This is a textbook for the senior undergraduate or graduate student beginning a serious study of Xray crystallography.
It will be of interest both to those intending to become professional crystallographers and to those physicists, chemists, biologists, geologists, metallurgists and others who will use it as a tool in their research. All major aspects of crystallography are covered  the geometry of crystals and their symmetry, theoretical and practical aspects of diffracting Xrays by crystals and how the data may be analysed to find the symmetry of the crystal and its structure. Recent advances are fully covered, including the synchrotron as a source of Xrays, methods of solving structures from powder data and the full range of techniques for solving structures from singlecrystal data. A suite of computer programs is provided for carrying out many operations of dataprocessing and solving crystal structures  including by direct methods. While these are limited to two dimensions they fully illustrate the characteristics of threedimensional work. These programs are required for many of the problems given at the end of each chapter but may also be used to create new problems by which students can test themselves or each other.
An introduction to Xray crystallography
An introduction to
Xray crystallography
SECOND EDITION
M.M. WOOLFSON
Emeritus Professor of Theoretical Physics University of York
CAMBRIDGE
UNIVERSITY PRESS
PUBLISHED BY THE PRESS SYNDICATE OF THE UNIVERSITY OF CAMBRIDGE
The Pitt Building, Trumpington Street, Cambridge CB2 1RP, United Kingdom
CAMBRIDGE UNIVERSITY PRESS
The Edinburgh Building, Cambridge CB2 2RU, United Kingdom 40 West 20th Street, New York, NY 100114211, USA 10 Stamford Road, Oakleigh, Melbourne 3166, Australia © Cambridge University Press 1970, 1997 This book is in copyright. Subject to statutory exception and to the provisions of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. First published 1970 Second edition 1997 Typeset in Times 10/12 pt A catalogue record for this book is available from the British Library Library of Congress cataloguing in publication data Woolfson, M. M. An introduction to Xray crystallography / M.M. Woolfson.  2nd ed. p. cm. Includes bibliographical references and index. ISBN 0 521 41271 4 (hardcover).  ISBN 0 521 42359 7 (pbk.) 1. Xray crystallography. I. Title. QD945.W58 1997 548'.83dc20 965700 CIP ISBN 0 521 41271 4 hardback ISBN 0 521 42359 7 paperback Transferred to digital printing 2003
Contents
Preface to the First Edition Preface to the Second Edition 1 LI 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 2 2.1 2.2 2.3 2.4 2.5 2.6 3 3.1 3.2 3.3 3.4 3.5 3.6 3.7 4 4.1 4.2 The geometry of the crystalline state The general features of crystals The external symmetry of crystals The seven crystal systems The thirtytwo crystal classes The unit cell Miller indices Space lattices Symmetry elements Space groups Space group and crystal class Problems to Chapter 1 The scattering of Xrays A general description of the scattering process Scattering from a pair of points Scattering from a general distribution of point scatterers Thomson scattering Compton scattering The scattering of Xrays by atoms Problems to Chapter 2 Diffraction from a crystal Diffraction from a onedimensional array of atoms Diffraction from a twodimensional array of atoms Diffraction from a threedimensional array of atoms The reciprocal lattice Diffraction from a crystal  the structure factor Bragg's law The structure factor in terms of indices of reflection Problems to Chapter 3 The Fourier transform The Fourier series Numerical application of Fourier series
Page x xii 1 1 1 7 9 12 15 16 20 23 30 31 32 32 34 36 37 42 43 48 50 50 56 57 59 64 67 72 74 76 76 79
viii 4.3 4.4 4.5 4.6 4.7 4.8 Fourier series in two and three dimensions The Fourier transform Diffraction and the Fourier transform Convolution Diffraction by a periodic distribution The electrondensity equation Problems to Chapter 4 Experimental collection of diffraction data The conditions for diffraction to occur The powder camera The oscillation camera The Weissenberg camera The precession camera The photographic measurement of intensities Diffractometers Xray sources Imageplate systems The modern Laue method Problems to Chapter 5 The factors affecting Xray intensities Diffraction from a rotating crystal Absorption of Xrays Primary extinction Secondary extinction The temperature factor Anomalous scattering Problems to Chapter 6 The determination of space groups Tests for the lack of a centre of symmetry The optical properties of crystals The symmetry of Xray photographs Information from systematic absences Intensity statistics Detection of mirror planes and diad axes Problems to Chapter 7 The determination of crystal structures Trialanderror methods The Patterson function The heavyatom method Isomorphous replacement The application of anomalous scattering Inequality relationships Sign relationships
Contents 83 85 92 94 99 99 106 108 108 112 118 125 130 135 140 143 150 151 154 156 156 162 169 173 175 179 188 190 190 196 208 210 215 227 229 231 231 233 249 255 267 274 282
5 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9 5.10
6 6.1 6.2 6.3 6.4 6.5 6.6
7 7.1 7.2 7.3 7.4 7.5 7.6
8 8.1 8.2 8.3 8.4 8.5 8.6 8.7
2 9.9
General phase relationships A general survey of methods Problems to Chapter 8 Accuracy and refinement processes The determination of unitcell parameters The scaling of observed data Fourier refinement Leastsquares refinement The parametershift method Problems to Chapter 9 Physical constants and tables Appendices Program listings I STRUCFAC II FOUR1 III SIMP1 IV FOUR2 V FTOUE VI HEAVY VII ISOFILE VIII ISOCOEFF IX ANOFILE X PSCOEFF XI MINDIR XII CALOBS Solutions to Problems References Bibliography Index
290 297 298 301 301 307 309 317 320 322 325 327 328 333 335 336 339 346 349 350 352 353 354 366 367 395 397 399
9 9.Contents
8.1 9.3 9.5
.4 9.8 8.
Bown and Dr S.
. medicine. Xray crystallography is sometimes regarded as a science in its own right and. described in terms of two or three parameters. It has now become clear that there is wide acceptance of the SI system of units and byandlarge they are used in this book. Indeed. There has been no attempt to compete in depth with specialized textbooks. there has been steady progress to the point where now several complex biological structures have been solved and the solution of the structures of some crystalline viruses is a distinct possibility. since a great deal of the basic literature uses this unit. it is a meeting point of many disciplines .. physics.have been excluded.mathematics. At that time the full consequences of this discovery could not have been fully appreciated. the conventional boundaries between scientific subjects often seem rather nebulous. biology. broad treatment. and closely associated topics which fall outside the scope of the title . From the solution of simple crystal structures. for the crystallographer. 325326. chemistry. A brief explanation of the SI system and some important constants and equations are included in the section Physical constants and tables on pp. In writing this book the aim has been to provide an elementary text which will serve either the undergraduate student or the postgraduate student beginning seriously to study the subject for the first time. geology. indeed. However the angstrom unit has been retained as a unit of length for Xray wavelengths and unitcell dimensions etc. metallurgy. electron. University of Cambridge and to my colleague. complete in itself. For those who wish to go further it should be regarded as a foundation for further study.and noncrystalline materials. it has also been found desirable to restrict the breadth of treatment. On the other hand. Dr P. to many other scientists it is only a tool and.for example diffraction from semi. However. as such. For those who wish to go no further it is hoped that the book gives a rounded. for reading the manuscript and for their helpful criticism which included suggestions for many improvements of treatment. some of which are listed in the Bibliography. Fleet of the Department of Mineralogy. fibre technology and several others. G. which explains the principles involved and adequately describes the present state of the subject. Main. I am deeply indebted to Dr M. there are many professional crystallographers who devote all their efforts to the development and practice of the subject.Preface to the First Edition
In 1912 von Laue proposed that Xrays could be diffracted by crystals and shortly afterwards the experiment which confirmed this brilliant prediction was carried out.and neutron diffraction .
Preface to the First Edition
My thanks are also due to Professor C. A. Taylor of the University of Cardiff for providing the material for figs. 8.9 and 8.10 and also to Mr W. Spellman and Mr B. Cooper of the University of York for help with some of the illustrations. M.M.W.
Preface to the Second Edition
Since the first edition of this book was published in 1970 there have been tremendous advances in Xray crystallography. Much of this has been due to technological developments  for example new and powerful synchrotron sources of Xrays, improved detectors and increase in the power of computers by many orders of magnitude. Alongside these developments, and sometimes prompted by them, there have also been theoretical advances, in particular in methods of solution of crystal structures. In this second edition these new aspects of the subject have been included and described at a level which is appropriate to the nature of the book, which is still an introductory text. A new feature of this edition is that advantage has been taken of the ready availability of powerful tabletop computers to illustrate the procedures of Xray crystallography with FORTRAN® computer programs. These are listed in the appendices and available on the World Wide Web*. While they are restricted to twodimensional applications they apply to all the twodimensional space groups and fully illustrate the principles of the more complicated threedimensional programs that are available. The Problems at the end of each chapter include some in which the reader can use these programs and go through simulations of structure solutions  simulations in that the known structure is used to generate what is equivalent to observed data. More realistic exercises can be produced if readers will work in pairs, one providing the other with a data file containing simulated observed data for a synthetic structure of his own invention, while the other has tofindthe solution. It can be great fun as well as being very educational! I am particularly grateful to Professor J. R. Helliwell for providing material on the new Laue method and on imageplate methods. M. M. Woolfson York 1996
*http: //www.cup.cam.ac.uk/onlinepubs/412714/412714top.html
xu
1 The geometry of the crystalline state
1.1
The general features of crystals Materials in the crystalline state are commonplace and they play an important part in everyday life. The household chemicals salt, sugar and washing soda; the industrial materials, corundum and germanium; and the precious stones, diamonds and emeralds, are all examples of such materials. A superficial examination of crystals reveals many of their interesting characteristics. The most obvious feature is the presence of facets and wellformed crystals are found to be completely bounded by flat surfaces flat to a degree of precision capable of giving highquality planemirror images. Planarity of this perfection is not common in nature. It may be seen in the surface of a still liquid but we could scarcely envisage that gravitation is instrumental in moulding flat crystal faces simultaneously in a variety of directions. It can easily be verified that the significance of planar surfaces is not confined to the exterior morphology but is also inherent in the interior structure of a crystal. Crystals frequently cleave along preferred directions and, even when a crystal is crudely fractured, it can be seen through a microscope that the apparently rough, broken region is actually a myriad of small plane surfaces. Another feature which may be readily observed is that the crystals of a given material tend to be alike  all needles or all plates for example  which implies that the chemical nature of the material plays an important role in determining the crystal habit. This suggests strongly that the macroscopic form of a crystal depends on structural arrangements at the atomic or molecular level and that the underlying factor controlling crystal formation is the way in which atoms and molecules can pack together. Theflatnessof crystal surfaces can then be attributed to the presence of regular layers of atoms in the structure and cleavage would correspond to the breaking of weaker links between particular layers of atoms.
1.2
The external symmetry of crystals Many crystals are very regular in shape and clearly exhibit a great deal of symmetry. In fig. l.l(a) there is shown a wellformed crystal of alum which has the shape of a perfect octahedron; the quartz crystal illustrated in fig. l.l(ft) has a crosssection which is a regular hexagon. However with many other crystals such symmetry is not evident and it might be thought that crystals with symmetry were an exception rather than a rule. Although the crystals of a particular chemical species usually appear to
The geometry of the crystalline state
Fig. 1.1. (a) Alum crystal. (b) Quartz crystal.
ia)
(b)
have the same general habit a detailed examination reveals considerable variation in size and shape. In particular one may find a selection of platy crystals looking somewhat like those shown in fig. 1.2(a). The shapes of these seem to be quite unrelated but, if they are rearranged as infig.1.2(b), a rather striking relationship may be noted. Although the relative sizes of the sides of the crystal crosssections are very different the normals to the sides (in the plane of the figure) form an identical set from crystal to crystal. Furthermore the set of normals is just that which would be obtained from a regular hexagonal crosssection although none of the crystals in fig. 1.2 displays the characteristics of a regular polygon. While this illustration is essentially twodimensional the same general observations can be made in three dimensions. Although the crystals of a given species vary greatly in the shapes and sizes of corresponding faces, and may appear to lack symmetry altogether, the set of normals to the faces will be identical from crystal to crystal (although a crystal may occasionally lack a particular face completely) and will usually show symmetry that the crystals themselves lack. For example, fig. 1.3(a) shows the set of normals for an octahedron. These normals are drawn radiating from a single point and are of equal length. This set may well have been derived from a solid such as that shown in fig. 13(b) but the symmetry of the normals reveals that this solid has faces whose relative orientations have the same relationship as those of the octahedron. The presentation of a threedimensional distribution of normals as done in fig. 1.3 makes difficulties both for the illustrator and also for the viewer. The normals have a common origin and are of equal length so that their termini lie on the surface of a sphere. It is possible to represent a spherical distribution of points by a perspective projection on to a plane and the stereographic projection is the one most commonly used by the crystallographer. The projection procedure can be followed infig.1 A(a). Points on the surface of the sphere are projected on to a diametral plane with projection point either 0 or O\ where 00' is the diameter normal to the projection plane. Each point is projected from whichever of O or O' is on the opposite side of the plane and in this way all the projected points are contained within the diametral circle. The projected points may be conventionally represented as above or below the projection plane by full or open circles. Thus the points A, B, C and D project as A\ B\ C and D' and, when viewed along 00', the projection plane appears as in fig. lA(b).
1.2 The external symmetry of crystals
Fig. 1.2. (a) Set of apparently irregular platelike crystals. (b) Crystals rearranged to show parallelism of faces and underlying hexagonal symmetry.
(b)
Fig. 1.3. (a) Set of normals to the faces of an octahedron. (b) Solid whose faces have same set of normals as does an octahedron.
(a)
(b)
The geometry of the crystalline state Fig. 1.4. (a) The stereographic projection of points from the surface of a sphere on to a diametral plane. (b) The final stereographic projection.
(b)
We now consider the symmetry elements which may be present in crystals  or are revealed as intrinsically present by the set of normals to the faces. Centre of symmetry (for symbol see section below entitled 'Inversion axes') A crystal has a centre of symmetry if, for a point within it, faces occur in parallel pairs of equal dimensions on opposite sides of the point and equidistant from it. A selection of centrosymmetric crystals is shown in fig. 1.5(a). However even when the crystal itself does not have a centre of symmetry the intrinsic presence of a centre is shown when normals occur in
1.2
The external symmetry of crystals
collinear pairs. The way in which this shows up on a stereographic projection is illustrated infig.1.5(b). Mirror plane (written symbol m; graphical symbol —) This is a plane in the crystal such that the halves on opposide sides of the plane are mirror images of each other. Some crystal forms possessing mirror planes are shown in fig. 1.6(a). Mirror planes show up clearly in a stereographic projection when the projecting plane is either parallel to or perpendicular to the mirror plane. The stereographic projections for each of the cases is shown infig.1.6(b).
Fig. 1.5. (a) A selection of centrosymmetric crystals. (b) The stereographic projection of a pair of centrosymmetrically related faces.
(b)
Fig. 1.6. (a) Crystals with mirror planes. (b) The stereographic projections of a pair of faces related by a mirror plane when the mirror plane is (i) in the plane of projection; (ii) perpendicular to the plane of projection.
The geometry of the crystalline state
Rotation axes (written symbols 2, 3, 4, 6; graphical symbols
An Hfold rotation axis is one for which rotation through 2n/n leaves the appearance of the crystal unchanged. The values of n which may occur (apart from the trivial case n = 1) are 2, 3,4 and 6 and examples of twofold (diad), threefold (triad), fourfold (tetrad) and sixfold (hexad) axes are illustrated in fig. 1.7 together with the stereographic projections on planes perpendicular to the symmetry axes.
Inversion axes (written symbols 1, 2, 3, 4, 6; graphical symbols
o, none, A , <f>, $ ) The inversion axes relate crystal planes by a combination of rotation and inversion through a centre. The operation of a 4 axis may be followed in fig. 1.8(<z). The face A is first rotated about the axis by n/2 to position A' and then inverted through O to B. Starting with B, a similar operation gives C which in its turn gives D. The stereographic projections showing the symmetry of inversion axes are given in fig. 1.8(6); it will be noted that T is identical to a centre of symmetry and T is the accepted symbol for a centre of symmetry. Similarly 2 is identical to m although in this case the symbol m is more commonly used. These are all the symmetry elements which may occur in the external form of the crystal  or be observed in the arrangement of normals even when the crystal itself lacks obvious symmetry. On the experimental side the determination of a set of normals involves the measurement of the various interfacial angles of the crystal. For this purpose optical goniometers have been designed which use the reflection of
Fig. 1.7. (a) Perspective views and views down the axis for crystals possessing diad, triad, tetrad and hexad axes. (b) The corresponding stereographic projections.
no matter in what part of the body of the crystal they originate.
1.3
The seven crystal systems
Even from a limited observation of crystals it would be reasonable to surmise that the symmetry of the crystal as a whole is somehow connected with the symmetry of some smaller subunit within it. (a) A perspective view of the operation of an inverse tetrad axis. (b) Stereographic projections for T. 1. 2. The idea of a structural subunit was first advanced in 1784 by Haiiy who
. indeed. are often parallel to the crystal faces. 3.13
The seven crystal systems
Fig. If a crystal is fractured then the small plane surfaces exposed by the break.8. 4 and 6.
2=
light from the mirrorlike facets of the crystal to define their relative orientations. show the same angular relationships to the faces of the whole crystal and.
He argued that the cleavage process. three inverse tetrad axes and four triad axes.1.9. However if some other crystal forms which can be built from cubes are examined. The cube has a centre of symmetry. for example the regular octahedron and also the tetrahedron infig. Various crystal shapes which can be built from cubic subunits: (left) cube.1.10(fo) for description of rhombohedron). then it is found that the special angles between faces are those corresponding to a cubic subunit and to no other. indivisible. having six mirror planes. Some materials do crystallize as regular tetrahedra and this crystal form implies a cubic subunit. rhombohedral structural unit and that the triad axis of the crystal as a whole derives from the triad axis of the subunit (seefig. The common characteristic shown by all crystals having a cubic subunit is the set of four
Fig. All these elements of symmetry are shown by the octahedron but the tetrahedron. Haiiy's ideas lead to the general consideration of how crystals may be built from small units in the form of parallelepipeds.9. Thus. Infig. the crystal as a whole may exhibit less symmetry than its subunit. (right) tetrahedron. shows less symmetry than the cube.9 is a cube built up of small cubic subunits. This has a threefold axis of symmetry and by successive cleavage Haiiy extracted from calcite crystals small rhomboids of calcite. It is found that.The geometry of the crystalline state
was led to his conclusions by observing the cleavage of calcite. it is true that in this case the subunit could be a rectangular parallelepiped which quite accidentally gave a crystal in the shape of a cube.
1
ii
. if repeated many times. six diad axes. generally the character of the subunits may be inferred from the nature of the crystal symmetry. would eventually lead to a small. four triad axes and three tetrad axes. (centre) octahedron. It is instructive to look at the symmetry of the subunit and the symmetry of the whole crystal. in some cases. nine mirror planes.1. 1.
/?.
(a)
(b)
(c)
. for example.10(a)). representing a onefold axis. The main characteristics of the seven crystal systems and their subunits are given in table 1.1 there is given the essential symmmetry for the seven crystal systems but. These two crystal classes may be shown conveniently in terms of stereographic projections as in fig. (a) A general parallelepiped subunit. y (fig.1.and conversely all crystals having a set of four triad axes are cubic. 1. different symmetry arrangements are possible. (c) The basic hexagonal subunits which are packed as shown to give hexagonal symmetry. As has been previously noted 1 is the symbol for a centre of symmetry and the symbol 1. Similar considerations lead to the conclusion that there are seven distinct types of subunit and we associate these with seven crystal systems. for each system. b. 1.1 \{a) and (b). corresponds to no symmetry at all. The projections show the set of planes generated from a general crystal face by the complete group of symmetry elements.1. The subunits are all parallelepipeds whose shapes are completely defined by the lengths of the three sides a. The possible arrangements for the monoclinic system are now considered.4 The thirtytwo crystal classes
triad axes . 1.
Fig. 1. may or may not have a centre of symmetry and this leads us to refer to the two crystal classes 1 and 1 within the triclinic system.4 The thirtytwo crystal classes In table 1. (b) A rhombohedron showing the triad axis. c (or the ratios of these lengths) and the values of the three angles a. A crystal in the triclinic system.10.
the mirror plane is perpendicular to the triad axis. An alternative name for mm is 2m and again the identity of the third symmetry element may be inferred. 1. the combination of symbols 3m implies that the mirror plane contains the triad axis and the trigonal symmetry demands therefore that a set of three mirror planes exists. For example. the symmetry associated with the third axis need not be stated. For the seven systems together there are thirtytwo crystal classes and all
. The orthorhombic and trigonal systems give rise to the classes shown in fig.11. illustrated in fig.13.10(6)) or as hexagonal a=b^ c a = P = 90°. The seven crystal systems
System Triclinic Monoclinic Orthorhombic Tetragonal Trigonal Subunit No special relationships a^b^c 0 5* a = 7 = 90° a^b^c a = p = y = 90°
a = b 7^ c
a = p = y = 90° a = fr = c (X = 0 = y ^ 90° (see fig. (b) a mirror plane and (c) a diad axis and mirror plane together. 1. This omission is permissible due to the fact that the two orthogonal mirror planes automatically generate a diad axis along the line of their intersection and a name such as 2mm therefore contains redundant information. Some interesting points may be observed from a study of these diagrams.12. It may also be noted that.10
The geometry of the crystalline state
Table 1. 7 = 120° (see fig. for the crystal class 3/m. have (a) a diad axis. 1.10(c)) a=b=c a = p = y = 90°
Essential symmetry of crystal None Diad axis or mirror plane (inverse diad axis) Three orthogonal diad or inverse diad axes One tetrad or inverse tetrad axis One triad or inverse triad axis
Hexagonal
One hexad or inverse hexad axis Four triad axes
Cubic
Fig. Stereographic projections representing the crystal classes {a) 1 and (b) I.1.
(a)
(b)
These. On the other hand. 1. 1. this class is identical to the hexagonal class 6 and is usually referred to by the latter name. for the orthorhombic class mm.
1A
The thirtytwo crystal classes
11
Fig. Stereographic projections representing the three crystal classes in the monoclinic system (a) 2. is called a point group. it strongly implies that there is some corresponding symmetry within the subunit itself.
32
Trigonal
Orthorhombic
crystals may be assigned to one or other of these classes. While the general nature of the basic subunit determines the crystal system.12. (b) m and (c) 2/m.13. The collection of symmetry elements which characterizes the crystal class.
Fig. 1. crystallizes with some element of symmetry. and which must also be considered to be associated with the basic subunit. If a material. It will be seen later that the point group is a macroscopic
. for each system there can be different elements of symmetry associated with the crystal. satisfying some minimizationofpotentialenergy criterion. Stereographic projections representing the three crystal classes in the orthorhombic system and the six classes in the trigonal system. 1.
. Similar arguments apply in three dimensions in that many different triclinic unit cells can be chosen to represent the structural
Fig. However in this case there is one rectangular unit cell and this choice of unit cell conveys more readily the special rectangular repeat features of the overall pattern and also shows the mirror plane of symmetry. It is well to note that the unit cell may not be an entity which can be uniquely defined.5 The unit cell We shall now turn our attention to the composition of the structural subunits of crystals. 1. 1.14 there is a twodimensional pattern which can be thought of as a portion of the arrangement of atoms within a crystal.14. when reproduced by close packing in three dimensions. A twodimensional pattern and some possible choices of unit cell. Several possible choices of shape and origin of unit cell are shown and they are all perfectly acceptable in that reproducing the unit cells in a closepacked twodimensional array gives the correct atomic arrangement.12
The geometry of the crystalline state
manifestation of the symmetry with which atoms arrange themselves within the subunits. In fig. gives the whole crystal is called the unit cell. The parallelepipedshaped volume which. 1.
15.1. for this indicates far more clearly the symmetry of the underlying structure. 1.15.4 the ideas were advanced that the symmetry of the crystal was linked with the symmetry of the unit cell and that the disposition of crystal faces depends on the shape of the unit cell. in the first instance. Infig.3 and 1. 1. The mirror line can be located (we take the normal to it as the b direction) and the angles made to this line by the faces can be found. to restrict attention to a twodimensional model. We shall now explore this idea in a little more detail and it helps. when the set of normals to the faces is examined we have no doubt that the unit cell has a tetrad axis of symmetry.17 the face AB is formed by points which are separated by la in one direction and b in the other. One customarily chooses the unit cell which displays the highest possible symmetry. The crystal is apparently irregular in shape but.5
The unit cell
13
arrangement.
. In §§ 1. It is required to determine the ratio of the sides of the rectangle from measurements of the angles between the faces.16 the set of normals reveals a mirror line of symmetry and from this we know that the unit cell is rectangular. For the twodimensional crystal in fig. The reason why a square unit cell with a tetrad axis gives fourfold symmetry in the bulk crystal can also be seen.1)
Fig. A twodimensional crystal made up of unit cells with a tetrad axis of symmetry. is clearly given by tan 6 = b/2a. The angle 0.7. which the normal AN makes with the b direction.
(1. DE and the other faces related by tetrad symmetry are also favoured because they lead to the same condition at the crystal boundary.1. A crystal made of square unit cells is shown infig. If the formation of the faces AB and BC is favoured because of the low potential energy associated with the atomic arrangement at these boundaries then CD.
The relationship between the crystal face AB and the unit cell.16 are 32° 12r. 1. 6 3 0 ^ = 0.
The geometry of the crystalline state
a
s. (1.14
Fig.3)
. = 1.946^.17. 43° 24' and 51° 33' so that we have * = 0 . 1.= tan0. a m (1.2)
The angles 0 for the crystal in fig.260^. A twodimensional crystal built of rectangular units. 1.16.
/ \
/
\
\
\ \ \
\ \
\ \ \ \\
N
\ S.
a /
\
/
/
B
If the neighbouring points of the face were separated by na and mb then one would have mb tan 0 = — or . \
• •
/ /
\ \
\ \
/ /
\ \ \
— /
Fig.
18. A twodimensional crystal based on an oblique unit cell.18. b/k where h and k are two integers.1. crystal class.630 x ? = 0.260 x \.260:1. 2b. For a real crystal. has intercepts OA' and OB' of the form a/1 and b/2. The line AB' parallel to AB.6 Miller indices In fig. Goniometric measurements enable one to determine the crystal systems. Now it is possible to draw lines parallel to the faces such that their intercepts on the unitcell edges are a/h. the task of deducing axial ratios can be far more complicated. Another type of twodimensional crystal is one based on a general oblique cell as illustrated infig. b and CD by steps of 3a. a 1 3 1 From this we deduce the ratio b:a = 1.3) and these are found to give . axial ratios and interaxial angles.946 x \ = 1.the line with
Fig. / /
/ / / / / / /
/ /
/ / A / / / y
/ /
/
/
/
//
//
/ /
// /
y /
/
/
\
/
\
/
\
/ / / /
• • '
y/
/ / /
/
y ~7
A
/
\\
A
/
/ / \
/ /
A /
/ /
/ /
7
/
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^ /A \
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A
. 1. for example. The integers h and k may be chosen in other ways . All the above ideas can be carried over into three dimensions. The only unconsidered type of twodimensional crystal is that based on a hexagonal cell where the interaxial angle and axial ratio are fixed. Many choices of unit cell are possible for the oblique system. 1.6
Miller indices
15
We now look for the simplest sets of integers n and m which will satisfy equation (1.19 is shown the development of two faces AB and CD of a twodimensional crystal. where one is dealing with a threedimensional problem. 1.= 0. similarly CD' parallel to CD has intercepts a/2 and ft/3. The crystal symmetry shown here is a diad axis (although not essential for this system) and one must deduce from the interfacial angles not only the axial ratio but also the interaxial angle. Face AB is generated by steps of 2a.1. This example is only illustrative and it is intended to demonstrate how measurements on the bulk crystal can give precise information about the substructure.
However. One property of this lattice is that if it is placed over the structural pattern then each point is in an exactly similar environment. If we have any repeated pattern in space.2) face for the cell infig. The two unit cells are quite different in appearance but when they are packed in twodimensional arrays they each produce the same spatial distribution.1. we can relate to it a space lattice of points which defines completely the repetition characteristics without reference to the details of the repeated motif. In three dimensions there are fourteen distinctive space
.21.16 Fig.the top lefthand corner. b/3 and c/6 (note that the condition for parallel planes OA/OA' = OB/OB' = OC/OC is satisfied).21 is an alternative to that shown in fig.19 and 1. the unit cell infig.1.20 is based on the unit cell shown with OA = 3a.1. The lines A'B' and CD' which are parallel to the crystal faces AB and CD have intercepts on the unitcell edges of the form a/h and b/k where h and k are integers. parallel to a crystal face. In three dimensions a plane may always be found. 1. This face may be referred to by its Miller indices and ABC is the face (436). 1. If one point is chosen to represent the unit cell .19.1) face for the cell infig.
The geometry of the crystalline state
intercepts a/2 and b/4 is also parallel to AB. OB = 4b and OC = 2c.7 Space lattices In figs. no matter how the lattice is displaced parallel to itself.21 are shown alternative choices of unit cell for a twodimensional repeated pattern.1. The plane A'B'C is parallel to ABC and has intercepts OA\ OB' and OC given by a/4.21 is placed over the twodimensional pattern and it can be seen that.19 and 1. This is illustrated infig. we are here concerned with the smallest possible integers and these are referred to as the Miller indices of the face. The face AB which was the (1. However. no matter which unit cell is chosen. 1. such as the distribution of atoms in a crystal. 1. Returning to our twodimensional example.19 is the (1.19.22 where the lattice corresponding to figs. The crystal face in fig. 1. each of the lattice points will have a similar environment. one can find a triplet of integers (generally small) to represent the Miller indices of the face. The Miller indices are related to a particular unit cell and are therefore not uniquely defined for a given crystal face. the centre or any other defined point then the array of cells is represented by a lattice of points and the appearance of this lattice does not depend on the choice of unit cell. b/k and c/l on the unitcell edges. 1. which makes intercepts a/h.
The faces AB and CD now have different Miller indices. Firstly there are seven simple lattices based on the unitcell shapes appropriate to the seven crystal systems. i. It is appropriate in this case to take the unit cell as the full line rectangle and to say that the cell is centred so that points separated by \at\b are similar.20. 1. 1. Such a lattice is nonprimitive.e.23.1. 1.
Fig.19. The lattice (small dark circles) represents the translational repeat nature of the pattern shown. there is one point associated with each unit cell of the structure. k and / are integers. An alternative unit cell to that shown in fig. The plane A'B'C is parallel to the crystal face ABC and makes intercepts on the cell edges of the form a/h.
17
Fig.21.7 Space lattices
Fig. But other space lattices can also occur. Consider the space lattice corresponding to the twodimensional pattern given infig. 1. The three possible types of nonprimitive lattice are:
. the primitive rhombohedral lattice is usually denoted by R. b/k and c/l where h.
• *
lattices known as Bravais lattices. Six of these are indicated by the symbol P which means 'primitive'. 1. lines connect the points to clarify the relationships between them.24. The unit of each lattice is illustrated in fig.1. This could be considered a primitive lattice corresponding to the unit cell shown dashed in outline but such a choice would obscure the rectangular repeat relationship in the pattern.22.
The fourteen Bravais lattices.18
Fig.23.
The geometry of the crystalline state
Monoclinic P Monoclinic C
Orthorhombic P
Orthorhombic C
Orthorhombic /
Orthorhombic F
(1st Part)
. 1. The accompanying diagrams show the environment of each of the lattice points.
23. 1. (2nd Part)
. 1. (cont)
Fig.7
Space lattices
19
Fig.1.23.
Any space lattice corresponds to one or other of the fourteen shown and no other distinct space lattices can occur.1. Twodimensionl pattern showing two choices of unit cell . A few minutes' study of the figures will confirm the truth of the last statement. primitive and nonprimitive. \b. 1. \c giving a point at the intersection of the body diagonals of the basic unit of the space lattice. 1. For each of the lattices. The symmetry elements which were previously considered were those which may be displayed by a crystal (§ 1. This is associated with elements of symmetry within the unit cell itself and we shall now consider the possibilities for these symmetry elements.
Cface centring .20
The geometry of the crystalline state
Fig. \b in the C faces of the basic unit of the space lattice. B and Cface centring. The seven nonprimitive space lattices are displayed infig. and /centring . for the periodic repeat pattern of the atomic arrangement gives new possibilities for symmetry elements.8 Symmetry elements We have noted that there are seven crystal systems each related to the type of unit cell of the underlying structure. A crystal is a single unrepeated object and an arrangement of symmetry elements all associated with one point can represent the relationships of a crystal face to all symmetryrelated faces. the constituent points have similar environments.general oblique (dashed outline) and centred rectangular (full outline).equivalent to simultaneous A. In addition there are thirtytwo crystal classes so that there are differing degrees of symmetry of crystals all belonging to the same system. A list of symmetry elements which can be associated with the atomic arrangement in a unit cell is now given.
.23.in which there is a translation vector \a. The situation is different when we consider the symmetry within the unit cell.24. Fface centring.2) and it was stated that there are thirtytwo possible arrangements of symmetry elements or point groups. A and Bface centring may also occur.where there is a translation vector \a.
(/) The operation of 3i
.8 Symmetry elements
21
Centre of symmetry (1) This is a point in the unit cell such that if there is an atom at vector position r there is an equivalent atom located at — r.
• r
id)
U'l
A\
.V
(M
0
& i LLJ* :.25(a) has centres of symmetry at its corners. (a) A centrosymmetric unit cell showing the complete family of eight distinct centres of symmetry. This gives rise to other centres of symmetry which bisect the edges of the cell and lie also at the face and body
Fig. Since all the corners are equivalent points the pairs of atoms A and A related by the centre of symmetry at O are repeated at each of the other corners. 1.25.1.
ST. (d) A view down a tetrad axis of symmetry showing the other symmetry axes which arise. (c) A unit cell showing glide planes. 1. The unit cell in fig. (b) A unit cell showing mirror planes. (e) The operation of a 2X axis.
1. and all subsequent new points. which are placed at the levels y =  and y = §. if perpendicular to c.  — y. These points. and the second a reflection in P2 followed by a displacement^ + ^a. z) then thefirstoperation generates a point an equal distance from the plane y = £ on the opposite side with x and z coordinates increased by £. It must be emphasized that Am is merely a construction point and the net result of the operation is to generate A2 from Av The repeat of the pattern gives a point A2 displaced by — b from A2 and we can see that A2 and A x are related by another glide plane parallel to the one through O and displaced by ^b from it. Px and P2.25(c)) the point A1 is first reflected through the glide plane to Am and then displaced by ^a to the point A2.22
The geometry of the crystalline state
centres. c. The description of this symmetry element is simplified by reference to the vectors a. Mirror plane (m) In fig. z + {). For the operation of a dglide plane perpendicular to b there are required two planes. If we begin with a point (x. f — y. For an aglide plane perpendicular to the b direction (fig. b.e. n.and cglide planes perpendicular to one of the other directions. B\. The first operation is reflection in P1 followed by a displacement ^c + ^a. The plane passing through 0 generates the points A2 and B2 from Ax and Bv The repeat distance perpendicular to the mirror plane gives equivalent points A\. the point (x + ^ .v 2 y
i +z
4I7
ly
iy
. An nglide plane is one which. 1. The second operation.25(b) there is shown a unit cell with mirror planes across two opposite (equivalent) faces. y. Glide planes (a. i. While these extra points are also centres of symmetry they are not equivalent to those at the corners since they have different environments.— v
z
X A. d) The centre of symmetry and the mirror plane are symmetry elements which are observed in the morphology of crystals. One may similarly have an aglide plane perpendicular to c and also b. The glideplane symmetry element operates by a combination of mirror reflection and a translation. respectively. For each initial point there are two separate operations generating two new points. A2 and B'2 and it can be seen that there arises another mirror plane displaced by \a from the one through O. The diamond glideplane d is the most complicated symmetry element and merits a detailed description. b and c which define the edges of the unit cell. similarly generates a point (x — £. involving the plane P 2 . may be subjected to the same operations and it will be left as an exercise for the reader to confirm that the following set of eight points is generated: x
44v
y
4.z + ^). Now we are going to consider a symmetry element for which the periodic nature of the pattern plays a fundamental role. gives a displacement component ^a + b.7
 +x
Y
ly
44.
1. Before describing a few of the 230
. respectively. the symmetry element RD along the a direction involves a rotation 2n/R followed by a displacement (D/R)a.1. 1. respectively. It is clear that Al9 A'2. 1.7. A3 and A± and this pattern is repeated about every equivalent tetrad axis. The point Ax is operated on by the tetrad axis through O to give A2. In general. the latter point being displaced by a from Av The difference between 3X and 3 2 can either be considered as due to different directions of rotation or. Rotation axes (2. A system of diad axes also occurs and is indicated in the figure. the new feature which arises for a repeated pattern is the generation of subsidiary axes of symmetry other than those put in initially. they are not included here as inversion axes. The same operation repeated on A2 gives A\ which is the equivalent point to Ax in the next cell.1. 65) These symmetry elements.e. This may be seen in fig. alternatively. 61? 6 2 . 3. 4. Thus the operation of the symmetry element 2X is entirely consistent with the repeat nature of the structural pattern. The point A x isfirstrotated by an angle n round the axis and then displaced by ^a to give A2. through the centre of the cell. 6) The modes of operation of rotation axes are shown in fig. 6) The action of the inversion axis R is to rotate the point about the axis by an angle 2n/R and then invert through a point contained in the axis. The point Ax is rotated by 2rc/3 about the axis and then displaced by ^a to give A2. like glide planes. respectively. The behaviour of a 2X axis parallel to a is shown infig. Since T and 2 are equivalent to a centre of symmetry and mirror plane.2 a list of symmetry elements and the graphical symbols used to represent them.25(d) which shows a projected view of a tetragonal unit cell down the tetrad axis. 1. 4. nonequivalent to the one through 0. Two further operations give A3 and A\. play no part in the macroscopic structure of crystals since they depend on the existence of a repeat distance.9 Space groups Symmetry elements can be combined in groups and it can be shown that 230 distinctive arrangements are possible.25(e). 63 . Screw axes (2X. 3 1? 3 2 . The two arrangements produced by these symmetry elements are enantiomorphic (i. as due to having the same rotation sense but displacements of ^a and fa. The actions of the symmetry elements 3j and 3 2 are illustrated in fig.9 Space groups
23
These coordinates show that there are two other glide planes at y = f and y =  associated with displacements c + £a and ^c — ^a. 6 4 . There is given in table 1. in mirrorimage relationship). Each of these arrangements is called a space group and they are all listed and described in volume A of the International Tables for Crystallography. A^ and A'£ are related by a tetrad axis. Inversion axes (3.25(/). 41? 42? 4 3 .
reflecting the smaller number of possible systems. rectangular. 4 and 6 mirror line m glide line g. 32 42.24
The geometry of the crystalline state
Table 1. lattices and symmetry elements. two types of lattice . 65 Inversion axes 3 4 6
71 •
A
Rotation axes
•
AA
• ****
A
space groups we shall look at twodimensional space groups (sometimes called plane groups) which are the possible arrangements of symmetry elements in two dimensions.43 62> 6 3 . 3.primitive (p) and centred (c).
Type of symmetry element Written symbol Centre of symmetry Perpendicular In plane of to paper paper Mirror plane Glide planes m ab c glide in plane arrow shows of paper glide direction Graphical symbol
—1 —v
1
\
glide out of plane of paper n 2 3 4 6 Screw axes 2. There are only 17 of these.
. and symmetry elements rotation axes 2.oblique.2. Thus there are: four crystal systems . 6 4 . square and hexagonal.
27 the centring of the cell is seen in that for each structural unit with coordinate (x. 1. represented by an open circle.26. The twodimensional space group cm as it appears in International Tables for Xray Crystallography. The twofold axis is at the origin of the cell and it will reproduce one of the structural units. 0).\).at the points (x. ^ No.1. 5 cl ml m Rectangular
0 O
O O
o
O 0 O
o
o
Origin on m
. 1. The righthand diagram infig. \ + y). The four centres of symmetry are all different in that the structural arrangement is different as seen from each of them.9
Space groups
25
We shall now look at four twodimensional space groups which illustrate all possible features. In addition. No.1.^) and ({. the mirror line is shown relating empty open circles to those with commas within them.27. 2
P2\
2
Oblique
O
O O
/o
I
Origin at 2
Rectangular cm This rectangular space group is based on a centred cell and has a mirror line perpendicular to the y axis. y) there is another at (^ + x. The twodimensional space group p2 as it appears in International Tables for Xray Crystallography. Infig.26 in the form given in the International Tables. the twofold axis manifests itself in two dimensions as a centre of symmetry.1. The significance of the comma is that it indicates a structural unit which is an enantiomorph of the one without a comma. What is also
Fig. (0.
Fig. It will be seen that three other centres of symmetry are generated . in the way shown. The righthand diagram shows the symmetry elements. Oblique p2 This is illustrated in fig.27 shows the symmetry elements in the unit cell and mirror lines are indicated at y = 0 and y = \. y) = (\. 1.
29 the sixfold axis generates six structural units about each origin of the cell. Square pAg This twodimensional space group is illustrated infig. although it was not a part of the description of the twodimensional space group.26
The geometry of the crystalline state
apparent. which is a rhombus with an angle 2it/3 between the axes. the related structural units are enantiomorphs. As can be seen infig.28. Because of the reflection part of the operation. Wherever a pair of structural units are related by either a mirror line or a glide line the enantiomorphic relationship is shown by the presence of a comma in one of them. 16
o
Origin at 6
. The twodimensional space group p6 as it appears in International Tables for Xray Crystallography. Starting with a single structural unit there are generated seven others. 1. the resultant eight structural units are the contents of the square cell. Square 4mm p4g m No. 1. two sets of glide lines at an angle TI/4 to each other and a set of mirror lines at n/4 to the edges of the cell. The twodimensional space group p4g as it appears in International Tables for Xray Crystallography. Hexagonal 6 No. is the existence of a set of glide lines interleaving the mirror lines.1.28 and shows the fourfold axes.1. A pair of threefold axes within the cell is also
Fig.29. The operation of a glide line involves reflection in a line followed by a translation ^a. 12
o o o o
0
o O o O o o o o
O O
Origin at 4
o o
O
Hexagonal p6 As the name of this twodimensional space group suggests it is based on a hexagonal cell.
Fig.
The complete arrangement of symmetry elements is shown in the righthand diagram offig.9
Space groups
27
generated. The diagram on the righthand side shows the distribution of symmetry elements. this is taken as the b axis. (iv) an assigned spacegroup number and (v) the spacegroup name according to the HermannMauguin notation with.1. b and c axes (where appropriate). as given in the International Tables.31 do not appear in the International Tables but they assist in a description of the generation of the complete pattern starting with a single unit. is reproduced infig. by convention. 1.29. The mirror plane gives A3 from A2 and the
.30. The unique axis for monoclinic space groups is the one perpendicular to the other two and. This convention is interpreted as meaning that if one coordinate is + £ then the other is —t. (ii) the point group. underneath. then the groups represented by O and 0 are enantiomorphically related. The cell is shown in projection and the third coordinate (out of the plane of the paper). The letters shown infig.1. The operation of the space group Pi as shown in the International Tables for Xray Crystallography.1.30. 2 PI
0
1
7
/ 0 +
/ •/
O+
o t
/ /
o
o
/
Origin at T
Monoclinic Cm This space group is based on a monoclinic Cface centred cell with the mirror plane perpendicular to the unique axis. with respect to an origin at a centre of symmetry. Triclinic PI This space group is based on a triclinic primitive cell which has a centre of symmetry. The representation of this space group. reading across the page.1. (iii) symmetry associated with a. the older and somewhat outmoded Schoenflies notation. The comma within the opencircle symbol indicates that if the symmetry operation is carried out on a group of objects and not just on a point. Triclinic 1 0 PI No. Having established some general characteristics of space groups by the study of some relatively simple twodimensional examples we shall now look at five threedimensional space groups where the third dimension introduces complications not found in two dimensions. is indicated by the signs associated with the opencircle symbols.
Fig.301. The information which headsfigs.1.35 is taken from the International Tables and. is (i) the crystal system. We start with the structural unit Ax and generate A2 from it by the operation of the Cface centring.
If a space group is developed from first principles. If this occurs in the point group it must also be so for any space group based on the point group. then the emergence of new symmetry elements. as has been done here. It can be found by inspection that other symmetry elements arise. Ax is related to AA and A2 to A3 by glide planes which interleave the original set. 1.28 Fig. Monoclinic P2Jc This space group is based on a primitive. often suggests an alternative and preferable choice of origin. unique axis b
centring gives 4 4 from A3.32(a) these basic symmetry elements are shown together with the general structural pattern produced by them. The International Tables gives this space group with the unitcell origin at a centre of symmetry and the structure pattern and complete set of symmetry elements appears in fig. where the original two sets of screw axes do not intersect. 1. In fig.25(a). is found to give a third set not intersecting the original sets and
. 1. The other possible arrangement. If we start with two sets of intersecting screws axes and generate the structural pattern from first principles we end up with the arrangement shown in fig. The pairs of units A4.31. 1. particularly centres of symmetry.
The geometry of the crystalline state Monoclinic m +0 O+
C 1 ml
No. 1.33(<z) which corresponds to the space group P21212.4 in some point groups certain symmetry elements appear automatically due to the combination of two others. Orthorhombic P212121 This space group is based on a primitive orthorhombic cell and has screw axes along the three celledge directions. +OO+
o+
+OO+ Origin on plane m. The name does not appear to define completely the disposition of the symmetry elements as it seems that there may be a number of ways of arranging the screw axes with respect to each other. As was noted in § 1. The + signs against each symbol tell us that the units are all at the same level and the commas within the open circles indicate the enantiomorphic relationships. 8
£w
+0 O+
The letters have been added.32(6). This constitutes the entire pattern. A2 and Al9 A3 are related by a centre of symmetry at a distance \c out of the plane of the paper and a whole set of centres of symmetry may be found which are related as those shown in fig. The operation of the space group Cm as shown in the
International Tables for Xray Crystallography. monoclinic unit cell with a 2l axis along b and a oglide plane perpendicular to it. It may be seen that this combination of Cface centring and mirror planes produces a set of aglide planes.
23
7222
+ OOo o+ i+o o i i . (b) The description of P2Jc as given in the International Tables for Xray Crystallography.2.32. This gives the space group Origin at 112 in plane of 2 . 1.9
Space groups
29
Fig. P2x2x2 P 2.2 No. 14
P2Jc
C52b
o
oiO+ i +0
o o+ i0 (
o 0+
oi
o o+
Origin at T.) Orthorhombic 222 7222
222
Orthorhombic
N o .
iiQ
O+
(a)
o.i . This gives the space group oK.1. o (b) The development of the structural pattern for +o +O three sets of 2 t axes O+ o+ which intersect.33.2. (From International (a) Tables for Xray Crystallography. 2 . 7222.o
o+
Monoclinic 2/m
P1 2Jc 1
No.2. (a) The development from first principles of the structural pattern for the space group P2Jc. 1.o oi+ + o oOO +
+ooo o+ —i
+o OO
Origin at 222 (b)
.
. 18 (a) The development of the structural pattern for + +O P_ two sets of 2 t axes o+ o+ which intersect. unique axis b (b)
Fig.
io o + i+o
o
io o+
.
for example P2Jc and P212121 are well known by most crystallographers. We should notice that the diad axis is automatically generated by the other two symmetry elements.
Orthorhombic
mml
Abal
No. an aglide plane perpendicular to b and a diad axis along c. afoglideplane perpendicular to a. 1.35.34 which is the space group One can have three sets of screw axes in a different arrangement. The diagrammatic representation of this space group. This space group is the one shown in fig.4 it was illustrated for a twodimensional square unit cell how symmetry within the cell influences the way in which cells associate to form
. other space groups occur much more rarely and these would usually be studied.34.
Fig.1.
Fig. The space group P2 1 2 1 2 1 as shown in the International Tables for Xray Crystallography.30
The geometry of the crystalline state
gives the structural arrangement shown infig. as given in the International Tables. Some space groups occur frequently.41
Abal
o+ o+ i+o +o
i+o
©+ +Q
+o
o+ OH
t
I
^
t If I
' *
o+
i+o
+o
o+
Origin on 2
The determination of a crystal structure is usually a major undertaking and the first task of the crystallographer is to determine the space group (chapter 7) and to familiarize himself with its characteristics. 1. is shown in fig. 1. on an ad hoc basis.35.33(b)/222. Orthorhombic 222
oio+
i + O!
i+o o oi
Origin halfway between three pairs of nonintersecting screw axes
Orthorhombic Aba2 The symbols tell us that there is Aface centring. 1.10 Space group and crystal class In §1. For example. The space group Aba! as shown in the International Tables for Xray Crystallography. if one starts with three sets of intersecting screw axes onefindsthat three sets of diad axes are also generated and that the unit cell is nonprimitive. as required. 1.
1 A unit cell has the form of a cube.
Fig.1. mirror planes in the crystal are formed in response to both mirror planes and glide planes in the unit cell. Find the crystal system and suggest a name for the space group.
Problems to Chapter 1 1. The formation of the faces of a crystal in the process of crystallization takes place in such a way that the crystal has a configuration of minimum potential energy.Problems to Chapter 1
31
the complete crystal. 1. (b) (100) (210). give rise to a crystal diad axis since the external appearance of the crystal will not be affected by atomicscale displacements due to a screw axis. any association of cells giving a particular face will be matched by an associated face related by a crystal diad axis. Similarly. The space groups described in this chapter. 1.2. in the macroscopic aspect of the whole crystal.36. However a screw axis in the unit cell will also. Diagrams for Problem 1. If the unit cell contains a diad axis then clearly.
o+ o+
+ 0
. 1. are: Space group
P\ Cm
Point group
m 2/m 222 mm!
r
P2Jc P212121 Aba!
A study of the crystal symmetry can be an important first step in the determination of a space group as for a particular point group a limited number of associated space groups are possible. (e) 14. with the corresponding point groups. Find the angles between the normals to pairs of planes whose Miller indices are: (a) (100) (010).0
o+
Ho
o+
(a)
+O
Oi(b)
0
0(c)
+o
. (c) (100) (111).2 The diagrams infig. (c) Pm. by symmetry.3 Draw diagrams to show a set of equivalent positions and the set of symmetry elements for the following space groups: (a) P91 (b) p4mm.36 show a set of equivalent positions in a unit cell. However the art of examining crystals by optical goniometry is now largely ignored by the modern Xray crystallographer who tends to use only diffraction information if possible. (d) P2/m. In the International Tables the point group is given for each of the listed space groups. (d) (121) (111).
1 the point O represents a scattering centre. in
Fig. Representation of the radiation incident on and scattered from a point scatterer. The type of scattering we are going to consider can be thought of as due to the absorption of incident radiation with subsequent reemission.
32
. Clearly. 2. the scattered radiation emanates in all directions with some spatial distribution about the point O. this is shown in thefigureby drawing a conical bundle of rays with apex at the point O representing the rays scattered within a small solid angle in some particular direction.1
A general description of the scattering process To a greater or lesser extent scattering occurs whenever electromagnetic radiation interacts with matter. The blue of the sky and the haloes which are seen to surround distant lights on a foggy evening are due to the Rayleigh scattering of visible light by molecules of gas or particles of dust in the atmosphere. The absorbed incident radiation may be in the form of a parallel beam but the scattered radiation is reemitted in all directions.1. 2. In fig. The spatial distribution of energy in the scattered beam depends on the type of scattering process which is taking place but there are many general features common to all types of scattering. The incident radiation is in the form of a parallel monochromatic beam and this is represented in the figure by the bundle of parallel rays. However. Perhaps the bestknown example is Rayleigh scattering the results of which are a matter of common everyday observation. Thus for parallel incident radiation the intensity may be described as the power per unit crosssection of the beam.2 The scattering of Xrays
2. The intensity at a point within a beam of radiation is defined as the energy per unit time passing through unit crosssection perpendicular to the direction of propagation of the radiation.
3) Yo is the amplitude of the wave.x/c)]. If the incident radiation falling on O is in the form of a simple monochromatic wave then the variation with time of the displacement y of the incident wave can be described by the equation y = A cos(27ivr). t) =f26^cos[_2nv(t . It is mathematically convenient to write the equation of a progressive wave in complex form as 7=r o exp[27iiv(rx/c)] = Yo cos[27iv(r . For a particular type of scatterer it will be a function of the scattering angle denoted by 28 infig.1 A general description of the scattering process
33
this case. The scattered wave will have a displacement at the point P (fig. the intensity of the scattered radiation will depend on the distance from 0 and there will be an inversesquare law falloff of intensity with distance.a j .x/c)] + i Yo sin[27tv(r . (iii) The inversesquare law of reduction of intensity with distance for the scattered radiation causes the falloff of amplitude to be inversely proportional to distance D.2)
The influence of the factors (i). (ii) and (iii) may readily be seen in equation (2. With this nomenclature one can express the time dependence of the disturbance at P in fig. The displacement at P can now be described by y(26.6).1)
where v is the frequency of the radiation and A its amplitude.2. The quantity/^ is a constant of proportionality with the dimension of length which is a function of the scattering angle and will be referred to as the scattering length. In Xray diffraction theory the scattering angle is conventionally denoted by 29 (and not simply by 6) as this leads to simplifications in notation in later developments of the theory and is also associated with the historical development of the subject (see§ 3. (2. This quantity as is called the scattering phase shift. 2.1 as
. t) with respect to that at the origin (0.2). (2.D. 2. the real part of the expression is the displacement and the ratio (imaginary part/real part) is the tangent of the phase of the wave motion at (x.1) which will depend on a number of factors: (i) The distance OP ( = D) will introduce a phase shift with respect to the scattered wave at O of —inD/X where X is the wavelength of the radiation.D/c) . This can also be expressed as —2nDv/c where c is the velocity of propagation of the radiation. The intensity of the scattered radiation is thus usually described as the energy scattered per unit time per unit solid angle in a particular direction and is therefore a measure of what is happening at the scatterer itself. (ii) The scattering process itself may introduce a phase shift so that the scattered wave at O will be retarded with respect to the incident wave at O.1. (2.3)
In equation (2.2.0).
The use of the distinct symbols to represent the differently defined incident and scattered beam intensities should be noted. 2. Since the scatterers are identical the scattering phase shift as will be the same for each. t) =/ 29 ^exp[27iiv(t .2 where radiation is incident on two identical scattering centres Ox and O2.
2. Hence.34
The scattering of Xrays
y{26D.2 to emphasize the threedimensional nature of the phenomenon we are considering.D)=f2e^ (2.2
Scattering from a pair of points
Consider the situation shown in fig.i a j . Under this condition the scattered radiation which arrives at P has been scattered from Ot and O2 through effectively the same angle 26. (2.D/c) . for the radiation arriving at P the phase difference of the radiation scattered at O2 with respect to that scattered at Ox is
Fig.2. The planes defined by (i) Ov O2 and the incident beam direction and (ii) OUO2 and P are indicated infig. 2.
So
Incident radiation
Scattered radiation
.6)
The intensity of the scattered beam in terms of power per unit solid angle is given by J2e = or ]2 x D 2 =f2dKA2
where K is the constant relating intensity to (amplitude)2 and / 0 is the intensity of the incident beam on the scatterer. a point at a distance r from Ox which is very large compared to the distance OlO2.
(2.4)
The amplitude of the disturbance at P due to a single scatterer is then given by t!(2d.
0.5)
and the phase lag of the disturbance at P behind the incident wave at 0 is aOP = 2nvD/c + as.2. Scattering from a pair of point scatterers. We shall find the resultant at P.
Scattering from a pair of points
35
«Oio2=^(CO2
+ O2D).8)
Two unit vectors § 0 and S are now defined which lie.2.8).{exp[27iiv(r . The amplitude of this resultant is (2. The vectors So/X and S/X in the incident and scattered directions have equal magnitudes 1/1.iaj[l + exp(2iurs)].9) may be replaced by an equivalent vector s=^ giving olo2 = 2nT's(2n) The vector s is highly significant in describing the scattering process and a geometrical interpretation of it is shown infig. O2D = . respectively. (2.D/c) . from equation (2.12) If the displacement due to the incident radiation at Ox is described by equation (2.iaj + exp[27iiv(t — D/c) — ias + 27iirs]} = /2e^exp[2itiv(t .
(2.13)
a ( 2 1 0)
Fig.3.t) =/2.1) then the resultant disturbance at P. If the vector joining O1 to O2 is denoted by r then CO2 = rS0.D/c) . 2. along the directions of the incident and scattered beams. The relationship of s to So and S.
S()/l
S/A
.3. It can be seen from simple geometry that s is perpendicular to the bisector of the angle between So and S and that its magnitude is given by s = (2sin0)/A.9) The bracketed quantity in equation (2.r § and thus. a distance D from Ol9 will be given by y(209D. (2.
The amplitude of the disturbance at P due to scattering at Ox is represented by the vector AB and that due to scattering at O2 by the vector BC. (b) A phasevector diagram for a pair of point scatterers with a general point as phase origin. However in this description we have given a special role to one of the scatterers.36
The scattering of Xrays
which. 2. D)
B
(a)
.. On. The phasevector diagram can be drawn with more generality if one measures phases with respect to radiation which would be scattered from some arbitrary point 0 if in fact a scatterer was present there. 2. 2.15)
(a) A phasevector diagram for a pair of point scatterers with one point as phase origin.
(2.D) and differs in phase from the radiation scattered at Ox by the angle 0. if the positions of Ox and O2 with respect to O are given by the vectors rx and r2. using equation (2. Then.4.
(2.. 2.D)[exp(27tiiys) 4. 27irs.4(a).D). and the angle between them equals the difference of phase of the radiation scattered from O1 and O2.5). equation (2. may be expressed in terms of the amplitude of scattering from a single unit as
rj2(26.. rt(29.exp(27iiiyr)] and the phasevector diagram appears as in fig.D) =
exp(2iurs)]. Ol9 with respect to which as origin all phases are quoted.D) = f7(20. The resultant AC has magnitude rj2(29.. If the position of the scatterer at Om is denoted by its vector displacement
Fig.
0. We are interested in the amplitude of the disturbance in some direction corresponding to a scattering vector s at a distance which is large compared with the extent of the system of scatterers.3 Scattering from a general distribution of point scatterers Let us now examine the scattering from a system of identical point scatterers Ov O 2 .14)
This equation is interpreted in terms of a phasevector diagram in fig.14) appears as ri2(20. Both these vectors have the same magnitude.
15) we find (2. D) appearing outside the summation. However it is sometimes possible to have the scatterers with differing phase shifts and.4
Thomson scattering
37
rm from some origin point 0 then. that it may appear in a number of modified forms. unbound and unrestrained) electrons was first given by J.
Fig.17)
where the scattering length for each of the scatterers now appears within the summation symbol. 2nrh • s
.5). This is the usual situation with Xray diffraction. 2.e. 2. we have assumed that they all have the same associated values of as. J. A phasevector diagram for six nonidentical scatterers. We shall find later that equation (2.
(2. When the scatterers are nonequivalent the scattering amplitude must be written rjn(2e. when this happens. 2.5 for the case n = 6.5.2.4 Thomson scattering We have discussed the results of scattering by distributions of scatterers without concerning ourselves with the nature of the scatterers or of the scattering process. by an extension of the treatment which led to equation (2. although we refer to the scatterers as nonequivalent. useful information may be obtained (§8. when the symmetry of the atomic arrangements within crystals is taken into account. It will be evident that.17) is the basic equation for describing the phenomenon of Xray diffraction and.16) That this equation applies to identical scatterers is revealed by the factor 7/(20. It turns out that the scatterers of interest to us are electrons and the theory of the scattering of electromagnetic waves by free (i. The phasevector diagram for nonidentical scatterers is shown in fig.D)=
= ^ Z (fie)] exp(27iir/s). Thomson.
In fig. 2.6) then theory tells us that the scattered radiation at P. The electron will have corresponding components of acceleration of amplitudes
Fig. although the incident radiation is unidirectional. is undergoing an oscillation such that the acceleration is periodic with amplitude a (fig. Thus the process may be envisaged as the absorption and reemission of radiation and. Here.7 a parallel beam of electromagnetic radiation travelling along OX falls upon an electron at O.18)
which is perpendicular to OP and in the plane defined by OP and a. If an electron at 0. which is travelling in the direction OP.
Acceleration vector
Electric vector
Direction of scatter
. The vectors are both in the plane of the diagram. If we have the straightforward case where the incident radiation is a single. continuous and monochromatic wave then the acceleration of the electron will undergo a simple harmonic variation and the incident and emitted radiation will quite obviously have the same frequency. the scattered radiation will be emitted in all directions. of charge e and mass m. The relationship of the components of the electric vector of scattered electromagnetic radiation at P to the components of the electric vector of the incident radiation at 0. 2. The amplitude of the electric vector E of the incident wave is perpendicular to OX and may be resolved into components E± and £l perpendicular to and in the plane OX P.6. 2. The relationship of the electric vector of scattered electromagnetic radiation at a point P to the acceleration vector of an electron at 0.7. £0 is the permittivity of free space. 2. We wish to determine the nature of the scattered wave at P. Fig. has an electric vector of amplitude E=
ea sin (/>
4nsorc2
(2.38
The scattering of Xrays
The basic mechanism of Thomson scattering is simple to understand. When an electromagnetic wave impinges on an electron the alternating electricfield vector imparts to the electron an alternating acceleration. and classical electromagnetic theory tells us that an accelerating charged particle emits electromagnetic waves.
22)
The factor 1/m2 in equation (2. Although we have been thinking about a simple.2. defined as the power per unit solid angle scattered through an angle 20 is given by 1
Af^—Yn^^cos 2\4n£ c m (1 +
2 o
2
20)10. continuous. (2.4
Thomson scattering
39
and
Applying equation (2. A complicated incident wave may be analysed into simple components (see chapter 4) and the resultant electron acceleration and reradiation may be found by adding together the effects of the simple components.6 we shall investigate the form of the scattering from the total assemblage of electrons contained in an atom. the lightest nucleus. which has the dimensions of length and equals 2. If the intensity of the incident radiation is Io and if this radiation is unpolarized then = CI0. the proton.21)
The intensity of the scattered radiation. Thus E± and E^ may be thought of as the components of the amplitude of any arbitrary electromagnetic radiation arriving at O.82 x 10~15m. In all the processes concerned with the scattering of Xrays the electrons are bound into atoms and in § 2. monochromatic.22) shows why electrons are the only effective scatterers.
(2. Thomson scattering is coherent.18) we find the electric vector components of the scattered wave at P as
1
4n£orc2m e2cos 20
and
1 1
4n£orc2m
The quantity e2/4n£oc2m. is referred to in classical electromagnetic theory as the radius of the electron. that is to say there is a definite phase relationship between the incident and scattered radiation. electromagnetic wave all the theory described above can be applied when the incident radiation is complex in form. in the case of a free electron the scattering phase shift is n.
. has the same magnitude of charge as the electron but 1837 times the mass. say.
40
The scattering of Xrays
It is instructive to determine the proportion of the power of a beam incident on a material which will be scattered. The power d^J scattered into the solid angle dft.
.22) we have
e2
2
\4ne0c mj
(1 + cos 2 y)I0 sin y dy. /?/ 0 .
(2. defined by the region between the surfaces of the cones of semiangles y and y + dy. is the power per unit area of the incident beam).24). 2. 2. The number of electrons traversed by the beam per unit length of path is n/i and hence the total power scattered per unit path is. the intensity. is called the scattering power of the material and is
Fig. by equation (2. The solid angle between the surfaces of the coaxial cones of semiangles y and y + dy is the area of the annular region on the surface of the unit sphere.25)
3 \4ii£oc m
The ratio of % to the power in the incident beam.23)
Hence the total power scattered by a single electron is (1 + cos 2 y)sinydy
\4%soc2m
_8TC/
}
°
X2
(
2
2
3 \4%eoc m
°'
(2. First we calculate the total power scattered for each individual electron.8 the point O represents the electron and OX the direction of the incident beam.8. In fig.24)
For a material containing n electrons per unit volume immersed in a parallel incident beam of crosssectional area /? the power of the incident beam is jS/0 (since 7 0. Pnlo(2. is
and since dQ = 27tsinydy and <fy is given by equation (2.
This experiment barely detected the presence of Thomson scattering as there were very few (less than ten) scattered photons per pulse.22) to be made (see Problem 2. Later work using highercurrent electron beams and more powerful lasers has enabled a direct confirmation of equation (2. The scattered light was of two types . For example a material of specific gravity 1.2 consisting of light atoms (say of atomic weight less than 30) would contain about 3 x 1029 electrons m~3. a 75 mA. whose wavelength was unshifted. In an experiment by Fiocco and Thompson (1963).some was scattered by the electron beam and there was also stray light reflected from the walls of the apparatus. The advent of the laser has made possible the direct measurement of Thomson scattering by the interaction of light from a ruby laser with an intense electron beam.
Fig. 2. illustrated in fig. If it is assumed that all the electrons in a material are free we can make an estimate of the fraction of the incident radiation which is scattered.9. This value of n substituted in equation (2.
(2. could be prevented from reaching the detector. This laser gave a burst of 20 joules of light in about 800 fxs and the light measured by the photomultiplier detector had an intensity about 10 ~ 8 of that of the incident beam. However for the scattering which normally occurs when Xrays interact with matter the electrons are bound with various degrees of strength to the nuclei of atoms. magnetically focussed to give an electron density within the beam of 5 x 1015 m~3 was crossed by a beam from a ruby laser. The central feature of this experiment was that it was possible to separate the stray light from the Thomsonscattered component. 2. The arrangement of components of the Fiocco and Thompson (1963) experiment.4
Thomson scattering
41
c = —— =
3 \4nsoc2m n. Since the crystals used in Xray diffraction usually have dimensions less than 1 mm it will be seen that only 2% or less of the incident Xray beam is scattered.2.
Collector for un scattered radiation
.9. This shift was about 260 A and with a suitable filter the stray radiation.26)
The quantity o is the fraction of the incident radiation scattered per unit length of path (one metre in SI units).3 at the end of this chapter).26) gives a — 20. Since the scattering was from rapidly moving electrons (speed about onetenth of that of light) there was a Doppler shift in frequency. 2kV electron beam.
10(a) the incident photon moves along the direction PO and. 2.
Incident photon he energy = —
\ Recoil electron energy = jmv2 (a)
Scattered photon _ momentum magnitude
J7 6
Recoil electron momentum magnitude = mv
Incident photon momentum magnitude = hjX (b)
.10(fr) is shown the appropriate momentum vector diagram. From the conservation of energy in the elastic collision we find that
he he 1 2
T ~ X + dX + 2™V or. Infig. moves off along OQ while the electron recoils along OR. momentum must also be conserved and in fig. making usual approximations.
A
(2.27)
In addition to energy. (b) Momentum vector diagram for Compton scattering. It is a valid approximation to ignore the change in magnitude of the momentum of the scattered photon and thus we deduce from simple geometry that
±mv = .10. has the same wavelength as the incident radiation. It is best described in terms of the elastic collision of a photon with an electron.42
The scattering of Xrays
2. 2. This latter component is due to what is known as Compton scattering and it is incoherent with the incident radiation. (a) Velocity vector diagram for Compton scattering of a photon by an electron. the second part has a wavelength longer than that of the incident radiation with the difference of wavelength depending on the angle of scatter. that associated with Thomson scattering. after collision with the electron. The first part.5
Compton scattering Experimentally it is found that the radiation scattered by materials consists of two parts.2.28)
Scattered photon he energy =
Fig.sin 6.
T2'
he
(2.
6 The scattering of Xrays by atoms We are now going to consider how Xrays are scattered by electrons which are not free but are bound into definite energy states in atoms. Since the electron can only exist in discrete energy states then Thomson scattering must correspond to no change of energy of the electron and Compton scattering to a change of energy of some allowed magnitude. The maximum possible change of wavelength is for back scatter when 26 = % and this gives dk = 0. The solution of the wave equation for an atomic electron gives a wave function. equation (2. equals the value given by Thomson's formula.048 A. from which the distribution of electronic charge is found by
p = \V\2 (2. Such a treatment shows that for a particular atomic electron the total intensity of scattering.22).27) and (2.024(1 .28) we have <U = — sin20 me or dX = — ( 1 . x¥. (2.30) The change of wavelength is seen to be independent of the wavelength of the incident radiation and depends only on the scattering angle. we are faced with the position that any change of direction of the photon on being scattered must be accompanied by an electron recoil to conserve momentum and hence a loss of energy of the photon to conserve energy. 2.2. This latter change might be between one bound state and another or the electron might be ejected completely from the atom.cos 20) A.6
The scattering of Xrays by atoms
43
Eliminating v from equations (2.29)
If the physical constants are now replaced by their magnitudes we find (U = 0. it shows that the coherently scattered component can be found from first principles by taking account of the fact that the electronic change is distributed and not located at a point. Thomson. both Thomson and Compton.c o s 20). While this change of wavelength is small it is quite significant for Xrays with wavelengths of the order of 1 A. We shall see in the following section how these apparently diverse conclusions have been reconciled. Furthermore. From the theoretical point of view there can be only Thomson scattering from a classical free electron and only Compton scattering from a wavemechanical free electron.and Compton scattering both occur but to determine the relative amounts of each type one must resort to a complete wavemechanical treatment of the scattering process. however. In general Thomson. Classical theory regards light as a wave motion and the scattered light as a continuous outpouring of radiation from the scatterer simultaneously in all directions. When light is regarded in terms of photons.31)
.and Compton scattering are examples of that dichotomy in physics summed up by the phrase 'waveparticle duality'. (2.
An elemental volume for spherical polar coordinates. if the scattering vector is s and if the coordinate system is so arranged that s is parallel to the axis from which i// is measured.n — ij/. ij/. for example. In the special case when  *F . 2. <f>) there is another point P' with coordinates (r. Thus.
. then the charge associated with a small elemental volume is p{r)r2 sin ij/dr dij/d(/> (fig. If the electrondensity distribution is spherically symmetric then it is also centrosymmetric and this enables simplifications in equation (2. then the total amplitude of coherently scattered radiation may be found from equation (2.11.44
The scattering of Xrays
where p represents the charge density in electron units per unit volume. we express the positional parameters in spherical polar coordinates with respect to the centre of the atom as origin.32)
J r = O J\J/ = O J ^ = 0
since r*s = rs cos \jt.n + <> (see fig. For every point P with coordinates (r. We take the amplitude of the scattered wave from the small elemental volume as Cs x charge where Cs is some constant dependent on the scattering vector s and we obtain the amplitude from the whole electron as
As = C s p(r)r2Qxp(2nirs cos i/f)sin \// dr d ^ dcf) (2. is spherically symmetric we may represent the electron density by p(r). 2. The contribution of two elemental volumes round P and P' will give a resultant. If. the form of which can be appreciated by adding two terms such as
Fig.11) and the same electron /) density. and therefore p.17) with integration replacing summation.32) to be made.11). Note particularly that the integration limits for \jj and 0 do cover the whole of space. 2.
r = 0. It is clear from this that As is a real quantity for a centrosymmetric distribution of electron density and that equation (2. pa(r). This may be found from equation (2. where the integration can be over any finite volume of space around the origin. say (As)o.34) by noting that a point electron at the origin has an electron density p(r) = d(r).32) can be rewritten as As=cA p(r)r2cos(2nrs cos ^)sin x// Ar d\jj d 0 (2. i.33)
The fact that p(r) is independent of \\t and 0 enables one to integrate over these latter variables giving
For a given value of s we shall now find the scattered amplitude from p(r) as a fraction ps of that amplitude. which would be given by a point electron at the origin. and J <5(r) dt? = 1.e. The delta function d(r) has the property S(r) = oo.
.36) where we recognize that p depends only on the magnitude of s by dropping the vector notation in the subscript. by definition
.00
4TI Jr = O
5(r)r2dr=
1
then it follows that
From this we find (2. For a deltafunction electron density there is no contribution to equation (2.34) away from the origin and since sin(27i rs)^ 2nrs and. If an atom contains Z electrons then the total electron density.6
The scattering of Xrays by atoms
45
) + exp[27iirs COS(TI — \jj)~] = exp(27iirs cos \j/) + exp( — 2nirs cos \j/) = 2cos(2iirscos^).2. will be the sum of the densities of the individual electrons.
However the Compton scattering from one atomic electron is incoherent with respect to that scattered by any other and hence the total intensity from all the electrons is obtained by adding the individual intensities from each of the electrons. for the six electrons of the carbon atom calculated from Slater's approximate analytic wave functions. 4nr2p(r).
(2. Infig.12(a) there are given the radial electrondensity distributions.36) that since for s = 0 (9 = 0) we have
V 2
)
then p0 = 1.
(2. although usually made. From equation (2. when radial symmetry is assumed (and this is an assumption which. This is derived from equations (2.38)
Atomic scattering factors are well tabulated in vol. ? }X^2«>
j= 1
(2.36) we can see that the intensity of coherent scattering from an atomic electron is p\^ 2Q and hence. For light atoms the Hartree selfconsistent field method of computing wave functions is usually employed. Thus we have ^Comp. We now define an atomic scattering factor fa as the ratio of the amplitude of the coherent scattered radiation from an atom to that from a single electron situated at the atomic centre. for radiation scattered in the incidentbeam direction there is no incoherent component. In fact there are two Is electrons.37) and is
4\^dr=i>s). while for heavy atoms the ThomasFermi approximation may be used.on = Z{1(P S ). two 2s electrons and two 2p electrons. Ill of the International Tables for Xray Crystallography. is not really justified for 2p electrons) the 2s and 2p electrons give equivalent radial electrondensity distributions. As 6 increases so p decreases but the rate of decrease is less for those electrons which are most tightly bound in the atom.40)
It will be seen from equation (2. since the total intensity of scattering as revealed by wave mechanics is J2By the intensity of the Compton scattering must be (1 — Ps)^2o.2.39)
and
ji]
/sin(27irs)\
2 2 (
. Hence.37)
The amplitude of coherent scattering from the total electron density will be obtained by adding the amplitudes for the electrons taken individually.
. We can now investigate the nature of Compton scattering from atoms.
(2.36) and (2. Various models of atoms have been used to give electrondensity distributions.46
The scattering of Xrays
pJr) = I pfo).
(a) The radial electrondensity functions of Is and 2s electrons of a carbon atom as defined by Slater's analytic wave functions.0
1.0 Is
0.
1. 2.12.0
. (b) The amplitude of scattering from the Is and 2s electrons.2.6
The scattering of Xrays by atoms
4nr2p(r)
47
Fig. (c) The atomic scattering factor/ a for the carbon atom and the coherent and incoherent scattered intensities from a single atom.5
2.0 r (a)
2.
2. Radiation of wavelength X falls on the scatterers along a direction which is normal to the row.1 Four identical coherent scatterers are placed in a row with a distance 31 between neighbours. determine the scattered amplitudes and intensities as fractions of that which would result if all four scatterers were at one point.15 A " 1 . (a) For scattering angles 26 = 0 to 180°.41) and (2.36). it appears that for a single atom the incoherent scattering is quite appreciable for high values of s. is for regions of space where sin(2nrs)/2nrs is close to unity and hence ps will also be closer to unity.39) and is also shown plotted infig.
Problems to Chapter 2
2.41)
*•*/
«
1
//•%
A
^ \
Zx/*
I
I* PYHI
/P
VI
(\Y
r=z

l /
dil
— 'TC i
I
/
CAUI
Z. very large numbers of atoms cooperatively scatter so that the amplitudes of the coherent scattering from different atoms add together whereas for the incoherent scattering it is the intensities which add.2. For the analytical expressions (2. 2.12(a).36)
A *\ I 0 / f\ \ *** .2. for carbon.C i / I
""
U7 — " x
^ TTT
\^«"*^/
Jr = O
and
C
2V C 2 ~~ 4 7 1
S
)
yFsns
(4 + 4u V ) 4 '
In fig.42) where. Thus when we consider the diffraction of Xrays by crystals incoherent scattering may generally be ignored.
.\**• *
MMM v
(2. Plot the results.12(fe) there are plotted the values of (ps)ls and (ps)2s and it can be seen how the tighter distribution of electron density for the Is electron leads to a slower falloff in the value of ps.12(c) together with^f the total coherent scattered intensity from a single atom. However under the conditions of the diffraction of Xrays from crystals. The incoherent scattered intensity is found from equation (2.77 A " 1 and c2 = 6. c1 = 10.48
The scattering of Xrays
From the Slater formulae we find c3 pls(r) = — exp( — 2cxr) and (2.42) we find from equation (2. The total coherent scattering amplitude/ a is found by adding together the values of ps for the individual electrons and this is shown infig.12(c). For a given value of s(9) if more of the electronic charge is concentrated at low values of r then more of the contribution of the integration. The much tighter distribution of the Is electrons can be appreciated from fig.. in steps of 20°. equation (2.
Problems to Chapter 2
49
(b) For the same values of 20 find the phases of the resultant scattered radiation with respect to that from a scatterer at one end of the line.01 steradian.2A" 1. Calculate. A detector is arranged to collect the light scattered through an angle of 45° from a solid angle of 0. 2. falls on the scatterers. by steps of 0. approximately.46A" 1 . moving along the direction of a body diagonal of the cube.4 A lithium atom contains two Is and one 2s electrons for which the Slater analytic wave functions are
and x//2s = (ci/96n)*rexp( . (Note: to calculate points for plotting the curves the recommended intervals are p l s : r = 01. and perpendicular to.0 A p2s: r = 02.2 A.10A" 1 and c2 = 2. the number of photons entering the detector. What is the ratio of the intensity of the scattering along the direction of one of the sides of the cube compared to that which would be obtained from a single scatterer for the same scattering angle? (Note: there are two directions to be considered. and (b) the incoherent scattering from a single Li atom.\c2r) where cl = 5.0 A and p:s = 02. Show graphically the radial electron densities for a Is and 2s electron and the amplitude of the coherent scattering from each of them.1 A. Plot also the intensity of (a) the coherent.) 2. the electron beam.3 In an experiment to investigate scattering from free electrons a fieldemission discharge of 2 kV electrons of 5000 A is confined within a cylinder of 4 mm diameter. one representing forward and the other backward scatter. 2.) by steps of 0.2 Eight identical coherent scatterers are placed at the corners of a cube of side L A parallel beam of radiation of wavelength A.
.0A" 1 by steps of 0. A Qspoiled ruby laser produces a 10 joule pulse of duration shorter than that of the field emission and this passes in a fine pencil through the centre of.
which are equal. and at some distance which is large compared with the extent of the lattice. The terms on the righthand side all cancel except the first and last. is 4. and we have sin(7inas) This equation can be found to hold also for n even. each atom separated from its neighbour by a vector distance a. expressed as a fraction of that from a point electron at the origin.1)
where/a is the atomic scattering factor. in the reasoning which led to equation (2. We are now going to examine in detail the influence of the periodic nature of the atomic arrangement in the diffraction of Xrays by a crystal. In a direction corresponding to a scattering vector s. as the coordinate origin.=/. if the centre of symmetry is used as origin. (3. The analysis of the present case is simplified if we assume that n is odd and if we take the centre atom.3 how to compute the resultant scattered amplitude. The scattered radiation from each of the atoms is coherent with respect to that from all others and we have seen in § 2. It is useful first of all to consider diffraction from a single row of n atoms. Previously. the amplitude of the scattered radiation. I cos(27i<zas). This expression can be simplified as follows:
a
2 sin(7ta*s)
{sin(7irca*s) — sin[7i(n — 2)a # s]
+ sin[7i(n — 2)a's] — sin[7t(w — 4)a*s] + • • • + sin[7t(2 — n)a*s] — sin[7t( — n)a*s]}.33). which is at the centre of symmetry.2) must give the magnitude of
.1
Diffraction from a onedimensional array of atoms A crystal consists of a threedimensional periodic arrangement of atoms each of which will scatter an incident Xray beam. it was found that the scattering amplitude from a centrosymmetric arrangement of scatterers is real if the centre of symmetry is used as origin.3 Diffraction from a crystal
3. and equation (3.
where h is any positive or negative integer. However. we can determine the corresponding value of (Kn) by noting that
[
sin2(nx) sin 2 *
M 2 _ n2
=— — n . 3. (2) Between the main maxima there are n — 1 minima. As a*s progresses from 0 to 1 we can see the development of the three minima and two subsidiary maxima. both sin(iina*s) and sin(7ia*s) are zero.
(3. In fact the positions shown as subsidiary maxima in fig. and n — 2 subsidiary maxima.
sin (Tea • s)
0. (3) The width of a main maximum is 2/n and the maxima therefore get narrower as n increases. 3.4)
In fig. The case n = 4 can be followed in the sequence of phasevector diagrams shown in fig. The functions sin2(5ita*s) and sin2(7ia*s).3 are close to but not actually at the maxima. (1) The main maxima of (Kn)2 occur whenever a#s equals an integer. It is evident that the ratio of these two functions will be periodic with a repeat distance of unity so that if (Kn)2 = n2 for a*s = 0 it is also equal to n2 for a#s = h.5
. 3. The vertical scale of these graphs has been adjusted to reveal more clearly the relative variation of (Kn)2 as a*s changes.1.5
1. where h is an integer.3.1 there are plotted the functions sin2(7ina#s) and sin2(7ia's) for n = 5. 3.0
1.2. If we look at (Kn) we see that for a»s = h.
(3. In fig.1 Diffraction from a onedimensional array of atoms
51
the scattered amplitude no matter what origin is chosen.3. 3. (4) The main peak is twice as wide as the subsidiary ones. The maxima of(Kn)2 lie close to the maxima of sin2(7i/ia*s). being closer
Fig. 5 and 7. The following then are the general characteristics of the functions (Kn)2.say. where (Kn)2 is zero. for the range a*s = 0 to 1 the function (Kn)2 is shown graphically for n = 3.3)
and it will be instructive to examine the properties of (Kn)2 as a function of a#s for various values of n. (5) The ratio of the heights of the main to subsidiary maxima increases as n increases. The intensity of scattering is given by
sin2(7ia#s)
=/ 2 (K n ) 2 .
Diffraction from a crystal 10
1.045. is given by
sin2[7i(3/2n)] and the ratio of height of the first subsidiary peak to the main peak is
= ^ 1 = 0.2. we may write the positions of the maxima of (Kn)2 as 2m + 1 a*s = — . 2n Thus the height of the first subsidiary peak. As n tends to infinity. 3. that for m = 1. m = 1 to n — 2. when the two sets of maxima tend to coincide.0
the larger the value of n and the faster the variation of sin2(7trcas) compared to sin2(7ia*s).5a)
. The intensity of scattering from rows of 3.
(3.52
Fig. 5 and 7 scatterers as functions of a*s.
For very large n (theoretically n = oo) we deduce that
.3.5b)
We may note that this ratio falls oflf rapidly with increasing m and that for large n all the subsidiary peaks of appreciable magnitude are very close to the main maximum. we find
(Kn)(2m+ l)/2n _ 4
(Knf0
(2m + 1) V
(3.3.
First minimum
First subsidiary maximum a s—i
A_ C E
Second minimum
Second subsidiary maximum
Third minimum a s=5
A
B
C
D
+ E
Main maximum as = 1
Similarly for the mth peak. Phasevector diagram showing the formation of maxima and minima of intensity for a row of four scatterers. as long as m « n.1
Diffraction from a onedimensional array of atoms Main maximum a •s=0
53
Fig. 3.
. The various values of h define a whole family of cones whose surfaces indicate directions in which the diffracted intensity is nonzero.7)
It should be particularly noticed that the lines representing the incident beam. 3.cos \jfat0) = hL (3.6)
This condition is the one which will be found to apply in the diffraction of Xrays by crystals where. etc. These are represented in fig. There can also be found the condition for diffraction from a onedimensional array of atoms from a more direct physical point of view. As the angle \jja 0 is varied so the circles shown in fig.6 . in the packing of the unit cells in any one direction. row of atoms and diffracted beam are not necessarily coplanar and for a particular angle \jja 0 and integer h the permitted angle \\ia defines a cone of semiangle \jja whose axis is the row of atoms. which is so large that the complete array of atoms can be considered as situated at the point O. 3.5(fc). or
a{cos \\ia . 3. for h = 3.4 radiation is shown falling on the row of atoms. finally.5(a) where one of the cones is illustrated. staying always perpendicular to and with their centres on the line OP.AD = hi where h is an integer.) until.5 slide round the sphere.54
Diffraction from a crystal
there is no significant diffracted intensity except under the condition a*s = h (an integer).
. 3. and the other cones are represented by their circular intersections on the sphere.
Fig. when \j/a 0 = 0 the situation will appear as in fig. and we consider the resultant in a direction making an angle y\ia with the row.4. n is rarely less than several hundred. (3.1. the incident radiation making an angle \j/a>0 with the row. 3. For reinforcement of radiation scattered from neighbouring atoms we must have CB . In fig. For h = 0 we see from equation (3.7) that \j/a = \j/a0 and hence the incident beam must lie on the surface of this cone. New circles will appear at the rear of the moving system of circles (h = — 5 . The relationship of incident and diffracted Xrays to a row of atoms. Thus if \\ia 0 is made steadily smaller the circle h — 3 will shrink and finally disappear while the other circles move round the sphere towards the point P. Where the crystal is very small there can be some spreading out of the diffraction pattern and this effect is discussed further in §6.
8)
Since S and S o are unit vectors making angles i//a and \jja0.6) and (3.
Incident ray
h=

(a)
h =
Direct ion ^ of arra> and of incident ray (*) It should be noted that the two conditions for diffraction to occur. are equivalent. respectively. 3.6) and (2.1
Diffraction from a onedimensional array of atoms
55
Fig.5. equations (3. From equations (3. (b) The orders of diffraction which occur when the incident beam is aligned with the row of atoms.
.3.7).10) we have
(3. (a) The allowed cones of diffraction from a onedimensional array of atoms shown by their intersections with a sphere.
7) follows immediately from equation (3. If the angles made by the incident and diffracted beams with the a and b directions are \\ia 0.for example the circles h = 1 and k = 2 intersect in the two points U and F.3.56
Diffraction from a crystal
with a then it is clear that equation (3. Thus for a particular
Fig. It will be seen that the two families of circles intersect .(i) that the radiation scattered by the atoms of separation a shall constructively interfere.2 Diffraction from a twodimensional array of atoms We can now progress to the consideration of diffraction from a twodimensional array of atoms (fig. These are represented infig.7 by the two families of circles on the surface of the sphere.10) The equations (3.6) which can be defined in terms of two vectors a and b. The relationship of incident and diffracted Xrays to a twodimensional array of atoms.10) define two families of conical surfaces with axes along the a and b directions. 3. Thus the lines OU and OF lie simultaneously on the two cones h = 1 and k = 2 and OU and OF are possible directions of a diffracted beam. 3.9) where h and k are two integers. ij/a.6. and (ii) all the radiation scattered by atoms of separation b shall constructively interfere. respectively.8).
. \jjb0 and \//b then these conditions can also be written as and &(cos^cos^ ftf() ) = (3. 3. these being the intersections of the cones emanating from the point O. The condition that the radiation scattered by all the atoms of the array shall constructively interfere can be broken down into the pair of conditions . This leads to the pair of equations a#s = h
and
(3.
We should note that.11)
c(cos \j/c — cos ^Ct0) = U.
Array direction along b Incident beam h= 
Array direction along a
direction of incident radiation diffracted beams are produced in discrete directions as indicated by the intersection points infig.12). The three conditions are a*s = h c*s =
or
(3. it passes through the point h = 0. Although the circle h = 3 appears infig.7. which describe the conditions under which diffraction can
. 3.8). The integer pairs (hk) are equivalent to orders of diffraction from a twodimensional grating.3
Diffraction from a threedimensional array of atoms
57
Fig.3 Diffraction from a threedimensional array of atoms The extension of the ideas of the previous two sections to diffraction from a threedimensional array of atoms is quite straightforward. since the incident beam must lie on the surface of both the cones h = 0 and k = 0.7 and to each diffracted beam a pair of integers (hk) can be assigned.3. The condition that all the atoms should scatter in phase in some direction can be broken down into the three conditions that atoms separated by a or by b or by c should so scatter where the vectors a. 3. The cones of diffraction corresponding to the a and b directions of the array are shown by their intersections on a sphere. 3.12)
where the angles are as previously defined. These equations. k = 0 on the surface of the sphere.7 no diffracted beam can occur for h = 3 because it does not intersect any of the k circles. b or c are the three vectors which define the array (fig. in the form (3.11) or (3. Diffracted beams are formed along the lines joining 0 to all the intersections of circles.
(3. their significance will be further explained in the following section.3.3.
This approach also shows us another new feature of the problem. Wherever it falls
. Looked at in this way the problem seems a very formidable one and this is not. except h = 0.10 that the vector S o which is along the incident direction can lie anywhere along the surface of a cone of semiangle ^rc — 9 whose axis is the direction of s. then the family of cones corresponding to various values of h does not move while the other two families of cones vary.12) are possible directions of a diffracted beam?' These latter three angles are to be 'possible' in the sense that for fixed vectors a.3.58
Fig. If we now wish to know what condition does give a diffraction beam we can approach the problem in two ways. That there is some solution can be appreciated by an examination offig. \j/c 0) such that the values of ij/a.9 the cones defined by equation (3. i/^?0. We can stipulate the triplet of integers (hkl) and ask ourselves the question . We can see from this that if there is any solution at all to the problem then there is a whole family of solutions. 2. ij/b and \j/c given by equations (3. the best way to approach the problem. 3. since an incident and diffracted direction corresponding to such a vector s would be what we are looking for.3) and contain s in the plane they define. This will be the normal situation when an incident beam has an arbitrary direction in relation to the array. Rather we should ask ourselves whether we can find a vector s which satisfies equations (3.e. through which passes one member of each of the families of circles and therefore no general diffracted beam can be produced.12) are illustrated for a typical case by their intercepts with a sphere. We can see now that there is an important new feature in this figure which has not appeared before. in fact. The magnitude of the scattering vector s gives the angle 6 and the incident and diffracted beams must each make an angle %n — 6 with s (as in fig. There is no point on the surface of the sphere. b and c the angles are not independent and must therefore be related in the correct way. 3.9. In fig.11). The relationship of incident and diffracted Xrays to the vectors which define a threedimensional array of atoms. For a particular pair of indices k and / the point of intersection on the sphere will move as the crystal rotates. Incident ray
Diffraction from a crystal
Diffracted ray
take place are known as the Laue equations and they are of central importance to the subject of Xray crystallography. say the a axis. / = 0. If the crystal is rotated about some axis. k = 0. \\ih 0. It is clear from fig.8. 3.'How do we select a direction of incident beam (i.
b and c directions of the array are shown by their intersections on a sphere. a**b = a**c = 0. 3.11. 3. (3.4 The reciprocal lattice We are now going to consider the Laue equations in the form (3.
Array direction along c Array direction Jilong a
k=
Array direction along b
Straightthrough beam
Fig. / = 0). defined by the vectors a. s and S must always be coplanar. A diffracted beam would be produced along a line joining 0 to any trisection of circles. 3. k = 0. The three vectors § 0 .3.11) and examine the problem offindingscattering vectors s which will satisfy these relationships for a given set of integers (hkl).9. The conical surface is the locus of the incident and diffracted beams for a particular scattering vector s. The cones of diffraction corresponding to the a. None occurs in the case shown (except h = 0. 3.
0
on one of the stationary h circles a diffracted beam will be produced corresponding to that particular combination of h. k and /. b and c and illustrated in fig. Consider the unit cell. We define a new vector a* by the following relationships: a**a = 1.4
The reciprocal lattice
59
Fig.10.13) Since the scalar product of a* with both b and c is zero then it must be perpendicular to each of them (or zero) and is hence perpendicular to the
.
k and / are three integers. Two other vectors. The magnitude of s gives the diffraction angle 20 from equation (2. of how to set the crystal to give the (hkl) reflection.14) and we shall see that the reciprocal relationship will also show itself in other ways. is also fixed relative to the crystal.15)
which follow from the relationships (3.
(3. and in the plane defined by the incident beam and s. Such a reciprocal lattice point can be denoted by the vector ha* + /cb* + /c* where h. The 'reciprocal' nature of this lattice as compared to the real space lattice is suggested by the nonzero diagonal elements of the relationships (3. 3. This fixes the direction of a* and its angular relationship with a. it turns out that this value is unique. It is possible to define a point of the reciprocal lattice by three integers giving the displacement from the origin in units of a*. and this then gives the scattering vector s = ha* + /cb* + /c* (3. 3.60 Fig.16)
which. b and c. b and c define a space lattice.12) and the crystal (and hence s) is positioned so that the incident beam makes an angle ^it — 6 with s. Now we look at the following equations: (ha* + /cb* + /c*)a = h (ha* + /cb* + /c*)b = k (ha* + /cb* + /c*)c = /
(3. The relationship of the reciprocallattice vector a* to a. We have now completely solved the problem. also making an angle ^rc — 6 with s. When space lattices were discussed in §1. As we saw from fig. First one finds the reciprocal lattice. in principle at any rate.11. therefore.10 this does not give a unique relationship between the incident beam and the crystal. b* and c*.11) it is clear that the vector ha* + /cb* + /c* is a possible value of s which satisfies the Laue equations for the indices (hkl) and. b* and c*. b* and c* define another lattice which is given the name of reciprocal lattice. in fact. which is fixed relative to the crystal.
. can be similarly defined and we now have the complete set of relationships aa* = 1 ab* = 0 ac* = 0 ba* = 0 bb* = 1 b e * = 0 c a * = 0 c b * = 0 cc* = 1.14). The condition a*#a = 1 then fixes its magnitude and so it is completely defined.
Diffraction from a crystal
plane defined by them.7 it was pointed out that.15) and (3. so the vectors a*.14)
Just as the three vectors a. The diffracted beam will then be observed. Comparing equations (3.
b. y.
.czk. The vectors a*. there are an infinity of possible choices of unit cell. although different vectors a*. ft. /?. i. b*. c and interaxial angles a. (3. if different vectors a.12 for a twodimensional example.cj 4. However it can be shown that for a particular space lattice the reciprocal space lattice is unique. b and c. This is illustrated in fig.12. Alternatively the space lattice may be described in terms of a2 and b2 and the reciprocal lattice correspondingly in terms of af and bf but the lattices themselves remain the same. The space lattice is shown by black dots and the reciprocal lattice by open circles. The vectors a x and hx can be used to define the space lattice and these lead to vectors a? and b^ describing the reciprocal lattice. 3.18)
Fig. First let us derive an expression for the volume of the unit cell. c. We shall now derive some relationships involving these quantities.17) To give the volume in terms of the scalar quantities a. b* and c* will define the reciprocal lattice. b and c are chosen to define the real lattice then. y*. j and k so that a = ax\ + aj 4.3. A unit cell of the crystal can alternatively be defined by the cell edges a. b and c in terms of any orthogonal set of unit vectors. 3. b. c* and a*. /?*. the reciprocal lattice will be unchanged. (3. This is given by the triplescalar product of the three sides as K=a*bx c. b* and c* by which it is defined are dependent on the nonunique description of the space lattice in terms of the vectors a. Similarly there will be a reciprocal unit cell derived from this which can be defined by a*. It can be shown that similar considerations apply to the reciprocal lattice. it is advantageous to express a.azk b = bxi + bj + bzk and = cxi 4. a. A given space lattice and corresponding reciprocalspace lattice described in terms of different unit cells and related reciprocal cells. y.4
The reciprocal lattice
61
although for a particular atomic arrangement the space lattice was fixed.
1 (p.62 The volume of the unit cell can now be written as ax V = K ay az
Diffraction from a crystal
by bz
(3.25) There is a simple relationship between V and F* which is not obvious from equations (3.22)
c*b c*c
If the interaxial angles are a.24)
VV* = bx
b*
.19)
The value of a determinant is unchanged if the rows and columns of the determinant are interchanged and it therefore follows that ax
ay az
by
r
a
x
ox c x
by
c
K
c. By similar reasoning we may also find *.a.
f CLyCy H
cxax + cyay F c z a cxbx + cyby Yczb.25) but which may be found as follows:
ax ay by az bz
(3._ cxcx
4" CyCy H~czcz
(3. p and y as defined in table 1.
K
X
ay
y
(3.24) and (3.a. (3.22) followed by evaluation of the determinant gives V2 = a2b2c2(l — cos 2 a — cos 2 P — cos 2 y + 2 cos a cos p cos y) or V= abc(l — cos 2 a — cos2/? — cos 2 y + 2 cos a cos P cos y)*. (3.18) that this reduces to V2= ba c*a bb be . 10) then we have a*a = a2 b*b = b2 c*c = c2 a*b = b*a = afecosy b#c = c*b = cb cos a and c*a = a*c = ac cos p (3. A
a
c.23)
and substitution of these values in equation (3.
Mx
bxbx bxcx^bzbz
L
aA
f.ayay 1.21)
b2cz
It can be confirmed from the expressions (3.20)
c The rules for multiplying determinants are like those for multiplying matrices so that
Wx 4.
+ azb* + azc* ac* bc* c# c*
b Q.17)
and since a* is parallel to b x c (both these vectors are perpendicular to the plane defined by b and c) then we must have bxc
a* = •
(3.
0 0 1
(3. For example we have a*a* = 1 from the relationships (3. b.a* <*>x aya\
63
* + az3 * .27)
The magnitude of these equal vectors must be equal and hence be sin a
a* =•
(3. gives
1 0 0
FF* = 0 1 0 = 1.4
The reciprocal lattice .24). c and a.26
This shows once again the reciprocal relationship of the reciprocal lattice to the real space lattice.14) and a bxc = 1 from the relationships (3. from the relationships (3. a. We can rewrite equation (3.14). /?. Any one of the parameters of the reciprocal lattice may be expressed in terms of the parameters of the real lattice and vice versa. y and the corresponding reciprocallattice quantities in equation (3. By cyclic permutation of a.28a) other relationships may be found.28a)
where Fis given by equation (3.* f
=
"xK + ayb.28a) as sin a = ~bc
and since
V*
we find
sin a = •
andc =
V*
(3.28b)
y*
. is similarly related to the reciprocallattice parameters. The real space parameter.3. "
a C
x x
+ ayc*
a •b* b •b* c •b*
+ czaf bxb*xf bybf + bzb? cxb*x + cyb* + czb* + cyc* + czc* bxct Hh byc* + bzc*
cxa$
T CyUy
bya* + bzaf
= ba*
ca*
which.
16).2 cos a cos /? cos y)} F* = a*b*c*(l — cos2 a* — cos2 p* — cos2 y* 4.5 Diffraction from a crystal . If we consider the atoms labelled A alone then they form a threedimensional array and from this array a nonzero diffracted beam can occur only if the Laue equations are satisfied. This can be pictured as a closepacked threedimensional array of unit cells within each of which there is a similar distribution of atoms.13 eight unit cells are shown with four atoms in each unit cell.28b). A summary of all these relationships is given in table 3.29)
If we have dealt at some length with the reciprocal lattice and its properties it is because of its great importance in Xray crystallography. Thus the total crystal can be divided into four component intermeshed arrays and the diffraction from the whole
.64 Table 3. It is useful to think of the crystal having rigidly attached to it a real space lattice and also a reciprocal lattice so that.1.abc sin psiny y*
sin
F* P = l7rzrr———.1. The magnitude of s can be found from equation (3. The same remarks apply to the array formed by atoms of type B. o* ac sin p . .— . for s2 = ss = (fca* + fcb* + /c*)(/m* + fcb* + /c*) = h2a*2 + fe2fe*2 + / V 2 + 2hka*b*cosy* 4.2hla*c* cos j8* + 2/c/b*c* cos a*. Summary of relationships
Diffraction from a crystal
V = abc(l — cos2 a — cos2 p — cos2 y 4. C or D alone. as the crystal moves. With this idea in mind many of the concepts of Xray crystallography can be understood much more clearly. 3. In fig. so do the lattices. afrsiny *
F* F a*b*c* sin p* sin J sina*=.the structure factor We must now look at the details of the arrangement in a crystal structure. this can be thought of as a small part of a very large array which forms the complete crystal.2 cos a* cos /?* cos y*)* FF* = 1 * be sin a . a*fr*c*sina*siny*
V sin/?* = ate sin a sin y
siny =
n^h^n*
F . 3. siny*=sina*sinj5* cin ^v* cm K* abc sin a sin j5
Again by cyclic permutation of the symbols and by interchanging real and reciprocal parameters new equations can be found from equation (3.
(3.
write
i= Z /.5 Diffraction from a crystal . 3. times a factor /4exp(27iir/1s) + /Bexp(27tiiys) + /cexp(2n. We shall see in § 3. 3./
A
/
/
/
/
/
crystal will be the sum of the contributions from the four components. if there are N atoms in the unit cell. we may.3. with respect to an electron at the origin of the cell it occupies. A group of eight unit cells containing four atoms per unit cell. one at each unitcell origin.5. It can be divided into a real and imaginary part and written as
lB
hkl
(3. The total scattered amplitude from the crystal will thus be that from an array of electrons.the structure factor
Fig. Hence there will be a diffracted beam from the whole crystal only when the Laue equations are satisfied and the Laue equations can thus be seen to be the controlling factor for diffraction from any threedimensional periodic arrangement of atoms.
(3.exp(27Uiys).6. •A » / / . We shall refer the scattering from each component array of atoms to that which would be obtained from an array of point electrons at the origin points of the unit cell . will be /4exp(27iir^*s) and the same ratio will apply for all the atoms A with respect to electrons at all the origins.A /
65
a
/
/ /
'
/
•A
/
/
r /•ry / /* /
A. (3.14(a).13.ircs) +/Dexp(27iirDs). The scattering of any one atom A.30) The scattering vector s will correspond to a triplet of integers (hkl) and. is called the structurefactor and the integers h.32)
where (3.marked O infig. The composition of the structure factor Fhkl can be seen in a phasevector diagram and is shown in fig.33a)
.31)
The quantity Fhkb which we notice is a function of the contents of one unit cell.13.6 the reason for referring to the diffracted beam as a reflection and at the same time we shall discover that the indices of the reflection are the same as the Miller indices defined in § 1. Each atomic type forms a space lattice. in general. k and / are referred to as the indices ofthe reflection.
33b)
There is clearly a phase angle <t>hkl associated with Fhkl which is given by Bhkl
Ahki
(3. (a) Phasevector diagram for a structure factor with contributions from four atoms.66
Fig.34)
where Bhkl and Ahkl have the signs of sin (j)hkl and cos (j)hkb respectively. (b) Phasevector diagram for a structure factor corresponding to a centrosymmetric structure.
. (3. 3. Imaginary axis
Diffraction from a crystal
/D
' <t>hki
Akki
J^^
t
2nxL • s /
s
Real axis
(a)
Imaginary axis
Real axis
(b)
and = X/)sin(27tiys).14.
6 Bragg's law
67
The intensity of the diffracted beam from the total crystal. von Laue
. 3. the expression for the structure factor is found by taking only the real part of equation (3. which often occurs. consisting as it does of large numbers of unit cells. 3.3.a phenomenon we noticed with the space group P2Jc when we considered that space group in §19. with the centre of symmetry as origin.36)
This explains why a centrosymmetric unit cell is always referred to a centre of symmetry as origin in the International Tables .6 Bragg's law In 1912. At this time it had been deduced indirectly from the geometry of crystals that they were almost certainly in the form of a threedimensional periodic array of atoms. will clearly be proportional to
<^hkl ~ I Fhkl I
=
A h k l + Bhkl
N
N
= 1 1 //)[cos(27tiys)cos(27iiys) f sin(27tiys)sin(27i. This only confirms what we know from physical considerations anyway. is when the structure has a centre of symmetry. An important case. for we could hardly expect the intensity of the diffracted Xray beam to depend on an arbitrary choice of an origin or an arbitrary unit cell. von Lauefirstproposed that Xrays might be diffracted by crystals.35)
The intensity is thus seen to depend only on the interatomic vectors and not on the actual atomic coordinates which depend on an arbitrary choice of origin.31) to give ^ = 1 / ^ 0 8 2^/8). In § 2. In fig. A phasevector diagram for the structure factor of a centrosymmetric structure shows very convincingly why the F is real. From the known values of Avogadro's number.6 we noted that for a centrosymmetric distribution of scattering material the amplitude of scattering is real.
(3.3. Other types of symmetry lead to other special forms of the structurefactor equation and this is dealt with in some detail in §7. (3. atomic weights and crystal densities the average distance apart of the atoms was found to be of the order of 12 A and it could be presumed that the crystal repeat distances would be of the order of tens of angstrom units.14(b) the scattering contribution is taken in turn from pairs of atoms which are centrosymmetrically related and after every pair of steps in the diagram one is always back on the real axis. Thus for a centrosymmetric unit cell.iys)] or
N N
Jf
= Y Y //cos[27i(r — rVs].
as the phase difference for rays reflected from A and B is CB .as we know from experimental observations. A number of sets of equispaced parallel lines are shown which pass through all the scatterers and.3. However this condition would be true for any value of 6 and we must now explain why it is only for special angles that the reflection can occur .16(a) this can be clearly seen. To do this we must bring in the distance between the parallel reflecting planes. it is only necessary to show that reflection from any point on one plane is in phase with that from any point on another plane to show that the total reflection from the two planes is in phase. caused a stir of excitement throughout scientific circles. Since reflections from all points in one plane are in phase.3.16(fc)].68
Diffraction from a crystal
reasoned that an optical diffraction grating repeat distance was some few times the wavelength of visible light and the same relationship might obtain between the repeat distance in a crystal and Xray wavelengths. In 1913. The condition for reinforcement is clearly given by
BA' + A'C = nX
where n is an integer. A selection of sets of parallel equally spaced lines on which lie all points of an array of scatterers.15. according to the Bragg picture. This inspired prediction was confirmed by Friedrich and Knipping whose Xray pictures. Bragg gave the first mathematical explanation of the actual positions of the Xray diffraction spots. W. 3. The two points we shall consider are A and A' separated by the distance d which is the interplane spacing [fig. these planes would act as partial reflectors for Xrays.
. When a parallel wave train falls on a specularly reflecting surface the conditions are such that reflection from any two points of the surface will give rays in phase in the reflected beam. 3.15.AD = 0.L. Infig. crude by modern standards as they were. We can follow the main lines of his explanation by considering diffraction by a twodimensional array of scatterers as infig. For reasons which will be clearer later we shall only
Fig.
It can be seen now why we refer to the diffracted beams as 'reflections' and why the angle between the incident and diffracted beam is denoted by 29 and not simply by 9.17(fc) there are shown the lines with indices (42).17(a) the indices of the lines shown are (21) and in fig. in terms of X and the spacing of the reflecting planes. 3. 0. (b) Parallel rays reflected from points on neighbouring partially reflecting planes are in phase when Bragg's law is obeyed. b/k. (a) Parallel rays reflected from different points of a plane are in phase after reflection. d. These we shall refer to as the indices of the Xray reflection and the spacing of the planes so defined is denoted by dhkl. 3.16.37)
This is the expression known as Bragg's law and it gives the permitted angles of reflection.in fact alternate ones are completely empty. Now the latter lines are not all atomrich .6
Bragg's law
69
Fig.17(a) in terms of the twodimensional unit cell which is outlined then it can be seen that they correspond to directions given by intercepts of a/2 and b/\ on the cell edges. 3. If we look at the atomrich lines in fig. From fig.16(fo) we can see that BA' = A'C = dsinO giving 2dsin9 = X. c/l where h. In terms of Bragg's law the angle 9 corresponding to such a spacing is given by sin0 =
2dA2
but this can also be expressed as
sin0 =
2X 2d 21
Seen in t h i s w a y . a reflection from t h e line with indices ( 2 x 2 2 x 1 ) can b e r e g a r d e d as a s e c o n d .
(3. In fig. 3. k and / are three integers. In three dimensions one would have atomrich planes parallel to the planes defined by three points with intercepts on the unitcell axes of a/h.3. 3.o r d e r reflection (difference of p a t h 2X b y reflection
.
//////.A
'// (a)
A' (b)
consider the case n = 1.
m
. Let us see if we can now relate Bragg's law to the Laue equations for. For three dimensions this generalizes to being able to consider reflection from planes with indices (nh nk nl) as the nthorder reflection from planes with indices (hkl). Ifh. if they are describing the same phenomenon. 3.18 there is shown part of a threedimensional unit cell with planes drawn corresponding to the indices (hkl).70 Fig. they must be closely related.6. (a) The (21) reflecting lines for a particular twodimensional unit cell. In fig.17.18 OD is perpendicular to ABC and since OA = a/fc then
OAdhkl = j
= OAx dhklcosx = d .
Diffraction from a crystal
(a)
(b)
from successive lines) from the lines with spacing d21. 3. (b) The (42) reflecting lines for the same unit cell. 3. k and / have no common factor then these planes would be those with Miller indices (hkl) according to the definition given in § 1. In fig.
Successive (hkl) reflecting planes with interplanar spacing dhkl.39b) the values of dhkl may be deduced for a particular unit cell and set of indices.
71
Direction of b axis
Thus
"hkl
and similarly
din
and
"hkl
d? hkl
= 1
(3. assuming a unique solution for s. In terms of magnitudes
5 = l/dhkl
(3.12).39b)
or. 2. as indeed is d which we have seen is parallel to s.38)
Comparing this with equations (3.3 and interpret S o and S as vectors along the direction of the incident and reflected beams from a mirror reflection then clearly s is perpendicular to the plane of the mirror. From equations (3. we must have
1
= <V<*few
(3. 3.11) we see that.18.39a)
that is to say that s is a vector in the direction of dhkl but with a magnitude l/dhkl. We could construct a reciprocal lattice by first
.3.6 Bragg's law
Fig.37).29) and (3. from equation (2. 2sin0 1
which is a rearranged form of equation (3. If we look again at fig.
/c* should leave us in no doubt that it would do so. 3. In the foregoing description of Bragg's law we have treated only the case of one atom per unit cell. b/k and c/l. y. Whether or not one is formally justified in thinking of a diffraction process in terms of speculartype reflection is not too certain from the physical point of view but. If the cell edges are denoted by the vectors a. since the two types of description are mathematically equivalent. there is no harm in doing so.exp(27ur/s)
Fig.16). 3. 3. b and c then the vector position of an atom would be r = xa + yb f zc
(3. as in fig.20. Thus we say that an atom has coordinates (x. k and / and now we can rewrite equation (3. Previously.7 The structure factor in terms of indices of reflection It is convenient to express the positions of atoms in the unit cell with respect to the chosen origin in terms of fractional coordinates.
.19 for a twodimensional unit cell containing three atoms per unit cell. y and z are three fractional numbers in the range 01. 3. 3.18. z) where x.72
Diffraction from a crystal
drawing planes with intercepts a/h. if there are many atoms per cell then one should think in terms of many sets of reflecting planes of spacing dhkl each with a different reflecting power and so interleaved that the reflected rays from each set interfere with each other. Thinking of Xray diffraction in terms of Bragg's law is often very convenient and we shall have recourse to this description of the diffraction process from time to time. in equation (3. then finding the normals to these planes from 0 and then marking the points along the normal distance 1/d from 0. A twodimensional structure with three different atoms showing interleaved reflecting planes.19. we have found an expression for s in terms of h. This situation is shown in fig.31) as
N
Fhki= Z /. That this would produce a lattice of points is perhaps not selfevident but the identity of s separately with dhkl/dlkl and with /za* +fcb*4.40)
as is shown for the point P in fig.
There is a useful concept of a weighted reciprocal lattice where we associate with each reciprocal lattice point the corresponding J>m.y.3.43)
The experimentally observed intensity of a diffracted beam is proportional to Jhkl and it can be seen from equation (3. equation (3.43) that Shu = Jhki(3.35) becomes
N N
^hu
=
Z ^ffjcos{2'^[Mxi
~ xj) + Kyi ~ yj) + Kzi •
(3.44)
This equation holds whether or not the crystal structure has a centre of symmetry.y.14) we find
Fm = Z ffi*pl2ni(hxj + kyj + bjf].41)
In the case of a centrosymmetric structure the structurefactor equation appears as Fhki = Z ffios[2n(hXj + kys + Izj)]. Equation (3.
(3. 3. (3. The form of the structurefactor equation.44) implies that the weighted reciprocal lattice always has a centre of symmetry. The relationship of the vector OP = r to the fractional coordinates of P(x.z). as we shall see. This important intensity relationship is known as Friedel's law. using this nomenclature.
= Z ffixpl2ni(xjBL + yjb + zf)(h&* + fcb* + /c*)].42)
and.
7=1
(3.z) are known for particular indices of reflection (hkl). for normally. In appendix I there is given a FORTRAN® program STRUCFAC which can be used to calculate structure factors for any twodimensional space
. From this and the relationships (3. is the most useful one in practice.41).7
The structure factor in terms of indices of reflection
73
Fig. one wishes to calculate structure factors when the atomic coordinates (x.20.
15A.601 A.002 A. The output from STRUCFAC is stored in the data file SFl. The reader should examine the FORTRAN® listing which is liberally provided with COMMENT ' C statements so that all features of the program may be seen.74
Diffraction from a crystal
group. 3. such as provision for anomalous scattering (chapters 6 and 8) and a temperature factor (chapter 6) which have not yet been dealt with but these can be ignored for now and the program used to solve Problems 3. c = 10.
Problems to Chapter 3 3.05 and plot the resultant amplitude as a function of a#s. a = 100.4 and 3.5°. If Cu Koc radiation is used (X = 1.3 A unit cell has the following parameters: a = 5A b = 10A. Calculate the observable structure factors for this projection taking all necessary information from Problem 3.4. 3.7°. (i) (ii) (iii) (iv)
. (1978) B34 23842). c = 15A. Find what orders of diffraction will be produced and the angle the diffracted beams will make with the row.2 for a row of six scatterers at intervals of a*s = 0. Determine the parameters of the reciprocal cell. Perales and S.2°. This file should be kept as it may be used as input for Problems to other chapters.DAT. The projection down the b axis has the centrosymmetric twodimensional space group p2. 3.4 The crystal and molecular structure of the phenylethylammonium salt of fosfomycin.2. Find the spacing of the (321) planes. p = 102. b = 6.C 9 H 6 OPO^.1 Draw diagrams similar to those shown in fig. If the Xray wavelength is 1.3°.21 A. y = 120°. p = 95.54 A. 3. It contains facilities. C 8 H 1 2 N + . y= 115. The noncentrosymmetric monoclinic space group is P2V The cell dimensions are: a = 11. b = 6.5 The caxis projection of the phenylethylammonium salt of fosfomycin has the noncentrosymmetric twodimensional space group pg. and the cooordinates of the nonhydrogen atoms (the hydrogen atoms will make a small and negligible contribution to the structure factors) in one asymmetric unit are shown in table 3. the name of which may be changed by the user. Find the volume of the real and reciprocal cells.6 A crystal of density very near 1.542 A (Cu Koc radiation) then use the program STRUCFAC (appendix I) to calculate the complete set of observable structure factors for this projection. was solved by A.2 x 103 kgm" 3 is found to have a unit cell with a = 5. a = p = 90°. 3. GarciaBlanco (Ada Cryst.H 2 O. c = 8.2 A parallel beam of radiation of wavelength X falls on a row of scatterers of spacing 5X so that its direction makes an angle of 30° with the row.5.54 A) what is the angle of diffraction (20) for the (321) reflection? 3.994 A.
7220 0.2500 0.9165 0.3482 0.1748 0.6140 0.0150 amu atomic weight of hydrogen (mean isotopic mixture) = 1.1141 0.4017 0.4 Atom
X
y 0.0740 0.4363 0.2621 0.3587 0.6598 x 10" 2 7 kg
.2156 0.1194 0.4318 0.2755 0.2655 0.7318 0.3982 0.1001 0.9542 0.2.2740 0.3650 0.3322 0.1479 0.0083 amu 1 amu =1.0654 0.3229 0.7347 0.3394 0.0697 0.9017 0.7909 0.7892 0.2676 0.2229 0.4021 0.3677 0.0693 0.2737 0.1303 0.1194 0.Problems to Chapter 3
75
Table 3.1433
z 0.4928 0.6519 0.6410 0.3238 0.2564
(i) How many molecules of chemical formula C 6 H 1 2 are there in the unit cell? (ii) Give a better estimate of the density. Note: atomic weight of carbon (mean of normal isotopic mixture) = 12.0717 0. Coordinates for Problem 3.4479 0.9551 0.1560 0.9882 0.2670 0.9011
P
O(l) O(2) O(3) O(4) O(water)
N
C(l) C(2) C(3) C(4) C(5) C(6) C(7) C(8) C(9) C(10) C(ll)
0.
If.\a.1
The Fourier series Let us consider a function f(X) which is singlevalued. with afinitenumber of maxima and minima and which is defined in the range \a ^ X ^ . continuous (except for afinitenumber offinitediscontinuities).
76
. sin[27i(Z/a)] and sin[27i2(X/a)]. sin{2n(X/a)} and sin{2n2(X/a)}. with factors of two outside the summation signs.4 The Fourier transform
4. 4.1) we make use of the following relationships:
to)
2a
Fig. It will be seen that the main characteristic of cos[27i/i(X/a)] is that it is an even function of X whereas sin[2nh(X/ay] is an odd function of X. The functions cos{2n(X/a)}. for a given f(X). We need not be too troubled by the various mathematical restrictions placed on the function f(X). In fig. we have adopted because it simplifies the forms of expressions we shall obtain by subsequent manipulation.1)
This particular form of the series.
h=l
(4. Within this range such a function may be represented by a series of sine and cosine terms of the form i(X) = Ao + 2
i
Ahcosl2nh— ) + 2
\
a
( X Bh sin (27i/2—).1.\a the functions cos[2u(Z/a)]. we wish to determine the coefficients in equation (4. cos{2n2(X/a)}. all the functions with which we shall find ourselves concerned are going to be very well behaved.1 there are shown in the range \a ^ X ^ . cos[27t2(*/a)]. known as the Fourier series. 4. We might look at the form of some of the terms which are included in the summation.
cos 2n(n + m)— dX = 0 (4. for an integer H. Other results follow from equations (4.a / 2
^ . / X\ cos 2nn— dX = a
(4.2)
a/2
V
a
(4.a/2
f
x\
(
x\
sin [ 2TIM— I cos [ 27im— I d X
J«/2 V */ i rfl/2 r
=
V
/ x~\
fl
i ra/2
r
L
xi
"A
sin 2n(n + m)— dX + 
sin 2n(n .m)— dX .4. (4.4).a )dX =\
V
)
Ja/2 ~ L2
+\
2
cos (2n2n
V
«/ J
]\dX
= + \a.3)
J
for n = 0 (since then cos[27in(X/a)] = 1 for all X).
.4)
/a/2
)
r
r
%a/2
(
x\ (
x\
cos I 271/1— Icosl 2nm— )dX
Ia/2
\i
.4) can be seen infig. The results (4.8)
The final result we shall require is
f
. a/2
unless n = ± m when
I cos f 2 7 i n .6) fl Ja/2 V aJ Ja/lll ^ V /J
We can also find
.
(4.
r
Z
%a 2
'
( x\
dX = 0
a
sin [2nn\
(4.) d ^ = I i + ^cos(27i2n.) \dX = \a.2) and (4.7) 2 2 a Ja/2 ±m when aA L J"«/2 L A unless n=
. For example. (4. where n is an integer.3) and (4.L n and We now note that.dX = 0 (4.a/2
2
J«/2
sin 27in— I sin 27im— IdX
f
x\
a)
f
x\
a)
ir
=
fl/2
\
\
r
/ v
xn
a/2
i ffl/2
r
x~i
cos 2u(n .2).m)— dX = 0
2 a 2 \ Ja/2 for all J«/2 m.m a .4.1 from the fact that there are equivalent matching positive and negative regions in the cosine and sine functions.2cos 2n(n .5) ) a L J Ja/2 L J
/
» .a/2
«/2
sin2 2nn.1
The Fourier series
77
ra/2
(
x\
cos [2nn— dX = 0 Ja/2 \ <*/ for n # 0.a/2
V */ V cos 2n(n + m)— dX 4. and
for all integers n.
14)
J
where A_h = Ah.9). What we are doing here is to extend the range of indices to all integers.10)
)
and.sin( .78
The Fourier transform
Ca/2
(
x\
Ca/2
(
x\
f ( Z ) c o s [ 2 n H — ) d X = A0\ c o s [ 2 % H .dX.13)
£
h=oo
Bhsm(2nh\
\
)
a
(4. If we now write Ch = Ah + iBh then Qexp X\ ( X .6) and (4.12) and (4.14) are consistent with what we would obtain from equations (4.15)
(Ah + iBh) cos 2nh— .a/2
/ X\ f(X)cos(2nH)dX
(4. B_h = — Bh and Bo = 0.2TL/Z— + C_^exp I 2ufc— V a \ a / (4.)dX
h=l Ja/2 \
fl
/
\
a
/
oo
fi=l
p
fl/2
/
\
X
a
\
)
/
\
y\
+ 2X Bj
Ja/2
sin 2icfc.
Ja/2 Thus we have
If' AH = \
fl
)
.cos 2icfl.1) can be rewritten as f(X)= £ ^cos(2iifc)+
h=oo \
a
(4. a V ) Ja/2 The expression (4. both positive and negative. we find that all the components on the righthand side are zero except for
Ca/2
2AH
(
\
x\
(4.dX a Ja/2 V ) Ja/2 \ "J oo [a/2 / y\ / y\ + 2 £ Ah\ cos [2nhcos 2 T I # .9) and sin 0 = 0.i sin [2nh—)\ a a
r ( x\ L V )
( x\
a
t x\\ \ )\
( X\\
a
+ (Ah 
Y
iBh) cos 2nh— + i sin 2nh —
= 2^cos\2nh—
(
L
x\
a)
V
)
\
+ 2B.13) since cos 6 = cos( — 9). from equations (4.dX
a
(4.5).sin 2u/z —
( x
\ a
\
)A
.12)
Ja/2
a/2
V
a
)
and similarly we find l Ca/2 C ( x\ BH = \\ f(X) sin 2nH . sinO = . (4.11)
a
cos2 2nH— )dX = AHa. The relationships between the Fourier coefficient which are given in equation (4.
< .4. (4.15).13).
(4.16) and (4.18) are not of much value for numerical work. involving as they do complex quantities.> .)dX
(4.18)
«/
f(X) exp 2nih 
Ja/2
Relationships of the form (4..)dX
a
J
In addition.2 Numerical application of Fourier series The best method of getting a 'feeling' for the properties of Fourier series is actually to do some numerical calculations.12) and (4.12) cos [2%H. for .13) we find l Ca/2 ( x\ Ch = \ f(X)cos[2nh)dX
aja/2 \ ")
)al2
\
<*)
a/2
a
(
\
x\
dX. for .)dX+.2 X . (4.h).19)
i r"/2i
+
/
x\
J
cos(2nH)dX
cos 2 T I H ..17)
l Ca/2 ( x\ + if(Z)sin (2nh. (4.4.16)
If we examine equations (4. from equations (4. + B_hsm\2n(h)\.> . 2 2 a 4 2 a 4 Then from equation (4. If we are dealing with onedimensional functions then the equations we shall want to use are (4.2
Numerical application of Fourier series
79
X^ x\ f X] ( X = Ahcosi2nh—\ + A_hcos\ 2%(h)— + ^ s i n ( 2nh — sin 2it( .< . To illustrate the application of these relationships we shall consider the function shown infig..1).12) and (4.14) then it is clear that we may write
f(X)= £ CkaJ2nih\
h=ao \
a
(4.I
+
( 1 + 2—)cos2uH—)d^ + M
cos2Ti/f—W
..and . 4.17) and (4.< .2 which is 1 X 1 f(X) = 1 . but they are a neat and concise form of expression for a Fourier series and the integrals which give the coefficients.< 4 0 4
= T..
20)
From equation (4. f(X) = f( — X)) and the Fourier series which represents it must contain only even (i. Infig. Having obtained the values of the coefficients Ah we are now in a position to see how well we can synthesize f(X) from = Ao + 2 V A.1013 0.2. It can be seen how the summation gradually evolves towards the correct shape and the result with h = 10 is a very good representation of the
.4.6250 0.13) to determine the coefficients BH it would be found that they are all zero. for {a
The crosses show the values of the reconstituted function computed from the Fourier series with /i = 10.0113 0
0.0056
0. ^1^. 4. The function f{X) = .2 the result of having ftmax = 10. 3 and 7 and in fig.0041 0.cos 2nh— . for h = 0 to 10 are:
h 0 1 2 3 4 5 6
(4. cosine) terms.3 there are shown the results of terminating with hmax = 1.4.21)
10
0. 4.e.e.0020
In practice one must always terminate the summation at some point and the similarity of the computed f(X) to the true function will depend on the number of terms in the summation.80
The Fourier transform
XX XX X XX XXX XX XXJ
Fig. If one formally goes through the process of using equation (4.0021 0
0.12) it can be seen that Ao = (I/a) x area under the curve and this can be confirmed for this simple function by an examination offig.0013 0. The coefficients.0506
0..
and these integrations give AH = T772
~ C0S V for H ^ ° and ^o = "V)
(4.2. This could be predicted from the fact that f(X) is an even function of X (i.
It is a very simple program.4.2
Numerical application of Fourier series
81
a/2
a/2 (c) hmax = 7
0 f(x) 1.0
all
0. so that f( _ X) = f(X) and the latter are odd. 4.
function. one could represent the function by the summation with any desired degree of precision by increasing the number of terms. The computed values are shown by dots.f(X).3. 4.which can be in more than one dimension . it exploits the symmetry of cosine and sine functions in that the former are even functions. and (c) hmax = 7. (b) hmax = 3 (since A4 = BA — 0 this is equivalent to hmax = 4). indeed. Even hmax = 3 gives quite a good reproduction of i(X) with the main discrepancy being in the region of the origin. An early and important contribution to this problem was made by Beevers and Lipson (1934) who precalculated components of individual contributions to the series on strips of cardboard which were provided in convenienttouse wooden boxes. In the early days of crystallography. written to be easy to understand.was a formidable one. before electronic computers were available.3 were made with the computer program FOUR1 given in appendix II. The summations shown infig.2 using a Fourier series with: (a) hmax = 1. In
.4. Simulation of the function shown in fig.5
a/2
0
a/2
Fig. the task of computing a Fourier series . so that f(X) = .
By placing strips under each other. One may replace all the limits a/2. in a little more detail. As a check for the user the last figures is the sum of the 16 values.2. a/2 by a.4.5. It is also convenient to change from the variable X which has the units of a to the variable x = X/a so that x is now a fractional coordinate defined in the range \^x^ —^orl^x^O. Let us suppose that we have a periodic function f(x) but that f(x) is now not an analytical function but one which is known in graphical or tabular form.5. 4.
Often it is convenient to define a function in the range of X from 0 to a and it is clear that the Fourier series can be applied to this range. Such a function. Thus the summation gives a periodic function of spacing a and the Fourier coefficients Ah corresponding to the f(X) shown infig. sine (odd h) and sine (even h) which could then be combined using symmetry to give the whole range. The odd ^ t h s are on the reverse side.0 in the relationships (4.5. 4. for X = Xx + ma where m is any integer. one could conveniently do the summations over the quarter range separately for cosine (odd h).2) to (4. 4.
Fig.22a)
.2 actually reproduce the periodic function shown in fig.2 also reproduce the function f(X) defined in the range 0 ^ X ^ a as shown infig. cosine (even h). equation (4. indeed. 4. The first thing we notice is that although we have originally stated that f(X) is defined in the range — a/2 ^ X ^ a/2 the series can be summed for values of X outside this range. We wish to carry out by a numerical method the integrals
f(x)cos(27i/zx)dx
(4.
31 C E 19 31 13 21 29 3 27 25 6 30 18 15 31 10 23 28 0
(4) 
Let us now examine the properties of the Fourier series. 4. The strip gives the value of — 31 cos(27i x 19 x n/60) where n goes from 0 to 15.6 both graphically and also tabulated at intervals of ^ in x. whose periodicity is unity is shown in fig. The coefficients Ah which reproduced the f(X) defined in the range — a/2 ^ X ^ a/2 in fig. which is the equivalent of going from 0 to \a in steps of a/60.4.1 that the functions are completely defined in the range 0 to \a and the way that the complete range is generated from the partial range depends both on whether it is a sine or a cosine and also on the parity of h.82
The Fourier transform
addition to the even and odd symmetry of cosine and sine functions it will be seen fromfig.4. From the properties of the sine and cosine functions it is clear that the series has the same value for X = Xl9 for X = Xx + a and. CE indicates that it is a cosine strip for even Y^ths.4. 4.
Fig.13).1).4. The periodic function reproduced by the Fourier series which is derived from the function i(X) shown in fig. A typical BeeversLipson strip is shown infig. A typical BeeversLipson strip giving 31cos(27t x 19 x n/60) where n is from 0 to 15.4.
. This replaces an integral
by . Simpson's Rule is equivalent to adding the areas of parabolae fitted to three function values at points defining successive pairs of intervals.4.23b) The coefficients obtained from these summations are shown in table 4. For example if we have a twodimensional.22) can be replaced by the summations
60
(4.22b)
There are various methods available for numerical integration and in appendix III there is given a simple program. singlevalued and
. . from a to b is divided into an even number of intervals N each of width h and the weights wn follow the pattern 1 4 2 4 2 .£ wB
h
N nh
)
where the range of x values.6. SIMP1.23a) and
60
(4.
and Bh = (4.3
Fourier series in two and three dimensions
83 60x f(x) 10 1 1 12 13 14 15 16 17 18 19 76 79 81 83 84 85 85 84 83 80 60x f(x) 20 21 22 23 24 25 26 27 28 29 79 76 73 70 66 63 60 55 50 47 60x f(x) 30 31 32 33 34 35 36 37 38 39 42 39 37 34 32 35 41 51 62 74 60x f(x) 40 41 42 43 44 45 46 47 48 49 90 106 117 123 126 126 123 120 113 104 60x f(x) 50 51 52 53 54 55 56 57 58 59 60 95 85 78 71 65 60 56 52 51 50 50
60x f(x) 0 1 2 3 4 5 6 7 8 9 50 51 52 54 57 60 63 66 69 72
(a) Fig. Using this method the integrals in equation (4.3 Fourier series in two and three dimensions The Fourier series can also be used to express two. for applying The Simpson's Rule method. 4.and threedimensional functions. The small disagreements are due to rounding off the calculated values of Ah and Bh and the termination of the series.6. 4. 2 4 2 4 1 .1 up to h= 15 and these values of Ah and Bh are used with FOUR1 to reconstitute the function f(x) which is shown in table 4. These results may be compared with the tabulated values of the original function given in fig. 4. A nonanalytical function f(x) shown graphically and by a table.2.
Bhk = — B^ and Boo = 0. 64 0.+ kfc=oofc=oo D L \ "
£
£
r
/ x
y
(4.51 42 117. 32 22 73. 36 34 32.82 15 84. 31 58 50.60 51 85. 77 11 78. 38 10 0. 05 26 59. 11
a
Table 4. 43 38 61. 84 2. 10 B(h) 4. A reconstruction of the function shown in fig.52 24 66. 20 4 56. 97 17 84.75 45 125.24)
where Ahk = Aa. 04 18 82. 47 0.25a)
^J. 98 44 125.07 0. Y) defined in a parallelogram whose sides are the vectors a and b.99 50 94. By mathematical arguments similar to those used in § 4. 61
continuous function f(X. 17 0.23) for the function shown in fig. 16 29 46.82 19 80. 89 32 36.90 52 77.24 30 42.Y)=
AhkcoS \2ii(h.2 we can find
i c12 cb'2
Ahk = —
r / x
L V
a
Y\I
h
f(X. 91 n
f (x) 2 52. 4. 16 35 34.2.09 10 75. We use the convention that H = — h. The coefficients found by equations (4.58 40 89. 00 B (h) 5.08 h 3 7 11 15 A(h> 0.21 25 63. 01 14 0. F)cos 2TI / I . 48 6 0. 42 56 55. then we may write
f(X. 10 6 63. 23 0. 60 36 41. 02 41 105.25 43 123.51 33 33. 93 7 65. 24 0. 4.03 2. 14 9 72. 05 0. 68 27 55. 03 0. 02 0.45 0.50 48 112.09 B(h) 0.97 37 51. 70 39 74. 12 0. 14 h 1 5 9 13 A(h) 2. 83 0. 83 6 68. 88 59 49. 07 0.21 21 76. 22 0.61 54 65.6 using the coefficients given by table 4. 01 5 60.01 h B(h) A(h> 2 15. 13 0.1 in the program F0UR1
THE COORDINATES ORE X/ft = n/N WHERE N = f (x) 0 50.27 13 82. 80 12 81.08 31 39. 5 2 28 50. 26 0.+ k\
\dXdY
(4. 48 60 50.6 as obtained by the program SIM PI
h 0 4 12 P(h) 71.1.21 55 59.22 46 123. 16 0.20 n f <x> 1 51. 10 57 52. 09 20 78. 22 0.29 16 85. 32 23 69.84
The Fourier transform
Table 4.00 1. 44 n n 60 f (x) 3 53.33 53 71.89 0.f l / 2 Jfc/2
)\
.17 47 119. 73 14 84.82 49 104. where the coordinates X and Y are measured in the directions of a and b.
+ k\ \dXdY. 4.or threedimensional region of space the series itself had a periodic nature.
ab
(4.
(4.17) and (4.27) and (4.28)
J a/2 J b/2
L
V^
^/J
There are corresponding equations for a threedimensional Fourier series applied to a function f(X. b and c.Z)= t
and
h=a0k=O0i=O0
t 1
=Lf/2 r r.+ kf+ I.+ / c .28) are
f(X.1 are shown in the X Y plane infig.7(fe) in relation to the volume defined by a ^ X ^ 0.1 are shown infig.4J(a) and the planes corresponding to cos{27t[3(X/a) + (Y/b) + 2(Z/c)]} = 1.4.or threedimensional Fourier summation.MdXdYdZ.18) we change our variable of summation from h to s = h/a and make F(s) = aCh. The final equations corresponding to (4. Y) = Y and V C^exp
L
r / x Y\I
(4.4
The Fourier transform
85
and
i c"12 r 6 / 2
Bhk = — If we write C» = 4 * + iBhk then we have f(X. Y.Y. b ^ F ^ O and c ^ Z ^ 0.
L V
a
b c
(4.4.d ^ d r .25b)
f(X. then f(X) = fj F(s) exp( .
a
bc J _a/2 J b/2J c/2
exp27ii( h.31)
. two. Y)sin \2% [h.30)
)\
Infig. The contours corresponding to cos{27i[3(X/a) + 2(Y/ft)]} = 1. 0 and . 0 and . Z) defined in the parallelepiped given by the vectors a.4.4 The Fourier transform We have seen that although the functions we have been representing by a Fourier series were defined in some one. It is not quite so straightforward to represent the terms in a two.1 are shown the forms of some of the terms included in a onedimensional Fourier summation.2nisX) (4.27)
li= — oofc= — oo
l Ca/2 Cb/2 V f x Y\l Chk = —\ PMOexp 2 u i U .26)
27ii[h— + k T ) \
\ / A
(4. If in equations (4.
and
a/2
f(X) exp(27iisX) dX. (b) Intersections of the faces of a unit cell with planes for which cos 2it I 3— + . Negative regions are shaded.
•a/2
(4.+ 2 . 4.I = 1 (thick full line)
f
/ X
Y
ZY] c/J
L
V a
b
= 0 (thin full line) = — 1 (thick broken line).86
The Fourier transform
(a)
Y Fig.7. The discrete values of s ( = h/a) become very close together and values of F(s)
. (a) Contours in the X Y plane of
tb)
s 2re( 3 — h 2—1 = 1 (thick full line)
L
V a
b)\
= 0 (thin full line) = — 1 (thick broken line). Negative regions are shaded.32)
Now let us consider what happens when a becomes very large.
8 there is shown. etc. ± 2/a. The rectangular blocks have areas (l/«)R{F(s)exp( — 2nisX)} and the total area of these blocks from s = — oo to s = + oo will equal f(X).35)
exp(2nisX)dX.36) is called the inverse Fourier transform to indicate the difference between the two forms.31) is clearly a real quantity (see equation (4.36)
R{F(s)exp(27risX)j
7
a
6
a
5
a
4
a
3
a
2
a
1
a
1 2
a a
3 a
4 a
5 a
6 a
7 a
Fig. or as a tends to infinity. 4. 4. Sometimes the integral in equation (4.4
The Fourier transform
87
determined from equation (4. so F(s) tends to be a function of a continuously variable s and one will then have f(X)
However we may now take out the 'realpart' symbol within the integration for the integral will still be real without this (see equation (4.4.32) for neighbouring values of s should not be very different.33)
where R(z) means the real part of z. a typical set of R{F(s)exp( . ±(l/a). Thus we have as a • oo
f
R{F(s) exp( 
2nisX)}ds.2nisX)} for s = 0.
.
(4. The sum in equation (4. ± I/a. In fig. Values of R{F(s)exp(27iisX)} at s = 0.34)
and
J A functiona f(X) related to F(s) in the way shown is defined as the Fourier transform of F(s) and similarly F(s) is the Fourier transform of f(X). ± ( 2 / 4 The sum of the areas of the blocks gives f(X). for a particular value of X.8.16)). On this point it should be stressed that if the transformation from f(X) to F(s) involves a negative sign in the exponential term then the back transformation from
J" "f
F(s) exp( 
(4.14)) and thus can be expressed as
art
(4.
(4. But if a is very large.
The position of a point in the parallelepiped whose sides are the vectors a.38) and (4. b* and c* defined by the equations (3. (4.14) and we may define a vector s by s = fta* + fcb* + Zc*.
We shall now generalize our description of Fourier transforms to the threedimensional function given in equations (4. it will be noticed that the width of the central maximum of F(s).
US
(4. This is a characteristic relationship between a function and its Fourier transform. 4. (4.42)
The function F(s) is shown in fig.+ Z. b and c there will be reciprocal vectors a*.40) and (4. b and c may be represented by r = Z a + Y 6 + Zt (4.37)
where a.35) and (4. 6 and c are the unit vectors in the directions of a.36) we find
f(r)= F(s) exp( . This may also be written as r = X+ Y. b and c.39)
If we now write F(s) = VChkl then by similar arguments which lead to equations (4. The Fourier transform of f(r) is F(s). 4.40)
and F(s)= f(r) exp(27iisr) dv (4.9(fo).41)
In equations (4. The two signs can both be reversed .
.this is only a matter of the way the transformation is defined in the first place in equation (4. a function in a reciprocal space in which an element of volume is dv*.15) where one could also have taken
Ch = AhiBh.9(a).88
The Fourier transform
F(s) to f(X) must have a corresponding positive sign. The Fourier transform is given by F(s)= ' = ™ ^ .30). is 2/a and is thus reciprocally related to the width of the function f(X).29) and (4.38) a b c Corresponding to a. We can see the mutually reciprocal nature of the two quantities r and s from the relationships (4. between the two points at which it falls to zero.39).2TUST) dv*
J V*
(4. To illustrate the calculation of a Fourier transform we consider first the onedimensional function
ry "v/"\ 1 f 1
^
V
<»' 1
f(X) = 0 for  X  > \a which is shown in fig.41) f(r) represents a function of position in some space represented by the vector r in which an element of volume is dv.
(d) The Fourier transform of the function shown in (c) F(s)=
. \a
<: \a
(b) The Fourier transform of the function shown in (a) F(s) = 
(c) The function f(X) = 2.0
0 (a)
J— x
f(X)
2.9.\X\>\a. \a ^ X ^ \a = §.4.4
The Fourier transform
89
1. 4.0'
\a
0 (c)
Fig. (a) The function
= 1.
44) we substitute kX = rj we find
F1(s) = 
f2(!. Another function of great importance to the study of Xray diffraction is the Dirac ^function.)exp(2*i!>. The Gaussian function (4. (4. This is illustrated infig. = F 2 ( 0
(4.9(c) and (d) which show f(Z) = 2for ia^X^ia Ofor \X\ >{a and the corresponding Fourier transform F(s) = us There are a number of analytic functions whose Fourier transforms are of interest.2n2a2s2) (4.45)
Thus when f2(X) has l/fc times the lateral spread of f^X) we find that F2(s) has k times the lateral spread of Fx(s). (4. where ft(X) = kf2(kX).4.90
The Fourier transform
if the lateral scale of the function changes by a factorfcthen the transform changes by a factor l/fc.2 and 3 are shown together with the corresponding Fourier transforms.43)
The function f2(X) has l/fc times the lateral spread of fX(Z) and is scaled by a factor k so that
The Fourier transform of f^X) is given by 00 Fx(s) =
f
f^X) exp(2nisX) dX f2(fcX) exp(27iisZ) dX. We can see this by considering the transforms of two functions fx(X) and f2(X). This function has the following properties: d(X) = 0.44)
= k
J oo
If in the integral (4. for X # 0
5(0) = oo
. The inverse relationship of the width of these functions can be readily seen.46)
which is another Gaussian function.48) for a = 1.47) (4. (4.49) . Infig.4.10 the Gaussian functions (4.48) which is normalized to have unit area under the curve has a Fourier transform F(s) = exp( .)di.
4
The Fourier transform
0. 4. 2 and 3. at the limit where a = 0.50)
It is not the sort of function we can draw but we can imagine it like the functions shown in figs. This result would also be found from the general expression (4. (c) and 4.2
^
n =
2
\
a= 3 0.48) we make a > 0 then i(X) > S(X) and.1
0.9 (a).0
0. (4. 4.51)
. In fact we can find the Fourier transform of the ^function by noting that if in equation (4.4
Fig.2 s
0.10 as the width of the curve tends to zero.5
0.1 
y^^
2 X
1. The function f(X) = (2na2)~±exp(jX2/a2) for a = 1.4 \ \ 0. we have the Fourier transform of the 5function given as F(s) = 1. a — l\
91
0.3
0.10.
and its Fourier transforms F(s) = exp(27tVs 2 )
and 5(X)dX = 1.4.
from (4.14)) and with weight 1/ V where V = a*b Ac. 4.40) and (4. This result can be extended to three dimensions. The Fourier transform of this is F(s)=
which.a)Qxp(2nisX)dX <5(X)exp[27tis(X
The functions d(X).11 together with the corresponding Fourier transforms.
D
We can have a 5function located at a point other than the origin.a) (4. Then if we take cj)(X) = exp(2%isX) we have <5(Z)exp(2iusX)dX = exp(O) = 1. Thus if we have f(X) = 8(X .52). (4. b and c (as defined by the relationships (3.92
The Fourier transform
j:
d(X)<l)(X)dX = 4>(0)
(4.5 Diffraction and the Fourier transform In equation (2. Of particular interest is the set of ^functions defining a onedimensional lattice of spacing a where it will be noticed that the transform is another set of ^functions of weight I/a defining a lattice which is reciprocally related to the first.53)
then this represents a (5function at X = a. 4.56)
— cc 1= — oo
a set of ^functions at the nodes of the lattice which is reciprocal to that defined by a.(nia + n2b + n3c)].17) the amplitude of scattering from a distribution of n scatterers was found to be
. gives F(s) = exp(2nisa).55)
« i = — oo n2— — o o « 3 = — oo
The Fourier transform of equation (4. A set of (5functions located at the nodes of an infinite threedimensional lattice defined by the vectors a.41) which give the general relationship between any threedimensional function and its Fourier transform.(/ia* + fcb* + / c * ) ]
(4.
(4. S(X — a) and various composite functions derived from the ^function are illustrated schematically in fig.54)
j: j:
S(X .55) is
F s
( ) =4 I
f i = — oo k=
I
I 5[s . The function f(r) and F(s) are related by the equations (4. b and c may be represented by
f
W=
t
t
t
5[r .52)
which is a fairly obvious result.
F(s) 1
93
o
(5function at origin
x
0 F(s) = 1
HX)
Real part
F(s) Imaginary part
0
a
I
x
^ \ ) 1
(^function at X = a
\
\
/
F(s) =
0 
\
\
/
A' a
a a x <5functions at X = a and X = .5 Diffraction and the Fourier transform Fig.a
1 " ~a
1 a
1 a
Infinite array of ^functions of spacing a
Infinite array of ^functions of spacing I/a and weight I/a.
(4. Various composite functions involving ^functions and their Fourier transforms. If we have a continuous distribution of electron density p(r). 4. then we can imagine that our space is divided into a number of small
.D)]j is the amplitude of scattering at a distance D from thejth scatterer at an angle 26 with the incident radiation.57)
where [rj(20. expressed in electrons per unit volume.11.4.
60a)
By substituting u = X — v and then v = u we find also
. For a particular value X the formation of the function g(X — u) is also shown in fig.6 Convolution Let us consider two functions f(X) and g(X). 4.
J — oo
(4.40) that the inverse transformation is also valid and that p(r)= F(s) exp( .12(b).
. Then the integral (4. this is shown in fig. 4. it will be seen that this function may be produced from g(w) by (i) inversion about the point u = X and (ii) translation of this point to the origin. The convolution of these two functions is defined by c(X)= f(u)g(X . 4.60b)
The operation of convolution is represented by the symbol * and we may write c(X) = f(X)*g(X) = g(X)*f(X). In fig.00
c(X)=
g(u)f{X . (4.58) Jv where the integration is over the whole volume of space in which p(r) is nonzero. g(X — u) and their product f(w) g(X — u). The operation by which g(X — u) is produced from g(u) is referred to as folding g(w) about X. 4.2nisr) dv*
J V*
F(s)=
(4.u)du.60a) which defines c(X) is given by the shaded area. for the particular example we have considered. Thus the scattered amplitude from such a small volume will be p(r)dv times as much as that from an electron at the same position.12(d). (4.12(a).61)
To understand what is meant by the convolution process let us take the two functions f(w) and g(w) shown in fig.u)du.12(c) there are shown superimposed the function f(w).41) it is clear that F(s) is the Fourier transform of p(r). 4. The result of doing this for all values of X completely defines the function c(X) and.59)
where the integration is carried out over the entire volume of the reciprocal space in which s is defined. From this we find that the total scattered amplitude from the distribution of electron density p(r). If equation (4.58) is compared with equation (4.94
The Fourier transform
volumes dv within each of which there is an effective point charge p(r)dv electrons. We can also infer from equation (4. expressed as a fraction of that from a point electron at the origin.
(4. is given by p(r) exp(27iisr) di. The relationship between diffraction and Fouriertransform theory has now been established and the application of Fouriertransform ideas to the consideration of Xray diffraction will be found to be most useful.
4. (d) The complete function c(X) = f(X)*g(X). (c) The derivation of f(u)g(X .4. (a) Functions f(w) and g(u). Add the resultant curves to obtain c(X).6
Convolution
95
(a)
\%(Xu)
0 (b)
X
c(X) =
Fig. {b) The function g(X .u). Plot g(w)<52ln with origin at centre of nth strip for all n. is to express c(X) as a summation by
. The steps in the process are:
(i) (ii) (iii) (iv)
Divide f(w) into strips of width du.12.un)du c(X) = f f(u)g(X . which can be used to determine the whole function c(X) at once.
.u). Find the areas of the strips <52In = f(un)du.
Another method. The shaded area gives c(X) = f(X)*g{X).u)du = du—>0 J where the summation is for the n values of un at the centres of the strips of width du which cover the nonzero ranges of the function f(w).
12(4
85 90 63
I
U
(a)
f{uun)g(un)Su
\ U2
"3 U5 "7 U 4 U6
. In (b) the eight weighted and displaced images of f(w) are shown and in (c) they are added to give the total function c(X). from equation (4. 4. for convenience. The proof of this result is fairly straightforward and is now given.w) exp{27iis(X . which is of particular interest to crystallographers. (a) g(w) divided into strips of width 3u.96
The Fourier transform
This process is illustrated in fig. the convolution theorem. 4.13.u)}dX
J
\du.63)
This may be rewritten as
i=
JU= GO
g(w) exp(2jisw)
L J 00
f(X . (b) The superposition of the functions f(w .62)
C(s) =
f(X . There is a theorem. (c) The sum of the superimposed functions rescaled to agree with fig.Mjg(Mj<5w. In (a) there is shown the division of g(w) into eight strips and the relative areas are given.60b) gives
% oo / i% oo
r
J c
c(X) exp(27iisZ) dX
(4.
J — oo J — oo
(4. (4.64)
Fig.u)g(u) exp(27iisX) du dX. This states that if there are two functions f(X) and g(X) whose Fourier transforms are F(s) and G(s) then the Fourier transform of c(X) = f(X)*g(X) is C(s) = F(s)G(s).13 where. 4.36) we have C(s)
which. the roles of the functions have been reversed. From equation (4.
52) since g(u)f(X . This can also be found by applying the expression (4.14 where the function g(X) is a spiky function of very small width.
(4.6
Convolution
97
The integral in the square brackets is independent of u (substitute y = x — u) and equals F(s) and it follows that C(5) = ¥(s)G(s).14. If the function g(X) is normalized to have unit area under the curve then the convolution c(X) differs very little from f(X). 4.u)du 8(u)f(X . We can express this as F(s)G(s) exp( .65)
It may be deduced from the reciprocal nature of Fourier transforms that c(X) is the transform of C(s) and is also the transform of the product F(s)G(s).
f(X)
(X) = f ( A > g m
. or (4.4.2niXs) ds = f(X)*g(X).67)
•j:
Fig. (4. 4.u)du = f(X). is little different from f(X). If we take this process to the limit so that g(X) = 8(X) then we should find that c(X) = f(X). Thus we have the general result that the Fourier transform of a product of functions is the convolution of the transforms of the individual functions.68)
r
J c
f(X)g(X) exp(27iiXs) dX = F(s)*G(s). (4. The convolution of f(X) and g{X). a spiky function with unit area under the curve.66)
Let us look again at the process of convolution and in particular the case shown in fig.
98
The Fourier
transform
Extending the application of equation (4.52) we can determine the convolution of f(X) with 5(X  a). This is c(X)= d(u  a)f(X  u) du
J — oo
= f(Xa) and this result is illustrated in fig. 4.15.
Fig. 4.15. The convolution of with a ^function not at the origin.
c(X)
(4.69)
0 a
This process is taken another stage by considering the convolution of f(X) with an infinite linear array of 8 functions given by
g(X)= X d(Xna).
n = — oo
(4.70)
The convolution is given by
c(X)= £
f(Xna)
(4.71)
and c(X) is a periodic function of spacing a. What is more if f(X) is completely defined in the range 0 ^ X < a (or any range of width a) then a unit of c(X) is identical in appearance with f(X) in the defined range. This point is illustrated in fig. 4.16. Thus it may be seen that any periodic pattern of spacing a may be considered as the convolution of one unit of the pattern with a (5function at the nodes of a lattice of spacing a. The result may be extended to three dimensions. A threedimensional periodic function may be considered as the convolution of one unit of the pattern, contained within the parallelepiped defined by the vectors a, b and c, with a set of
Fig. 4.16. The convolution of f(X) with a ^function array.
4.8
The electrondensity equation
99
^functions at the nodes of a threedimensional lattice defined by the vectors a, b and c. In particular, the electron density within a crystal may be considered as the convolution of the density within one unit cell with the threedimensional realspace lattice of spacing a, b and c. 4.7 Diffraction by a periodic distribution In §4.5 the relationship between diffraction and the Fourier transform was established and this is exemplified by equations (4.58) and (4.59). The scattered amplitude, as a fraction of that scattered by a point electron, is the Fourier transform of the electron density. Thus, from equation (4.65) and the periodic nature of the electron density in the crystal, the scattered amplitude is seen to be the product of the transform of the electron density within one unit cell of the crystal with the transform of a set of ^functions at the nodes of a unitcell lattice which covers the volume of the crystal. The transform of this set of (5functions will, for all practical purposes, be the same as the transform of an infinite set  that is another set of ^functions at the nodes of the reciprocal lattice. Thus the diffracted amplitude for the whole crystal can be thought of as the Fourier transform of the electron density in one unit cell of the crystal, F(s), sampled at points of the reciprocal lattice, s = /ia* + /cb* + /c*. Since the weight associated with each of the reciprocallattice 5function points is 1/K(see equation (4.56)) the scattered amplitude corresponding to the point (hkl) of the reciprocal lattice is given by (l/V)Fhkl where the reciprocallattice vector is now indicated by the triplet of integers (we write F(s) = Fhkl). If the diffracted amplitudes are expressed as a fraction of that from an array of point electrons at the chosen origins then F ^ is the structure factor as defined in § 3.5. The structure factor is also given by equation (4.58) if the integration is carried out over the volume of the unit cell and if p(r) is expressed in electron units per unit volume. 4.8 The electrondensity equation In equation (4.59) an expression has been given for the electron density in a crystal in terms of the scattering amplitudes F(s) expressed as a fraction of the scattering from a point electron. For the whole crystal, assumed to be infinite in extent, F(s) exists only at reciprocal lattice points and has weight at these points equal to (l/V)Fhkl. Thus we may take equation (4.71),
p(r) = F(s) exp( — 2TUST) dt;*,
J V*
and replace it by P« = i
h=
I
— oo k=
I
I
— ao 1= — oo
F»ki exp(  2irisr).
(4.72)
In this equation if Fhkl is the normal structure factor then p(r) will be the electron density expressed in electrons per unit volume. The electron
100
The Fourier transform
density is completely defined in one unit cell; substituting r = xa + yb + zc and s = /m* + fcb* + lc* we find
=± t
h=
i
t
— co 1= — oo
FhklQxp{2ni(hx
+ ky + lz)}
(4.73)
— ao k=
where x, y and z are the fractional coordinates of a point in the unit cell. The electrondensity equation can take different forms depending on the space group of the crystal structure. For example with a centre of symmetry at the origin all the F's are real and, since FJ^J = Fhkh we find
^ t
t
t
FhklCos{2n(hx + ky + lz)}.
(4.74)
h = — o o f c = — o o i = — oo
The various forms of the structurefactor equation (3.41) and the electrondensity equation are given for each of the 230 space groups in the International Tables for Xray Crystallography. Some examples of this spacegroup dependence will be given later, in chapter 7, where it is shown that the distribution of the values of  F  or \F\2 can give spacegroup information. The structurefactor equation (4.58), written in terms of indices of reflection (hkl) and fractional coordinates within the unit cell (xyz), is
hkl
Jx = Jy = O Jz = C For the class0 of structure factors for which / = 0
'J IT
1
p(xyz) exp{2iii(hx + ky f /z)}dxdydz.
(4.75)
r1 r 1 r r1
i
p(xyz)dz exp{27ti(/*x + ky)}dxdy. (4.76)
Fhk0 = V \
To attach a meaning to the integral in square brackets in equation (4.76) consider the total electron content in the fine filament parallel to the z axis in the unit cell shown in fig. 4.17. The crosssection of this filament in the xy plane is a and \// is the angle between the z axis and the normal to the xy plane. The electron content of the small shaded volume shown is p(xyz)a cos \\t cdz and hence the total electron content in the filament is p(xyz)dz. If we now imagine that we project all the electron content of the unit cell along z on to the xy plane then the electron density at the point (xy), expressed as electrons per unit area, will clearly be given by
, i
•J
p(xyz)dz.
(4.77)
From equations Jo (4.77) and (4.76) we find
4.8
The electrondensity equation
101
—f I"
Jx=OJy=O
pp(xy) Qxp{2ni(hx + ky)}dxdy exp{27ii(/ix + ky)}dxdy,
(4.78)
p(xy)
where 91 is the area of the xy plane of the unit cell. It can be seen that Fhk0 is the Fourier transform of the twodimensional function, the projected electron density pp(xy). Consequently, by analogy with our previous results, we may write
hkO
where da is an element of area in the xy plane and
1 00
I
pp(xy) exp{2ni(hx + ky)}da
(4.79)
Z
** h=
— oo k= — oo
F
hkoQXP{  2ni(hx + ky)}.
(4.80)
The Xray crystallographer frequently wishes to compute electron density since this gives a picture of the atomic arrangement in the crystal. At the resolution corresponding to the Xray wavelengths usually used, the electron density has its highest value at the location of the atomic centre and the separate atoms of the structure are usually well resolved. The electrondensity equation (4.73) contains imaginary quantities on the righthand side but of course p(xyz) is a real quantity. In § 3.5 the structure factor was given as F = where
Am=
A
hki^ ~
lB
hkl
N
:os{2it(/i*i + kyj +
(4.81a)
and
Fig. 4.17. Electron density projected on to the xy plane.
/
102
N
B
The Fourier transform
hki = Z fJsin{27c(focJ. + kyj + /z,.)}.
(4.81b)
There is also a phase angle, (j)hkb associated with each structure factor given by Bhkl tan0^ = — . From the equations (4.81) it can be seen that l^lhl^il and <kn= j^ and Bhkl = F fcWsin0fcW so that from equation (4.81) we find Fhkl=\Fhkl\exp(i(j)hkl). (4.86) (4.85) <t>mI cos (b (4.83) (4 84) (4.82)
In addition from fig. 3.14(a) we see that = \ j?
Let us now consider the contributions to the summation on the righthand side of equation (4.73) of two terms of indices (hkl) and (hkl). This will be Fhu
ex
P{ ~~ 2jii(/zx + ky + lz)} + F^j exp{2ni(hx + ky + lz)}
=  Fhkl  exp{ — 2ni(hx + ky + /z) + i ^ j } +  Fm  exp{27ii(/zx + /cy + lz) + i</>M/}
= 21 i 7 ^  COS{2TI(/IX + ky 4 /z) — 0^k/} =  .FMj  COS{2TI(/ZX + /cy + /z) — 0 M J
+  i ^ l COS{2TI(/ZX + fcy + lz) — ^fcy}.
(4.87)
From the form of equation (4.87) it follows that one may rewrite equation (4.73) as
1 oo oo
\ ^
oo
V ^ I r ' I ( f \ / 1
i f
Z
i
l
\
I
" ^
/
A
O
O \
\ = Z_j 00 —
i
\ \ r \ PnQ< /1Tl/iV  +  K A 7  4  / 7 I _ tlKl I I V ' J ' / = / —/ 00 I
/7) > TtlKl)
id. X X l V /
The corresponding equation for computing projected electron density becomes
PP(^) = W £
£
Ffctocos{27i(/Ix + /cy)</)MO}.
(4.89)
"^ fi =  oo k =  oo
In equation (4.88) can be seen the nub of the problem of determining crystal structures. The structure amplitudes, the  F 's, can be derived from the observed intensities of Xray reflections but the phase angles </> cannot
4.8
The electrondensity equation
103
Fig. 4.18. The zaxis projection of Dxylose. The dashed contour is at 3eA~ 2 and the others at intervals of 2ek~2. The positions of carbon and oxygen atoms are shown by the line framework. (From Woolfson, 1958.)
be directly determined. If the phases of the structure factors are known then the crystal structure is known, for one can compute the electron density from equation (4.88) and the atomic centres are located at peaks of electron density. The electron density is usually computed at the points of a uniform grid covering the unit cell and contours of constant electron density may then be drawn. An example of such a contour map is given in fig. 4.18 which shows a projection of the electron density of Dxylose. It will be noticed that the carbon (c) and oxygen (o) atoms may all be clearly seen but no trace of the hydrogen atoms is evident. The contribution of the single electron of the rather diffuse hydrogen atom has been swamped by the contributions of the heavier atoms. However, with careful experimental measurements and special computing techniques hydrogen atoms can be detected and we shall return later to this problem. It is more difficult to present an electrondensity map in three dimensions. This can be done by computing twodimensional sections keeping one coordinate constant. These can be examined sectionbysection or reproduced on transparent material (glass or plastic) and stacked so as to get a direct threedimensional view of the electron density. The advent of modern computer graphics has given the crystallographer very powerful ways of examining and utilizing threedimensional maps. On the computer screen there can be projected stereoscopic pairs of images of surfaces of constant electron density, reproduced by cagelike structures, and these are accompanied by viewing glasses. In one system the stereo images are projected on the screen alternately and glasses worn by the viewer are equipped with optoelectronic devices synchronized with what is happening on the screen so that the left and right eye see different images. If the switching rate is high enough, greater than about 30 Hz, then there will be no flicker and a constant threedimensional image will be seen. With a threedimensional view of the electron density available it is then possible
104
The Fourier transform
to fit a structure to it and the computer graphics packages provide the means to fit ballandspoke, or other, models to it. To give an idea of the power of a stereoscopic image there is shown infig.4.19 a stereo view of some overlapping molecules of 4(2carboxyvinyl)acyanocinnamic acid dimethyl ester. By holding the figure at a comfortable distance many readers will be able to fuse the two images to obtain a stereoview of the molecules.
Fig. 4.19. Stereopair of overlapping molecules of 4(2carboxyvinyl)acyanocinnamic acid dimethyl ester (Nakanishi & Sarada, 1978).
In appendix IV there is provided a program, FOUR2, for computing twodimensional electron density. This will accept the output of the program STRUCFAC and can be used to do some of the problems at the end of this chapter. Since STRUCFAC produces a whole semicircle of data in reciprocal space the program FOUR2 is simplified by being able to treat the space group as pi. The most efficient programs for carrying out this kind of calculation employ the socalled Fast Fourier Transform algorithm. However, although FOUR2 is less sophisticated in its approach it does have some efficient features such as factorizing the calculation in the x and y directions and using some of the symmetry of cosine and sine functions. Transforming equation (4.89), using the results (4.84) and (4.85) applied to the twodimensional structure factors we find
Bs(/c,x)}cos(27i/c3;)
X{B c (/c,x)  A%(k, where
Ac(k, x) = Y Ahko COS(2TI/DC)
h
(4.90)
(4.91a)
(4.91b)
4.8
The electrondensity equation
105
Bc(k,x) =
YJBhk0cos(2nhx)
(4.91c)
Bs(k,x)
=YJBhkOsin(2nhx).
(4.9 Id)
The summations over h only need to be done for x = 0 to 0.5, the remainder of the range being found from the symmetry of the cosine and sine functions. Similarly, for each value of x, the two summations over k need only be done for y = 0 to 0.5 and then combined for the whole range of y using symmetry again. One of the first decisions to be made when computing an electrondensity map is the grid spacing to be used along each of the unitcell axes. If the grid is too fine a great deal of needless computing is done whereas if the grid is too coarse then interpolation between grid points will be uncertain. The rule which gives the best interval is to take, along the a axis for example, intervals of £/imax where hmax is the maximum h index being included in the summation. Thus, if hmax = 14, intervals of jg are indicated although, in practice, one would take some slightly different and more convenient interval  for example j$ or ^ . The output of FOUR2 is scaled values of projected electron density at grid points. To visualize the actual projected density, contours of constant projected density can be drawn. An example of part of a map with density contours is shown in fig. 4.20 and should be used as a guide to the reader in drawing contours for Problem 4.7 which follows.
Fig. 4.20. Part of the projected electron density produced as a solution of Problem 4.7 with contours drawn at the level of 20 and 30 in the arbitrary scaled units of projected density produced by the program FOUR2.
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5 9. 4.0 9.80 0.30 0.40 0. 4.0 31.5 37.5 Determine the Fourier transform of f(x) = (27i)~iexp[ — i(x — 2) 2 ].35 0.4 Find by an analytical approach the convolution of f(x) = sin(27ix).
. (ii) f(x)=l\x\9l^x> 1 = 0.05 0.20 0.95
Fig. 4. O^x^ 1 x < 0 or x > 1
and = 0.1 (or given in the solution on page 374) reconstruct the function f(x) by use of the program FOUR1 given in appendix II.106
The Fourier transform
Problems to Chapter 4 4.50 0.0 22. 4.= hkl
r
F = hkl
r
F = F = hkl * hkl
1
F hk I'
Derive a modified form of the electrondensity equation for this space group. = 0. 4. Compare the answer you get by the straightforward method with that found by considering f(x) as the convolution of g(x) = (27i)"*exp( .21 both graphically and in tabulated form use the program SIMP1 to compute the Fourier coefficients Ah and Bh for h = 0 to 5.70 0. x>l.5 29.0 11.0 7. Periodic function for Problem 4.3 Find the Fourier transforms of the functions a^x^a (i) f(x) = e. 4.75 0.55 0.\x2) with h(x) = d(x .0 8.0 30.5
0.15 0.60 0.  x  > a. f(x) = 0. Over what portion of the unit cell must p(xyz) be computed in order to completely determine the structure?
X
f(x) 20.00 0.90 0.fcx .25 0.0 13.1 For the periodic function shown in fig.1.0 16.65 0.0 36. Ix> i
4.5
X
fW
16.2).85 0.5 34.5 7.5 12.5 26.21.45
0.2 With the coefficients found in Problem 4.6 For the space group Pmmm the following relationships exist between structure factors:
r * hkl
i7_ hkl
r
rp hkl
p
r
.0 23.10 0.
7 Using the output file containing the structure factors generated in Problem 3.4 (p.
. 74) calculate a projected electrondensity map using the program FOUR2 given in appendix IV. Remember that the name of the input datafilefor FOUR2 must be the same as that of the output file of STRUCFAC.Problems to Chapter 4
107
4.
Rotation axis A
Path of end of vector s. If. As the crystal rotates about OA so does the vector s and the angle between s and — S o decreases until the
Fig. and s continuously changes. Since the vector — s corresponds to the reflection with indices hk T which is.1
The conditions for diffraction to occur
The basic conditions under which Xray diffraction occurs from a crystal were given in § 3.2. In fig. a diffracted beam results. 5.44)]. where 6 is the Bragg angle. we also note its motion. The angle between s and — § 0 is a and that between — s and — S o is n — a. In fig. the magnitude of this vector is (2 sin 0)11.1 there is depicted a crystal.1. 5. The range of angles between s and — § 0 as the crystal rotates may be followed in fig. in general. If the incident Xrays make an angle jpi — 6 with s then a diffracted beam is produced coplanar with the incident beam and s. 10. We recall that there is associated with each set of indices a reciprocallattice vector s = ha* + /cb* + Zc*. if ever the angle \// between — § 0 and s becomes %n — 6. 5. Let us see how the crystal can be systematically moved to a position for a particular diffracted beam to be produced. As it does so the angle between the direction of the incident beam. The motion of the scattering vector s as the crystal rotates.5 Experimental collection of diffraction data
5. and its direction is normal to the Bragg reflecting planes. equivalent to the hkl reflection [see equation (3. We denote the direction of the incident beam by the vector § 0 and. an incident beam of Xrays and the appropriate reciprocallattice vector s. the crystal is rotated about the axis OA perpendicular to 10 then the whole reciprocal lattice rotates with it and the end of the vector s will move along the indicated circular path.
108
.3. 5.2(a) is one extreme position where the vector s points in the same general direction as the incident beam and is in the plane defined by 10A. for example.
7
The conditions for diffraction to occur
109
Fig. 5. 5. The angle between — s and — S o is always the supplement of that made by s with — § 0 . It is
. The variation of these angles as the crystal is rotated through 2it is plotted in fig. Further rotation of the crystal and of s reduces the angle between s and — S o until finally s is again in the plane defined by 10A and the angle between s and — S o is equal to n — a [fig. (a) One extreme position of the scattering vector where it makes the minimum angle with the direction of the incident beam.5. Paihofcnd ofs
Perpendicular planes containing all directions shown
ib)
position shown in fig.2(d) for a = 150°. (b) The scattering vector making an angle rc/2 with the incident beam.2(c)].2(b) is reached when the angle equals %n. 5.
Plane containing all directions shown
CL.2. 5.
« = 50°i i
i
2
i
i
I
30
60
90
120
150
180 id)
210
240
270
300
330
360°
Angle of rotation of crystal from position shown in (a)
clear that as long as ^K — 9 is greater than 30 ° (71 — a in general) there are two positions of the crystal when diffracted beams are produced corresponding to the vector s and two more positions (71 removed from the others) when diffracted beams are produced corresponding to the vector — s.110
Fig. however. where the axis of rotation of the crystal is perpendicular to the direction of the incident beam.s. is a particularly simple one to analyse.§„ /
^^^^
_
^ — I
hkl
hkl reflections \
i I i
reflection ^ i
s
. There is an interesting geometrical way of looking at the diffraction condition which can be very helpful in considering more general axes of rotation. The situation we have considered here. (d) The variation of the angle between s and —S o and —s and —S o as the crystal rotates.s and .
. If.^ 80 \ ^ ^^\^ / 60 ^ 71 40 — 9 = 20° *_u
1
Position shown in (c)
i
•
Angle between . 5.Angle between 160 L s and . ^71 — 6 < 30° then no diffracted beams will be produced corresponding to either s or . (com) (c) Second extreme position of the scattering vector where it makes the maximum angle with the direction of the incident beam.
Experimental collection of diffraction data
Plane containing all directions shown
» o £ c o C
c
g>
•*
Position shown in (b) 180 ° .S o 140 »20 hkl ^S^VJ^ 100 _ reflection J^C.2(d). These points are illustrated by drawing the lines corresponding to ^71 — 6 equal to 50° and 20° in fig.2. 5.
Infig. Hence CP is parallel to OD and gives the direction of the diffracted beam. If C is^the centre of the circle then CP equals CO and therefore C^PO equals POC and is also equal to POD.4(a) the locus of the end of the vector s as the crystal is rotated is shown and this cuts the sphere at P and Q. The sphere of reflection.10 represents the direction of the incident beam and a sphere is drawn which passes through the crystal at 0. The diffracted beam must be along OD which makes an angle %K — 6 with OP. 5.3. The condition for a diffracted beam to be produced is now seen to be that the end of the scattering vector s. When the tip of the vector s touches the sphere the corresponding reflection is produced. The direction of the diffracted beam can also be found from this geometrical construction. By rotation of the crystal about some axis any diffracted beam can be produced as long as the end of the scattering vector can be made to lie on the surface of the sphere. 5A(b) a crosssection of the sphere of reflection in the plane IOP is shown. which is attached to the crystal at O.7
The conditions for diffraction to occur
111
Infig. has 10 as a diameter and is of radius 1/L Let us assume that there is a reciprocallattice vector s whose end just touches the sphere at P.5. should just touch the surface of the sphere. Since 10 is a diameter the angle IPO is ^it and consequently 10P (= (j>) is related to s by
5 =
X '
(5. When the crystal is in such a position that the vector s is along OP or OQ a diffracted beam is produced with indices hkl appropriate to the vector s. One can now follow the process of rotating the crystal about an axis not perpendicular to the incident beam by using the concept of the sphere of reflection. The sphere of radius 1/1 which is defined above is known as the sphere of reflection or Ewald sphere.5.2)
But when the angle between the incident beam (actually with reversed direction) and the scattering vector s is ^rc — 6 a diffracted beam is produced.
Sphere of reflection
Incident beam direction
•
.3.5.1)
However since s = (2sin0)//l this gives
(5. The condition for this is that
Fig. In fig.
hk 7) may not occur (as in fig. {b) CP gives the direction of the diffracted beam. The powder is usually formed into the shape of a cylinder either by containing it in a plastic or thinwalled glass container or by mixing the powder with an adhesive material and shaping it before it
.112
Fig. 5.4. Axis of ^rotation of crystal
Sphere of reflection
Experimental collection of diffraction data
Diffracted beam direction
ol \7 rotation £"\ of crystal
^
ui
ui)
(5. The sphere of radius 2/2. 5.3) where 2/1 is the diameter of the sphere of reflection.4(c). It should be noticed that the reflection corresponding to — s (i. 5A(d)).3) is known as the limiting sphere.
5. If a possible reflection is not produced by rotation of the crystal about some particular axis then the situation must be like that shown in fig. 5.2
The powder camera
Frequently it is necessary or convenient to diffract Xrays from a specimen in the form of a fine powder.e. (d) s does not but — s does cut the sphere of reflection as the crystal is rotated. (c) Neither s nor — s cuts the sphere of reflection as the crystal is rotated.4(c)) or may occur (as in fig. centred on O within which a vector s must lie in order to satisfy equation (5. The end of the vector s describes a circular path which does not intersect the sphere. With these ideas at our disposal we can now consider the various types of apparatus by which Xray diffraction data may be collected. (a) As the crystal rotates the end of the scattering vector touches the sphere of reflection at P and Q.
6(c). The locus of the diffracted beams for a given hkl from all the crystallites of a powder specimen. If the powder is fairly coarse so that the crystallites are larger in size and fewer in number then the diffraction lines will not be uniform but tend to be rather spotty as infig. A beam of monochromatic Xrays is collimated by passing it through afinetube (or through a slit system) and falls on the specimen. that a crystal will reflect over a range of positions near to that corresponding to the Bragg angle so that the number of crystallites giving a particular reflection might be quite high.5.5. this film comes from a camera for which both the incident and straightthrough beam pass through holes in the film. This can be overcome by rotating the specimen as then many more of the crystallites contribute to each of the diffraction lines.6(c) have been taken with and without rotation of the specimen. the locus of all such diffracted beams is a cone of semiangle 29 with apex at the specimen. as is shown infig. which is not diffracted.that is to say. The volume of the individual crystallites in a typical powder might be about (5 \imf so that in a specimen of total volume (1 mm)3 the total number of crystallites will be of order 107.5. Such a specimen will be a myriad of tiny crystallites arranged in random orientations. It should be mentioned here.6(fo) andfig. For a particular reflection there will be a large number of the crystallites in a diffracting position . is contained in a black paper envelope to protect it from the light and is wrapped round the inside of the cylindrical camera as shown.5. 5. The diffraction pattern is recorded by thefilmas the intersection of cones similar to the one shown infig. Let us examine what happens when a monochromatic Xray beam falls on such a specimen.5. respectively. with their scattering vectors for this reflection making an angle %n — 6 (or very near) with the reversed direction of the incident beam. 5. The direct beam.6(a). Thefilmsshown infig. Any crystallite giving the reflection will produce a diffracted beam making an angle 20 with the incident beam and.When thefilmis straightened out it appears as in fig.5 with thefilm. 5. Powder cameras vary somewhat in their design but the arrangement of components for a fairly typical type of camera is shown schematically in fig.5.6(b). passes through a hole cut in thefilmand is absorbed by a beam trap. Thefilm.5. Frequently the data required by the Xray crystallographer are a
Fig.
Diffracted beams from different crystallites
Direct beam
.5.2
The powder camera
113
dries hard. This is necessary as otherwise this radiation would be scattered by thefilmand fog it over a considerable area thereby obscuring some of the diffraction pattern at low Bragg angles.in the form of a strip. the improvement in appearance produced by rotation is evident. anticipating some of the results of the next chapter.
5.6.Motor for roiaiing specimen
Beam (rap
Film
I
Fig. (c) A powder photograph without rotation of the specimen. (6) A powder photograph with rotation of the specimen.
(c)
. (a) A typical arrangement for a powder photograph.
The incident highly monochromatic Xray beam is very well collimated which means that the angular spread of the powder lines is reduced as much as possible.5) Thus the number of reciprocallattice points within the limiting sphere will be ^=VQV. as shown infig. The diffracted radiation is measured by some form of Xray photon counter (see § 5.5. 1. e. (5. To get some idea of this problem let us consider how many reflections might be obtained for a crystal structure with a moderatesized unit cell say of volume 500 A3. Many materials of great potential technological importance. new technology and new theory has given the powder method a fresh lease of life. 1. for some reason. In fact many diffracted beams will have similar 26 values (similar magnitudes of s). may sometimes only be obtained in the form of fine powders. diffracted beams may overlap completely.7(a).
.54 A. is by means of the diffraction angle 29.6)
If the wavelength of the Xrays is that for Cu Ka radiation.7(b). not only does this give a problem of identification but. The resultant intensity profile.5.g.2
The powder camera
115
complete set of diffracted intensities together with the corresponding indices of reflection hkl From a powder photograph the only way of determining the indices of a diffraction line.7) with a veryfineentrance slit which is slowly rotated about the central axis of the instrument. from equation (3. more important still. then the total number of reciprocallattice points equals / 2 \3 — — x 500=^=4000. assuming that one knows the unitcell parameters. hightemperature superconductors. Their powder diffraction patterns may be collected with a powder diffractometer. A combination of new needs. sixfold or eightfold coincidences of equivalent reflections but nevertheless it can be seen that for all but the smallest unit cells the data consist of a large number of independent items.For space groups of higher symmetry there may be fourfold.54y The number of independent reflections will be lower than this . If two or more beams fall on top of one another then it is impossible to ascertain the intensities of the individual components of the composite line and valuable information is lost. The total volume within the limiting sphere is
and the volume of the reciprocal unit cell will be. K* = (500A 3 )\ (5.for example reflections related by Friedel's law have the same Bragg angle and the same intensity and always overlap on the powderfilm. a schematic representation of which is shown infig.5.26). impracticable. The overlap problem is so severe that powder photographs are normally not used for the purposes of collecting data for structure determination unless the alternative of obtaining data from a single crystal is.
the converse process to convolution as described in § 4.5. these are restricted to fairly simple compounds where the overlap is not too severe.12. (a) A schematic representation of a powder diffractometer. There have been a number of successful computerbased methods for carrying out the deconvolution of powder patterns but. There are some deconvolution problems which cannot be solved by any form of analysis.8(c) and some model shapefig.5.6 and illustrated in fig. The convolution of the two gives the profile shown infig.5. Specimen \
Experimental collection of diffraction data
Collimator
Counter
• Xrays
Motion of counter (a) 10000 9000 8000 7000 2 6000  5000 u 4000 3000 2000 1000 0
uu
10 20 30 40 50 60 20 (b) 70
•J. In fig. 4.1
80 90 100 110 120
can be drawn by a pen recorder and also stored in digital form for subsequent computer analysis.5. (b) A typical powderdiffractometer trace. then it should be possible. 5.1. together with the fine entrance slit of the counter ensures high resolution in the diffraction pattern. albeit of different intensities and. 5. Although the incident Xray beam is well collimated and highly monochromatic which.L . The deconvolution problem is to find fig. This is because the small crystallites of which the powder specimen is formed will diffract over some small angular region around the Bragg angle.7. if this shape is known.8(a) there is represented an idealized powder diffraction pattern of ^function powder lines with different intensities and infig. The theoretical basis of this line spread will be found in equation (3. at least in principle.8(ft). 5.8(a) givenfig. The problem is one of deconvolution. However the crosssections of the diffraction lines will all be of the same shape.8(&) the standard shape of each line.29) that
. For example for a cubic crystal with cell dimension a it is found from equation (3.116
Fig. on the whole.ill 1. to unravel the total intensity pattern as a sum of individual singleline contributions.3) which gives the shape of diffraction pattern from afinitearray of scatterers and the theory of this is enlarged in §6.8(c). there is nevertheless a considerable overlap of diffraction lines.
For a cubic crystal. Most commercial powder diffractometers will be provided with a range of software for deconvoluting the diffraction patterns and also for carrying out Rietveld refinement. This will occur with pairs of indices [(550). (b) The shape of an isolated powder line. lattice parameters and lineprofile shapes which are all modified to give the best possible fit with the observed powder pattern. Powder cameras are often used for the identification of materials. although this information can be used subsequently in the process of structure refinement. simple permutations of indices just give equivalent reflections which do not present a problem for powder diffraction analysis.5. The number of parameters which could be accommodated by this method is of the order of 100. (c) The actual powder pattern . An important contribution to the use of powder patterns was made by H. However.4) for refining atomic positions.2
The powder camera
117
Fig. (710)] and [(410). He described a mathematical leastsquares procedure (see § 9.the convolution of (a) and (by
10°
20°
10°
20 (c)
20°
4sin 2 0
= Ah2 + k2
n
(5. For
. to refine crystal structures.8. thermal vibration parameters (§6. M. Rietveld in 1967 who showed how it was possible to use the whole pattern. in general the number of exactly overlapping powder lines is usually sufficiently small for the crystal structure analysis to be completed without using the information from them. (443)]. (a) An idealized b function powder pattern. 5. including the overlapped lines. (322)] and the triple of indices [(621). (540).7)
Thus any combinations of Miller indices giving the same values of h2 + k2 +1 2 will give exactly overlapping powder lines which no deconvolution process can disentangle. which means that it can only be applied to comparatively simple structures.5).
The relative intensities of powder lines may depend on the shape of the crystallites in the specimen and this may differ from sample to sample. Powder photographs can also be used to identify completely unknown materials. A large number of materials of all types have the major features of their Xray powder patterns listed in a set of ordered cards known as the Powder Diffraction File.9.9.5. It may be necessary to ascertain the form of alumina being produced under different sets of conditions and the most convenient way of doing this is by taking Xray powder photographs.118
Experimental collection of diffraction data
example in an industrial process one of the products may be alumina which can exist in a number of different forms. The crystal is glued to a suitable
Fig. 5.3
The oscillation camera The simplest type of singlecrystal camera in common use is the oscillation camera shown schematically infig. A typical arrangement for an oscillation camera. The information on one of the cards includes the dspacings (which can be derived from the Bragg angle by equation (3.37)) and relative intensities of the strongest lines of the pattern.
5.
Film
Collimator — Goniometer head
Housing for rotating and oscillating mechanism
. If the material to be identified is a mixture of two or more materials in unknown proportions then identification of the components can often be extremely tedious. if not absolutely impossible. The strongest three lines are displayed at the top of each card and they are listed in the order of the dspacings of their strongest lines. Consequently identification of materials by the Powder Diffraction File is sometimes not straightforward and requires some patience and ingenuity. These can be compared with a set of photographs covering the complete range of forms of alumina and identification would usually be straightforward and unambiguous.
5. As the crystal rotates so the Xray reflections are produced one by one and are recorded by thefilm. we canfindthe length of the a axis of the unit cell.wrapped in black paper to protect it from the light. a fine glass fibre) and this is attached to the rotatable goniometer head.12). say the a direction. we know that all the diffracted beams will lie along a series of cones coaxial with the a axis. at twothirds its natural size. the size of the crystal and the spread in wavelengths of the Xrays. For normal incidence \jja 0 = %n and the first of the Laue equations becomes acosi//a = hi.542 and 1.5. The Xray beam is collimated and is perpendicular to the axis of rotation of the crystal.10.5. Adjustments of the arcs and slides enable one to set a prominent axis of the crystal coincident with the axis of rotation of the goniometer head.3 mm and the reader may.11 shows.When thefilmis developed and straightened out the diffraction spots are found to lie on a series of straight lines which are the locus of the intersection of the cones of diffraction with the film (see fig. is mounted inside a metal cylinder which.10). the plane perpendicular to the a axis containing the incident beam and the cones corresponding to other values of h are shown infig. Thefilm. From the distances between these straight lines. The goniometer head consists of two perpendicular sets of arcs for rotating the crystal and two perpendicular slides for lateral motion of the crystal. As the crystal is rotated about the a axis then.10)
Fig. confirm that the unitcell axis about which the crystal was rotated was of length 11. from the Laue equations (3. a reproduction of a photograph taken on an oscillation camera.
. The camera diameter (2r) was 57. This prominent axis may be one of the main edges of the crystal so that the axis can be set quite accurately by observation through the microscope which is usually attached to the camera.0 A. (5. in position in the camera.389 A may be seen. by direct measurements on the film. The Xrays used were unfiltered copper radiation and the layer lines for both Cu Ka and Cu K3 radiation (see §5. is coaxial with the rotation axis.8)
The 'cone' corresponding to h — 0 is.3
The oscillation camera
119
support (e.8) we may eliminate \jja to obtain a (r2 + dl)* hV (5. called layer lines.5. We shall assume for now that a prominent axis has been so set and that it corresponds to the direction of one of the edges of the unit cell. 5.g.8) of wavelengths 1. There are errors of measurement of distances on the film which are aggravated by thefinitesize of the spots due to the divergence of the Xray beam. From a rotating crystal photograph the unitcell dimension may usually be found with an accuracy of about 1%.10 it is clear that if the camera radius is r then the distance of the line with index h from that with h = 0 is given by
By the use of equation (5. for normal incidence. Fromfig.
The diffraction cones with the incident beam normal to the oscillation axis which is also a prominent cell
Experimental collection of diffraction data
h= 4
Fig. 5. A typical oscillation photograph (twothirds natural size).11.
. 5.10.120 Fig.
M
• .
5. The crystal can also be accurately set about an axis on an oscillation camera and then transferred on its goniometer head to one of the more elaborate cameras which are described later. The effect of missetting of the crystal in
. 10 or 15° being the usual ranges. Although the separation of the diffraction data into layers makes the situation better than for powder photographs there is still nearly always some overlap of diffraction spots. In fact one rarely takes rotation photographs where the crystal rotates continuously.12. The cams are so designed that. apart from the inevitable discontinuities at the ends of the range. 5. the angular speed is uniform.
/
•
Diametral plane containing incident beam Zero layer of reciprocal lattice
Diffracted beam
Prominent axis of crystal
(a)
\h\
Changes in the physical dimensions of thefilmswhen they are processed are also important sources of error. (a) Location of the zero layer when the crystal axis is tilted from the rotation axis in a vertical plane containing the incident beam.3).the determination of unitcell dimensions and crystal system (see §7. Oscillation cameras are rarely used for the collection of intensity data but are sometimes used for the preliminary examination of crystals . (b) Locus of zero layer in relation to cylindrical film. The cameras are provided with mechanisms operated by cams which enable one to oscillate the crystal toandfro through a few degrees . (d) Appearance of zero layer on the flattened film when the lower part of the crystal axis is tilted towards the incident beam. The photograph in fig.11 is an oscillation photograph and it will be seen that the spots are all resolved.5. (c) Appearance of zero layer on the flattened film when the upper part of the crystal axis is tilted towards the incident beam. With a small angle of oscillation there are many fewer spots on thefilmand the chances of overlap are thereby much reduced.3
The oscillation camera
Axis of rotation Sphere of reflection Plane perpendicular to rotation axis
121
Fig. 5.
12 then a rotation through %n gives the fig.12(a). 5. The indexing of oscillation photographs can best be done by a graphical
. Now in this case the layer line in the central region of the film is almost straight and makes an angle s with the 'ideal' line corresponding to a perfectly set crystal. If both layer lines are recorded on the samefilmand if one. a rotation of the crystal changes the circle of intersection of the zero layer with the sphere of reflection but. The intersection of the zero layer with the sphere of reflection is shown for this situation in fig. we can. to a first approximation. and also the zero layer of the reciprocal lattice. if the oscillation angle is small. This situation is shown in fig.13 situation and the correction can be made as before. Such an appearance indicates that the crystal axis is tilted in a foreandaft direction such that the top of the crystal is tilted towards the viewer. ignore this change. If we transfer to the actual camera. In practice. as in fig. This 'ideal' line does not actually appear on the film. The other simple type of missetting is when the crystal axis is displaced from the rotation axis in a plane perpendicular to the direction of the incident beam. 5. one would take the first oscillation picture with the two arcs along and perpendicular to the direction of the Xray beam. 5A3(a) and this appears on the cylindrical film as in fig.13 the two layer lines at 180° separation are recorded and the error in setting is corrected on the arc perpendicular to the beam.5.5. The figs.12(c). 5.12(d). The angle between the two straight sections of the layer lines is 2s which can be measured easily and the crystal is known to be in the position corresponding to the second (weaker) layer line.13(c) and (d) show the appearance of the zero layer on theflattenedfilmfor both senses of tilt of the crystal axis. If the missetting has the major characteristics offig. say thefirstrecorded.122
Experimental collection of diffraction data
an oscillation photograph can best be examined by considering two simple types of missetting. If the missetting has the major characteristics shown in fig.5. although one can usually guess its position to within a degree or so. 5. However if the crystal is rotated through 180° and another oscillation picture is taken about this new position then one has gone from situation (c) to situation (d).12(ft). 5. By taking a succession of photographs and correcting the setting each time the crystal axis can be set along the rotation axis with a high degree of precision. the relationship of the zerolayer line to the plane perpendicular to the rotation axis is shown. the viewer being taken as looking along the direction of the incident beam. any general missetting position can be thought of as being compounded of the simple types. Because the axis of rotation is slightly displaced from the crystal axis. is made stronger than the other then the appearance of the film will be as shown infig. The sphere of reflection with centre C is shown. in order to set a crystal. Let usfirstconsider a crystal the prominent axis of which is displaced by an angle s from the axis of rotation in a plane containing the rotation axis and the Xray beam. If P is a reciprocallattice point then a diffracted beam is produced in a direction given by CP.13(e). When thefilmis opened out and placed so that we are looking at it in the direction travelled by the incident Xray beam then the zero layer appears as infig.13(5). 5. For a tilt in the opposite sense the appearance of the zero layer is shown in fig. and therefore the angle s cannot be directly measured. 5.
(b) Locus of zero layer in relation to cylindrical film. (a) Location of the zero layer when the crystal axis is tilted from the rotation axis in a plane perpendicular to the incident beam. 5.5
The oscillation camera
Axis of rotation Zero layer of reciprocal lattice Diametral plane containing incident beam Plane perpendicular to rotation axis
123
Fig. As the crystal rotates so does the reciprocal lattice and reciprocallattice points pass through the circle of reflection giving diffracted beams as they do so.14(a) there is shown a section of the zero layer of the reciprocal lattice of a crystal situated at 0 and the diametral plane of the sphere of reflection (the circle of reflection) which contains the incident beam. The relative motion of the circle and the reciprocal lattice can also be shown by keeping the reciprocal
. 5. (e) The double zero layer produced by taking two oscillation photographs with the crystal rotated 180° in between. (d) Appearance of zero layer on the flattened film when the crystal axis is tilted in a clockwise direction as seen looking along the direction of the incident beam.13.
Sphere of reflection
Diffracted beam
beam [a) Axis of
Prominent axis of crystal
Zero laver
rotation
/Axis of rotation
process which will be illustrated for the zero layer.5. In fig. (c) Appearance of zero layer on the flattened film when the crystal axis is tilted in an anticlockwise direction as seen looking along the direction of the incident beam.
Now let us see how to solve the converse problem . (d) A fit of (c) on the reciprocallattice system.14(c) and also on the set of arcs which are centred at 0 and whose
Fig.knowing the sin 6 values of the reflections and on which side of the incident beam they occur how do we find the set of reciprocallattice points to which they correspond? We know that the points must lie within two areas arranged as in fig. 5. (a) The diametral plane of the sphere of reflection containing the zero layer. (e) An example for the reader. 5. For an oscillation of 15° the extreme positions of the circle are shown in fig.14.limits of incident \ beam
[a]
(c)
(e)
.14(fc) and for each of the reciprocallattice points within the shaded areas a reflection may be produced.124
Experimental collection of diffraction data
lattice fixed and rotating the circle. 5. (b) For the range of oscillation shown all reflections within shaded area may be produced. (c) The measured values of s marked as arcs within the region in which reflections may occur.
Incident beam
0
Extreme .
5A4(d). In addition it will have demonstrated how useful is the concept of the reciprocal lattice in interpreting the results which one obtains.4 The Weissenberg camera While it is quite feasible to collect complete sets of Xray intensity data with an oscillation camera the inconvenience of indexing the photographs is such that they are hardly ever used for this purpose. 5. at the scale of the reciprocal lattice. If a transparent replica of fig. There are also
Fig. The reader may try for himself the problem of fitting the arcs in fig. {a) Layerline screens set for the zero layer. not difficult to understand. If the principles of the oscillation camera have been dealt with in some detail it is because it is a simple camera. Such afitof arcs to points (not all perfect because of errors of measurement) is shown in fig.15. (b) Layerline screens set for an upper layer. in which one can readily see the basic principles of Xray diffraction from crystals.
Incident beam
1 \
Layerline screens
Incident beam
. the Weissenberg camera.14(e) on to the same net.14(c) is placed with O over the origin of a reciprocallattice net and is pivoted about O a position will be found when each of the sections of arc passes through a reciprocallattice point. We shall now examine a more convenient instrument. Similar considerations apply to the indexing of nonzero layers although this introduces some additional complications.4
The Weissenberg camera
125
distances. 5. 5. 5. 5.15(a) there is shown a crystal mounted on a goniometer head with an Xray beam incident normal to the axis of rotation. In fig.5. which makes the task of indexing photographs quite straightforward and which also enables a whole layer of information to be collected at one time without overlap difficulty. correspond to the sin 8 values of the observed reflections.
15(b) a higher layer is allowed through. In the Weissenberg camera the crystal is oscillated. 5. and it is mechanically coupled to the rotation of the crystal in such a way that it slides backwards and forwards as the crystal oscillates toandfro.5 mm/angular degree. Let us consider fig. the range of the oscillation being under the control of the user and may be greater than 180°.16. The coordinate parallel to the slit is proportional to 20. 5.17(fo)).11 (a) which represents the diametral plane of the sphere of reflection containing the incident beam. inserted into a cylinder and placed coaxial with the screens will record only a single layer but. In fig. and we may write
x = kij/.17(c) we are shown onehalf of the film with the location of the slit indicated and also the line corresponding to 6 = 0. is proportional to the angle through which the crystal rotates. 5. If spots are produced at different times then they will be displaced from one another along the direction of the motion of the film.5.3 angular degrees per radian) and k = 0. The general effect of the film motion is to spread the data in a single layer over the whole area of the film and no overlap of spots can possibly occur. 515(a) the screens are adjusted to let through the zero layer and in fig.12)
Some typical values of these constants are 2r = 57. 5.126
Experimental collection of diffraction data
shown a pair of cylindrical metal screens which can be adjusted so that a circular slit occurs between them and this slit can be so arranged that one and only one of the layer lines passes through it. It should be recalled that the diffracted beams occur wherever a reciprocallattice point passes through the sphere of reflection and although two reflections may have the same Bragg angle they will not be produced at the same time. Turning back to fig. (5. </>). which measures the distance travelled by the film. In fig. The point Q may be taken as the origin of a Cartesian coordinate system. The film holder can move along the direction of its axis. there will be overlap of spots for diffracted beams which pass through the same points of the slit (same values of Bragg angle). the angle of diffraction and we may write y = 2rO (5. Thefilmin a Weissenberg camera can either be mounted in two halves or can be in one piece with a beam stop attached to the collimator and inside the layerline screens (fig.3 mm (note there are 57. which is also the axis of oscillation. A film.11)
where r is the radius of the film cylinder. say if/. The crystal and the film are at one of the extreme positions of their periodic motions and we wish to determine where on the film the diffracted spot will fall. The x coordinate. Diffracted beams in other layer lines will strike the screens and be absorbed.17(a) we can see that the reflection will be
. The distance travelled by thefilmholder is linearly related to the angle of rotation of the crystal. A succession of positions through one cycle of the motion is shown infig. 5. The reciprocallattice point P is in the zero layer and has coordinates relative to O of (s. Wherever the crystal passes through a position for a particular reflection to occur thefilmis always in the same relative position and the diffracted beam strikes the same point of the film. if the crystal is completely rotated.
135°
5
.4
The Weissenberg camera
Film
127
Fig. 5.5.13)
The spot will thus occur on the film with coordinates
.of motion of film
\j/=
0
\f/=
45°
o= 45°
= 90°
»// = 90°
. Diagram to show successive positions of a rotating crystal and the linked motion of the camera for a 180° oscillation in a Weissenberg camera.135° = 180°
produced when the crystal has rotated into such a position that the reciprocallattice point originally at P has moved to Pf.
Screens
Direction .16. The angle through which the crystal rotates is
:
2
(5.
parallel straight lines of slope — 2r/k. 5.18(<z) there is shown a representation of a polar coordinate grid in reciprocallattice space. A Weissenberg picture may be regarded as a distorted projection of the reciprocal lattice. The two thicker lines in
. The angular coordinate 0 is measured from some arbitrary origin and the radial coordinate s is the magnitude of the normal reciprocallattice vector.14) we find. The slope of this line. for example. that y = —— x + r(n (5. eliminating 6.14) Suppose that we have in the zero layer a line of reciprocallattice points collinear with the origin which might. it is a straight line.
Experimental collection of diffraction data
Film Back stop
Incident beam Collimaior
tb)
[a] Line of centre of slit Incident beam Row of reciprocal lattice spots
0 = 0
Line of
x centre of gap (c)
id]
(5. In fig. The lines of constant <j> at equal increments of <j> appear as a set of equidistant. Such a row of spots is shown in fig. (b) The arrangement of film in a Weissenberg camera. since (j) is constant.18(£). 5. and. — 2r/k.17. (a) The reflection corresponding to the point P occurs when it has rotated to point F. 5. be one of the prime axes we select for the reciprocal lattice. 5. For all these points 0 has the same value and from the two equations (5.128 Fig. is a function of the design constants of the camera. The corresponding grid in Weissenberg space is shown in fig. as shown by the diffraction spots.11)) the lines of constant s at constant increments of 5 in Weissenberg space are parallel but not equidistant. Since s is proportional to sin 9 and the y coordinate is proportional to 8 (see equation (5. (c) A row of reciprocallattice points collinear with the origin.15)
This is the locus of the reciprocal lattice points on the film.17( d) together with the section of the sphere of reflection.
<t> = 9 0 °
Circles at 0.2 0.18.8
/
/ f/ / / / / / / / / / // / / 1 f / I / / / / / • i / / / / / ' 1/ / / / / / / < • / / / / 1/ / i / / / / / / / / .0.)
.2 1.) (c) The transformed grid within a region which could occur on a Weissenberg film.
I
%
0 8?/ /
7
p/
///I / / / / / 7777
/7/
(b)
/ / // / / ///
.0 0.5 mm/angular degree.
/ 1 2. (Halfscale for 2r = 57. 5.2 1.
/ /
/
/ /
/
/
/
/
/
/
1/ / / / / / / / / / / .8 (c) 1.0 1.2 IX increments of s
<t> = o
As = 2.0
= 180°
= 0 / 180°
= 90°
<> = 180° /
1
7 //////////// in/ / / / / / / / / / / 7 7 0 87 / / / / / / / / / 1 / 7/ /
/ 1.2 0.180°
(f> = 270°
<f) = 360°
1. (a) The diametral plane of the sphere of reflection containing the incident beam marked with a polarcoordinate system.6 1.4 1.8 0.4 0.5 mm/angular degree. k = 0.360°
= 180°
(b) The transformation of the grid shown in (a) in Weissenberg space.4 1. /11 / 1/ / / 1/ / / / / / / / JLLL / I / / ' / / /:
' /
/ / / /
t (
///// / /// / 7 /////////////// /// / / / //////////// /.3 mm. / .6 0.6 / / / / /
/
// /////// / / / / 7 7 7 7 / / t i l
///7 w///.0 L L/ / / • : <t> = 270° 6 .3 mm.8 1. 0.f / / / / / / / / /
/
Fig.4 0. (Halfscale for 2r = 57.6 0. k = 0./ '/ / / /
/ / .
The derivation of the precise form of these curves is fairly straightforward but we shall not derive them here.5.19(b).18(fc) correspond to the complete line (j) = 0° plus (j> = 180° in fig. sometimes.21. 5.15 the incident Xray beam is normal to the rotation axis for all the layer lines. by applying scaling factors.5.5. Usually this operation presents little difficulty but.19(a) contained within the limiting circle of radius 2/1 The spacing of the lines is 0. Now let us suppose that in the zero layer of the reciprocal lattice we draw two sets of parallel lines within the limiting circle as is shown in fig.5. from equation (3.1 of the radius of the limiting circle and when they are plotted in Weissenberg space they appear as shown in fig. It is more usual to use the 'equiinclination method' for taking upperlayer photographs.20(a) could be regarded as zerolayer reciprocallattice points with each of which there is an associated intensity and the Weissenberg diagram would give a diffracted spot at each corresponding point. The incident Xray beam and the diffracted beam make the same angle with the rotation axis as illustrated infig. If a number of adjacent spots are too weak to be seen in an otherwise highly populated row corresponding to
. Buerger (Wiley). 5. respectively. one chart showing these curves can be used for all layers. The detailed theory of equiinclination Weissenberg diagrams for upper layers is to be found in Xray Crystallography by M.5 The precession camera The Weissenberg camera gives a distorted map of a reciprocallattice layer which.5. The points P and F are equivalent and the rectangular area shown infig. 5. The equiinclination method has the advantage that the family of curves corresponding to parallel lines in a reciprocallattice layer have the same shape regardless of which layer is taken and. (5.130
Experimental collection of diffraction data
fig. 5. In the arrangement shown infig.20(fr) and these are labelled with indices h and k. as we have seen. 5. the reader should study this figure for a short time to see the relationship between the reciprocalspace diagram and that in Weissenberg space. the angle \i between the incident beam and the axis is. It is possible to find the locus in Weissenberg space of a set of lines parallel to the thicker one in fig. It is normally fairly easy to see the families of curves on which the spots lie and therefore to index the reflections. 5.18(a). 5.20(a). The actual Weissenberg photograph shown in fig.20(fe).20(b). In Weissenberg space these will appear as in fig. 5. such a set of lines is shown in fig.16) It should be noted that the angles corresponding to x//a0 and ij/a in equation (3. It should be noticed that the arrangement of slits and film movement for the Weissenberg camera results in the diffraction spots falling on a rectangular area of the film. 5. this process can lead to errors.18(a).18(c) is equivalent to that shown infig. The intersections of the sets of lines infig.12) are n — jn and fi. 5. The lines of the grid are shown infig.12).5. given by 2a cos [i = hX. can be translated back to the actual reciprocallattice layer by means of standard charts.20(c) may be compared to fig.18(fe). particularly when the unit cell has one or more long axes. J.
(b) The transformation of {a) in Weissenberg space. (Halfscale for 2r = 57.2/A
Limiting circle
Fig.)
.5 mm/angular degree. (a) A set of equidistant parallel lines in the diametral plane of the sphere of reflection.Parallel lines at spacing 0. 5.3 mm. k = 0.19.
)
Experimental collection of diffraction data
8 6 4 2 0 2 4 6 8 1012 14 I I I I I I I II I I I i I I I I ! I I I i I I II I I I 0=88. it is convenient to obtain directly an undistorted picture of the reciprocal lattice. (a) Two sets of equidistant parallel lines in the diametral plane of the sphere of reflection.. k = 0.
.5 mm/angular degree. However even when the unitcell edges are all of moderate dimensions.132
Fig. In such a case it would be an advantage to have a camera which would give an undistorted map of the reciprocal lattice.5° (a)
A = 12
(b)
a line of reciprocallattice points then it is possible to misindex the higherorder reflections....3 mm.J.
— 12 10
— 6
</> = 1 8 0 ° " "
. 5. This can be caused by very slight mispositioning of the Weissenberg chart on the photograph. (b) Part of the transformation of (a) in Weissenberg space.. The location of a spot in relation to its fellows may then be determined by a straight edge alone and the possibility of error is much reduced.4 2 6 = 0°0k
f
.20.5°
.
.
. although such errors can be avoided by very careful measurement on the photograph this can be a tedious process. (Halfscale for 2 r = 57.. "441 0=268.
of the reciprocal lattice. 5. say at F.one which is simple to understand and illustrates the general principles of the method. 5.
Fig.5.5
The precession camera
133
Fig. The equiinclination arrangement for higher layer Weissenberg photographs.
Incident beam
respectively. with the rotation axis. If 0 is the centre of the sphere then the direction of the diffracted
. Only onehalf of the film is shown.) (c) A Weissenberg film corresponding to the lattice shown in (b). say the nth. If any reciprocallattice point lies on this ring of intersection. then the corresponding Xray reflection is produced. In fig. The sphere of reflection is shown and also the intersection of the sphere by an upper layer. Diffracted beam Conical surface on which lie all diffracted beams of this layer line
Axis of rotation of crystal
It was shown by de Jong and Bouman (1938) that a camera could be designed which would represent without distortion a layer of the reciprocal lattice. 5.20 (cont.21. We shall examine here a special case of the de Jong and Bouman arrangement. The incident and diffracted beams make angles
7i — \i and n.22(a) there is represented a crystal at C with an incident Xray beam normal to a prominent cell axis whose direction is CD. Natural size.
The way in which
. as it does so the nth layer slices through the sphere of reflection cutting it in the ring shown. With the arrangement described all the diffracted beams from the nth layer would lie on the surface of a cone with apex 0 and if aflatpiece of film was placed perpendicular to OE then the separate layers would appear as rings of spots on thefilm. The accessible area of the nth layer is the annular region shown shaded. The reciprocallattice layer would rotate about the point C in its own plane and one could record data corresponding to lattice points within the annular region shaded in the figure. {a) The intersection of the nth layer of the reciprocal lattice with the sphere of reflection. rotates about CD.134
t Axis of rotation Region of mh layer which can be recorded C
Experimental collection of diffraction data
Axis of rotation . which it will do twice on each revolution. Diffracted beam
Diffracled
Circle of intersection of nth layer and sphere of re flee [ion \
Incident
Incident beam
\y
0
( rystal
Layerline screen
ib)
Sphere of reflection
^ Axis of Axis of rotation of film CJS> rotation of crystal Film * Layerline screen
Cross section of sphere of re flee I ion
Fig. (b) A layerline screen arranged to allow through only the nth layer.
beam is given by OP. (c) If the film is rotated about C" with the same angular velocity as the crystal an undistorted projection of the reciprocallattice section is produced. Whenever a reciprocallattice point lies on the circle of intersection. 5.522(b). spreads out the record of the diffraction data by moving thefilm.each ring being the intersection of the appropriate conical surface with the plane of thefilm. a diffracted beam is produced along the direction joining 0 to the reciprocallattice point. like the Weissenberg method. with its origin at the point C. The de Jong and Bouman method.It is possible to separate one layer line by interposing in the path of the Xrays a metal screen with an annular slit cut into it.22. If the crystal is rotated about its prominent axis then the reciprocal lattice. The central ring of metal is kept in place byfinecellophane or plasticfilmwhich is almost completely transparent to Xrays. It helps to visualize the situation if we imagine the crystal actually located at 0 rotating about the line OE while the reciprocal lattice is displaced from it with its origin at C and rotating about CD with the same angular velocity as does the crystal. The relationship of this layerline screen to the crystal and incident beam is shown infig.
are used and these are normally doublecoated.6
The photographic measurement of intensities
135
this is done may be followed by reference to fig. If the spots on the film are similar to one another in appearance then one can produce an intensity scale by exposing one reflection along a strip offilmfor various lengths of time with the Xray tube running under constant conditions. A typicalfilmproduced by a precession camera is shown infig. to some extent. This was a layer of fluorescent material placed behind the film in such a way that the Xrays passed through thefilmand then hit the screen. as will be clear from fig. Many other experimental arrangements are possible and their various advantages and disadvantages have been discussed by Buerger (loc. The point C" is the projection from 0 of the point C on to the plane of thefilm.23. The bulk of the exposure of the film was caused by the photons of visible light released by the screen rather than by the direct Xray beam itself. The exposed points on the film are thus a projection of the reciprocallattice layer from the point O on to the plane of the film and the developed film will show a true undistorted picture of the reciprocallattice layer. In fact the camera which is most frequently used to record diffraction data on an undistorted reciprocallattice net is the Buerger precession camera.5.If thefilmis rotated about an axis through C" parallel to CD at the same angular velocity as the reciprocal lattice then the line joining O to any reciprocallattice point in the nth layer always intersects the same point on the film.
. 5. It will be noticed that the experimental arrangement which has been described is incapable of giving the zerolayer data and also presents considerable mechanical difficulties for layers close to the zero layer.22(c) which shows a crosssectional view in the plane of the sphere of reflection containing the incident beam.23. However. We shall not attempt to describe the complexities of the precession camera here. Thus whenever a particular reciprocallattice point passes through the circle of intersection the diffracted beam strikes the same place on the film.6 The photographic measurement of intensities Xray crystallographers have relied and. 5. 5.5. However. such screens are rarely used now. cit). still do rely on the photographic recording of diffraction data. fast films. For a given wavelength the precession camera records less of reciprocal space than does the oscillation or Weissenberg camera and therein lies its chief disadvantage. Before very fast films were available it was customary to use an intensifying screen. Usually one does not try to measure the intensities of the reflections by an absolute method. to increase their sensitivity still further. The eye is very good at comparing intensities for spots in the intermediate range of density but is less efficient for spots which are either very faint or very dense. very sensitive to Xrays. that is covered with sensitive emulsion on both sides. it enables angular measurements to be made more easily. for our purpose a description of the de Jong and Bouman arrangement suffices to explain the basic theory of methods of this type. This enables all layers to be recorded and for the layers to all be on the same scale. The relative intensities of the diffraction spots can then be determined by comparison with the scale.
We shall use the term 'energy' to denote the total energy of the diffracted beam. This effect may be seen infig.20(c) where at high Bragg angles the Kax and Ka2 wavelengths (see §5.5. by differentiation and rearrangement. since the total energy is proportional to the quantity Jhkl in equation (3. For instance. From Bragg's law. The reasons for the variation in spot appearances are manifold. Xray crystallographers are guilty of lax terminology here and use the word 'intensity' to denote total energy.43).
Experimental collection of diffraction data
It is frequently found that the recorded diffraction spots are not all of similar appearance and then it is not the intensities of the spots we wish to measure but the total energies of the Xray beams which have produced them.136 Fig. A typical photograph from a precession camera. the spots tend to become more diffuse at higher Bragg angles due to the finite bandwidth of the Xray spectral lines.23.8) produce resolvable diffraction spots. equation (337). However a more important reason for the spread of diffraction spots is
.17)
Id cos 9
and since cos 9 decreases as 9 increases so the diffraction image becomes more diffuse for high 9. we find d9 = (5. 5.
Hence the length of the blackened region is
lx =T\l/T v\ = \lvx\.25. as when one is using the Weissenberg camera. For example if A'B' = / and the total time for formation of the diffraction spot is T then the diffracted beam scans from A' to B' at an average velocity //T. the collimator serves only to cut down the background radiation and so to reduce fogging. If one were to use just the density of the spot then a contracted spot would be
Fig.
Useful Xrays Xray source
:
Collimator
Crystal
*~ N onuseful Xrays which coniribute to film fogging
Fig.6
The photographic measurement of intensities
137
divergence in the Xray beam. 5.
B
Film
. Divergence of the incident Xray beam to the finite size of Xray source and crystal. (5./ + vx. 5. 5.24.18a)
Similarly it can be found that if the film is moving in the opposite direction the length of the blackened region is
/ . 5. We must now examine the problem of measuring the energy of reflections when the spots on the film can be so varied in appearance. When the formation of a diffraction spot in this way is considered together with motion of the film.
(5. A rotating crystal.24). Different parts of the crystal reflect as the crystal rotates and the diffraction spot on the film grows from one end. will diffract Xrays from different parts of itself as it rotates. illuminated by radiation coming from a range of directions.18b)
Thus spots of the same energy may appear in different forms .5. the crystal may diffract from point A to give a diffracted beam AAr and at some later time when it has rotated further it could diffract from point B to give a diffracted beam BB'.25. Afilmplaced in the position indicated would be blackened in the whole region from A' to B'. In fig. for example. If the film moves in the direction from A to B' at a velocity v then the relative velocity of the scan relative to the film is //T — v (this may be negative).one may be contracted and more dense while the other may be extended and less dense. The beam divergence is usually defined by the Xray source and the crystal (fig. it is found to lead to the extension of some spots along the direction of film motion and a contraction of others.
It is possible to scan the diffraction spot with a fine
Fig. Fast films are particularly prone to a high fog level. The quantity one is really trying to measure is the total energy T of the radiation producing the spot or. The fog level may vary a great deal and depend on the duration and temperature of storage of thefilm. 5.0
1. However the general character. Ideally when comparing diffraction spots with an intensity scale it is better to be in the range of £ corresponding to the steepest part of the curve for it is in this region that small differences of E can most readily be detected by eye. The behaviour of films on exposure to radiation depends on the wavelength of the radiation and also very critically on the developing process. that is to say that the effect on the film is proportional to the total exposure E as measured by the product of beam intensity and time. expressed as a relationship between D and E. 5.19)
where the integration is over the whole area of the diffraction spot. The blackening of a photographic emulsion is measured by its density defined by
1
10
fractional transmission of light'
(5.0
Fog level
log£
.26.
3. for that part of the film.138
Experimental collection of diffraction data
judged as more intense than an extended one. However the quantity E will vary from point to point of a given spot and when the spots are all of different areas it is not easy to assess the relative values of T defined in equation (5. A typical curve of density vs log (exposure) for an Xray film.26.Film obeys the socalled reciprocity law.19). Since intensity is a measure of energy per unit area per unit time then £ is a measure of energy per unit area.0
2. the total number of photons falling on that region of thefilm.the cleanliness of the developing andfixingsolutions and also exposure to ambient cosmic radiation before use. what amounts to the same thing. usually resembles that shown in fig. D = 2. The quantity we wish to determine is then given by T= \EdA (5. There is no simple photometric method whereby measuring the attenuation of a beam of light passing through the whole spot gives a reasonable measure of T.20)
Thus if a certain region of afilmtransmits 1 % of incident light then.
5. at the end of every cycle of operations of the camera. This is illustrated infig. One such instrument.19).28 a Weissenberg picture. Automatic densitometers are available which enable rapid and quite accurate assessments to be made of the quantity Tin equation (5. Quite high precision can be reached by the mechanicalintegration method.
[a)
(b)
.5. This is a device which. Thus the total exposure at P is H£ where the sum is over the points of the grid and.
Fig. Because of the spreading out of the diffraction data longer exposures are required and weak spots may be missed altogether.19) is then computed automatically. the transmitted light being measured by a sensitive photocell. moves thefilmin such a way that consecutive images of the same diffraction spot fall on the film with displacements corresponding to the points of a small rectangular grid. one would normally use an integrating mechanism either with a Weissenberg or a precession camera.6
The photographic measurement of intensities
139
beam of light. The background round the spot is also measured and the integral in equation (5. The multiple image will have a flat plateau at its centre the density of which will correspond to a total exposure proportional to T.5. to a first approximation. However the very weak spots can be measured on nonintegrated photographs and related to the integrated data by comparison with stronger spots with similar shapes. since this summation is. The point P in (b) for example has been subjected to exposures from each of the images and these exposures come from points similar to those shown in the grid in (a). to determine D (and hence E from the known DE relationship) at the points of a grid covering the spot and hence to find Ton a relative scale from the sum E£. computercontrolled. scans the spots with a small source of light produced on the screen of a cathoderay tube. For accurate photographic work.27.27 where 25 images of the single diffraction spot shown in (a) are represented with displacements on a 5 x 5 grid in (b). The superposition of several images of the diffraction spot on a film to produce a uniform plateau of intensity at the centre.19). it will be proportional to T The usual practice is to compare the densities of the plateaux with a scale the elements of which are small uniform spots made by exposure to the direct Xray beam through a circular aperture. Once the film has been taken the actual measurements can be made at about one spot per second or even faster. There is shown infig. proportional to the integral in equation (5. normal on one half and integrated on the other.5.
At the higher counting rates proportionality between photonfluxand counter discharges is lost because of the increasing
. the residual ions in the tube must be removed. This discharge can be detected electronically and amplified to operate a recording instrument. such that a discharge does just not take place but so that the apparatus is in a critical condition. After each discharge the counter must be quenched that is to say.7
Diffractometers The energy of diffracted beams can also be measured by a counting device which records individual Xray photons. In practice up to about 3000 photons per second can be counted with a GM counter. A potential is maintained between the electrodes.the molecules of which absorb ions and dissociate rather than produce fresh ions.29 shows a schematic GM counter.140 Fig. The cathode is a metallic cylinder and the anode a wire along the axis of the cylindrical glass envelope.28. 5. A Weissenberg film showing unintegrated spots on the righthand side and integrated spots on the lefthand side. This can be achieved by having an organic vapour in the tube . of the order of 1000 volts.methylene bromide is effective .5.
Experimental collection of diffraction data
5. A single Xray photon falling on the gas in the tube can produce primary ions which in their turn produce a cascade of secondary ions and a discharge through the counter. The GeigerMuller counter has been used for this purpose andfig. The time for a GM counter to restore its initial condition after discharging is called the 'dead time' of the counter and is typically of the order 10 " 4 seconds.
This is so much greater than the rate at which Xray photons would arrive in a diffracted beam that the scintillation counter gives a count proportional to the total energy of the beam .g.2. This is similar to a GM counter but operates below the Geiger threshold. A typical fullyautomatic fourcircle diffractometer is shown schematically
. Each time an electron collides with an electrode it is energetic enough to produce several secondary electrons each of which is accelerated in the field to the next electrode and produces several more. If a highfrequency electronic system is used the scintillation counter is capable of counting of the order of 107 to 108 events per second. It is possible to incorporate a counter in a diffraction instrument based on any of the geometrical arrangements we have previously considered.5. Discharge counters have largely been superseded by the scintillation counter where the radiation first falls on afluorescentmaterial the visible light from which is subsequently detected by a photomultiplier arrangement. we have already mentioned a powder diffractometer which records with a counter rather than film. 5.that is to say. in § 5. An Xray photon entering the counter produces a pulse of height proportional to the energy of the Xray photon. Proportional counters also have the advantage of a short dead time (~ 10~7s) and so give a linear response at high counting rates. are called diffractometers and.30 a typical setup is illustrated. A schematic GeigerMuller counter. The crystal can be placed in a diffracting position. The photon of visible lightfirstfalls on a photoemissive surface which generates a photoelectron. Infig.7
Diffractometers
Cylindrical cathode [_
Fig. the counter placed so as to receive the diffracted ray and the counting rate will then be a direct measure of the power of the beam. that the probability of two Xray photons arriving so close together that they cannot be counted separately becomes vanishingly small. Consequently the voltage pulses produced are small (~ 1 mV) and require amplification. Another type of counter is the proportional counter.5. rather than taking a photographic record. This has the advantage that pulses due to unwanted photons (e. secondorder reflections with wavelength A/2) can be recognized and eliminated.29. This cascade effect can give a millionfold or more amplification factor and the final pulse of current can be amplified electronically and fed into a counting system.
Amplifier Anode
T
Glass envelope
probability that photons will arrive in the dead time when they cannot be counted. The layers of 'venetianblind' electrodes are each at about 100 volts higher potential than the one before. Devices incorporating counters.
The accuracy which can be obtained with diffractometers depends on a number of factors. A schematic view of a scintillation counterphotomultiplier arrangement. Another possible source of error is the statisticalfluctuationswhich are to be expected in the diffracted beam. we should note that this 'true' number is not available to us
. 5. This requires a stabilized power supply for the tube but in addition one should monitor a reference reflection from time to time to ensure that there is no variation in the intensity of the incident Xray beam. By the 'true' number we mean the average number of counts per unit time. The term 'fourcircle' refers to the number of rotational motions available and in the instrument shown three of these are associated with the crystal and one with the counter. If in a given time t. They can automatically determine the orientation of the crystal. usually by means of a socalled direct method as described in §8. N counts are made then the standard error in the number of counts is y/N. there is a 68% probability that the 'true' number of counts is in the range N ± y/N. multiplied by t. the rotation axis corresponding to this motion is called the 20 axis.31 . a 95% probability that it is in the range N ± 2y/N and a 99. 5. Modern singlecrystal diffractometers are computercontrolled and are provided with sophisticated software to carry out many tasks.the <j). x and Q. This means that. Using the stored intensity data the computer can then solve the crystal structure.142 Fig. For a particular reflection the counter is set at a position corresponding to the Bragg angle. as ascertained by counting for an infinite period. The counter rotates about a vertical axis so that the plane containing the incident and diffracted beam is always horizontal.31.5. Such positioning can be achieved by rotation of the crystal about the three axes shown in fig.30. Once this has been done the diffracted beam can be produced by positioning the crystal so that the scattering vector s makes the correct angle with the incident and diffracted beams. move the crystal and detector to record each diffracted beam and also control the time each beam is measured to optimize the accuracy of the measurements. axes.8.7% chance of it being in the range N ± 3^/iV. It is important that the Xray tube output should be kept absolutely constant with time as the data is collected. from normal statistics. Photosensitive cathode \
Experimental collection of diffraction data
Scintillator
Anode
—_ Electron paths
1012 layers of 'venetianblind' electrodes
infig.
where hundreds of thousands of items of data must be collected. 5. A typical count rate for a strong reflection would be about 30000 counts per second. or automatic densitometers. A typical fourcircle diffractometer. while a weak but observable reflection could give a count rate of 310 counts per second. it acts as a noise in the presence of which the signal must be measured. is the inevitable background count. It is also obvious that for weak reflections one must count over a considerable period of time to get reasonable accuracy.32. T.
143
20 Rotation
. M.31. Willis (Cambridge University Press). A disturbing influence. especially for the weak reflections.5. W. In this device. illustrated in fig. molybdenum.8 Xray sources
Fig. x a n d ^ . A complete account of the use of diffractometers is given in Single Crystal Diffractometry by U. diffractometers. 5.1% we need 106 counts and so on. The diffracted beam power will thus be proportional to N/t with a fractional standard error
N N
(5. they are potentially the most accurate and certainly a very convenient means of collecting diffraction data.only the number N. make possible what otherwise would border on the impossible. The counter rotates about the 20 axis in one plane and the crystal may be orientated in any way by the three axes of rotation (j>. The number of counts which can be made is clearly limited by the time available to collect the data. However.8 Xray sources Over the years the most important source for the production of Xrays for the crystallographic community has been the sealed hotcathode tube.21)
Thus to have a standard error of 1% we must make 10000 counts. whatever the difficulties with the use of diffractometers. cobalt or some
. Arndt and B. For the study of the crystal structure of large biological molecules. electrons from a heated filament are accelerated through a potential difference V towards an anode on which there is a disk of tarket material .copper. 5. for 0.
c the speed of light and Ex and E2 are the higher and lower energy levels of the shell electrons. are Ag(0. Within the L shell two slightly different energy levels occur so that the Mo Koc radiation consists of two close components Mo Ka x [X = 0.2896A). Some of the energy lost by the electrons on striking the target is converted into electromagnetic radiation in the form of Xrays and. Mo. indicating the most energetic Xrays produced.9360A) and Cr(2. eV. If the accelerating potential is increased then eventually a point will be reached where the impacting electrons can eject inner core electrons from the target element. 5.144
Fig. 5. It shows the characteristic Mo Koc (2. Elements of lower atomic number than chromium will give longerwavelength radiation that will be heavily absorbed by the exit window of the Xray tube while those with a larger atomic number than silver will give a very high ratio of background continuous radiation to characteristic radiation thus making them less convenient for crystallographic use. with the wavelengths of their Ka x radiation shown in parentheses. Cu(1. for example from an L to a K shell. Xrays from the line source are viewed obliquely through the beryllium windows so forming an effectively compact source. At this point a different source of Xrays becomes available when an electron moves from one level to another within a target atom. the wavelength of which will be given by he ExE2
(5. then there will just be a continuous intensity distribution of Xrays as shown in fig.70926 A) and Mo Ka 2 (X = 0. to the K shell. Fe(1.33(fo). respectively. will have energy corresponding to all the energy of one electron. A sealed hotcathode Xray tube. = 0.6578A). 5. The target materials generally used in these sealed Xray tubes.71354 A) with intensities in the ratio of about 8:1. The output from a molybdenum Xray tube operating at 35000 V is shown in fig. Ni(1. if the accelerating potential V is sufficiently low. going into a single Xray photon.22)
where h is Planck's constant.5405A).33(a). The lower limit of Xray wavelength 2min .32.5594A).7097 A) and Mo Kp (1 = 0. Xrays Water out
Experimental collection of diffraction data
Beryllium window Xrays
Heated filament Evacuated enclosure
other metal.6323 A) peaks derived from electrons moving from the L and M shells. This gives rise to what is called characteristic radiation.7889A). Co(1.
.
8 Xray sources
Fig. and to stop the target melting this heat is removed by water cooling. the appearance of the Xray source remains constant. In this device the target is in the form of a cylinder which spins about its axis so that the energy dissipated by the electron beam at the target is spread out over a much larger area. as it spins. 5. including the continuous background. following the direction of the electronemitting filament. corresponding to about 600 W of power being dissipated at the target. or nearmonochromatic radiation is required and filters are used to eliminate as much as possible of the unwanted radiation. This puts a very heavy demand on the water cooling system and should the cooling water be cut off for any reason then the target would quickly melt.0
That part of the energy of the electrons striking the target which is not converted into Xrays.4
0.2.2
0. A normal Cu Xray tube will run at 30 kV with an electron current of 1520mA.8 Wavelength (A) (b)
1.0
Wavelength (A)
0. The electrons fall on the target along a line. shown in fig. the great majority of it. so that only the desired characteristic radiation is transmitted.8
1. is converted into heat. For most Xray crystallographic purposes monochromatic.6 (a)
0.
0. The first synchrotrons were built as machines for
. In practice there are safety devices based on monitoring the water pressure and its flow which prevent this from happening. This makes the cooling problem soluble for currents of up to 200 mA. This is viewed obliquely so that the effective source is compact and roughly square.33. Since about 1970 sources of Xradiation have become available which are many orders of magnitude more powerful than any laboratory source. The principle by which the filters operate is explained in § 6.5. It is possible to produce even more powerful laboratory Xray generators by using a rotating anode tube. 5. (a) Continuous radiation
145
from a sealed Xray tube with a tungsten target at an operating voltage of 30000 V. These are synchrotron sources of which many now exist as national and international facilities.32. (b) Output from a molybdenum tube at 35OOOV. The target must be well shaped so that.
are designed to maintain the electron currents over periods of typically 220 hours. path by means of dipole bending magnets. Synchrotron radiation has many interesting properties.
Bending magnet Radiation
. was built in Tokyo and the first multiuser. whenever electrons pass through the bending magnets they are in a state of acceleration and hence. A typical synchrotron is shown infig. 5.34. in the particlephysics applications they could then be used for collision experiments. However. according to the laws of classical physics.K. These specialized machines. technically known as storage rings. A typical storage ring arrangement. Electrons are injected at about 10 MeV from a linear accelerator into a booster synchrotron which then increases the energy of the electrons to about 500 MeV.5. was built in the U. prior to transmission into the main synchrotron.146
Experimental collection of diffraction data
accelerating electrons and positrons to high energies for experiments in particle physics.K. The number of bending magnets is usually 16 or more and the diameter of the ring is of the order of 30 m for a major installation such as the SRS at Daresbury in the U. the SOR. the SRS. The first storage ring. For some years the use of synchrotron radiation was a parasitic activity accompanying particlephysics experiments but. This was a nuisance to the particle physicists who had to pump energy into the radiofrequency cavities to compensate for this loss but this radiation. soon attracted the attention of other scientists including crystallographers. The energies of these are gradually ramped up by passage through radiofrequency cavities to 24 GeV and they are steered into a closed. highenergy storage ring for research purposes.34. It is strongly
Fig. they lose energy in the form of electromagnetic radiation. some of similar design to the Daresbury machine but with better working characteristics and others optimized either for softer (longerwavelength) radiation or for harder radiation. which covered the range from infrared to Xrays. approximately polygonal. Eventually the electrons are isolated in orbit in the ring and. at Daresbury in 1980. This has been succeeded by many other machines. later. new synchrotrons were built specifically designed to optimize the radiation output.
5. The absolute scale of the power spectrum will depend on other factors.24)
where the electronbeam energy is in units of GeV and the dipole magnet field B is in tesla.41C.5. the spread in the vertical direction is very small and is given in radians as 5c/> = me2 IE
(5. m the mass of an electron and c the speed of light.64/(££2)
(5.9 A.35. The universal power spectrum curve for synchrotron radiation. is illustrated infig. E = 2. For the SRS.18) et seq. The critical wavelength.2 T so that kc = 3. One such insertion device. situated in the straight sections between the bending magnets.8 Xray sources
147
polarized. is given by = 18. The beam passes through a series of dipole magnets of alternating polarity so that it undergoes small oscillations perpendicular
Fig.5. which is useful in many scientific applications and which has to be taken account of when interpreting Xray intensities (see equation (6.23) we find that the vertical angular spread of the radiation is 0. For the SRS.25 milliradians or less than l'of arc. The bending magnet radiation is fanned out in a horizontal direction since it is emitted tangentially over the whole of its curved path through the magnet.35.
10u
10"
10"
10"
1
10
100
Wavelength/Ac
.0 GeV and B = 1. The output characteristics of a synchrotron source can be modified by what are called insertion devices. On the other hand.36(<z). The electrons do not form a uniform stream but occur in bunches separated in time by 10" 8 10~ 9 s.). as shown in fig. which corresponds to the greatest output of energy per unit wavelength. E = 2. in angstrom units.0 GeV and inserting this value in equation (5. and is characterized by a critical photon wavelength Xc which divides the curve into two parts such that there is as much energy generated above Ac as below it. called a wiggler. 5. The peak of the curve is approximately at 1. in particular the electron current which for the SRS is 200 mA. The output of radiation is pulsed with a similar frequency and this gives the possibility of doing timeresolved experiments on nanosecond timescales. The power spectrum of radiation produced from a dipole bending magnet is always of the same shape.23)
where E is the electronbeam energy.
Where monochromatic.37.38 there are shown the increases in available flux during the twentieth century. On the other hand. compared with that from the bending magnets. The availability of synchrotron radiation has revolutionized Xray crystallography as well as many other areas of science. Infig. (b) The power spectrum in terms of Xc. the critical wavelength of the bending magnets. or nearmonochromatic radiation is required the use of a tuned undulator can give greatly enhanced useful fluxes of Xrays by having the wavelength of interest at the centre of one of the harmonics. The output of a singlepole wiggler and a multipole wiggler.
to its general direction of motion. This leads to interference effects whichfirstlycause a reduction in the angle of the output cone but also lead the output spectrum of radiation to be in the form of a series of narrow harmonics. thus modifying the field. The wavelengths of the output from an undulator can be tuned by varying the gaps between the magnets. as seen from equation (5.36. 5.148
Experimental collection of diffraction data
Radiation
^ —
N
s
(a)
N
Electrons
A multipole wiggler
A singlepole wiggler Bending magnet radiation
0
log aac)
(b) Fig. as shown in fig. The magnetic fields are perpendicular to the figure with the nearer pole of each magnet indicated. if there are several wiggles then each of them produces its own radiation and the total output is the sum of that from all of them. The
. is shown infig. An even more important insertion device is the undulator which is similar to a wiggler except that the deviation of the beam is smaller and constrained to be within the output cone of the radiation (~ 1 milliradian).24). If there is only a single wiggle in the motion of the electrons then there is just a wavelength shift of the output curve. capable of giving several times the field of the normal bending magnets and so decreasing the critical wavelength. 5.5. (a) Three dipole magnets giving a singlewiggle Wiggler.536(b). The energy of the electron beam E is unaffected but the magnets can be of the superconducting kind.
For synchrotron radiation where.K. the intensity varies smoothly around the wavelength of interest it is more common to use a crystal monochromator. Brilliance is a measure of the intensity of wellcollimated monochromatic radiation which can be delivered on to a specimen. A difficulty with crystal monochromators is that they also
.39 then not only is the emergent beam parallel to the incident one but the quality of the monochromatic radiation is much improved. The form of output from an undulator with the energy concentrated in harmonics. Photon Factory at Tsukuba in Japan. U.37. if monochromatic radiation is required. For sealed Xray tubes. 5.A. filtering by metallic foils can produce a beam in which most of the radiation is within a characteristic line of the target.
149
log (A)
Fig.8 Xray sources
Fig.
I
SPRING 8 ESRF
Photon factory
I
i
1900 1920 1940 1960 Year 1980 2000
o
various machines indicated are the SRS at Daresbury.38. 5. 5. SSRL at Stanford in the U. This involves the use of a single crystal which has a very strongly reflecting set of Bragg planes so that for radiation of the required wavelength X the beam is directed at an angle ^it — 9 to the normal to the planes where 9 is given by equation (3.. ESRF at Grenoble in France and SPRING 8. an 8 GeV machine at Hirama Science Garden City in Japan.5.37). Even the best monochromator will give a finite bandwidth of radiation in its output but if a pair of monochromating crystals is used as shown in fig. The increase in available brilliance since 1900.S..
at a rate of 10 ^is per pixel.as otherwise the image will be greatly weakened. usually a HeNe source. After the image is stored on the plate it is scanned by a laser beam. where X is the wavelength of interest and n is an integer. BaFBr: Eu2 + . called an imaging plate. If the intensity (or the structure amplitude) is much greater for the (hkl) reflection than for any multiple of it then this may not be too serious and the situation can be further improved by the addition of a simple absorption filter. The action of a twocrystal monochromator. crystal monochromators are also required to be robust and also not to deteriorate in the Xray beam. Subsequently. The image plate is also convenient for recording Xray diffraction images but. The plate is coated with a storage phosphor. As well as satisfying particular requirements with respect to their diffracting properties.39. The BaFBr phosphor. as shown in fig. 5. in a layer about 150 \im thick. the latter will be able to record a pattern even from a weakly scattering biological crystal within the required timescale.a day at most .40. the release time of PSL being about 0. It is in the solution of biological structures that the imageplate system has most to offer. which is about the limiting resolution of the system.
Experimental collection of diffraction data
reflect wavelengths X/n. which has the property that when it is irradiated with Xrays some electrons within it are excited into higher quasistable energy states. when exposed to visible light.8 ^s from the time of light stimulation.9 Imageplate systems In 1983 a lightstoring device. is a very efficient absorber of Xrays. the trapped electrons lose energy and emit ultraviolet light of wavelength 390 nm . 5. 5. The PSL from each illuminated pixel is guided by fibre optics to a photomultiplier detector. The wavelength of the PSL radiation is sufficiently different from that of the stimulating light that the latter can easily be removed by a filter. a synchrotron source.a process known as photostimulated luminescence (PSL). it is only suitable for experiments where all the data can be collected and the pattern read out within a few hours . either of the rotatinganode variety or. This gives the requirement for a powerful Xray source. The plate is organized in pixels. better still. the signal from which goes into
. 100 x 100 jum in dimension. A common experimental arrangement is for the image plate to be the recording part of a precession camera. because there is gradual leakage of the trapped electrons. This means that the (hkl) reflection is being produced for X while the (nh nk nl) reflection is being produced for X/n.150 Fig. It should also be noted that if a crystal monochromator is being used to isolate the characteristic radiation from a sealed tube then the removal of the X/n radiation is less important since this will be within the lowerlevel background continuous radiation. was developed for medical diagnostic radiography.
41. The angle between the direction of the incident radiation and the normal is also fixed but if that angle is ^n — 6 for some wavelength present in the incident beam then radiation of that wavelength will form a reflected (diffracted) beam. 5.6
0.2
Wavelength (A)
a digital storage and imageprocessing system. dynamic range and precision of imageplate systems give them a growing role in Xray crystallography. was taken with a stationary crystal and. In general.10
The modern Laue method
100
151
Fig. A representation of such a system is shown in fig. A characteristic of the Laue method is that all the diffracted beams are produced at the same time and this can have important advantages. a continuous source of Xrays. One of the great problems with biological crystals is that they are degraded by Xrays so that if the same crystal is used for a long time the quality of the data steadily gets worse. particularly in the analysis of biological crystals.2
0.0
1. effectively. From the Bragg point of view in the Laue experimental arrangement the reflecting planes corresponding to the (hkl) reflection arefixedin direction. The sensitivity. Again.5. there are usually some variations of sensitivity in different parts of the image plate but these are normally less than 1. due to the photomultiplier tube for example.
•2
50
i
i
i
i
0. produced by Friedrich and Knipping in 1912. when the diffraction pattern will clearly show a corresponding symmetry (see §7.40. but it is no worse than for film. There is a little background noise in the system.4
0. The picture was crude but was good enough to verify von Laue's idea that crystals could diffract Xrays.10 The modern Laue method The very first Xray photograph.330 A is due to barium. Traditionally this problem of crystal decay has been met by using
. The absorption edge at 0. 5. particularly for protein crystallography. 5.8
1. The degradation of the crystal is not just due to the total Xray dose but also involves a time element. Laue photographs are very difficult to decipher and the only simple information they give is when the incident beam is aimed along a symmetry axis. as is the normal to those planes. The intensity of the PSL is linearly related to the Xray intensity over a wide range of about l:10 5 .3).6%. The absorption of the imaging phosphor BaFBr:Eu 2 + as a function of wavelength. The Xrays produce free radicals within the crystal by breaking off extremities of the protein molecules and it is the diffusion of these through the crystal that seems to do the damage.
The second problem is a little more difficult and can be understood in terms of Bragg's law. by the dimension of one pixel. in conjunction with a synchrotron source. is that since each spot corresponds to a different wavelength of Xradiation then it is necessary to interpret the intensity of a spot relative to the power spectrum of the source. This can be written as
(5.42. causing it to undergo some shortlived structural change.nk.37). Scanning
Experimental collection of diffraction data
Laser beam Limits of scan Optical fibres To photomultiplier. it can give a data set in a fraction of a second.nl =
d
hkl/n
and we may write
A/n
(5. Another possible application is if an experiment is carried out on the crystal.152
Fig. This change may then be investigated by recording its Laue diffraction pattern while it is in the transient state.26)
d
nh. data storage and image processing
Motion of plate 200 mm
individual crystals for only a limited time so that a whole batch of crystals would be required to collect a single set of data.41.25)
where dhkl is the spacing of the reflecting planes for the Miller indices (hkl). The Laue method offers an alternative approach since. which is well known for synchrotron radiation and possibly also the quantum efficiency of thefilmfor different Xray wavelengths. say exposing it to a laser beam. The scanning mechanism for an imageplate system. and the simplest. If we now consider the reflection with Miller indices (nh nk nl) then
(5.27)
. While it is quite a complicated pattern it can be seen that the reflections all lie on families of curves. equation (3. nevertheless. some problems to be solved. 5. A Laue diffraction photograph taken with synchrotron radiation for a crystal of the protein concanavalin A is shown infig. Knowing the orientation of the crystal it is possible to calculate the position of each diffraction spot and hence to index every spot on the film.5. At the end of each laserbeam scan the plate is moved in the direction shown. There are. The first.
The Xrays falling on the crystal have an upper and lower wavelength limit . and no reflection with higher indices will be present if the maximum possible k index is less than 76. R. 5. Under the conditions of the experiment Amin = 0.)
This means that in the Laue photograph all the spots for reflections (nh nk nl) will overlap for all n. for conconavalin A so that n cannot be greater than 4 for any reflection. it has been shown by Cruickshank and Helliwell that for most realistic experimental arrangements more than 85% of reflections on Laue pictures should be single spots without overlap and 95% should be either without overlap or singly overlapped. Laue photograph of the protein concanavalin A taken with Daresbury SRS wiggler radiation with exposure time of 19 ms.28)
where lx is the intensity due to reflection (hkl) and I2 is that due to reflection
. (Courtesy of J. because 17 is a prime number.0 A.0 A and 0.42. Let us assume that two diffraction spots overlap corresponding to reflection (hkl) with wavelength X and reflection (2h 2k 21) with wavelength A/2 and the combined intensity on the top film is I T = /i + I 2 (5.10
The modern Laue method
153
Fig. This is achieved by having a multiple film pack separated by layers of absorbing material. Again if a reflection such as the (17 38 2) is recorded then no reflection with smaller indices can be coincident with it.5 A and Amax = 2. Even when there is overlap the problem of separating the intensities due to the components is possible in principle. The absorption of Xrays in materials is wavelength dependent (§6.5 A. The problem is not quite as bad as it might seem atfirstsight.2. respectively.5. In general.2). Helliwell.
48°. reflections are produced in the zerolayer line making the following angles with the incident beam.154
Experimental collection of diffraction data
(2h2k2l).13°. 116°. 3 from the zerolayer line. To left looking in direction of beam . + a2l2.2 (a) An oscillation photograph is taken with Cu Ka radiation the rotation being about an axis of length 7. 78°. 85°.29)
From equations (5.13°. 130°. 41°. If the absorber reduces the intensity of radiation of wavelength X by a known factor ax and that of wavelength X/2 by a known factor a2 then the intensity on the bottom film is given by JB = aj. What are the indices of these reflections? Which reflections in the observable range are too weak to be observed? 5. 102°. 62°.5 mm. 2.9 A and can be rotated about the b axis.54 A) falls on the crystal normal to the rotation axis. 14.30)
With three films separated by two layers of absorbing material it should be possible similarly to unravel the intensities of three overlapped spots on the top film. (5.3 mm find the distances of the layer lines h = 1. (b) An oscillation photograph is taken with Cu Ka radiation and gives layer lines whose distances from the zerolayer line are as follows: h= 1 h=2 h=3 4.
The camera diameter is 57.JB)/(a x . 125°.2 A.3 For a certain crystal a* = 0. (5. 114°. When a 15° oscillation photograph is taken with Cu Ka radiation about the c axis. What is the length of the a axis? 5.
Problems to Chapter 5
5. To right looking in direction of beam .15.9 mm. By what angle must it be rotated for the (702) reflection to be produced? 5. The crystal is in the reflecting position for the (907) reflection.3 mm. An incident beam of Cu Ka radiation (X = 1.29) the separate components in the top film may be found as
and I2 = (aJT .1 A crystal has an orthorhombic unit cell with a = 11. The problems of the Laue method are such that crystallographers will usually prefer to use methods involving moving crystals and monochromatic radiation but for special applications the Laue approach is a useful additional technique. 9. 152°.20 A " 1 and y* = 80°. 90°. 61°. If the camera diameter is 57. 152°. b* = 0.28) and (5.3 mm.4 and c = 8.a2). 75°.4 A normalbeam zerolayer Weissenberg photograph is taken with Cu Ka radiation giving the (hkO) reflections for an orthorhombic crystal for
.
5 The energy of the electrons in a synchroton is 3.19(fo) and confirm that they follow the form of the curves shown in that figure.0 and b = 6. What field must be produced by the wiggler magnets? 5. 5. When the crystal is at the end of its traverse the Xray beam points straight down the a axis. On the top film the sum of the intensities of the overlapped spots is 262 and on the lower film 106. What is the critical wavelength and the vertical divergence of the emitted radiation? It is required to reduce the critical wavelength to 0.5 mm per degree of rotation.0 GeV and the bending magnet fields are LIT. Find the coordinates on the film of all possible reflections of the type 1/cO and T/cO. Assume that the oscillation is through 180°.3 mm and the translation constant of thefilmis 0. which is known to have overlapping (231) and (462) reflections is recorded on two films separated by an absorbing layer.5 A with a wiggler. Plot these on a replica of fig.0 A. What are the individual intensities of the two spots on the top film?
.6 A Laue photograph.Problems to Chapter 5
155
which a = 8. 5. the diameter of the camera is 57. The absorber allows through 30% of the shorterwavelength radiation and 60% of the longerwavelength radiation.
We shall now look at the problem of determining the total energy in a particular diffracted beam produced during one pass of the crystal through a diffracting position. This power is clearly proportional to / 0 and one can define the reflecting power by
where P(0) is a quantity with the dimensions of area. Fx(s). in a particular position corresponding to an angle 6 let the power of the reflected beam be (dE/dt)e. The crystal will reflect over a small range of angles around the 'ideal' position for a reflection (hkl). the weight associated with the point (hkl) being (l/V)Fhkl. This area phkl is called the integrated reflection. for this is a factor which must be present in every diffraction experiment. Because of various factors such as divergence of the incident beam and crystal imperfection the detailed shape of this curve is less important than the total area under the curve. 6.6 The factors affecting Xray intensities
6.1
Diffraction from a rotating crystal
It has been seen that methods of recording Xray intensities usually involve a crystal rotating in the incident Xray beam. However. Consider a crystal completely bathed in an incident beam of intensity / 0 . Let us first look at the situation when we have a stationary crystal in a diffracting position. there is a reciprocal space within which is defined the Fourier transform. and fixed relative to it.1 there is shown a typical curve relating P(0) to 6. The imperfectcrystal case we shall not consider here but we shall be concerned with the size of the crystal. the configuration we shall take is that the crystal is rotating about some axis with a constant angular velocity co and that the incident and diffracted beams are both perpendicular to the axis of rotation. In fig. For a theoretically perfect crystal of infinite extent the value of Fx(s) would be zero everywhere except at the nodes of a (5function reciprocal lattice. In order to do this we must make some assumptions about the geometry of the diffraction process. Associated with the crystal. Thus when the crystal is rotated with an angular velocity co ( = dO/dt)
156
. of the electron density of the crystal. if the crystal is imperfect in some way there may be nonzero Fx(s) well away from the reciprocallattice points and for a finite crystal there will be a small region of appreciable Fx(s) around each of the reciprocallattice points.
As in the onedimensional case. We shall now examine the problem of finding Ehkl. A typical curve for reflecting power as a function of 6. P(0)
157
dd coE. illustrated by fig.1 and by applying equation (2. 6. this factor will give the same shape of distribution about each reciprocallattice point.3)
The component of equation (6.2. b and c. the distance at which the factors first fall off to zero.
. Let us assume that we have. 3.22) as
L^S« electrons ^0
sin 2 (7ta's) sin2(7iiVcC's) sin2(7ic*s)
sin2(ixb#s)
(6. is of order (Naa)~l. Hence the total weight associated with the 'shape factor' is of order (NaNbNc)/(abc) = N/V where N is the total number of unit cells in the crystal and V the volume of the unit cell. kl h
(6.6.2)
where Ehkl is the total energy in the diffracted beam when the crystal sweeps through the diffracting position. i. In a direction corresponding to a scattering vector s the intensity of scattering can be found by a simple extension of the results in §3.e.3)
# sin2(7iiVfla*s) sin2(iiiVbb) s) sin2(7iNcc ( f l ) ( b ( c*s)
sin2(7ia*s)
sin2(7tb*s)
sin 2 (7ies)
is a 'shape factor' associated with the distribution of intensity around each reciprocallattice point.1 Diffraction from a rotating crystal
Fig. say. (N^)'1 and (JVcc)1. This rough assessment will be confirmed later. We saw in §3.1. respectively.1 that a finite onedimensional array of scatterers gives some scattering away from the directions of the main peaks and the same is true for a finite threedimensional lattice. Clearly as 5 • 0 so the height associated with this peak tends to N^NlN* while the width in each of the primary directions. aniVfl x Nb x iVc threedimensional array of point electrons with the array defined by the vectors a.
within which resides all the intensity associated with this particular reflection. the centre of the sphere of reflection.(s)2
(6. surfaces of constant intensity need not be ellipsoidal and what is shown is purely illustrative. In general the value of Fx(s) over the surface of the sphere will be small unless a reciprocallattice point lies on or very near the surface which is the condition we have previously noted for a diffracted beam to occur. represented by the ellipsoidal surface. has associated with it a small volume. with indices (hid).158
Fig. The intersection of a small region of the crystal Fourier transform as a shaded area round the point P. 6.
F. «/s. with the sphere of reflection. this subtends an angle X2da at C and the total energy scattered through it in time dr is
dEhkl =
(6.6. The situation for the particular diffraction geometry we are considering when the crystal is passing through a diffracting position is shown in fig. while the origin of Fx(s) is situated at O.2 the value of the transform is Fx(s) then this means that in the direction CP the intensity of scattering. Of course no such sharp boundary really exists.
The factors affecting Xray intensities
Let us now examine this question in more detail. if at the point P infig. 6. The volume is shown just entering the sphere of reflection and its surface of intersection with the sphere is that shown shaded which has total area a.4)
and in a small solid angle dQ in the direction CP the total scattered energy per unit time is Js dQ.6.22) we may write
2
1 + cos2 20. Within this surface is shown a very small area da. We may consider that the incident Xray beam is scattered in all directions.5)
and hence the total energy scattered during the total time T of the passage of
.3(a). is  Fx(s)2 times that which would result from a point electron at C.2 the crystal may be considered at C.2. Hence from equation (2. The reciprocallattice point P. Infig.
159
it) the small volume through the sphere of reflection is (6. It can be seen that a volume dadz of the transform moves through the small element of surface of the sphere. rotates by an angle codt in a time dt and the transform surface da moves to Q while P moves to F. 6.3(b) the plane COP is shown and the area da at Q on the surface of the sphere. From the diagram it is easily seen that if
.6)
JT Ja
It should be noted that as time changes so different crosssections of the volume pass through the sphere. (b) The small shaded volume between Q and Q passes through the area a on the sphere of reflection as the crystal rotates through an angle codt. (a) A schematic view of the passage of the region round a reciprocallattice point through the sphere of reflection as the crystal rotates. The crystal. and its associated reciprocal space.1 Diffraction from a rotating crystal
Fig.6. In fig.3. 6.
This leads to a#s = rj.9)
since (j) =^= 9 for the whole region of interest around the reciprocallattice point. as we have already noted.12a)
. Then a point s in reciprocal space will have coordinates (rj.IU/
^ S ~~ L ^ s J electrons * I r hkl I
where we now assume that we are only interested in s at.9)
_P
*" " ^
/
e2 yi+cos 2 20
2 sin 29 '
hkl
° \4Ti80c2m)
'
f sin2(7iiVflas) sin2(?i Nbbs) sin2(nNccs) JVhki sin2(7ia*s) sin2(7cb's) sin2(7ic*s) The integral in equation (6. £. since dadz is an element of volume in reciprocal space. or very close to.8)
which.£b* + Cc*. The effect of replacing point electrons by the electron distribution in a unit cell is to give the complete distribution of electron density in the crystal and the intensity of scattering from this is
$ _ r <f I
v IF
12
(fi 1 CY\
^O.6) can now be rewritten as (6. It is convenient to consider a set of coordinate axes with a*.12c) (6.160
The factors affecting Xray intensities OQ = s( = ——^ ) then dz = scos0 x codt.12b) (6.11) as (6.. We may now rewrite equation (6. \ * / The integration (6.11) should be taken in a region around the reciprocallattice point (hkl) but. Substituting from equations (6. the shape factor is the same for all reciprocallattice points and so we can carry out the integration around the origin.7)
z
Jascocos</>
(6. c#s = C and a volume element is given by dv = F*df/d^dC where F* is the volume of the reciprocal unit cell.10) into equation (6. b* and c* as the units of measurement along the three appropriate axial directions. the reciprocallattice point (hkl).3) and (6. b#s = <!. Q so that s = rja* 4. can also be expressed as
Ehkl=
Jsdv
(6.
6. The other trigonometric factor 1/sin 26 is called the Lorentz factor and depends on the diffraction geometry. The term ^(1 + cos2 29) is called the polarization factor and it should be noted that it depends on having an unpolarized incident Xray beam.2
sir2'^
sin 2
where the limits of integration include the area of interest around the reciprocallattice point. we see that the integrals have yielded a contribution N/V where N is the total number of unit cells in the crystal. The volume of the crystal is given by Vx = NaNbNcV so that the total energy in the diffracted beam is given by X3 ( e2 \ 2 l + c o s 2 2 0 F .2
J. Once the Lp factor has been applied to the observed intensities one is left with intensities
. if each of the intensities is multiplied by 2 sin 26/(1 + cos 2 26) the effect of the polarization term and the diffraction geometry will be removed. For the geometry which led to equation (6. B of the International Tablesfor Crystallography. K* = 1/V. This was the result earlier found by orderofmagnitude considerations.17)
One can see in equation (6. Hence we may write
This new integral is nonperiodic and the integrand falls off so rapidly with rj that the limits can be replaced by oo and — oo to give
rj) sm2(nrj) n2 n2rj 2
.1 that for large Na.„
IO
(6. for example. we are only interested in the region in which nrj is small. for example.18).18) the effect of various factors in the diffraction process. The individual integrals may be simplified in two stages. Firstly we know from § 3.15) is well known in diffraction theory and it equals Na. From equation (6. The Lorentz and polarization factors.^
The definite integral on the righthand side of equation (6. where Kis the volume of the unit cell.1 Diffraction from a rotating crystal
161
EhkI
~ coIo{4ns0c2m)
1
2sin20
FMI2K
*J. from equation (3.13) we now have
Since.26). are tabulated for various diffraction geometries in Vol. combined and referred to as the Lp factor.
63 x 10 3 4 Js and c.18) to be proportional to the volume of the crystal.4 there is depicted an Xray beam of intensity / having its intensity changed to / + d/
. it must be pointed out that although equation (6. it appears that the intensity in the direction of the diffracted beam will be increased fourfold. Let us find the order of magnitude of the total energy in a diffracted beam for a typical situation.162
The factors affecting Xray intensities
proportional to  Fhkl\2 (ignoring other corrections) and. is proportional to the volume of the crystal used. the velocity of light. 6. =6.18) was derived for a regular parallelepipedshaped crystal it is applicable to any shaped crystal. A typical copper Xray tube of 1 kW rating probably delivers about 1 watt of characteristic Kot Xrays which is emitted over a solid angle of 2n steradians (a hemisphere). This is seen in equation (6. these intensities are required if one is to solve the crystal structure. that is the conversion of the energy of the electromagnetic radiation to thermal energy. It is instructive to look at the effect of the crystal size on the energy in the diffracted beam. from the results in § 3. The crystal will be about 100 mm from the target and if we assume that the radiation is emitted uniformly and that the collimator allows the crystal to be completely exposed to Xrays. then the intensity of the incident Xray beam is
We now take
20 =
TI/2
A=1.54A Kx=1012m3 F=500A 3 co = 0. with the larger crystal the distribution of intensity around the reciprocallattice point is more condensed and effectively occupies onehalf the previous volume.1.e. and also by scattering. However. 6. =3 x 10 8 ms" 1 we find for this example n=^= 104. Planck's constant. In fig.05 radians s and we find This is equivalent to a number of Xray photons n = he From the values of h. If the volume of the crystal is doubled then. as we shall see in chapter 8.2 Absorption of Xrays When Xrays pass through a material their intensity is attenuated by absorption. This means that the overall increase in total energy is just doubled. i.
The law which will always be found to hold is d/_ / ~" or. 6.
. 6. An incident beam entering a crystal would. In addition. The quantity exp( — fix) is known as the attenuation factor.5 the effect of absorption on the intensity of the Xray reflection can be seen. If the crystal was an ideal. respectively. without absorption. but for the effect of absorption.19)
(6. small equal volumes in the vicinity of P and Q would give equivalent contributions to the emergent diffracted beam.
by passage through a thickness dx of material.
Fig. If we examine fig. have the same intensity at all points of the crystal for example at the points P and Q. When absorption is taken into account it can be seen that the incident beam at P will have a lesser intensity than at Q because of the longer path to P in the crystal and in fact the intensity at P will be IOQ~^XP while that at Q is IOC~^XQ.5. The diffracted beam from F is reduced in intensity by absorption by a factor Qn(xp+X£) a n ( j t k e p OS iti on i s similar for all other points in the crystal.4. The variation of the path lengths of the incident and diffracted beams for diffraction from different regions of the crystal. integrating and putting I = Io when x = 0.20)
The quantity n is known as the linear absorption coefficient of the material and it has the dimension of inverse distance. perfect crystal we should have to take account of the coherence of the radiation scattered from different parts of the lattice.6.2
Absorption of Xrays
163
Fig.
i = 1 r>e
(6. The attenuation of an Xray beam after passing through a small distance in a material. 6. Similarly the diffracted beam from P will be more attenuated in going from P to P' than does that going from Q to Q\ the attenuation factors being e " ^ and e~"*Q.
fi(x + *')}•
(6. The crystal crosssection is divided into a number of equal areas.We
. for such a perfect crystal the simple theory is.8(b).6. the gaps between them are nonparallel and of random thickness so clearly there can be no systematic relationship between the phases of radiation scattered from different parts of the crystal which are in different blocks.6. for example the ten shown in fig.6.6. For the crystal shown infig.Ox to O1O in thefigure. If. The fraction by which the total intensity is reduced by absorption is given by
. In practice perfect crystals are rare and usually we have what approximate to ideal imperfect crystals of the type illustrated schematically infig. The contribution to the diffracted beam of small volume dv is reduced by absorption by a factor exp{ . inadequate in a more fundamental way.
The factors affecting Xray intensities
This would mean a modification of the theory from which equation (6. we have a platy crystal similar to that shown infig. assumed ideally imperfect.8(a) then for one reflection most rays have a path like ABC while for another reflection the rays might be similar to DEF. The crystal consists of a mosaic of small blocks. in any case.21)
When fi is large the absorption factor A can have a large effect and must be corrected for if accurate results are required from the eventual structure determination. However. the small volume dv will contribute to the diffracted beam an intensity proportional to Q~tl(x+X)dv. absorption was ignored. each block being perfect but separated by faults and cracks in the crystal from other blocks. for example.= f
JV Fig. 6. as will be seen later.7. and the centres of these areas are found . 6. in this theory. 6.18) was derived since.7. A schematic diagram of a mosaic crystal.6. If the incident and diffracted rays are all in the plane of the plate then one can determine the approximate value of A by a graphical method. The small blocks are usually of the order of a few microns in dimensions. Thus to get the total intensity of scattering from the complete crystal we add the intensities of the radiation scattered from different regions of the crystal.164 Fig.
2 Absorption of Xrays
Fig.
165
HIM
(a)
now approximate the integral (6.23)
where dn is the number of atoms in the path of the beam per unit area and /ia. The simplest materials to consider are those which consist of a single element. is known as the atomic absorption
.?
(6. 6.22) this gives A = 0.044. follow in table 6. For the attenuation of a beam going through such material one may write
—
(6. For the example shown in fig.22)
where the total area is divided into M smaller areas. of course. B of the International Tables for Crystallography. which depends on the element. From equation (6.1. We shall now take a look at some general aspects of absorption with a view to discovering the general rules which govern it and also to finding how to determine \i for materials of known composition. the labour involved in the calculation also increases. (b) Approximate graphical method of calculating absorption factors by dividing crystal into small regions. assuming ju = 5 x 103 m" 1 . However if it is possible to shape the crystal by grinding it into a sphere or a cylinder then absorption factors can be expressed in the form of tables and these are given in Vol. for example. some of these are very sophisticated and will compute values of A for crystals of somewhat irregular shape.21) by the summation
.8(2?) the details of the calculation.8. 6. The accuracy of this method of calculating absorption factors is increased if a greater number M of points is taken but. For a sphere of radius R. the absorption factor is a function of fiR and sin 6 only and can be very concisely tabulated.6. Computer programs have been written to calculate absorption factors. (a) For a crystal of very unequal dimensions absorption corrections can vary greatly from reflection to reflection.
0112 0. or lose energy through the Compton effect. the value of /ia steadily reduces as X decreases. Within the atom.25 4.85 0.85
1. At the point P the photon energy is insufficient to eject any of the electrons of an unexcited atom and the photons either interact with the whole atom increasing its energy of motion.43 0.15 4.47
0.0039 0.27 0. XM*. However at Q the photons have just enough energy to eject an L m shell electron.14 0..42 0.90 1.14 0.2471 0.43 0.) i + Xi All linear dimensions are in mm
exp{ .97 0.50 7. with a further reduction of X.0159 0.56 0. 6. with energies he/A.90 1. However if the wavelength is reduced to the value of Q the value of /ia sharply increases and then.80 4.25
coefficient.14 0.23) can be transformed to be in terms of the distance traversed by the beam.and there are several of them . If experiments are done to measure /ia as a function of the wavelength of the Xradiation the results appear as in fig.50 5. which is equivalent to increasing its temperature..0009 0.41 0.9.)} 0. Between the absorption edges the general falloff of the absorption curves follows a form close to fia = CZ*X5/2 (6.28 0.43 0. Starting with a long wavelength.55 4.38
0.83 0.24)
where Z is the atomic number of the material and C is a constant which depends on the nature of the two flanking absorption edges.14 0. Point (0
The factors affecting Xray intensities
X x. will have more energy for smaller X and hence one should expect them to be more penetrating.43 0.14 0.47 1. They can be understood in terms of the electronic structure of the atom. In fig.10 the slab of material has unit crosssectional area.42 0.0144 0. 1. electrons exist in definite energy states and the absorption edges correspond to energies hc/X which are just sufficient to eject an atomic electron from the atom.0144
1 2 3 4 5 6 7 8 9 10
0. say at the point P.57 0.40 2. and thickness dx.85 2.11 0.166 Table 6.n{xt + x. The Xray photons.0578 0. /ia decreases again.are known as absorption edges. If it contains dn atoms then the total mass of material is Mdn/NA where M is the atomic weight and NA is Avogadro's
.69 0. These sudden discontinuities in atomic absorption coefficient . Similar effects occur corresponding to the other atomic electrons and gives a whole series of absorption edges. + x.14 0.47 0.0608 0. Equation (6. a new mechanism for interaction of the photon and the atom becomes available and results in a sharp increase in absorption. 6.14 0.05 4.0112 0..
Although }im has been introduced by considering the absorption of elementary material it can also be used for mixed materials or compounds. K3 Ka
number. 6.
Unit area
Xray beam direction
. and thickness dx.19) and (6. An Xray beam traversing a slab of material of unit crosssectional area.23) as (6. The density of the material is given by _Mdn and we can now rewrite equation (6.26) M or M (6.10. 6.6. If the element is nickel then the Cu Ka and Cu Kp wavelengths are as shown.25)
We have written fim = \ijp where jum is called the mass absorption coefficient.27) (6.26) Comparing equations (6.9. Variation of absorption coefficient with wavelength for a typical element.2 Absorption of Xrays
167
Fig. The important property which makes the mass absorption coefficient a useful quantity is that it is completely independent of the state of the
Fig.
The attenuation factor for the beam is then given by equation (6.54 A is 0.2 x 1 0 3 k g m " 3 Na atomic weight 23 fim(X = 1.460 X 1. By such means one can determine linear absorption coefficients for any material when the individual elemental mass absorption coefficients and the density and composition of the material are known.2 x H x 10. solid and liquid sulphur.1mm.
JJL/P
is the same for
Thus if one tabulates for elements their mass absorption coefficients for various wavelengths then linear absorption coefficients for elements can be deduced no matter in which state they exist.67 x 10 4 m" 1 .54A) = 10. Thus
/'diamond = (/Oc + diamond = 0.0m 2 kg" 1 Cl atomic weight 35 [im(A = 1. 2 x 103 x f f k g m " 3 .62 X 10 3 Hi" * /White = fan)c + Pgraphite = 0.25 X 10 3 Hi" ' = 1. water and steam. This means that jnm = ice.0 + 2.28)
where the summations are taken over all the elements in the compound and p p represents the partial density of the element within the compound.diamond.2 x ff x 3.86 X l O 3 ! * " 1
This same principle can be extended to determine the linear absorption coefficients of mixtures of elements or compounds by using the relationship
/'compound = Z /'element = Z ftnPp (6.03 X 10 3 m~ X Amorphous = (/Oc + Pamorphous = 0.54 A) = 3.168
The factors affecting Xray intensities
material. Thus the value of jxm for the element carbon for X = 1.88 X l O ^ " 1 = 0.54 A) in passing through a slab of NaCl of thickness 0. solid CO 2 and CO 2 gas.67 x 104 x 10" 4 ) or 0.460m2 kg" x and from this we can find the linear absorption coefficient for the three forms of carbon . An example will illustrate more clearly how one uses this equation.6m 2 kg" 1 . The following information can be found in tables: Density of NaCl = 2.188.20) and is exp(1. C of the International Tables for Crystallography.460 X 2. We shall determine the attenuation of a beam of Cu Ka radiation (X = 1. graphite and diamond. Mass absorption coefficients for the elements are listed in Vol.6) x 10 3 m" 1 = 1. Thus \i = (2. graphite and amorphous carbon black.
.460 X 3. The proportion of the two elements by mass is Na: Cl = 23:35 so that the partial densities are
and (p p ) cl = 2 .52 X 10 3 m " * = 1.
6. respectively. in which is represented the passage of the incident Xray beam through the material and the formation of the diffracted beam.0075 of the K(3 and thus constitutes a very efficient filter.3 Primary extinction So far in our consideration of diffraction from a crystal we have assumed that the atoms are under the influence of an incident beam whose intensity has been modified only by absorption in the crystal.8 the use of absorption filters to remove unwanted radiation from an Xray source was mentioned. However.389 A.11. Iffig.9 represents the atomic absorption coefficient of nickel then the Cu Ka and Cu K3 wavelengths are shown as Ka and K3. A schematic representation of the formation of a diffracted beam originating from points distributed throughout the crystal. The density ofNi is 8. 6.542 and 1. 6. which is the energy required to eject an electron from the K shell. We imagine that the Xradiation is 'established' in the crystal which is therefore occupied by a continuum of radiation. In fig. and it is usually required to remove the shorterwavelength component.6. Every point in the crystal is under the influence of the incident beam and also some part of the diffracted beam which is moving in a different direction. respectively.44 of the Ka radiation but only 0. For example.57 and 27. It is clear that the absorption is far less for the Ka radiation. a sealed copper tube will give as its main characteristic output Cu Ka and Cu K(3 radiation of wavelengths 1. beam
Diffracted beam
. Incident .3 Primary extinction
169
In § 5. The K absorption edge for copper.9 x 10 3 kgm~ 3 and hence the linear absorption coefficients are 4. We shall first investigate the propagation of a plane wave through a crystal in the direction of the incident radiation.11. 6.12 there is represented a section in which
Fig. it is clear that this simple picture is not really true.5 m2 kg" 1 . the element one less in atomic number than copper is nickel (atomic number 28) and its K absorption edge falls between the CuKa and CuKfS wavelengths.6. the mass absorption coefficients of Ni for Cu Ka and Cu K(3 radiations are 4.1 x 104m~1 and 24. For example. must be at a wavelength shorter than either the Ka or K0 radiations.A foil of thickness 20 fim ( = 2 x 10~5m) transmits a fraction 0. If the crystal is in a strongly reflecting position the extra effect of the diffracted beam component will not be negligible. However if we look at fig.5 x 104m~1 .
For r = 0. However some small part of the Xradiation will be scattered by the scatterers Q so that the point P.12(6) that radiation from all the points on the ring of radius r will arrive at P with the same phase relationship. starts from O and is directed in the direction AO that is along the negative real axis.6.13(a). ar = % and the first part of our phasevector diagram. illustrated infig.29a) where the % is the Thomson scattering phase shift. (a) The formation of a plane wave front from wavelets originating from a plane of scatterers. The phase lag behind the radiation coming from Q will be
*
or
< 4 >
The phase lag ar with respect to the unscattered radiation coming from Q is given by (6. 6.170 Fig. (b) All radiation originating in the annular region arrive at P with the same phase relationship. We imagine that the points Q are sufficiently densely packed so that the plane containing them may be considered as a uniform partially scattering plane. is at any time also receiving some radiation coherently scattered by each of the points Q. It is clear fromfig. for example.
The factors affecting Xray intensities
New w a v e front
Old wave
front
there are scatterers through a plane labelled Q1 to Q5.6. Most of the radiation passing through the plane <2i2s will n o t t>e scattered and will eventually pass through the plane containing the point P in a time which depends on the distance Q3P.12.
.
29b)
On the phasevector diagram the contribution of a small annular region of radius r and thickness dr will be a line segment. Taken together. {a) Phasevector diagram for radiation originating from a plane of scatterers and arriving at a plane wave front. dropping the subscript r. (6. {b) Radiation going along OA without being scattered is reduced in intensity due to destructive interference with radiation doubly scattered at C and O.31) The geometrical shape corresponding to equation (6. is 7t/2 ahead in phase of the radiation arriving from the nearest scatterer.29b) and (6.6. where the change of angle is proportional to arc length. Thus we have dqr =
r
2nrdr
2
\r +d2f
(630)
where K is some constant. whose length will be proportional to the area of the annulus and inversely proportional to the distance s. The resultant.
171
(a)
By differentiating equation (6. 6.31). dqr. is a circle. OC. equations (6. This latter factor is equivalent to an inversesquarelaw falloff for intensity.3 Primary extinction Fig. With only the
.13.30) give.29a) we find
r
Inrdr X(r2 + d2)r
(6.
When a crystal is producing a Bragg reflection there is no phase difference introduced by path differences from the scatterers arranged on a lattice. Since the primary beam is reduced in intensity so is the diffracted beam and the total energy of the reflection is less than that indicated by equation (6. These equations express the fact that each beam is depleted by scattering into the other beam and enhanced by scattering from the other
. 2 x n/2) out of phase with the unscattered radiation and destructive interference will result. He considers that in some volume element of the crystal the intensity / 0 of the beam in the incident direction and the intensity / of the beam in the diffracted direction are related by
and ^L = .e. The effect of primary extinction is very much reduced if the crystal is nonperfect and if the mosaic blocks are small. A different theoretical approach by Zachariasen (1967) has the conservation of energy as one of its fundamental hypotheses. As r tends to infinity the end of the line approaches C which is so situated that OC is approximately at right angles to OA. This is equivalent to K being a slowly decreasing function of r and the result of this is for the phasevector diagram to become a spiral rather than a circle. Crystallographers sometimes dip their crystals in liquid air to reduce the effect of primary extinction. It can be shown that at any point in the crystal the diffracted wave is also n/2 behind the incident unscattered radiation. The unscattered radiation passing along OA is joined by radiation doubly scattered at C and O. However in the above analysis we have ignored an obliquity factor which takes account of the fact that scattering is strongest in the forward direction and falls off with increasing angle of scatter. This theory. and a is the diffracted power per unit distance and intensity. 6.172
The factors affecting Xray intensities
considerations given above this is what the phasevector diagram would look like. 6. At any particular point in the crystal the only diffracted radiation which has a special phase relationship with the incident beam is that which arises in the same mosaic block and this will be of negligible intensity if the blocks are small. Thus the scattered radiation has a n/2 phase lag with respect to that unscattered in a forward direction.cl + alo (6.32)
where tx and t2 are lengths in the directions of the incident and diffracted beams.13(6). suffers from the drawback that energy seems not to be conserved. The thermal shock to which the crystal is thus subjected produces the desired effect of breaking it up into a mosaic structure. In fig.18). The primary beam is reduced in intensity and so is the diffracted beam and one might well ask where all the energy has gone. This will be n (i. For a = 2it the end of the line will be at 0' and as a increases it moves along the dotted path shown in fig.13(5) there is shown the incident beam passing through a crystal and some rays which have been doubly 'reflected'. respectively. which is the one usually given in elementary texts.
through a small
. When the crystal has a mosaic structure. of initial power 70a. In fig. the result corresponding to equation (6. that some of the energy goes into the diffracted beam. The factor by which the diffracted intensity is reduced for a spherical specimen and for low scattering angles is given by (6. 6. For small aT this is approximately
0()
Lot
(6. 6. where the incident beam enters the crystal. We cannot explore here the full depth of Zachariasen's treatment of these equations but a selection of the solutions he obtains will give the general pattern of his results. consisting of very small mosaic blocks. with domain size small compared to that of the whole crystal. However when the crystal is in a diffracting position there is available another mechanism for removing energy from the incident beam that is to say.14 the passage of the incident beam. The sum of the two equations gives
which is the condition for the conservation of energy. These equations are augmented by the boundary conditions that. This process is quite independent of the phenomenon of diffraction and could be recorded by measuring the attenuation of a beam of Xrays passing through slabs of material.34) where Ms the mean path length in the crystal and equals \r for radiation passing straight through a sphere. the angle the beam makes with the 'ideal' direction as given by Bragg's equation and clearly a falls off very rapidly with s and is significantly only for small s.35a)
which is an exact solution for an infinite plane parallel plate when the incident and reflected beams make the same angle to the normal to the plate. The coupling constant a is clearly a function of £. / 0 equals the intensity of the incident Xray beam and / = 0.35a) is (6. Since d is less than the value of o for a perfect crystal a reduction in primary extinction results from mosaic structure.35b) where Tis the mean path through the whole crystal and 6 a mean o for the distribution of orientations of the domains.6. there is another type of extinction process which may occur.4 Secondary extinction It is found that even when a crystal is ideally imperfect.4
Secondary extinction
173
beam into itself. We have already found that the intensity of an Xray beam is attenuated by its passage through a material by the absorption of some of the Xray energy and its conversion to thermal energy.
For a complete sweep of the crystal through a reflecting position there will be some average // given by Q(0).8(fc) and table 6.14.630 x 1 0 3 m " 1 whereas the normal linear absorption coefficient is only 1.36b)
The magnitude of \i — \i can be very considerable.613 A).5 x 10 3 m" 1 (// = 5.044 to 0. If the value of// is 5. 6. closer to the incident Xray beam.1)) which is a measure of the power of the diffracted beam from this small element of the crystal. If the mosaic blocks were all precisely parallel then all of them would diffract simultaneously and the secondary extinction effect would be the same as that for a perfect crystal.174
Fig. Crosssectional area i
The factors affecting Xray intensities
P(0)Io
mosaic element of a crystal is illustrated.36a) where Q(0) is the reflecting power per unit volume of the mosaic element. for the (200) reflection with Rh Ka radiation {X = 0. If we now consider a crystal similar in shape but
. Secondary extinction can be thought of as a shielding effect which exists at a point in a crystal due to diffraction by the layers of crystal above it .0 x 10 3 m~ 1 ) then the numbers in the column n(xt + x[) are all increased by 10% and the value of A changes from 0. (6. for example some experiments by Bragg. However if the mosaic blocks have a range of orientations then they do not all diffract together as the crystal is rotated and the shielding effect is consequently reduced.1.that is. One would not expect to find secondary extinction with a powder sample where only a tiny fraction of the crystallites are diffracting at any one time. The overall result of this additional depletion is effectively to raise the linear absorption coefficient from // to //(0) where
(6. The emergent beam power is depleted firstly by an amount filoat due to ordinary absorption and secondly by an amount equal to P(0)/ o (equation (6. This can be illustrated by the example shown in fig. the value of // = 1. This phenomenon is known as secondary extinction and it is difficult to eliminate by any treatment of the crystal. James and Bosanquet (1921) with rock salt crystals showed that.070 x H ^ m " 1 .035 or by about 19%. Since secondary extinction is equivalent to a change in the linear absorption coefficient of the material of the crystal its proportional effect on intensities is reduced if very small crystals are employed. Effective increase in absorption coefficient due to diffraction. 6. It certainly can be reduced to some extent by increasing the imperfection of the crystal.
for example the time of transmission of Xrays through the crystal. It is probably rather more accurate to say that the complete crystal structure corresponds to an arrangement of minimum potential energy and where. A further reduction by a factor of two in the dimensions gives A^ = 0. The first thing to note is that the frequencies of vibration of atoms are very low in relation to the sort of times in which we are interested . To begin with let us take one unit cell of a onedimensional structure containing N atoms per unit cell where thejth atom has mean fractional coordinate xj and. the diffraction pattern being produced is that of a 'frozen' crystal in which all the atoms are stationary and displaced by some distance from their mean positions. We are going to assume that all the atomic vibrations are completely uncorrelated so that averaging processes can be carried out for individual atoms. a change of 12%.
6.6. = 0. These vibrations will affect the relative coordinates of the atoms and hence the diffraction pattern and we shall now investigate this phenomenon. The total intensity pattern that we get over any long period of time is a timeaverage of the patterns which are obtained at successive instants. For the most part crystallographers accept that only a few very strong reflections will be affected by secondary extinction and these do not usually interfere with the processes of determining or refining crystal structures. for example. so in practice there is a limit to the smallness of the crystal which can be used.349 and secondary extinction now gives a 6% reduction of intensity. at some instant of time.5
The temperature factor The picture we have created of a crystal is that of a rigid stationary assemblage of atoms bound together in a periodic pattern. For this reason we may imagine that. Every atom in a crystal structure is bound to numbers of other atoms by bonding forces of various types and the position of the atom is that corresponding to the minimum potential energy. Thus we get a modified view of a crystalline solid in which all the atoms are vibrating about their mean positions with amplitudes which increase as does the temperature of the solid. a substance crystallizes in two different forms it means that two arrangements exist with potential energies virtually equal to each other and lower than that of any other arrangement. at any instant of time. If an atom is disturbed from its equilibrium position it experiences a restoring force tending to move it back again and we can see that the atom can acquire thermal energy by oscillating about its equilibrium position. We must now consider how the picture is modified by the presence of thermal energy because thermal energy on the atomic scale is energy of motion.381 and A^. = 0.145. an absolute displacement from that position uy If all the other unit cells were in a precisely similar state the structure factor of index h would be given by
. However this reduction of crystal size and reduction of secondary extinction is bought at the expense of lowering the diffraction intensities.165 and A p.5
The temperature factor
175
with its dimensions reduced by a factor of two we find A^ = 0.
42).41)
It can be seen that the overall result of the thermal motion of the atoms is effectively to modify their scattering factors to UJ]T =ffxp(Sn2u2sm2e/A2).44) (6. exp ( 2icifc^ ) ^ exp f .and since we are considering a particular s and since Uj and (/> are independent of each other we may write (s'U •) = s Uj cos (j). (6.
7=1
(6.45)
. We write for the structure factor at some temperature T
[7/Jr = £ ffi*P (2nih^)exp(2iufac.. varies with time. (6.37) since Uj varies from one unit cell to the next and. without the introduction of 6.) = 1 + Inih^.42)
If the threedimensional case is now considered it will be found that the equation corresponding to (6. in a more convenient form.43)
where 0 is the angle between the vectors s and u. appears in the form /27i2(su/}.38) together with h/a = 2 sin 6/A gives
JV
l 7 J r = E/.40a)
(6.2n2h2 %\ fl a
(6.37)
/
The actual structure amplitude in a direction corresponding to h will be a time and space average of equation (6. within one unit cell.38)
where exp{2nih(Uj/a)} is the average value of the diplacement term. so we have
\" 2
2iii/z— j ^= 1 — 2n2h2 ^ or.)
(6.40b) substituted in equation (6.176
The factors affecting Xray intensities
" ( U \ = £ ffxp 2nih ^ exp(27ii/zx)..39) \ aJ a a For simple harmonic or other symmetrical vibrations u} = 0.exp(87i 2w?sin 2 0/i2 )exp(27ii^). In all practical cases Uj is small enough to be able to write approximately expf Inih^.40b)
\
/
V
)
The result (6.
7=1
\
a
(6.2n2h2% (6. Now (s*Uj)2 = 52w2 cos 2 (j) (6.
6. There is a uniform probability distribution for the ends of a randomly oriented unit vector to fall on any point of the surface of the sphere so that the probability that it falls within any specified area.5
The temperature factor
177
Fig.15. 8TL 2 W
(6. is replaced by su±j where u±j is the magnitude of u7projected on s. The probability of the vector terminal being within the shaded annular region is (27i sin (j) d(j))/4n so that the average value of cos 2 <j) is cos 2(/>= Equation (6. da.
The value of cos 2 (j) is the average value of cos 2 4> where <f> is an angle between some random direction and a particular direction.46) where u] is the mean square displacement of the atom from its mean position The threedimensional and onedimensional formulae can be expressed in similar terms if S'u.6. 6. If
= 8TL2W 2 .49)
and the quantity Bj is known as the temperature factor of the jth atom. is da/47i. The annular ring on the sphere of unit radius gives the probability of a random angle in the range Oit being between <p and d<£.
. One may then write
T
= fjQxp(

j sin 2 9/X2)
(6.48)
then
UJ]T
=ffxp(
9/A2)
(6.15 the direction of s is shown along OA and a sphere of unit radius centred on 0. In fig.47)
where u2Lj is the mean square displacement of the atom perpendicular to the reflecting planes.43) may now be written (6.
k and / then for thejth atom one will see the timeaveraged electron density. In general.16.16(b) the atom P will move mainly at right angles to the bond NP. as illustrated infig. By and large. The quantity [/}]T. In fact this is rarely so and the magnitude and mode of vibration of an atom will depend very much on its environment. In that case we have (6. (a) Atom B vibrates most strongly in the plane perpendicular to AB. have an equal probability distribution in space . is the Fourier transform of the timeaverage of the electron density for the range of positions taken up by the vibrating atom. so to speak. Directions of oscillation in plane perpendicular to AB
(a)
(b)
. 6.
Fig. Similarly if one had a group of atoms of the type shown infig. (b) Atoms Q and R should have a larger amplitude of vibration than does atom P.50) or for intensities (6.51) The factor by which the observed intensities are reduced by thermal vibrations. less energy is involved in changing bond angles than in changing bond lengths. so that an atom out on a limb.6. exp( — 2Bsin2 6/A2).16(a).178
The factors affecting Xray intensities
We have tacitly assumed above that the vectors u.an assumption of vibrational isotropy. However for all but the most accurate work it is usually sufficient to assume that the thermal vibrations are isotropic and that the values of B are the same for all atoms. the scattering factor of the vibrating atom. the surfaces of constant timeaveraged electron density approximate to ellipsoids and in the most precise crystalstructure analyses the parameters which describe these ellipsoids are determined (see §9. will tend to oscillate mainly in the directions perpendicular to the bond. Vibration of the bond NP will also affect the atoms Q and R whose motion is augmented even more by vibrations of the bonds PQ and PR.6. If an electrondensity map is computed with the structure factors [Fhk J T for all h.3). is known as the DebyeWaller factor.
r x 
In practice the value of B can be found from the experimentally determined values of ^hkl. the method of doing this is described in §7. 10 . DebyeWaller factor. The dependence of B on the absolute temperature Thas been theoretically investigated by Debye who produced a formula whose application is limited to materials which are elements. moving independently of all the others. 20 .2369 0.1153 0. then its vibrational motion in the alternating electricfieldof an incident electromagnetic wave might be governed by an equation of the form mx + gx + kx = Eoe exp(iatf).7866 0..0215 0.6 Anomalous scattering In determining scattering factor equations as in § 2.5.6.52. where m is the atomic mass. 06 .6 Anomalous scattering
179
Table 6.8521 0. kB is Boltzmann's constant
and
xjo
f e^ p ^d1£ .0183 25 . 0. 08 . and for the limit of Cu Ka radiation (sin 6/A =^ 0.0067 30 . 0.IB sin2 0/k\ for three values of B (in A2) sin 0/A 02 .2 for various values of B and sin 6/L For B = 3 A2.4493 0.0025
Typical values of temperature factors fall in the range 23 A2 and. If we consider one atomic electron.0773 0. it will be seen that the intensity is reduced to about 10% of its unmodified value.53)
.1653 0. to illustrate their order or magnitude. DebyeWaller factors are given in table 6. h is Planck's constant.8187 0. 6.65). for example. exp( . (6.5273 0. 0. 04 .6 it has been assumed that all the atomic electrons are unrestrained and undamped so that the scattering phase shift is % for each of them. If© is the characteristic temperature of the material and x = &/T then the formula is .2.0408 0.3829 0.
57)
the phase shift of n with respect to the oncoming wave E = E0Qxp(icot) is made more evident.
CD YYl
(6. Substituting this in equation (6. k the restoring force per unit displacement. Eo and co/2it are the amplitude and frequency of the incident wave and it is assumed that there is a damping force gx proportional to the velocity.56) as x = J ^ i exp{i(cor + 7i)} (6.56)
This represents an oscillation of the electron with the same frequency as the oncoming wave but 71 out of phase with it .54b) we obtain
(col — co2)2m2 + g2co2 (col ~~ a)2)2m2 + g2co2
(6. without recourse to complex notation.53) m is the electron mass.54a)
(6. The steadystate solution of this equation is x = ^exp(icor) where Eoe Eoe[(k .55a)
o*
and t a n s = . In our present classical model the amplitudes of vibration of atomic electrons are
.i^ 2 (k — co m) + igco (k — co2m)2 + g2co2 Another form of solution.co2m) .180
The factors affecting Xray intensities
In equation (6. gC°2 .as is shown by the negative amplitude. is x = R cos(cot + s) where
E
(6. By writing equation (6.55c) k — arm For an unrestrained and undamped electron one would have k = 0 and = 0 giving
x= ^eXp(icot).58)
When co = co0 and the damping constant g is small it can be seen that the amplitude of oscillation of the electron would be very large.. (6. When/c # 0 there is a resonance frequency corresponding toco = co0 where
k — a>lm = 0
so that we may write k = colm.
61b)
For a Thomsonscattering electron one would have <\>A = 1 and cj)B = 0 so that. Thomsonscattering theory is only truly applicable for co > oo and in the vicinity of an absorption edge the vibration of the electron.63a)
Let us consider a diffraction situation where we have an iron atom in the crystal and Cu Ka radiation {X = 1. for the imaginary part. that which has a wavelength corresponding to the absorption edge.60)
and Xo would correspond to one of the absorptionedge wavelengths shown in fig. 2 J'2 OQ — co ) m
^ „" .co ) m
2
22 2
+ g2ao2
(6.61a)
and. if the absolute Thomson contribution to the scattering factor of this electron is p0. However.
gco3m
<t>B = j—2
{col . The critical wavelength Xo is given by Xo = — (6.co2)2m2 + g2co2
2X2~2
2~^
(6.9. other than as free electrons) while the others would be
.56). we can express the real and imaginary components of the amplitude of the scattered wave as fractions of that from a free electron by dividing the components in equation (6.
— (O2)m2
^
=
(co 0 .59) that when co » co0 their behaviour is not very different from that of a free electron.74 A and is at a greater wavelength for all the other absorption edges so that we might expect the two K electrons to scatter anomalously (i. — W = = POWA . the angular frequency co0 is that for an Xray photon with just enough energy to eject the electron from the atom. from a quantumtheory point of view. for the real part. The K absorption edge for iron is at 1.6 Anomalous scattering
181
continuously and infinitely variable.°. even for these. Po 2
+ g co
(6. we can see from equation (6. will be very different from that predicted by the Thomson formula. The electrons which are most tightly bound to the nucleus and therefore have the highest value of k are the K electrons but. i.6.59) by the amplitude given in equation (6. 6.1) = ^ .54 A) is being used. These fractions are.e. then the actual contribution is
Po = Poi^A = Po + Pi + P2I (662)
q2co2
where Pi
and
= nJrh . The amplitude of the scattered wave will be proportional to the amplitude of the electron vibration.e. and hence its scattering.
083 x 1 0 1 9 s ~ \ If we write — = ij/— m co then we find
<t>A = ^ and 4.182
The factors affecting Xray intensities
closer in behaviour to free electrons.64)
(6.224 x l O ^ s " 1 and co0 = 1. is when the velocity is least.53) we have implied. what amounts to the same thing.65a)
The actual behaviour of the electrons will depend very much on the value of \j/ or. occurs when the acceleration is greatest which. However we can calculate an orderofmagnitude value for a mean damping constant g. For the two wavelengths concerned co = 1. and therefore the greatest damping resistance.61^ .66)
The total distance it travels in unit time is D = 4R x frequency =
71
(6. In fact this does not tie in with our picture of a harmonically vibrating electron because the greatest radiation of energy. that the damping force is proportional to the velocity.67)
and therefore the mean force it experiences due to the radiation of energy would be
F
Q e2Ra}3
The mean velocity of the electron also equals D so that the average force per unit velocity becomes _ F ne2co2
We can test this mean value of damping constant to see whether or not it
.that is to say. By writing the damping term as gx in equation (6. that g is a radiationdamping constant. for a simpleharmonic motion. One possible mechanism which would give us an estimate of the value of g is the radiation of energy by the electron . It can be shown by a simple extension of equation (2. cpB = 2(6.65b)
(6. on the value of g. on the contrary.18) that an electron vibrating with an amplitude R emits energy at an average rate
6
=
1 2 ^
(6.
(6. is the mechanism by which Xradiation is absorbed by the atom and transformed into heat.2 x 104 times the amplitude of a Thomson electron. cf)B = 1.74)
If the intensity of the incident beam is / then this is also the energy passing into the block per unit time and equation (6.6. Another approach which can give us a rough estimate of g is by consideration of the mass absorption coefficient of the element in question. If there are N absorbing electrons per unit volume then the total energy absorbed per unit time by passing of the beam is ° dx. For an electromagnetic wave the electricfield strength and intensity are related by
. If the K absorptionedge wavelength is being scattered then the two K electrons should be oscillating more strongly than any others.55a). whatever its origin. The damping force acting on the electron is gx and when it moves through a distance dx does work d W = gxdx = gx2dt or. which implies that the electron is vibrating with 1. R = E0e/gco0 so that
A us F2p2
=
(6. shows that radiation damping is far too feeble to offer an explanation of the anomalous scattering effects which are actually observed.2 x 104. or is very close to that wavelength. (6. When co = co0.74) represents the change of this intensity. say d/. from equation (6.6 Anomalous scattering
183
gives sensible values for the scattering fractions cf)A and cj)B when the incident radiation has the wavelength of the absorption edge. For co = co0 we have
cj)A = 0 and <PB = 48g o c 3 m co0m — = 2— (670)
or. Let us assume that the damping force.
d W = gR2co2 sin2(cot + e)dt.72)
^r
2 •
(6 73)

Now let us consider the situation when the radiation passes through a thin slab of material of thickness dx and of unit crosssectional area.71) Since the average value of sin2(cot + e) is \ we have as the rate of loss of energy through damping forces for each K electron o2. This very large value. when numerical values are substituted.
Idx. It will be noticed in fig.38). The results of this calculation are shown in table 6.77)
where \i is the linear absorption coefficient of the material.75)
d/= . 2. (6.78)
where NA is Avogadro's number and if we assume two fully effective K electrons for each atom then N — 2n and
9 =
For an iron atom at its K absorption edge fim = 46 m 2 kg "* and M = 56 so that
If this value of g is used for all frequencies then <\>A and cj>B can be computed as a function of frequency or wavelength. if we refer to the normal atomic scattering factor as / 0 . From equation (2.19) to obtain Ne2 = u 2gcs0 or Ne2 ^ (6. then we have
/o = i iPsh
J=I
If the nonanomalous contribution of the two K electrons is taken to be unity for each then we can write the actual scattering factor as
.3. Now the K electrons are the ones most tightly bound to the nucleus of the atom and the ones which most closely resemble point electrons. for a reasonable range of sin 0/A.12(fo) that the scattering contribution of the K electrons of carbon do not fall off very rapidly with sin 0/L For an iron atom where the K electrons are even more tightly bound the falloff will be even less and.76) to indicate a reduction of the intensity of the beam.76) 2gcs0 The negative sign is put into equation (6.184 I = E2cs0 so that Ne2
The factors affecting Xray intensities (6. may be neglected altogether. If the density of the material is p and the atomic weight M then the number of atoms per unit volume is n= ^NA (6. we can now compare equations (6.76) and (6.
40 1.1) and f2 = 2<\>B.20 0.1) 0.62 1. An important consequence of anomalous scattering is that it causes a breakdown of Friedel's law.42 0. The general form of the classical solution is quite good except that it predicts a finite f2 for X > /lK whereas the quantummechanical theory gives / 2 = 0 under this condition.98 2.12 0.6 Anomalous scattering
185
Table 6.84 3.19(a) and the equality of  Fhkl \ and  FMT\ can be seen.00 0.31 1.81b)
The terms/i and/ 2 are.00 4.3 and in fig.18 0.75 0.99 0.18.12 0.00 0.06 0. 6.00 0.42 0.09 0.77 4.20 0.47 0.17.00 0.71 0.84 1.33
<t>B 0.82)
.16
i/2 where / i = 2{(t>A .25 0. (6.25 1. respectively.00 1. Then Fhkl = #exp(i(/>) + (/ + i//)exp(27iir5s) = [Kcos(/> +/cos(27iiys) — /'sin(27iiys)] + i[R sin 0 + / ' cos(27ir5s) +/sin(27ir5s)] and similarly FMT= [Rcoscj) +/cos(27tiys) +/'sin(27ir 5 's)] + i[R sin 4>+f cos(27tiys) /sin(27ir 5 s)].42 0. However if the scattering factor of thefifthatom has anomalous components then  Fhkl  is no longer equal to  F^T\.66 0.75 1.50 0. Let the contribution to Fhkl of the other four atoms be R exp(/0) and the scattering factor of the fifth atom b e / + if.00 1.
Afl.06 1. A quantummechanical treatment of anomalous scattering has been given by Honl (1933) and the results obtained for iron from this theory are shown infig.00 1.6.83)
(6. the real and imaginary changes in the scattering factor due to anomalous scattering and these are shown in table 6.50 2.75 2. The separate contributions of the five atoms to the (hkl) and (Ek 7) structure factors can be shown on a phasevector diagram as in fig.81a) (6.40 0. 6.50 1.94 2.54 8.3.08
/ i = 2{(j>A . It should not be expected that this rather crude theory based on classical ideas should give good agreement with experiment but it does give a reasonable qualitative picture.
0.
(680) (6.6. Let us consider a noncentrosymmetrical structure containing five atoms in the unit cell.00 1.
apart from a small change in the magnitude of t h e / is to rotate the contributions to FhM and FMJboth in the same sense.186
Fig. The anomalous scattering components / i and f2 for iron from the classical theory. for centrosymmetric structures.
.5. Anomalous scattering can be an important aid to structure determination and the method by which this is done is described in §8. This breakdown of Friedel's law is also shown in fig. Friedel's law is retained. 6A9(b) where it will be seen that the effect of the anomalousscattering component. 6.
The factors affecting Xray intensities
1.83) it will be seen that  Fhkl  ^  F^j\.17.82) and (6.0
From equations (6. The reader may readily confirm by drawing similar diagrams that.
18.0
.6 Anomalous scattering Fig.0
2. The anomalous scattering components /i and f2 for iron from the quantummechanical theory. 6.6.
187
Si
10
1.
b = 12.0.19.0 and c = 10. A beam of Cu Ka radiation (X = 1. (a) Friedel's law for a noncent rosymmetric structure without anomalous scattering.
The factors affecting Xray intensities
(b)
Problems to Chapter 6
6.02 radians sec ~*. 6.1 A crystal of volume 1 0 ~ 9 m " 3 is rotated about its c axis at an angular velocity of 0.54 A) of intensity l O W m " 2 is incident on the crystal at right angles to the axis of rotation.28 x 1 0 3 k g m " 3 has the chemical composition C 1 4 H 2 2 S 2 P 2 .188 Fig. The structure is orthorhombic with a = 6. (b) The breakdown of Friedel's law with one anomalous scatterer. What is the linear absorption coefficient of the material for Cu Koc radiation?
. How many photons will there be in the (240) diffracted beam for a single passage through the reflecting position if  F 240 1 = 120? 6.2 A material of density 1.0 A.
300 0.96 and/ 2 = 1.Problems to Chapter 6
189
Element H C P S
nm{k = 1.00. c of lengths 2.2.250 0.286 0.
.429 0.4 if the overall temperature factor for the structure is 3.54 A) 0.81
Atomic weight 1 12 31 32
6.525 0.714 0.393
c c c
Calculate the structure factors of type (hkO) with STRUCFAC for Cu Kot radiation (X = 1. b.425 0. 6.0 x 10 3 m" 1 what is the absorption factor for the (240) reflection? Use the graphical method described in § 6. 1.41 9.3 The crystal in Problem 6.300 0.0 A2 and that bromine has anomalous scattering components /i = — 0.0 A2.542 A). 6.525 0.625 0. b = 7. Note the breakdown of Friedel's law.00 and y = 110° has a projection with the following structure:
Atom Br N C C 0.1 is a block with sides parallel to a.00 and 0.46 7. given that the overall temperature factor is 3. If the linear absorption coefficient of the material is 5.00.400 0.643 0.46.4 Recalculate the structure factors in Problem 3.50mm. respectively.5 A crystal of space group PI with a = 10.04 m 2 k g " 1 0. The program STRUCFAC (appendix I) can be used for this calculation.571 0.
Such measurements should be carried out on many crystals for there is a tendency for crystals to exist in a number of slightly different forms in each of which some facets may not be present. In fig. if the direction of the field was reversed then some electron density would move out from between the nuclei and the bond length would increase. It may happen that the outer electrons of atom B are more shielded from the nucleus than are those of atom A and hence they may more easily be displaced. The two atoms are bonded together and the electron density is distorted from the configuration it would have for the superposition of that from two isolated atoms. so that the aggregate effect would be to change the physical dimensions of the crystal. Let us see what mechanism can produce this effect. The sign of the change of dimensions
190
. in favourable circumstances.4 measurements of crystals with an optical goniometer can. conversely. and in varying degrees. may be such as to enhance the buildup of electron density in the bond. For a crystalline material thefieldwill produce an induced polarization and all the bonds would be affected in one or other of the two possible ways. l. Byandlarge. This will have the effect of attracting the two nuclei inwards and so of shortening the bond. the physical principles involved and the apparatus which may be used for the tests. If the pair of atoms is placed in an electricfieldthis will lead to a displacement of the negatively charged electron cloud with respect to the positively charged nucleus.
Piezoelectric effect The first physical phenomenon we shall consider is that of piezoelectricity. when incorrect conclusions are drawn from optical goniometry it is in the direction of assigning too high a symmetry to the crystal. This is the process whereby when a material is placed in an electricfieldit undergoes a mechanical strain and. as shown in fig.7 The determination of space groups
7.\(a) there is a schematic representation of a pair of atoms with their surrounding electron density. The distortion is in the sense of building up extra electron density in the bond between the atoms which tends to attract the nuclei inwards and hence keep them together. This diminution in bond length would be small and dependent on the first power of the field. However it is sometimes possible to be reasonably sure by means of such measurements that a crystal structure either has or does not have a centre of symmetry. Consequently the net migration of electrons. We shall briefly consider these.1(6). when the material is mechanically strained it becomes electrically polarized and produces a field in its environment. 7. reveal the crystal class.1 Tests for the lack of a centre of symmetry As we have seen in § 1. the measurements of which can be used unequivocally to detect the lack of a centre of symmetry in a crystal structure. There are a number of physical properties of crystals.
This effect is used in the quartzcontrolled oscillator.2(a) a onedimensional crystal structure is illustrated and it will be seen that there are four different types of bond which.3. The netflowof charge will lead to a polarization of the material and hence afieldwill be produced around it.7. the natural frequency of one of the modes of mechanical vibration of the crystal controlling the electrical oscillation of a circuit coupled to it. if the material is physically strained. such as AB and A'B\ whose contributions to the change of dimensions are equal and opposite so that there is no externally observable effect.
(b)
would depend on whether the shortening or lengthening of bonds predominates. On the other hand. 7. The
. (a) Representation of electron density associated with a pair of bonded atoms.1
Tests for the lack of a centre of symmetry
191
Fig.7. (b) Change of electron density in an electric field. the electronic charge will flow in and out of the regions between nuclei. depending on their nature. A very simple type of piezoelectriceffect tester is shown infig.1. Infig. The piezoelectric effect is reversible so that. for the centrosymmetric structure shown infig.7. can give an overall increase or decrease in the dimension of the crystal.1. However it should be noted that an overall effect can only occur for a noncentrosymmetric crystal.2(2?) there will always be pairs of bonds.
3. 7. A piezoelectriceffect detector. it is because the charges on the surface are usually neutralized by stray charges on particles of dust. 7. (a) A onedimensional noncentrosymmetric structure. This is the electrical polarization of a crystal shown by the development of opposite charges on two opposite faces of a crystal when it is heated. that frequency.
Variablefrequency oscillator
Fig. is placed between the plates of a condenser which is in series with a variablefrequency oscillator and a loudspeaker. no bonds in one unit cell are related.2. At any particular frequency the current in the circuit will depend on how many of the crystals have a mode of vibration at. 43 2.
The determination of space groups
(a)
A
O
B B' • o o •
A'
O
(b)
o o •
O
o o
sample. Thus it is inferred that in a pyroelectric crystal there exists permanent polarization which suggests the presence of electric dipoles
. the vibrations of the various crystals go in and out of resonance and a series of clicks is heard from the loudspeaker. etc. does not permit a piezoelectric effect. bonds exist in pairs in opposite directions. In addition Wooster (1938) showed that the symmetry of one point group. When the frequency is slowly changed however. (b) A onedimensional centrosymmetric structure. In fact since a crystal must always be at some temperature it suggests that pyroelectric crystals should be polarized even at room temperature and.
Crystals
Loudspeaker
It must be emphasized that while the detection of the piezoelectric effect certainly denotes the lack of a centre of symmetry no conclusion is possible from a negative result as the piezoelectric effect may be present but just be too feeble to be detected. if this is not observed. The frequency of the oscillator is well above the audio range and so nothing is heard from the loudspeaker. in the form of a large number of crystals.192
Fig. or close to. Pyroelectric effect Another physical property which can be detected in noncentrosymmetric crystals is that of pyroelectricity.
Mean positions of charged groups at room temperature
Oscillations induced by heating
Optical activity A material is said to be optically active if. which are optically active when crystalline.4 the situation is depicted where on heating the crystal the mean distance apart of the charged atomic groups. notably organic molecular substances. A very simple form of pyroelectric test is to insert into a specimen consisting of small crystals a heated glass rod. The precaution should be taken of repeating the experiment with a cold rod to ensure that some other effect is not causing the adhesion. The same is true of structures with planes of symmetry or inversion axes. The above test is not a very sensitive one and other types of test are possible. such as quartz and certain inorganic salts. 7.
Fig. If this is so then the additional polarization due to heating can be ascribed to asymmetric oscillation of the dipoles. and therefore the mean dipole moment is increased by raising the temperature. and for these the optical activity is clearly a property of the molecular structure. If the crystals are pyroelectric they will develop charges on their surfaces. Clearly centrosymmetrical structures cannot be optically active since centrosymmetrically related objects are also enantiomorphically related and a centrosymmetric structure is its own enantiomorph.7. The two contraryrotating forms of the material are enantiomorphs. vaporized or in solution. the sets of normals to the faces being mirror related in the two types of crystal. Asymmetric oscillations of charged groups give rise to increased mean dipole moment as temperature increases. For organic materials the optical activity is associated with the tetrahedral
. If looking towards the source of light gives a clockwise rotation the crystal is said to be dextrorotatory. When materials are optically active they often exist in two forms which rotate the plane of polarization in opposite senses. otherwise it is laevorotatory. induce opposite charges on the rod. Some materials. are optically active in the crystalline state but not when fused or dissolved in solution. and so adhere to it. when planepolarized light passes through it the plane of polarization is rotated. This means that it is the specific arrangement of atoms in the crystal that determines the optical activity. that is to say that structurally they are mirror images of each other. Sometimes this shows itself in the crystals themselves. There are other substances.1
Tests for the lack of a centre of symmetry
193
within the crystal. In fig. However tests for pyroelectricity are rarely performed by crystallographers so we shall pursue this topic no further. molten. 7.4.
However no conclusion can be drawn if optical activity is not detected. The polarizer and analyser are initially adjusted so as to give no passage of light when the tube is full of solvent. 1. light passing through any other than a cubic crystal is usually split into two components polarized at right angles. If the crystals are soluble then the solution can be tested by means of the apparatus shown in fig.5. (a) Enantiomorphically related fourbonded carbon atoms. The light is planepolarized by a polarizer P (a Nicol prism or polaroid sheet for example) and after passing through the tube of solution traverses the analyser A. 7. This is illustrated in fig. If light passes through when the solvent is replaced by solution then the dissolved crystals must consist of molecules of one enantiomorph and so the space group cannot be centrosymmetric. 7.5(a) for two carbon atoms with four different atoms attached to each. as we shall see in the following section.
w
w
(a)
HO
OH
OH
HO
OH (b)
HO
.194
The determination of space groups
arrangement of bonds around a carbon atom bonded to four other atoms. (b) Enantiomorphic forms of tartaric acid. the two arrangements are enantiomorphically related. 7.5(b) two enantiomorphically related molecules of tartaric acid are shown. The effect might be too small to be detected or the crystals may be a mixture of the two enantiomorphic
Fig.6. It is not too simple to observe optical rotation from crystals because. In fig.
7. mainly electrons.
P A
195
Solution
forms (racemic mixture) and hence neutralize the effect of each other in solution.A cos cot + \Au.1 Tests for the lack of a centre of symmetry
Fig. of frequency v. cos 2cot (7.2) (7. The effect of this is that when a beam of light.7. In some crystals there are certain directions in which the phase correlation is preserved and then there can be a very high efficiency for second harmonic generation . If for a region round a small element of charge there is a lack of symmetry then the vibration of the charge element in an electric field due to a light wave can be anharmonic. There is a snag connected with harmonic generation. When there is a centre of symmetry then to any displacement form such asfig. due to dispersion the different frequencies of light travel at different speeds in the crystal and hence there is a loss of phase correlation for the second harmonic generated at different points along the path of the incident beam. This provides a very sensitive means of detecting the lack of a centre of
.1).1)
and it can be seen that the displacement has a constant component which is equivalent to a polarization of the material and also one of twice the incident frequency. coherent inphase displacement.6. It is due to the fact that the restoring force per unit displacement of charge is a variable and is less for displacements in one direction than for the other. This is only likely to occur appreciably at highfields(high intensity of light) and the general form of the vibration is shown in fig. like fig. U(a) with a = 0. equation (7. However since the nonlinear component will only be appreciable for high intensities it requires the light from a pulsed laser to easily observe these effects. passes into the crystal then a second harmonic of frequency 2v is generated.2. Let us assume that the vibration has the form x = A cos cot(l + a cos cot) which is that shown in fig. Then x = \Ai 4.l(b) and. A simple polarimeter.for example 20% for potassium dihydrogen phosphate. 7J(a). The form of displacement. It should be noted that harmonic generation may occur only for a noncentrosymmetric crystal. is rather special and for more general displacementtime relationships third and higherorder harmonic generation is possible. Frequency doubling Light is propagated in materials by inducing vibrations of the charged components.7J(a) there is another. within it. the second and higher harmonics do not appear. l. in combining these two.
already considered two optical properties associated with noncentrosymmetrical crystals . A commercial instrument incorporating these ideas. dealing fully with the subject of crystal optics. In fig. some of which are referred to in the bibliography. It is found that the refractive index of a crystal sometimes varies with direction and the way that this happens is related to the crystal system. 7.2 The optical properties of crystals We have. has been produced by the North American Philips Corporation. In this section there is given a very brief account of the subject which. 7. Another revealing property of a crystal is its refractive index or. There are many excellent text books.196 Fig. (b) Oscillation of electrons in centrosymmetric relationship to those in (a). For other readers there is appended to this section a short summary of the information which can be elicited by the examination of crystals with a microscope. inevitably. A typical pulse from a moderatesized ruby laser contains 1 joule of energy or about 10181019 photons. One way of envisaging the variation with direction of the refractive index
. 7.7. the SHA or Second Harmonic Analyser. what amounts to the same thing. must fall short in clarity from that of a longer treatment.
The determination of space groups
1 
1 (b)
symmetry.8 the specimen is a quantity of small crystals randomly oriented so that some may be well placed for most efficient harmonic generation. The light passing through the crystals is filtered to remove most of the primary frequency and then passed into a grating spectrometer set at the second harmonic frequency. in the previous section.optical activity and frequency doubling. For those readers with some preliminary knowledge about the behaviour of light in crystals it is hoped that the material given here will be informative. (a) Asymmetric oscillations of electrons giving rise to harmonic generation. A fairly straightforward photocell can detect 1000 photons so that a second harmonic conversion efficiency of about 1 part in 1015 should be detectable. A second filter will remove any primary radiation which reaches the slit S by random scattering and the second harmonic can be detected by the photocell P. the velocity of light in the crystal.
The cubic symmetry implies that any physical properties of the crystal are identical in the three mutually orthogonal directions along the axes.8.
Kilter
Laser
Crystals Grating spectrometer
of a crystal is to consider a point source of light within the material and to note the limits of the disturbance after some time T. For an isotropic material such as glass the disturbance will. The light from a point source within such a crystal will be found to split into two components which are polarized at right angles to each other and which in general have different refractive indices. If we consider a plane wave front.10. after a time AT. The rayvelocity (or wave) surfaces may be of two types which are shown in one octant of a set of cartesian axes in fig. 7. All points on this surface will act as a new source of light and so the wave front spreads out preserving its spherical symmetry. The axis of the spheroid along the unique axis equals the radius of the spherical surface. if the surface of the disturbance was not a sphere it would have to be something else having cubic symmetry. The following points will be noted: (i) One of the wave surfaces is spherical while the other is an oblate spheroid (negative uniaxial crystal) or a prolate spheroid (positive uniaxial crystal). extend out to a spherical surface. 1. 7. Thus it would be possible to interpret the
. as one would expect. The next type of crystal we shall consider is the uniaxial crystal which is a crystal having a unique axis and belonging to the trigonal.7. 00'O". by Huygens' construction. PP'P". 7. It is found that a crystal belonging to the cubic system behaves in a similar way. as in fig. In addition the properties in sets of directions related by the triad or tetrad axes would also have to be identical. the new position of the wave front. then it is possible to determine. Harmonicgeneration detector.9(a) and the planes through the surfaces containing the unique axis are shown in fig. A spheroid is an ellipsoid with two equal axes and in this case the equal axes are perpendicular to the unique axis so that the spheroid has circular sections perpendicular to the unique axis.9(b). moving through the medium. tetragonal or hexagonal systems.2
The optical properties of crystals
197
Fig. (ii) The surface has been called a rayvelocity (or wave) surface and this is not to be confused with a wavefront which is a surface of constant phase moving through the crystal.
7.7. Thus infig. PP' and QQ\ moving at different velocities and with their electric vectors in the directions shown. The striations indicate the electricvector direction.9(a) also indicate the directions of the electric vector for the plane wave moving in the appropriate direction in the crystal.7.198 Fig. (a) Ray surfaces of uniaxial crystals.11.9. (iii) The striations which define the surfaces infig.
The determination of space groups
[a]
spheroidal wave surface as the envelope of the wave fronts moving outwards in various directions in the crystal as is shown infig.12 the initial unpolarized wave front. It will be noted that the unique axis is also a direction in which a plane wave of any state of polarization (or unpolarized) will always move with the same velocity and for this reason it is termed the optic axis of the crystal. whose normal is in the direction OP is split into two components.1. It must be
. 00'.
in particular this implies that all directions are optically equivalent
.9 (b) Sections of the ray surfaces containing the optic axis.
Optic axis
(h)
stressed that the optic axis represents a direction in the crystal not a particular line.10. The crosssections of the spheroidal surface perpendicular to the optic axis are circular.
There is a certain selfconsistency in the form of these surfaces. 7. Wavefront generation by extraordinary ray component. 7.
Fig.2
The optical properties of crystals
799
Fig.7.
Again. 7.
Direction of optic axis
Direction of electric vector
Electric vector perpendicular to plane of figure
One of the properties shown by uniaxial crystals is double refraction. Two images of the spot are seen . This can be seen if one looks at a small spot on a piece of paper through a parallelsided slab of calcite. A piece of Polaroid held above the slab and rotated extinguishes the spot images in turn at positions separated by TI/2.200 Fig.
The determination of space groups
perpendicular to the optic axis. no matter in which direction in space the light travels. For trigonal.one where expected along the normal to the slab but the other displaced from the normal.12. 7. tetragonal or hexagonal symmetry one would expect sets of directions related by these symmetries to be equivalent and hence it can be seen that if the surface is to be any sort of ellipsoid at all it has to be a spheroid. if one looks at the spherical surface one sees that the electricvector directions are all perpendicular to the optic axis. showing that the light forming each of the images is planepolarized and that the planes of polarization are perpendicular to each other. Ray front as envelope of wave fronts. If the calcite slab is rotated as
.
Fig. Generation of wave fronts and direction of electric vectors for the two components in a uniaxial crystal. and hence optically equivalent.11.
The experimental arrangement is shown schematically infig.
Path of E when crystal rotates
(a) Extraordinary wave front
Ordinary wave front
\
4
O'
(b)
. The rays and waves which behave like those in an isotropic medium and give rise to the image 0 are called the ordinary rays and waves. (b) Production of ordinary and extraordinary images in a uniaxial crystal.7.2 The optical properties of crystals
201
illustrated infig. (a) Path of extraordinary image when crystal rotates. one moving normal to the surface and the other at some angle to the normal. does not move whereas the unexpected one. However the electric vector is always in the plane of the wave front or is tangential to it if the wave front is not planar.13.13(a) then the expected image.13(b) which shows a principal section of the calcite slab. a section containing the optic axis. which is also perpendicular to the surface of the slab. A plane wave front 00' falls normally on the surface and it can be seen that it is split into two plane waves.7. This latter wave front is not normal to its direction of motion. 0.14(a). that is to say. The reason for this behaviour may be followed infig. 7. An experiment which clearly identifies a uniaxial crystal is to examine it in convergent light between crossed Polaroids (or other devices for producing planepolarized light). light from an extended source S passes through
Fig. The wave front is a surface of constant phase while the direction of motion of the light is the direction in which the energy moves and these need not be perpendicular to each other.7.7. E. rotates about 0. the others are called extraordinary rays and waves.
202
Fig. (d) The relative amplitudes and directions of the components for various rays in the cone.14. (c) The division of the cone of light into two components.
The determination of space groups A
Viewing system
(b)
t(c)
Ordinary component
Extraordinary component (d)
. (b) Cone of light of semiangle 9 entering the point 0 of a crystal. 7. (a) Experimental arrangement for observing a crystal in divergent light.
the ordinary wave surface. light passes through for a whole range of angles contained within a fairly wideangle cone.9(a). 1. Infig.72
The optical properties of crystals
203
a polarizer P and a lens L so that. The circles correspond to striations on the sphere.7.14(d) we look at the situation in (b) straight down the optic axis and we also show the striations corresponding to the wave surfaces in fig. If. It should be noticed that this conclusion for the points B and F (also B' and F') is independent of 6 and so this produces in thefieldof view a dark cross as is shown infig. Appearance of uniaxial crystal in convergent light between crossed Polaroids with optic axis perpendicular to crystal face.7A4(b) there is represented a cone of light passing in at the point 0 of the crystal and making an angle 6 with the optic axis which is here assumed to be normal to the crystal face.7. in practice. When this ray reaches the crossed Polaroid analyser A it will be completely absorbed and so no light gets through the system in a direction corresponding to B.7. Infig.7.14(c). After passing through the crystal and a crossed Polaroid analyser A the light is viewed by what amounts to a telescope focussed at infinity so that what is seen at any point of thefieldof view is representative of the light passing in some direction through the crystal over the whole of its area. 7. This is shown infig. Within the crystal the original cone will split up into two separate cones corresponding to the two wave surfaces in a uniaxial crystal but once they emerge from the crystal they will again each form a cone of semiangle 6. on the other hand. at all points of the crystal. the relative displacement of the two emergent cones will. It is clear from (d) that a ray passing through the point B of the cone produces only an extraordinary ray in the crystal since there is no component of the electric vector in the direction of the circular striations.15.3)
Fig. The direction of the electric vector for light passing through P is shown by the striations and this is also shown by the doubleheaded arrows at the base of the cone.15. the extraordinary wave surface.14(c) that there will be a phase difference between the components introduced by passage through the crystal given by
(7. It can be seen infig.
. We now consider the separation of the original cone into the separate cones. the direction of the light corresponds to the point D where OD makes an angle it/4 with OB then two components pass through the crystal which are of equal magnitude. be very small. Similarly a ray passing through the point F of the cone produces only an ordinary ray and again is blocked by the analyser. and the radial lines to striations on the spheroid.
Fig.7. the two components in the crystal are unequal in intensity and one does not get complete blackness when 0 is a multiple of 2n. Resultant when cf) = Directions of polarization of components passing through the crystal
2TT
Plane polarized
Circularly polarized
Plane polarized
Circularly polarized
Plane polarized
If the crystal surface is parallel to the optic axis then the appearance of the field under the same experimental conditions as infig.17. 7. It is clear that as i increases from zero so < monotonically increases from zero (ft = // when i = 0). 7. Resultant of adding two perpendicularly planepolarized beams of light with various phase differences. 7. This gives a dark point in the field of view. 7.15 and when this is seen it denotes a uniaxial crystal. We can see / > in fig.204
The determination of space groups
where \i and // are the refractive indices for the two polarization directions and i is assumed to be the same for both rays.7. Optic axis
. We have assumed that the light is monochromatic and that one obtains only patterns of light and dark regions.16 how the two components recombine for various values of (j> between 0 and In. For other ray directions.17.16.14{a) is shown infig. The complete resultant field of view is shown in fig. Appearance of uniaxial crystal in convergent light between crossed Polaroids with optic axis contained in the crystal face.and this cannot go through the crossed Polaroid A. When <j> is a multiple of 2n the recombined beams give a resultant equivalent to that entering the crystal . with the same value of 6 but given by C and E on either side of D. If white light is used then the condition for blackness in the field of view varies with the wavelength and the result is a series of coloured rings although the dark cross is retained.
Fig.
7. tetragonal and hexagonal systems. the refractive index of light is independent of its state of polarization.that the electricvector direction is equivalent for each of them and along the Y direction.these are crystals belonging to the trigonal.20.19 where two points. The optic axes are shown as OQ and OQ' in fig. The same consistency will be found for the circular boundaries in the X Y and YZ planes. The surface characteristics can also be appreciated by their intersections with the principal planes which are shown in fig.14 then the resultant field of view shows the presence of the two optic axes.7. This point is illustrated in fig. the optic axes are directions in which there is a single phase velocity and they are the normals to the common tangent planes to the two parts of the surface. Along the unique axis of the crystal. Biaxial crystals have two optic axes but they are not in the directions OP and OP'. on a plane wave front are used as origin points for Huygenstype wavelets to construct a new position of the wave front.7. 7. 7.18(a). For other directions light breaks up into two components polarized at right angles to each other and moving with different velocities. Summary 1. If a biaxial crystal is used in the experimental arrangement of fig. for example. The striations represent the direction of the electric vector for a plane wave tangential to the surface at the point in question. monoclinic and orthorhombic systems are known as biaxial crystals and their ray surfaces are much more complicated than those for uniaxial crystals. O1 and O2. Two examples of these forms are shown in fig. It can be seen that rays travelling out to the circular boundary all travel with the same velocity and this is consistent with what is seen infig. 7. These latter are known as ray axes. It can clearly be seen that if the wave front is parallel to the common tangent plane to the two parts of the surface then there is only a single phase velocity. a typical ray surface is shown infig. 7. (b) Uniaxial .18(a) which shows that all directions of the electric vector occur at P. In the XZ plane. 7. The surface is represented in one octant of a set of rectangular Cartesian axes and is completed by mirror reflection in each of the principal planes. on the other hand. the curves of intersection are a circle and an ellipse. In the X Y plane the two curves cross over and so a ray moving in the direction OP has the same velocity for any plane of polarization.18(fc).7.2 The optical properties of crystals
205
Crystals belonging to the triclinic.18(a).these are isotropic in their optical properties and behave optically like a noncrystalline material such as glass. This definition of an optic axis also applies to the uniaxial crystal for which the ray axis and optic axis are identical. This is evident from fig. In terms of crystal optics crystals can be divided into three types: (a) Cubic .18(fc). called the optic axis.
. If the crystal face is perpendicular to the bisector of the acute angle between the optic axes then the appearance will take a symmetrical form dependent on the orientation of the polarizer to the line joining the optic axes.
.Fig. {a) Ray surfaces for a biaxial crystal.18. 7. (b) Intersection of ray surfaces with principal planes of Cartesian axes.
The optic axis is along the direction in which both rays have the same phase velocity.19.2 The optical properties of crystals
Fig. Other forms of these patterns exist and can be recognized. These are the two optic axes of the crystal.17 . 7.20.
(c) Biaxial .a biaxial crystal with the normal to the crystal face bisecting the acute angle between the optic axes.a uniaxial crystal with the optic axis contained in the crystal face. 7. 7. Some characteristic patterns are shown: (a) Fig.7. 7. There are two directions in which light of any polarization moves with the same phase velocity. If a crystal is viewed in convergent light between crossed Polaroids as in fig. Combined wave front
207
Fig. monoclinic or orthorhombic systems.20 . 7. It is perpendicular to the common tangent surface to two parts of the ray surface. Appearance of a biaxial crystal in convergent light between crossed Polaroids for two different orientations of the crystal. (b) Fig. 2.14(a) then one can usually distinguish which type of crystal one is dealing with.a uniaxial crystal with the optic axis normal to the crystal face. (c) Fig.these are crystals belonging to the triclinic.15 .
. 7.
Fig. The orientation of the crystal can be determined by examination with a microscope.3 The symmetry of Xray photographs The very first type of Xray diffraction photograph.
. (b) A Laue picture down a hexad axis. For this type of arrangement one obtains a large number of diffraction spots . All orders of the same set of Bragg planes will overlap with the spots produced by different wavelengths (see §5.21.10). 7.21(a) there is depicted the crystal at 0 and a reciprocal lattice point at P. (a) With Xray beam down triad axis three equivalent points fall on sphere of reflection together. the Laue picture. 7.indeed. For some X the sphere of reflection will pass through P and with all wavelengths available diffraction may take place for any reciprocallattice point on the incidentbeam side of the plane through the crystal perpendicular to the incident beam. An important characteristic of this type of examination is that it is rapid and therefore well worth doing with a new and unknown crystal. identification and composition determination are also possible in some circumstances.208
The determination of space groups
3. 7. was made by diffracting white (nonmonochromatic) Xrays from a stationary crystal. In fig. one should obtain almost a complete set of diffraction data.
.41). say b. This will be seen infig.21(6). When an oscillation photograph shows a mirror line then it is certain that the space group is at least monoclinic and if mirror lines are located about two different axes the symmetry must be at least orthorhombic (a third axis giving a mirror line must also then be present). a twofold screw axis or is perpendicular to a mirror plane then \Fua\ = \Flia\ = \Fw\ = \FaT\.exp{27ii(/zx. A typical Laue photograph taken down a hexad axis is shown infig. will reveal the presence of all the symmetry
.5)
from which relationship (7. (x.7. Thus with a diad axis *m = I /.2\(a) the incident beam is directed along a trigonal axis so that there are two other reciprocallattice points P' and P" equivalent to P and related to it by the trigonal axis. z) mirror plane (x. It is evident that the value of X which gives the reflection P will also give those corresponding to the symmetryrelated ones. (x. z)./z. + lz)} = I /.3 The symmetry of Xray photographs
209
The Laue photograph is particularly suited to detecting symmetry axes if the Xray incident beam is directed along. (7. which can be obtained from Xray photographs. The symmetry of the weighted reciprocal lattice. \ + y. is a diad axis.7.22 which shows that the reciprocallattice points (hkl) and (hkl) cut through the sphere of reflection simultaneously. P' and P".)cos{27i(/2xj + Izj)}
J=i
(7. all of the same intensity.[exp{27u(foc.4) follows. The reader may confirm that relationship (7.4) We can deduce this relationship from the basic structurefactor relationship. by noting that for these symmetry elements there are pairs of atoms with related positions as follows: diad axis (x.7. z). the symmetry axis. Infig. Even if the axis is slightly offset from the incident beam the trigonal symmetry will still be evident.. y. (x. + kyj + lz$ + exp{2ni(hxj + ky3 . z). If an oscillation photograph is taken about a 2 or 2 x axis or about an axis perpendicular to a mirror plane then the photograph will have the zero layer as a line of mirror symmetry. The triangles of spots will not be equilateral and they may vary slightly in intensity since they are produced by different wavelengths but the overall evidence from the whole photograph is usually unmistakable. One can also detect on other kinds of Xray photographs sets of equivalent reflections (other than Fhkl and F^j) which give information about symmetry elements in the crystal.. or very close to. z). y.7. For example if a unitcell axis.)}]
j=i
= £ 2^exp(27ii/cj. y.4) also follows for the other two symmetry elements and also for any tetrad or hexad axis. z) screw diad axis (x. y. These will form an equilateral triangle of spots on the film. + ky. equation (3. y.J.
7.1. glide planes and nonprimitive lattices.for example screw axes. in general.
The determination of space groups
Incident beam
elements associated with the various crystal classes except for a centre of symmetry. these are known as the eleven Laue groups. They are associated with the crystal classes in accordance with table 7. Such systematic absences are always found whenever there is present a symmetry element which involves a translation .reflections which are systematically zero because of spacegroup considerations rather than accidentally zero (or unobservably small) due to the particular arrangement of atoms in an asymmetric unit. z).22.4 Information from systematic absences The types of information we have considered so far have enabled deductions to be made about the crystal system or even the crystal class. Cface centring Atoms occur in pairs with coordinates (x.210 Fig. 2 or 2l axis the points (hkl) and (hlil) touch the sphere of reflection simultaneously. The type of observation we shall consider in this section is that of systematic absences . There are only eleven possible symmetry arrangements for diffraction data. With Xray beam perpendicular to 2. only a limited amount of data is recorded at any one time and this is usually from some asymmetric region of the reciprocal lattice. Because of Friedel's law all weighted reciprocal lattices have a centre of symmetry whether or not the crystal structure has one. It should be noted that Friedel's law does not imply that every Xray photograph will have a centre of symmetry since. 7. y + ^. z) and (x + \. The structurefactor equation can be written as
. We shall consider the systematic absences due to some of the more commonly occurring types of symmetry element. y. If the Xray diffraction data are examined in greater detail there can often be found sufficient information to enable the space group to be determined unambiguously or at least to be narrowed down to a choice of two or three.
7b) (7. When this type of systematic absence is found the presence of Cface centring is established.7. 6mm.j)cos{27i(/ixJ. 6. + kyj + lZj)} + exp{27ti( — hxj + kyj — lZj) + Tii/c}]. z) and (x.9a)
and.1.. 23. From this we see that for Cface centring there are systematic absences given by Fhkl = 0 for h + k odd for any /.) Now i</>) = exp i(0 + 2rm) and (2n (7. m3 43m. for k odd. 32.izj)}
(7. y. mm2.
F
(7. 3m 6/m 6m2. 4.
Laue group 1 2/m mmm 4/m 4/mmm 3 3m 6/m 6/mmm m3 mbm Crystal classes 1. 1 m.4
Information from systematic absences
211
Table 7.
. 3.
2/m mmm 4/m 42m. z).8)
hki = Z 2//exp(27ii/cj. m3m
4/mmm
6/mm
+ ty +
exp{27ii(/ixi + kyj + /z.7) we find. 2. 622. 4mm. for k even.7a)
/c)}]. 432. 222. 422.4.
(7. 3 3m. \ + y. 6. From equation (7.6)
where n is an integer. 4. 2X axis parallel to b Atoms occur in pairs with coordinates (x. The structurefactor equation can be written as Fkki = I /)[exp{27ii(/zx.
\\for / even.23. There follows in table 7. Fm = £ 2ffxp{2ni(hxj + lzj)}sin(2nkyj). The reason for this is that the (hOl) data corresponds to that from a twodimensional projection of the structure down the y axis.212
The determination of space groups
Fm = Z 2/jexp(27iifc^sin{2ii(/ixJ + Izj)}
j= i
(7. This is shown infig.10a)
The systematic absences which arise from these equations are that Fhol = 0 for / odd. It should be noticed that a cglide plane can only be diagnosed if a lattice absence does not interfere.9b)
An examination of these expressions will show that the type of systematic absence which can occur is that FOkO = 0 for k odd. This means that for the layer k = 0 only those reflections are observed for / even. cglide plane (perpendicular to b) Atoms occur in pairs with coordinates (x. \ + z). z) and (x.
(7. Monoclinic.10b) z). This gives. Fhkl = Z 2ffixp{2ni(hxj + lzj)}cos(2nkyj) and. for an Aface centred lattice Fhkl = 0 for k + / odd for any h and. The twodimensional coordinates for this projection are (x. Whenever this systematic absence is found without others affecting reflections for which both h and / are not zero then the existence of a 2X axis parallel to b is established.2 a selection of some of the more common lattices and symmetry elements and the systematic absences which follow from them. Thus the systematic absences due to the cglide plane would be masked. if one breaks the projected cell into two by drawing the line z = \ then the two parts are equivalent. Case 1. (7. in particular. this gives Fh0l = 0 for / odd for any h. All reflections observed except 0/cO for k odd. y.7. The space group is P21.
. For example. y. z) and (x. for / odd. The cell must be primitive with a 2X axis along b. in the projection there is an effective unit cell with d = \c and this gives rise to the systematic absences which are observed. We shall now look at a few cases where systematic absences give spacegroup information. if one had only these data available then one would judge that the c* spacing was twice as large as it really was or that the cell parameter was onehalf of its true value.
Case 2. The possible space groups are C2.3.6.23. Crystal projection down b axis perpendicular to which there is a cglide plane. 2j  to b axis 0/cO for A = 2w + 1 2±  to c axis 00/ for / = 2n + 1 A B C F
k + / = 2n + 1
None hOl for /i = 2n + 1 /z/cO for h = 2« + 1 Okl for fc= 2n + 1 hkO for /c = 2« + 1 = 0/c/ for / = 2nf 1 = hOl for / = 2n •f 1 Okl for /c + / = 2« + 1 M)/ for h + / = 2rc + 1 hkO for /i = 2n + 1
Fig. ml 2. Cm or C2/m.7.4. say b.4. 3. there must be along one axis. The observed absences are hkl for h + k = 2n + 1. The cell must be Cface centred but otherwise no other symmetry element is indicated by the systematic absences.6 J a ± to b axis /i + / = 2n + 1 L a _ to c axis h + fc = 2rc + 1 fr ± to a axis /i. Pm or P2/m. the way of distinguishing
. A monoclinic cell with no systematic absences would be P2. 7.
Lattice P Absences None Symmetry element Absences
T. Monoclinic.2. / not all odd fr J_ to c axis or all even I h + k + l = 2n + l c _L to a axis c ± to b axis n l t o o axis Symmetry element «_L to b axis 2 j  to a axis hOO for h = 2n + 1 «_L to c axis .4
Information from systematic absences
213
Table 7. a 2 or 2 ( = m) symmetry axis or both. However since the system is monoclinic. /c.
The incident beam CO falls on the crystal at O and produces a reflection in the direction CO' due to the reciprocallattice point Of touching the sphere of reflection. that there is a foglide plane perpendicular to the a axis. 7. The space group is therefore P2 1 2 1 2 1 .24. This is a process of double reflection where the beam reflected from one set of lattice planes is reflected from another set of planes which happens to be in the correct orientation. 7. Hence the space group is Ibca. The other reciprocallattice point P on the sphere of reflection
Fig. The observed absences are for /zOO with h odd 0/cO with k odd 00/ with / odd. Case 3. They occur when two reciprocallattice points touch the sphere of reflection simultaneously and their formation can be followed by reference to fig. Case 4. Production of Renninger reflections. a oglide plane perpendicular to the b axis and an aglide plane perpendicular to the c axis.24. The phenomenon was first pointed out by Renninger (1937) and the reflections so produced are called Renninger reflections.6 and similar methods can be used for the facecentred cells.214
The determination of space groups
these is discussed in §7.
. Orthorhombic. Orthorhombic. There is a diffraction phenomenon which can sometimes interfere with the identification of symmetry elements from systematic absences. The cell is primitive with a 2X axis along each cell axis. The systematic absences are for
hklfovh + k + l = In + 1
Ofcf for M for M hkO for k = In + 1 / = In + 1 h = 2n+L
The systematic absences tell us that the lattice is /centred.
the presence or absence of a centre of symmetry does impress itself on the diffraction data but in a way which does not reveal itself without a certain amount of analysis .11) has a mean
X= £ ^
and a variance
. the direction of a forbidden reflection for the incident beam CO. the doublereflection process will happen only for a restricted range of wavelengths of the characteristic radiation being used.' Let us see what this means. Of course if P was not a point corresponding to a systematic absence a Renninger reflection would still occur and this would enhance the intensity of the primary reflection and would appear as an experimental error in the data. There are no restrictions on the distribution functions of the variables x and the distributions can all be different. The sum of the variables (7. In fact. Renninger reflections can usually be recognized by their very sharp. In order to derive these distributions it will be necessary to use an important theorem of statistical theory . Thus a reflection would be produced in the direction CP.5 Intensity statistics
215
corresponds to a systematic absence and so will not give rise to a reflection due to the incident beam CO. This states that: The sum of a large number of independent random variables will have a normal probability distribution with mean equal to the sum of the means of the independent variables and variance equal to the sum of their variances. Now let us assume that an incident beam falls on the crystal in the direction CO'. the beam leaving the crystal along CP. If the intensities corresponding to the reciprocallattice vectors sx and s3 are both strong the Renninger reflection can be very prominent. The reflected beam CO' due to the reciprocallattice vector sx can thus be reflected again.7. with the possible exception of optical goniometry. as was shown by Wilson (1949).the centrallimit theorem. has enabled a centre of symmetry to be positively detected. In practice if one has overwhelming evidence of a given type of systematic absence with one or possibly two faint reflections disturbing the pattern then one should suspect that the systematic absences are genuine and that Renninger reflections are occurring. 7c5 Intensity statistics None of the techniques we have previously considered. We now centre the reciprocal lattice at 0' and it is clear from thefigurethat O'P corresponds to a reciprocallattice vector s3( = s2 — sx).through the distribution of the structure amplitudes or intensities. We consider a number N of independent random variables Xj (j = 1 to N) which have means Xj and variances aj. nondiffuse appearance.
14)
which means that the probability that the sum lies between X and X + dX is P(X)dX.) = 2fj cos(27ihT.17a)
.15)
where the summation is over one asymmetric unit. Comparing equation (7. However all the terms in the summation are not independent because for an atom at r7.216
The determination of space groups
o2 = I a2 .(X .) = 0 and hence x~j = 0.is given by the wellknown expression OL] = X ~ 2 .XJ2. Since Xj = 0 then a] = 4/? cos2(27thT.19) (7. The structure factor equation can be written
where h is the reciprocallattice vector.). Thus the mean value of the structure factor is given by F=YJx~j = 0 and its variance is given by (7.16)
If we assume a random distribution of atomic positions then all positions in the unit cell are equally probable and cos(27thr.5.20) (7.
(7.17b) (7. This theorem can now be applied to the distribution of the structure factors for a centrosymmetric structure..13)
The probability distribution of X is given by the normal distribution
.X)2/2<72} (7.15) with equation (7. The equation can be rewritten as the sum of a number of independent terms as Fh= £ 2/}cos(27ihr..) to Xj so that Xj = 2fj cos(2uhTJ.11) it will be seen that we should equate 2fj cos(2iihTJ.) (7. (7.) = 2/ 2 since the mean value of cos 2 6 is 0.there is also one at —Vj.18) (7. The variance of x.
For such a structure we have
=A
where
= I/)C0S(27lhT.22) any further to see how one could use it to distinguish a centrosymmetric structure we shall first find the corresponding distribution for a noncentrosymmetric structure. It can only be an approximation to the true distribution since we know that F
N
has a maximum possible value of £ fp whereas the Gaussian curve extends from — oo to + oo.21) The distribution function of F is now given by
(7.5 Intensity statistics
217
(7. The centric distribution function.
. A more exact theory has been given by Klug (1958). 7.thus
Fig.7. is shown infig.25.25.7.22)
The form of this function.)
The distributions of A and B can be found separately . the normal Gaussian curve.. Before looking at the properties of equation (7.
is given by ?(A)?(B)dA dB = (Tt
1
exp( .24)
The region defined by the above probability is shown infig. (b) Region of complex space for which structure amplitude is between  F  and  F  + d  F .A2/X)
(723a)
and similarly :(7iE)"exp(B 2 /Z). 7. Imaginary part off
Real part
Imaginary part
off
Real part off
.218
The determination of space groups
so that
P(A) = (7iE
. . (7. F 2/S)dv4 dB.
(7.23b) Since A and B are the real and imaginary parts of the structure factor they can be plotted on an Argand diagram.26(a) and since dAdB is an element of area in the diagram we can say that the
Fig.7.26. and also that B lies between B and B + d£. (a) Region defined between A and A + dA and between B and B + dB for a complex structure factor. The probability that A lies between A and A + dA.
7. is
which gives
i>
(7. 7. it should be noted that these terms are used only for the distribution functions and not for the symmetry of the structures which produce them which are centrosymmetric and noncentrosymmetric. The acentric distribution function. In fact what these distribution functions mean is either: (i) for a particular structure factor at a point of reciprocal space where £ has a known value the probability that its value (or magnitude) lines between F and F + dF (or  F  and  F  + d F ) is given by Pj(F)dF (or
J
(ii) for a region of reciprocal space where £ is constant (or approximately so) the proportion of structure factors (or amplitudes) which lie between F <mdF + dF(or \F\ and  F  + d  F  ) i s PT(F)dF (or P
Fig.7. which is that the value of Z is not constant over the whole of reciprocal space.27. 7.26)
The form of this distribution is shown infig. How can the distributions represented by equations (7.22) and (7.26) be used to distinguish the two types of structure? There is one snag which prevents one from plotting the distribution curves directly. The two distributions are referred to as centric and acentric respectively. that is within the shaded area shown in fig.
.27 and is quite different from that which obtains for a centrosymmetric structure.5 Intensity statistics
219
probability that a structure factor lies in a small region of area dS round a point distant  F  from the origin is
Hence the probability that the structure amplitude lies in the range  F  to  F  + d  F .26(b).
As an example in fig. This process is illustrated in table 7. We now take overlapping regions covering the sinfl ranges 0.28)
(7.33)
2
\F\2?1(\F\)d\F\ = X
(7. which is centrosymmetric.4. 1958) together with the values of  F  and  F 2.1 in sin 9 and within each annular region are counted the number of points.30) and (7.33) are sufficiently different to give a discriminating test. Very often axial structure factors. 0. In addition the structure factors at low sin 6 values tend to be statistically unreliable (Wilson.29)
so that
M T = . In fact the space group can be unambiguously determined as P2Jc. and for each range determine  F \ and  F 2 and then the value of M.637. 00/.4 and it will be seen that the value of M seems to decrease with increasing sin 9. 7. This is probably due to the
.27)
o
and
12 \F\2= .28 there is shown one quadrant of a rectangular reciprocallattice net for the h = 0 layer for dicyclopentadienyldiiron tetracarbonyl (Mills.. but we shall treat the Okl data as though the space group was completely unknown.
71
(7.
l—oo
(^J
2F 2 P T (F)dF = Z
(7. £  F  and ZF 2 . etc.785. i. For the centric distribution (7. are atypical and are real even when the projection is noncentrosymmetric and these will be ignored in determining the values of  F  and  F 2.20. These results are shown in table 7.30)
For the acentric distribution ^^icZ)* o and (7.e.2. (7. 1949) and will not be used for sin 6 < 0.5.= 0.31)
f00
F = Jo so that Mx = ^ = 0. The net is divided by arcs of radii which increase by 0.30.32)
The two values given in equations (7.220
The determination of space groups
There is a quantity which enables one to distinguish the two types of distribution and is independent of Z and that is M== .3.. 0/cO.
30.40.8 0.5 0.  F  and  F  2 for (0/c/) data of dicyclopentadienyldiiron tetracarbonyl.3 0.20.9 0. However the average value of M is 0.80.60.7.70.50.6 0.612.5 Intensity statistics
221
Table 7.
large number of unobserved reflections at high angles whose contribution.7 0.91.0 No.28.4 0.3. if measurable.
sin 6 range 0. of points 3 6 8 9 12 16 11 18
nn
60 133 181 104 130 166 84 49
IF 2 1814 3843 5027 2096 2094 3434 1238 267
Fig. 7. giving a fairly clear indication that the projection is centrosymmetric
. would change substantially the values of  F  and IT7!2.
728 0. This is defined by
(7.222
The determination of space groups
Table 7.791 0.36)
7=1
and expresses Fh in the form of a summation then equation (7.7 0. including the temperature factor.0
IF
193 314 285 234 296 250 133
ZF2
5657 8870 7123 4190 5528 4672 1505
\F\ 21. and not the stationaryatom scattering factors one finds in the published tables..5 0.34) becomes Uh = £ rtj exp(27iihr.70.8).).4 0.4.34) that the fjS are the actual scattering factors for the atoms.8 0.616 0.3 4.9 0.570 0. If one writes (7.1 10. (7.34)
Since
and for a real structure factor
(7.81. Crystallographers frequently find it convenient to use structure factors corrected for falloff in 6 and the unitary structure factor is particularly useful (see §§ 8.60.4 22.8 11.6
\F\2
M 0.674 0.7 and 8.30.407
629 634 419 200 197 173 52
In order to get meaningful values of M it was necessary to divide the reciprocal net into regions in which Z did not vary overmuch.500 0. in particular the higher the atomic number the more tightly bound are the electrons and the less rapid is the relative falloff of/ However one usually
.6 9. will vary with sin 0 since the ratio of scattering factors for different atoms does not remain constant.50.35)
It is assumed in equation (7.
No.6 0.40.4 16.37)
When the structure contains atoms of more than one type the quantities rip known as the unitary scattering factors.20. of points
9 14 17 21 28 27 29
sin 6 range 0.
We can determine this factor from the condition that.38)
6 = £ n).105. \Uf = e.4.11/ 2A) where (7.29.015 and e = 0. Dicyclopentadienyldiiron tetracarbonyl has two molecules of Fe 2 (CO) 4 (C 5 H 5 ) 2 in the unit cell.39) (7. The factor J~§ applied to the  F 's will give  U 's and y/4> is shown plotted in fig. If the point O of the scale is pivoted at the origin of the reciprocal lattice then the reading of the scale at the reciprocallattice points gives the factor which changes  F  into \U\. no = 0.
( 4) 72

In order to determine IPs from observed data we note from equations (7.20.5 Intensity statistics
223
makes the assumption that the w/s are constant over the whole of reciprocal space.29. 7. for an annular region in reciprocal space after the factor has been applied.3. We shall ignore hydrogen since it contributes negligibly to the scattering and we take/ F e :/ o :/ c = 21:4:3 over the whole range of sin 0 which gives nFe = 0. The values of <j) for the other values of sin 9 may be found similarly.
For a structure with N equal atoms in the unit cell
(7. By analogy with what we have had previously. A smooth curve is drawn as close to the points as possible and the curve is extrapolated at both ends.0536/629.7. corresponding approximately to sin 8 = 0. the value of  F  2 is 629.020. In table 7. Hence the best estimate of the factor <f> which one should apply to  F  2 's at sin 6 = 0.29) and (7. nc = 0.32) that for both the centric and acentric distributions we shall have (7.40)
and
JU>i?
\U\2 = s. also shown in fig.4 in the sin 6 range 0.0536. can be prepared.U2/2s) and Pi(l L/1) = 11/1 exp( . the distribution functions of the unitary structure factor for centrosymmetric and noncentrosymmetric structures. From this curve a linear scale. respectively. are P T([/) = (27i£)*exp( .43)
/ > The  U  2 's can be obtained from the  F  2 's by applying some factor < which depends upon sin 6. 7.3 to convert them into  U  2 's is 0.
.
0
The complete set of £/'s for dicyclopentadienyldiiron tetracarbonyl is given in fig.6
0. The values of E can be obtained from the L/'s by
.7
0.8
0.44)
The normalized structure factors have distribution functions
(7. 7.' h '
l
(7.
The determination of space groups
o
0
0.30. 7.8
1.3 0. Another type of structure factor corrected for sin 6 falloff which is sometimes used is the normalized structure factor defined by
I F I2 I2 .5 0.29.45)
and (7.4
0.0
i i I i i i i  i 11iiiii[i
0. Curve for y/4> and chart for deriving  U \ fromF.0
3.6 sin0
0.46) For either distribution \E\2 = 1 and it can also be seen that the distribution functions are completely independent of the structural complexity.0
2.1
0.2
0.224
Fig.9
1.
7.5 Intensity statistics
Fig. 7.30. 100  U  for (0/c/) data of dicyclopentadienyldiiron tetracarbonyl.
225
k . I——^ 14 "21^^.i > 16 28 16 33 21 32 40 6 44 33 10 9 6 6 1 43 36 33 0 33 6 16 13 17 6 32 1 3 22 27 15 18 21^ 6 21 27 1 1 37 20 3 1 30 20 34 36
r. o
15 24 1 1 40 5 28 1 1 5 2 42 17 40 1^ 1 12 36 0 20 12 0 3 1 1 3 12 17 0 0 26 0 29 10 8 13 ^K0 2l\
A to .\ . *\
4 31 1 3 24 100
0
A • \ " \
 38 (7.47)
0
In appendix V there is given a FORTRAN program, FTOUE, which converts  F 's to either  U 's or  E 's by calculating the factor < v /$. The values of \F\2 are calculated in overlapping regions of sin# and, for calculating  U 's, the values of £ x ( F  2 )~* (i.e. (/>) which converts  F  2 to  U  2 are found and associated with the average value of sin 6 in each region. Coefficients are found for a bestfit parabola of the form =
a
+ b sin 9 + c sin2 6
(7.48)
which is then used for finding the conversion factor from  F  to  U  for any reflection from its associated sin 6. If  E 's are required then a different scaling factor is used. In practice it may be found that the values of y/ip deviate considerably from the best parabola, both above and below the curve. This is particularly true for protein structures where strong structural features, for example helices or planes, impose a variation of average intensities with (sin 0)1L A test which is frequently used to detect a centre of symmetry is the N(z) test suggested by Howells, Phillips and Rogers (1950). This is a cumulative distribution curve for intensities and N(z) is the fraction of reflections with intensities less than or equal to z times the mean intensity. If one is using
226
The determination of space groups
data with a sin 6 falloff then one must always compare an intensity with the local average to determine the appropriate z. However if one has  U 's or  £/2 's available then for any reflection \U\2 z =^U
£
(7.49)
It is straightforward to derive the theoretical forms of N(z) from PT(£/) and P x ( U ). For PT((7), N(z) is the proportion of IPs with values between and — y/zs thus
N
i( z ) = I
Prfl/Jdl/ = erf( /  j
(7.50)
where
is the welltabulated error function. Similarly N t (z) = Jo These two functions are tabulated in table 7.5 and shown graphically in fig. 7.31. For dicyclopentadienyldiiron tetracarbonyl the values of  U  corresponding to various values of z and the numbers of reflections with \U\2 less than ze are also shown in table 7.5 and N(z) is also plotted in fig. 7.31. It is clear from this that the projection is centrosymmetric. The general quality of Nx(z) and NT(z) can be seen in the distributions P x ( F ) and PTCF) plotted in figs. 7.27 and 7.25 where, in particular, it will be noticed that the centric distribution has a higher proportion of small Ks. It was shown by Lipson and Woolfson (1952) and by Rogers and Wilson (1953) that other types of distribution could occur when there were molecules with noncrystallographic centres of symmetry in the unit cell. In fig. 7.31 is shown the N(z) curve for a hypercentric distribution which occurs when there are in a unit cell two centrosymmetric molecules related by a crystallographic centre of symmetry (fig. 7.32). It will be noticed that the distribution has an even higher proportion of small intensities than the centric one. The form of the distribution has been given by Lipson and Woolfson; one important property which it has, as have all other distributions, is that  F  2 = Z, so that the procedure described for determining IPs is still valid. The various distribution functions described in this section depend on randomness of the atomic positions. When there is a very heavy atom in the unit cell, equivalent to a nonstatistical aggregation of scattering power, or when atoms are in special positions (§8.1), the distributions can depart markedly from those which have been described. In such cases tests involving the moments of the distributions can be used (Foster & Hargreaves, 1963a, 1963b; Pradhan, Ghosh & Nigam, 1985). Pjd 1/ )d 1/1 = 1  exp(  z). (7.51)
7.6
Detection of mirror planes and diad axes
227
Table 7.5.
For Fe2: (CO) 4 (C 5 H 5 ) 2 No. , <  F  N(z) 0 25 30 37 42 47 50 50 53 59 59 85 0.00 0.29 0.35 0.44 0.49 0.55 0.59 0.59 0.62 0.69 0.69
z 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Nx(z) 0.00 0.09 0.18 0.26 0.33 0.39 0.45 0.50 0.55 0.59 0.63
NT(z) 0.00 0.25 0.35 0.42 0.47 0.52 0.56 0.60 0.63 0.66 0.68
\u\
0.00 0.07 0.103 0.127 0.146 0.164 0.179 0.194 0.207 0.220 0.23! 1.00
Fig. 7.31. The cumulative distribution curves for the following distributions: acentric (equation (7.51)); centric (equation (7.50)); and hypercentric (from symmetry shown in fig. 7.32).
N(z) 1.0 
Hypercentric x Centric Acentric
0
0.1 0.2 0.3 0.4 0.5 0.6
0.7 0.8
0.9 1.0
7.6
Detection of mirror planes and diad axes The only common symmetry elements for which detection techniques using diffraction data have not been described are the diad axis and the mirror plane. In fact one frequently needs to distinguish these two. For example, the space group of a monoclinic structure with no systematic absences is one of P2, Pm or P2/m. The last of these is centrosymmetric and can therefore be isolated by an N(z) test but, if the test indicated a noncentrosymmetric structure, one would still be left with the choice of P2 or Pm. It can be shown that when there is a mirror plane, perpendicular to the b
228 Fig. 7.32. Structure for which centrosymmetrical groups are related by a centre of symmetry; this gives rise to the hypercentric distribution.
The determination of space groups
axis let us say, then the value of  F \h0l  2 is 2Z or twice the average value for general reflection intensities. For a mirror plane atoms occur in pairs with coordinates (x, y, z) and (x, y, z) and the structure factor equation become
F
hki = Z 2fj
7=1
= Ahh
iBhhl.
(7.52)
Since Ahkl = Bhkl = 0 we have A\kl equal to the variance of Ahkl which, by the centrallimit theorem, gives
Zj} x cos2(27i/cy7)
7=1
Similarly B^kl = ^Z and hence
(7.53)
However for k = 0
2
x COS2{2TI(/ZX,.
= 2 =
and
2 _
B2hOl = 2 1 .
(7.54)
Another, and easier, way of deducing this relationship is to see that the fcaxis projection will show complete overlap of pairs of atoms due to the
Problems to Chapter 7
229
mirror plane. Thus, in projection, there are \N doubleweight atoms and the effective value of Z, Zm, becomes I
2
= 22.
(7.55)
In a similar way the presence of a diad axis along b shows itself in that  FokO  2 is TL. Pairs of atoms are related with coordinates (x, y, z) and (x, y, z) so that projected on to the b axis they overlap at (0, y, 0). Since, in general, there are fewer reflections involved this test for a diad axis is normally less reliable than that for a mirror plane. In order to apply these tests all the observed data must be on the same relative scale and the method of achieving this is described in § 9.2. It is also necessary to compare the values of  F 2 for similar narrow ranges of sin 9 and not for all the data together, since 2 will not have the same average over the whole threedimensional reciprocal lattice as it has for a one or twodimensional projection.
Problems to Chapter 7 7.1 What systematic absences are given by the following symmetry elements? (a) /centred lattice, (b) nglide plane perpendicular to b, (c) 3X axis. 7.2 Identify the space groups given by the following sets of systematic absences: (a) Primitive monoclinic lattice: 0/cO only present for k = 2n, hOl only present for / = In. (b) Primitive orthorhombic lattice: Okl only present for k + / = 2n, hOl only present for h = In, hOO only present for h = 2n, 0/cO only present for k = 2n, 00/ only present for / = In. 7.3 In table 7.6 are given the (hOl) and (Okl) data for mtoluidine dihydrochloride (Fowweather & Hargreaves, 1950). By comparing intensities with the local averages, determine N(z) for each projection and determine whether they are centrosymmetrical or noncentrosymmetrical. The data are given in order of sin 6 and hence may be taken in overlapping groups of consecutive items. 7.4 Using the output file generated in the solution of Problem 3.4, use the program FTOUE to find the normalized structure factors ( E 's) for the (hOl) reflections of the phenylethylammonium salt of fosfomycin. Plot the values of ^/^ found by averaging in sin 9 regions and compare with the curve given by equation (7.48). You may request output of the values of a, b and c (equation (7.48)) when running FTOUE.
^.H^H^^CSJfN)^^,
s
fN O O O OO CN
o o
O
o o c3 oo o o o o o oo oo
O oo vo O
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SO fN
o oO
O
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r O O
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s r
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8 The determination of crystal structures
8.1
Trialanderror methods The object of a crystalstructure determination is to locate the atomic positions within the unit cell and thus completely to define the whole structure. Sometimes there are special features in the diffraction pattern, the space group or the suspected chemical configuration of the material under investigation which enable a guess to be made of the crystal structure or at least restrict it to a small number of possibilities. In the early days of the subject, when methods of structure determination were poorly developed, only the simpler types of structure could be tackled and trialanderror methods based on such special features were commonly used. That is not to say that such techniques are now outmoded  no crystallographer would ignore the information from special features if it was available, but he does not rely on such information as much as hitherto. One type of situation which is of great importance and is always sought by the crystallographer is when spacegroup considerations lead to thefixingor restricting of the positions of atoms or whole groups of atoms. If a centrosymmetric unit cell has only one atom of a particular species (or an odd number) then that atom (or one of them) must be at a centre of symmetry. In a case with an odd number of atoms in a cell with a diad axis one of the atoms would have to lie on the diad axis. Similarly, in some situations, an SO4 group may have to be symmetrically arranged on a triad axis as shown infig.8.1. It is also possible to gain stereochemical information from spacegroup requirements so that a molecule may be found necessarily to have a centre of symmetry or a diad axis of symmetry within itself. An interesting example of a structure determination using this sort of information is provided by the hydrocarbon fluorene, a molecule of which is shown in fig. 8.2. This was solved by Brown and Bortner (1954) whose Xray data showed the crystal system to be orthorhombic, of space group Pna21 or Pnam with four molecules per unit cell. The unitcell dimensions were a = 8.50, b = 5.71 and c = 19.00 A. Subsidiary evidence showed that the space group was probably Pnam for which in general there are eight symmetryrelated positions. The only way in which fourfluorenemolecules can be accommodated in the cell is if the molecule itself has a mirror plane which coincides with the crystallographic mirror plane. This could mean either that the molecule is precisely planar and lies completely in the mirror plane or that the line AB in fig. 8.2 is a mirror plane for the molecule. The latter alternative was considered the more likely and, if the molecular shape was assumed to be known  approximately at any rate  then the crystal structure could be defined in terms of three parameters. These could be the
231
232 Fig. 8.1. An SO 4 group arranged on a triad axis.
The determination of crystal structures
x and y coordinates of the point A and the angle made by the line AB with the y axis. For the a ox b axis projections there are only two parameters. Structure factors were calculated for various positions of the model molecule and reasonable agreement of calculated and observed (hOI) and (O/cZ) structure factors was found for the point A at position (0.353, 0.431, 0.250) with AB making an angle 30.5° with the y axis.
Fig. 8.2. An outline of the carbon atoms of fluorene.
As a measure of agreement between observed and calculated structure factors crystallographers use a quantity called the reliability index or residual defined by (8.1) The Fo's and Fc's are the observed and calculated structure factors respectively and, of course, for them to be comparable the Fc's must include the temperature factor. The way that one can determine the temperature factor from the observed data is described in § 9.2.
One can try various combinations of signs for the few structure factors and. The intensities of the Bragg peaks will correspond very closely to those from a 50:50 mixed structure and there will be an apparent centre of symmetry. particularly if one has some initial idea of the stereochemistry of the substance under investigation.3. if a particular  Uh  is very large. where the (202) reflection is the one which is very strong. the final electrondensity map is shown in fig. This occurs when the structure consists of'unit cells' in which the atoms are arranged in two or more possible ways and where the arrangement from cell to cell varies randomly. If there are a few very strong reflections with high unitary structure factors then these alone can reveal the structure. 8. then the atoms will tend to have coordinates r such that cos(27th*r) is either near +1 for each of them or near — 1. once the crystallographer has his foot in the door. It can occasionally be very profitable to play about with wire models of the unit cell and of the molecules.8. The sets of lines corresponding to cos{2n(hx + lz)} = ± 1 are shown. For a centrosymmetric structure. A computer can also be used systematically to explore various methods of packing to achieve sensible intermolecular distances and structurefactor agreement (Milledge. so to speak.2. A word of warning should be given about pseudosymmetry arising as a result of statistical disorder.8.3(fc). 8. lines can be drawn corresponding to cos(27th*r) = ± 1 depending on which sign is being tried.3(c) where it can be seen that in the foaxis projection of paranitroaniline (Abrahams & Robertson. The separate molecules may be linked by hydrogen bonds or may have to be separated by van der Waals distances.2
The Patterson function
233
Once a trial structure has been found which is close enough to the true structure to give a low value of R then one can refine the structure by the routine procedures which are described in chapter 9. Infig. 8. When the structure is a molecular one then the shape of the unit cell and the restrictions on location imposed by symmetry elements may enable a trial structure to be found from packing considerations alone. To show how well this indicated the correct position. Such a statisticaldisorder situation is illustrated in two dimensions infig. 1948).S3(a) there is shown a diagram given by Dunitz (1949) demonstrating how six strong reflections revealed the position of the molecule in the foaxis projection of 1. the crystal structure is all but solved. Another example in which information was gained from only one very strong reflection is shown in fig. However one would know from packing considerations that the two arrangements of atoms could not occur simultaneously in one cell and this would also be revealed by the electrondensity peaks which would be half the normal height. 1962). the sign taken in each case being indicated in the diagram. in two dimensions.4.2 The Patterson function We have seen that the lack of knowledge of the phases of structure factors prevents us from directly computing an electrondensity map and so
. all the atoms lie along the direction of the (202) planes.4tetraphenylcyclobutane. The whole crystalstructure problem consists of getting the first trial structure.
{a) The six strong reflections which showed the 6axis projection of 1. (c) The /?axis projection of pnitroaniline showing the molecule lying along the (202) direction (from Abrahams & Robertson. 1948).
.4tetraphenylcyclobutane (both {a) and (b) from Dunitz.3.( + J401
Fig. 8.2.3.2. 1949).4tetraphenylcyclobutane. (b) The 6axis projected electrondensity map for 1.3.
showing the positions of the atoms in the unit cell.72) will show that the transform of ( 1 / F ) ^ is p( . The transform of (l/F)F h is p(r). V (8. it can be seen that FH is the complex conjugate of Fh so that F hFH =  Fh  2 .3)
Ideally.8. 8. say.6 that the transform of a product of two functions is the convolution of their separate transforms and this gives
v
p(i#(r . from equation (4.4.4) and (8. From equations (8.2
The Patterson Junction
235
Fig. Patterson (1934) suggested as an aid to structure determination the use of the function
(8. But we found in §4.r) = I//(Y). With the operation of Friedel's law we have  Fh \2 =  Ffi  2 and so the Patterson function is real and may be written as 1 = £F h  2 cos(27ihr). A twodimensional statistically disordered structure.
(8.u)dt> = vr^I
h
~ 27iihr).81).2) it now appears that
. and a few moments study of the electrondensity equation (4.4)
The righthand side can be simplified because. the values of Fh and \Fh\2 are finite only at the points of the reciprocal lattice.2)
where r = xa + yb + zc is a position in unitcell space and h = ha* + /eb* + Zc* is a reciprocallattice point coordinate.
(8. Then
1 (£). we see that ^(r — u) = p(u)p(u — r) dt? or. We suppose that in fig.5)
This enables us to interpret the function P(r). since P(r) is a centrosymmetrical Jv function from equation (8. replacing r by — r we find P(r) = P( . The reader should examine equations (4.
.6)
Let us now find a physical interpretation of the Patterson function. The electron density p(r) will be in units of electrons per unit volume (or area or length depending on the number of dimensions of the representation) while the structure factor Fh will be in electron units.75) to see that they are consistent with this set of dimensions. 8.236
The determination of crystal structures
l' e x P( .u) di.72) and (4.2) and (8. = P(r). A representation of two similar electrondensity maps displaced by a vector r.r) = V\
)v
p(u)p(u + r) dv.6) indicate that the dimensions of P(r) are (electrons)2 per unit volume. 8.3).
equivalent unitcell origin at O' such that 00' = r. Jv
p(u — r) and P(r) = V
(8. This gives a consistent dimensional system if fractional coordinates are always used and volume integrals are taken over the unit cell in dimensionless units of volume which are expressed in terms of fractions of the unitcell volume. If the integration in equation (8.
Fig.5.2 ™ h * r ) = V I P(u)<A(r .5 we represent the electron density with the origin of one unit cell at 0 and superimpose on it the electron density with the p(u)p(u + r)du Jv represents the product of the staggered electrondensity functions integrated over the complete unit cell outlined boldly in the figure. A brief word about the units of P(r) should be given here.6) is over a dimensionless volume then both equation (8.
The contribution to the Patterson function of two atoms separated by a vector r will be a diffuse peak centred on r. which will be well resolved. if there was no overlap of Patterson peaks. or the overlap was slight. (a) Two peaks of electron density. When two such maps are overlapped with a displacement r the value of P(r). The Patterson function will be a superposition of peaks derived from all the pairs of atoms in the unit cell. for i = 1 to N and. which can be seen from equation (8. 8.(j = 1 to N) they will give rise to a set of Patterson peaks at positions rt — r. give rise to N(N — 1) vectors (ignoring the null vectors of an atomic position to itself) and the corresponding Patterson peaks are more diffuse than the electrondensity peaks.. = 1 to N. as given by equation (8. The N peaks in an electrondensity map. In fact the resolution of Patterson maps is usually rather poor and this is what should be expected. 8.7) Fig.8. A wellresolved electrondensity map shows regions of isolated electron density symmetrically disposed about the atomic centres.5.8. The N null vectors give a large peak at the origin. then the function P(r) would show the positions of all the interatomic vectors in the cell.2
The Patterson function
237
What should the Patterson function P(r) show? Clearly it will be large if strong regions of electron density overlap in the displaced electrondensity maps illustrated infig.6).8.3). Infig. (b) Overlap of peaks when two electrondensity maps are displaced by a vector
(a)
(M
. If there are several strong regions of electron density separated by the vector r the P(r) will show the total effect of this and will consequently have a large value.6(a) there are seen two atomic peaks of a onedimensional electrondensity map. In fact this is equivalent to saying that the value of P(r) will be large if strong regions of electron density are separated by a vector r in the unit cell. depends on the product of the p's over the range for which they are nonzero.6. This will be the integrated product for the shaded region in fig.6(fc). An examination of this figure should make it clear that the maximum integrated product will occur when the atomic centres exactly overlap and that the width of a Patterson peak will be wider than that of an electrondensity peak. since
(8. Thus if there is a set of atoms in positions r.
. — r. In terms of the cell with sides d and c the coordinates
. xj and — r. indeed.)
r) . The total Patterson density associated with a vector between two atoms of atomic numbers Z{ and Z} is equal to Z{Z. of twodimensional space group p2. quite complex crystal structures can be solved from an interpretation of the Patterson function. In the event that the structure is centrosymmetrical there is a systematic overlap of some peaks to give doubleweight peaks. 8.7(a) there is shown thefoaxisPatterson projection for 2amino4..84.z1 — z 2 )and ±(xx + x29zx + z2).r. For atoms with coordinates ri9 —rt. will contain two molecules which must therefore be related by the twofold axis (the same as a centre of symmetry in two dimensions) and each molecule is expected to look like that shown in fig.2z 1 ) and ±(2x 2 .(r.and r.
(i) Peaks due to heavy atoms
If there are a few atoms (perhaps only two) which have a higher atomic number than the remainder then the peaks due to these may well stand out in the ruck of minor peaks and give clear interatomic vectors.28 A and p = 108°. In fig. and double peaks at ± (r • — r7) and ±(rt + r^). again in conformity with the centrosymmetric nature of P(r) as shown by equation (8. c = 10. b = 3. single peaks at + 2rf. 1948). Thus there should be four chlorine atoms in the simple cell with coordinates + (xl9 zx) and ± (x2.. Due to the aglide plane thefcaxisprojected cell shows two equivalent parts so that a simpler cell with a' = \a and d = c can be considered. thus if a structure contains carbon atoms (Z = 6) and chlorine atoms (Z = 17) the types of peaks present and their weights are C—C weight 36 C—Cl weight 102 Cl—Cl weight 289. Despite the overcrowded nature of Patterson maps useful information can frequently be derived from them and.45. The space group is P2Ja with a = 16. ± 2r.3).. the interatomic vectors.( Tjij
r)
or. are
r
i ~~ (~~
r
i)
r
i — rj
r
i~(~
T
j)
r'jh
r. respectively.2z 2 ) and doubleweight peaks at ±(x x — x2. 8. z2) and hence one should expect singleweight peaks at ±(2x 1 . apart from the null vectors. to summarize.238
The determination of crystal structures
The other vectors occur in centrosymmetric pairs r..7(fc).. This simple cell. — i\.
rjirj
r.6dichloropyrimidine (Clews & Cochran. The two heaviest peaks of the Patterson map are those marked C and D which have heights of 326 and 323 units. Some common situations which occur and give rise to recognizable Pattersonmap features will now be considered.
7. (b) A molecule of 2amino4.6dichloropynmidine. (a) The fraxis Patterson projection for 2amino4.y
Cl (b)
{a)
Scale of Angstrom units
a/2
1
0
1
Scale of Angstrom units Fig.) (c) The electrondensity map for the /?axis projection of 2amino4. 8.6dichloropyrimidine.6dichloropyrimidine. (c)
. (Parts (a) and (b) from Clews & Cochran. 1948.
shows this vector marked by an X.2z 2) = ( .8.7(fl). 1948) projected down the a axis. For example. zx + z2 = 0.015.306). 8.6dimethyl2hydroxypyrimidine(Pitt. 8.8). If it is assumed that they are the two types of doubleweight Cl—Cl peaks then we have xx h x 2 = 0.376. z1z2 = 0.0.665. In fig. 8. For example the structure may contain benzene rings or linked rings as in anthracene (fig.2z2 ).z2) = ( 0.153). The vector AB occurs repeatedly and the Patterson projection.0. Other types of symmetry element or space group can give vectors in special positions.9(a) there is shown the arrangement of the molecules of 4.321. Even though a single carboncarbon vector might not be strong enough to be seen in a Patterson map the superposition of several of them may well stand out.0.0. Substantial peaks are found in these positions shown as B and A in fig.624.228. The carbon atoms of the anthracene molecule and some of the interatomic vectors which occur repeatedly.4). giving (x 1 . For these positions we should expect to find two singleweight Cl—Cl peaks at (2xx. In fig.665.306) = (0.0.240
The determination of crystal structures
of these peaks are (0. (Hi) Spacegroupdependent vectors
It has been seen that a centre of symmetry gives an exact overlap of pairs of Patterson peaks.z 1 ) = (0. 8. The final electrondensity map for this projection appears in fig.7(c).477.015). 2zx) and (2x 2 . given in fig. From the above coordinates these would be (2x^22^ = (0. Once the chlorine atoms had been located. the determination of the complete structure was a routine matter (see § 8.0. 8. 8.0.188.
.336) and (2x 2.0.8 there is shown a selection of vectors which occur repeatedly in the anthracene molecule. x1x2 = 0. (ii) Overlap of parallel vectors
Very often the arrangements of atoms in a crystal structure have a great deal of symmetry which is unrelated to the crystal symmetry but is concerned with stereochemical factors.288. 8.168) and (x2.954.9(6). the twodimensional space group
Fig.321) and (0.
8.6dimethyl2hydroxypyrimidine.9.8.2
The Patterson function
241
Fig.
• = H2O
(a)
(b)
pgg has atoms in general symmetryrelated positions ±(x.2y) double weight ±(i + ± ( i i + 2y).2x.These four related positions give vectors (except null vectors) single weight ±(2x.y). 1948). {b) The Patterson peak marked with an X corresponds to the repeated vector AB in (a) (from Pitt. ±(i ~ x>i + y). We now look at an example of the finding of heavy atoms from spacegroupdependent vectors for a structure in projection with space
.2y). ±( . (a) The arrangement of molecules in the aaxis projection of 4.
0. calculated with the program STRUCFAC for Cu Ka radiation (X = 1. 0) and the doubleweight 2 vector (% 2y). (a) The twodimensional space group pmg(p2mg\ (b) The artificial structure C 4 H 4 N 2 C1 2 . These are discussed further in §8.583). 8. are given in table 8.8.542 A).which gives a centre of symmetry in projection.175.125.0. 2y\ (\ + 2x.10(a)).333). which we shall be using to illustrate various methods of solving structures. (x.10.0. From knowledge of the structure. The Patterson map has space group pmm and other vectors are generated by the mirror planes.10(fr).833) and we also have a = 10 A and b = 6 A. and the two singleweight vectors at positions B and C. The positions of the atoms in one asymmetric unit of the unit cell are: Cx (0. The vector is not on
Fig.3. y). Cl (0.083). The structure is an artificial one.100. [Chlorine contributions to the structure factors are listed in table 8. There is also a glide plane g perpendicular to y and these two symmetry elements generate a twofold axis .8.175.0. y).] Since chlorine (Z = 17) is much heavier than the other atoms the Cl—Cl vectors should be clear in the Patterson map. The molecule has a mirror plane which sits on the crystallographic mirror plane m perpendicular to x. The complete set of structure factors. C2 (0. (C2H2NC1)2.8.11.1 and the program FOUR2 uses the magnitudes to generate the Patterson map shown infig.11. y). 7
O
plmg O 0
mm
Rectangular
o
Origin at 2 (a)
(b)
. For this space group the coordinates of symmetryrelated atoms are: (x. (\ — x. the highest nonorigin peak infig. N (0. pmg © © © 0 No.242
The determination of crystal structures
group pmg (fig. y) giving rise to singleweight vectors (2x. The mirror and glide planes are indicated m and g. 8. shown infig. respectively.2. (j + x. the doubleweight vector is found at A.
2 2 . 13. 10. 36*. 12. 15 2 1 . 1 4 .
1 1 . 11.
18.
11. 20. 18. 25. 20. 11. 13. 30^. 30}
9. 2 1 . 13. The vector between such a pair of atoms is (2x. 1 1 . ™ 9 10 11 12 13 14 15 16 17 18 15.
15. 12. 18.
15 7. 16. 13.
7. ' l 9 . 11.
2 1 . 16. 18. 1 0 . 20. "28V. 8. 9. 26. 12.
30V 2 1 . 26. 10. 9. 1 1 . 17. 1? 77 47 77
12. 19.
16 iq 18. 19. 25.
13.
12. 27. 1 1 . 15.% 2 2 . 9. 13. 19. 2 1 . 1 3 .
30/31. 12. 19. 12. 12. 14. 11.y. 12. 9. 14. 9. 15. 9. 10.
3 0M
1 1 . 9.
15. lot" 12. X N 34. 15. 30. 16. 15. 16. ^ 2 . 11. 18. 24. 14. 17. 17. 15. 17. 10.
?6T "25 . 12
1 3 . 9.
23. 13. 12. 9. $6. 8. 2*0.1
243
Fig. 11. 19. 33\
10. 13.
A^^3 # 6. the special peaks along y = 0 and x = \ at A and C are sufficient to determine the position of the chlorine atoms and peak B can then just be used as confirmation. 1 1 . 18 . 11. 17. 14. 10. 30\
13. 10. 14. 1 2 . 7 14
21. 14. 11. 8. 11. 19. 12 12. 11. 19. 12.
14
1 2 . 44 \ 10 . 1 3 . 10. 2 0 . 22. 11. 1 2 . 11. ^ 11. 3 6 / 44 I 1 8 . 23. 33\. 15. 12. 1 3 .11. 13. 15. 18.
1 3 . 10. 11 12 9 14 10 20
1 4 . 12.
24.
21. 14. 9. 1 1 . 16. 9. 9. 10.
3 6 . . 13. 13. 14. 9. 24. 26.
12. if the symmetry element 2X is present along the b direction then atoms will be related in pairs with coordinates (x. 14. 8. 13. but a high proportion of the peaks should be associated with the systematic peaks which show the structure projected down the b
.
12. 17 . 18.8. 23. 1 2 . 3 0 / 37. 19. 12. > " ( 22. 21. 16. 18. 15. 14. 19. 14. 8. 14. 11.
21 22 23 24 25 26 20 10 14 9 12 29 30 31 11 10
15. 2 1 . 27. 9. 12. 2 1 . 8. 14.
10 14 9
15. 15. 22.^23. >1 9
17. 15. 13. 7. of course. 16.11 are spacegroupdependent vectors and these generally occur when a symmetry element involving a translation is present. 10.
2 3 . 10 12. 20. 11 11 12 14 15 14
11. 14. 16.
3^3 7 :Vo r
13.
14 . 25. The vectors at the special positions A and C infig. 14. 13. 12.
10. 8.
2 5 . 11. The Patterson function for C 4 H 4 N 2 C1 2 . 26. 2 1 . 11. 36. 13.
26"! ""23. 17. 2 7 . 24. 15. 17.. 20. 14. 18. 10. 20. 20. I '33^18.
9. 17. 2 1 . 12.
15. 19. 13. There may. 16.23. 3 0 / 3 7 .
18~. 12 . 9.z) and (x. 8. 3 0 / ^ 3 1 . 15. 16. 2 8 f 23. 14. 11. 20. 19. 9. 16. 13. 10. 17. 12. 12. 15.
13. 13. 17. 8. 18.
2J5 < 1 2 . 8.
27>30f'26. 12 1 9 . 13. 20. 14. 9. 11. 11.
30* 2 1 . 1 0 . 26. 2 3 . 10.
10.
18. 27. 14
7 . 9. 15. 14. 16.^ + y.2
The Patterson function
1. 10. 25.
12. 16. 24. 25. 7.
11.
23. 11. 11.
1 1 . 15. 14. 10. 17. 8." 26r"26. 7./34~25^. 9. 11. 2 1 . 1 1 . 15. 12. 13. 25. 1 5 . 25. 12. 11 11 22
13. 8. 14. 11. 14. 17. 12.^ l^< 26.
10. 14. 7. 30/>. 13. 27. 15. 22. 10. \. 14.
2 2 . However. 15. 1 1 . ^21.
2 1 . 8. 15 . 17. 19. 18. 16. 11. 11. 1 5 . 10. 8. 23. 7. 16. 7. 12. For example.
13. 20. 12. 13.z). 27.
I S I S
the centre of peak B because of other vectors nearby. 9. 7. 33<'*44
161 2 3 . 18. 11. 11. 1 1 . 11.
9. 9.
13. D 12. 1 1 . 17. 18. 11. 1 5 .
30S27«?'2O.
11
12
z ^ 
13
14 14. 12. 9. 13. 19. 13. 8. 14 12. 1 1 . 26.
11.
10. 12. 13. 17. 17.} 2 5 .
58 "
. 12. 19. 14 18. 2S. 14. 14.
20. 23. 2z) and hence the section of the threedimensional Patterson map y = \ should show all the vectors of this type. !<f. 9.
16. 15 . 16. 3 6V 44 23.8. 11 10
17. 15. 9. 18. 2117. 1 2 .
1 8 .
13. 1 6 . \ ^ 18. 13.* 1 9 . 17. 11. 18. 10 . 8.
9. 15. 18. 31'.
11. 7. 19. 15. 25. 19. 10. ^ 3 6 . 11. 14. 31r» 1 7 . 37. 12. 21.
2 1 . 11.5705 FACTOR CONVERTING TO DENSITY/UNIT AREA IS TOP LEFT OUTPUT WITH Y HORIZONTAL AND ORIGIN 0 0 100 58^37^/13. 18. 11. 16. 11. 12. 17. 2 1 . 16.
7. 11. 9. 18. be other peaks in this section due to the accidental occurrence of vectors with a component y = \. 11 16.. 2 1 . 12. 13. 10. 12. 2 0 . 20. "27 6 17 10
0. 10. 9. 2 3 . 15. 23.
2 8 . 0. 2 1 . 14. 13.
1 5 . 7. 10. 36 .
18. 15. 25.
96 24.33 32.
8 8
8
8
9 9 10 10 11 12
5
1 4 1 4 2 0
0 3 6
2 5
20.
0.13 20.24 180. 0. 180.
5
0 3
180.
0. 15.
0.
180.43 10.
0.
180.
0.
h
11 11 10
k
1 4 3 2 5
F
PHI
180.28 46. 0.06 18.
180.07 10.47
3.91 30.
180.93 180. 0.38 20.00 1.
180.
0.244
The determination of crystal structures
Table 8. 0.80 180. 2. 0.43 13.
2 0 .91 4. 21.
0.32 9.11 11.96 24.43 1 3 .28 23. Note the systematic absences.
0.
6
1 4 7 2 5 1 4
180.
k 2 3
2 1 4
F
4.
5 5
6
180.88 180.
0.
0.55 10.00 3.07 180.53 15.
180. 29.
0. 5 6 180.
0.
180.91 4.80 0. 0.01 32.98 180.
180.
6.
0.
3 3 3
2 2 1 1
6
2
180.
0.
0.00 30.36 34.26 13.
180.28
23.39 18.
0. 22.
0.
180.
180.06 21.
0. 2 4
180.56 4.74 180.68 15.
0.80 19. 180.58 21. 180.
20.67 0.
6
6
180.29 1.33 8.
9 9 8 8
7 7 6 6
2 5 2
5
5
5 4 4 4
2 5 2
5 1 4 7
3 3
2 2 1 1 1
3 6
2 5 1 4 7
3
6 1 4 7 2 5 0
0
0 1 1 2
2
2
3 6
1 4 7 2
3
3 3 4 4 5 5 5 6 6 7 7 7 8
5
0
3 6
1 4 0 3
6
2
3. 0.
0.53 17.08
0.
0. 0.28 1.30 0.
0.
0.
9 9 8 8
7 7
10. 180.51 0.91 3.
0.
0.60
180.
h 12 11 10 10 9 k 1
F 6.
6
7 7
0.
0.00 0.30 180. 16.88 23 .
180.68 15. 49.
2
5 0 3
0.
0.
h
12 11 10
2
1 4
3
1 4 1 4 1 4 1 4 7
8 8
7 7
6 6 5
5 5 4 4
3 3
2 2 2 1 1 0
3 6 2 5
1 4 7
22.
180.27 12. 4. 0.93 180. 0.89
180. The complete set of structure factors for the artificial structure (C2NC1)2 as output by STRUCFAC PHI is the phase angle in degrees. 14.56 9.67
1.1.12 0.20 180.
5 5
4 4
6
2
180. 180.81 0. 0.36 34.27 19.
0.
180.
180.
0.75 180.00 16.69 49 .32 9.89
180.93 5.
0.36
14.70 26.82 63. 12.
180.
5
1 4 7 3
180.00
180.51 7.
0.31 180.20 4.60 46.
0. 180. 180. 0. 0.
0.
0. 0. 0. 0 7 180.71 2.
2 2 3
3 4 4 4 5
15.81 14 .
0.65 39.56 5.
0.00 180.
0. 0.
0. 0. 0.53 26.
180.13
0.56 4.93 3.55 8.12 0.
0. 0.
0. 180.
0.
3 6 3
6 3 6 3
180.64 7.47 0.63 144.00 0.65 39.20 10.56 9.15
.38
2.36 0.81 5.79 11.69 0.71 8.
0. 180. 3.16 2 7 .02 11. F(h.91 30.68 17.80 19.08 0. 14. 180. 10.00 1.39 18. 0.
180.
0.
0
0 0 1 1 1 2
6
1 4 7 2
0.29
180. 14 .
180.
0 0
1 1 1 2
2 5 0 3
6 1 4 7
180.
0 3
0
3
1 4 2
180. 180.06 7.00
PHI 0. 0.74 27.15 0.98 180. 180.81
2.
0. 0.49 15.
5 6
6
5 0
3 6 2 5 1 4
180.91 180.79 11.20 10.08 0.69 12.
0. 0.
0.53
9
9 10 11 11 12
2 0 3
1
5.82 11.02 11.53 17.15 0.38 23. 0.68 16.
180.69 3.43 17.
0.
2 3
3 3 4 4 4 5
5 0
3 6 1 4 7 2
1.11 17.
180.
0.49 0.67
PHI 0.65 0. 180. 4.69 0. 180.08 0.
8 8
9 9 10 10 11 11 12
0.64 7.65 0.67 0.96 19. 0.75 14. 180.
0.27 18. 0) = 0 for h odd.
6
7 7
0.65 0. 19. 0 0 180. 17.96 19.
0.06 17.
0.15 32.31 20.63 7.
0. 0. 0.17 25 .17 25. 0.43 9 .00 18 .88 4. 0.89 12. 0. 0.44 13.89 12.43 13. 0. 0.00 0 .99 13. 0.99 13 .00 42.03 0. 180. 180. 0. 180. 180. 0.37 21.39 17 .2 The Patterson function Table 8. 180.96 24 .07
PHI
180. 0. 0. 180.00 29.26 9. 0.87 0.00 0. 0.00 14 .26 26 . 180.93 68. 180.00 0.61 4 . 180.80 14 .87 15 .54 8. 0.
h
12 11 10 9 9 8 8 7 7 6 6 5 5 4 4 4 3 3 2 2 1 1 1 0 0 1 1 1 2 2 2 3 3 4 4 4 5 5 5 6 6 7 7 8 8 8 9 9 10 11 11 12
k 2 3 2
1 4 2 5 2 5 2 5 2 5 1 4 7 3 6 2 5 1 4 7 2 5 0 3 6 1 4 7 2 5 0 3 6 1 4 7 2 5 1 4 0 3 6 2 5 2 0 3 1
F
4 . 180. 0.34 22.00 16. 180.46 15.18 11 . h
12 11 10 10 9 8 8 7 7 6 6 5 5 5 4 4 3 3 2 2 2 1 1 0 0 0 1 1 2 2 2 3 3 3 4 4 5 5 5 6 6 7 7 7 8 8 9 9 10 10 11 12
k
1 2 1 4 3 1 4 1 4 1 4 1 4 7 3 6
F
4. 0. 0.21 31.35 0. 0.18 11 .73 0 . 180.08 12.11 4. 180. 180. 180.09 38 . 180.19 0.55 26. 0. 180.21 8 . 0.07 0.08 12. 0.85 27 . 180.26 14 . 0.16 0 .83 29 . 0. 180.88 14 .2. 0. 0.43 13.87 22 .93 5.78 16 . 180. 0. 180. 0. 0.34 22 . 0.46 15.87 12. 180. 180. 0. 180.93 5 . 180.87 12. 0.00 0. 180.00 0 .80 8.81 7.03 37 . 180.16 31. 180.26 27. 180.16 0. 180.56 15.10 14 .91 4.00 0.37 21.00 0. 180. 0. 0.99 4.23 0 .07 13. 0. 0. 0. 0. 0. 180. 0.03 13 .15 0.08 4 .00 0 .1 shows that the indications of sign given by chlorine are mostly correct. 0. 0.21
PHI
0.11 29.
h
11 11 10 9 9 8
k
1 4 3 2 5 3 6 3 6 3 6 3 6 2 5 1 4 7 3 6 2 5 0 3 6 1 4 7 2 5 0 3 6 1 4 7 2 5 0 3 6 2 5 1 4 0 3 0 3 1 4 2
F
14 .35 27.61 4. 0.29 0 . 0. Chlorine contributions to the structure factors o/(C 2 H 2 NCl) 2
245
PHI is the phase angle in degrees. 0. 0.81 26.85 0 .31 4. 0.16 27.90 31 . 180.81 0. 180. 0. 180. 0. 0.83 22. 180.34 18. 0. 180.87 22.00 0.95 12. 180.21 7 .38 0. 180.98 9 . 0.07 13. 180. 180. 180. 0. 0. 0.31 0 . 0.39 14 . 0.54 8. 180.04 0 .93 18. 180. 0.
8 7
7 6 6 5 5 4 4 3 3 3 2 2 1 1 0 0 0 1 1 1 2 2 3 3 3 4 4 4 5 5 6 6 6 7 7 8 8 9 9 10 10 11 11 12
2 5
1 4 7 3 6 1 4 7 2 5 0 3 6 1 4 7 2 5 0 3 6 1 4 0 3 6 2 5 1 4 1 4 2 0
. 180.21 7.03 13.31 15 .26 4 .01 16.92 43.49 29. 180. 180.01 12. 180. 0. 180.00 0 . 180.00 0 . 180.90 0. 0.13 26.00 0. 0. Comparison with table 8.92 26.26 27. 0. 0. 0. 0. 0. 0.02 10 .08 14 .99 27.08 0 .23 0. 180. 0.15 0. 180. 0. 0.96 24.43 14. 180.19 0.91 4. 0.31 26. 180.73 37. 0. 0. 180. 180.26 15. 180.39 14. 180.57 13 .09 8. 0. 180. 0. 0.8.33 17.82 4. 180. 0.00 14. 0.83 22.02 10. 0. 0.00 0.00 30. 0.34 7 .04
PHI
180.26 4. 180.00 0. 180.38 43. 0. 180.10 4 . 180.39 17. 180.81 26 .56 14.57 13.82 4 .29 0. 0. 0. 0.
A very powerful technique for making use of Patterson maps is by the use of superposition methods.11 A and p = 98. A section of the Patterson function which shows spacegroupdependent vectors is called a PattersonHarker section (Harker. b = 6.\.2z).8.z) and ± ( i + x>\ ~ y>z) a n d the vectors between related atoms.5° and four molecules of C1C 6 H 4 IO 2 per unit cell. The effects of spacegroup symmetry which lead to relationships between the phases of equivalent reflections. 8.12 are the iodineiodine vectors corresponding to ± ( i + 2x.2y.12.246
The determination of crystal structures
axis at double scale.12. For all orthorhombic structures one has
hkl
I2 = \Fm\2 = \Fhkl\2 = \Fhkl\2 = \Fm\2
=
\2 = \Fhn\2 = \Fhkl\2
and the Patterson function of all primitive orthorhombic space groups is Pmmm. are lost in the Patterson function for which \F\2 is used as a coefficient.y.
The two heavy peaks infig.2z) and hence the iodine position may be derived.
1 0 1 2 3A LnlnJ 1 1 I 1 I 1
. 1948). are:
single weight ±(2x. 1948). 1936).4. It can be shown (Buerger. The PattersonHarker section y = ^ for pchloridoxy benzene (from Archer.2z) double weight + & £ + 2y.2y. The Xray measurements gave the space group as P2Ja with a = 14. ±(2x.0).13(a) a set offivepoints and in (b) the vector set derived from
Fig. 8.£. To see how this can be done there is shown infig. apart from null vectors. 1950a) that for the 230 space groups there are only 24 possible Patterson symmetries. The symmetry gives related coordinates ±(x. It should be noted that the symmetry of the Patterson function need not be the same as that of the structural group. It was shown by Wrinch (1939) that if the complete set of vectors between atoms was available it would be possible to recover the original atomic positions. this was used to solve the structure of parachloridoxy benzene (Archer. c = 8.8.2z). ±{\ + 2x.50. An example of a PattersonHarker section is given in fig.
if the original unit is centrosymmetric as in fig.14(a) giving the vector set (b) and if the overlap is made on a singleweight peak then a single image of the set of points is produced. « single peak. If two of the vector sets are now superimposed with a relative displacement equal to that of one of the single vectors then a number of points exactly overlap.
(a)
#
® ®
® ®
D I
(c)
these points. For second set: (] origin peak. 8.13. (c) Superposition on a singleweight vector. then two images of the original set of points result. It will be appreciated that this method depends on having available the vector set and this is not what one usually has from a Patterson function. and errors in the observed data can lead to randomfluctuationswhich are as big as some of the smaller peaks. On the other hand. Incidentally it should be noticed that if the displacement of two vector maps corresponds to a doubleweight vector. If the relative positions of more than two points of the original set are
.2
The Patterson function
247
Fig.8. These are shown in (c) and they show the form of the original set of points plus the centrosymmetrically related set connected with dashed lines. Similarly superposition with anrcfoldvector displacement gives n distinct images. Q double peak.14(d).  double peak. 8. The Patterson peaks are spread out and overlap.
to A
noncentrosymmetric set of points. 8. as in fig. (b) The vector set. For one vector set: ^ origin peak. a single peak.
13). (a) A centrosymmetric set of points. (c) Superposition on a singleweight vector. (d) Superposition on a doubleweight vector (symbols as in fig. There are
. there will always be a number of chance peaks which will confuse the image obtained from the overlap function. 8. secondly.248 Fig.14. it is usually difficult to find a singleweight peak and. 8.
The determination of crystal structures
(b)
(c)
id)
known then the image of the set of points can be recovered by multiple superposition. firstly. (b) The vector set. This type of procedure is very necessary when one is using a real Patterson function.
8.l) then the individual peaks retain their spherical symmetry. However to take the observed \F\2 will probably lead to very diffuse peaks giving considerable peak overlap. say. Sometimes the contribution of the heavy atoms can dominate to the extent that most of the F s will have the same signs as the C's. In fact if one modifies the JF 2 'S by any smooth function of s ( = 2sin0/. If the displacement of the two map origins is R then one can find the product function P(r)P(r + R) or the sum function P(r) + P(r + R).3
The heavyatom method
249
various functions of the overlapped Patterson maps which can be taken.3 The heavyatom method When a structure contains a large number of light atoms and a few heavy atoms the structure can frequently be solved in a straightforward way. By taking the minimum function one reduces the amount of spurious information in the result. or by a handdrawn function on graph paper . A function proposed by Buerger (1950b) is the minimum function. which means the least of the two quantities P(r) and P(r + R).1 times the average of  F  2 near the centre of the sphere. If the contribution of the heavy atoms to the structure factor of index h is Ch then we have
Nn
F
h = ch + Z /)cos(27ihT</) = Ch + Kh. The negative regions thus introduced may reduce or eliminate other peaks. Either a Fourier synthesis can be calculated with the signs of the C's completely accepted or discretion can be exercised and the sign only accepted if the magnitude of C is sufficiently high. The quality of Patterson functions can be improved by various sharpening procedures. 8.8)
where N is the total number of atoms in the unit cell. In selecting the heavy
. A standard technique of solving a stereochemical problem is to prepare a heavyatom derivative of the substance in question. M{P(r). on the other hand. Let us consider a centrosymmetric structure containing in each unit cell n heavy atoms whose positions can be located through the use of the Patterson function.it is not a very critical operation. With judicious sharpening one can pick out useful vectors which would otherwise be lost. P(r + R)}. Oversharpening. If r and r + R correspond to the positions of peaks of interest then each of the peaks should at least have a single weight but might be heavier because of the accidental overlapping of peaks. The modification can be made with an analytical expression. A 'ruleofthumb' which gives reasonable results is so to modify the \F\2 that the average value of the modified  F \2 for the region near the edge of the sphere of reflection is about 0. Ideally one would like the Patterson map corresponding to point atoms but if one tries to achieve this by using \U\2 instead of  F  2 then the termination of the Fourier series leads to considerable diffraction ripple around the peaks.
(8. such as exp(Ks2). leads to the appearance of greater resolution but the extra peaks can be of diffractionripple origin and some of them can be quite spurious. When the relative positions of a number of atoms are known the use of the minimum function can lead to the solution of quite complicated crystal structures.
respectively. On the other hand. indicates that the average contributions of the light atoms and heavy atoms to an intensity should be equal.22) it can be seen that. it is possible to determine the probability that the sign of the structure factor is correctly given by the heavyatom contribution. The modified data file was then input to FOUR2 to give fig.
(8. 8. enables the output file from STRUCFAC to be modified and this has been used to make the structure amplitudes zero for the 20 reflections for which there are no sign indications and to change the signs (phases) of the 8 incorrectly indicated by the chlorine contribution.11)
.250
The determination of crystal structures
atom a careful balance has to be struck. The program HEAVY listed in appendix VI.and righthand sides of equation (8.11) and the chlorine atom forms a substantial part of the total scattering power. A ruleofthumb which works well if there are a number nL of almostequal light atoms and a number nH of heavy atoms is to have
I/ 2
heavy atoms
= I/ 2
light atoms
(89)
which. in fact. 8. The program STRUCFAC was used to calculate structure factors from the chlorine positions alone and these are shown in table 8.8) it can be deduced that if F h and Ch have the same sign then
lKkl= ll^hliqjl
whereas if Fh and Ch have opposite signs then
\Kh\ = \Fh\ + \Ch\.8.10(b).2 (p. If the heavy atom is too light it will be a poor determiner of signs and the structure will not be soluble.K 2 /2I') (8.10b)
From equation (7. From equation (8. The left. Of the 156 structure factors there are 14 for which the chlorine contribution is zero (excluding 6 structure factors which are systematically zero) so that no sign indication is given. the contribution of too heavy an atom will so dominate the intensities that the errors in intensity measurement may become comparable to the contribution of the lighter atoms. from structurefactor statistics alone and not taking account of any other information. In this example all the signs of the structure factors were taken as those of the chlorine contributions but. The position of the chlorine atom could be determined from the Patterson function (fig. the probability distribution of Kh is given by P(K) = (27il')"iexp( .29) and (7.32). from equations (7.15.9). are 289 and 121. Of the remaining 136 structure factors all but 8 have their signs indicated correctly by the chlorine contribution and 4 of these 8 have very small structure amplitudes. a Fourier map which shows clearly the positions of the light atoms. The principle of the heavyatom method can be illustrated with the synthetic structure (C2H2NC1)2 shown earlier infig. ignoring the hydrogen atoms. 245).10a)
(8.
1.
1.
7. 0.
1 .
1. 4 . 2.
4.
8.2 . 5. 5. 0. 1. . .
1. 1. 13 .
3. 2. 5.
6.
g
7 q
5.
10.4 . 4. 3 . 9.
4.
.
4 9.
0. 2. .
2.
2. 2.
0 .
18. 4
7
1.
0 . by P+_exp{(Fh[CJ)2/2E'}
T) ( / I T7 I 1 I /"> I \ 2 / ^ W V V * /
The expression (8.
1.3 .
.
3.
9 7 9 3 1 .
^2}J 2 / 7 )
6. 2. 2.
where Z' = £ / ? .
9 11 3 2 8 2 3
2 . 1 . 3.
15 /"* "" \ 2 . Expression (8.
2. .
0.
9.
1. 1 7 4.
.
0. 1 1 .
. 4 .
0. 4. 3 1 7 4 3
2 .>l
S
. 4. 4 . 5 2 1 6 2 7 2 6 2 4 3 4 2 6 2 7 2 6
.
As . . . . 8.
. 3 . 9. 3 . 8. 1.
3. 10. 4. . 1.4 . 1 0 . 1.
. 3.
1 8 .
6.
. 12 .
1. 14. 5. 9.
.
9 3
. 3.
2. 2.
5. 2.
4. 2. 3.
0. 0.
. 7. 2 10
A
"
V'2.
2. 1. 3. 8.2 . 15 v
1. 5. 2*7.1 .
6. 8 7. 7. 0.
7 0 6 0
5 1 7
. 1. .
1. .
0. 1.
4 .
1. 9.13)
. 10. 3. 27 . .
5.
0. 2.3 .
2. 0.
4. .
6.2 .
3 9 7 9 11 3
2 8 2
2. 1.
14 . 2{. 23/ 3.
3."* s 5. 1. 9.
6. 3. . 0.2 2 . 3 . 4 . 5 . S .
1. 4. .
.
17. 7 . 5. 6. .
6.12) can be simplified to (8.1 0 . . . t * 2. 2. 4 .
4.2 .
5.
2. 12. 13 5 2 5
?
1. 0. 3 . 5.
8.
5.
3.
7. . 5.
3
11
3 . 1 9 . 9.
.
0. 3. 4. 3.5 .
3.
3.
• " 2 . 19 / 9
4 9
2
6. 7.
6. 5.
1.
t
9
7
9 3 9 3 9 7 9 11 3 2 8 2 3
11
4. .
0 .
4 . 0. 3. x5^« .
4.
1.4 . 0.3
The heavyatom method
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 0. .
3. 2
3. 2. .
7 . 19s.'25 " l 8 . 3. 2. 7. 2 .
3.
1.
4. 2. 10. 4 .
0. 7 .11) to determine the relative probability of having the two values of  X h  given by equation (8. 6.
9. . . 4 . . 9. 0. . 4 .
5. 4 .f4. 9. 2'5~ 14 . 11
19
12
. . .
0.
5 8 3 3 3.
9. 1. 1 2.
lift'
1.
11 9 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
7
A2
4 .
9
9
7
9 3 1
. To. 2 . 4.
2 .3
7 . . 3 6 .
4 . 1. The probability that Fh and Ch have the same sign. 10 . 5.
7 1
.2 . . 3. 1 7 . 5.1955 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT 10 11 12 13 14 15 16
251
Fig.
0. 4. 6. 4 .
Q. 0. 4 .
0. 5 9. .
4. 2.15.
1. The light atoms are in the positions outlined by a single contour. 0.
4. 7.
0.
4. 6. 27.
7
2.
2
0
.10).3 .
2.
9. 10 4 . 10. 5.
9.
4.
4
3. 2. 0. . .
j= 1
will be related to the probability that they will have opposite signs.6
4 .^XP/.
2.
1.
10.3 . 12 . . .
. 0. 2. 0 .
4. \
in
V?'
1.
9..9 2 .
4 . Fourier map for C 4 H 4 N 2 C1 2 with signs given by the chlorine atoms.
in
. .
7
2. 4 .
7. 1.
2.
17 18 19 20
3
9 7
2
5 4
4.
?
7. P_.
1. . 3.
1 .
2. 8. P + .J7~ V .
1. 6.
8
.
5. 2.
1
2. 7 . 4.
2. 9. 2. 12 . .
0. 3.
.
8.
2.
3. 4 . 1. 7
5. 12. 4 .
2. 4.
.
4. 0. 6.
8. . 1 1 .5 . .
5
2.
2.
12 . 9.
2. 1 3 .
2 5. 6. . . 5 . . 1. 7. 1 7 . 2.
9. 2. 0. 1.7 . 9
7
2.
2. 5.
3. 14 . 3. 13 125
V.
7.
3.
0.3 .
4. . 1 .12) uses the distribution (8.
9.
23 i
10.
3. 11 2. 5.1 2 .
1 3
. /
4. 2. 0.
3.
7. 1 5 . 9. 1 . 7.
.
8. 4.
5.
. 3. 1. (25.3 . 5.1 . 1. 8 .
13.2 .
6. 12 . 0. 4 .
3 3 8 5
. 12.
26^ 2.
7.
27*\ 5 /
1 .
1.
0.
5. 5.8. 4.
6 . 4.
1 . 0. 6.
2 26
6
4
6
2. 1 . 2.
6.
The heavyatom method can then be used to try tofindthe remainder of the structure . for example by matching vectors from some symmetric part of a structure with the peaks of a Patterson map. This will give rise to a Fourier synthesis which has a false centre of symmetry and it may be difficult to pick out the peaks corresponding to the structure. 1959. For the example we have used here the advantage would be hard to detect because perfect data are being used and the heavyatom contribution is relatively large.and righthand sides of equation (8. The map calculated is
. However if there is only one heavy atom then this may be arbitrarily placed at the origin and all the phases are indicated as zero.although the term 'heavy atom' applied to the method is somewhat inappropriate in such a situation. The synthesis with modified coefficients gives a clearer density map than is obtained by accepting all signs from the heavyatom contribution or any arbitrary scheme of accepting or not accepting the heavyatom sign. There are cases where. If there are two equal heavy atoms then the situation is similar since the centre of the pair may be taken as origin and all the phases will be 0 or it.15) (8. The Fourier coefficients used for the synthesis are Fhx(2P+l)x(signofCh). However if there was one chlorine atom in the presence of. In this case the atoms which are clearly indicated in the map can be added to the heavy atoms and the new combination of atoms in known positions will give more reliable sign indications. The contribution of chlorine would be much less reliable in this case and a map with properly weighted coefficients would be much easier to interpret.in the sense of having the highest signaltonoise ratio.252
The determination of crystal structures
and if we use the relationship P + + P_ = 1 then we obtain P + =Hitanh(Fh C h /r). A new map may then reveal further atoms and the process can be repeated until the structure is completely determined. for a lightatom structure some fragment of the structure can be found.14)
Woolfson (1956) showed that a Fourier synthesis can be calculated with weighted F s which gives the greatest signaltonoise ratio in showing the light atom. say. Sim (1957. 30 carbon atoms then the left. (8. Sometimes the first map obtained by the heavyatom method does not give all the light atoms but rather a fragment of the remainder of the structure.9) would be 289 and 1080. 1960) has made a statistical analysis of the errors in the phase angles obtained from the heavy atoms alone and has also found the weighting scheme for structure amplitudes which gives the best Fourier synthesis . respectively. The heavyatom method can also be of value for solving noncentrosymmetric structures. When there is a noncentrosymmetric heavyatom group which can be located by Patterson methods then the phase from this group can be used as a first phase for a Fourier synthesis.
3
The heavyatom method
253
p'(r) = £ W(h)F(h)cos{27ihT .375.17)
where 7X and / 0 are modified Bessel functions and X = 2  F(h) 11 C(h)  /E'.5 
An illustration of the use of Sim weighting is given by application to the synthetic structure C 3 H 5 N 2 ONa 2 . 8. C (0.958).0.16.
.0. C (0. The synthetic structure C 3 H 5 N 2 ONa 2 . Na (0. 0(0. space group pg with a = 8 A.
h
(8.125.
Fig.219.#1)}.0.167).583). N (0.417).344. The coordinates of atoms in one asymmetric unit are: Na (0. I\(X) I0(X) iQ_
0.437.17.937.
Fig.156.063.250).667).16.0. The Sim weighting curve.125).17. 8.8.375). 8. C (0. b = 6 A. 8. The form of I^Xyi^X) as a function of X is shown in fig.0. illustrated in fig.0.0.16)
The weight imposed on the structure amplitude is W(h) = I1(X)/I0(X) (8. N (0.0.
7. 4. /
7.
15.1 2 .
13 5 2 7
12.
7. — —
< 0. 4
6
0.
57""77 — 2T
17.
2. 4 3. 16/
4 .542 A) for the complete structure and the contributions of the sodium atoms. 2.
. 2 3 .
^9. 5 '
11/ 5. 11 6. 6 8 11
V
.^ . 9V
4 8. 9.
4. but the other atoms appear less clearly and some spurious density can also be seen. 8. 8.
0.and righthand sides of equation (8. 5. "~2*". 8
1 9 .N 3 7.4 show the structure factors for Cu Ka radiation (X = 1.
1. 4.8..^ v l l . .
Fig. 1.1212. s 7.
14. excluding hydrogen.
5.
7 . 14"
x
{ 4.2 .
6 8 13
19.
20.14. 0. 12. 1 6 . It will be seen that the sodium atoms tend to give reasonable phase estimates.
3. 6. 6. The program HEAVY was used to produce an input file for FOUR2 which had Simweighted Fourier amplitudes and the phases from the sodium contributions.
* 1.
" 16.1. 5.
8.
2. 4
16. f"l4
.
19 • # '
l \
0.
5.
^97_
h /
6.
2.
8.
. mostly within 60° or so. In this case the heavy atoms are not so dominant as in the previous synthetic structure (C2H2NC1)2.
4 . 8.
4 . 4.
*>
1. 3.
6. 1. 8.
2
0 ."'f2T
7 . 1 8 * 1 3 ." l o . 4. .
. .0
V V ) 12 . 4. If only a fragment of the nonheavyatom structure can be found from a Simweighted map then the iterative procedure described for centrosymmetric structures can be used. 1.
1.15*»
Na
VIOO.
3.
1.
2 2 9
_2
. . 16. < 1 4 . 14 . 1 6.
8. 3.
5.1231 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT 10 0 1
2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
11
12
13
14
15
16
17
18
19 20
3 2
0 15 23 / 20 12 1 14 10 5 7 5. 0. 8.
7
19
is'
V
5? ( 1 3 \ 7 5 \ 92
5 10 6 8
~dr
NS^ 9^
8.
\
5
^. 3 . 8. 8.
11? t
8.
1T
6. the sodium atoms appear clearly. 24. 1 6 . but with some notable exceptions. 1.
8 10 7
^
7
4 . The resultant map is shown infig.
l l T . 17 1 6 .
5.
) 5.254
The determination of crystal structures
The sodium atoms are regarded as 'heavy' and the left.. 0.
17.1 .
2. 6. The use of Simweighted Fourier syntheses is an important procedure in Xray crystallography for going from a knowledge of a partial structure to a complete structure determination. .
97
15.
9'. 1 2 . 11. . respectively. 3 V I 3 . \ 19.
r.
20. 13. ""* 6L
5. and tables 8. 1.
14. 6.^i3r
13.. 137 24. 3. 8. .i
2.18."
V
— ~"
16. 4 1
5
*8. 6. 6.
^ £ . 7 . 5
5.
23 24
11 3
8\ l 9
2. 13.9) are.
N
5 . 16
12.
4 . However with stereochemical knowledge of the molecule the map can be interpreted to lead to a complete solution of the structure. 3. 13.1 . 3 . 1 1 .
24.
\
12. 5.
5. 3.
0 4
8.
4 .
0. / ' 9.
4. 2 1 '? . 14. 14 . respectively. 2. 12 • l^ .
N5.
3. 2 4 .
3.
4 . 3. 8. 12 . 9. 8. ^
8.«s . • . i 10^ 15. 4. 1 4 . 16.
^16. 3.
4 . 1 5 .3 and 8. 2.
.
11.4 . 4.
\7.
16
/9.
. because they have been the source of the phases. 3 3 0
19 18'
'
. 6.
3. 8 4 1 3 7 10
H
. \
1Z.18.
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 0.
{3
5 ^ 0
j
4 . 1 9
10 J 2 3 . 5.
0.13
5.
5. 6 . 3 . 9^
12 . 6. 19 r* "5. .1 3 .
'7 0.
5. 7. 0.
V
.
\M>
5. 1. . 242 and 270. 7 ./ 13.
6.
13 ' ' '(
\
Na .
8.O.1
17 7
0. 8. 7. V
16.
10/15.
.
5
. Fourier map for C 3 H 5 N 2 ONa 2 with phases from the sodium atoms and Sim weights. 4.
1.
4 2
' 14
V
>
X"
16.
2. 101 2 3 . 16.
6.
/ 2
7 11
4 .
3. 2.
4 ^ 14 . 6.
10. ) l 2 4 . 3~" T. 1.
"1 N 2.
4. 5 .
"VI. \ k 9. • 4. 4
.
1.
3. 12 .
18. 13. 6.
3.
4. 12 "" — " 7. . 5. 5. 6.3
1.
17. 4 4 ..J
i 3 6
v 8.
3
(16. 3. 16.
9. i 2 1 20
19 9 17
' >&
ll)
5.
C
4.8
2. 1
5 . 4 .
8.
43 A 16.6dichloropyrimidine
.but can be less simple.45 A 4.
L
2amino4.4 Isomorphous replacement
255
8. Two crystal structures bearing this sort of relationship to each other are termed isomorphous and from the differences in their diffraction patterns it is often possible to obtain a complete structure determination. For example. The molecular forms of the isomorphous compounds 2amino4methyl6chloropyrimidine and 2amino4.19.6dichloropyrimidine. 1948) which differ in that the methyl group of the first is replaced by a chlorine atom in the second. in fig. 8.85 A 10. the atoms must be similarly arranged except that in one case a methyl group is replaced by chlorine. Sometimes the substitution can be fairly straightforward .
H H—NL
2amino4methyl6chloropyrimidine
H H—N.4
Isomorphous replacement Very often it is possible to have chemically similar materials in which one or more atoms or groups in one compound are replaced by one or more similar atoms or groups in the other.6dichloropyrimidine (Clews & Cochran.31 A 10.28 A 109° 108°
An examination of the Xray data reveals that the diffraction patterns are strikingly similar in appearance and it is clear that. 8. in terms of crystal structure.8.00 A 3. Let us take the case where we have two isomorphous structures which differ in having n atoms of type A in one replaced by atoms of type B in the other.one halogen atom for another or one alkali metal for another . Then the structure factors of vector index h for the two compounds can be written as
Fig.19 there are shown the molecular forms of 2amino4methyl6chloropyrimidine and 2amino4. The cell dimensions of the two structures are:
P
methyl chloro 16. The crystals of the two materials look rather similar (long needles) and both have four molecules in a monoclinic unit cell of space group P2Ja.
53
20.23 18.86 8.65 14. 24. 54.
0. 180.82 10. 135.
73. 46.72 15.98 15.15 8.63 4.82 10. 180.
125.12 11.
139.03 4.50 16.
48.
93.53 11.41 4.
4.08 3.63 7.97 8.13 5. 170.93 28.
107. 19.71 6. 174.01 9.19 4.49 10.
149.
0.36 28.03 6.97 4.05 16.
170.01 7.23 8. 0.28 14. 0. 99.
128.97 4.71 36. 131. 139. 53.51 0. 180.82 8.66 0.05 16.95 10.83 5. 40.
132.
75.84 14. 48.68 26.65 0.62 15.
164.
0.
h 10 9 8 7 7 6 6 5 5 4 4 3 3 3 2 2 1 1 0 0 0 1 1 1 2 2 3 3 3 4 4 4 5 5 6 6 7 7 8 8 9 10
k 1 2 2 1 4 2 5 2 5 2 5 1 4 7 3 6 2 5 0 3 6 1 4 7 2 5 0 3 6 1 4 7 2 5 1 4 0 3 0 3 1 0
F
4.00 0. 138.15 8.01 9.
35.02 11.24 32. 14.51 2.59 6.10 11. 45.
179. 115. 125.
46.03
12.
41.38 4.87 11. 130.33 14. 16. 0. 70. 174.71 15.
0. 180. 10. 87.87 11.
46. 132.23 36. 149.
139.83 5.93 28.84 14.12 11. 166.
140. 1.10 6. 159.02 11. 69.15 32.33 8.49 10.57 15.51 30.
.72 15.27 5.27 5. 34. 22.00 17. 180.
41.
1.
156. 50.
16.57 4. 126.
167. 153.01 7.
h 10 9 8 7 7 6 6 5 5 4 4 3 3 2 2 2 1 1 0 0 0 1 1 2 2 2 3 3 3 4 4 5 5 5 6 6 7 7 8 8 9 10
k 2 3 3 2 5 3 6 3 6 3 6 2 5 1 4 7 3 6 1 4 7 2 5 0 3 6 1 4 7 2 5 0 3 6 2 5 1 4 1 4 2 1
F
PHI
3.83 6. 105.76 6.24 3. 147.76 14.
145. 146.
179.
125. 161.16 26. 161. 11. 48.83 4.256
The determination of prystal structures
Table 8.08 3.95 5. 168.63 7.08 16.57 8. 169.
45. 1.19 4.08 4.37 1.00 28.37 17.
21.69 5. 108.61 5. 135.41 17.62 6. 65.13 5. 161. 69.
180.
27.
53. 134.15 14.69 3.95 18.
75. 110.24 3. 77.50 0.36 30.
49.
33. 80.21 14.30 14. 22. 167. 4 .
0.38 4.95 10.02
PHI 1.00 13.30 14. 108.95 6. 180. Structure factors for the synthetic noncentrosymmetric structure C 3 H 5 N 2 ONa 2 PHI is the phase angle in degrees.96 13.
81. 45.3. 20.61 5. 45.03 2.96 12.24 19. 139. 128.21 14. 0.
132.30 13.37 1.76 11. 138.63 4.76 11.37 124.
0.
h 9 8 8 7 6 6 5 5 4 4 4 3 3 2 2 1 1 1 0 0 1 1 1 2 2 2 3 3 4 4 4 5 5 6 6 6 7 7 8 9 9 10
k 1 1 4 3 1 4 1 4 1 4 7 3 6 2 5 1 4 7 2 5 0 3 6 1 4 7 2 5 0 3 6 1 4 0 3 6 2 5 2 0 3 2
F
PHI
12.16 17.
100.86 8. 10. 55.00 12.
48.30 14.
77.
54 150. 90.
3 3
2
0.4 Isomorphous replacement Table 8. 30.09 4. 6 .11 6. 120. 60.02 20.17
150.91 6. 30.
3
1 4 1 4 1 4 7 3
6 . 0.00 0. 180. 90. 30.83 6.46 0.24 13.
4. 180.27 15.19
0.16 150. 180. 150. 30.64 11. 8. 120. 7.57 0.50 0. 90.01 6.62
4.
0. 7. 3 8 120.18 4. 120.60 0. 60. 1 7 . 60. 150.43 9.43 9.17 60.43 30.66 60.00 0.39 10.18 30. 120. 30.20
30.37 0. 8. 150.43 1 3 . 7 4 150.94
3 6
1 4 7
0
0 0 1 1 2
0. 6 .16 180. 11. 0 . 90. 0.15 12.
0. 0.
0. 17.10 12. 0.80 0.00 4. 2 7 .78 13.92 0. 60.19 0.51 120. 30.95 30.00 0. 0. 12.38 120.87 0.74 6.11 120. 20. 30. 9 6 150. 12. 60.
0. 60.93
6
2
2
1 1 1
5
1 4 7
0 0
1 1 1 2
2
5 0
150. 150. 60.93
0. 120.83 6.54 7. 0. 14 .00 27.27 0. 60.08
0. 60.27
60.
0. 0.24
8 9
9 10
0 3 6 2 5 2 0
3 2
8. 30. 2 0 120. 90. 0. 60.81 180. 20. 1 5 180. 60. 0. 150.00 0.09
h 10
k
F
PHI
9 8
7 7 6
2 3 3 2
5 3
6 5
5 4 4
3 3 2 2
2 1 1
6 3 6 3 6 2 5
1 4 7
4.38 24.09 0.19 20.01 30.16 0. 90. Contributions to the structure factors of the Na atoms of the synthetic noncentrosymmetric structure C 3 H 5 N 2 ONa 2 PHI is the phase angle in degrees. 8 3 120.21 7. 150. 8. 150.62 180.95 20.66 11.
2
2
8.64
5
1 4 1 4
7 8 8 9
10
2
1
180. 90.39 30.
h 10 k 1 2 F
257
PHI
9 8
7 7 6 6 5
2
1 4 2 5 2
5
4 4 3 3 3 2 2 1 1 0 0 0 1 1 1 2 2 3 3 3 4 4 4 5 5 6
5
2 5 1 4 7
3
6 2 5
0
3 6 1 4 7
2
5
0
3 6 1 4 7 2
5
1 4
6
7 7 8
0
3
8
9 10
0 3
1 0
60. 0. 120.
5
4 4 4
8.00 0. 0. 180.00 0.
. 0.87 15. 30. 0.62
4.
2 5 0 3 6
1 4 7
90.83 11.00 0. 8.55
14. 120.03
7.46 11.27 150. 120. 60.06 0.51 7.66 17.04 0.57 30. 4.80 120. 8. 30.
60.37 15. 90. 8 7 60. 30. 30. 150. 60.37 12. 10.48 20.13 6.02
4.
60. 5.50 0.37
3 3
4 4 4
2 5 0 3 6
1 4
5 5 6 6 6
7 7
0.
2
2
3 6
1 4 7
3
3
3
4 4
5 5 5 6 6
7
2 5 0 3 6
2
8.94 9. 0.15 150.00
12. 180. 13.02 0.19 9.91 6 .21 6. 120.01 0. 26.04 0. 30. 5.8. 90.96 26. 44.4.62 26. 90.
h 9
8 8
7 6 6 5
k 1 1 4
F
PHI
5.02 90. 0 1 150.09 12. 1 3 120.87 15. 90. 0. 150.08 0.10 0. 120. 180.04 90.00 90. 90. 7.04 11.66 5.00 4.
60. 120.55
16.03
24. 150. 7.06 0. 30.
 (Fh)B  = 7 8 . \(Fh)B\ = 1 0 . = 20. Let us consider  (Fh)A  = 92.19).2. then the signs of the F s may be found. (Fh)B = + 78. The signs of (Fh)A and (Fh)B will both be established as positive in this example. Ch = . = 1 2 . we have (8. if the value of Ch is known as. / . Another set of values might be \(Fh)A\ = 8. Let us now consider the situation for a centrosymmetric structure when we do not know the sign or magnitude of Ch. / .15).ZA = 18) or O by S (ZB — ZA = 8). Since.20) it can be seen that (Fh)A — (Fh)B ( = ^ h ) is the structure factor for scatterers of scattering factors/. The values offA.19) +fACh
For centrosymmetric structures these equations can lead directly to phase information. from equations (8. = 1 2 . \ (Fh)A  and  (Fh)B  will be known.fB. Ch=2. If this summation is written as Ch we have (Fh)A = Kh and (Ft)B = Kh+fBCh. = 20. allowing for some errors of measurement. If we accept that only rarely will a sign change occur then we know the magnitude of \jjh but not its sign. the only reasonable values for the structure factors are (Fh)A = + 8 and (Fh)B = — 10. The situation where the F's have opposite signs is quite rare if the isomorphouslyreplaced (abbreviated to ir) atoms are not too powerful scatterers. / .
The only reasonable solution of equations (8. It is possible with careful measurements to record structure factors with sufficient accuracy to measure the changes of scattering due to replacements of Na by K (ZB ZA = 8). when the isomorphouslyreplaceable atoms are in special positions. Kh = + 117.).)
7=1
and (FJB = Kh +fB £ exp(27iihT.. Cl by Br (ZB .258
The determination of crystal structures
(h)A = Kh +fA t exp(27iihr7. (8. (8.20) and the value of the righthand side is +16. for example. — fB at the positions of the ir atoms. However a Fourier synthesis with \jj^ as coefficients will give a Patterson map of the difference of the two structures which should show
. Clearly it is important that the two sets of data should be reasonably well scaled together. From equation (8. / . is (Fh)A = + 92.18)
where Kh is the contribution of the atoms common to both structures and the summation is over the positions of isomorphouslyexchangeable atoms.
0. 3. 2. 1.
y.
3. 2. 1. 7. 2. 8 .
1. 5.1 and 8. 9. 18 .
2. 2. 11. 1.
2.
3.
1.
1. 1.
1. 2.
3. 1 .
0.
3. 2. 0.
7
2. 1. 1.
0. 8. 14
0 . 2. 5.
5
6
7
1
9
10
11
12
13
1
14
15 1 . 9.
3.
3. 1.22.
1.
1. 0. 2. . 2 . 1. <j
12.
V
1.
4 .
3.
5.
• W
.
2.U. . 1.
1.
2. 1. 1 .
1. 1.
0. 12 .
19V 2.
2. . 10.2 .
6.
IV
a
1.
N
1.
1. 2. 2. 1.
3 5 2 2 4 2 3 2.
2. 1.
0.. 3. 1 2 . 7 0 6
. 1.
1.
1.
1 . .
3. 9. 0. This process can be followed by using the data from the artificial twodimensional structure (C2H2NC1)2 shown earlier infig.
2.
7 .
1. 2.
1. 4.
6. 4.
2. .
7. 0.
16
17
18
19 20
2 .
5.
1. This has been used for the present pair of isomorphous compounds and the difference Patterson function is shown infig. 2.8.
4. 3. 9. 3.
r
12.
4. 9. .
1.
1.
1Y "
. 0.
0. 5. . 7
7. 4.
3. 6.
3.
6 . 4. 5.
7. 0.
2. 5.
5. 1. 6. 0.
1.
2. 2 0 .
11. 0. 2. 1. 0.
11.
2. 2.
.
1. 1. 0.
2.
2 2 5
2.
2"
9 2
11 . 3.
1. 2. 2.
7 . 3. 2.
2.
4. 0.
4 . 2. 9.
5. 3. 3. There are three independent vectors indicated
Fig.. 8. 2. 3
4 . 5.
1
7 . . 2.
2.24.8. 5.
2.
3 5 8 1 1 16
.
8.1 . 4. 8. .
1. In appendix VII there is given the computer program ISOFILE which takes output files from STRUCFAC for two isomorphous compounds and prepares an input file for the Fourier synthesis program FOUR2 with Fourier coefficients of magnitude ( FA \ — \ FB \ )2 with zero phase.
1. 0.
5.
2. 9. 8. .
3. 2.
1.
1.
1.5.
1. 3. 3.
5.
0. 4. 13.
9.
2.
2. 3. 1
12.
4.
2 .
2.
2. 4.
4 .
0. 0.
3. 6.
2.
1.1 . 1. 2. 3.
3.
3. 2. 3.
3. 2. 5.
4.
3.
4. 3. 2..1 . ' 2. 9. 6. .
2.
3.
2. 8.
0.
1.
3. 1.
4 . 1.
0 . 12. 3.
2. 5. 6.
3.
11
^2l\ 2. 1. 6. 0.
(4 0 7 7 2 9 2
. . 6. 3.
4.
.
1. 0. 8. 1.
6. 3. 9.
OUTPUT WITH Y HORIZONTAL AND ORIGIN 0 0 100 L/ 1
7
2
3
7
4
X. 3.
3.
1. l ) . " " 6
1. 1. 12. 3. 0.
0. 4. 9. 0. 4. • 2. . 2. 2. 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31
2. 2.
3.
4 . 1.
2.
3. 3. 5.
1. . 1.5 shows that only 18 of the 156 structurefactor signs are different.
2.1 .
8.
4 . 2. 5.
1.
2.
. 5. 3. 2. 4 .
3. 1. 2. 2. . 0.
V
lt
1 7 3 1 3 1 3 7 1
3.
/ 4 . 2.
6 . 18 ' 6.
1. 6.
3
5. 3. 3. 0.
0.
2 7 9 0.
\
10. 0. 16 1
2(
V .
.
4 .
10. 3. \
13.
3.
1.
0.
8. 3.
2. 0. 3. 2. 2.
3.
1. 1.
3. .
4.7
7. 2.
3. 6.
0.
6.
10 .4
Isomorphous replacement
259
peaks only at positions corresponding to vectors between the ir atoms. 3.
4
1.
21//
2
'Is. 3. 2.
2.2 .2 . 6.
3. 2 2 T 16V
6.
4 . 1. 3.
1.
2.
5. 4. 1. 2.
2. 2.
1.
1.
3. . 1.
0.
6.10(b) together with data for the isomorphous structure (C2H2NF)2.
1.'
1. 24 .
4. 3.
>7 4 • (£
^ 2 4 v^ 4 .
4. 6. 3.
1.
2.
6. If this simple Patterson map can be interpreted then the positions of the ir atoms will be found and the signs of the structure factors can be determined. the structure factors for which are given in table 8. ^23.
'3.
9
1. 5. 0. 0. 5. 2.
0.
1. 13.
2.
4. 3.
0. 2.
2
A ' 2. 5. 8.
2.
6.
1.
3. .2 .
4. 8. 1.
1.
2. 4. 8. . 3. 0. 0.
2.
1. . 3.
7. 0. 5. 6. 2.
9. 1. .
2. j 4 . 5. 0.
1.
5. 1. 6.
7. 12. 2. .
uTV
V
2. 0. .
1. 3.
1.1 .
8. 2. 2. 6.
3. 2. 5.20. 1. 2. '4 9T
4. 1. 8 5 3
1. 1. 1. 3. 3.
.
1.
1. 2 .
5.
3. 3. 2.8. 0.
7
1.\ 4.
6.
4.
4 . 3. 3.
7 . 1.
4 .
7
2.
0. .
0. 6.
1. 1. 12. 1. 0.
2. 8. 5.
4 .
2. 3.
4 .4 .
0.
4.
20 v
2. 6. 1.
5.
6
3.2 .
3. 3 . 22.1 4 . 2.
1.18.
2. 1. 5.
1.
1. 2.20.
2.
7
2. 3.
1. 3. 3. A comparison of tables 8.
1.
4 . 2. . 5. Difference Patterson function for the isomorphous structures (C 2 H 2 NC1 2 ) 2 and (C 2 H 2 NF 2 ) 2 . 9.
.
20 2. 0. 0.10 0.09 6. 0. 180.69 32.81
PHI
180. 0.00 11. 0.93 3. 180. 0.11 18.33 3.56 0.55 5.98 0. 180. 0. 0. 0. 180. 0. 0. 0.00 3.55 2. 0.32 12. 180. 0. 0.64 7.36 0. 180. 0.23 30. 0. 0. 0. 180. 180.85 11.5. 0.52 12. 180.12 5.06 3. 0. 180.3 0 4.93 7. 180. 180. This structure and (C2H2NC1)2 are isomorphous.41 6. 180.00 10. 180.41 0.18
PHI
0. 180.11 10. 180.91 4. 180. 180. 0. 180. 180.43 0. 180.64 4.43 11.07 3. 180.82 0.23 30. 180. 0.64 4.1 and note that 18 of the 156 structure factors have different signs.40 1.75 14.19 1. 0. 0. 0.02 2.18 1.58 3. 0.50 20.59 0. 180. 0. 0. 0. 180. 0. 0.
h 12 11 10 10 9 8 8 7 7 6 6 5 5 5 4 4 3 3 2 2 2 1 1 0 0 0 1 1 2 2 2 3 3 3 4 4 5 5 5 6 6 7 7 7 8 8 9 9 10 10 11 12 k 1 2 1 4 3 1 4 1 4 1 4 1 4 7 3 6 2 5 1 4 7 3 6 1 4 7 2 5 0 3 6 1 4 7 2 5 0 3 6 1 4 0 3 6 2 5 1 4 1 4 2 0
F
4.91 4.88 3. 180.68 1.01
PHI
0. 0. 180.58 12.58 12.71 7. 0.15 32. 180.74 7.02 1. 180. 180. 0.55 0.36 11. 180.62 3.52 16. 180. 180.96 1. 0. 180.02 3.55 0.98 13.98 16.22 2.64 46.93 5. 0. 0. 0. 0.18 1. 180.52 5.23 4. 0. 0. 180.15 11.07 32. 180. 180. 0. 0.91 10.88 16. 0. 0.68 1. 180.69 5. 180. 0.82 0.67 1.36 0.90 16. 180. 0. 180. 180.10 5.77 6. 180.07 3.00 10.00 1.00 0. 180.19 32 . 0.69 0.15 6.55 13 . 0. 180. 0. 0.02 7.98 0.06 1. 0. 0.85 3.91 4.06 3. 180. 0. 180.40 10.77 6. 180. 0. 0.81 0.15 6.260
The determination of crystal structures
Table 8.75 14. 0. 0.65 2. 180. 0. 0.89 8.59 0.75 4. 180. 180.11 18.52 12. 0. 180.52 16. 180.51 10. 0.69 0.55 0. 180.
. 0.06 10. 180.56 0.74 6.91 6.85 3.36 0. 180.75 14.15 0. 180. 0.91 4. 0.06 10.07 3. 180. 0.15 0.33 3. 0.65 1. 0. 180.90 112.39 2.56 23.00 0. 0.00 1. 180.88 13.74 0.65 1.00 0. 0.88 6.
h
12 11 10 9 9 8 8 7 7 6 6 5 5 4 4 4 3 3 2 2 1 1 1 0 0 1 1 1 2 2 2 3 3 4 4 4 5 5 5 6 6 7 7 8 8 8 9 9 10 11 11 12
k
2 3 2 1 4 2 5 2 5 2 5 2 5 1 4 7 3 6 2 5 1 4 7 2 5 0 3 6 1 4 7 2 5 0 3 6 1 4 7 2 5 1 4 0 3 6 2 5 2 0 3 1
F
6. 0. 0. 180.32 12. The complete set of structure factors for the artificial structure (C 2 H 2 NF) 2 as output by STRUCFAC PHI is the phase angle in degrees. 180. 0.80 7. 0. 180. 180.89 8.11 6.06 1.93 3.87 0. 180.67 3. 180. 0.71 0.85 11. 180. 0.30 5.39 2. 180.50 20. Compare the structure factors with those given in table 8. 0.
h
11 11 10 9 9 8 8 7 7 6 6 5 5 4 4 3 3 3 2 2 _ ~\ 1 0 0 0 1 1 1 2 2 3 3 3 4 4 4 5 5 6 6 6 7 7 8 8 9 9 10 10 11 11 12
k 1 4 3 2 5 3 6 3 6 3 6 3 6 2 5 1 4 7 3 6 2 5 0 3 6 1 4 7 2 5 0 3 6 1 4 7 2 5 0 3 6 2 5 1 4 0 3 0 3 1 4 2
F
1.96 1.80 7.22 3. 180.12 3.22 14.39 6. 0. 0.01 13. 180.20 2. 180. 180.
From a knowledge of the stereochemistry of the material a consistent set of peaks can often be selected and the structure thus solved. For noncentrosymmetric structures it is not possible precisely to define the phases of the structure factors. 2y). respectively. The peaks due to vectors between the non ir atoms will not appear in this difference Patterson function. If instead of one ir atom there are several which are all replaced when going from one structure to the other then the situation is somewhat different. If there is a single ir atom then one can arbitrarily choose this as an origin for the unit cell and.in this case the magnitude of the phase is determined but not its sign. With centres O and O' one draws the arcs of circles of radius  (Fh)A  and  (Fh)B . 0) and doubleweighted (^.21)
These equations can be expressed in the form of the diagrams given in fig. as in (b\ with PQ coincident with P'Q\ the appearance of the joint diagram suggests a method of determining the phases. The quantities which are known in these diagrams are/^ and/ B and also  (Fh)A  and  (Fh)B . However the solution is not unique for the arcs also cross at R and so there is an ambiguity of phase . If the difference between I (^h)^ I a n d I (F\)B I i s small compared with Kh then the arcs of circles intersect at a very acute angle and the error in the phase due to errors in the experimental determination of structure factors may be very high. What are determined unambiguously are the real parts of the structure factors (Fh)A and (Fh)B. It will be left as an exercise for the reader to confirm that the three vectors have the required relationship and that the peaks indicate correctly the position of the Cl (or F) atoms in the structure. If one computes a Fourier synthesis as for a centrosymmetric structure with these real parts as coefficients then one obtains an image of the structure with the addition of a centre of symmetry. From a point P one draws two lines PO and PO' equal in length XofA and/ B . Thus if the ir atoms are
. If the two diagrams are drawn together.3 can be used to complete the structure determination.4 Isomorphous replacement
261
in the map which for the space group pmg are at (2x. The Fourier map has twice as many peaks as atoms and for each pair of centrosymmetrically related peaks one must be selected and the other rejected.8. 2y). If the ir atoms in one or other of the isomorphs form a sufficiently high proportion of the total scattering power of the structure then the heavyatom method described in § 8.21(a). If the difference of weight of the ir atoms is considerable then a Fourier summation with coefficients  (Fh)A  2 —  (Fh)B  2 will contain peaks corresponding to vectors between the ir atoms of weight ZA — Z\ and other peaks due to vectors between the ir atoms and other atoms of weight (ZA — ZB)Zj. (\ + 2x. 8. Once the positions of the ir atoms have been located then it is possible to find probable signs for the structure factors in the way indicated previously. from equation (8. These intersect at Q and define the complete diagram.19). This process is made more difficult by the overlap of peaks in the map and also by false peaks due to experimental error. the corresponding structure factors for the two isomorphs appear as (Fh)A =fA + Kh and (Fh)B=fB + Kw (8.
64 = 192 and (ZA .21. 8. If the Patterson function of the sulphur compound is computed there will be S—S peaks of weight 256. {b) Construction to determine magnitude of phase angles. and there will also be a number of C—C peaks of weight 36.262 Fig.
The determination of crystal structures Q
[a)
(b)
oxygen and sulphur in the two compounds and the remaining atoms are carbon then the weights of these peaks are Z2AZ2B = 256 . Once the configuration of the ir atoms has been
.ZB)Zj = 8 x 6 = 48. (a) The components of FA and FB due to a single isomorphous atom and the remainder of the structure. S—C peaks of weight 96. The superiority of the difference Patterson for picking out vectors between the ir atoms should be evident from these figures.
22. The method of producing a diagram for determining phases is shown in fig.
=
(8. with contribution Kh as shown in fig.22(fe) and follows closely the principle used in fig. 8. From fig. (a) The components of FA and FB due to a group of isomorphouslyreplaceable atoms and the remainder of the structure. The angle A0 h is found as follows: (i) From the triangle O'OQ
cos
.24)
.4 Isomorphous replacement
263
determined. then the contribution of these atoms.22(5) the phase of Kh is seen to be either (f>x h 4.23)
(iii) from the triangle O'PQ again
c o s A</>h =
Fig.22.22)
(ii) from the triangle O'PQ
(8. and an origin specified with respect to this group of atoms. 0 r are identical and the resolution of the structure factors into the contributions of the ir and non ir atoms is shown in fig. in this case the ambiguity of phase is not simply just one of sign and the real part of the structure factor is not determined. 8.22(a).8. 8. 8.
(8. 8.21.A0 h or cj)xh — A0 h . XA anc * XB> c a n t>e determined. The phases of these contributions with respect to the origin. 8. (b) Construction to determine the phase angles showing the phase ambiguity. Since the positions of the ir atoms are assumed known then completing the structure determination consists of finding the remaining atoms.
B (0.23 at A (0.874.0.937. In our particular case it would involve calculating <5(r) = p Z I *h I {cos(27ihr .583) give the Patterson peaks in fig. C 3 H 5 N 2 ONa 2 . It is often possible to recognize the correct structure from such a map.500. gives the Fourier summation shown in fig.
( 2 x 2 . A (0. If A0 h is small.17. The correct terms will form an image of the structure without the ir atoms and the incorrect terms will give a random background noise. T h e coordinates
(x^yj = (0.
v
(8.h a n d ^xM t 0 P r °duce a tape suitable for input to FOUR2 with structure amplitudes  Kh \ cos A(/>h and phases 4>x h so that the summation (8. y
l
.0.A</>h) + cos(27thr . 8. £ ) .y2) and four independent nonnull vectors (2xl9j). from this map the complete
.500).374.167). 8.25b)
h
One of the two terms for each h in equation (8.25) can be made. However.874. so that the two possible phases differ by n then the corresponding term is eliminated.25a) = ^ Z I ^h I c °s A0 h cos(27ihr .23. With two independent 'differenceir atoms' and space group pg there are four ir atoms in the unit cell with coordinates (xl5 y x). (x1x2. which has a noncentrosymmetric option and produces an output file with amplitudes F A 1  2 —  F N a  2 and zero phase.25b) it is seen that the terms of the Fourier summation have phases corresponding to the heavyatom contributions and structure amplitudes weighted according to the values of A0 h .0. The structures we shall use are the one shown earlier in fig.500). This is used with FOUR2 to give the difference Patterson shown in fig.250) and (x29y2) = (0. ( — x l5 \ + y x).0. and the supposedly isomorphous structure. so that the two possible phases are not very different. marked Sp. (x2.24. Structure factors are calculated for both of these using STRUCFAC and these files are used by ISOFILE.y2) and ( — x 2 . 8. On the other hand. then the structure amplitude is modified very little. XB.437.0. in the map. because of the noise in the map. This shows all the nonir atoms although. In the form of equation (8. C 3 H 5 N 2 OA1 2 . if A0 h = it/2. i 4. used as an input file for FOUR2.667) and C (0.<j>xM + A0h)} (8. Schoone & Bijvoet (1951) and others have recommended dealing with the singleisomorphousreplacement (SIR) ambiguity by the calculation of a synthesis in which both possible phases are used.25a) will be correct. their positions are slightly displaced from peaks and there are also two significant spurious peaks. The output file from ISOCOEFF. If the coordinates were not known and the map had to be interpreted then the overlap of two peaks would create an extra interpretational problem but in view of the fact that there are only three significant independent nonorigin peaks and no other peak on the line y = \ the problem could easily be solved.y 2 ) a n d (x1+x29^
+ y
1
. This is done by the program ISOCOEFF which is given in appendix VIII. 8.0Zfh). We shall look at how this works in practice by means of a simulation.(j>xM . The next stage in the simulation is to use the data files giving the sets of structure factors FAh and FB h together with files from STRUCFAC giving %Ah.y2).264
The determination of crystal structures
Bokhoven.0.
7 .
6. 10. 11. 17 .
9. 1 4 .4
Isomorphous replacement
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 1. 10. 14 . 9. 1 2 . 13 6. 16. 1 4 . 12. 5. 13 .
16. 9.
6. 7. 12 . 13. 14. 13 . 13 . 13 . 9. 12
6. in
" 7
1 ^ 18 . 10. 1 4 . 1 3 . 10. 1 4 .
12 . 16. 1 1 . 12 . 11.
6. 11.
9. If a native protein crystal is soaked in solutions containing heavyatom compounds then these are sometimes absorbed by the crystal at specific sites in the protein molecules. 10. 1 4 . 16. 11. 8 . 13
8
8 9
10 11 12 13
13 8
10 11 12
9 . 12 . 13 .1 5 . 11 .
?* A
21
13. 8. 1 0 . 15. 9 . 10. 1 2 . 10. 1 2 . 11. 16 . 13. 10. 16.
17. 15. 13
9.
9. 11. 11. In practice. 21.
4.
13 11 11
c'13. 15. 4 . 1 0 . 1 4 . 9. 16. 15. 2 2 > *43"
•n
\\n
14
1?
a. 16. 13. 13 . There are four Patterson peaks with A being an overlap of two peaks. the situation may not be so straightforward but a 'best' phase can nevertheless be found. 9 .24. 14. 14 .
4 . 12 14 . 14. 10. 16. 11. 11 . 14 . 1 5 . 8. 16. 10. 1 5 . 6. 14 . 11. 11. 14 . If. qq i no 4.1 4 ^ 18 •
in
8 v 1? 
structure determination would be straightforward.
8. 14. 1 4 .
. 11. 1 5 . 10 5. 13 . 16. 16. 1 4 . 12 . 16. 2 11 .
7. 2 4 . 12 . 1 4 . Because proteins are such large structures the addition of a heavyatomcontaining group will only disturb its immediate environment and the bulk of the structure will be undisturbed. 2 0 ^ • 2 7 '
2 8 . 9. 12 . 1 2 . 15.say 23 A. 9. 9 . 5.
. 12 . 7 .
. 5 .
8. 13 . The multipleisomorphousreplacement (MIR) method has been very important in the development of protein crystallography. for example. 8.5705 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT
0 0 1 2 3 4 5 6 7 100 43 1 13 12 12 9 12 1 2 Tl 3 4 5 8 6 10 7 7 8 9 10 11 12 15 13 7 14 10 15 8 16 1 7 17 14 18 19
265
Fig. 9. 15. 13. 13 . 10.
11. 1 2 . 8 . 33'' 54T . 21. 15. 9.
5.
AI
2. 12. 8. 1 4 . 10. 21. 2. 1 4 . 8. 1 3 . 1 5 . 9
7 . 10.
7 .
15. 1 2 . 10. 9 . 12. • 13 9. 1 2 . 8. . 14. the isomorphism may only be valid to a limited resolution . 9. 13 . r
5. 6. 13 .11. 2 7 . 12
8.
4.
8.
)33 N « 1 1 . 5. because of errors in the data. 20. 13. 14.
B. 3 . l
9. 10. 11. 22. 11 . 16. 17.
11 . 13. 9. 13.23. 14. 8 14. 12. 13. 11. If there are several different isomorphs then the phase ambiguity can be resolved.
12. 16. 14 . 11. 11.
. 10. 1 2 .1 1 . 13 . 14 . 12. B and C and the pair AB gave phase indications (j)AB(l) and (j)AB(2) and for other pairs of isomorphs there were pairs of phase indications (j)BC(^\ <t>BcQ) anc* <I>CAW> <t>cd?) ^ e n the correct phase should occur as one member of each pair of phase indications and so be recognized. 9. 10. 13. 15. 9. 13. 13. 8 . 12 15. 13. 14. 13 . N. 12 .
6.
<
2. 16. 1 4 .
7. 12.
10 . 1 0 . 13. 13 .
8. 14 . 11. 9. 11. 12.
9. 14 . 1 3 .
29^15 A
9. 13 . 10. 8. 1 2 . 16. 2 8 . 10. 13. 2 7 . 8. 10. 2 6 .
8. 9. In this case the heavyatom derivative will be isomorphous with the native protein although. 2 4.
9 . 13.^29r• 21*. 11. 1 1 . 12 .
4 . 10. 5 . 16. 11 . there were isomers A.
15 16 17 18 19 20 21 22 23 24
8
13 12 9 12 12 13 1 43 100
17. 22.. 14 . 23. 10. 12.
O
7. 15.8. 15. 3 . 11. 11.1 2 .
9. 10. 14.
11 10
11 . 1 5 . 15. 16. 12
8. 14
14 . 13. 26. 10. 11
4 . 10. 8. 9. 14 . 14. 8 . 15. 1 2 . 1 4 . 10. 13. 11 .3 2 6 . 14. 12 13 . 6.
20
1 4 12
18 14 18
1 7. 27r•
13 .12. 23 . 1
2.2 4 . 8. 11.
9. 11
20 •* 4 . 8.
14. 7 . 11. 16. 1 2 .1 0 . 11. 1 5 . "
6. 12. 14 . 14 . .1 4 . 21. 11 . Different derivatives may have the heavy atoms attached at different sites in the
.
»22. 8. 7 .
.
10. 7 . 11. because some atoms are displaced in the derivative. 1 2 . The difference Patterson for the isomorphous compounds C 3 H 5 N 2 ONa 2 and C 3 H 5 N 2 OA1 2 . 10. 12. 1 0 . 13 . 13. 10. 21. 14 . 6. 16 14 15
4.
6. 13. 3 3< »22.
14 . 1 2 . 4 . 15. 10. 1 4 . 9
8. 10.
6. 6. 10. 12. 11.
13 . 10. 11. 13 . 11. 13 . ^50 . 12
15 ^29: 1 5 . 10. 14. 13.
. 7.
9. 13.
7 . 15 14 16
7. 8 . 12.
. 10.
2. 18 . 1. 4. 4. 2 0 . A complete review of methods dealing with multiple isomorphous replacement (MIR) has been given by Woolfson and Fan (1995).
3. 1. 1 2 . 0. 5.8. 0. 6 .
3 9
. 2.
3.1 6 .
• • s
/ J72)
18.
39'" 3 ^
8. The peaks of the map correspond to the ambiguity and the spread around each of the peaks is related to the probable errors of measurement. 1 6. 21 \
La. 3. 4s. By considering the probable errors of measurement each experiment gives a probability curve for the phase looking something like that infig.
6 2
7 6
S 3.
15. 1 2 . 1 3 . 2.
5 3
.2 0 .
I
14. 1 8 . 5. 1. ^
. 8.
1 8
€25
3. \l4. 10.
7
.
1.
6. 1.
1. 1 9
. . 9.
21
7 . 34 .9 4 . 7
2.
>3 / 7
9
10. . 11
8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
13 7 9 12 18 5 6 11 0 3 13 0 15 9
16. 3. 2^5 — 1 3< 0 . 5. from each of which there is a phase ambiguity. 3.1 8
12. . . 8.
3 11 16
2 2 : •69\^58.
9. Curves from four different experiments and the product of the four curves are shown in fig. It will be seen that.
•
3 1
31
/
6 4
. 2 0 . 8.2 3 . 7. 12 . 26
2
(JX\ ) I
2 . A general approach to combining information from MIR experiments. 0
10. 7. 2 7 . 12. . . 6. 10
6. 3
1 10
6. 13^ .
3. 1 7 .
/16. 8.
2.
3. 7.
8
8 1
.
1. 6.
6. .
10.
"11
8. 1
23^ ^ 8 20
^. 12 .
.
c
rr
i . 21) «41. /
2.
5. 2 0 .
1 .
3. 7. .
3
4 7
3
12 3
.1 6 . 1 6 . 1.2 3 .
12. 0. .
8.
. 10 .
2
. 3 . 2. 7 .
/'6. 1
. . 14.2 .
12. ni. 2 2 . ~*3*" 18
20 V
12.
3
it
4. 9.^ 2O.
. 20.24 '
12. 15. 15.
0.<34 7 \ y . 3 4 .
1 14 6 \ 6
.
11.
Sp
4.
1
3
4 11
•
\
4.
3
7. 12.
14. . 4
5.6 . . . 8.
1.
6.21 " 8
5. 0.1 8 . 0 1. \ \^_ > ——^ 7. . "^6 7* 7 1 8 .
^59
J\ 7
2 0 .
2
9.
i. . 1 2 .
3.
1. .'v 2.266 Fig. 7
4 .
3. 12
Sp'
17" 4. 1
8. 2
1.
4 . 3
9.24.
4 . 11.. For very precise measurements the two peaks become sharp and narrow. 6.
The determination of crystal structures
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 0. 25. 3 .
.
(
1
9. 30\
9.1 .1 .
8. which shows the positions of the light atoms.
6. considered in the form of a number of SIR experiments. . 20 O 4<~~55s 14
1. 26. 5
3. 8. 1.
8. . Again.
2. *—*v • .
3.
\V 3.
14
* ir"
protein. 20 .
7. if the A0 associated with the ambiguity is small then the two peaks may coalesce to give a unimodal distribution.
14. Spurious peaks are marked Sp. 10 . 5.
5 . . 3.
5
.
. 5. 2. 3. was suggested by Blow and Crick (1959). 5 6 11 0
. 6.26. 27.
2.
22. derived from the heavyatom positions in C 3 H 5 N 2 ONa 2 and C 3 H 5 N 2 OA1 2 . v 3.
0.4 . although each individual experiment gives a rather diffuse curve the overall probability curve can define the phase quite well. 1.1 .
3.
9. . 11.
8 . 2 0 . 13. 16.
9
7
26.1 2 .25. 15 .
3.
. 8.0483 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT 9 10 11 12 13 14 15 16 17 18 19 20
15. 12.
10.
6
. 1.
2. 1. 16. A Fourier summation. I *" • 1 0 .
3.
7 . ll^3 . 5. if the measurements are very poor then the probability may vary little over the whole 2TI range.
30/7^
4. 21 N 16 . 13. 26 . 2C ^ !2\ 9. 12
1. . 2 0 . 3. 9 7 .
8.
13 0
4. 5.
9 16
V. 16 12
• &
7 2 \ *18
. 12 .
3 . 7.
\
4 1 .
6. each derivative gives two possible values for the phase of the protein but with several different derivatives a unique 'best' phase for the protein can usually be found.\ ln
Z56v
7.
8.26. We shall now see how to exploit this difference to solve crystal structures.6 anomalous scattering was described as a phenomenon which influences the intensities of Xray reflections and causes a breakdown of Friedel's law so that \Fh\ / I F_h .25.5
The application of anomalous scattering
P(0(h))
267
Fig.5
The application of anomalous scattering In §6. A Blow and Crick probability curve for a phase from singleisomorphousreplacement (SIR) data. 8.27(a) there is shown the way that Fh may be decomposed into the
. 8. (ad) Crick and Blow probability curves from different pairs of isomorphs multiplied together to give (e) a unimodal probability
P(0)
(a)
8. Infig.8.
Fig.
In practice it is found preferable to use only some of the largest anomalous differences for these are most likely to have magnitudes close to the correct ones. so that the contribution F2h is known. The decomposition of F _ h is also shown. If the anomalous difference is large then the true Patterson map must have a large coefficient but some large coefficients for the true Patterson map will be small in the corrupted map. By reflecting the construction for F_h in the real axis the diagram shown in fig. 8.
. which is equivalent to the structure factor for normal scattering. and the imaginary part of the anomalous scattering. subscript N. This means that there is both a phase and magnitude ambiguity. 8.27. In practice Flh is usually much smaller than FN h and it is acceptable to find the phase corresponding to the total real scattering.268
Fig. if the positions of the anomalous scatterers are known.27(b) it is then obvious that
\F2M\>±\\Fh\\F_h\\.28(b) from which it is clear that the phase alternatives are </>2 h ± A(/>h.h
(a)
(b)
nonanomalous contribution FN h and the real and imaginary components of the anomalous scattering.
The determination of crystal structures
N. This gives a phase ambiguity of the same form as that found for isomorphous replacement. Since  Fh  and \F_h\ are found by experiment then if the positions of the anomalous scatterers can be determined the two possible phase values will be known. is either F N 1 h or F N2fh . From the triangle with sides 2F2 h.26)
A map with coefficients ( jFh  —  F _ h  ) will be a corrupted Patterson map for the anomalous scatterers where each Patterson coefficient has been multiplied by an unknown factor which reduces its value. 2F2. the real part of the anomalous scattering. This is shown in fig.28(<z). subscript 2.h and F h .
2
(8. 8. ( Fh \ — \ F_h \ ) 2 . there are two ways to produce such a triangle and these are shown in fig. (b) Reflecting F _ h in the real axis produces a triangle with sides F*_h. It is assumed that if there is more than one anomalous scatterer then they are all of the same kind so that F2h is perpendicular to Flh. 8. (a) The decomposition of F h and F _ h in terms of the nonanomalous scattering. One way of finding the anomalous scatterers is to compute a Pattersontype map with coefficients which are the square of the anomalous differences. subscript 1. respectively. Flh and F2 h. 8. FN h + Flh which has the same magnitude for both possible phases. However. Fh and F_ h in fig. \F_h\ and 21F2 h . then the nonanomalous scattering contribution.27(b) is obtained and it can be seen that a triangle is produced for which the lengths of the sides are  Fh.
The anomalous components of the scattering factor are. However. very small and normally.29 withfig. (b) Finding the total real scattering gives only a phase ambiguity. Ideally the map should show only the vectors linking the anomalous scatterers but.29.29 although the coordinates found will be slightly different from the true coordinates. 8. since the coefficients of the map are not those of a true Patterson function the map obtained is somewhat corrupted.28. in a real case. The output file from STRUCFAC was used as the input file for ANOFILE. Table 8.h ^s known in both magnitude and phase then finding the normal structure factor F N j.8.542 A) was used. Having determined the positions of the anomalous scatterers. chosen to give reasonable values of/t and/ 2 . B and C appear but B and C are slightly displaced and that there are also smaller false peaks present./X = 0. Another interesting way of resolving
. for which Cu Ka radiation (X = 1. the remainder being made equal to zero by ANOFILE.25). This gives an output datafilewhich can be input to FOUR2 to give the required anomalousdifference Patterson map. the quantities F2h for different h can be calculated so defining the phase alternatives for each reflection and then a double synthesis can be calculated as given in equation (8. so that F2. gives an ambiguity both in magnitude and phase.490. Only onequarter of the largest anomalous differences are used. if Co Kax radiation (X = 1.17 where the Na atoms are the anomalous scatterers.8. for Na.8. It should be noted that the Xray wavelength used here for anomalous scattering.29 than forfig. in fact.8.5
The application of anomalous scattering
269
Fig. the anomalous scatterers would be heavier elements with the wavelength tuned to give large anomalous effects. given in appendix IX. which is shown infig. It is possible to interpretfig.8.331 and/ 2 = 0. Comparing fig.8. This table was produced by STRUCFAC which contains a facility for including anomalous scattering.196.
\Fh\
(b)
We now illustrate this process using the synthetic structure C3H5N2ONa2.789 A) was used with Fe as the anomalous scatterer then/j = — 3.936 A) for which.6 shows the structure factors calculated for Fe Kax radiation (A = 1.8. since we are dealing with idealised calculated structure factors we can use the very small differences in  Fh  and  F_ h  seen in table 8.23 we can see that peaks A. (a) If the positions of the anomalous scatterers are known.186 and/ 2 = 0. For example. shown earlier infig.6 for our illustration. 8. also gives lower resolution forfig.23.
270
The determination of crystal structures
Table 8.6. Structure factors for the noncentro symmetric structure C 3 H 5 N 2 ONa 2 with anomalous scattering by the sodium atoms PHI is the phase angle in degrees. The anomalous components of the scattering factor are/j =0.186 and / 2 = 0.196. h 8
7 7 6
k
1 1
F
3
1
6 6 5 5
4 4 4 4
3
4
2 3
1 2 4
_2 3
3 2 2 2 2 1 1 1 1 0
5 2 3 5
1
3
4
6
1
3
4
6
0
0
0 0 0 1 1 1 1
2 3 5 6
1
2
4
2
2 2 2 2
5 0
1
3
4 6
3 3 3
3 4 4 4 4 5 5 5
0 2 3
5 0
2 3 5 0
2
6 6 6 6
7 7 8 8
3 0
1
3
4 1 2 0 1
4.87 14.33 6.84 14.46 15.27 8.61 14.70 14.63 14.80 6.12 11.95 12.02 15.92 8.19 11.64 16.39 18.44 9.81 7.71 5.15 8.97 29.05 4.50 124.75 19.92 0.00 0.00 14.10 4.64 29.48 28.59 15.61 17.76 16.39 18.44 9.81 7.71 2.97 15.92 8.19 11.64 16.69 6.12 27.29 11.68 2.28 14.70 14.63 15.53 14.46 15.27 8.61 14.13 14.07 15.71 4 R7
PHI 81.
h 8
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8.5
The application of anomalous scattering
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 0.0009 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT 9 0 1
2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
271
Fig. 8.29. The anomalousdifference Patterson map for C 3 H 5 N 2 ONa 2 .
10
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the phase ambiguity for onewavelength anomalous scattering (OAS) by using anomalous differences will now be described. Let us write the scattering factor of an atom as
where the imaginary component is nonzero only for an anomalous scatterer and is the f2 of equation (6.80) and the real component for an anomalous scatterer, (fj)R, differs slightly from the nonanomalous value and is the/ 0 +/i of equation (6.80). The structure factor of index h can now be written as
N N
F
h = Z (/j)*ex P( 27lih#r/) +
J
(8.27) Z A/} exp(27tihT;).
The complex conjugate of F h is given by ex
n = I (/;)* P( 
 i I A/) exp( 
(8.28)
The form of the second summation follows from the result that the complex conjugate of iei0 ( = i cos 0 — sin (/>) is — i cos 0 — sin 0 which can be
272
The determination of crystal structures
written as — ie"i<iP. From equations (8.27) and (8.28) we find
N
(/))i?exP(27lih#r i) + * Z A/} exp^Trihr,.)
r
N N
i
x
Z (fj)R™P( ~ 27tihr,.)  i £ Afj exp(  27iihr,.) .
(8.29)
Similarly we find that
2
rN
N
ex
• i
(8.30)
J
I F.h  =  ^ I (/^exrf  27uhr,.) + i £ 4/) P( " ^ ^ J
x
[ £ (/^exp(27iihrj)  i £ Afj exp(27iihri)].
U=l 7=1
By combining equations (8.29) and (8.30) one obtains l^hl 2 + l^hl 2 = and \f  2 _  p_ 2 _ 2 V V M / / / ) (/.) — Af(f) } sin{27ih#(r — r)}. (8.32a) If in equation (8.31) we write (^c)h = \{ \ Fh \ +  F_h  } then it is clear that (i/^c)h is the hth Fourier coefficient of a function which has peaks at rk — Tj. These peaks will have Fourier transforms which, at the point in reciprocal space corresponding to the index h, have values (fk)R(fj)R + AfkAfj. This peak will be like a normal Patterson peak except that when one or both of the atoms is an anomalous scatterer the peak is very slightly modified in weight and form. The Fourier synthesis with V~l(\j/\ as Fourier coefficients gives a function P c (u) which will thus be similar to a normal Patterson synthesis obtained with nonanomalous scattering data except at points corresponding to the vectors involving anomalous scatterers. Equation (8.32a) is the basis of a much more interesting function first discussed by Okaya, Saito and Pepinsky (1955). It simplifies our consideration of this function if it is assumed that there is only one anomalous scatterer in the unit cell, i.e. the one for which; = 1. Equation (8.32a) then becomes
N
2 2 2
Z Z WRWR
+ A/fcA/)}cos{27ih(r,  r^)} (8.31)
I ^h I2 ~ I Fh I2 =
2
Z
A
fi(fk)R sin{27ih(rfc  r j } .
(8.32b)
If we write (ij/s\ = \Fh\2  \F _h\2 then (i^s)h =  0A s ) h  lt should now be clear that (^s)h is the Fourier coefficient of an odd function Ps(u) which will have a peak corresponding to the transform of Afx(fk)R at (xk — r x) and a peak corresponding to the transform of — Afx{fk)R at —(rk — r1). The function Ps(u) is given by
). (8.33)
8.5
The application of anomalous scattering
273
This function will have peaks from an anomalous scatterer, say atom m, to any other atom, say atom n, of weight approximately proportional to AfmZn and peaks from atom n to an anomalous scatterer, atom m, of weight AfmZn. The significance of this anticentrosymmetric function is that it not only gives a pattern of peaks, positive and negative, which can be used to solve the structure but the absolute direction from an anomalous scatterer to other atoms is clearly indicated. Thus if the positive directions of the axes with respect to the crystal are defined and the record of the reflection of index h is distinguished from that of index — h then the absolute configuration of the crystal structure can be determined. When a molecular structure exists in enantiomorphic forms then, if it contains an atom for which a suitable wavelength can be found to give anomalous scattering, the absolute configuration of the enantiomers can be determined. Without anomalous scattering the diffraction patterns of the two forms are identical and they cannot be distinguished. To illustrate the principle of the Ps(u) function there is shown infig.8.30 a hypothetical structure in space group pi with the sulphur atom acting as the anomalous scatterer. Anomalous structure factors were calculated using STRUCFAC and the output was used as input for PSCOEFF (appendix X). This program produces an output file with amplitudes and phases which, used as input for FOUR2 gives a Psfunction map. The map, reproduced infig.8.31, shows positive peaks from the anomalous scatterer to other atoms and negative peaks in the reverse directions. Because two carbon atoms are nearly centrosymmetrically disposed about the sulphur atom the positive and negative peaks related to these two atoms partially cancel each other  although the peaks can still be clearly seen. Synchrotron sources of Xrays (§ 5.8) can give radiation tuned to a particular wavelength and increasingly this is being used to make anomalous scattering measurements for a given structure at several different wavelengths. The anomalous scatterers have values offx and/ 2 which depend on the Xray wavelength and if the wavelengths used are tuned to be close to an absorption edge for the anomalous scatterer then there will be large changes in the anomalous components of the scattering factor (seefig.6.17). Manywavelength anomalous scattering (MAS) overcomes the phase ambiguity of OAS (Woolfson and Fan, 1995). Anomalous scattering can also be used to resolve the ambiguity of phase
Fig. 8.30. The synthetic structure
274 Fig. 8.31. The Psfunction map for C5H9S. Positive contours are drawn with solid lines and negative contours with dashed lines.
The determination of crystal structures
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 1.1507 OUTPUT WITH X HORIZONTAL AND ORIGIN BOTTOM LEFT 0 20 0  2 . 11 25
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9
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which results from the use of a single pair of isomorphous compounds. If the simplest case of a single ir atom is taken then the phase ambiguity is shown in fig. 8.32. When Xrays are used for which the ir atom Z scatters anomalously, a component Afz is added to the scattering factor (ignoring the change in the real part) and the new structure factor is shown infig.8.32 as OQ or OR depending on whether it was originally OQ or OR. Since OQ and OR' will have different magnitudes it will be possible to distinguish which of the phases is the correct one. Another way of combining SIR and OAS is by the probability curve method illustrated earlier infig.8.26. Although the atomic positions for both isomorphous replacement and anomalous scattering are the same, the central phases of the phase ambiguities, 0xh and (/>2?h, will differ by it/2 so that the multiplication of the probability curves will not give a symmetrical result. 8.6 Inequality relationships In 1948, Harker and Kasper showed that inequality relationships existed between the structure factors and that these relationships could occasionally lead to definite information about the phases of structure factors. To derive these relationships, the Cauchy inequality can be used. This is
N
I KI
where a} and b} can be real or complex quantities.
(8.34)
8.6 Inequality relationships Fig. 8.32. The resolution of the phase ambiguity from isomorphous replacement with anomalous scattering.
275
We shall apply this inequality to derive relationships between unitary structure factors. The assumption will be made that the unitary scattering factors, the n's remain constant over reciprocal space. If the structure contains atoms of equal weight, or nearly so, this assumption will be justified; if there are heavy atoms present then, since their scattering factors fall off more slowly with sin 6 than do those of light atoms, the assumption is not really valid. Consider the unitary structure factor h = X nj exp(27tihr;). (8.35)
Taking a^ = y/rij and bj = ^Jnj exp(27iihTJ) then from Cauchy's inequality we find (8.36) Since exp(27iihT;) = and
N
Tj) + i sin(27ih*r7)  =
inequality (8.36) gives
(8.37)
276
The determination of crystal structures
This is a fairly obvious inequality and not a useful one, since by the very way in which Uh is defined it must be true. However more useful results are obtained as soon as we take account of the presence of symmetry elements. Thus for a centre of symmetry we have Uh = £ n,.cos(27ihr,.).
7=1
(8.38)
Putting cij = y/rij and bj = v /^cos(27ihr J ) we find
u
l < I
7=1
n
j
x
I ";cos2(27ihr,.).
7=1
(8.39)
Now
N N N
£ njCOS2(2nh'Tj) = \ £ nj + \ £ n</cos(27c2hT</.)
7=1 7=1 7=1
so that ^ h ^ l + ^h). (8.40)
This inequality can be used to give the sign of £/2h; if it is written in the form ^2h >2Ull (8.41)
this can be seen a little more easily. If  Uh \ and  t/ 2ll I are both sufficiently large then one can show that (72h must be positive. Thus if  Uh \ = 0.6 and  £/ 2h  = 0.5 then, since from inequality (8.41) U2h ^  0.28, it is clear that U2h must be positive since the negative sign for Ulh would contravene the inequality. Let us now see what inequalities result from having a twofold axis. Atoms will occur in pairs with coordinates (x, y, z) and ( — x,y, —z) and the unitarystructurefactor equation appears as Um = £ nj exp(27ii/c^)cos{2Ti(/i^ + Izj)}.
7=1
(8.42)
For dj = y/rij exp(2nikyj) and bj = y/njCOs{2n(hXj + Izj)} this gives
\Uhkl\2^^l + U2h<oai). (8.43)
This inequality can be very useful. Thefoaxisprojection is centrosymmetric and it is possible to determine the sign of a large structure factor V2K02l if any of the structure factors Uhkl has a sufficiently high magnitude. If, together with the twofold axis, there is a centre of symmetry then the unitarystructurefactor equation has the form
N
Uhkl = Z ";cos(27tfcy;)cos{27t(/zx; + IZJ)}.
7=1
(8.44)
This can lead to two different inequality relationships depending on the
8.6 Inequality relationships
277
way the summation terms are partitioned. For aj = y/njCOs(2jikyj) (and bj = y/rij cos{2Ti(hXj + Izj)} we have
U2hkl < *(1 + l / 0 , 2 W X l + t/2*.o.2i) (845)
while for a,. = ^/n^ andfey= ^/rijCOs(2nkyj)cos{2n(hXj + /z,)} the inequality becomes
U2hkl ^ i ( l + £/0,2*,0 + l/2*.O.2I + ^ 2/,,2*,2/)(846)
The general rules for formulating inequalities of this type should be now be apparent. The unitarystructurefactor equation is written down for the particular space group with which one is dealing, the summation terms are partitioned in all possible ways and, for each partition, an inequality relationship can be deduced. The reader should be able to confirm the following inequalities for the space group Pljm for which the sets of related atoms have coordinates ±(x,y,z), ±(x,±y,z): U2hkl < i { l + ( and UL < i U + ( " l)**Vo, 2 I + ( " l)*t/o,2*,o + U2ht2kai}. (8.48)
1)*£/ 2 *,O,2/}{1
+ (  l?U0f2ht0}
(8.47)
We now consider a number of situations for P2Jm and study the conclusions therefrom. (1)  Uhkl  = 0.5,  U2Mt2l  = 0.3,  UoaM  = 0.1. The lefthand side of the inequality equals 0.25. If ( — l)kU2h02l *s negative then the maximum value of the righthand side of inequality (8.47) is 0.25 x 1.1 x 0.7 = 0.19. Thus (  l)kU2htOf2l must be positive. This proves that V2h02l is positive if k is even and negative if k is odd. (2)  Uhkl  = 0.4,  U2hMl  = 0.25,  UoaKO  = 0.25. The lefthand side of the inequality equals 0.16. If ( — l)kU2hiOt2l and ( — i)kUOt2ktO are both negative then the maximum value of the righthand side of inequality (8.47) is 0.25 x 0.75 x 0.75 = 0.14. However if either of them is positive or both then the inequality can be satisfied. Hence one can only show in this case that at least one of ( — l)kU2h0 2l and (  l)*l/o,2fcfo m u s t be positive. (3)  Uhkl  = 0.5,  t / 2 M t 2 I  =  U0Mt01 = 0.05,  U2K2K2l  = 0.3. From inequality (8.47) it can be shown that at least one of ( — l)kU2h0 2l and ( — l)k£/o,2fc,o must be positive. From inequality (8.48) it can be shown that U2K2k2l must be positive. There is another type of inequality relationship which can be deduced by forming the sum and differences of unitary structure factors. We have
N
Uh + UW= ^ ny{cos(27ihri) + cos(27ih/rJ)}
}sin{7t(h .5.\ = 0.}.50) and (8.53) is equivalent to (8. We shall consider a number of examples. For each of these triple products if two of the t/'s are known in sign then the sign of the third U will be found.0.h')r.4.52) can be combined into a single inequality (I ^ h I + I Uw ) 2 ^ {1 + s(h)5(h')t/h+h. is that either or both of the triple products of signs s(h)s(h')s(h + h') and s(h)s(h')s(h ..50) while if s(h)s(h') is negative then (8.50) while if they have opposite signs (8.). Uw.53) into ( I ^ h I + I Uh. (8.  ) 2 ^ {1 + 5(h)5(h>(h + h')  l/ h + h.45.52) are valid for a given set of l/h.
The lefthand side equals 1. give rise to definite relationships between structure factors.53) is equivalent to (8.54) cannot be satisfied. Let Uh and Uw be known in both magnitude and sign as 0. 1 .278
N
The determination of crystal structures
= £ 2nj cos{7i(h + hOrJcosfrfli .52) gives a lefthand side equal to 0.  = L/ h _ h . If Uh and Uw have the same sign then one uses (8. if the U's are sufficiently large..h') are positive.)2 < (1 + Uh+h'Xl + ^hh)Similarly ^h " t/ h ' = I " 2njSin{7i(h + h')r.Uh. (8. As a next step one can transform (8.}{l + s(h)s(h')£/h_h.  } h')L/ h .51) (850)
and the corresponding inequality becomes (Uh .\ = \Uh_h.45 and —0. is positive the inequality cannot be satisfied so that Uh+W must be negative. =  t / h + h . This means that (8.3 and  Uh_h.l/ h+h .h')r. = 0. ^h+ir anc * ^ h .)2 < (1 .52) is used to get the largest lefthand side.54)
This relationship is interesting in that what it can show. Then inequality (8.
.49)
we find (Uh + l/ h .(7h_h.52). (1) \Uh\ = \Uh. respectively.81 and it can be seen that if Uh+h. It can easily be shown that unless both the triple products of sign are positive then the inequality (8. (2) L/ h  = L/ h .\ = \Uh+h.50) amd (8.52)
Both the inequalities (8.)(l .} (8.} (8..  = 0 .h ' an<^ ^ e y can > u n der suitable circumstances. Taking the partition aj = and
(8.53)
where s(h) means 'the sign of Uh\ The reader should confirm that if s(h)s(h') is positive then (8.h ^}. and  Uh+W \ = 0.
0) it will be
N
(8.45).36 ^ (1 + 0.3025 and since this is less than the lefthand side the assumption cannot be valid.45. 0.50) shows that the assumption is invalid. At least one of the triple products must be positive otherwise the inequality cannot be satisfied.that the signs of a number of structure factors may be chosen arbitrarily.36. and Uh_w are both negative then the use of inequality (8.6 Inequality relationships
279
The lefthand side equals 0.}] or [F ]i =( — \)h[F ] (8.6. Suppose we take one centre of symmetry C as the point (0.64. A parity group is a set of structure factors whose three indices are odd or even in the same way. We consider the situation I Uh  = 0. For example if a structure factor with respect to C as origin can be written as
N
C^Jooo = Z fjcos{2n(hxj + kyj + Izj)} then with respect to an origin at (£.45X1 . For either (8.55)
DF/iJioo = Z fjCOs[2n{(h(Xj . with respect to this origin. Then as the origin is moved to other centres of symmetry the signs of the structure factors will change. \Uh.0.50) and (8.52) the lefthand side has value 0. Similarly if one assumes that Uh+h. is positive.50) or (8.i) + kyj + Jz.52) as the following example will show. 1961).52) we have the righthand side equal to (1 . The only valid assumption is that Uh+W and Uh_w have opposite signs when either of the inequalities gives the valid conclusion 0.0.  = 0.8.
The lefthand side equals 0. In fact inequality (8. Before we do this.56)
.54) does not completely replace (8. we should acquaint ourselves with a useful piece of information . The reason for this is the existence of a number of nonequivalent centres of symmetry which may be chosen as origin. Let us assume that Uh+h. from (8.0.36.45) = 0.0) and one structure factor from each parity group each of which.45)(l .  Uh+W  =  Uh_w  = 0. As the origin is moved from one centre of symmetry to another so the signs of the structure factors will change but they change in such a way that all the members of one parity group change together.. and Uh_w are both positive. We shall demonstrate the application of inequality relationships by the solution of the caxis projection of tetraethyl diphosphine disulphide (Dutta and Woolfson. however. The inequality is satisfied even if both the triple products are negative and no conclusions can be drawn.0.
41) we must have l/ 4 $ greater than —0.0. and Uh_h>. In two dimensions there are four origins available and one may arbitrarily select the signs of two reflections taken from different parity groups of oe. We find
From inequality (8. Further progress can now be made with inequality (8.54). eoe and ooe. The twodimensional space group is p2 implying only a centre of symmetry. the two U's can be shown to be positive and they must therefore be structure invariants otherwise their signs would change with change of origin. 8. hkl parity
Origin eee oee eoe
The determination of crystal structures
eeo
ooe
oeo
eoo
ooo
(0. This may conveniently be done by preparing a transparent replica (tr) of fig. At this point two originfixing signs may be chosen. if one takes three linearly independent reflections from three different parity groups and not including eee then all eight (23) combinations of signs occur at one or other of the origins. The reader may check that the products of signs in these three columns is always positive. l/ 4 $ must be positive. where adding the parity of the indices gives eee.
.7. If three groups are taken. The eee group does not change its sign with change of origin and these structure factors are therefore called structure invariants. The logical nature of these sign determinations should be noted. eo and oo. The reader should make a tr of fig. It is clearly advisable to choose large  U 's and two which satisfy the rules for selection are U3 ~n and (76 7 which are both taken as positive.33. On the other hand. then the product of three such structure factors (called linearly dependent) is also a structure invariant. i)
+
+
+
+
+
+
+
+
(U0)
(111\
The complete pattern of changing signs is shown in table 8. First one can look for pairs of large  U 's of indices of form Uh and U2h to see whether inequality (8. 8.37 and hence. h'.0. With threedimensional data we are thus enabled to select three such reflections and arbitrarily to fix their signs (as positive. To use this inequality it is necessary to select four indices of form h. from its magnitude. The  U  data for tetraethyl diphosphine disulphide is given in fig. h + h' and h — h'.33. say) and this amounts to fixing the origin of the cell.41) can be applied.0) (0. 8.33 and try finding sets of four indices in this way.7.280 Table 8. such as oee. If the origin of the tr is placed over Uh of the figure then under the Uw and U _w of the tr are seen Uh+h. Similarly U82 can also be shown to be positive.
It will be noticed that progress so far has only enabled signs to be determined as positive since all the initial signs were positive.42 5(2. this will merely give a signdevelopment pattern where a large peak will build up at a nonorigin centre of symmetry. If the sign of U^ is indicated as p then one may find: h
U47 = 0.6 Inequality relationships
281
86 42 65 42 0 0 0 0 45 0 0 0 0 0
0 85 91 0 45 0
0 0
0 0
0 0
0 0
0 0 51 34 44 0 0 34 61 18 0 0 0 0 0 0 0 0 0 17 0 0 0 0
9
0
0 20 54 26 28 73 58 13 70 65 15 56 55 0 6 0 42 75 43 14 28 0 8 0 17 0
0 63 45
0 62 46
0 33 70 36
16 33
0 49 35 0 69 53 12
0 21
53 35 23 39 41
0 38
0 21 42 52
0 42 49 0
0 48 30 20 14 0 6 41
17 16 30 33 57 42 30 13 17
14 13 61
0 26 49 6 0
17 14 10 10 0 0 0
X
0
30 42 57 41
10 10 14
12 49 26
0 52 61 0 0
14 33 30 8 6
16 17 14 20 30 48 0 38 0 41
0 49 42
0 53 69 0 35 49 0 0
0 42 21 0 33 16 0 18 34
39 23 35 53 21 0 46 62 0 0 0 0 0 0 0
0 28
14 55 56 0 65 70
15 36 70 33 13 45 63 0 0 0 0 0
0 43 75 42 0
0 61
58 73 28 26 54 20 0 0 0 0 0 0 0 0 0
0 45
44 34 51
0 45
0 42 65 42 0 86
0 91 85
Fig. 8. This situation cannot be avoided by choosing one or more originfixing signs as negative.65 ^
I/5t5 =
Conclusion 5(3. The values of \00\Uhk0\ for tetraethyl diphosphine disulphide. However it is known for this as for all other l/'s that I UI < 1 and it can be shown that U5t5 must be positive no matter what is the value of Ullt$.86 I l / 1 0 t l 4  = ? I l/ 2 f 0  = 0.h'
I U10\
Conclusion
= 0.5)= + 1
The last relationship is interesting in that one of the E/'s is outside the observed region.57
h . Once progress in sign determination is baulked by an inability to relate fresh signs to ones already determined then it is possible to introduce sign symbols.30 5(1. If it is known that there is no atom at the origin then we must expect the progress in determining new signs to break down at some stage.85p U6'ri = 0.33.45 h'
\U3O\ = 0.S5p
h'
U37 = 0m
h + h'
l/7l4 = ?
h .7 = 0.
A few sign determinations follow: h l / 4 s = 0.8.0) = p
.0) = p
< .57
h + h' t/3 0 = 0. When all the signs for a structure are positive then a Fourier synthesis gives a very large peak at the origin.0) = + 1 5(7.h' Uo1 = 1/ 7 g I = 0.6) = + 1 5(5.
If the number of symbols is n then there are 2" possible sets of signs and.1. 1961). (8. In fact it was possible to determine both p and q by the use of inequalities (8. can show that s(h + h')s(h — h') = — 1. b sin a
. For N > 40 or so it is extremely unlikely that the use of inequality relationships alone will enable the structure to be solved. 8.3%) will be greater than 0.50).34. as we have seen.52) and (8. For tetraethyl diphosphine disulphide most of the large unitary structure factors were found in terms of two symbols p and q.54).62pq U5
= OJOq pq2 = p = . This structure was solved by the use of the simple basic inequalities for PI.42 U9
= 0.282
The determination of crystal structures
Whenever progress stops then another symbol can be introduced.65
l/3*2 = 0.52) which. If there are N equal atoms per centrosymmetric unit cell then the L/'s will have a normal distribution with variance N~* and mean zero.
The Fourier synthesis based on the inequalityderived signs is shown in fig.38<? q = . The electrondensity map with inequalitydetermined signs for tetraethyl diphosphine disulphide (from Dutta & Woolfson. inequality relationships can only be used with the simplest structures. In general. Thus h h' h + h'
5
h — h'
5
Conclusion
^ 7 3 = 0 I U2 0  = 0. For N = 36 this means that very few  U 's (about 0.34 and it can be seen that this shows the form of the molecule quite well. At the end of the signdetermining process one should have determined the signs of a number of the largest l/'s in terms of a few sign symbols. Only one in twenty structure factors should have a magnitude greater than two times the standard deviation.41).63 U7[6 = 0.2 = 0 I U5]i\ = 0. 8.50) and (8. (8.1
^2. one might recognize the correct structure in one of them. or 2N~ % and three in a thousand should be greater in magnitude than 3N " *.5 and one needs to have a fair number of I U 's this large in order for inequalities to be effective. if Fourier syntheses are calculated for all these.(8. 8. For space groups with more symmetry other inequalities may be used but it is found in practice that it is with the simple inequalities that most progress is made.54) it can be shown that if the corresponding  U 's are all sufficiently large then
Fig.7 Sign relationships From inequality (8.
57) was probably true.
Fig.7 Sign relationships
283
s(h)s(h>(h . shown in fig. From equation (3. Let us consider a structure containing equal resolved atoms as demonstrated by the onedimensional electrondensity distribution in fig.31) we may write for three dimensions
F
h=
Z /h ex P( 27lih ' r .57)
In 1952 Sayre. From equations (8.58) and (8.6 that the Fourier coefficients of p(r)2 will be given by the selfconvolution of the Fourier coefficients of p(r).
(8. resolved atoms in one dimension.35(fc).59)
where Gh is the hth Fourier coefficient of p(r)2 and gh is the Fourier transform of a 'squared' peak. x (a)
Pix)2
x (b)
. (8. 8.1 0 = + 1. resolved atoms in one dimension. 8.59) we may write say. 8. The value of/h also corresponds to that of the Fourier transform of an atomic peak at the point corresponding to h in reciprocal space. Cochran and Zachariasen separately showed that even when the  U 's were smaller than was necessary to satisfy the inequality relations it could still be shown that equation (8.58)
where/ h is the scattering factor for each of the atoms.35(a). Sayre's approach to this problem is the one we shall consider.)
(8. We may also write
G
h
=
(8. If this electron density p(x) is squared to give p(x)2 then this distribution. also consists of equal resolved peaks.60)
It follows from the convolution theorem given in §4. (a) p(x) for equal. (b) p(x)2 for equal.8.35.
284
The determination of crystal structures
From equation (4.64)
The reciprocallattice distance s is related to the structurefactor index h by s=a so that (8.62)
where u is the distance from the centre of the atom. The results are shown in table 8. the length. applies to any equalatom structure whether centrosymmetrical or not. What can be seen from these equations is that if F h is
. ±0.61) with a centrosymmetrical onedimensional model structure. known as Sayre's equation.361 and ±0. Hence. It will apply to one. The electron density in the atoms was taken as
p(u) = e2*»2 (8.67)
Structure factors were calculated for the structure and the two sides of equation (8.66)
y^
V
(
^Y
(8.60). the area.61) were then compared. This had atoms at ±0. we find
This equation. from the convolution theorem
Lr
U V
VLF
Ly^W h
LF
i/^hh'
h~
v
and.8.or twodimensional data if the atoms are resolved in the appropriate projection and then /.72) it can be seen that the Fourier coefficients of p(r) are (l/K)F h and similarly the Fourier coefficients of ph(r)2 will be (l/V)Gh. or A. The agreement of the two sides of the equation is excellent.113. ±0.65) (8. any disagreement is due to the termination of the Fourier series and to slight overlap of the electron density between atoms. using equation (8.234. Sayre actually used his equation to solve a crystal structure but generally this is not feasible.61). and this gives a scattering factor
The squared density was p(u)2 = Q^u2 with a Fourier transform gs = ^~^\ (8.438 in a cell of length 20 A. of projection will replace Kin equation (8. Sayre illustrated the application of equation (8.
lFhFh
a h.}.68)
where « means 'probably equals'.8.62 0.72 0.68) is true was worked out for the equalatom case by Woolfson (1954).7
Sign relationships
285
Table 8.64 0.37 0.35 1.17 0.54 1.48 1.28 0.41 0.48 1. Cochran and Zachariasen also arrived at this probability relationship although by different lines of reasoning.)
j= i
N/2
= £ 2nJcos(27ih/ri)cos{27i(hh/)TJ.35 0.78 0.71b)
.66 1.48 0.29 0.h') « 1 (8.03
large then any large products on the righthand side of equation (8.38 0.}
N/2

X 2nisin(27ih/TJ.76 0.41 2.16 0.03 0.36 0.36 0.00 0.07 0.07 0.38 1.61) are likely to have the same sign as Fh or s(h)s(h')s(h .38 0. We write the unitary structure factor as the sum of independent terms
N/2
u
h = Z 2nicos(27ihrJ.47 0.
(8.78 0.35 1.05 0.69)
This can be written as
N/2 N/2
^h = I "j + Z Pj
where
(8. 0.54 1.41 2.
h 0 1 2 3 4 5 6 7 8 9 10 11 12 13
F
h 5..)sin{27i(h .70)
(8.10 0.03
h
5.41 0.10 0.78 0.)sin{27i(h 
h^
(8.79 1.80 1.71a) and
pj = 2rijsin(2Txh/r7.66 1.05 0.72 0.52
0.8. The probability that equation (8.52 14 15 16 17 18 19 20 21 22 23 24 25 26
F
o.27 0.h')r.77 0.37 1.30 0.03 0.81 0.00 0.
79)
If we take sin2(27ihTJ) = cos2(27ihTJ) = \ then we find for equal atoms o2h = N\ (8..76).} = 2n/cos(27th'r/) x cos{27i(h . from equations (8.77)
since the values of sin(2iihTJ..h')*^.
7=1
(8. We also have
(8.74)
taking the product of the averages is valid since the two quantities are independent..73 )
Now a.78)
As long as Uh>Uh_h.h')r.as long as  Uh  is not exceptionally large. 00+ KPjTA
7=1 7=1
2
( 8 .18)
N/2 N/2
<= I (*.) = 2rij x — x (cos 2jthr/ )
2
N
= cos(27ihrj) = Uh. = 2n/cos(2iih'r/)cos{27t(h . When the atoms are equal rij = N'1 and
N/2
2n/ {cos 27thT/.76)
Pj = 2n/sin(27th'T.80)
. This gives.) x sin{27i(h .72) and (8.72)
and a variance from equation (7.h')^.) x sin2{27i(h .) are equally probably positive and negative and not constrained by the value of Uh .h')r..}.} = 0
(8.75)
(8.. Hence
^ = 2N'UWU^.} (8.
7=1
(8.286
The determination of crystal structures
The centrallimit theorem tells us that the probability distribution of Uh is normal with a mean
N/2 N/2
^h = I OLJ + £ pj
7=1 7=1
(8. is not too large we can write
N/2
h Z—i
j
N/2
/^
• j
7=1
N/2
7=1
= X 4n 2 cos2 (27ih r r j) x cos 2 {2ii(h
7=1
N/2
X 4n 2 sin2(27ihrJ.
N/2
u
h = Z 2AT1L/h>Uh_w = Uh Uh_h.
9 there are shown some typical values of P+(h.h') then P + (h.987 1.500 0.p.994 1.Uh. By inequality relationships he was able to find the signs of forty structure factors in terms of five sign symbols.h')  l/h  or s(h')s(h .540 0.h')# 1 in some situations where inequalities apply. Next Zachariasen extended the sign information and found relationships between the symbols by the use of (8.).9. in practice.84) where the summation was taken for all products of structure factors for Table 8. However. The probability of it having each of these values is proportional to the ordinate of the distribution (8.Uh_h.81). (8.83) tend to be somewhat lower than those given by the more precise theories although the expression does become more accurate as N increases. The expression also gives P+(h.r. In table 8. 40 and 80 and for a range of values of 0 = ( UhUh.2 0.7
Sign relationships
287
Thus for a particular pair of unitary structure factors Uw and Uh_w the
distribution of the values of Uh is = (2TCAT *) exp{ .1 0. have been given by Cochran and Woolfson (1955).)2}.000 80 0. h') for N = 20.68).\).8.993 40 0.500 0.4 0.520 0. respectively.h') = 1 we can find P+(h.h') = i + $tznh(N\UhUh. if we denote the probabilities by P+(h.h') + P_(h. (8. one is not normally interested in the exact probabilities when one is using expression (8.0 0.782 0.928 0.h') and P_(h.5 N = 20 0.s.757 0.h) _ exp{ ±N(\Uh\ ~ 1 E W .h')  Uh' . The probabilities given by equation (8.
U 0. and ones which apply to structures with nonequal atoms. Bertaut (1955) and Klug (1958).000 1.000
.±N(Uh .Uh_w  )*. These relationships were first used by Zachariasen (1952) in solving the structure of metaboric acid.896 0.579 0.3 0.83) More accurate probability expressions.510 0.r I ) 2 } ^UMO " exp{iV(l/ h  +  l / h ^ h _ J ) 2 } "
2Nl v v CXP(2iV U U u
' > >U (8.500 0. These two values correspond to s(h)s(h')s(h — h') being positive and negative.654 0. the tripleproduct sign relationship (t.82)
Since we must have P+(h.Ukh.81)
However we know the value of  t/h  and the value of Uh is either s(h>(h .
78 U5.27
=1 I/7f5 = 0. b = 12. 5 = 0. We should note that.81.58
l/ 7 .57
=0.24
I U0.3 = 0.3 = 0. It will be noticed that if the summation is negative then P+(h) < \. 1958).r.57 t/ 7 .8)= + 1 . This relationship is an approximation to the more accurate relationship (8.s. until virtually all the larger l/'s have their signs determined.8 = 0. 2 = 0.5) = +1
*(0.p. with the introduction of more sign symbols. As an example we consider the determination of signs for the caxis projection of Roussin's red ethyl ester (Thomas.5)^5(2. This would be taken as an indication that s(h) = a and b = 4.26 l/2i3 = 0. (8.36 should be marked on a transparent
.8 = 0.36 there is shown a stage where 23 signs are determined in terms of four symbols. Infig.k) = (l)h+ks(h.nl = ?
f/14t0l
h . 8. One can easily go further and find explicitly what all the symbols represent but the process has been stopped here to demonstrate the application of the t.67. equivalent reflections in neighbouring quadrants have signs related by s(h. for this space group.01 A and /? = 111°24/.74a l/3fll =0 5(7.26 l/ 7fl = 0.3)
= 5(5.i
h + h' IUl2.87)
The two originfixing reflections are chosen by taking
S(7.58 U 0.14a U7.85) which has an associated probability ) (886)
where P+(h) is the probability that Uh is positive.8.3 I = 0. c = 7.h' 1^2.288
The determination of crystal structures
which signs or sign symbols were known.84) it might be found that the separate products in the summation were aaaaababab.5) = + 1 and a = + 1 5(2.3) =5(2.78
U7fl
h' ^5.k).3) =41
Inequalities can be applied.2) = + 1
= 0. All the signs and symbols in fig. The structure has two molecules of (NO)4Fe2S2(C2H5)2 per unit cell and has space group P2Ja with a = 7.74a = 0.21
Conclusion 5(2. The caxis projection has the twodimensional space group pgg and the table of  U 's is shown in fig. In a typical application of equation (8. Robertson & Cox.36.1. If other indications gave b = + 1 it could soon be accepted with some confidence.
The first few stages of sign determination by inequalities give: h ^7. 8.
10. Some points of interest are: (a) Sign relationships (as distinct from inequality relationships) do occasionally break down and three examples of breakdown can be seen. For example. c.7
Sign relationships
289
1 1 22 1 1 57
6 78 17 74 + 0 68 3
74 17 78
6 57
f b 28 48 14 60 37 38 22 56 32 13
+ + b 0 56 22 38 37 60 14 48 28
+ +
0 58 22 41
8 29 20 24 5 21 d 19 41
3 24 20 29
19 21
8 41
22 58
0 32 7 13 0 0
e c 7 31 24 35 18 47
d 12 42 12 41 d 33
e c c 5 47 18 35 24 31
0
e 0 14 25 35 47 24 38 19 35 + + 6 24 18 27
d 9 33
c e 9 35 19 38 24 47 35 25 14 _ _ 9 27 18 24
d 14 20 38 18 40 18 22 16 30 16
9 16 27 16
d 6 22 18 40 18 38 20 14 0 16
17 30
b b 0 10 38 12 37 23 15 26 12 25 18 20
17 14 35
+ 28
b b 20 18 25 12 26 15 23 37 12 38 10
26
+ 26
b 0 10 38 12 37 23 15 26 12 25 18 20 _ _ 6 24 18 27
b
X
+ 26
26
+ 28
35
14
b b 20 18 25 12 26 15 23 37 12 38 10 + + 9 27 18 24
0 16
d 14 20 38 18 40 18 22 0
13
d
6 22 18 40 18 38 20 14 0 7 0
9 16 27 16 d 9 33 d 33
e c 0 14 25 35 47 24 38 19 35 c 7 31 24 35 18 47
e •
e c 9 35 19 38 24 47 35 25 14
19 21
d 5 21 19 41 8 29 20 24
d 12 42 12 41 3 + 0 68
+
c e c 5 47 18 35 24 31 8 41 22 58 0 32
32
0
+ 58
+ 22 41
3 24 20 29
+ b + 28 48 14 60 37 38 22 56
+ 57 +
+ 0 56 22 38 37 60 14 48 28
+ 74 + +
b
6 78
17 74
17 78
6 57
1 22 1 1 1
Fig.8. An inspection of this table reveals that the almost certain values for the symbols are b = + 1 .5) with sign symbol c gives indications c « be. bd. d.8. If the magnitudes of the l/'s are taken into account one finds from equation (8.86) that P + (6.35.
symbols and signs then give probable sign indications for these new U's.36. The origin of the Values of 1001 Uhk01 for transparent sheet is then moved in turn to lie over points in the figure whose Roussin's red ethyl ester signs have not been determined and for which  U  ^ 0. bd.10. c = d = e = — 1 and when these are taken the final column of table 8. (b) The sign of U6t5 seems not to be given.
.5) = 0. c. The results of doing this gives the independent indications shown in table 8. d. e.10 gives the sign indications for the new (7's. all of which confirm the indications in table 8. superimposing on (3. The overlap of showing inequalityderived signs
and symbols. sheet so that they exactly fit over the ones in the figure. c. (c) Superimposing the chart on points for which signs or symbols have been found can give symbol relationships directly. In calculating this probability it has been assumed that there are 32 equal atoms in the unit cell.89 which is a correct indication that the sign is positive. be.
c.cd
•
6. bd. be. . 8. 1..c. 6..d. be. were not really valid.d
+ + + + + + + .d. 1964a).b. 3.cd. d ..d.d.
4 5 8 8 9 10 11
b.. d.85) as soon as possible.) 1
v
+ </>hh')}h'
(888)
If equation (8. . Cochran and Penfold (1952) used a procedure very similar to that just described.8 General phase relationships Sayre's equation (8.c. d
b.84) or (8. 0. k Independent indications Indications with
b = — c = —d — —e — \ 4.10.c.g. 1. However when only a few terms (perhaps only one) are known on the righthand side then the most probable value of 0 h .290
The determination of crystal structures
Table 8. is that given by those terms. Karle and Karle have systematized this process into what they call 'the symbolicaddition procedure' and very complex centrosymmetric structures can be solved in this way (e.c. 3 .) exp(i</>h_h. b ' —. This suggests that a reasonable method of tackling sign determination is to assume the inviolability of some of the strongest sign relationships .e _ _ _ _ _ _ —..in fact to treat them as inequalities . on which their solution seemed to rest. in the form of a threephase relationship. c.( d.b. —b. h.
(889a)
.61) applies quite generally and for noncentrosymmetric structure factors can be written as I *h I exp(i0h) = ^Y  Fh. c. ed ed _ 9 —9 — 9 b.88) is written with IPs or £'s instead of F s then the summation must be over an infinite number of terms because the data then corresponds to point atoms for which there is no scatteringfactor falloff. b. c. c.e
— + + + . 2. c. However when the structure was solved they found that they had overestimated some of the unitary structure factors so that the inequalities. Thus with a single term involving reflections with indices h' and
hh'
<A> = K + hw
or.b.b.+. —d.+ _ _j_ ___ —— _ _ _ _ _l_ _l_ _l_ _l_ ______ _ _ _ _ _ _ _
In solving the structure of Lglutamine. c . 0 3. Karle & Karle. . 1 Fh_h. <</>h>.d + .and then to use relationship (8.  exp(i</>h. be.
90a)
Equation (8.<t>hh' ~ ° (modulo 2n)
291 (8. h') for that relationship the smaller the difference one is likely to get. The general form of the probability distribution of c/>h has been given by Cochran (1955) and is shown in fig.92)
Karle and Karle (1964b) solved the structure of Larginine dihydrate. on the righthand side of equation (8. If equation (8. The actual value of 0 h will in general be different from the most probable value given by equation (8.44)) instead of U's was first given by Karle and Hauptman (1956).£ h _ h .90a) with £'s (see equation (7. If there are a number of pairs of phases which.89a).90c)
If the atoms in the structure are not all equal then N. (8. This equation is referred to as the tangent formula and it has played a very important role in the development of direct methods of solving crystal structures.. (8.17).90) is used to estimate 0 h then the same probability relationship is valid except that jc(h. is
</>h_h .89a) but the larger the value of ?c(h. the first noncentrosymmetric structure to be solved by direct methods. h') is replaced by ah where ^h = T\ + B\. 8. much as was done for signs in the
. h') the smaller is the variance of the distribution and the more likely it is that the estimated value from equation (8.h) = 2AT*£ h £ h .8. is replaced by a more complicated expression but normally its value will not be very different from N.8 General phase relationships h ~ <t>h'. which has a better theoretical basis. Another form of the tangent formula. all contribute to an estimate of </>h then the probable value of tan 0 h may be found from
<tan 0h> = ±
. They used what they called the symbolic addition method in which unknown phases are represented by letter symbols.)
<tan 0h> = X
=
^ h
where *(h. the number of atoms in the unit cell.37. It is of the form
P( I <t> 
l
/ 0 is the modified Bessel function which also appears in equation (8.89) will be close to the true value.89b)
which means that the combination of three phases has a distribution about 0 or some multiple of 2n. The larger is jc(h.
(8.
anything from 50 to 1000 different sets of phases will be generated. After several cycles the phases converge to stable values and one phaseset has been obtained. The Cochran distribution. <tan0 h >=Jil h>(h. 8. may be given initial weights of 1. One very simple program. 8.0.37.
The determination of crystal structures
0.) where w(h) is proportional to {(7^)2 + (B™h)2}*. RANTAN.1
1 i
20
40
60
80
100
120
140
160
180
solution of Lglutamine. They tend to
= ^ (893)
.38 and clearly shows every atom. Subsequent to this important structure solution other procedures were developed which were amenable to implementation by computer and the vast bulk of smalltomediumsized structures are now solved by directmethods computer programs.4
0. It is a socalled multisolution method where several sets of phases are generated and are then tested by variousfiguresof merit to see which are the most plausible. A new weight is also found but the phase is not changed to the new value unless the new weight is bigger than the previous weight.89b). For each reflection in turn a new phase estimate is found from the weighted tangent formula using current phase estimates for all other reflections. In RANTAN a set of reflections of large  E  are given random phases and these are then subjected to an iterative refinement by the tangent formula. Because of the way the phases are determined the phases of each phaseset give reasonable satisfaction of the threephase relationships (8.292 Fig. the density map obtained with £'s as coefficients. Different initial random phase sets give different final phasesets and. + <Ah_h.h')cos(</> h . However. obtained by the Karles is shown in fig.25 but other reflections. An initial system of weights is set up. for RANTAN a weighted form of tangent formula was used . depending on the size of the structure.5 0. which define the origin for example. was developed by Yao (1981).h')sin(0h.h>(h. The socalled £map.2
0.3
cu 0. the initial weight for each general reflection is usually 0. Manyfiguresof merit have been suggested from time to time but they all depend on how well certain expected conditions are satisfied.
(2) A subset of large  E 's is found for which  E \ > 1.
N(12)
N(5) C(7) O(2)
N(9) #
(a)
4^010) C(4) \J^CIS) /
Nil 1)
AN
H2O(2)
o
H2O(1)
be rather complicated but a very simple figure of merit. (4) A map is calculated with magnitudes of coefficients w(h)  £(h)  and current phase estimates. a simple twodimensional form of RANTAN which can be applied to structures with any twodimensional space group. From Sayre's equation it is evident that the phase obtained from equation (8.
. We can illustrate the application of direct methods with MINDIR (appendix XI). the values of  Ek  are small but the large  E 's go into the summations which give the a's. The values of a are just proportional to the magnitude of the righthand side of equation (8. Another simple figure of merit is Z = 2>k
k
(8. (3) Random phases are generated for the subset of reflections and weights of 0.61) which can also be written in terms of £'s.0.8
General phase relationships
293
Fig.8.93) is just that from squaring the density of a map with coefficients w(h)£(h).95)
where. is (8. k)  values in a form given by the output of FTOUE. not now used. The aaxis projection of a threedimensional electrondensity map for Larginine dihydrate with 400 phases determined by phase relationships (from Karle & Karle.38. 1964b). 8. This figure of merit can best be understood in terms of Sayre's equation (8.25 are allocated.61) so this figure of merit is simply saying that if  E  is small for normal density then it is expected to be small for squared density.94) where the h's are for all large  Eh  and all large  E 's are used in evaluating the a's . The steps in MINDIR are: (1) A file is read in giving h. in this case.which is just a measure of how well the threephase relationships are satisfied. k and  E(h.
as given by equation (8. (9) Return to (3) and repeat until a chosen number of phasesets has been generated.95). The following points will be noted. Solution 17 had the highest value of CFOM. The correct positions of the light atoms all fall on positive density although two do not fall within contoured regions. 1. 8. as we have seen with MINDIR.
/ min
(8. These figures of merit are scaled to have a maximum value of 1000 and output for each phaseset. rather than by squaring the map and producing large
.39. Also output is a combined figure of merit. (6) For each reflection a new weight is calculated. squaring and Fouriertransforming the map is carried out and the final weights and phases are accepted unconditionally.94). If this does not reveal the structure then MINDIR can be run again using a switch which simply finds any other designated phaseset from afileand then computes and outputs the map without rerunning the complete program. the application of the tangent formula is tantamount to squaring the electrondensity. The sodium atoms appear clearly but overweight compared with other peaks in the map. Finding new phases in series.3 and Z. (7) If there have been less than 16 cycles of refinement or if the mean change in phase is greater than 2° then go back to (4). This is a common feature of solutions produced with the tangent formula because. which tends to increase density differences and makes heavier atoms appear stronger than they should be. The program automatically produced a map for solution 17 which is shown in fig.96)
A max
A mm
/ max
The subscripts refer to the maximum and minimum values of A and Z for all the phasesets generated and CFOM would have a value of 2.5.17 and the output file from this was used with FTOUE to give a set of  E 's. by the tangent formula.11. followed by solution 43 with a value 1. as given by equation (8. This was used as input for MINDIR which generated 50 phasesets and gave the list of figures of merit shown in table 8. for all  E 's < 0.330.8. All these features are seen in the results from the large and complicated directmethods computer packages which are commonly used. (8) A final cycle of calculating a map. Structure factors were calculated with STRUCFAC for the artificial structure. CFOM.321. shown earlier infig. with space group pg. Otherwise go on to (8). one at a time. for all  E 's > 1.294
The determination of crystal structures
(5) The map is squared and Fouriertransformed to give Fourier coefficients G(h). (11) MINDIR automatically outputs the map for the largest value of CFOM.0 if it had the greatest value of A and the least value of Z and a value of zero if it had the least value of A and the greatest value of Z. but to a lesser extent. in addition there is a considerable amount of spurious density. If this is greater than the previous weight then the new phase and weight are accepted. (10) For each phaseset calculate A. defined as CFOM =
A A
~
i4 in
"
+
Z
™* ~ Z .
7 336.9 796.043 983.0 35 37 400.9 238.021 1.5 984. Again.7 5 369. If.9 1. dampens the squaring effect.025 1.7 277.2 1.013 996.8 964.2 990.3 925.330 17 628. is that the structure obtained may be the true structure or its enantiomorph.1 1.6 928.
THE SEED USED IS 9000 CFOM SOLN Z A 1 948.191 1.060 1.5 404.111 49 952. Organic molecules very often occur in either a righthanded or lefthanded form represented by the prefixes D (dextro) or L (laevo).6 1.5 991.9 152.244 889.025 1.6 11 942.1 1.263 1.5 112.145 21 399.9 648.0 35.7 1.0 988. Nevertheless the general principles of direct methods are well illustrated by MINDIR. y) to (x.213 0. as with almost all other methods.7 940.2 985.5 955.8 23 426.3 970.116 258.0 1.2 517.7 64.1 1. when solving an unknown noncentrosymmetric crystal structure when only the experimental  F 's are available.034 1.078 963.0 1000.042 19 264.6 408. Figures of merit from MINDIRfor the structure C 3H 5N2 ONa2
The values of A and Z are as given in equations (8.6 1.3
Z 198.023 1.4 847.003 1.3 243.147 45 47 349.155 1.5 339.0 1.113 1.3 177. in three dimensions the ratio of the number of data employed to the number of atomic positions to be determined is much greater than in two dimensions and gives better resolution of the structure.4 926.031 263.7 44 .8 1. either form could be found by the structuresolving method.6 25 27 941.219 1.3 1.000 152.0 410.0 766.8
General phase relationships
295
Table 8.1 555.8 1.2 399. For that reason.031 426.321 43 705.128 7 488.38.5 268.2 872.7 986.0 1.1 29 761. The two forms are related to each other as a left hand is to a right hand and two molecular structures of different chirality may be arranged so as to be
.4 730.0 300.7 785.8.8 925.95).0 980.11.133 1.102 3 889.000 1. A characteristic of direct methods when applied to noncentrosymmetric structures.5 41.5 971.159 499.011 734.3 1. it should be noted that 400 reflections in three dimensions have gone into the £map given infig.3 41.2 516.051 997.8.1 136.5 991.940
numbers of new phases in parallel. CFOM.0 851.0 1.4 80. for example. y) then the magnitudes of the structure factors are unchanged.8 257.6 479.1 1.7 716.4 15 314.137 1.4 1.3
CFOM 1.140 1.5 996.175 928.060 998.9 9 1000.5 817.6 264.94) and (8.9 1.9 966.8 1.5 1.158 404.117 1.7 1.132 1.7 39 41 854.9 239.4 1.4 285.011 33 725.6 31 996.3 931.028 1.101 950. Solution 17 has the highest combined figure of merit.001 1.2 1.295 707. the positions of all atoms are changed from (x.262 1.3 972.6
SOLN
2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50
A
311.122 1.267 1.9 1.7 13 656.
10. .
2. 12 . .2 8 .1 4 . . 5
2
2 . 8.
. .
8 . >. . 11 7.3 .20 . 1 4 .8 . . . 9 . . The exception to the rule that either enantiomorph may be found in the structure solution is when anomalous scattering is used. 23 .
. 4 . 5 . 9 .1 1 .7 . 17' ' 16 . 24
.
^ 3 .18 .12. .
5
8.
9 6
33
r'l4 '14 . 13 . 12 .10 .
6 .3 .3 .2 7 . t 5 .
5.1 3 .2 .1 . . 16 .
29 30 31 32
4 11 .
5
1
. 6 . 0.
~ c ~)
5 . . .
5 . 5 .1 2 .5 . 10 .
"3
• L
. . . "V
21

0.
.2 1 .
6 5
. 6 . 13
j 7
V 32". 3 . . .
9 ^2 2
"
17. 12 . 5. 7 .
4
.1 .12 .24 . If for one enantiomorph  F(h)  >  F(h)  then for the other  F(h)  <  F(h)  and so the solution may be found for the correct form of the crystal.27. 3 .12. 1 . . 19 /l4.2 .
9 .
3. . 7. 6 4 2 2 4
.20.
5 . .
J
7
—er
18 3 7 4 7 20 5
. 1 0 . 2 2
7
8 . 18
. 16.6 .
1
2 .5 .1 9 . 2 4
N
. 12 1
v
N
14 5
2
. 8.^. 3 .
. 12
12 28
2 14 2 3
. . .2 7
\ . 3.17. 4. 30 ^ 1 1 . .2 0 . .1 1 . 8.
2 A. 1 9
(33 s
. 24 ( 19/.15 .16 .2 0 . .1 .7 .1 8 . . 3
9
2.
x13.
3 . 13
i?
26
32
Na
.
. Infig. 14 >
}ij
. 7 . 2 .5 . 3. 14 .16 . 4.1 6 . 13.20 . 20 5
11 22
. 13 . 20
. 1 . 4 .8
6 3 2
. .18 . . . . 2 3 < 11.9 . 8. r \ 2 7. 5.2 .9 . . 13. 2 . . The directmethods solution of C 3 H 5 N 2 ONa 2 from the program MINDIR.1 .
3. .id\
. 15 . 4 .
2. . 9 . 4 .
2
. . . 7 .1 8 . 5 3 . 18. .
1 .
c
1 2 6.1 3 .
.
4 ..
'3
.
i . . .3 1 . 6 . 2
^5
2 .1 1 .
vio.
4
• 11.
N
. .
3/
i\
'13
3
.2 7 .1 .16.20. . . 17
2.
.6 . 2.
1.5 . 3 . 6 .
7
! .15. "9. . 11 .1 4 .7
1
. 0
1
23
. . 6 1 7 8 16 1
' 7 . . .1 . 10 .5 .26 . 6
1. 0 / 15 \ "3
4 7 2
2
3 . Z = 314.1 0 . . .1 628. 7. . . 6
3
"20
4 32
7
3 .296 Fig.1 5 . 17 . ^ 2 8 ^ . 5. . 6
V •Y
•
. 32 7 32
4 . 2. 4
.39 has a change both of origin and enantiomorph compared to the structure shown infig.
5
26. 28 . 16 . 12 . . .
. . ^\
7
\
.2 8 .1 5 .
5. 330
11
12
3
13
14
15
16 17 1?
32
1 1
q
i? .' 39 i
(7Z
8
.
.
4. 3 .10.
A3 . . 19 2 .1Z.4 = 628.
X
9 ^ 2 ^ 3
JL4 .1 4 .
7
v20. .
4. . . 3 . 17 .31. 9
. . .)
SOLUTION NUMBER 17 A.V
.1 3 . 17 . 1 5 .
w
I
related by either a centre of symmetry or a mirror plane.
8 5
10. 8 .5 . . 6.2 1 .
4 .2 .
0. "NaT
1 ° . .1 4 .
.
5.1 1 .
. . .2 9 .8. 8 . 4.12 .39.20.1 1 . . . 12. 2. . . 18\^
5
2
.a?. 3 6
1 2
3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
13 7
20 27
0 15 21 24 7' 9 5
14
27 .1 . . 10
21 22
23 24 25 26 27 28
19 2
11 15 18
3 9 6
8 4.
7 .42 . 10
c
if.2 7 .8.27. 6 . The solution shown in fig.
3 10 11 23
7
V 3 9 .2 9 .
. 4 .
12
6 5 7 1 2 7 10
.19 . .2 9 .3 . .
7 .1 2 . 16.
1. . 4 6 . 11.0. .12 .10 . 12.3 .10 .330.1 2 .10 . 12 . 1 0 .1 and CFOM = 1.19. . (Solution 17 from table 8. . 11 • 2 l 20. CFOM = OUTPUT WITH Y HORIZONTAL AND ORIGIN
The determination of crystal structures
314.
. .15 . 9. 27 ) 5 \ 1. 1 . 122. 2 .13 .0 TOP LEFT 10
0
1 . 3 . 5 .1 1 . 17.4 2 . 5 . 1
3. 2
3. 18 ~
r
3
1. 2.
. . 8 .
11.
• J
?> 5 . 15 . . 13 . .1 .1 1 S 9.2 .
6
6.
9.
.1 0 .3 . . 1 8 W 4 . 2 . 7.1 3 . 4 . 2.2 0
6 15.1 0 . . . 23
2. . . 8 5 . 2 .
9. . 7 7. 13 . 7 . 5 . 5 .4 .) " 3 .
1 15
( 14.2 .
7
{ r'i3. 1 0 .40 two enantiomorphic structures are illustrated.1 4 . 3. 10 . .
1.18 . .
2 12
. 3.
11
7. in this case the molecules in the two enantiomorphs are related by a mirror plane.1 5 .^22.
7. \~ '
2
. .2 9 . . 5
. 1. 9
.16.
4. 23.9 .
0. /o.1 . .8 . .
1. .
3.
2 .
fX
fsO* *32 •1
V
2. 9 . . .1 3 .8.
y4l) ' 5 .
.
2 13 6 3 2
IS.7
11
4
. 10. 13 . 19 T . Z. 27 •1 0 .11 with .1 . 2.1 4 . . . 16. 2.
8.6 .
2 3 ^ 1 3 .
• t}\
. 8
6 16
4. . 15
9 .1 5 . 3 . . 7 . . 18 .3 . .
*v
. . . 1 4 . 7 .
\^—
1 .12. .
where high resolution (~ 1 A) data of good quality are available it has been shown that small proteins with up to 500 or so atoms in the asymmetric unit can also be solved by direct methods. metallic alloys and minerals are often threedimensional frameworklike structures and frequently they involve arrangements of atoms in special positions.unlike isomorphous replacement where the addition of a heavyatomcontaining group somewhat distorts the structure so that isomorphism breaks down at higher resolutions. the Patterson method. 8. have led to tremendous advances in the subjects of biochemistry and biophysics. perhaps to the point where it may become the method of choice. The oldest of the systematic approaches. However the widescale availability of synchrotron radiation is changing the pattern in macromolecular crystallography so that the use of anomalous scattering should increase. On the other hand. even for tackling structures of very great complexity. iron. Indeed. as molecular structures. An illustration of enantiomorphic structures in two dimensions. or pseudoorganic. structures. for example.40.direct methods are usually used because they are so automatic. they are clearer for demonstration purposes.9 A general survey of methods Fig. calcium or even sulphur. This is partly because the majority of structures solved are of this type and also because. Many native proteins contain atoms suitable for anomalousscattering experiments. applied to proteins and other macromolecular structures. For most smalltomedium structures .8. The examples given in this chapter have tended to be organic. The methods which have had the greatest impact on structural crystallography are the heavyatom method and that of isomorphous replacement which.up to 150 or so nonhydrogen atoms in the asymmetric unit . and anomalous differences can be relied upon to the resolution limits of the data . still has an
.9
A general survey of methods The range of methods available to the crystallographer represents a formidable armoury.
297
8.
1 The caxis Patterson projection of the structure of cuprous chloride azomethane complex (Cu 2 Cl2 C 2 H2 N 2 ) is shown infig.600). C (0.0.0 A ~ 2 . (v) Calculate a Fourier synthesis with program FOUR2 and data file SF.875. C (0.3 A structure which is isomorphous with that described in Problem 8.375.0. (iii) Use ISOFILE to find the coefficients of the difference Patterson and place them in data file SF.4 A twodimensional structure. C (0.2 has sulphur replaced by oxygen.500). again for X = 1.200). (i) Calculate the structure factors for the sulphur compound for X = 1.0.656. C (0.0. C (0.542 A with temperature factor B = 2.0.0.350). The space group is P\ with one molecule per unit cell. (iv) Use the program HEAVY to produce a data file. SF. b = 5 A and y = 95°. 8. (iii) Run FOUR2 with SF.150.298
The determination of crystal structures
important role to play.542 A and temperature factor B = 2. (i) Calculate structure factors for this crystal.175.41.
Problems to Chapter 8
8.469.563. C (0.350.125.375.650).DAT. (i) Calculate structure factors with STRUCF AC for Xray wavelength k = 1.500). (iv) Use FOUR2 to calculate the difference Patterson.600).0. S (0. Solve the crystal structure as completely as possible.600).0. 8. An isomorphous compound exists with oxygen replacing sulphur.DAT to give a difference Patterson and locate the ir atom.750). putting the result in data file SF2. C (0.DAT. for example it can be used to locate heavy atoms as the first stage of solving a complex structure. There are also available very powerful imageseeking Patterson methods which often succeed when direct methods have failed.0. Confirm that
.542 A and temperature factor B = 2. (iii) Calculate the contribution of the S atoms with STRUCFAC.813.0. C (0. with a = 10.0. (ii) Calculate a Patterson function with FOUR2 and find the position of the S atom.0 A" 2 .0. C (0.750). (ii) Run program ISOFILE to give coefficients for a difference Patterson in an output file SF. as sometimes they do.300).DAT. space group pi with a = 8. C (0.DAT. has atoms with the following coordinates: S (0.800).DAT to find the remaining atoms.313. b = 5 A and y = 98° has the following content of one asymmetric unit: S (0.0.075. 8.DAT with the phases given by S and structure amplitudes with centrosymmetric heavyatom weights.0 A " 2 using STRUCFAC and place the results in file SF1.2 A twodimensional structure of space group p2.325.850). (ii) Similarly calculate structure factors for the oxygen compound and place in file SF2.300).0.8.DAT. S (0.
639.41.500). 0(0. (iii) Use the output file from ANOFILE as input to FOUR2 to generate an anomalousdifference Patterson map.9 0
299
\ 0
\ 0. (vii) Use the program ISOCOEFF with the data files SF1.111. 1.6
\ 0.778.7 0. b = 6.500.0.292). 8.0 A and y = 98°. 1.472.8
\ 0.0.1 0.9
\ 0
this can be interpreted as vectors from the three ir atoms.2 0.DAT and SFIRB. 0 0.500).167). (v) Calculate structure factors for the sulphur atoms alone and place in data file SFIRA.0.Problems to Chapter 8 Fig. (ii) Use the datafilefrom STRUCFAC as the inputfileto ANOFILE to generate anomalous difference coefficients.8 0.1
\ \ \ 0. C (0.3 0.2 0.611.7
\ 0.0.3 0.DAT. C (0.846. (i) Calculate structure factors with STRUCFAC including the anomalous contributions from sulphur.250).500). (iv) Interpret the map to show that it is consistent with the peak between the sulphur atoms.389. N (0. 0(0.5 0.500.5 Data is taken for the structure described in Problem 8.667).DAT. (i) Calculate structure factors for k= 1.DAT.DAT to generate the Fourier coefficients of a map which should show the carbon atoms.0.936 A) is used giving anomalous scattering from the remaining two sulphur atoms with/ x = 0. space group pi with a = 9.6 0. SF2. C (0.1).0. (vi) Calculate structure factors for the oxygen atoms alone and place in data file SFIRB.0.833). O (0.6 A twodimensional structure.4
\ \ 0.833). has atoms with the following coordinates: Hg (0.542 A using STRUCFAC
. The caxis Patterson projection of Cu 2 Cl 2 C 2 H 2 N 2 (see Problem 8.625).167.0. SFIRA. C (0. C (0.0.4 0.DAT.385 and/ 2 = 0.0.0. Fe Kax radiation (2. = 1.333.5 0. (viii) Use FOUR2 with the output file from ISOCOEFF andfindthe carbon positions.4 with the modification that the second sulphur atom is replaced by carbon.
0. has atoms with the following coordinates: 0(0.792).8 A twodimensional structure.0.0.583).389. (ii) Use the output file from STRUCFAC as input to PSCOEFF to generate Fourier coefficients for a Psfunction map. C (0. 0. C (0.7 The aaxis projection of dicyclopentadienyldiiron tetracarbonyl (Mills.0 A and y = 100°. 1958) has twodimensional space group pgg.167).5.12.278.9.0.12. (ii) Use FTOUE to produce a data file with £'s.139.0. (i) Calculate structure factors with STRUCFAC.1 and/ 2 = 8. space group p2 with a = 9. b = 6.300
The determination of crystal structures
with anomalous scattering for the mercury atom for which fx = . C (0. (iii) Use the E datafilewith MINDIR to find a directmethods solution of the structure.306. (iii) With the output file of PSCOEFF as input to FOUR2 calculate a P s function and find the positions of all atoms relative to the mercury position. C (0. The values of 1001 U \ are listed in table 8.167.
k
2 4 6 8 10 12
I
0 0 0 0 0 0
100 C/ 43 6 33 40 33 16 33 36 1 6 9 10 44 6 32 21 16 28 14 18 15 27 22
k 4 5 6 7 8 9 10 1 1 12 1 3 1 2 3 4 5 6 7 8 9 10 1 1 12 13
/ 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3
100 t/ 1 3 32 6 17 1 3 16 6 33 0 21 36 34 20 30 31 20 37 1 1 27 21 6 21 0
k
0 1 2 3 4 5 6 7 8 9 10 1 1 12 1 2 3 4 5 6 7 8 9 10 4 4 4 4 4 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 5 5 5
100 U\ 40 17 42 2 5 1 1 28 5 40 1 1 24 15 0 17 12 13 31 0 12 20 0 36 12
k
/
1001 £/ 1 1 13 8 10 29 0 26 0 0 7 21 100 24 13 31 4 9 16 38 0 28 0 0
1 2 3 4 5 6 7 8 9 10 1 1 12 13
L L L L L I I I
) o :
i : I I 2 : ) 3 :
11 5 0 6 1 6 2 6 3 6 4 6 5 6 6 6 7 6 8 6 9 6 1 7 2 7 3 7 4 7 5 7 6 7 7 7 0 8 1 8 2 8 3 8 4 8
. By the use of inequality and sign relationships determine signs for the large l/'s. (Note: for this space group Pom = ("~ 1) Foki) 8.0.333).583).
Table i $.389. C (0.333). 8.
van der Waals distances.1. However the accuracy with which these quantities can be determined will depend not only on the accuracy of the atomic coordinates but also on the accuracy of determination of the unitcell parameters.002 A in a bond of length 1.
+ 2hla*c* cos jS* + 2klb*c* cos a*. By oscillating an orthorhombic crystal about an a axis in such a way that the centre of the oscillation range has the c axis pointing at the collimator one will record equivalent reflections (0/c/) and (Ofe/) on the zero 301
.29) we have
6
= h2a*2 + k2b*2 + / 2 c* 2
S=
A. In a method proposed by Farquhar and Lipson (1946) a singlecrystal photograph is taken with a camera arranged as in fig. By the measurement of layerline spacings or from Weissenberg photographs one can usually measure cell edges to about 1 % and angles with an error of about \°. (9.1) Equation (9. What will be done is to select an example of each of the main types of method to illustrate the ranges of techniques and accuracy which are available.1) takes on special forms for the various crystal systems.1
The determination of unitcell parameters
When a crystal structure is solved and refined the solution appears as a set of fractional coordinates from which can be determined bond lengths and angles. For some other purposes more accurate unitcell parameters may be required . etc. This would correspond to less than 0. The collimator passes through a hole in the film so that reflections for 6 close to 90° are recorded near the centre of the film .9 Accuracy and refinement processes
9. 9A(a).500 A and rarely is this order of accuracy really required. The order of accuracy of cell dimension required to match that of coordinate determination is about one part in a thousand or perhaps a little better. Once the reciprocalspace quantities have been found they can be transformed into crystalspace quantities by the relationships in table 3. There has been a great deal of work in this field and it would be difficult to mention it all.for example for measurement of thermal expansion coefficients of crystalline materials or for investigating small changes in cell parameters with changes of composition of the material.not at the edge as is usually the situation. The basic idea behind all the methods is to measure the Bragg angle for a number of reflections. From equation (3. This is related to the reciprocallattice constants as follows.
The value of 9 for a particular reflection is found by measuring the distance x between equivalent reflections.302
Fig. (a) The arrangement of the film in the Farquhar and Lipson camera. (b) A symmetrical oscillation diagram for the Farquhar and Lipson technique. The collimator passes through the central hole and highangle reflections are near the centre of the film. 9.9.9A(b) and the zero layer on the straightenedoutfilmis represented infig. (c) The appearance of the zero layer of the film.9.1(c).
Accuracy and refinement processes
Collimator
I II
M
O
(c)
I
I
II
II I
layer symmetrically disposed about the centre of the film.1.1 (a) that
. The indexing chart for a photograph produced in this way is shown infig. If the camera radius is R then it is clear fromfig.
This provides the basis of an extrapolation technique to eliminate errors due to this cause. Optical goniometry (Groth. The graph for this is shown in fig. At lower angles the lack of resolution leads to a fuzziness of the spot on the film.1
The determination of unitcell parameters
303
The values of 9 are measured for a number of highangle reflections. The overall accuracy of the method is about 1 part in 20 000 if care is taken in measuring the quantities x but even if the x's are measured more roughly.0003 kX. (iii) As will be seen from fig. (ii) At high angles the a x a 2 doublet is resolved and the position of the reflection can be measured more precisely. 1910) gave the axial ratios as a:b\c = 0.3)
Farquhar and Lipson illustrated the method by determining the axial lengths for thallium hydrogen tartrate.2(a) and the scatter of the points was taken as an indication of an incorrect ratio c/b. This can be seen from d(sin0) = cos0d0.9. with a steel scale for example. one finds —k2 + / 2 cosec0.7275.1(b) the highangle reflections will be those for large values of / and low values of k.9099 ± 0. (9. 9. 9. From equation (9.00202 A and was used before Xray wavelengths had been precisely related to the centimetre.2(b) was obtained and extrapolation to 9 = 90° gave the value c = 7. However the effect of errors in x or R can be seen to diminish and to tend to zero as 9 • n/2. The advantages of this are: (i) Since x will be comparatively small the effect of film shrinkage is minimized. The a and b axes were similarly determined and Farquhar and Lipson discussed the extension of the method to the measurement of unitcell parameters for monoclinic and triclinic crystals. The unit kX is given by l k X = 1.4) were plotted as a function of sin2 9. (9. not 9. For a ratio c/b = 0.6976:1:0.4)
With the value of c/b given by Groth the values of 9 were measured for a number of reflections and the values of c calculated from equation (9. for the Okl reflections of an orthorhombic crystal. and for a given error dO the error in sin 9 reduces as 9 > 90°. an accuracy of 1 part in 500 is still attainable. A new principle for measuring unitcell parameters was introduced by
. 9. They are therefore very suitable for precisely determining the value of c since a small error in b will not matter very much. (iv) The quantity which appears in equation (9.71975 however the graph in fig.1) is sin 9.1).
As used by Weiss et al. The crystal was then moved by steps of \° within this range to locate the position even more closely and finally intensities for a fixed exposure were recorded at steps of 3' with a very finely collimated beam of Xrays to find the position of maximum reflection.71975
7. The apparatus was accurately made and a finely collimated incident beam of Xrays was used.4 the position of the reflecting planes is shown for the two positions of a (hOO) reflection. By measurement of (M)0). the angle between the a* andfo*axes. 9. the normals are along ON and ON'.90 sin20 (a)
0. In fig. the position of maximum reflection could be found to within + 1 ' .00
0. NON'. It should be clear from this figure that when the crystal is halfway between these two positions the a* axis lies along the direction of the incident beam.80
Weiss et a\. It should be clear from the figure that the angle turned through by the crystal. 1946).
Accuracy and refinement processes
7. for the two positions in which the reflection occurs.00
1
1
0.90 c/h = 0. equals 26. For crystals which reflect over 15' of arc.304
Fig. b* and c* could be found directly. (1948).92 059 0310
068
o o
* . (a) A Farquhar and Lipson graph for an incorrect axial ratio. This method was also used by Bond (1960) who used a counter to record the diffracted beam.90 sin20 (b)
0.80
1.7.7275 c/b = 0. This involved the measurement of the angle between two positions of a crystal when it gives the same reflection on opposite sides of the incident beam. In fig. with angles measured on the goniometer circle of the oscillation camera the method gave an accuracy of about one part in 104. 9.91
o
0210
049
7.3 the normal to the reflecting planes is perpendicular to the rotation axis and.2. 9. Corrections
.9099 kX
CD
o
X 7. One is thus able to measure all the reciprocalcell parameters and thereby deduce the realcell parameters.89
1. due to the finite size of the crystal and its mosaic structure. was first to locate the crystal position for the desired reflection to within 5° by taking 5° oscillation pictures. The technique used by Weiss et a\. (0/c0) and (00/) reflections the values of a*. Thus if the crystal is being rotated about the c axis and (hOO) and (0/c0) reflections are recorded then it is possible to deduce y*. (b) The improvement of the extrapolation when the axial ratio is corrected (from Farquhar & Lipson.
and gives an accuracy of better than 1 part in 103.9. The two reflecting positions with normals along ON and ON'. which are usually available anyway.1
The determination of unitcell parameters
Incident beam
305
Fig. Bond claimed an accuracy of about one part in 106.
. An automated instrument on similar principles has been built by Baker et al. The method rests on the fact that sin 6 can be determined for highangle reflections from the separation oia1a2 doublets. 9.
Reflected beam for position 2
Reflected beam for position 1
Position 2
Position 1
Fig.3.4. (1966) who have measured lattice parameter changes due to radiation damage and also coefficients of thermal expansion. A method proposed by Main and Woolfson (1963) is useful in that it uses information from Weissenberg photographs.
Reflected beam position 2
Unit cell in position 1
Unit cell in position 2 Position 1
Reflected beam position 1
were made for the various errors that could occur and the temperature of the crystal was kept constant. The accuracy claimed is one part in 107. Location of the a* axis from the two positions which give an (M)0) reflection. 9.
Putting s = 2 sin 6/1 and differentiating equation (9. The measurements on the films can be made very quickly with a travelling microscope and the parameterrefinement process is carried out by a standard computer program. Since there are more equations than unknowns one can find a leastsquares solution (see § 9.Wca*fo*siny*dy*.8) we find
from which sin0 may be found. 9.10)
Approximate values of the reciprocalcell parameters will be known and they can be used to evaluate the coefficients on the righthand side.1) by using the approximate lattice parameters.7) and (9. Although t cannot be measured very accurately. On the lefthand side one makes s equal to the measured value and ds = s — sc where sc is obtained from equation (9. d/J* and dy*.4). etc. (9./c/fc*c*sina*da* .
. The quantities a* + da*. (9.5.± ^ . For Cu Ka radiation and a camera diameter of 57.306
Accuracy and refinement processes
We write Bragg's law for Ka2 radiation as sin0 = ^ and for the slightly different wavelength of Kax radiation A0) = ^ .lhc*a* sin P*dp* . dft*.3 mm the relationship between sin 6 and t is shown in fig. To determine the lattice parameters. the value of sin 6 is determined much more accurately. perhaps with an error of 3% or so for a 1 mm separation.. From equations (9. dc*. are better approximations to the reciprocallattice parameters and can be used for the next cycle of refinement. doublet separations are measured on zerolayer photographs so that more doublets are measured than there are parameters to be determined.6) (9.5)
Subtracting and using the approximation sin ^A6 = ^A0andcos^A0 = 1 we have A0(cot 6 .7)
where t is the separation of the doublet on the film perpendicular to the camera axis and r is the radius of the camera. da*.8) (9. This process yields a set of linear equations in the quantities da*.A0) = A2/1 For a zerolayer Weissenberg photograph 2A0 = t/r (9.1) we find sds = (h2a* + hlc* cos p* + hkb* cos y*)da* + (k2b* + kha*cosy* + klc* cos a*)dfo*
+ (l2c* + Ikb* cos a* + lha* cos jS*)dc* .
With diffractometers.995
0.
0. The methods mentioned in this section are only a small selection of those available. The relationship between sin 6 and the separation of the aja reflections in a Weissenberg photograph. the running conditions of the Xray tube can be strictly stabilized and the number of counts in a given time will then be a measure of the
.998
307
Fig. (1960) 13. 9.980
t (mm)
An extension of this technique so that measurements on higherlayer photographs can be utilized has been given by Alcock and Sheldrick (1967). for example.985
0.990
0.5. 81850.9.2
The scaling of observed data 0. A number of papers from a conference on The Precision Determination of Lattice Parameters' at Stockholm in 1959 will be found in Ada Cryst.2 The scaling of observed data Thefirstproblem of the crystallographer in collecting diffraction data is to make sure that it is all on the same relative scale. 9.
the diffraction spots on differentfilmsmust be related to each other by empirical processes. a factor of three or so being the usual attenuation in going from onefilmto the one below. (Fm)r is the structure factor corresponding to scattering factors for atoms at rest and the exponential term is the DebyeWaller factor (§ 6.IB sin 2 0/P)
(9.1). The total intensity range of the spots may well be 100000:1. 9. the Lp factor (§ 6. Once the data have been put on the same relative scale then various corrections can be made to them . a film which showed the weakest spot would be too overexposed to measure the strongest.Thesefilmswill differ from each other in intensity due to the absorption of thefilmitself.5 which is that
Fig.9) they are still used in some laboratories and may make a comeback by the resurgence of the Laue method (§5. Although collection of data byfilmmethods has largely been superseded by diffractometer (§ 5.6.10). Film pack 1 Film pack 2 Film pack 3 Intensity 10 io
2
103
104
105
106
. Arranging three packs of three films to cover an intensity range 10 5:1. If the measured intensity of the (hkl) reflection is denoted by Ihkl then we have
= K  (Fhkl)r 2exp( . Even if one considers a single layer of data taken with a Weissenberg camera there are several numerical relationships to be established. By comparing the intensities of spots in the conveniently measurable range one can quite easily deduce a filmtofilm scaling factor. 9. and a film which gave the strongest spot at a convenient intensity would not show the weakest.for example for spot shape (§ 5. By remeasuring one particular reflection from time to time one can be sure that the scale of one's measurements is remaining steady.5).11) that the temperature factor B is the same for each atom and is isotropic. and absorption factor A (§ 6. It is implicitly assumed in equation (9. This will comfortably cover the range 100000:1 or even greater and provide enough common measurable reflections in successivefilmsto give welldeterminedfilmtofilmratios.11)
where K is some scale factor. which would be too dense. In general when a Weissenberg photograph is taken a pack offilmsis placed in thefilmholder .6).7) or imageplate methods (§ 5. when collecting data on film. The greatest range of intensity which can be comfortably measured on onefilmis about 100:1 (two units of density).308
Accuracy and refinement processes
intensity. The common reflections in intersecting layers will then provide the means of putting the data all on the same scale. A scheme for taking three separate photographs using a pack of threefilmsat a time is shown in fig. Normally.6. When threedimensional data are being collected then it is necessary to measure the data in layers taken about two different axes.2).very often threefilmsbut occasionally up tofive. In order to determine the values of K and B we can make use of the result in § 7.
Once the structure has been solved the observed data can be scaled to those calculated and the differences in the observed and calculated data then give a measure of the accuracy of the atomic parameters. The net shows one asymmetric unit of the reciprocallattice layer k = 0 and arcs of radius sin0/>l = 0.1(b) and a straight line through three of the points is shown. The values of ln«/ 0 >/iy are plotted in fig. In table 9. The innermost point has been ignored. this has been allowed for by taking E0 = 2Le while </#> is the average for the observable reflections. However.1. Such a procedure was first suggested by Wilson (1942) and the graph is known as a Wilson plot. etc. From equation (9. and the errors from this method of scaling are seen to be comparatively large.1 there are derived the values of \n((Ie}/?. If we consider together a number of observed intensities all within a narrow range of sin 9 then we may write from equations (9. The value of { J ^ ) f° r ^ e reflections which are not systematically absent is twice the average for a general reflection. Since the space group is P2Ja the (hOl) reflections only occur for h even.
(9.40.either a trial structure or a phaseset for the structure factors.3 Fourier refinement We have seen in chapter 8 that there are a large number of ways to solve a crystal structure.IB sin2 9/X2) (9.'0 is that computed for s = 2<sin2 9/A2}*. Infig.9. one needs only a rough scale to set about the task of structure determination. 1951) with intensities corrected for Lp and absorption factors. the number of reflections in the corresponding annular region is small but in any case Wilson gives reasons for not using data for low values of sin 9/X.12) the structure factor has been denoted as that for atoms at rest and the scattering factors will therefore be those tabulated for rest atoms..13) we find
Thus if the data are divided into ranges of sin 9 and ln«/0>/Z0) is plotted against sin2 9/X2 one should obtain a straight line whose slope is —2B and whose intercept on one axis is In K. are drawn.'d) for four ranges of sin2 6/A2. 9. 0.2. Let us imagine that a structure has been solved by a method that leads to
. 9. It is assumed in this table that <sin2 9/A2} is the average for the extremities of the range and the value of T.33.3 Fourier refinement
309
<J\I 2 >= £ / ? = £. The values should be approximately B = 4.3 and K = 0.12) </.0 and K = 0.9. initially.12)
In equation (9. From the graph one finds B = 2.1(a) is shown a reciprocallattice net for thefraxisprojection of salicylic acid (Cochran. Basically these methods give information of one of two types .13)
where </0> is the average of the intensities in the sin 9 range and Z0 is the value of Z for the particular mean value of 9.> = K(\Fr\2}Qxp(2Bsin2e/l2) .11) and (9.
10.310
Accuracy and refinement processes
Table 9.8 2.5 1448 206 1. 9.125 0.40 0.452
fu
3. (a)
f
p—
/1140
78 ^*
103
0
124
0
No
\ 16 \ \ 7\ \ 7 \ 58 0
A
A8
t 2 /
3
27'
1
4
176
285
0
52 /
112 /
104
9
188
216
0 \
\
475
8 /
I
414
49
334
1 6 6 \ 10
^72 \ 29^
A
21
?3C
262
56
1
ln
IT
1.9 2.5 /sin 2 0\ /sin 2 0\±
fo
\Y~ // \1T // \Y~
0.3 0.0 250 33 2.2
IF
.7.158 0.20.354 0. (a) Reciprocallattice net for the 6axis projection of salicyclic acid (Cochran.1 sin2* 0.95 0. 1951).40.71 0.0
2.8 1. (b) Wilson plot for the fraxis projection of salicylic acid.4 0.205 0.1.5 2.1
0.025 0.04
Fig.2 0.6 3.0 370 67 1.2 688 170 1.30. Calculations for determining the Wilson plot sinfl/A range 0.4 1.255 0.0 0.6
I n
Ve>
5.065 0.
the Fc's.30 for a noncentrosymmetric structure would indicate a satisfactory.1).9.16a)
If the structure is centrosymmetric this will appear as Pr = "pZ 5(h) I (fo\ I cos(27ihr)
h
(9. From the new positions another set of Fc's can be calculated and this will give a lower value of R. the F0's.3
Fourier refinement
311
a trial set of atomic positions . If observed structure factors are compared with structure factors calculated for a structure with the correct number and type of atoms in randomly incorrect positions the most probable values of R would be 0. first trial structure. The situation with a centrosymmetric structure is that the refinement process is terminated when the signs of the calculated structure factors are the same for two successive cycles.2TU1IT + i</>h}. To put the observed structure factors. as given in equation (8. on an absolute scale they could be multiplied by the factor K~* deduced from a Wilson plot (§ 9. In order to test the plausibility of the structure one would calculate structure factors and compare them with those deduced from the experimental data. An electrondensity map is calculated with the magnitudes of the observed structure factors and the phases from the calculated structure factors.586 for a noncentrosymmetric structure and 0.e.828 for a centrosymmetric structure (Wilson. Once an acceptable set of calculated structure factors is available a cyclic process of refinement can be initiated. 1950). or at least plausible. We can take as a rough rule that a value of R less than 0. This electrondensity map will indicate positions for the atomic centres which will be displaced somewhat from those originally inserted and the new atomic positions should be a better estimate of the true atomic positions.2) while the calculated structure factors. the reliability index.for example by an examination of a Patterson function.10 depending to some extent on the complexity of the structure and also on the accuracy with which the data were collected. once a trial structure has been obtained it is customary to determine the multiplying factor which puts the observed structure factors on an absolute scale as
where the summation is over all the structure factors for which Fc is found. typically. i. with noncentrosymmetric structure factors.
h
(9. The agreement between the observed and calculated structure factors is expressed by R. on the other hand. the phases change continuously and when to terminate the
. Pr = } l I (po\ I exp{ . The significance of the value of R depends on whether or not the structure has a centre of symmetry. After a number of cycles of this process the solution will converge and. In fact.02 and 0. should include a temperaturefactor term exp( — B sin2 6112) where B is also given by the Wilson plot.16b)
where s(h) is the sign of the calculated structure factor.40 for a centrosymmetric structure or less than 0. one will be left with an R somewhere between 0.
Imaginary axis
. in addition to this. (Fo\ the observed structure factor of index h.perhaps only for some subset of the data may give a rough but adequate picture of the structure from which a trial set of coordinates may be found and refinement initiated.18b)
Fig. We may now write
1
(9. i. If in the completely refined structure the phase angles <\>^ and 0 h are not very different then it is clear that (9. 9. The errors in the F0's will lead to an error in the electron density and we can estimate the extent of this. It has been assumed above that one began with a trial structure but the same process is valid if one starts with a trial phaseset instead. the limitation in the amount of data being collected. Let pr be the calculated electron density.18a) where (9. p'r be the electron density for errorfree data. that there should be many more items of data than there are parameters to be refined. there is also an error due to series termination. and F^ the errorfree structure factor.e.17)
In fig. It should be stressed that for effective refinement the problem should be greatly overdetermined . 9.that is to say. The Fourier synthesis with the trial phases .8 (Fo)h and F^ are depicted on an Argand diagram.8.312
Accuracy and refinement processes
refinement process is a matter of judgement. What are the underlying causes of error in this process? There will of course be errors in the measurements of the Fo's but. The observed structure factor (Fo)h with the errorfree structure factor Fh on an Argand diagram.
When X is the wavelength of the Xradiation being used then the explorable volume of reciprocal space is n(2/>i)3 and.10. If the structure contains 40 carbon atoms (Z = 6) and Q = 0.9.21) that
(9.21)
where M is the total number of terms in the summation and a(F) is the standard deviation of the errors in Fo which are assumed to be uncorrelated with the magnitude of Fo. since the volume of a reciprocal unit cell is V~1.18) r h exp(27tihT + i£h). If the standard deviation of pT from p'x averaged over the whole cell is o(p) then Mp)} 2 = (Apr)2 or a{p) = —o{F) (9. we find M = (32TI/3)F>1~ 3 . This gives ^(p) = J—HL {2(j(F).
h
(9.25)
We can now make some orderofmagnitude assessment of a(p).20)
In deriving equation (9.22) (9. For atoms which are not too heavy and for an average temperature factor one finds that
N
P(0)=^0. that is to say that the average error in
. For example with V = 500 A 3 .24) where Q2 is the constant of proportionality linking  AF 2 with  Fo \2 and P(0) is the value at the origin of the Patterson function.8 Z Zj.
(9.5) we can find that the probability distribution of Apr will be normal with a zero mean and a variance
W
h
2

(9. 1 = 1.14eA~3.20) and (9. (9.23)
Another assumption which could be made about the errors of measurement is that  A F  2 is proportional to F O  2 .20) the result was used that exp(ia) = 1.19)
From an application of the centrallimit theorem (§ 7.23) that <7(p)=^0.17) and (9.54 A and a(F)=^ 1 electron we find from equation (9.3
Fourier refinement
313
Combining equations (9. From this assumption one would have from equations (9.
27)
The slope of Ap may be assumed constant over a small range so that
(9 28)

In addition. What will affect the peak position will be the gradient of Ap in the vicinity of the atomic centre.31)
Fig. The shift in a peak maximum due to the gradient of the error in electron density.
. If the maximum is displaced a distance AX from the true atomic centre.9. and a uniform raising or lowering of the electron density in the neighbourhood of an atomic peak would not affect the precision with which this could be determined. However in normal circumstances what one is concerned with are the atomic coordinates. from Taylor's theorem (9. then one has for a maximum of p + Ap
]
JX=AA:
=
°
=0.26)
or . is given by the wellknown result
c
d2p/dx2 {l+(dp/dx) 2 p
(9. Cx.314
Accuracy and refinement processes
measuring a structure factor is of the order of 10% of its magnitude.29) Now the curvature of p.9 which shows p and p + Ap in the vicinity of a maximum of p which represents the atomic position. we find a(p)^ 0. taken as the coordinate origin.9.30)
and at the atomic centre where (dp/dx)x = 0 = 0 this gives (9. 9.9. The actual errors of electron density would be of interest if one was looking for evidence of a redistribution of electron density in some particular chemical bonding situation.15^ A" 3 .
(9. This can be seen in the onedimensional example infig.
where /imax is the 'index' (perhaps nonintegral) corresponding to sinfl = 1.36)
where o(F\ the standard deviation of the errors in the Fo's.35)
h
k
I
The origin of the unit cell has been placed arbitrarily at the centre of the atom of interest.2 so that
V2 = 0. This ratio may easily be found to be equal to 0. In fig.38) (9.34)
h
k
I
which gives
= G'o = p E Z E . we obtain (9. is assumed not to be correlated with  Fo  and M is the number of terms in the summation. From equation (9. A few moments study of this should convince the reader that (/i2/^max) i s ^ e meansquare distance in a sphere of unit radius from a diametral plane. 9. Thus. 8 ^ .10 there is shown the limiting sphere with the various layers of constant h.
V
(9.. Hence the error in coordinate will depend on the slope produced by the electrondensity errors at the atomic centres and one can make an assessment of the magnitude of this on a statistical basis.2™h I AF*i IexpG&H).37a)
and. with the value of M found previously.2ra(/tx + ky + Iz) + iZM}
V
(9.z = p i l l I AFm I exp{ ..19) in terms of the individual Cartesian coordinates we have *Px.37b)
.2/JLX (9.3
Fourier refinement
315
From this we find ^
0
Go
(932)
The general threedimensional result corresponding to equation (9. since /imax = 2a/A then h? = 0 . If we write equation (9.9.35) we can deduce that G'o should have a normal probability distribution with zero mean and with standard deviation
9JT
G{G0) = —{Mh2fo(F)
(9.32) replaces differentiation by partial differentiation thus
One can find a good estimate of C o by assuming that the atomic peak changes position but not shape so that C o is the curvature at the centre of the 'perfect' electrondensity distribution.
This gives (9.40). In equation (9. To change this to rate of change of electron density per unit distance along the x direction. Hence
= 32. we must divide by the cell edge a. r is the distance from the atomic centre.
= 3
Accuracy and refinement processes
h = 2
I
h =
2
h=
3
where it should be noted that the units of G'o are rate of change of electron density per unit increase of fractional coordinate.316 Fig.32) and is
(9. from equations (9.41) gives a{AX)
_iHr«W'Y.6
VX
(9. the curvature at the centre can be found by differentiating twice with respect to r and then making r = 0.o(F) Zp \pj \VX
(9. 9. Go. Layers of constant h within the limiting sphere.39) and (9.42)
which.41) The standard deviation of the error of coordinate may be obtained from equation (9.43a)
.40)
where p is typically about 4 A 2 for an atom of moderate weight with an average temperature factor.10.39)
A representation of the electron density near the centre of an atom which is often found useful is
pr2)
(9.
t h atom can be expressed as (Bj + ABp xj + Ax.45)
The correct parameters for the . yj + Ayp zj + Azj) and hence we can write
N/2
f
sin 2 01 (9. .
(9. 9.v . For simplicity of our discussion we shall assume that the structure is centrosymmetric and the temperature factors are isotropic. with p = 4A~ 2 . will have diffraction ripples.
— G(F) Z
.4
Leastsquares refinement
317
or..47)
. + Iz.) + k(yj + Ayj)
+ l(zj + Azj)}l As long as the errors in the parameters are small this enables us to write (F0\u ~ (Fe)m = AFhkl and (9.^ j c o s ^ l M x .43b)
Thus with V= 500 A 3. + Ax.4 Leastsquares refinement Let us imagine for now that we have an errorfree set of  Fo 's and an almost correct set of atomic coordinates and temperature factors.)}.44)
where the twodimensional electron density is given by
The effect of series termination is rather less easy to deal with. it is as though the scattering factors for the atoms sharply terminate at 5 = 2/A and this means that the computed electron density for an atom. The calculated structure factors will be given by
N/2 /
s:n2
gx
(FXki = I 2/)exp I . instead of smoothly decreasing with increasing distance from the atomic centre. Z = 6 and a(F) = 1 electron then It can be shown that for a projection of area 91 the standard deviation of a coordinate error is
2n2
.
(9. These will be particularly disturbing round a heavy or even moderately heavy atom (sulphur for example) and the error induced in the coordinates of a neighbouring atom can be greater than that due to errors in measurement of the  Fo 's.46)
= I 2/Jexpj .54 A.
J
A
(9.(Bj + A ^ . X = 1. Effectively.BjjfJ
cos{2n(hxj + ky.9.
the quantity
h
h
(^)h}2
(949)
is a minimum. One such scheme proposed by Hughes (1941) takes co = constant for  Fo  < F l i m and co oc 1/ Fo  2 for \FO\> Flim where F l i m is some chosen upper limit of  F J for a constant weight. ignoring secondorder small quantities.48) can be produced for each reflection and. This solution is the one such that when the parameters are changed to Bj + ABp Xj + Axp etc.(F'X = AFh ."£ (J^ABJ
+ . From Taylor's theorem we find.48). in general. Another weighting scheme suggested by Cruickshank et al. When a reasonable set of weights has been found. each equation is multiplied throughout by the appropriate weight and a leastsquares solution of the modified set of equations is then sought in the usual way. The equations are linear in the corrections to be made to the parameters and.48) when the solution is inserted and it is the minimization of this quantity which is usually implied by the term 'leastsquares solution'. ideally.. there will be many more equations than parameters.48) An equation of type (9. if a subset of these equations was taken such that the number of equations equalled the number of parameters then the correct parameters could be found and recalculated values of the F c 's would then equal the F0's. Errors of measurement tend to be related to the actual value of  Fo  and many weighting schemes have been proposed based on the value of  Fo .). (1961) is co = (a +  Fo  + c\ Fo  2 )~ x where a^=2Fmin and c —2/F max . that
N/2
and hence
(F„)„ . However in practice the  F J ' s are not errorfree..
(9. If the measured  Fo  is expected to have a large random error then the value of AF may well be dominated by this and the AF may not be very useful in indicating the changes to be made in the atomic parameters. where (F'c\ is the revised calculated structure factor.318
Accuracy and refinement processes
(9. It is possible to weight the equations according to the expected reliability of the quantity AF. The quantity which is being minimized in this case is
.51)
Hence Rs is the sum for all the equations of the squares of the differences between the lefthand sides and righthand sides of equations (9. and so one finds a leastsquares solution of the complete set of equations (9.. where F m i n and F max are the minimum and maximum observed intensities. Thus for space group PT with 40 atoms in the unit cell and hence 160 parameters there could be 2000 or more independent reflections.
in the n unknown x's...52) A brief description will be given of the standard process for finding a leastsquares solution of a set of equations.55) is one member. Thus equation (9. The first equation of the normal set is obtained by multiplying each equation by its coefficient of x x and then adding together the modified equations.. This is illustrated below: a\1x1 alxal2x2 a\1xl + a21a22x2 alxalnxn = axlbx a21a2nxn = a21b2 (9. The solution of this normal set of equations is the required leastsquares solution of the original set.9.54) where A is the (m x n) matrix
al2ax
a
ml
a
m2'"amn
and x and b are the column vectors
and
The first step in the solution is to reduce the equations (9. of which equation (9.55)
Z \ Z flsiflSr
l ls=l
n
C m
=
Z
s=l
If this process is repeated by multiplying by the coefficients of x2..53) to a normal set of equations. x 3 .53) can be written (9.
.53)
A description of these equations is most neatly given in the terminology of matrix algebra. etc. In general there will be m equations for n unknowns xx x2. xn where m> n and these can be written as
a21x1 + a22x2 + •
«ml*l + am2*2 +
+ a2nxn = b2 (9.4
Leastsquares refinement
319
(9.. in turn there is obtained a set of n equations.
.56)
2l'"aml
a
A=
a
22'"am2
(9.57)
\n
a
2n'"amn
This gives as the solution vector for the x's
1
Ab
(9.5 The parametershift method The methods of refinement so far discussed occasionally run into trouble in unfavourable circumstances. If a projection is being refined and there is some overlap of atoms then Fourier methods are difficult to apply because of the interference of the overlapped atoms with each other. 9. is the parametershift method of Bhuiya and Stanley (1963). A fairly complete account of leastsquares refinement methods can be found in Computing Methods in Crystallography edited by Rollett (1965).un give a value of residual
. which works well even under the difficult circumstances described above.58)
where (AA)~l is the inverse matrix of A A. even in three dimensions where overlap is no problem the refinement process will not work if the trial coordinates are not very close to the correct positions. leastsquares methods are also difficult to apply in such circumstances and. These latter include a scale factor for the  Fo 's. Excellent standard computer programs are available which make the refinement process quite automatic once the data are provided. Further details of this are given in Computing Methods in Crystallography. the coefficients for anisotropic temperature factors and even the scattering factors themselves if it is felt that the quality of the observed data justifies this.. The technique of leastsquares refinement can be used for noncentrosymmetric structures and other types of parameter can also be refined. Again. From the final value of Rsw the standard errors of the final parameters can be estimated. Let us say that the structure can be described in terms of n parameters whose initial values ul9 u2..320
Accuracy and refinement processes
In matrixalgebra terminology the normal set of equations is obtained as AAx = Jib where A is the transpose of A and is the (n x m) matrix
a
(9.. indeed. A very successful method of refinement. In practice the crystallographer need not get deeply involved in the mathematical complexities of refinement by the leastsquares method.
. typically in the initial stages of refinement one would have k — 5 and Aux — 0. .02 A. The first parameter is shifted to the value which gives the lowest residual and the other parameters are treated in turn in the same way.37 and it was decided just to refine the coordinates for thefirstcycle. The initial value of R was 0.60)
which would not be valid for the large shifts which might be used.9. This has space group pgg and contains sixteen carbon atoms and two nitrogen atoms in the asymmetric unit..11. An example given by Stanley (1964) was the caxis projection of naphthocinnoline.37 to 0.33 in two cycles and then could refine no further. 9. un) = R(uuu2.5
The parametershift method
321
In the parametershift method the first parameter is varied in steps of Aut from ux — kAux to ux + kAux and the 2/c f 1 values of R are calculated for each value..02 A for both x and y and the progress w of the first refinement cycle is shown in table 9. It should be noted that the 2/c + 1 values of R are worked out by exact calculation and not by R(u1 + kAul9u2.11.2. whereas with the leastsquares method it would be unlikely that the parameter would climb out of the local minimum. The steps can be quite large. at the end of the range of investigation. Once the complete set of parameters has been shifted in thefirstcycle one begins again with uv As the residual is reduced so the steps Au are also reduced since the parameter space must be explored more closely as the correct values are approached. 9. dR —kAul9 cu1 (9. The parametershift method is very fast in application and the time taken by the computer is proportional to the product of the number of parameters
Fig.. The residual R as a function of parameter shift showing the parameter at a false minimum.5 Al When leastsquares refinement was tried on this projection it reduced R from 0.
N
2
1
. The advantage of this method is that it can move atoms away from false positions which give a local minimum of R.... the parametershift method would move the parameter to N. The values of k and A were 5 and 0. It turned out when the refinement was complete that the rootmeansquare displacement of the atoms from their initial positions was 0. The refinement was very rapid and all the atoms were displaced to the extreme end of their permitted range for at least one of the coordinates. This is shown in fig.
The unit cell contains four molecules of C 7O 3 H 6 .2.10 0. The ratio a:b determined by optical goniometry is 0.21. The diameter of the camera is 57.3185 0.5 observed (hkO) intensities. The leastsquares method.
Atom no.3425 0.2 A monoclinic crystal is mounted so as to rotate about the unique b axis and a beam of Cu Ka radiation is directed on to the crystal normal to the rotation axis.10 0.2898 0.10 0.10 0.3549 0. Use a Wilson plot to put
. of salicyclic acid (Cochran.10 0.3091 0. If the angles between reflecting positions on opposite sides of the incident beam for various reflections for Kax radiation were as given in table 9. which involves eventually the inversion of a matrix of order n.10 0.3651 0.2994 0.7500.10 0.3045 0.10 0.02 0. The space group is P2Jc with a = 11. the number of parameters.3.3593 0.10 0. on the other hand.3233 0.4. determine a and b.52. 9.10 0. b = 11. takes a time proportional to n3.5418 A) and the distances between equivalent reflections on the film are as given in table 9.10 0. 1953).
Problems to Chapter 9 9.3277 0.10 0.10 0.3 There are given in table 9. c and p.1 An oscillation photograph of an orthorhombic crystal is taken on a camera modified in the way described by Farquhar and Lipson (1946).06 0.10 0. find a.10 0.2947 0. where one often uses approximate methods of solving the normal equations. it could be argued that the parametershift method should be used instead.10 0.92A and ji = 91°. corrected for Lp and absorption factors. in the early stages of leastsquares refinement.10 0.10 0. c = 4.10
R
0. Because of this.08 0. If the radiation used is Cu K04 (1 = 1.10
Ay(A)
0.3323 0.322
Accuracy and refinement processes
Table 9.10 0.10 0.3449 0.10 0. 9.10 0.06 0.10 0.3376 0.
Ax(A)
0.2850
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
and the number of reflections.10 0.10 0.10 0.08 0.10 0.3 mm and the crystal is oscillated about the c axis.3497 0.3138 0.08 0.10 0.
3.18 32. the unit cell has volume 300 A3 and the rootmeansquare error of the observed structure amplitudes is 0.400).100.83 24.5 electrons and is not correlated with the magnitude of  Fo . Calculate structure factors for these coordinates with the same B and X as in (i).4 (i) Estimate the rootmeansquare error of electron density when data are taken from a crystal with Cu Ka radiation (X = 1.0 A ~ 2 and Xray wavelength X = 1.542 A.0. 0.0.150).200.950.4.0.3.5 (i) Calculate structure factors with STRUCFAC for the synthetic structure C 3H5 N2ONa 2. (ii) Under the conditions of part (i) what would be the rootmeansquare error in the x coordinate (in A) for a carbon atom when the electron density near the maximum is given by equation (9. N (0.83 38. C (0.480.400.
h 1 1 1 1 6 6 k 1 2 3 / 0 0 0 0 0 0 Distance (mm) 51.6A"2? 9.0. C (0. 0(0.54 A). Take the temperature factor B = 2.000.20
4 5 6
Table 9.
h 3 4 5 0 0 0 0 3 4 /c 0 0 0 0 0 0 0 0 0 / 0 0 0 4 5 6 7 4 5 Angle 64° 31' 90° 46' 125° 42' 61° 9' 78° 56' 99° 24' 125°41' 129° 4' 85° 15'
the data on an absolute scale and also determine an overall temperature factor.200).09 46. Na (0.350. This gives simulated observed structure amplitudes.0. 0. the coordinates for which are given in § 8.40) with /7 = 3. 0.000). This gives calculated structure amplitudes and phases.275). C (0.400).600). (ii) Approximate coordinates are available as follows: Na (0.50 50.Problems to Chapter 9
323
Table 9.
. 9. N (0.650).200.
(vi) Calculate structure factors for the new coordinates. Use this program with the output from (i) and (ii). h
0
k
/
h 2
k
13 14 1 2 3 4 5 6 7 8 9 10 11 12 13 14 0 1 2 3 4 5 6 7 8 9 10 11 12 13 1 2 3 4
/ 5 0 1 407 23 28 226 94 31 0 2 1 9 34 1 1 260 35 63 9 17 61 263 2 7 26 1 69 0 0 134 3 22 107
h 5
k
5 6 1 8 9 10 11 12 13 0 1 2 3 4 5 6 7 8 9 10 11 12 13 1 2 3 4 5 6 7 8 9 10
/
126 21 5 16 11 8 2 0 1 300 67 124 21 19 10 23 18 4 10 4 1 0 1 92 134 40 6 19 22 2 3 0 3
h
k
/ 0 1 58 2 43 11 76 19 27 7 11 7 0 0 0 0 6 35 86 9 7 3 11 0 0 0 22 0 1 18 98 18 17
h
10
k
1 8 9 10 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 1 2 3 4 5 6 0 1 2 3 4
/
11 4 2 1 1 0 1 0 19 13 0 9 1 1 2 1 0 4 1 2 8 10 4 7 2 0 3 0 5 3 3 2 1
1
2
2 142 4 246 6 63 24 8 1 10 1 12 14 0 1 529 2 112 14 3 4 83 7 5 6 225 67 7 8 0 2 9 10 19 11 6 6 12 0 13 14 1 0 211 1 1140 4 2 13 3 4 194 3 5 6 122 47 7 42 8 2 9 10 50 11 10 12 38
3
6
4
7
5
1 11 12 8 0 1 2 3 4 5 6 7 8 9 10 11 12 9 1 2 3 4 5 6 7 8 9 10 11 10 0 1 2 3 4 5 6
11
12
13
12
(iii) A program CALOBS is available (appendix XII) which combines the observed structure factors and calculated phases in an output file suitable for input to FOUR2 and also gives a reliability index. (vii) Using CALOBS find the new residual.324
Accuracy and refinement processes
Table 9. (v) Contour the map and find new estimates of the coordinates. (iv) Using the outputfilefrom CALOBS as input to FOUR2 calculate a map.
.5.
Thus the millimetre (mm) is an acceptable unit. Field E due to charge q at distance r is given by
4nsor2
where e0 is the permittivity of free space.602 x 9.675 x 6. The force on a charge q in a field E is given by F = qE.381 x 6.110 x 1.854 x 10" 19 C 10" 31 kg 10" 27 kg 10" 27 kg 1023mol~1 10" 2 3 JK" 1 10" 34 Js 10" 19 J 108 m s ~ * 10" 12 F m ~ * 325
.022 x 1. The electricfield amplitude £ in a beam of electromagnetic radiation of intensity / is given by cs0 Some useful physical constants: electron charge electron mass atomic mass unit proton mass Avogadro's number Boltzmann's constant Planck's constant electron volt speed of light permittivity of free space 1.Physical constants and tables
Among the basic units used by the SI system are the following: length mass time current Some other metre kilogramme second ampere units derived
m
kg
s A
from these are:
newton N = kgms" 2 force J = Nm energy joule W ^Js"1 power watt electric charge coulomb• C = As V = WA" 1 electric potential volt electric capacitance farad F = Acceptable multiples or submultiples can be used which differ from the basic unit in steps of 103.626 x 1.998 x 8.660 x 1.602 x 2.
6 56.241 2.22 34.462 1.114
7.544 0.82 9.7902 1.483 0.44 8.2 108 Br 30.76 2.21 8.397 1.90 2.6 115 152 144 190 234 305 Hg 47.740 0.31 2.70 11.40 2.376 0.250 5.2909
0.60 5.34 6.56
17.47 4.91 13.64 31.366 0.00 11.400 0.07 7.96 5.481 0.5 114 108 142 175 229 S 3.600 3.99 6.000 7.65 3.7 0.31 5.545
The mass absorption coefficients in SI units (m2 kg l) are onetenth of the tabulated values.000 0.0848 2.34 8.8 42.2 0.000 2.9 1.010 2.44 4.0 66.23 9.27 4.00 14.48 67.7565 1.70 23.581 2.4 79.11
16.404 0.8 70.71 8.84 11.52 1.33 12.426 1.25 1.320
6.21 2.071 0.570 0.00 9.944 1.17 10.571 0.71 2.00 1.010 0.60 4.3 0.8 16.421 0.333 0.00 23.54 6.07 6.700 0.52 8.3922 1.9 O 0.00 32.2 74.6208 1.59
10 x Mass absorption coefficients fi/p(m2kg
H Li 0.56 4.811 0.67 5.5418 1.19
80.67 2.502 1.65 47.64 3.02 4.4 99.9373 2.83 7.76 8.Scatteringfactor table
sinO
Li
N
O
Na
Al
Cl
Fe
Br
Hg
0.96 C 0.6 Na 1.00 13.000 5.000 6.944 1.187 0.01 5.215 1.512 1.495 0.2 48.33 11.31 38.
.7107 1.8 46.0 19.177 0.77 13.6 18.350 1.916 5.015 0.68 20.89 55.9 93.094 3.0 58.71 5.41 9.29 3.269 1.374
11.22 1.3 Al 1.14 59.380 0.6323 0.550 1.714 1.77 8.14 11.0 106 122 161 152 200 246 318 Fe 14.80 1.7 38.00 9.444 1.338 1.69 4.2 74.98 1.5 238 308 349 52.8 36.7 58.5 0.263
8.16 36.47 7.322 1.8 0.1 64.7 87.88 3.60 6.040 0.31 7.0 14.218 1.1 85.82 4.4 27.650 0.464 0.507 0.8 50.7 27.823 0.0 0.685 1.64 7. The values come from the International Tables for Xray Crystallography and are in units (cm 2 g~ I ).00
26.443 0.1 34.90 11.00 15.27 15.126 3.4 82.566 1.5 95.371 0.84 6.88 6.5 89.52 11.04 42.9 116 152 P 2.203 4.0 14.3 30.950 1.433 0.2 23.28 3.29 6.78
13.44 4.55 66.83 5.51
35.8 22.513 0.024 0.77 5.435 0.217 0.43 28.625 3.6 0.31 8.459 0.8 79.007
3.47 9.85 4.5 44.5 13.15 3.1 0.200 0.64 5.31 52.89 5.93 10.16 7.9 117 166 216 245 312 298 377 446 547
AgKp AgKa MoKp MoKa CuKp CuKa CoKp CoKa FeKp FeKa CrKp
CrKa
0.59 7.09 16.716 0.5
*)
N 0.698 1.00 75.5608 0.84 18.69 8.98 1.634 4.130 0.43 27.741 1.82 20.536 1.6 11.32 3.71 3.21 22.032 0.0
1.60 7.8 74.78 11.99 7.03 0.3 17.251 0.6 72.32
15.09 5.4970 0.05 6.4 0.1 103 136 129 170 209 272 Cl 4.
cam.Appendices
The FORTRAN® listings given in these appendices relate to programs described and illustrated in the text and used for the solutions to examples. In addition.ac. Readers are advised to examine the listings before use as they are well provided with COMMENT. when running the programs users are guided by screen output and these should be carefully followed. C. In particular. statements which describe the workings of the programs. in that the output files from some of them become the inputfilesfor others. it is important that datafile names should be correctly given and in all programs it is possible to designate the names of the input files if the default values are invalid.html
327
.cup.Uk/onlinepubs/412714/412714top. These files can be downloaded free of charge from http://www. They are heavily interrelated.
1.5.1.1.1.0.0.0.0.IEND(20).0. 1 = 1.0.NATOM(I) THEIR COORDINATES .0.ATYPE(I) NUMBER OF ATOMS OF EACH TYPE IN THE ASYMMETRIC UNIT .5.1.1. FNAME*10 PARAMETER (PGG='pl p2 pm pg cm pmm pmg pgg cmm p4 p4m p4g p3 + p3mlp31mp6 p6m ') PARAMETER (ATOM='H LI C N O F NA AL P S CL FE BR HG END') THE FOLLOWING DATA STATEMENTS GIVE FOR ALL THE 17 PLANE GROUPS THE NUMBER OF ASYMMETRIC UNITS IN THE CELL AND CONSTANTS FOR CALCULATING THE POSITIONS OF ATOMS EQUIVALENT TO (X.0.(EQP(7.5.1.0/ DATA NAU(2).1.0.(EQP(4.(EQP(3.0.0/ DATA NAU(12).0.0.1. 0.NAU(17).1.0/ DATA NAU(4).(EQP(1.0.0.1.0.72).0.0.I).1.(EQP(6.0.0.0.12)/2.5.0.1.1.0.I).1.24)/4.0.0.0.0.1.0.5/ DATA NAU(10).5.0.1.0. F*X+G*Y+H).1. DIMENSION EQP(17.0.1.1. +1.0.5.1.0.0.0.0.0.0.1.0.0.0.0.0.I).I).1=1.1.0.1. IEND.PHI(1000).0.0.0.1.0.0.0.0.0.0.1.1.1.(EQP(9.1=1.0.HT * CHARACTER PGG*(*) .0.1.0.0/ DATA NAU(ll). +0.0.1.0.0.0.0.5/ DATA NAU(9).24)/4.48)/8. Y WHETHER OR NOT THIS TYPE OF ATOM SCATTERS ANOMALOUSLY IF SO THE VALUES OF F' AND F".1=1.0.1.1.5.0.0.1.0.0.0.0.0.0.0.5/ DATA NAU(6).0.0. 24)/4.0.5.1.0.0.1.0.0.5.1.I).0.0.24)/4.0/ DATA NAU(8).1.I).36)/6.0.0.0.0. F & PHI.0.0.1.1.1.0/ DATA NAU(7).0.0.(EQP(5. +0.1.0.0.1.1.5/ DATA NAU(5).5.1.0.0.0.0.1.0.1.0.1.KT(1000) INTEGER HMAX.1=1.0.1.(EQP(11.1.0.0.0.1.0.1.328
Appendices
C C C C C C C C C C C C C C C C C C C C C C C
C C C C
Appendix I PROGRAM STRUCFAC THIS CALCULATES STRUCTURE FACTORS FOR ALL THE 17 PLANE GROUPS.0.1.0.0.0.0.1.0.(EQP(13.5.1. DATA NAU(l).0.0.0.0.0.I).1.1.1.0.(EQP(10.5.1=1.0.0.0.0.1.1.0.1.0.0.1.0.0. THE INITIAL PART OF THE PROGRAM REQUIRES THE INPUT OF THE FOLLOWING INFORMATION: XRAY WAVELENGTH .Y(100)fF(1000).0.0.0. +1.0.0.0.XLAM CELL DIMENSIONS AND ANGLE .0.0. PLANE GROUP .18)/3.0.1.0.1.0.0.1.MTYPE(13)/NATOM(20). THE NUMBER OF DIFFERENT TYPES OF ATOM IS LIMITED TO 20 BY THE DIMENSIONS OF IBEG.0.0.5.X(100).1.I).0.X.24)/4.0.0.1=1. C.0.1.1.1.I).0.1.1.1.FP(20) +FPP(20). THE MAXIMUM NUMBER OF ATOMS IN THE UNIT CELL IS LIMITED TO 100 BY THE DIMENSION OF THE ARRAYS X & Y.(EQP(2.0. 0.(EQP(12.1.1=1.0.IBEG(20). +1.5.1.0.1.0.1.1.0.1.12)/2.0.1.1. GAMMA NOTE THAT OTHER PROJECTIONS CAN BE USED IN WHICH CASE A.1.1.1.0.0.0/ DATA NAU(3).1.0.0.0. FP AND FPP AND THE MAXIMUM NUMBER OF REFLECTIONS FOR WHICH STRUCTURE FACTORS ARE CALCULATED IS LIMITED TO 1000 BY THE DIMENSIONS OF THE ARRAYS HT.0.0. +1.0.(EQP(8. FOR EXAMPLE.0. B.1.1.0. +HT(1000). KT.1. +1.0.1=1. ASYMB*3 .0.1=1.1.1.0. +1.0.0.0.0. +1.0.0.I).0.1. BE REPLACED BY A.1. +0. P G M .0.0.1.0.1.0.1.H.0. GAMMA MAY.12)72. +1.1.1.0. IT WILL DO SO BOTH FOR NORMAL AND FOR ANOMALOUS SCATTERING.0.0.5/ DATA NAU(13).0.0.0.1.5.1.A# B.0.1.0.0.0.48)/8.5.0. 0.1. 0.1. ATOM* ( ) .0/ DATA NAU(14).0.1.1=1.1.0.1.0.1.48)/8.1.1.I).1=1. Q*4 .I).PG CONTENTS OF THE CELL IN THE FORM OF: TYPES OF ATOMS .0.1=1. BETA SO THE INSTRUCTIONS GIVEN BY THE PROGRAM WILL HAVE TO BE INTERPRETED ACCORDINGLY.0.0.1.I).0.5. Y) IN THE FORM (C*X+D*Y+E.1.0.1.0.0.0.0.0. +1.0.0.0.0.1.1.1=1.0.0.0.0.6)71.0.5.0.1.5.5.(EQP(14.0.I).0.0.5.5.1.0.0.0.0. 1. +1.0.0/
.0.0.0.0.0.1.1.
pmg.0. P.DAT' 68 WRITE(6.0.1. NA.1.1. p2.EQ. O. BR.1.0.1.1.0.0.1. pgg.0/
c
C OPEN (UNIT=9.0.0.1.ONE OF THE FOLLOWING '')') VIRITE{6.1.72)/12.I).' (" INPUT CELL DIMENSIONS A.1.1.0. p31m. pmm.I). p3.NE.1.OR INPUT END IF ALL ")') WRITE(6.1. WHICH CONTAINS H K F AND PHI '')') WRITE(6.0.0.'y')GOTO 66 IF(Q.0.1.1.1.0.1.0.0.1.0.(EQP(17.'(" INPUT THE NUMBER OF ATOMS OF THIS TYPE IN ONE '')') WRITE(6.1.0. 50) PG 50 FORMAT(A4) FORM IDENTIFYING INTEGER 1 TO 17 FOR PLANE GROUP NX=INDEX(PGG.EQ.DAT".0.'(// Note: use lower case symbols as shown '')') READ (5.0.1.1.0/ DATA NAU(16).1. +1.15)GOTO 33 A NEW TYPE OF ATOM HAS BEEN IDENTIFIED.1.0.0.0. FILE=FNAME) WRITE(6.1.0. N.0. C.0.0.1. pm.0.'')') WRITE(6.1.1.1.1.THE NUMBER OF DIFFERENT TYPE OF ATOMS IBEG AND IEND ARE ARRAYS WHICH FLAG THE FIRST AND LAST ATOMS OF THE VARIOUS TYPES IN THE COORDINATE LIST NTOTAT=0 NOTYPE=0 IBEG(1)=1 2 WRITE(6.0.0.1.'('' READ IN THE FILENAME [<= 10 CHARACTERS] '')') READ(5.0. p4g. F. NOTYPE=NOTYPE+1 MTYPE(NOTYPE)=NASYMB WRITE(6.1.NE.0.58)FNAME 58 FORMAT(A10) 67 OPEN (UNIT=10.1.EQ.0.'('' INPUT ATOMIC TYPEONE OF H.0.Q.0.1.'('' INPUT XRAY WAVELENGTH IN ANGSTROMS '')') READ(5.1.' {' ' pi.I). pg.1.Appendices
*29
DATA NAU(15).36)/6. +1.'(" THE OUTPUT FILE.1.OR.0.1. ' ( " ASYMMETRIC UNIT ' ') ') READ(5.1.NX)GOTO 1 NOW INITIALISE THE FOLLOWING QUANTITIES: NTOTAT TOTAL NUMBER OF ATOMS IN THE CELL.0.1. p6m '')') WRITE(6.0.1.GAMMA READ IN PLANE GROUP SYMBOL AND TRANSLATE INTO IDENTIFYING INTEGER 1 WRITE(6. +1. (EQP(15.0. 14 = HG. S.0.0.*)A.0.0.0. ASYMB) +2 NASYMB=NX/3 IF(NASYMB*3.0/ DATA NAU(17).1.0.1.1. +1.0. FE.1.EQ.*)XLAM WRITE(6.1.NX)GOTO 2 IF(NASYMB.0.1 = 1. 2 = LI.0./ (// IS NAMED "SF1. ' ( ' AND GAMMA IN DEGREES ' ')') ' READ(5.1. cm.0.1.0.0. DO YOU WANT TO CHANGE IT Y/N'')') READ(5.0.0.*)NATOM(NOTYPE) INPUT COORDINATES
C
C
C C C C
C C
C
C
. +1.0. NX=INDEX (ATOM.0.'n')GOTO 67 GOTO 68 66 WRITE(6.0.'Y'.1.1.0.0.1.50)Q IF(Q.36)/6.0.1.0.1.0.0. CL.0. HG .1=1.'')') WRITE(6.B.0.1.0.1.1.0.'N')GOTO 67 IF(Q.60)ASYMB 60 FORMAT(A3) GENERATE A NUMBER FROM 1 TO 14 TO IDENTIFY THE TYPE OF ATOM WHERE 1 = H.0.0.0.1=1.'(" INPUT PLANE GROUP .0.0.0.1. p6.B [IN ANGSTROMS '')') WRITE(6. LI.0.1. p4.'(" AL.1.1. ' ( ' COORDINATES HAVE BEEN READ IN " ) ') ' READ(5. FILE='LPT1') CHANGE NAME OF OUTPUT FILE IF REQUIRED FNAME='SF1.0. NOTYPE .'(" p4m.(EQP(16.0.PG)+3 NPG=NX/4 IF(NPG*4.0. OR 15 TO END INPUT. cmm.0. p3ml.0.EQ.0.
6*J2)*XX+EQP(NPG.ONE ATOM PER LINE '')') ' WRITE(6.' ( ' INPUT COORDINATES X.'y')GOTO 80 IF(Q. REFLECTIONS WITH k >= 0.EQ.NOTYPE 7 TESTAS=TESTAS+FP(I)**2+FPP(I)**2 ALL INPUT IS NOW COMPLETE.EQ.OR. Y .6*J1)*YY+EQP(NPG.'Y'. NOW STRUCTURE FACTORS ARE CALCULATED TO THE LIMIT OF RESOLUTION GIVEN BY THE XRAY WAVELENGTH.'('' IF YOU ENTER A COORDINATE INCORRECTLY THERE " ) ' ) WRITE(6.6*J5)*XX+EQP(NPG.'N')GOTO 3 IF(Q. FPP(NOTYPE) GOTO 2 AT THIS STAGE ALL ATOMIC COORDINATES HAVE BEEN INPUT IN CASE OF ERROR THEY MAY NOW BE DISPAYED WITH A POSSIBILITY OF CHANGING ANY INCORRECT ONE 33 WRITE(6.EQ.'('' IS THIS TYPE AN ANOMALOUS SCATTERER? Y/N'')') READ(5.6*J3) Y(NTOTAT) =EQP(NPG.6*J2)*XX+EQP(NPG.'(" IS AN OPPORTUNITY LATER TO CORRECT IT '')') DO 5 I=1 / NATOM(NOTYPE) READ(5.'n')GOTO 3 GOTO 33 80 DO 90 1=1.*)XX.OR.'('' INPUT REPLACEMENT X.6*J5)*XX+EQP(NPG.0*A/XLAM)
.330
Appendices
C
C C C
C C C
C
C C C C C C C
WRITE(6.NTOTAT. * ) XX.EQ. IF ANOMALOUS SCATTERING IS PRESENT THEN THE COMPLETE CIRCLE IS CALCULATED.6*J) 90 CONTINUE IF ONE IS NOT '')') 3 WRITE(6 / '(' / INPUT TEMPERATURE FACTOR.50)Q IF(Q.'('' DO YOU WANT TO INSPECT THE COORDINATES? Y/N " ) ' ) READ(5 / 50)Q IF(Q.*)BTEMP PROVIDE A TEST QUANTITY FOR THE PRESENCE OF ANOMALOUS SCATTERING TESTAS=0 DO 7 1=1.EQ. HMAX=INT(2.EQ.S FACTOR'')') READ(5. 6*J) 5 CONTINUE IEND(NOTYPE)=NTOTAT IBEG(NOTYPE+1)=NTOTAT+1 IF THIS ATOMIC TYPE IS AN ANOMALOUS SCATTERER THEN THE REAL AND IMAGINARY PARTS OF THE ANOMALOUS COMPONENT OF THE SCATTERING FACTOR MUST BE GIVEN 16 WRITE(6.Q. FIRST CALCULATE MAXIMUM INDICES.EQ.'Y'.6*J3) 72 Y(I+J1)=EQP(NPG.NAU(NPG) WRITE(6 / 200)X(I) # Y(I) 200 FORMAT(2F8.'Y '.EQ.50)Q IF(Q.6*J4)*YY+EQP(NPG.'y')GOTO 71 IF(Q.4) 70 W R I T E ( 6 / ' ( " DO YOU WANT TO CHANGE THIS? Y/N'')') READ(5.Y '')') READ (5 . WRITE(6.EQ.EQ.NAU(NPG) NTOTAT=NTOTAT+1 X(NTOTAT)=EQP(NPG.Q.6*J4)*YY+EQP(NPG.*)FP(NOTYPE). YY DO 72 J=1.OR. NORMALLY A COMPLETE SEMICIRCLE OF STRUCTURE FACTORS WILL BE CALCULATED ALTHOUGH THE ASYMMETRIC UNIT OF RECIPROCAL SPACE CALCULATIONS ARE FOR ALL INDEPENDENT MAY BE SMALLER THAN THIS.'N')GOTO 90 IF(Q.YY GENERATE COORDINATES OF ALL SYMMETRY RELATED ATOMS DO 5 J=1.'N ')GOTO 2 IF(Q.'('' REQUIRED THEN INPUT 0 '')') READ(5.Q. 6*J1) *YY+EQP(NPG.'(" INPUT REAL AND IMAGINARY PART OF A.EQ.'n')GOTO 90 GOTO 70 71 WRITE(6.'n ')GOTO 2 GOTO 16 6 WRITE(6.'y ')GOTO 6 IF(Q.NAU(NPG) X(I+Jl)=EQP(NPG.EQ.
OE4)PHI(NOREF)=0 10 CONTINUE WRITE(10.1.IEND(I) Z=6.0)GOTO 10 NOW CALCULATE (SIN(THETA)/LAMBDA)**2 AND CHECK THAT < SLIM SL2=CO1*H*H+CO2*K*KCO3*H*K IF(SL2. IF THERE IS ANOMALOUS SCATTERING THEN BOTH F(h k 1) AND F(h k 1) ARE CALCULATED.KMAX IF(K.F(I).1.0E12)GOTO 10 NOREF=NOREF+1 HT(NOREF)=H KT(NOREF)=K F(NOREF)=SQRT((SUMA+SMAASM)**2 +(SUMB+SMBASM)**2)*BTFAC PHI(NOREF)=ATAN2(SUMB+SMBASM.Appendices
331
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KMAX=INT(2. CO2 AND CO3 ARE USED FOR CALCULATING SIN(THETA)/LAMBDA COl=0.KT(I).0E12)GOTO 15 TEST FOR ATOM TYPE I AS ANOMALOUS SCATTERER IF(FP(I)**2+FPP(I)**2.GT.1.1.0174533) SLIM IS THE LIMITING VALUE OF (SIN(THETA)/LAMBDA)**2 AND NOREF RECORDS THE TOTAL NUMBER OF REFLECTIONS.H.LT.0.2958 IF(F(NOREF).LT.1=1.LT.SUMA+SMAASM)*57.25/B/B CO3=0.GT.LT.5/A/B*COS(GAMMA*0.PHI(I).NOREF)
.*)NOREF.0E12)BTFAC=EXP(BTEMP*SL2) F(NOREF)=SQRT((SUMA+SMAASP)**2 +(SUMB+SMBASP)**2)*BTFAC PHI(NOREF)=ATAN2(SUMB+SMBASP.2 831853*(H*X(J)+K*Y(J)) PSUMA=PSUMA+COS(Z) 26 PSUMB=PSUMB+SIN(Z) SUMA=SUMA+SCF*PSUMA SUMB=SUMB+SCF*PSUMB TEST FOR PRESENCE OF ANOMALOUS SCATTERING IF(TESTAS.0 IF(BTEMP. SUMA=0 SUMB=0 SMAASP=0 SMAASM=0 SMBASP=0 SMBASM=0 DO 15 I=1.SLIM)GOTO 10 SL=SQRT(SL2) NOW THE STRUCTURE FACTOR IS CALCULATED.(HT(I).NOTYPE CALL SUBROUTINE TO DERIVE SCATTERING FACTOR [SCF] FOR ATOM OF TYPE I FOR SIN(THETA)/LAMBDA = SL CALL SCAT(MTYPE(I)fSLfSCF) PSUMA=0 PSUMB=0 CALCULATE CONTRIBUTIONS TO REAL AND IMAGINARY PARTS OF THE STRUCTURE FACTOR OF ATOMS OF TYPE I DO 26 J=IBEG(I).LT.1.HMAX DO 10 K=0.0E4)PHI(NOREF)=0 IF(TESTAS.EQ.SUMA+SMAASP)*57.1.0E12)GOTO 15 SMAASP=SMAASP+PSUMA*FP(I)PSUMB*FPP(I) SMAASM=SMAASM+PSUMA*FP(I)+PSUMB*FPP(I) SMBASP=SMBASP+PSUMB*FP(I)+PSUMA*FPP(I) SMBASM=SMBASMPSUMB*FP(I)+PSUMA*FPP(I) 15 CONTINUE NOREF=NOREF+1 HT(NOREF)=H KT(NOREF)=K BTFAC=1.LT. SLIM=1/XLAM/XLAM NOREF=0 DO 10 H=HMAX.25/A/A CO2=0.2958 IF(F(NOREF).AND.O*B/XLAM) C01.
1.2.41.332
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WRITE(9.60.1=0.47.0.54.43.1.22.11.007/ DATA (SF(2.1.00.NOREF) 100 FORMAT(3(16.10)/I.1.31.16.43.84.34.10)/l6.878. +0.5.1. NA.4.404.07.71.6.0.1.2.00/ DATA (SF(12.16.263/ DATA (SF(5.000. +5.1=0.47.338.10.10)/3.00.F8.1.1.56/ DATA (SF(11.100)(HT(I). DIMENSION SF(14.3.218.I=1.18.IO)J=9 IF(J.SCF) THERE NOW FOLLOW THE SCATTERING FACTORS FROM INTERNATIONAL TABLES FOR ATOMS H.19/ DATA (SF(14.130.64.I).14.350.000.33.83.13.15. +5.462.0.91.72.944.11.1=0.EQ.010.71.2.83.481/ DATA (SF(7.241.3.69.10)/9.2.312.1.0.691.52.1.698.6.015.67.0.76. +1.SL.741.59.70.33.1.10)/ll.1*J)**2+B*(SL0. +5.1.3.481.I). PARABOLIC INTERPOLATION IS USED TO OBTAIN THE SCATTERING FACTOR FOR SIN(THETA)/LAMBDA = SL.4.1.65.7.44.00.032.1) IF(J.12.0:10) DATA (SF(1.J))/0.34. N.77.7.1.I).2.48.7.5.4.27.I). +15.4.14.Jl))/0.56.1=0.14.3.29.47. +42.I).251.I).7.13.634.1=0.1.4.322.02 B=(SF(I.6.8.71.1=0.J) RETURN END
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.00. +0.4.0.5.1.444. +1.10)/7.7.5.04.1.00.6.1*J)+SF(I.550.1.2. +9.20.566.114/ DATA (SF(4. CL.0.1.99.581.5.99.88.J+1)+SF(I.02. C.27.59.000.1=0.82.0. +2.00.4.823.29.6.1.11.760.53 6.000.000.513.31.293.521.00.34.64.1=0.F(I).650.685.O)J=l A=(SF(I.78.010.2.I).2.320/ DATA (SF(3.28.42 6.1=0.587.9.3.8.1.950.0.9.I). +1.700) 700 FORMAT(3(24H h k F PHI )) WRITE(9.269.6.374/ DATA (SF(6.000.0.78/ DATA (SF(8.7.13.735.27.2.KT(I).4.0)) STOP END SUBROUTINE SCAT(I.5.7. FE.EQ.23.8.Jl)2*SF(I.600.4.31.96.10)/l5.9. AL.20.00.8.6.0.67.1.1=0.071.10)/13.11.10)/80.6.00.10)/26.5.15.82.10)/l7.8.944.397.2.044.88.3. S.203.126.3.76.31.0.23.93.9.040.21.958.75.I).05.59/ J=INT(SL/0.31.1.I).3.I).502.1 FOR SIN(THETA)/LAMBDA.I). O.215.00.89. BR AND HG AT INTERVALS OF 0.64.09.21.2 SCF=A*(SL0.28.J+l)SF(I.I).I).0.714. +2.84.60.PHI(I).10.1=0.1.1=0. P.11/ DATA (SF(10.10)/35.40.68.1=0.10)/6.8. LI.23. +3.38.094.1=0.51/ DATA (SF(13.F6.47.6.250.10)/8.024.32/ DATA (SF(9.811.17.32.3.
B(h) OR F(h).B FORM IF NECESSARY. ' ( ' VALUE OF h IS 50.HMAX)HMAX=H GOTO 3 START THE SUMMATION. ")') ' CLEAR A. TO TERMINATE DATA INPUT' ') ') ' WRITE (6.EQ.*)H IF(H. HMAX=0 3 READ(5.EQ.l)GOTO 12 GOTO 13 12 WRITE(6.N/2
. SYMMETRY ABOUT THE ORIGIN IS USED BY DOING SEPARATE SUMMATIONS FOR THE COSINE AND SINE TERMS FOR X/A FROM 0 TO 1/2 AND THEN COMBINING THEM. FOR THE TERM OF'')') WRITE(6. THE OUTPUT RANGE FOR X/A CAN BE EITHER (1/2.1/N.*)N WRITE(6./('/ INPUT h(+ve) FOLLOWED BY EITHER A(h).N/2 X(I)=A(0) Y(I)=0 DO 6 J=1.HMAX ARG=TPI*FLOAT(J*I)/N X(I)=X(I)+2*A(J)*COS(ARG) 6 Y(I)=Y(I)+2*B(J)*SIN(ARG) 5 CONTINUE DO 8 1=0.50 A(I)=0 50 B(I)=0 READ IN DATA.'(" INDICATE INTERVAL OF X/A AT WHICH FUNCTION IS'7)7) WRITE(6.OR.0.'(" IF DATA IS IN FORM A & B THEN INPUT 0 '')') WRITE(6. THE MAXIMUM'')') WRITE(6.FILE='LPT1' ) TPI=6.2831853 CONSTANT TO CONVERT DEGREES TO RADIANS DTR=0.GT.Appendices
333
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Appendix II PROGRAM FOUR1 THIS PROGRAM COMPUTES A ONEDIMENSIONAL FOURIER SERIES.'('' CALCULATED.IC(0:200) .EQ.YY IF(KEY.1)GOTO 11 GOTO 7 11 WRITE(6.100)GOTO 4 READ(5.1/2) INPUT 0'')') WRITE(6.IOUT. BY INPUT OF EVEN INTEGER N <=200 //) /) READ(5.Z (0:200) INTEGER H.PHI(h) [in degrees].*) KEY IF(KEY. VALUES OF A.'(" F(h).0174533 WRITE(6. ' (" FOR OUTPUT OF X/A IN RANGE (1/2. B'')') WRITE(6.OR.EQ.B(0:50) .0. PHI(h). A [OR F] . ALSO FIND HMAX.B(h) OR '')') WRITE(6.0)THEN A(H)=XX B(H)=YY GOTO 2 ENDIF A(H)=XX*COS(DTR*YY) B(H)=XX*SIN(DTR*YY) 2 IF(H.HMAX CHARACTER*4 NC. DIMENSION X(0:100) .1)./ (// AND F MUST ALL BE < 1000. *) IOUT IF(IOUT.1) INPUT 1'')') ' 7 READ (5.'(" INDEX 0 INPUT 0. 0.1/2) OR (0.*)XX.KEY.A(0:50) . THE INPUT COEFFICIENTS CAN BE IN THE FORM EITHER A(h). B ARRAYS DO 50 1=0. ' ( ' H = 100. ' ( ' FOR THE RANGE (0.EQ. 4 DO 5 1=0.Y(0:100) . CONVERT TO A.FX NC='n' FX='f(x)' OPEN(UNIT=9.EQ.'('' IF IN THE FORM F & PHI THEN INPUT 1 '')') 13 READ (5.
IX.FX. OUTPUT STAGE BEGINS.Z(I).NC.1=0.N) 200 FORMAT(4(18.334 IF(IOUT. WRITE(9.F7.NC.A4)) WRITE(9.2)) STOP END
.EQ.FX 150 FORMAT(4(6X.FX.' ( ' '')') ' WRITE(9.13) WRITE(9.2 00)(IC(I).100)N 100 F0RMAT(41H THE COORDINATES ARE X/A = n/N WHERE N = .NC.A4.150)NC.FX.0)THEN IC(I)=IN/2 Z(I)=X(N/2I)
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Z(Nl)=X(N/2I)+Y(N/2I) GOTO 8 ENDIF IC(NI)=NI Z(NI)=X(I)8 CONTINUE CALCULATION COMPLETE.
'n')GOTO 5 IF(ANS. ' ( ' DO YOU WANT TO CHANGE THIS? Y/N " ) ') ' READ(5.AC.2831853 WRITE(6.2F7.A4) ) WRITE(9.1=0. '')') DO 1 I=0/NNl WRITE(6.F6.'('' IN STEPS OF l/N.ANS.'(" WILL BE AN OPPORTUNITY TO CORRECT IT LATER.*)F (I) 1 CONTINUE 3 WRITE(6.'('' INPUT HMAX FOR THE CALCULATION [<=50] '')') READ(5.14.FILE='LPT1') TPI=6.Appendices
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Appendix III PROGRAM SIMP1 THIS EVALUATES THE INTEGRALS FOR FINDING A(h) AND B(h) BY SIMPSON'S RULE.EQ.*)HMAX THE VALUES OF A(h) AND B(h) ARE NOW TO BE CALCULATED DO 10 H=0.'Y'.NN.ANS.250)(I#A(I). FOR QUADRATURE AS AN'')') ' WRITE(6.0/NN B(H)=BB/3.EQ.25)ANS IF(ANS.EQ.*)NN WRITE(6.0/NN 10 CONTINUE OUTPUT RESULTS 150 F0RMAT(4 ( 4 X ^ 4 ^ 4 .'('' INPUT N VALUES OF f(x) FOR x = 0 TO 1l/N '')') WRITE(6.lH]) READ(5.'y')GOTO 6 GOTO 7 6 WRITE(6.25)ANS 25 FORMAT(Al) IF(ANS.' ( ' INPUT THE INTERVAL.1H/.13.HMAX) 250 FORMAT(4(15.200)I.' (' INPUT REPLACEMENT f(x) '')') ' READ(5f*)F(I) 5 CONTINUE 2 WRITE(6.EQ. BECAUSE OF THE PERIODIC NATURE OF f(x) THE SUMMATION IS DONE OVER THE POINTS 0 TO Nl (NOT N) AND THE POINT 0 IS GIVEN WEIGHT 2 RATHER THAN 1 AS USUAL. 3X.OR.F(I) 200 FORMAT(4H X =. IF YOU MAKE AN ERROR THERE '')') WRITE(6.2)) STOP
.'Y'.HMAX CHARACTER*4 HC.HMAX AA=0 BB=0 W=4 SUMMATIONS FOR A(h) AND B(h) DO 12 J=07NNl W=6W ARG=TPI*H*J/NN AA=AA+W*F(J)*COS(ARG) BB=BB+W*F(J)*SIN(ARG) 12 CONTINUE A(H)=AA/3.EQ.'('' DO YOU WANT TO CHECK THE VALUES OF f(x)? Y/N ")') READ(5.BC#ANS*1 HC='h' AC='A(h)' BC='B(h)' OPEN(UNIT=9. REAL F(0:199)fA(0:50)fB(0:50) INTEGER H.I3.100)I 100 FORMAT(11H INPUT f{X[.2) 7 WRITE(6.'y')GOTO 4 GOTO 3 4 DO 5 I=0.EQ. l/N.B(I).'n')GOTO 2 IF(ANS.7H f(x) =.OR.OR.EQ.OR.ANS.'N'.ANS.'N'.'('' EVEN INTEGER N <= 200 '')') READ(5.NNl WRITE(6.EQ.
AC(0:15. THERE IS A PATTERSON FUNCTION OPTION IN WHICH CASE THE SCALING FACTOR IS ELECTRONS**2/ANGSTROM**2.'N'.55)FNAME 55 FORMAT(A10) 2 OPEN(UNIT=10.50)ANS 50 FORMAT(Al) IF(ANS.0:30).ANS. WRITE(6.15 DO 1 K=0.'N'. '')') READ(5. +CSY(0:60). TO TAKE ACCOUNT OF THE LIMITED WIDTH OF PRINTER PAPER THE OUTPUT IS IN SECTIONS WHICH HAVE TO BE JOINED SIDEWAYS.'n')GOTO 94 GOTO 95 93 DO 96 I=1.PHI(500) INTEGER H.0:60).Y COORDINATES USED IN PROGRAM STRUCFAC.B AND GAMMA (degrees)'')') WRITE(6. +AS(0:15. +F(500). THE DENSITY IS SCALED TO A MAXIMUM VALUE OF 100 AND THE SCALING FACTOR TO CONVERT TO ELECTRONS/ANGSTROM**2 IS GIVEN.BC(0:15.*)AA.ANS.LIST(0:60).DIR*1.'('' REMEMBER .KK(500).' ( ' MAKE SURE THAT THEY ARE CONSISTENT WITH THE '')') ' WRITE(6.0:30).336
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Appendix IV PROGRAM FOUR2 FOUR2 CALCULATES A TWODIMENSIONAL PROJECTED ELECTRON DENSITY MAP FROM STRUCTURE FACTORS INPUT FROM THE OUTPUT FILE OF STRUCFAC.EQ.NOREF IF(ABS(HH(I)).'y')GOTO 3 GOTO 4 3 WRITE(6.K)=0 1 CONTINUE FNAME=/SF1.GT.FILE=FNAME) HMAX=0 KMAX=0 INPUT THE CELL DIMENSIONS A & B AND THE CELL ANGLE GAMMA.EQ.'('' DO YOU WANT THE PATTERSON OPTION? Y/N '')') WRITE(6. DIMENSION A(15:15.'Y'.'y')GOTO 93 IF(ANS.0:15). ' DO YOU WISH TO CHANGE THE NAME? Y/N'')') READ(5.0:30).OR.'('' INPUT CELL DIMENSIONS A.DAT/ 4 WRITE(6.'Y'.BS(0:15.I=1.CSX(0:60).K)=0 B(H.OR.KK(I).PHI(I).50)ANS IF(ANS.OR.FNAME*10.EQ.NOREF) 95 WRITE(6.'('' ISOFILE THEN YOU SHOULD INPUT N '')') READ(5.2831853 CONSTANT FOR CONVERTING DEGREES TO RADIANS DTR=0.NOREF F(I)=F(I)*F(I) PHI(I)=0 96 CONTINUE 94 DO 77 I=1.IF THE INPUT TAPE IS FROM PROGRAM'')') WRITE(6.EQ. FOR ECONOMY THE OUTPUT IS ON AN ORTHOGONAL GRID AND THE SCALING WILL NOT BE ACCURATE ALONG THE AXES.ANS.'n')GOTO 2 IF(ANS.BB.BT*6 DATA NPAGE/15/ OPEN(UNIT=9.0:15).*)NOREF.GAMMA AREA=AA*BB*SIN(DTR*GAMMA) READ(10.'('' X.HH CHARACTER ANS*1.HMAX)HMAX=ABS(HH(I))
.EQ.EQ.ANS.DAT.RO(0:60.0174533 CLEAR A AND B ARRAYS DO 1 H=15.15 A(H.FILE='LPT1') TPI=6. B(15115.0:30).'(" READ IN FILENAME [<= 10 CHARACTERS] '')') READ(5.HH(500).' ( ' SF1. THE VALUES OF HMAX AND HMIN MUST BE <= 15 AND THE MINIMUM GRID SPACING IS 1/60.(HH(I).' ( ' IT IS ASSUMED THAT THE INPUT DATA FILE IS NAMED'')') ' WRITE(6.OR.F(I).EQ.EQ.
THE REMAINING REGION FROM X = 1/2 TO 1 WILL BE GIVEN BY SYMMETRY.HMAX IF(H.K) *ZIN 13 CONTINUE THE SUMMATIONS OVER X FOR AC.5 DO 16 IY=0.IX)BS(K.IX)+AS(K. THE F(0. IX) =AS (K. IX) =BS (K.NX)) ZIN=CSX(MOD(H*IX+NX16NX4. AS.Appendices
337
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IF(KK(I). K) *COZ BS (K.NY 11 CSY(I)=COS(TPI*I/NY) NOW DO THE SUMMATIONS AC.K) *ZIN BC (K.0 IF(IX. THEY SHOULD BE DIVISIBLE BY 4.NY 15 RO(IX.0)/2. DO 15 IX=0.EQ.'('' X Sc Y DIRECTIONS. BC AND BS AFTER CLEARING ARRAYS DO 12 1=0.K.BC AND BS ARE FOR X = 0 TO 1/2.IX))*ZIN 16 CONTINUE THE DENSITY TABLE IS NOW COMPLETE AND IT IS SCALED TO A MAXIMUM MAGNITUDE OF 100.EQ.IX)) *COZ ++W*(BC(K.NY)) RO(IX.IX)+BS(K.NX 10 CSX(I)=COS(TPI*l/NX) DO 11 1=0. THE NUMBER OF DIVISIONS IN THE'')') WRITE(6.KMAX COZ=CSY(MOD(K*IY+NY16.AND. J)=0 12 CONTINUE DO 13 K=0.KK(I))=F(I)*SIN(DTR*PHI(I)) 77 CONTINUE INPUT OF DATA COMPLETE WRITE(6.NX)) AC (K.IY)=A(0.IX))*COZ + +(BC(K.J)=0 AS(I.NXl DO 20 J=0. K) *COZ AS (K.EQ.30 AC(I.IY)+W*(AC(K.IX))*ZIN RO(NXIX. IT HAS HALF THE WEIGHT OF THE OTHER TERMS AND ITS CONTRIBUTION IS NOW LOADED INTO ARRAY RO WHICH WILL CONTAIN THE SCALED DENSITY. IX) =BC (K.NY)) ZIN=CSY(MOD(K*IY+NY16NY4.*) NX.IY)+W*(AC(K.NYl
. THESE TABLES ARE USED IN THE SUMMATIONS WHICH FOLLOW AND THEIR USE IS FAR MORE EFFICIENT THAN CALCULATING EACH SINE AND COSINE AS IT IS REQUIRED.NY DO 16 K=0. IX) +B (H.NX/2 DO 13 H=HMAX.NX/2)W=0. IX) +B(H. IX) =AC (K.IX)AS(K.15 DO 12 J=0.NX/2 W=1. IX) +A (H.GT. J)=0 BS(I.KMAX)KMAX=KK(I) A(HH(I).J)=0 BC(I. DO 10 1=0.NX DO 15 IY=0.KMAX DO 13 IX=0.0.0) TERM HAS BEEN EXCLUDED.0 DO 16 IX=0.' (" INPUT NX AND NY.IY)=RO(IX. NY NX4=NX/4 NY4=NY/4 NX16=16*NX NY16=16*NY TABLES ARE NOW SET UP OF COS(2*PI*N/NX) AND COS(2*PI*M/NY) WITH N FROM 0 TO NX AND M FROM 0 TO NY.'')') READ (5.IY)=RO(NXIX.0)GOTO 13 COZ=CSX(MOD(H*IX+NX16. RMAX=0 DO 20 I=0.KK(I))=F(I)*COS(DTR*PHI(I)) B(HH(I).AS. IX) +A(H.
(RO(IX. ' ( ' " ) ') ' DO 25 IY=NY.1 WRITE(9.NX)THEN DIR='Y' BT=' TOP' M=NY/NPAGE+1 L=l ENDIF WRITE(9.'('' '')') WRITE(9.LT.IY).A1.NY RO(I.23H HORIZONTAL AND ORIGIN .700)CAF 700 FORMAT(42H FACTOR CONVERTING TO DENSITY/UNIT AREA IS.'('' '')') DO 2 6 IX=0.'('' '')') WRITE(9.N2) 150 FORMAT(5X.5H LEFT) IF(L.200)IX.(RO(IX.2114) WRITE(9.IY=N1.0) WRITE(9.M WRITE(9.'('' '')') 2 6 CONTINUE 45 STOP END
. J) ) . DO 25 N0=l.RMAX)RMAX=ABS(RO(I.21F4.N2) 200 FORMAT(I4.BT 100 FORMAT(13H OUTPUT WITH .IX=N1.150)(LIST(I).Appendices
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IF(ABS(RO(I.4) DO 66 1=0.EQ.NX WRITE(9.J) 21 CONTINUE CALCULATE FACTOR WHICH GIVES PROJECTED DENSITY FROM PRINTED VALUES CAF=1/FAC/AREA OUTPUT THE FACTOR WRITE(9.A6. FOR OTHER AVAILABLE PAGE WIDTHS THIS CAN BE ALTERED BY THE DATA STATEMENT NEAR THE BEGINNING OF THE PROGRAM.2X.M)N2=NY WRITE(9.N2) WRITE(9.1)GOTO 30 THE MAP IS PRINTED IN SECTIONS WHICH MUST BE JOINED AT SIDE EDGES.EQ.'('' '')') 25 CONTINUE GOTO 45 30 DO 26 N0=l.M WRITE(9.I=N1. DIR='X' BT='BOTTOM' M=NX/NPAGE+1 L=0 IF(NY. J) ) 2 0 CONTINUE FAC=100/RMAX DO 21 1=0.I=N1.NX DO 21 J=0.100)DIR.EQ.F8.'('' '')') Nl=(N0l)*NPAGE N2=NPAGE*N0 IF(N0.150)(LIST(I).M)N2=NX WRITE(9.60 LIST(I)=I 66 CONTINUE FIND A CONVENIENT ORIENTATION FOR THE OUTPUT WHICH IS THAT WITH THE LEAST NUMBER OF DIVISIONS ACROSS THE PAGE. THE NUMBER OF GRIDPOINTS ACROSS THE PAGE IS NPAGE WHICH IS SET AT 15.IY).200)IY.GT.0.'('' '')') Nl=(N0l)*NPAGE N2=NPAGE*N0 IF(N0.N2) WRITE(9.J)=FAC*RO(I.
AVSUMF2(30).C. REAL F(1000). THE QUADRATIC FORMULA IS THEN USED WITH THE S FOR EACH REFLECTION TO CONVERT THE VALUE OF F TO U OR E.'E'.F2LIST(100).OR.'('' INPUT CELL DIMENSIONS A. A BEST FIT OF THE KIND " FACTOR = C(1)+C(2)*S+C(3)*S**2 " [s = SIN(THETA)] IS FOUND TO FIT THE CONVERSION FACTORS AND <SIN(THETA)> FOR EACH GROUP.N2.'('' '')') ITOT=0 6 WRITE(6.NUMLIST(100).C(3).HG. THE F'S ARE FIRST SORTED INTO GROUPS FOR OF ROUGHLY 40 IN ORDER OF INCREASING VALUE OF SIN(THETA).N. " ) ') ' WRITE(6. THESE FACTORS ARE THEORETICALLY WHAT IS REQUIRED TO CONVERT F**2 TO U**2 OR E**2 AT <SIN(THETA)> FOR EACH GROUP.Appendices
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Appendix V PROGRAM FTOUE THIS PROGRAM ACCEPTS THE OUTPUT FROM STRUCFAC AND CONVERTS THE F's INTO EITHER U'S OR E'S.Q.EQ. WRITE(6.50)Q IF(Q.OR.NATOM(13). '')') WRITE(6. +IEND(0:30) CHARACTER Q*4.THETLIST(100).'U'.GAMMA NOW CALCULATE FACTORS WHICH WILL BE USED LATER TO FIND VALUES OF SIN[THETA]/LAMDA COl=0.'n')GOTO 2 GOTO 3 1 WRITE(6.U (or E) IS'')') WRITE(6. WHICH '')') WRITE(6.'u')THEN IUE = 1 GOTO 4 ENDIF IF(Q.'('' ONE ASYMMETRIC UNIT] IS INPUT IN THE FORM X 1 . EACH GROUP A CONVERSION FACTOR IS FOUND WHICH WILL.Q. " ) ') ' READ(5.25/B/B CO3=0.AVTHET(30).OR.'('' DO YOU WANT U OR E? (U/E) '')') READ(5.BR.B.FILE='LPT1') FNAME='UE.'('' NAMED UE.DAT FOR SUBSEQUENT USE. B [IN ANGSTROMS] AND'')') WRITE(6.UE(1000) INTEGER ISYMB(13).KT(1000). FOR U'S.Q.0174533) WRITE(6.'('' THE OUTPUT FILE WHICH CONTAINS H.'('' AND Nl IS THE TOTAL NUMBER OF THAT TYPE.25/A/A CO2=0.HT(1000).'('' INPUT ATOMIC TYPE'')')
.CU*1.S.NA.EQ. ' ( ' MUST BE ONE OF H.DAT' WRITE(6. +EPS(30). N 1 " ) ' ) WRITE(6.'('' INPUT THE RADIATION WAVELENGTH IN ANGSTROMS'')') READ(5.'N'.EQ.ASYMB*3.EQ. DO YOU WANT TO CHANGE IT? (Y/N)'')') 3 READ(5.AL.OR.'('' THE CONTENTS OF THE WHOLE UNIT CELL [NOT JUST'')') WRITE(6.LI.FNAME*10. MAKE <U**2>= SIGMA(f**2)/(SIGMA(f))**2 OR. FOR E'S MAKE <E**2> = 1.DAT.'('' X2.ATOM*(*) PARAMETER (ATOM='H LI C N 0 NA AL P S CL FE BR HG END') OPEN(UNIT=9.ETC WHERE XI IS THE TYPE OF ATOM.5/A/B*COS(GAMMA*0. ' ( ' GAMMA IN DEGREES.'y')GOTO 1 IF(Q.'e')THEN IUE=2 GOTO 4 ENDIF INPUT THE ATOMIC CONTENTS OF THE WHOLE UNIT CELL 4 WRITE(6.75)FNAME 50 FORMAT(A4) 75 FORMAT(A10) 2 OPEN(UNIT=10.CL.FE.50)Q IF(Q.EQ.O.'('' READ IN THE FILENAME [<= 10 CHARACTERS] '')') READ(5.EQ.EQ.'Y'.P.*)A.Q.FILE=FNAME) INPUT THE UNIT CELL DATA WRITE(6.EQ.*)XLAM DECIDE WHETHER TO OUTPUT U'S OR E'S.K. THESE ARE THEN PLACED IN A FILE UE.
'('' IF ALL ATOMS HAVE BEEN INPUT THEN INPUT END'')') READ(5.GE.50)Q IF(Q.DAT.ASYMB)+2 NASYMB=NX/3 IF(NASYMB*3.NX)GOTO 6 IF(NASYMB.IOO)ITG=100 THETLIST(ITG)=THETLIST(ITG)+STHET F2LIST(ITG)=F2LIST(ITG)+F(I) **2 NUMLIST(ITG)=NUMLIST(ITG)+ 1 2 0 CONTINUE NOW FIND GROUPS OF 40 OR SO FOR FINDING AVERAGES THESE GROUPS WILL SLIGHTLY OVERLAP DO 21 1=1.05)GOTO 20 ITG=INT(100*STHET)+l IF(ITG.'('' INPUT NUMBER OF ATOMS OF THIS TYPE IN WHOLE CELL'')') READ(5.KT(I). ' (" INPUT THE FILE NAME YOU WANT [<= 10 CHARACTERS] " ) ') READ (5.14)GOTO 7 ITOT=ITOT+1 ISYMB(ITOT)=NASYMB WRITE(6.NOREF) EACH REFLECTION IS READ IN AND VALUES OF NUMBER OF REFLECTIONS SIGMA(F**2) AND SIGMA(SIN[THETA]) ARE FOUND FOR SIN[THETA] RANGES OF 0.GT.'n')GOTO 9 GOTO 10 8 WRITE(6.340
Appendices
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WRITE(6.DAT' 10 WRITE(6.0.OR. 75) FNAME 9 OPEN(UNIT=11 / FILE=FNAME) READ(11.O5 ARE EXCLUDED SINCE THEY DISTURB THE STATISTICS.100)GOTO 30 GOTO 31 ENDIF 3 0 CONTINUE IF THE FINAL GROUP HAS MORE THAN 2 0 MEMBERS THEN IT IS ACCEPTED OTHERWISE IT IS ADDED TO THE PREVIOUS GROUP IF(SUM.'N'.OR.*)NATOM(ITOT) GOTO 6 THE DATA FROM STRUCFAC CAN NOW BE READ IN 7 FNAME='SF1.EQ.DUMMY.LT.40)THEN IEND(IX)=I IX=IX+1 IN=I IF(IN.EQ.NE.EQ.(HT(I).EQ.'Y' .01. FIRST ALL ARRAYS ARE CLEARED DO 66 1=1.1=1.EQ. DO YOU WANT TO CHANGE THIS? (Y/N)'')') READ(5.Q.100 SUM=SUM+NUMLIST(I) IF(SUM.Q.NOREF STHET=XLAM*SQRT(CO1*HT(I)**2+CO2*KT(I)**2CO3*HT(I)*KT(I)) IF(STHET.'y')GOTO 8 IF(Q. REFLECTIONS WITH SIN[THETA] LESS THAN O.20)IX=IX1
.100 THETLIST(I)=0 F2LIST(I)=0 NUMLIST(I)=0 66 CONTINUE DO 20 1=1.F(I).30 IEND(I)=0 21 CONTINUE IEND(0)=l IX = 1 IN=1 31 SUM=0 DO 30 I=IN.'('' THE OUTPUT FILE FROM STRUCFAC IS ASSUMED TO BE'')') WRITE(6 / / ( / / NAMED SF1.EQ.*)NOREF.100)ASYMB 100 FORMAT(A3) NX=INDEX(ATOM.LT.
EPS.IX.2)THEN FACTOR=SQRT(1.'N'.0 GOTO 89 ENDIF SUM1=O SUM2=0 DO 87 1=1.ITOT IA=ISYMB(ITOT) CALL SCAT(IA. IEND(l) TO IEND(2) . DO 40 1=1..OR.'n')THEN IABC=0 GOTO 93 ENDIF GOTO 94 93 IF(IUE. CALL PARAFIT(AVTHET.'y')THEN IABC=1 GOTO 93 ENDIF IF(Q.STLAM.'('' GIVEN IN EQUATION 2. NOW THERE ARE CALCULATED THE AVERAGE F**2 IN EACH GROUP AND <SIN[THETA]>.0/AVSUMF2(I)) GOTO 62 ENDIF SUM1=O SUM2=0 DO 61 J=l.C) C(l)+C(2)*s+C(3)*s*S GIVES THE CONVERSION FACTOR FROM F TO U OR E THE PROPER VALUE OF E(0.ITOT NN=ISYMB(I) CALL SCATFAC(NN.EQ.EQ.IX STLAM=AVTHET(I)/XLAM IF(IUE.Appendices
341
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IEND(IX)=100 THE TOTAL NUMBER OF GROUPS IS IX.0) IS KNOWN AND IS NOW CALCULATED 94 WRITE(6.IEND(I) SUMF2=SUMF2+F2LIST(J) SUMTHET=SUMTHET+THETLIST(J) NSUM=NSUM+NUMLIST(J) 41 CONTINUE AVSUMF2(I)=SUMF2/NSUM AVTHET(I)=SUMTHET/NSUM 40 CONTINUE NOW CALCULATE CONVERSION FACTORS FOR CALCULATION OF U OR E DO 60 1=1.0.OR.IX SUMF2=0 SUMTHET=0 NSUM=0 DO 41 J=IEND(I1).SCF) SUM1=SUM1+NATOM(I)*SCF SUM2=SUM2+NATOM(I)*SCF**2 87 CONTINUE
.Q..EQ. b AND c '')') WRITE(6.50)Q IF(Q.EQ.SCF) SUMl=SUMl+NATOM(J)*SCF SUM2=SUM2+NATOM(J)*SCF*SCF 61 CONTINUE FACTOR=SQRT(SUM2/AVSUMF2(I))/SUMl 62 EPS(I)=FACTOR 60 CONTINUE A BEST PARABOLIC FIT IS NOW TO BE FOUND TO GIVE EPS AS A FUNCTION OF SIN[THETA]/LAMDA [=s].0) OR U(0. THE BEGINNINGS AND ENDS OF THE GROUPS ARE IEND(O) TO IEND(l).Q..EQ..48? Y/N '')') READ(5.0.1)THEN Z = 1. IEND(IXl) TO IEND(IX).'('' DO YOU WANT TO OUTPUT THE VALUES OF a.'Y'.EQ.
8.00.741.83.32/ DATA (SF(8.I).UE(I).7.77.33.698.811.5H c = .KT(I).95*Z 91 CONTINUE ALL F's HAVE NOW BEEN CONVERTED TO U OR E.3. P.60.114/ DATA (SF(4.007/ DATA (SF(2.1.6.1=0.40.0.EQ.6.O.O.5. DIMENSION SF(13.550.I).0.15. THEY ARE NOW WRITTEN ON A FILE FOR FUTURE USE.64.13.1.1. +5.823.16.I).47. NA.241.(HT(I).EQ.00.10)/ll. CL.71.EQ.AND.1=0.000.566.5.KT(I).34.4.72.3) 95 CU='U' IF(IUE.0.44.024.4.10)/l3.040.33.1. O.11.8.444.2.I).EQ.1=0.130.88.27.0.10)/l7.1.54. +5.83.250.634.374/ DATA (SF(6.NOREF IF(HT(I).3.3)) STOP END SUBROUTINE SCATFAC(I.4. C.UE(I).1 FOR SIN(THETA)/LAMBDA.11.6.NOREF) 400 FORMAT(3(5X.96.34.5.4.02.650.300)CU.7.71.944.9.404.9.1.89.10)/7.1.7.263/ DATA (SF(5.2.13.29.05.I).00.1.462. PARABOLIC INTERPOLATION IS USED TO OBTAIN THE SCATTERING FACTOR FOR SIN(THETA)/LAMBDA = SL.99.60.15.521.5.4.3.51/
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.000.2.10)/15.322.400)(HT(I).*)IUE.E9.8.64.6.00. BR AND HG AT INTERVALS OF 0.CU 300 FORMAT(3(16H H K .21.7.00/ DATA (SF(11.21.16.010.10)/16.0.1.NOREF.09.000.0)THEN UE(I)=Z GOTO 90 ENDIF 90 CONTINUE DO 91 I=1.00.1. +0.EQ.I=1.84.10)/26.69.1. LI. +1.126.426.6.88.0.56/ DATA (SF(10.000.31.944.6.EQ.I).1=0. +5.481.1.0.KT(I).99.3. FE.3X)) WRITE(9.1=0.31.0)GOTO 95 WRITE(9.3.GT. +2.76.2)CU='E' WRITE(9.00.5.KT(I).600.1.010.0:10) DATA (SF(1.269.10.11/ DATA (SF(9.12.685. IF(UE(I).1=0. AL.CU.59.23.20. b AND c ARE WRITTEN IF REQUESTED IF(IABC.3.29.1=0.0. N.8.7.E9.0.10)/1.17. S.3 97.SL.0.95*Z)UE(I)=0.4.7.218.3.I).714.4.10)/8.2.350.I=1/NOREF) THE VALUES OF a.68.015.I).500)C 500 FORMAT(5H a = .47. +1. +9.32 0/ DATA (SF(3.8.28.2.581.53 6.9.3.67.251.215.4.1=0.82.0.950. +1.10)/3.1.SCF) THERE NOW FOLLOW THE SCATTERING FACTORS FROM INTERNATIONAL TABLES FOR ATOMS H.1=0.000.094.2.AND.10)/6.07.513.A1) WRITE(9.1.1=0.71.I5.0)GOTO 91 STHET=XLAM*SQRT(CO1*HT(I)**2+CO2*KT(I)**2CO3*HT(I)*KT(I)) CONV=C(1)+C(2)*STHET+C(3)*STHET**2 UE(I)=CONV*F(I) CHECK THAT THE CALCULATED E IS NOT BIGGER THAN E(0) WHICH CAN HAPPEN FOR A LARGE STRUCTURE FACTOR TAKING INTO ACCOUNT THE INACCURACIES IN SCALING.14.I).F7. +0.76.NOREF IF(HT(I).1.I).1.0.200)CU 200 FORMAT(11H VALUES OF .1.56.4.I).6.071.E9.338. WRITE(10.3.00.6.11.I3.47.00.1.542
Appendices Z=SUM1/SQRT(SUM2) FIND E(0) 89 DO 90 I=1.032.1=0.0.203.5.502.5H b = . +3.23.1.3.0.A1.2.2.78/ DATA (SF(7.7.
59/ J=INT(SL/0.K))
343
11
. S.INDXR(NMAX).N IF(IPIV(J).59. 1986.J A(K.41.10)735.02 B=(SF(I.EQ.3 DO 7 K=1. DO 13 J=1.91.IO)J=9 IF(J.Jl))/0.Y(I). B.MP).3 C(I)=B(I) 8 CONTINUE RETURN END SUBROUTINE GAUSSJ(A.MP) PARAMETER (NMAX=50) DIMENSION A(NP.J+1)+SF(I.K)=0.00.11.27. 2 CONTINUE B(J)=0.K) 7 CONTINUE 6 CONTINUE CALL GAUSSJ(A.2 8.3 8. DIMENSION X(NDATA).N IPIV(J)=0 CONTINUE DO 22 1=1.B(NP.INDXC(NMAX) DO 11 J=1.32. J) =A(J.1=0.3 DO 2 K=l. C(2).22.48.N.93. NDATA. +15.Vetterling.J) RETURN END C C C C C C SUBROUTINE PARAFIT (X.B.T.K)).Teukolsky & W.J) )/0.1*J)+SF(I. IT USES THE SUBROUTINE GAUSSJ WHICH IS DERIVED FROM "NUMERICAL RECIPES" BY W.82.3 DO 5 K=1.04.EQ.64. C) THIS SUBROUTINE FINDS THE COEFFICIENTS C(l). 1=1 TO NDATA.N IF (IPIV(K).J+l)SF(I.A(3.IPIV(NMAX).1)THEN DO 12 K=1. +42.23. C(3) TO GIVE THE BEST FIT OF Y(I) =C(1)+C(2)*X(I)+C(3)*X (I)**2 TO A SET OF POINTS X(I).NE.10)780.1) IF(J.34.NP).Y(NDATA).A.Press.P.78.H.3.C(3).O) THEN IF (ABS(A(J.00.B.47.O)J=l A=(SF(I.65.N BIG=0.M.31.52.14.84.EQ.43.J A(J.31. Y.Jl)2*SF(I.FUN(3) DO 1 J=l.70.3).1=0.18.3.75.1*J)**2+E*(SL0.3 A(J.NDATA FUN(1)=1 FUN(2)=X(I) FUN(3)=X(I) *X(I) DO 4 J=l.67.31.Flannery.Appendices DATA (SF(12/I).K)=A(J.20. 1 CONTINUE DO 3 1=1.1.10.9.I).NP. PUBLISHED BY Cambridge University Press.BIGJTHEN BIG=ABS(A(J.19/ DATA (SF(13.27.2 SCF=A*(SL0.GE.1) DO 8 1=1.13.B(3).K)+FUN(K)*FUN(J) 5 CONTINUE B(J)=B(J)+Y(I)*FUN(J) 4 CONTINUE 3 CONTINUE DO 6 J=l.43.
L)=B(LL.INDXR(L))=A(K.EQ. LI. DIMENSION SF(13.ICOL) A(ICOL.ICOL)=1.SL.M DUM=B(IROW/L) B(IROW. S.INDXR(L)) A(K. FE.ICOL)=0.ICOL) A(LL.M B(ICOL.0:10)
C C C C
.L)=A(LL. 0.L)A(ICOL.1 IF(INDXR(L).ICOL). C.L)=B(ICOL.INDXC(L))THEN DO 23 K=1.L)B(ICOL.344
Appendices
12 13
14
15
16 17
18 19 21 22
23 24
IROW=J ICOL=K ENDIF ELSE IF (IPIV(K).N DUM=A(K. P. DO 16 L=1.N DUM=A(IROW/L) A(IROW/L)=A(ICOL/L) A(ICOL/L)=DUM CONTINUE DO 15 L=1.INDXC(L)) A(K.N A(LL.INDXC(L))=DUM CONTINUE ENDIF CONTINUE RETURN END SUBROUTINE SCAT(I. N.N A(ICOL/L)=A(ICOL/L)*PIVINV CONTINUE DO 17 L=1.M B(LL.1 FOR SIN(THETA)/LAMBDA. CL.GT.L) B(ICOL.SCF) THERE NOW FOLLOW THE SCATTERING FACTORS FROM INTERNATIONAL TABLES FOR ATOMS H.ICOL)THEN DUM=A(LL. AL.1.NE.NE.NE.O. PARABOLIC INTERPOLATION IS USED TO OBTAIN THE SCATTERING FACTOR FOR SIN(THETA)/LAMBDA = SL.L)*DUM CONTINUE ENDIF CONTINUE CONTINUE DO 24 L=N./A(ICOL.ICOL) THEN DO 14 L=1.) PAUSE 'Singular matrix. NA. BR AND HG AT INTERVALS OF 0.L)=B(ICOL.N IF(LL. DO 18 L=1.L)=DUM CONTINUE ENDIF INDXR(I)=IROW INDXC(I)=ICOL IF (A(ICOL.L)*PIVINV CONTINUE DO 21 LL=1.' PIVINV=1.l) THEN PAUSE 'Singular matrix' ENDIF CONTINUE ENDIF CONTINUE IPIV(ICOL)=IPIV(ICOL)+1 IF (IROW.L)*DUM CONTINUE DO 19 L=1.
741.7.1.698.130.I).J+l)SF(I.566.9.4.16.4.11.I).Jl)2*SF(I.685.2.43.14.0.5.I).76.550.99.1.3 8.0.23.0.218.0.Appendices
345
DATA (SF(1.1=0.1.5.1.10)/35.1) IF(J.13.3.462.J))/0.2 8.215.2.6.0.64.1.10)/I.23.20.I).263/ DATA (SF(5.350.32.84.99.10)/7.7.91.31.70.426.82.944.944.32/ DATA (SF(8.27.536.114/ DATA (SF(4.68.09. +1.0. +15.203.1. +0.1.EQ.6.52.4.34.071.0.094. +1.8.11.I). +5.1.2.75.000.31. +42.9.64.3.6.10)/l7.1=0.4.581.1=0.9.48.000.1=0.60.15.10)/8.88.251.I).22. +0.322.I).64.00.56/ DATA (SF(10.714.59/ J=INT(SL/0.502.521.18.10)/80.10)/l5.950.1.007/ DATA (SF(2.600. +5.00.21.3.65.44.1=0.0.0.I).67.71.67.404.4.IO)J=9 IF(J.15.14.J) RETURN END
.4.1.1.5.4.00.7.78.00.05.29.56.60.00.024.13.I).2.59.31.11/ DATA (SF(9.0.34.00.04.0.1=0.11.1=0.84.88.000.10)/l6.0.96.31.83.1=0.3. +1.27.823.6.1=0.72.10.3.250.241.11.1=0.3.31.1=0.34.6.8.010.6.1*J)+SF(I.J+1)+SF(I.3.6.1.5.320/ DATA (SF(3. +5.41.2 SCF=A*(SL0.000.000.634.28.338. +2.444.12.77.47.126.2.00.27.269.10)/6.71.481.9.7.29.16.21.6.2.10)/26.47.1.1=0.07. +9.7.010.1.7.032.8.3.O)J=l A=(SF(I.2.1*J)**2+B*(SL0.8.2.I).76.17.513.71.83.0.Jl))/0.10)/3.47.I).811.015.02 B=(SF(I.EQ.69.I).23.1.1.19/ DATA (SF(13.5.1.13.02.78/ DATA (SF(7.1.397.1=0.89.59.I).4.51/ DATA (SF(12.7.40.8.040.4.00.1. +3.10)/l3.650.93f10.00.5.00.33.00/ DATA (SF(11.43.33.20.1.10)/ll.82.47.3 74/ DATA (SF(6.54.
'('' DO YOU WANT TO TAKE THE STRUCTURE AMPLITUDE'')') WRITE(6.'Y'.'n')GOTO 12 IF(ANS.'('' FOR THE HEAVY ATOM STRUCTURE IS CALLED SF2. DO '')') WRITE (6.EQ.'('' DATA FOR INPUT TO FOUR2 IS CALLED SF.DAT.50)ANS IF(ANS.ANS*1.ATYPE*3.' ( ' IT IS ASSUMED THAT THE FILE CONTAINING THE DATA'')') ' WRITE(6/'('/ FOR THE WHOLE STRUCTURE IS CALLED SF1. DATA FILES ARE READ IN [SF1.'')') WRITE(6.'('' WITHOUT WEIGHT? Y/N '')') READ(5.OR.EQ.'y')GOTO 5 GOTO 6 5 WRITE(6 / '(" READ IN THE REQUIRED FILE NAME ")') READ(5.EQ.ANS.'N'.346
Appendices
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Appendix VI PROGRAM HEAVY THIS PROGRAM ALLOWS A SIMULATION OF A HEAVYATOMMETHOD SOLUTION OF EITHER A CENTROSYMMETRIC OR NONCENTROSYMMETRIC STRUCTURE.50)ANS
.DAT & SF2.'Y'.ANS.'('' OR N FOR A NONCENTROSYMMETRIC STRUCTURE '')') READ(5.OR.EQ.'y')GOTO 2 GOTO 3 2 WRITE(6.DAT' 6 WRITE(6.DAT OR OTHER CHOSEN NAMES] CONTAINING THE OUTPUT FROM "STRUCFAC" FOR THE WHOLE STRUCTURE AND FOR THE HEAVY ATOMS RESPECTIVELY.ANS.'Y'.EQ.DAT.'n')GOTO 1 IF(ANS.EQ.ANS.EQ.DAT' 3 WRITE(6.DAT.EQ.EQ.'N'.MTYPE(14) CHARACTER FNAME*10.OR. HAS THE PHASE OF THE HEAVY ATOM CONTRIBUTION AND MAGNITUDE OF THE WHOLE STRUCTURE MODIFIED BY EITHER THE SIM WEIGHT FOR A NONCENTROSYMMETRIC STRUCTURE OR THAT GIVEN BY WOOLFSON FOR A CENTROSYMMETRIC STRUCTURE.'Y'. ' ( " YOU WANT TO CHANGE IT? Y/N ")') READ(5.ANS.OR.OR.EQ.F2(1000) .50)ANS IF(ANS. REAL Fl(1000) .'n')GOTO 4 IF(ANS. SUITABLE FOR INPUT TO "FOUR2".ANS. THERE IS ALSO AN OPTION FOR ACCEPTING THE HEAVY ATOM PHASE WITHOUT WEIGHTING THE MAGNITUDE.EQ.'N'.ANS. DO '')') Y/N " ) ' ) WRITE (6.DAT' 9 WRITE(6 / '(" IT IS ASSUMED THAT THE FILE CONTAINING OUTPUT'')') WRITE(6.EQ.'(" READ IN THE REQUIRED FILE NAME '')') READ(5/100)FNAME 1 OPEN(UNIT=10.PHI(1000) INTEGER H(1000)fK(1000)/NATOM(14).EQ.EQ.'N'.ANS. THE OUTPUT FILE.OR.50)ANS 50 FORMAT(Al) IF(ANS.OR.'('' DO YOU WANT TO CHANGE IT? Y/N '')') READ(5.FILE=FNAME) FNAME='SF2.50)ANS IF(ANS.'y')GOTO 8 GOTO 9 8 WRITE(6 /'(// READ IN THE REQUIRED FILE NAME '')') READ(5/100)FNAME 100 FORMAT(A10) 7 OPEN(UNIT=12/FILE=FNAME) 46 WRITE(6.OR.EQ. ' ( " YOU WANT TO CHANGE IT? READ(5.ATOM*(*) PARAMETER (ATOM='H LI C N O F NA AL P S CL FE BR HG END') FNAME='SF1.'(" IT IS ASSUMED THAT THE FILE CONTAINING THE DATA'')') WRITE(6.EQ.'n')GOTO 7 IF(ANS.'y')THEN KEY=1 GOTO 13 ENDIF GOTO 46 12 WRITE(6/'('/ INPUT C FOR A CENTROSYMMETRIC STRUCTURE ")') WRITE(6.100)FNAME 4 OPEN(UNIT=11/FILE=FNAME) FNAME='SF.
K (I) .OR.NOTYPE CALL SCAT(MTYPE(J).'('' WHOLE UNIT CELL '')') READ(5 .LT.0174533) WRITE(6.'')') WRITE(6.'('' INPUT ATOMIC TYPE . CL.150)ATYPE 150 FORMAT(A3) GENERATE A NUMBER FROM 1 TO 14 TO IDENTIFY THE TYPE OF ATOM OR 15 IF ALL ATOMS HAVE BEEN READ IN NX=INDEX(ATOM. (H (I) .5658*X0. CO2 AND CO3 ARE USED FOR CALCULATING SIN(THETA)/LAMBDA C01=0.ANS. LI.OR.5/A/B*COS(GAMMA*0. I = 1. B.EQ.0106*X*X*X 36 F1(I)=F1(I)*FACTOR
.SL.NOREF) READ(11.EQ. Fl (I) . ' ( " ATOMS HAVE BEEN READ IN ' ') ') READ(5.NE. F.'(''THERE ARE NOW INPUT THE TYPES AND NUMBERS '')') WRITE(6.'('' INPUT CELL DIMENSIONS A. BR.EQ. K (I) .34. ' ' ) ' ) ' WRITE(6. S.'('' AND GAMMA IN DEGREES '')') READ (5.1.EQ. FOR SMALLER VALUES OF X A POLYNOMIAL APPROXIMATION IS USED.*)NOREF.'(''NOTETHE NUMBERS ARE FOR THE WHOLE UNIT CELL!")') NOTYPE=0 30 WRITE(6. N.SCF) SIG=SIG+NATOM(J)*SCF*SCF 32 CONTINUE X=2*F1(I)*F2(I)/SIG GOTO(33. (H (I) .'c')GOTO 10 IF(ANS. ' ( 'OF ATOMS WHOSE COORDINATES ARE NOT KNOWN.Appendices
347
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IF(ANS.'N'. F2 (I) .6.GT. 35 IF(X.15)GOTO 40 NOTYPE=NOTYPE+1 MTYPE(NOTYPE)=NASYMB WRITE(6. *) A.ATYPE)+2 NASYMB=NX/3 IF(NASYMB*3. IF X>6 THEN IT IS EFFECTIVELY 1. P. 33 FACTOR=1 IF(F2(I).0E6)FACTOR=0 GOTO 3 6 THIS GIVES THE WEIGHT GIVEN BY WOOLFSON 34 FACTOR=EXP(X) FACTOR=FACTOR/(1.NX)GOTO 30 IF(NASYMB. FE.'C.PHI(I)/ I = 1/NOREF) WRITE(6.ANS.ONE OF H.0+FACTOR) GOTO 36 THERE FOLLOWS A CALCULATION OF THE SIM WEIGHT. B IN ANGSTROMS '')') WRITE(6.25/B/B CO3=0. GAMMA CO1.*)NOREF.EQ. * )NATOM(NOTYPE) GOTO 30 40 DO 31 I=1/NOREF CALCULATE THE VALUE OF (SIN(THETA)/LAMBDA) SL=SQRT(H(I)*H(I)*CO1+K(I)*K(I)*CO2H(I)*K(I)*CO3) SIG=0 DO 32 J=l.'n')GOTO 11 GOTO 12 10 KEY=2 GOTO 13 11 KEY=3 13 READ(10.1304*X*X+0. PHI(I) .25/A/A CO2=0.'('' NA. HG OR END IF ALL '')') WRITE(6.35)KEY THIS GIVES UNWEIGHTED STRUCTURE AMPLITUDE UNLESS THE HEAVY ATOM CONTRIBUTION IS ZERO WHEN THE TERM IS REMOVED FROM THE SYNTHESIS.0)THEN FACTOR=1 GOTO 3 6 ENDIF FACTOR=0. AL. C.' (" INPUT THE NUMBER OF THIS TYPE OF ATOM IN THE'')') WRITE(6. 0.
481.1. NA.00.0.6.19/ DATA (SF(14.944.18. +42.760.0.33.15.338.78/ DATA (SF(8.29.2 SCF=A*(SL0.010.16.16.944.811.I=1.09.462.536.374/ DATA (SF(6.10)/9.481/ DATA (SF(7.9.0.691.4.2.20.64.1.96.29.1.47.2.Jl))/0.71.1.250.7.21.11.00.000.6.10)/l7.6.3.7.2.6.32/ DATA (SF(9.76.I).12.00.27.10.2 8.9. 8.10)/ll.34.4.59 .6.4.312.65.PHI(I).5.9.1.I).587.000. +1.13.47.8.13.23.*)NOREF.1=0.J) RETURN END
.1.3.I).83.320/ DATA (SF(3.00.1=0.76.502.78.600.3.10.1=0.07.0:10) DATA (SF(1.99.9.735.1) IF(J.823.2.269.0.32.64.4.00.0.70. BR AND HG AT INTERVALS OF 0.2.0.IO)J=9 IF(J.99.11.5.I) .21.322.032.31. +5.48.1.350.00.4. AL.31.SL.1 = 0.SCF) THERE NOW FOLLOW THE SCATTERING FACTORS FROM INTERNATIONAL TABLES FOR ATOMS H.1.1.1. +0.0.10)/15.071.K(I).91.I). CL.024.00.EQ.23.2.566.263/ DATA (SF(5.31.31.34.1*J)**2+B*(SL0.3.3.33. LI.15.60.444.581.203.10)/6. P.7.64.10)/16.47. S.71.68.I).38.000.10)/8.14.1.0.8.040.10)/7.67.1.EQ.I).43.348
Appendices
31 CONTINUE WRITE(12. +2.(H(I).5.10)/26.93.4.1=0.1=0.4.10)/I.J+l)SF(I.714.10)/3.3 97.I) . +1.000.6. +0.741.878. +5. 0.685.60.2.34.47.1.10)/80.31.89.20.241.05.521.41.14.0.1.2.1=0.010.0.1.251.6.28. +5.11.44.6.3. +15.1=0.04.I).00/ DATA (SF(12.8.1 = 0.4.77.2.4.02 B=(SF(I.00.1=0. C. FE.88.293.56.Jl)2*SF(I.1.1=0.75.72.54.007/ DATA (SF(2.NOREF) STOP END
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SUBROUTINE SCAT(I.5.094.044.0.17.13 0.I). DIMENSION SF(14.59/ J=INT(SL/0.71.02.0.84.10)/l3. +2.23.7.1.43.27.1 FOR SIN(THETA)/LAMBDA.550.5. +3.I).215.59.1=0.11.1*J)+SF(I.126.00.650.7.1.22.1=0.3.000.I).69.3.27.698.513.958. +9.3.0.6.5.1.J))/0.950.J+1)+SF(I.Fl(I).7.7.I).88.1.634.5.1. +1.56/ DATA (SF(11.000.O)J=l A=(SF(I.83.00.51/ DATA (SF(13.82.404.13.8.11/ *DATA (SF(10.218.10)/35.8.114/ DATA (SF(4.67.40.I).1=0.015.426.1.1. N.52.82.84.1. PARABOLIC INTERPOLATION IS USED TO OBTAIN THE SCATTERING FACTOR FOR SIN(THETA)/LAMBDA = SL.
EQ./(// [<= 10 CHARACTERS] ")') READ(5.1).KTAB(I.DAT.2).2).ANS*1 OPEN(UNIT=9.'Y'.KTAB(1.NE. IF NONCENTROSYMMETRIC THEN THEY ARE FA**2 .NE.EQ.'N'.' (" INPUT FILES '')') 101 STOP END
.ANS. REAL FTAB(1000.2))**2 GOTO 12 11 FTAB(I.ANS.50)FNAME2 OPEN(UNIT=11.=10 CHARACTERS] '')') READ(5.1).(HTAB(1.' (" THE PROGRAM IS ABORTED.1=1. 8 DO 9 1=1.100)ANS IF(ANS.1)FTAB(I.OR.OR.ANS.1=1.DUMMY.PHI(I).FTAB(1.DAT/ 1 WRITE (6.(HTAB(1.'n')GOTO 2 IF(ANS.1)=(FTAB(1.NOREF GOTO(10.Appendices
349
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Appendix VII PROGRAM ISOFILE THIS PROGRAM TAKES DATA FILES FROM STRUCFAC FOR TWO ISOMORPHOUS COMPOUNDS.' (" THE INDICES ON THE TWO INPUT TAPES DO NOT AGREE")') WRITE(6. ' ("SF1.2).FILE='LPT1') WRITE(6.'N'.'C.*)NOREF.NOREF) GOTO 101 99 WRITE(6. IF NOT THEN THE PROGRAM IS TERMINATED WITH AN ERROR MESSAGE.1).NOREF) 7 WRITE(6.'(// [. DO YOU WANT TO CHANGE THIS? Y/N ")') READ(5.FTAB(1.KTAB(1.EQ.FTAB(1.EQ.FB)**2.FILE=FNAME) READ(10. ' (" READ IN FILENAME [<= 10 CHARACTERS] " ) ') READ(5. ' (" INPUT C FOR A CENTROSYMMETRIC STRUCTURE OR N " ) ') WRITE(6.1).FILE=FNAME1) WRITE(6.11)KEY 10 FTAB(I.2)**2 12 IF(HTAB(I.KTAB(1000.1).'n')GOTO 6 GOTO 7 5 KEY=1 GOTO 8 6 KEY=2 THE OUTPUT TAPE WILL NOW BE PRODUCED. THEY ARE COMBINED TO GIVE AN INPUT TAPE FOR FOUR2 TO GIVE A DIFFERENCE PATTERSON MAP.EQ.PHI(1000) INTEGER HTAB(1000.OR. A CHECK WILL BE MADE THAT THE INDICES ON THE TWO INPUT TAPES CORRESPOND. IF THE STRUCTURE IS CENTROSYMMETRIC THEN THE COEFFICIENTS ARE (FA .ANS.100)ANS 100 FORMAT(Al) IF(ANS.2).EQ.'c')GOTO 5 IF(ANS.2))GOTO 99 IF(KTAB(I.2))GOTO 99 PHI(I)=0 9 CONTINUE WRITE(12.NOREF) READ(11.'('' READ IN THE NAME OF THE SECOND DATA FILE '')') WRITE(6.1=1. CHECK PRINTOUTS OF ")') WRITE(6.KTAB(1.(HTAB(1.50)FNAME 2 OPEN(UNIT=12.OR.2).' ("IT IS ASSUMED THAT THE OUTPUT DATA FILE IS NAMED")') WRITE (6. HOWEVER.1).2) CHARACTER FNAME*10.1)**2FTAB(I. BECAUSE THE COEFFICIENTS ARE ALREADY IN PATTERSON FORM FOUR2 SHOULD BE USED IN NORMAL MODE NOT IN PATTERSON MODE.EQ.1).FILE=FNAME2) 50 FORMAT(A10) FNAME='SF1.FB **2.*)NOREF.5O)FNAME1 OPEN(UNIT=10.'y')GOTO 3 GOTO 1 3 WRITE(6.EQ.DUMMY.FNAMEl*10.HTAB(I. ' ( " FOR A NONCENTROSYMMETRIC STRUCTURE " ) ') READ(5.1)=FTAB(I.'(" READ IN THE NAME OF THE FIRST DATA FILE ")') WRITE(6.FNAME2*10. IN BOTH CASES THE PHASE IS PUT AT ZERO.*)NOREF.1).
ANS.OR.EQ.ANS.EQ.DAT.ANS.OR.EQ. DO YOU WANT TO CHANGE THIS? Y/N '')') READ(5.FIRB(IOOO) .OR.OR.'N'.EQ.'n')GOTO 11 IF(ANS.'('' DO YOU WANT TO CHANGE THIS? Y/N '')') READ (5.FNAME *10 SET NAME OF INPUT FILE FOR STRUCTURE A FNAME=/SF1.K(1000) CHARACTER ANS * 3.50)ANS IF(ANS.OR.EQ.100)FNAME 11 OPEN(UNIT=11/FILE=FNAME) SET NAME OF INPUT FILE FOR IR ATOMS A FNAME='SFIRA.'Y'.EQ.'(''READ IN NAME OF FILE [<= 10 CHARACTERS] '')') READ(5.'n')GOTO 21 IF(ANS.'Y'.'')') WRITE(6.ANS.' ( ' DO YOU WANT TO CHANGE THIS? ' Y/N '')') READ(5. REAL FA (1000) .'y')GOTO 32 GOTO 3 3 32 WRITE(6.50)ANS IF(ANS. 50) ANS IF(ANS.350
Appendices
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Appendix VIII PROGRAM ISOCOEFF THIS PROGRAM CALCULATES THE FOURIER COEFFICIENTS AND PHASES FOR A DOUBLE FOURIER SUMMATION GIVEN THAT THE POSITIONS OF IR ATOMS AND THE STRUCTURE AMPLITUDES FOR THE TWO ISOMORPHOUS STRUCTURES ARE KNOWN. THE PRINTOUT OF WHICH WILL BE THE DOUBLE FOURIER SUMMATION.'('' INFORMATION FOR STRUCTURE A IS IN FILE SF1.'n')GOTO 1 IF(ANS.FB(1000) .'Y'.'y')GOTO 22 GOTO 23 22 WRITE(6.FIRA(IOOO) .'(" IT IS ASSUMED THAT THE STRUCTURE FACTOR '')') WRITE(6.EQ.DAT/ 3 WRITE(6.EQ.ANS.EQ.DAT' 33 WRITE(6/'('/ IT IS ASSUMED THAT THE STRUCTURE FACTOR '')') WRITE(6/'('/ INFORMATION FOR IR ATOMS B IS IN FILE '')') WRITE(6/'('/ SFIRB.'N'.DAT.'y')GOTO 2 GOTO 3 2 WRITE(6.'(''READ IN NAME OF FILE [<= 10 CHARACTERS] '')') READ(5.100)FNAME 21 OPEN(UNIT=12/FILE=FNAME) SET NAMES OF INPUT FILE FOR IR ATOMS B FNAME='SFIRB. THE SIMULATION REQUIRES: (i) STRUCFAC OUTPUT FILE FOR STRUCTURE A (ii) STRUCFAC OUTPUT FILE FOR STRUCTURE B (iii) STRUCFAC OUTPUT FILE FOR IR ATOMS A (iv) STRUCFAC OUTPUT FILE FOR IR ATOMS B THE OUTPUT FILE WILL BE SUITABLE AS AN INPUT FILE FOR FOUR2. PHI (1000) INTEGER H(1000).'(''READ IN NAME OF FILE [<= 10 CHARACTERS] '')') READ (5.EQ.DAT.'N'.ANS.EQ.EQ.'(''READ IN NAME OF FILE [<= 10 CHARACTERS] '')') READ(5.EQ.OR.DAT' 23 WRITE(6/'('/ IT IS ASSUMED THAT THE STRUCTURE FACTOR '')') WRITE(6/'('' INFORMATION FOR IR ATOMS A IS IN FILE '')') WRITE(6/'('' SFIRA.ANS.100)FNAME
.'Y'.50)ANS 50 FORMAT(A3) IF(ANS.EQ.OR.EQ.'n')GOTO 31 IF(ANS. DO YOU WANT TO CHANGE THIS? Y/N '')') READ(5.OR.100)FNAME 100 FORMAT(A10) 1 OPEN(UNIT=10/FILE=FNAME) SET NAME OF INPUT FILE FOR STRUCTURE B FNAME='SF2.ANS.EQ.'y')GOTO 12 GOTO 13 12 WRITE(6.'N'.DAT.'')') WRITE(6.DAT' 13 WRITE(6/'('/ IT IS ASSUMED THAT THE STRUCTURE FACTOR '')') WRITE(6/'('' INFORMATION FOR STRUCTURE B IS IN FILE SF2.
0*FB(I)*FIRB(I)*CPSI) APPLY EQUATION (8.FA(I).EQ.0/FB(I) +/(FIRB(I)FIRA(I)) CHECK FOR COS(PSI) WITHIN PROPER LIMITS. FB (I) .0.24) TO FIND COS(DELTA PHI) CDPHI=(FB(I)**2XK**2FIRB(I)**2)/2.'(''READ IN NAME OF FILE [<= 10 CHARACTERS] " ) ' ) READ(5.0/XK/FIRB(I) FA(I)=XK*CDPHI 10 CONTINUE WRITE OUTPUT FILE WRITE(14. (H (I) .'y')GOTO 42 GOTO 43 42 WRITE(6.EQ.'Y'.(H(I). FA (I) .CPSI) APPLY EQUATION (8.PHI(I)1/NOREF) READ(12. K (I) .K(I).1.' ( ' DO YOU WANT TO CHANGE THIS? ' Y/N '')') READ(5/50)ANS IF(ANS.*)NOREF.GT.NOREF APPLY EQUATION (8.'('' DOUBLE FOURIER SUMMATION WILL BE IN SDF.'('' IT IS ASSUMED THAT THE OUTPUT FILE FOR THE '')') WRITE(6.DAT.'n')GOTO 41 IF(ANS.PHI(I)1/NOREF) = READ(H. IF NOT BRING TO LIMIT IF(ABS(CPSI). #PHI(I)/ I = 1/NOREF) CALCULATE VALUES OF K*COS(DELTA PHI) DO 10 I=1.Appendices
351
31 0PEN(UNIT=13/FILE=FNAME) SET NAME OF OUTPUT FILE FNAME='SDF.EQ. (H (I) . / I = 1/NOREF) READ(13.0)CPSI=SIGN(1.FILE = FNAME) READ IN ALL DATA FROM INPUT FILES = READ(10.23) XK=SQRT(FB(I)**2+FIRB(I)**22.PHI(I)/I=1/NOREF) STOP END
.*)NOREF.EQ. K (I) .*)NOREF.100)FNAME 41 OPEN(UNIT=14.OR.ANS.ANS.OR.DAT' 43 WRITE(6.*)NOREF. '')') WRITE(6.'N'.*)NOREF.22) CPSI=((FIRB(I)FIRA(I))**2+FB(I)**2FA(I)**2)/2.
352
Appendices
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Appendix IX PROGRAM ANOFILE THIS PROGRAM TAKES THE OUTPUT FILE FROM STRUCFAC FOR ANOMALOUS SCATTERING AND GIVES AN OUTPUT FILE WITH FOURIER AMPLITUDES (F(H)F(H)).EQ.EQ.ANS.'y')GOTO 12 GOTO 13 12 WRITE(6.'N'.'n')GOTO 11 IF(ANS.NOREF1.DAT ")') WRITE(6.DAT '')') WRITE(6.fY'.100)FNAME 100 FORMAT(A10) 1 OPEN(UNIT=10.OR.GT.EQ.EQ.1=1. REAL F(1000). ' ( " DO YOU WANT TO CHANGE THIS? Y/N ' ')') READ(5.'(" THE OUPUT FILE IS ASSUMED TO BE SANO.0.DAT' 3 WRITE(6.EQ. READ(10. 2) STOP END
.K(1000) CHARACTER ANS*1.2 IF(F(J).XLIM)F(I)=0 36 CONTINUE READ IN TO FILE FOR INPUT TO FOUR2 NOREF2=NOREF/2 WRITE(11.GT.19 XLIM=(1.05*1)*DIFMAX NUM=0 DO 31 J=1/NOREF1.*)NOREF2. THIS CAN BE USED AS INPUT TO FOUR2 TO CALCULATE A PATTERSON FOR LOCATING THE ANOMALOUS SCATTERERS. (H(I).DIFMAX)DIFMAX=F(I) 20 CONTINUE DO 30 1=1. ' ( ' DO YOU WANT TO CHANGE THIS? ' Y/N ' ') ') READ(5.EQ.ANS.50)ANS 50 FORMAT(Al) IF(ANS.DAT' 13 WRITE(6.NOREF1.EQ.K(I).'y')GOTO 2 GOTO 3 2 WRITE(6.K(I).'n')GOTO 1 IF(ANS. FNAME='SF1.F(I).ANS.PHI(1000) INTEGER H(1000).00.2 IF(F(I).OR.1=1.'Y'.50)ANS IF(ANS. FNAME*10 GIVE THE NAME OF THE INPUT DATA FILE.LT.GT.NOREF1.PHI(I).OR.XLIM)NUM=NUM+1 31 CONTINUE IF(FLOAT(NUM)/FLOAT(NOREF).NOREF) DO 10 1=1. SINCE THE REFLECTIONS ARE IN ADJACENT PAIRS WITH INDICES h AND h THE OUTPUT FILE HAS ONLY ONE HALF THE NUMBER OF REFLECTIONS AND THE STRUCTURE AMPLITUDES ARE THE DIFFERENCES OF NEIGHBOURING F VALUES ON THE INPUT FILE.EQ.125)GOTO 35 30 CONTINUE 35 DO 36 I=1.FILE=FNAME) FNAME='SANO.F(I)#PHI(I).OR.'('' THE INPUT FILE IS ASSUMED TO BE SF1.(H(I).'(" READ IN THE FILE NAME [<= 10 CHARACTERS] ")') READ(5/100)FNAME 11 OPEN(UNIT=11/FILE=FNAME) MODIFY ARRAY F TO CONTAIN ANOMALOUS DIFFERENCE.*)NOREF.'(" READ IN THE FILE NAME [<= 10 CHARACTERS] ")') READ(5.2 F(I)=ABS(F(I)F(I+1)) 10 CONTINUE IDENTIFY ABOUT 25% OF THE LARGEST ANOMALOUS DIFFERENCES AND PUT THE REMAINDER EQUAL TO ZERO IN OUTPUT FILE DIFMAX=0 DO 20 I=l/NOREFl/2 IF(F(I).ANS.'N'.
K(I)fF(I).2 X=(F(I)**2F(I+1)**2) F(I)=X*X PHI(I)=90.OR.EQ. REAL F(1000).EQ. GIVES A PSFUNCTION MAP.EQ.OR.F(I). SINCE THE REFLECTIONS ARE IN ADJACENT PAIRS WITH INDICES h AND h THE OUTPUT FILE HAS ONLY ONE HALF THE NUMBER OF REFLECTIONS ON THE INPUT FILE.NOREF1. READ(10.DAT '')') WRITE(6.0*SIGN(1. 100)FNAME 11 OPEN(UNIT=11/FILE=FNAME) MODIFY ARRAY F TO CONTAIN ANOMALOUS INTENSITY DIFFERENCE MAGNITUDES AND ARRAY PHI TO CONTAIN PI/2 OR PI/2 DEPENDING ON WHETHER F(h)**2F(h)**2 IS POSITIVE OR NEGATIVE.ANS.DAT' 13 WRITE(6.50)ANS IF(ANS.'('' READ IN THE FILE NAME [<= 10 CHARACTERS] '')') READ(5. THIS WILL GIVE THE PSFUNCTION.Appendices
353
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Appendix X PROGRAM PSCOEFF THIS PROGRAM TAKES THE OUTPUT FILE FROM STRUCFAC FOR ANOMALOUS SCATTERING AND GIVES AN OUTPUT FILE WHICH.'n')GOTO 1 IF(ANS.EQ.(H(I).'N'.*)NOREF. FNAME*10 GIVE THE NAME OF THE INPUT DATA FILE.OR.'N'.'y')GOTO 12 GOTO 13 12 WRITE(6. USED AS AN INPUT FILE FOR FOUR2.ANS.K(I).PHI(I).1=1.'(" THE OUPUT FILE IS ASSUMED TO BE PSF.'y')GOTO 2 GOTO 3 2 WRITE(6.(H(I).EQ. FNAME='SF1.PHI(1000) INTEGER H(1000)fK(1000) CHARACTER ANS*1.ANS.0/X) 10 CONTINUE READ IN TO FILE FOR INPUT TO FOUR2 NOREF2=NOREF/2 WRITE(11. ' ( ' DO YOU WANT TO CHANGE THIS? ' Y/N ")') READ(5/50)ANS 50 FORMAT(Al) IF(ANS.*)NOREF2.'Y'.'n')GOTO 11 IF(ANS.EQ.EQ.'C' THE INPUT FILE IS ASSUMED TO BE SF1.OR.PHI(I)/I=1/NOREF) DO 10 I=1.NOREF1.EQ.'(" DO YOU WANT TO CHANGE THIS? Y/N '')') READ(5.'Y'.DAT '')') WRITE (6.ANS.'(" READ IN THE FILE NAME [<= 10 CHARACTERS] '')') READ (5.100)FNAME 100 FORMAT(A10) 1 OPEN(UNIT=10/FILE=FNAME) FNAME='PSF.DAT' 3 WRITE(6. 2) STOP END
.
(6) DO ONE LAST CYCLE ACCEPTING NEW PHASES REGARDLESS OF WEIGHTS.KMAX.*)IBEST GOTO 76 C ENTER SPACE GROUP AND CELL DATA
C C C C C C C C C C C C C Q C C C C C C C C C C
.PG*4 PARAMETER (PGG='pl p2 pm pg cm pmm pmg pgg cmm p4 p4m p4g p3 + p3mlp31mp6 p6m ') COMMON RO.' (" READ IN THE NUMBER OF THE PHASE SET FROM THE")') WRITE(6.NOREF.LIST(0:60) CHARACTER ANS*3.H.E.EQ.FILE='LPT1') PI=4.DIR*1. (5) RETURN TO (1) UNLESS NUMBER OF TRIALS EQUALS NTRIAL.OR. ' ( ' BEGINNING THEN INPUT "B1" ') ') ' WRITE(6.25.50/ OPEN(UNIT=9. THE STEPS IN THE PROCESS ARE: (1) GENERATE RANDOM PHASES FOR ALL REFLECTIONS AND GIVE INITIAL WEIGHTS 0.HMAX.ANS. HOWEVER. REAL RO(0:60.NY.354
Appendices
Appendix XI PROGRAM MINDIR
c
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USER PLEASE NOTE THIS PROGRAM CONTAINS A RANDOM NUMBER GENERATOR WHICH USES INTEGERS. (2) CALCULATE A DENSITY MAP. SOME COMPILERS HAVE DEFAULT INTEGERS WITH ONLY 16 BITS WHICH IS NOT SUFFICIENT. ACCEPT NEW PHASE AND WEIGHT ONLY IF NEW WEIGHT IS GREATER THAN PREVIOUS WEIGHT.FNAME*10.Z(500). THEN APPLIES SIMPLE FIGUREOFMERIT TESTS AND THEN COMPUTES THE EMAP WITH THE HIGHEST COMBINED FIGURE OF MERIT.HMAX.'b')GOTO 79 IF(ANS.O VC=1/CV MARK=0 80 WRITE(6.0:60)fE(1000). +CFOM(500). (4) COMPARE WITH PREVIOUS PHASES.A(500).'P'. THE INITIAL INPUT IS AN OUTPUT FILE FROM FTOUE WITH E'S. IF THIS DOES NOT GIVE A SOLUTION THEN IT SUBSEQUENTLY COMPUTES AND PRINTS EMAPS FOR ANY PHASE SET SELECTED BY THE USER. (3) FOURIER TRANSFORM THE SQUARED MAP AND FIND NEW PHASES AND WEIGHTS.'p')THEN MARK=1 GOTO 78 ENDIF GOTO 80 78 WRITE (6.'(" IF YOU ARE RUNNING THE PROGRAM FROM THE7')') WRITE(6.EQ.'('' RUN THEN INPUT "P" '')') READ(5.50)ANS IF(ANS. WITH WEIGHTS AND SQUARE.'B'. IF MEAN CHANGE IS LESS THAN 2 DEGREES OR IF THIS IS SIXTEENTH REFINEMENT CYCLE THEN GOTO (5).K.WAIT(1000).PHI. OTHERWISE RETURN TO (2).WAIT DATA NPAGE.OR. (7) OUTPUT FIGURES OF MERIT INCLUDING COMBINED FOM.NTRIAL/15.EP(1000).
THIS PROGRAM GIVES A SIMULATION OF A DIRECTMETHODS SOLUTION FOR EITHER A CENTROSYMMETRIC OR A NONCENTROSYMMETRIC STRUCTURE. (9) THEREAFTER USER REQUESTS EMAP FOR DESIGNATED PHASE SETS. IN THAT CASE THERE WILL ALWAYS BE A COMPILER OPTION WHICH GIVES LONG INTEGERS AND THIS SHOULD BE USED.EQ.ANS.BT*6 CHARACTER PGG*(*).0*ATAN(1.PHI(1000)fFP(1000)fPHIP(IOOO).NX.'('' IF YOU WANT TO PRINT A MAP FROM A PREVIOUS'')') WRITE(6. (8) THE MAP FOR THE BEST FOM IS OUTPUT.EQ.K(1000).WATE(1000) INTEGER H(1000). IT FINDS A NUMBER OF SETS OF PHASES WHICH SATISFY THE TANGENT FORMULA.0) CV=PI/18O. ' (" PREVIOUS RUN YOU WISH TO PRINT " ) ') READ(5.
l)GOTO 177 READ(10.50)ANS IF(ANS. DO YOU WANT TO CHANGE IT? Y/N'')') READ(5. p4.'')') WRITE(6.'('' INPUT XRAY WAVELENGTH IN ANGSTROMS '')') READ(5. p3ml.'n')GOTO 101 IF(ANS.NOREF EP(I)=E(I) IF(E(I).EQ.NOREF) IF(IUE.' ( ' READ IN NUMBER OF ATOMS IN THE UNIT CELL'')') ' READ(5.' ( ' INPUT CELL DIMENSIONS A.K(I).NSG)GOTO 107 WRITE(6.*)AC.EQ.OR.PG)+3 NPG=NSG/4 IF(NPG*4. ' ( " AND GAMMA IN DEGREES ' ' ) ' ) READ(5.'y')GOTO 2 GOTO 3 2 WRITE(6.1)THEN WRITE(6.ANS. DO YOU WANT TO CHANGE IT? Y/N'')') READ(5.(H(I).EQ.'C' pi.FILE=FNAME) 76 FNAME='DIRECT.O)E(I)=0 12 9 CONTINUE E(M0)=0.'N'.OR.'')') READ(5.B [IN ANGSTROMS '')') ' WRITE(6. pg. STORE ALL VALUES OF E IN EP AND SELECT SUBSET OF LARGE E'S ALSO LOCATE POSITION OF E(0) EMAX=0 DO 129 I=1. pm. p2. pgg. 51) PG 51 FORMAT(A4) FORM IDENTIFYING INTEGER 1 TO 17 FOR PLANE GROUP NSG=INDEX(PGG.100)FNAME 100 FORMAT(A10) 1 OPEN(UNIT=10.'(''INPUT THE REQUIRED NAME.'(''NAMED DIRECT.'Y'.ONE OF THE FOLLOWING ' ' ) ' ) WRITE(6.'n')GOTO 1 IF(ANS.NE.OR.'N'.BC.ANS.E(I).*)XLAM WRITE(6.EQ.NOREF. pmm.GT. p3.0/SQRT(FLOAT(NATOM)) FNAME='UE.GAMMA READ IN PLANE GROUP SYMBOL AND TRANSLATE INTO IDENTIFYING INTEGER 107 WRITE(6. p6. ' ( " INPUT THE REQUIRED NAME.DAT' 103 WRITE (6.EQ.ANS.'y')GOTO 102 GOTO 103 102 WRITE(6.'')') READ(5.EQ.'(''IS NAMED UE.'Y'. cm.DAT. p6m " ) ' ) WRITE(6.'(''U VALUES HAVE BEEN INPUT INSTEAD OF E'')') STOP ENDIF END OF DATA INPUT.*)IUE.100)FNAME 101 OPEN(UNIT=11 / FILE=FNAME) REWIND(11) IF(MARK.EQ.5*E(M0) CALCULATE THE INTERVALS FOR EMAP HMAX=0 KMAX=0
. cmm.EQ.EMAX)THEN EMAX=E(I) M0 = I ENDIF IF(E(I).50)ANS 50 FORMAT(A3) IF(ANS.EQ. p31m. p4g.EQ.ANS.Appendices
355
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79 WRITE(6.*)NATOM FAC=2.DAT.OR.'C' Note: use lower case symbols as shown '')') READ (5.'('' INPUT PLANE GROUP .'C' p4m.DAT' 3 WRITE(6.I=1.l. ' ("IT IS ASSUMED THAT THE PROGRAM OUTPUT FILE IS'')') WRITE(6. pmg.'(''IT IS ASSUMED THAT THE INPUT FILE FROM FTOUE'')') WRITE(6.LT.
000'')') READ(5.GT.15)KMAX=15 NX=4*HMAX NY=4*KMAX ALLOCATE RANDOM PHASES.EQ.0.NOREF FP(I)=SCALE*FP(I) 53 7 CONTINUE RF=4.NOREF SUM=SUM+(WAIT(I)*E(I))**2 53 6 CONTINUE SCALE=SUM/FP(MO) DO 537 I=1.NTRIAL IEND=0 GENERATE INITIAL SET OF RANDOM PHASES CALL RANFAZ(NPG/H/K/NOREF/PHI/IDUM.*)IDUM ISEED=IDUM IDUM=IDUM NTRIAL SETS OF PHASES WILL BE GENERATED DO 10 ITRIAL=1.NOREF WAIT(I)=0.J)=RO(I.NY RO(I. NOW CALCULATE NEXT PHASES UNLESS IT IS FINAL CYCLE SUM=0 DO 536 I=1.GT.356
Appendices
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DO 5 I=1/NOREF IF(ABS(H(I)).GT. DO 667 I=1. WRITE(6.GT.WAIT(I))INEW=INEW+1 538 CONTINUE IF(INEW.HMAX)HMAX=ABS(H(I)) IF(ABS(K(I)).J)**2 12 CONTINUE CALL FTMAP(FP.15)HMAX=15 IF(KMAX.GT. DO 12 1=0.' ( ' INPUT A SEED FOR THE RANDOM NUMBER GENERATOR'')') ' WRITE(6.NOREF WATE(I)=FAC*E(I)*FP(I)/RF IF(WATE(I). CALCULATE WEIGHTS FOR THE NEW PHASE ESTIMATES.5 571 INEW=0 DO 538 I=1.1. A SEED IS REQUIRED FOR THE RANDOM NUMBER GENERATOR.0 IF(WATE(I).0 ADJUST THE CONSTANT RF UNTIL AT LEAST ONE PHASE IS CHANGED.25 DO 555 I=1. FIRST A FACTOR MUST BE FOUND WHICH CONVERTS COEFFICIENTS FP TO THOSE OF SQUARED DENSITY.RF.5 GOTO 571 ENDIF PHASES CHANGED IF WATE > WAIT.51)THEN RF=RF0.1)THEN WAIT(I)=WATE(I) GOTO 667
.25 555 CONTINUE ICYCLE=0 70 CALL EMAP THE EMAP HAS BEEN CALCULATED.2. RF HAS A MINIMUM VALUE OF 2.NOREF IF(IEND.GT.EQ.NX DO 12 J=0. HOWEVER.MO) INITIALISE WEIGHTS TO 0.'C' AS AN INTEGER BETWEEN 0 AND 10.GT.AND.0)WATE(I)=1. IT IS NOW SQUARED. FOR FINAL CYCLE ALL WEIGHTS AND PHASES ARE CHANGED.PHIP) THE STRUCTURE AMPLITUDES OF THE SQUARED MAP ARE IN ARRAY FP AND THE PHASES IN ARRAY PHIP.KMAX)KMAX=ABS(K(I)) 5 CONTINUE IF(HMAX.
OR.2.GT.0Z(I))/(1000.0*AMIN/AMAX ZMIN=1000.Appendices
357
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ENDIF IF(WATE(I). I = 1.GT.0AMIN)+(1000.GT.0)DEL=360.WAIT(I).LE.E(I) .PHI(I) .0*A(I)/AMAX Z(I) =1000.0 Z(ITRIAL)=0 DO 637 I=1.LT.EQ. WRITE (11.1)GOTO 115 CHECK THAT THERE HAVE BEEN AT LEAST FIVE CYCLES IF(ICYCLE.EQ.0DEL SUM=SUM+DEL PHI(I)=PHIP(I) 13 CONTINUE IF(SUM/NOREF.0.ZMIN)ZMIN=Z(I) 737 CONTINUE DO 837 I=1.AMIN)AMIN=A(I) .NOREF PHI(I)=PHIP(I) 159 CONTINUE GOTO 370 ENDIF CHECK FOR CONDITION THAT EITHER THERE HAVE BEEN 16 CYCLES OF REFINEMENT OR THAT MEAN PHASE SHIFT IS LESS THAN 2 DEGREE SUM=0.0*ZMIN/ZMAX CALCULATE COMBINED FIGURE OF MERIT DO 937 I=1/NTRIAL CFOM(I)=(A(I)AMIN)/(1000.NOREF) 10 CONTINUE ALL SETS OF PHASES HAVE NOW BEEN GENERATED TOGETHER WITH FOMS.NTRIAL A(I)=1000.0ZMIN) 93 7 CONTINUE WRITE(9.LE. *)NOREF.WATE(I).231)ISEED
.0)GOTO 60 370 ICYCLE=ICYCLE+1 IF(ICYCLE.3)A(ITRIAL)=A(ITRIAL)+ FP(I)*WAIT(I) IF(EP(I).999999)THEN WAIT(I)=WATE(I) ELSE PHIP(I)=PHI(I) ENDIF 667 CONTINUE IF(IEND.GT.180. (H(I).0E8 ZMIN=1.5)Z(ITRIAL)=Z(ITRIAL)+ FP(I) 637 CONTINUE WRITE THE SOLUTION ON AN OUTPUT TAPE.0*Z(I)/ZMAX 83 7 CONTINUE AMIN=1000.ZMAX)ZMAX=Z(I) .5)THEN DO 159 I=1.K(I).GT.AMAX)AMAX=A(I) .LT.0E8 DO 737 I=1.1.NOREF IF(E(I).16)GOTO 60 GOTO 70 NOW DO A FINAL CYCLE WHERE ALL THE WEIGHTS AND PHASES ARE CHANGED. 60 IEND=1 GOTO 70 CALCULATE THE FIGURES OF MERIT FOR THIS TRIAL.GT.LT. WAIT (I) .0. NORMALIZE THE FOMS TO MAXIMUM OF 1000 AMAX=0 ZMAX=0 AMIN=1. 115 A(ITRIAL)=0.NTRIAL .NOREF DEL=ABS(PHI(I)PHIP(I)) IF(DEL.0 DO 13 I=1.
WAIT(II).CFOM(I). CFOM = .I=1.0/ROMAX 68 CONTINUE DO 166 1=0. Z.NTRIAL) 300 FORMAT(2(I6 f 2F8.CBEST)THEN CBEST=CFOM(I) IBEST=I ENDIF 65 CONTINUE 177 REWIND(11) DO 66 I=1 / IBEST READ(11.Z(I).GT.23H HORIZONTAL AND ORIGIN .14.14) WRITE(9.*)NOREF.EQ.CFOM(IBEST) 650 FORMAT(16H SOLUTION NUMBER.KMAX)KMAX=ABS(K(I)) 715 CONTINUE IF(HMAX.17) WRITE(9.NX DO 68 J=0.4X)) WRITE(9.500)DIR.NOREF) 66 CONTINUE DO 715 I=1.GT.GT.15)KMAX=15 NX=4*INT(0. ' ( ' ' ' ) ') ' CBEST=0 DO 65 I=1 / NTRIAL IF(CFOM(I).F6.300)(I.1.J)*100.5H LEFT)
.LT.60 LIST(I)=I 166 CONTINUE OUTPUT BEST OR CHOSEN MAP FIND A CONVENIENT ORIENTATION FOR THE OUTPUT WHICH IS THAT WITH THE LEAST NUMBER OF DIVISIONS ACROSS THE PAGE.14H A.A6.NX DO 67 J=0.HMAX)HMAX=ABS(H(I)) IF(ABS(K(I)).PHI(II).1.NX)THEN DIR='Y' BT=' TOP' M=NY/NPAGE+1 L=l ENDIF DO 444 IL=1.1)THEN WRITE(9.5) CALL EMAP SCALE THE EMAP READY FOR OUTPUT ROMAX=0 DO 67 1=0.II=1.6 444 WRITE(9.3X.GT.NY RO(I.F9.3) 652 WRITE(9.4X)) WRITE(9.GT.5) NY=4*INT(0.358
Appendices
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231 FORMAT(17H THE SEED USED IS.J)).(H(II).15)HMAX=15 IF(KMAX.650)IBEST.A1.3.K(II) . DIR= / X / BT='BOTTOM' M=NX/NPAGE+1 L=0 IF(NY.200) 200 FORMAT(2(28H SOLN A Z CF0M.'('' '')') WRITE (9.75*HMAX+0.ROMAX)ROMAX=ABS(RO(I.2F8. E(II).Z(IBEST).J)=RO(I.75*KMAX+0.J)) 67 CONTINUE DO 68 1=0.651)IBEST GOTO 652 ENDIF 651 FORMAT(16H SOLUTION NUMBER.BT 500 FORMAT(13H OUTPUT WITH . ' ( ' ' ' ) ' ) ' IF(MARK.NOREF IF(ABS(H(I)).A(IBEST).NY IF(ABS(RO(I.GT.A(I).
150)(LIST(I).BC(0:15.M)N2=NY WRITE(9.21F4.'('' '')') WRITE (9.0:15). ' (" ")') 26 CONTINUE 45 STOP END
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SUBROUTINE EMAP EMAP CALCULATES A TWODIMENSIONAL EMAP FROM THE OUTPUT OF DIRECT WITH PHASE CHANGES CONTROLLED BY WEIGHTS.EQ.Appendices
359
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IF(L.K(I))=E(I)*WAIT(I)*COS(DTR*PHI(I)) B(H(I). 200)IY.IX=N1 / N2) 600 FORMAT(I4. ' ( ' " ) ') ' 25 CONTINUE GOTO 45 30 DO 26 N0=l.HH COMMON RO.0:30).0:30). DIMENSION A(15:15 f 0:15) # B(15:15. VALUES OF HMAX AND HMIN MUST BE <= 15 AND THE MINIMUM GRID SPACING IS 1/60.' (" ")') N1=(NO1)*NPAGE N2=NPAGE*N0 IF(N0.'('' '')') Nl=(N01)*NPAGE N2=NPAGE*N0 IF(N0.EQ.600)IX.1)GOTO 30 THE MAP IS PRINTED IN SECTIONS WHICH MUST BE JOINED AT SIDE EDGES.KK)=0 B(HH.HMAX. FOR OTHER AVAILABLE PAGE WIDTHS THIS CAN BE ALTERED BY THE DATA STATEMENT NEAR THE BEGINNING OF THE PROGRAM.KK)=0 1 CONTINUE DO 77 I=1 .NX. THE NUMBER OF GRIDPOINTS ACROSS THE PAGE IS NPAGE WHICH IS SET AT 15. KMAX^OREF.2114) ' WRITE (9..AC(0:15 f 0:30).M WRITE(9.0:30).WAIT(1000).K(I))=E(I)*WAIT(I)*SIN(DTR*PHI(I)) 77 CONTINUE NX4=NX/4
.EQ. DO 25 N0=l.(RO(IX.0) WRITE(9.K.IY). H.M)N2=NX WRITE(9.CSX(0:60).K(1000).0174533 CLEAR A AND B ARRAYS DO 1 HH=15 / 15 DO 1 KK=0.IY=N1.N2) WRITE (9. NY.IY). +AS(0:15.2831853 CONSTANT FOR CONVERTING DEGREES TO RADIANS DTR=0.M WRITE(9.N2) WRITE(9.150)(LIST(I).PHI(1000) INTEGER H.2X.I=N1. WAIT TPI=6. HMAX. E.H(1000).' ( ' '')') ' WRITE(9.' (" '')') DO 26 IX=0 / NX WRITE(9. +CSY(0:60).I=N1. PHI.N2) 150 FORMAT(5X. ' ( ' ' ' ) ' ) DO 25 IY=NY / 0 / 1 WRITE(9 . NOREF A(H(I). +E(1000).RO(0:60.15 A(HH.BS(0:15.(RO(IX.0:60).
0.0)/2.J)=0 BS(I.IY)=RO(IX.HH. J)=0 12 CONTINUE DO 13 KK=0.NY 11 CSY(I)=COS(TPI*I/NY) NOW DO THE SUMMATIONS AC.IX)+B(HH.IX)AS(KK.IY)=RO(NXIX.IX))*COZ + +W*(BC(KK.IX))*ZIN 16 CONTINUE THE DENSITY TABLE IS NOW COMPLETE.NY. THE E(0.PHI.15 DO 12 J=0.NX/2 DO 13 HH=HMAX.NX 10 CSX(I)=COS(TPI*I/NX) DO 11 1=0. NO ATTEMPT IS MADE TO SCALE THE AMPLITUDES REAL RO(0:60. RETURN END SUBROUTINE FTMAP(FP.K.AF(15:15.0) TERM HAS BEEN EXCLUDED.KK.E.H.0:15).EQ.NY)) ZIN=CSY(MOD(KK*IY+NY16NY4.NX DO 15 IY=0.NX/2 W=1. DO 15 IX=0.EQ. DO 10 1=0. THESE TABLES ARE USED IN THE SUMMATIONS WHICH FOLLOW AND THEIR USE IS FAR MORE EFFICIENT THAN CALCULATING EACH SINE AND COSINE AS IT IS REQUIRED.KK)*COZ BS(KK.IX)=AC(KK/IX)+A(HH.AS.PHIP) THIS CALCULATES THE FOURIER TRANSFORM OF THE SQUARED EMAP .IX)=BC(KK.WAIT(1000) INTEGER H(1000).NX)) AC(KK.30 AC(I.KMAX.NX)) ZIN=CSX(MOD(HH*IX+NX16NX4. IX) =AS (KK. BC AND BS AFTER CLEARING ARRAYS DO 12 1=0.0:15). IX) +A (HH.J)=0 BC(I.360
Appendices
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NY4=NY/4 NX16=16*NX NY16=16*NY TABLES ARE NOW SET UP OF COS(2*PI*N/NX) AND COS(2*PI*M/NY) WITH N FROM 0 TO NX AND M FROM 0 TO NY.IX)BS(KK. IX) =BS(KK.0:15).NOREF.E(1000).0:15).IX)+B(HH. KK) *ZIN BC(KK.HMAX.0)GOTO 13 COZ=CSX(MOD(HH*IX+NX16. IT HAS HALF THE WEIGHT OF THE OTHER TERMS AND ITS CONTRIBUTION IS NOW LOADED INTO ARRAY RO WHICH WILL CONTAIN THE EMAP.KMAX DO 13 IX=0.0:60).IX))*COZ ++W*(BC(KK.PHIP(1000)fFP(1000).BC AND BS ARE FOR X = 0 TO 1/2.B(1:60.K(1000) COMMON RO.EQ. +BF(15:15.A(1:60.G(h).KK)*ZIN 13 CONTINUE THE SUMMATIONS OVER X FOR AC.0 DO 16 IX=0.CSY(0:60).NY)) RO(IX.HMAX.5 DO 16 IY=0.IX)+AS(KK. +CSX(0:60).J)=0 AS (I.0 IF(IX.IY)+W*(AC(KK.PHI(1000).IX)+BS(KK.IY)=A(0.AND. THE REMAINING REGION FROM X = 1/2 TO 1 WILL BE GIVEN BY SYMMETRY.HMAX IF(HH.IY)+W*(AC(KK.KK)*COZ AS (KK.KMAX COZ=CSY(MOD(KK*IY+NY16. AS.NX/2)W=0.NY 15 RO(IX.WAIT NX16=16*NX
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.NX.IX))*ZIN RO(NXIX.NY DO 16 KK=0.
NX)) AF(HH.NOREF FP(I)=AF(H(I).KK)+A(IX.Appendices
361
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NX4=NX/4 NY16=16*NY NY4=NY/4 TPI=8.KEY(1000) RANDOM PHASES ARE ALLOCATED TO ALL REFLECTIONS.NX COZ=CSX(MOD(HH*IX+NX16.K(1000).NX)) ZIN=CSX(MOD(HH*IX+NX16NX4.NX DO 12 KK=0/KMAX DO 12 IY=1.K.0*ATAN(1.NY)) ZIN=CSY(MOD(KK*IY+NY16NY4.NY)) A(IX.KK)=0 B(IX.KMAX DO 16 IX=1.HMAX DO 15 KK=0.KMAX AF(HH/KK)=0 BF(HH/KK)=0 14 CONTINUE DO 15 HH=HMAX.M0) REAL PHI(1000) INTEGER H(1000).KK)=0 11 CONTINUE DO 12 IX=1.KMAX A(IX.IY)*ZIN 12 CONTINUE NOW FOR EACH H AND K DO THE SUMMATIONS OVER X FIRST CLEAR ARRAYS DO 14 HH=HMAX.KK)=AF(HH. KK)*COZB(IX.0/TPI SET UP COSINE TABLES FOR USE IN SUMMATIONS DO 1 1=0.NY COZ=CSY(MOD(KK*IY+NY16.HMAX DO 14 KK=0.KK)*ZIN BF(HH.
SYMMETRYRELATED
.KK)*COZ 16 CONTINUE FF=SQRT(AF(HH/KK)**2+BF(HH.H. 20 CONTINUE RETURN END
SUBROUTINE RANFAZ(NPG.PHI.NX 1 CSX(I)=COS(TPI*I/NX) DO 2 1=0.KK)=FF BF(HH. KK)=B(IX.KK)=PHIF*CONV 15 CONTINUE TRANSFER MAGNITUDES AND PHASES TO ARRAYS FP AND PHIP DO 20 I=1.KK)*ZIN+B(IX. PHIP(I)=BF(H(I).KK)**2) PHIF=ATAN2 (BF(HH/KK) ^ F C H H ^ K ) ) AF(HH.KK)+A(IX.NOREF.NX DO 11 KK=0.NY 2 CSY(I)=COS(TPI*I/NY) SUMMATION OVER THE Y DIRECTION FOR PARTICULAR K AND X VALUES FIRST CLEAR ARRAYS DO 11 IX=1.KK)=BF(HH.IDUM.IY)*COZ B(IX.KK)=A(IX/KK)+RO(IX.KK)+RO(IX.0) CONV=360.
DGOTO 206 XX=RAN2(IDUM) PHI(I)=0 IF(XX.11.EQ.NOREF KEY(I)=0 103 CONTINUE DO 203 I=1.8.EQ.3.NOREF XX=RAN2(IDUM) PHI(I)=360.14)NPG 1 DO 101 I=1.13.EQ.NOREF IF(KEY(I) .K(J).K(I))GOTO 604 GOTO 504 604 KEY(J)=1 PHI (J)=PHI(D +(1.DGOTO 203 XX=RAN2(IDUM) IF(K(I).4.0)GOTO 303 PHI(I)=360.AND.GT.0*XX GOTO 403 303 PHI(I)=0 IF(XX.H(I).NOREF XX=RAN2(IDUM) PHI(I)=0 IF(XX.EQ.EQ.5)PHI(I)=180 102 CONTINUE GOTO 500 3 DO 103 I=1.0 504 CONTINUE 204 CONTINUE GOTO 500 6 DO 106 I=1.13.0
.DGOTO 204 XX=RAN2(IDUM) IF(K(I).NOREF IF(KEY(D .0*ATAN(1.0.6.11.DGOTO 503 IF(H(J).EQ.EQ.0)GOTO 304 PHI(I)=360. PI=4.AND.H(I).EQ.EQ.K(J).EQ. THE PROGRAM CAN BE APPLIED TO ALL 17 TWODIMENSIONAL SPACE GROUPS.K(I))GOTO 603 GOTO 503 603 KEY(J)=1 PHI(J)=PHI(I) 503 CONTINUE 203 CONTINUE GOTO 500 4 DO 104 I=1/NOREF KEY(I)=0 104 CONTINUE DO 204 I=1/NOREF IF(KEY(I) .0.GT.0)**K(D)*90.0) GOTO (1.GT.5)PHI(I)=180 403 DO 503 J=I+1.14.0.EQ.6.01.7.2.DGOTO 504 IF(H(J).Appendices
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REFLECTIONS ARE ALLOCATED PHASES WITH THE PROPER RELATIONSHIPS.GT.0.6.10.NOREF IF (KEY (J) .0*XX GOTO 404 304 PHI(I)=0 IF(XX.5)PHI(I)=180 404 DO 504 J=I+1.0* (1.00*XX 101 CONTINUE GOTO 500 2 DO 102 I=1.NOREF KEY(I)=0 106 CONTINUE DO 206 I=1.5)PHI(I)=180.14.NOREF IF (KEY (J) .
GT.DGOTO 308 IF(H(J).DGOTO 208 XX=RAN2 (IDUM) PHI(I)=0 IF(XX.208 IF(KEY(I) .EQ.K(J).EQ.0 DO 308 J=I+1/NOREF IF (KEY (J) .K(I))GOTO 408 GOTO 308 408 KEY(J)=1 PHI(J)=PHI(I)+(1.GT.DGOTO 307 IF(H(J).EQ.0*(1.0*(1.EQ.H(I).AND.H(I).K(I).EQ.NOREF KEY(I)=0 108 CONTINUE DO 208 1=1.EQ.NOREF KEY(I)=0 110 CONTINUE DO 210 1 = 1.K(I).EQ.K(J).H(I))GOTO 410 IF(H(J).H(I))GOTO 410 GOTO 310 410 KEY(J)=1 PHI(J)=PHI(I) 310 CONTINUE 210 CONTINUE GOTO 500 11 DO 111 I=1.01.NOREF KEY(I)=0 111 CONTINUE
363
.0.DGOTO 210 XX=RAN2(IDUM) PHI(I)=0 IF(XX.H(I).0.EQ.AND.EQ.EQ.Appendices DO 306 J=I+1.EQ.DGOTO 310 IF(H(J).K(I))GOTO 406 GOTO 306 406 KEY(J)=1 PHI(J)=PHI(I) 306 CONTINUE 206 CONTINUE GOTO 500 7 DO 107 I=1/NOREF KEY(I)=0 107 CONTINUE DO 207 I=1/NOREF IF(KEY(I) .NOREF IF (KEY (J) .EQ.EQ.EQ.01.0)**H(I))*90.0)**(H(I)+K(I)))*90.EQ.EQ.NOREF IF (KEY (J) .NOREF IF (KEY (J) .K(J).GT.5)PHI(I)=180.0 307 CONTINUE 207 CONTINUE GOTO 500 8 DO 108 I=1.0 DO 310 J=I+1.AND.DGOTO 207 XX=RAN2(IDUM) PHI(I)=0 IF(XX.0 3 08 CONTINUE 2 08 CONTINUE GOTO 500 10 DO 110 I=1.K(J).AND.K(J).5)PHI(I)=180.EQ.AND.5)PHI(I)=180.K(I))GOTO 407 GOTO 3 07 407 KEY(J)=1 PHI(J)=PHI(I)+(1.0.DGOTO 306 IF(H(J). 210 IF(KEY(I) .0 DO 307 J=I+1.
AND.16)PHI(I)=0 IF(NPG.H(I))GOTO 414 IF(H(J).EQ.AND.0PHI(I) CONTINUE CONTINUE GOTO 500 DO 114 I=1/NOREF KEY(I)=0 CONTINUE DO 214 I=1/NOREF IF(KEY(I) .EQ.K(J).EQ.0.K(J).0.K(J).EQ.0 DO 313 J=I+1.K(J).EQ.0 IF(NPG.H(I).AND.0 CONTINUE CONTINUE GOTO 500 DO 113 I=1/NOREF KEY(I)=0 CONTINUE DO 213 I=1.AND.AND. K(I).K(I))GOTO 514 IF(H(J).K(I).0 IF(NPG.EQ.EQ.AND.K(J).K(I).AND.H(I)K(I))GOTO 514 IF(H(J).EQ.5)PHI(I)=180.K(J).EQ.DGOTO 311 IF(H(J).EQ.GT.EQ.DGOTO 313 IF(H(J).K(J).EQ.H(I)K(I))GOTO 614 IF(H(J).0 DO 311 J=I+1/NOREF IF (KEY (J) .19)PHI(I)=0 IF(NPG.EQ.364
Appendices
511 411 311 211 13 113
413 513 313 213 14 114
DO 211 I=1/NOREF IF(KEY(I) .AND.EQ.EQ.EQ.EQ.EQ.K(J).H(I).EQ.K(J).EQ.H(I)+K(I))GOTO 513 IF(H(J).EQ.H(I))GOTO 411 IF(H(J) .19.EQ.EQ.AND.EQ.K(I))GOTO 414 IF(H(J).NOREF IF (KEY (J) .0*(1.H(I)K(I).K(I).0)**(H(I)+K(I)))*90.AND.EQ.K(J).16.H(I))GOTO 411 GOTO 311 KEY(J)=1 PHI(J)=PHI(I) GOTO 311 KEY(J)=1 PHI(J)=PHI(I)+(1.K(J).K(J).AND.DGOTO 211 XX=RAN2 (IDUM) PHI(I)=0 IF(XX.0.H(I))GOTO 413 IF(H(J).AND.K(I).AND.XX.EQ.EQ.EQ.XX.EQ.01.H(I)+K(I).5)PHI(I)=180.K(I). K(I).K(J).NOREF IF(KEY(I) .K(I).EQ.AND.EQ.AND.EQ.H(I)+K(I).K(I))GOTO 411 IF(H(J) .H(I)K(I))GOTO 413 IF(H(J).EQ.K(J).H(I)K(I).H(I)K(I).H(I))GOTO 514 IF(H(J).H(I).AND.EQ.EQ.EQ.K(I).13)PHI(I)=XX*3 60.EQ.H(I))GOTO 511 IF(H(J) .AND.EQ.H(I))GOTO 511 .EQ.H(I)+K(I))GOTO 714 IF(H(J).K(J).DGOTO 213 XX=RAN2(IDUM) IF(NPG.EQ.H(I))GOTO 614 GOTO 314
.H(I))GOTO 714 IF(H(J).H(I))GOTO 513 GOTO 313 PHI(J)=PHI(I) GOTO 313 PHI(J)=360.K(J).GT.AND.EQ.H(I)+K(I))GOTO 414 IF(H(J).EQ.AND.K(J).EQ.H(I)+K(I).EQ.EQ.AND.K(J).EQ.0 DO 314 J=I+1/NOREF IF(H(J).5)PHI(I)=180.K(I).EQ.EQ.AND. IF(H(J) .DGOTO 214 XX=RAN2(IDUM) PHI(I)=XX*360.K(J).GT.
0 COMES FROM "NUMERICAL RECIPES" BY W.RM=1.EQ.97 IDUM=MOD(IA*IDUM+IC.EQ. B.9 7.P.OR. CAMBRIDGE UNIVERSITY PRESS.0PHI(I) IF(NPG.1)PAUS E IY=IR(J) RAN2=IY*RM IDUM=MOD(IA*IDUM+IC.IA=1366.0 TO 1.PRESS. FUNCTION RAN2(IDUM) PARAMETER (M=714025.0)THEN IFF=1 IDUM=MOD(ICIDUM.H.Appendices
365
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414 PHI(J)=PHI(I) IF(NPG.M) ENDIF IY=IDUM J=l +(97*IY)/M IF(J.FLANNERY.LT. S.LT.15)PHI(J)=360 PHI (I) GOTO 314 514 PHI(J)=360.M) IR(J)=IDUM 1 CONTINUE IDUM=MOD(IA*IDUM+IC.0.15)PHI(J)=PHI(I) GOTO 314 614 PHI(J)=PHI(I) GOTO 314 714 PHI(J)=PHI(I) 314 CONTINUE 214 CONTINUE 500 PHI(MO)=0 RETURN END THE FOLLOWING FUNCTION ROUTINE WHICH GENERATES RANDOM NUMBERS IN THE RANGE 0.EQ.IC=150889.IFF.VETTERLING.0/M) DIMENSION IR(97) DATA IFF/0/ IF(IDUM.T.OR.A.M) IR(J)=IDUM RETURN END
.TEUKOLSKY AND W.GT.M) DO 1 J=l. 1986.J.
*)NOREF.NOREF) NOW CALCULATE AND OUTPUT THE RESIDUAL SUMDIF=0 SUM=0 DO 40 1=1.'N'.EQ.OR.'('' F[OBS] AND PHI[CALC] IS COMB. DO YOU '')') WRITE(6.'('' IT IS ASSUMED THAT THE FIRST FILE CONTAINING'')') WRITE(6. DO YOU WANT TO CHANGE '')') ' Y/N '')') WRITE (6. (H (I) . THE OUTPUT FILE COMBINES THE OBSERVED F's WITH THE THIS CALCULATED PHI'S AND IS SUITABLE FOR INPUT TO FOUR2. NOREF) FNAME='SF2. 50) ANS 50 FORMAT(Al) IF(ANS. '')') READ(5. K (I) .EQ.'(''THE F[OBS] IS SF1.ANS.*)NOREF.'(''READ IN THE FILE NAME [<= 10 CHARACTERS].ANS.FNAME *10 OPEN(UNIT=9.K(I).OR.EQ.'y')GOTO 22 GOTO 23 22 WRITE(6.ANS. FI.OR.'(''TO CHANGE THIS? Y/N '')') READ(5.K(I). DO YOU WANT '')') WRITE(6.EQ.'(''READ IN THE FILE NAME [<= 10 CHARACTERS].F6. THE PROGRAM ALSO OUTPUTS THE RESIDUAL FOR THE CALCULATED F's. '')') READ(5. REAL Fl(lOOO) / PHI2(1000).FILE=FNAME) WRITE(12.'Y'.FILE='LPT1') FNAME='SF1. 50) ANS IF(ANS.EQ.'y')GOTO 12 GOTO 13 12 WRITE(6.3) STOP END
.'('' WANT TO CHANGE THIS? Y/N '')') READ (5.EQ.'N'. PROGRAM ENABLES THE FOURIER REFINEMENT OF STRUCTURES.Fl(I).ANS.ANS.DAT.100)FNAME 11 OPEN(UNIT=11 / FILE=FNAME) READ(11. ' ( 'THIS? READ (5 .1=1.'y')GOTO 2 GOTO 3 2 WRITE(6.366
Appendices
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C
Appendix XII PROGRAM CALOBS THIS PROGRAM COMBINES OUTPUT FILES THE FIRST OF WHICH IS IN THE FORM GIVEN BY STRUCFAC AND HAS "OBSERVED" F'S AND THE SECOND OF WHICH HAS "CALCULATED" F's AND PHI'S FROM AN APPROXIMATE STRUCTURE.NOREF SUMDIF=SUMDIF+ABS(F1(I)F2(I)) SUM=SUM+F1(I) 40 CONTINUE RESID=SUMDIF/SUM WRITE(9.EQ.'('' IT IS ASSUMED THAT THE OUTPUT FILE CONTAINING'')') WRITE(6.'('' IT IS ASSUMED THAT THE SECOND FILE CONTAINING'')') WRITE(6.DAT' 13 WRITE(6.EQ.PHI2(I).DAT' 23 WRITE(6.OR.300)RESID 300 FORMAT(39H THE RESIDUAL FOR THE INPUT F[CALC] IS .'Y'.F2(1000) INTEGER H(1000).K(1000) CHARACTER ANS *1.'N'.OR. 1 = 1.DAT.OR.100)FNAME 100 FORMAT(A10) 1 OPEN(UNIT=10 / FILE=FNAME) READ(10.'n')GOTO 11 IF(ANS.(H(I).1=1.'(''READ IN THE FILE NAME [<= 10 CHARACTERS]. Fl (I) .DAT.50)ANS IF(ANS.EQ.DAT' 3 WRITE(6.'Y'.100)FNAME 21 OPEN(UNIT=12.F2(I).NOREF) FNAME='COMB.'n')GOTO 21 IF(ANS.ANS.EQ.'n')GOTO 1 IF(ANS.*)NOREF. '')') READ(5.(H(I).EQ.EQ.PHI2(I).'(''F[CALC] AND PHI[CALC] IS SF2.
26 0 or 180° 20 or 160° 40 or 140° 60 or 120° 80 or 100° Amplitude 1.767 0. If graphical processes are used then precise numerical agreement should not be expected.000 0. overleaf.1 If unit vectors 1. as shown in the International Crystallography.966 0. s = 2 sin 0/2 and the angle between r and s is 6. (a) 90°.2 (a) Orthorhombic Pmml.948 Intensity 1.899
Tables for
Xray
367
. r2 = 92/2. (b) Monoclinic. as a fraction of that from four scatterers at the origin.876 0.3 The diagrams. The amplitude. Chapter 2 2. is ^{cos(27ir1's) + cos(2inr2's)} where rx = 32/2.248 0. (d) 19° 28'. (b) 26°34/ . (c) 54° 44'. Pljc. are given in fig. Table II1. j . 1. PA. 1.062 0.983 0. 11. This gives the amplitudes and intensities listed in table II1. (c) Tetragonal.000 0. The angle a between two planes is given by cos a = A1*n2.Solutions to Problems
The solutions are given with outline derivations where appropriate.1 (a) With the centre of the group as origin the atomic coordinates are ±32/2 and ±92/2. Chapter 1 1. £ are taken along the edges of the cube then the unit normal to the plane with Miller indices (hkl) is n = (hi + k] + fc)/(h2 + k2 + l2f.
2 x 10" 16 joule.012.0. This gives 29 0 or 180° 20° or 160° 40° or 140° 60° or 120° 80° or 100° 0 0° 14° 321° 323° 335° 2.3.7 x 107 m s~ *._3*)
From this it may be found that the ratio of the scattered intensity to that for a single scatterer is the same in both directions and equals 0. so that s. Solution to Problem 1.0).1. r2 = 61 and r 3 = 91.0). say.i£.1).3 A 2 kV electron has energy 3. the quadrant of < being such that the / > / signs of B and A are the signs of sin (> and cos (/>. The phase angle required. If
. 11. S2 = ( .
Solutions to Problems
o
o
o
o o
oooo
o
Origin on g (a)
O0O0
p ©
o
0
°0
0
O0°
Origin at 4mm
(b) With one end of the group as origin the amplitude of scattering compared with that of a single scatterer at the origin is 1 + exp(27tiiys) + exp(2Ttir2s) + exp(27iir3s) = A 4. (/>. Sx = (1. Equating this to \mv2 the electron velocity is found to be approximately v = 2. =
and
: = A(l_3*_3*.0. where r± = 3/1.368 Fig. is given by tan 0 = B/A.2 For an origin at the centre of the cube the scatterers have coordinates
±(\1MM\ ±(RR &\ ±(& &Rand ±(& " R "i4The
unit vectors in the direction of the incident and scattered beams are So = 3"±(1. 2.1.
)
369 /_©+
0+
_0+ Origin on plane m. The number of electrons traversed by the
. unique axis c
+0O+
+0O+
Origin on plane m. This gives / = E/ST. unique axis b (c) 01®+
_ / 0 +
/
/
0+ 0+ 0O
W
0+ 0O
/
/
Origin at centre (2/m). unique axis c
+0
0O
O O+O O + Origin at centre (2/m). (cont. This gives n ^ 9 x 10 19 electrons m 3.Solutions to Problems
Fig. unique axis b id)
+ 0 O+
+o + o 0+
+Q
+0
0+
i+o 01+ OH
+O
0+
0+
+0
Origin on 4
the electron beam has n electrons per unit volume and its crosssectional area is a then the current is 1 = nave. If the laser pulse has intensity /. duration x and crosssectional area s then the energy of the pulse E = 1ST. 11.
21 0.0 0.71 0. The energy of one photon is hc/L Assuming 2 ^ 7 x 10~7m this gives about 106 photons collected by the detector.0 0.6 0.
2sin0/.00 0.8 2. Table II3.92 2.4 1.2 1.34 1.8 2.26 0.76 2.00
9.69 1. 2.370
Solutions to Problems
light beam.0 0.93 3.20 0.i 0.4 0.08 0.24 1.9 1.89 0.95
. is approximately 4 x 10 ~3 sn since the diameter of the electron beam is 4 x 10" 3 m.42 0.65 2.04 0.00 1.1 0.33 0.00 1.11 0.00 0.52 0.8 1.65 0.32 0.27 0.3 0.46 2.02 r 0.0 4nr2pls 0.82 2.0
4™2p2s
0.0 1.44
The amplitudes of scattering from these electrons and the intensities of coherent and incoherent scattering from the atom are given in table II3.7 0.6 1.81 0.4 0.42 1.
This gives ET = 2.44 0.0
Pis
Pis
^Thomson
''Compton
1.2 x 10~ 13J.8 1. JV.00 0. Table II2.29 0.6 1.2 0.10 0.86 2.43 0.00 4.4 0.77 0.91 2.01 0.2 0.4 1.78 2.2 0.21 0.
r 0.48 0./tdQ = iN[ = 2 x 10"3n ( / e2 V =.97 0.6 0.04 0.0 1.47 0.03 1.00 0.46 0.16 0.2 1.10
0.4 The radial electron densities for a Is and 2s electron of a Li atom are listed in table II2.00 0.8 0.5 0.42 0. The total energy in the scattered beam is ET = .(1 + cos2 20)/idQ \4ns0c2mJ e2
r\
V (1 + cos220)£dQ.41 0.17 2.16
1.6 0.16 2.
12 0.90 0. fc* = 0.15 0.00
a*s 0.41 1.46 1.35 1. 3.26.73 1.6 From V = abc(l — cos 2 a — cos 2 /? — cos 2 y + 2 cosa cos /? cosy)* the volume of the cell is 2.3
(i) a* = 0. Table IIIl.70 0.20 0. F* = 1.00 0. The probable value of N is 2 and this gives a density for the crystal of 1.17 3.35 0. a* = p* = 90°.
a*s 0.55 0.95 1.60 0.76 36.73 0. c* = 0. (iii) d321 = 1.82 1.67 1. 3.46 9.061 x 10 3 kgm" 3 .067 A " 1 .5 In table III4 there is presented the complete output of STRUCFAC.
h 0 1 2 _3 4 <a A 30° 00' 48° 14' 62° 13' 74° 34' 86° 13' h 5 6 7 8 9 97° 42' 109° 31' 122° 16' 137° 14' 159° 04'
3.2 x 103 kg m " 3 the number of molecules would be N = 2.115.85 0.76 9.2 The orders of diffraction h and angles il/a are given in table III2.1 The values of K6 and K\ are given in table IIIl.53 2.08 0.00 0. Table III2.68 1.25 0.00 1.Solutions to Problems
371
Chapter 3 3.68 3.00
3.00 26.80 0.47 26.75 0.10 0. y* = 60°. If your solution agrees with this then the remainder will certainly be correct.05 0.47 0.00 0.00 0.50 K6 6.00 2.45 0.636 x 10~ 2 8 m 3 .00 0. (iv) 29= 80° 4'.231.00 0.30 0.12 1. Notice the relationships between the structure factor magnitudes and phases of reflections with indices (h k 0) and (h k 0).
.00
Kl
36.08 5. 3. (ii) V= 650A 3 .41 0.00 0.00
K6 0.65 0.00 5.3974 x 10~ 25 kg and for a density of 1.54 x 1 0 " 3 A " 3 .82 0.67 0. The mass of one molecule is 1.00 0.17 6.00 0.00 0.4 In table III3 there is presented a selection of the output of STRUCFAC.50 0.53 0.40 0.00 1.20 A.00 0.35 0.
089 5.0 180.0 7 180.0 160.0 4 180.487 19.619 7.0 0.0 3 180.910 0.0 0.0 12 180.0 0.0 180.0 180.673 18.194 38.264 5.894 3.0 1 0.0 5 0.769 8.0
.415 7.0 11 0.858 11.0 180.0 0. •'
idO.0' 14 180.0 180.0 6 180.000 40.119 26.459 4.0 180.0 0.716 17.0 0.211 22.0 0.EOS 3.228 13.0 3 180.713 6.0 180.022 35.754 1.479 7.512 13.070 9.858 13.294 3.0 0.764 40.0 _ i ••
3 2
c.499 15.672 8.
h 14 13 12 12 11 11 10 10 10 9 9 9 8 8 8 7 7 7 6 6 6 6 5 5 5 4 4 4 4 3 3 3 3 2 2 2 2 1 1 1 1 1 0 0 k
I
F
21.992 7.688 11.0 180.471 0.0 0.0 0.816 4.0 180.0 0.834 2.932
PHI
2 1
4
L.352 12.158 42.534 13.0 9 180.0 0.0 8 180.987 3.0 160.0 0.755 24.080 9.167 20.861 2.0 0.0 180.735 39.005 65.0 6 180.0 2 180.0
5 1 4
7 /
2 5 3 3 6 9 3 6 9 2 5 8 11 3 6 9 1 4 7 10 1 4 7 10 1 4 7 10 1 4 7 10 13 2 5
0.363 29.0 180.023 27.548 1.0 180.0 0.0 180.0 9 180.0 8 0.0 1 0.861 57.692 256.0 7 180.347 16.981 27.0 7 0.0 160.724 19.0 2 180.0 180.194 27.0 180.0 180.O 13 180.0 8 0.263 8.0 0.456 6.0 0.0 0.0 10 180.0 180.0 0.0 180.664 3.0 0.0 180.0 0.438 15.160 6.241 12.0 5 180.540 10.733 7.541 7.061 56.143 5.0 0
2 5 3 6 1
4
I
7 1 4 7 10 3 6 9 1 4 7 10 2 5 3 11 2 5 8 11 2 5 8 11 2 5 6 11 0 3 6
0.0 160.910 1.0 180.0 6 180.0 0.641 1.490 21.817 4.0 0.914 6.0 0.507 3.0 7 0.985 4.0 180.0 160.729 18.0 180.352 30.0 0.0 0.0 0 160.378 3.584 2.0 2 0.491 8.241 6.0 0.825
PHI
h
k
a
F
4.623 0.0 180.952 67.0 3 180.0 13
0.0 1 0.670 32.0 5 0.0 0.850 43.0 0 180.7% 9.0 4 180.0 180.280 13.292 22.430 12.0 4 180.160 IE.944 20.639 2.0 0.188 15.114 6.067 27.0 0.0 0.510 8.349 1.989 22.039 10.746 5.0 2 0.836 2.0 180.693 5.0 0.0 10 180.0 180.501 13.0 3 0.333 23.0 0.0 160.0
0.0 12
4 34
130.091 3.213 22.0 0.0 0.756 44.0 0.
180.0 4 0.977 1.372
Solutions to Problems
Table III3.0
.392 16.730 11.692 27.0 5 0.386 1.845
PHI
h
k
i
F
•5.694 14.0 0.519 11.372 12.0 180.106 28.644 19.0 0.180.0 180.132 4.0 180.0 180.0 180.490 33.0 0.0 180.027 26.388 5.614 16.0 10 0.165 21.0 13 180.228 2.373 6.432 4.947 8.0 0.986 9.0 1 180.295 0.269 8.0 180.0 0.0
11 11 11 10 10 9 9 9 8 6 6 7 7 7 6 6 6 6 5 5 5 5 4 4 4 4 3 3 3 3 2 2 2 2 1 1 1 1 0 0 0
7 3 6 * 4 7 2 5 8 2 5 8 1 4 7 10 2 5 6 11 3 6 9 12 3 6 9 12 3 6 9 12 3 6 9 12 1 4 7
180.181 4.039 6.943 8.
322 3 9..4 52.051 57..6 22..032 22. 3 12.9 3..099 145. 3 17...762 2 30.7 2.. 262
io
•~9
9 8 8 7 7 6 6 6 5 5 4 4 3 3 3 2 2 1 1 0 0 0 1 1 1 2 2 3 3 3 4 4 4 5 5 6 6 6
E 5 E 5 E 5 1 4 7 3 6 2 El.1 93...051 57. 6 4.1 7.3 26.798 23. 8 16.2 20. 7 13.866 19...045 17.045 1 35.344 113.0 135.. 146 150....762 86..6 E IS .5 26.9 E3.396 149.3 130. 9 21. 1 3.496 155.364 11. 799 0. 902 58.. 7 2. 741 171.. 0 7. 941 30.262 175.9 12. 417 41.9 30..3 54.5 20.0 17.933 127.3 180.5 16..071 177. 3 41.2 3.732 6
. 9 32. 7 2. 000 59.094 2. 1 6. 822 139.056 64.908 34.6 20..9 16.. Oil 54.4 160.729 12. 2 19. 5 20.958 126.357 IE..9 134..9 12. 284 180. 182 70.837 7. 745 180.7 30. 1 46.278 15. 0 12.7
4
3 3 2 2
_p
1 1 0 0 0 1 1 2 2 2 3 3 3 4 4 5 5 5 6 6
8..324 35.7 11. 4 9.. 0 2.1 139.3 40. 7 36.941 6 2 32. 13.8 20.231 144....4 12.706 11..391 El .422 3.6 22..661 4 11.713 155.1 73.605 150.4 46.644 44.1 0.. 623 156.046 7 12.
373
h 14 13 IE 11 11 10 10 9 9 8 8 7 7 6 6 5 5 5 4
k 1 2 1 4 2 5 3 6 3 6 3 6 2 5 1 4 7 3 6 2 5 1 4 7 3 6 1 4 7 2 5 0 3 6 1 4 7 2 5 0 3 6 1 4
F
PHI
h 14 13 IE 11 il 10 9 9 8 8 7 7 7 6 6 5 5 4 4 4 3 3 2 2 1 1 1 0 0 1 1 1 2 2 2 3 3 4 4 4 5 5 5 6 6
k E 3 3 E
c
F
PHI
h 13 IE IE 11 io
k 1 1 4 3 1
F 9.0 0.458 6.2 124.. 2 12.864 33..562
PHI 165.4 12.8 145. 4 10.933 5 0 34. 642 80.729 9.6 15. 6 9...6 118..379 43..605 10. 9 42.499 70.126 120.889 7 7.8 116..146 4 10.5 43.000 3 6 24.393 17..902 121.221 171.1 12.6 16.3 139.658 31. 323 2.644 3 6 16.173 153.7 18.300 14..299 0 10.162 2.741 8..5 170.. 643 150.0 47.. 126 59.869 52.4 117.000 0. 869 52..641 8.732 117.162 132. 0 8.091 149.4 14 .4 14.. 934 107.661 9. 394 125.8 170.346 176 ...2 0. 1 10... 046 43.9 0. 9 0.13b 4i.182 70.827 148 .b77 i0.524 138.Solutions to Problems Table III4.. 0 20.786 18. 6 62.392 24.0 . 4 16.9 125.032 30.422 4 19. 094 63.0 104.325 12.5 11..323 173... 7 35.205 30.. 9 11. 1 10..287 77.637 96 .623 23.934 5 0 256. 000 80...1 7..4 30.097 S. 5 11.8 14. 6 1.7
3 * 4 1 4 1 4 7 3 6 2 5 1 4 7 3 6 2 5 1 4 7 2 5 0 3 6 1 4 7 2 5 0 3 6 1 4 7 2 5
8...763 6. 002 113.6 17.. 964 180.278 9.490 36.655 1 70.3 176..0 167.3 117.002 9.6 1.622 18.... 000 15. 0 25.. 1 9. 2 7.1 29.7 150.. 958 126.7 20.102 3 25.417 41.9 66. 4 22.161 6..4 1.8 179. 287 102. 7 30.6 154. 1 10. 0 14. 221 171.499 5 13. 889 134.9 11.. 6 2.4 7. 0 11.533 37. 102 55.8 22..642 99.6 16. 6 7.4 162.099 7 6.0 11...364 2 10. 2 17.7 11. 1 22. 4 19. 0 9.3 40.299 7.Oil 5 1 36.874 160. 562 11.
6 8.187 3.379 41.374
Solutions to Problems Table III4.6 31.3 149.0 .392 23. 35 9. 25 10.978 11. {continued)
h k F PHI h k F PHI h k F PHI
6 7 7 6 8 9 9 10 10 11 11 12 12 13 14
a
7 2 5 0 3 6 2 5 1 4 1 4 1 4 2 1
18.52 8. OO 12.4 180.3 83.763 7.071 20.0 146.822 13.0 145.091 18. 26
4.9 149.0 14.0 0.1 .181 6.173 12.0 .864 22.4 148.136 19.3 (i) F(S) =
4n2s2
—fccos(2Tisa)]+ k}.524 25.713 9.0 0.5 25.036 13.300 12.0 . 15
B(h)
0.827 18.4 160.2
7 7 7 8 8 9 9 9 10 10 11 11 12 13 13 14
0 3 6 1
4
0 3 6 2 5 2 5 2 0 3 2
25.9 156.9 137.458 6.9 139.21.2 The output from FOURl is as follows.1 0.387 8.2 0.07 16.0 . 47 22.1 40. 11 9.968 18.57
a
12 16 20
f (x) 26.2 3.4 7. 02
6.0 42.0 26.
THE COORDINATES ARE X/G n O 4 n 19. 31
h 1 5
A (h)
0.837 12. 49 7.6 142.346
160.868 8.658 14.1 The output from SIMPl should be as follows:
h 0 4
A '( h ) 20.324 8. 40 30.4 139.3 66.786 10.4.9
7 7 7 8 8 9 9 10 10 11 11 12 12 13 14
1 4 7 2 5 1 4 0 3 0 3 0 3 1 0
22.706 11.874 7. 76
B< h ) .496 8.396 14.3 21.0 144.056 2.5 163. 09 16.3 36.798 8. This may be compared with the table given infig. 37 34.677 10.325 17. 17
h 3
A (h) 0. 00 0.1 180. 97 1 5 9 13 17 n/N WHERE N = f (x) 23. 62
B (h) 0 .637 1. 45 7. 97 .0 25.766 16.533 12.8 155. 22 19.299 7.97 31. 17
4.908 16.391 22.357 14. 04 13.9 130. 05 .056
2.0
Chapter 4 4.0 170.4 115.0 162.344 14.27
B(h)
.4 155. 71 n 2 6 10 14 18 20 n 3 7 11 15 19 f (x ) 29.231 12.641 16.8 0.1 144.
(ii)
.3 62.1 180.8 14.490
180. 20
h 2
A (h) . 09 36. 57 37.097 20.
5. 24. Hence Fourier transform of g(x)*h(x) = exp( —
J 00 00 00
2R2S2
+ 47ii5).
4.3. 13. Fourier transform of h(x) = exp(47tis). exp{ .5 (2u)*
= exp( — 2n s
2 2
+ 4TUS). The reflections too weak to be observed have indices (420). I is zero 2 if two of h. the angle through which the crystal must be rotated is ij/ = (n/2) — 6 + (j) and the intersection will be with the lower section of the circle.4 \>x —i ^ x ^ I
i ^ y. (hk) inside circle and (h'k1) outside.20. (340) and (410).4 Fig. The reflections which are observed are indicated. I are zero 1 for h = k = I = 0.0 mm. 4
c(x) = O c(x) = — {1 + sin(27ix)}
2TI
/)/ Y  ^v^/ —
1
^
. k.
. y and z. 9.1}. respectively. Vl shows the fit of the reciprocal lattice on to the arcs within the allowed regions of reciprocal space.2 (a) 6. For a point inside the circle. It will be found that if a reciprocallattice net is rotated over a diametral section of the sphere of reflection then one must rotate the net 54° between the (907) and (702) reflections. 4. I is zero 4 if one of h.91.2n2s2 + 47iis) exp{ . k.y. If this region is found in the map then the map is almost certainly correct.2 .X X Z o)Wk2FllWcos(27cftx)cos(27cfcy)cos(27i/z) where coM/ = = = = 8 if none of h. Chapter 5 5.fa . x
sin(27ix)
71
 < x< H
.7 Part of the projected density is shown in fig.01 A. (b) The layer lines indicate a = 9.fa .
Fourier transform of g(x) = exp( — 2n2s2). 10.5.97. 5.27iis)2}dx
J — oo
4.oo
c(x) = — {sin(27ix) .6 p{x. V2 shows two reciprocallattice points. 4. k. 5.3 Fig.1 This problem can be solved graphically.2)2}exp(27iix5)dx .z) = .Solutions to Problems
375
4.^ 4 ^* ^ ^* J2.
The range of summation is 0 — \ for x.
From equation (5. respectively.
Table V1.108 x 10" 3 1 x ( 3 x 108)2 = 1.0' or 0 + 0 .24) the critical wavelength in angstroms is given by _ 18.706 x 10 " 4 radians 3 x 109 x 1. With the y coordinate on the upper section taken as positive and on the lower section taken as negative the (x.
= ^ + 0 .the angle of rotation in the two cases being.
h 1 1 1 1 1 k 1 6 5 4 3 2
x(mm) y(mm) 65 /i 1L L I L I L L L L L L [ L [ k 1 6 5 4 3 2 1 0 2 3 4 5 6 7 x(mm) y(mm)
T T T T 0 T 1 T 2 T 3 T 4 T 5 T 6 T 7
61 68 74 80 85 6 16 42 67 72 71 69 66 61 55
51 40 31 23 16 9 5 9 16 23 31 40 51 65
t T
35 29 25 21 19 18 23 53 76 88 5 10 16 22 29
65 51 40 31 23 16 9 5 9 16 23 31 40 51 65
5. the intersection can be with either the upper section or the lower section .y) coordinates on the film are as listed in table V1.5 From equation (5.602 x 10~ 1 9
= 35".
.883 A.64 '"BE2 where B is in tesla and E in GeV.376
Solutions to Problems
For a point outside the circle. Inserting the given values Xc = 1. This gives
?JL
9.1
and
A reflection will be produced if 0 ^ \j/ ^ 180°.23) the vertical divergence of the beam is given by me2 E where E is the energy of the electron beam.
. Vl. Diagram for solution 5.4.6 Let the intensities of the (231) and (462) reflections be lx and / 2 . respectively. / / Incident beam
/ /
^ Direction
of
^
b
(h'k')
rotation
1^
Section of sphere of reflection
1
A
a
5.Solutions to Problems
Fig. The (462) reflection corresponds to the shorter wavelength so that / ! + / 2 = 262 and i + 0. V2. Diagram for solution 5.(460)
(100)
(100)
(440)
Fig.3/ 2 = 106.3.
377
.
22 0.00002 0. = 91.108 58 = 0.0109.00 10.27 x' (mm) 0.1 3.45 4.
Point 1 2 3 4 5 6 7 8 9 10 x (mm) 0.44 1.82 0. The details of the calculation are given in table VI1.12 5.60 • x') exp{ x')}
t
0. Division of the crystal for the absorption calculation.2 4720 m " 1 .04 1.12 0.378
Solutions to Problems
Solving the simultaneous equations gives I.27 0.27 0.65 6.36 1.00075 0.80 9.20 7.85 x + x' (mm) 1. VI1.3 The reflecting planes make an angle 45° with the cell edges and 6 = 21.108 58
A=
Fig.93 1.82 0.
6\ \ \ \ \ \ \ \ \
Direction of reflecting plane
i
I
I
1
i
i
i
i
1 mm
.66 1.62 0.20 7. I2 = 170.44 1.
0.27 0.003 70 0. 6.53 1. VI1.80 2.50 0. The crystal can be divided into ten regions as shown in fig.20 7.56 x 108. Chapter 6 6.49 0.27 0.00012 0. 6.33.00075 0.009 56 0.62 0. Table VI1.005 52 0.67.00111 0.60 2.09 1.3° for the (240) reflection.20 5.44 1.62 0.00075 0.22 0.82 0.08630 0.62 0.82 0.
353 9.184 1.694 6.047 1.0 0.0 180.767 21.0 0.0 0.469 9.769 12 .0 0.0 0.494 9.031 0.028 8.238 5.0 180.000 38.533 12.290 4.415 8.0 180.926 6.044 8.0
180.902 23. Compare this solution with that of Problem 3.0 11 0.012 5.207
180.296 8.639 2.925 17.0 180.0 0.0 180.512 2.0 0.0 180.0 180.0 0.0 0.0 0.0 180.968 5.0 180.0 0.490 0.672 36.0 180.0
0.0 0.0 180.0 0.920 1.604 19.0 180.114 8.0
0.0 0.557 4.118 61.713 7.102 55.0
0.0
0.535 14.570 64.0 0.0 0.640 1.0 180.0 180.0 0.0 14 180.0 11
0.0
0.0 180.
Table VI2.891 0.840 9.0 0.0 180.880 2.0 0.556 3.0 180.792 1.466 2.0 0.0 180.629 3.0 180.206 21.0 0.978 1.213 5.0 180.278
180.0 180.370 1.907 2.0 180.359 8.0 180.0 180.928 5.0 180.472 20.852 4.0 180.0
8
11 2 5 8 11 0 3 6
180.041 1.992 13.0 10 0.Solutions to Problems
379
6.127 2.0 180.334 32.0
9
9 8 8
8 7 7 7 7 6 6 6 5 5 5 5 4 4 4 4 3 3 3 3 2 2 2 2 1 1 1 1
180.385 0.702 6.431 9.0
180.201 20.308 1.597 5.0 0.0 0.898 26.0 180.847 1.661 8.0 180.306 17.0
180.480 0.0 13
0.0 180. If your solution agrees with this then the remainder will certainly be correct.0 0.0 12 180.717 7.393 14.405 5.0 180.0 0.394 8.0 180.4 and notice that the effect of the temperature factor becomes more pronounced for reflections with higher Bragg angles.0
2 5
8 11 2 5 8 11 2 5
1.0
180.0 180.842 13.0 10
2 3 2 5 3 6 2 5
8
3 6 1 4 7 1 4 7 10 3 6 9 1 4 7 10
180.0 0.0 180.0 0.883 2.257 12.269 8.291 6.085 14.346 42.058 4.0 180.455 23.0 180.0 0.044 13.381 4.024 27.0 180.0 180.0 0.0 10 180.323 2.0 0.0 180.582 0.0 0.011 1.0 0.0 0.432 4.025 53.0 0.796 0.684 25.220 7.135
4.0 180.427 5.507 3.380 0.344 1.0 0.0
.0
0 0 0
0 0
3 .0 0.0
4
4 4 3 3 3 3 2 2 2 2 1 1 1 1 0
6
9 12 3 6 9 12 3 6 9 12 3 6 9 12 1 4 7
180.0 180.0
0.
h k F PHI h k F PHI h k F PHI
14 13 12 12 11 11 10 10 10 9 9 9 8 8 8 7 7 7 6 6 6 6 5 5 5 4 4 4 4 3 3 3 3 2 2 2 2 1 1 1 1 1 0 0
l 2 1 4 2 5 1 4 7 2 5 8 3 6 9 3 6 9 2 5 8 11 3 6 9 1 4 7 10 1 4 7 10 1 4 7 10 1 4 7 10 13 2 5
6.0 180.0
180.0
13 13 12 11 11 11 10 10 9 9 9 8 8 8 7 7 7 6 6 6 6 5 5 5 5 0.0 180.0 0.0 180.168 6.929 5.0 180.0 0.0 180.0 0.235 1.902 16.654 4.0 0.0 180.0 0.0 180.572 6.995 5.145 3.0 4
l 4 3 1 4 7 3 6 1 4 7 2 5 8 2 5
8
1 4 7 10 2 5 8 11 3
0.0 180.387 3 .369 8.216 9.0 0.127 256.803 2.201 34.0
0.0 0.0 0.0 180.422 6.418 0.0 180.745 0.283 7.0 0.612
180.371 9.075 10.496 3.0 0.0
180.581 0.0
0.428 0.0 0.748 2.547 1.0 180.4 In table VI2 there is presented a selection of the output of STRUCFAC.872 7.078 9.585 1.0 180.0 12
180.114 0.029 3.0 180.041 6.191 2.677 2.
691 15.951 17.576 19.159 20.095 29.754 13.166 11.8 1 37.2 78.459 13.6 2 171.336 17.0 94.9 26.014 15.581 25.471 11.5 43.5 174.504 21.5 54.991 11.0 5 122.1 136.196 15.041 19.5 8 90.6 3 127.3 121.7 158. Neighbouring pairs of structure factors form Friedel pairs (hkO) and (hkO).921 13.082 20.9 0 71.743 11.473 16.3 71.137 28.6 42.6 0 3.128 17.577 16.0 21.606 26.889 20.402 13.396 17.7 10 86.459
93.988 12.011 175.215 22.3 43.7 79.6 91.0 141.996 22.705 28.5
82.193 20.0 124.239 17.5 8 8 172.6 139.1 173.0 6.5 41.508 20.2 54.5 100.104 47.1 16.009 22.843 18.2 1 1 134.212 26.
PHI PHI PHI
12 11 10 10 9 9 9 8 8 8 7 7 7 7 6 6 6 6 5 5 5 5 5 4 4 4 4 4 3 3 3 3 3 2 2 2 2 2 1 1 1 1 _ \ 1 0 0 0 0 0 0 1
1 1 1 2 1 2 4 1 3 4 1 2 4 5 1 2 4 5 1 2 4 5 7 1 3 4
6 7
2 3 5 6 8 1 3 4
6 7
1 2 4 5 7 8 1 2 4 5 7
8
0
13.6 3 59.538 11.587 22.6 78.529 13.3 5 57.3 94 .7 36.5 133.594 11.0 119.5 27.910 18.299 80.634 12.920 14.1 90.808 32.4 115. Note the breakdown of this condition.538 18.2 89.2 1.8 48.248 15.554 12.1 177.0 7 7 124.320 21. Without anomalous scattering these would have equal amplitudes and opposite phases.083 15.853 17.4 33.070 13.393 20.5 32.5
2 4 5 7 8 2 3 5 6 8
1 3 4 6 7 0 1
3 4 6 7 9
0
23.657 19.534 25.034 24.0 67.420 25.6 6 40.297 16.3 7 41.3 2 1 123.6 23.4 30.8 9 9 63.5 145.514 20.659
81.670 20.118 22.820 25.8 91.100 21.278 27.722 21.5 11 23.079 37.7 4 166.555 25.1 2 2 83 .660 23.1 91.9 132.055 36.3 146.0 46.8 39.5 98.0 8 8 93.228 26.681 24.7 7 7 131.2 179.815 18.3 28.536 25.7 139.0 90.5 13.4 11 11.7 8 7 57.7 0 169.603 29.3 2.838 23.651 11.0 20.858 24.013 14.8 0 4.636 71.6 129.5 73.582 18.7 1
1 2 1
3
1 3 4 2 3 5 1 3 4 6 1 3 4 6 1 3 4 6 7
2 3 5 6
1
13.0 41.367 17.7 0 175.045 29.480 15.9 96.811 13.155 17.8 1 63.987 13.334 11.0 12.406 25.338 11.9
6 6 6 5 5 5 5 4 4 4 4
4 3 3 3 3
3 2 2 2 2 2 2 1 1 1 1 1
1 2 2 3 2 3 1 2 4 5 2 3 5 6 2 3 5 6 2 3 5 6 1 2 4 5 7 1 3 4 6 7 1 2 4 5 7 8 2
0 0 0 0 0 0 0
1
3 5 6 8 0 2 3 5 6 8 9
1
13.859 16.2 65.2 3 123.9 176.793 15.416 16.6 133.564 21.055 32.849 27.8 3 2 7.9 140.116 14.690 16.3 4 4 18.8 52.682 17.3 38.0 5 136.8 10 119.945 15.380
Solutions to Problems
6.092 22.956 20.7 125.5 30.777 16.2 6 87.933 14.3 10 112.160 29.924
136.1 130.1 167.9 178.4 10 164.9 9 9 49.901 14.751 19.853 29.332 16.6 87.4 7 7 43.767 13.091 23.4 9 82.116 21.2 142.974 14.4 100.573 10.379 172.997 22.552 15.999 20.9 50.3 5 4 109.8 18.812 17.0 11 125.4 115.6 19.834 15.797 19.5 175.8 3 151.695 17.5 Part of the output of STRUCFAC is shown in table VI3.592 19.9 133.6 178.354 1.7 6
8.545 21.1 88.837 14.937 22.9 0 125.709 11.093 49.962 26.0 87.8 1.776 14.2 6 6 92.2 49.2 71.7 137.582 14.9
.179 29.7 175. Table VI3.582 17.0 176.740 69.5 51.521 14.201 19.505 26.2 101.4 8 11.3 75.184 121.728 20.904 16.625 21.0 12 124.2 172.5 7.159 18.524 12.5 3 48.553 14.4 0 82.6 100.3 5 33.5 22.872 20.524 105.352 15.6 77.
(hOl) data N(Z) 0.823 0.321 6 9 7 9 0.Solutions to Problems
381
Chapter 7 7.4 0.63 0.243 4 14 14 5 0.845 0.105
.4 The first part of the output is given as table VII2.28 0.078 0.33 0.303 1. (b) Fhol = 0 for h + I = In + 1.5 0.238 9 3 4 9 0.1 0.234 0.760 0.323 1.3 0.810 0.259 4 11 11 5 1.523 0.598 0. 7.035 1 11 11 2 0.766 0.458 0.
a = 0.675 10 11 9 1 0.511 0.717 1.35 0. 7 0 1 E .140 1.7 0.0 2 VALUES OF E H K E H K E 14 1 14 2 0.274 5 12 12 6 0.988 0. JFOkO = 0 for h ^ 3n.8 0.028 7 14 14 8 0.793 13 9 1.50 0. This gives the results shown in table VII1.3 For each projection the reflections are taken in groups of twenty and the intensities are compared with the average within the group.9 1.414 0.40 0. This indicates that the (hOl) projection is centrosymmetric and the (0/c/) projection is noncentrosymmetric.033 0.652 0.003 0.851 0.367 13 8 0.011 0. Table VII1.47 0.563 0.313 2 13 13 3 0.505 0.124 5 13 13 6 0.064 0.272 1.62
7.20 0.423E01 b = 0 .118 2.123 1.837 0. If your results agree with this then you may assume that the remainder is correct.65 0.2 (a) P2 1 /c.221 10 2 10 0.812 12 3 0.0 0.431 11 10 11 11 0.730 0.365 9 9 9 10 0. Table VII2. 6 4 8 E .803 0.390 10 5 10 6 0.48 0.13 0.50 0.6 0.151 8 10 10 9 0.2 0.511 0.43 0.367 0.0 2 c = 0 .038 3 0.20 0. (c) For 3l axis along ft.506
H 14 14 13 13 13 12 12 12 12
K 3 6 1 4 7 1 4 7 10
E
IX
11 11 10 10 10 10 9 9 9 9
3 6 9
1 4 7 10 2 5 8 11
1.70 (0/c/) data N(Z) 0.40 0.998 0. (ft) Pna2v 7.60 0.219 7 11 11 8 0.56 0.1 (a) Fhkl = 0 for h + k + I = In + 1.073 0.68 0.494 12 8 12 9 0.439 0.099 12 2 0.
VIII7. If the reflections are divided into four groups (k even.3 8. odd) + — + + + — + — — + y = 0. 2 / of weight 289 Cu—Cl at x + x'.5 8. / odd). and (k odd. (k even.VIII3 and clearly shows the S—S (or O—O) vector. These can be clearly seen in the difference Patterson map which is given in fig. The complete set of signs for this projection is given in table VIII1.600).1 Let the coordinates of Cu atom be x. The anomalousdifference Patterson map is shown in fig.2
8.60 for N
8.100).0. Atomic no.188. of Cu = 29 and of Cl = 17. Thus there are the following peaks: single weight single weight double weight double weight x = 0.x\y — y' of weight 986.4
8. y. Other solutions are possible which represent transformation to other centres of symmetry as origin.y + / of weight 986 Cu—Cl at x . The Patterson map is shown infig. / odd). The final Sim map is shown in fig.6).438.7
. It would be difficult to interpret it completely for the positions of the light atoms but several could be approximately located. They are at x = 0.193 / = 0. Peak B gives the S—S vector (2x. and of Cl atom be x'.
Examination of the Patterson function gives
Superposition methods can be used to locate the two other atoms. The highest nonorigin peak corresponds to the S—S vector. Where there are alternative peaks it may be necessary to try both to see which one gives a plausible solution.382
Solutions to Problems
Chapter 8
8. VIII6.67 for C. The final map giving the carbon positions is shown in fig. even) (even.0. 2y) at (0.250.0. y = 0. VIII5. ±(0.05 and x = 0. The Psfunction map is given in fig. / even). Check that these give vectors with the other atoms which are consistent with the Patterson. even) (odd. VIII4. odd) (odd. The vectors between the sulphur atoms are at ±(0.700) and ±(0.249 Cu—Cu at 2x.146.6
8. (k odd. / even).2y of weight 841 Cl—Cl at 2x'.27 y = 0. / . then multiplying complete groups by the signs given below corresponds to transforming to the three other origins: (even.VIII1 and it will be seen that there are two major peaks other than the origin peak. VIII2. The two atoms not on peaks are approximately centrosymmetrically arranged about the mercury atom so their densities partially cancel each other. The difference Patterson map is shown infig.074 x' = 0.3.0.
15. 33 42. 17. 27 25.
22.
y
3
V
^ 2 6 . 21. 21. 48 . 18. 19 . 15. 19 . 33. 16. 22 . 17. 24
^ 2?
21. 20. 15.43. 19. 25. 17. 23. 26 17. 28. 15 . 23. 19. 2 1 . 23 . 2 2 . 29. 28. 14 . 37 36. 22. 23. 27. 19. 21.
21. 32. 23 . 17 . 17. 27. 2 7 . 16. 44. 15 . 30. 21. 17. 23 . 22. 21. 28.28
28. . 24. 22. 32. 18. 44._3L. 43. 28 139 \ 20. 25. 26 . 21 21. 23. 31. 19. 27. 25. 28. 29. 22. 19 21. 17 . 16. 22. 15. 2 2 . 27. 19. 22. 25. 38. 16. 19. 22 21.7. 22. 19. 22.
Fig. 26.
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 3. 18 . 17. 15. 29. 15. 28. 31. 22. 17. 28. 20. VIII8) showed the complete structure. 21. 14. 26
19. 15. 28. 26. 21. 17. 24. 22. 22. 25 . 17. 32. 26. 26 . 19. 22. 28. 14.
A
l: /'
(
23. ?1
28. 21. 20. 19. 22 • 30<r N 48. 25. 35 N 24. 27. 19. 22. 19. 24. 44. 1 4 . 17 . 2 2 . 19. 17. 21. . 32. 20.'27. 2"8. 25. 20. 21
4 32. 16. 16.8 The solution obtained will depend on the seed for the randomnumber generator chosen for MINDIR. 25. 17. 21 . 22. 38 44. 25. 28. 3 20.4333 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT 0
Q 1
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16 i no
100 66 27 22 21 30 42 39 28 25 21 19 26 33 37 33 26 19 21 25 28 39 42 30 21 22 27
2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
J>
•^5
/ 27.
t /
19. 15. 19. 25. 15. 21. 15. 19. 2 5 . 20. 17. 25 36. 20. 28^ 2B 23. 21.Solutions to Problems
383
8.
J2 . 36 . 46 . 25. 20. 27. 3 2 O
. 16. 24. 2 3 . 30. 20 . 22. 22. 27 . 25
2k. 36 /24. 18 . 26. 26. 16 18. 21. 18. 2 8 X 4 6 S 23 . 17. 16. 19. 22. 22. 21. 31
22. 15. 17. 18 20. 15. 22. 19. 15. 23. \40. 17. 17 . 17. 24. 16. 19. 44 . 21 31. 24. 19. 29. 21 17. 17. 22. 19 25. 17. 17 26. 26. 36. 351. 31. 1 9 22 . 2 0 . 25. 18. 28. 21. 19. 17. 17. 16. 19. 25. With seed = 3000 the data in table VIII2 was found and the automatic solution corresponding to set 33 (fig. 25.
16. 21. 42. 31'""
18. 26 32. 28. 25
16. 14. 22. 15. 18.^ s
66 46. 33. 31. 19. 19 . 25. 22. 18. 39 22. 21 16. 27 28. 21. 30. 17. 23. 22 24. 19. /42 • \ 1 46. 2 3 . 26 . 26.
2. 17. 17. 43 26. 21.
19. 36'. 27. 42
/L. 22. 17. 19 . 18. 18. 38 . 21. 19. 25. 14. 17. 15. 30. 22 . 31. 14. 25. 19. 22 . 21 ." 100
I
<66
. 18. The Patterson map showing SS vectors. 25. 17. 14. 2 6 . 25. 22. 20. 44. 25. 22. 2 3 . 29. 19. 2 1 ^ 2 3 ^ 19. 1 8 . 40. 16. 19. 21. 43.
y. 33 22. 51 38. 18. 17. 30» 23. 31. 24. 16. VIII1. 15. 15. 15. 22. 22. 22. 19
23. 51.
O l 6. 2. 2 0. 2. 24" I 4 .• .8 f 4. 12. 1. 8.
25 .
14 2 . 12*7 "12. 2. 0.
''lO 190. 3.
o. 5. *4 • ^ . 13:* 17r ' 9. 3.
i
n
n
_9
n
n
. 3 1 0 4 1 3 1 4 0 1 3 1 1 0 1 4 2 0 6 11 1 9. 2 3
8. 5. 4.
1
2. VIII2. 4. 1. •>
2. 5 2
12. 7. 1.
I
< *25. 6. 1. 2. 6. 4 2. 23 . 2 1 3. 1 1. 0. 2. 127. 2] 0 6
8. 0. 3. 12 . 14\"
\ 11/ 7. 1. 3. 6 1. 3. 2. 1 7. 0. 11.
1
3. 1 1. 3 .
4 . ? 6.
9 1. 8 2. 3. (12 3.2 .— 10 0. 7. 0. 7 3. 1 3. 6.
4 . 16. . 1 3. 1 3.
i
1. 5.
1. 4. 7. 13. 25 . 1. 8. 1 3 . 0
^ v
4 4. 1. n.13. 3 . 2 . 1 1. 3 . 1. 3.29 \ 3. \ 7 . 1. 8. 8 2 4. 12.384 Fig. 1. 9.
5. 10. n
2.
. 1 5.
ro
4 . 6
3 2. .
"Nl. 1 1
. 10 2. 0. n
ro CN
3. 1 0 1 4. 6. 5. 26.
0.1371 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT 10 11 n 2 3. 1. 1. 11. 3.
8 0. 7.
3. 7 8. 2 1 3.
1. 5.
1. 1. 4. • * 8 6. 9.
5. l ) .
o
0. 20 . 12. 1.
1. 2. 0. 4. 2. 1.
9
2. 20/ 24
j
Solutions to Problems
0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 11 6 0 2 4 1 0 1 1 . 3.
3. 1.
7 .
2
4. 4. 14.
¥•
*27. 0. 7 2 4 4. 1 . 6.
)!i
2 7 n 4. n
6. 1. 6
4.
3. 6
s
7.
3. 4.
I
2.
2
3. 4.
4 . 19. 1 3 1 0
6 . 4. 1. 5.\. 6. 1. 2 1. 8 3 2
3
1 3
1
3 6.
3. 1. 2? . 19 \ I 8. 9. 4 0. 1 .v67
•3. 7.
q
1. 3. 2. t 7. 18 / 31.
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 0. 0 8. 2. V 7 9. 1. 2 . 2. 1.
6
yo
.
12
13
14
15
16
n. 1. 4.
3. 3 1. ^ ^1 7. 11 . 8 6 6 1 6. . 13. 1. 2 1 2. 2. 17. 3. 2. 7 2 3 1
6. 22 * J
2.
2. 1 4 0. 4 . A Simweighted map based on the sulphur positions. 2. ^ 3 4. 1. 5.
7. 3. 2. 1. 14 . 6. 8.
12 4. 1 2. 10. 8.
3.
A23. 2 4. 3. 1 4 5. 8.
0. 6. 8. 3 4.
6. 2. 5. 7. 2 5. 1. 1 6.
7 6 3. 6. 4
3
s
4
0. 3 1
3 . 3
9. 8. 2. 1 1.1 6.0. 1. 2 . 0
3.
ft
o
1 1.
2. 1. 0. 3 . 8.
4. 7. The difference Patterson map clearly showing the isomorphously replaced atom. 2.
8. 2.
8. 0. 1 ? 3. 12 . 9. 0 . 4. 18
0.
8.
7. 5. 0 . 10 3. 2. 8.
7 . 8. 8. 7. 4 . 6. 1. 10 7.
0 .
5 . 2 . 3 .
14. 6. 2. 1. 1.
4 . 4. 14. 5. 2. 4. 11
V
2 . 5. 4 . 1. 1. 4 . 10. 7. 2. 12. 5. 11. 13. 9. 1. 5. 10. 8. 0 4. 4. 4
4. 0.
it
1 2 8 5
inn
5 —97 " 9. 2. 6. 3. 6. 1. 7 .
8. 4. 9.
)l8. V 39. 2 .
5. 5. 2. 2 1. 1
1
4 .
4 . 4 .
n
4. 3 . 3. 0.
n
n
A/. 2. 2. 4
51 $20% 100
o
2 .
2.
0. 2
0.
2 5. 8.
o
6.
4 . 14. 5. 10. 3*8^
2 . 5.
I. 5. 5.
1. 9. 2 4. 10. 8. 5. 7. 11
1
n
n
o
7
. 1. 9. 5. 4 . 8. 5 8. 8. 5. *5 * 4. 4.
8. 6 1
2 . 8. 1. 2. 1. 2 . 7. 5. 6. 5.\ ^ 4. 4. 13 . 1. 0
0
7. 1. 1.
4
5
6
7
8
1
9
10
11
12
13 1
14
7
15
16
n
5.
9. 7 .
(f
3.
2 . 0. 2.
3. 2 .
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 0. 3. 2 . 1.
6. 2.
T?>>^12. 3
.
n
6.
1.
0. 3. 2. 2 S
1. 5. 10. 9. 11. 2 0 ? 0. 0. 6. 2.
2 . 1. 1 . 4 3. 1.
4.
2. 1. 13. 2. 8.3 .
3 . 9. 7
7. 14. 2. 9.
1. 1. 3 . 2. 5 . 1.
1. 3. 4. 2 4. 11 .
2 . 2. 0. 8.
4. 2. 6 . 2. 2 .
2 . 5. 1. S
7
?
1 2
2 . 7 1 2 8 5 2 0 2 3 2 2 5 2 2 3 2 0 2 5 8 2 1 7 5
3. 2. 2. 8.
5 . 4 .5607 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT
385
0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 100 51
1
2 7 )/*>
3 1 7. 0. 6. 1. 0 . 5. 6 . 1.
4 . 3. 3. 3. 5.
8. 2. 1. 2.
6 . 7.
2. 1. 6. 1. 1. 9
1
_^
1. 1.
3.
1.
4 . 0
1. 8. _^ . 11. 2. 2. 9. 2. 6. 5. 8. 0. 2. 8 9.
13". 1. 3. 3. 0. 9. 8. 0. 4 . 2.2 . 2 . 2.
5 . 1. 3 .
6. 4. 1 ?
0. 4. 2. 2^> N 3 . VIII3. 0 2. 7. 3. 8. 5. 1. 3. " 7*" 10 1. 0. 7. . ? 1 6 9
4. 4. 2. 5. 9. 0. 4. 3. 14 . 0. 2. 2.
o
1.
9. 11. 2. 4 . 4. 1. 6. 2. 2.
6. 4 . 3 . 2. 6. 2. 1. 10. 3.
n
4 . 1.Solutions to Problems Fig. 2. 3
1
7 . 1 .
5
?
1 0. 1. 2. 1. 14 . 5. 2.
5. 6. 5. 2. 2. 2. 4. 3 5.
5. 13. A difference Patterson map showing the six vectors between the sulphur (or oxygen) atoms. 1 5 . 11.
6. 7.
2 1 •/ 31 ^ 1 5 . 8.
8 10 . 5 9. 7. 10.
3 . 5.
3 7 11 6. 8.
7. 6. 3.
3. 6. 17 . 9. 6. 2.
7. 6. 1 2 .>
32. 10.
6 9.
2. 13. 8. 2 . 6. 9. 5. 4. 11. 7.
27 28
59 100
10. 0. 1 7 . 5.386 Fig. 4. 4 4 . 7. 8. 6. 6. 5. 4
23
6 . 8.
L
10. 9 11. 6 .
6. 6. 6. 3.
8.
7. ^ 2 1 . 9. 13 .. 9. 12. 8. 4.
6. 6. 11. 3 3 .
Vo.
1. 3. 6. 6
7. 6. 7 . 9. 3 . 7. 3. 7 5 . 3. 5. 33
6 3 7 6 1 5 4 5 8 5 4 5 1 6 7 3 6 6 8 7 10
7.
5. 4.
5. 12. 11. 2 1 .
7 . 14. 3. 4. 7. 4. 8. 3. 9. 6. 6. 5. 3. 5. 1
3. 1 1 . 9. 1 . 3. 3. 4. 5. 5 4 . 9.
4.
5. 5 6.
1.
10 . 5. 14. 7. 7. 3.
1. 6. 6. 5
4
10 . 6. 1 1 .
3
6. / 3 4 . 11. 3 4 .
5.
7.
3 1 . 9. 12. 10. 3. 6 . /
7 . 5 . 6. 2. 8. 8. 4.
5. 6 7. 7.
8. 5
7. 6. 9.
. 11.
FACTOR CONVERTING TO DENSITY/UNIT AREA I S 4 .
I . 6.
6. 6. 10.
8. 6. 8. / 9. 9.
7 .
5. 6. 3. 4.
76>
27. 9
6. 1 0 . 4. 10. 2. 6 .
8. 7.
6. 7. 4. 10. 2. 8.
14
15'
16
o
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
100 59 10 7 8 6 6 3 7 6 1 5 4 5 8 5 4 5 1 6 7 3 6 6 8 7 10
U. 3. 5. 10. 6. 16. 12. 5.
8. 3.
4. 10. 5. 5
12 ./ S
18. 3. 4. 9.
9. 3. 5. ^19^. 6. 18.
9. 11.
7 7. 5. 19. 6.
to
3 . 0. 10. 9.
4. 5 . 19 . 1 0 .
sa. 2. 5. 6. 5 5 5 7 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT
0 1
M
Solutions to Problems
2
3 q
4 ^ 2 .
7.
12 . 9. 4 .
* 21/' "2*9 "
7.
5 \
6
7 1
8 6 7. 6. 19. 4. 3. 6 . 9.
10 7 8
8 .
4. 5.
11. 4. 2. 4. 6.
5
6.
g
3. 2. 7 10 .
2. 15. 5. 3. 8. VIII4. 3 6 7 2 .
5. 12. 3. 15.
9 . 1. 10. 3 2 . 1 5 .
5. 10. 6. \ s .
7. 5. \34 1 1 .
3. 8. 8. 3. 23
5. 13. 8. 3. 4. 6. 6. 6. 6.
1
8.
2.
4.
t
10. 6. 3. 3. 3. 6. 4.
9.
8. 7.
10 9. 23> 20
12 . 7. 1 6 .
3. 4. 9 4 .
6.
9.
10. 5. 3. 15.
"VV
isif inn
Lo
. 5. 3. 4. 6. 10. 8. 2. 5.
4. N31.
7.
3. 8 5 .
8. 2. 9. 5. 10.
6. 9. 8. 5. 9. 7 . 15.
6.
7 .
9
10 ?
11 3
12
13 9. 8. 4. 6. 12. 10. 11. 9. 4.
2. 10. 1. 8. 21. VIII4.
9.
5. 10. l. 2. 11. 2 8 . 9. 18.1
5. 4. 2. 19. 6. 1.
8. 2. 21. 0. 12
7. 15. 12 . 8. 25.
3 .
6. 18.
10. 14. 17. 3. 4. 41. 19. 18. 24. 4. 10. 2. 15. 2. 3. 3.
8. 14 . 3. 20. 8. 3. 1 3 . 1. 13. 16. 22.
2. 18. 13. 9. 8.1 0 . 14.
0. 1. 25. 14
3 . 2.
3.
d
2. 12. 0
7. 10. 23 . 6. 17. 22. 11. 1. 21. 28.
1.
0. 2. 28.
31. 16 J 8. 16. 56T 43 . 13. 12. 23. 23 . 2 5 . 17. 11. 17. 13. 59/ 5. 33. 12 . 6. 7. 13.
41. 4. 1.
9. 10. 2. 1. 3. 16
2.
9. 14. 19. 34. 8. 1. 13. 3 3. 10.
9 3
32. 13. 6. 52.
6. 15. 15. 16. 12. 17. 23.
/53T
26.
2. 9. 14.
3. 14. 3. 14. 13. 9. 6. 10. 9. 3. 22. 18. 48. 22.30. 13 .
9. 37
2.
12. 38.1 0 . Map showing the carbon atoms with phases from sulphur atom positions as deduced from fig.
9. 22. 12. 10.
3 4
6. 13. . 13. 2. 42.
6. 25. 19. 12. 45. 6.
9.
7 . 4. 7. 10. 16. 29. 19. 8. 11. 16
6. 11. 1. . 13. 11. 1. 1.
3.
0
7.
7 11
9. 3. 5. 18. 5. 14. 26 2.
9 _7 4
4
0. 29. 6. 9. 34. 0. 4. 39 9. 11
5. 3. 11. 13. 35. 14. 26. 8.
35.
8. 14.
8. 2. 5. 3 6 . 7. 2. 5. 7. 3. 1 6 . 8. .
16. 14 .
11
9. 5. 2
8. 24.
6. 10. 29. 19.1 5 .6 . 6.1 0 .
3. 9. 21. 18. 17. 18. 39*. 34. 4. 7. 6. 3. 2 . 13. 7. 20 9. 18. 9 11 2 3 3 4 2 7 0 21 34 26 16 16 16 4. 5. 2. 25. 8. 13.
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 0. 13. 19. 12.
9. 1. 12. 8. 13. 0.
2
2. 15. 30 9. 31. 3. 7. 8. 10. 15. 5
1
91
n
1i
n
. 14. 17. 11. 12. 16. 2.
2.4 5 .
10 .
2.0392 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT 10 11 12 13 14 15
387
16
o
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 5 21
•\>
37.
10. 2 . 14. 24. 2. 7.
2. 11. 2 0 .
9. 7 0. 7 . 13 . 12. 22. 10. 21. 0. 5. 8 9.
6. 58TN 1 5 .
0. . 2 5 . 5. 4. 24. 4. . 3. 4. 11. VIII5. 4. 3.
3. 24. 15.Solutions to Problems Fig. 7. . 28. 30
24. 4.
0.
8.
4. 12 . 15. 0.
4.20 1. 40. 12. 19.
16. 7. 36. 7. 7. 10. 8 0
4 2 6 6 9
11
9.N22. 2 5 . 23 .
2. 1. 16. 13. 4. 22. 9. 0. 3. 12. 7.
6. 16. 16. 14. 3.
4. 13. 26. 1. 21. 13. ^ 1 . 12. 21
8.
35. 2 . 36. 4 . 32. 12.32 . 20. 4 3. 22.
lb . 17. ?O . 22 .
2. 24 33. 9. 4 .
6. 17. 7
9.
q
1//
rnn
.
I i
1.35. 0. 29. 6. 7. 45 30. 3.15. 2.
2. 11. 12. 2.
^ 3 8 . 8 . 12 . 20. 19\ 2 ." 15 3. 16?" 3.
2
r
37. 30. \ V 9 11.0065 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT
Solutions to Problems
0
1
2
3
4
5
6
7
8
9
10
11
12
1 4
13 .29 . 20. 12. .
12 30. 11. 18.
1 16. 5 .
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 0. 16 . VIII6. 11. 8. 16.6 . 3 . 28. 8. 10
j
5. 20.20 . 19
5.45 . 36. 4 . 9.388 Fig. 11. 28. 14. 10 5. 11. 15 3 12. 16
34.15 . N > 7 . 7 10. 3. 10 . 19 7.
17. 2.
7 . 12 .
18. 15.
*•
13.1 1 . 39 34. 15. 10 9.43 . 19. 4. 20.
1. 1
23 . 10 . 7.28 . 10 . 38. 33. 2<)J 13. 27.
2./22T 0. 20.
/
3. 7. 6 . 17. 21. 6 7 . 16
2 18. 1. 21. 19. 16
7 . 13. 25i
12 . 1. 11 10 .26 .
7. 15. 2. 2. 2 / 6 .30 . 6 . 2 4 * \ 2 .
* • « . 4
12. 10 0 \ 7. 1.
1. lfe> 19
9. 4. 3 .91
14
q
15
16 inn
o
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
100 72 23
kh
10 2. 21. 3
5. . 8. / 5. 9 . 6. 9
\?o.12
4. 2. 1. 4 . 7 . 0. 2.36. 3 . 11. 43 29.12 . 26. 6. 4 . 13. 3 4. The anomalousdifference Patterson map. 19 ) 18 . 10. 19 2 16 10 3 1
f
2. 20. 10. 11
16 27.
N2. 11. 14. 3. 34. l 8. 16. 10. 9
14 . 9.
12 14.'39 . 8. 11.10 .15
•Si
10. 31. 2.12 . 11.
k\ \
0. .
K
. ^23 . 2 5. 19 23 16 15 9 16. 11 . 14.19 . 30.
91
7. 15. \ 25 . 2.1 4 . 6 . 6. 24. 12.2 . 17. 14 . 10. 10 . 18. 3fV9. 0. 8. 1. 29. 20. 16. 7. 5. 1. 14.11. . 12. 12.18 . 17. 20. 12. 3. 3. 14. 16 5. 15 5 .
2. 12. 10 . 3. 20. 10
6 . 14 .
12. 9 . 15. 18. 15 3. 9. 32 15. 6 . 8. 1. 1. 7 . '. V3. 14 . 10.
4. 5 . 4. 20 & * 0. 3.
/o?
23 \ 4. 10 . 16 8. 36.15. 10.18
^ 37. 7. ^22^. 11. '11 . 7. 4. 3
5. «*4.17. 11 1 A
3.
0 . ? 9 6.\b
t
ir.25 . 8 . 23
% 24.•>o. 0. 6 . 5. 2. 20. 2.
y
25. 10.23 . 2. 16. 30. 16 2 . 18. 12 32.37. 6. 26. 11. 5. 20.14. 14
11 . 15.26 . 5.24. 20. 4. 5. 4 . 7. 10.i o s 15. 7. 24
1
/o./12. 28 23. 24. 12. 4.34 . 72 100
ft
21. 24T ^ 3 5.2T?
^J16.
10. . 11. .31 . 77 . 0. 35. 56. 11.1 5 .2 5 .
4 . 13.
12. 20. 32 . 10. \
15.
7. . . . 46
\
67. 60.6 2 . .18. 62 57
50\
47 .
3 7 . 15. 4 4 .43 .
&
79 89 .24. 46.5 1 . 70. 2 1
1
6.
84. 25. 23 .1 4 .
. .15
4. . 4
16.18. 17 . 19 20 .10. 68.5 2 .43 .52.
\
•
5 3
\ 79. 42. 48 . 49 . 26. 1 .
~T?T . . 3 9. 37. . 21. . 15.35. 11 . 62. 20
33.
83. 47. 11
8 . 36 . 14 74.3 9 .59.6 3 . 2 5 . 12 1. 68. 2 1 . 12 5. 44.6 8 . 8
4 . 45. A
44 .2 1 . 89.
5.
9. 14. 23 14
45
4 7s
26. 5 0
1
. 11. . 37. .1 0 . . 16. 44 . 20. 36.46 . . 55. 12 . 64. 81.3 2 .7 . 97. 97. 20 .
30. 27
58>^ 5 8 I 52 39 32 33
\
5 2 ^ 43^. 1 . 9.25 . 41. 6. 19. 12 1 . 58 X 4 4 . 28 . 11 . 35. 12.28. . .1 6 . 25. 1 1 . 11. 37 1. 16.
8 . The Psfunction map showing its antisymmetric form.5 . 27
29. . 40
T
65. 16. 7 .89. 14 0 . 18 . 16 0.
20 . 20. 72 . 25.7 1 .
5
1
6
1
7
8
9 4
10 n 41
4 4 1
15
i 1
16 n
17
1
18
19
i
20
0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
0 1 2 5 14 19 12 3 15 16 5 8 12 8 0 8 12 8 5 16 15 3 12 19 14 5 2 1 0
n
2. 15 18 .5 2 . 35. .
. 37.1 0 . 8
0 8
v
83
N
0 51. 24.3 4 . 75.
FACTOR CONVERTING TO DENSITY/UNIT AREA IS 243.
2 3 .. 16.
5.5 4 .
8 . 75. 89 .
23.2 4 . 11
25. 9. 5 7 . 16. 40 .
62. 52 . 3 . .64. 62 . 79.
V4
1
47. 1 . 48. \32. 12
1. 31 44 . 9 . . 2 8 .
8.10 . 8. 5
19. . 56. 1 .
28. 50.42 .16 . 21 59. 15 . 58. 35. 11. 67 . . 7. 36 3 5 . . . 46. . 12.2 1 . 46. 44 . 43
11.Solutions to Problems Fig. 25 . 43 .
58. 28. 12 . 2 3 ..— 7 2 :^65.5 1 . 20 . 26. 1. .1 7 . 75
V
/61.6 . 41. 83 .69. 75.1 2 . 37
34.8 . 49.
1 3 . 33 9. X. 5. 33 . 34. 74 .3 2 . 19. 26 . 11 .
8. 16
14.6 8 .
6 4 . 15.47. . VIII7. 3 5 .9 .5 . 28 .
18. 9
1 . 39.4 . 48
35
25.
/
6*7 . 34. 14
2 4 . 35. 78. 58.16. 84. . 15.50 63 71. 69 . 23 .30. 19 9 7 . 23 .
31 0 . 65.
13
13. 44 58. 58. 55. . 2 8 . . 3 0 .
7 . 8 2 .2 5 .5 2 . 14 .
20. 28
10. 17 25 36.11 .2 1 . 9. 23 . 35 44 . l 9 . 67. . 46 32.56. 64. .
"" N
/
56. 3 7. 21. 50.19 . .
169.6 . 24
25. 53 28 . 19 7 . 13 . . 12
/43.2 1 ."50 . 6 3 . 43 39. 2 10 . "578
""Ve. 5 29 . 27. 1 6 . 5. 47. 9 .28 .21.. 6.83. 60.8131 OUTPUT WITH Y HORIZONTAL AND ORIGIN TOP LEFT
0 1
1
389
2
3
1
4 n
7 25 . 65. . 28 . 89. . 6. 1 2 . 13.
6 0 . . 51. 3
10.2 8 . 27. 9. . 28. 22 .
3 9
3 .
11.
75.
6. 27.5 0 .28. 21
17 .1 3 . 37 .
18.
3. 52 . 3. .1 1 . 43.5 2 .2 7 . 4
4 .3 0 . 52< 52751.
11 9 . 2 . 28 . 62 .3 7 . 2 0 . '44
N
3 1 .
11.
&
56. 53 .
.5 . 47 . . 61. 37. 5. .
1
89
54 1 44 '28
2 4 .56 .
/
13
13 . 15. 25 . 6 . . 18 . 48
60 . 94. 18. 9 . 4 . 22 . 43.
"6J. 62. 79 . 5 10 . . 7. 67. 62. 1 8 . . 19 .5 7 . 13 28.37. 41.1 1 .5 8 .
. .
Xs ) 2 8
31.
^.
1
7 .
17.
.2 .4 .
1.
1 20 5
in
9.9
4 10 3 3 7
c. . .2 3
. . . .1 4 . 0. 20 .37
33.1 6 . 23. 0. 7 .
.2 7 . .
9 .1 4 . 4 . 5.
1. .3 .
.
N 2. 4 .
0
8.15 . .3 .28 .
6
9
7.2 4 .
37 28
17
12
5 24 23 2 10
16. CFOM = AND ORIGIN 4
5
832. 6
.
. 1 3 . 6. 6.8 . 8. .
9.
•513
20
1
14.7 . 1.
?R
4 6 1.
.8 .
.
5. . . 26.
9 . 5 .
IB
23
fi
"*
fi. . 20. 11 . \ »
4*9 >
Ur
1. .
5. 30.5 .13 . . . 11
12.
' \ f/\ 1 3 .
1.
8.
53/
0.
"5
11. 6 10.3 . 0.
6. . 10.1 8 . .1 3
4
11 .
5. . 12.8 . 10 2
4 . An automatic structure solution from MINDIR.
. . 10
.0 TOP LEFT 8 9 10 11
12
1.
12.1 0 . .
11
4 1
1 16 8
2.
2. . 32. .. 22 30. 3. .
4
2 . 5. 9. .3
?1 14
6 2 6 9 3 1 9
8.6 . 4 .1 6 .12.
4.
7. 4. 19. . 8. 4 .^
.
9. 8.
SOLUTION NUMBER
0UTPUT
33 2 3
^
WITH Y H 0 R I Z 0
™L
A .
7. 5. 3. 36. 7.1 0 .
17
1. 33. 6
13 —a* 10
12 23 10
2
3.8 .
~
5
.2 8 .28
.1 6 ^54 .
5
. 0. 33. .666
0
0
1
1 «
6
7
13
14
15
16
17
18 13 . .
5?V
19 .2 7 . 6 6 9
.
\
3. z. . .
3. 3 . . R 12
) \ 3.
5.
.10. . 6 .
4
28. 2 3 *
7. 2.
12
4
. 19 . 15 3.390
Solutions to Problems
Fig.
. . 23 . 33. 9
3 .
_ 7. 2 3 5 4 5 .
10.
11
26
. 3 . . 13 . .13 .
14.16.12 . .10. 8. 9.33
% 9 . 5 3 :/.8 .
2
5 . 24 5 . .1 1 .
10 23 12
10
5. 1.
24. 9.
13
4 . 8. 17 . 4 .3 .9 268. .1 2 . 8. 23 .
28
9 2
8. 1 0
1. 11 .
16.10.10. 8
4
. . . 11. 3 .
5. 2. 18 .1 0 .
i
8 5.19.
. 4 . 9. . 10.
5.
13N. 3. 1 1
6 7 8 9 10 11 12
13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
13 5 20 1 4
4. .
7.
f
13.
1 2 3 4 5
9 6 13 26 11
20. . .
5.
13
1 (7? 49\ .
%
. 12 .5 .1 1 10. 27. "~23 . 44 f
7 0 7
\
13 11
26 13 6 9
10
.
^Z
6.
4
10. 35^ ^6< .7
A
4 . 15 . 5
.
6.
2.. 11
9
9.
1. .1 5 .
7. 9. 4. .11. . 19. 14 .2 .18.
2 . 3. 8.
2 4 4 5 3 2 17 3
10.
4 . 1.1 5 . 5 . .
4. 3.
4 9
54/
3*
3 8
13
4 1 20 5
49/
. .
7
9. 11. 8. 19. 10 33. 28.
3
9.1 0 7 . 2. 11 .12.
1 1
•
<i PS
$
. 9. 10. 3.
11 . . 13 4
2.
22
1 3
1 n
11 22
3 . 1R
10
18.
^
11.1 6 . 9 .
2. 42*.
4
11.
7. .
2. ^22. 17 .
7
3
.1 0 . 1 9 .20.3 .
5 23
26. . .2 0 .
13
. 9 13 10. 38 . . 0
7 7 3 3
18 .2 0 .6 . 1. 16 2. 3. 1 2 .10 . 2. .
26
18
10
11
5^3> V \ .13
21.18 . .
19
20
.2 . ^ 5 30 27.1 2 4 .14. 8 23 . .5 .1 0 . . . 11
7.8 . 2 .11 .5 .
9. 6 . 9. 18 .
7 .
.3 0
28
. 22. 2 .
. 9.2 7 _ .9 . 11
11. . . 1 ? . . 5.1 4 .
12.
.6 .2 1 . 4. N
it
6.
10. 2.3 .1 2 . 2.38. 1 7 . .
13
6 9
16.1 3 4 2 7 2. 9.2 3 .1 1 . 13.
0 .3 7 . 2. . . t . 7. 13. .
6
\
1 3 . "28
7. 1 0 . 22. 14. .2 3 13.
10
8 4 10
.
10 5 2 6
8 . V I I I .2 3 11.1 1
. 11
2
i
7.
.48 • / « .9 . 18 . 5 .36. . 28 37 26
. 2.8 .
9.
.1 2
8.
. 13 . 15. 17.1 0 . . . 23 5. .8 .
1 4 4
. 7 . 20 0.9 . 10 10.6 .
.
0 .1 3 . 13.1 8 .1 3 . .4 .
6.
8.
7 .
17 .10. 17.20
"13
1 9
5 8
6
3
n
1_
32.4
_. . . 11 . . 14 .
6 11 650 .0 411.045 655.6 27 659 .817 1.6 571. 0 1000 .0 1.396 1.163 1.3 698.9 35 349 .5 597.263 805.3 770.355 0.041 0.171 1.2 450.075 1.7
SOLN 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50
A 646.201 722.1 1.3 49 381 .7 5 358 .6 1.9 1.315 670.9 748.8 608. 080 916.5 810.0 1.6 13 454 .1 440. 39 409 .8 730.0 1000 .8 634.6 1.2 41 443 .0 565.7 1.263 779.314 1. 048 610. 666 832.9 1.8 549.
Table VII2.2 1.9 640.2 33 268 .285 1.5 543.3 800.0 800.9 664.6 1.0 1. 077 614.6 17 416 .3 479.3 1.176 846.3 1.2 421. 079 588.2 759.2 319.3 668.017 1.3 1.7 1.3 1.087 1.317 707.9 356.2 601.3 3 544 .2 21 1 0 0 0 .
THE SEED USED IS 3000 Z SOLN CFOM A 1 296 .336 0.1 367.1 31 393 .026 563.140 1.Solutions to Problems
391
Table VIII1.057 527.8 1.
sign 0 0 0 0 0 0 / sign / sign 11 0 1 2 3 4 5 6 7 8 9 1 2 3 4 5 6 7 0 1 2 3 4 / sign
10 12 1 2 3 4 5 6 7 8 9 10 11 12 13 0 1 2 3
4 5 6 7 8 9 10 1 1 12 13 1 2 3 4 5 6 7 8 9 10 1 1 12 13
2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3
+ — — — + — +
u
+ — — _ — + — + + + + + +
u
0 1 2 3 4 5 6 7 8 9 10 1 1 12 1
2 3
4 5 6 7 8 9 10
4 4 4 4 4 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 5 5 5
+ +
u = unobserved.8 758.2 557.4 9 286 .3 348.964 1.3 258.5 608.0 19 284 .959 1.1 659.020 1.9 754.3 1.7 1000.2 1.7
CFOM 1.079 1.785 0.1 394.2 0.1 505.8 29 464 .259 889.1 411.0 1.8 37 651 .8 1.144 573.880 617.2 1000.152 1. 000 23 821 .1 15 316 .7 7 491 .9 481.206 698.000 47 475 .035 538.9 784.3
Z 370.4 0.3 524.245 887.271 706. 204 715.9 45 1000.000 0.3 543.1 1.7 513.7 693.950 598.970
.4 1.5 711.284 1.7 513.160 1.2 25 355 .1 43 528 .292 1.6 428.155 1.4 1.
9560 0. A straight line as close as possible to the other points gives K = 0. We now find a ^ ^ s i n j S ) " 1 = 5.30 and B = 2.23091 A " 1 and the next four reflections similarly give c* = 0.001 A.4) gives the results presented in table IX1.9231
a(A) 6.4 (i) 0. (ii) 0.8140 0.j8* = 120° 0'.392
Solutions to Problems
Chapter 9
9. Table IX1.020 6. 9.
.
h k 1 7 7 7 6 6 1 2 3 4 5 6
e
64° 27' 66° 35' 70° 35' 77° 45' 64° 55' 73° 54'
sin 2 0 0.747.016
A plot of the determined values of a against sin2 6 shows considerable scatter.2 In the (hOl) layer of the reciprocal lattice we have s2 = 4S11^ ° = h2a*2 + l2c*2 + 2hla*c*cosP*.3 The data is plotted on a reciprocallattice net and is divided into regions of sin 6/1 enabling table IX2 to be constructed.8421 0. 9.0874eA" 3 .001 A and
9. For a monoclinic lattice P = 180° . A best straight line for the other points gives a = 6.008 6. (400) and (500) reflections one finds an average value of a* = 0. The final reflections give cos/?* from
O5k
(4 sin 2 8/A2) .16496A" 1 . Plotting ln«/>/Z) indicates that the innermost point does not fit the general trend.h2a*2 
l2c*2
and the mean value of cos /?* is 0.0060A.499 97 which gives /?* = 60° 0'.002 ± 0.013 6.2) and (9. Try the calculation again with a/b = 0.012 6.6 A" 2 .1 The calculation using equations (9.8895 0.
A
From the (300).005 6. in particular the last two points give values which are far too high.8203 0.
12. 10. 12.
x
\ 15. 18
19. 12.1 .
16. C (0. 16.
2C
L
16. " 1 8 . 9.
10.1 0 . 4.
if/ % isb. 4 .
1.
/ 16. 7.
4.390).
2. 1 1 .
4.
8. .4 . 5.
•s 16. 7. 5 . 4. 5. 46'
/ I . 9. .
8.
\
6.28
481 235 129 85 72
483 265 143 81 50
7.s 12. 53. 8. 11.
3. 14.48^7^. 7. 5 . .
5. / 1 2 . 5. 5. 1. ' 9.
H3. 13. 17. 2. 5. 1 5 . 9. 1. 16.
v
2 4 j 15 10
1. 11.11. 0. 1 1 .
5. 9. 15. 17.
0.4 9 ^ o ' > \1 1 . 6.
7. 8. 16.
14. 10.
11^ 21. 8. 1.46 2.
10.
1. ^ 1 ^ . .1 .
1. 8. 2. 23.
13. 1. 13. 12. 2.
2. 6. 14. 3. 15. 9.1 . 1.
s
21.
r^ . ' q
8.
7.
1. 15. . 3*2. 2. 0.
* 3. 1.
16.125 0. 2. . 1. 1.
6. 22<
22
1
13.
3
/°'
7?
86 7 8 6 4 1 5 9 1 7 4
11 . 16. 4. O (0. 8.
8
9. 5.0.
15r . 5.1 . 6. 17.
V
. 10. 3. 2. 11.5 . 2.
22
7.
0. . 1.
10.
29. 21/. 3.
14 . 2.0. \ 19/ 8.
7 .30.
24. 6.390).0. 5. 5.690).
3
2
.
\ \ 3 . 7.
FACTOR CONVERTING TO DENSITY/UNIT AREA I S TOP OUTPUT WITH Y HORIZONTAL AND ORIGIN
0. 9. 12. 5. 15.025 0.7 5 .13.391. 4.
7 .0.401 for the original estimated coordinates and the map shown in fig.1 80. 2.6 59. 6. 3. 15. 12.
^0^1^
7.
\\10. 3.
0. 12. 49. 10. . 4 . .84
9.205 0.
0.40.
2. 12.1 .
15. 8.1 .
4. .2f.
9.
24* l).
3. 7. 11. 9.. 5.1 1 .A
' 7
LtK)r94>\38.
1. 18
20 ' 2 9 .
12. 17. 1 1 . 7. 10.
9.
M t /
19r15.
1.
5. 5.
22.
15. 10.20.
27. \ \ \ 5>.2 0.
29.3 . 2. 6. 10.
3 : 7"
.
^
.10. 8. 15.
1.
7 . 5. 0.83 1.
6.1016 LEFT 9 10
11 12 13 14 15 16
0
1
2
3
4
5
6
7
8
17
1 •}
18
19
20
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
3 2 5 18 49 49 8 6 7 8 6 4 1 5 9 1 7 4 15 10 5 9 3 2 5 7 6 8
2.0.
17. 8. 3. 10. 6.014.
9
20{
8.
*27~
31.0. 7 . 1. /
1? /
^V
/S7\
40
21 A . 8. 15.158 0. 49. 8. 13. 5.
5. . 1 2 . 10. 2.8 .
0. 8.
2. 16. 10.1 .
5. 11.
13.
12. 7.
5. 12 .
8. i i ? ^21_. 4. C (0. 8. 1. .452 0. 2. 1.
q
9. 5. 4. 8. 1.
8. 2. . 5. 12.
6.552
I 964 500 272 166 122
</>
99. .196.5 0._ 14".255).30.3 0. 4. N (0. 7.50. The map obtained as the first stage in a Fourier refinement procedure. 1. 2.8 .
3. 40*. 7.065 0.
4.
Fig. 1.353 0. C (0.
7. 12
15'. 11.333. 1 \ 8. 5.
7./ \ 23. 7.
8.
5.155). IX1. IX1.
7.
15.2 . 1 4 .1 3 . 1. 8.

s
ior
1.3 14. .
< 9. 9 4 ^ 10
^
9
10. 2. 21*7
5 3 ^ ^ 9
2.
18> s 30. 5. 3 . 11.
>
•
•
10. 17. 15. 1 .
\6.
10.
38. 8. 3. 8.
1. 3. 24N
13 . 12.305
0.943. 1 5 . 8. 12.
1.
4. 5. 2. 2.
i
4 . 10. Na (0. 7. 6. .
12.
2. 1. 4. 5. 2. 22. .2 .
12*.7
ln2 2.
)v
0.
sin0 A 0. 3. Revised coordinates estimated from the map are: Na (0.
1. 2. 20. 20.
7 .9. 11. 0.255 0. 9.
2
\
29
13.1 . _15< 1 1 . ^ 3 \ 8.475. 16. 9.1 1 . ?*=• 92. 9.
30 .52 2. 5. 9.0. ( ^
6.
N
1 .
. . 2. 1 1 .605). 15.1 . 8.
3 ^ \ " . 4. 5. 9.
9. f
5 7 6
A. 2. 32.
"o". 4 .6 /sin 2 0\
/sin 2 0\ *
28/ c 2 12/O2
\ *1 \ * 1
0. 8.
19.1 0 .200). . 2. 6.
7.5 CALOBS gives a reliability index of 0.
7 .114.
23. 4. 3.4 0.
10.
6.0
1. 1.. 7.
2. 0. 35. 1.
8.
3. 1. .Solutions to Problems
393
Table IX2.
4 . 8.
360. However.394
Solutions to Problems
Structure factors calculated with these new estimates gave a reliability index of 0. this does not prevent the refinement from taking place. It should be noted that the origin is free to move along the y direction in this space group and that as the refinement proceeds there may be a gradual drift of y coordinates towards higher or lower values.
.
(1933). W. Soc. E. E. 7.W. D. (1950b). J. (1966). E. W. Cochran. 64. R. 70. W. 210. M. 720. H. 814. D. 16. S. 35. J. 58. 1. 381. (1948).R. M. (1963). W. Beevers.K. 3. E. & Robertson. C. 4. Sitsungsberichte der Kgl. W. Dunitz. C. (1950). Ada Cryst. 8256. Ada Cryst. 4. Cochran. Ada Cryst. W. Phys. 4. 1737. D.N. 473. Phil. (1948). W. W. (1955). Oxford: Pergamon. Chem. 89. (1963a). Computing Methods and the Phase Problem in Xray Crystal Analysis. (1963). J. Mag. Buerger. 36. Proc. Ada Cryst. Bokhoven. (1955).M. 16. Lovell. 12. Bellamy. Am. & Penfold. Soc. M. F. & Bosanquet. 14.R. Archer. Ada Cryst. 41. Chemische Kristallographie. F. 17. Phys. (1952). 3.M. & Truter. & Thompson. Acad. Acta Cryst 23. 275. (1941). Cochran. 65.L. 1. Cruickshank. Ada Cryst. W. 63. & Hargreaves. Ada Cryst. 4. Phil. Honl.S. 1. 1133. D. 17.C. Mag.E.M.W. (1913). Bhuiya. G. & Bijvoet.
395
. Acta Cryst. L. J. A. (1960).D. H. & Lipson.M. Ada Cryst. Alcock. Bragg. & Rogers. C. (1961). M. (1951). Pilling. 200. (1946). Proc. Buerger. J. 6. Ada Cryst.H. B. Phil. & Hargreaves. Lond. (1963b). M. 456. (1934). 309.J. Foster. F. Cochran. Clews. Bertaut. W. Ada Cryst. Baker. D. Friedrich. D. Ada Cryst.M. 376. R. 62557. 3. N. 16. D. Letters 10. M. J. A. A. Brown. Acta Cryst. M. (1936). (1938). (1950). Fiocco. S. (1954). 81.W. Hughes. A. (1921). Krist. J. 5. Acta Cryst. 260.C. R. Soc. & Cochran. & Kasper. Cochran. C. Phys. (1950a). Z. 2. C. Harker. E. Ada Cryst..C. E. J. 178. (1959). James. & Woolfson. Blow. George.F.B. 252.. A. (1949). 1.D. Knipping. Rev. W. & Causer. H.L. 1124. W. & Sheldrick. 1. 5. (1912) InterferenzErsceinungen bei Rontgenstrahlen. Bond. Chem. Groth. Bujosa. Acta Cryst. G.F. & Stanley. S. 139. (1955). Ada Cryst. M. M. M. 981. Ada Cryst. Dutta. Phillips. W. 376. Camb.J. & Woolfson. Sci. Ann. H. 98. Farquhar.References
Abrahams. 8. Ada Cryst. J. J. & Bouman. (1967). Cochran. M. 30322. Ada Cryst. Fowweather. F. T. (1948). 8. B. 13. (1951). Schoone. de Jong. W. & Lipson. Bayerischen Akademie der Wissenschaften zu Miinchen. M. (1948). F.C. Acta Cryst. P. (1961). pp. 544. Nat. P. 465. 794. 8. (1953). H. (1910). Bragg. & von Laue. & Bortner. Proc. (1952). G. & Crick. Acta Cryst. 43.A.M. Foster. & Hargreaves. (Leipzig) 18. Harker. 1. Ada Cryst. Howells. Phys. J. Nature 210. 644. Leipzig: Engelmann. A.
O. 1. Wilson. M. 536. Karle. Dordrecht: Reidel. 46. Guilderland. & Woolfson.C.. & Hauptmann. 16. Milledge. Acta Cryst.D.T. Acta Cryst. Klug. Acta Cryst. C. 11. W. B. M. Wrinch. H. Acta Cryst. Phys. Y. A. 150. A. 17. (1953).F. Thomas.H. J. Woolfson. 835. W. Vol. 267. & Nigam. A. 1356. II.C. Mathematical. J. Oxford: Pergamon. 511. Weiss. W. & Cox. & Fan.J. U. Sim. J. Swarthmore. 439. Wooster. L. Phil.M. 22. S. (1958).M. (1978). H. Vol. (1964b). Cochran. (1995). Crystal Physics. 97. (Ed. Karle. 635. J. Vol. 9. 10. (1958). 5. Acta Cryst. J. Roy. A. H. Mills. Nature. Acta Cryst. (1937). W. M.C. Berry) Joint Committee on Powder Diffraction Standards (JCPDS). Y. M. Krist. 83. SpaceGroup Symmetry. 60. (1978). 68. (1955). 61.M. B34. 5. Mag. (1967). 151. A. 238. A. 152. 804. G. (1948). O. G. Proc. 372. (1948). S.396
References International Tables for Xray Crystallography. International Tablesfor Crystallography. Lipson. Zachariasen. J. & GarciaBlanco. M. A. Acta Cryst. Woolfson. 318. Acta Cryst. PA 19081. J. 439. International Tablesfor Crystallography. M. H. H. L. (1967). Sim. H.L. B34. S.M. & Cole. C. New York: Adenine Press.C. (Ed. Acta Cryst. Acta Cryst. Okaya. M. & Karle. Wilson. Pradhan.J. (1965) Computing Methods in Crystallography. & Sarada. 515. (1942). (1985). Vols. Reitveld. 3. Birmingham: The Kynoch Press. Robertson. 23. (1954). Renninger. Nakanishi. 7. Cambridge: Cambridge University Press. Acta Cryst. Y. Dordrecht: Reidel. 620. (1952). L. Dordrecht: Reidel. Acta Cryst. Acta Cryst. (1964).. Physical and NonPhysical Methods of Solving Crystal Structures. 558. 11.S. Woolfson. (1958). (1956). (1952). Woolfson. 11. D. A. 17. 397.H. Ghosh. Acta Cryst. 599. M. Sim. J. A. A. Phys. Pitt. 6. 13. (1959). 107. I.S. & Pepinsky. 566. Soc. 27. International Tables for Crystallography. Zachariasen.M. A. (1962). Acta Cryst. D. I. E. J. Acta Cryst. H. A. 6. Acta Cryst. J. Acta Cryst.J.G. Stanley. Acta Cryst. Acta Cryst. & Wilson. Acta Cryst. Physical and Chemical Tables. (1934). A. (1939). Acta Cryst. 2. (1938). 17. (1964a). Z. Rogers. 9. I. 1857. (1957). 12. G. Acta Cryst. & Karle. Acta Cryst. (1981). Main. W. 98. Karle. (I960). M. Acta Cryst. 642. 98. Patterson. 332. (1958). Structure and Statistics in Crystallography. Yao. Acta Cryst.X. Saito. A. Wilson). M. R. Acta Cryst. (1950). E. J. Powder Diffraction File.. Cambridge: Cambridge University Press.F. G.A. Rev. D. 393. Rollett.
. W. (1963). Rev. 1028. P. 168. 813. 731. 1601 Park Lane. Wilson. Reciprocal Space. (1952).. D. A37. III. G. 11. (1956). & Woolfson. Perales. Sayre. (1949). 1.
James. Xray Diffraction.A.C. Crystal Structure Analysis: A Primer. Wilson. Crystals and Xrays. S. W. R. Macromolecular Crystallography and Crystallographic Statistics. F. London: Macmillan. Robertson. Structure Determination by Xray Crystallography. N. R. W. R.C.J.. D. 1974. Singapore: World Scientific.W. Kaplow. & Palmer.) Anomalous Scattering. Kato. The Interpretation of Xray Diffraction Photographs. 1985. London: Bell. 1965 Schenk. McKie. New York: Plenum. 1987. Wilson. 1971. H. The Optical Principles of the Diffraction of Xrays (The Crystalline State. & Speakman. Vol. Imperfect Crystals and Amorphous Bodies. 1948.C. 1958.E. London: Bell. San Francisco: Freeman. B. Bacon. AzarorT. J. 1966.P. Oxford: Pergamon. S. R. Pepinsky.. Ramachandran. 1962. R.. 1968. 1961. A. Xray Crystallography. G. They represent a selection of a very large number of books in the field. 1963. many of them specialist texts. Oxford: Blackwell.T. D. 397
. Cracknell.N. Xray Structure Determination. The Crystal Structure of Solids. M. New York: McGrawHill.J.A. 1948. & Cochran. R. Ramaseshan. Oxford: University Press. K. & McKie.. 1978. & Parthasarathy. P. Computing Methods in Crystallography. Crystals and their Structures. 64076. & Lorrain. Henry.Bibliography
The books given in the list below. London: Methuen. Rollet. 1960.. U. H.J.V. 1973.F. G. New York: Wiley. London: Edward Arnold. 1986. & Willis. 1969. Buerger. Weiss. A. Guinier.J. P J . (Eds.B. J.H. A.S. Fourier Methods in Crystallography.A. J.) Direct Methods. An update. R. & Young.C. K. & Abrahams. Robertson. A. The Determination of Crystal Structures (The Crystalline State. R. Lonsdale.. London: Longmans. (Eds.F.M. & Srinivasan. & Trueblood. appears in the Journal of Applied Crystallography (1982) 15. New York: Wiley. An Introduction to Crystallography. (Eds. Single Crystal Diffractometry. 1966. & Wooster. between them cover a much wider range of material and go to much greater depth than does this introductory textbook..) Computing Methods and the Phase Problem in Xray Crystal Analysis: Glasgow. Glusker. S. 3). L. Vol.S. Ladd. Essentials of Crystallography. Lipson.) Xray Diffraction in Crystals.N. Neutron Diffraction.C. Stout.W. Oxford: University Press. G.M. Megaw and published in 1965 by the International Union of Crystallography Commission on Crystallographic Teaching.P. New York: Macmillan. & Forsyth.H. Xray Crystallography. H. 2).C. produced by Dr J. H. C. Arndt. (translated by Lorrain. Oxford: Pergamon. L. M. Phillips. Brown. Copenhagen: Munksgaard. James. 1965. & Jensen.W. Oxford: Pergamon. J. London: Bell. 1970.M. Cambridge: University Press. Lipson. J. A comprehensive list is given in the Crystallographic Book List edited by Helen D. 1975. N.
Cambridge: University Press. Woolfson. M. New York: Adenine. Guilderland. H. Oxford: University Press.398
Bibliography Taylor. Woolfson.) Structure & Statistics in Crystallography. & Fan Haifu. 1995.J. Wilson. 1961. Direct Methods in Crystallography. C. London: Bell.M. A.A. Optical Transformations. Xray Optics. (Ed. Physical and NonPhysical Methods of Solving Crystal Structures.
.J. & Lipson. A. Wilson.C.C.M. London: Methuen. 1964. 1985. M. 1962.
287 Bhuiya. formation of 13 faces. energy states of electrons in atoms 46 equiinclination method for Weissenbeg camera 130 errors in electrondensity maps 312 et seq. E. 133 Bragg. calculations of 164 for sphere and cylinder 165 acentric intensity distribution 219 Alcock. G. M.W.L. 286
centre of symmetry 21.249 calcite 8.L. W. 266 bodycentred lattice 20 Bokhoven.G.H. W. 194 energy in diffracted beam 156 et seq. from twodimensional array 56 et seq. E. and Friedel's law 185 and solution of crystal structures 267 et seq.
399
. S. 231 Buerger. F. J. rules for selection 279 Archer. 205 cuprous chloride azomethane complex 298 deadtime of GeigerMuller counter 140 of scintillation counter 141 Debye theory for temperature factor 179 DebyeWaller factor 178 deconvolution of powder lines 116 delta function 45. 30 faces. symmetry 7 systems 7 crystal monochromator 149 cube. normals to 2 habit 1 optics 196 et seq. 288 Crick. W. 99 from linear array 50 et seq.6dichloropyrimidine 255 2amino4methyl6chloropyrimidine 255 ANOFILE 269. 4. from threedimensional array 57 et seq. 90 disordered structures 233 divergence of Xray beam 137 double refraction 200 Dunitz. coordinate errors from errors in data 331 et seq. 246 Larginine dihydrate 293 Arndt. radius of 39 electrons in atoms 43 et seq. 135. 233 Dutta. 56. 231 Bosanquet. 255.M. 279 electromagnetic radiation 32. 223. Brown. C. 305 beam trap 113 BeeverLipson strips 81 bending magnets Bertaut. 266 Cruickshank. 304 Bortner. Bijvoet.C. D. 58 continuous white radiation 144 convolution 94 et seq. 90
densitometers 139 density of film 138 densityexposure relationships for film 138 dextrorotation 193 diad axis 6 detection from intensities 227 diad screw axis from systematic absences 211 dicyclopentadienyldiiron tetracarbonyl 220. J. 200 CALOBS 323. 290. from a crystal 58. 174 Bouman. 38 electron density contours 103 equation 99 et seq. 283.246. E. H. 130. grid spacing for 105 in projection 103 electron. 174 Bragg's law 67 et seq. F. M.W. K.J. C. 153. 285. anthracene 240 arbitrary signs. 67 190 detection of intensity statistics 215 et seq. A. 291. centric intensity distribution 219 characteristic radiation 144 characteristic temperature 179 cleavage 1. 23. 309 Cochran distribution 291 coherence of Thomson scattering 39 combined figure of merit 294 Compton scattering 42 et seq. 320 biaxial crystals 205 et seq. T. 264 Bond. 136 Bravais lattices \1 et seq. relation to Thomson scattering 43 from atoms 46 cones of diffraction 54. M. 318 crystal classes 9.N. W. 143 atomic absorption coefficient 165 atomic scattering factor 46 atomic vibrations 175 axial ratios.B. relationship to Fourier transform 92 ripples from series termination 317 diffractometers 140 et seq. N. C. J. 8 Clews. symmetry elements of 8 cubic system 10 optics of 197. M.. 366 Cauchy inequality 274 cell dimensions from layer lines 119 centrallimit theorem 215. 307 alum 1 2amino4. 287. determination of 13 Baker. J. 264 Blow. 300 difference Patterson function 285 diffraction conditions for 58. D. enantiomorph and phase relationships 297 enantiomorphic relationships in unit cell 25. C.Index
Abrahams. from series termination 317 counter GeigerMuller 140 scintillation 141 standard errors of measurement 142 Cox. M. U. S.J. 233 absorption edges 166 absorption of Xrays 162 et seq.352 anomalous scattering 179 et seq.H. D.6dimethyl2hydroxypyrimidine 240 Dirac (5function 45. 108 et seq.W. 255 Cochran.
207 oscillation camera 118 et seq. S. P. 70. 226 noncentrosymmetrical structure. Friedel's law 73.350 ISOFILE 259. definition of 87 of crystal 156. photograh 208 layer lines from oscillation camera 119 layerline screens 126 leastsquares refinement 311 et seq. optical goniometers 6.J.291.J. R. 349 isomorphous replacement 255 et seq. detection by intensity statistics 219 et seq. 8 Okaya. Y. 233 Mills. Fowweather. 205 Honl 185 Howells.229 Harker. 226 FOUR1 81. Miller indices 15 et seq. 205. Hartree selfconsistent field method 46 Hauptman. optical 6 grid spacing for electrondensity maps 105 Groth 303 Hargreaves. R.400
Ewald sphere (sphere of reflection) 111 extraordinary rays and waves 201 facecentred lattices 20 detection by systematic absences 210 facets 1. H. G. H.C. 226 glide planes 212 detection by systematic absences 212 Lglutamine 292 goniometer head 119 goniometers. I. 267 Friedrich 68 FTOUE 225. 31 ordinary rays and waves 201 originfixing signs 279. wedges 135 intensifying screen 135 International Tables for Crystallography 23 International Tables for Xray Crystallography 254 et seq. 48 indices of reflection 65. 73 inequality relationships 274 et seq. for noncentrosymmetrical structures 252 Helliwell. 225 Hughes.354 minimum function 249 mirror planes in a crystal 12 in a unit cell 21.292 Kasper. F. 7 Fan. convolution 94 et seq. use for crystal optics 201 et seq. 235.R. Nigam. 173. 210. 174
Index Bravais 17 space 16 et seq. 220. M. 290. 303. 287 integrated reflection 156 integrating method for intensity measurement 139 intensity of diffracted beam 67 of radiation 32 photographic measurement of 137 statistics 215 et seq. 226. S. 205. 264 and anomalous scattering 274 James. 292 Karle.346 heavyatom method 249 et seq. 117 Milledge. 22 detection in cell from intensities 227 moment tests for symmetry elements 226 monoclinic system 9. 119 group 210 method 151 et seq. 70. 290. normalized structure factor 224 octahedron 1. optical activity 193 et seq.. effect of missetting 121 indexing of photographs 122 setting of crystals 121 Pc(u) function Ps(u) function 272 272
Karle. 266 Farquhar. 197. 287 Knipping 68 kx unit 303 laevorotation laser 41 lattice 193
.. 207 mosaic crystal 163. weighting schemes for 318 limiting sphere 112 linear absorption coefficient 163 calculation for compounds 167 linearly dependent structure factors 280 Lipson. 274 Klug. 246.M. Hf. 41 fluorene 231 Foster. 318 Huygens' construction 197 hypercentric intensity distribution 226 /centred lattice 20 imageplate systems 150 imperfect crystals 164 incoherent scattering 42. 79 in two and three dimensions 83 et seq.322 figures of merit 293 film packs 308 films densityexposure relationship of 138 double coated 135 fog level 138 filters for Xrays 168 Fiocco. D. E. 300 MINDIR 293. O. inversesquare law 33 inversion axes in crystals 6 in unit cell 23 ISOCOEFF 264. numerical examples 79 et seq.W. 280 orthorhombic system 11. 153 hexad axis 6 hexagonal system 10. 305 mass absorption coefficient 167 matrix notation 319 metaboric acid 287 microscope. A. S. H. Laue equations 58. Fourier series determination of coefficients 78 form of 76.157 of Dirac ^function 91 of Gaussian function 90 of point lattice 92 of product of functions 97 relationship with diffraction 92 et seq.W. 303. 226. E. 74 Gaussian function 90 GeigerMuller counter 140 Ghosh. 274 HarkerKasper inequalities 274 et seq. G. 70.333 FOUR2 104. J. 291 Hauy 8 HEAVY 254. A. and phase ambiguity 261. L. 272 optic axis 198 et seq. 229 frequency doubling in crystals 195 et seq. 46. J. 115. 174 multiple isomorphous replacement (MIR) 265 N(z) test 225 et seq. periodic nature of 82 fourcircle diffractometer 141 Fourier transform calculation of 88 et seq. F. D. 322 Lorentz factor 161 Lp factor 161 Main. 336 Fourier refinement 309 et seq. 11. S. 186.339 GarciaBlanco.
34. 353 pseudosymmetry 233 pyroelectric effect 192 et seq. J. G. 207 trigonal system 10. series termination errors 317 Sheldrick. 328 structure factor 65. 66 phase velocity 205 phenylammonium salt of fosfomycin 74. 205 identification of 200 unit cell 12 et seq. 240 planes of relection 68 point group 11. 283. J. 41 Thomson scattering 37 et seq. 226 precession camera 130 et seq. 264 scintillation counter 141 screw axes 23. space lattices 16 et seq. detection of 191 Pitt. 252 SIMP1 82. breakdown of 289 probability of 285 et seq.
401
stereoimages 104 STRUCFAC 73. 307 sign relationships 283 et seq. 197. 39. detection of 193 quartz 2. systematic absences 210 et seq. B.4tetraphenylcyclobutane 233 thallium hydrogen tartrate 303 Thomas. G. total by electron 40 scattering vector 35. 158 standard errors of counter measurements 142 Stanley. 226 rotating anode Xray source 145 rotation axes in crystals 6 in unit cells 23 Roussin's red ethyl ester 288 Saito. 235 Patterson function 233 et seq. M. Y. tangent formula 291. 170.. 197. paramtroanilinG 233 Patterson. Pradham. scattering 33 phasevector diagram 36. piezoelectric effect 190 et seq. 181 experimental measurement of 41 relationship to Compton scattering 46 mtoluidene dihydrochloride 229. synchrotron radiation 145 et seq. D. 205 tripleproduct sign relationship 278. Powder Diffraction File (PDF) 118 powder diffractometer 115 et seq. D. unitcell parameters. 108. 288 ThomasFermi method 46 Thompson.T. determination of 301 unitary structure factor 222 et seq. scattering phase shift 33. equation of 33 PSCOEFF 273.3. 99 phase angle of 66 structure invariants 280 superposition methods 246 symbolic addition method 292 symmetry elements in crystal 4 et seq. 37. 44. 205 Rayleigh scattering 32 reciprocal lattice 59 et seq. Sim. 335 Simpson's rule 82 Sim weighting 253 Slater's wave functions 46 space groups 23 et seq. M. 244 225 photographic measurement of intensities 135 er seq. in unit cell 20 et seq. 285 undulator 147 uniaxial crystals 197. 290 salicyclic acid 309 scaling of data 307 et seq. 53.H. 288 Robertson. 225. table of 24 symmetry information from photographs 208 et seq. 179 scattering power 40 scattering. 180 Schoone. 193 quenching of GeigerMuller counter 140 racemic mixture 195 radiation damping 182 RANTAN 292 ray axes 205 rayvelocity surface 197. primitive lattice 17 probability curves for MIR 266 progressivewave. scattering angle 33 scattering factor 46 scattering from centrosymmetric distribution 44 scattering from general distribution 36 scattering length 33 scattering of Xrays by atoms 43 et seq. D. J. 230 transpose of matrix 320 triad axis 6 trialanderror methods 231 triclinic system 9. 102 phase relationships 290 et seq. determination from observed data 308 et seq. 229 Phillips. 117 Rietveld refinement 117 Robertson. pulsed form 146 polarization 146 power spectrum 146 vertical spread of beam 146 synchrotron sources 145 et seq. 20. 72. 13 tetraethyl diphosphine disulphide 279 tetragonal system 10. 31 polarization factor 161 potassium dihydrogen phosphate 195 powder camera 112 et seq. R. E.R. R. 205 tetrahedral bonding of carbon 194 tetrahedron 8 1.285 Sayre's equation 284. residual (reliability index) 232 for randomly incorrect structures 311 for trial structures 311 rhombohedral lattice 17 rhombohedron 8 Rietvelt.. A. 74 phase problem 103 phase of structure factor 66. 10.C. H. 320 statistical disorder 233 stereographic projection 32 et seq. 292 temperature factor 175 et seq. A. and spacegroup dependent vectors 240 dimensions of 236 for centrosymmetric function 238 peaks between heavy atoms 238 peaks between parallel groups 240 peak shapes 237 sharpening of 249 symmetry of 246 PattersonHarker section 246 Penfold.Index parachloridoxy benzene 246 parametershift method 320 et seq. tetrad axis 6.J. 272 Sayre.C. 233 Rogers. L. spacing of reflecting planes 69 et seq. and indices of reflection 60 weighted 73 reciprocity law for film 138 reflecting power of crystal 156 refractive index 196 reliability index (residual) 232 Renninger reflections 241 et seq. symmetry of 20 et seq.G. D. 11.M. J. 28 sealed hotcathode Xray tube 143 secondary extinction 173 et seq.2. van der Waals 301 vibrations of atoms 175 volume of reciprocallattice cell of unit cell 62 von Laue 67
62
. 58. 290 Pepinsky. phase shift. E. 272 Perales. 205. sphere of reflection 111. primary extinction 169 et seq.
266. 305 Wrinch. W.309 Wilson plot 309. 205 weighted reciprocal lattice weighting Fourier coefficients 252. 253 weighting scheme for leastsquares refinement 318 Weiss. A. D. coordinates of reflections in 126 et seq. H.T. symmetry from 208 et seq. 292 172 283. xylose 103 Yao. 285.
Zachariasen. O. wiggler 147 Willis. 246
Index
Xray photographs.M. M. B.322 Wilson statistics 251 et seq. 287
. 285.226. 287. M.C. JX.402
wave front 197 wave function 43 waveparticle duality 43 wave surface 197. M. 226. 143 Wilson. 279. Woolfson. 215. Xray sources 143 et seq. 303 Weissenberg camera 125 et seq. equiinclination method 130 extension and contraction of spots 137 layerline screens 126 Weissenberg photographs 126 et seq. J. 252.