Figure 11 TEM images of concentrically arranged layers of WS2 at (a) low magni-
fication and (b) higher magnification where the WS2 periodicities are
evident.

MxWO3, known as intergrowth tugnsten bronze (ITB),56 where M is, typically,

an alkaline element. They are built up from the intergrowth of WO3 and HTB
(hexagonal tungsten bronze) units. The WO3 slabs have a distorted ReO3-type
structure, i.e., [ReO6] octahedra sharing corners. The HTB units consist of
hexagonal tunnels, derived from six [WO6] octahedra which share corners.
Notice that these tunnels constitute another example of cavities, of about
0.5 nm, for substance incorporation. Depending on the width of these two units
different intergrowths can occur. Moreover, they can be ordered, i.e., recurrent
intergrowths or disordered involving short-range order phenomena. In the first
case, a homologous series with members exhibiting different periodicities,
depending on the slab sizes, is attained. Figure 12 is an HREM image showing
the 2H-WS2 encapsulated KxWO3, which exhibits a quite ordered contrast
arrangement corresponding to the ordered intergrowth between two HTB
layers, which define one octahedral [WO6] layer in the block, and five octahe-
dral layers of the WO3 block. It can be defined as a (1,5)-ITB.57 These recurrent
intergrowths are induced in WO3 due to the introduction of an alkaline
element. The WO6 skeleton is modified forming hexagonal channels, in which
the alkaline element is placed, in order to accommodate the compositional
changes.

4 Compositional Variations in Confined Spaces:

A General Case
This example of ITB allows introducing the concept of non-stoichiometry,
which has been widely studied in oxides exhibiting the related perovskite
structure, derived from the ReO3 type by occupying the empty octahedral
Nano and Mesoporous Materials: A Study by HREM 739

Figure 12 HREM image of KxWO3 encapsulated inside 2H-WS2. The HTB and WO3
recurrent intergrowth is shown.

sites. Perovskite type can easily accommodate compositional changes without

substantial modification of its structural skeleton. There are several mecha-
nisms, extensively reviewed in the literature58–64 going from defects randomly
distributed to new superlattices, as a consequence of ordered arrangements
induced by the compositional changes. Notice that, in any case, these modifi-
cations take place in a confined space leading to changes at the nanometre scale
in one dimension.
A very common problem of non-stoichiometry in perovskites is the accom-
modation of anionic vacancies, which can lead, as in the ITB case, to recurrent
intergrowths. For instance, this is the case for LaBaCuCoO5.265 in which a five-
fold perovskite superlattice is observed as a consequence of the recurrent
intergrowth of two blocks showing 2ac and 3ac periodicities (ac being the basic
parameter of the cubic perovskite). The five-fold periodicity is observed in
Figure 13. Crystallographic imaging processing (CIP) studies suggest that the
2ac and 3ac blocks are related to the polyhedra sequences . . .POhP. . .
and . . .PP. . . (P  square-pyramid, Oh  octahedron) respectively, which
constitute structural units related to YBa2Fe3O8 (POhP)66 and YBaCuFeO5
(PP).67 The final potential map resulting from the CIP study together with the
740 Chapter 44
polyhedral sequence representation has been included as an inset in Figure 13.
Furthermore, the oxygen content on LaBaCuCoO5.2 can be reduced, under
controlled atmosphere in a thermobalance, leading to single phases for the
LaBaCuCoO4.8 and LaBaCuCoO4.4 compositions. From the structural point of
view it is worth mentioning that the five-fold order is kept in the reduced
phases, whereas differences in the periodicities inside the two types of block are
appreciated by CIP. These differences involve a reduction of the central
distance in the three-fold periodicity block. This fact can be interpreted as a
consequence of modifications of the coordination polyhedra in the three-fold
periodicity block according to Oh- Pc- L (Pc  square planar, L  linear
coordination) while the two-fold block is not altered. The ensemble of these
results allows the proposal of a topotactic reducing process for LaBaCuCoO5.2
through the following sequences: . . .POhP PP . . . - . . . PPcP PP . . . -
. . . PLP PP . . . as schematically represented in Figure 14. Notice that this
process affects a plane of atoms in the structure between two layers of square-
pyramids involving a confined space in which chemical modifications can be
performed. The elucidation of this topotactic reduction process has been
possible due to the use of HREM. Moreover, since it affects the oxygen
environment of Cu/Co cations, the use of electron crystallography has been
invaluable in solving the local atomic arrangement for image interpretation.

Figure 13 HREM image of LaBaCuCoO5.2 where the recurrent intergrowth between

blocks of 2ac and 3ac periodicity can be observed. The inset shows the final
potential resulting from CIP study. The polyhedra sequence derived is
depicted.
Nano and Mesoporous Materials: A Study by HREM 741

Figure 14 Schematic representation of the topotactic reducing process of LaBaCu-

CoO5.2 through the 3ac periodicity block.

5 Conclusions
In this chapter several examples of compositional accommodation in solids
(mesoporous, tubular compounds and bulk materials) have been reviewed.
Mesoporous materials can incorporate substances inside, as drug delivery
systems, but also exhibit an interesting surface chemistry promoting, for
instance, the formation of hydroxyapatite in contact with SBF. Tubular
structures, either organic or inorganic, provide confined spaces with sizes in
the nanometre range along one dimension, which allows the incorporation of a
variety of substances whose size is also limited by the host matrix. Similarly,
confined spaces can also be found in ‘‘bulk’’ materials. Herein, two classical
problems concerning both cationic and anionic non-stoichiometry have been
described. In both cases, KxWO3 and LaBaCuCoO51d, modification of the
coordination polyhedra happens, leading to recurrent intergrowths of different
basic structural sequences. All the above examples include structural problems
of local nature which require the use of HREM and associated techniques such
as local analysis by means of EDS and electron crystallographic methods, such
as CIP, for interpretation. In this sense, it is worth mentioning that the
advances in instrumentation (lenses, digital electronics, detector technology)
have allowed to solve complex phenomena associated with the new develop-
ments of materials chemistry but also the elucidation of different types of
structural imperfections such as twinning, intergrowths, Z-type faults, and
dislocations present in hitherto uncharacterized materials. On the other hand,
increasing the available resolution has been, since long ago, aimed through
improvements encompassing, again, either instrumental development of the
microscope but also with the use of electronic crystallography, which has had
enormous importance in order to obtain information from unstable substances.
Concerning instrumentation, the initial efforts were directed to higher acceler-
ating voltages and a few years ago to field emission source microscopes which
742 Chapter 44
provide higher coherence and the possibility of analyzing small regions. The
most recent improvements are due to the introduction of aberration correctors
which have provided interpretable resolutions under 0.1 nm at intermediate
voltages. This opens a promising future for structural knowledge.

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CHAPTER 45

In Situ Direct Observation at

Atomic Scale Twinning
Transformations and the
Formation of Carbon
Nanostructures in WC
PRATIBHA L. GAI,a,b,c C. C. TORARDId AND
E. D. BOYESb,c,e
a
Department of Chemistry, University of York, Heslington, York YO10
5DD, UK; b Department of Physics, University of York, Heslington, York
YO10 5DD, UK; c The York JEOL Nanocentre, University of York,
Heslington, York YO10 5DD, UK; d DuPont, Central Research and Develop-
ment, Wilmington, DE 19880-0356, USA; e Department of Electronics,
University of York, Heslington, York YO10 5DD, UK

1 Introduction
We report direct atomic resolution-in situ environmental transmission electron
microscopy studies of atomic level twinning transformations in tungsten car-
bide powders in reducing gas environments. Our results demonstrate that the
dynamic twin structural transformations play a direct role in the formation of
nano-tungsten and carbon nanostructures. We propose a model for atomic
arrangements of the reacting twin structures to explain the dynamic gas-carbide
interaction leading to the nanostructures.
The performance of materials is fundamentally governed by atomic scale
reactions under operating conditions. The dynamic atomic scale reactions
of carbides of transition metals under operating conditions are of great

745
746 Chapter 45
importance in heterogeneous catalysis, nanoelectronics devices and fuel cell
technologies.1,2 Active hexagonal tungsten carbides (WC) are employed as fuel
cell electrodes,1,3 hydrogenation catalysts4,5 and for applications in nanoelec-
tronic devices including as barrier layers5,6 and cutting tools.5 In addition, WC
systems are of interest as catalysts in a number of diverse reactions, including,
for example, the hydrogenation of benzene to cyclohexane,4 isomerization of
2,2-dimethylpropane,7 methanation,8 ammonia decomposition,9 ammonia syn-
thesis10 and as electrocatalysts in fuel cell technologies.3,11,12 The dynamic
nature of the carbide as a function of the reaction environment and temper-
ature is crucial in determining the activation and deactivation in the catalytic
reactions, the performance of fuel cell devices and electrical conductors. The
current understanding of the operation of WC, however, is based on ex situ
chemical studies which have considered only a perfect WC structure.1–13 A well-
ordered WC structure is uncommon as it is inherently a defective struc-
ture.11,14,15 In addition, obtaining insights into the behaviour of WC in these
reactions based on ex situ studies (whereby reacting samples are cooled to room
temperature (RT) and are removed from the reaction environment for charac-
terization) has been difficult, since ex situ studies often do not accurately
represent dynamic reaction conditions. Previous studies have not mentioned
atomic structural studies of defective WC in reaction environments despite the
fact that a number of technological reactions over WC, including fuel cell and
catalytic technologies, employ hydrogen containing gases. This has hindered
the understanding of the performance of WC.

2 Experimental Procedures
Spectrographically pure WC powders were obtained from Aldrich Chemical
Company, Inc., MI, USA and from other manufacturers. WC powders from
different manufacturers exhibited the same structural properties. WC particles
were dispersed in alcohol and supported on finely meshed, high purity titanium
as well as nickel microscope grids for in situ environmental transmission
electron microscopy (ETEM) studies. Crystallites extending over the edge of
a grid bar were selected for the study. The pioneering development of atomic
resolution in situ ETEM under controlled environments by Gai et al.,16–18
equipped with a reaction chamber inside the microscope, was used for direct
real-time imaging of dynamic gas–solid reactions at the atomic level. The
ETEM is capable of atomic resolution (B0.2 nanometers (nm)) under gas
pressures of a few mbar and reaction temperatures of up to 1000 1C . Gas–solid
reactions can be monitored in real time.16–20 The design16–18 of atomic resolution-
in situ ETEM by Gai and Boyes has been adopted by TEM manufacturers
(FEI)21 for commercial production and the resulting commercial instruments
are in use in academia and industry.22 Reduction experiments were performed
in the ETEM using very low doses of electron beam currents (below the
threshold for beam damage) in controlled, flowing 20% H2 in carrier He gas,
and in other reducing gases including methane and ethane, and at temperatures
In Situ Direct Observation at Atomic Scale Twinning Transformations 747
ranging from RT to B940 1C, to obtain dynamic reaction sequences in real
time.
Since a number of chemical reactions over WC employ hydrogen, this gas
was selected for our detailed studies. Calibration studies were carried out in the
ETEM on samples under the same experimental conditions without the elec-
tron beam (with the beam switched on for a few seconds only to record the final
state of the material), and the results were checked with the in situ data to
ensure no invasive beam damage. Measurements of reaction products under
similar conditions were performed on larger amounts of samples ex situ in a gas
reaction chamber connected to a mass spectrometer and used for the nano-
structural correlation. Reduction of the carbide was found to be slower below
450 1C and faster above this temperature.

3 Results and Discussion

WC particles exhibited extensive atomic level twin boundary defect structures
(Figure 1a). In the crystallography of simple structures, the twin has a lattice
which is a mirror of the host lattice.23 The twinning in the carbide is consistent
with the fact that structural homogeneity is rarely achieved in WC prepara-
tions.14,15
Figure 1b is an atomic resolution image of the twin boundaries in WC in the
(1 0 0) crystallographic orientation. The image reveals that the atomic twins
are along the [0 0 1] direction and lattice modulations along [0 1 0]. WC is
hexagonal (space group P-6m2), with a ¼ 0.2906 nm and c ¼ 0.2838 nm.14,15,24
In the hexagonal lattice, the 4 axes (hkil) of Miller-Bravais indices are abbre-
viated to (hkl), where i ¼
(h+k). Thus, (10
10) is the (1 0 0) crystallographic
orientation. The (0 0 1) lattice planar spacings of 0.28 nm and the (0 1 0) lattice
spacings of 0.25 nm are clearly resolved in the image. The lattice spacings (dhkl)
in the hexagonal structure were obtained by using the formula:25
2
ð1=dhkl Þ ¼ ð4=3Þðh2 þ hk þ k2 Þ=a2 þ ðl=cÞ2

Figure 1c shows an electron diffraction pattern of WC in (1 0 0), with the

main (0 1 0) and (0 0 1) reflections indexed. To exclude the possibility of three-
dimensional configuration for the atomic twins, we imaged complex bicrystal-
line WC grains. Figure 1d is an atomic resolution image of a bicrystalline WC
grain in (1 0 0) and (0 0 1) crystal projections denoted by A and C, respectively.
The image clearly demonstrates that the twin structures are present in (1 0 0),
but are absent in (0 0 1), thus establishing the planar nature of the twins.
We observed the same thin area of the WC sample in situ, in real time, under
dynamic reaction conditions of 20% H2/He at a pressure of B3 mbar, at
operating temperatures. The studies on both types of the support grids showed
the onset of reaction at B450 1C. Figure 2a shows atomic twin defects in the
sample at RT and Figure 2b shows the dynamic image recorded of the same
area which is reacted for B15 min at B450 1C. Figure 2b of the reacting WC
demonstrates the elimination of almost all of the atomic scale twin structures
748 Chapter 45

Figure 1 Atomic resolution image of (1 0 0) hexagonal WC. (a) Profuse twinning

observed in WC particles. (b) Atomic scale twin boundary structures along
the [0 0 1] direction with lattice modulations along [0 1 0]. (c) Electron
diffraction pattern of (1 0 0) WC. 001 and 010 reflections are indexed. (d)
Atomic resolution image of a complex bicrystalline WC grain, showing the
presence of twin defects in (1 0 0) but their absence in (0 0 1) orientation,
denoted by A and C, respectively. The image clearly demonstrates the
planar nature of the atomic twins.

and the transformation to tungsten metal. The presence of the metal was
confirmed by electron diffraction (Figure 2c) and by compositional analysis
using electron-stimulated energy dispersive X-ray (EDX) spectroscopy in the
electron microscope. Figure 2c shows the emergence of {1 0 0} reflections
(indicated by arrows) due to cubic a-W (with a ¼ 0.316 nm) in the parent
crystal. Complete ordering was observed after B4 h.
Further reduction up to 650 1C showed the presence of W nanoparticles,
amorphous carbon, graphitic carbon (both as sheets and in onion shaped
In Situ Direct Observation at Atomic Scale Twinning Transformations 749

Figure 2 Atomic resolution in situ ETEM of real-time reduction of the same thin area
of WC sample in 20% hydrogen/He gas: (a) room temperature; (b) dynamic
reaction at 450 1C, indicating the elimination of almost all of the twins; (c)
dynamic electron diffraction pattern of (b) indicating the emergence of {1 0 0}
cubic tungsten reflections (arrowed).

rings). At higher temperatures of 850–900 1C, carbon nanostructures, including

with contrast indicative of single wall carbon nanotubes (CNTs) were observed
in a few thin areas of the specimen. The growth of CNTs was observed to be
faster on nickel grids. The precise role of the influence of the grids on the rate of
the reaction is yet to be understood. These results are summarized in Figure 3.
Figure 3a shows WC in 20% H2/He at 650 1C showing W nanoparticles and
amorphous carbon, Figure 3b shows graphite rings, W nanoparticles, a small
number of long CNTs and amorphous carbon at 900 1C. Figure 3c shows
an enlarged area of (b). Figure 3d shows more CNTs after about 5 h. The
750 Chapter 45

Figure 3 In situ ETEM studies of the thin area of WC in 20% H2/He at 3 mbar: (a) at
650 1C showing amorphous carbon and tungsten particles; (b) the formation
of what appear to be a few long single wall CNTs at 900 1C with W
nanoparticles and graphite (onion shaped) rings (sample supported on nickel
grid); (c) enlarged area of Figure 3b; (d) more CNTs after 5 h (the individual
tube spacing is about 1.4 nm).

formation of CNTs in these experiments is consistent with the production of

CNTs on the surface of a-silicon carbide single crystal wafers.26 The findings
are also consistent with reports of chemical vapour deposition studies per-
formed by flowing propylene or acetylene gas environments over Ni which
showed the formation of single wall CNTs above 700 1C.27
Figure 4a shows the structure of WC in (1 0 0) crystal projection. The carbide
adopts a hexagonal crystal structure with nonmetallic carbon atoms in the
In Situ Direct Observation at Atomic Scale Twinning Transformations 751

Figure 4 (a) Structural schematic of hexagonal WC in (1 0 0) orientation (a ¼ 0.2906

nm and c ¼ 0.2838 nm). W atoms are shown in green. Carbon atoms (in
black) occupy interstitial positions. (b) Structural schematic of WC in (0 0 1).
(c) Projection of one layer of the WC structure on (1 0 0), showing a possible
twin boundary structural model along [0 0 1] (arrowed), consistent with the
experimental observations. Carbon atoms gathered in the defects react with
hydrogen and diffuse out. This is accompanied by readjustments of the
atoms to create the metal structure.

interstitial positions between the metal atoms. Twin structures are believed to
form in carbide grains during their synthesis, accommodating the disorder and
re-order of the crystal structure during the grain growth to minimize the grain
boundary energy.23 Although precise mechanisms of the WC transformation
are not understood, we propose a possible structural and compositional model
for the atomic twin boundary structure along [0 0 1], based on our in situ
electron microscopy observations of the formation of nano-W and carbon
nanostructures . This is shown in Figure 4b in the projection of one layer of the
WC structure on (1 0 0) with carbon atoms gathered in the boundaries. We
752 Chapter 45
believe that in reducing hydrogen containing environments, WC with atomic
twin structures is thermodynamically unstable and there is a strong driving
force for the reduction of the carbide. Relatively loosely bound carbon atoms in
the twin structures interact with the H2 gas and diffuse out of the surface. This
is accompanied by readjustments of atomic positions to produce a stable
energy configuration of W and carbon nanostructures. At higher temperatures,
any methane formed is expected to decompose over the nanoparticles.

4 Conclusions
On the basis of our newly discovered dynamic atomic scale interactions
between a reactive tungsten carbide and reductive gas environments, we con-
clude that the reaction kinetics of the carbide are altered by diffusion processes
along atomic twin boundaries. In situ observations demonstrate that dynamic
atomic twin structural transformations in WC play a key role in the single step
production of carbon nanostructures and tungsten metal. The studies have
implications in the production of carbon structures and in understanding the
chemical reactivity of the carbide in commercially important catalysis, energy
and nanoelectronics technologies. We further speculate that similar atomic
level interfacial transformations are likely in other transition metal carbides as
well as in transition metal nitrides.

Acknowledgements
The authors thank L.G. Hanna, T. Borecki, C.E. Greer and W.J. Marshall of
DuPont for technical assistance, the University of York, Yorkshire Forward,
the EU and JEOL Ltd for support for the Nanocentre.

References
1. S.T. Oyama, The Chemistry of Transition Metal Carbides and Nitrides,
Blackie Academic and Professional, London, UK, 1996.
2. G.S. Ranhotra, A.T. Bell and J.A. Reimer, J. Catal., 1987, 108, 40.
3. B. Vidik, J. Lematre and L. Leclerque, J. Catal., 1986, 99, 439.
4. J.S. Lee, M. Yeom, K.Y. Park, I. Nam, J.S. Chung, Y. Kim and S. Moon,
J. Catal., 1991, 128, 126.
5. H. Bohm, Electrochim. Acta., 1970, 15, 1273.
6. D.V. Baxter, K. Coulson, M. Chisholm, S. Chuang and C.D. Minear,
Chem. Commun., 1998, 1447.
7. R.S. Williams, J. Linee, T. Tsai and J.H. Pugh, Mat. Res. Soc. Symp. Proc.,
1986, 54, 335.
8. R. Levy and M. Boudart, Science, 1973, 181, 1477.
9. S.T. Oyama, J. Catal., 1992, 133, 358.
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10. M. Boudart, S.T. Oyama and L. Leclerque, Proc. 7th Int. Cong. Catal.,
1980, 1, 578.
11. Gmelin Handbook of Inorganic and Organic Chemistry, W. Suppl. A5b, 137,
Springer-Verlag, 1991.
12. T.D. Massalski, Am. Soc. Metals, 1986, 1–2, 599.
13. H. Okamoto, G. Kawamura, A. Ishikawa and T. Kudo, J. Electrochem.
Soc., 1987, 134, 1645.
14. P.N. Ross and P. Stonehart, J. Catal., 1977, 48, 42.
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B105, 10037.
16. P.L. Gai and K. Kourtakis, Science, 1995, 267, 661.
17. E.D. Boyes and P.L. Gai, Ultamicroscopy, 1997, 67, 219.
18. P.L. Gai, Adv. Mater., 1998, 10, 1259.
19. P. Crozier, R. Sharma and A. Datye, Microsc. Microanal., 1998, 4, 228.
20. P.L. Gai and E.D. Boyes, Electron Microscopy in Heterogeneous Catalysis,
Institute of Physics Publishers, UK and USA, 2003.
21. FEI/Philips Company, News Views Dev. SEM TEM, Scope, 1998, 9, 11.
22. T.W. Hansen, J. Wagner, P.L. Hansen, H.T. Topsoe and S. Dahl, Science,
2001, 294, 1508.
23. A.H. Cottrell, Introduction to Metallurgy, Arnold Publishers, UK, 1971.
24. Crystal Data Determinative Tables: Inorganic Compounds, ed. H.M. Ondik
and A.D. Mighell vol. 4, National Bureau of Standards (USA) and JCPDS
International Centre for Diffraction data, 1969, 99.
25. P.B. Hirsch, A. Howie, R. Nicholson, D.W. Pashley and M.J. Whelan,
Electron Microscopy of Thin Crystals, Kruger Publishers, New York, USA,
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CHAPTER 46

A Survey of the Bi2O3–MoO3

Binary System
DOUGLAS J. BUTTREY
Center for Catalytic Science and Technology, Department of Chemical
Engineering, University of Delaware, Newark, DE 19716, USA

It is a pleasure and an honour to have the opportunity to provide a contribu-

tion to this volume in honour of Sir John Meurig Thomas on the occasion of
his 75th birthday. I was introduced to John by C.N.R. Rao in the summer on
1982 at a Gordon Conference on Solid State Chemistry held in Plymouth, New
Hampshire. In 1984, with funding from Bob Grasselli’s catalysis group at the
Standard Oil Company of Ohio (SOHIO), John invited me to join his group in
Cambridge as a postdoctoral fellow. Naturally, my work with John involved
the characterization of bismuth molybdates by transmission electron micro-
scopy. Our papers together with David Jefferson on the fluorite commonality in
bismuth molybdates and on the new phase, Bi38Mo7O38, came about from that
period. John’s contagious enthusiasm for research and mentoring nature was
as truly inspiring then as it is today. My wife and I had a wonderful 19 month
stay in Cambridge, and our time spent there with John and his lovely wife
Margaret will always be treasured. It has been our good fortune to have had
numerous opportunities to meet with John through the intervening years and
with increasing frequency, a trend that we hope to continue for years to come.

1 Introduction
Bismuth molybdates have been extensively studied for about four decades, with
most of the early effort directed at catalytic applications for selective oxidation
and ammoxidation of olefins.1–5 Today, multicomponent derivatives of these
materials remain as the dominant catalysts for propene-fed conversions.
Incorporation of a variety of additional elements into the bismuth molybdates,
such as Fe, Ce, K and V, has a promotional effect, but the underlying structure
and chemistry is fundamentally tied to the parent bismuth molybdate system.
754
A Survey of the Bi2O3–MoO3 Binary System 755
Selectivities as high as about 95% can be achieved for conversion of propene to
acrolein and in excess of 90% for propene to acrylonitrile.5 Demand for
acrolein is driven by its use as an intermediate in the synthesis of various
secondary products such as glycerin, methionine and 1,3-propanediol, as well
as direct use as a biocide. Annual production of acrylonitrile worldwide has
grown steadily since 1960 and now approaches a kilogram for every person on
earth6! The enormous market for acrylonitrile is tied to use in production of
synthetic fibres, ABS and SAN plastics, and other miscellaneous end products.
While the interest in catalytic issues continues, more general interest and
potential for other applications has increasingly broadened the scope of inves-
tigation. Interest in the exceptional oxide ion conductivity of bismuth moly-
bdates,7–10 which was apparent early on in catalytic studies using 18O labeling,11
has become quite significant in the last 5 years or so. These efforts are ultimately
aimed at potential fuel cell applications, though concerns about stability will
have to be addressed. Applications in conductance-based sensors for ethanol
and other organics have been driving another segment of the research commu-
nity to explore these materials.12–15 Still others have been motivated by lumi-
nescent properties16 and acousto-optic behaviour.17–19
The Bi2O3
MoO3 phase diagram includes many phases and has been the
subject of several studies.20–23 It is well established for Bi/Mo r 2.6, but
remains only partially characterized for the more Bi-rich compositions, and
previously unknown phases have been identified recently.24 In this chapter, an
overview of the structure and properties of this system, and the trends across
the phase diagram, will be provided.

2 Selective (Amm)oxidation and the Mars–van

Krevelen Mechanism
The commercialization of processes for selective oxidation and ammoxida-
tion of propene began at SOHIO (now British Petroleum) in the 1950s with
the discovery of a silica-supported bismuth phosphomolybdate catalyst,
Bi9PMo12O52, for the acrolein process.2 The corresponding ammoxidation
process followed with an added step involving acrolein ammoxidation over
MoO3. Further developments led to a single-step ammoxidation process and
ultimately to the commercialization of this technology by SOHIO with bismuth
molybdate catalysts in the early 1960s, based on developments led by Grasselli
and Barrington.4 This SOHIO process remains dominant in the manufacture of
acrylonitrile today.
The mechanisms of both selective oxidation and ammoxidation of propene
over bismuth molybdates have been extensively studied. Abstraction of an
a-H to form a symmetrical allylic intermediate is the rate-determining step
and involves a lattice oxygen adjacent to bismuth (III). This was proposed
on the basis of isotopic labeling experiments by Adams and Jennings24,25 and
was subsequently confirmed in other studies.4 Oxygen as O2
bound to Mo
in the selective oxidation case provides for oxygen insertion into the allylic
756 Chapter 46
2

intermediate and, similarly, NH at a surface Mo site is responsible for
nitrogen insertion in the case of ammoxidation.4,24–26
While the propene is oxidized, the catalyst is concomitantly reduced.
Reoxidation of the catalyst to complete the cycle is a crucial part of the overall
catalytic cycle. Decoupling of this reoxidation step from the surface site at
which reactants adsorb and react with the catalyst in a sacrificial manner is of
central importance. The description of the general nature of this decoupled
mechanism for reduction and reoxidation is attributed to the Dutch workers
Mars and van Krevelen (M–vK) as reported in their landmark paper27 in 1954.
The M–vK mechanism involves a dynamic mass balance in which oxygen
vacancies created at the active site during reaction are replaced by incorpora-
tion of O2 into the lattice at a different surface site. The net result is spatially
separated catalyst reduction and reoxidation steps in which oxygen vacancies
are created and eliminated, respectively. The key to efficient operation of such a
mechanism is adequate diffusion of lattice oxygen (or equivalently, diffusion
of the vacancies) so that an overall steady state process is maintained while co-
feeding the catalyst oxidant (oxygen) and reductant (propene) without destroy-
ing the catalyst. The M–vK mechanism has been found to play a role in many
catalytic oxidation processes.
The bismuth molybdates and their multicomponent counterparts,5 with the
appropriate composition and structure, provide each of the necessary require-
ments considered above, i.e. the site for abstraction of the a-H, the site for
oxygen (or nitrogen) insertion, dynamic reoxidation at the catalyst surface
by O2, and facile diffusion of lattice oxygen. To better understand the role of
composition and structure, and perhaps to contemplate prospects for rational
design of new catalysts related to those presently in use, it is helpful to
understand the bismuth molybdates as a family and to consider which ones
are active and selective as compared with those that are not. Though there have
been many studies of this system and multicomponent variations over the last
40 years, our understanding of the crystal chemistry and the overall phase
diagram has improved significantly in recent years.

3 The Bi2O3
MoO3 Phase Diagram Revisited

3.1 Cataloguing the Phases
At present, there are at least 16 phases reported in the Bi(III)–Mo(VI)-O system.
Arranged from Mo-rich to Bi-rich compositions, these are: a-Bi2Mo3O12,17,28,29
b-Bi2Mo2O9,30,31 g(L)-Bi2MoO6,32–35 g(I)-Bi2MoO6,33,35–37 g(H)-Bi2MoO6,33,38,39
d(L)-Bi26Mo10O69,40 d(H)-Bi26Mo10O69,41,42 Bi8Mo3O21,43 Bi14Mo5O36,43
L-Bi6Mo2O15,44 H-Bi6Mo2O15,43,44 Bi10Mo3O24,45 Bi21Mo4O43.5,46 Bi38-
Mo7O78,47,48 L-Bi14MoO2449, and H-Bi14MoO24.21,48,49 Updating previous
models for the phase diagram20–23 to include those phases that have only recently
been identified leads us to propose the updated version shown in Figure 1. Low-
temperature phases with compositions in the range 8/3 r Bi/Mo r 10/3 were
A Survey of the Bi2O3–MoO3 Binary System 757

Figure 1 Phase diagram for Bi2O3 – MoO3. The bismuth-rich region is not well studied;
phase boundaries are based on findings from various studies.20–24,28–49

very recently described as belonging to a homologous series43 with the form

Bi2n14MonO6(n11) with n ¼ 3, 4, 5, 6. This list may not yet be complete since the
most Bi-rich part of the phase diagram has not been exhaustively explored; it is
possible that there are other phases yet to be found, most likely in the range 38/
7oBi/Moo14/1. Ling et al.50 report increasingly disordered variants of Bi38-
Mo7O78 in this range as the Bi/Mo ratio is increased in specimens prepared with a
final annealing at 900 1C.
Among the 16 phases, only three are recognized as active and selective for
propene (amm)oxidation. These are a-Bi2Mo3O12, b-Bi2Mo2O9 and g(L)-
Bi2MoO6, all of which are positioned towards the Mo-rich side of the composi-
tional range. The role of composition and structure in distinguishing these three
catalytic phases from the larger group is an important issue to be addressed in
the context of the requirements we associate with the catalytic mechanism.
Similarly, the attributes of other phases will be considered in terms of the
properties they exhibit and opportunities for applications.

3.2 Structural Evolution

The crystal structures of the a-, b- and g(L)- phases were solved to a reasonable
level of certainty several decades ago, with improvements in the details of each
resolved in more recent years using more advanced approaches. Even with
single crystals, structural details can be difficult to work out in such structures
using X-ray methods due to the dramatic difference in scattering from bismuth
(Z ¼ 83) versus oxygen (Z ¼ 8). Neutron powder diffraction (NPD) has proved
very useful in more recent years for elucidating the finer details of these
structures.
758 Chapter 46
All but two of the bismuth molybdate phases have structures that are easily
recognized as fluorite derivatives. The two exceptions are the low- and inter-
mediate-temperature polymorphs of Bi2MoO6, which are n ¼ 1 Aurivillius-type
forms and are layered structures with the general formula Bi2n
1MonO3n11. The
common fluorite building block of the majority of phases was recognized over
two decades ago54 and remains true now, even with the addition of many newly
characterized phases. Fluorite-type oxides ideally have compositions of the
form MO2, such that the average metal valence should be +4. In the case of
oxidized bismuth molybdates, the metal valences are fixed at +3 for bismuth
and +6 for molybdenum. Those with fluorite-type frameworks must be non-
stoichiometric in either the metals or oxygen if Bi/Mo a 2. If Bi/Moo2, then
there are metal vacancies present and if Bi/Mo 4 2, then the composition must
be oxygen deficient with respect to fluorite. a-Bi2Mo3O12 and b-Bi2Mo2O9 are
the only phases with Bi/Moo2; consequently, 1/6 of the metal sites of a and 1/9
of the metal site of b are vacant. g(H)-Bi2MoO6 is the only fluorite form with an
average metal valence of +4, and hence it is a stoichiometric fluorite derivative.
On the bismuth-rich side, oxygen nonstoichiometry relative to fluorite seems
to be manifest as changes in the intrinsic coordination numbers, rather than
involving identifiable oxygen vacancies. The fluorite forms are readily identified
using powder XRD or selected area electron diffraction (Figure 2); the fluorite
subcell gives rise to intense reflections characteristic of (distorted) FCC with a
subcell lattice constant near 5.7 Å. The superstructure representing the true unit
cell is then evident from the weaker reflections. In the case of Bi26Mo10O69, the
fluorite substructure is modified somewhat by a slight periodic shearing of the
cation arrangement with every half-unit cell along c. This involves a shift in
isolated MoO4 tetrahedra42 accompanied by some statistical disorder in iso-
lated Bi columns, while the larger Bi columns remain in an intact fluorite
pattern. Isolated Mo tetrahedra are readily envisioned as derived from an
idealized fluorite parent by allowing four of the eight oxygens from the first
coordination sphere to relax from ideal distances of about 2.45 Å to typical
tetrahedral Mo–O distances of roughly 1.75 Å.
A further generalization becomes apparent when the cation distributions are
compared across all of the fluorite derivatives. The Bi sites tend to cluster into
columns that extend continuously in one or more directions through the crystal
lattice (Figure 3). In the phases having Bi/Moo2, it is these bismuth columns
that contain the required metal site vacancies. The borders of these Bi columns
are surrounded by ‘‘sheets’’ of isolated, and often distorted, MoO4 tetrahedra,
and often these tetrahedra appear as pairs.

3.2.1 Polymorphism in Bi2MoO6

The low-temperature polymorph of Bi2MoO6 is a naturally occurring but
scarce mineral known as koechlinite. The structure of the Aurivillius form is
characterized by alternating {MoO4}2
layers and {Bi2O2}21 bilayers that
are stacked along the b-axis. The {MoO4}2
layers are usually described as
octahedral, but are severely distorted due to the second-order Jahn–Teller
A Survey of the Bi2O3–MoO3 Binary System 759

Figure 2 Representative selected area electron diffraction patterns from several of

the bismuth molybdates. (a) a-Bi2Mo3O12 [201], (b) a-Bi2Mo3O12 [100],
(c) b-Bi2Mo2O9 [110], (d) b-Bi2Mo2O9 [100], (e) g(H)-Bi2MoO6 [100], and
(f) g(H)-Bi2MoO6 [301]. The most intense fluorite-like reflections give the
expected nearly square pattern for the {100}F subcell and ‘‘O2-diamond’’
pattern for the {110}F subcell patterns; weaker superlattice reflections pro-
vide evidence of the true unit cells and proper zone assignments.
760 Chapter 46

(a) (b)

[201]

[010] b

a c
(c) (d) c

a
c

a

[010]
 (H)
[010]

(f)
(e)

[001]
a
a
 (H) [001]
b b

Figure 3 Structural views of some of the fluorite-related bismuth molybdates: (a)

a-Bi2Mo3O12 [010] ‘‘scheelite projection’’, (b) a-Bi2Mo3O12 [201] principle
fluorite projection, (c) b-Bi2Mo2O9 [010] projection, (d) d(H)-Bi26Mo10O69,
(e) g(H)-Bi2MoO6 [001] ‘‘Latin cross’’ projection, (f) e-Bi38Mo7O78 proposed
cation arrangement in the [001] projection. Note that in each case, the
fluorite subcell axes are oriented along the chosen true-cell zone axis as well
as vertically and horizontally in the projections so as to produce the
approximately square pattern of metal sites expected in projection from
the fluorite substructures. Bi (yellow), Mo polyhedra (blue), O outside
polyhedra (red), metal vacancies (grey).

distortion characteristic of small and highly charged d0 octahedral transition

metals. This ‘‘out-of-centre’’ distortion serves to lower the energy of vacant 4d
orbitals such that they can interact with filled oxygen 2p states. The distortion
produces four short (1.74–1.90 Å) and two adjacent long Mo–O bonds (2.21
and 2.29 Å). One can equally well envision the four short bonds as being
in a distorted tetrahedral configuration, which would then leave them as
isolated rather than corner-shared. Figure 4 shows the [100] projection of
g(L)-Bi2MoO6 using the conventional distorted octahedral view and the
corresponding ‘‘isolated tetrahedral’’ counterpart; room temperature atomic
A Survey of the Bi2O3–MoO3 Binary System 761

Figure 4 Comparison of (a) conventional corner-shared ‘‘4+2’’ distorted octahedral

rendering and (b) ‘‘isolated’’ distorted tetrahedral rendering of g(L)-Bi2MoO6
in the [001] projection. Bi (yellow), Mo polyhedra (blue), O outside polyhedra
(red).

coordinates used here are the same in both views. The clear distinction between the
Aurivillius packing arrangement and the fluorite forms is in the spatial relation-
ship between the molybdenum layer and the bismuth interfaces immediately
above and below it, which are perovskite-like rather than in an FCC-like pattern.
Polymorphism in g-Bi2MoO6 has been the subject of considerable contro-
versy,33,35–37,51–53 associated with the transition between the g(L) and g(I)
forms. This controversy is associated with the subtle nature of the reversible
second-order g(L) 2 g(I) transition. Several studies based on combined XAS
with XRD51 and Raman spectroscopy54 have suggested that this transition is
associated with a change in the strong molybdenum octahedral distortion such
that it approaches tetrahedral coordination on heating; however, temperature-
dependent NPD refinements35 show that while the coordination of moly-
bdenum polyhedra does evolve significantly, this is not a simple progressive
shift from distorted octahedral towards distorted tetrahedral coordination. In
fact, the neutron and X-ray diffraction data do show an incommensuration
with diminishing amplitude with increasing temperature on approach to the
g(L) - g(I) transition,35 disappearing above the transition temperature. These
seemingly different descriptions might be reconcilable if the incommensuration
is associated with long-period variations in the local geometry of tilts of the
distorted MoOx polyhedra. Powder refinements based on the Aurivillius subcell
would reflect an average polyhedral environment, but XAS and Raman would
reflect local geometries. Perhaps the tilts modulate to produce the long-period
incommensuration.
The high-temperature polymorph, g(H), occurs above a first-order recon-
structive transition at 604 1C. This polymorph is a fluorite derivative charac-
terized by a 3  4  1 fluorite supercell with isolated tetrahedra surrounding
bismuth-rich columns having a ‘‘Latin cross’’ pattern39 consisting of 14 bis-
muth sites, as well as an isolated bismuth column, when viewed in the [001]
projection (Figure 3e).
762 Chapter 46

3.2.2 The Cation Deficient Structures: a-Bi2Mo3O12

and b-Bi2Mo2O9
The traditional way of viewing the a-phase has been to consider it as a defective
(cation-deficient) scheelite rather than fluorite, and to view it down the [010]
zone (Figure 3a), which represents the catalytically active surface; however, it is
important to recognize that the scheelite family, based on the mineral CaWO4,
is a subset of the broader family of fluorites. Rotating the view by 901 about the
principle fluorite-type directions reveals that a-Bi2Mo3O12 is in fact comprised
of pairwise Bi columns and vacancies (see Figure 3) extending along the [201]
(Figure 3b) and the ½10 1 (not shown, but very similar in appearance to [201])
directions of the true unit cell.54 Note that cation vacancies, represented as grey
spheres, are dispersed within zig-zaged strings of Bi sites as can be seen running
vertically in Figure 3a; every third metal site is vacant in the sequence.
The most obvious Bi columns in the b-phase extend in the [010] direction with
a square cross-section of four bismuths when viewed in projection (Figure 3c);
again vacancies are distributed among the Bi sites in these columns. Rotating by
901 along either principal fluorite subcell axis reveals isolated Bi columns
extending indefinitely in the two perpendicular directions.
An important distinction between a-Bi2Mo3O12 and most of the other
fluorite derivatives is that all lattice oxygen sites bridge between molybdenum
and bismuth sites. In b-Bi2Mo2O9, g(H)-Bi2MoO6, and others with large cross-
section bismuth columns, some oxygen sites bridge between adjacent bismuth
sites and are not involved in coordinating molybdenum. This may have cata-
lytic significance in that these oxygens bound only between Bi sites are the ones
that form strong covalent bonds to Bi.

3.2.3 The Bismuth-Rich Phases

Bi26Mo10O69 has enlarged Bi columns with a symmetrical cross (‘‘rosette’’)
pattern of 12 Bi sites (Figure 3d), which can be described as [Bi12O14]N
columns.40–42,55,56 This column pattern is very similar to the ‘‘Latin cross’’
configuration in g(H) (Figure 3e). Another similarity with other fluorite deriv-
atives is that Bi26Mo10O69 has isolated Bi columns. As stated earlier, all of the
Bi-rich phases with Bi/Mo 4 2 are expected to contain oxygen vacancies
relative to the parent fluorite ideal. Based on ideal fluorite, this phase would
ideally have 72 oxygens, so in this sense it is deficient by three oxygens per
formula unit from this perspective. On the other hand, the refined structure
indicates an ‘‘ideal’’ stoichiometry of Bi26Mo10O68 based purely on coordina-
tion environments, so from this perspective it is superstoichiometric by one
oxygen. The actual stoichiometry seems to truly be Bi26Mo10O69 since there is
no indication of unpaired electrons associated with MoV, as would be required
with only 68 oxygens. The nature of the stoichiometry dilemma has been the
subject of a number of studies,42,55,56 but as yet there appears to be no clear
understanding. The possibilities either involve an interstitial oxygen site with
partial occupancy,42 solid solubility of Bi on Mo tetrahedral sites55 (which
A Survey of the Bi2O3–MoO3 Binary System 763
alters the metal stoichiometry), and a combination of bismuth vacancies and
minor substitution of Bi for Mo on tetrahedral sites.56 Vannier et al.41 and Vila
et al.43 have noted that the [Bi12O14]N ‘‘rosette’’ pattern is a common feature of
a number of other mixed metal bismuth-containing oxides and consider the
g(H)-phase to contain such a rosette plus two additional Bi sites (in [001]
projection) to then complete the Latin cross pattern. In another paper, Vila
et al.45 have proposed that Bi10Mo3O24 contains wavy bismuth layers rather
than columns; however, it appears that full refinement has not yet been
achieved. This is the n ¼ 3 member of the homologous series Bi2n14Mon
O6(n11). This low-temperature series consists of fluorite-based monoclinic su-
percells, all of which have the unique axis parallel to a principal fluorite
direction in which the cell constant, b, is approximately 5.64 Å, i.e. based on
a single fluorite subunit in this direction, similar to the unique axis in g(H) and
d(H). The c and b cell parameters evolve systematically as n increments,
generating 13-fold, 16-fold, 19-fold and 22-fold superstructures,43 while a and
b remain the same. Figure 5 shows the relationship (in projection) between the
fluorite subcell and the supercells for the homologous series, as well as g(H) and
d(H) for comparison.
A likely cation distribution for Bi38Mo7O78 is presented in Figure 3f, based
on a combination of high resolution images47 and structure factor considera-
tions based on X-ray diffraction intensities; unfortunately a full refinement

chs6 Bi8Mo3O21
21 (n=6)
Bi14Mo
Bi o5O36 (n=5)
5
chs5
L-Bii6Mo2O15 (n=4)
(n
n=4)
chs4 Bi100Mo3O24 (n=3)
Bi (n=
n 3)
(H)-Bi
(H)-B
Bi26Mo
o10O69
chs3
 (H)
(H)-Bi
)-Bi2MoO
MoO6

bγ

cF
cδ
aF cF
ahs aδ aγ
aF

Figure 5 Comparison of unit cell projections of the fluorite subcell with various
bismuth molybdates having a single fluorite unit repeat normal to the
drawing.
764 Chapter 46
remains elusive. In this model representation, the oxygen coordinates have been
set somewhat arbitrarily pending refinement. The Bi columns are readily
apparent in multiple directions and with different geometries. In some direc-
tions the columns can be quite large in cross-section,47,54 but none of these
column projections seem to show the rosette motif.
The low- and high-temperature forms of Bi14MoO2421,48,49 seem to break
from the above trend in the sense that there is not enough molybdenum content
to create sheets or even threads of continuity through the structure. The low-
temperature form is monoclinic and transforms at about 22 1C to a closely
related tetragonal variant. These are isomorphous with low- and high-tempera-
ture forms of Bi14WO24,48,49,57 and are quite closely comparable to the defect
fluorite end member, d-Bi2O3, one of the best oxide ion conductors known. The
molybdenum sites are in the form of isolated tetrahedra that exhibit orienta-
tional disorder about high symmetry positions in the structures. The low-
temperature form has a reduced set of statistical orientations compared with
the high-temperature form.49

4 The Stereochemical Influence of Bi Lone Pairs

4.1 General Considerations
Bi(III) has the electronic configuration [Xe]4f145d106s2. The 6s2 lone pair in
Bi(III), as well as in Tl(I), and Pb(II), plays an important role in terms of both
structure and properties because of its stereochemical and steric influence. This
steric effect contributes to distortions characteristic of materials containing
elements in N-2 states, where N is the group number. The commonly observed
asymmetry has been traditionally explained as arising from mixing of the 6s
atomic states with the unoccupied higher-energy 6p states near the Fermi level
to produce a filled 6s–6p hybridized orbital, which is the sterically active and
chemically inert lone pair. One ideally expects to find MX3E geometry, where
M is the metal, X the ligand, and E the lone pair. This classical view is at odds
with the fact that 6s electrons are quite relativistic, which increases separation
in energy between the 6s and 6p states58–60 and argues against simple hybrid-
ization. While oxides consistently exhibit strong steric effects from the lone
pair, other coordinating ligands do not always produce such asymmetric sites
with 6s2 species. The example of rocksalt-structured PbS with a perfectly
symmetric Pb(II) site is often considered as a case in point, for which the lone
pair does not distort the local environment61; however, a-PbO does exhibit
strong asymmetry due to the lone pair. Likewise, TlF has a stereochemically
active lone pair, but TlCl and TlBr do not show asymmetry.62 Ligands clearly
influence the symmetry of the nonbonded pair.
In a recent combined XPS and XES study, Payne et al.63 show clear evidence
for O2p ligand interactions mediating the mixing of 6s and 6p metal states in
both a-PbO and a-Bi2O3. This study confirms that rather than being a chemi-
cally inert entity, the lone pair can be significantly influenced by coordinating
A Survey of the Bi2O3–MoO3 Binary System 765
ligands. They also show that the dominant contribution from the Bi 6s partial
density of states is at the bottom of the valence band, rather than near the
Fermi level as had previously been widely assumed to rationalize the traditional
metal hybridization argument. It is instead the O 2p states that are at the top of
the valence band, and these serve to mediate hybridization of 6s and 6p bismuth
states.
In the bismuth molybdates, the lone pairs are widely believed to be important
for the rate-determining initial a-H abstraction step in olefin selective oxidation
and ammoxidation.1–6 The mixing of O 2p character with the Bi 6s and 6p
states must surely have important consequences for our understanding of
the chemical influence of the Bi(III) lone pair on the a-H abstraction step in
olefin oxidation, as well as on the nature of structural distortions. Long ago,
Andersson64,65 pointed out that the effective volume occupied by the lone pair
in oxides is similar to that of an oxide ion, so the lone pair steric effect can be
similar to that of an extra ligand. For this reason, diffusion of lattice oxygen
is strongly influenced by lone pair orientation, as in the case of d-Bi2O3.66–68
What is less obvious is how the hybridization with O 2p states enhances the
a-H abstraction, and more specifically, which oxygen site(s) is (are) directly
involved.

4.2 Locating the Lone Pairs

Lone pair orientation can be inferred from reliable structural refinement data,
since the electron–electron repulsion between lone pairs and between lone and
bonded pairs is significant. The key issue is that the oxygen coordinates must
be confidently determined in order to assess orientation, which means that
neutron data are preferred for adequate structure refinement. Bond valence
analysis69 can be used to obtain valence vectors70,71 at the Bi sites. The valence
vector should point in a direction directly opposite to the direction in which the
lone pair is oriented. Such an analysis applied to b-Bi2Mo2O9 and g(H)-
Bi2MoO6 shows that the lone pairs clearly point in directions that perpendic-
ularly fan outwards from the larger Bi columns for those Bi sites that are
immediately adjacent to Mo tetrahedra (Figure 6).
The Bi sites confined to isolated (single site cross-section) columns have very
small valence vectors with essentially zero component along the column axis.
This may result from statistical variations in lone pair orientation, resulting
in diffraction evidence that averages the environment perpendicular to the
column, or may be indicative of a symmetric lone pair state. If the lone pair
is asymmetric in the isolated columns, then the adjacent Mo tetrahedra
should show local disorder, or there could be an incommensurate modula-
tion of orientations. In either case, anomalous oxygen thermal parameters in
refinements should reveal this. Because of the larger numbers of parameters in
Rietveld refinements of these structures, the usual approach has been to use
a single isotropic thermal parameter for all oxygens, which would mask the
disorder.
766 Chapter 46

Figure 6 Lone pair orientation in a-Bi2Mo3O12, b-Bi2Mo2O9, g(L)-Bi2MoO6 and

g(H)-Bi2MoO6. Yellow arrows indicate the locations of [201] and [10-1] Bi
channels in a-Bi2Mo3O12. Oxygens opposite the lone pair vectors have bond
valence sums that indicate overbonding. Note: For a-Bi2Mo3O12, the col-
umns are paired as was shown for the [201] zone in Fig. 2(b). For clarity,
only single Bi rows are shown in the half unit cell [010] projection above; the
compliment to each of these rows in the next layer up/down (i.e. not shown)
would have the lone pairs pointed in the antiparallel directions. Bi (yellow),
Mo polyhedra (blue), O outside polyhedra (red), metal vacancies (grey).

In the g(H)-phase, there are yet another set of Bi sites, namely those within
the Latin cross columns that are fully surrounded by other Bi sites. These sites
have the lone pairs oriented nearly parallel with the column axis, except for
slight off-axis canting.39 Evidence for similar lone pair arrangements is found
internal to the large [Bi12O14]N columns in Bi26Mo10O69 and substituted
variants,56,57,72 and is readily confirmed by valence vector analysis on our
NPD refinement results for Bi26Mo10O69.42
In the case of a-Bi2Mo3O12, the lone pairs are somewhat more difficult to
analyze. There are two crystallographically distinct Bi sites in the a structure.29
It should be noted that the Mo polyhedra are sometimes described as five- or
six-coordinate, but with four short Mo–O bonds (ca. 1.65–2.05 Å) and one or
two longer bonds (ca. 2.2–2.5 Å); we will ignore the distant oxygen(s) and treat
these as distorted tetrahedra for the present discussion. Applying valence vector
A Survey of the Bi2O3–MoO3 Binary System 767
29
analysis to the refined coordinates from the study of Theobald et al., we find
that the Bi(1) lone pair points nearly parallel to [101], adjacent to Mo(3) faces,
and towards a nearby Mo(2) tetrahedron (Figure 3). The Bi(2) lone pair is
canted so as to bisect the [201] and ½10 1 column axes, pointing into a gap
between Mo tetrahedra (Figure 6a).
The g(L) structure is noncentrosymmetric, resulting in two distinguishable
Bi2O2 layers, and consequently, the lone pairs have an asymmetric steric
influence on the polyhedral tilts. The lone pairs in both layers point away
from the bilayer centre and are canted towards the gaps created by the
polyhedral tilts (Figure 6c). At 604 1C, the g-phase transforms irreversibly to
the high-temperature polymorph,39 g(H), which was discussed earlier.

4.3 Identifying Associated Oxygen Sites

Assuming that the surface geometry is sufficiently similar to the bulk, the lone
pairs pointing outwards from the Bi columns and towards neighbouring Mo
polyhedra have been generally accepted as the ones involved in the initial a-H
abstraction at an oxygen site bridging between Bi and Mo to generate an allylic
intermediate.5,6,73 Justification for similar bulk and surface compositions was
provided by Grzybowska et al.74 in a combined XPS/UPS study of the a, b and
g(L) catalysts to probe the relationship between surface and bulk composition
under various conditions. Samples measured under conditions of catalytic
oxidation of propylene with co-fed oxygen flow were found to have similar
Mo/O and Bi/O ratios to those of freshly prepared samples for each of the
phases, indicating that the catalysts have closely matched surface and bulk
compositions, and are fully oxidized.
As can be seen in the cases of the a- and b-phases, all Bi sites in nonisolated
columns have the lone pairs directed towards neighbouring MoO4 tetrahedra.
Oxygen sites bound to bismuth and nearly opposite to the lone pairs in both
phases have the strongest bonds to Bi and seem to be the most likely candidates
for accepting the a-H. Some useful geometric and bond valence sum data for
the oxygen sites strongly bound to Bi in a-Bi2Mo3O12 are compiled in Table 1.
These values have been obtained from the NPD study of Theobald et al.29 Of
the 12 crystallographically distinct oxygens, all of which belong to the tetra-
hedral coordination sphere of one of the three distinct Mo sites, only O(2),
O(3), O(6), O(7) and O(10) form strong bonds with Bi. Of these, O(3) is unique
in being strongly bonded to two bismuth sites.
In the b-phase, out of 18 crystallographically distinct oxygens, only two form
strong covalent bonds with Bi: O(1) and O(2). These sites are located near the
centre axis of the square (2  2) column and nearly opposite the lone pairs, each
forming three covalent bonds to Bi neighbours in the column. Based on
refinement results of Chen and Sleight,31 geometric and bond valence sum15 data
for bonding of these oxygen sites to Bi in b-Bi2Mo2O9 are compiled in Table 2.
The g(L)-phase has lone pairs pointed toward MoOx polyhedral faces from
both of the distinguishable Bi2O2 layers, independent of whether they are
 768

Table 1 Geometric and bond valence sum data associated with covalently bound oxygen sites in the a, b and g(L) phases.
Bi 0 site O site M00 site Bi 0 –O–Bi00 angle E–Bi 0 –O angle Bi 0 –O distance (Å) M00 –O distance (Å) Oxygen BVS
a-phase
Bi(1) O(3) Bi(2) 110.791 128.41 2.230 2.299 1.94
Bi(1) O(10) Mo(1) 130.941 144.01 2.220 1.905 2.12
Bi(2) O(2) Mo(1) 131.401 132.21 2.164 1.861 2.23
Bi(2) O(3) Mo(3) 130.071 101.51 2.299 2.052 1.94
Bi(2) O(6) Mo(2) 134.291 105.31 2.331 1.773 2.20
Bi(2) O(7) Mo(3) 119.471 119.51 2.187 1.904 2.38
b-phase
Bi(1) O(1) Bi(2) 107.241 136.61 2.209 2.40
Bi(1) O(2) Bi(2) 107.781 147.71 2.154 2.33
Bi(2) O(1) Bi(4) 120.431 145.61 2.201
Bi(2) O(2) Bi(4) 117.011 136.11 2.239
Bi(4) O(1) Bi(1) 120.831 142.81 2.127
Bi(4) O(2) Bi(1) 121.811 132.21 2.173
g(L)-phase
Bi(2a) O(2) Bi(2b) 118.161 156.11 2.170 2.22
Bi(2b) O(2) Bi(2a) 126.51 2.224
Bi(1a) O(3) Bi(1b) 113.061 159.01 2.161 2.39
Bi(1b) O(3) Bi(1a) 116.41 2.245
Chapter 46
A Survey of the Bi2O3–MoO3 Binary System 769
viewed as distorted corner-shared octahedra or distorted isolated tetrahedra.
The repulsion from these lone pairs matches with open spaces created by the
polyhedral tilts. Oxygens located on the midplane of each of the Bi2O2 layers,
O(2) and O(3), are also strongly bonded to Bi. Geometric and bond valence
sum15 data for bonding of O(2) and O(3) to Bi in g(L)-Bi2MoO6 are found in
Table 1, based on refinement of NPD data35 at 300 K.

5 Linking Structure to Catalysis

5.1 Making the Connection to Propene Oxidation
and Ammoxidation
Although there is a general consensus that an oxygen bonded to Bi(III) is
responsible for this rate-limiting first hydrogen abstraction, there seems to be
no confident assignment of the crystallographic oxygen sites involved. Various
proposed mechanisms are surveyed in a review by Hanna,76 but the conclusion
is basically that bismuth is important for the initial step and that the details
remain vague. The function of the lone pair has been commonly attributed to
the imparting of partial radical character to an adjacent oxygen bridging
between Bi and Mo, and consequently abstracting the a-H to produce H, but
the specific oxygen site associated with this is not clear. In fact, it seems highly
unlikely that an oxygen bridging between Bi and Mo can be the abstraction
site for b-Bi2Mo2O9 or g(L)-Bi2MoO6, since none of the strong bonds to Bi
that may be mediating the lone pair hybridization are also bridged to Mo
polyhedra. Only in the case of a-Bi2Mo3O12 do we find such bonds bridging to
MoOx, and in fact, all of them do.
Ono et al.77,78 have used Raman spectroscopy with 18O as a tracer in an
attempt to assign bands to specific oxygens that are involved in the oxygen
insertion step in a-Bi2Mo3O12. They conclude that candidates for involvement
in oxygen insertion are the pairs O(10)–O(5), O(10)–O(2) and O(5)–O(2), if the
allyl is centred at the Mo(1) tetrahedron, but argue that O(10)–O(2) should be
eliminated based on the excessive separation of 3.5 Å relative to the allyl bond
width of about 2.4–2.5 Å. In this case, the obvious candidate for the a-H
abstraction is O(10), since only it belongs to Mo(1) and also forms a short bond
to Bi(1); it is about 1441 from the lone pair, consistent with the anticipated
hybridization. This seems to suggest that specifically the O(10)–O(5) pair is
directly involved in the mechanism at Mo(1) of a.
Ono et al.77,78 also consider involvement of Mo(2) in a-Bi2Mo3O12, for which
pairs from each of O(3), O(6) and O(9) are implicated. They eliminate the O(3)–
O(6) pair based again on excessive separation. Interestingly, we have only O(6)
bridging from Mo(2) to nearby Bi(2). O(6) forms a strong bond to Bi(2), but is
at an angle of 1051 from the lone pair. This suggests that the O(6)–O(9) pair is
directly involved in the mechanism at Mo(2) of a.
They do not consider Mo(3) for the oxygen insertion site, arguing that Bi
ions are not present there; however, O(7) does bridge between Mo(3) and Bi(2)
770 Chapter 46
with a strong Bi–O bond (2.187 Å) and forms a reasonable bond angle with
respect to the lone pair. O(3) also bridges Mo(3) to Bi(2), but the bond is
somewhat weaker. Finally, note that the bond valence sums for these oxygens
with strong bonds to Bi tend to be over 2.00 in a, b and g(L), with the exception
of O(3), indicating that they are ‘‘overbonded,’’ and as such seem most likely to
abstract hydrogen to form an –OH. Since O(3) is not overbonded, this site
might indeed be inactive.
An entirely different mechanistic scenario involving surface oxidation of
Bi(III) to Bi(V) has been proposed by Jang and Goddard75 to explain the a-H
abstraction, and it does not require Bi lone pairs at all. In this model, based on
Bi4O6 molecular cluster calculations, the abstraction of the a-H would not be
energetically favourable at a Bi(III) site, but might be favourable at a Bi(V)
surface site under strongly oxidizing conditions. The fact that these catalysts
can perform for a fairly extended period under anaerobic conditions by
sacrificing lattice oxygen without dynamic M–vK replacement27 would seem
to argue against this. Also, Bi(V) is very difficult to stabilize.
Following the initial H abstraction, a symmetrical allyl forms and a series of
redox and acid–base steps result in the oxygen insertion for selective oxidation
to acrolein, or nitrogen insertion in the case of ammoxidation.5,6,79–82 In the
case of acrolein formation, the initially formed p-allyl becomes an anion in
an acid–base step, and then becomes oxidized by the Mo site as oxygen
binds through nucleophilic addition to form a s-allyl complex. A second
hydrogen is then abstracted from the s-allyl complex to form acrolein. In the
process, ‘‘vacancies’’ are generated, which distribute throughout the bulk
by diffusional exchange with lattice oxygen. We should be cautious with the
term vacancy here, since this is not likely to be a simple point defect, but
should rather involve a change in local coordination of pairs of Mo sites
such that two isolated MoO4 tetrahedra accommodate loss of one oxygen
between them by corner-sharing to produce a Mo2O7 doublet, or some
similar complex defect site. Finally, reoxidation of the lattice by co-fed di-
oxygen via the M–vK mechanism27 replenishes oxygen deficiencies to complete
the cycle.

5.2 Photocatalysis
Interest has been growing in the last few years in compounds of d0 metals for
photocatalytic splitting of water to generate H2 and O2 using ultraviolet (UV)
radiation,83 and for other conversions. In a very recent paper by Shimodaira
et al.84, g(L) is reported to be photochemically active for oxygen evolution from
silver nitrate in the visible, and the performance improves with increased
crystallinity. They also used plane-wave based density functional calculations
on unit cells of a, b, g(L) and g(H) to characterize the nature of valence and
conduction bands states. Interestingly, for all four phases they seem to be in
agreement with the Payne et al.63 findings for Bi2O3, i.e. that O 2p states mainly
contribute to the top of the valence band. Shimodaira et al.84 further state that
A Survey of the Bi2O3–MoO3 Binary System 771
the conduction band is derived from mostly Mo 4d orbitals mixed with some
contribution from Bi 6p.

6 Lattice Oxygen Mobility and Oxide Ion

Conductivity
The nature of oxygen sites across the bismuth molybdate phases can be divided
into groups related to the character of bonding they are involved in. The very
short Bi–O bond lengths involve oxygens with high bond valence sums39 (42.0)
indicating high covalency, and these have been shown to have small thermal
parameters.55 Oxygen sites associated with the Mo polyhedra show low valence
sums39,55 and large thermal parameters. The combination of a covalent ‘‘skel-
eton’’ of covalently linked bismuth sites (Figure 7) with flexible molybdenum
polyhedra that are amenable to oxygen nonstoichiometry is ideal for oxygen
transport and ionic conductivity. As described by Vannier et al.,55 these
attributes can be classified by dimensionality: three-dimensional cases such
as derivatives of d-Bi2O3 that are stabilized with low levels of substitution of
dopants, two-dimensional examples such members of the Aurivillius family,

Figure 7 Local environments and lone pair orientations; (a) cluster from a-Bi2Mo3O12
with Bi(1) down, Bi(2) up, Mo(1) forward left, Mo(3) upper right, and Mo(2)
back left and shared; (b) cluster from b-Bi2Mo3O12 22 bismuth column
with Bi(1) and Bi(2) paired, Bi(3) (top and bottom) opposite metal site
vacancy; (c) Bi(2) bilayer from g(L)-Bi2MoO6.
772 Chapter 46
and one-dimensional examples such as Bi26Mo10O69. In each case, the rela-
tionship between lone pair orientations and pathways for oxide ion and
vacancy migration is obviously important.
Surveying our entire phase diagram, it is clear that, with the exception of
a-Bi2Mo3O12, we have a family of phases comprised of compositional and
structural variants that satisfy the conditions above. a-Bi2Mo3O12 is a special
case where bismuth sites are paired to form covalent clusters that are organized
along with vacancies to form criss-crossed 21 columns. In a sense, it is a mix
of zero and one-dimensional covalency, in that the one-dimensional columns
are not contiguously bonded along the column axis due to the presence of
periodic vacancies. The skeleton is comprised of columns of weakly-linked
doublets (Figure 7a), and therefore is more like a spinal cord than rigid. The
b-Bi2Mo2O9 is clearly dominated by the 22 columns forming a one-
dimensional example. g(L)- and g(I)-Bi2MoO6 are Aurivillius derivatives,
therefore clearly of the two-dimensional variety; and these also have high
conductivity.85,86 g(H)-Bi2MoO6 is again one-dimensional with its Latin cross
columns (Figure 8 a,b), and is an excellent ionic conductor85 comparable to
YSZ. Bi26Mo10O69 with the symmetrical-cross channels is yet another one-
dimensional case (Figure 8 c,d). The proposed wavy layered structure of the
new homologous series, Bi2n
1MonO3n11, seems to fit into the two-dimensional
group, and measurements show that these are good conductors.9,43,45 The
proposed cation arrangement put forward in this chapter for Bi38Mo7O78
would be a three-dimensional member, as would Bi14MoO24. It is quite
reasonable to have expected that we find facile oxygen transport permitting
excellent M–vK behaviour, as well as impressive oxide ion conductivities, as a
common attribute of the entire bismuth molybdate system.
Based on pair potentials, modeling of oxide ion transport in g(L) by Dad-
yburjor and Ruckenstein83 shows that the apical oxygens (using the octahedral
view and referring to oxygens between Mo and the Bi2O2 layer) are highly
mobile and that these oxygen are likely to be the ones inserted in selective
oxidation. They further argue that this vacant site is replenished by other apical
oxygens, such that the vacancy diffuses through the lattice and is eventually
replaced by gas phase oxygen at a remote surface site.
Three other factors influencing oxide ion transport are the presence of metal
site disorder,49 substitutional defects,56,87–89 and nonstoichiometry56 in some of
the phases. Substitutional solid solutions based on g(L) can have conductivities
as much as three times higher than the pure end member.82 Cation vacancies in
a and b leave significant room in the lattice to further facilitate diffusion.

7 Summary
Surveying the full family of bismuth molybdates brings into evidence the
importance of covalently linked bismuth columns or bilayers surrounded by
isolated molybdenum polyhedra as a unifying characteristic. The key features
that lead to the multiple functionalities for bismuth molybdates are the
A Survey of the Bi2O3–MoO3 Binary System 773

Figure 8 Comparison of the covalent network within the large Bi columns in g(H)-
Bi2MoO6 and Bi26Mo10O69. (a) [100] profile view of the g(H) Latin cross
column, (b) clinographic view looking down the Latin cross column, (c)
[010] view (on-axis) of the Bi26Mo10O69 symmetrical cross column, (d)
clinographic profile view of the Bi26Mo10O69 column, Bi (larger white
spheres), O (small grey spheres at bond intersections), E (lone pairs: white
spheres near the bismuth sites).

combination of (i) facile oxygen diffusion, (ii) the presence of the lone pair on
bismuth coupled with opposing strongly bonded oxygens that hybridized with
the lone pair, and (iii) the site geometry with Mo polyhedra adjacent to the
bismuth columns. Across the phase diagram, the known phases all seem to be
exceptional oxide ion conductors, as one would expect from fluorite derivatives,
including the Aurivillius type as a modified form with a fluorite-like bilayer.
The catalytic applications are favoured towards the compositions with Bi/Mo
not too far from unity because of the need to have dual functionality: initial H
abstraction at Bi and oxygen (or nitrogen) insertion at an adjacent Mo. The
774 Chapter 46
more Bi-rich phases tend to have large-diameter Bi columns, which leave some
of the Bi sites without Mo neighbours. These Bi-rich phases are drawing
increasing attention for their oxide conduction properties, perhaps with poten-
tial for use in fuel cell applications, if they can be rendered sufficiently stable.

Acknowledgments
I would like to thank Prof. Tom Vogt for helpful discussions, and I would like
to thank Xin Li for his kind assistance with the many of the structural figures in
this chapter.

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CHAPTER 47

An Investigation of the Surface

Structure of Nanoparticulate
Systems Using Analytical
Electron Microscopes Corrected
for Spherical Aberration
RIK BRYDSON AND ANDY BROWN
Leeds Electron Microscopy and Spectroscopy Centre, Institute for Materials
Research, SPEME, University of Leeds, Leeds LS2 9JT, UK

1 The Importance of Surfaces in Nanoparticulate

Systems
The surface area to volume ratio of a particle increases with decreasing
diameter and this can have profound implications for the case of nanoparticles
less than ten nanometres in size. The large proportion of atoms at, or near,
surfaces, combined with the need to minimize the overall Gibb’s free energy of
the system may lead to substantial changes in the atomic and hence electronic
structure of the surface and/or bulk of the nanoparticle, ultimately altering the
physical and chemical properties of nanoparticles and their arrays relative to
their larger counterparts.1
Thus it is clear that there is a critical requirement to analyse the surface
structure and chemistry of nanoparticles at atomic resolution. Of course high
resolution scanning probe microscopies (SPM) can provide very important
images of surface structures and also provide highly localized measurements of
surface electronic structures and mechanical properties (for example see Ref. 2).
However transmission electron microscopy (TEM) or its scanned, focused
probe variant (scanning TEM (STEM)), whilst traditionally regarded as pro-
viding images of the projected internal structure, can also provide projected
778
Investigation of the Surface Structure of Nanoparticulate Systems 779
images of the surface structure of nanoparticles, even, in many cases, when they
are embedded within another material and are inaccessible by SPM. As we will
demonstrate, particularly when combined with spherical aberration correction
of the principal imaging lens, TEM and STEM can actually provide compar-
ative measurements of the differences between bulk and surface structure in
quite complex systems.

2 Aberration Correction in Electron Microscopy

At high resolution, conventional TEM and bright field STEM imaging both
employ the interference in the image plane between the unscattered incident
beam and at least one Bragg diffracted beam emergent from the exit surface of
a thin specimen to provide phase contrast images of the projection of its
electron scattering potential and hence, under certain conditions, the projection
of its atomic lattice. Unfortunately these images, besides simply reflecting the
orientation and composition of the specimen, are also sensitive to other factors
such as specimen thickness, lens defocus and the inherent characteristics of the
imaging or probe-forming lens (summarized in the concept of a contrast
transfer function (CTF); for a more detailed explanation see Ref. 3). In
contrast, STEM high angle annular dark field (HAADF) imaging employs
the detection of Rutherford-scattered electrons which are incoherently scat-
tered to much higher angles than the coherently Bragg scattered electrons; this
direct high angle scattering by the atom columns is proportional to the average
atomic number raised to the power of approximately 1.7. Both imaging
techniques rely on the specimen being oriented such that the atomic planes
or columns of interest in the specimen can be projected along the incident beam
direction. However, owing to its incoherent nature, HAADF imaging of such a
specimen orientation provides a much more directly interpretable image of the
projected atomic structure, with increases in image intensity being related to
increases in atomic number or thickness of the specimen in a relatively simple
fashion.
In recent years, it has become possible to correct spherical aberration, CS, in
electromagnetic lenses employed in electron microscopes and this improves the
resolution of either a TEM image forming lens or, alternatively, a probe
forming lens in STEM (because, in the latter case, one can form a smaller
probe and hence a more highly resolved scanned image). STEM employs a
lens corrector based on a set of quadrupole and octapole lenses prior to
the main probe-forming lens,4 whilst TEM utilizes a hexapole corrector after
the main imaging lens.5 Relative to these probe forming or imaging lenses, these
correctors introduce negative aberrations which can cancel with those inherent
in the primary imaging system – correction in (S)TEM is currently possible to
fifth order and can allow the formation of images with resolution below
0.09 nm at electron accelerating voltages of 100 or 200 kV. Two spherical
aberration-corrected electron microscopes have been installed in the UK prior
to 2004: a VG HB501 STEM with a NION corrector at Daresbury Laboratory
780 Chapter 47
(SuperSTEM) and a JEOL JEM 2200FS TEM with hexapole correctors at
Oxford University; both can routinely achieve an image resolution of 0.1 nm
either in terms of HAADF images (STEM) or bright field images (TEM),
respectively. These substantial improvements in electron microscopy image
resolution can provide additional detail in bulk structures and, of particular
interest here, these are also retained in images of defects and surface structures
in nanomaterials.6,7
It is clear that reducing the spherical aberration in a lens will lead to an
increase in image resolution, although in the case of phase contrast imaging one
should note that there is a corresponding drop in contrast. However, as alluded
to above, there are additional benefits of aberration correction. In STEM these
include an increased analytical sensitivity since the current becomes concen-
trated in an electron probe that is not only smaller but has a substantially
reduced intensity in its tail, making highly localized analysis of a projected
atomic column or surface layer more accurate. Furthermore there is an
increased clarity in images of surface structure and this is also reflected in
TEM aberration correction. In conventional TEM, the use of (spatially)
coherent cold field emission or Schottky emission sources is known to lead to
the problem of image delocalization at surfaces or internal defects/grain
boundaries; here one is sampling the undamped oscillations of the (contrast)
transfer function of the image forming lens well beyond its point resolution.
This causes the projected images of surfaces, for example, to exhibit numerous
lattice fringes extending beyond the surface and arising from the rapidly
varying reversals in the CTF at spacings beyond the point resolution of the
lens system. This results in corresponding reversals in image contrast (scattering
centres can change from black to white and back over a smaller spatial range)
and these image artefacts complicate analysis and interpretation of the exact
surface structure. A reduction in CS increases the lens point resolution and
largely removes these contrast reversals.
Aberration-correction in (S)TEM is therefore extremely beneficial for imag-
ing the projected surfaces of crystalline nanoparticles. Here we provide two
examples of the use of aberration corrected STEM and TEM in providing a
detailed understanding of the differences between the surface structures of iron
oxide/hydroxide-based nanoparticles produced either by synthetic methods and
imaged in a vacuum or biogenically and imaged within tissue extracted from
the human liver.

3 Aberration Corrected TEM and STEM of Synthetic

Magnetite Nanoparticles
Iron oxide nanoparticles play a key role in numerous important technological
applications including catalysis, high-density data storage and also for targeted
drug delivery and cancer treatment in biomedicine. The iron oxides Fe3O4 and
g-Fe2O3 are both ferrimagnetic and, when nanodimensioned, often exhibit
octahedral or cube-octahedral morphology. Such nanoparticles should contain
Investigation of the Surface Structure of Nanoparticulate Systems 781
only one single magnetic domain that would be significantly affected by
thermal fluctuations when measured at room temperature over laboratory
timescales. There is however evidence to suggest that they may possess a non-
uniform spin structure at the surface of the nanoparticle and this could affect
the exact magnetic behaviour. Hence there is a strong interest in the study of
the surfaces of such iron oxide nanoparticles, as it becomes crucial to charac-
terize these effects if we are to have well defined and predictable properties for
precise technological applications.
Fe3O4 (magnetite) has an inverse spinel structure and consists of a cubic close
packed lattice of oxygen anions. Although this lattice provides both tetragonal
(A) and octahedral (B) interstitial cation sites, only a quarter of the available
sites are filled: in a unit cell, 8 Fe2+ cations occupy the B sites, whilst 16 Fe3+
cations are equally distributed between both A and B sites. Bulk Fe3O4 exhibits
predominantly {1 1 0} and {1 1 1} growth faces, with {1 1 1} planes providing the
majority surface of octahedral or cube-octahedral particles. The {1 1 1} planes
of magnetite consist of layers of either anions or cations, but are never mixed; a
model of the {1 1 1} Fe3O4 surface viewed down the o1 1 0> direction is shown
in Figure 1. When the model {1 1 1} surface terminates in octahedral cations as
shown at the top of Figure 1, the terminating plane is expected to be composed
of alternating columns of half occupied and fully occupied octahedral (B)
cation sites. Figure 1b shows how, in this particular projection, the fully
occupied B cation columns form a distorted hexagonal pattern within the bulk
structure. g-Fe2O3 has a defect spinel structure similar to Fe3O4 but with a
larger number of cation vacancies, where the number of vacancies depends on
the degree of non-stoichiometry (i.e. there exists a solid solution between Fe3O4
and g-Fe2O3). The extra vacancies in the g-Fe2O3 structure are usually thought
to be accommodated in the octahedral sites and it has been suggested that the
mechanism of g-Fe2O3 formation from Fe3O4 is via a topotactic process
involving the diffusion of Fe2+ ions from within the particle to the surface,
where they oxidize to Fe3+ leaving behind a lattice vacancy.
Iron oxide nanoparticles may be fabricated using standard wet chemical
routes such as the reduction of iron chlorides with ammonia under a nitrogen
atmosphere.8 Batches of nanoparticles can be synthesized either with nominally
bare surfaces or with a surfactant coating such as lauric acid, to stabilize
against aggregation.9,10 A full characterization of such samples using both
X-ray and electron diffraction and TEM imaging revealed that the nano-
particles were almost exclusively single crystalline in nature, and were a mixture
of spherical and faceted particles with an average projected particle diameter of
approximately 8 nm and a near normal size distribution.9 As expected, the bare
nanoparticles showed a greater tendency to be faceted than the lauric acid
coated nanoparticles. Diffraction showed the particles to be a mixture of Fe3O4
and g-Fe2O3 phases, either on the inter- or intra-nanocrystal level. High
resolution TEM of {1 1 1} surface facets of cube-octahedral and octahedral
shaped particles shows an enhanced contrast of the atomic columns at their
projected surfaces; this is present at both minimum contrast and Scherzer
defocus and does not contrast invert at different negative defocii. Figure 2c
782 Chapter 47

Figure 1 (a) Model of a Fe3O4 crystal observed down the o1 1 0>direction with the
different occupation possibilities for the {1 1 1} planes indicated. The light
grey spheres represent iron cations, and the darker spheres oxygen anions.
The octahedral iron sites are labelled B, and the tetrahedral sites A. Solid
black circles indicate columns where all the octahedral (B) iron sites are fully
occupied and dotted black circles where only half the sites are occupied.
A distorted hexagonal pattern formed by the fully occupied octahedral
columns is visible. (b) Image corresponding to the model in (a) tilted to
show the occupancy along the fully occupied and half occupied octahedral
columns.

presents one example of this enhanced contrast in images taken from a

nanoparticle viewed down the o1 1 0> direction using an aberration corrected
TEM with a thermally assisted field emission source (JEOL-JEM 2200FS
FEGTEM at the University of Oxford). Here an indirect reconstruction of a
series of images recorded at different defocii has been used to recover the
complex specimen exit wavefunction based on the assumption that the nano-
particle is a weakly scattering object. With this method higher order aberrations
(which have not been corrected) can be measured and compensated for,
providing a further increase in interpretable resolution and in this case allowing
Investigation of the Surface Structure of Nanoparticulate Systems 783

Figure 2 (a) Phase and (b) modulus of the reconstructed exit wavefunction. (c) Shows
an overfocus bright field HRTEM image of an uncoated nanoparticle from
the corresponding focal series taken on the double aberration corrected
JEOL JEM-2200FS FEGTEM at the University of Oxford. The particle is
viewed down the o1104 direction. Cations appear white in (a) and (c) and
appear dark in (b). Enhanced contrast is clearly visible along the surface
atomic columns. A disordered sub-surface cation structure is marked by a
black arrow in (a).

a particularly clear image of the projected atomic columns at the particle

surface to be obtained (Figures 2a and b). The modulus of the reconstructed
exit wavefunction after transmission through the nanoparticle (Figure 2b) is, to
a first approximation, similar in intensity to that of the unscattered incident
beam (the region of vacuum next to the particle) suggesting that the weak
(scattering) object approximation may be valid. If this is so, projected columns
of cations will appear dark in the modulus and bright in the phase (since
scattering from the atomically heavier cations will dominate over that from the
anions and the cations advance the phase of the incident electrons). This can be
seen in Figures 2b and 2a respectively and indicates that the enhanced contrast
observed can be attributed to the presence of excess cations. Comparison with
the model magnetite crystal structure identifies this {1 1 1} surface as a layer of
octahedrally co-ordinated cations and the extra intensity can be interpreted as
excess cations occupying the alternating columns of the half-filled octahedral
sites present in the bulk structure; there is similar intensity on every column at
the surface whereas only alternate columns of corresponding layers further in
the structure have similar intensity. The brightest columns within the nano-
particle have the expected symmetry and spacing of the distinct ‘‘hexagonal’’
pattern of the fully occupied octahedral cation columns in the model structure
(the B columns in Figure 1 marked with a solid circle). Detailed multislice
simulations of these images for a variety of model Fe3O4-based structures with
different surface terminations have indicated that all of the B sites at the {1 1 1}
surface would need to be filled with cations in order to create contrast effects
comparable to those observed in experimental high resolution TEM images.11
Similar contrast enhancement in TEM images is also observed at {1 1 1} surface
facets of g-Al2O3 which is isostructural with g-Fe2O3.
784 Chapter 47

Figure 3 HAADF STEM micrographs of iron oxide nanoparticles shown with line
intensities taken along adjacent {1 1 1} planes. Columns displaying enhanced
intensity (marked with black arrows) are found on the terminating planes.
Image recorded on a dedicated aberration corrected STEM VG-HB501.
Note, there is a large contrast range in the image, however the range between
saturation has been narrowed to enhance the visibility of the atomic
columns.

Corresponding aberration corrected STEM HAADF images of a similar

nanoparticle, shown in Figure 3, reveal the same distinctive ‘‘hexagonal’’
symmetry of the fully occupied {1 1 1} octahedrally co-ordinated cation col-
umns for a particle viewed at or very near to the o1 1 0> zone axis, although
otherwise not much detailed contrast is apparent. The latter could be caused by
a tilt of the nanoparticle off the major zone axis or, alternatively, by a reduction
in cation order within it. This reduction in cation ordering is consistent with the
presence of a highly defective g-Fe2O3 type structure immediately below the
surface of the particle, potentially arising as a result of the diffusion of internal
cations to the surface layer. This effect is also apparent in the HRTEM images
as an amorphous-like layer just beneath the projected surface of the nanopar-
ticle (indicated by the black arrow in Figure 2a). As already discussed, the
additional vacancies in the g-Fe2O3 structure are thought to occur in octahedral
positions, and may be a result of the topotactic transformation of Fe3O4 to
g-Fe2O3. Figure 3 shows the STEM HAADF integrated line intensities taken
Investigation of the Surface Structure of Nanoparticulate Systems 785
along the {1 1 1} edge of the nanoparticle, and also along corresponding {1 1 1}
planes within the structure. The last of these, corresponding to the surface of
the particle, shows an overall increase in intensity, suggesting an increase in
cation occupation in the available octahedrally co-ordinated cation sites at the
surface of the nanoparticle, compared with those planes further within the
particle. It also shows a more uniform intensity distribution on the columns,
corresponding to a more uniform filling of the octahedral sites. Note there is a
monotonically decreasing background under the column intensities, owing to
the change in thickness along the {1 1 1} surface facet when a cube-octahedron is
viewed in this orientation.
The combination of aberration-corrected bright field TEM and high angle
annular dark field STEM has clearly revealed that magnetite crystals, formed
via a controlled, synthetic colloidal route and in the absence of a surfactant
layer, form highly faceted cube-octahedra. Owing to the minimization of surface
energy, the surfaces of these cube-octahedra terminate in low index planes such
as {1 1 1}. If a low index plane terminates at a nanocrystal surface, then the
charge balance of the crystal as a whole is highly dependent on whether the
surface is terminated by either anions or cations due to the relatively high
proportion of surface atoms in the nanoparticle. Analysis of the TEM and
STEM images suggests that the magnetite {1 1 1} surface facets reconstruct to
become distinctly cation-rich. If the edges of a pure Fe3O4 or a g-Fe2O3
nanoparticle were to terminate in a cation layer, cation vacancies need to be
introduced below the terminating surface layer in order to maintain the overall
charge balance and hence stoichiometry of the particle, assuming the anion
sublattice is unaltered. It is believed that such considerations may be intrinsic for
the case of synthetically produced oxide (or compound) nanoparticles in the
absence of adsorbed surface layers. The inclusion of surfactant layers appears to
result in magnetite nanoparticles with more spherical morphologies and would
tend to suggest that, in this case, surface energy considerations are less impor-
tant. We now compare these results with studies of biogenic nanoparticles,
whose nucleation and growth are mediated by self-assembled protein shells.

4 Aberration Corrected STEM of Ferritin Mineral

cores In Situ within Human Tissue Sections
In the human iron cycle, excess iron is temporarily stored by ferritin molecules
located within cells. Ferritin is the major iron storage protein and plays an
important role in iron metabolism due to its dual function of iron detoxification
and turn-over. The structure of the iron-rich core of individual ferritin mole-
cules has been widely studied by transmission electron microscopy (TEM).
However, the exact core structure and morphology remains controversial and
somewhat ambiguous. Ferritin is generally accepted to consist of a 12–13 nm
diameter protein shell that houses iron in a 6–8 nm diameter central cavity. In
animal cells, the protein shell is made up of a 24 strong, non-covalent assembly
of subunits of two types: heavy and light; the subunits are polymerized with
786 Chapter 47
regions of four-fold three-fold and two-fold, symmetry around the protein
shell as a whole. The iron is stored as an inorganic complex similar to the
hydrous ferric oxide mineral, 6-line ferrihydrite (6LFh), and the central cavity
has a theoretical capacity of around 4500 iron atoms.
The mineral ferrihydrite is known to be sensitive to exposure to the high-
energy electron beam of (S)TEMs12,13,15 such that increasing accumulated
electron dose leads to a migration of iron (originally in the form of 100%
Fe3+) from octahedral sites to tetrahedral sites and ultimately to a reduction of
iron from the Fe3+ state to Fe2+. Furthermore the mineral core of ferritin is
embedded in organic tissue which is itself notoriously beam sensitive and yet all
previous investigations of the structure and chemistry of ferritin cores have not
properly addressed the issue of electron beam induced transformation of the
core. We have applied aberration-corrected STEM at accumulated electron
doses ranging from 6  103 to 1.6  108 electrons nm 2 and at dose rates
ranging from 70 to 1.88  107 A m 2, where we know from a systematic
experimental investigation that minimal structural and chemical change occurs
in the mineral core as a result of electron beam irradiation. Such studies provide
vital information on the morphology, structure and iron-loading of ferritin
cores within tissue and we believe some of the findings may be generic in terms
of biogenically produced nanoparticles, particularly those undergoing rapid
turnover of species.
Figure 4a shows a STEM HAADF image of cytosolic ferritin within thin
sections of liver biopsy (from a patient with hereditary type 2, juvenile
haemochromatosis). The image has been recorded in the electron dose range
described previously. The mineral cores appear bright due to the relatively high
atomic number of the iron atoms in the core compared with the organic
material in the surrounding tissue. In order to best preserve the local chemistry,
only unstained biopsies have been examined and although the biopsies are
unstained, it is possible to visualize some of the main cellular structure in the
HAADF images and thus locate the relative position of the ferritin within the
cell (which is a major advantage over bright field TEM of unstained biological
sections). The higher resolution HAADF images clearly show polycrystalline
cores with crystalline regions surrounded by an amorphous surface structure
(Figure 4b). This is in sharp contrast to synthetic 6LFh crystallites, which are
clearly facetted similar to the synthetic magnetite crystals shown in Figure 2. In
the core second from the left in Figure 4b, only the bottom-right corner of the
core is oriented such that iron atom columns are visible (i.e. only the bottom-
right corner is close to a zone axis). The disordered surface of the ferritin
mineral cores would be expected to provide an ideal site for the dynamic
turnover of iron.
Finally, we address the question of the three dimensional morphology of the
ferritin mineral cores. From 133 STEM HAADF images of 1241 hepatic
ferritin cores, it can be seen that many cores have a subunit structure exhibiting
a near cubic symmetry with a low density central region (Figure 4a). We have
employed a conventional single particle analysis routine to produce a 3D
reconstruction of an average core from a series of HAADF projection images.
Investigation of the Surface Structure of Nanoparticulate Systems 787

Figure 4 (a) STEM HAADF image of ferritin located within the cytoplasm of a section
of human liver tissue, the mineral cores clearly stand out against the tissue
background; (b) higher magnification image of individual cores; (c) one
selected view of the preliminary three dimensional reconstruction of a cyto-
solic ferritin core generated by single particle analysis and image processing
(EMAN software) of images of some 750 cores with similar iron loading.
788 Chapter 47
This routine is designed for identical objects with random orientations in thin
layers and is commonly applied to low dose electron cryo-TEM images. Since
ferritin molecule cores in human tissues have different amounts of iron filling, it
is not valid simply to reconstruct an average based on every core image.
However, it is possible to obtain an absolute quantification of the number of
iron atoms in any particular core by using the technique of electron energy loss
(EEL) spectrum imaging in the STEM. Here EEL spectra of the Fe L2,3-
ionization edge and the corresponding EEL low loss region are acquired from
each 1 nm2 pixel over a whole core which allows the quantification of the
number of iron atoms in each pixel.14 Summing these results for each pixel over
a particular core can provide an absolute quantification of the number of iron
atoms in the core and this technique has been applied to 16 individual cores
with significantly different iron loadings. Since the specimen thickness is to a
first approximation uniform (because it was prepared by sectioning with an
ultramicrotome), the HAADF image contrast of a core can be taken to be
solely sensitive to the atomic number of the constituent atoms of the imaged
material. Thus we have then used the EEL quantification results to calibrate the
contrast level in a HAADF image of any particular ferritin molecule core. As
expected, there was found to be a linear correlation of the normalized HAADF
image intensity of a given core to the absolute amount of iron it contains (as
estimated by EELS) from the 16 ferritin cores measured in this way. This linear
fit is then used as a calibration to pre-classify the iron content of each of the
1241 individual cores imaged, in order to obtain a distribution of iron loading
in ferritin within a tissue section which is found to range from 500 to 3000 iron
atoms per core. The final 3D reconstruction was developed from images of
cores with the most common iron loading (1200–1600 iron atoms versus a
maximum threshold of 4500 iron atoms) and is shown in Figure 4c. This
reconstruction of the most common ferritin core in the liver tissue section is
seen to possess eight subunits in a cubic arrangement that reflects the symmetry
of the protein shell (regions of four-, three- and two-fold symmetry) of the
molecule and its eight, three-fold symmetry, entry channels for Fe2+. Note that
the subunits do not quite meet in the centre of the reconstructed core (i.e. there
is a hole in the reconstruction in Figure 4c) and this is consistent with a core
containing only B30% of its maximum possible loading.
Combined with the high resolution information from the HAADF images
(Figure 4b), the reconstruction suggests how the protein shell may template the
growth of the mineral core; iron ions once in the central cavity agglomerate and
nucleate at the eight separate entry points to the cavity forming distinct
subunits that can crystallize and with continued iron input can grow inwards
until the cavity is fully occupied. Given that some 30% of the atoms in a 5 nm
particle are located at or near its surface suggests that the high specific surface
area of such a structure enables rapid acquisition and release of iron thus
facilitating ready response to the requirements of the body. A new schematic
model for the core growth process is shown in Figure 5. It is well known that
Fe2+ ions travel into the ferritin central cavity through the eight hydrophilic
three-fold symmetry channels in the shell and then oxidize and form the mineral
Investigation of the Surface Structure of Nanoparticulate Systems 789

Figure 5 Schematic cross section of an hepatic ferritin molecule (viewing direction:

normal to one of the four-fold symmetry channels in the protein shell),
depicting the proposed core-formation mechanism. (a) Early stage of iron
deposition in the molecule’s central cavity. The sites near the ends of the
three-fold symmetry iron entry channels are favourable areas for the
incoming Fe21 to deposit and to be oxidized. (b) As the iron cellular
concentration becomes elevated, more Fe21 ions are shuffled into the ferritin
molecule, rapidly deposit and oxidize on the surface of the Fe31 already laid
down near the entry channels; consequently, core subunits are formed. (c)
With higher iron-filling, a cubic-like core structure with eight-subunits (four
shown) is constructed and Fe31 ions diffuse inwards forming closely packed
crystalline structures of ferrihydrite (dark red circles) in contrast to the
loosely packed (yellow) Fe31 ions. (d) An HAADF image of a single ferritin
molecule core of similar iron loading and lying in a similar orientation to the
schematic.

cores beyond the exit of the channels. At the early stage of the core formation,
molecules may contain more than one crystal nucleus near the exit of each of
the eight entry channels (Figure 5a). As the iron level in the cell increases, more
Fe2+ ions are loaded into ferritin and these deposit at the surface of the existing
core (Figure 5b). Once one of these nuclei reaches a critical size it will become
thermodynamically stable, forming a subunit and will compete successfully for
further incoming Fe2+, possibly at the expense of other neighbouring nuclei
due to its lower free energy; eventually, a cubic-like structure of eight connected
790 Chapter 47
lobes or subunits at each corner is evidently formed (Figure 5c compared with
Figure 5d). Since the inner surface of the core subunits is less accessible to
incoming iron compared to the outer surface, a hole is commonly left in the
centre of the mineralized core and the likelihood of completely filling this is low.
Given that phosphorus has been suggested to be a surface component of a
ferritin core, one can speculate from the above model that phosphorus may
preferentially bond to the loosely packed Fe3+ ions at the surface of the core
(yellow circles in Figure 5c) such that it may inhibit crystallization within the
subunits and lead to the disordered surface structure seen in Figure 4b. The
exact role of phosphorus could be investigated by controlling the STEM probe
to average many EEL spectra from the core surface of many ferritin molecule
cores, each recorded at an appropriately low electron dose.

5 Conclusions
The development of practical schemes for aberration-correction in transmission
electron microscopy has led to a renaissance in the application of the technique.
Here we have shown how aberration corrected TEM and STEM can give
important information on the surface structure of nanoparticulates. In partic-
ular we have highlighted the significant differences between the surfaces of
synthetic nanoparticles and those formed in situ within biological tissue.

Acknowledgements
RB would like to express his sincere gratitude to Professor Sir John Meurig
Thomas for the friendship, guidance and supervision provided to him during
his early scientific career; in particular instilling in him the legacy of his
scientific philosophy and his interest in electron microscopy which has contin-
ued to this day and which, hopefully, he has attempted to pass on to APB.

References
1. R. Brydson and C. Hammond, in: Nanoscale Science and Technology, ed.
R.W. Kelsall, M. Geoghegan and I. Hamley, Wiley, Chichester, UK, 2005.
2. A.R. Lennie, N.G. Condon, F.M. Leibsle, P.W. Murray, G. Thornton and
D.J. Vaughan, Phys. Rev. B, 1996, 53, 10244.
3. P. Buseck, J. Cowley, L. Eyring (eds), High Resolution Transmission
Electron Microscopy and Associated Techniques, Oxford University Press,
Oxford, UK, 1992.
4. N. Dellby, O.L. Krivanek, P.D. Nellist, P.E. Batson and A.R. Lupini,
J. Electron Microsc., 2001, 50, 177.
5. M. Haider, H. Rose, S. Uhlemann, E. Scwan, B. Kabius and K. Urban,
Nature, 1998, 392, 768.
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6. B. Kabius, M. Haider, S. Uhlemann, E. Schwan, K. Urban and H. Rose,
J. Electron Microsc., 2002, 51, S51–S58.
7. P.E. Batson, N. Dellby and O.L. Krivanek, Nature, 2002, 418, 617.
8. S. Khalafalla and G. Reimers, IEEE Trans. Magn., 1980, 16, 178.
9. G.R. Lovely, A.P. Brown, R. Brydson, A.I. Kirkland, R.R. Meyer,
L.Y. Chang, D.A. Jefferson, M. Falke and A. Bleloch, Micron, 2006, 37,
389.
10. G.R. Lovely, A.P. Brown, R. Brydson, A.I. Kirkland, R.R. Meyer,
L.Y. Chang, D.A. Jefferson, M. Falke and A. Bleloch, Appl. Phy. Letts.,
2006, 88, 093124.
11. D.A. Jefferson, Philos. Trans. Mat., Phys. Eng. Sci., 2000, 358, 2683.
12. Y. Pan, A. Brown, R. Brydson, A. Warley, A. Li and J. Powell, Micron,
2006, 37, 403.
13. Y. Pan, A. Brown, R. Brydson, A. Warley, J. Powell, A. Bleloch, M. Falke,
U. Falke, K. Sader and J. Trinick, Proc. Int. Microsc. Congr. IMC16, 2006,
1, 112.
14. R. Brydson, Electron Energy Loss Spectroscopy, Bios, Oxford, 2001.
15. Y. Pan, A. Brown, R. Brydson, A. Warley, A. Li, J. Powell, A. Bleloch,
U. Falke, M. Falke and C.C. Calvert, Eur. Microsc. Congr. 2004 Proc.,
2004, III, 167.
Closing Chapter
CHAPTER 48

Design and Chance in My

Scientific Research
JOHN MEURIG THOMAS
Department of Materials Science and Metallurgy, University of Cambridge,
New Museums Site, Pembroke Street, Cambridge CB2 3QZ, UK

1 Introduction
In common with many other natural philosophers, I believe that tools and
techniques play at least as important a part in the evolution of scientific and
technological progress as do ideas and theories. To substantiate this statement one
need think only of the telescope and the optical microscope, the mass spectro-
meter and the chromatograph, not to mention the numerous variants of X-ray
crystallography that have been deployed by solid-state, surface and materials
chemists in the last 80 years. But important as techniques and new instruments are
in governing scientific growth, it is also vitally important to have alongside one (as
students or colleagues) key individuals who possess the intrinsic skills, commit-
ment and enthusiasm to develop and exploit the newly available equipment.
Other factors are also relevant, for example, an expert technician, graduate
student or post-doctoral colleague may help translate a dream into reality by
constructing devices that are not commercially accessible. And even if one is
blessed by financial support from research councils, governmental institutions
or private industry, it is sometimes vital that instrument manufacturers are alert
to the needs of the experimentalist so that novel and crucial attachments (such
as an electron spectrometer to a high-resolution microscope) may be incorpo-
rated to standard equipment.
Looking back over 50 years of fundamental research, I am acutely conscious
of the fact that I have relied quite heavily on both simple and sophisticated
tools and techniques to reach the goals that I set out to attain. In rough
chronological order these include:
(i) Optical and electron microscopes;
(ii) Various kinds of spectroscopies such as soft X-ray-stimulated and
UV-stimulated photo emission measurements;
795
796 Chapter 48
(iii) ESR, NMR, FTIR and Raman studies, as well as electron-energy-loss
spectroscopy and X-ray absorption fine structure at near and extended
edges (XANES and EXFAS), made possible through access to synchro-
tron radiation; and
(iv) Various kinds of diffraction experiments involving either electrons, or
X-ray or neutrons; and, thanks to synchrotron sources, both energy-
dispersive (powder) X-ray diffraction (EDXRD) and four-circle X-ray
diffractometry for the determination of the structures of minute single
crystals. A special feature of synchrotron radiation is that it allows one
to record X-ray absorption spectra (XAFS) and X-ray diffractograms in
parallel and in a time-resolved fashion, an invaluable method of prob-
ing, in situ, the short- and long-range order of heterogeneous catalysts.

Whereas many of these techniques have been used intermittently within my

research group, my devotion to electron microscopy, ever since I began to use it
in the early 1960s, has never wavered. It was fortunate that I saw a good deal
earlier than my contemporaries in other departments of chemistry, the great
potential that electron microscopy has to elucidate a vast range of intriguing
chemical problems (especially solid-state science).
Over and above the tools and techniques that one chooses to deploy, there
are other vital determinants that govern progress in one’s scientific research.
These include the books and articles that one reads, the lectures that one hears
and, above all, perhaps, the intellectual energy, manipulative dexterity and
determination of one’s students, collaborators and colleagues. All these factors
can make the difference between success and failure.
I have always tried to pursue my research with passion and commitment.
When it progresses well, my spirits can be raised to the brink of ecstasy. When it
goes badly, I can become enveloped in saturnine gloom. And chance – that
‘‘divine creator’’ as Pushkin called it – can play an extremely important role in
one’s scientific life. Whilst I console myself with Pasteur’s dictum that ‘‘chance
favours the prepared mind’’, I nevertheless feel that, on many occasions, I was
unprepared to reap the benefits of chance conversations or encounters with
scientists in contiguous or distant disciplines.
In describing the role of design and chance in my work, I feel that a
chronological path through my career is also perhaps the most logical one to
follow. Consequently, I shall highlight some of the lessons, incidents and
significant achievements in my research, starting from my days as a graduate
student in the Universities of Wales and London and at my first post-doctoral
post at the UK Atomic Energy Authority.

2 Swansea, Queen Mary College (QMC) and

Aldermaston (1954–1958)
As was the rule in the 1950s, all research students in Physical Chemistry
pursuing PhDs in schools around Britain spent at least a year (their first)
Design and Chance in My Scientific Research 797
building the apparatus and tools that, in conjunction with their supervisors,
they considered essential to reach their goals. Whilst I never became an expert
glassblower nor a wizard in electronics, I did succeed in assembling a glass
vacuum system, McLeod gauges for low pressure measurements and an ana-
lytical facility – a thin platinum wire that, in the presence of O2 and CO could,
by judicious use, determine CO:CO2:O2 ratios at low pressures. I also acquired
from my supervisor, K.W. Sykes, the habit of following the recent literature in
my and my co-students’ research fields. I was fortunate that one of my co-
students was Wyn Roberts (a lifelong friend) who purchased newly published
monographs, such as B.W.M. Trapnell’s ‘‘Chemisorption’’, and who set a fine
example as a devoted and hard-working experimentalist.
In retrospect, our resources at Swansea were relatively sparse, and progress
was slow. The Departmental microbalance (there was only one) had to be
booked a week in advance, and it took a morning to weigh a sample to the fifth
decimal place. But our spirits were high. We were well taught; and the visiting
lecturers to the student Chemical Society were of uniformly high quality (e.g.
M.H.F. Wilkins, D.H. Everett, Sir Robert Robinson, J.S. Anderson, who
all became or were already Fellows of the Royal Society and two won the
Nobel Prize).
Because of the lectures that I was required to give as an officer of the student
Chemical Society – one on ‘‘Diffusion and its Chemical Importance’’ and one
on ‘‘Magnetic Resonance Spectroscopy and the Chemist’’ – I read every word
of R.M. Barrer’s ‘‘Diffusion in and through Solids’’ and almost every paper
that appeared up to 1955 on NMR and ESR spectroscopy. Both these exercises
influenced my attitudes and enlarged my knowledge enormously.
The undergraduate course at Swansea, though very thorough in what it
covered, did not include any reference to crystallography. I therefore taught
myself the rudiments of this important field from Dame Kathleen Lonsdale’s
semi-popular book on the subject. I remember how jubilant I felt after being
allowed to take powder X-ray diffraction photographs (in the Department of
Metallurgy) of my graphite samples, and being able to work out from my films
that the C–C bond length in the basal plane was 1.42 Å. I also vividly remember
encountering the word ‘‘dislocation’’ in the context of crystal growth in a
review article by A.R. Ubbelohde.
At QMC it was again necessary to assemble one’s own high-vacuum glass
apparatus – I was investigating the surface properties of evaporated carbon
films and of crystallites of diamond and graphite – a task which entailed
considerable reliance on the expert departmental glassblower.
In retrospect, it was not a wise decision on my part to go and work as a
Scientific Officer in the Atomic Weapons Research Establishment (AWRE),
Aldermaston when I completed the work for my PhD in October 1957. When I
had applied, three months earlier, I was under the impression that I would be
trained to pursue studies in electron diffraction, which, for reasons I still cannot
fathom, I thought would excite me. On arriving at AWRE, I was given a dismal
task involving electrodepositing thin films of metals on uranium. Whilst I
disliked this work, I was fortunate to share an office with a graduate in
798 Chapter 48
Metallurgy from Newcastle (then in the University of Durham) and from him I
began to learn the language of dislocation theory and found out that the
authoritative text on this subject was by A.H. Cottrell: ‘‘Dislocations and
Plastic Flow in Solids’’. This book, along with a few others – notably F. Seitz’s
masterly tome on the theory of metals and alloys, Mott and Gurney’s concise
monograph on electronic processes in ionic crystals and Linus Pauling’s
extraordinary analysis of the nature of the chemical bond – was of critical
importance in making me a solid-state chemist.
By the time I left Aldermaston to take up an Assistant Lectureship in
Physical and Inorganic Chemistry at the University College of North Wales,
Bangor, in September 1958, I was inwardly convinced that the main thrust of
my creative research work would focus on the chemical consequences of
dislocations and other defects in solids. And just before I left Bangor (as a
Reader in Chemistry) to take up the Chair and Headship of the Edward Davies
Chemical Laboratories in the University College of Wales, Aberystwyth in
October 1969, I wrote the following1:
For over 30 years physicists and metallurgists have interpreted the properties of
solids in terms of well-defined deviation from a perfect structure, the so-called
dislocation. But chemists have tended to show a reluctance to use this concept,
possibly because they were charmed by x-ray crystallography into believing that
the solid state is a paradise of faultless regularity. It is as well to remember that
most crystals, like most human beings, are imperfect; and often the more subtle
the imperfection, the more interesting the consequence.
A correlation between chemical reactivity and crystalline imperfections, which
is the main theme of this article, was noted quite early in the history of chemistry.
In 1834, Faraday2 demonstrated that the efflorescence of sodium carbonate
decahydrate was facilitated when the crystal surface was scratched. And it was
another polymathic chemist, Michael Polanyi who, 100 years later,3 first formu-
lated the notion of dislocation.
Dislocations (or line defects), which are best envisaged in solids that are
partially deformed, separate the parts of a crystal which have undergone slip from
those which have not. In an edge dislocation (the type described by Polanyi and
independently by Taylor4) the direction of slip is perpendicular to the line (EE 0 in
Figure 1); in a screw dislocation (first described by Burgers5) the directions of
slip and the line itself are parallel (SS 0 ). An edge dislocation is equivalent to the
insertion of an extra half-plane into the solid; but a screw dislocation effectively
converts a crystal into one helicoidal surface. For topological reasons, dislocations
must either close in upon themselves (to form loops) or emerge at free surfaces.
From a geometrical viewpoint the most important single characteristic of a
dislocation is its Burgers vector – this designates the magnitude and direction of
slip. The extra energy (per unit length) U due to the presence of a dislocation in a
crystal is given by
U ¼ atb2 ð1Þ

where a is a numerical factor close to 0.5, t is the rigidity modulus and b the Burgers
vector.6 The entropy change DS associated with the formation of a dislocation can
Design and Chance in My Scientific Research 799

Figure 1 A dislocation line. One end is of pure screw character (SS 0 ) and the other
pure edge (EE 0 ). The slip plane is ABCD, and slip has already occurred over
the shaded area.

also be computed 5,6 even when the line is perfectly flexible, the maximum value of
TDS at room temperature can never exceed about 3 kT. Since the creation of a
dislocation requires energy in the range 102 to 103 kT, it is evident, from the
equation DG ¼ DU – TDS, that dislocations are thermodynamically unstable, unlike
point defects.
Dislocations are present in crystals for a variety of reasons – accidents of
growth, supersaturation of point defects (as a result of rapid quenching) – and
may also be introduced by compression or extension. In heavily dislocated solids,
as many as 1012 lines may emerge per cm2 of surface: at the other extreme, it is
feasible for a solid to be prepared that is free from dislocations, e.g. certain
specially grown crystal whiskers.

3 Bangor; ‘‘Arm Chair’’ and ‘‘Zig-zag’’; Visit to Penn

State; and the Popularization of Science
My teaching load was heavy in my first 6 years or so, amounting to some 150
lectures per annum and an average of 9 hours per week of supervision and
organization of laboratory practical courses. Research work could only be
pursued during the vacations or in the evenings. As luck would have it scientists
at UKAEA Harwell offered me a grant to investigate the factors that influenced
800 Chapter 48
the kinetics of the oxidation of graphite – in view of the then great commercial
importance of the graphite-moderated, gas-cooled nuclear reactor. Attendance
at the 4th Biennial Conference on Carbon, held in 1959 at the University of
Buffalo, New York (now SUNY at Buffalo) convinced me that I should acquire
single crystals of natural graphite and examine their topographical features
prior to and after controlled oxidation in dry air, oxygen or carbon dioxide
(C+CO2 - 2CO).
There was no optical microscope in the department, so I purchased a second-
hand one in an antique-cum-pawn shop in Llandudno (for d8), and then, with a
fine workshop technician, Ken Syers, we built a home-made illumination
system that consisted of a car headlamp bulb, and a specially machined
dural-metal reflector that focused light that had passed through a heat-absorb-
ing glass on to the graphite surface.7 The Departmental Kodak camera, whose
primary function was for photographing all in-coming students once a year,
became our means of recording dislocation-etch pits, twin planes and surface
steps; and with my first research student (Miss Glenda Hughes), we made
significant progress in elucidating the dependence of the rate of oxidation on
crystallographic direction and upon the nature of the crystalline defect at which
enhanced reactivity was observed. An interference objective lens (and sodium
light) enabled us to determine the exact depth of etch pits and hence the rate of
oxidation perpendicular to the basal plane. We recorded kinetic anisotropies,
activation energies and absolute rates of oxidation along and perpendicular to
the basal planes. I also coined the terms ‘‘arm chair’’ and ‘‘zig-zag’’ (faces),8
terms that are now universally utilized in descriptions of carbon nanotubes and
graphene layers.
P.L. Walker, Jr, who headed a large group at Penn. State University, had
heard me present an account of my work at a conference organized in Imperial
College in March 1962 by A.R. Ubbelhode. This prompted him to invite me to
spend 3 months in State College, Pennsylvania in the summer of 1963. It was
there, with the hot-stage microscope used by the coal petrographers and
palynologists, that I carried out in situ, time-lapse cinematographic studies of
catalytic channelling (by a large variety of metals) on graphite surfaces. This
work was well received at the first International Conference on Carbon, held in
Tokyo in June 1964. It also prompted the AERE, Harwell team to repeat such
work using in situ electron microscopy.
In addition to studying the topography of graphite, I also explored the
gasification of another layered mineral, molybdenite, thereby finding evidence
for the important role of screw dislocations in governing the reactivity of this
mineral, MoS2, also. As a result of having a new chemistry building at Bangor,
more sophisticated equipment became available, and one of the items that I was
able to purchase was a low-power electron microscope. It was, however, ideally
suited to do what I wanted, namely employ the ‘‘gold-decoration’’ technique to
good effect. On warming a solid (whose surface topography is to be deter-
mined) and, at the same time, evaporating gold metal from a distant source,
surface mobility is so high that individual atoms tend to accrete and will
preferentially nucleate (decorate) any surface step – even those that are just
Design and Chance in My Scientific Research 801
monatomic height. By placing the thin decorated solid (graphite or MoS2,) into
the electron beam of the microscope, the gold nanoparticles are readily
rendered visible, since they scatter strongly. In this way I could image spiral
oxidation pits that were nucleated at emergent screw dislocations.
I found it possible to determine extremely minute concentrations of ‘‘vacan-
cies’’. Expansion of the vacancy, by oxidation either in O2, NO or CO2 gives rise
to a ‘‘hole’’ of monatomic depth (3.35 Å on graphite, ca. 6 Å on MoS2). Gold
decoration delineates the precise site of such vacancies. We found that their
concentration in natural graphite (emanating from Ticonderoga, New York) was
less than 1 in 1010 atoms of carbon.9,10 We could however create new vacancies
by allowing excited atoms of oxygen (generated by UV-irradiation) to impinge
on the basal surface of graphite. (At present there is great interest in probing the
vacancy concentrations in graphite and graphene sheets using other methods.)
Intrigued by Michael Faraday’s observation in the 1830s that scratching the
surface of a crystal hydrate gave rise to enhanced efflorescence at and around
the scratch marks, I decided to investigate, topographically, the surfaces of
calcite crystals and was able to deduce from etch pits and (thermal) decompo-
sition centres, the slip planes along which dislocations freely moved during the
strain suffered by crystals on gradual heating. The decomposition ‘‘volcanoes’’
were readily apparent microscopically in beautifully aligned arrays at the points
of emergence of the dislocations, that moved on the slip planes. The paper in
Nature11 detailing this work, I subsequently learned, marked a turning point in
the study of solid-state decompositions by others, notably in Israel.
My knowledge of dislocation theory deepened considerably at Bangor
through discussions with Robert Cahn, who, from 1962 to 1965 was Professor
of Materials Science there. I read the seminal book on electron microscopy
and dislocations by Hirsch et al.12 as well as the one by Amelinckx,13 which was
heavy going. But I learned, to my advantage, that dislocations could dissociate
into partials and such effects gave rise to stacking faults, an idea which I
capitalized upon in my Aberystwyth days, and which excited Kathleen Lons-
dale when she visited me there in 1970 (see below).
I also became familiar with fluctuation theory, and its critical importance in
governing the sensitivity of measuring instruments – such as a vacuum micro-
balance which my Ph.D. students Brian Williams and Eurwyn L. Evans had
built for general physico-chemical purposes14 – through an initial social contact
(in the College Refectory) with a colourful and extremely able Dutch physicist,
Johannes Poulis. He was on sabbatical leave in E.R. Andrew’s Department
of Physics at Bangor. I admired Andrew enormously because of his well-
organized approach to science – my first-ever Departmental Seminar, on the
interaction of gases and solid surfaces,15 was given at his invitation in his
superbly run Department – and especially because of his invention of the now
universally used magic-angle-spinning (solid-state) NMR technique.16 At the
symposium he organized to celebrate the opening of his new building in
Physics, I heard memorably lucid lectures from NMR giants such as Abragam
and Hahn, whose passion for clarity of exposition was equalled only by the
depths of their scientific insights.
802 Chapter 48
At the Department of Physics in the early 1960s were two extraordinarily
bright young Welsh research students, Gareth Roberts and Robin Williams,17
who played football with my versatile PhD student J.O. Williams (known
throughout Wales, for he was an international (soccer) footballer, as ‘‘J.O.’’). It
was through ‘‘J.O.’’ and his contacts in Physics that I became acquainted with
‘‘space-charge currents’’ in solids, a topic in which the theoretician in Physics
R.H. Treadgold, who supervised Gareth and Robin, excelled. This, in turn, led
me to appreciate the phenomenon of carrier injection (from an appropriate
electrode) into a poorly conducting solid. Could one, I thought, induce an
organic hydrogen-bonded solid or an inorganic hydrate to become a protonic
conductor using a proton-injecting electrode. For Li2SO4
H2O the answer
turned out to be ‘‘yes’’.18 But with the organic solids, such as imidazole, that I
studied with gifted colleagues such as G.P. Jones19 (an NMR expert) and T.J.
Lewis20 (a versatile electronic engineer) we saw no evidence of Grotthuss
conduction.
Though not strictly scientific, in the creative research sense, I began at
Bangor to pursue my interest, which remains unabated, in the popularization of
science. The Department of Extra Mural Studies in Bangor, as well as the
North Wales Branch of the Workers Educational Association (WEA) invited
me to lecture, in Welsh, to lay audiences from Bala to Mold, from Abersoch to
Amlwch. And for two long winters I lectured to a WEA class in Llangefni
(again in Welsh) on the ‘‘History and Origins of 20th Century Science’’, using
Herbert Butterfield’s classic tome and Mansel and Rhiannon Davies’s gem
(in Welsh) on that general theme.
The work that ‘‘J.O.’’ and I did on the role of crystalline imperfections in
governing the reactivity as well as the electronic and spectroscopic properties of
organic molecular crystals drew much worldwide attention. (I should mention
parenthetically that it was on reading Martin Pope’s beautiful article on electric
currents in organic crystals – in Scientific American – that I was inspired to
write my first paper on anthracene.) On the strength of it I was invited to lecture
and research at the Weizmann Institute by Schmidt and Cohen. I was able to
show how photoactive solids (like acenaphthylene) exhibited enhanced ease of
dimerization at dislocations.21 This work, done just before I left Bangor for
Aberystwyth, provided another turning point in my career. I set out deliber-
ately to elucidate the nature of defects in numerous kinds of molecular crystals.
This was one of my objectives when I had the freedom to run my own
Department at the University College of Wales, Aberystwyth.

4 Aberystwyth: Adventures in Photoelectron

Spectroscopy, Clay Mineralogy and Catalysis,
High-resolution Electron Microscopic Imaging,
and the Photophysics of Organic Solids
Because I inherited a well-run department, I had the freedom not only to extend
my electron microscopic studies, but to open several new avenues of
Design and Chance in My Scientific Research 803
investigation. As a result of seeing an interesting paper by Linnett in Nature,
shortly before leaving Bangor, I came across reference to Kai Siegbahn’s
monumental work on ESCA (electron spectroscopy for chemical analysis,
which is synonymous with X-ray induced photoelectron spectroscopy (XPS)).
I read every word of his lengthy and elegant Report on ESCA (to the US Air
Force). It educated me further in solid-state and surface physics; and it
prompted me to apply to SRC for my own instrument, which arrived in early
1971 from A.E.I. Manchester. A productive collaboration ensued with Mickey
Barber. On one of his visits to Aberystwyth we charted some six new areas of
investigation of the surface and bulk properties of solids. This led to great
success in clarifying the nature of the surfaces of carbon fibres, graphite (and
later diamond), and of the electronic band structure of solids. Success was also
achieved in the study of intercalation and in correlating Mössbauer parameters
with those of XPS, as a result of collaboration with Mike Bancroft in Canada
and with Mike Tricker who had joined me in Aberystwyth from London,
and we demonstrated later the value to structural chemists of photoelectron
diffraction.22
A bright Sri Lankan Ph.D. student, Tilak Tennakoon, also joined me
because, inter alia, he had read that I had an interest in cricket! As a result
of listening to John White (Oxford) describe his neutron-scattering work on
montmorillonite clays (at a meeting in Harwell), I resolved to deploy all the new
physico-chemical tools to clarify the structures of numerous members of the
layered silicate and aluminosilicate minerals, including montmorillonite, hecto-
rite, beidellite, mica, talc and vermiculite. Apart from achieving most of these
objectives we also discovered important new catalytic processes, involving the
exploitation of the unusual chemistry associated with the interlamellar spaces
of these clay minerals. The work of Howard Purnell and Jim Ballantine at
Swansea in collaboration with that of my team at Aber, attracted the attention
of John Cadogan who had just taken over as Research Director of the BP
Centre at Sudbury-on-Thames. Later (in my Cambridge days) this cooperation
flourished further and we discovered numerous new catalytic routes to prepare
ethers, esters, thioethers, amines and alkylated aromatics. One of the most
important advances, patented by BP on our behalf,23 was the discovery of how
to synthesize ethyl acetate in one step by the addition of acetic acid to ethene in
the interlamellar (acidic) spaces of clays:
CH2 ¼ CH2 þ CH3 COOH ! CH3 COOC2 H5
This was one of the first examples of ‘‘green chemistry’’ to be reported. (This
procedure, with different solid catalyst, is now employed by BP to manufacture
ethyl acetate, an important solvent, on a massive scale 4220,000 tonnes p.a.).
Because of the enormous cross-sections associated with photoelectric emis-
sion, XPS (and UPS) comprehensively transformed the study of chemisorption
and surface science. Prior to the arrival of XPS, there were no really sensitive
tools available to the physical chemist for determining the nature and extent of
sub-monolayer species bound at solid surfaces. Taking a lead from Siegbahn,
my colleagues and I showed that we could readily identify and characterize
804 Chapter 48
24
bound oxygen at carbon surfaces. In particular, we showed that, whereas the
prismatic faces of graphite retained nearly a monolayer of bound oxygen, the
basal surfaces were essentially free of such chemisorbed species.25 By using
single crystals of MoS2, we showed, in a fruitful collaboration with Robin
Williams, how angular variation of UV-stimulated photo emission enabled us
to determine the electronic band structure of this archetypal layered chalco-
genide.26 This initiated much subsequent research elsewhere on angle-resolved
photoemission.
Convinced that a powerful electron microscope was essential for my brand of
solid-state chemistry, the SRC awarded us the funds to purchase the best
Philips microscope then available, the EM300. It proved invaluable in tracing
the progress of intercalation of transition-metal chalcogenides,27 it enabled us
to track staging in the intercalation of graphite and, in the hands of my PDRA,
Eurwyn Lloyd Evans, we discovered28 an incommensurate structure in a
graphite–iron chloride intercalate, one of the first ever reported examples.
David Jefferson joined my team (from Mineralogy in Cambridge) and he did
some elegant work on stacking disorders in wollastonite and pseudowollasto-
nite (CaSiO3). And when Miguel Alario Franco, originally from Spain, joined
my group from Brunel University, he quickly mastered electron diffraction and
high-resolution imaging. In so doing we introduced great simplifying features
in the family of grossly non-stoichiometric ‘‘phases’’ exhibited by CrO2x. We
were, in fact, ‘‘seeing’’ crystallographic shear of the kind that J.S. Anderson
et al. had earlier reported in Oxford on the TiO2x system.29
To my delight, when ‘‘J.S.’’ reached retirement age as Head of the Inorganic
Chemistry Laboratory in Oxford, he asked if he could join me – as he put it
jocularly – as a ‘‘post-doc’’. I jumped at the opportunity; and ‘‘J.S.’’ arrived
with his right-hand man, John Hutchinson. They also brought as ‘‘dowry’’ a
handsome Siemens, high-resolution microscope. Great things on silicate and on
block-structures – the latter done experimentally by one of our very best Aber
graduates Sian Crawford – soon emerged. And when David Jefferson and Bob
Millward applied the multi-slice simulation (of high-resolution images) method
of Moodie and Cowley, my Department in Aber was one of the foremost in the
world in the electron microscopic (real-space) study of complex solids.30
Amongst other things we were the first to demonstrate that H.R.E.M. (high-
resolution electron microscopy), used properly, could routinely identify single
graphene sheets,31 a fact which became important decades later when single-
walled carbon nanotubes became all the rage. At Aberystwyth at that time, and
in joint work with Walker and Thrower in the U.S.,32 we also could routinely
prepare multi-walled carbon nanotubes, one example of which is shown in
Figure 2.
After ‘‘J.O.’’ and I perfected methods of growing high-purity single crystals
of anthracene, we and our collaborators (Gari Owen and Juliusz Sworakowski,
from Wraczow) could, by judicious deformation, introduce known numbers of
well-defined dislocations into this archetypal organic molecular crystal. We
then showed how the lifetimes and mobilities of electrons and holes in
anthracene were governed by crystalline defects. And in a fruitful collaboration
Design and Chance in My Scientific Research 805

Figure 2 High-resolution electron micrograph (two views) of a carbon nanotube

taken in 1974.

with Digby Williams and Wilhem Siebrand, at the NRC Ottawa, we experi-
mented successfully on the luminescent properties of undeformed and deliber-
ately deformed anthracene. Triplet and singlet exciton lifetimes (and trap
depths) could be deduced from our measurements,33 and this attracted much
attention from the world consortium of ‘‘molecular crystal’’ scientists. (I was
invited to give a plenary lecture at their Symposium in Philadelphia in 1970 and
again at the same series of Symposia in Santa Barbara. Attendance at those
events brought me in touch with new, and lasting, friends such as Martin Pope,
Ahmed Zewail, Mostafa El-Sayed, Jan van der Waals and Gil Sloan. Gil had
the courage to take his sabbatical leave from Dupont at Aberystwyth in 1973.)
Deformation of anthracene, if done in a certain way, so my Ph.D. student
Gordon Parkinson discovered, could produce a new metastable phase of ant-
hracene.34 Bill Jones, another Ph.D. student of mine, likewise, found that a
combination of stress and low temperature – we had built a liquid N2-cooled
stage in one of the three electron microscopes at Aber – produced a new phase of
crystalline pyrene. In no time at all, Subramaniam Ramdas, an expert compu-
tational chemist, who had joined me as PDRA from C.N.R. Rao’s group,
worked out from known atom–atom potentials (in the manner popularised by
Kitaigorodskii) what the new structures of these metastable phases might be.
Knowing the space-group as well as the unit-cell dimensions from selected-area
electron diffraction, and assuming that these aromatic molecules retained their
planarity, we could compute the new structures! Quite a breakthrough in
806 Chapter 48
microcrystallography. (Later, after I moved to Cambridge, Ramdas, Parkinson,
Mike Goringe (at Oxford) and I had a productive collaboration with
Massimo Simonetta and his ingenious crystallographer colleague, Carlo Maria
Gramaccioli, from Milan. This joint work enabled us to compute the dynamics,
i.e. the phonon spectra, as well as the statics of the new metastable phase of
anthracene.34)
Bill Jones and Gordon Parkinson, through Sir Peter Hirsch’s generosity to me,
were able to visit and work at the liquid-He-cooled electron microscope operated
by Linn Hobbs and Mike Goringe in the Oxford Department of Metallurgy and
Materials. This helped us uncover new features about dislocations in organic
solids such as p-terphenyl (studied elegantly by Bill Jones) and other aromatic
solids. We found that martensitic transformations occurred just as readily in our
organic molecular crystals as in martensite and austenite themselves.
While at Aberystwyth, a distinguished Egyptian solid-state scientist, Adli
Bishay, from the American University in Cairo, invited me to give three lectures
a week for seven weeks there in ‘‘exchange’’ for a week’s holiday on the Nile
in Upper Egypt. Culturally this was fascinating for me and my wife. Scienti-
fically it was worthwhile because, apart from interacting with able young
people (notably Jehane Regai), I took a keen interest in the chemistry and
physics of glasses and the incredible history of ancient Egypt, which has always
fascinated me.
At Aberystwyth also, I pursued, especially with ‘‘J.O.’’, how the luminescent
properties of organic solids depend critically on crystal structure, a topic in
which Gil Sloan’s experience proved invaluable.35,36 And we jointly investi-
gated, with Stan Moore and Gari Owen, two very bright Bangor graduates, the
electrical properties and thermal reactivity of ammonium perchlorate.
I also started work that I designated crystal engineering,37,38 a topic that is
now of major interest world-wide. My own efforts in this direction started
almost by accident, and in the following manner. Shortly after taking up the
Headship of Chemistry at Aberystwyth, I learned that a large fraction of the
employees of Unilever Research Centre in Port Sunlight were ‘‘Aber’’ chemi-
stry graduates – selected by the management because these graduates, having
been well taught by C.W. Davies, C.B. Monk and Mansel Davies, were thor-
oughly versed in solution chemistry and in crystal nucleation. The Director of
Research at Port Sunlight, Dr Brian Pethica, invited me to write him a two-page
report that dealt with the role of solid-state chemistry in the future evolution of
the subject. This I did; and as the contribution of Unilever to the Aberystwyth
centenary appeal (in 1972), I was given d5k per annum for 5 years, provided I
gave one or two research talks at Port Sunlight every year. This, in turn, led me
to solve a problem that was then exercising the Unilever researchers: how could
one enclathrate hydrogen peroxide in a ‘‘benign’’ solid which, upon dissolution
in water, would release the desired bleach, H2O2? With another PDRA, John
Adams and an Aber graduate Robin Pritchard, we solved this problem with two
such enclathrating hosts: guanidinium oxalate dihydrate37 and the mixed salt,
4Na2SO4
NaCl
2H2O2.40 (At Cambridge, some years later my group returned
to crystal engineering in purely organic molecular systems.)
Design and Chance in My Scientific Research 807
Topochemistry and topotaxy had always interested me, ever since I first came
across the work of the German pioneer, Kohlschutter.41 It clarified my
thoughts greatly when, in 1974, the Royal Society invited me to give a review
lecture on solid-state chemistry. The resulting article (Topology and Topography
in Solid-State Chemistry42) is still cited often; and, inter alia, it began to
highlight the key role of dislocations in governing the chemistry of solids.

5 Aberystwyth: Stacking Faults, Rapid Phase

Transitions and the Photochemistry
of Organic Solids
According to well-known principles in organic photochemistry, it was expected
that the photo-dimerization of 9-cyanoanthracene would yield cis dimer,
because of the mutual orientation of neighbouring molecules within the crystal.
The dimer that is formed, however, in the trans one; and this unexpected
product mystified the organic chemist. My colleagues and I showed that a
plausible explanation for this observation is the occurrence of dislocations on
the active slip planes (221). Within stacking fault regions, bounded by partial
dislocations, the monomer molecules are in trans registry (see Figure 3).
Molecules at such stacking faults act as traps for the excitation energy provided
by UV-irradiation, and reaction (photodimerization) ensues at these sites.43
Gradually, with low-temperature stages and fibre optics, it became possible
(through TEM) routinely to probe the microstructure of a range of organic
molecular crystals such as pyrene, p-terphenyl, anthracene using selected area
electron diffraction, dark- and bright- field imaging on in situ photodimeriz-
ations.44 We (i.e. Gordon, Donato Donati, Ching Fai Ng and others) could
also account45 for the hitherto inexplicable and rapid single-crystal - single-
crystal phase transitions of molecular-ionic solids (such as the cyclooctane
molecular cationic salt of a perchlorate reported by Paul et al.46). Partial

Figure 3 Crystals of 9-cyanoanthracene, when they contain stacking faults brought

about by partial dislocations on (221) slip planes will generate many pairs of
incipient dimers that are trans to one another.
808 Chapter 48
dislocations, and their rapid movement through this solid rationalizes the
nature and rapidity of the process.
Martensitic transformations were discovered47 in other organic solids, nota-
bly 1,8-dichloro 10-methyl anthracene, a material to which I had been intro-
duced by J.P. Desvergne, H. Bouas-Laurent and Guilio Guarini. And the
nature of the photodimerization products in this solid, and in 1,8-dichloro
9-methyl anthracene could be interpreted in terms of partial dislocations.48
Three other noteworthy events occurred during my days at Aberystwyth. Sir
George Porter (GP) invited me to give a Friday Evening Discourse at the Royal
Institution (RI). Second, I spent three months on sabbatical leave at the IBM
San Jose Research Laboratories in California. I subsequently learned from GP
that my Discourse, and the demonstrations that I carried out during my
account of ‘‘Adventures in the Mineral Kingdom’’ (when inter alia I disclosed
some striking high-resolution electron micrographs of the precious minerals
such as jade, beryl and cordierite), had influenced him in pressing the Council
of the RI (in 1986 when he announced his resignation as Director) to appoint
me as his successor.
At San Jose, apart from having access, via Don Burland, to sophisticated
lasers which I lacked in Aberystwyth – and which enabled us to do some unique
site-directed photochemistry in crystals of anthracene49 – I struck up a friend-
ship with an emigré-Scottish chemist, Colin Fyfe (ex-Dundee) who was in
California also on sabbatical leave from the University of Guelph. He taught
me a great deal about solid-state and fluid-phase NMR, and we soon designed
an experiment (carried out with Jim Lyerla) involving organic species inter-
calated within a layered mineral (hectorite) that gave beautifully resolved lines,
even though we did not rotate the solid hectorite sample (in the magnetic field).
So mobile were the intercalated species (xylenes and certain ketones and
lactones) that we uncovered some important facts relating to keto-enol
equilibria of some selected species that were restricted in two-dimensions
between the aluminosilicate sheets.50
The third event of note involved my collaboration with the Department of
Mineralogy at the Natural History Museum in London. Because I wanted to
exhibit some spectacular minerals of various kinds (precious, gigantic, fluores-
cent) at my Friday Evening Discourse in the RI, I got to know Dr Clive Bishop,
the Head of Mineralogy at the Museum. Soon we were collaborating by
combining high-resolution electron microscopy (HREM) with ultramicro-
chemical analysis using the electron beam and an energy-dispersive detector
for the liberated (characteristic) X-rays that gave us the precise, local, compo-
sition of a volume that was typically not much more than 106 unit cells of the
mineral (attogram quantities, 1018 g, in other words). The problem that we
solved, involving my bright Ph.D. student Sian Crawford, was the structure–
composition relationship among the serpentine minerals: lizardite, chrysotile
and antigorite, the three basic and inter-related forms of these minerals.
Combined HREM and XRE (X-ray emission) quickly showed why lizardite
was flat and platey – the curvature seen in specimens of chrysotile and
antigorite arises because the mesh repeat of the tetrahedral (SiO4) sheets and
Design and Chance in My Scientific Research 809
the octahedral (MgO6) sheets are different. In lizardite, however, some Al is
substituted into the SiO4 linked tetrahedra, thereby making its mesh essentially
the same as that of the (MgO6) sheets.51

6 Aberystwyth in Retrospect
The 9-year period that I spent in the University of Wales, Aberystwyth were
sublimely happy ones, partly because of the individuals with whom I interacted.
The principal, Sir Goronwy Daniel, was a giant of a man both physically and
as an academic administrator. Originally a geology graduate from Aberyst-
wyth, he took a D.Phil. in statistics at Jesus College, Oxford and, later, he
became Chief Statistician for the Ministry of Fuel and Power. Later still he was
the principal civil servant in the Welsh Office, where he had major responsi-
bilities in organizing the investiture of the Prince of Wales in Caernarvon Castle
(in 1969). Two of his top administrators in the College at Aberystwyth, Tom
Arfon Owen (the Registrar) and Emrys Wynn Jones (Deputy Registrar), along
with Sir Goronwy ran the College superbly.
This rubbed off on all Heads of Department. Whenever I had an acute and
seemingly insurmountable departmental problem (e.g. the need to expand the
Chemical Laboratories so as to accommodate extra instrumentation), these
men always sought ways to help me.
The Department achieved high visibility both nationally and among chemists
world wide, a fact reflected by the number of distinguished visitors we could
attract to lecture to us. For example, from the U.S., George Pimentel, Kenneth
Pitzer, H.C. Brown, R.M. Glaeser, Martin Pope, Roy Gordon, and Roald
Hoffmann (who gave us a dazzling performance as Chemical Society Centenary
Lecturer); other overseas visitors included Haruo Kuroda, V.V. Boldyrev,
Wolfgang Baumeister, Gerhard Wegner, C.N.R. Rao, P.W.M. Jacobs and
Mendel Cohen; and, from the U.K., Jack Linnett, Ralph Raphael, David
Buckingham, Ron Mason, John White, Richard Barrer, Moelwyn Hughes, J.S.
Anderson, Geoff Allen, R.J.P. Williams, Archie Howie, Ray Egerton, A.R.
Ubbelohde, R.W. Cahn, John Cadogan, Trevor Evans, F.C. Frank, A.R.
Lang, Pratibha Gai, C.A. Coulson, Kathleen Lonsdale and Dorothy Hodgkin.
When each of the last-three-named individuals visited the Department, I asked
them to design their lectures so as to be palatable to lay audiences and school
children, and I advertised in the local press the lectures that were to be given.
The response was heart-warming. Gordon Parkinson, my Ph.D. student, drove
Dorothy Hodgkin all the way from Oxford, a fact that she never forgot. And
Kathleen Lonsdale was so intrigued by our solid-state photochemistry work
(Figure 3 above especially) that she resolved that my group should be invited as
exhibitors in a Royal Society Soiree in July 1971.52
The students (undergraduates and graduates) at Aber were good and hard-
working; one of them has recently been appointed as Head of Chemistry at
Cambridge. The laboratory was well-equipped (and especially strong in dielec-
tric, infrared and other forms of spectroscopy). It attracted outstanding
810 Chapter 48
PDRAs (some mentioned earlier) and staff from other European universities:
solid-state chemists like Guilio Guarini and Donato Donati, University of
Florence; Salah Morsi from Alexandria, Egypt and Jehane Ragai from Cairo;
Bernard Bach from Nancy; Henri Bouas-Laurent and Jean-Pierre Desvergne
from Bordeaux; Isao Ikemoto from Tokyo; Julian Palomino Morales from
Cordoba, Miguel Alario Franco from Madrid, Jerzy Pielaszek from Warsaw,
and Ching Fai Ng from Hong Kong.
Once a month, on average, I gave popular scientific lectures (chiefly in Welsh)
in villages and towns throughout Wales. I also gave several lectures to school
children and their teachers, and I was regularly interviewed on radio and
television on topics of general scientific interest. It was fascinating to listen to
the response of expert Welsh bards when I told them (with copious visual aids)
about the poetry of science, during the course of which I would compare the
creative instincts and actions of artists and scientists.
Many firm offers of Professorships came to me from other universities
(Liverpool, Birmingham, Manchester, London and Edinburgh) all of which I
declined. Then I heard on the grapevine that the University of Cambridge was
likely to invite me to succeed Jack Linnett as Head of their Department of
Physical Chemistry, which, shortly after I was elected FRS (in March 1977), they
duly did. Dame Rosemary Murray, the then Vice-Chancellor, phoned me up and
offered me the job, which ‘‘J.S.’’ urged me to take. My wife and I agonised over
the decision, for we were very happy on the Cardiganshire coast, tucked away in
an idyllic region behind the Welsh hills. Advice from Jack Lewis, David Buck-
ingham and Ralph Raphael convinced us it was wise, scientifically and perhaps
otherwise, to move from West Wales to East Anglia. I began my duties in
Cambridge (and as Professorial Fellow at King’s College) on 1 April 1978.

7 Cambridge and the Expansion of my Activities

in Solid-State and Surface Chemistry
The first 5 years of my period as Head of Physical Chemistry in Cambridge
were among the busiest of my life. It was quickly apparent that there were great
opportunities to balance the outstanding gas-phase (and spectroscopic) acti-
vities of the Department with condensed-matter chemistry, particularly solid-
state and surface chemistry. I wanted, too, to shift the world attitude that then
prevailed in regard to the study of solid catalysts from the preoccupation with
adsorption and the structure of adsorbed layers to in situ investigations of solid
catalysts. I also wanted to design new catalysts and test them both with ex situ
and in situ methods of the most powerful kind.
Shortly after reaching Cambridge, I succeeded in being awarded an SRC
grant for the most powerful high-resolution electron microscope then in
existence, the JEOL 200CX (with 200 keV electrons). I also took my Philips
EM300 to Cambridge; and with Gordon Parkinson, David Jefferson, Bob
Millward and Bill Jones’ help, I acquired for a ‘‘knock-down price’’, from
Professor Ellis Cosslett (Old Cavendish) and from Ray Smallman
Design and Chance in My Scientific Research 811
(Birmingham) two other old (surplus to needs) microscopes which we re-built
as one (for liquid N2, low-resolution work on our organic solids).
With other government grants and generous support from BP Sunbury, Du
Pont, AERE (Harwell), N.C.B., Unilever and numerous Royal Society and
other (competitive) awards, as well as modest support from the University
itself, I also acquired the following key items: an X-ray powder (Philips)
diffraction system with an Anton Parr high-pressure stage; a high-resolution
solid-state (Bruker 400) NMR spectrometer; an Evans and Sutherland com-
puter graphics system (with which Ramdas did pioneering work); and Perkin
Elmer FTIRs and a scanning calorimeter. The workshop staff as well as the
glassblowers and photographers in Physical Chemistry were outstanding, so we
fashioned much new (and non-purchasable) equipment.
But, in addition to this essential equipment, I had also brought devoted and
able co-workers from Aberystwyth, and, as well, I was able to welcome other
outstanding senior workers from abroad, particularly Hachiro Nakanishi and
Wataru Ueda (as Ramsay Fellow) from Tokyo, Osamu Terasaki from Tohoku
(thanks to a Royal Society Guest Fellowship), K.J. Rao and S. Vasudevan from
Bangalore, Armin Reller from Zürich, Doug Buttrey from Purdue, Robert
Schlögl from Münich, Marc Audier from Orleans, Brian Williams from South
Africa, Carlo Maria Gramaccioli from Milan, Mark Hollingsworth from Yale,
Xinsheng Liu from Jilin and Wen Shu Lin from Shanghai, Tilak Tennakoon from
Sri Lanka, Jose Gonzalez-Calbet from Madrid, and – originally from Cracow –
from Imperial College, Jacek Klinowski, who played a pivotal role in much of
what I set out to do. Sabbatical visitors also contributed greatly to our efforts:
Les Bursill from Melbourne, Jack Lunsford from Texas A and M, Bob Cotts
from Cornell, Joe Wong from G.E. Schenectady and Gautam Desiraju from
Hyderabad. And the quality of research students, from outside Cambridge
(Lynn Gladden and Noel Thomas, Bristol; Kenneth Harris, St. Andrews; Michael
Anderson, Edinburgh; Ian Gameson, Swansea; Charis Theocharis, Brunel;
Andreas Nowak, Oxford; Wuzong Zhou, Fudan; Allan Pring, Monash, Australia;
Rik Brydson, Leeds) as well as the home-based ones (Carol Williams, Adrian
Carpenter, Simon Kearsley and Paul Wright) was superb. Most of these
students and PDRAs now hold Professorships, Readerships or senior positions
in industry.
With this army of devoted and inspired collaborators I witnessed many
turning points in my research in the early 1980s. In broad terms they occurred
in the following fields:

1. The structure, properties and nature of Si, Al ordering and the uptake of
adsorbates and reactants by zeolites.
2. The ‘‘real-space’’, structural imaging by electron microscopy of numerous
categories of minerals.
3. Electron-energy-loss spectroscopy/microscopy.
4. Crystal engineering and diffusionless reactions in the organic solid state.
5. The exploration of the properties, structures and dynamics of urea
inclusion complexes.
812 Chapter 48
6. The structure and nature of gross non-stoichiometry in complex, mixed-
metal oxides.
7. Novel analytical techniques, including X-ray-induced photoelectron dif-
fraction; in neutron scattering and in Compton scattering.
8. Discovery of numerous methods of organic synthesis by clay catalysis.

Apart from the contributions made by members of my own research group, I

benefited greatly through my collaboration with other groups, notably those
of Howard Purnell and Jim Ballantine (Swansea), Tony Cheetham (AKC)
(Oxford), Richard Catlow (CRAC) (London), Colin Fyfe (CAF) (Canada) and
(greatly) with Peter Edwards in Inorganic Chemistry at Cambridge. I was
responsible for introducing AKC, CRAC and CAF to zeolite science. These
main fields will now be elaborated.

7.1 Zeolites
Prior to the startlingly good resolution achieved in the high-resolution imaging
of zeolite-A (by Bursill et al.53 that we published in 1980) only Menter’s classic
work,54 done at much lower resolution (in the mid-1950s), had previously
shown the stark openness of the architecture of zeolites. Our work stimulated
great activity, by ourselves and others, and several noteworthy landmarks were
reached. These included:
(i) The direct-imaging of ZSM-555 and of ZSM-5-ZSM-1156 intergrowths
(see Figure 4), thereby revealing the internal structure (down two
principal zone axes) of the MFI zeolite before single-crystal X-ray
crystallography had solved its detailed structure.
(ii) Terasaki et al.57 found evidence for quite unexpected (rotational) co-
incidence boundaries, like the O7.O7 R22.51 one shown schematically
in Figure 5 for zeolite-L. (This picture later became the cover illustration
of a Greek textbook in mathematics – see chapter by Terasaki). The
existence of such boundaries greatly diminishes the diffusivities of
molecules in the commercially important zeolite-L (which is the basis
of the now commercial catalytic conversion of n-hexane to benzene).
(iii) Another unusual structural feature to emerge from our HREM studies
was estuarine defects in dealuminated zeolite-Y.58

Above all, however, what our HREM studies contributed to the structural
understanding of zeolites, was the existence of intergrowth structures within a
given, ostensibly pure zeolitic host. The first specific example that we elucidated
was the case of faujasite. My colleague, Marc Audier,59 found direct (real-
space) evidence for the co-existence of slivers of the hitherto hypothetical Breck
Structure 6, which is simply the hexagonally stacked analogue of the cubic
faujasite, now called EMT. A regularly and multiply twinned faujasite is
synonymous with the Breck Structure 6; the FAU and EMT frameworks are
the cubic and hexagonal extremes (EMT has since been prepared in a struc-
turally pure form60). Just as ZSM-5 (s) and ZSM-11 (i) are two framework
Design and Chance in My Scientific Research 813

Figure 4 Intergrowths of ZSM-5 (s) and ZSM-11 (i).

end-members,55 so it becomes possible to envisage an almost infinite family of

recurrent intergrowths (e.g. sisi . . ., ssissi . . ., siisii . . .). The same is true of
many other families of zeolites, notably the various members (gmelinite,
chabazite, offretite, erionite, cancrinite, sodalite) that belong to the so-called
ABC-6 group (see Figure 6).61 Indeed we soon found direct, real-space evidence
that the ZSM-23 framework structure (first-solved62 by my Ph.D. student Paul
Wright) is a recurrently twinned variant of zeolite theta-one.63
Another significant turning point to emerge from HREM was the observa-
tion (done jointly with Terasaki et al.64) that the uptake of some guest
(sorbents) such as Se into certain zeolite hosts (such as mordenite) occurs in
a spatially non-uniform manner.64
Yet another turning point in zeolite science resulted (initially) from a message
I received from Lovat Rees that Lippmaa and Engelhard65 had been able
directly to detect Si:Al ordering in zeolite-A. I quickly realized that it was
magic-angle-spinning NMR (MASNMR), of the 29Si nucleus, that was being
used. With the great efforts of Klinowski and Fyfe we made huge advances in
the study of zeolites by 29Si and 27Al high-resolution solid-state NMR. What
we established were the following:

(i) A method of determining Si/Al ratios non-destructively in the frame-

work of zeolite structures from the intensities of the 29Si(nAl) peaks
814 Chapter 48

Figure 5 A coincidence boundary detected by Terasaki, Ramdas and Thomas in

zeolite-L.

alone. (Earlier methods involved either destructive wet-chemical ana-

lysis, or laborious X-ray fluorescence measurements).
(ii) Identification, via 27Al NMR, of the extent of octahedrally and tetra-
hedrally linked Al31 ions.
(iii) A re-evaluation of the Si, Al ordering schemes in zeolites X and Y.
(iv) An ability to monitor the detailed structural changes of zeolites during
the course of de-alumination.
Design and Chance in My Scientific Research 815

Figure 6 Recurrent intergrowths in the ABC-6 family of zeolites were discovered by

HREM (see Ref. 61).

(v) The important ability to be able to resolve crystallographically distinct

tetrahedral sites in silicalite and ZSM-5. In 1982, three papers66,67 of
mine appeared in Nature (two were back-to-back!) on these topics, one
in J. Chem. Soc., Faraday Trans.68 and one in J. Phys. Chem.69 We were
also able to deduce a useful equation70 relating 29Si chemical shift to the
average T–O–T angle.
(vi) In so far as neutron scattering (from zeolites) was concerned, Tony
Cheetham and I registered important advances in elucidating the chemi-
stry of zeolites by

 proving that the 4:0 ordering scheme exists in zeolite-A (from a study
of Tl1–zeolite-A);71
 providing direct proof of cation-hydrolysis in La31-exchanged zeo-
lite-Y cracking catalysts by detecting La(OH)21 exchangeable ions in
the super-cage and Od–Hd1 bonds (as acid sites) on the oxide
cage;72 and
 localizing active sites73 in zeolitic cages through a neutron-powder-
profile analysis and computer-simulation of deutero-pyridine bound
in gallozeolite-L. (This was the first structural determination of the
location of an organic molecule absorbed within a zeolite or any
microporous catalyst or adsorbent.)

In pursuit of the chemistry and physics of zeolites, I talked to Peter Edwards

about an early experiment of Barrer, who had diffused sodium into an
816 Chapter 48
1
Na -exchanged zeolite-A and obtained evidence of a cluster cation from ESR
measurements. Peter saw the golden opportunity that faced us. With his ESR
instrument and our expertise (especially Jacek Klinowski’s experience in zeolite
science) we repeated and greatly extended the early work on alkali metal ions
and metallic clusters inside zeolites.74–76 Not only did we see Na431, K431 and
Rb431 cluster cations, we also saw K321 ions and many other comparable
species. In retrospect, our work obviously prompted much activity elsewhere;
and Osamu Terasaki and his colleague Yasuo Nozue in Tohoko University
discovered77 that potassium clusters incorporated into zeolite-A exhibit
ferromagnetism.
In all this work on zeolites, Ramdas’ supreme skills in computational
chemistry and computer graphics did much to bestow upon us world primacy
in this field – see, for example, Figure 7 illustrating the cluster ions of the alkali
metals inside zeolite-A, and also the location of sorbed xenon inside zeolite rho,
that had been studied experimentally by Paul Wright, Trevor Rayment and Ian
Gameson.78 In addition, I had Bob Millward’s expertise as an electron micro-
scopist, and his command of the multi-slice computer programs (of Moodie
and Cowley) to aid in the reliable interpretation of HREM images. This greatly
assisted the BP Research Centre to solve their important new zeolite catalyst,
theta-one.

Figure 7 (a) ESR spectra reveal the existence of Na431 clusters in zeolite-A and (b)
XRD powder diffractometry reveals the location of adsorbed xenon in
zeolite rho.
Design and Chance in My Scientific Research 817
Trevor Rayment’s skill in devising apparatus for the powder X-ray diffracto-
meter at both low temperatures (when alkyl chlorides or xenon were adsorbed)
and high temperatures, where the migration of exchangeable cations could be
tracked during catalytic activation (which he and Carol Williams studied so
effectively79), was invaluable. Michael Anderson almost single-handedly build
a sensitive IR set-up to explore the Brønsted acidic properties of deuterated
zeolites (and deuterated alkanes in contact with non-deuterated acidic zeolites).
This yielded definitive results, as did his work on de-alumination with Jacek
Klinowski and also his exploration of the subtle difference in framework
aluminium sites in zeolite omega.80

7.2 Real-Space Crystallography: Direct Structural Imaging

of Minerals
Apart from the zeolites, there were other solids of geochemical interest that I
had begun to explore in Aberystwyth. Prominent among these were the chain-
silicates, notably the archetypal pyroxene, wollastonite; the pyroxenoids
(rhodonite, pyroxmangite and ferrosilite); the amphiboles, particularly nephrite
jade; and sheet silicates like chloritoid and stilpnomelane, all brought to my
attention by David Jefferson.
What we discovered by imaging these solids was quite spectacular. Thus,

(i) The various samples of the amphiboles (nephrite jade) which the British
Museum provided, and whose provenance ranged from Rhodesia to
China to New Zealand, contained triple-chain defects, and in some
instances, quadruple-chain, quintuple-chain and even hexuple-chain
regions surrounded by regular (double-chain) silicate structures. This
was a major discovery,81 which was independently confirmed by geo-
chemists at Harvard and Arizona State University.
(ii) The pyroxenoids (empirical formula MSiO3, M ¼ Ca, Sr, Mg, Mn, Fe,
etc.) proved equally fascinating. Our studies, led by David Jefferson,
revealed in unprecedented detail the unit cell level stratigraphy that
these minerals (natural and synthetic) displayed (see Figure 8). In fact,
when David Jefferson and I arrived in Cambridge, Ellis Cosslett and
David Smith were just about to commission their 600 keV electron
microscope; and they wondered what the best sample would be to test its
performance. Not only had we thinned samples of wollastonite avail-
able, we had also done a ‘‘through-focus’’ series of computed images.
The correspondence between what was observed and what was com-
puted was very good, and Nature published our Letter.82 By joining
forces with Richard Catlow and his group in London, we could
rationalize the subtleties in structural behaviour in terms of the known
atom–atom potentials that Richard and his group had compiled.83
(iii) The hollandites and other tunnel structures were revealed uniquely well,
at atomic-scale resolution, by the studies pursued by Allan Pring.84,85
818 Chapter 48

Figure 8 HREM readily reveals the unit-cell level stratigraphy within the pyroxenoid
family of minerals (MSiO3, where M ¼ Ca, Mn, Fe, etc.) of which wol-
lastonite, pyroxmangite, rhodonite and ferrosilite are members.

These exercises greatly clarified the way in which hollandites were

effective in burial of the kind of materials generated in nuclear waste.
(iv) The structure of the extremely hard (second only to diamond) and
complex mineral rhodizite was solved by Pring, Jefferson and me from
HREM images, one of the very first minerals to respond to such
determination.86
(v) I also had witnessed in the Nobel Symposium in Stockholm, to which
I had been invited, the enormous potential (which I described in
Nature87) that real-space imaging could play in the solid-state chemistry
of the future.

7.3 HREM and Electron Energy Loss Spectroscopy (EELS)

of Simple Solids and Complex, Non-Stoichiometric Oxides
Fresh impetus to my interest88 in EELS was given to us by the arrival on
sabbatical leave of Ray Egerton, who taught us how to extract quantitative
Design and Chance in My Scientific Research 819
compositional data from our raw data. Plasmon spectroscopy we explored to
good effect in determining the composition of binary alloys;89 and, with Rik
Brydson, it became clear (thanks to joint work with Vevedenski in London)
that, with light elements much as boron, beryllium and aluminium, we could
justifiably talk about determining the nature of oxygen coordination numbers
around these light elements from the ‘‘finger print’’ EELS spectra that they
exhibited.90 Brian Williams, aided by Gordon Parkinson and Craig Eckhardt,
convinced me of the value of the Compton scattering of electrons measured by
electron microscopy. In particular, we probed the ‘‘structure’’ of amorphous
carbon by Compton scattering and showed91 that such a solid, in our case, was
predominantly graphitic. This emerged from the measured momentum density
of the valence electrons92 in the ‘‘unstructured’’ solid. It also proved possible, in
favourable circumstances, to deduce from ‘‘white line’’ (L3/L2) EELS meas-
urements, the number of d-electrons present in transition-metal oxides.93 And
we had an exciting time, prompted by Joe Wong, who came on sabbatical from
GE in Schenectady, elucidating by HREM and EELS the nature of semi-
insulating polycrystalline silicon and its interface with single crystal silicon,94 a
project which involved collaboration with Archie Howie in the Cavendish
Laboratory.
With the current availability (2007) of aberration-corrected electron micro-
scopes, the combination of HREM and EELS (coupled with energy-dispersive
X-ray emission XRE) is likely to boost still further the power of electron-based
methods in chemical, surface and materials science.
Non-stoichiometry as a phenomenon, in complex oxides especially, is well
studied by HREM in combination with selected-area electron diffraction. The
behaviour of CaMnO3 (a perovskite) when it is progressively reduced to yield
CaMnOx, where x is 2.50oxo3.00, was beautifully charted by Armin Reller. It
was possible95 to pin-point the precise nature of the highly ordered oxygen
vacancies in, for example, CaMnO2.50, CaMnO2.556, CaMnO2.66, CaMnO2.75
and CaMnO2.80. With the arrival in 2003 of aberration-corrected HREM
instruments,96 paradoxical as it may seem, oxygen vacancies in such key
materials as ceramic superconductors (e.g. in YBa2Bu3O7d) may be readily
‘‘seen’’.97
Wuzong Zhou, who joined my group (with no prior electron microscopic
experience) from Fudan University, China, very quickly mastered (for his
Ph.D.) what needed to be accomplished in the study of non-stoichiometric and
complex mixed oxides (such as those formed from solid solutions of Bi2O3 and
a range of other oxides like TiO2, V2O5 and Nb2O5).98,99 It transpired, quite by
chance, as was demonstrated by Tony Harriman, that a large family of
photocatalysts based on Bi2O3 could be readily prepared.100 It so happens that
Bi2O3 is a classic example of the defect-fluorite structure, and is best repre-
sented as Bi2O3& (where & signifies an oxygen vacancy).
With all the information that could be retrieved from HREM in conjunction
with analytical electron microscopy (by either XRE or EELS and selected-area
electron diffraction), we were able to discover altogether new structures
exhibited by complex oxides (some of which were of key catalytic interest).
820 Chapter 48
101
Into this category came the new layered bismuth tungstate material brought
to our attention by Bob Grasselli (during sponsorship of work by his (then)
company, SOHIO in Cleveland). The financial support from this source also
enabled me to recruit Doug Buttrey as a PDRA. He did excellent work on the
bismuth molybdates. To our delight, we discovered that very many of the
ostensibly crystallographically unrelated polymorphs of bismuth molybdate
could all be related102 back to the defect-fluorite structure and superlattices
thereof. And our HREM led us to the discovery103 of a new molybdate phase,
Bi38Mo7O78, that is still of considerable scientific interest.
Pratibha Gai, after establishing initial contact in my Aberystwyth days, kept
in touch with my group intellectually. She did some elegant work on many
complex oxides, and with E.D. Boyes, ‘‘saw’’ proof of the existence of cry-
stallographic shear planes in ReO3-derived, non-stoichiometric oxides, from
HREM studies. Our interests converged again during the emergence of the
ceramic (warm) superconductor era.104 Later, because she is one of the few
electron microscopist to image the extremely beam-sensitive aluminophos-
phates (ALPOs), see below, we combined forces with her (mainly Jiesheng
Chen, Paul Wright, my other colleagues and I) to solve, by stochastic methods,
the atomic structure of a recalcitrant transition-metal (framework) exchanged
ALPO catalyst.105
The phenomenon of intercalation (of iron carbonyls, iron chlorides or
organometallic entities) exhibited by graphite was also much elucidated by
the application of HREM,106 selected-area diffraction and also by laser-Raman
spectroscopy which Robert Schlögl brilliantly exploited in our in situ studies of
the uptake of SbCl5 by single-crystal graphite.107 The spectroscopic changes of
the lattice modes of the host told us the extent of uptake, and the local modes
told us precisely the chemical nature of the intercalated species. The use of
combined techniques to resolve hitherto intractable structural problems proved
fruitful on numerous occasions, just as it did when we established108 by solid-
state 29Si MASNMR, Raman spectroscopy and electron microscopy that in
stishovite, a high-pressure form of silica, the silica is in octahedral coordina-
tion. (It had been my good fortune that in 1977, I had met Malcolm Nicol in
UCLA, and he carried out the Raman spectroscopy and provided the samples.)

7.4 Crystal Engineering, Diffusion-free Solid-State Reactions

and Structural Mimicry
I had formulated ways of carrying out certain kinds of crystal engineering in my
Aberystwyth days (see Refs. 39 and 40); and through reading Kitaigorodsky’s
work and following the experience I had gained in the Weizmann Institute, I
was keen to extend the kind of concepts that I had outlined42 in my Royal
Society Review Lecture in 1974. I proposed some further ideas at the Interna-
tional Conference of Physical Organic Chemists that met in York109 in 1979,
where I first met the great John D. Roberts of Caltech. But it was the arrival of
Hachiro Nakanishi from Tokyo (as a PDRA) and Noel Thomas as a graduate
Design and Chance in My Scientific Research 821
student (from Bristol) as well as Charis Theocharis (from Brunel University)
that gave Bill Jones and me extra momentum in this field.
We soon zoomed in on a fascinating single-crystal to single-crystal photo-
dimerization with benzylbenzylidene cyclopentanone monomers110 and shortly
thereafter we were engineering crystals so as to control the photoreactivity of
the reactants and the crystallinity of the products.111 Moreover, thanks to
Mike Hursthouse’s help with the crystallography, we could monitor the
precise crystallographic course of this (single-crystal) photodimerization112
(see Figure 9).
Following our intuition, and the atom–atom calculations that Ramdas was
carrying out, we took advantage of substituting methyl for chlorine groups
attached to benzene rings, so as to steer crystallization in a desired fashion.113
And we played tunes, along with Gautam Desiraju (who was on a short
sabbatical in my group) with the notion of structural mimicry, whereby one
molecule (with its ‘‘own’’ structure) takes up that of the host molecular
crystal.114 Unifying many of these concepts and insights, Noel Thomas,
Ramdas and I proposed a new approach to the crystal engineering of organic
solid-state compounds.115
When Kenneth Harris joined my group from St. Andrews,116 I put him on to
the well-studied problem of photodimerization of the a- and b-forms of cinnamic
acid, a field extensively studied by Schmidt and Cohen in the Weizmann
Institute. The stacking of the monomers of cinnamic acid in the b-crystallo-
graphic form is one in which there is translational symmetry (see Figure 10).

Figure 9 Within crystals of benzylbenzylidene cyclopentanone, photodimerization

occurs in a single-crystal - single-crystal (diffusionless) transformation (see
Ref. 110).
822 Chapter 48

Figure 10 Photodimerization within the b-phase of cinnamic acid may leave isolated,
untransformed monomers (see text and Ref. 117).

Kenneth was the first investigator of this system (in nearly a hundred years of
study) to ask the question: ‘‘How many isolated monomer molecules remain
unreacted at the completion of U.V. irradiations, once all the possible dimeriz-
ation options have been exhausted?’’ Some residual, unreacted monomers must
remain, unlike the situation prevailing in the a-cinnamic acid form (where
adjacent molecules are related by a centre of symmetry). I confessed to Kenneth
that I was not smart enough to solve the intricate mathematics involved, so I sent
him to speak to my friend, David Williams, the Professor of Mathematical
Statistics in Cambridge. In the fullness of time, Kenneth solved this mathemat-
ical problem elegantly: he was, as a Ph.D. student, the senior author, with two
FRSs as his co-authors.117

7.5 Urea Inclusion Complexes

I had always regretted that, because very few (hardly any) important zeolites
occurred as good quality single crystals, it was not possible to conduct elegant
solid-state structural and reactivity studies on them, in the way that one could,
for example, do with graphite8 or diamond118 or certain organic crystals119
which I had studied earlier. When Kenneth Harris and my new PDRA (from
Yale) Mark Hollingsworth started interacting within my group, a striking new
Design and Chance in My Scientific Research 823
opportunity arose: one could readily grow quite large single crystals of urea
(and thiourea) that accommodate linear molecules of a wide variety of kinds. It
was well known that hydrocarbons (paraffins) could fit snugly inside the
channels of urea. But now, with Kenneth and Mark together, very exciting
opportunities arose: very many linear organic peroxides (e.g. diacyl peroxides)
could be ‘‘placed’’ inside the urea host. (For a plan view of such channel
complexes and further information about this fascinating field, the reader is
referred to the chapters by K.D.M. Harris and by M.D. Hollingsworth).
Here were golden opportunities to explore the detailed solid-state chemistry
of photo-produced (separated) radical pairs, which we were quick to capitalize
upon.120 Using Peter Edwards’ ESR instrument we followed, via zero-field
splitting measurements, the precise changes in distance separating the individ-
ual radicals from one another, as the cold solid (after irradiation to create the
two radicals, as shown in Hollingsworth’s first illustration in this book) was
gradually heated.
In due course, much elegant crystallography and physico-chemical insight
on the part of Kenneth Harris led to deeper appreciation of the structure of
these inclusion complexes (with guests such as chlorocyclohexane, for
example).121,122
Later, on his own initiative, Kenneth Harris uncovered a wealth of unprece-
dented new properties exhibited by these fascinating complexes. Initial exten-
sion of this work by him focused on understanding periodic structural
properties (with particular interest in the experimental assessment and theo-
retical understanding of incommensurate versus commensurate behaviour),
dynamic properties, host-guest chiral recognition, and the structural and
dynamic aspects of order–disorder phase transitions. A beautiful paper123 on
the quantitative analysis of guest periodicity in one-dimensional inclusion
compounds was published by Harris and Rennie (the latter having joined me
as a scholar on vacation at the RI: his mathematical skills were so good124 that I
immediately encouraged him to interact with KDMH).

7.6 Clay Catalysis: Synthesis of Commodity Chemicals and New

Reactions that Take Place in the Interlamellar Regions
of Sheet Silicates
Early work (done at Aberystwyth), like the novel reactions125 of hydrocarbon
complexes of metal-ion exchanged sheet silicates such as montmorillonite, was
known to open up interesting possibilities, the thermal dimerization of trans-
stilbene being just one example.125 My work with Howard Purnell and
Jim Ballantine on cation-exchanged acidic clays (modified natural ones and
synthetic variants) established a wide variety of other (solvent-free) methods of
producing bulk chemicals, one of the most important (later patented by BP)
being the facile synthesis126 of esters by direct addition of acids to alkenes. We
also evolved effective methods to synthesize esters, amines and may other
products.127,128 Alkylation reactions, such as the formation of cumene and the
824 Chapter 48

Catalyst
+ H3C C CH2
H H+

synthesis of primary alcohols could also readily be effected129:

Catalyst
H2C CH2 + H 2O CH3CH2OH
H+

We also explored the merits of pillared clays, which we investigated in situ by

MASNMR, FTIR and powder X-ray diffractometry.130
Towards the end of my period in Physical Chemistry at Cambridge, I also
gave considerable thought to such topics as the design of new porous solids,131
activating the C–H bond,132 and – a topic that I had explored earlier at
Aberystwyth – ascertaining the environment of guest species in minerals and
other crystals.133
All these topics were to be re-united in my days at the Davy Faraday
Research Laboratory (DFRL) of the RI, along with earlier attempts to follow
(in situ) the structure of the iron catalyst in the synthesis of ammonia.134

8 The Davy Faraday Laboratories of the Royal

Institution of Great Britain
In 1986, when I relinquished the Headship of Physical Chemistry in Cambridge,
there were over twenty or so active collaborators (graduate students, PDRAs,
staff members and visitors on sabbatical leave) that attended the lunch-time
group meetings I convened every Monday (see Figure 11). On taking up the
post as George Porter’s successor at the DFRL and RI, I knew from the outset
that my group would have to contract considerably, that I could not transfer
from Cambridge to London the cutting-edge, world-class equipment I had
acquired (electron microscopy, solid-state NMR, powder X-ray diffractometers
and spectroscopic tools of various kinds). I knew also that the recruitment of
bright young graduate students to my group would now be more difficult, but I
also knew that Tony Cheetham (who had been appointed as a Visiting
Professor at the DFRL) would bring along some graduate and Part II students
from Oxford. I took (on soft money) two PDRAs from Cambridge, Tilak
Tennakoon and Carol Williams, who had completed their Ph.D.s with me, and
a recent graduate, Ingrid Pickering, and I quickly acquired an outstanding
PDRA from the Dyson Perrins Organic Laboratory (at Oxford) Peter Maddox.
Kenneth Harris remained in Cambridge to finish his Ph.D., but he regularly
visited the DFRL. Dr Yashonath, one of C.N.R. Rao’s bright computational
chemists, also joined us at the DFRL and, shortly thereafter, Dr Stachurski
Design and Chance in My Scientific Research 825

Figure 11 The solid-state chemistry group (with some missing members) in

Cambridge in 1986.

from the Polish Academy, Warsaw, and Dr John Couves (ex-University of

Kent) soon followed.
The EPSRC awarded me a competitive rolling grant (for personnel, equip-
ment and running costs) and some helpful research support was also provided
by Unilever, Shell and BP. The Kirby-Laing Foundation gave me a substantial
grant to purchase an X-ray diffractometer for our rotating anode system,
together with a quadrupole mass spectrometer, and the Laura Ashley Foun-
dation gave me 5 years of support to recruit teenagers as research assistants in
my team during those students’ ‘‘gap year’’.
Andreas Nowak and Steven Pickett came as PDRA and graduate student,
respectively, with Tony Cheetham from Oxford. Later, one of Tony’s ex-
D.Phil. students Richard Jones returned from Canada to join us; and we also
welcomed a charming and hard-working Chinese graduate student, Yan Xu,
from Jilin University. Later, two remarkably effective PDRAs (Dr. Natarajan
from Madras and Dr. Jiesheng Chen from Jilin) joined my team, as did the
hard-working Gopinathan Sankar from Bangalore. It was my great good
fortune that Paul Wright, who had earlier joined Shell in the Netherlands,
returned to my team as a pivotal member, to be joined later by Leo Marchese
from Torino. Much later, two other gifted individuals became DFRL members,
Thomas Maschmeyer from Sydney and Robert Raja from Pune, India.
A 1-year PDRA from the MPI Mülheim, Markus Dugal, was also an inval-
uable member of the team.
826 Chapter 48
But what was my plan – my ‘‘designed’’ research vision in 1986? It had two
main strands:

 to study solid catalysts under in situ conditions,

 to devise new ways of synthesizing open-structure solids that could
enable me to design new catalysts consisting of well-defined, single sites.

Most researchers in the field of heterogeneous catalysis adopt a reductionist

approach to the design of new catalysts: the individual steps involved in overall
catalytic conversion – the processes of adsorption, surface rearrangements and
reconstructions, desorption of products and the diffusion of products to and
from exterior surfaces – are analysed in great detail and the resulting informa-
tion is then used to interpret the behaviour of existing catalysts with a view to
generating new ones. In my view, this approach seldom – very, very rarely –
leads to the arrival of a new, effective solid catalyst. (An exception is to be
found in the work of Besenbacher and co-workers135 who, using STM, were
able to design an idealized, nickel (single crystal) catalyst for ethene hydrogen-
ation in which monatomic steps on the Ni(111) surface were deliberately
‘‘poisoned’’ by adsorbed silver to prevent the rupture by hydrogenolysis of
ethene).
My approach to the design of new heterogeneous catalysts is fundamentally
different from that of the reductionist. I use what may best be described as an
‘‘emergent’’ or ‘‘integrated’’ policy. I focus on the precise atomic architecture of
the catalytically active site – its determination under operating conditions, its
assembly and scope for its modification, and the subtleties of its mode of action.
Armed with such information and the extensive structural and preparative
principles of solid-state chemistry, and augmented by lessons derived from
other branches of the subject (including organometallic chemistry, computa-
tion, enzymology and organic and inorganic chemistry). This has enabled my
group to design numerous new catalysts capable of facilitating conversions that
were hitherto deemed either impracticable or very difficult to effect – (see
below, and the chapters by Maschmeyer, by Wright and Zhou, by Marchese
et al. and by Raja).

8.1 Targeting In Situ Catalytic Studies

As well as the conscious act to design a compact rotating anode X-ray
diffractometer plus mass spectrometer set-up at the DFRL, with which we
were able to chart136,137 the movement of Ni21 ions within a Ni-exchanged
zeolite-Y catalyst (for the trimerization of acetylene to benzene) during the
course of thermal activation, we also set up in situ FTIR equipment to probe
adsorption, diffusion and catalytic dehydration of alkanols at acidic zeolites.
We gained enormous advantages by collaborating with Kirill Zamaraev and his
team at the Boreskov Institute in Novosibirsk in this aspect of our adventure.
Precise quantitative data pertaining to the individual rates of the above steps as
Design and Chance in My Scientific Research 827
well as the overall general influence of confinement of the reactants within
zeolite pores were gleaned in this way.138,139 Whereas chance has often played a
big role in my scientific life, no finer example may be cited than my association
with Kirill Zamaraev. I met him in June 1984 at the lunch organized by
Gerhard Ertl after the morning session of the 8th International Congress on
Catalysis in Berlin. We were seated next to one another, and he proceeded to
interrogate me about certain aspects of my plenary lecture which I had just
delivered. His English was perfect – and his scientific knowledge seemed
encyclopaedic. I happened to say that of all the chemical phenomena that I
had encountered, the most enigmatic was that of quantum mechanical tunnel-
ling. He then proceeded to give a dazzling account of the origins of its
discovery, and the best way of picturing it conceptually. During the course of
his exposition it transpired that he had been taught physics as an undergraduate
in Moscow by Landau and Kapitza. (He also told me that, late one night in his
parents home in Moscow, the great N.N. Semenov phoned him up to ask if he,
Kirill, could give him some tutorials in quantum mechanics. Apparently,
amongst the cognoscenti of Russian physical scientists, the young Zamaraev
had become known as a rising star. Later, at a tender age he was invited to
succeed the aged G.K. Boreskov as Director of the Catalysis Laboratory in
Novosibirsk.) His science and his friendship I shall treasure forever, and a
sadness overtakes me even now when I read some of our joint articles (see Refs.
139–141). He passed away in the summer of 1996.
In 1989 when I appointed Richard Catlow to the Wolfson Chair of Natural
Philosophy at the DFRL, my efforts were greatly speeded up chiefly because his
and my interaction (which had already been initiated in my Cambridge days)
intensified.142
The computational power that Richard Catlow brought with him extended
in a most satisfying manner what Tony Cheetham and I had initiated through
the appointment of Yashonath (who had just completed a PDRA post in
Klein’s group at the University of Pennsylvania). We were pleased to be among
the first to use Monte Carlo methods in determining the siting, energetics and
mobility of saturated hydrocarbons inside zeolitic cages, and our first143 of
several144 papers on this topic was published in Nature in 1988. Tony Cheetham,
elsewhere in this book, has given a lucid account of how our small team at the
RI, interacting with researchers at Shell, Amsterdam, moved on to molecular
dynamic treatment of alkane diffusion in zeolites.
One of Tony’s bright young Oxford colleagues, Julian Gale, joined us from
time-to-time, with satisfying consequences in our successful attempts (with
Richard and his ex-student Rob Jackson) to interpret the behaviour of organ-
ically pillared clays.145
On the experimental front, Ingrid Pickering and Peter Maddox completed an
elegant in situ study of the structural changes accompanying a lithium-nickel
oxide catalyst during the high temperature oxidative coupling of methane,146
and Peter and Yan Xu147 succeeded in our first ever synthesis of aluminium
phosphate (ALPO) molecular-sieve catalysts. Ingrid and Peter quickly learned,
from Tony Cheetham, how to employ his Rietveld refinement program, and
828 Chapter 48
1 148
this was used to solve the structure of K -zeolite-L. Ingrid and my PDRAs
Peter, John Couves and Eric Dooryhee had great pleasure in collaborating with
Mike Sheehy and David Madill, two outstandingly versatile technicians whom
I had inherited from George Porter and David Phillips (Richard Catlow’s
predecessor as Wolfson Professor) in designing cells and a reliable set-up for
quantitative studies of gas–solid interactions by powder X-ray diffraction
analysis.149 This apparatus we put to good effect in testing the catalytic activity
of the ceramic superconductor (known to be readily reduced to a sub-
stoichiometic state) YBa2Cu3O7x. We discovered150 that this solid functions
as a Mars-Van Krevelen type of sacrificial catalyst, where the CO plucks the
oxygen from the solid, and gaseous O2 restores the original composition.
Having immersed myself rather gradually into the study of the new (Union
Carbide generated) ALPOs, SAPOs and MAPOs, Tony and I (using his solid-
state NMR, operated by the bright Clare Grey at Oxford) investigated the
solid-state and catalytic chemistry of the methanol to olefin conversion (MTO).
The paper that Yan Xu, Clare, Tony and I published151 came out just before
the elegant one by my two former collaborators (in Cambridge) Klinowski and
Anderson in Journal of the American Chemical Society on the same theme.
The family atmosphere that pervaded the DFRL in those days had a unique
quality. It had been a feature of the RI ever since the halcyon days of Sir
W.H. Bragg, when he was Director from 1920 to 1942, and again when his
successors, Sir Eric Rideal and Sir Lawrence Bragg (my predecessor but one)
were at the helm. At the time of writing (2007) there are no technicians
employed by the DFRL any more and the mechanical and glass-blowing
workshops have been closed.

8.2 The Daresbury Synchrotron and Collaboration

with Neville Greaves
Even as early as 1979, when I organised a summer school in King’s College,
Cambridge, with my colleague Richard Lambert,152 I had been eager to embark
on full-blooded in situ studies of heterogeneous catalysis. The first paragraph of
the preface to ‘‘Characterisation of Catalysts’’ reads as follows:152
Unlike the situation that prevailed only a few years ago, several tech-
niques are now available for carrying out in situ, dynamic studies of
catalysts. Until recently, essentially all the methods used for catalyst
characterisation could be classified as either post-mortem or pre-natal, in
the sense that tests were carried out either on the expired, poisoned or
partly consumed catalyst or, alternatively, on the newly prepared, preac-
tivated or ‘simulated’ solid. Great progress was achieved in this way, a
fact borne out by the virility of the chemical industry in which heteroge-
neous catalysts continue to play a crucial rôle.
My own chapter in this book highlighted EXAFS, radioisotopes, neutrons,
Raman spectroscopy, FTIR and magnetic resonance. In retrospect, we see that
Design and Chance in My Scientific Research 829
all these, except neutrons (because, inter alia, they demand large samples) have
been very helpful for in situ investigation of catalysts.
Following discussions with Jerzy Haber in the early 1980s, I convinced him –
not that he needed to be – that X-ray absorption spectroscopy (XAFS) had
already become a sine qua non in catalysis research. But the trouble was, little
access to synchrotron radiation was available in the U.K. (the situation was
very different in Japan, and quite good in Germany). In 1982, Roman
Kozlowski, one of Jerzy Haber’s PDRAs, joined me in Cambridge and Robert
Pettifer in Warwick (a joint appointment supported by the SRC). We had great
difficulties; but we did succeed to record the first genuine XAFS study of a real-
life catalyst, V2O5 supported on TiO2 (which selectively oxidizes ortho-xylene to
phthalic anhydride153). Useful as this work was – and it taught me a great deal –
it was far removed from the kind of in situ studies (on single crystals and on
organometallic catalysts immobilized on oxide supports) that Haruo Kuroda
and Yasuhiro Iwasawa were doing in Japan.
When I invited Haruo Kuroda to Cambridge in 1985 to tell us about the
Japanese ‘‘Photon Factory’’ – their high-flux synchrotron – I felt convinced
that XAFS alone, and, if possible, in conjunction with other measurements,
was the way forward for in situ studies of solid catalysts.
Shortly after I took up the Directorship of the RI, Professor Alan Leadbet-
ter, formerly of Exeter, was the Head of the Central and Synchrotron Facilities
at Daresbury. He invited me to give a review lecture there. And, afterwards, I
had a long chat with Neville Greaves and told him how excited I had been to see
the work of Joe Wong et al. on XAFS studies of a range of vanadium oxides.
Neville’s response was superb. He became as convinced as I was that we had to
collaborate, which is what we did (from 1987 to 1996) on the application of
XAFS (both extended and near-edge, EXAFS and XANES). Special cells were
built. Neville, Andy Dent and his other colleagues acquired the requisite
instrumentation; and, in the fullness of time, we set up the first combined
XAFS-XRD (X-ray diffraction) facility in the world to explore solid catalysts
in situ. John Couves, Eric Dooryhee, Carol Williams (after she returned from
Novosibirsk) and later Richard Jones, Sankar, Jiesheng Chen, David Waller, as
well as Richard Catlow from time-to-time joined in this adventure. Paul Wright
and Gareth Derbyshire were also part of the team. And so it came that we
published one of the papers of which I am most proud (see Figure 12).154–156
Soon we improved the technique of combined XAFS-XRD further by
incorporating a fluorescence detector (see Figure 13) which gave us much
greater sensitivity in our measurement of XAFS spectra.
Numerous applications followed. We ‘‘watched’’ the production of a sup-
ported metal catalyst on a high-area oxide (i.e. Cu on ZnO154). We followed the
course of Ti41 ions in MCM-41 impregnated samples (for epoxidation) – this
work was done jointly with Avelino Corma157 – we also established the precise
atomic architecture of both the Brønsted active site and the redox active site in
CoIIALPO-18 and CoIII-ALPO-18.158 (The point to remember here is that both
these active sites are located at the accessible, three-dimensional surface of the
microporous (open structure) catalyst. What is in the bulk in these solids is
830 Chapter 48

Figure 12 Title and abstract of the first published paper describing the combined use
of XAFS and XRD to determine both short- and long-range order. This
approach enables the atomic detail of a catalytically active site as well as
the structural integrity of the solid to be simultaneously determined.154

simultaneously at the surface. This is why conventional bulk methods of

analysis (XAFS and XRD) are, at one and the same time, surface techniques.)
But perhaps our most perspicuous contribution159 came when, through a
fortunate concatenation of circumstances, Maschmeyer, Rey, Sankar and I
charted the preparation, the activation, the catalytic turnover, the gradual loss
of catalytic activity and its reactivation, all in situ, in the case of TiIV-centred
epoxidation catalysis, which is described in detail in Maschmeyer’s chapter in
this book. I say fortunate circumstances because Thomas Maschmeyer, whose
idea it was to use the titanocene (and whose knowledge of immobilization of
organometallic entities on oxides was considerable) entered my laboratory, to
my delight, just when Fernando Rey, who had come from Corma’s laboratory,
Design and Chance in My Scientific Research 831

Figure 13 The experimental set-up that yields the XRD patterns (from the position-
sensitive detector) and the XAFS spectra to be recorded in parallel either
by fluorescence detection or by absorption.155

had worked out a rapid, simple and reliable method of preparing mesoporous
silica of high area, and just when Sankar was at his most effective as a
synchrotron-based expert. I had earlier, in an article I was invited to write in
Nature,160 made the point that, with the arrival of mesoporous silicas (like
MCM-41), the stage was now set for large precursor catalysts to be immobi-
lized at the inner walls of such silicas, and that quite bulky reactants could
readily reach (by rapid diffusion through the mesopores) the active sites. (I also
said that enzymes could also be considered as anchored catalytic entities inside
the pores. This has subsequently been done by Hodnett and by Paul Wright.)

8.3 Computational Chemistry and Collaboration

with Richard Catlow
There was an element of opportunism associated with my recommendation to
the Council of the RI that the Chair of Natural Philosophy that became vacant
at the DFRL in 1989 should be filled by Richard Catlow. Not only had I been
collaborating with him already, it was clear that, if he were to join us, he could
guide me and my small group into rich computational chemical pastures.
Moreover, he was a top-quality person (whom I had frequently invited to talk
to my Monday lunchtime group meetings in Cambridge); he was a decent
832 Chapter 48
human being; a prodigiously hard-working man, who, as well as his compu-
tational skills, was aux fait with developments in synchrotron science. In
addition, he could be relied upon to equip the DFRL with cutting-edge
computational facilities. Richard was also genuinely interested in the popular-
ization of science, and was especially keen to give lecture demonstrations to
school children of all ages, a very important facet of the work of professors at
the RI. Little time elapsed, after his appointment, before all these hopes of mine
were fulfilled.
Richard Catlow has always attracted gifted graduate students and PDRAs;
and that soon became apparent when he, Clive Freeman and I started to
interact by computing the location and energetics of organic molecules in
microporous adsorbents and catalysts, where we combined ‘‘docking’’ proce-
dures with MD computations.161 Soon, with our joint Polish PDRA, Zbigniew
Kaszkur, Richard and I were engaged in computing the location of chloroform
and dichlorobenzene in zeolitic solid adsorbents and finding satisfactory agree-
ment with directly measured locations (via synchrotron radiation).162
But perhaps one of the most satisfying collaborations that Richard and I had
on the computational front was the one that involved Joachim Sauer163 (who
had visited us at the RI). This entailed an atom-atom approach to the study of
bridging hydroxyl groups in zeolitic catalysts: in particular a simulation of the
structure, vibrational properties and acidity in protonated faujasites (H-Y
zeolites). So good was the agreement between, for example, the computed
and observed IR frequencies of the loosely bound protons to the bridging
oxygens that we convinced the world of the great value of the computational
approach. Very many comparable adventures soon ensued: a combined
molecular dynamics-Rietveld powder diffraction study of the location of
1,4-dibromobutane in zeolites;164 a short review on the modelling of solid
catalysts;165 a computational analysis (well ahead of its time) of the energetics
and lattice dynamics of germanium-containing zeolitic solids;166 a critique on
simulating and predicting crystal structures;167 a computational study142 of the
adsorption of the four isomers of butanol in silicalite and H-ZSM-5, which
complemented my earlier experimental studies with Carol Williams and
Zamaraev.138,139

8.4 Other Turning Points at the DFRL

One of my former associates at Cambridge, Wataru Ueda, on returning to
Japan began to collaborate with my team in the difficult task of ‘‘oxidizing’’
methane to useful C2 products: some novel solid-state structures were explored
by him and us (largely Kenneth Harris and John Williams ) and we found168 a
novel structure (and solved it !) in the material Cs2Bi10Ca6Cl12O16. It had been
a gleam in my eye ever since Wataru had joined us in Cambridge that
Aurivillius and Aurivillius-Sillen structures, exemplified by Figure 14, could
function as effective selective oxidation catalysts for hydrocarbons. This indeed
turned out to the case; and even simpler structures, based on bismuth
Design and Chance in My Scientific Research 833

Figure 14 An example of a mixed Aurivillius-Sillen structure, typified by PbBi3ReO8Cl2,

a catalyst for the oxidative dehydration of methane (after Thomas et al.169).

oxychloride, and we discovered170 several new catalysts for the oxidative

dimerization of methane to form C2-compounds on a variety of so-called
Arppe’s phase of the oxychlorides of Bi, La and Sm.
Many other exciting ventures were opened up at the DFRL, two particularly
important ones being: (a) the formation and full characterization of DAF-1171
(Davy Faraday No. 1, designated DFO by the International Zeolite Society).
This was largely the effort of Paul Wright (see his chapter with Wuzong Zhou
on a full account of the story, and for an illustration of its unique structure);
and (b) the uptake of water by the acid catalyst H-SAPO-34 (which is described
in this book both by Cheetham and by Marchese). One of the reasons why
H-SAPO-34 was of critical importance was because theoretical computations
by others indicated that no H3O1 ions should be formed during the uptake of
water. Our FTIR and, later, neutron scattering, work left no doubt that H3O1
ions were definitely formed.172
In addition, Jiesheng Chen opened up a large family of new catalysts173
(MAPO-18, M ¼ Mg, CoII, Zn, . . .) which smoothly convert methanol to light
834 Chapter 48
174
alkenes, predominantly C2H4 and C3H6; Natarajan et al. discovered the first
open framework cobalt phosphate containing tetrahedrally bound CoII (this
material had interesting magnetic properties); Sankar led the way in our
combined QuEXAFS-XRD technique175 in high-temperature solid-state chemi-
stry when he showed how our in situ method could track the conversion of a
precursor zeolite into the important ceramic cordierite; we also were able176 to
probe by combined XAFS-XRD the onset of crystallization of a microporous
catalyst (Co-ALPO-5) in which we could identify, in solution, a pre-monitory
change of coordination of the CoII ions from octahedral to tetrahedral, prior to
the actual formation of crystalline nuclei; and, in a profitable, short collabo-
ration with Keith Ingold (to whose laboratory my PDRA Richard Oldroyd
went for a few months), we established that the TiIV-centred catalysis of the
epoxidation of cyclohexene by hydroperoxides was a radical-free (rather than a
free radical) reaction.177
Two other significant advances were made during that era in the DFRL: the
preparation (by R. Xu et al.) and characterization by XAFS of a layer
titanosilicate in which TiIV was in 5-fold coordination (square pyramidal as
in the mineral fresnoite),178 and the development, largely by Dewi Lewis,179 of
the Zebedde code for the de novo design of structure-directing agents for the
synthesis of microporous solids generally. Using the Zebedde approach we
succeeded in synthesizing a new molecular-sieve catalyst, DAF-4,180 which
converts methanol preferentially to ethene and propene.

8.5 Editorial Initiatives at the DFRL and RI

In addition to writing short (or long) reviews on strictly scientific topics – an
exercise that I always find illuminating and helpful in identifying future,
worthwhile projects – I also was expected to produce reviews and articles (as
well as numerous181 public talks) on Michael Faraday and the RI in the time
immediately preceding and following the bicentenary celebration (in September
1991) of the birth of Faraday, and pressing for first day postal stamps, bank
notes and public exhibitions to be organized in his honour.182 I was also
engaged in much editorial work and the writing of various monographs and
texts.
From the strictly scientific viewpoint, it has turned out – thanks to the
brilliant work done by Zewail and his team – that my speculations about
‘‘femtosecond diffraction’’184 and the possible dawn of a new era in structural
chemistry has been one of my most significant and accurate predictions.
Zewail, from 2004 onwards, building on his femtosecond skills, has revolu-
tionised electron microscopy. My review of 90 years of diffraction,185 since it
was first demonstrated by the Braggs, has also proved satisfyingly useful in that
it has prompted much new work. A selection of the editorial work, which
brought me into written and sometimes verbal contact with scientists whom I
had long admired and from whom I acquired good scientific habits, is given in
Table 1.
Design and Chance in My Scientific Research 835
Table 1 A Selection of my editorial work and my reviews of popular and
frontier science while working at the RI.
 Selections and Reflections: the Legacy of Sir Lawrence Bragg (co-editor with Sir
David Phillips). Contributions by Linus Pauling, Lord Todd, Dorothy Hodgkin,
Max Perutz, John Kendrew, Francis Crick, Sir Aaron Klug, Sir Nevill Mott,
James D. Watson, Sir Brian Pippard, Lord Porter, Jack Dunitz, Ullie Arndt,
A. Guinier, H.S. Lipson, Charles Taylor and others (Science Reviews Ltd, 1990).
 Curiosity, Chance, Paradox and Perspective in the Chemistry of Materials
(Sesquicentenary Issue of J. Chem. Soc. Dalton Trans., 1991, 555–563).
 Perspectives in Catalysis (co-editor with K.I. Zamaraev) (IUPAC and Blackwells,
Oxford, 1992).
 In Praise of Michael Faraday, Chem. Br., 1991, 27, 765–766.
 Femtosecond electron diffraction, Nature, 1991, 351, 694.
 Science at interfaces: the metaphor and the reality – a bicentennial assessment of
Michael Faraday, J. Chem. Soc. Faraday Trans., 1991, 87, 2865–2870.
 Michael Faraday and the Royal Institution: The Genius of Man and Place.
Monograph published by Institute of Physics, 1991; translated into Japanese,
1994, and Italian, 1997.
 Michael Faraday and his Contemporaries, J.M. Thomas and A.B. Pippard.
A Handlist for the Exhibition at the National Portrait Gallery, 1991.
 A Personal View of Michael Faraday and the Royal Institution, Bull. History
Chem., 1991, 11, 4–9.
 Sir Humphry Davy who Abominated Gravy . . ., Adv. Mater., 1991, 3, 582–589.
 Solid Acid Catalysts, Scientific American, 1992, 266, 85–88.
 The genius of Michael Faraday, Engineering Science, 1992, 20–27 (written version
of Watson Centennial Lecture at California Institute of Technology, September
1991).
 I Michael Faraday er Anrhydedd (in praise of Michael Faraday – in Welsh),
Y Gwyddonydd, 1992, 29, 102–106.
 New Methods for Modelling Processes within Solids and at their Surfaces
(co-edited with C.R.A. Catlow and A.M. Stoneham), O.U.P. and Royal Society,
1993.
 Turmoil in Higher Education, Proc. of Joint HEFCW – Univ. of Wales Conf.,
Cardiff, 1993, 1–20.
 Syr Humphry Davy (A Welsh article on the life and work of Davy),
Y Gwyddonydd, 1993, 30, 31–39.
 Tales of tortured ecstacy: probing the secrets of solid catalysts, Faraday Disc.,
1995, 100, C9–C27. (A celebration of Physical Chemistry to mark the 100th
Discussion Meeting of the Faraday events.)
 Michael Faraday een Kerstventelling (in Dutch), Nat. Tech., 1996, 12, 74–85.
 Davy et Faraday: Deux Genies Contrastes (in French), Actualite Chim., 1997, 3,
23–27 et 4, 29–34.
 Landmarks in the evolution of heterogeneous catalysis, with P.A. Wright and
R.G. Bell, Bull. Soc. Chem. France, 1994, 131, 463–485.
 Turning points in catalysis, Angew. Chemie Int. Ed., 1994, 33, 913–937.

Note: In 1988 a new journal, with G.A. Somorjai and J.M. Thomas as Co-editors in Chief, Catalysis
Letters, was started and another Topics in Catalysis, in 1994. With A.K. Cheetham and
H. Inokuchi, J.M. Thomas initiated Current Opinion in Solid-State and Materials Science.
836 Chapter 48
The last two reviews in Table 1 were written versions of the opening review
talk (on turning points in catalysis) that I gave at the First Europacat Sympo-
sium, held in Montpellier in September of 1993.

9 Return to Cambridge, Collaborations with Brian

Johnson and Paul Midgley. Tomography and
Enantiocatalysis
Many of my friends have told me that I should never have resigned the
Directorship of the RI. Although it was not disclosed until much later
(2002), my reasons for doing so were personal. My wife’s cancer had returned
in late 1989, and the medical advice was that she would live longer if she were
relieved of the gruelling entertainment and organization associated with Friday
Evening Discourses and other public events at the RI. So, in late 1991, when
Lord Cledwyn of Penrhos (Pro-chancellor of the Federal University of Wales)
and others (including the former Prime Minister, Lord Callaghan) pressed me
to become Deputy Pro-Chancellor (based in Cardiff, for 3 days a week) I
accepted the offer. It meant that, as a family, we could live in our Cambridge
home again, and Margaret’s arduous duties were eliminated. In 1993, however,
I was elected Mater of Peterhouse; and Margaret thought that she could cope
with the not inconsiderable but less stressful duties of being Master’s wife
(which she did magnificently). To my delight, Colin Humphreys, as Head of
Materials Science in Cambridge, immediately offered me space in that Depart-
ment where I was (and still am) made most welcome. His successors as Heads of
Department186 have all given me considerable support in the very happy and
distinguished Department that they ran and run. (In 2002, as soon as my term
of duty as Master of Peterhouse ended, the University of Cambridge conferred
upon me the title of Honorary Professor in Solid-State Chemistry.)
But, from the time I resigned as Director of the RI and DFRL in 1991, I still
continued to pursue much of my research at the DFRL (supported by rolling
grants from EPSRC), and, in addition to my interaction with Richard Catlow
and others there, I began some new ventures with two exceptionally gifted
PDRAs: Thomas Maschmeyer, who came with a sky-high reputation from the
University of Sydney, and Robert Raja, who had graduated in the National
Chemical Laboratory, Pune (and who had won a prestigious Research Fellow-
ship from the Commissioners of the Royal Exhibition of 1851). With my other
colleagues they added new impetus to my research – see their chapters in this
book for more details. In particular, we constructed at the DFRL one of the
most versatile and compact in situ cells for following catalytic reactions
involving liquids, gases and solids, with automatic (microprocessor-operated)
microanalytical facilities capable of extracting microlitre samples from the
reactor to enable us to record kinetic runs. We also set up a facility (that could
be transported to the synchrotron) for in situ studies of XAFS, XRD and
chemical conversion (followed by mass spectrometry, FTIR and
Design and Chance in My Scientific Research 837
chromatography). Many of these features and the results they yielded in
environmentally friendly (often solvent-free) conditions were described in my
Linus Pauling Lecture at Caltech in 1999.187 This equipment was used for
the first-ever, in situ XAFS-XRD study of a solid-liquid catalytic system, the
selective oxidation of cyclohexane, where we saw structural changes in the solid
catalyst during the induction period,188 prior to the onset of catalysis.
From 1998 onwards, I focused exclusively on single-site heterogeneous
(solid) catalysts for environmentally benign processes. Their advantages are
many, as has been described elsewhere.189 Above all, they enable one to evolve
a proven, reliable strategy for the design of new catalysts.
In my travels to and from Cambridge and the DFRL, I once had an
unpremeditated meeting (on the train) with Brain Johnson that had far-
reaching consequences. We quickly agreed that by combining his vast experience
in organometallic chemistry with my resources at the DFRL (they were later
transferred to Brain’s laboratory) we would have unique opportunities, especially
in hydrogenation catalysis. Thomas Maschmeyer, Sankar, Robert Raja, Doug
Shephard, Wuzong Zhou, Lynn Gladden, and later Paul Midgley, and many of
Brian’s bright graduate students, Matthew Jones, Tanya Khimyak, Sophie
Hermans, Marcus Klunduk and Stuart Raynor, as well as Tim O’Connor,
Stefan Bromley and Matthew Weyland (the latter being Paul Midgley’s Ph.D.
student) played a critical role in our development of high-performance nano-
particle bimetallic catalysts, such as that illustrated in Figures 15 and 16.190,191

Figure 15 On a background where the white spots denote the location of individual
Ru6Sn nanoparticle hydrogenation catalysts, a schematic drawing shows
how the nanoparticles are thought to be bound at the walls of the
mesoporous silica support (after Thomas et al.190).
838 Chapter 48

Figure 16 Some of the facile selective hydrogenations that are catalysed by the
bimetallic nanoparticle Cu4Ru12C2, drawn schematically inside the open-
ing of a single pore of mesoporous silica.190

Brian Johnson’s hospitality, cooperation and expertise was crucial in fostering

the highly successful years of collaboration that we pursued in Cambridge.
Tomography, using scanning transmission electron microscopy (see chapter
by P.A. Midgley), played a critical role in this facet of my work. It was the
shrewd suggestions of Paul Midgley, concerning Z-contrast scanning electron
microscopy and the collaborative work that he and I did with Pratibha Gai
and Ed Boyes, that convinced me that scanning electron tomography192,193
would provide unique new insights into supported catalysts, particularly those
of the (high Z) precious metal group (Pt, Pd, Rh, Ru, etc.) on light high-area
supports (especially mesoporous silicas). A recent review, co-authored with
Paul and our two associates Ana Hungria and Edmund Ward194 summarizes
the huge potential that electron tomography has in chemical, biological and
materials science.
The extension of my work on bimetallic nanoparticles has subsequently
involved fruitful collaboration with Rick Adams and Burjor Captain at the
University of South Carolina (see their chapter), and this has taken us into the
exciting field of trimetallic nanoparticle catalysis, to which our Spanish PDRA
at Materials Science, Ana Hungria, has made significant contributions.195
Another significant turning point that had its origins in the DFRL,
prompted by suggestions made by Thomas Maschmeyer, came to fruition
during my active collaboration with Brian Johnson and his students, but which
Design and Chance in My Scientific Research 839
involved (initially) Thomas Maschmeyer and (later and crucially) Robert Raja.
This is the new approach to heterogeneous enantioselective catalysis involving
spatially constrained chiral organometallic (mainly Pt, Pd or Rh cations and
N-containing chiral ligands). Full details have been given elsewhere.189,190
Expert contributions of Matthew Jones, Kenneth Harris196 as well as access
to the unique equipment in the Bayer Laboratories at Leverkusen, made the
key difference between success and failure in this new approach (which has
since been taken up by Can Li and others197 in China, Korea and the
Netherlands) to producing enantiopure products.

10 The Present
Throughout my scientific career, I have been able to interact constructively
with old and new colleagues, particularly with former members of my research
groups. Exciting new prospects are opening up in the application of aberra-
tion-corrected electron microscopy198 to the study of nanoparticle catalysts,
for example; and altogether new kinds of solid-state NMR experiments
involving liquid–solid interactions have recently emerged199 thanks to Kenneth
Harris’ ingenuity. Moreover, with the Diamond Synchrotron Facility about to
become operational, there are opportunities, which I am exploring with
colleagues,200 of carrying out quite new types of investigations of solid
catalysts and photocatalysts. It also seems likely that electron-wave hologra-
phy, especially for the investigation of micromagnetic materials, could con-
tribute much to solid-state science. And the prospect that trimetallic
nanoparticle catalysts may be able to play a key role in sustainable develop-
ment – just as Ru10Pt2 bimetallic ones have done for the conversion of
muconic acid, which is derivable from corn, into adipic acid201 – is one that
awaits further exploration.
Now, in the autumn of my days, my interest in solid-state chemistry,
materials and surface science is greater than ever it was. I am nourished
intellectually through my continuing collaborations (Paul Midgley and Brian
Johnson in Cambridge, Robert Raja in Southampton, Kenneth Harris in
Cardiff, Rick Adams in Carolina) and by the stimulating and congenial
atmosphere of the Department of Materials Science in Cambridge and the
Fellowship at Peterhouse. I have a book half (re-) written on catalysis with
Lynn Gladden and W. John Thomas, another with Robert Raja, and yet
another is planned on the new era in electron microscopy with Ahmed Zewail.
One of the greatest pleasures, cerebrally, for me these days is to keep abreast of
the pulsating pace of Zewail’s work on‘‘4D Ultrafast Electron Diffraction,
Crystallography and Microscopy’’. In his seminal review202, he pays me hand-
some compliments for noticing the enormous potential of his work on femto-
second diffraction in 1991. In my Nature ‘‘News and Views’’ I said184 ‘‘If the
experiment (that Zewail can now do) does indeed prove successful it will mark the
dawn of a new era’’. What I see, inter alia, in Zewail’s recent remarkable
breakthroughs is the time-dimension being added to many of the electron
840 Chapter 48
microscopic experiments that I have myself pursued over the years – but also so
very much more.202–206
I end with a reference to my hero since my schooldays, Michael Faraday
(Figure 17). It was when my physics Mistress in South Wales, Irene James, told
her class about the life and achievements of Michael Faraday some 60 years
ago, that the flame of science was lit in my heart and in my mind. To be
appointed in 1986 one of his successors at the RI, and to occupy the Fullerian
Professorship that was created for him, was the greatest scientific honour I have
had bestowed upon me. At the RI, I sat in the chair used by Faraday and wrote
at his desk. When I retired at night, the bathroom furniture had a brass plate
bearing his signature; and each time I gazed at it, I felt, knowing how
prodigiously hard he used to work, that I had not done enough to earn a
night’s sleep. All but a few of the papers and books written by Faraday – there
were over 450 in all – were authored solely by him. This is but one of the
reasons why he is regarded as perhaps the greatest experimenter and natural
philosopher of all time.

Figure 17 Portrait of Michael Faraday (when he was in his mid-forties) by Thomas

Phillips. One of his favourite mottos was: ‘‘Work, finish, publish’’.
Design and Chance in My Scientific Research 841

References
1. J.M. Thomas, Chem. Britain, 1970, 6, 1.
2. M. Faraday, Phil. Trans. Roy. Soc., 1834, 55.
3. M. Polanyi, Z. Phys., 1934, 89, 660.
4. G.I. Taylor, Proc. Roy. Soc. A, 1934, 145, 362.
5. J.M. Burgers, Proc. K. Ned. Akad. Wet, 1939, 42, 293.
6. A.H. Cottrell, Dislocations and Plastic Flow in Crystals, Oxford Univer-
sity Press, Oxford, 1953.
7. E.E. Glenda Hughes, K. Syers and J.M. Thomas, J. Sci. Instrum., 1962,
39, 485.
8. E.E. Glenda Hughes and J.M. Thomas, Nature, 1962, 193, 838.
9. J.M. Thomas, C. Roscoe, K.M. Jones and G.D. Renshaw, Phil. Mag.,
1964, 10, 325.
10. O.P. Bahl, E.L. Evans and J.M. Thomas, Proc. Roy. Soc. A, 1968,
306, 53.
11. G.D. Renshaw and J.M. Thomas, Nature, 1966, 209, 1196.
12. P.B. Hirsch, A. Howie, R.B. Nichalson, D.W. Pashley and M.J. Whelan,
Electron Microscopy of Thin Crystals, Butterworths, London, 1965.
13. S. Amelinckx, Dislocations in Crystals, Academic Press, London, 1964.
14. E.L. Evans, B.R. Williams and J.M. Thomas, J. Sci. Instrum., 1966, 43,
263.
15. J.M. Thomas, Sci. Prog., 1962, 50, 46.
16. E.R. Andrew, A. Bradbury and R.G. Eades, Nature, 1958, 182, 1659.
17. (a) Gareth Roberts first became a member of the teaching staff in Bangor.
Later he worked in the Xerox Co., USA; then as a Professor in Coleraine
and later at the Universities of Durham and Oxford. An FRS, he was
knighted in 1995; (b) Robin Williams was also a staff member at
Coleraine, and later a Professor of Physics at Cardiff, before becoming
Vice-Chancellor at the University of Wales, Swansea; (c) ‘‘J.O.’’ did a
post-doctoral period in Michigan State University, returned as a member
of my staff at Aberystwyth, then became Professor and Head of Chemi-
stry at UMIST before taking up the post of Chief Executive at the North
East Wales Institute of Technology.
18. T.A. Clarke and J.M. Thomas, Trans. Faraday Soc., 1969, 65, 2178.
19. J.T. Daycock, G.P. Jones, J.R.N. Evans and J.M. Thomas, Nature, 1968,
218, 672.
20. J.M. Thomas, J.R.N. Evans, T.J. Lewis and P. Secker, Nature, 1969, 222,
375.
21. M.D. Cohen, I. Ron, G.M.J. Schmidt and J.M. Thomas, Nature, 1969,
224, 167.
22. J.M. Thomas, Nature, 1979, 279, 755.
23. J.A. Ballantine, J.H. Purnell and J.M. Thomas, U.S. Patent 4,499,319
(1985).
24. J.M. Thomas, E.L. Evans, M. Barber and D. Swift, Trans. Faraday Soc.,
1971, 67, 1875.
842 Chapter 48
25. M. Barber, E.L. Evans and J.M. Thomas, Chem. Phys. Lett., 1973, 18,
423.
26. R.H. Williams, J.M. Thomas, M. Barber and N. Alford, Chem. Phys.
Lett., 1972, 17, 142.
27. J.M. Thomas, E.L. Evans, B. Bach and J.L. Jenkins, Nature Phys. Sci.,
1972, 235, 126.
28. E.L. Evans and J.M. Thomas, J. Solid State Chem., 1975, 14, 99.
29. M.A. Alario Franco, J.M. Thomas and R.D. Shannon, J. Solid State
Chem., 1974, 9, 261.
30. D.A. Jefferson, G.R. Millward and J.M. Thomas, Acta Cryst. A, 1976, 32,
823.
31. G.R. Millward, J.M. Thomas and D.A. Jefferson, J. Microsc., 1978, 113,
1.
32. E.L. Evans, J.M. Thomas, P.A. Thrower and P.L. Walker, Carbon, 1973,
19, 441.
33. D. Goode, Y. Lupien, W. Siebrand, D.F. Williams, J.M. Thomas and J.O.
Williams, Chem. Phys. Lett., 1974, 25, 308.
34. S. Ramdas, G.M. Parkinson, J.M. Thomas, C.M. Gramaccioli, G. Filip-
pini, M. Simonetta and M.J. Goringe, Nature, 1980, 284, 153.
35. B.P. Clarke, J.M. Thomas and J.O. Williams, Chem. Phys. Lett., 1975, 35,
251.
36. J.O. Williams, B.P. Clarke, J.M. Thomas and G.J. Sloan, Chem. Phys.
Lett., 1977, 48, 560.
37. J.M. Adams, R.G. Pritchard and J.M. Thomas, J. Chem. Soc. Chem.
Commun., 1976, 358.
38. J.P. Desvergne, H. Bouas-Laurent, R. Lapouyade, J.M. Thomas, J.
Gaultier and C. Hauer, Mol. Cryst. Liq. Cryst., 1976, 32, 107.
39. J.M. Thomas, Nature, 1981, 289, 633.
40. J.M. Adams, R.G. Pritchard and J.M. Thomas, J. Chem. Soc. Chem.
Commun., 1978, 288.
41. H.W. Kohlschütter, Naturwissenshaften, 1923, 11, 865.
42. J.M. Thomas, Phil. Trans. Roy. Soc., 1974, 277, 251.
43. M.D. Cohen, Z. Ludmer, J.M. Thomas and J.O. Williams, Proc. Roy.
Soc. A, 1971, 324, 459.
44. W. Jones and J.M. Thomas, Prog. Solid State Chem., 1979, 12, 101.
45. G.M. Parkinson, J.M. Thomas, J.O., Williams M.J. Goringe and L.W.
Hobbs, J. Chem. Soc. Perkin Trans. 2, 1976, 836.
46. I.C. Paul and G.T. Go, J. Chem. Soc. B, 1969, 33.
47. W. Jones, J.M. Thomas and J.O. Williams, Phil. Mag., 1975, 32, 1.
48. J.P. Desvergne, J.M. Thomas, J.O. Williams and H. Bouas-Laurent,
J. Chem. Soc. Perkin Trans., 1974, 363.
49. D.M. Burland and J.M. Thomas, Chem. Phys. Lett., 1978, 57, 163.
50. C.A. Fyfe, J.M. Thomas and J.R. Lyerla, Angew. Chemie Int. Ed. Engl.,
1981, 20, 96.
51. E.S. Crawford, D.A. Jefferson, J.M. Thomas and C. Bishop, J. Chem.
Soc. Chem. Commun., 1978, 986.
Design and Chance in My Scientific Research 843
52. At that Soiree, my young enthusiastic colleague ‘‘J.O.’’ was describing our
in situ electron microscopic studies of anthracene to Sir Lawrence Bragg,
whom he had not recognised. JO’s first question to him was ‘‘Do you
know much about diffraction?’’.
53. L.A. Bursill, E.A. Lodge and J.M. Thomas, Nature, 1980, 286, 111.
54. J.W. Menter, Proc. Roy. Soc. A, 1956, 236, 119.
55. J.M. Thomas, G.R. Millward and L.A. Bursill, Phil. Trans. Roy. Soc. A,
1981, 300, 41.
56. J.M. Thomas, and G.R. Millward, J. Chem. Soc. Chem. Commun., 1982,
1380.
57. O. Terasaki, S. Ramdas and J.M. Thomas, J. Chem. Soc. Chem. Co-
mmun., 1984, 216.
58. J.M. Thomas, Proceedings of the 8th International Congress on Catalysis,
Berlin, 1984.
59. M. Audier, J.M. Thomas, J. Klinowski, D.A. Jefferson and L.A. Bursill,
J. Phys. Chem., 1982, 86, 58.
60. F. Delprato, L. Delmotte, J.L. Guth and L. Huve, Zeolites, 1990, 10, 546.
61. G.R. Millward, S. Ramdas and J.M. Thomas, Proc. Roy. Soc. A, 1985,
399, 57.
62. P.A. Wright, J.M. Thomas, G.R. Millward, S. Ramdas, and S.A.I. Barri,
J. Chem. Soc. Chem. Commun., 1985, 1117.
63. J.M. Thomas, G.R. Millward, D. White and S. Ramdas, J. Chem. Soc.
Chem. Commun., 1988, 434.
64. O. Terasaki, K. Yamazaki, J.M. Thomas, T. Ohsuna, D. Watanabe, J.V.
Sanders and J.C. Barry, Nature, 1987, 330, 58.
65. E. Lippmaa, M. Magi, A. Samoson, G. Engelhardt and A.R. Grannier,
J. Am. Chem. Soc., 1980, 102, 4889.
66. J. Klinowski, J.M. Thomas, C.A. Fyfe and G.C. Gobbi, Nature, 1982,
296, 533.
67. C.A. Fyfe, G.C. Gobbi, J. Klinowski, J.M. Thomas and S. Ramdas,
Nature, 1982, 296, 530.
68. J. Klinowski, S. Ramdas, J.M. Thomas, C.A. Fyfe and J.S. Hartman,
J. Chem. Soc. Faraday Trans., 1982, 78, 1025.
69. J.M. Thomas, C.A. Fyfe, S. Ramdas, J. Klinowski and G.C. Gobbi,
J. Phys. Chem., 1982, 86, 3061.
70. J.M. Thomas, J. Klinowski, S. Ramdas, B.K. Hunter and D.T.B.
Tennakoon, Chem. Phys. Lett., 1983, 102, 158.
71. A.K. Cheetham, M.M. Eddy, D.A. Jefferson and J.M. Thomas, Nature,
1982, 299, 24.
72. A.K. Cheetham, M.M. Eddy and J.M. Thomas, J. Chem. Soc. Chem.
Commun., 1984, 1337.
73. P.A. Wright, J.M. Thomas, A.K. Cheetham and A.K. Nowak, Nature,
1986, 318, 611.
74. P.P. Edwards, M.R. Harrison, J. Klinowski, S. Ramdas, J.M. Thomas,
D.C. Johnson and C.J. Page, J. Chem. Soc. Chem. Commun., 1984,
982.
844 Chapter 48
75. M.R. Harrison, P.P. Edwards, J. Klinowski and J.M. Thomas, J. Solid
State Chem., 1984, 54, 330.
76. P.P. Edwards, J.M. Thomas and P.A. Anderson, Acc. Chem. Res., 1996,
29, 23.
77. Y. Nozue, T. Kodaira, S. Ohwashi, T. Goto and O. Terasaki, Phys. Rev.
B, 1993, 48, 12253.
78. S. Ramdas and J.M. Thomas, Chem. Britain, 1985, 21, 49.
79. J.M. Thomas, T. Rayment and G. Williams, J. Chem. Soc. Faraday Trans.
I, 1988, 84, 2915.
80. J. Klinowski, M.W. Anderson and J.M. Thomas, J. Chem. Soc. Chem.
Commun., 1983, 525.
81. L.G. Mallinson, D.A. Jefferson, J.M. Thomas and J.L. Hutchinson, Phil.
Trans. Roy. Soc. A, 1980, 295, 537.
82. D.A. Jefferson, J.M. Thomas, D.J. Smith, R.A. Camps, C.J.D. Cato and
J.R.A. Cleaver, Nature, 1979, 281, 51.
83. C.R.A. Catlow, J.M. Thomas, S. Parker and D.A. Jefferson, Nature,
1982, 295, 658.
84. A. Pring, D.A. Jefferson and J.M. Thomas, J. Solid State Chem., 1984, 55,
125.
85. A. Pring, V.K. Din, D.A. Jefferson and J.M. Thomas, Mineral. Mag.,
1986, 50, 163.
86. A. Pring, D.A. Jefferson and J.M. Thomas, J. Chem. Soc. Chem. Co-
mmun., 1983, 734.
87. J.M. Thomas, Nature, 1979, 281, 523; see also D.A. Jefferson, J.M.
Thomas, G.R. Millward, A. Harriman and R.D. Brydson, Nature,
1986, 323, 428.
88. J.M. Thomas, Inorganic Chemistry Towards the 21st Century, M.H.
Chisholm (ed), ACS Publications, Washington DC, 1983.
89. T.G. Sparrow, B.G. Williams, J.M. Thomas, W. Jones, P.J. Herley, D.A.
Jefferson, J. Chem. Soc. Chem. Commun., 1983, 1432; see also B.G.
Williams, G.M. Parkinson, C.J. Eckhart, J.M. Thomas and T.G. Spar-
row, Chem. Phys. Lett., 1981, 78, 434.
90. R.D. Brydson, H. Sauer, W. Engel, J.M. Thomas and E. Zeitler, J. Chem.
Soc. Chem. Commun., 1989, 1016.
91. B.G. Williams, T.G. Sparrow and J.M. Thomas, J. Chem. Soc. Chem.
Commun., 1983, 1434.
92. J.M. Thomas, B.G. Williams and T.G. Sparrow, Acc. Chem. Res., 1985,
18, 324.
93. T.G. Sparrow, B.G. Williams, C.N.R. Rao and J.M. Thomas, Chem.
Phys. Lett., 1984, 108, 547.
94. J. Wong, D.A. Jefferson, T.G. Sparrow, J.M. Thomas, R.H. Milne,
A. Howie and E.F. Koch, Appl. Phys. Lett., 1986, 48, 65.
95. A. Reller, J.M. Thomas, D.A. Jefferson and M.K. Uppal, Proc. Roy. Soc.
A, 1984, 394, 223.
96. C.L. Jia, M. Lentzen and K. Urban, Science, 2003, 299, 870.
97. J.M. Thomas and W. Zhou, ChemPhysChem., 2003, 4, 927.
Design and Chance in My Scientific Research 845
98. W. Zhou, M. Alario Franco, D.A. Jefferson and J.M. Thomas, J. Phys.
Chem., 1987, 91, 512.
99. W. Zhou, D.A. Jefferson and J.M. Thomas, J. Solid State Chem., 1987,
70, 129.
100. A. Harriman, J.M. Thomas, W. Zhou and D.A. Jefferson, J. Solid State
Chem., 1988, 72, 126.
101. D.A. Jefferson, J.M. Thomas, M.K. Uppal and R.K. Grasselli, J. Chem.
Soc. Chem. Commun., 1983, 594.
102. D.J. Buttrey, D.A. Jefferson and J.M. Thomas, Phil. Mag., 1986, 53, 897.
103. D.J. Buttrey, D.A. Jefferson and J.M. Thomas, Mater. Res. Bull., 1986,
21, 739.
104. J.M. Thomas and P.L. Gai, Supercond. Rev., 1991, 1, 1.
105. P.A. Wright, S. Natarajan, J.M. Thomas, R.G. Bell, P.L. Gai, R.H. Jones
and J. Chen, Angew. Chemie Int. Ed., 1992, 31, 1472.
106. E.L. Evans and J.M. Thomas, J. Solid State Chem., 1975, 14, 99.
107. R. Schlögl, W. Jones and J.M. Thomas, J. Chem. Soc. Chem. Commun.,
1983, 1330.
108. J.M. Thomas, J.M. Gonzalez-Calbet, C.A. Fyfe, G.C. Gale and M. Nicol,
Geophys. Res. Lett., 1983, 10, 91.
109. J.M. Thomas, Pure Appl. Chem., 1979, 51, 1065.
110. H. Nakaniski, W. Jones and J.M. Thomas, Chem. Phys. Lett., 1980, 71, 44.
111. W. Jones, H. Nakaniski, C.R. Theocharis and J.M. Thomas, J. Chem.
Soc. Chem. Commun., 1980, 610.
112. H. Nakaniski, W. Jones, J.M. Thomas, M.B. Hursthouse and M. Motevalli,
J. Chem. Soc. Chem. Commun., 1980, 611.
113. W. Jones, S. Ramdas, C.R. Theocharis, J.M. Thomas and N.W. Thomas,
J. Phys. Chem., 1981, 85, 2594.
114. W. Jones, C.R. Theocharis, J.M. Thomas and G.R. Desiraju, J. Chem.
Soc. Chem. Commun., 1983, 1443.
115. N.W. Thomas, S. Ramdas and J.M. Thomas, Proc. Roy. Soc. A, 1985,
400, 219.
116. He came on the advice of his Professor, Peter Wyatt, who was an
Aberystwyth graduate and who had felt that I would be able to guide
Kenneth sensibly in his Ph.D. studies. In retrospect, I cannot thank Peter
enough for his generous and (to me) still rewarding gesture.
117. K.D.M. Harris, J.M. Thomas and D. Williams, J. Chem. Soc. Faraday
Trans., 1991, 87, 325.
118. S. Evans and J.M. Thomas, Proc. Roy. Soc. A, 1977, 353, 103.
119. H. Bouas-Laurent, J.P. Desvergne, R. Lapouyade and J.M. Thomas,
Mol. Cryst. Liq. Cryst., 1976, 32, 107.
120. M.D. Hollingworth, K.D.M. Harris, W. Jones and J.M. Thomas,
J. Inclusion Phenom., 1987, 5, 273.
121. K.D.M. Harris and J.M. Thomas, J. Chem. Soc. Faraday Trans., 1990, 86,
2985.
122. K.D.M. Harris and J.M. Thomas, J. Chem. Soc. Faraday Trans., 1990, 86,
1095.
846 Chapter 48
123. K.D.M. Harris and A.J.O. Rennie, J. Chem. Phys., 1992, 96, 7117.
124. Andrew Rennie later graduated with first class honours in mathematics at
Trinity College, Cambridge.
125. M.J. Tricker, D.T.B. Tennakoon, J.M. Thomas and S.H. Graham,
Nature, 1975, 253, 110.
126. J.A. Ballantine, M. Davies, J.H. Purnell, M. Rayanokorn, J.M. Thomas
and K.J. Williams, J. Chem. Soc. Chem. Commun., 1981, 8.
127. J.A. Ballantine, J.M. Thomas and J.H. Purnell, J. Mol. Catal., 1984, 27,
157.
128. J.H. Purnell, J.M. Thomas and J.A. Ballantine, Clay Miner., 1983, 18, 347.
129. M.P. Atkins, Top. Catal., 2003, 24, 185.
130. D.T.B. Tennakoon, W. Jones and J.M. Thomas, J. Chem. Soc. Faraday
Trans. I, 1986, 82, 3081.
131. J.M. Thomas, Nature, 1986, 322, 500.
132. J.M. Thomas, Nature, 1985, 314, 669.
133. J.M. Thomas, Nature, 1979, 279, 755.
134. T. Rayment, R. Schlögl, J.M. Thomas and G. Ertl, Nature, 1985, 315,
311.
135. J.V. Lauritsen, R.T. Vang and F. Besenbacher, Catal. Today, 2006, 111,
34.
136. J.M. Thomas, C. Williams and T. Rayment, J. Chem. Soc. Faraday Trans.
1, 1988, 84, 2915.
137. P.J. Maddox, J.M. Thomas and J. Stachurski, Catal. Lett., 1988, 1, 191.
138. C. Williams, M.A. Makarova, J.M. Thomas, K.I. Zamaraev, Catal. Lett.,
1980, 4, 261; see also J. Catal., 1991, 127, 377.
139. K.I. Zamaraev and J.M. Thomas, Adv. Catal., 1996, 41, 335.
140. J.M. Thomas and K.I. Zamaraev, Angew. Chemie Int. Ed., 1994, 106, 316.
141. J.M. Thomas, Obituary of K.I. Zamaraev in The Independent, 22nd July
1996.
142. C.R.A. Catlow, A.A. Shubin, J.M. Thomas and K.I. Zamaraev, Proc.
Roy. Soc. A, 1994, 446, 411.
143. S. Yashonath, J.M. Thomas, A.K. Nowak and A.K. Cheetham, Nature,
1998, 331, 601.
144. S.D. Pickett, A.K. Nowak, J.M. Thomas, B.K. Peterson, J.F.P. Swift,
A.K. Cheetham, C.J.J. den Ouden, B. Smit and M.F.M. Post, J. Phys.
Chem., 1990, 94, 1233.
145. J.D. Gale, A.K. Cheetham, R.A. Jackson, C.R.A. Catlow and J.M.
Thomas, Adv. Mater., 1990, 2, 487.
146. I.J. Pickering, P.J. Maddox and J.M. Thomas, Angew. Chemie Int. Ed.,
1989, 28, 808.
147. Y. Xu, P.J. Maddox and J.M. Thomas, Polyhedron, 1988, 8, 819.
148. I.J. Pickering, P.J. Maddox, J.M. Thomas and A.K. Cheetham, J. Catal.,
1989, 119, 261.
149. I.J. Pickering, D. Madill, M. Sheehy, J. Stachurski, P.J. Maddox, J.W.
Couves, E. Dooryhee and J.M. Thomas, J. Chem. Soc. Faraday Trans.,
1991, 87, 3063.
Design and Chance in My Scientific Research 847
150. I.J. Pickering and J.M. Thomas, J. Chem. Soc. Faraday Trans., 1991, 87,
3067.
151. Y. Xu, C.P. Grey, J.M. Thomas and A.K. Cheetham, Catal. Lett., 1990,
4, 251.
152. J.M. Thomas and R.M. Lambert (eds), Characterization of Catalysts,
Wiley, Winchester, 1980.
153. R. Kozlowski, R.F. Pettifer, J.M. Thomas, J. Chem. Soc. Chem. Co-
mmun., 1983, 438; see also same authors in J. Phys. Chem., 1982, 87, 5172.
154. J.W. Couves, J.M. Thomas, D. Waller, R.H. Jones, A.J. Dent, G.E.
Derbyshire and G.N. Greaves, Nature, 1991, 354, 463.
155. J.M. Thomas, G.N. Greaves and C.R.A. Catlow, Nucl. Inst. Methods B,
1995, 97, 1.
156. J.M. Thomas and G.N. Greaves, Science, 1994, 265, 161.
157. G. Sankar, F. Rey, J.M. Thomas, G.N. Greaves, A. Corma, B.K. Dobson
and A.J. Dent, J. Chem. Soc. Chem. Commun., 1994, 2279.
158. J.M. Thomas, G.N. Greaves, G. Sankar, P.A. Wright, J. Chen, A.J. Dent
and L. Marchese, Angew. Chemie Int. Ed., 1994, 33, 1871.
159. T. Maschmeyer, F. Rey, G. Sankar and J.M. Thomas, Nature, 1995, 378,
159.
160. J.M. Thomas, Nature, 1994, 368, 289.
161. C.M. Freeman, C.R.A. Catlow, J.M. Thomas and S. Brode, Chem. Phys.
Lett., 1991, 186, 137.
162. Z.A. Kaszkur, R.H. Jones, J.W. Couves, D. Waller, C.R.A. Catlow and
J.M. Thomas, J. Phys. Chem. Solids, 1991, 52, 1219.
163. K.-P. Schroeder, J. Sauer, M. Leslie, C.R.A. Catlow and J.M. Thomas,
Chem. Phys. Lett., 1992, 188, 320.
164. Z.A. Kaszkur, R.H. Jones, D. Waller, C.R.A. Catlow and J.M. Thomas,
J. Phys. Chem., 1993, 97, 426.
165. C.R.A. Catlow and J.M. Thomas, Phil. Trans. Roy. Soc. A, 1992, 341.
166. A.R. George, C.R.A. Catlow and J.M. Thomas, J. Solid State Chem.,
1993, 104, 6.
167. C.R.A. Catlow, J.M. Thomas, C.M. Freeman and P.A. Wright, Proc.
Roy. Soc. A, 1993, 442, 85.
168. K.D.M. Harris, W. Ueda, J.M. Thomas and G.W. Smith, Angew. Chemie
Int. Ed., 1988, 27, 1364.
169. J.M. Thomas, W. Ueda, J. Williams and K.D.M. Harris, Faraday Disc.
Chem. Soc., 1989, 87, 33.
170. W. Ueda, F. Sakyu, Y. Morikawa and J.M. Thomas, Cat. Lett., 1991, 10,
83.
171. P.A. Wright, R.H. Jones, S. Natarajan, R.G. Bell, J. Chen, M.B. Hurst-
house and J.M. Thomas, J. Chem. Soc. Chem. Commun., 1993, 633.
172. L. Smith, A.K. Cheetham, R.E. Morris, L. Marchese, J.M. Thomas, P.A.
Wright and J. Chen, Science, 1994, 271, 799.
173. J. Chen and J.M. Thomas, J. Chem. Soc. Chem. Commun., 1994, 603.
174. J. Chen, R.H. Jones, S. Natarajan, M.B. Hursthouse and J.M. Thomas,
Angew. Chemie Int. Ed., 1994, 33, 639.
848 Chapter 48
175. G. Sankar, P.A. Wright, S. Natarajan, J.M. Thomas, G.N. Greaves, A.J.
Dent, B.R. Dobson, C.A. Ramsdale and R.H. Jones, J. Phys. Chem.,
1993, 97, 9550.
176. G. Sankar, J.M. Thomas, F. Rey and G.N. Greaves, J. Chem. Soc. Chem.
Commun., 1995, 2549.
177. R.D. Oldroyd, J.M. Thomas, T. Maschmeyer, P.A. MacFaul, D.W.
Snelgrove, K.U. Ingold and D.D.M. Wayner, Angew. Chemie Int. Ed.,
1996, 35, 2787.
178. M.A. Roberts, G. Sankar, J.M. Thomas, R.H. Jones, H. Du, J. Chen, W.
Dang and R. Xu, Nature, 1996, 381, 401.
179. D.W. Lewis, D.J. Willock, C.R.A. Catlow, J.M. Thomas and G.J.
Hutchings, Nature, 1996, 382, 604.
180. D.W. Lewis, G. Sankar, J.M. Thomas, C.R.A. Catlow and D.J. Willock,
Angew. Chemie Int. Ed., 1997, 36, 2675.
181. In 1991 alone I gave thirty-seven general (popular) lectures on Faraday
and the RI, mainly in English, but there were a few in Welsh.
182. I succeeded in all these, the d20 note carrying Faraday’s image being the
most satisfying, although the exhibition that I helped mount at the
Natural Portrait Gallery183 was also a great thrill.
183. J.M. Thomas and A.B. Pippard, Michael Faraday and His Contemporar-
ies, Handlist of the National Portrait Gallery, 1991.
184. J.M. Thomas, Nature, 1991, 351, 694.
185. J.M. Thomas, Nature, 1993, 364, 478.
186. Alan Windle, Derek Fray and Lindsay Greer, all Heads of Department at
various times.
187. J.M. Thomas, Angew. Chemie Int. Ed., 1999, 38, 3588.
188. T. Maschmeyer, R.D. Oldroyd, G. Sankar, J.M. Thomas, I.J. Shannon,
J.A. Kleptko, A.F. Masters, J.K. Beattie and C.R.A. Catlow, Angew.
Chemie Int. Ed., 1997, 36, 1639.
189. J.M. Thomas, R. Raja and D.W. Lewis, Angew. Chemie Int. Ed., 2005, 44,
6456; J.M. Thomas and R. Raja, Top. Catal., 2006, 40, 3.
190. J.M. Thomas, B.F.G. Johnson, R. Raja, G. Sankar and P.A. Midgley,
Acc. Chem. Res., 2003, 36, 20.
191. R. Raja, S. Hermans, J.M. Thomas, B.F.G. Johnson and T. Khimyak,
Angew. Chemie Int. Ed., 2001, 40, 4638.
192. M.A. Weyland, P.A. Midgley and J.M. Thomas, J. Phys. Chem. B, 2001,
105, 7882.
193. P.A. Midgley, M. Weyland, J.M. Thomas, P.L. Gai and E.D. Boyes,
Angew. Chemie Int. Ed., 2002, 41, 3804.
194. P.A. Midgley, E.P.W. Ward, A.B. Hungria and J.M. Thomas, Chem. Soc.
Rev., 2007, 36, 1477.
195. A.B. Hungria, R. Raja, R.D. Adams, B. Captain, J.M. Thomas, P.A.
Midgley, V. Golovko and B.F.G. Johnson, Angew. Chemie Int. Ed., 2006,
45, 4782.
196. M.D. Jones, R. Raja, J.M. Thomas, K.D.M. Harris and B.F.G. Johnson,
Angew. Chemie Int. Ed., 2003, 42, 4326.
Design and Chance in My Scientific Research 849
197. C. Li, H. Zhang, D. Jiang and Q. Yang, Chem. Commun., 2007, 547.
198. E.P.W. Ward, J.M. Thomas, I. Arslan, A. Bleloch and P.A. Midgley,
Chem. Commun., 2005, 2805.
199. M. Xu, K.D.M. Harris, J.M. Thomas and D.E.W. Vaughan, Chem-
PhysChem., 2007, 8, 1311.
200. R. Raja, M. Tromp, J. Evans, R.D. Adams, B. Captain, M. Anpo and
others, all of whom are now among my active collaborators.
201. J.M. Thomas, R. Raja, B.F.G. Johnson, T.J. O’Connell, G. Sankar and
T. Khimyak, Chem. Commun., 2003, 1126.
202. A.H. Zewail, Ann. Rev. Phys. Chem., 2006, 57, 65.
203. N. Gedik, D.-S. Yang, G. Logvenov, I. Bozovic and A.H. Zewail, Science,
2007, 316, 425.
204. J.M. Thomas, Angew. Chemie Int. Ed., 2005, 44, 5563.
205. K.D.M. Harris and J.M. Thomas, Cryst. Growth Des., 2005, 5, 2124.
206. H.S. Park, J.S. Baskin, O.-H. Kwon and A.H. Zewail, Nano Lett., 2007, 7,
2545.
 Appendices: Tributes
to Sir John Meurig Thomas
APPENDIX 1

Tribute to John Meurig Thomas

on the Occasion of His 75th
Birthday

It is a special pleasure to have the opportunity to write this tribute to my great

friend John Meurig Thomas. We are approximate contemporaries and
were colleagues in chemistry at Cambridge from 1978, when he came from
Aberystwyth to be Professor and Head of the Department of Physical Chemis-
try, until his departure to be the director of the Royal Institution of Great
Britain in 1986, and we have remained friends ever since. Although we were
based in different departments – I was in the Department of Organic and
Inorganic Chemistry on the south side of the building in Lensfield Road and
Physical Chemistry occupied the north side, and we had separate tea rooms –
we talked frequently. Our styles differed somewhat, in that John led a large
team of scientists and has a very lengthy publication list, but we found many
common interests and synergies. Our younger daughters were in the same form
at the Perse School for Girls and they became, and have remained, good
friends. We have a common interest in sport and particularly in cricket; we
opened the batting together for the team of the President of Queens’ College
against the students one summer afternoon, and both of us are supporters of
Cambridge University Cricket Club. We have urged each other on whilst
cycling to the Institute of Astronomy in West Cambridge for a Faculty Board
meeting when we were running a little late. And John and I are both recipients
of honorary DSc degrees from the University of Sydney. He came from South
Wales and I from New South Wales.
John’s research has produced major advances in many branches of physical
chemistry. I have particularly admired his designs for efficient inorganic cata-
lysts that are expanding the scope of clean technologies and his development of
new techniques for characterising solid catalysts. He and his collaborators have
made important contributions to electron microscopy, electron energy-loss
spectroscopy, solid-state nuclear magnetic resonance, X-ray diffraction,
X-ray absorption spectroscopy and neutron scattering. His is a remarkable
record of achievement and there is more to come. He is much in demand as a

853
854 Appendix 1
lecturer; I shall not forget his plenary lecture on the role of new catalysts in
clean technology delivered to the World Chemistry Congress in Brisbane,
Queensland in July 2001.
John is a cultured man with a prodigious memory – he recalls with apparent
ease poems, quotations, music and history, as well as jokes. His command of
the English language sets a standard for us to aspire to, and this despite English
being his second language. We learn new words – like eupeptic – through
reading his writings and scurrying to the dictionary. He enlivens any gathering.
On this 75th anniversary I wish him many further successes and much
happiness, and my wife and I express our gratitude for his friendship.

David Buckingham

Professor A.D. Buckingham, CBE, FRS

Emeritus Professor of Theoretical Chemistry,
University of Cambridge, UK.
APPENDIX 2

John Meurig Thomas and the

Royal Institution
I am a biologist, not a physical chemist, so I can only write of John as a friend,
not a colleague. These are just some personal reminiscences.
I first met John Thomas in 1987, when he was Director of the Royal
Institution (RI). I went there with two others representing the Clothworkers’
Company, to learn about the RI’s Mathematics Masterclasses, and to decide
whether we should recommend support of them by our Company. We were so
impressed, not only by the importance of the subject but also by John’s
presentation of it that we did recommend support on quite a large scale, and
this has continued ever since. It is one of the main components of the
Company’s charitable activity. The need to improve the teaching of mathe-
matics in this country is now widely recognized, for example by the Royal
Society, but I think it is fair to say that the RI, under John’s leadership, was the
first in this field.
From this first meeting there followed an invitation to give a Friday evening
lecture at the RI. Since I was professor of human nutrition I chose as my subject
‘‘The Diet of Ancient Greece and Rome’’. In those days – I do not know if it is
still like that now – the Friday lectures were formidable affairs. At 9 pm
precisely a large door is thrown open and you walk in and begin your lecture,
which has to finish in precisely one hour, with no introduction beforehand and
no questions afterwards. Looking back, I am surprised that I made the course,
particularly after the generous hospitality at dinner of John and Lady Thomas.
Later the boot was on the other foot. I went to a lecture John gave on Sir
Humphry Davy at the National Portrait Gallery. I am not good at lectures, seldom
enjoy them and easily go to sleep; but not at this one – it held me spellbound, not
only the content but John’s eloquence. I have never heard a better lecture.
The last time I saw him we had breakfast together in Cambridge when Lady
Thomas was terminally ill. I came away feeling how wonderful to have as a
friend a man of such wisdom and compassion.
John Waterlow

Professor John C. Waterlow, CMG, FRS

Emeritus Professor of Human Nutrition,
University of London, UK.
855
APPENDIX 3

Sir John Meurig Thomas:

An Unforgettable Person

Occasionally, I am asked something like, ‘‘You have been around for quite a
while. Who is the most unforgettable person you have ever known?’’ That is a
difficult question, because several might qualify and yet the name of John
Thomas certainly springs to mind as very high on the list and is easy to say with
true conviction.
Later, you might hear from the questioner, ‘‘I was very interested in your
reply and, although I have heard of John Thomas, I wanted to find out more, so
I went to the Internet and found that Google lists 239,000,000 John Thomas
items. What can I do now?’’ You can see why astute parents named John as
John Meurig Thomas in anticipation of the perceived need to have him
identified as a very unique John Thomas. So, if you enter John Meurig Thomas,
Google lists 60,300 entries and 29,500 entries for Sir John Meurig Thomas. The
nice thing is that all of the entries seem to be to our hero of the day.
In contrast, for John Roberts, Google produces 74,000,000 entries and John
D. Roberts, 47,100,000 very non-specific entries. But Google almost immedi-
ately asks, ‘‘Did you mean John G. Roberts?’’ (Chief of Justice, US Supreme
Court). So Meurig is a great help to being sure you have the right John
Thomas. The appellation Sir, normally suggests an Englishman, but that is
definitely incorrect. Sir John is Welsh, almost defiantly so, proud of his
ancestry, and his love of speaking, both in native Welsh and in English about
his region in the United Kingdom.
John was born in a coal-mining town in Wales. His interest in science was
stoked by learning in school about Michael Faraday and, judging from his
subsequent career, Faraday seems to have become his number one hero.
John received his BSc at the University of Wales in Swansea and his PhD at
the University of London. He started his academic career at the University of
Wales at Bangor in 1958, then moved to Aberystwyth in 1969, where he was
head of chemistry. The next steps were in 1978 to heading up physical chemistry
at Cambridge, and from 1986 to 1991, he was Director of the Royal Institution
in London, where he occupied the chair created for Michael Faraday. He was
also Director of the Davy-Faraday Research Laboratory. Following those

856
Sir John Meurig Thomas: An Unforgettable Person 857
experiences, he had his feet more or less firmly planted all at once in the Royal
Institution, Cambridge and Wales. He does research at the Royal Institution,
he was Master of Peterhouse College (the oldest of the Cambridge colleges) for
10 years and is honorary visiting professor in Wales at Cardiff.
His research career started on the properties of solids, particularly zeolites, as
studied by electron microscopy, neutron scattering, X-ray and synchrotron
radiation diffraction. This effort morphed into catalysts – especially for organic
reactions, often oxidation. He is apparently the current world leader in research
which could result in winning the Barton Challenge, a $5000 prize for the first
synthesis of adipic acid from n-hexane in at least 85% overall yield.
His glory in the catalyst field is championing single-site catalysts, where one
site does all, even of transformations you might think should require several
steps with different catalysts for each step. In this area of research, he has
uncovered not only currently useful commercial reactions, but also others of
real commercial as well as ‘‘green’’ potential.
He has published more than 1000 papers, two textbooks on heterogeneous
catalysts and a wonderful biography of Michael Faraday. Awards, honorary
society memberships and professorships, he has them; many more than can be
related here.
Sir John is a marvelous person, well spoken, a fabulous storyteller and a
fantastic writer (when he does an obituary, he brings you the real essence of his
subject and sets it in beautiful prose).
Those of us that know him at all well are swept off our feet by his
encyclopaedic memory. He will typically say something like, ‘‘On July 16,
1993, at the formal dinner, I asked you about ‘‘blank’’, and you answered,
blank, and blank. How do you feel about that now?’’ Sometimes other people
ask similar, but far less specific, questions. However, about 90% of the time, the
reply attributed to me seems to be something I feel I could never, ever have said.
John’s memory of such situations does not have that problem. I just hope when
John reports what I said at sometime was actually as well stated as he makes it
sound.
Last year, I had the honour of introducing John to a Caltech seminar
audience and was able to give his seminar title in a phonetic version of my
ancestors’ native Welsh:
MAN-TEI-SHION AH RAG-OH-LUG-ON SOLED AH KHAN-NOL-
VAN-EYE EN MAUTH.
People like John are indeed unforgettable!
John D. Roberts

Professor John D. Roberts,

Institute Professor of Chemistry Emeritus and
Former Provost and Chairman of Division of
Chemistry and Chemical Engineering,
California Institute of Technology, USA.
APPENDIX 4

John Meurig Thomas on His

75th Birthday

It does not happen often that a friendship initiated somewhat late in life
blossoms within a relatively short period of time into a relationship, which one
can normally only expect to achieve within a lifetime. But this is precisely the
case when John and I met quite unexpectedly only a few years ago.
I can be mathematically precise in stating the date and in describing the
event. In fact, we would not have met had it not been for the providential
intervention of my wife at a critical moment!
The occasion was my election to the Honorary Fellowship of the Academy of
Medical Sciences. The award ceremony was scheduled to take place at St
Bartholomew’s Hospital, London and the citation to be presented by an old
friend from my Manchester University days, Lord Turnberg (Leslie Turnberg),
a former distinguished President of the Royal College of Physicians, London.
It was a day when unbeknown to me a march was due to take place starting
in the Holborn area of London during the course of the afternoon. A vast
crowd had assembled; taxis and buses had stopped running. I naturally pan-
icked at this sight as it was quite impossible to reach the venue in time for the
ceremony, except by underground as walking was out of the question. I had
given up using the ‘‘tube’’ some 10 years earlier as a result of a very claustro-
phobic experience and I resolutely refused to go down into Holborn Station. It
was only my wife’s determination in allaying my fears which finally overcame
my resistance to take the underground train. We arrived at Barts just as the
proceedings were about to commence!
At the end of the presentations I was chatting with some friends when a
gentleman came up and introduced himself – this was John Meurig Thomas,
who had been invited (at the last minute) to the event by our mutual friend,
Keith Peters. John had heard another mutual friend, Max Perutz, talk of my
great interest in music. We had a long and delightful conversation and agreed
to see each other again. I realized immediately that I had the rare good fortune
of meeting a person with profound knowledge and achievements and I was very
much taken by his warm friendly outgoing manner and personality. Being
somewhat sensitive to ‘‘sound’’ I could tell immediately that he had a very

858
John Meurig Thomas on His 75th Birthday 859
musical and resonant voice and it was not difficult to identify him as belonging
to that unique Celtic Race – the Welsh! with their great tradition of music, and
particularly choral singing.
I learned later that John was a leading figure (an Honorary Bard) at the
National Eisteddfod of Wales and a highlight in his career was when he became
Vice-President of the Cambridge University Music Society in 1995!
The beginning of our friendship I always likened to that unforgettable last
scene in the legendary 1942 film Casablanca. Rick, played by Humphrey
Bogart, had just shot the dreaded Gestapo chief at the airport and, when the
police patrol car came up responding to the shooting, the local police chief
Louis (Claude Rains) tells them to ‘‘round up the usual suspects’’. Realising
that they would both be arrested, they walk away together into the misty
distant twilight to join the free French forces with Rick’s final words in the film:
‘‘Louis, I think this is the beginning of a beautiful friendship’’.
Well, without the necessity of shooting anyone, we established a ‘‘beautiful’’
friendship!
I discovered that the positions John had held in his life and the depth of
knowledge and scholarship in both his own subject and deep insight in the arts
were quite extraordinary.
To name but a few of his many important positions in academia: Professor at
Aberystwyth and Cambridge, Director of the Royal Institution, Master of
Peterhouse, Cambridge, Member of Council of the Royal Society, but his
distinguished CV is simply too vast to be given in full here.
As a retired, geriatric and out-of-date pharmacologist, I can hardly be
expected to know much about John’s particular field of solid-state and mate-
rials science, but I know he has made outstanding contributions and is
acclaimed as an international authority in his subject.
Apart from his outstanding scientific achievements, John is a superb writer
and orator. I have read quite a number of his publications also on more
generalized topics and they are full of erudition and profound knowledge and
understanding of the subject matter. Reading his obituaries of distinguished
personalities brought these individuals vividly back to life for me.
Seeing John in action as an orator is quite an experience. He is a born
communicator and this quality was dramatically brought home to me on one
occasion when I invited John to be opening speaker at the launch of one of my
CDs of vocal recordings, which took place at the Royal Institution. We had a
large and distinguished gathering with many true cognoscenti! John, without a
single note, gave us a masterly presentation of the venue in which we found
ourselves and its historic scientific significance, in which such luminaries as
Davy, Faraday, Dewar, the Braggs (W.H. & W.L.), Dale and George Porter
worked. Modesty, of course, forbade him to mention his own name in this
connection. John then proceeded to give us an account of the importance of the
area surrounding the Royal Institution. It was a dazzling performance!
Being in John’s company is always a very special pleasure, and at the end of
our usual three-hour sushi luncheon I feel that we have hardly covered the topics
on which he has so much to contribute. John is in great demand as a lecturer all
860 Appendix 4
over the world, while at the same time picking up highly coveted honours. He
simply has to travel so extensively because he is wanted everywhere. As a result,
he cannot obey one of Charles Darwin’s less known principles. In the words of
the great man himself ‘‘I am convinced it is a most ridiculous thing to go around
the world: when by staying quietly, the world will go around you’’!
It is such a privilege and pleasure for me to have been asked to provide an
appreciation of John for this Festschrift, and I do so with great humility to be
able to make my personal contribution to a great man at an important stage in
his life. On behalf of my wife, family and myself, we wish him many more years
of happiness and good health to carry on with his outstanding work in his life’s
journey. And we can still expect great things from John in the future; after all
many are the scientists, artists, physicians, architects and musicians and men of
letters who have accomplished great things at a ripe age. Ancient rabbinic
writings tell us that when men reach an advanced age they have developed
many qualities – of which wisdom is one – and are able to impart this to their
friends and colleagues, of a younger generation.
But let me conclude by mentioning just a few outstanding personalities who
have still achieved great things in the fullness of their years: Monet painted
some of his finest water lilies at Givenchy; Hokusai, the Japanese woodblock
artist aged 80 and at the height of his fame, exclaimed ‘‘If I were given 10 more
years, I promise to become a real artist’’; Verdi wrote his two operatic
masterpieces Otello and Falstaff in very advanced years; Neville Mott did his
Nobel prize-winning physics after he had officially retired here in Cambridge;
Haydn wrote his Creation and Seasons in his 70s; Heinrich Schütz, Bach’s great
predecessor, wrote some of his finest church music in his 80s; and, finally,
Goethe wrote his West–Eastern Divan in his 70s and some of his outstanding
poetry in his early 80s, not forgetting his amorous advances to much younger
ladies! Goethe also considered himself to be somewhat of a scientist and even
had his arguments with Newton about the theory of light and the nature of the
rainbow. In his famous poem Phenomenon, Goethe wrote (free translation)
‘‘Be of good cheer old fellow
Do not lose heart
Though your hair be white
You shall still find love’’
A poem immortalized by Brahms and Wolf.
John – may all these blessings be yours!

Ralph Kohn

Dr Ralph Kohn, FRS

The Kohn Foundation,
London, UK.
APPENDIX 5

Remembering a Period of Work

with Sir John Meurig Thomas

I met Sir John at a conference in Long Island, in 1968. That was a tumultuous
year in US politics, and if I remember correctly, we talked about public issues.
We did get around to science, and found that the crystal growth I was doing at
DuPont matched well with the work on characterization of defects in organic
crystals that John was carrying out. We resumed that conversation at the 1970
Molecular Crystals Symposium in Philadelphia. At the end of the program, I
invited him to visit my family in Wilmington, after which he made a counter
invitation: that I spend some time working with him in Aberystwyth.
There were family reasons not to do so immediately, but John repeated the
invitation and on Boxing Day 1972 Sonia and I arrived at Heathrow with our
sons Jonathan and Victor, in a nearly empty 747. The drive to Aber was
harrowing (windshield wipers failed in heavy rainstorm as we drove through
Rhyader) but we got there and were welcomed with great warmth by John and
Margaret, and ultimately by the whole family at Edward Davies Chemical
Laboratory. John and Margaret had found a lovely house (Tir-a-Mor) for us
on Cardigan Bay, and we were soon ‘‘at home.’’ We were helped to understand
local customs by the fact that John had subscribed to the Cambrian Times for us,
several months before our arrival. When informed of this, our mutual friend Dick
Merrifield asked if this publication was a successor to the pre-Cambrian Times.
I had brought with me some crystals of anthracene and related PAH’s
(polycyclic aromatic hydrocarbons) containing radio-tagged impurities and set
to work studying macro- and micro-distribution of impurities by autoradio-
graphy. John introduced me to the celebrated (for football prowess as well as
chemistry) J.O. Williams, who patiently taught me etching and microscopy
techniques, so that we could learn something about effects of physical defects
on impurity retention.
In no time at all I was ‘‘one of JMT’s team,’’ greatly enjoying interaction with
the international group of students and post-docs. Our boys were enrolled
in the Ardwyn School, which was near the lab, and they were frequent visitors
to the lab and more particularly to our lunch spot, Morgan’s Cafe, where they
cadged coins for purchases in the nearby sweets shop.

861
862 Appendix 5
During our stay, JMT was host to numerous distinguished visitors, including
Prof. Martin Pope (who was awarded the Davy Medal last year) and Prof. H.C.
Brown, who later won the Nobel Prize in Chemistry. During these social
occasions, we became aware of Sir John’s prodigious memory, and his ability to
focus totally on personal as well as scientific facts. Many years after our visit, he
reminded me that we were standing in the Aber post office when I first outlined
for him my reasons for scorning Richard Nixon. (In more recent visits, that
event comes up in the context of outlining even better reasons for scorning
George Bush.)
The relationship forged in Aber was the basis for a long series of visits by Sir
John to the DuPont Central Research and Development Department, involv-
ing many DuPont scientists.
Non-scientists may believe that scientists are cold and dedicated only to
work. JMT, while working for decade after decade at the peak of his consid-
erable intellectual power, has nurtured and shown the warmest of relations and
commitment to his family and to the enormous international family of friends
and colleagues who cherish his friendship and devotion. It is a rare and valued
privilege to be included in this circle, and to have the opportunity from time to
time, to welcome him in our home as an old friend. It was an especial pleasure
to visit with daughter Naomi last February, when the BBC Welsh National
Orchestra visited Wilmington. Naomi was a very small child when we first met
her, and it was wonderful to be brought together again through her music.

Gilbert Sloan

Dr Gilbert J. Sloan,
E.I. Du Pont de Nemours Experimental Station (retired),
Wilmington, DE, USA.
APPENDIX 6

Reflections on John Meurig

Thomas on the Occasion of His
75th Birthday

The occasion of this Festschrift to honour John Meurig Thomas, a great

scientist, humanist and polymath, brings back a flood of memories. It is an
honour to be part of what should be a parade of admirers of this unique man.
John is a dear friend, a most helpful, thoughtful, gifted and informed scholar,
and an utterly delightful personality.
I first met John back in 1970 at an Organic Crystals Symposium in Phila-
delphia. Because his everyday speaking was sheer poetry, I asked whether he
was related to Dylan Thomas or Gwyn Thomas. Little did I know that in
Wales, to have the surname Thomas was to be as gifted as Anonymous. About
the writer Gwyn Thomas, I will have more to say.
John has on several instances mentioned my role in getting him to focus on
organic crystals, where he used his awesome prowess in the analysis of crystal
structure and its imperfections, to clarify quantitatively the part they play in
affecting their electronic properties. That inspiration came to him from an
article describing the electronic properties of anthracene I wrote in the Scientific
American in 1967, 40 years ago. That same article also impressed Professor Sir
Nevill Mott, who, a few years later, asked me whether I would be interested in
writing a monograph for the Clarendon Press of Oxford University Press on
this new field of organic electronics. I agreed, not really knowing what a burden
it would place on me, my family, my co-author, and my research. I had then
become the Co-Director of the Radiation and Solid State Laboratory at New
York University, and later, the Director, which added to my responsibilities. As
I later describe, John proved to be of invaluable assistance in the preparation of
that book.
We met again in 1971 in Nottingham at a Faraday Society meeting. My wife
and younger daughter Deborah were at that meeting. We became good friends,
and I had the good fortune to be invited to a conference to be held in 1973 in
Aberystwyth. John met us in Bristol in his car, and guided my wife and me as
we drove to Aberystwyth. On a later tour of the local countryside, with John

863
864 Appendix 6
inside the car as a guide, we learned that John was not only a great scientist, but
a philosopher, a poet, and a teller of tales in a voice filled with such cadence and
colour as to make one oblivious to the passage of time. It so happened that the
day was coming to a close as we approached Tintern Abbey; the setting sun lit
up the white faces of the cattle as they were returning to their barn, and being
with John made it a perfect setting for the words of Thomas Gray:
The curfew tolls the knell of parting day,
The lowing herd winds slowly o’er the lea. . .
At Aberystwyth we were fortunate to meet John’s talented wife Margaret. As is
well known, John is Welsh, body and soul. This was also true of Margaret, and
their two wonderful daughters Lisa and Naomi, both of whom still can speak to
each other in that strange but beautiful language. We also met Gilbert and
Sonia Sloan with whom we became bonded, certainly in part for our mutual
admiration of Gwyn Thomas, a writer of unearthly wit and mastery of the
English language, insufficiently known in the U.S. John of course knew of and
was an admirer of Gwyn Thomas and subsequently sent us Gwyn’s weekly TV
reviews from the local newspaper, so that we could share his pleasure in them.
John’s father and brother were miners, as was the family of Gwyn Thomas. It
so happened that before John met us in Bristol, we had already visited Gwyn
and his wife Lyn. Gwyn, born and raised in the Rhonda Valley, told of the time
he had received a scholarship to study at Oxford, where the other students were
from well-to do families. When they learned that Gwyn’s father was a miner,
the look of horror on their faces was dispelled as soon as Gwyn informed them
that his father fortunately was unemployed.
The book that emerged from the invitation of Sir Nevill Mott, ‘‘Electronic
Processes in Organic Crystals,’’ appeared in 1982 with the late Charles E.
Swenberg as co-author. This book became a classic. In the course of writing the
book, John informed and enriched my discussion of crystal defects and trapped
charge, and their influence on the mobility of charge carriers in organic crystals,
a subject that he had mastered. The bulk of this book will do justice to his great
advances in designing catalysts with enzyme-like abilities to effect reactions
under mild and environmentally benign conditions.
John was always proud of the accomplishments of his daughters, especially
in their later years. One story he told of Naomi, who at the age of 4, was
becoming fascinated with words and wondered how they came to mean what
they did. She looked about her, spied the curtain, and questioned the origin of
the word ‘‘curtain.’’ She then announced that someone had looked at that piece
of cloth and decided to call it ‘‘curtain.’’
Over the years, John has sent me copies of talks he had delivered; their
subject matter is encyclopaedic. His memory is phenomenal, and in addition to
science, his knowledge of history is extraordinary, particularly of personalities
from Wales. I have learned about William Morris, who was an artist and
decorator, who designed wallpaper, and the eponymous chair. He also sent me
his talk on David Lloyd George, which revealed to me the contributions of one
of the greatest Prime Ministers. He presented me with the biography of
Reflections on John Meurig Thomas on the Occasion of His 75th Birthday 865
Churchill by Roy Jenkins. My opinion of Churchill had not been favourable,
but Jenkins’ book convinced me that much of the freedom we enjoy today
hinged on this one man. John was a great admirer of Faraday, who was a
formative influence on John’s youthful interest in science, and his writings on
that genius are gems. There is scarcely a subject on which one cannot get an
informed comment from John.
Last year, in the course of one of his many speaking engagements in the
United States, John stopped by in New York and spent one day and night at
my brother’s home, overlooking Central Park. Together we then unexpectedly
attended, participated in and enjoyed a spontaneous memorial to John Lennon
who had been murdered years ago at that corner.
Most recently, I met John in London at the Royal Society’s Anniversary on
November 30, 2006, when I was awarded the cherished Davy Medal for my
‘‘pioneering studies on molecular semiconductors.’’ In London too, my daugh-
ter and I were fortunate to be guided in the area between my hotel and the
Royal Society by John, who filled that small region with historical treasures
from his phenomenal memory. In particular, I remember the inconspicuous
spot covered by two stone steps, used by the Duke of Wellington to assist him
in mounting his horse.
Many years ago, he stayed in our modest guest room several times (now
converted to a computer room), and shared meals and gentle talk about our
mutual friends at our kitchen table. John has never forgotten his humble roots.
Although he has received honours almost beyond enumeration, including being
Director of the Royal Institution of Great Britain, Master of Peterhouse at
Cambridge, and knighted, he has maintained his old friendships, always
inquiring about the wives and families of his many friends.
We feel privileged to be part of his worldwide friendships. On this occasion of
his 75th birthday, we wish him good health and the love that sustains him in
times of sorrow.

Martin Pope

Professor Martin Pope,

Emeritus Director of Radiation Laboratory,
New York University, USA.
APPENDIX 7

Bangor 1966–1969; Aberystwyth

1969–1973; Some Fond
Reflections

Imagine having returned late to Bangor, in the early hours, from an away
University rugby game and the following morning awaiting the arrival of the
chemistry lecturer for a dose of thermodynamics. Just imagine! Then in bounds
the Tigger of science fresh from his research laboratory. ‘‘Just look at these
photos’’, we were implored. And so we listened willingly to a breathless, brief
summary of the latest results from Dr Thomas’ research group, presented with
his now legendary clarity. We even felt like members of the research group. But
then on to thermodynamics and he made that digestible, especially by inter-
spersing the equations with colourful stories of the renowned chemists, many of
whom he had visited.
Then on to Aberystwyth to do a PhD with Professor Thomas, Head of
Department and the late lamented John O. Williams. What a team and what a
pace and now I was part of the research team. I was to study the kinetics of
vaporization of certain crystals and was sent lots of preparatory reading over
the summer of 1969 in order to hit the ground running. More excitement when I
grew, from the melt, a large crystal of anthraquinone. If there had been
champagne at hand, corks would have popped.
But amidst the whirl there was always time found for reflection, encourage-
ment, scientific and pastoral guidance and appreciation of the efforts of the
research team, a team which was growing and becoming more international by
the day. We worked with visitors from USA, France, Egypt, Russia, Yugoslavia,
Poland, and many other countries, all of whom contributed scientifically and
personally to the delight of studying in Aberystwyth with Professor Thomas. In
addition, Mrs Thomas will also be fondly remembered by all members of the
research group as a warm hostess on many occasions providing an oasis of home
cooking, home comforts and conversation.
Meanwhile, however, Professor Thomas did not stay in the research labo-
ratory. He spread his wings into popularizing science and gave many demon-
stration lectures to schools and the public with a variety of specially-built kits

866
Bangor 1966–1969; Aberystwyth 1969–1973; Some Fond Reflections 867
including, I recall, a mass spectrometer featuring a number of painted
ping-pong balls. These forays were to serve him well later at the Royal
Institution and subsequently throughout his spectacular career.
Aberystwyth finished for me with a one year post-doctoral fellowship still
benefitting from the wise words and support of Professor Thomas. I then went
to Imperial College to work with David Trimm, followed by the Midland
Region Research Laboratories of the Central Electricity Generating Board
and thence to the science department of the North East Wales Institute in
Wrexham. In every facet of my career I have used the lessons learned from my
days in Bangor and Aberystwyth with the now ennobled Professor Sir John
Meurig Thomas.
I and my family, Lynne, Rhys and Elen have always maintained contact with
John over the intervening years, he visiting our home in Wrexham on a number
of occasions, and we would like to congratulate him on his outstanding
contributions to chemistry, science and life in general. This book and sympo-
sium are worthy tributes to a worthy human being.

Stan Moore

Dr Stanley V. Moore,
Principal Lecturer,
North East Wales Institute of Science and Technology,
Wrexham, UK.
APPENDIX 8

Aberystwyth 1970–1973.
Reflections and Lessons Learnt

I arrived in Aberystwyth in October 1970, following three years as undergrad-

uate at the Physics Department at University College of North Wales, Bangor.
I was enthusiastic to start research – an enthusiasm that has remained with
me to this day, although I now work in diverse and multidisciplinary areas
rather than on a specific topic. I was privileged to be able to join the research
group of Professor John Meurig Thomas and the late Dr J. O. Williams – J.O.
as he was always known. Although I had not been taught by J.M.T. as an
undergraduate, I was inspired by a lecture he had given in Welsh during my
time at Bangor.
These were exciting times. My research topic was to understand the electrical
properties of ammonium perchlorate as part of the understanding of the
chemical decomposition process of this material. I also became involved in a
study of the electrical properties of anthracene under charge injection condi-
tions. These measurements provided an understanding of the electronic band
structure of organic materials that has technological applications in solid-state
electronics and opto-electronics. The results were not always as predicted, a
valuable lesson that has stayed with me. J.M.T. continuously encouraged his
students, being sympathetic during difficult times. We were always in awe of his
great and diverse knowledge base, not only in science but other fields such as
literature and history.
In those days, the Edward Davies Chemical Laboratories, the first purpose-
built chemical laboratory in a British university, had an international reputa-
tion with workers from Sri Lanka, the USA, Poland, France and elsewhere.
This provided someone like myself, from a rather parochial background in
North Wales, an appreciation of the wider world. J.M.T. maintained this
international reputation for high quality science and few weeks went by when
we were not visited by leading scientists of the day. The equipment we used was
also state-of-the art in its day. I remember being extremely proud of my
electronic thermometer – an analogue temperature display using a therm-
ocuple. In 1973 J.M.T. purchased a Wang computer. Although by today’s
standards it is probably equivalent to a scientific pocket calculator, at that time

868
Aberystwyth 1970–1973. Reflections and Lessons Learnt 869
it revolutionized my experimental programme since I was able to display results
in a short time after taking measurements and determine trends before pro-
ceeding further. The cost at that time, if I recollect, was about d2000. This was a
substantial sum in those days and is an example of his foresight perhaps
captured in the words of Admiral Fisher: ‘‘the best is the cheapest’’.
I also remember my excitement of meeting Professor Vladimir Boldyrev –
‘‘my first Russian scientist’’ – and that his journey from Moscow to Novo-
sibirsk took longer than from Moscow to Aberystwyth. From the mid-1990s
onwards I conducted a programme of science and technology exchange with
Russia, always remembering this first meeting. I am still intrigued with the
novel approaches to problems taken by scientists from that country. During the
course of my first visit to Russia, my colleague and I ended up quite unexpect-
edly, and to our delight, in the office of Professor Aleksandr Prokhorov, 1964
Nobel Prize Winner (along with Charles Townes and Nicolay Basov) for
fundamental work on the principles of lasers and masers. The General Physics
Institute of the Russian Academy of Sciences was renamed in his honour
following his death in 2002.
I also fondly remember the famous ‘‘Russian radio lamp’’, presented to
J.M.T. by a friend during his time at Bangor. This is an intriguing combination
of old technologies (a kerosene lamp) and high technology components
(a bismuth telluride thermcouple array). This could generate sufficient current
to drive an old-fashioned valve radio and the devices were used in isolated
communities in the former Soviet Union. I demonstrated this during J.M.T.’s
lecture to visiting sixth-formers and literally turning the wick up at the appro-
priate moment would bring the radio to life. Remembering this, I retrieved the
lamp (Figure 1) in 1993 from Mr. A.J.S. Williams, former senior lecturer in
organic chemistry at Aberystwyth for the purpose of demonstrating Russian
technology.
Figure 2 is the departmental photograph of the Edward Davies Chemical
Laboratories for 1973. In October of that year, I joined the Ministry of Defence
and apart from two years at the Home Office stayed there for 30 years in
research, development, a liaison post in Washington DC and finally on a
programme of evaluating science and technology in other countries and
arranging collaborative programmes. I kept in touch with the Aberystwyth
team over the years. During the 1980s, I had a fruitful collaboration with J.O.,
by this time Professor J.O. Williams at UMIST, on optical switching. This led
to patents, a PhD thesis, post-doctoral sponsorship and included novel work on
Langmuir–Blodgett films, fashionable at that time.
I have kept in touch with Sir John over the years. During my time in
Washington (1987–1990), he was Director of the Royal Institution. I remember
sending a flyer from a pizza restaurant in Michael Faraday Court, Reston,
Virginia. This was used as the basis of a slide to illustrate the world renown of
Faraday! Co-incidentally, I noticed the street sign during a recent visit to BAE
Systems at Reston, two weeks before writing this and it reminded me of this
earlier event. I regularly attended discourses at the Royal Institution during his
tenure and we share an interest in the historical predictions for science and
870 Appendix 8

Figure 1 Russian radio lamp with hand-written instructions by Mr. O. Dyson Jones,
Chief Electronics Technician, Edward Davies Chemical Laboratories, for
the use of the Decca radio.

technology. I hosted several meetings with Russian visitors at the Royal

Institution, the Council Room where Faraday and others had once sat pro-
viding an inspiration for fruitful discussions. On a tour of the Royal Institution,
the guests were particularly interested to hear that the discovery of the electron
was first announced during the Friday evening discourse given by Sir J.J.
Thompson on 30 April 1897.
Since 2003 I run my own consultancy – Annwvyn Solutions – with customers
in government, industry and education. But even now, I employ the basic
principles that I learnt during my time at Aberystwyth: always ensure that I
have consulted the literature before starting on any work, network as much as
possible with workers in interdisciplinary fields, and that making mistakes
provides humility and learning that is part of scientific endeavour and indeed
life in general.
Finally, I have, at the time of writing, just put into practice some words of
wisdom spoken by Sir John as guest speaker at a Bangor students’ reunion
dinner on 2 October 2004. I had been consulting for a company in Belfast for
some time and working on a problem with results that were unsatisfactory to
both the client and myself. I was reminded of part of that after dinner speech
mentioning the fundamental importance of defining problems before they can
be solved. Once this was done, providing the solution to our problem was in
principle reasonably straightforward. The other issue we were faced with,
Aberystwyth 1970–1973. Reflections and Lessons Learnt 871

Figure 2 Departmental photograph, Edward Davies Chemical Laboratories, for

1973.

insufficient data, was remedied by accessing the literature since fortunately I

had a recollection that the data required might exist in a University of London
doctoral thesis of the mid-1990s. This is a working example of lessons learnt
from Sir John.
Sir John has provided such inspiration for many. I for one am extremely
grateful and privileged to have been his student.
Gari Owen

Dr Gari P. Owen,
Annwvyn Solutions, Kent
and Ministry of Defence, London, UK.
APPENDIX 9

Molecular Modelling Input to

Organic Solid State and Zeolite
Chemistry: Reminiscences
(1975–84)

It was in March 1975 that my wife and I first met Professor John Meurig
Thomas at Aberystwyth railway station on a cold and wet afternoon. To make
sure that we settled down comfortably, he not only took care of our hotel bills
for a month but also took us on motoring and walking tours nearby. I even
remember watching village cricket in Crickhowell with him one sunny Sunday
afternoon. I still have fond memories of Boxing Day afternoons spent with
JMT and his family, where it did not take very long for the conversations to
inevitably take a technical turn!
In Aberystwyth, we had eminent scientists like Prof. Mansel Davies, Prof.
J.S. Anderson and a highly multi-disciplinary group of researchers. What was
extremely rewarding in terms of my research and education was the constant
flow of excellent speakers and eminent scientists that JMT could attract to that
part of Wales. It is no wonder that, from the time I joined his group in
Aberystwyth, I continued to value his friendship and research throughout my
career in Aberystwyth, Cambridge, BP Sunbury and Imperial College, London.
In this short account I would like to share my reminiscences of some of the
work done during my association with JMT and its timely impact on our
research at that time.
In the course of extensive experimental activity on the characterisation of
organic solids and surfaces undergoing photoreactions, phase transitions, etc.,
the modelling techniques we employed introduced an additional analytical tool
to help rationalise and understand the experimental observations. The first such
study was on crystalline p-terphenyl1 which on cooling to 110 K underwent a
phase change from P21/a to P 1 with a doubling of the unit cell along a and b.
The transition involves the so-called ‘rotational disorder’ in which the indivi-
dual molecules become non-planar. By evaluating the pairwise interactions
between non-bonded atoms, it was possible to elucidate the nature of this
872
Molecular Modelling Input to Organic Solid State and Zeolite Chemistry 873
transition and, in particular, determine semi-empirically the conformations of
the non-planar molecules in, and the lattice parameters of, the stable low
temperature phase – in good agreement with the subsequent X-ray and neutron
diffraction refinement.
We next employed constrained optimisation techniques on large unit cells to
mimic the presence of extended planar faults (i.e. stacking fault or anti-phase
boundary) of a particular type in organic molecular crystals. From the calcu-
lations we were able to estimate the extra energy involved in accommodating
such a fault in the crystal. For example, in the case of 1,8-dichloro-9-methyl-
anthracene for which much experimental data was already available on the
nature of structural faults and their influence on solid state photodimerisation,
we were able to show2 that for a (100) fault plane the lowest energy is achieved
1 
by incorporating a translation vector of ð10 Þ½2 50
and a small degree of folding
of the constituent molecules in and adjacent to the plane of the fault. Such
molecular relaxations gave rise to incipient ‘trans dimers’ in the fault plane, an
unusual observation verified by experiments. We extended such studies to 1,5-
dichloroanthracene3 where we showed the presence of orientational point
defects as a possible cause for the discrepancy in the ratios of head-to-head
versus head-to-tail dimers formed upon photo irradiation in the solid and in
solution. Similarly, we could rationalize4 the unexpected occurrence of racemic
crystals of hexahelicene, which happens to have a chiral space group, in terms
of enantiomeric intergrowths of pure P and pure M forms. Computations
showed that the interfacial energies associated with such intergrowths are
minimal at (100) planes. We also pointed out, as in the case of the low
temperature phase of pyrene5 and 9,10-diphenylanthracene,6 how constrained
optimisation of cohesive energies of molecular solids could give good starting
coordinates for structural refinements from X-ray or neutron diffraction data.
When JMT moved to Cambridge in 1978, the group started expanding
rapidly both in number and range of research interests. It was appropriate that
with him in the Chair of Physical Chemistry, the wall in the canteen was made
to be removed to facilitate integration with the Organic and Inorganic chemists
on the other side. The arrival of visiting scientists and academics also added to
the depth and breadth of research in the group. When the new experimental
focus in the group shifted to zeolite chemistry in 1980, there was tremendous
excitement and intense competition from other illustrious groups in industry
and academia. The weekly group discussions held on Sundays, in the Physical
Chemistry department in Cambridge, became a day long event, often demand-
ing immediate attention and research.
The success in controlled dealumination of aluminosilicate frameworks and
their 29Si-MASNMR spectra provided a fertile ground for new interpretation
of Si,Al ordering in a number of zeolites. For example, we simulated a number
of structural models7 of synthetic faujasites (zeolites X and Y) with Si/Al ratios
ranging from 1 to 2.45 and their predicted intensities of the five peaks corre-
sponding to the local Si(nAl) n ¼ 4,3,2,1,0 environments. For the first time we
also reported8 the highly resolved (29Si-MASNMR) spectra distinguishing the
24 distinct tetrahedral sites in silicalite – our simulations also predicted the
874 Appendix 9
distribution of these sites in the observed spectra. Next, we showed9 that the
29
Si MASNMR spectra of ZK4 point strongly in favour of the 4:0 rather than
3:1 ordering previously proposed and that the abnormal position (chemical
shift) of the Si(OAl)4 MASNMR signal in zeolite A and in ZK4 was due to the
presence of the nearly linear T–O–T linkages in the aluminosilicate framework
[there was an amusing incident concerning this work – when Professor J.V.
Smith of the University of Chicago was our guest at a lunch in King’s College,
he happened to mention some recent but unpublished NMR work showing that
zeolite A could indeed have 4:0 ordering, we immediately produced the then
already completed manuscript on ZK4 to confirm the interpretation]. A natural
extension of these arguments resulted in a simple correlation10 between iso-
tropic chemical shifts and T–O–T (T ¼ Si or Al) angles in zeolite frameworks.
During the early 1980s the group made much progress in the high resolution
transmission electron microscopy (HRTEM) of zeolites, particularly those with
high Si/Al ratios which rendered them stable to the electron beam. When the
HRTEM images of ZSM-5 and ZSM-11 frameworks were first published11 the
importance of computer simulation of images became obvious, particularly in
distinguishing closely related frameworks. For the first time we started using
molecular graphics to project the images of various assumed models of ZSM-5
and ZSM-11 intergrowths12 and subjected them to optical diffraction to
compare with the corresponding electron diffraction patterns. We were then
able to characterise the average lengths of intergrowths in the sample studied.
These techniques were exploited13 in greater detail in the understanding of
stacking faults in the (001) planes of the ABC-6 family of zeolites (e.g. offretite,
chabazite, cancrinite, etc.) and in the direct imaging of these materials. It was
indeed remarkable to observe and characterise the presence of a coincidence
boundary (O13O13R32.21 Superstructure) in zeolite L14 when one part of the
crystal is rotated with respect to another. Finally, in the X-ray powder
diffraction (Reitveld profile refinement), we used models derived from electron
diffraction, adsorption data and space group limitations in arriving15 at a
structure of ZSM-23 – it was found to be a recurrently twinned version of theta-
1 (ZSM-22), the structure of which was examined in BP.
I must also mention the tremendous progress made in the computing front
around this time, both in the hardware and software – interactive computing
was just starting then. This, and the presence and collaboration of scientists and
experts from several countries, made my stay with Professor Sir John Thomas
intellectually challenging and satisfying.

S. Ramdas

Professor S. Ramdas,
Former Professor of Computational Chemistry,
Imperial College, London,
and ex-Senior Research Scientist at the BP Central Research Laboratory,
Sunbury-on-Thames, UK.
Molecular Modelling Input to Organic Solid State and Zeolite Chemistry 875

References
1. S. Ramdas and J.M. Thomas, J. Chem Soc., Faraday 2, 1976, 72, 1251.
2. S. Ramdas, J.M. Thomas and M.J. Goringe, J. Chem. Soc., Faraday 2,
1977, 73, 551.
3. S. Ramdas, W. Jones, J.M. Thomas and J.P. Desvergne, Chem. Phys. Lett.,
1978, 57, 468.
4. S. Ramdas, J.M. Thomas, M.E. Jordan and C.J. Eckhardt, J. Phys. Chem.,
1981, 85, 2421.
5. W. Jones, S. Ramdas and J.M. Thomas, Chem. Phys. Lett., 1978, 54, 490.
6. J.M. Adams and S. Ramdas, Acta Crystallogr., 1979, B35, 679.
7. S. Ramdas, J.M. Thomas, J. Klinowski, C.A. Fyfe and J.S. Hartman,
Nature (London), 1981, 292, 228.
8. C.A. Fyfe, G.C. Gobbi, J. Klinowski, J.M. Thomas and S. Ramdas, Nature
(London), 1982, 296, 530.
9. J.M. Thomas, C.A. Fyfe, S. Ramdas, J. Klinowski and G.C. Gobbi,
J. Phys. Chem., 1982, 86, 3061.
10. S. Ramdas and J. Klinowski, Nature (London), 1984, 308, 521.
11. J.M. Thomas and G.R. Millward, J. Chem. Soc., Chem. Commun., 1982,
1380.
12. G.R. Millward, S. Ramdas, J.M. Thomas and M.T. Barlow, J. Chem. Soc.,
Faraday Trans. 2, 1983, 79, 1075.
13. G.R. Millward, S. Ramdas and J.M. Thomas, Proc. R. Soc. London, Ser.
A, 1985, 399, 57.
14. O. Terasaki, J.M. Thomas and S. Ramdas, J. Chem. Soc., Chem. Commun.,
1984, 216.
15. P.A. Wright, J.M. Thomas, G.R. Millward, S. Ramdas and S.A.I. Barri,
J. Chem. Soc., Chem. Commun., 1985, 1117.
APPENDIX 10

Reflections of a Cambridge
Undergraduate

It is a pleasure to offer this short contribution to the volume celebrating the

75th birthday of Professor Sir John Meurig Thomas. My brief is to provide a
personal reflection, as someone who was taught as an undergraduate in
Cambridge by Sir John during his tenure as Professor of Physical Chemistry.
I have taken as my reference sources my own memory and my preserved
undergraduate notes.
My first contact with Sir John was in the Lent Term of 1985 when, as part of
1B advanced chemistry he gave a lecture course entitled ‘‘Introduction to
Surface Chemistry’’; with the summary aim (Figure 1) ‘‘This short course covers
the chemical principles required for an understanding of the nature of the adsorbed
state and the mode of action of most of the known types of heterogeneous catalysts
for gas-solid reactions’’; no easy task in eight lectures!
At this stage of our education the undergraduate class had only minimal
exposure to this branch of chemistry; ‘‘A’’ level inorganic chemistry taught at
school had a strong solution and analytical bias and the first year course at
Cambridge given the previous year by Brian Johnson had concentrated largely
on inorganic thermodynamics and main group chemistry. Thus, Sir John had
the challenge of enthusing approximately 150 undergraduates in an entirely
new field of chemistry. However, it was clear that this would be a challenging
few weeks given the somewhat worrying (to an undergraduate) advice at the
end of his comprehensive lecture notes that ‘‘you are strongly advised to attempt
all of the attached problems. . .’’ which doubled the length of the handout. The
course itself introduced the full range of techniques available at that time for
probing catalysts including this author’s first exposure to ‘‘the powerful tech-
nique of Transmission Electron Microscopy’’. In all cases these techniques were
carefully illustrated by reference to processes of industrial and academic
importance. Sir John also described the characterisation of a wide variety of
important catalysts including zeolites (succinctly summarised by this author in
his notes as ‘‘zeolitic materials are full of useful holes’’). As anyone who has
attended one of Sir John’s numerous invited and plenary lectures knows, they
are always exquisitely planned and precisely executed and this undergraduate

876
Reflections of a Cambridge Undergraduate 877

Figure 1 Summary of the Part 1B advanced chemistry course as provided by Sir John
in 1985. The marginal notes are those of the author written during the first
lecture.

course was no exception. Thus we finished the course (and in my case almost all
of the questions) with a comprehensive introduction to the field of hetero-
geneous catalysis.
My second contact with Sir John happened one year later, in rather different
circumstances which (although I did not know it at the time) would turn out to
be a defining moment in my own career.
Having survived the Part 1B exams we returned to Lensfield Road (Cambridge)
in October 1985 to begin the final year of our degree course as Part 2 students.
Although this may seem to be a linear transition in status it was in practice a
step function. Part 2 students were allowed to use the Chemistry library and
even had their own coffee room in the centre of the Part 2 laboratory. An
important component of the Part 2 course was a ‘‘research project’’ which
required all of us to spend a term (8 weeks) working within a research group on
a specific project. The choice of projects available was vast, ranging from bio-
organic synthesis through to theoretical chemistry. The author’s first choice
was a project investigating zeolites using a brand new solid state nmr spectro-
meter recently installed in the department; at that time one of only a handful in
the UK. For those of us who now have responsibility for major instruments I
now realise that this was a brave move by Sir John letting (untrained) under-
graduates loose on complex and expensive instruments. Having made my
choice, as fate would have it I was asked to see Sir John (with my project
partner Dr Mike Doyle). Sir John kindly explained (in great detail) that the new
instrument was still being commissioned and hence was not ‘‘suitable’’ for
undergraduate research. He suggested as an alternative that we might be
interested in a project investigating complex Bi–W oxides using high resolution
TEM. Given my introduction to this technique in Part 1B this appeared to be
an excellent substitute, offering the exciting possibility of ‘‘imaging atoms’’ at
the incredible (to an undergraduate, at least) resolution of 0.25 nm. Thus, I had
my first exposure to high resolution TEM which has subsequently formed the
cornerstone of my entire research career (see Ref. 1 for recently published data
on complex oxides now recorded at a resolution approaching 0.1 nm).
I count myself as fortunate that I had the opportunity to meet Sir John on
two occasions as an undergraduate; the first providing my first exposure to
catalysis (and indirectly metallic nanoparticles which formed the basis of my
878 Appendix 10
PhD supervised by one of the editors) and the second shaping my research
career by providing my first opportunity to use TEM.
In summary my recollections of Sir John as an undergraduate are as an
inspirational lecturer and as a wise mentor.
In 2007 I am proud to count Sir John as one of my newest collaborators
(looking at the current generation of heterogeneous catalysts with the now
substantially improved instruments) and I look forward to many more years of
working with him.

Angus Kirkland

Professor A.I. Kirkland,

Professor of Materials,
University of Oxford, UK.

Reference
1. A.I. Kirkland, S. Haigh and J. Sloan, Ultrahigh resolution imaging of local
structural distortions in intergrowth tungsten bronzes, Utramicroscopy,
2007, 107, 501.
APPENDIX 11

Sir John Meurig Thomas

There are moments in one’s life that stand out and on reflection mark a true
turning point. For me one such event occurred just over ten years ago when a
chance meeting with Sir John on the London train was to bring about a
fundamental change in my research direction and lead me into new, exciting
studies of real catalytic systems based on our previous work. At the time, he
and his co-workers were deeply involved in work on catalysts based on
mesoporous solids, and had shown that extremely active hydrogenation and
oxidation catalysts could be produced by the incorporation of transition metal
ions onto the inner walls of the mesoporous material. My own work had
developed from work on metal clusters together with Sir Jack Lewis earlier in
Cambridge on studies of nano-particles prepared by wet chemical methods. In
his usual infectious style Sir John described his chemistry and we both recog-
nised that the possibility of depositing nano-particles within the mesopore was
highly attractive. That was the beginning of a long, fruitful and highly enjoy-
able collaboration which lasts till today, and Sir John, on this very happy
occasion, I should like to thank you for that inspirational turning point on the
9.15 London Express.
I had of course met John well before this train journey. I well remember
attending an International Meeting in Sheffield and being introduced to him at
an evening reception. Our conversation moved rapidly through rugby onto
chemistry, and to my intense pleasure and I must admit surprise he began to
discuss a recent communication I had published on the structure of the binary
carbonyls. His detailed knowledge of my work was highly inspirational, and I
was immediately aware not only of his ability to read, understand, and recall
the work of others but also of his kindness taking care to encourage them in
their endeavours.
On another occasion I remember attending a lecture by Sir John at The
Royal Institution. His fluency and lecturing style truly impressed me and I
recall casting an eye over the audience, they were totally captivated. But it was
his final remark that caught us all: ‘And there’s the magic – you see!’. His
lecturing style is brilliant. He informs, he excites and he entertains. He never
ignores the work of others, and I am deeply grateful for the attention he has
drawn to my work – not only that carried out in association.

879
880 Appendix 11
Then there are the jokes and stories. I recall so many happy times when
together usually in the company of others we have entertained ourselves, and
hopefully our guests with tales of for example your telephone conversation with
your family solicitors (Davies, Davies and Davies), of the Welsh/Italian village,
Portmerion, and so on.
John you have been an inspiration to us all. I very much look forward to
celebrating this wonderful occasion with you and to a long and sustained future
period of collaboration and it goes without saying to topping up my fund of
stories.

A Very Happy Birthday!

Brian Johnson

Professor B.F.G. Johnson, FRSE, FRS

Emeritus Professor of Inorganic Chemistry,
University of Cambridge, UK.
APPENDIX 12

Getting the Details Correct

I joined John’s group as a raw graduate student, fresh from a slightly

frustrating Ph.D. using classical methods of diffuse X-ray scattering to study
disorder in silicates. What attracted me to the group from the outset was John’s
determination to get right down to the detail in disordered solids, rather than
merely being content with the average picture. In the early seventies this was
very unusual, especially in Chemistry. For someone whose studies were rooted
in traditional X-ray diffraction, working in the Aberystwyth group was like a
breath of fresh air, with the (then) new technique of high resolution electron
microscopy to master, and a vibrant group in which to work.
In the early days in Wales we studied such diverse systems as graphite and
graphitic carbons, clay minerals and other sheet and chain silicates. In retro-
spect our interpretation of results may sometimes have been naı̈ve, as experi-
ment ranged well ahead of theory at the time: however, some truly significant
advances resulted, such as the first observation of ‘‘staging’’ in intercalated
graphite, the detection of relatively long-range order in disordered single and
double-chain structures, and the observation of defect-separated fibrils within
individual asbestos fibres. In today’s world, this would be innovative nano-
science, but the term had not then been coined. Then came the move to
Cambridge and with it a new field of interest, the zeolites. Here a combination
of electron microscopy, solid state NMR and neutron diffraction led to a much
more complete understanding of these very complex materials. These studies
then extended into the crystallographically bizarre world of mesoporous solids
and their interaction with metal nanoparticles. As ever, the driving force was
their role in catalysis. By then my involvement in metal oxides had led me away
from the main work of the group, but I must confess to a feeling of envy when
looking at some of the publications which resulted!
As a young postdoc it is very difficult to comprehend the effort and
determination which goes into managing a large and successful research group,
particularly one which is expanding in a field which is by no means mainstream
chemistry. It is only now that I can appreciate fully just how much energy John
must have put into keeping the group at the top of the solid-state chemistry
field in Britain. One of my enduring memories of the time in Wales was
spending several evenings explaining to John the mathematics of image

881
882 Appendix 12
formation in the electron microscope. It amazed me that the boss had both the
time and the patience to assimilate all these trivial details, but as he said, ‘‘if you
are going to write about it then you have to get the details correct’’. And write
he did. The legacy of his work in the solid state is incontestable: countless
publications, many of which have set the standard for others to follow. But
there is also a hidden legacy. John’s efforts gave many young scientists, myself
included, their first steps on the ladder of an academic career. Successful science
today is almost as much about management as research. We were lucky that
John was so capable in both areas.

David Jefferson

Dr D.A. Jefferson,
Reader in Crystallography,
University of Cambridge, UK.
APPENDIX 13

Tribute to Sir John Meurig

Thomas on the Occasion of His
75th Birthday

For me, Aberystwyth and JMT will always remain synonymous. As a final year
undergraduate at UCL, arriving in the springtime in Aber from the big smoke
was like finding Paradise, with the Edward Davies Chemical Laboratories
nestled comfortably between the sparkling sea and the gentle hills. I arrived, at
the recommendation of JMT, by train (‘‘The Rheidol Valley railway is one of
the most picturesque train journeys in Britain, Gordon’’), only to find myself
wrestling with the pronunciation of ‘‘Cymru’’ (‘‘Prifysgol’’ I did not even
attempt at this stage) in order to find my destination. When I did reach the
chemistry department, my linguistic attempts were put to shame by JMT’s now
legendary mastery of my native tongue.
My immediate impressions of JMT were his immense enthusiasm, warmth
and inclusiveness, and his literally encyclopaedic knowledge. It struck me how
he was personally interested in a prospective student for the new MSc course in
solid state chemistry. He fired my interest in his research, and regularly
interrupted his discussions in Welsh with J.O. Williams about their latest
results on anthracene, in order to give me an English translation.
Excited by my visit, and furnished with a good supply of JMT’s recent
reprints, I happily settled down on the return journey to read about his
proposed chemical analogue to the demonstration by Hirsch et al. of the
control dislocations hold over the mechanical properties of solids. Specifically,
he proposed using transmission electron microscopy to investigate the role that
dislocations, or line defects, play in controlling the chemical reactivity of
organic crystals, and that was something I now wanted to be part of.
Another characteristic of JMT’s that I was soon to enjoy is his ability to
attract an eclectic and international cohort of collaborators and visitors. What
an exhilarating environment for a young researcher! Moreover, many of the
people I met through JMT have remained good friends throughout the ensuing
years. I was quickly immersed in this experience as, a week into my PhD at
Aber, JMT arranged for me to enjoy the wonderful opportunity of working for

883
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the next few years at Oxford in the then Department of Metallurgy led by Sir
Peter Hirsch. There I had the privilege to enjoy the people, expertise and
facilities of that great Department, as well as the atmosphere of the City of
Dreaming Spires, whilst pursuing the research direction that had inspired me
on my first visit to Aber.
My links with JMT and Aber were not lessened by this move. JMT visited
Oxford (I remember after one visit PBH calling me to his office to tell me he was
so impressed with JMT’s recall of the Encyclopaedia Britannica, which JMT
had started reading sequentially from ‘‘A’’, that he almost rushed out and
bought an edition himself ), and I frequently paid visits to Aber. Indeed I acted
as a ferry service sometimes, from a set of tiles for Margaret’s kitchen
renovation to, most memorably, taking Professor Dorothy Hodgkin from
Oxford to Aber and back (having seen the state of my student mini, for this
event JMT relaxed his normal fiscal control and paid for me to hire a new car
for the weekend).
Anecdotes involving JMT are legion, and it is not my aim to give an
exhaustive account of my own role in some of them. Rather my theme is to
illustrate the longstanding relationships and friendships JMT engenders in
those he meets. Thus, when JMT moved to Cambridge I was happy to accept
his invitation to join him. After a number of years there, I struck out on my
own and joined the BP Research Centre in Sunbury. It was with some
amusement that when I responded to the Director’s invitation to meet with
one of their consultants, I discovered he was none other than . . . JMT.
Thereafter began a regular series of meetings and continued collaboration.
Shortly after JMT moved to the RI, I accepted a Chair in Crystallization in
Australia, where even down under we remained in touch, and I recently had the
pleasure of being JMT’s guest when he was awarded an honorary DSc by the
University of Sydney.
So, in summary, it is a great pleasure to congratulate Sir John on his 75th
birthday. His contribution to science and beyond is unquestionably broad and
deep. I am personally grateful for the many opportunities he has opened up for
me, and for the way he has, through various ups and downs, maintained his
infectious enthusiasm, support and loyalty. Whilst Sir John has achieved ever
increasing success, and moved on to greater and greater heights, what most
endures for me, surpassing even his erudition, are his warmth and friendship,
which I first experienced in that happiest year as his MSc student in Aber.

Gordon M. Parkinson

Professor G.M. Parkinson,

Curtin University, Australia,
and Research Manager, ALCOA, Western Australia.
APPENDIX 14

Solid State Chemistry and the

Edward Davies Chemical
Laboratories

My first contact with Professor Sir John Meurig Thomas was in the autumn of
1970. I was one of a small group of final year undergraduates (perhaps twenty
or so) in the Edward Davies Chemical Laboratories in Aberystwyth. John was
beginning a lecture course that, unknown to me at the time, would fashion my
future research career. In the space of a few weeks we were introduced to the
rapidly developing area of solid state and surface chemistry. We learnt of
ESCA and high-resolution electron microscopy and the challenges associated
with studying surfaces and solids at the atomic level.
Chemistry at Aberystwyth from 1969 to 1978 was truly international and
exhilarating. Despite its relative isolation – no trains on Sundays! – John
managed to attract the top chemists of the day to give Departmental Lectures
or a series of research seminars. Kathleen Lonsdale, Dorothy Crowfoot
Hodgkin and many others lectured to full and appreciative audiences. Aberyst-
wyth became a world-class centre for solid state chemistry.
John’s natural enthusiasm and energy created within his group a very strong
research culture with MSc and PhD students working long hours alongside
post-docs and visitors. Two Senior Research Associates, John (J.O.) Williams
and Eurwyn Evans, helped coordinate and direct the research. My own PhD
project on defect analysis in organic crystals benefited from the arrival of a
Philips EM300 electron microscope (with liquid nitrogen cooled single tilt
holder) and on occasion a very early generation video recorder (borrowed from
the Audio Visual Aids Department) to record beam-induced dynamic processes
in some of our crystals. The microscope was also used to study the oxidation of
carbon surfaces and provide high resolution images of various minerals and
oxides. Also developed was optical microscopy for etch-pit analysis of defects
in solids such as ammonium perchlorate. Intensive work on cationic clays, in
terms of structural characterisation and catalytic application, began.
Research followed into the use Mössbauer Spectroscopy and the recently
developed technique of Conversion Electron Mössbauer Spectroscopy

885
886 Appendix 14
(CEMS), both of which complemented the surface studies made possible by the
arrival of an AEI ES 200A electron spectrometer.
Collaborations were numerous and world-wide – academic and industrial
visitors came from Spain, France, Poland, Russia, the U.S., Canada, India,
Egypt, Israel and elsewhere. Department spirit was strong with visitors, after a
day in the Department, being introduced to cricket during summer evenings.
The Chemistry Department football team, consisting of staff and students and
named appropriately Carotenoids, seemed to win all the local trophies! One
could feel the excitement and commitment associated with being part of an
internationally recognised laboratory.
In 1975 I went to the Weizmann Institute to work with Professor Mendel
Cohen. John and I corresponded regularly during this period and it was with
real enthusiasm that I looked forward to returning as a Staff Demonstrator in
October 1976. Two further years of active research continued until John was
elected to the 1920 Chair of Physical Chemistry at Cambridge. I was fortunate
to be able to join John in his move to Cambridge and participate in his new
phase of research. John’s enthusiasm, energy, commitment and scientific vision
would ensure that he and the team he brought together would continue the
tremendous progress being made in solid state and surface chemistry.

Bill Jones

Professor W. Jones,
Head of Department of Chemistry,
University of Cambridge, UK.
Subject Index
Ab initio approach, 297–8
Aberration correction, 723–5
Accessible volume, 232
Acetophenone hydrogenation, 200
Acetyl benzoyl peroxide, 366
carbon dioxide interchange, 367–71
end-for-end rotation, 367–71
Acid-base entity, 590
Acrolein
oxidation, 512–14
synthesis from propene, 755
Acrylonitrile, 755
synthesis, 578–86
Active regions, 399–402, 423–5
Active sites, 399–402, 409
computational approaches, 411
design of, 519–33
features of, 407
frameworks holding, 404–6
ill-defined, 426–9
mobility at, 421–3
allosteric systems, 423
minor mobility, 421–3
Sn-Beta, 641–2
1,3,5,7-Adamantane-tetracarboxylic
acid, 77
Adams, Ian, 652
Adams, John, 806
Adams, Rick, 838
Adipic acid, 417, 625, 626, 629
production from sustainable resources,
631–2
Adsorbents, 123–37
AIPO-5, 397, 628
AIPO-18, 397
AIPO-31, 628
AIPO-36, 397
Alcohol oxidation, 561–4
Alkali halides, 287
Alkanes, 25
Alkyl radical generation, 569
Allen, Geoff, 809
Allosteric systems, 423
ALPOs, 16–17, 76, 222, 609
preparation, 616
ALPO-5, 520
ALPO-11, 520
ALPO-kan, 618
scanning electron microscopy, 618
Alumina, melting curve, 166–7
γ-Alumina, 597–8
Aluminium, distribution in SAPOs, 608
Aluminium tri-(2,6)-diphenylphenoxide,
640
Aluminoarsenates, 222
Aluminophosphates see ALPOs
Aluminosilicates see Zeolites
6-Aminohexanenitrile, 354, 356
(S)-(-)-2-Aminomethyl-1-
ethylpyrrolidine, 625
Ammonium heptamolybdate, 598
Ammonium sulphate, 626
Ammoxidation catalysis, 577–87
bismuth molybdates, 769–70
888
MoV(Nb,Ta)(TeSb)O system, 578–86
acrylonitrile yield, 582
active centre, 581
site isolation, 582
symbiosis between phases, 581, 583
propane, 514–17, 584
Amorphisation, 171–6
double well potentials, 176–7
negative melting curves, 171–2
zeolites, 172–6
Amorphous solids, computer
modelling, 185–6
Amphiboles, 817
Analysis, 22
Anderson, J.S., 797, 809
Anderson, Michael, 811, 817
Andrew, E.R., 801
Anionic-surfactant-templated
mesoporous silica, 673–4
9,10-Anthracendicarboxylate-bridged
compounds, 145–8
crystal packing, 148
powder X-ray diffraction, 146, 147
Anthracene, 288, 292
Antigorite, 808
Aperiodicity, 302–33
incommensurate materials, 304–22
diffraction properties, 307–12
energetic aspects, 312–14
physical properties, 314–22
structural aspects, 307–12
structural classification, 304–5
urea inclusion compounds, 305–7
quasicrystalline materials, 323–30
crystal engineering, 324
design of, 324–9
future directions, 329–30
Apollonian tessellations, 218
Arm chair configuration, 800
Armstrong, Henry E., 287
Arrhenius plots, 278
Arsenopyrites, XPS studies, 654, 655
Ashtray structure, 193
Atom-atom method, 289–93
weaknesses of, 293
Subject Index
Atom-atom pair potential curves, 291
Atomic force microscopy, 97, 719
faujasitic structures, 104
silicalite, 112, 115
zeolite A, 97, 98, 101, 105, 106, 107
zeolite Y, 104
Atomic level twinning transformations,
745–53
Atomistic modelling, 443
Audier, Marc, 811, 812
Auger electron spectroscopy, 481
Aurivillius structures, 832
bismuth molybdates, 758, 761, 771
Aurivillius-Sillen structures, 832–3
Avogadrite, 239
Avogadro, Amadeo, 239
Bach, Bernard, 810
Back-projection, 715, 716
Baeyer-Villiger oxidation, 641
Ballantine, Jim, 803, 812, 823
Bancroft, Mike, 803
Barber, Mickey, 803
Barlow, William, 240
Barrer, Richard, 809
Barrer, R.M., 95, 797
Barthomeuf, Danielle, 609
Bartlett, Paul D., 362
Basket 1 structure, 193
Basket 2 structure, 193
BCT framework, 232
Bednorz, J.G., 53
Benzene, 297–8
2,2’-bis(4S)-4-Benzyl-2-oxazoline, 625
Beryllophosphates, 222
Berzelianite, 239
Berzeliite, 239
Berzelius, Jöns Jacob, 239
Beta-cages see Sodalite cages
Betteridge, Paul, 14
Biesinger, Mark, 654
Biewer, Michael, 365
Bioactivity, 729–30, 733
4,4’-Bipyridine, 78
Bishay, Adli, 806
Subject Index
Bishop, Clive, 808
Bismuth citrate, 735, 737
Bismuth lone pairs, 764–9
associated oxygen sites, 767–9
location of, 765–7
orientation of, 766
Bismuth molybdates, 754–77
ammoxidation, 769–70
Aurivillius type, 758, 761, 771
bismuth lone pairs, 764–9
bismuth-rich phases, 762–4
cation deficient structures, 762
fluorite type, 758, 760, 763–4, 774
Latin cross configuration, 760, 762,
773
lattice oxygen mobility, 771–2
oxide ion conductivity, 771–2
phase diagram
cataloguing of phases, 756–7
structural evolution, 757–64
photocatalysis, 770–1
polymorphism, 758–61
propene oxidation, 769–70
scheelite projection, 760
Boisen-Gibbs-Bukowinsky energy, 212
Boldyrev, V.V., 809
Boltzmann distribution, 644
Bomb 1 structure, 193, 194
Bomb 2 structure, 193
Boreskov, G.K., 827
Born, Max, 287
Bouas-Laurent, Henri, 808, 810
Boyes, Ed, 838
Bradley, Donal, 339
Bradley, F.C., 138
Bragg, William Henry, 240, 287
Bragg, William Lawrence, 240, 287,
365, 828
Breck, D.W., 95
Breck Structure, 812
see also Faujasite
Brillouin scattering, 169
Bromley, Stefan, 837
11-Bromoundecanoyl peroxide
crystal packing, 372
889
preservation of asymmetry, 372–6
rotation, 372–6
site exchange, 372–6
Brønsted acidity, 611
Brønsted sites, 441, 442, 449–50
computational analysis, 613
designed distribution, 616–19
faujasite, 449–50
H-SAPO-34, 605
Bronzite, XPS studies, 658, 659, 660
Broom, Ron, 718
Brown, Adam, 339
Brown, H.C., 809
Brydson, Rik, 811, 819
Bubble 1 structure, 193, 194
Bubble 2 structure, 193
Buckingham, David, 6, 809, 810
Buckingham, Jill, 6
Buckminster fullerene, 56
Bulk matrix catalysts, 429–35
electron flow, 431–4
flow between sites, 431
molecular flow, 434–5
proton transfer, 434
semi-conductors, 431
Burland, Don, 808
Burn, Paul, 339
Burns, Roger, 652
Burroughes, Jeremy, 339
Bursill, Les, 811
Busche, Daryle, 139
Butane oxidation rate, 574
Butterfield, Herbert, 802
Buttrey, Doug, 811, 820
Bydson, Rik, 721
13
C chemical mapping, 464–8
13
C DEPT-MRI, 464–8
Cadogan, John, 803, 809
Cahn, Robert, 801, 809
CAL-1, 614, 615
scanning electron microscopy, 618
CALPHAD approach, 39, 41
Cancrinite, 224, 813
Cancrinite cages, 224
890
ε-Caprolactam
conventional synthesis, 625, 627
solvent-free synthesis, 630
Captain, Burjor, 838
Car-Parrinello approach, 182
Carbido-pentaruthenium carbonyl
clusters, 535–7
Carbon dioxide
FTIR, 365–6
FTIR frequencies, 378–9
as mechanistic probe, 366–7
Carbon dioxide interchange, 367–71
Carbon monoxide, photocatalytic
oxidation, 500–3
Carbon nanoparticles, 745–53
Carbon nanotubes, 728, 734–8
formation of, 749–50
multi-walled, 722, 723
single wall, 728, 734
Carbonic anhydrase, 416
Carpenter, Adrian, 811
CAT(0) complexes, 216
Catalysis, 123–37
active regions, 399–402, 423–5
active sites, 399–402, 409
computational approaches, 411
design of, 519–33
features of, 407
frameworks holding, 404–6
ill-defined, 426–9
mobility at, 421–3
Sn-Beta, 641–2
ammoxidation, 577–87
bulk matrices, 429–35
choice of ligand atom, 403–4
choice of metal atom/ion, 402–3
effectiveness factor, 458
enzymes see Enzymes
enzymes vs solid state, 396–440
gold, 550–67
gold-palladium, 550–67
direct synthesis of hydrogen
peroxide, 558–61
oxidation of alcohols, 561–4
gold/carbon, 553–8
Subject Index
current density, 557
cyclic voltammetry, 556
green chemistry, 623–38
hybrid, 392–4
hydrocarbon oxidation, 568–76
in situ studies, 826–8
intra-pellet molecular diffusion,
469–70
metallic, 429
molecular, 388–90, 411–12
molecular “ionic” cluster, 426
non-adjacent sites, 418–21
particle size effects, 427–9
photocatalysis, 492–506
silica-grafted titanate, 386–8
solid heterogeneous, 405
solid state, 417–18
non-adjacent sites, 421
solid state cluster, 427–9
types of, 398
Catlow, Richard, 16, 76, 165, 443,
812, 817, 827, 829, 831–2
Ceramic cuprates, 52
Cerius software, 231
Chabazite, 124, 49, 604, 813
FTIR spectroscopy, 614–16
H-SAPO-34, 604
SAPO-34, 17, 125
structure, 17
Characteristic energy, 313
Charge flipping, 251–2, 253
Cheetham, Tony, 812, 815, 824, 825, 827
Chemical mapping, 460–8
1
H observation, 460–3
13
C observation, 464–8
Chemical periodicity, 57
Chemical synthesis, 22, 23–5
alkanes, 25
element combinations, 24
Chen, Jiesheng, 825, 829, 833
Chippindale, Anne, 17
Chiral catalysts, 632–6
Chiral ligands, 635
Chiral porous coordination polymers, 79
Chiral structures, 674–6
Subject Index
Chitinase, 413
Chloro effect, 295
Chromium oxides, 133–4
Chromium-MCM-41, 500–3
Chrysotile, 808
Citronellal, cyclization, 641, 642–6
adsorption, activation and reaction
energy, 644
conversions and
diastereoselectivity, 645
beneficial factors, 649
effect of solvents and water, 646–9
stereoselectivity, 644
Clark, Howard, 138, 651, 652
Clathrasils, 118, 228
Clathrates, 64
Clausius-Clapeyron relation, 166
Clay catalysis, 823–4
Clay mineralogy, 802–7
Clean technology, 623–38
Co-structure directing agents, 673
Cobalt acetate, trimeric, 524
Coenzymes, 413
molybdenum, 420
Coenzyme B12, 413, 415
Cohen, Mendel, 363, 364, 809
Coherent structure imaging, 689–91
Collective framework distortion,
679–81
Commensurate materials, 305
Compartmentalized cascade
reactions, 520
Complexity, 250–7
in structural solution, 250–1
Compositional range, 124–5
Compositional variations, 738–41
Computational chemistry, 831–2
Computer modelling, 180–207
amorphous solids, 185–6
crystal structures, 183–5
defect structures and energies, 187–8
defects in semiconducting oxides,
197–9
enantioselectivity in Ru(II)
hydrogenation catalysis, 199–204
891
methods, 182–3
motivation and background, 180–1
nanocluster structures and energies,
191–4
pre-nucleation and polymorphism,
195–7
reactivity, 189
sorption, 188–9
surface structures and properties,
186–7
synthesis, nucleation and growth,
189–91
Configurational spaces, 37–9
Contrast transfer function, 779
Coordination sequence, 225, 227
Core loss spectroscopy, 694–5
Corma, Avelino, 829
10,5-Coronene, 326
Corundum, melting curve, 167
Cosslett, Ellis, 810
Cottrell, A.H., 798
Cotts, Bob, 811
Coulomb energy, 293, 294–5, 296, 298
Coulson, C.A., 809
Couves, John, 825, 828, 829
Crawford, Sian, 808
Cristobalite, 213
Cross polarizations magic angle
spinning NMR, 349
Crowther, Tony, 720
CRYSFIRE program, 143
Crystal architectures, 221–38
Crystal engineering, 324, 820–2
Crystal growth, 98–102
defects, 99
faujasitic structures, 102–5
modelling, 119
zeolites, 98–102
Crystal structure modelling, 183–5
Crystal structure prediction, 183–5, 298
Crystalline molecular sieves, 222–3
Cu+/ZSM-5 catalysts, 503–5
Cu2+/Y zeolite catalysis, 503–5
Cyclobutane, 290
1,4-Cyclohexanedimethanol, 546
892
Cyclohexanol, 629
Cyclohexanone, 629
Cyclohexyl hydroperoxide, 629
Cyclooctanol, 569
Cyclooctanone, 569
Cytochrome P450, 413, 414
3D atom probe, 706–7
DAF-1, 126, 127
DAF-5 structure, 190
Dainton, Lord, 4
Daniel, Sir Goronwy, 809
Dantus, Marcos, 5
Daresbury synchrotron, 828–31
DASH program, 143, 147
Davies, C.W., 806
Davies, Keith, 14
Davies, Mansel, 806
Davis, Rhiannon, 802
Davy, Humphrey, 239
Davydov, Aleksander, 3
Debye Model, 167–8
Debye-Scherrer pattern, 172
Debye-Waller factors, 169, 262
Deductive approach, 22–50
materials discover, 43–4
Deep centres, 274–7
vs shallow centres, 279–81
Delaney symbol, 229, 230
Delaunay tessellations, 218
Dempsey’s rule, 449
Dendrobates histrionicus, 334
Density functional theory, 182–3,
411, 443, 528, 571, 640
Deprotonation, 591
Designer templates, 125–7
Designer zeolites, 208–20
Desiraju, Gautam, 821
Desvergne, Jean-Pierre, 808, 810
Dewar, Sir James, 6
Dexter transfer, 342
DFT code, 31
Diastereoselectivity, 645
beneficial factors, 649
effect of solvents and water, 646–9
Subject Index
Diels-Alder reactions, 390
Diffraction contrast microscopy, 688–9
Digital analysis of lattice images, 703
Dimethylformamide, 78
Dimethylterephthalate, 545, 548
Diopside, XPS studies, 658, 659
(1R,2R)-(+)-1,2-Diphenylethylene-
diamine, 625
Diphenylferrocenyl palladium
dichloride, 524–5
Dirhenium cluster complexes, 539–40
Dislocations, 798, 799
Dislocation density, 699
Dislocation imaging, 687–97
electron microscopy, 688–93
coherent structure imaging, 689–91
diffraction contrast microscopy and
transmission channelling, 688–9
incoherent structure imaging, 691–3
weak beam imaging, 689
new methods, 694–6
shortcomings of
background contributions, 694
projection failures, 693–4
Disordered states, 486–90
Dispersion energy, 296
Dispersive kinetics, 315
Displacive modulation, 308
Dissolution-reprecipitation, 596–8, 600
Distributed charge methods, 293–4
Diundecanoyl peroxide, 347, 348
Donati, Donato, 807, 810
Dooryhee, Eric, 828
Double rotation technique, 443
Double well potentials, 176–7
Dream reactions, 552
Dresselhaus, Millie, 18
Drude model, 58, 61, 71
Drug delivery systems, 729–34
Dugal, Markus, 825
Dutta, Prabhir, 104
Dynamic kinetic resolution, 531
Earl and Deem database, 213
Eckhardt, Craig, 337, 819
Subject Index
Edge, 228
Edwards, Peter, 812, 815, 823
Edwards, Sam F., 51
Effectiveness factor, 458
Egerton, Ray, 818
Einstein, Albert, 286, 588
El-Sayed, Mostafa, 3, 805
Electric field gradient splitting, 653
Electric permittivity, 592
Electroluminescence, 339–40
Electron density mapping, 254–6
Electron energy loss spectroscopy,
721–2, 788, 818–20
Electron microprobe, 240
Electron microscopy
aberrant correction, 779–80
dislocation imaging, 688–93
coherent structure imaging, 689–91
diffraction contrast microscopy and
transmission channeling, 688–9
incoherent structure imaging, 691–3
weak beam imaging, 689
InGaN, 700–1
microporous/mesoporous crystals,
667–86
nanoparticulate systems, 778–91
see also various modes
Electron paramagnetic resonance,
347, 363
Electron spin resonance, 493
Electron tomography, 711–26
aberration-corrected instruments, 723–5
cluster-to-crystal transition, 723–5
further developments, 720–5
in physical sciences, 715–18
STEM, 711–14, 719
nanoscale structures, 721
three-dimensional imaging, 715
Electron transfer, 570
Electrophilic oxidation, 575
Electrostriction, 592
Element combinations, 24
Eley-Rideal mechanism, 480
EMC-2, 130
EMT framework, 215
893
Enantiocatalysis, 836–9
Enantioselectivity, 199–204, 634
End-for-end rotation, 367–71
Energy landscapes, 26–8
computational approaches, 28–34
experimental exploration, 36–7
non-physical explorations, 34–6
Energy materials, 57–8
Energy minimisation, 182
Energy-filtered transmission electron
microscopy, 700
Energy-generating devices, 58
Energy-storage devices, 58
Engelhardt, Günter, 443
Enthalpy
of formation, 24, 31
free, 45
Enumeration
non-systematic structural, 226–8
tiling theory, 228–30
cis-Enynes, 334–8
Enzymes, 396, 398, 412–17
adjacent sites, 413
clusters in, 426–7
hydrolytic, 415–17
metallo-enzymes, 402
non-adjacent sites, 418–21, 427
oxidative, 413, 415
solvents, 404
substrates, 404
thermal stability, 404
see also individual enzymes
Epsilon-cages see Cancrinite cages
Ergodic regions, 38, 45
Erionite, 449, 813
Ertl, Gerhard, 827
Eskimoite, 243, 244, 246–8
ETS-10, structure, 100, 102
Euler, Leonhard, 34
Europium coordination polymers, 83, 84
Evans, Eurwyn Lloyd, 801, 804
Evans, Trevor, 809
Everett, D.H., 797
Evolutionary algorithm methods, 184
Ewald, Peter Paul, 287
894 Subject Index

EXAFS, 130, 495, 501, 521, 523, 527–8 5-Fluorouracil, molecular forms, 195, 196
Exciton localisation, 700, 707–8 Fourier spaces, 717
in-localised hole wave functions, Fourier transforms, 252, 277
707–8 Fourier transform infrared
quantum well thickness fluctuations, spectroscopy see FTIR
707 spectroscopy
Experimental exploration, 36–7 Framework density, 225
Extended X-ray absorption fine structure Framework energy, 231
see EXAFS Frameworks, 196
Eyring transition state theory, 406 229-5-8058871, 214
BCT, 232
Face, 228 EMT, 215
Fajans, Kasimir, 287 FAU, 215
Faraday Discourse, 4–5 FER, 210–11
Faraday, Michael, 801, 840 holding active sites, 404–6
Farina, Mario, 352 MFI, 212, 215, 218
FAU framework, 215 NPO, 232
Faujasite, 102–5, 130, 224, 258, 812 RWY, 232
atomic force microscopy, 104 UFI, 232
Brønsted sites, 449–50 Franco, Miguel Alario, 804, 810
coordination sequence, 225 Frank, F.C., 687, 809
Cu(I) sites in, 450–4 Free enthalpy, 45
hexagonal, 215 Free-energy diagrams, 406–11
structures, 444–5 Freeman, Clive, 832
Fcc structure, 670–1 Freezing, 165–6
FDU-12, 130 Friedrich, Walther, 287
Fenske-Hall molecular orbital Friend, Richard, 334, 338
calculations, 539 FTIR spectroscopy, 365–6, 493
FER framework, 210–11 chabdazite-related SAPOs, 614–16
coloured graph, 211 H-SAPO-34, 611, 612
Fermi level, 276, 280 zeolite H-ZSM-5, 617
Fermi-Dirac statistics, 63 Fullerenes, 728, 734–8
Fernandez, Jose-Jesus, 720 Function group interaction energies,
Ferritin, STEM studies, 785–90 351–6
Fixed-bed reactors, 457–78 Fyfe, Colin, 443, 808, 812
chemical mapping, 460–8
1
H observation, 460–3 Gai, Pratibha, 809, 820, 838
13
C observation, 464–8 Galactose oxidase, 413
imaging flows field, 470–6 Gale, Julian, 16, 827
single-phase flow, 470–1 Galloarsenates, 222
two-phase flow, 471–6 Gallophosphates, 222
Flanigen, Edie, 16 Gameson, Ian, 811, 816
Flexible electronics, 272 Gault, François, 550
Fluorite type bismuth molybdates, Gay-Lussac, Joseph Louis, 239
758, 760, 763–4, 774 Gaylussite, 239
Subject Index
Gell-Mann, Murray, 5
General utility lattice program, 216
Genetic algorithm methods, 184
Geochemistry, 596–7
Geometric group theory, 217
Gibbs free energy, 217
Gibbs’ phase rule, 42
Gillman, Henry, 139
Gismondine, 258
Gladden, Lynn, 811, 837, 839
Glaeser, R.M., 809
Global equilibrium, 37
Global minimum structures, 192
Global optimisation, 191
Glycerol oxidation, 553
Gmelinite, 449, 813
Gold, 551
Gold catalysis, 550–67
Gold-manganese alloys, 669–84
structural modulation of mesoporous
crystals, 670–6
2d-hexagonal p6mm structure, 674–6
anionic-surfactant-templated
mesoporous silica, 673–4
multiply twinned crystals, 671–3
structural modulation of
microporous crystals, 676–86
zeolite Beta, 681–3
zeolite LTL, 679
zeolite MOR, 676–8
zeolite SSZ-24, 679–81, 682, 683
structure, 670
Gold-palladium catalysis, 558–64
direct synthesis of hydrogen
peroxide, 558–61
oxidation of alcohols, 561–4
Gold/carbon catalysis, 553–8
current density, 557
cyclic voltammetry, 556
Goldschmidt, V.M., 34
Gonzalez-Calbet, Jose, 811
Gordon, Roy, 809
Goringe, Mike, 13, 806
Grafting process, 593
Gramaccioli, Carlo Maria, 806, 811
895
Grand Canonical Monte Carlo
techniques, 188
Graph theory, 35
Graphitic carbon, 749
Grasselli, Bob, 754, 820
Gray, Harry, 139
Greaves, Neville, 828–31
Green chemistry, 623–38, 803
Green, Malcolm, 139
Greengard’s algorithm, 217
Greenhouse gases, 632
Grey, Clare, 17, 828
Gross indium-rich clusters, 700–1
Grotthus conduction, 434
Growth fronts, 105, 106
Guarini, Guilio, 808, 810
Guest exchange, 318–22
Guest substructures, 304
distribution of, 315–17
Gustavite, 243, 244
1
H chemical mapping, 460–3
H-SAPO-34, 604–22
Bronsted sites, 605, 607–16
catalysis of methanol-to-olefin
process, 607–16
FTIR spectroscopy, 614, 615
HAADF see STEM-HAADF
Haber, Fritz, 287
Haber, Jerzy, 829
HADES code, 181
Haemochromatosis, 721, 722, 786, 787
Haemoglobin, 401
Hale, George Ellery, 5
Hall effect, 278
Hamilton, James, Faraday: The life, 600
Hard templating method, 132
Harris, Kenneth, 3, 7, 349, 811, 821,
822, 823, 824, 839
Hartree-Fock code, 31
Hartree-Fock method, 182
Heat of formation, 66
Hermans, Sophie, 837
Heterogeneous catalysis, 479–91
Heteropoly acid, 640
896
Heterosupramolecular chemistry, 593
Hexachlorobenzene, 295
Hexachloroplatinic acid, 590
Hexagonal close packing, 670
Hexagonal tungsten bronze, 738
Hexamethylene diamine, 627
Hexamethyltetramine, 288
Heyrovskyite, 243, 244
High angle annular dark field see
STEM-HAADF
High Tc, 54–6
High-resolution electron microscopy,
55, 96
carbon nanotubes, 728, 734–8
fullerenes, 728, 734–8
mesoporous materials, 727–44
nanoporous materials, 730–4
zeolite L, 99
High-resolution transmission electron
microscopy see HREM
High-temperature superconductivity,
52–6
chemical control, 54
Highest occupied molecular orbital
see HOMO
Hills, Ken, 338
Hirsch, Sir Peter, 577, 806
Histrionicotoxin, 334, 335
HKUST-1, 116, 129
structure, 117, 118
Hobbs, Linn, 806
Hochstrasser, Robin, 3
Hodgkin, Dorothy, 809
Hoffman, Roald, 809
Hollandites, 817
Hollingsworth, Mark, 303, 366, 811, 822
Holmes, Andrew, 334
HOMO, 492, 538, 539, 541
HOMO-LUMO gap, 340, 341–2
single-site photocatalysts, 498
Hong, Suk Bong, 126
Host substructures, 304
Host-guest interaction, 313
energies of, 317
Host-guest materials, 727
Subject Index
Hot oxygen atoms, 574
Howie, Archie, 711, 809
HREM, 240, 818–20
lillianites, 242–8
Mo-based catalysts, 510, 511
modular crystallography, 241–2
Hughes, Glenda, 800
Hughes, Moelwyn, 809
Humphreys, Colin, 836
Hungria, Ana, 838
Hursthouse, Mike, 821
Hutchinson, John, 804
Hutchison, Clyde, 363
Hybrid catalysts, 392–4
Hydride complex activation, 543–5
Hydrocarbon oxidation catalysis, 568–76
electron transfer, 570
Hydroformylation, 403
Hydrogen
charge states, 276
in semiconductors, 272
Hydrogen chloride, dissociative
chemisorption at Cu(110), 479–91
chlorine induced step movement, 486
disorder and nucleation, 482–6
surface reactivity, 486–90
surface relaxation and “final state”
structure, 486
transient and disordered states, 486–90
Hydrogen fuel cells, 65
Hydrogen peroxide, 390
direct synthesis, 558–61
Hydrogen storage materials, 65–71
characteristics, 65–6
decomposition temperature, 67, 68
effect of destabilisation, 70
reduction in, 69
destabilisation, 69, 70
gravimetric densities, 67
metal-organic coordination polymers,
79–82
redox potentials, 68
volumetric densities, 67
Hydrolytic enzymes, 415–17
Hydroperoxidase, 413
Subject Index
Hydrotalocites, 599
Hydroxycarbonoapatite, 729
Hydroxyl nests, 258
Hydroxylamine, 630
Ikemoto, Isao, 810
In-localised hole wave functions, 707–8
Inclusion compounds, 64
Incoherent structure imaging, 691–3
Incommensurability, 251
Incommensurate materials, 304–22
diffraction properties, 307–12
energetic aspects, 312–14
physical properties, 314–22
distribution of guest molecule
environments, 315–17
molecular transport processes,
318–22
vibrational properties, 317–18
structural aspects, 307–12
structural classification, 304–5
urea inclusion compounds, 305–7
Indium oxide, 60
Indium-rich clusters, 700–1
3-D atom probe studies, 706–7
TEM evidence for, 704–5
Inductive approach, 26
InGaN
electron beam damage, 701–4
exciton localisation in, 700
indium-rich clusters, 700–1
quantum well LEDs, 698–710
strained, 708
transmission electron microscopy,
703–4
Inner sphere complex, 592, 596
Insulators, 272
Inter-molecular perturbation theory, 296
Inter-valence charge transfer, 512
Interactive Data Language, 718
Interatomic potential-based methods,
182–3
Intergrowth tungsten bronze, 738
Intra-pellet molecular diffusion, 469–70
Iridium, supported catalysts, 18
897
Iridium carbonyl clusters, 538–9
IRMOF-6, 80
IRMOF-9, 81
IRMOF-13, 81
IRMOF-14, 81
IRMOF-20, 81
Iron oxide nanoparticles, 781–5
IrSr2RECu2O8 cuprates, disordered
perovskite, 151–64
average structure, 154–60
chemical composition, 153–4
experimental, 152
magnetic properties, 162
microstructure, 160–2
synthesis, 153
Isopulegol, cyclization, 641, 642–6
adsorption, activation and reaction
energy, 644
conversions and diastereoselectivity,
645
beneficial factors, 649
effect of solvents and water, 646–9
stereoselectivity, 644
Itoh, Kenji, 138
Iwasawa, Yasuhiro, 829
Jackson, Rob, 16
Jacobs, Pat, 651, 652
Jacobs, P.W.M., 809
Jahn-Teller effect, 158
JANA software system, 251
Jefferson, David, 754, 804, 810, 817
Jennings-White, Clive, 337
Johnson, Brian, 624, 713, 836–9
Jones, Bill, 337, 338, 347, 805, 806,
810, 820
Jones, Emrys Wynn, 809
Jones, G.P., 802
Jones, Matthew, 837, 839
Jones, Richard, 17, 829
Jong, Krijn de, 716
K-A oil, 625, 626
Kaszkur, Zbigniew, 832
Kearsley, Simon, 366
898
Keast, Vicki, 712
Kendrick, David, 337
Khimyak, Tanya, 837
Kink sites, 105, 116
Kitaigorodski, A.I., 289, 324
Klein, Mike, 15
Klinowski, Jacek, 443, 811, 816, 817
Klunduk, Marcus, 837
Knipping, Paul, 287
Kochi, Jay, 139
Koechlinite, 758
Koster, Bram, 716
Kozlowski, Roman, 829
Kraft, Arno, 339
Kratos Axis Ultra spectrometer, 654
Kuroda, Haruo, 809, 829
Kurosawa, Hideo, 138
Laccase, 418–19
Lambert, Richard, 828
Lang, A.R., 809
Langmuir isotherm, 480
Langmuir-Hinshelhood mechanism, 480
Lanthanide coordination polymers, 83
Lanthanide phosphonates, 83, 84
Larmor frequency, 273, 277
Lattice constants, 32
Laurencia nidifica, 335
Leadbetter, Alan, 829
Lenard-Jones potential, 671
Lewis acid catalysis, 639–50
Lewis, Dewi, 833
Lewis, Jack, 51, 810
Lewis, T.J., 802
Li, Can, 839
Lichtenhan, Joe, 389
Ligand atoms, 403–4
Ligand field splitting, 653
Ligand tethering, 391
Light emitting devices, 340
Light-emitting diodes, 698–710
Light-emitting polymers, 338–41
Lillianites, 242–8
Lin, Wen Shu, 811
Lindemann ratio, 170
Subject Index
Lindemann’s melting rule, 167–71
Linnett, Jack, 809, 810
Lipoxygenase, 413
Lippmaa, Endel, 443
Lithium carbonate, E(V) curves, 33
Lithium halides, lattice constants, 32
Liu, Xinsheng, 811
Lizardite, 808
Local ergodicity, 26
Loewenstein’s rule, 449
Lonsdale, Dame Kathleen, 797, 801, 809
Loop coordination, 224–5
Low energy electron diffraction, 481
Lowe, Barrie, 95
Lowest unoccupied molecular orbital
see LUMO
LUMO, 492
Lunsford, Jack, 811
Lyerla, Jim, 808
Lysozyme, 400–1, 405
McBride, J. Michael, 337, 346
McClure, Don, 3
McIntyre, Steward, 654
Maddox, John, 183
Maddox, Peter, 824, 827
Madelung, Erwin, 287
Magic angle spinning NMR, 14, 349, 443
Magnetic resonance imaging, 457–78
13
C, 464–8
chemical mapping, 460–8
1H observation, 460–3
13C observation, 464–8
imaging flows field, 470–6
single-phase flow, 470–1
two-phase flow, 471–6
intra-pellet molecular diffusion, 469–70
Magnetite, 780–5
cis-Maneonene-A
structure, 335
synthesis, 336
Manganese porphyrin, 569
Manzer, Leo E., 138
Marchese, Leo, 17, 825
Marcus theory, 431, 432
Subject Index
Mars-van Krevelen mechanism, 571,
755–6
Martensitic transformations, 808
Maschmeyer, Thomas, 389, 825, 830,
836, 837, 839
Mason, Ron, 809
Materials chemistry
foundations, 52–6
four elements of, 56–7
intellectual foundation, 56–7
Materials design, 43–4
Materials discovery, 43–4
Materials synthesis, 44
Maxwell, James Clerk, 365
Mazzite, 258–70
scanning electron microscopy, 260
structure, 259
see also Zinc-aluminosilicate mazzite
MCM-41, 129, 130, 131, 385–91, 634
chromium catalysts, 500–3
HREM studies, 730–4, 735
STEM HAADF imaging, 714
MCM-48
HREM studies, 730–4
tomographic voxel projections, 720
Meerwein-Ponndorf-Verley
oxidation, 641
Melanophlogite, 669
Melt-quench approach, 185
Melting, 165–71
Clausius-Clapeyron relation, 166
Lindemann’s melting rule, 167–71
melting curve of alumina, 166–7
Melting curve of alumina, 167
Menthol synthesis, 639–40
Mesoporous materials, 129–34
for catalysis, 130–2
electron microscopy, 667–86
HREM studies, 729–34
non-silicate, 132–4
silicas, 129–30
Metal organic vapour phase epitaxy, 700
Metal oxides, 17–19
Metal-organic coordination polymers,
76–94
899
4f metals, 83–4
d-block, 77–9
p-block, 90–1
uranyl-organic coordination polymers,
84–90
Metal-organic frameworks, 77, 78, 114,
116, 128–9
adsorption and hydrogen storage
properties, 79–82
drug delivery, 82
HKUST-1, 116, 117, 118
Metallo-enzymes, 402
Methane oxidase, 413
Methanol synthesis catalysis, 189, 190
Methanol-to-gasoline process, 606
Methanol-to-olefin process, 06
H-SAPO-34 as catalyst, 607–16
2-Methy-2-butene, 464–5
Methyl mandelate, non-phosphine-
based production, 632–6
Meurigite, 239
MFI structures, 212, 215, 444–5
crystallographically distinct sites, 445–9
Cu(I) sites in, 450–4
relative energies, 448
sphere packing, 218
Mica, 287
Michaelis-Menton equation, 437
Microporous aluminophosphates, 76
Microporous organic-inorganic hybrids,
127–9
Microporous solids, 123–37
compositional range, 124–5
designer templates, 125–7
electron microscopy, 667–86
synthesis and study, 124–9
titanium silicate, 386
Midgley, Paul, 7, 836–9
MIL-53, 129
MIL-53as, 91
MIL-53ht, 91
MIL-96, 91
MIL-100, 82
MIL-101, 82
MIL-102, 82
900
MIL-n, 129
Miller indices, 307, 309, 311
Miller-Bravais indices, 747
Millikan, Robert, 5
Millward, Bob, 804, 810, 816
Minerals, 239–49
structural imaging, 817–18
see also individual minerals
Minimal surface-area principle, 670
Mirsky, Kira, 290
Mo-based catalysts, 507–18
acrolein oxidation, 512–14
activation energy for propane, 516
high-resolution transmission
electron microscopy, 510, 511
orthorhombic, 509–12
elemental composition, 514
propane ammoxidation, 514–17
surface area, 514
Raman spectroscopy, 511
reaction rates, 516
simulated rate constants, 516
structure, 508
trigonal, 509–12
Mo-oxide catalysts, 500
Modular crystallography, 241–2
MOF see metal-organic frameworks
MOF-2, 80
MOF-3, 80
MOF-4, 80
MOF-5, 80
MOF-CJ2, 82
Molecular beam epitaxy, 700
Molecular catalysts, 388–90, 411–12
non-adjacent sites, 418–21
Molecular Crystal Symposia, 3, 4
Molecular dynamics, 182, 187, 195
Molecular flow, 434–5
Molecular interactions, 286
ab initio approach, 297–8
atom-atom method, 289–93
distributed charge methods, 293–4
history, 285–8
non-bonded interactions, 290
penetration energy, 294–5
pixel method, 296–7
Subject Index
Molecular “ionic” cluster catalysts, 426
Molecular modelling, 872–5
Molecular packing methods, 185
Molecular prediction of chemical
compounds, 29
Molecular recognition, 346–61
function group interaction energies,
351–6
with interactional complementarity,
595
Molecular sieves, 640
crystalline, 222–3
structural description, 223–6
Molecular transport, 318–22
Molecularly defined catalytic
materials, 388–90
Molybdenum coenzyme, 420
Monk, C.B., 806
Monte Carlo analysis, 28, 81, 182
Monte Carlo Basin Hopping, 194
Montmorillonite, 640
Morales, Julian Palomino, 810
Morpholine, 609
Morsi, Salah, 364, 810
Mössbauer spectroscopy, 651, 653
Mott criterion, 58
Mott-Littleton method, 187, 197–8
MoV(Nb,Ta)(TeSb)O system, 578–86
acrylonitrile yield, 582
active centre, 581
site isolation, 582
symbiosis between phases, 581, 583
MoVTe(Sb)NbO system, 507
MRI see Magnetic resonance imaging
Müller, K.A., 53
Multi-quantum technique, 443
Multi-walled carbon nanotubes, 722,
723
Multiply twinned crystals, 671–3
Multisample concept, 36
Multiwall carbon nanotubes, 728
Muonium, 271
hyperfine constant, 280
spectroscopy, 272
spin precession signal in ZnO, 277
states in silicon, 275
Subject Index
Muons, 271–82
Larmor frequency, 273, 277
spin rotation spectra, 274
Murray, Dame Rosemary, 810
Muybridge, Eadweard, 6
Myoglobin, 401
Nakanishi, Hachiro, 811, 820
Nano-catalyst formation, 545–8
Nano-squares, 109
Nanocapsules, 531
Nanoclusters, structures and energies,
191–4
Nanoparticulate systems, 427–9
carbon, 750
catalysts, 631–2, 633
electron microscopy, 778–91
gold, 550–67
gold-palladium, 550–67
surfaces, 778–9
synthetic magnetite, 780–5
tungsten, 748, 750
Nanoporous materials, 95–122
crystal growth, 98–102
as drug delivery systems, 729–34
faujasitic structures, 103–5
HREM studies, 727–44
metal-organic frameworks see
metal-organic frameworks
modelling, 116, 118–20
pore size, 733
supersaturation, 109, 111–14
zeolite A transformations, 105–9
Naphthalene 1-2 dioxygenase, 413
Negative melting curves, 171–2
Neodymium coordination polymers,
83, 84
Nepouite, 596
Newton, Isaac, 285
Ng, Ching Fai, 807, 810
Nitrogen oxide decomposition
systems
Cu+/ZSM-5, 503–5
Ti-oxide/Y zeolite, 494–8
Nitrogenase, 432
901
Nitromethane, 196
Nitrous oxide, 625–8
Nitrous oxide-free synthesis, 628–31
NMR see Nuclear magnetic resonance
Non-bonded interactions, 290
Non-conductors, XPS studies, 651–64
Non-silicate mesoporous oxides, 132–4
Non-systematic structural enumeration,
226–8
Nowak, Andreas, 15, 811, 825
NPO framework, 232
Nucleation, 482–6
Nucleophilic oxidation, 575
Nylon-6
conventional industrial synthesis, 625–8
environmentally benign production,
628–31
Nylon-6,6
conventional industrial synthesis, 625–8
environmentally benign production,
628–31
O’Connor, Tim, 837
1-Octene hydrogenation, 468
Offretite, 258, 449, 813
Olation, 598
Olivine, XPS studies, 658, 659, 660
Omega structure, 259
Onminum-type carbon structures, 736
Optical coherence, 4
Organic materials
aperiodicity, 302–33
molecular interactions, 285–301
ab initio approach, 297–8
atom-atom method, 289–93
distributed charge methods, 293–4
history, 285–8
non-bonded interactions, 290
penetration energy, 294–5
pixel method, 296–7
photochemistry, 807–10
photophysics, 802–7
Organic peroxides, 362–81
Organic potential energy, 291
Orthopyroxenes, XPS studies, 657–8
902
Ostwald, W., 42
Ourayite, 243, 244
Outer sphere complex, 592–3
Owen, Gari, 804
Owen, Tom Arfon, 809
Oxidation reactions, 550–67, 568
electrophilic oxidation, 575
gold-palladium catalysts, 558–64
gold/carbon catalysts, 553–8
hydrocarbons, 568–76
nucleophilic oxidation, 575
targets for, 552
Oxidative enzymes, 413, 415
Oxide-supported catalysts, preparation,
589
Oxolation, 598
Packing effects, 290
Palatinus, Lukas, 257
Palladium, 534
Paraffin conversion catalysts, 578
Parkinson, Gordon, 337, 338, 365, 805,
806, 810, 819
Particle size effects, 427–9
Partitioning, 668
Paschen-Back regime, 277
Pate, Kevin, 367
Patterson function, 250, 252
Pauling, Linus, 5, 34, 287
Peierls barriers, 688
Penetration energy, 294–5
Pennington, Joan, 338
Penrose tiling, 323–9
nodes, 326
thick rhombus, 327
thin rhombus, 327
Pentane oxidation rate, 574
Perhydrotriphenylene, 352–6
Periodic Table, 2, 56, 57
Perovskites, 18, 738–9
disordered, synthesis, 151–64
non-stoichiometry, 739–40
Peroxidase, 413
Peroxy dicyclohexylamine, 630
Perutz, Max, 858
Subject Index
Peters, Keith, 858
Pethica, Brian, 806
Petricek, Vaclav, 251
Phase diagrams, 40
quasi-binary systems, 41
Phillips, David, 828
Phosphoglycerate kinase, 424
Phosphorescence, 342–3
Phosphorus, distribution in SAPOs, 608
Photocatalysis, 492–506
bismuth molybdates, 770–1
single-site, 493
catalyst design, 498–500
Cr-MCM-41, 500–3
Ti-oxide/Y-zeolite, 494–8
Photoelectron spectroscopy, 802–7
Photoluminescence, 340
Pickering, Ingrid, 824, 827
Pickett, Steve, 825
Pielaszek, Jerzy, 810
Pimentel, George, 809
Pippard, Sir Brian, 6
Pitzer, Kenneth, 809
Pixel method, 296–7
Plan view imaging, 694
Plane wave pseudopotential approach,
182
Plastocyanin, 406
Platinum-ruthenium tin cluster
complexes, 545
nano-catalyst formation, 545–8
Point of zero charge, 591
Poirier’s dislocation melting model, 169
Polanyi, Michael, 798
Polarization energy, 296
Polyamorphism, 171
Polydiacetylenes, 334–8
Poly(2,7-dibenzodiloles), 342
Poly(3,6-dibenzodiloles), 342
Polyethylene teraphthalate, 652
Polyfluorenes, 341–2
Polyhedral oligomeric silsesquioxanes,
294
Polymorph A, 100, 102
Polymorphism, 195–7
Subject Index
Poly(p-phenylene vinylene), 339
Polystannanes, 534
Ponyatovsky-Barkolov model, 172
Pooley, Guy, 338
Pope, Martin, 802, 805, 809
Pope, Wiliam, 240
Porous solids
mesoporous materials, 129–34
for catalysis, 130–2
non-silicate, 132–4
silicas, 129–30
microporous solids, 123–37
compositional range, 124–5
designer templates, 125–7
synthesis and study, 124–9
Porter, Sir George, 5, 808, 828
Potential energy, 31
Poulis, Johannes, 801
Powder X-ray diffraction, 140
9,10-anthracendicarboxylate-
bridged compounds, 146, 147
Power reflection coefficient, 61
Pre-nucleation, 195–7
Price, Sally, 294
Primitive cubic rod packing, 82
Pring, Alan, 817
Pritchard, Robin, 806
Product shape selectivity, 629
Projection requirement, 715
Propane ammoxidation, 514–17, 584
Propane oxidation, 507–8
rate of, 574
Propene, 755
Propene oxidation, 769–70
Propylene oxide, SMPO process, 388
Proton transfer, 434
Protonation, 591–2
Pseudo-symmetry, 252
Puddephatt, Richard J., 138
Purnell, Howard, 803, 813, 823
Pyramid structures, 105, 106
Pyridine-dicarboxylate, 86
3,4-Pyridinedicarboxylic acid, 86
2,4-Pyridinedicarboxylic acid, 86
Pyroxenoids, 817, 818
903
(S)-(+)-1-(2-Pyrrolidinylmethyl)-
pyrrolidine, 625
Quadruply bonded complexes
dicarboxylate linked, 141–5
electronic absorption spectra, 142, 143
intermolecular interactions, 144
Quantum dot superlattices, 64
Quantum well LEDs, 698–710
Quantum well thickness fluctuations, 707
Quantum wire arrays, 64
Quartz, 212
XPS studies, 658, 659
Quasi-binary systems, 41
Quasicrystalline materials, 323–30
crystal engineering, 324
design of, 324–9
future directions, 329–30
Quitenine, 79
Radon, Johannes, 715
Ragai, Jehane, 810
Raithby, Paul, 338
Raja, Robert, 713, 825, 836, 837, 839
Raman microspectrometry, 320–1
Raman spectroscopy
bismuth molybdates, 769
Mo-based catalysts, 511
Rao, C.N.R., 56, 754, 809
Rao, K.J., 811
Raphael, Ralph, 334, 335, 809, 810
Rapid phase transitions, 807–10
RARE imaging, 460, 463
Rate expressions, 396–9
Rayment, Trevor, 816, 817
Raynor, Stuart, 837
Reaction time, 560
Reactivity, 189
Realisable nets, 227
Redox potential, 569, 570
Rees, Lovat, 813
Regai, Jehane, 806
Reller, Armin, 811
Rennie, Andrew, 303–4
Repulsion energy, 296
904 Subject Index

Rey, Fernando, 830 Scheelites, 239, 760, 762

Reynolds number, 470 Schirmerite, 243, 248
Rhodium carbonyl clusters, 538–9 Schlögl, Robert, 811, 820
Rideal, Sir Eric, 828 Schmidt, Gerhardt, 363
Rietveld refinement, 14, 154, 155, 156, SCIBS, 211, 212, 215
510 Secondary building units, 223–4, 226
Roberts, Gareth, 802 Seebeck coefficient, 63
Roberts, Jack, 8 Segmuller, B.E., 348
Roberts, John D., 820 Selectivity, 577–87
Roberts, Wyn, 479–80, 797 Selenium, 676–8
Robinson, Sir Robert, 797 Semi-classical density sums see Pixel
Robinson, Wilse, 3 method
Rock-salt structure, 193 Semiconducting oxides, defect
Rosker, Mark, 5 modelling, 197–9
Ruthenium, supported catalysts, 18 Semiconductors, 272
Ruthenium(II) hydrogenation catalysis, band offset diagram, 280
enantioselectivity, 199–204 bulk solids, 431
Rutherford Appleton Laboratory, 272, silicon, 273, 274–7
273 zinc oxide, 273, 277–9
Rutherford scattering, 712 Septenary cuprates, 54
RWY framework, 232 Shallow centres, 277–9
vs deep centres, 279–81
Sankar, G., 76 Shephard, Doug, 837
SAPOs, 607 Shoppee, Charles, 480
preparation, 616 Siebrand, Wilhelm, 805
Si, Al and P distribution, 608 Siegbahn, Kai, 803
SAPO-5, 520 Silicas
acidity and island dimension, 613 amorphous surface, 595
SAPO-11, 613 anionic-surfactant-templated
SAPO-18, 613 mesoporous, 673–4
SAPO-31, 613 chiral mesoporous crystals, 675
SAPO-34, 17, 125, 127 mesoporous, 129–30
acidity and island dimension, 613 Silica-grafted titanate catalysts, 386–8
scanning electron microscopy, 618 Silicalite, 109, 111–14, 184, 347
Sb2Zn3-x, 252–7 atomic force microscopy, 112, 115
SBA-2, 130 morphology, 111
SBA-15, 129, 131, 132, 392–4 surface topography, 111, 112
HREM studies, 730–4 Silicates
SBA-16, 130 modified mesoporous, 130–2
Scanning probe microscopy, 102, XPS studies, 655, 656, 657
695–6, 778 Silicoaluminophosphates, 125, 222
Scanning transmission electron Silicon, 273, 274–7
microscopy see STEM in ALPOs, 610
Scanning tunnelling microscopy, 695 in SAPOs, 608
Scheele, Karl, 239 Silicophosphates see SAPOs
Subject Index 905
Silsesquioxanes, 386–8 STA-7, 127
metal catalysts, 388–90 Stacking faults, 807–10
Simplices, 229 Stearyl desaturase, 413
Simulated annealing, 28, 32, 184 STEM, 691, 711–14
Simulated body fluid, 730, 731 ferritin mineral cores in human tissue,
Single wall carbon nanotubes, 728, 734 785–90
Single-phase flow, 470–1 synthetic magnetite nanoparticles,
Single-site epoxidation catalysts, 385–95 780–5
Single-site heterogeneous catalysts, 624 STEM energy dispersive spectroscopy,
Single-site photocatalysis, 493 559
catalyst design, 498–500 STEM-HAADF, 546–7, 691–3, 711,
Ti-oxide/Y-zeolite, 494–8 713, 714, 779, 787
Site isolation hypothesis, 578–86 Stern-Volmer equation, 501
Size quantization effect, 492 Stone, Anthony, 294
Skutterudites, 64 inter-molecular perturbation theory,
Sliding mode, 318 296
Sloan, Gil, 805 Storage materials, 65–71
Smallman, Ray, 810 Structural mimicry, 820–2
Smith, J.V., 209 Structural solutions, 250–1
Smith, Luis, 17 Structure Commission of International
SMPO process, 386 Zeolite Association, 215, 219
propylene oxide, 388 Structure directing agents, 123, 609
Sn-Beta, 643, 644 alkylammonium, 126
catalytic active sites, 641–2 morpholine, 609
Soap bubbles, 668–9 tetraethylammonium hydroxide, 610
Sodalite, 224, 813 Styrene monomer propylene oxide
Sodalite cages, 107–8, 109, 224 see SMPO
Sodium chloride, 288 Superflip software, 257
SOHIO process, 755–6 Supersaturation, 109, 111–14
Solid heterogeneous catalysts, 405 Supported metal catalysts, 17–19
Solid state catalysts, 417–18 iridium, 18
non-adjacent sites, 421 ruthenium, 18
Solid state cluster catalysts, 427–9 Surface characteristics
Solid state reactions, diffusion-free, 820–2 charge, 591–2
Solvents computer modelling, 188–9
in cyclization reactions, 647–9 Mo-based catalysts, 514
viscous, 591–2 nanoparticulate systems, 778–9
water as, 590 reactivity, 486–90
Sorption, 188–9 silicalite, 111, 112
Space filling, 668 Surface relaxation, 486
Space groups, 209 Surface strings, 484
Space-charge currents, 802 Sustainable development, 623–38
Speck, Jim, 18 Sworakowski, Juliusz, 804
SPUDS program, 158 Syers, Ken, 800
STA-2, 127 Sykes, Keble, 480, 797
906
Symbiosis, 581, 583
Symmetry-constrained inter-site
bonding search see SCIBS
Synthetic magnetite nanoparticles, 780–5
Synthetic routes, 39–43
SYSTRE, 214
Szargan, Rudiger, 653
T-atoms, 210–11, 213, 223
Takasago process, 639
Taube, Henry, 139
Taylor, H.S., 399
TEM see Transmission electron
microscopy
Tennakoon, Tilak, 803, 811
Terasaki, Osamu, 96, 720, 811, 816
Terephthalic acid
conventional industrial synthesis, 625–8
environmentally benign production,
628–31
Tetraethylammonium hydroxide, 610
Tetrahedral silicates, 212
Tetrahydridotetraruthenium clusters,
537–8
Theocharis, Charis, 347, 821
Thermodynamic spaces, 37–9
Thermoelectric materials, 62–5
figure-of-merit, 62, 63
Thiele modulus, 458
Thomas, John Meurig, 3, 55, 124, 139, 165,
208, 215, 239, 337, 364–5, 624, 754
Aberystwyth, 802–10
Aldermaston, 796–9
American Chemical Society award,
588
Bakerian lectures, 4–3
Bangor, 799–802
Cambridge, 810–24, 836–9, 87507
Davy Faraday Laboratories, 824–36
Molecular Crystal Symposia, 3, 4
Penn State, 800–2
Queen Mary College, 796–9
Royal Institution, 13, 855
Swansea, 796–9
tributes to, 853–86
Subject Index
Thomas, Margaret, 5, 620, 624
Thomas, Noel, 820, 821
Thomson, J.J., 365
Three-dimensional imaging, 715
Ti-Beta, 125, 643, 644
Ti-MCM-41, 520
Tiling theory, 196, 228–30
Penrose tiling, 323–9
Tin, 534
Tin oxide, 60
Titanium oxide/Y-zeolite catalysts, 494–8
Titanium silicalite, 558
Titanium silsesquioxanes, 386–8
Titanocene dichloride, 520–2
surface reactions, 522
Titanosilicates, structure, 100, 102
Tomography, 836–9
Topological methods, 185
Transient states, 486–90
Transition metal cations, 441
Transition metal oxides, 133–4, 493
Transition state theory, 408
complications in, 410–11
Transitional metal oxides, 572
Transmission channelling, 688–9, 694
Transmission electron microscopy,
76, 208
InGaN, 703–4
synthetic magnetite nanoparticles, 780
zeolite Na-A, 96, 97
Transparent conducting oxides, 58–62
conductivity, 60
doping, 59
power reflection coefficient, 61
Trapnell, B.W.M., 797
Treadgold, R.H., 802
Treasurite, 243
Trickle flow, 471, 472
Trickle-bed reactors, 465–8, 471–6
Triosmium carbonyl clusters, 540–3
Triphenylstannane, reactions, 534
carbido-pentarutheniumcarbonyl
clusters, 535–7
dirhenium cluster complexes, 539–40
iridium carbonyl clusters, 538–9
Subject Index
platinum-ruthenium complexes, 545
rhodium carbonyl clusters, 538–9
tetrahydridotetraruthenium clusters,
537–8
triosmium carbonyl clusters, 540–3
Triphenyltin, 534
Triplet emitters, 342–3
Triply periodic minimal surfaces, 225
L-Tryptophanbenzyl ester, 625
Tunable copolymers, 341
Tungsten carbides, 745–53
atomic level twin boundary defects,
747, 748
carbon nanoparticles, 750
hexagonal, 751
Tungsten nanoparticles, 748, 750
Tunnel inclusion compounds, 305–7
Two-phase flow, 471–6
Two-solvents method, 132
Ubbelohde, A.R., 809
Ueda, Wataru, 811
UFI framework, 232
Ultraviolet-visible spectroscopy, 493
Unit operations, 589
Uranyl-organic coordination polymers,
84–90
3D framework, 87, 88
microporous frameworks, 89–90
Urea inclusion complexes, 305–7,
309, 347, 822–3
Valence sites, mapping of, 694–5
Van der Waals equation, 286
Van der Waals, Jan, 3, 805
Vanadium oxide, 571–2
Vanadium phosphate, 572
Vasudevan, S., 811
Vauquelin, Louis, 239
Vauquelinite, 239
Vegard’s law, 701
Vertex, 228
Vertex figure, 228
Vikingite, 243, 244–5
Vollmer, M., 42
907
Volume-spectroscopy, 722
Von Laue, Max, 240, 287
Von Neumann algebra, 217
Voronoi cells, 217, 668
Walker, P.L., 800
Waller, David, 829
Ward, Edmund, 838
Water, 590–600
in cyclization reactions, 647
as donor, 590
formation constants of complexes
in, 594
as H-bond intermediate, 592–3
as ionizing and dissociating
solvent, 590
as labile and weak delta donor-π
donor ligand, 593–6
as ligand, 592–3
as reactant, 596–9
as reaction product, 596–9
as transport agent, 599–600
as viscous solvent, 591–2
Water exchange rates, 594
Weak beam imaging, 689
Wegner, G., 338
Wellard, Nick, 334
Wells, A.F., 209
Werner-Zwanziger, Ulrike, 353
Weyland, Matthew, 717, 837
White, John, 803, 809
White, Jonathan, 338
Whitsel, Bonnie, 366
Wiedemann-Franz law, 64
Wilkins, M.F.H., 797
Wilkinson, Sir Geoffrey, 6, 140
Willemite, 261
Williams, Brian, 801, 811, 819
Williams, Carol, 811, 817, 829
Williams, David, 822
Williams, D.E., 290
Williams, Digby, 805
Williams, J.O., 364, 802
Williams, R.J.P., 809
Williams, Robin, 802
908
Wolf, Hans Christoph, 3
Wong, Joe, 811
Wong, Wallace, 338
Wright, Paul, 15, 17, 811, 816, 833
Wurtzite structure, 193
X-ray absorption fine structure, 493,
495, 521
X-ray absorption near edge structure
see XANES
X-ray diffraction, 287
X-ray energy dispersive
spectroscopy, 547
X-ray photoelectron spectroscopy, 481
non-conductors, 651–64
arsenopyrites, 654, 655
bronzite, 658, 659
diopside, 658, 659, 660
olivine, 658, 659, 660
orthopyroxenes, 657–8
quartz, 658, 659
silicates, 655, 656, 657
X-ray powder diffraction, 143
XANES, 521, 523
XPS see X-ray photoelectron
spectroscopy
Xu, Yan, 825
p-Xylene
bromine-free oxidation, 631
conventional oxidation, 628
Yashonath, 15–16
Zamaraev, Kirill, 826
Zebedde code, 126, 190, 218
Zeolites, 13–21, 76, 606, 727, 812–17
aluminium phosphates, 16–17
amorphisation, 172–6s
binodal, 233
Bronsted sites, 441, 442, 449–50
collapse of, 174–6
crystal growth, 98–102
designer, 208–20
feasible structures, 230–5
framework structures see Frameworks
Subject Index
as graphs, 209–12
hypothetical structures, 215, 233, 234
known, 215
modelling, 441–56
science of, 14–16
silicon-aluminium ordering, 14
trinodal, 234, 235
uninodal, 233
van der Waals surface, 15
Zeolite A, 224
amorphisation, 173
atomic force microscopy, 97, 98, 101,
105, 106, 107
collapse of, 174
crystal growth modelling, 119
dissolution process, 108–9, 110
nano-squares, 109, 110
sodalite cages, 107–8, 109
spiral growth, 100, 101
structure, 14, 100
transformations, 105–9
Zeolite Beta, 123, 124, 184, 520, 640
overgrowth, 681–3
Zeolite H-ZSM-5, 606
FTIR spectroscopy, 617
Zeolite JMT, 717
Zeolite K-L, 15, 16
Zeolite L, 449
crystal structure, 100
high-resolution electron microscopy,
99
Zeolite LTL, 679
Zeolite MOR, 676–8
Zeolite Na-A, transmission electron
microscopy, 96, 97
Zeolite Na-Y, 14, 53
Zeolite Rho, 15, 224
Zeolite SSZ-24, 679–81, 682, 683
Zeolite TS-1, 520
Zeolite X, 124
Zeolite Y, 104, 123, 124
atomic force microscopy, 104
Cu+ catalysts, 503–5
Ti-oxide catalysts, 494–8
Zeolite ZK-4, 14
Subject Index 909
Zeolite ZK-5, 224 thermogravimetric analysis, 264
Zeolite ZSM-5, 15, 123, 124, 125, 229–30 X-ray absorption spectrum, 264
Cu+ catalysts, 503–5 Zinc-blende structure, 193
NMR spectra, 447 Zinc-montmorillonite, 261
Zeolite ZSM-12, 520 Zinc oxide, 60, 193, 273, 277–9
Zeolite ZSM-48, 520 defect modelling, 197–9
Zeozymes, 623 Zinc sulphide, low energy structures,
Zewail, Ahmed, 303, 805, 839 193–4
Zhou, Wuzong, 811, 819, 833, 837 Zincosilicates, 222
Zig-zag configuration, 800 Zirconia
Zilm, Kurt, 349 hydrous, 640
Zinc-aluminosilicate mazzite, 258 infrared spectra, 192
core level photoemission spectra, 266–7 sulfated, 640
curve-fitting, 265 ZnBr2, 640
Fourier transforms, 265 Zr-Beta, 643, 644
powder X-ray diffraction patterns, 263 Zunyite, 287