C. GIACOVAZZO, H. L. MONACO, D. VITERBO F. SCORDARI, G. GILLI, G. ZANOTTI, M. CATTl
Edited by
C. GIACOVAZZO
Dipartimento Geomineralogico, University of Bari, ltaly and lstituto di Ricerca per lo Sviluppo delle Metodologie Cristallografiche, CNR, Bari, ltaly
INTERNATIONAL UNION OF CRYSTALLOGRAPHY OXFORD UNIVERSITY PRESS
OXFORD
UNIVERSITY PRESS
Great Clarendon Street, Oxford 0x2 6 D P Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide in Oxford New Yorlz Athens Auclzland Bangkok Bogota Buenos Aires Calcutta Cape Town Chennai Dares Salaam Delhi Florence Hong Kong Istanbul Karachi KualaLumpur Madrid Melbourne MexicoCity Mumbai Nairobi Paris S%o Paulo Shanghai Singapore Taipei Tokyo Toronto Warsaw with associated companies in Berlin Ibadan Oxford is a registered trade mark of Oxford University Press in the U and in certain other countries K Published in the United States by Oxford University Press Inc., New York O C. Giacovazzo, H. L. Monaco, D. Viterbo, F. Scordari, G. Gilli, G. Zanotti, M. Catti, 1992 The moral rights of the author have been asserted Database right Oxford University Press (maker) Parts of this work first appeared as Introduzione alla cristallografia moderna by M. Bolognesi, A. Coda, C. Giacovazzo, G. Gilli, F. Scordari, and D. Viterbo, edited by C. Giacovazzo, and published by Edizioni Fratelli Laterza, O 1985 First published by Oxford University Press 1992 Reprinted 1994,1995,1998,2000 All rights resewed. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this book in any other binding or cover and you must impose this same condition on any acquirer A catalogue record for this book is available from the British Library Library of Congress Cataloging in Publication Data Fundamentals of crystallography/C. Giacovazzo . . . [et al.]; edited by C. Giacovazzo. (International Union of Crystallography texts on crystallography; 2). Includes bibliographical references. 1. Crystallography. I. Giacovazzo, Carmelo. 11. Series. QD905.2.F86 1992 548dc2O 9127271 ISBN 0 19 855578 4 (Pblz.) Printed in Great Britain on acidfree paper by The Bath Press, Bath
Preface
Crystallography, the science concerned with the study of crystals, is a very old subject. However, only in this century has it developed into a modern science, after the discovery of Xrays and their diffraction by crystals. In recent years crystallography as assumed an increasingly important role in the modern sciences because o its interdisciplinary nature, which has acted as a bridge between, and often as a stimulus for, various rapidly evolving disciplines. Indeed, Chemistry, Physics, Earth Sciences, Biology, Mathematics, and Materials Science have all provided stimuli to the development of new crystallographic interests and techniques. In turn, crystallography has significantly contributed to the advancement of these sciences. Thus, while on the one hand crystallography has been enriched, on the other hand writing a textbook describing all of its aspects has been made more difficult. Recently, the demand for a compact book that gives a comprehensive account of the modern crystallographic subjects has increased. This volume should therefore be a useful and handy textbook for university courses that cover crystallography, fully or only partially. It should also be useful at the more advanced level required for doctorate studies as well as for experienced researchers. It was with these ideas in mind that I first set out to coordinate the in 1985, of a textbook in Italian (Introduzione alla cristallograjia moderna, Edizioni Fratelli Laterza, Bari) of which Fundamentals of crystallography is not only an English translation, but a completely revised and updated version with a new chapter on crystal physics. It was clear to me that (a) the book had to be written by several authors in order to take advantage of their specific expertise; (b) the different chapters had to be carefully harmonized in order to conform them to a unified plan. It seems to me that these two requirements are even more valid today and their achievement is entirely due to the creative cooperation of the coauthors of this book. Two of the coauthors of the Italian textbook, M. Bolognesi and A. Coda, were unable to carry out the translation and revision of their chapters. I wish to express my thanks for their valuable contribution to the previous edition. In this book their topics are treated by G. Zanotti and H. L. Monaco. An additional chapter on crystal physics has been written by M. Catti. I thank the three new authors for entering our team and all the authors for their enthusiastic participation in this project.
f
Bari, Italy August 1991
C.G.
Acknowledgements
We have the pleasant task of expressing our gratitude to Dr C. K. Prout and to Dr D. J. Watkin for encouraging us to write this book and for their useful advice. We have also to thank many friends and colleagues who have commented on the manuscript or given technical support. The cover picture was kindly provided by Professor A. Zecchina and Dr S. Bordiga, who used the ChemX software of Chemical Design Ltd, Oxford, UK. Thanks are also due from C. Giacovazzo to Mr D. Trione for his accurate and rapid typing of the manuscript, to Mr G. Pellegrino for his aid with the drawings and to Ms C. Chiarella for her technical support; from H. L. Monaco to Mr M. Tognolin for the figures, to Mr R. Pavan for the photographs, and to Mrs A. Migliazza for typing the manuscript; from F. Scordari to Professor F. Liebau for the critical reading of the silicate section and for helpful suggestions, Mr Trione is also acknowledged for the typing of the manuscript; from G. Gilli to Professor V. Bertolasi, Dr V. Ferretti, and Dr P. Gilli for their help in the critical reading of the manuscript; from M. Catti to Mr M. Bandera for his aid with the drawings.
Contents
List of contributors
1
Symmetry in crystals
Xlll
...
Carmelo Giacovazzo
The crystalline state and isometric operations Symmetry elements Axes of rotational symmetry Axes of rototranslation or screw axes Axes of inversion Axes of rotoreflection Reflection planes with translational component (glide planes) Lattices The rational properties of lattices Crystallographic directions Crystallographic planes Symmetry restrictions due to the lattice periodicity and vice versa Point groups and symmetry classes Point groups in one and two dimensions The Laue classes The seven crystal systems The Bravais lattices Plane lattices Space lattices The space groups The plane and line groups On the matrix representation of symmetry operators Appendices: 1.A The isometric transformations l . B Some combinations of movements 1.C WignerSeitz cells References
1.D The spacegroup rotation matrices 1.E Symmetry groups l . F Symmetry generalization
Crystallographic computing
Carmelo Giacovazzo
Introduction The metric matrix The reciprocal lattice Basic transformations Transformation from triclinic to orthonormal axes Rotations in Cartesian systems Some simple crystallographic calculations Torsion angles Best plane through a set of points Best line through a set of points Principal axes of a quadratic form Metric considerations on the lattices Niggli reduced cell Sublattices and superlattices Coincidencesite lattices Twins Calculation of the structure factor Calculation of the electron density function The method of least squares Linear least squares Reliability of the parameter estimates Linear least squares with constraints Nonlinear (unconstrained) least squares
viii
I
Contents
Leastsquares refinement of crystal structures Practical considerations on crystallographic least squares Constraints and restraints in crystallographic least squares Alternatives to the method of least squares Rietveld refinement The basis of the technique Some practical aspects of Rietveld refinement Analysis of thermal motion The effect of thermal motion on bond lengths and angles About the accuracy of the calculated parameters Appendices: 2.A Some metric relations between direct and reciprocal lattices 2.B Some geometrical calculations concerning directions and planes 2. C Some transformation matrices 2.D Reciprocity of F and I lattices 2.E Transformations of crystallographic quantities in rectilinear spaces 2.F Derivation of the normal equations 2.G Derivation of the variancecovariance matrix M, 2.H Derivation of the unbiased estimate of Mx 2.1 The FFT algorithm and its crystallographic applications 2.5 Examples of twin laws References
Introduction Thomson scattering Compton scattering Interference of scattered waves Scattering by atomic electrons Scattering by atoms The temperature factor Scattering by a molecule or by a unit cell Diffraction by a crystal Bragg's law The reflection and the limiting spheres Symmetry in reciprocal space Friedel law Effects of symmetry operators in the reciprocal space Determination of the Laue class Determination of reflections with restricted phase values Systematic absences Unequivocal determination of the space group Diffraction intensities Anomalous dispersion The Fourier synthesis and the phase problem Modulated crystal structures Appendices: 3.A Mathematical background 3.B Scattering and related topics 3.C Scattering of Xrays by gases, liquids, and amorphous solids 3.D About electron density mapping 3 .E Modulated structures and quasicrystals References
4
Experimental methods in Xray crystallography
Hugo L. Monaco
Xray sources Conventional generators Synchrotron radiation
3
The diffraction of Xrays by crystals
Carmelo Giacovazzo
Contents
I
ix
Monochromatization, collimation, and focusing of Xrays Data collection techniques for single crystals The Weissenberg camera The precession camera The rotation (oscillation) method in macromolecular crystallography Densitometry The singlecrystal diffractometer Area detectors Data collection techniques for polycrystalline materials Xray diffraction of polycrystalline materials Cameras used for polycrystalline materials Diffractometers used for polycrystalline materials Uses of powder diffraction Data reduction Lorentz correction Polarization correction Absorption corrections Radiation damage corrections Relative scaling Appendices: 4.A Determination of the number of molecules in the unit cell of a crystal References
5
Solution and refinement of crystal structures
Phase determination procedures Completing and refining the structure Difference Fourier method Leastsquares method Absolute configuration Appendices: 5.A Structure factor probability distributions 5.B Patterson vector methods 5.C Two examples of deriving phase information from positivity 5.D Probability formulae for triplet invariants 5 . E Pseudotranslational symmetry 5.F Magic integers 5.G New multisolution techniques 5.H Procedures for completing a partial model References
6
Ionic crystals
Fernando Scordari
The structure of the atom Atoms with a single electron Atoms with more than one electron Interactions between ions Notes on chemical bonds Ionic crystals Lattice energy: the contributions of attractive and repulsive terms Lattice energy: CFSE contribution Applications of lattice energy calculations Ionic radius Maximum filling principle Coordination polyhedra Radius ratio rule Applications of the concept of ionic radius
Davide Viterbo
Introduction Statistical analysis of structure factor amplitudes The Patterson function and its use The heavy atom method Advanced Patterson methods Direct methods Introduction Structure invariants and semiinvariants Probability methods Fixing the origin and the enantiomorph
x
1
Contents
Closest packings Pauling's rules Pauling's first rule Pauling's second rule Pauling's third rule Pauling's fourth rule Pauling's fifth rule Ideal and defect structures MX structures MX, and M2X structures MX3 and M,X, structures A,B,X, structures On the classification of silicates Liebau's crystallochemical classification Structural formulae Relationship between classification parameters and properties of the cations Appendices: 6.A Application of the concept of the packing coefficient (c,) 6.B Structural inferences from crystallochemical parameters References
7
Molecules and molecular crystals 465
Ring conformations Ring conformation and group theory Computation of puckering coordinates Molecular geometry and the chemical bond An overview of bond theories The VSEPR theory Valence bond (VB) theory Hybridization. The machinery Molecular mechanics Molecular hermeneutics: the interpretation of molecular structures Correlative methods in structural analysis Some threecentrefourelectron linear systems Nucleophilic addition to organometallic compounds Nucleophilic addition to the carbonyl group A case of conformational rearrangement Resonance assisted hydrogen bonding (RAHB) References
Gastone Gilli
Chemistry and Xray crystallography Crystal and molecular structure The growth of structural information The nature of molecular crystals Generalities A more detailed analysis of intermolecular forces Thermodynamics of molecular crystals Free and lattice energy of a crystal from atomatom potentials Polymorphism and the prediction of crystal structures Effect of crystal forces on molecular geometry Elements of classical stereochemistry Structure: constitution, configuration, and conformation Isomerism 465
8
Protein crystallography
486
Giuseppe Zanotti Introduction Protein crystals Principles of protein crystallization The solvent content of protein crystals Preparation of isomorphous heavyatom derivatives How isomorphous are isomorphous derivatives? The solution of the phase problem The isomorphous replacement method Anomalous scattering: a complementary (or alternative) approach to the solution of the phase problem The use of anomalous scattering in the determination of the absolute configuration of the macromolecule The treatment of errors
Contents
1
xi
The refinement of heavyatom parameters Picking up minor heavyatom sites: the differenceFourier synthesis A third approach to the solution of the phase ambiguity: realspace filtering Rotation and translation functions and the molecular replacement method Direct methods and the maximumentropy principle in macromolecular crystallography The interpretation of electron density maps and the refinement of the model The interpretation of electron density maps Interactive computer graphics and model building The refinement of the structure Protein structure General aspects Levels of organization of proteins: secondary structure Polypeptide chain description Higher levels of organization: tertiary and quaternary structure, domains, and subunits Groups other than amino acids Thermal parameters and disordered structures Solvent structure The influence of crystal packing Protein classification Appendices: 8.A Some formulae for isomorphous replacement and anomalous dispersion 8.B Translation functions 8.C Macromolecular leastsquares refinement and the conjugategradient algorithm 8.D Conventions and symbols for amino acids and peptides
References and further reading
,
9
Physical properties of crystals Michele Catti
Introduction Crystal anisotropy and tensors Tensorial quantities Symmetry of tensorial properties Overview of physical properties Electrical properties of crystals Pyroelectricity Dielectric impermeability and optical properties Elastic properties of crystals Crystal strain Inner deformation Stress tensor Elasticity tensor Examples and applications Piezoelectricity Symmetry properties of the piezoelectric tensor Crystal defects Experimental methods Planar defects Line defects: dislocations The Burgers circuit Xray topography of dislocations Energy of a dislocation Motion and interaction of dislocations Partial dislocations Smallangle grain boundaries Point defects Thermal distribution of defects Diffusion Ionic conductivity Appendix: 9.A Properties of secondrank tensors Further reading Index
Nec possunt oculi naturam noscere rerum: proinde animi vitium hoc oculis adfingere noli. Lucretius, De Rerum Natura, IV, 3867.
Contributors
Carmelo Giacovazzo, Dipartimento Geomineralogico, Universith di Bari, Campus Universitario, 70124 Bari, Italy; Istituto di Ricerca per lo Sviluppo delle Metodologie Cristallografiche, CNR, 70124 Bari, Italy. Hugo L. Monaco, Dipartimento di Genetica e Microbiologia, Sezione di Biologia Molecolare e Biofisica, Universith di Pavia, Via Abbiategrosso 207 27100, Pavia, Italy. Davide Viterbo, Dipartimento di Chimica, Inorganica, Chimica Fisica e Chimica dei Materiali, Universith di Torino, Via P. Giuria 7, 10125 Torino, Italy. Fernando Scordari, Dipartimento Geomineralogico, Universith di Bari, Campus Universitario, 70124 Bari, Italy. Gastone Gilli, Dipartimento di Chimica and Centro di Strutturistica Diffrattometrica, Universith di Ferrara, Via L. Borsari 46, 44100 Ferrara, Italy. Giuseppe Zanotti, Dipartimento di Chimica Organica, Universith di Padova, Via Marzolo 1, 35126 Padova, Italy. Michele Catti, Dipartimento di Chimica Fisica ed Elettrochimica, Universith di Milano, Via Golgi 19, 20133 Milano, Italy.
.
the links between molecules will become more stable. They can assume a random disposition. breaks in a completely irregular way. This is due to the fact that glass is formed by long. Can we then conclude that all solid materials are crystalline? For instance. liquid. As a consequence of our increased understanding of the structure of matter. If we reduce the thermal motion of a liquid. A distinctive property of the crystalline state is a regular repetition in the threedimensional space of an object (as postulated as early as the end of the eighteenth century by R. made of molecules or groups of molecules. randomly disposed macromolecules of silicon dioxide. a crystal necessarily has a number of defects at nonzero temperature and/or may contain impurities without losing its order. The thermal motion has sufficient energy to move the molecules away from the attractive field of their neighbours. Some crystals do not show threedimensional periodicity because the .Symmetry in crystals CARMELO G I A C O V A Z Z O The crystalline state and isometric operations Matter is usually classified into three states: gaseous. and solid. When it is formed from the molten state (glass does not possess a definite melting point. except for occasional collisions. Gases are composed of almost isolated particles. The molecules will then cluster together to form what is macroscopically observed as a rigid body. Furthermore: 1. but becomes progressively less fluid) the thermal energy which remains as the material is cooled does not allow the polymers to assume a regular pattern. is therefore retained when the cooling is completed. Usually glasses are referred to as overcooled liquids. and crystalline. which is subject to variation following changes in pressure. they tend to occupy all the available volume. J. However. but not calcite. the particles are not linked together permanently. can common glass and calcite (calcium carbonate present in nature) both be considered as crystalline? Even though both materials have high hardness and are transparent to light. while nonfluid materials with a very high degree of disorder are known as amorphous solids. it has become more convenient to classify matter into the three states: gaseous. characteristic of the liquid state. thus allowing liquids to flow. This ordered disposition of molecules is called the crystalline state. but an ordered pattern is more likely because it corresponds to a lower energy state. As a consequence liquids can only be slightly compressed. This disordered disposition. glass. extending over a distance corresponding to thousands of molecular dimensions. Haiiy). liquid. In liquids the attraction between nearestneighbour particles is high enough to keep the particles almost in contact.
or some exhaustive or in the theoretical sections of the International Tables for Cryst~llography). An important step is achieved by answering the following question: given two identical objects. If the congruence is direct. IMS). depending on their nature and on the thermodynamic conditions of their formation. when all points of the object undergo an equal displacement in the same direction. while here only its most useful results will be considered. As a consequence. The movement may be: (1) a translation. These examples indicate that periodicity can be observed to a lesser or greater extent in crystals.A. the basic concepts of which are described in Appendix 1. It has. according to whether the corresponding angles have the same or opposite signs. 171 and Appendix 3. which operations should be performed to superpose one object onto the other? The well known coexistence of enantiomeric molecules demands a second question: given two enantiomorphous (the term enantiomeric will only be used for molecules) objects. when conveniently heated. however. . which are the operations required to superpose the two objects? An exhaustive answer to the two questions is given by the theory of isometric transformations. the corresponding angles will also be equal in absolute value. in incommensurately modulated structures. all points on the axis will not change their position.E) that IMSs are periodic in a suitable (3 + d)dimensional space. Two objects are said to be congruent if to each point of one object corresponds a point of the other and if the distance between two points of one object is equal to the distance between the corresponding points of the other. The congruence may either be direct or opposite.[~~ In order to understand the periodic and ordered nature of crystals it is necessary to know the operations by which the repetition of the basic molecular motif is obtained. In this chapter the symmetry rules determining the formation of an ideal crystalline state are considered (the reader will find a deeper account in some papers devoted to the subject. one object can be brought to coincide with the other by a convenient movement during which it behaves as a rigid body. assume a state intermediate between solid and liquid. Some polymers only show a bidimensional order and most fibrous materials are ordered only along the fiber axis. more often it is the cause of favourable properties which are widely used in materials science and in solid state physics. been shown (p. Some organic crystals. In mathematics such a correspondence is called isometric. 2. which is called the mesomorphic or liquid crystal state. Although nonideality may sometimes be a problem. (2) a rotation around an axis.e. 3.2 1 Carmelo Giacovazzo basic crystal periodicity is modulated by periodic distortions incommensurated with the basic periods (i. It is therefore useful to introduce the concept of a real crystal to stress the differences from an ideal crystal with perfect periodicity. placed in random positions and orientations.
Symmetry in crystals ( 3 (3) a rototranslation or screw movement. which symmetry operations are performed. Symmetry elements Suppose that the isometric operations described in the preceding section. 9) in the axes 1. the plane is then called a glide plane. If the congruence is opposite. 6 axes (called two. the operation is called rotoinversion. sixfold axes) are shown in Table 1. since. which may be considered as the combination (product) of a rotation around the axis and a translation along the axial direction (the order of the two operations may be exchanged).1 their effects on the space are illustrated. (5) the product of a rotation by a reflection with respect to a plane perpendicular to the axis. while the description of translation operators will be treated in subsequent sections. an object is represented by a circle. and a 6 axis is at the same time a 2 and a 3 axis. 1.sign next to it indicating whether it is above or below the page plane. There is no graphic symbol for the 1 axis. 2. axes. known as inversion. p. Note that a 4 axis is at the same time a 2 axis. Axes of rotational symmetry If all the properties of the space remain unchanged after a rotation of 2nIn around an axis. In keeping with international notation. We will be mainly interested (cf. . not only bring to coincidence a couple of congruent objects. (3) the product of a rotation around an axis by an inversion with respect to a point on the axis. In the first column of Fig. If all the properties of the space remain unchanged after a given operation has been carried out. 4. The two objects may be brought to coincidence by the following operations: (1) a symmetry operation with respect to a point. but act on the entire space.1. its written symbol is n. (2) a symmetry operation with respect to a plane. this will be called a symmetry axis of order n . (4) the product of a reflection by a translation parallel to the reflection plane. 4. Axis 1 is trivial. known as reflection. three. with a + or . then one object will be said to be enantiomorphous with respect to the other. or planes with respect to . 6. In the following these elements will be considered in more detail. 3. the operation will be a symmetry operation. Symmetry elements are points. after a rotation of 360" around whatever direction the space properties will always remain the same. the operation is called rotoreflection. The graphic symbols for the 2. 3. four.
1. and screw axes. (b) axes 2 and 2. (d) symmetry pfanes normar to the plane of projection. . Graphical symbols for symmetry elements: (a) axes normal to the pfane of projection. inversion. (c) axes parallel or inclined to the plane of projection.4 1 Carmelo Giacovazzo Table 1. Arrangements of symmetryequivalent objects as an effect of rotation.1. 1. . (e) symmetry planes parallel to the plane of projection Fig.parallel to the plane of projection.
1. 6 axes. When the two enantiomorphous objects fall one on top of the other in the projection plane of the picture. 3 = 31. 2 = 1. According to international notation. (3) the 3 axis is equivalent to the product of a threefold rotation by an inversion: i. they are represented by a single circle divided into two halves. 9 we will be mainly interested in 1. 4 = 4. To each half the appropriate + or . if an object is represented by a circle. (4) the 4 axis is also a 2 axis. 6 axes coincide with those caused by an inversion axis (generally of a different order). 3. (5) the 6 axis is equivalent to the product of a threefold rotation by a reflection with respect to a plane normal to it. while their effects on the space are represented in the second column of Fig. The written symbol of this plane is m. 2. 6 can exist with appropriate translational components. We may note that: (1) the direction of the i axis is irrelevant. and their graphic symbols are given in Table 1. 2.1. 10 we will see that in crystals only screw axes of order 1. Axes of rotoreflection A rotoreflection axis of order n is present when all the properties of the space do not change after performing the product of a 2nln rotation around an axis by a reflection with respect to a plane normal to it. The effects on the space of the 1. 6 = 3. 4. the properties of the halfspace on one side of the plane are identical to those of the other halfspace after the reflection operation. In particular: i = m. From now on we will no longer consider the ii axes but their equivalent inversion axes.e. this will be indicated by 6 = 3/m. its enantiomorph is depicted by a circle with a comma inside. one of which contains a comma. 3 = 6. The written symbol of this axis is fi. . 4. Axes of inversion An inversion axis of order n is present when all the properties of the space remain unchanged after performing the product of a 2nln rotation around the axis by an inversion with respect to a point located on the same axis.Symmetry in crystals 1 5 Axes of rototranslation or screw axes A rototranslational symmetry axis will have an order n and a translational component t. 3. 3. 1. 4. (2) the 2 axis is equivalent to a reflection plane perpendicular to it. The written symbol is fi (read 'minus n' or 'bar n'). since the operation coincides with an inversion with respect to a point. As we shall see on p. On p. 2. if all the properties of the space remain unchanged after a 2nln rotation around the axis and the translation by t along the axis.sign is assigned.
if instead of placing the lattice point at the centre of gravity. Nevertheless we are allowed to choose different types of unit cells. we obtain the lattice of Fig. 1. We will speak of line. . where HOCl is a geometrical motif repeated at intervals a and b.2(b) is uniquely defined by the vector where u and v are positive or negative integers.. b. 112). The vectors a and b define a parallelogram which is called the unit cell: a and b are the basis vectors of the cell.2(c). Lattices Translational periodicity in crystals can be conveniently studied by considering the geometry of the repetion rather than the properties of the motif which is repeated.Cl o H . the point P is related to the origin 0 and to the basis vectors a' and b' through ( 4 v) = (112.6 1 Carmelo Giacovazzo Reflection planes with translational component (glide planes) A glide plane operator is present if the properties of the halfspace on one side of the plane are identical to those of the other halfspace after the product of a reflection with respect to the plane by a translation parallel to the plane. or in a threedimensional space. such as those shown in Fig. The cells in Fig. and space lattices. (c) corresponding lattice with some examples of multiple cells. On p. the lattice does not change.Cl /Cl . and c along three noncoplanar directions.2(b). the repetition geometry can be fully described by a periodic sequence of points. depending on whether the periodicity is observed in one direction. 1. 1. taking into account that the points on sides and on corners are only partially shared by the given cell. If the motif is periodically repeated at intervals a. having double or triple area with respect to those selected in Fig.Cl . 1.2(b). An example is illustrated in Fig. they are all characterized by the property that each lattice point satisfies relation (1. Therefore the position of the lattice with respect to the motif is completely arbitrary. plane. separated by intervals a. we locate it on the oxygen atom or on any other point of the motif.2(a). 1. In Fig. In this case each lattice point will still satisfy (1. If any lattice point is chosen as the origin of the lattice. since the four points at the corners of each cell belong to it for only 114.2(b) contain only one lattice point. Symmetry operations relating objects referred by direct congruence are called proper (we will also refer to proper symmetry axes) while those relating objects referred by opposite congruence are called improper (we will also refer to improper axes). H? ? ? H ? H? H ? H /C1 /Cl /Cl /Cl &C1 7 1 H /Cl H H H H ~ i ~ (a) R~~~~~~~~~ of a graphical motif as an . 11 we shall see which are the glide planes found in crystals. example of a twodimensional crystal. in a plane.2(b) four possible choices are shown. (b) corresponding lattice with some examples Of primitive cells. 1. For instance. The different types of unit cells are better characterized by determining the number of lattice points belonging to them. If we replace the molecule with a point positioned at its centre of gravity. These cells are called primitive. c along the same three directions. b. 1. The choice of the vectors a and b is rather arbitrary.1) with integer u and v.2(c) contain either two or three /Cl /Cl /Cl .1) but u and v are no longer restricted to integer values. 1. Note that. This collection of points will be called a lattice. The cells shown in Fig. the position of any other point in Fig..
If the chosen cell is primitive. then the values of u. Two lattice points define a lattice row. to be read as 'three. it is necessary to specify in a simple way directions (or planes) in which specific physical properties are observed. lattice points. Lattice rows and planes. and c are the X . opposing b. If the cell is multiple then u. For instance. 0.. and one on a face for 112. and planes defined by three lattice points rational planes. The above considerations can be easily extended to linear and space lattices. while the angles between them are indicated by a. The volume of the unit cell is given by where the symbol '. and y.. respectively. b. C. 1. and y opposing c (cf.' indicates the scalar product and the symbol ' A ' the vector product... The directions specified by the vectors a . The three basis vectors define a parallelepiped. Z crystallographic axes. and c.. Suppose we have chosen a primitive unit cell. and n integer. one. u. .2) Fig. b. Fig.Symmetry in crystals 1 7 points and are called multiple or centred cells. . (1.with no common factor among the indices. . 1. In a lattice there are an infinite number of parallel rows (see Fig. .. etc.3). a point on a edge for 114.. 1. w will have rational values. . each node is uniquely defined by the vector = ua II + ub + W C . double cells. define two different lattice points. This property may be used to characterize a direction in a unique way.e..4): they are identical under lattice translation and in particular they have the same translation period. . A lattice row defines a crystallographic direction. The two lattice vectors Q . called again a unit cell. Y. u. w in (1. Directions defined by two lattice points will be called rational directions. etc.with w.2) are bound to be integer for all the lattice points.4. can be uniquely defined by the vector Q. Directions and planes of this type are also called crystallographic directions and planes. given an origin 0 and three basis vectors a . depending on whether they contain two.. Several kinds of multiple cells are possible: i. The faces of the unit cell facing a . and Q. triple cells. u. the lattice properties related to them are called rational. B. To characterize the cell we must recall that a lattice point at vertex belongs to it only for 1/8th. This direction will be indicated by the symbol [3 1 21. two' and not 'three hundred and twelve'. but only one direction. For the latter in particular. . a Notation for a unit cell. The orientation of the three crystallographic axes is usually chosen in such a way that an observer located along the positive direction of c sees a moving towards b by an anticlockwise rotation. u. the direction associated with the vector Q9. with a opposing a . Crystallographic directions Since crystals are anisotropic. respectively. and c are indicated by A. three.. The rational properties of lattices Since a lattice point can always be characterized by rational numbers. Fig. b.
6. and Z at three lattice points is that characterized by a m value equal to the least common mutiple of h . 1.3 define the same direction..5). k . m l k . We can therefore conclude that eqn (1.1512. I.4) and (1..4) from the origin is m times that of plane (1. Y .4) where h .6 + and no common factor among the numerators: Q [3 9 21 to be read 'three'. k . The rational properties of all points being the same.5..4) m l h . = Q3. a family of identical and equally spaced crystallographic planes. It is then clear that the distance of plane (1. 0 . Then the equation of the plane is x'lpa + y'lqb + z'lrc = 1. 1. q. 0 ) and (0. r. These will also be crystallographic planes since each of them is bound to pass through at least three lattice points. the equation of the plane becomes xlp + y l q + z l r = 1. r ) with integer p. If we introduce the fractional coordinates x = x ' l a . q . In fact they .4). The first plane of the family intersecting the axes X . Let us now show that (1. and I can be deduced from (1. + lz = m (1. these are included within braces: ( h k I ) . 0. Thus Q112. Y . as m is varied. (1. We can therefore construct a family of planes parallel to the plane (1. To indicate that a family of lattice planes is defined by a sequence of three integers. . minus two'..312. by varying m over all integer numbers from m to +m. and n will be rational numbers. m l l . z = z l / c .4) represents a plane at a distance from the origin m times the distance of the plane The intercepts of the plane (1. and 1 are suitable integers. Some lattice planes of the set (236).5. The three indices h .4) defines. there will be a plane of the family passing through each lattice point. and 1 define the family and are its Miller indices.6. and Z at the three lattice points ( p .5). v. Crystallographic planes Three lattice points define a crystallographic plane. The indices of the former may therefore be factorized to obtain a common denominator . A simple interpretation of the three indices h. nine. 0 ) ) (0. w. the largest common integer factor of which will be 1. Z will be l l h .113 and Q512. For the same reason each lattice plane is identical to any other within the family through a lattice translation. k .3) Multiplying both sides by m we obtain hx + ky Fig. y = y ' l b . r (see Fig.8 1 Carmelo Giacovazzo When the cell is not primitive u. l l k and 111 respectively and those of (1.5). k .5) on X. Suppose it intersects the three crystallographic axes X . Y . Suppose that m is the least common multiple of p. q.
from which 0 k . this being the reason why it is impossible to pave a room only with pentagonal tiles (see Fig. Some examples of crystallographic planes are illustrated in Fig. and T".(a) Lattice points in a plane normal to the symmetry axis n passing through 0. there will be an n axis passing through each and every lattice point.7(a)) at T. 2. T. 15. + + + Planes (1. by varying m over all integers from m to +m. (1.8) belong to the same family. As a numerical example let us consider the plane which can be written as The first plane of the family with integer intersections on the three axes will be the 30th (30 being the least common multiple of 10. (110) (010) (zio) Fig. . Symmetry restrictions due to the lattice periodicity and vice versa Suppose that the disposition of the molecules in a crystal is compatible with an n axis. 1. The vector T' . and r in eqn (1. 6.Symmetry in crystals 1 9 indicate that the planes of the family divide a in h parts. We will then have lattice points (see Fig. 1. and 6) and all the planes of the family can be obtained from the equation lox + 15y 62 = m. 1.T" = mT where m is an integer value: in a scalar form 2 cos (2nIn) = m (m integer). q. We conclude that a family of crystallographic planes is always uniquely defined by three indices h. 1.9) is only verified for n = 1. we will assume that n passes through the origin 0 of the lattice.6) by their common integer factor we obtain x/3 y/2 z/5 = 1. (OkO). and C of the unit cell are of type (hOO). 4. Miller indices for some crystallographic planes parallel to Z ( Z i s supposed to be normal to the page). We observe that if we divide p. and 1 having the largest common integer factor equal to unity. T'. 1. 3. Planes parallel to faces A. (b) Fig.9) Equation (1.7) and (1.7. compatible with an ii axis and vice versa. and (001) respectively. parallel to that passing through the origin.6. Thus axes I 3. Since each lattice point has identical rational properties. being parallel to T.7(b).6. (hol). B.T" must also be a lattice vector and. Y. Let T be the period vector of a row passing through 0 and normal to n. Crystallographic planes parallel to one of the three axes X. Regular (b) pentagons cannot fill planar space. k. 4. and c in 1 parts. In particular each symmetry axis will lie along a row and will be perpendicular to a crystallographic plane. or (hkO) respectively. b in k parts. or Z are defined by indices of type (Okl). It is noteworthy that a 5 axis is not allowed. Without losing generality. and therefore a lattice. 3. we will have T' . A unit cell. As a consequence the disposition of lattice points must also be compatible with the same axis. 6 will also be allowed. compatible with an n axis will also be .
. (4/4)T. and 6. (2/4)T.10 1 Carmelo Giacovazzo Let us now consider the restrictions imposed by the periodic nature of crystals on the translational components t of a screw axis.1: the effects of screw axes on the surrounding space are represented in Fig. It follows that: (1) in (1. we will obtain. 4. of these only the first four will be distinct. in the first case a righthanded helix and in the second a lefthanded one (the two helices are enantiomorphous). . is also a 2 and a 32. 6.8. (1/4)T. with integer p .. The same applies to the pairs 4. 64 is also a 2 and a 3.. 61 and 6. and 63 is also a 3 and a 2. Screw axes: arrangement of symmetryequivalent objects..8. and by a 32 axis. 6. Note that: If we draw a helicoidal trajectory joining the centres of all the objects related by a 3. If we apply the translational component n times the resulting displacement will be nt. for a screw axis of order 4 the allowed translational components will be (0/4)T.. 3. In order to maintain the periodicity of the crystal we must have nt = p T . . and 6. . The nature of a screw axis is completely defined by the symbol n. . 2. (2) the nfold axis may be thought as a special screw with t = 0. 1.. 4. is also a 2 axis. Its rotational component must correspond to n = 1. (5/4)T.. (3/4)T. Suppose that this lies along a row with period vector T. Fig.10) p can be restricted within 0 s p < n . and 4. or For instance. The graphic symbols are shown in Table 1. 1.
2. will Table 1. Classes coinciding with other classes already quoted in the table are enclosed in brackets. The total number of crystallographic point groups (for threedimensional crystals) is 32. In a nonprimitive cell the condition 2t = p T still holds. b / 2 . (1/2)T. the symbol n/ri is used. and they were first listed by Hessel in 1830. Therefore 2t = p T . t = ( p / 2 ) T . 1. We will indicate by a. and l2 intersecting in 0 (see Fig. The problem of the coexistence of more than one axis all passing by a common point was first solved by Euler and is illustrated. while 1. Here we only give the essential results.e. by n the diagonal glides with translational components ( a b ) / 2 or ( a + c ) / 2 or ( b c ) / 2 or ( a + b + c ) / 2 . may coexist. c / 2 respectively. The simplest combinations of symmetry operators are those characterized by the presence of only one axis. The set of crystals having the same point group is called crystal class and its symbol is that of the point group.Symmetry in crystals We will now consider the restrictions imposed by the periodicity on the translation component t of a glide plane. The graphic symbols for glide planes are given in Table 1. . Let us suppose that there are two proper axes I . the combinations of proper and improper axes intersecting in a point. where p may be any integer and T any lattice vector on the crystallographic plane on which the glide lies. Singleaxis crystallographic point groups Proper axis 1 2 3 4 6 Improper axis Proper and improper axis 1 3 =m 31 4  (i[i i) = 212= 2jm (3[3 = 3) 414 = 4/m 616 = 6/m 6 = 3/m 5 5 + + 3 = 13 . These are called point groups. but now T is a lattice vector with rational components indicated by the symbol d. which can be a proper axis or an inversion one. (2/2)T. in Appendix 1. The I . If we apply this operation twice. . b. a proper and an inversion axis may be simultaneously present. with or without translational components. We will consider here only those combinations of operators which do not imply translations. c axial glides with translational components equal to a / 2 . i. of which only the first two are distinct. (3/2)T. Often point group and crystal class are used as synonyms. axis will repeat in Q an object originally in P.B. The 13 independent combinations of this type are described in Table 1. with a different approach. I 11 + + Point groups a n d s y m m e t r y classes In crystals more symmetry axes.2.As p varies over all integer values. both proper and improper.9). the resulting movement must correspond to a translation equal to pT. When along the same axis a proper axis and an inversion axis are simultaneously present. For p = 0 the glide plane reduces to a mirror m.e.1. the following translations are obtained OT. Also. even if that is not correct in principle. i. since the operators form a mathematical group and leave one point fixed..
Suppose now that in Fig. while their disposition in the space is shown in Fig. The only allowed combinations are n22. For these combinations the smallest angles between the axes are listed in Table 1. . while in Table 1.9.3. We may conclude that if one of the three symmetry operators is an inversion axis also another must be an inversion one. P and Q are therefore directly congruent and this implies the existence of another proper operator which repeats the object in P directly in R. Then the objects in P and in Q will be directly congruent.'. 422.10. 2 3 4 6 2 4 90 60 45 30 70 54 (22) (2 2) (2 2) (2 2) 31 '44" (3 3) 44'08" (4 3) repeat in R the object in Q.9 1.10. For each angle the types of symmetry axes are quoted in parentheses Combination of symmetry axes 2 2 2 2 3 3 2 2 2 2 3 2 cu (ded 90 90 90 90 54 35 (22) (2 3) (2 4) (2 6) 44'08" (2 3) 15'52" (2 3) B (ded 90 (2 2) 90 (2 3) 90 (2 4) 90 (2 6) 54 44'08" (2 3) 45 (2 4) Y (ded 0 Fig. .4 are listed all the point groups characterized by combinations of type PPP. 322. The Fig. 622. 432. 1. 1.3. PII. 432. For each combination of symmetry axes the minimum angles between axes are given. Therefore the third operator relating R to P will be an inversion axis.12 ( Carmelo Giacovazzo 11 P t' . 1. Note that the combination 233 is also consistent with a tetrahedral symmetry and 432 with a cubic and octahedral symmetry.5 the classes with axes at the same time proper and improper are given. IIP (P=proper. In Table 1. while the object in R is enantiomorphic with respect to them. 1. is a proper axis while 1. Arrangement of proper symmetry axes for six point groups. is an inversion one. Arrangement of equivalent objects around two intersecting symmetry axes. IPI. 233.0 Table 1. 233. 532 which in crystals reduce to 222. I = improper). In the two tables the combinations coinciding with previously considered ones are closed within brackets.
In Table 1. there will also be an m plane (or a ? axis) normal to the axis and passing through the intersection point. some molecules and their point symmetry are shown in Fig. In Tables 1. 1. there will also be a 2 axis passing through ? and normal to m. are one the enantiomorph of the other. since only two symmetry operators are independent.5. Of basic relevance to this is a postulate .6 are listed the conventional symbols used for the 32 symmetry classes. To help the reader. Crystallographic point groups with more than one axis PPP PI1 I P I IIP 1 13 (43 2 43 .Symmetry in crystals Table 1.4. the symbol 2/m% is too extensive. In any case the symmetry of the crystal will belong to one of them. It may be noted that crystals with inversion symmetry operators have an equal number of 'left' and 'right' moieties.2 rnlm Table 1. when considered separately. The conclusions reached so far do not exclude the possibility of crystallizing molecules with a molecular symmetry different from that of the 32 point groups (for instance with a 5 axis).4. these parts. Conversely. On the other hand. the complete list of symmetry elements in the class 2/m33 is 2/m 2/m 2/m?3333. each axis being proper and improper simultaneously results so far described can be easily derived by recalling that: If two of the three axes are symmetry equivalent. while binary axes in 422 differing by 45" are not symmetry equivalent. the threefold axes in 233 are symmetry referred by twofold axes.2. they can not be one proper and one improper.11. and 1. If an evenorder axis and a ? axis (or an m plane) coexist. It is very important to understand how the symmetry of the physical properties of a crystal relates to its point group (this subject is more extensively described in Chapter 9). for example. if m and ? coexist. 1.5 the symbol of each point group does not reveal all the symmetry elements present: for instance. Crystallographic point groups with more than one axis.
2E341mmo E E E E E E E EEE E EkEnmm .E E E E E E E E E Ekkbmm . .2 E 9 3 ~ ~ m wE E .
galena crystals (PbS. The indices of welldeveloped faces on natural crystals tend to have small values of h. In Fig. J. and in symmetry classes belonging to the cubic system the shape of the indicatrix is a sphere. enclosed in braces: {hkl). The morphology of different samples of the same compound can show different types of face. and different numbers of edges. a prism a set of equivalent faces parallel to a common axis. or octahedral habit (Fig. 1. blk. We shall now see how it is possible to guess about the point group of a crystal through some of its physical properties: 1. cubeoctahedral. Steno (1669) and D. (b) crystal with a sixfold symmetry axis. or hexagonal systems (see Table 1. The morphology of a crystal tends to conform to its point group symmetry. An important extension of this law is obtained if space group symmetry (see p. But at the same temperature crystals will all have constant dihedral angles between corresponding faces (J. etc. with point group 3m. 607). Accordingly. The origin within the crystal is usually chosen so that faces (hkl) and (hit) are parallel faces an opposite sides of the crystal. showing a symmetry higher than that of the point group. with different extensions. otherwise it is closed. the ellipsoid is a revolution around the threefold axis.13 some idealized crystal forms are shown.12(a)). point group m3m) tend to assume a cubic. Miller indices can be used as form symbols. Thus a pedion is a single face. 1. Rome' de l'Ile. A crystal form is named according to the number of its faces and to their nature. a pyramid is a set of planes with equal angles of inclination to a common axis. 1. the external form depending not only on the structure but also on the chemical and physical properties of the environment.6) the shape of the indicatrix is a rotational ellipsoid (the axis is parallel to the main symmetry axis). From a morphological point of view. Sodium chloride grows as cubic crystals from neutral aqueous solution and as octahedral from active solutions (in the latter case cations and anions play a different energetic role). L. This is in general a threeaxis ellipsoid: thus the lowest symmetry of the property 'refraction' is 2/m 2lm 2/m. The set of symmetryequivalent faces constitutes a form: the form is open if it does not enclose space. can be explained easily. trigonal. . cll on the reference axes (Bravais' law). (integers greater than six are rarely involved). with large intercepts alh. in the case of tourmaline. The variation of the refractive index of the crystal with the vibration direction of a planepolarized light wave is represented by the optical indicatrix (see p. or equivalently. Haiiy (17431822). Such faces correspond to lattice planes with a high density of lattice points per unit area. The orientation of the faces is more important than their extension. by considering that faces coincide with lattice planes and edges with lattice rows. following R. 17361790). 1.Symmetry in crystals 2. In crystal classes belonging to tetragonal. (a) Crystals showing cubic or cubeoctahedral or octahedral habitus. a pinacoid is a pair of parallel faces. the point group of the ellipsoid. For instance. B. 22) is taken into account: screw axes and glide planes normal to a given crystal face reduce its importance (DonnayHarker principle). This property. the observation of which dates back to N. Guglielmini (1688). The orientations can be represented by the set of unit vectors normal to them.12. the faces. a sphenoid is a pair of faces related by a diad axis. k. a crystal is a solid body bounded by plane natural surfaces. For example. This set will tend to assume the pointgroup symmetry of the given crystal 1 15 (b) Fig.
This phenomenon is described by a thirdrank tensor. which varies with temperature (pyroelectric effect. HgS. 6. see p. 606). 4. Piezo. Point groups in one and two dimensions The derivation of the crystallographic point groups in a twodimensional space is much easier than in three dimensions. and ii axes are not used. 3m. Nevertheless when these effects are not detectable. and these are indicated by the symbols: 1. m.and pyroelectricity tests are often used to exclude the presence of an inversion centre. 4. 6mm. no definitive conclusion may be drawn. 2mm. (b) arsenopyritf. 3. (c) ilmenite. 2. 1. The ten polar classes are: 1. 6. because of the piezoelectric effect (see p. Because of nonlinear optical susceptibility. The number of crystallographic point groups in one dimension is 2: they are 1 and m = (I). 4mm. The symmetry of a crystal containing only one enantiomer of an optically active molecule must belong to one of the 11 point groups which do not contain inversion axes.12(a) shows an m3m symmetry. A point group is said to be polar if a polar direction. (d) gypsum. The morphological analysis of a crystalline sample may be used to get some. class 32). Electrical charges of opposite signsmay appear at the two hands of a polar axis of a crystal subject to compression. mm2. light waves passing through noncentrosymmetric crystals induce additional waves of frequency twice the incident frequency. A polar axis is a rational direction which is not symmetry equivalent to its opposite direction. 5. 2. 6. class 32. For instance.13. 3. . It then follows that a polar direction can only exist in the 21 noncentrosymmetric point groups (the only exception is the 432 class. The total number of point groups in the plane is 10. 4. 3m. Thus. Along this direction a permanent electric dipole may be measured. 1. Some simple crystal forms: (a) cinnabar. 608): it occurs in all noncentrosymmetric groups except 432. class mmm. although not conclusive. 2. CaSO. in quartz crystals (SOz. Ferroelectric crystals show a permanent dipole moment which can be changed by application of an electric field. 4mm. but not at those of the threefold axis. and is very efficientL7] testing the for absence of an inversion centre. class 3. each sample of Fig. 6mm. 619). of its pointgroup symmetry..16 1 Carmelo Giacovazzo independently of the morphological aspect of the samples. as the piezoelectric tensor (see p. indication. class 2/m. where piezoelectricity can not occur). In these groups not all directions are polar: in particular a direction normal to an evenorder axis or to a mirror plane will never be polar. charges of opposite sign may appear at the opposite hands of the twofold axes.. Etch figures produced on the crystal faces by chemical attack reveal the face symmetry (one of the following 10 twodimensional point groups). Thus they can only belong to one of the ten polar classes. In fact the reflection with respect to a plane is substituted by a reflection with respect to a line (the same letter m will also indicate this operation). 3. FeTiO. 1. Fig. FeAsS. 7. m. and the sample in Fig.12(b) shows a sixfold symmetry if the normals to the faces are considered instead of their extensions. with no other symmetry equivalent directions. is allowed.
Point groups 1 and i have no symmetry axes and therefore no constraint axes for the unit cell. 4. m. These crystals belong to the tetragonal system. and 2/m belong to the monoclinic system. . 6mm. Classes 222. we will obtain a unit cell with angles a = P = y = 90" and with unrestricted a:b:c ratios. m3m] distributed as the diagonals of a cube can be referred to orthogonal unit axes coinciding with the cube edges. For the seven groups with only one fourfold axis [4. 6. and 2/m all present a 2 axis. Classes 1 and are said to belong to the triclinic system. For the crystals with only one threefold or sixfold axis [3. The presence of the threefold axes ensures that these directions are symmetry equivalent. 3m. 6/mm] the c axis is assumed along the three. which indeed form a centrosymmetric set. P. 422.4/m. 32. 6. If we assume these as reference axes. m3.or sixfold axis. the ratios a:b:c and the angles a . Crystals with four threefold axes [23.4. If we assume that this axis coincides with the b axis of the unit cell. 42m. mmm are characterized by the presence of three mutually orthqgonal twofold rotation or inversion axes. We will then have a = y = 90" and P unrestricted and the ratios a:b:c also unrestricted. y can assume any value. Crystals with symmetry 2. In particular this happens when the measured quantities do not depend on the atomic positions. In turn. 6. 62m. 432. the cells will be chosen in the most suitable way to show the symmetry actually present. This is called the cubic system. These classes belong to the orthorhombic system. 3. 6/m. 3. a and c can be chosen on the lattice plane normal to b. the presence of one of these axes will impose some restrictions on the geometry of the lattice.Symmetry in crystals 1 17 The Laue classes In agreement with Neumann's principle.4mm. both characterized by a unit cell with angles a = /3 = 90" and y = 120°. while a and b are symmetry equivalent on the plane perpendicular to c. mm2. The seven crystal systems If the crystal periodicity is only compatible with rotation or inversion axes of order 1. on the lattice plane normal to c. When these groups are collected in classes they form the 11 Laue classes listed in Table 1. m. The chosen unit cell will have a = P = y = 90' and ratios a :b:c = 1:1:1. physical experiments do not normally reveal the true symmetry of the crystal: some of them. 4/mmm] the c axis is chosen as the direction of the fourfold axis and the a and b axes will be symmetry equivalent. 622. 43m.6. but rather on the interatomic vectors. These point groups are collected together in the trigonal and hexagonal systems. 2. 3m. Groups 2. show the symmetry one would obtain by adding an inversion centre to the symmetry elements actually present. and ratios a:b :c = 1:1:c. for example diffraction. It is therefore convenient to group together the symmetry classes with common features in such a way that crystals belonging to these classes can be described by unit cells of the same type. The cell angles will be a = P = y = 90" and the ratios a:b:c = 1:l:c. respectively. Point groups differing only by the presence of an inversion centre will not be differentiated by these experiments.
In this section we shall describe the five possible plane lattices and fourteen possible space lattices based both on primitive and nonprimitive cells. This plane lattice has an oblique primitive cell. based on nonprimitive cells.14(d) a plane lattice is represented compatible with the presence of a fourfold axis. The cell is primitive and compatible with the point groups 4 and 4mm. (b) m .14. 2 m m (c) m. Nevertheless. but such a cell is seldom chosen. A unit cell with a rhombus shape and angles of 60" and 120" (also called hexagonal) may be chosen. This can be seen by choosing the rectangular centred cell defined by the unit vectors a' and b'. which can not be related to the previous ones.14(c) with a = b and y # 90" is compatible with m.4mm .14(a)) is compatible with the presence of axes 1 or 2 normal to the cell. each of the lattice points has a 2mm symmetry and therefore the lattice must be compatible with a rectangular system. 1.14(b) and 1. It is worth noting that the two lattices shown in Figs. A centred rectangular cell can also be selected. In Fig.14(c) are of different type even though they are compatible with the same point groups.2mm Fig.14(e) a plane lattice compatible with the presence of a three. Plane lattices An oblique cell (see Fig. In particular we will consider as different two lattice types which can not be described by the same unitcell type. There are also other types of lattices. This orthogonal cell is more convenient because a simpler coordinate system is allowed. These are called Bravais lattices. Note that the unit cell is primitive and compatible with the point groups m and 2mm. Each of these primitive cells defines a lattice type. 1. The five plane lattices and the corresponding twodimensional point groups.14(b) is a reflection line. In Fig. I I i i I (d) 4.18 1 Carmelo Giacovazzo The Bravais lattices In the previous section to each crystal system we have associated a primitive cell compatible with the point groups belonging to the system. 1. after Auguste Bravais who first listed them in 1850. 1. If the row indicated by m in Fig. This cell is primitive and has point group 2.or a sixfold axis is shown. Also the lattice illustrated in Fig. 1. 1. the cell must be rectangular. 1.
A cell which is at the same time body and face centred can always be reduced to a conventional centred cell. 1. In fact a cell which is at the same time A and B.0).1/3.2/3.15. b' = b. The conventional types of unit cell Symbol Type Positions of additional lattice points Number of lattice points per cell 1 2 2 2 2 2 4 3 Fig. Their fairly limited number can be explained by the following (or similar) observations: A cell with two centred faces must be of type F.1/2. 112).112. y = 90" a=b. y.8 the most useful types of cells are described. The lattice can then be described by a new A cell with axes a ' = a/2. Reduction of an I.1/3) . z) is repeated by translation into ( x .8 define the minimal translational components which will move an object into an equivalent one.1/2. For instance. The five plane lattices  1 19 Cell Oblique Rectangular Square Hexagonal Type of cell P P. + J Table 1.0) will then also be present.0. in an Atype cell.1/2.0.15).112~ (1/3.112. O). 1. an object at ( x .0. C P P Point group of the net 2 2mm 4mm 6mm Lattice parameters a. b.1/2.2/3). When these two lattice translations are applied one after the other they will generate a lattice point also at (1/2. (1/2. z n/2) with m and n integers: the shortest translation will be (0.y=120" The basic features of the five lattices are listed in Table 1.1/2) and (1/2. For instance an I and A cell will have lattice points at positions (1/2.0) (112.1/2. b. must have lattice points at (0. y a.1/2). y = 90" a = b. y + m/2. It is worth noting that the positions of the additional lattice points in Table 1. and c' = c (Fig.0.1/2) and (0.1/2) ~0.7 Space lattices In Table 1.1/2.8.and Acentred cell to an Acentred cell.1/2) (1/2.1/2. P I A B C F R primitive body centred Aface centred Bface centred Cface centred All faces centred Rhombohedrally centred (de scription with 'hexagonal axes') (112.1/2): a lattice point at (1/2.Symmetry in crystals Table 1.1/2. Let us now examine the different types of threedimensional lattices grouped in the appropriate crystal systems.1/2) (1/2. (2/3. l r 2 ) (0.7.
1. P and I. C. (b) reduction of an Icentred to an Acentred cell. It can be easily verified that because of the fourfold symmetry an A cell will always be at the same time a B cell and therefore an F cell. 1. A Bcentred monoclinic cell with unit vectors a. b' = b. while the unit vectors a. With arguments similar to those used for monoclinic lattices. When choosing a' = a. with angles a = /3 = y = 90" and general a:b:c ratios.16(d) a C cell with axes a. Thus only two different tetragonal lattices. described by P and C cells. b. c' = ( a c ) / 2 a typeC monoclinic cell is obtained. since the a and c axes can always be interchanged.16. c' = a + c. (c) reduction of an Fcentred to a Ccentred cell. An I cell with axes a. (d) reduction of a Ccentred to a P nonmonoclinic cell. 1. c) plane. angles a = y = 90". Therefore a lattice with a Btype monoclinic cell can always be reduced to a lattice with a P monoclinic cell. c is illustrated. the reader can easily verify that there are four types of orthorhombic lattices. In fact. the corresponding cell becomes an A monoclinic cell. A C cell is always amenable to another tetragonal P cell. b' = ( .16(c). 1. and not amenable one to the other. are found. c. b. + + + Orthorhombic lattices In the conventional orthorhombic cell the three proper or inversion axes are parallel to the unit vectors a. We will now show that there is a lattice with a C monoclinic cell which is not amenable to a lattice having a P monoclinic cell. Furthermore. c is shown in Fig. b' = b. Since c' lies on the (a. but this no longer shows the features of a monoclinic cell.16(b). p. a lattice described by an F monoclinic cell can always be described by a C monoclinic cell. Fig.16(a). If we choose a' = a . b. any triclinic lattice can always be referred to such a cell. A primitive cell is obtained by assuming a' = ( a + b ) / 2 . and the 2 axis lies along the diagonal of a face. It can then be concluded that there are two distinct monoclinic lattices. 1. An F cell with axes a. unrestricted p and a :b:c ratios.20 ( Carmelo Giacovazzo Triclinic lattices Even though nonprimitive cells can always be chosen. Monoclinic lattices: (a) reduction of a Cubic lattices In the conventional cubic cell the four threefold axes are chosen to be parallel to the principal diagonals of a cube. also. . c are parallel to the cube edges. Monoclinic lattices The conventional monoclinic cell has the twofold axis parallel to b. and F. c' = ( a c ) / 2 a primitive cell is obtained. P. the absence of axes with order greater than one suggests the choice of a conventional primitive cell with unrestricted a . Therefore. a' = b' # c ' . b.a b ) / 2 . c' = c. a = b. b' = b. Tetragonal lattices In the conventional tetragonal cell the fourfold axis is chosen along c with a = p = y = 90°. c is illustrated in Fig. the new cell will still be monoclinic. since y' # 90°. Therefore a lattice with an I monoclinic cell may always be described by an A monoclinic cell. and unrestricted c value. an A cell can be always reduced to a C cell. Because of symmetry a typeA (or B or C) Bcentred cell to a P cell. b. y angles and a:b:c ratios. If we choose a' = a. c is shown in Fig. In Fig. b. The latter is then amenable to a tetragonal I cell. I.
213) while for reverse setting centring points are at It is worth noting that a rhombohedral description of a hexagonal P lattice is always possible. Six triple rhombohedral cells with basis vectors a. terms of the c. the basis of the hexagonal centred cell is labelled a b. I.Symmetry in crystals 1 21 cell is also an F cell. Such lattices may also be described by three triple hexagonal cells with basis vectors UH..O. Rhombohedra1 lattice.213. The basis of the . (numerical fractions are calculated in . with unit vectors a R . . (a) Obverse setting. CR such that aR= bR = cR. P is the only type of hexagonal Bravais lattice. and the threefold axis along the UR + bR + CR direction (see Fig. axis). Centred cells are easily amenable to the conventional P trigonal cell.I . a = /3 = 90°. unrestricted c. 1. Hexagonal lattices In the conventional hexagonal cell the sixfold axis is parallel to c. Fig. with a = b... bH. and F which are not amenable one to the other. said to be in reverse setting. aR= PR = YR. unrestricted c. c. and y = 120". c. in the conventional trigonal cell the threefold axis is chosen parallel to c. There are three cubic lattices. bR. (b) the same figure as in (a) projected along c.17. CH defined according to[61 These hexagonal cells are said to be in obverse setting. O).I .17)) at (O. 1. (113. Three further triple hexagonal cells. I . can be obtained by changing a H and bH to aH and bH. Trigonal lattices As for the hexagonal cell. The hexagonal cells in obverse setting have centring points (see again Fig. P. 1. bk. rhombohedral cell is labelled a b. Because of the presence of a threefold axis some lattices can exist which may be described via a P cell of rhombohedral shape. a = /3 = 90") and y = 120".. with a = b..17).
e. b) plane is defined by a vector (P . and (ihkl) are symmetry equivalent planes. The 14 Bravais lattices are illustrated in Fig. Each triple rhomobohedral cell will have centring points at (O. with i = (u v).+ cH. others by a triple hexagonal cell. v = n . and cyclic permutations of a.1/3). O).0. a direction in the (a. In the first case the nodes lying on the different planes normal to the threefold axis will lie exactly one on top of the other.213. they are called holohedries and are listed in Table 1. A detailed description of the metric properties of crystal lattices will be given in Chapter 2. (213. Also. Following pp. [u . bH. For instance (1 2 3 5). i should be added to the first three indices in order to bring to zero the third index.j. 2mm. a hexagonal cell is chosen. v = (2n . to pass to the threeindex one. this may be represented by the coordinates: u = m . a k = aH ck=(aH+bH)+cH ck = a H+ bH + cH + CH. in the second case lattice planes are translated one with respect to the other in such a way that the nth plane will superpose on the (n + 3)th plane (this explains why a rhombohedral lattice is not compatible with a sixfold axis). 1. lattice directions can be indicated by the fourindex notation. ck. 6mm. symmetryequivalent a. CH by choosing: U ~ = U H + C H .m)/3.0)= ma nb. If we choose j = (m n)/3. a Fig.6 (note that 3m is the point symmetry of the rhombohedral lattice). bk = bH + CH.0)= ma + nb Od. .i w].j. In conclusion the direction [mnw] may be represented in the new notation as [uviw].n)/3. 1. b) plane is divided in i parts we can introduce an extra index in the symbol of the family.1/3.C for a different type of cell).e. If we introduce the third axis d in the plane. On the contrary. In two dmensions four holohedries exist: 2. we can write (P . then u = (2m . since (hkil). If the third axis (say d) on the (a. for crystals belonging to the hexagonal or trigonal systems.18. 1.22 1 Carmelo Giacovazzo ck can be obtained from a H . 78. and then i = (h k). 4mm.i v . The fourindex symbol is useful to display the symmetry. From the same figure it can be seen that the negative side of d is divided in h k parts. (hkil). There are seven threedimensional lattice point groups. bk=b. When. (2 0 2 3) represent three plane families in the new notation. A last remark concerns the point symmetry of a lattice. if a direction is already represented in the fourindex notation [uviw]. Intersections of the set of crystallographic planes ( h k l ) with the three . Since a decrease (or increase) of the three coordinates by the same amount j does not change the point P. The family of planes (hkl) (see Fig. i. then on the plane defined by a and b there will be a third axis equivalent to them. b daxes in trigonal and hexagonal systems.18) divides the positive side of a in h parts and the positive side of b in k parts. i = j.. some trigonal lattices may be described by a hexagonal P cell. (113. bk. (3 5 2 I).213). In conclusion. + + + + + + + The space groups A crystallographic space group is the set of geometrical symmetry operations that take a threedimensional periodic object (say a crystal) into itself. (kihl). i. i = (m n)/3.19 by means of their conventional unit cells (see Appendix 1.
9. The Schoenflies approach was most practical and is described briefly in the following. P4. Fddd. The others may be obtained by introducing a further variation: the proper or improper symmetry axes are replaced by screw axes of the same order and mirror planes by glide planes. As a consequence of the presence of symmetry elements. By combining the 32 point groups with the 14 Bravais lattices (i. the restriction that all symmetry elements must intersect in a point no longer applies (cf. however. We will call the smallest part of the unit cell which will generate the whole cell when applying to it the symmetry . however.) one obtains only 73 (symmorphic) space groups. 1116 we saw that 32 combinations of either simple rotation or inversion axes are compatible with the periodic nature of crystals. that when such combinations have more than one axis. . .B).e. In Fedorov's mathematical treatment each space group is represented by a set of three equations: such an approach enabled Fedorov to list all the space groups (he rejected. The 14 threedimensional Bravais lattices. P4132).Symmetry in crystals 1 23 Triclinic Cubic Trigonal Hexagonal Fig. . 1. several symmetryequivalent objects will coexist within the unit cell.19. P. F. They were first derived at the end of the last century by the mathematicians Fedorov (1890) and Schoenflies (1891) and are listed in Table 1. On pp. five space groups as impossible: Fdd2. 143d. I. The total number of crystallographic space groups is 230. Note.32. Appendix l.
Pbcm. Cmm2. Amm2.2. Fddd. 2 . Pnn2. lmma p4. ~ a 3 I& .3 ~ m 3 ~ d . P?. C2/m. Fmm2. Aba2. Cc P2/m.. P2.. Ccc2. 12.32. la3d operations an asymmetric unit. Cm. P43n. P222.Pnnn. Fm&.Pccm. PncZ. Pbca. p41.2121 Pmm2. F b m .. 143m. Pccn.Pnna..2. Fdd2. Space groups (and enantiomorphous pairs) that are uniquely determinable from the symmetry of the diffraction pattern and from systematic absences (see p. Cmma. PG2.. Pba2.2. It is nevertheless obvious that when rotation or inversion axes are present. Abm2. F43c. Pnma. C2 Pm. Fmmm. The asymmetric unit is not usually uniquely defined and can be chosen with some degree of freedom. P4. Pcc2. Point groups without inversion centres or mirror planes are emphasized by boxes Crystal system Triclinic Monoclinic m 2/m Orthorhombic Point group Space groups p1 P1 P2. 1 d Pm_3m.. F23. 1432.Pmna. p4.. . Pnnm. C222. F43m. Y . C2/c P222. 14. lm3m. Immm. P2.9._12.Pban. Pa&?. [i3 i 12221 mm2 mmm Tetragonal 4 Cubic (231 m3m P23. Ibca.lmm2.3. PmnZ. lba2. F a . Pn3m. PmcP.. P2.. 123. F&c. they must lie at the borders of the asymmetric unit.Pmma. PcaS. Ama2. 1 4 14.24 1 Carmelo Giacovazzo Table 1. Ibam. Cccm. Pna2. Pmmn. . P2.. Cmmm. Fm3. PC. Cmc2.2./c. P2. PrnBn. P2./m. Cmcm. F$32. Ccca. Cmca. Pn3n. F222. Pbcn. 159) are shown in boldtype. p . PmaP.Pcca.. Fm3m. 4 P4. Pbam. h a 2 Pmmm. l4?32 G P43m. The 230 threedimensional space groups arranged by crystal systems and point groups.32. P2/c. 1222.. C222. lm3.
P6222 (P6422).12 (P3212). P4. P4. 4.22 (P6522). a 4 sub 2 screw axis along z to which a diagonal glide plane is perpendicular. then the dyad (proper and/or of inversion) along x and after that the dyad (proper and/or of inversion) along [1?0] is specified. P6. The 230 space groups include 11 enantiomorphous pairs: P3. P4J2 (P4322). giving the nature of the unique dyad axis (proper and/or inversion). 2. and after that the dyad along [I101 is specified. For example. For monoclinic groups: only one symbol is needed. P6i (P65). there are 65 groups of this type (see Table 1. P41 (P43). For example. The combination of the Bravais lattices with symmetry elements with no translational components yields the 73 socalled symmorphic space groups. Biological molecules are enantiomorphous and will then crystallize in space groups with no inversion centres or mirror planes.mc has primitive cell. Two settings are used: yaxis unique. then the dyad (proper and/or of inversion) along x is given.32 (P4. P4.32). followed by triads (proper and/or of inversion) along [ I l l ] and dyads (proper and/or of inversion) along [110]. glide plane of type c normal to xaxis. The point group to which the space group belongs is easily obtained from the spacegroup symbol by omitting the lattice symbol and by replacing . The ( + ) isomer of an optically active molecule crystallizes in one of the two enantiomorphous space groups. P3. a reflection plane normal to x and an axial glide plane c normal to [ ~ I o ] . there is no need to specify symmetry along the yaxis.). For tetragonal groups: first the tetrad (proper and/or of inversion) axis along z is specified. an axial glide plane b normal to the x axis. For triclinic groups: no symmetry directions are needed.21 (P3. Cmm2. P6. the ( .&2 (P4&?. (P3.lnbc denotes a space group with primitive cell.9). the spacegroup symbol consists of a letter indicating the centring type of the conventional cell. For cubic groups: dyads or tetrads (proper and/or of inversion) along x . (P64).2). etc. Such a set is organized according to the following rules: 1. 4.Symmetry in crystals 1 25 According to the international (HermannMauguin) notation. means: primitive cell. Thus Pca2. 5. glide plane of type a normal to the yaxis. Only two space groups exist: PI and PI. We note that: 1. followed by a set of characters indicating the symmetry elements. twofold screw axis along z . F23. 3. 3. 6. an axial glide plane c normal to [110]. For trigonal and hexagonal groups: the triad or hexad (proper and/or of inversion) along the zaxis is first given. and z axis in the order. P6. For orthorhombic groups: dyads (proper and/or of inversion) are given along x.21). y. 2. zaxis unique. Examples are: P222. a sixfold screw axis 6 sub 3 along z. Because of the tetragonal symmetry.) isomer will crystallize in the other. P3.
21). confirmed Mighell and Rodgers' results and suggested a possible model to estimate the number Nsg of structures in each space group of a given crystal class: Nsg = Acc exp { BccE21sg . in the full symbols axes and planes are listed for each direction. the full international (HermannMauguin) symbol.26 1 Carmelo Giacovazzo the screw axes and the glide planes with their corresponding symmorphic symmetry elements. . Short and full symbols differ only for the monoclinic space groups and for space groups with point group mmm. the Patterson symmetry (see Chapter 5.20 and 1. 14. . the crystal system..) where A. Organic compounds tend to crystallize in the space groups that permit close packing of triaxial ellipsoids. the point group symbol. A more recent study by ~ilson. B. .. 327). Indeed most of the 11641 inorganic compounds considered by Mighell and Rodgers crystallize in space groups with orthorhombic or higher symmetry.[81According to this view./c. 2. make it easier because they shift the molecules away from each other.9% to C21c. Close to the graphical symbols of a symmetry plane or axis parallel to the projection plane the 'height' h (as a fraction of the shortest lattice translation normal to the projection plane) is printed. Mighell and Rodgers [9] examined 21 051 organic compounds of known crystal structure. [2].4% to P2. are parameters characteristic of the crystal class in question.2. ~ m 3 m ~ 3 m C2/m. While in the short symbols symmetry planes are suppressed as much as possible.Ccclmls. 12./c. The frequency of the different space groups is not uniform. P6Jmmc. rotation axes and reflection planes can be considered as rigid scaffolding which make more difficult the comfortable accommodation of molecules.. the other illustrates the arrangement of the symmetry elements. In order of decreasing frequency we have: Fm3m. 6/mmm. 3m. 3. the number of reflexion planes in the cell. all belong to the point group 4lmmm. The standard compilation of the plane and of the threedimensional space groups is contained in volume A of the International Tables for Crystallography. If h = 0 the height is omitted. Two types of space group diagrams (as orthogonal projections along a cell axis) are given: one shows the position of a set of symmetrically equivalent points. [m].2. 5. 13. For instance. In particular 35% belonged to the space group P2. P2. . and Cc. the space groups P4Jmmc. For each space groups the Tables include (see Figs 1. P4/ncc. 95% of them had a symmetry not higher than orthorhombic. where ionic bonds are usually present. Fd3m. and 6. C2/c. At the second line: the sequential number of the plane or space group. when present. m3m. . p. Symmetry elements at h also occur at height h + 112. At the first line: the short international (HermannMauguin) and the Schoenflies symbols for the space groups. ..lacd.6% to P2. .['~] based on a survey of the 54599 substances stored in the Cambridge Structural Database (in January 1987).. 4/mmm. 7. is the total number of structures in the crystal class. 1. m3.3% to PI. while screw axes and glide planes. is the number of twofold axes. The same results cannot be applied to inorganic compounds.
2 (see Appendix 1.2.21 descriptions of the space groups Pbcn and P4222 are respectively given as compiled in the International Tables for Crystallography.E) selected to generate all symmetrical equivalent points described in block 'Positions'. This is often a trivial task. origin.a point which is surrounded symmetrically ~ by the three 2. For example.B) .2. each point of which is left invariant only by application of an identity operation) and a list of special positions (a set of symmetrically equivalent points is in special position if each point is left invariant by at least two symmetry operations of the space group). symmetry generators (see Appendix l. the HermannMauguin symbol of the resulting plane group. Symmetry of special projections. The symbol adoptedr9]for describing the site symmetry displays the same sequence of symmetry directions as the space group symbol. For example. limiting possible reflections. A dot marks those directions which do not contribute any element to the site symmetry.20 and 1.2.2. 159) or special (it limits the contribution to the structure factor of the atoms located at that Wyckoff position). Three orthogonal projections for each space group are listed: for each of them the projection direction. The condition may be general (it is obeyed irrespective of which Wyckoff positions are occupied by atoms (see Chapter 3. For noncentrosymmetric space groups the origin is chosen at a point of highest symmetry (e..g. are given. Information about maximal subgroups and minimal supergroups (see Appendix l. In order to obtain space group diagrams the reader should perform the following operations: 1. but in certain cases special care must be taken. For example.Symmetry in crystals 1 27 4. The origin of the cell for centrosymmetric space groups is usually chosen on an inversion centre.2. The first three block columns give information about multiplicity (number of equivalent points per unit cell).. site symmetry (the group of symmetry operations which leaves invariant the site). Wyckoff letter (a code scheme starting with a at the bottom position and continuing upwards in alphabetical order). for ~ n 3 n descriptions are available. on the screw axis in P2. asymmetric unit. together with the location of the plane group with respect to the unit cell of the space group. In Figs. 5. The block positions (called also Wyckoff positions) contains the general position (a set of symmetrically equivalent points. axis in P2. 6. Information is given about: setting (if necessary). .E) is given. and the relation between the basis vectors of the plane group and the basis vectors of the space group. symmetry operations. A second description is given if points of high site symmetry not coincident with the inversion centre occur. 1. Some or all the symmetry elements are traced as indicated in the spacegroup symbol. and the second with origin at 3. in P ~ a 2 at . may be associated. 7. the three twofold screw axes do not intersect each other in P2. the first with origin at two 432. on the glide plane in PC.. at la2. but two of them do in P2. the origin for ~ 4 2 c is chosen at 4lc) or at a point which is conveniently placed with respect to the symmetry elements. To each Wyckoff position a reflection condition. p.
28 1 Carmelo Giacovazzo Pbcn No. 0 OlzS: Asymmetric unit Symmetry operations Fig. / n Patterson symmetry P m m m Origin at i on I c 1 OSxli. 1.lb 2 / c 2 .20. . Representation of the group Pbcn (as inlnternational Tables for Crystallography). 60 Orthorhombic P 2.
J + : . Positions Mulliplicity.) 1. t(0.)).z Maximal nonisomorphic subgroups 1 [2]P2. 60 Pbcn Generatorsselected ( I ) .y+i. 2.[2]1bam. [ 2 ] P r n c a ( 2 b 1 =b ) ( P b c m ) .y. Site Spmetry ( 1 0 0 ) .2.3.4.y+i.5. 8 [2]P2. ~ (2) x + ~ .5.7 [2]P2.[2]Bbab(Ccca).z++ ( 4 ) x+:.y+. l c ) 1. 7 . l = 2 n Symmetry of special projections Along [001] c 2 m m bl=b al=a Origin at 0. 1 = 2 n hkl : h + k .r ( 8 ) x'+:. ) ( [ 2 ] P b 2 n( P n c 2 ) 1 . [ 3 ] P b c n ( b 1 = b ) .22.6.7 IIa none IIb none Maximal isomorphic subgroups of lowest index IIc [ 3 ] P b c n ( a 1 = a ) .0 . 5 . (5) Coordinates Reflection conditions General : Okl : k = 2 n h01: 1 = 2 n hkO: h +k = 2n hOO: h = 2n OkO: k = 2n 001: 1 = 2 n Special: as above. z + ~ (3) f ..8 1 .O Along [ 1001 p 2g m al=ib b'=c Origin at x./b11(P2.5+: ( 7 ) x. 6 .0./c) 1.(P2. plus 8 d 1 (1) x (5)x ' . [ 3 ] P b c n ( c 1 = c ) 3 3 3 Minimal nonisomorphic supergroups I none I1 [2]Abma(Cmca). 3. Wyckoff letter. ( 0 1 0 ) .2) 1.O.4 [ 2 ] P1 1 2 . (2). 8 [2]Pbc2.i+i ( 6 ) x+:.3.[ 2 ] P b mn(2c1= c ) ( P m n a ) Along [010] p 2g m bl=a a'= Origin at O.z hkl: h+k=2n hkl : h + k .cn(Pna2.J'. 6 [2]P12/cI(P2/c) 1.4.[2]Pbcb(2a1= a ) ( P c c a ) .p. 2. Pca2 . j . (3).Symmetry in crystals 1 29 CONTINUED No.2.O.[2]Cmcm. / n ( P 2 .
. .10. which are listed in Table 1. 93 P4222 Patterson symmetry P 4/m m m Origin at 2 2 2 at 422 1 Asymmetric unit Olxli. 3. 0Izl$ Symmetry operations Fig.23 and 1. There are two line groups: p l and pm. New symmetry elements are then placed in the unit cell so producing the second type of diagram. Representation of the group P4. P . . . Once conveniently located. fall outside the unit cell.21. The plane and line groups There are 17 plane groups. they should be moved inside by means of appropriate lattice translations. . A periodic decoration of the plane according to the 17 plane groups is shown in Fig. . 2. 1. the symmetry operators are applied to a point P in order to obtain the symmetry equivalent points P'. OIySI. . The first type of diagram is so obtained. Two simple crystal structures are shown in Figs 1.30 1 Carmelo Giacovazzo Tet rag on al No. Some space group diagrams are collected in Fig.22. If P'.25. . 1. P". Any space group in projection will conform to one of these plane groups.24: symmetry elements are also located for convenience. 1.22 (as in International Tables for Crystallography). . . In the symbol g stays for a glide plane.
[21P42/nnm. 2 ) . ( a 1 = 2 a .f. t Generators selected ( I ) .[31P4232 I1 ( 2 ] 1 4 2 2 .x.2. = [ 2 ] F 4 . x.x.f.O f.O. Wyckofl kllcr. 2 2 ( a 1 =2a.i. [ 2 ] P 4 2 2 ( 2 c 1 =c) .O. [ 2 1 P 4 2 / n b c .x.O hhl : I = 2n 4 h 2.i f.+ f..f. .O.z Along [I001 p2n1tn a'=b bl=c Origin at x.O).z+: +.T f. 2 2 ( c ' 2 c ) .: f.7.i hkl : I = 2 n Symmetry of special projections Along [OOI] p 4 m m a'=a bl=b Origin at 0.f. [ 2 ] P 4 .. t (O. 2 2 .O.5. [ 2 ] C 4 .+ x.4 [2]P221(P222) l.a f b ) bl=c Origin at x. S~le symmetry (0.O.c1= 2 c ) ( 1 4 .b1= 2b.0).: x. plus Coordinates 4 4 o n .O Along [I101 p 2 m m a'= + ( . I . 2 2 (a1= 2 a . b 1 = 2 b ) ( P 4 .1. b l = 2 b ) ( P 4 2 2 2 ) Minimal nonisomorphic supergroups I I21P4Jmmc.f O.f+f hkl : 1 = 2 n 2 2 f 2.$ f.O.f.O.O.x.2.+ O. L f . ( 2 ] C 4 .2.+ x.+ O. 2 2 ) Maximal isomorphic subgroups of lowest index IIc [ 3 ] P 4 .6 [ 2 ] P 2 1 2 ( C 2 2 2 ) 1.+. 2 2 ( c 1 = 3 c ) .O O.2 x.1 1 ( P 4 2 ) 1. I). f. [ 2 ] P 4 J t n c m . z .3. (5) Reflection conditions General: 001: I = 2 n Special: as above.$.f.:. 2 2 ( c 1 = 2 c ) .2 . 1.2.+ hkl : I = 2 n hkl : I = 2n hkl : h + k + l = 2 n e 2 b 222. 2 .? Okl: I = 2 n Okl: I =2n 4 1 .x. 93 t (I .+ f. (2).8 IIa none IIb [ 2 ] P 4 .Symmetry in crystals CONTINUED 1 31 No. (3).22 2.$ Maximal nonisomorphic subgroups I (2]P4.+ it+. Positions Mulliplicily.22 +.x. ..
z of a point P to obtain the coordinates (x'. $1. A list of all the rotation matrices needed to conventionally describe the 230 space groups are given in Appendix 1. 1.  : 1 ! I  4  0 010 o+ 0 0+0 0   I  0 0+O o+ 0 0+0 o+ c . As we shall see in Chapter 2 its elements may be 0 .0 .y.22.0  TI1 1 + Fig. y'. Some space group diagrams. 1 and its determinant is f1. + On the matrix representation of symmetry operators A symmetry operation acts on the fractional coordinates x.32 1 Carmelo Giacovazzo C2 00+ 004 P 2/m o+ O+ 00+ 0". T is the matrix of the translational component of the operation.D. . 2') of a symmetryequivalent point P': The R matrix is the rotational component (proper or improper) of the symmetry operation.
2. 20. A P2.. Gaetani Manfredotti. Glide planes are emphasized by the shading.2.24. .Symmetry in crystals / 33 Fig. G. Calleri.23. Guastini (1975). 1. 4.. Ferraris. Struct. Cryst. Fig.561) and its symmetry elements (hydrogen atoms are not drawn). Commun. and C. A P2. A./c crystal structure (M. Viterbo. crystal structure (G. 73) and its symmetry elements (hydrogen atoms are not drawn). Chiari. and D. Viterbo (1966). D. 1. Acta Cryst.
.34 1 Carmelo Giacovazzo Table 1. . The 17 plane groups Oblique cell Rectangular cell Square cell Hexagonal cell P I .25. Tonetti. p3rn1. Nov 1990). p4. p6.~ 2 9 9c2mm . we obtain X' = CIX = RIX + TI. p4nm~ p4gt11 p3. A periodic decoration of the plane according to the 17 crystallographic plane groups (drawing by SYMPATI. 9. p6mrn Fig. If we then apply to r' the symmetry operator C2. we obtain X = C2Xf= R2(RlX + TI) + T2= R2RlX + R2Tl + T2. 920. ~ 2 m m P ~ V . When applying the symmetry operator C1= (R. a n .10. pg. 1.a computer program by L. TI) to a point at the end of a vector r. Loreto and M . pixel. ~2 pm. . p31n1.
.12) 1 35 where R2Rl is the rotational component of C3 and (R2T. Each of the 12 different operators of the group may be obtained as C'. R~T) (1. and one twofold axis. C3 = C2C1= (R2R1. 2. example. +T2) is its translational component. R2T1+ T2). When we take them into account. . + R + I)T]. we obtain all the six points equivalent to a point r by applying to it the operators CJ with j going from 1 to 6. Once we have defined the R and T matrices corresponding to an anticlockwise rototranslation of 60" around z. The theory of symmetry groups will be outlined in Appendix 1. We can then represent the symmetry operators of P6'22 as the product {C1){C2). the twofold axis operator.15) where T = mla m2b m3c is the set of lattice translations. So far we have deliberately excluded from our considerations the translation operations defined by the Bravais lattice type. + + Appendices 1.Symmetry in crystals Since the symmetry operators form a mathematical group. For instance. all the spacegroup operations may be written in "a very simple way. 1112). . j = 1. (1. (RJ' + . . e3). If only two generators are sufficient. Similarly there are two generators of the group P222 but three of the group ~ 4 3 mIn general all the . operator is of order six (similarly 2 and m are of order two).. . or as their product. In fact the set of operations which will transfer a point r in a given cell into its equivalent points in any cell are: { c ~ {c2} {c3} } (1. and therefore C1 = (R1. TI) which will bring r ' back to r. Obviously C6= I and C6+j= CJ. Since we must have C'C = I. Because of (1. Cl = C5.. When all the operators of the group can be generated from only one operator (indicated as the generator of the group) we will say that the group is cyclic. All symmetry operators of a group can be generated from at most three generators.E.A The isometric transformations It is convenient to consider a Cartesian basis (el. T) there will also be an inverse operator C' = (R'.12) C1 = [RJ.E. In the P6. The list of the generators of all point groups is given in Appendix 1.13) Let us now apply this result to the space group P6.12) we will also have R'R = I and R'T + T' = 0. In particular the operator C2= CC will be present and in general also the CJ operator. . where {C) indicates the set of distinct operators obtained as powers of C. If r is transferred to r' by C = (R. then C2 = C3 = I.14) where Rl is the inverse matrix of R. the generators of the space group P6. For this reason we will say that the 6. operations of a space group may be represented by the product {C1){C2){C3). because of (1.22 are 6. we will set C3 = I. or as C2. (1. a third symmetry operator must be present (see also pp. and if only one is sufficient. say the powers of 61. e2. Any transformation which will keep the distances unchanged will be called an isometry or . 6.
and then det R = f1. will also maintain the angles fixed in absolute value.4) leaves the origin point invariant. Since det (R . then this condition is satisfied. In order to find the other points left invariant we have to set Xo = X and obtain (1.R) det R = det (I .3) adds to each position vector a fixed vector and corresponds therefore to a translation movement. more properly.5a) will have solutions for X#O only if det (R . z ) into .A.A.I) = det (R .A.l) into two movements: X1=X0+T Xo = RX. from (1. When the translation is parallel to the rotation axis the movement will be indicated as rototranslation.4) must be a linear combination of the other two.A.R) = det (R . (1. if T = 0 the movement is a pure rotation.A. which is the locus of the invariants points. the movement described by (1. R indicates the transpose of the matrix R and I is the identity matrix. (1.4) is therefore a rotation.1) is R = I then the movement is a pure translation. Another example is the anticlockwise rotation around the z axis of an angle 8.A. the product) of a translation with a rotation around an axis. We will refer to direct or opposite movements and to direct or opposite congruence relating an object and its transform. In conclusion. A movement. + + Direct movements Let us separate (l. y.36 1 Carmelo Giacovazzo an isometric mapping or a movement C. ye2 ze3 is related to a point P'.R)RJ = det (I .I) = 0. a direct movement can be considered as the combination (or.I). Since the determinant of the product of two matrices is equal to the product of the two determinants. Therefore one of the three equations represented by (1. this will move r(x. The two independent equations will define a line. We note that X and X' are the matrices of the components of the vectors r and r' respectively. in the sense that a point P defined by the positional r x t o r r = xe. It will be a linear transformation.A.RR) = det [(I .e2 T3e3.2) we have (det R)'= 1. An example of direct movement is the transformation undergone by the points of a rigid body when it is moved. with positional vector r' = x f e l y1e2 zfe3by the relation + + + + with the extra condition RR= I or R = R'. If in eqn (1. depending on whether det R is +1 or 1. while T is the matrix of the components of the translation vector t = Tlel T. leaving the distances unchanged.A.
y'. then. C with the points A'. B'. y '. i. with (l. zl). the movement resulting from the combination of the rotation and translation operations is still a pure rotation around an axis parallel to 1 (see Appendix l. of the point P with its symmetry related with respect to the origin of the coordinate system. B.e. We may conclude that each direct movement.e. We will now show that any direct movement can be carried out by means of a translation or a rotation or a rototranslation. then the complete superposition can be achieved by a rotation R around an axis 1 passing through A'. which. Opposite movements An opposite movement can be obtained from a direct one by changing the sign to one or three rows of the R matrix. y'. R = Rl. On the other hand an opposite movement may be obtained as the product of a direct movement by a reflection with respect to a plane or by an inversion with respect to a point. Changing the signs of all three rows of the R matrix implies the substitution of the vector (x'.2). This operation is called a reflection with respect to the plane at z = 0. followed by a reflection with respect to a plane or by an inversion with respect to a point yields an opposite movement. when composed with a2. the movement is a translation.B. in agreement with (1. we substitute the vector ( x ' .A. z') through the transformation xl=xcosOysinO y1=xsin8+ycos0 which in matrix notation becomes X' = RX. y'. if not. Some combinations of movements Only those combinations of movements explicitly mentioned in this book will be considered (for further insight. This operation is called inversion with respect to a point.Symmetry in crystals 1 37 r1(x'. The product of R times al is a pure rotation around an axis parallel to 1. then it can be decomposed into two translational components a1 and a2. Let us suppose that an isometric transformation relates the three noncollinear points A.B). results in a rototranslation movement. one perpendicular and the other parallel to 1. stated laws may be interpreted The . the point P' with its symmetry related with respect to a plane at z = 0. when changing the sign of the third row. if also B and C superpose on B' and C'. If a is the translation bringing A on A'. C' respectively. z') with (x'. the reader is referred to the splendid book by Lockwood and ~acMillan[~I). For instance. y'. If 1 is perpendicular to a. If a is not perpendicular to 1.A. 2')) i. 2') with (x'. 1.5b) R' can be obtained by substituting 8 with 8 and it can be immediately seen that.
We may conclude that the product of the two reflections is a rotation of 2 a around 0 . 2. 2y around A. with respect to m. is OQ. The Silvester theorem states that consecutive anticlockwise rotations of 2a.about parallel axes. + + + . (a) Composition of two reflections.): in fact by first reflecting OQ with respect to m. The product is not commutative (m. In fact.B. Composition of two reflections. 1. 2P. BABC. C. The traces of the three axes on the plane of Fig. is OQ1 and the image of OQ. we obtain a 2 a rotation in the opposite direction. two successive rotations of 2 a and 2P around A and B respectively. When a = P. 1. (b) composition of two rotations about parallel axes. CBCA respectively and all these reflections cancel each other out. the third axis goes to infinity and the resulting movement is a translation.. (c) composition of two rotations. are at a dihedral angle a and intersect along a line.m.l(a) the two reflection planes m. In Fig. C respectively produce the identity. will be equivalent to a rotation of +(2a 2P) around C. in terms of combinations of symmetry operations if all the space is invariant with respect to the movements. l. B. and then reflecting the image with respect to m.m.B. The Silvester theorem relative to three parallel rotation axes. in symbols mlm2 = R.38 1 Carmelo Giacovazzo Fig. B. Since a P y = n. because of point 1. (d) composition of two rotations about axes passing through a point. by a rotation of 2 a around the axis through 0 . and m.B. the first through cuand the second through a. l. # m.1. the rotations are equivalent to reflection operations with respect to the three pairs of planes ACAB. the trace of which is in 0 . The image of OQ with respect to m.l(b) are A. It is possible to superpose OQ to OQ.
with 2y # (2a 2P). anticlockwise rotations of 2 a and 2P around OA and OB are equivalent to a 2y anticlockwise rotation around OC.1. 3.=T. P.a)/2 with respect to AB. Values of 1 different from 2. a . I). On the sphere there will . The three twofold axes will be perpendicular one to the other and can be assumed as the axes of a reference system.l). and these reflections cancel each other out. n13.B. and y are equal to n12. 4. The resulting movement brings AC to BD and can be achieved by a translation of DA = 2AB sin (a12) perpendicular to the direction of the rotation axes and at an angle of ( n . y in A. 3. The group of rotations is consistent with the symmetry of a tetrahedron. If A. n13 respectively and the area of the spherical triangle is nr2/6. 2P. 3. because of point 1. The 24 n / 2 angles meet four at a time at six vertices and the 48 n13 angles meet six at a time at eight vertices. p. A rotation and a translation perpendicular to the rotation axis combine in a resulting rotation movement around an axis parallel to the original axis. l. In symbols: R. .l(c) AC moves to AB by a rotation of a around A. B. 3. 2. C is therefore a symmetry axis of order p = 2nI2y = nly. 3. 2y around A. 3. (1.n)r2: + + + + + (a) Solution 1. 5. 2.1.1. n14 respectively and the area of the spherical triangle is nr2/12. then consecutive rotations of 2 a around A and of 2P around B are equivalent to a rotation of 2y around C. 2. We can then deduce the following point 3. This implies the presence of three twofold axes and of four threefold axes. 1.RI_. I). the inequality l l m l l n l l p > 1 follows. a . (1. B. 2. BOCCOA respectively. We will study this problem using the Silvester theorem treated in point 4. We can now consider the different solutions. 3. Since the sum of the angles must be greater than n. p. the three rotations correspond to the products of the reflections with respect to the pairs of planes AOCAOB. 5. a .B. 2. C are in a clockwise order. keeping in mind that the surface of a sphere of radius r is 4nr2 and that of a spherical triangle is ( a P y . n l n and nlp. In Fig. by a a rotation around B BA goes to BD. 3. I). 2.B. The angles of the spherical triangle are then nlm. l. Coexistence of rotation axes passing through a point: the Euler theorem. l. The possible solutions of this inequality are: 1. 4.l(d) let OA and OB be two symmetry rotation axes of order m and n respectively. 4. Because of the Silvester theorem. p. 6 correspond to noncrystallographic groups which occur as possible symmetries of molecules or as approximate local site symmetries in crystals. C respectively. (c) Solution 4. The angles a and P are chosen in such a way that 2 a = 2n/m and 2P = 2nln. On the sphere there will be 24 such triangles. (b) Solution 2.1. In fact. Since a + p + y > n. and y are equal to n/2. and y are equal to n12. AOBBOC. The binary axes are therefore always at 90' with respect to the 1 axis. 3. rotations of 2a. 2. In Fig.l(d) ABC is a spherical triangle with angles a . n13. The four threefold axes run from the centre to the points (1.Symmetry in crystals 1 39 In Fig. C leave the figure unchanged. The Silvester theorem relative to three rotation axes passing through a point. 2 with 1 integer >1. B. n l l respectively and A and B may be chosen on an equatorial circle with C as a pole. (. n12.
B. [I. [I. The three fourfold axeswill be perpendicular one to the other and can be assumed as the axes of a reference system.2. The c axis is normal to the plane. of four threefold axes. y ) plane as intersection P' of that plane with the line . The threefold axes are 1 located along the [I. 1. 11.1. The group of rotations is consistent with the symmetry of a cube and of an octahedron (see Fig. 1. 1. the 48 n / 3 angles meet six at a time at eight vertices and the 48 n / 4 angles meet eight at a time at six vertices. . A unit sphere is described around the crystal in C.40 1 Carmelo Giacovazzo Fig.3(a)). Stereographic projections of the 32 crystallographic point groups. The mutual disposition of the symmetry elements in the 32 crystallographic point groups is illustrated in Fig. 1. 1 directions. The 48 n / 2 angles meet four at a time at twelve vertices. the a axis points down the page.10). [I.2. 1. A stereographic projection is defined as follows (see Fig. 11.B.1]. where the so called 'stereographic projections' are shown. and of three fourfold axes will be present. and the b axis runs horizontally in the page from left ro right. 1. l. while the twofold axes are on the bisecting lines of the angles between the fourfold axes. be 48 such triangles. A point P (terminal of some symmetry axis) in the $ 2 hemisphere is defined in the ( x . A total of six twofold axes.8.
l.Symmetry in crystals 1 41 connecting the point with the south pole of the unit sphere. A conventional cell is a parallelepiped: as such it may be considered as a particular type of polyhedron. From point 5 we know that the coexistence of two orthogonal twofold axes passing by 0 .B. but not with the periodicity property of crystals. respectively. the regular pentagondodecahedron. Y. and Q' are the reflection images of Q with respect to S. axis normal to both of them and intersecting the first 2.B.4.C. Composition of two glide planes. axis orthogonally intersecting both axes will exist.4 let S and S' be the traces of two glide planes forming an angle a and 0 be the trace of their intersection line. (e) if two orthogonal screws are separated by 114 of a period (Fig. 12 vertices) and its dual. (c) if a pair of mutually perpendicular 2 axes is separated by 114 of a period (Fig. (b) Angular values occurring in m3m stereographic projection. then another 2 axis perpendicular to them and passing at (114. 20 vertices). the rotation angle AQB = 2a. and to the point 0. 7.5(e)) there will then be a new 2. l. will not be examined.B.B. 3. The reader can easily verify the following conclusions: (a) if one of the two axes is 2. In Fig. Fig. (a) Geometry of the stereographic projection. Composition of two twofold axes.3(b) parts of the stereographic projections for m3m are magnified in order to make clearer the statements made in the text. will exist. which is compatible with the symmetry of the regular icosahedron (20 faces. implies a third binary axis perpendicular to them and also passing through 0 (see Fig.B. The translational components OA and OB are chosen to lie on the plane of the drawing and Q is the meeting point of the axes of the OA and OB segments. This solution. 1.BS(d)). then another 2 axis. l. l. l. then a 2. axis at 114 froin the 2 axis. (b) if two 21 intersect in 0 (Fig. (d) Solution 5. 1. 1. poie 6. 1. 2.5(f)).3. at 114 from 0 and intersecting orthogonally the screw axis. with and without translational component.8. l.114) from 0 will be present. It is however of particular importance in Crystallography as symmetry of viruses molecules and in quasicrystals. l. (Fig.8.5(c)).B.BS(b)). . There are several families of polyhedra with which we can fill up the space Fig. then a third screw axis normal to them and passing at (114. (12 faces. Since S'S moves first A to 0 and then to B. The product S'S moves Q to Q' and then back to Q.114) from them will be present.5(a)). In Fig. WignerSeitz cells The 14 Bravais lattices are compatible with cells which are different from those conventionally associated to them. X. S'. Since S'S is a direct movement it leaves Q unchanged and corresponds to a rotation around an axis normal to the plane of the figure and passing through Q. (d) if a 2 and a 2. Composition of two glide planes. axis are separated by 114 of a period (Fig. If the point to be projected is in the 2 hemisphere then the north pole is used. Note that the two glides are equivalent to a rotation around an axis not passing along the intersection line of S and S'.
C.8. Each lattice point is connected with a line to its nearest neighbours. We then trace through the midpoints of the segments the planes perpendicular to them. by translation.C. These intersecting planes will delimit a region of the space which is called called the Dirichlet region or WignerSeitz cell. l. The length of the graphical symbol for screw axes i n the plane of the page corresponds t o half repetition period.1.D). The WignerSeitz cell is always primitive and coincides with the Bravais cell if this is rectangular and primitive.5.l(a) and two threedimensional examples are illustrated in Fig. Chapters 2 and 3) a cell conventionally known as the first Brillouin zone. There will be 14 first Brillouin zones corresponding to the 14 Bravais lattices. the first Brillouin zone of an I lattice will look like a WignerSeitz cell of an F lattice and vice versa. l(b. then. Fig. We recall here that to a lattice I in direct space corresponds an F lattice in reciprocal space and vice versa (see Appendix 2. 1. An example in two dimensions is given in Fig. A construction identical to the WignerSeitz cell delimits in the reciprocal space (cf.42 1 Carmelo Giacovazzo Fig. Examples of WignerSeitz cells. 1. c) . . 1. The Brillouin zones are very important in the study of lattice dynamics and in electronic band theory. A very important type is the one obtained through the Dirichlet construction. Various arrangements of three orthogonal binary axes.C.
together with the trace (sum of the diagonal elements) of a matrix. This number. They operate according to the relation X' = RX. This corresponds to changing the sign of all the elements of the original matrix. 3 =( O O i O . and third columns are the coordinates of the points symmetry related to points (1. trace 3 i 0 1 2 3 1 0 1 2 .0. O).1) respectively. o o i Direction [0 0 1 1 o o i l o o 1 1 0 (yg. and for the hexagonal and trigonal systems they are preceded by the letter H. are characteristic of the symmetry element: element 1234612346. determinant l l l l l i i i i i . They may be constructed using the following practical criterion: in the first. O). (0. 0 O 1 ) H 2 = 1 O O . but only the 32 matrices corresponding to proper symmetry elements. 0 1 ) 4 3 = 0 1 0 . o I 0' 0 1 0 0) Direction [0 1 01 ) 2 =( i o10 O .0. Direction [0 0 01 Direction [I 0 01 2 (~ 0 0 ° 1) o o i 0H 2 = 0 1 0 ( 1 ) o o i 4 ( l o O). The matrices are grouped following the directions along which they operate. Therefore in the following list we will not give all the 64 matrices necessary to describe the space groups. ( l o ~ 0 0 14 3 = O 0 1 . and (0. second. The determinant of a matrix will have a +1 or a 1 value depending on whether the represented operation is of rotation or of inversion type.1.Symmetry in crystals 1 43 1. The spacegroup matrices All the rotation matrices R needed to conventionally describe all 230 space groups will be listed. The matrix of the fi operator may be simply obtained from that of the n operator by multiplying by the matrix corresponding to the i operator: 0 i = ( i 1 1 o :).) i o o o i o .D.
44 1 Carmelo Giacovazzo Direction [ l 1 01 Direction [l 0 1 1 0 0 1 Direction [0 1 1 1 Direction [l i 01 Direction [ i 0 1 1 Direction [0 1 I] Direction [I 1 1 1 0 0 1 0 1 0 Direction [I 1 1 1 o i Direction [l 0 o o i i 1 1 l o o o i o .
If a group also possesses the commutative property gigj=gigi for any i and j..l) is = satisfied.Symmetry in crystals Direction [I 1 ?I 3 Direction [2 1 0] 1 45 ( ~ 0 0). negative. = ua vb wc with u. The number of different elements of a group is called the order of the group and can be finite or infinite. Since gJgnj= gnjgi = e. then G is said to be Abelian. or null integers. g . (2) the rational numbers. inversion. and zero). identity.. excluding zero. In this case e = 0. . . when the combination law is the sum. there is only one element e in the group such that eg = ge = g. g' = g. negative. An integer n may exist for which then gn+'= g. associativity. . (3) is infinite and nonAbelian. If n is the smallest integer for which (l.. Symmetry groups A group G is a set of elements g. g. = g.. . when the combination law is the vector sum: gl then e = g. v. With reference to the examples given above... the combination of two elements of the group is an element of the group gigj =gk. there will only be n distinct powers of g.E.. g2. (4) are infinite and Abelian groups. (2).E. then gnj is the inverse of gi. w positive. 0 i 0 Direction [ l 2 01. 1. If g is an element of G. gn+2 g2. (3) the set of all n x n sonsingular matrices under the product law: e is the diagonal matrix with aii = 1. all powers of g must be contained in G.. . .. the associative law (gigj)gk= gi(gjgk) is valid. each element g in the group has one and only one inverse element g' such that glg = ggl = e. when the law is the product: e = 1. (4) the set of all lattice vectors r.l = l/g. . Examples of groups are: (1) the set of all integer numbers (positive. .. with the following four properties: closure. 13 0 T o o (O O T ) 2 ' 1 0 0 . . (I). The element g is then said to be of order n and + + . for which a combination law is defined.
which are the generators of the group. 3. Any point group can be represented as the product of powers of at most three elements. All cyclic groups are Abelian. Each row (column) is different from any other row (column). Each element appears once and only once in a given row (or column) of the table. 2. would appear twice in the row. In order to demonstrate this statement let us consider the ith row of the table and suppose that there are two different elements gj and gk. List of generators for noncyclic point groups. 210101 or or and ~[ooI]. this property follows immediately from property 1. . but by multiplying the two equations by g. E . Then g. . We also note that the definition of the generators is not unique. When the physical properties of the group elements are not specified the group is said to be abstract.1. . gnl.ooland 2[olo1.E. is called cyclic.1. 1 i o ~ I 4 0 1 1?[0011 101 ~ [ I O O I ~2 [ i i o 1 T r r o o i ~2 [ i i o 1 ?[looit 4 i i o i 210011 3 1 o o i 1Triooi ~ 310011~ 21ioo~ the set of all powers of g is a group of order n: G I = (g. l the list of the generators of the noncyclic groups is reported. but the converse is not true.. g 2 . 2roio1 2~1001~ 210101 2[1001' 210011 2110011 ~ 1 0 1 0 1 ~ 210011 ~ [ ~ o o 3. in which all the elements are powers of a single generating element. gn = e).E. .' we obtain g. In Table l .2). For instance in the class 222 we may chose the generators 2[. 2. for which gigj = gigk = g. = g. For abelian groups the table is symmetric with respect to the diagonal. such as (1.. There are 2 1 proper generators in all Point group Generators Point group Jrn 62rn 622 6/m Generators 2/m 222 rnrn2 rnrnrn 422 4/ rn 4rn rn 42rn 4Jrnrnrn 32 3rn 4oro1. For a group of n elements this table has the form: We note that 1. in contrast with the hypothesis. From a mathematical point of view all its properties are determined by its multiplication table. An example of cyclic group of order n is the set of rotations around a given axis.46 1 Carmelo Giacovazzo Table 1.. . A group.] and 2[00. which are multiple of an angle a = 2nln..
2. For instance the three point groups 222.g3 = 3. 622 23 4/mmm 432. We note that all cyclic groups of the same order are isomorphous.H = (gl. 2/m and mm2 are isomorphous. g3. They must have the same order and may be considered as generated from the same abstract group. g4 = 2[1m1. 6. 62m. group 222: 1. group mm2.43m m3 6/mmm m3m Groups having the same multiplication table. g2 = 310011.2. g. m 2.g5 = 2[0101. 422. The multiplication table of the abstract group is In Table 1.. g2. 2.E.4 2/m. g3) is a subgroup of G.42m g/m 3m. = 1. . To show this let us choose g. are called isomorphous. 1. m. The subgroup H is proper if there are symmetry operations of G not contained in H. = 3l.3m mmm 4/m 4mm. i.Symmetry in crystals Table 1. (2) the point group 32 has elements g.E. even though their elements might have different physical meaning. 2.2 the 32 crystallographic point groups are grouped into 18 abstract groups and for each of them the defining relationships are listed. mm2. 1. group 2/m. m. 6mm. Examples of subgroups are: (1) the set of even integers (including zero) under the sum law is a subgroup of the group of all integers.. 222 6. Subgroups A set H of elements of the group G satisfying the group conditions is called a subgroup of G. m. 3 32. 3 4. g4 in the following way. The 18 abstract groups corresponding to the 32 crystallographic point groups Point group Order of the group Characteristic relations 1 47 1 i. 2.g6 = 2[iio1. 2.
the index of the subgroup 2 of the group 2/m is two. .5) the element e forms a class on its own. U T2 U . Conversely G may be considered a supergroup of H. .E. of conjugate elements. . In the previous example.e. Cosets Let H = (h.) form a left and a right coset of H respectively. . Since each element of G can not belong to two different classes.5) If g. (1.) be a subgroup of G and gi an element of G not contained in H. h2gi. . . it is possible to decompose G into the factorized set G = e U T. we had gihi = hk. 2. I m are subgroups of the point group 2/m. either have no common element or are identical one to the other. A coset is never a group because it does not contain the element e. . . In fact. is fixed and gk varies within G. The decomposition of the group 2/m into separate left cosets with respect to the subgroup 2 is: The number of distinct cosets obtained from the decomposition of a group with respect to a subgroup is called index of the subgroup. it would follow that gi = hkhjl. h2. Furthermore H can not have any common element with giH or Hgi. if for instance. contradicting the hypothesis. i. Subgroupgroupsupergroup relationships are very important in the study of phase transitions and of orderdisorder problems. . Then the products giH = (gihl. It can be shown that two right (or left) cosets. then the set of elements gi forms a class In agreement with relation (1. This allows us to decompose G with respect to H in the following way: It follows that the order of a subgroup is a divisor of the order of the group and if this is a prime number. . . In .48 1 Carmelo Giacovazzo (3) the point groups 1. Conjugate classes An element gi is said to be conjugate to an element gj of G if G contains an element gk such that gi = gklgjgk. the only subgroup of G is e and G must also be cyclic. .) and Hgi = (hlgi. A physical or geometrical meaning may be attributed to the classes. (4) 222 is a subgroup of 422. . gi would belong to H.. In general they will not be identical. g h . (5) the set T of all primitive lattice translations is a subgroup of the space group G.E.
i. Since g.form a group.5).H)'(gi~)= H'~&H = el We can now define a new type of group of order p. indicated by the symbol G/H: its elements are cosets of .l ~ g .2) = (1.4) the order of H is n/p. while n is the order of G. Because of (1. 2) = (1. 1 49 Conjugate subgroups Let H be a subgroup of G and g an element of G not in H. Normal subgroups and factor groups If the right and left cosets of the subgroup H are the same. They must contain complete classes.5) (see eqn (2.2)i. let the element g. Furthermore. called a factor group or quotient group.H and g. the subgroup (1. (2[iool. 2)m. (3.E. are each in a separate class.2i1. =g. Subgroups which are transformed into themselves by applying all the elements of the group.'Hg. Conversely. for the point group 32 three classes may be set up: (el.1) is not.Symmetry in crystals the transformation (1. m(1. are called invariant or normal. the operators identity. inversion.&H Besides. Then all the elements g . The following rules may be useful to set up the pointgroup classes: the classes are formed by one element only for the point groups up to orthorhombic.~ [ o I D ] .3'). 2~iiol. it is: (g. and reflection with respect to a mirror plane perpendicular to the principal symmetry axis (the axis with the highest order). if a subgroup is transformed into itself when applying all the elements of the group. Let H be a normal subgroup of G with index p.3.E. the following multiplication law may be established: (g. Hg.E. this means that each symmetry operator commutes with all the others.E. belong to H. the subgroup T of all the primitive lattice translations is an invariant subgroup of the space group G.3') is normal. H and glHg are conjugate subgroups. be a coordinate transformation due to a symmetry operator and the element gj a matrix operator related to another symmetry operation. For instance. is transformed by (1. This relation is still valid when g. is in H since both g.H&H) = giHHgj = giHgj = g.I As we will see later. in the group 32.7)). the corresponding left and right cosets must be equal. We observe that for H and all its distinct cosets. the operators belonging to the same class are changed one onto the other by coordinate transformations represented by the elements of the group. = H. while (1.e.H for every i. in an Abelian group the classes are formed by only one element. For instance the subgroup 2 of the point group 2/m is normal since 1(1. the character is identical for the matrix representation of all the elements of the same class. then g.
multiply it by an element not in H. (Z[iool.11).e. the point group G = 23: say Readers will find the four classes: and the ten subgroups 2[. (21. and G are invariant subgroups.1. 4H. The subgroup H = (e. g. i. obtain and We take now an element not in H or in 3[llllH. of which only {I).Z[oio]). .H. 211.50 1 Carmelo Giacovazzo rrl H.f. For instance. . (Z[iio17 invariant and the factor group with respect to H may be written as: H. . g2H . A homomorphic correspondence allows us to reduce the study of the multiplication laws of the group G to that of the multiplication laws of the smaller G / H group. Z[lool. In detail glH = H . G . . The relat~onbetween G and G / H is a n / p + 1 correspondence. 43). Isomorphism is then a special case of homomorphism for which there is a one to one correspondence. for the quotient group (2/m)/2. dence of this type (many + one) is called homomorphism and G / H is said to be homomorphic with G. 2) is (e). and we get .e. . To display many of the abstract definitions given so far. (1.6) becomes As a further example let us consider the elements of the point group 2[olol. q2 = 2. 4.E. (1.H + fp. 210101. . (4. 2[iiol). we consider as major example.Z[llol. 2[olo17 2[ooll): we Calculate now the factored group of H = (1. say 3[1111.Five classes may be formed: 4mm: e. say 3flll]. 43. 211.. The following multiplication table is for the quotient group (we assume = e).1. A correspon. Z[liol. Z[100]H7 Z[llop.
By loss of translational symmetry. P2212. Maximal nonisomorphous subgroups of C222 are also P222. Let us first recall the concept of proper subgroup. Maximal subgroups and minimal supergroups The number of subgroups of a space group is always infinite. 3[1111H.e.Symmetry in crystals 1 51 The group is now exhausted and we may write 3fl11]H) form a group under the On assuming g1 = e. Since the point group P of G is finite.4). All the maximal subgroups as of type t for any given G are listed in the Znternational ~ a b l e s type I maximal nonisomorphous subgroups (see Figs 1.. according to (1.E. or line groups. For example.. following multiplication table This group is homomorphic with G itself if we associate the elements in H to e. the number of subgroups. P1211. The index of the decomposition determines the degree of 'dilution' of the symmetry in H with respect to that in G. the set T of all the primitive lattice translations is a subgroup (invariant) of the space group. plane groups. the elements in 3elllH with the 'element' 3tl11]~. P222. from G = P212121 to H = P2. Further subgroups may be found by considering the set of all the translations defined by a superlattice. if G = (2222.g. while P1 is not maximal. 2. Those of lowest index are listed as IIc in the International Tables.21). P2J12. which have the same conventional cell: for practice1 . or space groups. Such subgroups are called Klassengleiche or k subgroups and are classified as type 11. A subgroup H is called proper subgroup of a group G if there are symmetry operations of G not contained in H. Such a dilution may be obtained in three different ways: 1. For every H. A subset of k subgroups are those belonging to the same space group G or to its enantiomorphic: their number is infinite and they are called maximal isomorphous subgroups. and therefore. For example.ll).20 and 1. by thipning out the lattice. Now we define maximal subgroups: a subgroup H of a space group G is called a maximal subgroup of G if there is no proper subgroup M of G such that H is a proper subgroup of M. rod groups. We are here interested only in subgroups which are space groups themselves. They may bp the sitesymmetry groups (groups without a lattice). i.l11H. P2. then {e.22. P112. a right coset decomposition of G relative to H may be made. of maximal subgroups. the elements in 3[111]H with the 'element' 3[. is finite. maximal isomorphous subgroups of lowest index are C222 with a' = 3a or b' = 3b and C222 with c' = 2c. Subgroups of this kind.. ribbon groups. P2.ll are maximal subgroups of P212121. For example. are called Translationengleiche or t subgroups. By eliminating some symmetry operators (e.
E. (with c' = 2c). Cmma. A scheme showing the subgroup and supergroup relationships for point groups is illustrated in Fig. ~ 4 r n 2~ 4 ~~ 2 b 2 ~ 4 n 2 P622. . P42. Ccca. 4. it will be easily seen that Laue symmetry is always a minimal supergroup of index 2 of a noncentrosymmetric point group. P422. or a maximal isomorphous k subgroup of G'. The minimal nonisomorphous supergroups of C222 are: of type t: of type k: Cmmm. P6. For k subgroups the point group P of G is unchanged.2. From the geometrical point of view w and wm are identical. and IIc subgroups are listed. By combination of 1 and 2. For example. F222. In this case both the translation group T and the point group P of G are changed. or a minimal nonisomorphous k. A set of maximal conjugate subgroups is referred to by a broken line.E.l a double solid line refers 422 to 222.52 1 Carmelo Giacovazzo reasons they are labelled as subgroups of type IIa.22.22. Cccm.2. G' is called a minimal supergroup of the group G if G is a maximal subgroup of G'. Limiting groups in two and three dimensions In two dimensions there are two types of point groups: For very large values of the order of the rotation axis the two types approach w and am respectively. Space groups with primitive cells have no entry in the block IZa. P222 (with a ' = a/2.2. I222 (with c' = 2c) and I2. 1. A theorem by Hermann states that a maximal subgroup of G is either a t subgroup or a k subgroup. For example. and our standard notation will be wm (the situation .2. l. Furthermore. Maximal invariant subgroups are indicated by full lines: if two or three maximal invariant subgroups exist with the same symbol then double or triple full lines are used. (with c' = 2c). IIa. . Thus in the International Tables only I. b' = b/2). 3.22. or a maximal nonisomorphous k. from 3m three conjugate subgroups of type m can be formed. IIb. Some further subgroups of C222 are C222. P4.1. Sometimes we are interested to the possible space groups G' of which a given space group G is a subgroup. Of course we will have a minimal t. Thus in Fig. or a minimal isomorphous k supergroup G ' of G according to whether G is a maximal t. These subgroups have conventional cells larger than that of C222 and are denoted as subgroups of type IIb. Maximal subgroups and minimal supergroups for threedimensional crystallographic point groups With trivial changes the definitions of maximal subgroup and minimal supergroup given above for space groups may be applied to threedimensional crystallographic point groups. P42. P6. Thus a dashed line refers 3m to m. from 422 two invariant subgroups of type 222 with index 2 can be formed (no symmetry operation of 422 refers one subgroup to the other). .
for a . magnetic field round a disc). mm (the symmetry of the two groups can be represented by a circular cone and by a circular cylinder respectively). in Chapter 1 we have represented the symmetry groups through square matrices of order 3. according to whether there is or not a mirror perpendicular to a axis . since q can be interpreted as a change of coordinate system. supergroup relationships for point groups (from International Tables for Crystallography). In accordance with this point of view. It is often possible to find a new coordinate system for which each matrix d .) then the two representations are said to be equivalent. a # a m occurs when the rotation direction is taken into account: i. Different representations of G may be obtained through a transformation of the type When condition (1. In the first case two groups can be identified. d 2 . 1.E.E. wm and w 2 .. In three dimensions a point group can include continuous rotations about one or about all axes (this is a consequence of the Euler theorem applied to such a limiting case). .1. d. then the matrices form a group D isomorphous with G.) and r2(dI. . . subgroup. Group.. in such a way that when gigj = g k also didj = d. w m Representation of a group If a square matrix d can be associated to each g E G .represents the case in mm which continuous rotation about any axis is allowed (the symmetry is represented by a sphere). The symbol . . These matrices form an isomorphous or exact representation of the group: the order n of the matrices is the dimension of the representation.e.Symmetry in crystals 1 53 Fig. .. .7) is verified for the two representations rl(d.
) defines the dimensionality of the representation.ds2). Sometimes dl and d2 can be further reduced.di2).' where dji) are themselves matrices. .. The matrices dl1). dj2). etc. Similarly dl2). . as well as (dl2).(")]= d.) form a'representation of the group. The complete set of characters for a given representation is called the character of the . . It can be shown that for finite groups the number of irreducible representations is equal to the number of classes.). d. and at the end of the process each matrix d j will be transformed into qld.di2). dill. For instance an isomorphous (reducible) representation of the point group 32 is Also the twodimensional irreducible representation and the onedimensional nonexact (homomorphic) representations exist: Character tables The sum of the diagonal elements of a matrix. dS1).q = diag [djl). . . .. .m). have the same dimension. . otherwise it is called reducible.54 1 Carmelo Giacovazzo is transformed into with dl of order m < n and d2 of order (n . . all have the same dimension. . elsewhere called trace. in group theory is called character and is indicated by ~ ( g It is obvious that ) ~(g. . then the representation is called irreducible.dS2)..d$'). dp). From the rule of the product of blocked matrices it follows that (dl1). . If this can not be obtained by any transformation. .
but there are only ten crystallographic groups (see p... In this space only symmetry operations transforming the space into itself will be allowed. 1 55 1. which is nonperiodic. The G2 groups 1.. which is nonperiodic. at least one line will remain invariant with respect to all symmetry operations. which transform that direction into itself. G$ groups. describing objects periodic in one direction and finite in the other two...I t. glides with translational component parallel to it and twofold axes. In a onedimensional space (a line). Only two groups of type G: are then possible.+ . .F. since a full treatment would exceed the limits of the present book.1. We may therefore consider reflection planes parallel or perpendicular to the invariant direction. Symmetry generalization Only a few intuitive elements of this subject are given. Besides the 1 and ? operators. G groups. t aat:2 at:2.t.Symmetry in crystals representation.. 1.. In a 'twodimensional space (a plane). For instance in the G: groups.F...a . the characters of two equivalent representations will be identical (the converse is also true). The reader is referred to specific texts or The symmetry groups G: A space may or may not be periodic in all its m dimensions.. In a twodimensional space. 2. 16). are allowed. There are seven Gf groups (the symmetries of linear decorations) which are represented in Fig. Each row of the table refers to a particular irreducible representation and each column to a given class... with m 3 n. G: groups. 1. The corresponding symmetry groups are indicated by GT.a 1.l. ~f (border) groups.m ++++t:zm IIm : t Fig. only two symmetry operators are conceivable: 1 and ? (which is the reflection operator m)..F. the only conceivable operators are those of rotation around an axis perpendicular to the plane and of reflection with respect to a line on the plane. Since the traces of two matrices related by a coordinate transformation are identical. only the symmetry operators (and their combinations).. Gh groups. The G1 groups 1. The number of (point) groups is infinite. It is therefore convenient to set them up in tables called character tables. where n is the number of dimensions of the subspace in which the group is periodic. The seven border groups 3. The only two (point) groups are therefore 1 and I . There are the 17 plane groups described on the pages 30 and 34. 2. they contain the translation operator. periodic in one dimension. ? . Several properties of a point group may be deduced from the characters of its irreducible representations alone.
2 mmc 4 22 .2 1m . There are 75 G: crystallographic groups. 2 and 3 axes perpendicular to it.2 3m 4m2 6m2 2 1 2 13C 2 C 4c2 6c2 . Rod groups may be considered as arising from the combination of onedimensional translation groups with point groups G.mc 3c 4. mmc 6 2 . 1116). the Table 1. The first position in the symbol indicates the axis (n or ri) along z. but there are only 32 crystallographic point groups (see pp.22 6.mc 2. The number of (point) groups is infinite (see Appendix l.mc 6.B)./m m2c 2. They describe threedimensional objects which are periodic in only one direction (say z).1./m 421m 6.2 mmc 2.2 3m 4m2 6m2 3 4 6 m . This must remain invariant with respect to all symmetry operations. The only allowed operations are therefore n and ri axes coinciding with z. 2. . G..F.22 312 4. In Table l.56 1 Carmelo Giacovazzo The G3 groups 1. There describe nonperiodic spaces in three dimensions.l the rod group symbols are shown alongside the point groups from which they are derived. groups. 2 . screw axes and glide planes with a translational component parallel to the invariant direction. The 75 rod groups Point group Rod groups 1 2 3 4 6 I m 2mm 3117 4m m 6mm m 2/m 4/m 6/m m2m 2 2 2 mmm 4 2 2 rnrnrn 6 2 2 mmm 12 222 32 422 622 1 1 2 3 4 6 I m 2mm 3m 4mm 6m m m 2/m 4/m 61m m2m 2 2 2 mmm 4 2 2 mmm 6 2 2 mmm 12 222 32 422 622 1 21 31 41 61 I c 2.F.22 3 4 6 . G: (rod) groups.
(b) for a square net. They are useful in describing the patterns of walls. at an atomic level. Glides in the z direction are denoted by c. The layer groups can be enumerated according to the five nets quoted in Table 1. also about a horizontal one. hexagonal) and contains the point groups compatible with the net and the corresponding layer groups.g. to x (and therefore symmetry related axes) and to diagonals directions. 43m.7 for the plane lattices. The groups of colour symmetry Groups in which three variables have a geometrical meaning while the fourth has a different physical meaning and is not continuous. m3m plus four second settings (this time the z axis is distinguishable from x and y: so 2 is different from 12. groups we may consider the G: groups. y) plane bisecting the previous ones. in describing structures with layer molecular units. These are the 230 space groups (see pp. The third and fourth positions refer: (a) for rectangular nets. each block divided by the subsequent by a double line: each block refers to a specific net (in sequence. the time. the phase of a wave function. . parallelogram.Symmetry in crystals 1 57 second position refers to axes (n or i i ) in the plane (x. . G: groups. rectangular. to x (and therefore to y) and to a diagonal direction. and. The number of point groups which can be used is 31: the 32 threedimensional point groups minus the five incompatible groups 23. panels. In a fourdimensional Euclidean space the symmetry groups G: may be constructed from their threedimensional projections G:.2 the 80 layer groups are divided in blocks. square. .~ symmetries of doubly periodic threedimensional objects. G: groups. the third position for axes in the (x. The first position in the layer group symbol gives the type of cell. The 6 . (c) for a hexagonal net. or 2/m from ?2/m. ~the ~ . 3. Let us denote by z the direction perpendicular to the layer plane. centred rectangular. 4. y) normal to the invariant direction. As subgroups of the G. thus passing from a threedimensional space into a space with dimensions m > 3. otherwise translational symmetry should also occur along the z axis. to x and y respectively. We can therefore introduce one or more additional continuous variables (e. Rotations can only occur about a vertical axis. m3. which are obtained by projecting the Gq groups along the axis normal to the singular plane. 2230).F.). are . It will be the vertical axis from now on: directions in the plane will be called horizontal. which are all well known. No more than one horizontal reflection plane can exist.groups 4 The threedimensional Euclidean space may be insufficient to describe the symmetries of some physical objects. ' ~ ] . 432. etc. In Table 1.). and if twofold. the second refers to the z direction. Thus there are 227 point groups G: and 4895 groups Gi. There are called layer groups and d e s ~ r i b e [ ~ .
ba 2 nrnm nbm 1rn 2mm m2m 2 2 2 mmm 12 222 .g m P.2 422 pA.2 p2 .a 2 2 2 mrnm 2 222 22.2 1m 4 4m rn 41rn 4 2 2 mmrn c l rn c.2 2 mmm P4 ~ 2 2 p4m2 p4grn p4/n 42 42.a pn2a p2ba pa2.2 r n g m P.22 plL brnm bm a P b b i Pbba22121 p.mrn cm2m 2 2 2 Cmmm c12 c222 .2.58 1 Carmelo Giacovazzo Table 1.2 clr n  4 422 4m2 P4 p4mm p4m/m 4 P. The layer groups Point group Plane groups 1 2 rn 1 Tim 1rn 2rnrn rn2m P1 P2 prn p2/m P1 plm p2rnm prn2rn pn2..F.m rn ng ~ 4 2 ~ 2 p4g2 p42rn p42.rn .m pb2rn pa2a pb2. P.m Pb p2/b plb p2bm pm2.A .2 2 Pl mmm rnbrn 22 2 222 22. 2 22 22 PP.2.
For the threedimensional groups with antisymmetry we observe that.2(c) the quasicubic magnetic unit cell of NiO has an . More complicated cases require more colours. identity after an inversion operation. 1. (c) antiferromagnetic superstructure of NiO (only ~ i ' +ions are shown). Classical groups involve only neutral points. axis. NiO is cubic with ac2: 4. such as those given in Fig. The polymorphism of NiO is due to its magnetic properties. In these conditions the threefold axis is unique and the structure is rhombohedral.F. identity after both an inversion operation and a change in colour. For instance: 1. group. and the term colour symmetry is used. l. NiO is rhombohedral with edge length a . If the cube is compressed (or extended) along one of the four threefold axes of the cubic unit cell then symmetry reduces from cubic to rhombohedral (the only threefold axis is the compression axis). Groups of this type are also called 'groups with antisymmetry' or 'blackwhite' symmetry. antiidentity (the two objects differ only in the colour). magnetic structure.2. Above 250°C the antiferromagneti~ordering is lost: the rhombohedral + cubic transition occurs and NiO displays ordinary paramagnetism.@)with a clear meaning of the symbols.2(c). Each Ni2+ ion has two unpaired spins (the [Ar]3d8 electronic configuration).. because of the existence of the antiidentity operation 1' (only the colour is changed).F. \ O 0 0 R44/ where R4.Symmetry in crystals 1 59 particularly important in crystallography. If we project a G: group. we obtain a G. The position and orientation of the magnetic moments of the cobalt atoms in the CoA1204structure (space group ~ d 3 m may be described by ) means of a twocolour group (see Fig. (b) geometrical relation between a facecentered cubic unit cell and a primitive rhombohedral unit cell. 1. New types of Bravais lattices.F. above 250°C. a material used in the ceramic and electronic industries.952 A and a~ =. as in Fig. 2. A general rotation matrix may be written in the form Fig.3.F. l.  2.177 A. In the groups with antisymmetry there will be four types of equivalence between geometrically related objects: identity.O. we will obtain a colour group G. l. = 1 or +1 depending on whether or not the operation changes the colour.2(a)) in which each colour corresponds to a given polarity of the magnetic moment. will come out. in which a 6. l. in Fig. axis is present. But. 60'4': aR approaches 60" with increasing temperature. the antitranslation operation t' = t l ' will also exist. As a further example let us consider the case of NiO. As an example.F. if we assign a different colour to each of the six atoms related by the 6. on a plane perpendicular to the axis. At room temperature the spins in NiO form an ordered antiferromagnetic array: layers of Ni2+ with net spin magnetic moments all in the same direction alternate with layers of Ni2+ with magnetic moments all in the opposite direction.2(b): the same set of lattice points is described by the primitive rhombohedral unit cell and by the facecentred cubic cell provided that aR= 60' exactly and a R = a/*.F. and. The relation between the two cells is shown in Fig. Examples of structure described by an antisymrnetry group: (a) CoAI. At room temperature.
E. Journal of Applied Crystallography. (1988). International tables for crystallography. R. including the traditional uncoloured lattices.3. Berlin. C. 9. R. (1978). 12. A36. Pergamon. Oxford. Space groups and lattice complexes. I. Acta Crystallographica. 70. Shubnikov. Dougherty. 4. C. 3. Fischer. and Kurtz. 13. I b ? ' Fig. (1957). and Cracknell. L. S. K. H . (1980). (1955). Reidel.. and Rodgers. N. V. Alexander. B. E. Bradley. 10. V. Wilson. Acta Crystallographica. Hellner. Oxford. and MacMillan. In three dimensions there are 36 black and white Bravais lattices. Krystallografiya. 8. Burzlaff. 5. Cambridge University Press. Mackay. J. J. K. 14. Zeitschrift fur Kristallographie. 9. A. 543. 145. Washington. Two antisymmetrical Bravais lattices. A. A. NBS Monograph 134. D. methods of structural crystallography. Vol.. 2.. (1983). P. (1981). Lockwood. H. . 321. It may be seen[14]that if the five Bravais lattices are centred by black and white lattice points (in equal percentage) then five new plane lattices are obtained.60 ( Carmelo Giacovazzo edge length twice that of the chemical unit cell. (1976). Alexander. and Donnay.F. Moscow. W. 7. ? fg / 9 References 1. Space group symmetry. Clarendon Press. A. A. A. P. The mathematical theory of symmetry in solids. National Bureau of Standards. A44. 328. Representation theory for point groups and space groups. E. Mighell. 10. K. V. Kitaigorodskij. 489. (1960). 715. Acta Cryst. 70. M. Zeitschrift fur Kristallographie. Modern crystallography I: Symmetry of crystals. (1964). (1929). 11. (1972). Coloured symmetry. b. Shubnikov. 367. Geometric symmetry. J. Vainshtein. Organic crystallochemistry. 5. H. Springer. J . D. (1929). A. 6. (1973). A. J.C. and Belov. and Herrmann. E. Dordrecht. 1.
For practical reasons some calculations useful in characterization of thermal ellipsoids are developed in Appendix 3. Fourier calculations. The metric matrix Let [0. and S is the determinant of the square matrix S. The following notation is adopted: rl. with respect to a coordinate system [0. Material is treated in order to answer daytoday questions and to provide a basis for reference. rl A r2 is their cross product. principal axes of the quadratic forms. c] the vector r will be written as where X is the coordinate matrix and A is the matrix which represents the basis vectors of the rectilinear coordinate system. For example. r will be the is modulus of r. c] be our coordinate system.). those which are of more frequent use have been selected: axis transformations. b. Among the various topics. b. S1S2 the (row by columns) product of two matrices S1and S2: S is the transposed matrix of S. a. and r2 is rl r2 = (xla + ylb . r2 denotes the scalar product between the two vectors rl and r2. The scalar product of r. torsion angles. geometric calculations (bond angles and distances. metric considerations on the lattices. a. The method of least squares and its main crystallographic applications are treated in greater detail. We will also distinguish between coordinate matrices and vectors.B . + zlc) . . structure factors.CARMELO G I A C O V A Z Z O Introduction In this chapter elements of crystallographic computing are described.. (x2a + y2b + z2c) =xlx2a2+yly2b2+ zlz2c2+ (x1y2+ x2y1)ab cos y + ( ~ 1 + X ~ Z ~ )cosIPC+ ( Y ~+zY ~ z ~cos~ c ~2 L ~ ) CY . .
A3 = c(zl .4) 3. b. 69) is equal to V2 (square of the volume of the unit cell).22) A2 = b(yl . A$ + 2A1A2COSY + 2A1A3cos P 2A2A3cos a. c and the angles between them. z.62 1 Carmelo Giacovazzo or.cos2 y  + 2 cos a cos P cos y) + 2xzac cos j3 + 2yzbc cos a (2. The value of its determinant is (2.GX.2) which (see Table 2. The cross product r2 A r3: 4. = r2= r then (2.) and (x2y2z2)Denoting A1 = a(xl .r~). We c8n now calculate the following: 1. gives d2 = A: A.3b) + + + 2.3~) which gives the modulus square of a vector. The scalar triple product rl r2 A r3: is the volume of the unit cell The following formulae of vector algebra are also recalled for future convenience: Some properties of the rotation component R of the symmetry operators . The interatomic distance d between two atoms positioned in (xl. G is the metric matrix.cos2j3 ..1 and p. If r. in matrix notation. also called the metric tensor: its elements define both the moduli of a.l(r. y.x2). (2. The angle 8 between two vectors cos 0 = ~.1) becomes r2 = XGX = x2a2+ y2b2+ z2c2+ 2xyab cos y G = a2b2c2(1 cos2 a .y2). (2.
can now be proved: 1. If a. A symmetry operator does not change the moduli of the vectors and the angles between vectors: i. . c be the elementary translations of a space lattice (called here a direct lattice). A second lattice. b). b. Multiplying the second eqn (2. 3. The modulus and sense of a*. r2. c define a primitive cell. in terms of moduli.11) by a is taken: a*. Ewald in 1921.e. from which = Crystallographic computing 1 63 . Therefore.9) by R gives GR= W G . the reciprocal lattice was introduced by P.. = XlRG~X2 XlGX2. lob). The value of p is obtained if the scalar product of both the sides of (2. the elements of R are integers. 2. According to (2. Indeed the relation Xr = RX transforms lattice vectors r into lattice vectors r r . b* to the plane (a. 2. reciprocal to the first one. b*. which satisfy the following two conditions: Equation (2. The reciprocal lattice Very useful in metric calculations (as well as in diffraction geometry). r. Both r and r r have integer components. c) and c* to the plane (a. Properties 1. 3 can be verified for the rotation matrices quoted in Appendix 1. Equation (2.10) also suggest that the roles of direct and reciprocal space may be interchanged: i. is defined by translations a*.a)=pV from which p = 1/V.10a) a* may be written as where p is a constant. b. Let a.1). ri = r. If only determinants are taken into consideration then R = f1 arises. c).a=l=p(b~c.e. according to (2.D. c* are fixed by (2. c*.9) can be symmetry rotation matrices in the coordinates system defined by G. Only the matrices R which satisfy (2. Equation (2.11) and its analogue may then be written as or. the reciprocal of the reciprocal lattice is the direct . b*.GX. consequently also the elements of R must be integers. X.10a) suggests that a* is normal to the plane (b.
However.1. .A: a summary is given in Table 2. and cubic lattices a* )I a. .( c* A a * ) . cos a* = COS @ / ( I + COS a ) . 2. assumes a very simple expression: Table 2. c* = l l ( c sin P). lattices are triclinic. . p*=n/3. In monoclinic lattices b* JJ b while a* and c* are in the plane (a. tetragonal. c): then a* = l / ( a sin p). Some relations between direct and reciprocal bases are discussed in Appendix 2.cos /3 cos y .13) It may be easily verified that the reciprocals of triclinic. v* c = v * (a* A b*).64 1 Carmelo Giacovazzo lattice.acsinp . c* 1) c. monoclinic. The scalar product of two vectors. . monoclinic. In detail: 1 . b = llb. and 3.D). the reciprocal of an F lattice is an I lattice and vice versa (see Appendix 2.(b*~c*). b* (1 b. V ' c* .a b sin y v v abc sin p sin y ' abc sin a sin y ' cos a  * . Relationships among direct and reciprocal lattice parameters. the first defined with respect to the reciprocal basis and the second to the direct basis. Some important properties of the reciprocal lattice are: 1 .1.cos2P . In rhombic.cos2 a . Inverse relationships are obtained by interchanging t h e starred by unstarred parameters b a*=. Therefore 1 a=. v 1 b = . a*=y*=n/2. themselves. 1 (2. c s i n a V ' sin a* = sin p* = sin y* = b*.cos2 y + 2 cos a cos P cos y)'I2 = abc sin a sin p sin y* = abc sin a sin p* sin y = abc sin a* sin /3 sin y v* = 1/v . b ) : For the rhombohedrical basis a* = p* = y * . . .cos a sin p sin y *~cosa~~sycosp cospsin a sin y *~cosacospcosy cosy sin a sin p v abc sin a sin p ' V = abc(1 . In trigonal and hexagonal lattices c* )I c while a* and b* are in the plane (a.
k.Crystallographic computing 1 65 2. c by . Since r i has the same direction as ON.= r r. Since r i is perpendicular to two lines in the (hkl) plane.1. b r .a l h . As well as for direct lattice. a metric matrix G* may be defined for the reciprocal lattice: It may be easily verified that Consequently (see (2. The vector r i = ha* + kb* + lc* is normal to the family of lattice planes (hkl). Consequently (BA) = blk .1 the plane of the family nearest to the origin is drawn. Basis transformations In threedimensional space the coordinate system defined by the base vectors a ' . Therefore (CA) = cll . In Fig. where dH is the spacing of the planes (hkl) in the direct lattice. r i (BA) = (ha* + kb* + lc*) (blk . 8 the vectors (A0). d H = (alh) . (B0) and (C0) are equal to alh.alh. b. . blk and cll respectively. c r may be defined in terms of the base vectors a. This may be proved by observing that dH is equal to the length of the normal ON to the plane ABC from the origin 0. it is normal to the plane. 2.17b) Specific expressions of d H for the various crystal systems are given in Table 2. If h. 2.2. 3. . 1 have no common factor.1) and (2. then Fig.3) for the direct lattice) from which d H = (h2a*2 k2b*2 1 2 ~ * 22hka*b* cos y* + 2hla *c*cos /3* + 2klb *c*cos is easily obtained. r .blk. (cB) = cll . . (CA) = r . The plane of the faniily (hkl) nearest to the origin. (CB) = 0 . In accordance with p.a l h ) = 0. 1 ria 4. + + + (2.
l ( $ sin2 a 21h 2hk + (cos y cos a . c and then using (2.cos2 y + 2 cos a cos fi cos y ) .cos p ) + (cos a c0s. Introducing (2. In matrix notation (2. The result is The unit cell volume defined by A' is V' = a' b' c' therefore. 2 + + .p .cos2 /3 . .1) a ' . b. c' for a.2.18) into the r' expression leads to + + + + The reverse transformation is X' = (M)'X.66 1 Carmelo Giacovazzo Table 2.cos2 a . The vector r = xa yb zc may be written in the new coordinate system A' as r' = r = x'a' y'b' z'c'. The algebraic expressions of 4. according A .20) provides the transformation rule for the components of the vector r while the vector itself is unaffected (r' = r) by a change of axes. b'.18) is written as The reverse transformation will be A = M'A'.COS y ) ca ab three equations (suppose the transformation leaves the origin invariant) are where mi. The metric matrix G' in A' may be calculated by substituting into (2.18). for the various crystal systems Cubic Tetragonal Orthorhombic Hexagonal and trigonal ( P ) Trigonal (R) Monoclinic Triclinic ( h2 + k2 + 1') sin2 a + 2(hk + hl + kl)(cos2acos a) 1 +2cos3cu3cos2~ a2 h2 I ? 1 ' 2hlcosP 2 . It should be noted that (2. any real numbers. 7 2 2 a sln fi b c sin /3 ac sin2P (1 .
25) are special cases of (2.a)a* + (r' b)b* + (r' c)c*).28) are special cases of (2. the following relations a* = (a* a*)a + (a* b * ) b + (a* c*)c b* = (b* a*)a + (b* b*)b + (b* c*)c C* = (c* a*)a + (c* b*)b + (c* c*)c are respectively obtained.22): Additional transformation rules are given in Appendix 2.26) They transform components defined in direct space into components defined in reciprocal space and vice versa.27) 2.~ Q ' ( M ) . . . In accordance with (2. A * = G * A or A = G A * . b' = b*. .5).. (2. The reader is referred to the splendid book by sandsr1]for further insight. Let us now apply (2. Relations (2.1) and (2. (2. for any transformation of axes the unit cell volume is multiplied by the determinant of the transformation matrix. 1. Thus.Crystallographic computing ( 67 to (2. .~ . c' = c* to a.20) X Q X = X ' M Q M X 'from which Q' = MQM or Q = M .20) X=G*X* or X*=GX.22) A special linear transformation is that which relates a' = a * . = Xax. Let us show that in this case M = Gl = G*. c (in this case A' will be replaced by A*).19).26) we have rl r2 = XlGX2 = XIX. which in matrix notation reduce to .23) r = a *. . In particular r2 = r*2= X X * is the square modulus of a vector. .24) On assuming in (2. b . The set of matrices conventionally used to pass from centred cells to primitive ones and vice versa is shown in Table 2. Let be a quadratic form defined in the coordinate system A.25) It is easily seen that relations (2.C. Similarly: (2. (2.26) are special cases of (2. . b *.19) and (2.1 (however. Write the vector r = xu + yb + zc as (in terms of reciprocal axes r' = r* = x'a* + y'b* + z'c* = (r' . (2. In accordance with (2.20) to derive the transformation rules of a quadratic form. V ' = V M . transformation matrices are not unique).E. Equations (2. c*.
e2 normal to a in the (a.). 2. = 0. If we choose (see Fig. = sin p sin a*= l/(cc*) is easily obtained. 12= 0. 2.30) The matrix M to use in E = MA is therefore 1/a cos y/(a sin y) a * cos p* 0 l/(b sin y) b * c o s a * c* . according to (2.18). blb. E = MA. and inversely A = M'E.. n.) = WIJL (2. m2 = sin y. e2. Let A= (I) and E= (i) be the crystallographic and the orthonormal bases respectively. Orthonormalization of crystallographic bases.cos p cos y)/sin y = sin p cos a*.. m l= cos y. by means of C Fig.2) el along a. Then. clc in E. m2. cos a = C mini = cos cos p + sin sin n2 i we obtain n2 = (cos a . m.68 1 Carmelo Giacovazzo Transformation from triclinic to orthonormal axes Geometrical calculations are often more easily made in an orthonormal than in a crystallographic frame. e. b) plane. (m.) are direction cosines of the unit vectors ala. 2. nl = cos p. from the relation Ci n: = 1 n. I.). then the unit vectors ala. /a i where (I. blb. Finally (fI))=(co:y from which =(bc:s c cos p cos p 0 0 siny sin p cos a* ll(c*c) 0 0 b sin y 0 c sin /3 cos a* l / c * )(. clc are referred to el. (n.. Therefore ClT=Cm?=Cn:=l.. Since m3 = 0. 1.2. e3 normal to el and e2 (and therefore parallel to c*). n2. I.2 it may be deduced that 1. Furthermore. i i From Fig. = 1.
el.31~) where sy. b*): e3 is then along c. c may be easily obtained if M is known. In this case M= and ~ l = ("d*~.~* 0 0 c*cosp* b*siny* .l l ( b ty sp*) ll(c s a tp*) M=( 0 0 l/b 0 ll(b t a ) ll(c s a ) and (2. y . . The volume of the unit cell defined by a. b. We obtain l l ( a sy sp*) l l ( b t a tp*) . Furthermore. e3] the anticlockwise rotation of a vector r through angle al about el or through a2 about e2 or through cu3 about e3 produces a vector r' = R. For example. c in terms of el. then the result . . ty stand for sin y. The family of all the possible transformations M which orthonormalize a given frame A according to E = MA may be obtained from the following decomposition of the metric matrix G of A: Such a relation is obtained by requiring that in (2. cy. the assumption made on p. since det (Ml Ml) = v2= G.21) the condition G' = I is satisfied. etc. and if (2. e2. c)). Rotations in Cartesian systems In a righthanded Cartesian coordinate system [0. if we express a. V =a b A c = det (M') is obtained. b. 62 according to which G is the square of the volume of the unit cell is also proved. cos y.30). and tan y.r where s = x . .5) is then used for calculating a b A c. el may be chosen along a* and e2 in the plane (a*.c * s i n p * c o s a llc l l a * cot y*/a* a cos /3 0 l/(b*siny*) b c o s a C Also. z . Indeed. we may choose el along a* and e2 along b (then e3 is in the plane (b. e2. e3 according to (2.Crystallographic computing 1 69 A crystallographic frame may be orthonormalized in infinite ways.
. 0 cos a2 c a s ia Rz(a3) = sin a3 cos a3 ( sin a . e2. . e2. Matrices corresponding to rotatoryinversion operations about el.(M)'. 0) Since the matrices are orthogonal.(M)~ (cos . the following relations hold: R(a) = Rl(cu) = Rl(a) = R(a). the same rotation in A is represented by R = MR. e2. .. Thus R (which is an integer matrix) may correspond to a symmetry axis along a in . (2. R. an orthonormal base E = (el.1)/2 cos x = 0 aflsinX/(2c) 1 c sin x / ( a f l ) 2 c sin Xl(afl) cos x Incidentally.30) and (2. eh. e2. e3 are obtained by changing the signs of all the elements. X ' = R.32) the integer 1 by 1. It should be noted that rotating r about el.. into a. e3 in anticlockwise mode is equivalent to rotating el.31) the matrices M and MI are from which R = MR. Rotation about the unitary vector I in a rectilinear coordinate system..l(a3)x = R.)X. According to (2. e] by a clockwise rotation through a about e3. 2 cos a . The traces of the matrices that represent proper rotations. e3 in clockwise mode. e3 are obtained by replacing in (2. e3] may be superimposed to the new framework [0. e2. .(a. . e3) may be chosen (E = M A ) such that el coincides with 1 In accordance with .(a3)E. according to Table 2. b. and. which corresponds to an anticlockwise rotation of a vector r in E. c).1 respectively.20). Matrices corresponding to rotatoryreflection operations about el. For example if the framework [0.32) a rotation about 1 in E is represented by R. el.70 1 Carmelo Giacovazzo and 0 cos a . ez. 0 sin a .E. rotatoryreflection and rotatoryinversion operations are 1 2 cos a. then E' = e. + See now some useful applications: 1. Given the crystal base A = (a. As an example we calculate in the hexagonal system the matrix corresponding to an anticlockwise rotation through x about a. Corresponding clockwise rotations are obtained by changing a.1.1 2 cos a . According to (2. it may be noted that the ratio a/c is unconstrained.
cot /3 sin x = 0. . Ry(q). I. I.(w).Crystallographic computing 1 71 the hexagonal system only if x =O.cqsqcw s q c o c q s q s o c q c q + and c q stands for cos q . n (onefold or twofold proper or improper axis). s q for sin I . etc.=( cos x + cot plsin x 0 c sin %/(asin p) 0 1 0 a sin xl(c sin$) 0 cos x . .29). where mij are suitable parameters. e. The overall effect of a sequence of three successive rotations R. Let I.. As an example.sqsqsw sqcq sqsw . the reader will easily verify that rotating r through 120" about e3 and then through 90" about el leaves r in r" where . R will correspond to a symmetry operator if n. 2. 3.. Sequence of rotations about the same axis or about different axes. Explicit expression for the rotationmatrix R about the unit vector I in an orthonormal system. the overall effect changes. according to (2.X = RX cqcw cqso c q s o + sqsqcw c q c o .) is chosen so that 1 coincides with el: then. . $ If the three rotations are made in different order. The matrix corresponding to a rotation about I in A is then where sx and cx stand for sin x and cos X.. Rx(q) on the vector r may be so described: from which X where = RxRyR. A new orthonormal system E = (el. e. be the direction cosines of 1 in the orthogonal system A. The reader will easily find that the general rotation matrix about b in the monoclinic system is .
e2. e2) and (e.3(a) two orthonormal frameworks [ 0 . (b) Spherical polar coordinates. Eulerian angles. The axis OK. e. (b) rotate through 8. about OK which will bring e3 into coincidence with e.72 1 Carmelo Giacovazzo and 4. 2.. el.. (a) Eulerian angles... (c) Return these coordinates into the system A. called the line of nodes. the rotation function corresponding to any desired rotation.31b) or (2. The Eulerian angles can also be used in order to calculate..20).31a) or (2. 2. where cei and soi stand for cos ei and sin Oi respectively. e. (c) rotate about e.. e.) planes and is perpendicular both to e3 and e. then according to (2. = M X = MR. = (M)lXA. M may be (2. If E = MA. E may be superimposed to E' by three anticlockwise rotations in the following order: (a) rotate about e3 by the angle 81 (OK and el are now identical). el. by O3 which then brings el to el and e2 to e. For example. Then XE transforms in XI. X. The simplest procedure could be: (a) Transform coordinates in A (say XA) into coordinates in E (say XE). = REuXE.31~). in any crystallographic system A. Then the inverse operation described in (a) has to be made. In Fig. (b) Transform the Cartesian coordinates into a rotated set of axes. Suppose now that r is a vector with coordinates X in the spacefixed system and coordinates X' in a bodyfixed system: then X and X' are connected by Fig.(M)'X~ so that the desired ~ rotation function is the full range of rotation operations is . The final coordinates are Xj. is the intersection of the (el.] are shown. e3] and [O.3.
furthermore. C.cx)c*s*sq. c ysx.4.cx)s2*cQ)sq.l3 of the rotation axis 1 by Il = sin I) cos q. . D.cx)s2*c2Q) s*sQ)sx+ (1 cx)c*s*cQ) cx + (1 . owing to (2. become cos w = cos a cos y . 2. The rotation about a given axis is specified by the angle x and the polar coordinates and q.4).c ~ ) c v s v c q . 2.C X ) C I ~ S ~ S Q ) cx + (1 .B for calculations concerning crystallographic directions and planes.(1 . Here we limit ourselves to the description of some calculations which occur very frequently in crystal structure analysis. 12. z are given by Since (2. sin a sin /3 sin o = Vb ab2c sin a sin y ' Fig. the torsion angle o(ABCD) is defined as the angle between the normals to the planes ABC and BCD (see Fig. viewed down BC. s*cQ)sx.3(b) the orthonormal coordinates x .. and is reversed by reflection or inversion.7) and (2.c x ) c 2 ~ R.32b) represents the anticlockwise rotation matrix about the unit vector 1 in an orthonormal frame we can replace the direction cosines 11. ( S~CQ)SX cvsx.(1 .(1 . According to the definition (see again Fig. B. = s * s q s ~ +(1 . and q : CX+ (1 . l3 = sin qj sin q. According to Fig. define the direction of the rotation axis. Note that w(ABCD) and w(DCBA) have the same sign. is clockwise.Crystallographic computing 1 73 Since Eulerian angles are difficult to visualize it is preferred to specify a rotation in terms of spherical polar coordinates (see Fig. Torsion angles For a sequence of four atoms A . the sign of a torsion angle does not change by rotation or translation. 2.4) cos o = (a A b ) (b A c) ab2c sin a sin y b .c~)sz*s2Q) Since all rotation operations qre included in Some simple crystallographic calculations The reader is referred to Appendix 2. 2.3(b)).(1 cx)s2*cQ)sQ) . and so obtain the expression of the rotation matrix Rsp in terms of the rotation angle x and the spherical polar coordinates q.. (a A b) A (b A c) b sin w = ab2c sin a sin y which.8). otherwise it is negative. l2 = cos q.sin /3 . Definition of the torsion angle w . By conventiod2] w is positive if the sense of rotation from BA to CD. y. 2.
. under the condition that n is a unit vector. but they are often assumed to be unitary.34) becomes ao.74 1 Carmelo Giacovazzo If the vectors a * . i (2. (2.1 that w coincides with P*. r2.ro and Note that N * S N * is the weighted sum of the squares of the distances of the atoms from the plane.35). multiplied by the weights of the atomic positions. where r.5) and ( 2 .36) with respect to . 7 ) ) where d is the distance of the plane from the origin of the coordinate system.35) Equation (2. a + n2b n. Setting to zero the derivative of (2.34) with respect to d gives from which d = N * [ ( F w j x j ) ( ? w.)'1 = N*Xo.34) The partial derivative of (2. The minimum of Q will be searched with respect to d and n:. c* reciprocal to a . is minimum. c are considered. the least squares plane coincides with the principal plane of least inertia. n z . B . = r. where rj = AX. b . Best plane through a set of points Consider a set of p atoms at positions rl.35) states that the plane passes through the centroid ro = Owing to (2. eqn (2. . n = n .B. This kind of problem is best solved by the method of Lagrange multipliers. . should be taken as being inversely proportional to the variances of the atomic positions in the direction normal to the desired plane. it may easily be seen from Table 2.d ) 2 . The function to minimize is thenL3] + + + = C w j ( A * x j. n. ..A ( N * G * N *. .c = A N = nFa* nib* ngc* = A*N* is the normal to the plane.. Such a plane is characterized by the minimum of the function (see eqns (2. . The weights w. The best plane through them is that for which the sum of the squares of the distances of the atoms from the plane. If the atoms are considered as point masses of weight w j . b * . r.1).
*Xi is the distance of the ith atom from the best plane and N i x . N. say A >AP 3 A Each eigenvalue of A gives a stationary value of Q ' : the three corresponding eigenvectors N NP. and N/TXI are useful to prepare a diagram of the projection of the system of atoms on to the best plane. which may be also written as (A. Best line through a set of points This problem is strictly connected to results described in the above subsection. The best plane corresponds to the eigenvalue A and coincides with the plane passing through ro and normal to . define the principal axis of inertia of the system of atoms when considered as points of masses w. . N is the corresponding eigenvector. Principal axes of a quadratic form Let be the quadratic form. . three different A values. the problem may be solved via the Lagrange multipliers by minimizing The derivative of q' with respect to N brings to from which (A .. The eigenvalue A gives the value of q in the n direction.Crystallographic computing 1 75 N* (in practice with respect to the components n:. w.37) as AN = A N and multiplying both sides for N* gives The eigenvalue A is therefore the weighted sum of the squares of the distances of the atoms from the plane. Furthermore. .38) is written as AN* = AN* and both sides .AG*N* = 0. The search of the best plane is remarkably simplified if Cartesian systems are used (then G = G* = I).. .hl)N = O ng. . Writing (2. Finding its principal axes is equivalent to finding the directions n in which q is stationary. . There are three solutions of eqn (2.37). It may be shown that the least squares line passes through the centroid ro of the atoms and is normal to the plane corresponding to the eigenvalue A.. and N* = GN is the general eigenvector the components of which are referred to the reciprocal axis.B.6)). .Al)N* = O where A = QG*. if (2.. . while A and N define the worst plane. which in general correspond to .E. SN* .37) where A = SG and N = G*N* (see Table 2. N. nz) gives (2. As in calculating the best plane through a set of points. 1). . Indeed. N (see eqn (2.
A. 0. : . The function to minimize is which.2592n3.0438 0.12) the problem may be solved in the same way on condition that G* and N* replace G and N respectively.00049..1515..04921.0354 (0.742. that condition may be written ($G .15151.0280.. Therefore N.. Let the orthohombic unit cell parameters be a = 8.0733 0. In an analogous way N~ = [0. = 0. If this conclusion is referred to the tensor U* = j3/(2n2).0352 0.76 1 Carmelo Giacovazzo are multiplied by N we obtain Substituting the three eigenvalues A. P13 = 0.01424.1097..0139.00038. q * = H$H = Pllh: + 2P12hk+ . 0. = [0. : If the quadratic form is referred to the reciprocal basis (i. = 0. derived with respect to N*. . N which represent the principal axes of q.. The corresponding secular equation is Expansion of the determinant produces the cubic equation which has solutions A. are the components of N.0125 (I::)).8991$.38a) provides the three eigenvectors N N.00906. in A) if n3. = 0.e.0132) 0. = [0. n2.0565 0. = 0. Using the first root gives 0.185n3.1677 0. 0. n. (see eqn (3.. P3.B.05871 and N.. into (2. The eigenvector N.475. (! = n3. P23 = = 0. b = 10. 0.. A. Since each eigenvalue A fixes the value of q* along the corresponding eigenvector. c = 5.. .448. P12= 0.0393. AB = 0. can be found in terms of n.0203 0.Al)N = 0 . = 0. 0. + P3. will have unitary modulus (remember that n. A.483.6) . Since the three equations are linearly dependent n. = +0. 0.00401.: n. As an example let us determine the principal axes of an atomic thermal ellipsoid for which PI1= 0. leads to the condition Since N = G*N*.00102.677.. n..0866. and n2.0210.. PZ2 0.
3) where u. are calculated by (2.151 A and 0.38b) so that Metric considerations o n the lattices The results obtained so far can be used to characterize lattices and their properties. where V is the eigenvector matrix transforms the basis A into a Cartesian coordinate system A' in which the axes are the eigenvectors of $.156& 0. The .. (2) the matrix M = (GV)l. A unit cell characterized by the three shortest noncoplanar translations is called a Buerger cell. which uniquely describes the lattice:[41 is primitive and it is built on the shortest three noncoplanar lattice translations (the ~elauna~[~] reduction procedure is also a suitable tool for the identification of a crystal lattice: readers will find careful description of it in some recent papers["']).E.38b) ) ) ~ where ( u ~ is the meansquare displacement along the ith principal axis. for the example above.[92101 Several algorithms can be used to obtain it. a special cell exists.185 A respectively. The reader will easily find. v.. The easiest is: lattice vectors of magnitudes r.8). w vary over the smallest integers set (usually between 3 and 3). However. It would be worthwhile remembering two basic properties of the eigenvectors: (1) eigenvectors corresponding to different eigenvalues are orthogonal to each other.the Niggli reduced cell. Because of (2... Niggli reduced cell A unit cell defines the lattice: conversely any lattice may be described by means of several types of cell. that the rootmeansquare displacements along the principal axes are 0. Indeed. $ transforms into $' = VG$GV.Crystallographic computing 1 77 the following relations follow: ( ~ 2= ) ~ 2n2 A3 (2. called . according to (2.
If gij are the elements of the metric matrix. the triclinic lattice described by a Buerger cell with may be described by means of four other Buerger cells having the same a. y = 104'28'. For 7 of the 14 Bravais lattices a unique Buerger cell exists. however. if (Ig23l + Ig13l + Ig121) = 1/2(g1. P = 93'36'.. The main conditions define a cell based on the three shortest noncoplanar vectors. not unique: if it is.C. In other lattice types up to five types of Buerger cell can be found (the values 4 and 5 occur only in triclinic lattices) according to whether some conditions on the parameters of the conventional cell are satisfied or not. This cell is. but with a = 60°00'. c values.1= g h = gj3 = a2/2.[''] while in a face centred cubic lattice (see later) two Buerger cells can be found. +gZ2) then gll a 2 18131 + 18121. b. if lg131= 1/2gll then g12= 0. .1 we get g. y = 75'31'. Positive reduced cell (all the angles <90°). a = 117'57'. Negative reduced cell (all the angles 290').if g12= 1/2gll then g13 s 2g23. Main conditions: (b) if k231 = 1/2g22 then g12 = 0. /3 = 93'36'. y = 104'28'. if g13 = 1/2gll then g12s 2gZ3. If we move to the primitive cell by means of the transformation matrix g. if lglzl = 1/2gii then g13 = 0. y = 100'48'. conditions (b) define the Niggli cell when there is more than one symmetrically independent Buerger cell. Main conditions: Special conditions: (b) if gz3= 1/2gZ2then g126 2g13. If we move to the primitive unit cell by means of the appropriate matrix quoted in Table 2. the Niggli cell is defined by the following conditions:[129131 1. P = 100°48'. then it coincidesiwith the Niggli cell.78 1 Carmelo Giacovazzo smallest three noncoplanar translations will be the Buerger cell edges. As an example of systematic ambiguity let us consider the facecentred cubic lattice with cubic edge a. It will be shown later that only the first of the five cells is the Niggli cell. Conditions (a) break down ambiguity when two cell edges are equal. = gi3 = gi3 = a2/4. For example. a = 113'58'. P = 86'24'. 2. a = 120"001.
A 'very efficient algorithm to derive the Niggli cell from any [ ~~ primitive cell is described by Krivy and ~ r u b e r .PI + 1x12 . ~ ' ~ ] For any Bravais lattice ~ i g g l i [defined the algebraic relations that the gijs ~] of the reduced cell must satisfy. As an example let us consider the triclinic lattice defined by the primitive .max.Crystallographic computing 1 79 1(1/2 112 01 1/2 112 01 0 1 1 1/2 11211 then we get Both the primitive cells are Buerger cells but the second violates the conditions (a): thus the first is the Niggli reduced cell. These cells are checked against a suitable file containing as complete as possible a file containing crystallographic data (the NBS Crystal Data File handles data of more than 60 000 materials). and then to the Niggli cell. and that may be equal to or larger than the symmetry of the crystal structure. For example. The type of Bravais lattice may be thus derived from the Niggli cell just by comparing the found with the expected relations. Some auxiliary procedures recently suggested by different are less sensitive to these error sources. analysis of Laue symmetry and of systematic extinctions. An advisable sequence may be: a unit cell is determined.["] It would be worthwhile recalling that the lattice symmetry determined via the Niggli cell is only of metric nature. The use of automatic procedures devoted to identify the Niggli cell may yield incorrect conclusions as a consequence of errors in the cell parameters or of rounding errors in the calculations. 1 (2) 1x12 . Reduced cells may be used: As a useful step for the correct definition of the space group (see also Chapter 3). for the cells defined in (1). G r ~ b e r [has shown that a cell is a Niggli cell if and only if the following ~~] conditions are fulfilled: (1) a b c is a minimum when calculated for all primitive cells of the lattice. Matrices which derive Niggli cells from Buerger cells are given by Santoro and ~ i ~ h e l l . space group choice.yI lcos crl + lcos p1 lcos yI lcos cr cos p cos yl + + + . in a facecentred cubic lattice the gij of the Niggli cell must satisfy gll = g22= g33. analysis of the latttice symmetry. As an effective tool for the identification and characterization of crystalline materials['91(as an alternative to powder methods in which the identification is based on matching diffraction positions and intensities).a + 1x12 . the reduced cell is derived together with derivative supercells and subcells (derivative cells are calculated to overcome possible errors made by the experimentalist). gI2= g13 = g23 = g11/2. The final steps from the Niggli cell to the conventional cell may be performed by means of suitable transformation matrices. An advisable sequence may the following:[181from the conventional cell to a primitive cell. It could be asked now if Niggli cell expresses some geometrical property.
03". 2.434 A. with equivalent terminology. This cell satisfies the geometrical properties suggested by Gruber. (1) twinning by merohedry takes place only if a superlattice exists with symmetry higher than that of the crystal lattice (2) crystallographic phase transitions often take place between the structures for which one lattice is a superlattice of the other. b = 9. The cell in L' is related to the cell in L by A' = MA. 3. Let A= (B) and A' = (f:) be two triplets of noncoplanar vectors defining two primitive cells in two different lattices L and L' respectively. It should be noted that if L' is a sublattice of L then L'* is a superlattice of L*. Then L and L' will coincide. The superlattice then belongs to a subgroup of the parent structure: indeed increasing cell dimensions causes a loss of translational symmetry.80 1 Carmelo Giacovazzo cell The Niggli cell is obtained from the previous one by application of the matrix 001/100/111: a = 8. y = 110.562 A. (2. /3 = lO6. Then A' defines a new lattice L' called a superlattice of L whose elementary cell is M times larger than the primitive cell in L.and sublattices are frequently related to important properties of the crystals. The knowledge of the possible superlattices of a given lattice limits the set of possible structures of a new phase. 4. In this case A = QA' and L is a superlattice of L'.97".39) Consider four important cases: 1. L' is a sublattice of L. or. That is of particular usefulness when the phases are simultaneously present in a polycrystalline sample and . c = 12. M is a rational matrix.070 A. M = QI where Q is a matrix with integer elements for which Q > 1. For example. Super.54". Sublattices and superlattices The term superlattice is commonly used for a structure closely related to a parent structure and having cell dimensions superior to that of the parent structure. The miis are integers and M > 1. The mii elements are integers and M = 1. a = 100. This case is described in the following subsection.
1 81 diffraction peaks having identical positions are generated.F. magnetic structures are based on cells often larger than those of the corresponding conventional chemical structure (see Figs. Consider two lattices L and L' with bases A and A'. 1.3.F. The energy of a polycrystal is higher than that of a single crystal with the same mass: the additional energy is stored in the grain boundary areas. = N''N is a matrix with rational elements.231 factorization of Xc of the a . 113 are obtained by applying the same matrices to the reciprocal lattice and then by calculating the lattices that are reciprocal to the resulting superlattices. In this case the CSL is defined as that superlattice (at 1 or 2 or 3 dimensions) of L and L' which contains all (and only) the lattice points incommon to L and L'. The lattices L and L' will have a common superlattice if a lattice point of L (defined by NA) can be found which is also a lattice point of L' (defined by N'A'): then NA = N'A'.3). In particular.2 and 1. Without loss of generality it will be assumed that the two lattices have one lattice point in common. Let N and N' be two matrices with integer elements. The unique matrices generating sublattices for M = 112.Crystallographic computing Table 2. To determine the CSL one has to find[22. Coincidencesite lattices Most materials of technological interest are used in their polycrystalline form. if an orderdisorder transformation occurs. Note that several other lattices could be defined having points in common with L and L' but all of them will be superlattices of the CSL. The mathematical model of the crystalline interfaces is today based on the properties of coincidencesite lattice (CSL) and related lattices.3 the unique matrices M are given generating superlattices for M = 2. taken as the origin of the coordinate systems. and depends on the orientations of the neighbouring grains. Their mechanical and chemical properties are controlled to a large extent by the boundary between crystallites. the ordered phase is characterized by a cell larger than that of the disordered phase.[^^] This number quickly gets large with M: in Table 2. Thus modern treatment of these materials tend to optimize the size of the grains and quality of the grain boundaries. For any value of M there is a finite number of matrices M that produce distinct super lattice^. or also where X. 3.
The DSC may be determined by means of a factorization similar to that used for X. The ratio between the volume of the CSL unit cell and the volume V of the crystal unit cell is called the multiplicity of the CSL and is denoted by Z (the analogous ratio for the DSC cell will be 1/Z). where u and u' are vectors of L and L' respectively.[251 With respect to the energy of the grain boundaries DSC lattices have the same importance as CSL: indeed translations by DSC vectors do not destroy the coincidence sites. then the boundary energy per unit area will be a minimum. Analogously.I A I or also A' = XdA. Such vectors are the geometrically possible Burgers vectors (energy considerations will dictate the most probable of them) of dislocations in grain boundaries. is the DSC lattice. The problem may ~e~a [ ~ r.40) Several attempts have been made to find the general solution of (2. where Xd= N'NI is a matrix with rational elements. The determination of all possible coincidence orientations with low values of Z is an important premise for the understanding of grain boundaries.82 1 Carmelo Giacovazzo type X. In this case the displacementshiftcomplete lattice (DSC) is defined as the sublattice with the largest volume of the primitive cell. It may be shown that in cubic lattices a CSL is obtained by a rotation 8 about an axis [uvw] coincident with a lattice direction if tan (812) = (u2 + v2 + ~ ~ ) l ' ~ / r n . The coarsest lattice which contains all vectors of the form u + u'. Special methods for the solution of this problem were developed for c u b i ~ . and the CSL basis will be NoA = N S ' . G' = XGX. [ ~ h . It may be also shown that: 1. then. owing to (2. If No and N satisfy such a factorization process then the DSC basis will be h NilA = NA'A'.21). two lattices L and L' will have a common sublattice if two matrices N and N' (with integer elements) can be found such that NIA = N I .40). ~ b ~~] be so stated: determine all the rotation angles 8 about a given lattice axis [UVW] which generate CSLs. which defines a cell with volume l/No times the volumes of the cell defined by A and 1/NA times the volume defined by A'. = N''N with the smallest possible values of N and N'. If the two lattices L and L' are congruent then one can be transformed into the other by means of a rotation: this is called coincidence rotation if L and L' have a CSL in common. All lattices which are sublattices of both L and L' will be sublattices of DSC. If N or N' are sufficiently small (a large fraction of points of one of the two lattices consists of coincidence sites) and if the boundary coincides with a dense net plane of CSL.[241 2. If A' = XA defines one of the required orientations. and ~ h ~ m ] o h e d r a l [lattices. If No and NI. satisfy this condition then No and N indicate the reciprocal fraction of A coincidence points (degree of coincidence) in lattices L and L' respectively. The CSL (DSC) of the reciprocal lattices is the reciprocal lattice of the DSC (CSL) of the two lattices. (2.: again we will look for the smallest possible values of N and N'. ~ ' ] ~ o n a l .
5. 1 83 I:= Twins Twins are regular aggregates consisting of individual crystals of the same species joined together i i some definite mutual orientation. If the twinning operations relating adjacent components are all identical then the twins are known as lamellar or polysynthetic twins (the components have a lamellar form parallel to the composition plane). I: = 5. It may easily be seen from the figure that the volume of the CSL unit cell is f o r m ~ d the vectors [210]. Polysynthetic twins may be on a microscopic or macroscopic scale. v. 2n/3 also occur but are less common. tetrad. n12. The operation is very frequently a rotation through n about a zone axis (in this case the axis is the twin axis and the twin is a rotation twin). u. when a higher symmetry crystal is cooled and converts to a lower symmetry structure). Denoting by N the number of odd integers among m. Supplementary information on the most common types of twin and some i Fig. w. w may be chosen withoyf restricting generality. by In Fig. Obviously diad. a = 2 if N = 2. 8 = 36'52'. If a triad is a twin axis the twinning operation may be equivalently described as a n/3. or hexad axes cannot be considered twin axes (at least for rotation through n). u.. Rotation twins of n/3. The black and the crosslike points belong to lattices 1 and 2 respectively. n. in reflection twins the composition plane is parallel to the twin plane. or 4n/3 rotation about the axis: conventionally the n rotation is preferred. The lattice direction [OOl] has been chosen as the rotgion axis: if we choose m = 3 then N = 2. If lattice 1 is shifted by a DSC unit with respect to latticg 2 the pattern shown in the figure is reproduced in another position. The CSL pgints are those on which crosslike and black points overlap. a = 4 if N = 4. There are three principal types of twin: growth twins (produced by accident as the crystal grows from its initial nucleus).21").Crystallographic computing where m is an integer. or a reflection in a lattice plane called the twin plane (the . [120]. for . Black and crosslike points are both part of the DSC lattice. (b): CSL i c and ~ s ~ j a t t i c e s the cubic (111) plane. twin is then a reflectipn'twin). Multiple twins consist of three or more components. [OOl]. 2. 3. In interpenetrating twins the twin c~mponentsintergrow so as to generate an irregular interface between components. (a): 6SL lattice and CSL unit cell for a rotatiop of a ~ ~ blanice about I0011. 2. a = 2.5(a). An example is illustrated in Fig. 2. and transformation twins (the product of a polymorphic transformation. whose units are evidently smaller than crystal units. A unitary greatest common divisor among m. i. A twin is called a contact twin if the two components are joined in a plane (known as fhe composition plane). From a geometrical p ~ i n of view a twin is characterized by the symmetry t operations which relate one individual to the other individuals in the composite crystal.5(b) the CSL with I: = 7 is shown for the cubic (111) plane ( 8 = 38.e.* . the multiplicity I: is given by m2+u2+v2+w2 a where a = 1 if N = 1. deformation twins (considered as a means of relieving the strain in$uced by some applied stress). v. In the case of a rotation twin the composition plane is parallel to the twin axis.
sufficiently dense. Friedel).5. (1)M will correspond to a reflection in the plane (hkl) normal to [uvw].40). The twin lattice is the lattice with the smallest cell that is common to both (or to all) individuals of the twin. The slight deviation. A recent classification[319321 divides the twin kingdom into two species. if a = 180°.41). and is usually less than 6". n: n = (vol. per node in twin lattice)/(vol. For n > 1 the twin lattice is a superlattice of the crystal lattice (see CSL in previous subsection). Such a lattice will show perfect continuity at the composition surface of the twin in case of TLS. for n = 1 the twin lattice coincides with the crystal lattice. for any twin rotation through a about the direction [uvw] there should exist a twin operation which is the combination of M and of the inversion of the lattice. Mallard. Obviously only matrices with M = 1 have to be considered: furthermore symmetry operators M must also be excluded since they are trivial solutions of (2. per node in crystal lattice). we are interested in the characterization of the twins in terms of lattice geometry. According to ~ r i e d e l [ twinning ~~] may occur because of the accidental presence in a lattice of a net and a row. in minerals. Twins are usually classified in accordance with the (preXray) theory developed by the French crystallographic school (Bravais. and their presence may be indicated by a high irreducible residual R in the attempted crystal structure determination. TLS twins with n > 1 are often found in highly symmetrical lattices. The twin law specifies the mutual orientation of the two twinned crystals: it is usually expressed in terms of the rotation necessary to bring one of the lattices into coincidence with the other. and may be so expressed:[341 crystal may twin if the condition is satisfied where M is a matrix with rational coefficients'. If M satisfies (2. giving rise to double or multiple diffraction spots: they are generally recognizable simply by optical observations. TLQS and TLS. is referred to as the twin obliquity w .84 1 Carmelo Giacovazzo morphological details are given in Appendix 2. TLS (twinlattice symmetry) twins show a single orientation of the reciprocal lattice so that they give rise to single diffraction spots: they are optically indistinguishable.41) M = (1)M also satisfies (2. which are exactly or approximately perpendicular. Friedel's necessary (but not sufficient) condition for twinning in triclinic lattices (specialized conditions can be found for the other lattice types) is that g11:g22:g33:g12:g13:g23 are. For example. and will suffer some deviation for TLQS twins. TLQS (twinlattice quasisymmetry) twins are characterized by two or more reciprocal lattices differently oriented. Here. for example. Friedel's rule may be obtained by 'a requiring G' = G in (2. or approach rational numbers.41): therefore. expressed in degrees. Occurrence of TLQS mostly depends on special relationships between cell parameters while the existence of TLS depend on the symmetry properties of the lattice. . A further criterion for subdividing twins is the twin index.
97) is impossible. four. In order to explain their diffraction behaviour. Twins in class I1 are characterized from the fact that the Laue symmetry of the crystal is lower than the crystal lattice symmetry. Structure determination is therefore not hindered but the determination of the absolute configurations (using the methods described on p.7. 2. they may be divided into two classes:[35] Twins in class I show the same crystal Laue symmetry as the lattice symmetry. Twins by hemiedry.7(a) the projection along the b axis of a monoclinic lattice with P = 90" is shown. In Fig. A scheme for twin classification is drawn in Fig. merohedrical twins have one or more symmetry operations which are present in the lattice and not in the crystal. except for anomalous scattering.6. Then at least one of the twin operations belongs to the lattice symmetry but not to the Laue symmetry of the crystal.classII Im Fig. and ogdohedry can be found: they are made by two. with that which would be measured on a single crystal. . ~~stwins TWINS nyy yy twins class I /\ class II Fig. n (wO") 1 . A scheme for the classification o f twins. 2. and eight crystals respectively. TLS. Accordingly. TLQS.7 some examples of twinning are collected. n =l. n=l(oiO"). 2. but we could also choose the mirror plane perpendicular to c ) . The o misfit is intentionally exaggerated. 2. Examples of twins (from reference 1361). tetartohedry. They were called by Friedel twins by merohedry since the crystal symmetry is merohedry of order n (subgroup of order n ) of the symmetry of its lattice. Then the twin operation belongs to the Laue symmetry of the crystal: in these conditions the set of intensities collected from the twin coincides. 2. together with its twinned lattice (the assumed twin operation is the mirror plane m perpendicular to a .Crystallographic computing 1 85 Twins of special interest are TLS twins with n = 1.[361 In Fig. TLQS.6.
2[100]. 2.E). g.[371 Denote by H and G the pointgroup symmetry of the crystal and the point group of its lattice respectively (G may be obtained by the process of cell reduction). b = 6. c = 5.6foo11.. Brazil. /3 = 99. The diffraction pattern will show then R3m symmetry.1]H) U ( W U ( ~ [ 0 0 1 . 1.. It may be seen that 2. The coset decomposition is therefore G = H U (2[.3[ooil. E G. (&El). The twin lattice unit cell is defined by a ' = 2a. two individuals) two reflections which are not equivalent by Laue symmetry contribute to a twin reflection:[381 then IFtn12 = a IFHl2 (1 . ~ ) . P' = /3 (but also a Bcentred orthohombic cell may be chosen.]. The same procedure.913 and c = 5. The twinrelated reflections are therefore (hkl). 2[ziol. In Fig.142. aquartz crystallizes in P3121 with a = 4. applied to a crystal with point group H = 4/m. operations (g. while a * is the common reciprocal lattice of the two lattices. (hki). the coset decomposition of G with respect to H may be made (see Appendix l. If the space group of the crystal is supposed to be ~ 3a TLS twin of .404 A.2[im]. 2.a ) lFHI2 a IFKI2 + ..2[iiol. 2. 2[110]. 2[nol.2[010]). In the case of hemiedry (twins in class 11. 2[1zol. referred by the twin operation (111) mirror plane. 2. 2pm1.a)IFKI2 + IFMI' = (1 .2[orol.3fhi1) {H.982. and therefore will contain the possible merohedral twin laws for a crystal of point symmetry H in a lattice of point symmetry G.7(c) the projection of a hexagonal lattice along the c axis is shown. four times larger than the original cell). 4 H) used for the (left) coset decomposition will lead to the superposition of the lattice onto itself.86 1 Carmelo Giacovazzo In Fig.7(b) the projection along the b axis of the monoclinic lattice of 1aspartic acid with a = 7. ~f0011. For example. are viewed along the direction [i10]. ~[Ool].7(d) the classical penetration twin of fluorite (CaF.6[m1]. and combined twinning respectively. Hence the twinrelated reflections are (hkl) and (&kt). Two cubic lattices.2[z101:3pmI. The twin lattice has a volume three times the volume of the original cell.1101. class I1 may be generated by reflection with respect to the plane m drawn in the figure. 3&. b' = b. In Fig.84" is shown: the lattice is also shown after a twofold rotation about the a " axis. An elegant derivation of twin laws by merohedry has been recently proposed. (&El). Any system of g. I and for DauphinC. z[lio]. 40011.617. correspond to the classical twin laws .) is described. Since H is a subgroup of G. c' = c. will decompose the metric symmetry group G = 4/mmm into G = H U (2[010]H). It is easily seen that 2a of the original lattice nearly coincides with 2ac of the rotated lattice. The crystal point group is 321 and the metric symmetry is 6/mmm: thus H G (1.
X. + Ts) = exp (Apis~)sin 2n H(R.E. s = 1.. Accordingly. An alternative procedure may be that of 'detwinning' reflection data: i. .H) cos 2n H(R. . The calculation of (2. the total number of symmetry operators) of the space group and t the number of symmetryindependent atoms.8)) H~. nj is the occupation number of atom j. and IFKI2 be calculated from observed IF. The structure factor may be then written as (see notation on pp.X. If the jth site is only partially occupied because of some statistical disorder then nj will be proportionally reduced. (2.^^ and IF.e.. . < 1 for atoms in special positions (the use of nj allows that summation over s is always extended from 1 to m. where mi is the number of different atomic positions which are symmetry equivalent to the jth atom. pis is the 3 X 3 temperature factor matrix for the atom j in symmetry position s. defined as mjlm.) = j=1 t x f A. nj = 1 for an atom in a general position. However.Crystallographic computing 1 87 where IF. and IFH12# 1FKI2are the intensities of the two overlapping reflections.^^ and 1FtKI2 twin reflection intensities. .5. m are calculated. j= 1 Aj and Bj are the contributions of the jth atom and of its symmetry equivalents to AH and BH respectively.36)) HR. and (see eqn (2. may be replaced by H.^^ according to can Previous knowledge of a is a necessary condition for the application of the above formulae: these cannot be applied if a = 0. n.X.42) will be simpler if. The algebraic relation between H and K is fixed by the twinning law.42a) (2.x.. alternative methods are available for such a specific case (see [36] and references quoted therein). T. Calculation of t h e structure factor Let m be the order (i. = HR. .e. a is the volyme are fraction of crystal 1. for a given H the symmetry equivalent indices H. A trial estimate of a may be obtained via suitable statistical tests on diffraction data:[3g411 may then be refined as an extra a parameter in adapted crystallographic leastsquares programs. independently of the atomic site type).524) where AH = BH= j=1 j=1 f x f njfoj(H) n. In this case (see eqn (3.foi(H) s=l m s=l x x m exp (H&. 1.42b) + B..H by As ~ j h .
Indeed. sin2 8/A2] + C. For space groups with centred unit cell s may vary only over the matrices not referred by nonprimitive lattice translations: AH and BH are then multiplied by the centring order of the cell.44) for every X.) sin 2 n (H..H.44) are then limited to the set of values. if the space group is centrosymmetric (origin on a centre of symmetry). For example.)] j=l For each j the maximum number of ujs (and vjs) to calculate is 24.46) we have to calculate p(x. The calculations may be performed in a trivial fashion starting from the list of symmetry independent Fhkl. in Pmmm independent Fhkl . 4 It should be noted that only nine parameters have to be stored for each element. (2. y . A more usual procedure is to approximate scattering factors by the sum of one or more Gaussian functions: for accurate structure factor calculations four Gaussians are used according to 1431 fo(8) = i=l C a. AH is then multiplied by 2 and BH is settled to zero (origin on a centre of symmetry).~.at the actual sin 8/A value may be obtained from the tables by interpolation. The summations in (2. s may vary only over the symmetry matrices not referred by the inversion centre. have been tabulated[421for all elements: their accuracy depends on the wave functions and on the numerical methods used. The crystal symmetry may be more conveniently exploited by combining in advance the terms containing the symmetrical structure factors. The values of fg. thus obtaining an expression valid for that given symmetry.li.88 1 Carmelo Giacovazzo We will then write eqns (2.x. Calculation of the electron density function According to (3.~. + AT.p. generating symmetry equivalents. Scattering factors f.)cos 2 n (HsXj + ATs)] f m s=l BH= C t [Cnj$(H) s=l m exp (A. r ) = 2/V + 2 2' 2' [AHcos 2 n ~ X BH sin Z ~ H X ] . and evaluating the sum in (2..44) where the prime to the summation implies that only half of the reflections (0. k. exp [b. 1) have to be considered.42) as AH = j=l C [ c njfhi(H) exp (.
.
The p values observed at 19 grid points (see Fig. The m e t h o d of least squares Linear least squares A very common problem found in physical sciences is the following: given a set of experimental observations ( 5 ) and a theoretical model which. A further reduction in the number of operations is obtained if the fast Fourier transform[441(FFT) algorithm is used.1). and R(xyz) can replace T(hyz) at the end of the process. . A typical process for locating maxima involves two stages: 1.. after its completion. Then the position of the maximum is obtained from the conditions 6p/6x = 6p/6y = 6 p / & = 0. 1 are obtained which minimize C19 (In p. Fig.44) the work to do is of the order n6 (say nhnknlnxnynz. involved and.In p. Six of these points are nearest neighbours.90 1 Carmelo Giacovazzo Then 1 p(x. By least squares the ten values a.J2 (nine degrees of freedom are retained). within every transform a single line of Fhk. 2. estimate their accuracy. large values of n the BeeversLipson technique makes a considerable is saving.8. find the values of parameters which give the best fit to the data.. etc. are stored. The 19 grid points used for peak search routines.8). . . . centred on that point for which p is largest. . The saving of the computer time may be so described: a onedimensional transform with n values of h and x requires n2 operations. while the FFT technique reduces this to 2n log. the line is no longer necessary: thus S(hkz) can values after the first transform. generates a set of calculated f values. and comment on the adequacy of the assumed model. Furthermore. The technique factorizes onedimensional into twodimensional transforms by a procedure quite similar to that of Beevers and Lipson (see Appendix 2. y) Z) = Vh=0 x " [COS 2nhxTl(hkz) + sin 2nhxT2(hyz)] which is again a onedimensional transform for fixed y and z : R(xyz) = x h T(hyz) exp (2nihx). . .44)? If p is calculated directly from (2. Why is this procedure preferable to the direct use of (2.. The saving is not impressive for n < 16 but becomes large for larger values of n (as in protein crystallography). if the BeeversLipson technique is used the work for the three + Thus for transforms is of the order n 4 (say nhnknlnz+ nhnknynz nhnxnyrtz). so it could be fitted by the function p(xyz) = exp (a + bx + cy + dz + ex2 +fy2 + gz2 + hyz + kzx + lxy). T(hyz) replace the corresponding set of Fhkl can replace S(hkz) after the second transform.. 2.where nh is written for the number of different h values. 2. from trial values of some parameters. n. . The full peak is expected to be Gaussian in shape. Electron density maps are usually not printed: frequently peak search routines are used to locate electron density maxima and to print their list in order of peak intensity.). There are . and twelve are next nearest neighbours.
. equal variances) was treated by Gauss who showed that. Suppose that a set of n experimental observations F(fljf2. . We will assume that errors e. the most satisfactory was that (say A) for which the residual where v  s= i=l x v? = w = minimum (v.fn) h is subjected to some random error e.. .e. . . . The case Mf = I (uncorrelated errors. The condition n > m emphasizes the fact that the parameters are overdetermined. estimates of the variances of such estimates. . due to the finite precision of the measurement process. m columns) of rank m which is assumed to be known.).fy)2 = n n i=l = VMT'V = minimum (2. and E = (el. among the various X. the most satisfactory estimate 2 is that for which the weighted deviance S= i=l 2 wiv?= x wi(A . Alternative approaches are briefly mentioned on pp. (2. .F")) is the variancecovariance matrix of rank n. This result suggests that..Crystallographic computing 1 91 several approaches for answering this problem. . v2. is available for which: (1) (2) . . Because of its wide use in crystallography we will mostly be interested in the method of least squares. vn) is given by V=FAX. x2. Then the observational equations may be written[451 as where A = {aii) is the n x m design matrix (n rows. when Mf is a diagonal matrix with elements (in this case errors on h and fi are statistically independent and pii = 0 for i # j). and where pii are the correlation coefficients. at the same time. . X. .48) ( F ) =F"=Ax where Mf = ((F . 4 X' is known to linearly depend on a set of m S n parameters (xl. have joint distributions with zero means and finite second moments: i. . en). e2. Our problem is to obtain satisfactory estimates g of the parameters X and...51a) where wi = 1/o?.F")(F . 1089.
Nf. unknown.57) M.56) If Mf is known within the scale factor K. Substituting K.53) the leastsquares estimate of X is obtained as It may be easily seen that 8 is independent of the scale of the covariance matrix.51b) In most applications Mf is taken to be diagonal. (2. for a general variancecovariance matrix. (Mf = K.H) an unbiased estimate of K. is given by k. where Nf (the working matrix) is known and K. Reliability of the parameter estimates It may be shown (see Appendix 2.54) B is a m x m symmetrical (bij = bji) square matrix. is available from the leastsquare treatment: so that the unbiased estimate of M. relative to the unbiased estimate 8 is given by M. is known: luckily (see Appendix 2.+.52) In accordance with Appendix 2. the most satisfactory solution 8 is given by S = bMTIV = minimum.52) leads to the so called normal equations B ~ = D (2. is completely determined only if K.. 'V = minimum. From (2.Nf) then where B. the relation (2.F. = ((8 .51) suggest that. is often called goodness of fit and denoted by GofF Linear least squares with constraints Assume that the parameters xi are not independent but are constrained to satisfy the set of b linear equations OX = Z (2. Relations (2.x ) ( ~ ) X ) ) = B .92 1 Carmelo Giacovazzo If Mf is not diagonal then = \iWV = bM.~A.Nf for Mf in (2. (2. (2.55) eliminates K. (2. is the working matrix calculated via the known Nf matrix.~ .60) . Indeed suppose that Mf = K.G) that the variancecovariance matrix M.53) where B = AM. According to (2. D = AM.
which is larger (see Appendix 2. +~lQ(~elQ)l(z 02)  (2. . shown that the expected value of the weighted deviance S is given by (3.'SV  . Eliminating I in (2. = (n .62) gives X =2 .p=l &j6~p +. 2. according to (2.f. xi.H it may be . Examples of local minima for the residual S. and Z is a column vector with b components. unless a good approximation S XO = (x: . . In this case the unbiased estimate of X may be obtained by considering the variation function S = V M ~ ~ 2X(QX .B~Q(QB~Q)~QB~.2 ) = 2(F . (2.60) is satisfied: l by X = (zKGR)(QB'Q)'.Z) . 2j.62) by B and~ requiring that (2. we obtain F M ~ A X A M ~ ~ A = 0. V where I is a column vector with b components (the Lagrange multipliers). To this aim each may be expanded : ) in a Taylor series about the point XO: +' 2 () parameters 6" 6 .51) will not usually provide a satisfactory 4 estimate for the parameters.AX)M. . . Then the residual S will have several local minima (see Fig. is (Bl is the variancecovariance for X) M = B1 .64) By a procedure analogous to that described in Appendix 2. XQ + Calling the solution X. may be written as X =X a B (.H) than the expected value of the unconstrained residual (3) = (VN'V) = (n .2XQ6X = 0.Crystallographic computing 1 93 where Q is a b m matrix of rank b. ).rn + b)lK. The value of I may be obtained by postmultiplying both sides of (2..~ ~ .) do not linearly depend on the X parameters. (2. .63) The variancecovariance matrix for X. . ~ ~ 6. Nonlinear (unconstrained) least squares Let us suppose that the observations F = (fl. The condition 6s" = 0 brings to 2 V M 7 ' 6 ~ 2X(Qx . x of X is available.65) Fig. . .9) and condition (2. Since 6V = A6X. . 2.9. gives which.m)lK.55).) = (VN~V)/K. . .
If the Taylor expansion is valid. AA will not be an unbiased estimate of AX. by taking into account two different situations: 1. To carry out leastsquares refinement of a crystal structure let us associate . according to which the new parameters X = X0 A 2 are used as a new starting model for the application of (2.s (structure factors moduli calculated from the structural model) and the IFHlos. it is described in the following. A large number of moduli JFHJo measured.65) (GaussNewton approximation) to get where derivatives are calculated in XO. Parameters are then refined in order to minimize the difference between the IFHl. 322).and In matrix notation where is the design matrix (compare (2. the problem has been reduced to a linear one: thus an estimate for AX. + + Leastsquares refinement of crystal structures Leastsquares techniques are widely applied in crystallography. and that the refinement of the parameters has been completed. 300). from which more satisfactory values X = X0 A% may be derived.94 1 Carmelo Giacovazzo If X is sufficiently close to X0 second and upper derivatives can be dropped in (2. 10917. Therefore for nonlinear problems an iterative procedure must be followed. The iterative process will continue until the changes A% are very small or zero: then it may be concluded that the leastsquares procedure has converged. are 2. The Rietveld technique for the analysis of powder diffraction data. Since in (2. In the following we will describe the application of leastsquares techniques to crystal structure refinement. say A% will be obtained in the same way as described in the previous paragraphs. thermal motion analysis (pp.47)). calculation of the Wilson plot (p. 10917). 74). 11720).66) second and upper derivatives have been ignored. calculation of least squares planes for molecular fragments (p.This technique is of general use for singlecrystal data and of remarkable usefulness also for powder data. Mf can still be considered as the variancecovariance matrix of AF if X0 is a good starting model.66): in each cycle the derivatives will have changed so that the design matrix has to be recalculated.66) with (2. and profile analysis in powder methods (pp. We will describe this technique on pp. point by point: the model parameters are then adjusted by the leastsquares method. Examples are: refinement of unit cell parameters from diffraction angles (see p. The entire diffraction profile is calculated and compared with the observed step profile.
.51). we expand in a Taylor series: then which. .} = {CwH[1FHIo lFH.55)) A% = BW1D provides the required solution. its is derivatives are also calculated in XO. in accordance with (2.Crystallographic computing 1 95 a weight wHto each IFHI.54)) for j = I . We have denoted IFH.Thus eqn (2. may be written as S = (AF ..lc the modulus of the ith structure factor calculated in XO. more explicitly. BAA=D or. rn.53) and (2.Then.^ AF = MT'AAF = {d.A AX) = W V = VMY'V. where D= AM. for each atom. The normal equations may be obtained by settling to zero the derivatives of S with respect to AX: a lFHlc =o axi In matrix form (see eqns (2. . . a parameter defining chirality in noncentrosymmetric space groups. thermal parameters (1 for . up to three coordinates (fewer if the atom is on a special position).A AX)W(AF . Parameters usually refined are: are overall scale factor (observed intensities are usually on an arbitrary scale).llc] lFHl H 1. we want to make minimum the quantity According to the previous subsection if a satisfactory model X0 is available.51b).66) is again obtained. according to (2. dxi Then (compare with (2.
.the second derivative of S with respect to K = is zero: therefore K is the parameter which converges faster. pi339 pi129 p j 1 3 ) p j 2 3 ) ) then 6A 6 Bi =cos g..)/6K IFH(.axji sxji where A . v are defined by eqns (2.swill be multiplied by 1 / K in order to lead them on the absolute scale.. The IFH(. xi. in increasing order of i we will refer to n. if we erroneously had chosen to minimize S'= .+ sin g. i = 1 .ZH w H ( K(FHIO  . are the contributions of the jth atom to A H and BH respectively. Then For isotropic motion (Q denotes here the thermal factor.20)). the site occupancy if the atomic position is statistically occupied because of some structural disorder. xji is the component UGq of the vibrational tensor U. z.. Therefore from which the following estimate for K is obtained Then the IFHJ.96 ( Carmelo Giacovazzo isotropic motion. Let us now calculate the explicit expressions of the derivatives for the various parameters. (see eqn (3. in order to avoid confusion with the normal matrix B) 3 .e. zit B. Consider the various cases: 1. p j 2 2 . p j l l . If xii is the ith parameter of the jth atom (i. Since 6 ( K IFH(. and B. 2 . y. xi. xji is an atomic coordinate: then where hi. or n. 2 . yi.43). Even if (FHJc on the absolute scale are and (FHIO a relative one.. and u. It should be noted that. up to 6 for anisotropic). xji is the overall scale factor K .so rescaled will work as observations in subsequent cycles of least squares.. 3 are the components of H. during a leastsquares refinement it is the on structural model which has to be refined and not vice versa.
An efficient way for determining the absolute configuration is based on measurement of the intensities of the Bijvoet pairs of reflections (see pp. 6. Then 5. In this case . with a readily computable precision a(q)/q. Thus Bijvoet pairs (h k I) and ( h k I) can be used for the assignment of chirality.the minimum could be found at K = 0 and with an extremely large thermal motion. A very efficient alternative procedure[47] considers the crystal as an inversion twin: I F ~ ( X= ~ ~x) ( ~ ~ 1+' x IF^^' ) (1 where (1 . e r s [ ~ ~ ] suggested a better procedure: a single leastsquares variable who q is introduced into every dispersion term (iqfy instead of $7) that contributes to the structure factor.gzo1l. While primary extinction is often negligible in singlecrystal studies. where N is the number of degrees of freedom (see p.symmetry equivalents have an intensity value different from that of. the effects of seconstw~extinction are usually corrected by means of the equation (Z0)corr = Zo(1 .88) : for the meaning of R). q is kept zero in the early stages of refinement: later it should converge to values close to 1 or 1. say R and R. where it is replaced by[4s501 (1c)corr = & ( I +gZc)l. 4. it cannot be directly used in leastsquares procedures.indeed (h k 1) and its. xji is the atomic occupancy factor. By merely reversing the signs of all the ifl' two R values are obtained (see eqn (5. In this case the symmetry of IFIo in reciprocal space degrades from Laue to the true pointgroup symmetry. For a given value of T one looks up Hamilton's tables R (1.. 103). The parameter x is refined: usually it converges in a few cycles to the final value. 164). More often only the asymmetric set of reflections is collected: then chirality may be fixed by the following procedure: (a) the structure is solved and refined by using real atomic scattering factors (and preferably absorptioncorrected data). (b) the final values of scale factor. Since this equation corrects observed quantities. (c) the ratio T = RJR: is used in the Hamilton test (the unweighted ratio R/R+ is usually regarded as an acceptable approximation).(h k 1) reflection and its equivalents. Reasons for considering the ratio test overoptimistic were given by ~ o . a ) to estimate a. coordinates.Crystallographic computing 1 97 IFH1c)2. is a parameter defining chirality in noncentrosymmetry space groups. and thermal factors are kept intact to calculate structure factors. xii is the secondary extinction parameter g (see p.x) and x are the fractions of the structure and its inverse in the macroscopic sample. . xi. N. 1659) when dispersion effects occur.
= f1 refers to two completely dependent parameters.98 1 Carmelo Giacovazzo where L is the Lorentz factor.' by $I($) in order to obtain M.' 3 = H K1> " where bcl is the ith diagonal element of B. If they are sufficiently small. = b. ' I ' 11 I1 pi.85) the goodness of fit ratio $I($) (see also eqn (5. Generally speaking. owing to the presence of systematic errors very often the working matrix Nf experimentally available is referred to Mf by an unpredictable relation much more complex than a scaling factor. According to eqn (2. = A N ~ ~ from which variance and covariance values for the A. pi. can range from 0 to f1: as a rule. Correlation coefficients between two parameters are given by 6 m).Nf): then A% will be insensitive to the scale factor K. In these cases the technique of multiplying the working variancecovariance matrix B. for the estimated parameters will strongly depend on it. Suppose now that Nf is known instead of Mf (= K../(b.1 nm mx = &B. an overall scale factor. may be highly questionable. the refinement process may be considered complete if the ratios (calculated shiftslstandard deviations) are sufficiently small (e.59) ($) nm where B. parameters may be calculated. pI.20. Then a square matrix B of order 361.. Practical considerations on crystallographic least squares Crystallographic leastsquares refinement may not be a trivial task.3) and (5. The standard deviations of the parameters are a useful guide during the refinement process. pi. for a structure of modest complexity (40 atoms in the asymmetric unit). The computing time .20. one of which has to be eliminated. s 0. P a suitable polarization factor.86)) should be also reported in publications as a global measure of fit. each one constituted by a summation on thousants of terms. for a total of 361 parameters. A report[511 of the International Union of Crystallography Subcommittee suggests that besides indices R or R.b. and 240 anisotropic thermal parameters should be refined. 120 positional.3 are frequent. less than 0.. with m = 361 x 36012 = 64 980 distinct elements will arise. Suppose that. while the matrix M.g. and K the scale factor.3).'=B.'.. In particular the variance of the es'timated parameters is given by C WH(AFH)~ oii= (bii). It is easily seen that increasing the number of observations reduces the variance of the parameters ((bii)' and n are mutually related in an inverse fashion so that the standard varies as If the quality of the data is improved then deviation WH = 1/ah will increase: since (bii)' varies inversely with w it follows that standard deviations of the parameters are proportional to a. n = 4000 reflections have been measured.)112. As already stressed.. as given in eqns (5.
(3) a high correlation will be found among the site occupancy and temperature factors if they are contemporaneously refined. That produces A. Thus the major advantage of the method is the lessened storage requirements for problems too large to be treated by a full matrix. A scheme for blockdiagonal approximation. or. . . . If an error A. but this is often unrealistic. = A. An alternative to the diagonal approximation is the blockdiagonal approximation. along the line yo A y = const. For example: (1) errors in the thermal parameters generate a systematic error (larger to high sin 8 / A ) on IF[. a block for all positional parameters and a block for all vibrational parameters with the overall scale factor. the 'best' value for x i s obtained by minimizing. 2. Indeed an error on a coordinate is compensated by errors on some other coordinates (see Fig. Each refinement cycle is faster. are 9 x 9 matrices comprising positional and anisotropic temperature factors (a 4 x 4 matrix for an isotropic atom).. but convergence is slower: so the complete refinement process requires more cycles and almost the same computing time. . nonnegligible correlations between some coordinates of the same atom may be found. or. is introduced. yo) is the true atomic position.g. one for each atom. the offdiagonal elements are sums of products which may be positive or negative. all the atoms in the same molecule could belong to the same block. The storage requirement for the block diagonal approximation is certainly smaller than for full matrix methods.11. Larger blocks are sometimes used. e. 2. That is equivalent to assuming a complete statistical independence among the parameters. computing time and storage rapidly increase with the complexity of the structure. A very large saving of computer time has been recently achieved by Fig.11. 2. + Fig.which on its turn produces a bias into the estimate of the scale factor K. The matrix B will then appear as in Fig. On the contrary.Crystallographic computing (Cpu) and the storage (St) needed for a 'structure factor calculationleastsquares refinement' cycle will comply with the following table: Step Cpu St 1 99 Calculate structure factors Calculate derivatives Calculate normal matrix Invert matrix Calculate shifts AX nrn nrn nrn2 m3 rn n rn rn(m + 1112 In accordance with the above table. therefore they are generally expected to be smaller than diagonal elements. P(xo. so that they are always positive and rather large.10). cos y. Accordingly computer storage and computing time may be reduced by setting all offdiagonal elements to zero (diagonalleastsquares approximation). the distance of the atom from the true position P. 2. also. the other blocks. A useful suggestion arises by observing that the elements on the principal diagonal of B are sums of squares. . a first block may involve the correlation between the scale and the overall thermal parameter.10. so that the task soon becomes prohibitive even for large and fast computers when largescale problems (thousands of parameters) are treated. (2) in oblique coordinate systems.
A critical point in least squares is the occurrence of large correlation coefficients among parameters: this can give rise to illconditioned (determinant close to zero) B matrices and therefore to serious problems for the calculation of B' and for the accuracy of AX. Provide easy ways for applying symmetry constraints to parameters of atoms in special positions. In some noncentrosymmetric space groups the origin may float in some directions. or x and z in Pm). Refinement in P2 is then carried out on four symmetry independent molecules. If the = pll and pzzare erroneously refined as if they were independent. The normal equations matrix will become singular if the atomic coordinates of one atom along the free directions are not fixed (e. 107) the sum of the free coordinates to a constant value. These are handled by not refining some .100 I Carmelo Giacovazzo application of the fast Fourier transform (FIT) algorithm. The question arises as to whether or not the space group is really centrosymmetric. The problem may be solved by constraining (or restraining. 2. let us suppose that refinement of two symmetry independent molecules has been unsatisfactorily carried out in P2/m. with respect to pairs of positional parameters referred by the inversion centre have equal moduli and opposite signs. = 0. so that B is singular. As a further example. the derivatives of IFI.. 4. 1. A more efficient procedure is that which modifies the normal matrix to limit the parameter shifts (not equivalent to dumping shifts after the matrix solution).g. see p. To overcome this difficulty small random shifts are applied to parameters when refinement moves from the first to the second space group. the matrix B will have two rows and two columns equal and will be singular. a singularity may occur when two atoms with the same x and y coordinates but differing by a 50 along the x axis are refined without using reflections with h odd. Such a practice was frequently used in the primitive least squares programs but provides incorrect estimated standard deviations unless the full variancecovariance matrix is used.1 for some details). following constraints will hold: Pll = fizz. However. 3. PZ3 P13= PI. The symmetry of the structural model is higher than the spacegroup symmetry in which refinement is made. the derivatives with respect to corresponding pairs of thermal parameters have equal moduli and signs. Then the new B matrix will be singular: indeed the imaginary parts of the structure factors are vanishing. An efficient leastsquares program should: 1. As an example. pairs of lines will be identical or opposite. For example if an atom lies on 4[rn11. Symmetry constraints are not introduced. That occurs when the following conditions hold. the matrix still remains illconditioned and further unpredictable shifts can be generated. FFT based programs allow fullmatrix refinement of protein structures at a reasonable cost (see Appendix 2. z in Pca2. Two atomic sites nearly overlap because of some structure disorder (or some error). Since the elements of B are sums of products of derivatives. the second two obtained from the first two by application of the inversion centre.
m degrees of freedom. Indeed variances estimated in this way are proportional to the intensities themselves: the consequence is that low intensities will systematically have lower variances than high intensities. That results in a bias in the estimate variances. anisotropic and/or anharmonic vibration. should not be based on counting statistics alone. Different types of errors can have similar effects and may be compensated by others.B. incorrect symmetry assignment. For example. absorption and extinction corrections tend to reduce intensities at low sin 6/Avalues more than at high values: thus errors in correcting these effects produce. w = 1 for all reflections is commonly used when a partial structure is under .IFHlc)and therefore the results of a crystal structure analysis: experimental accidents (fluctuating power in the incident beam. as a partial compensation. In the initial stages of refinement artificial weights may be used to accelerate convergence (e.. In the final stages the weights should reflect the accuracy of the should be deduced from an analysis individual observations (w. = 1/02(IFIO) of the experiment). that the averaged intensity is used in least squares. and that the variance based on counting statistics is combined with that arising from differences among symmetryequivalent data. In most cases the effects of each type of error cannot be estimated: then the standard deviation of individual intensity measurements is assumed as the standard deviation calculated from counting values plus an additional term which allows for errors of an undefined nature. background radiation. Then observations which are believed to be unreliable get very small weights. For large n . A long list of errors[521 affect the can values of the deviates (IFHlo. anomalous dispersion. correlation among observations. 369). in a z) hexagonal space group for an atom in special position at (x.m values x2/(n .[511 The possible presence of errors may be checked by observing that S is expected to be distributed like X2 with n . It should be stressed that estimated variances of observations. so that Analogous problems occur for thermal parameters: symmetry constraints on them are described in Appendix 3. errors in the thermal tensors. and therefore weights. if w. crystal damage by the incident beam. In these cases it is highly recommended that all symmetry equivalent reflections are measured. Unfortunately it is not trivial to assess the accuracy of observations and the correctness of the assumed model. For example.Crystallographic computing 1 101 parameters or by equivalencing atomic parameter shifts. h. thermal diffuse scattering. statistical fluctuations in quantum counts. refinement). disorder. 2. = l/& . The weights play a critical role in any refinement process. etc. crystals moving on their mounts.m) is expected to be close to unity: so. Allow for a variety of weighting schemes (see p.g.). errors in corrections for absorption. multiple reflections. extinction. the only independent positional variables are x and z. and consequently (the GaussMarkov theorem states that only if errors are random and uncorrelated it may be expected that the leastsquares methods give the best unbiased estimate of the parameters) in a bias in the parameter estimates which may be of some relevance in highprecision structure determinations. deviations from the isolated atom approximation.
Each jth sum should be nearly (n . For each ith interval the average (IFlo)i and the difference (AF). Wang and ~ o b e r t s o n [ modified leastsquares weights by adding to the calculated ~~] variance a term which is a fundion of the disagreement between the experimental and the expected distribution of the deviates. If some unexpected behaviour appears then one may guess that some source of error has not been taken into account. 2.IFJ. called outliers. The robustresistant techniques decrease weights when disagreement increases.H) for 3 is ( 3 ) = n . . or to many other reasons it may occasionally occur that a small number of data. Plotting (AF). Least squares are very sensitive to the presence of large residuals which. or parity of Miller indices. A naive approach.102 1 Carmelo Giacovazzo the expectation (see Appendix 2. reflections for which I 1 < qo(lF1) are often excluded from the refinement (q depends also on the F number of available data: q = 2. If a careful check does not suggest any new strategy the only way for lessening the effects of systematic errors is based on a weighting scheme based on the deviates (IFo[. having a high leverage. Higher values of q could bring to a unsatisfactory ratio number of observations/number of parameters).I&[). so avoiding any discontinuity in the process. A practical weighting criterion which takes into account all random experimental errors for which precise estimates are not available from experiment may be so described: the lFlorange is subdivided into a number of intervals each containing approximately the same number of reflections. versus (IF.m)(p.m. may be to discard outliers by setting to zero the corresponding weights. often used in practice. or intervals of Bragg angles. Allow for a proper choice of the number of reflections to be included in the refinement. 2. Due to some random or systematic errors.12. may cause nonnegligible distorsions in results.12) will show a distribution of points which can be approximated by an analytical function such as . or to avoid many lowquality data reducing the efficiency of the process. where p j is the number of terms in the jth subset. or to imperfections in modelling parameters. show a very large discrepancy with respect to the corresponding calculated values.): then the weighted sum of discrepancies for each subset may be analysed. 3. In order to save computing time. The weighting scheme will be designed in order to make differences (A&) constant. etc. Accordingly the set of observations may be divided in large subsets (any significant criterion may be used for obtaining subsets: intensity ranges. F0 p(lFl0) = a0 + a1 I 1 + a2 IFIi + a3 IF[:. thus More efficient empirical weights which make ( A F ) ~constant as a function of lFlo can be obtained through truncated Chebyshev polinomials. and weight should be suitably changed./n). Robustresistant techniques[551also use weights based on the deviates.= ((IFIo. Fig. 3 is a frequent choice.[) (see Fig.[531 But the above practices are not able to eliminate systematic errors or correlation among errors.))i are calculated.
a leastsquares refinement was first carried out up to the R(l) value on assuming that all the atoms have isotropic temperature factors (ml is the number of parameters)...m (very frequent in crystallography). [ He ~ ~ ~ ] ~ ~ considered the weighted residual (5. let us suppose that two leastsquares refinements based on the same number of parameters m and on the same number of observations n are carried out by two different investigators.b varied param.85). where x2 is the well known chisquare function: in these cases As an example.a the hypothesis can be rejected at the 100a% significance level (a significance level of a = 0. Sometimes the two models used for refinement involve a different number of parameters. The hypothesis 'the m parameters obtained by investigator 1 are consistent with the experimental data' may be rejected at the cu significance level if T > Rm. In the practice T = R(l)/R(2) is often used because usually Rw(1)/Rw(2) R(l)/R(2). For example one refinement is carried out where b parameters are held fixed. If a((F1) depends on I 1 such a practice preferentially F discards lowintensity reflections so introducing a bias in the process.Crystallographic computing However. where Rw(l) and Rw(2) (with Rw(l)> Rw(2)] are obtained from the two different models. the omission of observations is equivalent to assigning zero weights to them.m. The test compares T with the function 1 103  If the computed T satisfies T > Rm.. The problem of identifying meaningful changes in R produced when the model is altered has been faced by ~ a m i l t o n . Tables for Frn. were computed from Hamilton. The refinements resulted in two different R factors. Often. For large values .[56]but sometimes it discards important information (very unreliable results can be obtained when a structure with superstructure effects is refined without using weak reflections). and proposed the test (known now as Hamilton's test) based on the ratio T = Rw(1)lRw(2). a. that has little effect on the results.. of n .n m..05 is commonly used). say R(l) > R(2).88) instead of the conventional residual (5. Then Hamilton's test may be so modified: the value of T given by T= R (b fixed param. A subsequent refinement was carried out up to a residual R(2) < R(l) on assuming anisotropic atoms (m2>m1 is the number of parameters). varied) may be tested against values of For example. m .) R (all m param. The hypothesis 'all the atoms ..
lFHlcl [IFHI: .IFHI:]. which is highly improbable) when at least one of the following conditions occurs: 1. stops with the residual R(l). The ratio is particularly unfavourable for biological macromolecules. replaced by wk= wH/(4 IF^^!). the hypothesis that the correct space group is centrosymmetric may be rejected at the a significance level if A last remark on the crystallographic leastsquares technique concerns which function to minimize. While to a resolution of 0.3 A. while refinement in a noncentrosymmetric space group (say P2 or Pm) results in the residual R(2) < R(1). There is still a strong disagreement[51]over the question of whether S or S t should be used in refinement. In place of the function S defined by eqn (2. in D.21. [IFH10 .86 A (typical limit .2 and 0./G~j) by (6 and. Constraints and restraints in crystallographic least squares The accuracy of the derived parameters is generally small (e. The normal equations (2.g. it would be found that CC distances in a phenyl group were in the range 1. for which a(lF1) become infinite or extremely large (we must. If ml and m2 are the numbers of parameters for the two refinements. IFH1. so limiting the diffraction data to a resolution of about 2 A. owing to their intrinsic flexibility. Low ratio between the number of the observations and the number of parameters to refine. This is a nonlinear operation which may introduce a bias proportional to the variance of IFI2. Indeed.Furthermore the (2 formula a(lF()= a ( l ~ 1 ~ ) /IF() so widely used in practice is not appropriate F for zero or close to zero I 1 values. let us suppose that refinement in a centrosymmetric space group (say P2/m).7 A).68) still hold if w is .67) the function is sometime minimized. however. 6 IFHlc/6~j 2 IFH[. In favour of (FIrefinement it may be observed[s8] that 6 IFI2/6xi is small if IFI2 is small: thus weak reflections have too weak a leverage in IFI2refinement. mention that methods[613621 obtainfor ing more reliable I 1 and a((F1) from 1 ~ and ~o(lFI2) values are now F 1 available).104 1 Carmelo Giacovazzo vibrate isotropically' may be rejected at the a significance level if As a further example. the amplitudes of the thermal vibrations from the average positions are rather large (usually between 0. Arguments in favour of IF 12refinement are based on the observation[s93 that I F are obtained 601 I from intensity data via a square root.
If. Atoms with very large atomic number and very light atoms coexist in the unit cell. Derivatives with respect to such parameters are calculated from those for the atomic parameters Xi using the chain rule: i. yo. Assume A" = MA where M is given by (2.. say by about e. A rotation matrix R may be then defined which aligns A = (ey. 2. by 3 about the new e2. Rigid body refinemenP1 If the structure contains rather rigid molecular fragments of well established geometry (e. zo) parameters defining the position of some reference point and w. Only poor and scarce data are then available. some prior stereochemical information is available on parts of the structure its use in the leastsquares procedures may increase the degree of overdetermination of the system and improve the accuracy of the results. Then modest errors on the heavyatom parameters cause strong errors on the lightatoms parameters.g. q5 for the group orientation). Too high thermal motion. q5 to the matrix of normal equations.. 6 lFHIc .31~)or a similar matrix.) on to A' (say A' = RA): according to the discussion on p. e. e. For each rigid group of n atoms the number of independent positional parameters reduces from 3n to 6 ((xo.7 A the number of parameters is nearly equal to the number of the observations. etc. to keep the number of parameters small. ' ." = RX. The atoms concerned are initially regularized to some ideal geometry which is preserved during the refinement. Three methods will be briefly recalled here. v. (see Table 2.[641 For the jth atom of the group let Xi be the coordinates with respect to the system A defined by the conventional unit cell. The problem is now to calculate the appropriate contribution for the rigid parameters x. Then X.axo j=1 a lFH1c ax.E. Leastsquares calculations could be performed according to the following scheme. a single overall thermal parameter may be assumed for the group. the number of parameters to refine may be considerably reduced.. yo. zo. at 2. and. however. Xi" the coordinates with respect to an orthogonal cell of unit dimensions (say A ) oriented in some way with respect to A. Thermal parameters are usually considered to be isotropic. benzene rings).1) and The atomic coordinates so obtained may be used in the usual manner for calculating structure factors. presence of structural disorder.e. w. 72 the matrix R may be expressed as the product of three successive anticlockwise rotations. and by q5 about the new el. 3. Xi' the coordinates (in A) with respect to a set of orthogonal internal axes A'. 3 .Crystallographic computing 1 105 for small molecules) there are about 30 observations for each coordinate being refined.
In this last case the normal matrix has to be modified in order to take into account all physical parameters (the common practice fixes the thermal parameter of H. rigid body refinement is that used for putting hydrogen atoms into structures (Xray data). some bond distances and angles are fixed to given values.(XO) and 6 ~ ~ is 1the6 derivative of G calculated in XO. Sometimes H atoms are geometrically positioned at the end of each round of LSQ. etc. The size of the normal matrix is therefore reduced. The success of this method relies on the accuracy of the assumed geometry: if this is wrong systematic errors on other parameters will be introduced (e. At the end of calculations H and the reference atom will have the same positional estimated standard deviations. A technique related to. ~ ~ The normal equations can be derived by settling to zero the derivatives (with respect to Ax and A) of S: . Usually the available model X0 will not exactly satisfy (2. Constraints via Lagrangian multipliers In the absence of complete information on a fragment's geometry one may wish to fix some molecular parameters (e. In such cases Lagrangian multipliers can be used: the function to minimize is h where the (generally nonlinear equations) represent the fixed constraints. which is set equal to that of the reference atom). convergence is accelerated but there is no remarkable saving in computing time (derivatives with respect to each atomic parameter have to be calculated for each structure factor and chain rule implemented). but more frequently H parameters ride upon those of a reference atom (riding refinement). a group of atoms is held in coplanar arrangement.). but not coincident with. the symmetry of phenyl groups sometime deviates remarkably from the sixfold symmetry[651). for a group temperature factor B.69).g.. while the bond distance between them must have an estimated standard deviation equal to zero (if the full variancecovariance matrix is used in the calculation). The problem will be linearized by expanding both the IFHIcs the Gis in Taylor series: and where G: = G.g.106 1 Carmelo Giacovazzo and.
equations are obtained by expanding S in Taylor series and equalling to zero its derivatives (with respect to AX): The effect of restraints is therefore to add contributions to the elements of the normal equation matrix. In this situation the function to m i n i m i ~ e [ ~ ~ . If we recall. These functions are used as supplementary observations. expressed in terms of partitioned matrices. according to p. Thus parameters highly correlated can be found. is its standard (or optimal) value. For example. The normal . chirality (a restraint on the chiral volume about an asymmetric carbon atom may maintain the conformation in the correct hand). a restraint may be to set an interatomic distance d (bonded or nonbonded) to a given value taken from the literature. that where and so on. but this is expected since parameters are deliberately correlated by restraints. Another restraint may be: the sum of all the atomic coordinates along a polar direction can be fixed to its current value in order to keep fixed the centre of gravity of the molecule and so determine the origin. are where mjq = i(6G:/6xj). g. p.. Use of restraints Soft. bond and torsion angles. the approach is not very attractive for largesize problems: indeed the order of the normal matrix is increased. 564) and they concern van der Waals distances. Several other types of restraints can be imposed (see Chapter 8. 62.Crystallographic computing 1 107 The augmented normal equations. flexible constraints (say restraints) may be imposed to some functions of the parameters in order to permit only realistic deviations of their values from fixed standard ones. Even if a large variety of stereochemical constraints can be taken into account by the method. w is the weight to associate to the qth restraint. planarity of groups. ~ ' ] is where gq is the function describing the gth restraint. so that the order of the normal equation matrix is neither increased nor reduced. thermal .
When the number of restraints is sufficiently large the equations are overdetermined and refinement will also converge with lowresolution data. Also. let us suppose that the bond distance dj is to be restrained to a set value. etc. its logarithm is a monotomically increasing function of the argument. The likelihood function L is then given by Since P is everywhere greater than or equal to zero.exp~[e?/(2o?)] . 103). In statistical sciences the main alternative to least squares are maximumlikelihood methods. deficiencies which invite the application of alternative methods.m increase but oii(see p. If the error function is Gaussian then ~' P(ei) = ( 2 ~ o ? ) .47) are distributed according to some probability density function P(e). the sum of site occupancies of two or more atoms can be restrained to some fixed value when disorder problems occur. A basic difficulty of their use is to assess an optimal weighting scheme: indeed the first component of S is in electrons squared while the second may be considered an energy quantity. The approximate nature of the restraints well agrees with our approximate knowledge of the chemistry involved. An alternative criterion may be the use of the Hamilton's test (see p. Thus the maximum of L is attained when In L is a maximum. If the weights of Xray observations are (as usually) sufficiently accurate but on an arbitrary scale. A sensitive criterion may be to compare estimated standard deviations obtained by constrained and unconstrained refinements. the expected standard deviations) of the restraints and scale them with respect to the observations. positional and thermal parameters related by noncrystallographic symmetry.108 1 Carmelo Giacovazzo motion. where w plays the role of an effective force constant. 98) may be larger or smaller according to circumstances. That does not necessarily mean that the constrained solution fits less well to the data. Then the restraint equation / may involving di with estimated standard deviation o(dj) is given the weight Very small standard deviations make restraints equivalent to constraints. mechanism is to indicate the relative precisions (i. When constraints are applied both S and n . Alternatives to the method of least squares In the above sections some deficiencies of least squares have emerged. A convenient . the normalization factor &. Let us suppose that the errors e defined by (2. = CHw ~ ( A F ~ )~m )( ~ be obtained. potential energy functions. If refinement provides a bond distance differing from dj by several times a(di) it should be concluded that experimental data are in conflict with the fixed restraint. As an example. Applications of constraints and/or restraints in leastsquares processes usually lead to larger residuals than by unconstrained refinement.e.
We have so shown that. the leastsquares and the maximumlikelihood methods provide equivalent results. if errors are not distributed according to a Gaussian model.and in some more recent paper^. based on Jaynes' extension of Shannon's theory. in a paper by ~hirley[~'] . Conversely. If a (even imperfect) structural model is available then the intensity yi. and the theta and twotheta axes are then stepped to the next position. such a situation is very infrequent in crystallographic refinement. as well as maximumlikelihood methods. The reader will find general remarks on the various approaches. are far from being competitive with least squares in most of crystallographic applications. observed at the ith step may be compared with the corresponding intensity . indexing is a rather difficult task for relatively large cell volumes and/or lowsymmetry crystals. 293) may be collected in a step scan mode: intensity is measured for a given interval of time. where only rather imperfect estimates of the variances are available. and observations are weighted by the reciprocal of the variance. if the distribution of the errors is Gaussian. In L has its maximum when where wi = l/a:. and tests on their efficiency. since such methods can exploit more information. Because of unavailable experimental errors in the estimates of the diffraction angles and because of the frequent overlapping of peak intensities. Then Since the second and third terms are constant. the method of least squares does not lead to a maximumlikelihood estimate. Rietveld refinement The basis of the technique Powder diffraction patterns (see p. appropriate Miller indices are associated with observed reflections and simultaneously accurate unitcell dimensions are calculated. The pattern is then indexed: i. so that proper figures of can be used to distinguish between bad and good solutions. When this is available maximumlikelihood methods provide better estimates of the parameters.e. Parameters may also be estimated by maximum entropy methods. require the maximization of the entropy. they often provide more than one solution.Crystallographic computing 1 109 where a is the variance of the ith observation. But such methods. which. The above results also explain why least squares are practiclly the only ones used in crystallographic refinement: they only depend on the variance of the errors while maximumlikelihood methods require the knowledge of the distribution of the errors. However.[^"^^] This stage of analysis is followed by the examination of possible systematic absences to suggest a space group. Several approaches are today available for this aim: implemented in computer programs.
= B:~ + o. is the standard deviation associated with the peak (usually based on counting statistics) and a. the ~ ] ~ ~ model may be refined by minimizing by a leastsquares process the residual S = C Wi I~ io yic12 where wi. .k) is the reflection profile function. the detector system. possibly selected by a monochromator crystal with its specific mosaic spread). Lk is the Lorentzpolarization factor for the k reflection k. and parameters defining the functions G and yzb* The determination of an accurate model for the profile function G(Aock) is one of the fundamental problems in both singlepeak and in Rietveld analysis. is a suitable weight.g. Accordingly. . According to ~ i e t v e l d . 2 Lorentzian). Aerk= 28. (modif. is the calculated positon of the Bragg peak corrected for the zeropoint shift of the detector. The parameters to adjust by refinement include unit cell. the wavelength distribution in the primary beam (e. F is the structure factor. 2(1 + CIX.20k where 28. between monochromator and sample.. 1 Lorentzian). atomic positional and thermal parameters.k)l nHk ci l2 (Lorentzian). is that associated with the background intensity yib. the beam characteristics (as influenced by slits and collimator arrangements between the primary radiation source and monochromator. and between sample and detector). mk is the multiplicity factor. and G(Ae. (1 + c2xfk)2 'L 2 ~t Hk " (1 + c3xfk)1'5 ' 2Hk with 0 s q G 1 (pseudoVoigt). there are many choices of analytical peakshape functions.~. This is particularly true today when highresolution neutron and Xray spectra are available: deficiencies in the profile model are no longer lost in relatively large instrumental diffraction profiles.110 1 Carmelo Giacovazzo yic calculated via the model. given by (wi)' = 0. The shape of a diffraction peak depends on several parameters: the radiation source. yic is the sum of the contributions from neighbouring Bragg reflections and from the background: where s is a scale factor. We quote: (Gaussian) . (modif. oi.
Person VII becomes a Lorentzian.I).~ i c ) ~ ~iy?o]l'~* (3) The Bragg RB= C JZko .72) for the Lorentzian component. = X tan 8 + Y/cos 8 (2.. It is mainly due to insufficient shielding.. (5) The goodness of fit GofF = C wi(yio. terms are refinable parameters.70).. There is no well established approach to the background.)p 7tk (Pearson VII). to electronic noise of the detector system. Also RB is of considerable use since it depends on the fit of structural parameters more than on the profile parameters.Y .0. and/or X. C.Ikcll(CZko). C4= 21f8. and r is the gamma function. m./R. modified Lorentzian.5) 52(1 + 4c4x:. The background and its variation with angle is usually defined by refinement of the coefficients of a power series in 28: where the b. are obtained by partitioning the row data in accordance with the Ik. The FWHM is usually considered to vary with scattering angle according to (2. The values I. Hk is the fullwidth at halfmaximum (FWHM) of the kth Bragg reflection. and GofF since they show in the numerator the quantity being minimized .1. = ( U tan2 8 V tan 8 . ~ Xik = AOik/Hk.Crystallographic computing 1 111 r(B) r ( p . Y are variable parameters in the profile refinement. C1 = 4.. Besides analytical functions nonanalytical functions arising from an analysis of resolved peaks may also be usedL8'] to describe peak shape (in the Rietveld method the peak shape is not the end but a tool of the method). and Gaussian function respectively.71) (FWHM). When P = 1.[791 U. C3 = 4 (2213 I). V. W. 2. The most meaningful indices for the progress of refinement are R. ~ ) ~ /N ) = (R. values of the component peaks.P)/(X number of profile points and refined parameters respectively. The agreement between the observations and the model is estimated by the following indicators:[s11 /C (2) The weighted profile R.)~. to diffuse scattering. which (P should approach the ideal value of unity.w)'" + according to for the Gaussian component. where N and P are the (4) The expected R E = [ ( N . . = [C wi(yi0. to incoherent scattering (rather high for neutrons). All the above described parameters are introduced in the Rietveld refinement process according to (2. = 4 ( . Of some use also is the pure Voigt function which is the convolution of Gaussian and Lorentzian forms. It is easily seen that the pseudoVoigt function presents the mixing parameter rj which gives the per cent Lorentzian character of the profile.[781 (FWHM). where Co = 4 In 2.
silicon. Such an analysis allows one to set up the angular dependence of the peak shape. the values of FWHM obtained from refinement are used for a first estimate of the U . It is worthwhile mentioning that standard specimen data are also used for the determination of wavelength A (if necessary) and for the zeropoint calibration 28. and their FWHM can be set equal to that of al. Analogously.71) and/or of X . diffraction profiles from a standard specimen (e. If a Cu Xray source is used and a2 and a. the angles for a2and a3lines may be fixed according to their wavelengths. V. are not eliminated by some experimental device (i. The number of variable parameters in the profile function may be reduced by fixing a. in synchrotron or neutron experiments) a single peak may be represented by one or by a combination of the functions described in the previous subsection. corundum.e.72). one for each spectral component. and y. or quartz standard materials) devoid of crystallite size or strain broadening effects are collected: in this case f (28) may be represented by a delta function and (2.e.. W values in eqn (2. Y values in eqn (2.831 particular usefulness for complex structures.. The values of the profile parameters may be refined for each single peak collected from the standard: each peak is separated and analysed in a region with enough points to allow a good sampling of background on each side of the peak (a parameter for background may also be refined).g. In particular. intensity via a previous profilefitting experiment. The correct profile function is in general obtained by trialanderror methods from single well behaved profiles of the standard material. are the observed and calculated values at the position 28. A peak profile may be expressed as where b(28) is the background function. f(28) is a specimen related function. and a3 intensities relative to a. of the detector scale. For good experimental data the R value is expected to be around one per cent. Some practical aspects of Rietveld refinement The generation of instrument profile calibration curves usually precedes Rietveld refinement. a germanium monochromator) a compound profile consisting of three split functions has to be chosen.[80. and w(28) *g(28) is the socalled instrument function. The goodness of the profile fit is measured by where y.73) becomes If a single wavelength is used (i. This may be considered as the convolution of the function g(28) representing the diffractometer's optics and a second function w(8) representing the wavelength distribution of the incident radiation. As a first step.112 1 Carmelo Giacovazzo The use of restraints in the Rietveld method has proved to be of 82.. Analysis of the specimen profile f usually follows instrument profile .
The increase of N does not remarkably affect the conventional Rietveld agreement but decreases the parameter estimated standard deviations approximately in proportion to N'". are correlated themselves. The success of the Rietveld method is based on some fundamental requirements: 1. As a consequence the correlation among observations becomes higher with N = 10. For example. yield structural information nearly equivalent to a single integrated intensity count (even if the precision obtained by 1000 steps count may be higher than by 10 or 100 counts). Because of peak overlapping. a single Bragg reflection may be measured using 10.1 per cent significance point via the formula[891 where P is the number of leastsquares parameters involved in the calculations. . (b) integrated intensities are calculated and structure solved by direct or Patterson methods. p. for single peaks. dstatistics suggest that an optimum value of the step width is[901 between onefifth and onehalf of the minimum FWHM of well resolved peaks. The same intensities are then used in a fullmatrix leastsquares refinement as for singlecrystal structure determination. 100. together with their standard deviations and their correlations (see Appendix 3. 1000 and leastsquares residuals A.y . . this time error margins for each . Peaks generated by overlapping of more reflections are deconvoluted and integrated intensities of individual hkl are calculated. That can be provided by the following procedure:[911(a) deconvolution techniques and profilefitting methods are used to derive intensities Zk of individual reflections and to resolve overlapping peaks. A starting model for atomic positional and thermal parameters should be available in advance. i. In such a situation DurbinWatson dstatisti~s['~I may be used to assess the nature of correlation. The parameter d may be tested against the 0. For positive serial correlations adjacent A tend to have the same sign and d will be smaller than 2. A specific feature of Rietveld refinement is that the number ot observations N can be chosen arbitrarily large simply by decreasing the step interval in 28. Such an improvement is often fictitious. 184). whereas for negative serial correlation (alternating signs of adjacent A) d is expected to be larger than 2 (and smaller than 4).. It is based on the parameter For no serial correlation a d value close to 2 is expected.Crystallographic computing 1 113 calibration. 100. if d < Q or d > 4 . Specimen broadening of the profiles is often present: it is traditionally assumed to be Lorentzian if profile broadening is present. The observed intensities are not statistically independentFa7] and. The profile analysis of the full diffraction pattern is often used to peak positions and peak heights for each reflection: from them lattice parameters are calculated and refined in an iterative way. they tend to assume the same sign. = y.e.Q if consecutive terms are uncorrelated. Q < d < 4 .Q consecutive terms tend to have positive or negative serial correlation. or 1000 steps.A.
The crystallites should be of equal size.[92. g4 arises from specimen transparency (i.e.951~ ~ ~ [ or of trigonometric type1961 p is a parameter to refine in the refinement process. the acute angle between the preferred orientation plane and the diffracting plane k:. Particles much larger than 10 pm should be removed from the sample.[971 In this case unimodal distributions are inadequate to describe profile functions. Correction for instrumental aberrations[9s1001should be made. 913).e. That is not easy to achieve in practice. g2 is due to the varying displacements of the various parts of the flat specimen surface from the focusing circle. and unavoidable profile misfit errors will still appear at the end of refinement when observed and calculated patterns are compared. thus it may be introduced in a rather simple way in the fitting schemes and in Rietveld refinement. If a specimen spinner is used in the experimental setup the preferred orientation can be characterized by a few parameters only. Ik(corr) = IkPk(@). The problem is also minimized in neutron diffraction because of the large transmission specimen. from the . 4. Diffraction patterns of materials with single composition but two different distinct distributions of crystallite size (or of microstrain) could be characterized by profilebroadening effects with bimodal distribution. 2. 3.931 Traditionally preferred orientations are minimized by loose packing of the powder: however. sufficient compression improves homogeneity and reduces surface roughness effects.114 1 Carmelo Giacovazzo observation and correlation among reflections intensities could be processed to calculate a nondiagonal matrix Mf (see pp.[941 The most simple way to correct the intensities calculated from the model structure is to use an empirical correction function depending on @. which are responsible for profile broadening. as well as very small particles (<1pm). errors in the relative intensities may occur which limit the accuracy of the refinement process. Some geometries are less sensitive to this problem (i. Guinier cameras). g3 is due to the axial divergence (as regulated by Soller slit collimators). The crystallites should be randomly distributed. but it is severe when synchrotron radiation is used because the number of crystallites correctly oriented to reflect the parallel beam is much smaller.73) may be considered as the result of six specific functions: The function gl depends on the projected focal spot profile. If the preferred orientation is not taken into account. Pkmay be ~ a u s s i a n . The instrument function g in eqn (2.
. g4 broaden it asymmetrically and shift the peak from the theoretical position. Resolution of the pattern may be improved by mathematical technique^:[^^^^^^] i. in Fig. .._._.._... 5._)_._.._. As a consequence. . When a nonconventional diffraction apparatus is used one of the first choices to be made is fixing the wavelength. The resolution of the pattern as well as the signaltonoise ratio can be appreciably improved with carefully designed diffraction experiments. As may be seen from Fig._..._._.._..14 typical FWHM (instrumentonly contribution) are plotted against the diffraction angle for modern neutron diffractometer (N). The use of incident beam monochromators can further improve performances of conventional divergent beam diffractometry. .._)_. p._._.c.~.. and for a synchrotron powder diffractometer (S).. g5. g3. g6 is due to the possible misalignment of the experimental setup. so halving the number of lines in the pattern..e... The deleterious effects of the aberrations can be minimized by the use of appropriate analytical functions in Rietveld refinement or by a careful design and/or alignment of the instrument.._. N ~ A e D () I / H N . ._._._~ .. .[lo5]Indeed.._... Thus a useful compromise has to be chosen between the two requirements. FWHM for different experimental arrangements.. g5 is defined by the receiving slit. ..._..._._. this last containing the effect of instrumental broadening (see Appendix 3.._ .14...c._.. 2. and g6 broaden the profile symmetrically. In order to compare the performances of different experimental arrangements._.Crystallographic computing 1 115 penetration by the beam of a sample with finite absorption). the resolution of the remaining lines is improved._. /'  XCW ..o S I Fig._._. radiation and a diffractedbeam curved graphite monochromator) limiting vertical beam divergence to less than the standard value of 5". A short wavelength increases the number of accessible peaks but produces severe overlap of them. Functions defining the instrument function g. 185)...._.._. .._.[lo4] When higher resolution is needed for conventional Xray sources it is advisable to use the Kg doublet (but the total experiment time will increase). by deconvolution of the pure from the observed profile. component may be removed..A._._. while gZ.. for a conventional BraggBrentano with (XCS) and without (XCW) diffracted beam Soller slit (Cu K. Complex structures will produce peaks closely spaced and frequently overlapping: a long wavelength improves separation between peaks but reduces the number of accessible reflections which cannot then offset the large number of structural parameters to refine. ._._)_. .. .. the K._.._._.13._._.'. 2. ._._. . ._. the f~nal prof~le Fig.. only gl.~. 2.:._._./  XCS _.13..._._.a . 2._.. 0.2 /..
corresponding to 127 independent reflections.577 respectively (see Appendix 3B. Neutron data have smaller resolution (FWHM = 0. and 0. It is therefore not infrequent that the Rietveld method benefits by a combined use of neutron and Xray data.[79] Synchrotron intensity data show a very good instrumental resolution (FWHM = 0. 198) neutron refinement is expected to be more sensitive than Xray to oxygen positions.352. For example. where location of some dominant atoms may be easy but subsequent accurate location of very light atoms may be difficult. The best resolution is attained by synchrotron radiation: the probability of measuring single peaks is larger than for any other radiation source. Such information is often generated by complementary experimental techniques. improvement in precision may be obtained if lo9] refinement is carried out on the combined Xray and neutron data sets[llol). Neutrons have smaller resolution. 2. As an example in Fig.07" at 28 = 50") but a remarkable intensity decay with sin BIA: the attained maximum sin BIA value is 0. p. 0. This situation is just complementary to that occurring for Xray data. and 0 are 0. Owing to the smallness of crystallites and to the greater disorder present in the . If such conditions are not satisfied quantitative kinematic treatment leads to models of low accuracy and the Rietveld method may be applied in order to discriminate unsatisfactory structural models. It is not infrequent[lo6]that synchrotron data present so large a percentage of unique I. etc.40 Al.'08.) and on the available prior information which may be introduced into refinement. intensities of overlapping reflections of LaMo50. and also structures arising from the filter absorption edge are eliminated).b) observed (points). better treatment of profiles.. (however. Since the neutron scattering amplitudes for Cr. refinement with neutron data may be used to confirm results obtained with Xray data[79.35 A'. P.6" at 28 = 50") but no serious intensity decay with sin 8/A: the maximum sin 8/A value is 0. but a better signaltonoise ratio at high sin 8/A values. were broken up by considering electron diffraction patterns:[1091 14 symmetryindependent atoms were then positioned and their isotropic thermal motion determined.[82~112~1'31 Electron diffraction is a generally applied technique when chainfolded crystals are of minimal thickness and crystal deformation negligible. and difference profiles generated by powder samples of aCrP04 are shown. the structure solution may be difficult.53. higher resolution. When some heavy atoms are present in the structure or highangle Xray data are not attainable. As a further example we recall the application of the Rietveld method to polymers.116 1 Carmelo Giacovazzo background is kept essentially constant (indeed KO lines are removed at source. calculated (bold line). refinement is facilitated when some heavy atoms are present. The limits of the method depend on progress in experimental aspects (sample preparation.15(a. however. corresponding to 97 independent reflections. The Rietveld procedure has been applied to a very wide range of inorganic and organic materials[llll and scientific interest in this area is increasing (the present annual publication rate is approximately 100). Because of the narrow range of neutron scattering lengths. values that structure determination may be carried on by techniques identical to those used for singlecrystal data (for rather large structures specialized solution techniques have still to be applied[lo7]).
condensed rings. In other words. The above conclusion is valid also for small molecules. polymers the width of peaks is rather large for polymers so that overlapping events in their pattern are more frequent.g. rings. In spite of that. 323 A 10 20 30 20 (deg. 2. Analysis of thermal motion In biological macromolecules the rootmeansquare displacements of atoms from their mean positions are of the order of tenths of an angstrom. The apparent contradiction may be overcome by assuming a high correlation among the thermal motions of bonded atoms. Powder diffraction profiles for aCrPO. if an atom at a certain instant is out from its equilibrium position. On the other hand the allowed variations for covalently bonded distances are no greater than some hundredths of an angstrom. from: (a) the synchrotron Xray experiment. some other atoms coherently move in such a way that bond distances are chemically meaningful. Reflection positions are marked. (b) neutron experiment. Indeed more or less rigid groups of atoms can be found (e.Crystallographic computing (a) 1 1000 1 117 aCrP04 NSLS Cap I 1 l a r y Oat a 1.) 100 125 Fig.) 40 50 60 + 25 50 75 28 (deg.15. etc. discrimination among various structural models may often be accomplished provided prior information (size and shape of rigid molecular fragments) is adequately introduced into refinement.) .
where R= I + XP and P = ( 2 \12 11 The change of variable q = ~1 brings to where !. In the following. If the axis of rotation is correctly oriented but incorrectly positioned. will be its direction cosines). In accordance with Appendix l . it makes sense to analyse thermal motion in terms of translational and librational oscillatipns of these groups. the rotation and the translation component parallel to the axis do not vary. a rotation through x about the unitary vector 1 (I1. A the most general motion of a rigid body is a screw rotation. accurate to the level of quadratic approximation. such an analysis will be described on assuming a Cartesian coordinate system. but additional translation components perpendicular to the rotation axis are introduced.77) . 94) any correlation among fi tensors of different atoms is usually ignored. in such a system./ 0 (2. I. can be used upon infinitesimal rotations which do commute. Or also. terminal atoms such as the 0 atoms in carbonyl groups or H atoms in methyl groups have generally greater thermal motion than the atoms to which they are bonded.. if thermal ellipsoids correctly represent the thermal motion some a posteriori correlations among them can be found. According to p.e.76) u = ( U C )= ( t i ) + ( ~ ( 9 9 ) + () ~ ( q q + ((t9)A) ~ ) =T+A~+AS+SA (2. bond bending or torsional vibrations) the mean square displacement of pairs of bonded atoms should be approximately equal in the bond direction. since bond stretching vibrations have a much smaller amplitude than other sources (i. consider an atom at X = (xl. If is sufficiently small (2. To illustrate this representation of rotation. 71.32b) may be written as x X' = RX. is represented by relation (2.A.75) X'=(I+K)X=X+KX=X+AQ It may be concluded that the most general infinitesimal displacement of an atom in a molecular crystal from its equilibrium position is u=t+q/\r=t+(rlr)=t+Aq.[1141161 In the crystallographic leastsquares procedures (see p. Thus if the crystal contains moreorless rigid groups of atoms. For example. or. These operations do not commute in general.118 1 Carmelo Giacovazzo for which the internal molecular motion may be negligible and the thermal motion may be described in terms of a rigid body model. Thus the most general motion of a rigid body may be considered as the combination of a rotation with a suitable translation. x3) in a Cartesian coordinate system E. in longchain molecules the thermal motion normal to the chain should be greater than at right angles to it. luckily an adequate treatment of anisotropic thermal motion. However. 1.32b). The variancecovariance matrix for the displacement u is (2. x2.
.
75). L. S33.) .wA) so that (w2) = (w.g. only the differences SI1.added to S. and d = do+ s be the instantaneous separation. but simplified models of the vibrating system do provide useful estimates of the mean separation. S do not vary if D is.SZ2 S33. Often thermal motion analysis produces an excellent agreement between A'): sometimes observed and calculated U. but it has become clear that.? (e. Vice versa.Since their sum is zero the number of determinable components of S is eight: usually it is preferred to have the trace of S equal to zero. ((Au~. if the thermal motion is not negligible. Since A = A we will have D = kl where k is an arbitrary constant. of the order of low2 or more). if S in (2. If v and w are the axial and radial vectorial components of s respectively then d = do+ v w from which d = [(do v)' ~ ~ 1 " ~ .77) is replaced by S +D is obtained from which (2. the most suitable measure of an interatomic distance is the mean separation (usually longer than intermean distances). The effect of thermal motion on bond lengths and angles From a crystal structure analysis atomic coordinates are obtained which represent the centroid of a distribution of electron density arising from the combined effect of the atomic structure and of the thermal vibration.)') lJ2= (14) X worse agreement occurs (e. It may be noted that w is the difference between the projected instantaneous displacements w6 and wA of the two atoms B and A (w = w~ . For convenience consider a cylindrical coordinate system with axis z in the direction of do. Let dorepresent the separation of the mean positions of two atoms A and B.SZ2. . Such complex information is seldom available. w) yields + + + from which Express now the value of (w2) in terms of quantities which are experimentally accessible for three simplified models of thermal motion. It may be concluded that the values of Uij calculated from T. Usually interatomic distances are calculated as separations between a pair of atomic positions (distances from mean positions). or also to the inadequacy of the approximation (2. DisagreeA2 ment may be due to internal molecular motion of the atoms as well as to errors in the observed Uij.79) arises. TaylorMaclaurin expansion of d(v.120 1 Carmelo Giacovazzo S + D provided AD+DA=O is satisfied.Sll may be obtained from the observed 5 .2(wgw*) + (wi).g. Indeed. the average being calculated by taking into account the joint distribution of the thermal motion of the two atoms.
Then (2.Crystallographic computing We will examine three simplified models: 1. The rigid body model.81) and (2. If the thermal motion is assumed to be anisotropic. 3 (2. 1 121 According to (3 .19). . Let n be the unit vector about which a group of atoms oscillates with mean square amplitude (w2).) . 10a) where A3.10~) and (3.38b)) we can write (w:) = ( ~ 2 +) (w?ly) = (A1A+A2A)l(2n2). The atom B has all of the translational motion of the atom A plus an additional motion uncorrelated with the instantaneous position of A (riding motion).81) 2.( w W ( 2 d o ) .1(2n2) is the meansquare displacement of the atom A along do. that occurs for nonbonded atoms). The motion of the two atoms is not correlated (as a first approximation. Such a model well fits the case in which the riding atom B is strongly linked only to the atom A and the mass of B is considerably smaller than the mass of A (eventually summed to neighbouring atoms strongly linked to A. On introducing (3.80) (d) =do  + (dow2sin2 3 ) / 2 = do(l + w2sin2 312). / 8 n ~ (w:) = 2 ~ ~ / 8 where BA and BB are the thermal factors estimates arising from leastsquares calculations for A and B atoms respectively.82) in order to obtain (d).B.9a) we obtain where Xo represents now the direct lattice components of the vector do. Then ( 4 =do + ( ( ~ . . according to (3.82) Express now ( w i ) and ( w i ) in terms of the vibrational parameters usually obtainable from leastsquares refinements: the corresponding expressions could be introduced into (2.B. and (see eqn (2. 3. therefore ( 4 = do + ( ( ~ + ( & ) ) l ( W . as occurs for example if A belongs to a rigid group). we can write (w2) = d2(w2)sin2 3 dt(w2) sin2 3 where 3 is the angle between do and n. In accordance with (2.B. In this case (w2) = ( w i ) + ( w. 3 (2.82) become and respectively. Since 6d is perpendicular to d. If the thermal motion of the atom A is assumed to be isotropic then. A small rotation dw about n will produce over the interatomic vector d the variation 6d = (n A d) d o . (wk) = 2 ~ .81) and (2. n ~ . then a suitable coordinate system in the plane normal to do may be chosen.
1 we obtain where A.84) to the expression of cos a* in Table 2. Shortening of interatomic distances due to libration motion.[1161   About the accuracy o f the calculated parameters At the end of a structure analysis both positional and vibrational parameters are available.16. B3 = sin y(cos y . Shortening of interatomic distances will be more clearly deduced from Fig.) and (x. On applying (2. 2. (p. y2.84) to the relation (2. a .cos a cos y)a((p). yl. in Apply now (2.122 1 Carmelo Giacovazzo Fig.1 we obtain a2((a) = {a2(a)sin2 a + a2((p)(sin(p cos y + cos a*cos (p sin y)' + 02(y)(cos(p sin y cos a*sin (p cos ~ ) ~ ) l ( sa*sin (p sin Y ) ~ . This supplementary information is of primary importance in assessing the accuracy of the parameters themselves. b. The variance of the parameter f i n terms of variances of and covariances among other directly determined parameters p is If the pjs are uncorrelated then (2.83) reduces to As an example. 2. cos a + A3)2[A3: + c2(c?(z1) + a2(z2))] + (AlA2a(y) sin y)' + (AlA3a((p)sin (p)' + (A2A3a(a)sin a)2).16.. cos + A. z2) respectively. On applying (2. The radial displacement is approximately given by d . The libration axis n is normal to the page through 0 .cos o ) d((u2/2). + A3 cos a ) 2 [ ~ : ~+ b2(a2(yl)+ 02(y2))] : + (A. cos y + A. Thermal motion is expected to produce distortion also in apparent angles. Then + 1 a2(d) = 7 {(A1+ A2 cos y + A3 cos ( p ) 2 [ ~ T+ a2(a2(x1)+ a2(x2))] ~: d + (A.84) to the expression of V in Table 2. y are known. a librational meansquare amplitude of 10' may lead to shortening of interatomic distances of up to 0. (2. 2. B1 = sin a(cos a . d is the distance from P to the axis.3b) in order to derive a2(d2).d cos o d(1. As an example.where d is the distance between two uncorrelated atoms positioned in (xl. B2 = sin (p(cos (p .025 A. = a(b)/b. A3 = a(c)/c. let us calculate the standard deviations of the unit cell volume V and of the angle a*when the standard deviations of a. A.85a) .cos (p cos y)a(a). = o(a)/a. To study this type of effect the joint distribution of three correlated thermal motions has to be taken into account. together with variances of the parameters and covariances among them. c.cos a cos (p)a(y).
cos 8)/d2. = c20:. defined on p. Then (2.dAB (ABC) . any error in one position is completely correlated with the error in the other and where a is measured in the direction of a line joining the atomic centres. The covariances among the unit cell parameters are usually available from the leastsquares refinement of the unit cell parameters.. sin (ABC) .d~~cos (BCD))] cD sin (BCD) = If in the first expression dAB dBCand a common a2is assumed then a = 2a2(2 . : = a2&.85a) is simpler if the errors on the unit cell parameters can be neglected. = bZa. It may be observed that 20 (standard deviation for the distance of two completely correlated atoms) is larger than (standard deviation for the distance of two uncorrelated atoms: see eqn (2.cos cp)(l .85a) reduces to  For pairs of symmetryrelated atoms (2. and the general expression (2.cos o)]. = a and a2a. torsion angles. . : If in the second expression dAB dBc do.2 cos o cot (BCD)( cos dBc ..85b) for al = a2).cos cp(1.dAB cos (ABC) dAB (ABC) sin .Crystallographic computing ( 123 (2. and a common a2are assumed then a 2 ( o )= 4u2 [I . By an analogous technique the standard deviation^["^^^^] of bond angles. An additional simplification is obtained if the errors are isotropic (i.2 cos w cot (ABC)( . for a pair of atoms referred by an inversion centre. and leastsquares planes may be obtained. = b2at2 c2afZ a:) and the axes are orthogonal. d2 sin2 cp . In general any pair of atoms in a structure are neither completely independent nor completely correlated.dcD cos (BCD) cD sin (BCD) ~ B C . Thus. To assist the reader the simplified expressions of the standard deviations for bond angles 8 and torsion angles o are quoted: a&BcD) = dAB (ABC) sin2 2 + d& sin2(BCD) .e. equal bond angles (ABC = BCD = cp).. An estimate of the covariance between the positional parameters pi and pj is usually obtained from the structure leastsquares refinement (as the ijth element of the matrix M. 92).83) has to be invoked.85a) cannot be applied.
The conclusive inference is that the two bonds differ. then a statistical criterion may be used to decide if d l and d2 are significantly different.A Some metric relations between direct and reciprocal lattices Let us prove that V* = 1/V. If 6 is assumed to be distributed around zero according to a normal distribution with standard deviation a. = a.. It is often required to take a decision whether a bond lengtb or angle differ significantly from some others. According to (2. the quantity is evaluated and compared with the tables of the xi.85b) a(d) = 0. owing to second and third relations (2.003 A. = a. suppose that two independent CC bonds dl and d2 are found which differ by 0. = a.. y* from direct lattice parameters.39 times larger than a. p*. Derive now the expres .1 are obtained by cyclic permutation of the parameters.8) 1 V* =(b v3 A c ) . For example. [(c a A 1 b)a] =  v ' Derive now the values of a*. = 0.02A. Expressions for sin p* and sin y* quoted in Table 2. We are required to decide if a sample of n observed bond distances di is drawn from a common population or not.13) from which. distribution. According to the first eqn (2. Appendices 2.d2 is It is therefore found that the observed value of 6 is A = 3.12b). while the isotropic standard deviations for the atomic positions are a.124 1 Carmelo Giacovazzo Two simple examples on the use of the variances of the parameters in crystal structure analysis may be described: 1. By definition Owing to (2. sin a* = v abc sin p sin y is obtained.. If the di are assumed to be normally distributed about the mean (d).0042 A while the standard deviaton associated with 6 = dl . 2.
The family of planes H = (hkl) belongs to the zone [uvw] if Indeed if (2. r i .1) is verified then r i is normal to r. The condition that the point P(x.B Some geometrical calculations concerning directions and planes All crystallographic planes parallel to a given direction are said to belong to the same zone.cos a)/(sin p sin y).By definition 1 1 b*c* cos a*=(C A a ) .17a). According to p.B.7) and the above derived expression of sin a* gives cos a*= (cos p cos y . We require that the projection of r = xu yb zc onto the direction of r i be equal to n times the interplanar spacing d H : + + r . Angle 4 between two planes H. The planes HI. are coplanar. . 7 any vector ru = ua + vb wc defines the crystallographic direction [uvw] which is also the symbol of the zone. r i .2) . 2.B. H3 shall belong to the same zone if r i . H2.r i / r : = ndH= n l r i from which r r i = hx .1) 4. Symbol of the zone [uvw] defined by two planes HI and Hz. (a b*c* b*c* V2 . . z) lies in a plane (the nth of the set from the origin) of the family (hkl).Crystallographic computing 1 125 sion of cos a*. . (2. cos 4 = r H l . We derive now the following results: + 1. + ky + lz = HX = n. r i . 2. * * ' d H l d H 2 r irli 2 .1 may be obtained by cyclic permutation of the parameters. Then they shall define a cell in the reciprocal lattice whose volume is zero: 5.B. r ~ l r ~ 2 where r:. may be calculated by means of eqn (2. 3. Because of (2. The expressions for cos P* and cos y* quoted in Table 2. so that the planes (hkl) are parallel to ru. = (hlklll) and H2 = (h2k212): . Using (2. y. A b).
where rl and r2 are the positional vectors of the two points.r2) = 0. Plane normal to the unitary vector n:r n = d. these points give rise to the nth layer line in a rotation photograph when the crystal is rotated about the axis [uvw]. In terms of coordinates ("' X~XI x3 . k. P2. Plane determined by the three points Pi. 1 can be found for which ri A r u = (ha* + kb* +lc*) A (ua + v b + wc) =O. It is the same problem as in 5 above. Projection of the vector r. Line through the point Po and perpendicular to two unitary vectors u and v:(r .B. (2. 1 coincide with u.126 1 Carmelo Giacsvazzo 6.3) defines the reciprocal lattice points which lie on a plane normal to the direction [uvw] defined in the direct space. (2. w respectively (in other words the plane (uvw) is perpendicular to the direction [uvw].5) .ro) A (u A v) = 0. As it will be seen on p.B. . on to the unitary vector n (from now on we will denote by N and N* the matrices of the components of n with respect to direct and reciprocal bases respectively): 12. P3 whose positional vectors are P l . The required condition is therefore Note that the lattice vector ru = ua + vb + wc defines the direction [uvw] orthogonal to the planes (uvw) of the reciprocal lattice. p3:(r PI) ' (p2 pi) A (p3 PI) = 0.rl) A (r . 247. 1) of the reciprocal lattice lies in the nth (starting from the origin) plane of the set of planes (uvw) of the reciprocal lattice. 10. = a . but transferred in the reciprocal lattice. 8.Yl ") I 2221 23 =O. Indeed ru= 0 owing to the fact that a * ~ a = b * ~ b = c * ~ c andO u a * ~ v b + v b * ~ u . n = ~ * ~ = d . Therefore eqn (2.4) derives from (2. In cubic lattices h. Line parallel to the direction n and going through the point ro:(r ro) A n = 0.B. r3 =P3 is vanishing. where d is the distance of the plane from the origin. 7.= = 0. 13. v. Such a plane will exist if a triplet of integer numbers h.B. Line determined by two points: (r . P2. r 2 = p 2pl. 9. k.4) . It may also be written r . The condition that the point P(h.X1 Y Y1 y2yl Y3 . Condition for the existence of a lattice plane perpendicular to the direction [uvw].21 Equation (2. k.5): indeed the unit cell volume defined by the vectors i =P i . 11.
[I/$& i l f i .r .Crystallographic computing 1 127 14.1.7) 15.1: more explicitly .C. A3 = eie.2~ cos 8)(1 .d = 0: P(rl (1 n*) = rl . for an improper axis it is 1. any linear combination of the corresponding eigenvectors is an eigenvector itself. The corresponding eigenvalues are [O. Distance from P1 to the plane N*X . Furthermore. the basis vectors of a facecentred lattice.C Some transformation matrices Transformation matrices conventionally used to generate primitive from centred cells are shown in Table 2. The secular equation will be cos8A sin8 sin 8 det (R. Plane normal to the unitary vector n and through the point defined by ro: ( r . in a Cartesian system. let R = R. = eie.C. A = 1 is one root. For example. the basis vectors of a primitive unit cell for the same lattice. bF. 1: the eigenvectors are any three unitary vectors orthogonal to each other. the 1 1 in matrix 1 i 010 i 010 0 1 represents the twofold symmetry axis 211001 a hexagonal framework. 01.A = (1 ( + 0 0 1A . Principal axes of the symmetry operator R.7) n = rnln and d = d'lm have to be calculated. Projection of the vector rl on to the plane N*X . If the plane is defined by means of the equation r rn = d'. the identity operator has three eigenvalues 1. and AP=(aP.A)= 0. To give an example. ) ~ * 17. If sin 6' = 0 all the eigenvalues are real. [l/fl. before applying (2. 1. For a proper rotation axis the eigenvalue is + 1. The above result may be generalized to a rectilinear coordinate system: there will always be a real eigenvalue the eigenvector of which corresponds to the direction of the symmetry axis.B. ) . If sin 8 # 0 the other eigenvalues are A.( N * x .B.Al) = det cos 6' . Then Ap = MAF. If two eigenvalues are equal.) =o. 16. 2. cF). 01 respectively. .B.d = 0: D = N*Xl .1]. cp). (2. where M is one of matrices shown in Table 2. where rn is a general vector.6) (2.d. 0.D Reciprocity of F and I lattices Let AF = (aF. n = N*(xx. bp. The eigenvectors corresponding to the doubly degenerate eigenvalues 1 are normal to [loo] . A vector r along an axis of R should satisfy the eigenvalue equation Rr = Ar. 2. i/fi.
= (M)~R. (2. I ... according to (2.MX' (M)'T.* and A we obtain : where all of h. are integer numbers) or odd values (when hI.C. = RpX T. If we index the reciprocal lattice with respect to A. = R.1.. = (M)~R. These are just the conditions for systematic extinctions in an F lattice. according to the relationships A' = M A According to Table 2. will either assume even values (when h.18) (from A to A') transforms the space group symmetry operator C. = 21. Let us first prove that the basis vector transformation (2. from which : or. where R. are of type m/2. 2b:. A = QA:. = (Rk.1) The relation X. = (MIIT.1) with : the matrix which transforms an I cell into a P cell. 2c:.) into C. T. = (R. k . is transformed. which coin + + + ..20).E. = 2k1. 2. where Q coincides (see Table 2. n.). into MX.C. T.E. from which X. Transformation matrices M conventionally used to generate centered from primitive lattices and vice versa. p). 1.M. in matrix notation. T. 657. p / 2 with integer values of m.MX' T. It may be concluded that the reciprocal of an F lattice is an I lattice whose cell is defined by the vector 2a:. k. n/2.128 1 Carmelo Giacovazzo Table 2. 1 A = (M)IA:. k. 1.E Transformations of crystallographic quantities in rectilinear spaces In this paragraph we describe the transformation properties of crystallographic quantities not studied on pp. = 2h1..
*=GT.E. We obtain G''RYG' = (M)'G~R.E.16) in the first eqn (2.2) If the second of the equations (2.l x ' * = .9) is introduced into the first equation (2.*M' A and T * = MT.E. Then R. T) will have identical expression both in direct and in the reciprocal space.E.E. T.* = (R. which. In an orthonormal system a* = a.~R.G~ (R. Indeed.7) Note that (2. (2. The list of the symmetry operators in the reciprocal space may be obtained without inverting the various matrices. A particular case of (2.1). if R is a symmetry element in the direct space.Crystallographic computing 1 129 cides with (2.E.)l.5) are the transformation rules of the Miller indices (hkl). R. C * e C 1 * : introduce the first eqn (2. Owing to (2.3) In conclusion. b* = b.According to (2. A' = GIA'* = MGA*.21).2) in the first eqn (2.E. the set R operate in reciprocal space (however. Note that the trace of R is invariant under transformations such as (2. = (2.G*. We describe some of them: 1. Therefore any symmetry operator C = (R.)~GR.E.1) occurs when A' =A*.25).E.2) the following result is obtained R. may pertain to different symmetry elements). On postmultiplying both sides of this equation by GI* we obtain I = MG*~MG'*from which 4.E.. if the operator R is a symmetry element in the direct space. It is often useful to know the transformation rules valid in reciprocal space when the basis vector transformation A' = MA is performed in direct space.21). and R. Consequently.A. X*@X1*: by analogy to point (1) it may be obtained Note that relations (2. that gives 2.6) gives R * = MR. Furthermore R = R' holds. (R)' is a symmetry element in the reciprocal space.7) represents the transformation rules for the reciprocal space symmetry operators generated by a basis vector change in direct space. Q * e Q 1 * .E. as already obtained in Appendix 1.5) it will be x*Q*x* x l * ( ~ ) . 5.l). A* e A 1 * : according to (2.*=GR. introduced into (2.* A (2. c* = c and G = I.E. group properties guarantee that R' is also an element of the direct space symmetry group: therefore R is a symmetry operator of the reciprocal space symmetry group.l Q * ~ . which thus becomes GI*' = MG*IM.1). if the set of matrices R operate in direct space.E.*GM. 3. G * e G 1 * : let us introduce the first eqn (2.
E. (2. C ' . In this case the metric matrix will not vary: indeed. c) into A' = ( a ' .1.F.b ' .9)) to G. In accordance with eqns (2.19) and (2.X A M ~ ' F .E. C*.   from which Qr* = (M)'Q*M'. b*. T its translational part): C. c'). A*.8) The transformation rules obtained in this paragraph and on pp.(a. c*) and A'* ( a r * .E.8) As an example.b ' * . In accordance with (2.E. M~' By _applying to (2. A'* respectively.1. 657 are collected in Table 2. C'* are symmetry operators defined in A. G and G' are the metric matrices of A and A' respectively.130 ( Carmelo Giacovazzo Table 2.~ M ~ ' A X + ~(2.D) are (see Pi1 = P331 Pi2 = P137 Pi3 = P23) 2. A particular basis transformation is that corresponding to a symmetry operation. C (R. A'. G* and GI* are the metric matrices of A* = ( a * .20) a transformation R acting on the coordinates is equivalent to the transformation M = (R)' acting on the basis vectors. Find now the relationships existing between the matrices 8' and p defining the anisotropic temperature factors of the atoms related by a symmetry operator. In the table M is the matrix transforming A . Q and Q* are the quadratic forms of A and A*.1) the differential operator 6 we obtain (note that SX = 6X) . G' = (R)'GR~ which is identical (because of (2. Q* = MQ'*M. according to (2.21).F Derivation of the normal equations Because of (2. the reader will easily verify that the relationships existing in the cubic system along the components of p of two atoms related by the symmetry axis 311111 the matrix given in Appendix l.F.52) may be written as S = V M ~ ' V = F M ~ ' F .T) is a symmetry operator (R is its rotational part. c ' * ) respectively. Transformation relationships. b.1) A X .50) the parameter S in (2.
Subdivide the x axis in N parts so that .X)) = m. (9) = ((F .H. ((X .(X .55). the first two terms on the righthand side of (2.F)M.G.G Derivation of the variancecovariance matrix M x Because of (2.'F~ B X (F.1) According to (2.'(F .54) A' = B~AM. 2.56) may be written as M. Therefore 6s = ~(%)(AM.A~F)(B~AM.'AX .F ) and ( 2 . = 2.((X .~so that (2.Nf) then which coincides with (2. and with variancecovariance matrices of rank n and m respectively.~F) =0 from which (AM.A~F). For the same reason the third and the fourth terms are equal too.1) where N/2 s h ' < N/2.X)B(XX) where X = AIF.~ A M F.X) are random variables with zero means and finite variances.F.2) are 1x 1 matrices which are equal (My1 = ~ 7 ' ) .1) reduces to F ) .Crystallographic computing 1 131 Since X and 6X are vectors.I(F= F)) ~ A M Y ~ A ) ~ . 2.X)B(X .55) the eqn (2.F)Myl(F (F . Let us calculate (2.F)(F .'A)X = A M ~ ~ F .~(% 7 . In this condition it is possible to show[451 that ((F .F ) ) = n.1) Y Because of (2. ~F (2.). which coincides with (2. = ( ( B .H.(FM.~F .1.1 The FFT algorithm and its crystallographic applications Suppose that we want to calculate the onedimensional transform p(x) = h' F(h ') exp (2nihrx) (2.1) becomes M = B~AM.~ A M ~. eqn (2.54) and (2.53).H Derivation of the unbiased estimate of M.G.58).~M~M.1) for X = 2 : then 3 = FM.F)M.AM.~A ~F S = FM. B~AM.~((F .F))M.F.~F . Therefore I f Mf is known within a scale factor (Mf = K.x)M.'AB'= .x)). The expected value of 3 will then be . (2.~AB~ B'.
h.1y' 2 F(h) exp (2nihjlN) h =O where wN = exp (2nilN). . . 1 . . s . r . .1 ) . h o i ~ W f ~N ~ W h ~ i ~ i s1 p(j) = p(jo. . s . Because of the transformation h ' + h the negative indices are removed: furthermore.1. . r . ho)w. Then (2. T(jo.I)]:  + Similarly. If N is not a prime number. (N . As in the BeeversLipson procedure the expression (2.1 and jl=O.1 and ho = 0. .3) by the classical method requires N2 . 1. .1 . . Step 2: calculate forjo=O. . . . . .132 1 Carmelo Giacovazzo Denoting h' = h .. .) values can replace F(hl.1.1. While the evaluation of (2. W# = W . 1.1 . the expression jlr [O. the number of Fourier coefficients is chosen equal to the number of points in which p has to be calculated (the F array may h eventually be completed with a number of zeros).N/2 gives exp (2nih1x)= exp (2nihjlN) exp (nij) = (1y exp (2nihjlN) where 0 G h < N. . jl) = (1y ho=O h1=0 2 2 F(hl. . 1 . r . .1.3) may be calculated in two Step 1: calculate for jo = 0. (N . 1 . . ho) values in the memory of a computer since these last are no longer necessary.A. ( = O 1 .1 p(j) = (. ho) represents the F factor obtained by combination of hl and h ho in eqn (2. .2). say N = r s (of particular interest and simplicity is the case N = 2")) then the expression hls ho will generate all the integers h in the range [0.hoJ1wfljO h"io WN r1 where F(hl.1 1 1 j=jlr+jO Then and + jo will generate all the integers j in the range jo=O.21) becomes N.
. which are not displayed by single crystals. Calculations are organized into two steps: + + 1. 2. 6 FT * (2nik)F(H) These more recent developments have made possible the use of a fullmatrix leastsquares for macromolecule structure at a reasonable cost. 92). Besides calculating electron density maps. Step 1: All the atoms (in the asymmetric unit) which contribute to the electron density are selected. the FFT method is also used for the calculation of the structure factors when the number of atoms is very large and computing time has to be saved. the FFT method involves r(s r) operations in the first step and s(s r) operation in the second step. which provides structure factor magnitudes and phases.Crystallographic computing 1 133 operations. in accordance with p. the following properties of the Fourier transform hold: Real space Reciprocal space 6dr) 6Y etc. calculation of the gradient vector D and of the normal matrix B (see p. 145. For each of them the electron density is nothing else but the Fourier transform of the atom scattering curve corrected for thermal motion. with special references to minerals. Usually each atom is represented by a single Gaussian function (for low resolution data) or as the sum of two or three Gaussian components. 2. From the figures the reader will conclude that morphology exhibited by twins often shows reentrant angles. If N is sufficiently large that corresponds to a large saving of time. The overall model electron density map is sampled on a grid not too fine (that would greatly increase cost and computer storage) and not too coarse (in order to avoid too rough an approximation of the electron density). Step 2: The fourier inversion of the map is made. Besides structure factor calculations most of the steps involved in LSQ structure refinement can be performed by the FFT algorithm:[125~1261 the i.e. Indeed. Ten ~ i c k [ ' proved that ~~] the number of grids may be taken small by artificially increasing the B value of the atoms. The speed of steps 1 and 2 depends on the number of grid points in which the density has been sampled and on the number of terms in the Gaussian approximation to the atomic scattering curve.J Examples of t w i n laws Some examples of twin laws are described here. Too coarse a sampling grid would produce structure factors which are the sum of the desired ones and those with indices spaced away by multiples of N.
(b) penetration twin.4(b).J. a righthanded crystal is shown in Fig..1.l(c). (a) (b) Tetragonal system \Iiiil (c) / Cassiterite (SnO.134 1 Carmelo Giacovazzo A Cubic system Twinning according to the spinel law is commonly found in crystals of the class 43m. 2. Orthorhombic system Aragonite (CaCO. Fig.J. The twinning is due to the ability of structural layers parallel to (1102) to slide past each other. 2. Japan twins. In Fig. where the two cubes are rotated about [ I l l ] (classical mineral: fluorite).J. which are often polysynthetic. Twinning occurs on (1121. In Fig.J.). . An interpenetrant rotation twin about [ l l i ] is shown in Fig. 2. shown in Fig. or penetration. 2. (d) classical pentagonal dodecahedron of pyrite. The most important are listed below. presents the so called elbow twin.l(b). more frequently (1102) (see Fig. and the Brazil twin is displayed in Fig.4(c). (c) interpenetrant rotation twin. point group mmm.3(a)).J. point group 3m) is often (0001) (see Fig. point group 42m) are commonly tetrahedral. separated by a very irregular surface. Two right. Quartz (SiO. point group m3. contact twins with (1122) as twin and composition plane (see Fig. ( ~ i 0 2 and zircon (ZrSiO. The c axes intersect at 84'33'. Such types of twin are useless for electrical work.2.J. which often exhibit forms (111). Hexagonal and trigonal systems Twinning is rare in minerals of the hexagonal system and frequent in minerals of the trigonal system.J.J. ) Calcopyrite crystals (CuFeS. one pair of faces (1010) is common to both pairs of twins. This combines right.and lefthanded crystals in a penetration twin (often with plane composition surface). 2. 2. 3. twin plane {101).2..4(d)).J. point group 4/mmm). with (1120) as the twin plane. polymorphous with calcite) often twins on (110) faces.3(b)).4(e)). 2.J. (e) iron cross law. 2. 2. lamellar. 2.J.J. and may be detected in polarized light (the plane of polarization is rotated in opposite directions by the two parts of the twin). The elbow twin is also found in rutile .J.. . The twin plane (and the composition plane) in calcite (CaCO.. 2. Then the faces (10i1) of one individual and the faces (0111) of the other will coincide (see Fig.or two lefthanded individuals are combined. A lefthanded single crystal is shown in Fig.l(e). Spinel law.J. with (112) as the dominant form. with form e = (210): twinned crystals display the form shown in Fig. with c as twin axis. 2. Crystals of pyrite. Elbow twin.4(a).l(d) the classical pentagonal dodecahedron is shown. Brazil twins. 2. 2. This last twin is readily provoked by mechanical deformation (for example. 2. 2. contact. the pressure of a razor blade on a rhombohedron of calcite). (a) Twin plane (1 11). point group 32) twins in several ways.J.l(a)). frequently obey the iron cross law: they twin with (110) as a twin plane. The same law applies to the penetration twin shown in Fig.J.. 1. Twinning occurs with (111) as a twin plane (see Fig. 2. Dauphine twins.5(a) a single crystal of aragonite in shown. Fig.
. 2. . 2. Some examples of calcite twins. 2.J. (a) Plane {OOO1). or Manebach law.J.J. (d) Dauphin6 twin: interpenetration of two lefthand crystals. point group mmm) forms cruciform penetration twins: if the twin plane is (032) then the two individuals form a nearly rightangled cross (Fig. While Carlsbad twins are penetrating twins.6(b)). Fig.c)). The twin and composition plane is (021) in Baveno twins (see Fig. 2.6(a)).b. (a) Lefthanded quartz. Monoclinic system Orthoclase crystals (KAlSi. point group i] the albite law is often satisfied: twin plane (010) . 2. 2.08. 2. Na)(Al.J. Triclinic system In twins of plagioclase feldspars [(Ca. an oblique cross (angle =60°) is formed by twinning on (232) (see Fig. (c) Brazil twin: the twinning plane is indicated by a broken line. 2.J.7(a)).J.Crystallographic computing 1 135 in Fig. Staurolite (A14FeSi2010(OH). (b)righthanded quartz.8(a. Baveno.3. Twinning is often repeated and produces interpenetrant triplets of pseudohexagonal shape (Fig.5(d)).J. (b) twin plane {lio2). 2.J.5. and (001) in Manebach twins (see Fig. In the Carlsbad law c is the twin axis and (010) the composition plane (see Fig. Baveno and Manebach are usually contact twins. Quartz twins.7(c)). Si)A1Si208. Also common is the (b) Fig.J. in Fig. 2.4. 2.7(b)).5(b) a twinned crystal is displayed.5(c) the structural scheme of the twin is given. type of twinning usually multiple and polysynthetic (see Fig.J. point group 2/m) often twin according to the Carlsbad.
Orthoclase twins. (b) twinned crystal. (d) triplet. . (4 Fig. (c) Manebach twin. 2. (b) Baveno twin. Aragonite twinning. 2.8.7.J. Plagioclase feldspars. (a) Twin after {032}.6. (c) structural scheme of the twin. (b) twin after {232).136 1 Carmelo Giacovazzo Fig.5. (a) Single crystal.J. 1 1 (c) (c) Fig. (d) twin by pericline law. 2. (a) Single crystal. (c) polysynthetic albite twin. Fig. (a) Carlsbad twin.J. 2. (b) twin by Albite law.J. Staurolite twinning.
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4 and 2. This experiment was successfully performed by Friedrich and Knipping. In 1912 M. or refraction. and KI. if Xrays are used. Although the theory of diffraction is the same for all types of radiation. von Laue used Xray diffraction patterns for deducing the structure of NaC1. we shall consider Xray scattering with particular interest: some references to electron and neutron scattering are made in Appendix 3. 195 and 198. The vectors electric field E and magnetic field H are both orthogonal to the direction of wave propagation. in only few years. In such a way. In addition. L. both students of Rontgen. starting from an article by Ewald. The range of Xray wavelengths is placed between the ultraviolet region and the region of yrays emitted by radioactive substances. electrons. a student of Sommerfeld. von Laue. reflection. Let us recall some properties of electromagnetic radiation: 1. The refractive index of Xrays is very near to unity: for A = 2 A and for highdensity substances the difference from unity is of the order lop4. Thus. Several years later Sommerfeld measured an Xray wavelength of about 0. suggested the use of crystals as natural lattices for diffraction. In 1913 W. The interval of wavelengths of particular usefulness in crystallography ranges between 0. . or neutrons. 4. For this reason the Xrays cannot be focused by means of suitable lenses like ordinary light or electrons. However. being lo' for most cases. KC1. Bragg and M. KBr. they are mutually orthogonal and vary sinusoidally with time. the electromagnetic nature of Xrays and their usefulness in the determination of crystal structure was indisputably demonstrated. 3. The most important properties of Xrays were described by Rontgen in 1896.4 A. with equipment in common use in optics at that time he could not measure any effect of interference.The diffraction of Xrays by crystals CARMELO G I A C O V A Z Z O Introduction Crystal structure analysis is usually based on diffraction phenomena caused by the interaction of matter with Xrays.B pp. 2.5 A. Electromagnetic radiation propagates in a vacuum with the velocity c equal to 300 000 km s'. we cannot talk about a direct observation of objects by means of instruments equivalent to optical or electron microscopes.
they constitute the Compton radiation (see pp.ia]. 2. Thomson scattering Q . Other photons are scattered with a small loss of energy. 3. Readers not acquainted with such a mathematical concept are urged to consult Appendix 3. Let us orient the axes y and z of our coordinates system in such a way that the observation point Q defined by vector r is in the plane ( x . In this case the photon energy is used to remove one of innershell electrons of the absorber element. 1656) 1 Eod .142 1 Carmelo Giacovazzo The interaction of Xrays with matter essentially occurs by means of two processes: 1. 1856) with wavelength slightly greater than the wavelength of the incident radiation. exp Fig. and amorphous solids are described in Appendix 3.Eoi(e2/mc2) 9 = sin r . They constitute the scattered radiation with exactly the same wavelength as the incident radiation. Thomson showed that (see also pp. Major emphasis is given to diffraction by perfect crystals.C. r). Diffraction theory is described by making use of Fourier transforms. At the point Q we will measure the electric field Ed due to scattered radiation Ed= EOd [2niv(t . liquids. y). 3.X/C) is where EOi the amplitude of the wave and Ei is the value of the field at position x at time t. (a) A free charged particle is in 0: a plane monochromatic electromagnetic wave propagates along the x axis. The field exerts on the particle a periodic force F = eEi and therefore the particle will undergo oscillatory motion with acceleration a = F l m = eEi/m and frequency v. The photons can be absorbed by the atoms of a target and will increase its temperature. Let suppose that (see Fig. (b)Surface element at scattering angle 28.l(a)) a free material particle with electric charge e and mass m is at the origin 0 of our coordinates system and that a plane monochromatic electromagnetic wave with frequency v and electric vector Ei propagates along the x axis in positive direction.1. but basic elements of diffraction by gases. The present chapter is mainly devoted to the socalled kinematic theory of diffraction (only few brief remarks on some aspects of dynamic theory of diffraction are given on pp. Absorption phenomena will be discussed in Chapter 4. In accordance with classical theory of electromagnetism a charged particle in accelerated motion is a source of electromagnetic radiation: its field at r is proportional to acceleration and lies in the plane (Ei. Its electric field is described by equation Ei = Eoiexp 2niv(t . Some photons of the incident beam are deflected without a loss of energy.B). 1625 and Appendix 3.rlc) .A. Discontinuities in curves of absorption are caused by the photoelectric effect. This atom can come back to its minimal energy state by emission of a photon X whose wavelength is characteristic of the atom (fluorescent radiation).
If we want to obtain the total scattered power P we have to integrate (3.1) becomes e4 ZeTh = Zi 7 q. The term sin q. from now on and according to tradition. then I.. ~ mrc + If the primary beam is not polarized..3) gives the intensity scattered into a unit solid angle at angle 28.. It may be calculated that the total fraction of incident radiation scattered by one 'crystal' composed only of free electrons and having dimensions less that 1mm is less than 2 per cent. If the primary beam is completely polarized: (a) with Ei along the z axis. Equation (3. The total scattering 'crosssection' PI4 is equal to 6. Therefore. = ~~e~ 28/(m2r2c4).. then I. If K1 and K2 are parts of these two beams in percentage we obtain ZeTh = 4 e4 (K1 K2 C O S 28).The diffraction of Xrays by crystals 1 143 where q. The decrease of Ed with r is caused by the scattering of radiation in all directions. It suggests that the radiation scattered in the direction of the incident beam is maximum while it is minimum in the direction perpendicular to the primary beam. 303). which is a very small quantity.3) from 0 to n (see Fig. the symbol e will represent the electron charge. = 4e4/(m2r 2c4). 2nr2 sin 28 d(28) where (2nr sin28) r(d(28)) is the surface element at angle 28. 3.where 28 is the angle between the primary beam and cos2 the direction of observation. is the intensity of scattered radiation and Zi is the intensity of incident radiation. In terms of intensity eqn (3. the computation can be executed by decomposing the primary beam into two beams whose electric vectors are perpendicular and parallel respectively to the plane containing the primary beam and the scattered radiation being observed. then K1 = K2 = 112 and where P = (1 + cos228)/2 is called the polarization factor (see also p. a is the phase lag with which the charge reemits the incident radiation. In general. The scattered radiation will be partially polarized even if the incident . sin2 mrc where I. is the angle between the direction of acceleration of electron and the direction of our observation.l(b)). (b) with Ei along the y axis.7 x cm2/electron. This simple result excludes neutrons from the category of Xray scatterers because they do not have electric charge. and makes negligible the contribution to scattering by protons whose factor (elm)2 is about 18372 times less than that of electrons... is a polarization term: we 'see' only the component of vibration parallel to the observer and normal to the direction of propagation.
144 ( Carmelo Giacovazzo radiation is not.048) is reached for 28 = n (backscattering) which is small but significant for wavelengths of about 1A. Thus. BO = r s. 185) (3.r 9 so. if the beam is scattered first by a crystal (monochromator) and then by the sample the polarization of the beam will be different. Point scatterers are in 0 and O'. Interference o f scattered waves Here we shall not be interested in wave propagation processes. the Compton effect.2 two scattering centres are at 0 and at 0'. This fact permits us to omit the time from the wave equations.4) The following properties emerge from eqn (3. It is impossible to calculate interference effects for Compton radiation. which can be considered stationary. Besides. The scattering is coherent.B. 3. But experiments with light elements have revealed a completely different effect. Compton scattering is incoherent. One could suppose that scatterers composed of light elements with electrons weakly bound to the nucleus is a good approximation to the ideal Thomson scatterer.024 (1 . p. In Fig.so and s are unit vectors. Let so be the unit vector associated with the direction of propagation of the primary Xray beam.4): Ah does not depend on the wavelength of incident radiation. Ah (A) = 0.2. 3. These patterns are constant in time since they are produced by the system of atoms. according to Thomson.cos 28). Ah = 0 for 28 = 0. Consequently there is a difference in wavelength between the incident radiation and the scattered one which can be calculated by means of the relation (see also Appendix 3. The incident photon is deflected by a collision from its original direction and transfers a part of its energy to the electron. because there is a well defined phase relation between the incident radiation and the scattered one: for electrons a = n. Unfortunately it is very difficult to verify by experiment the Thomson formula since it is almost impossible to have a scatterer composed exclusively of free electrons. Compton scattering The process can be described in terms of elastic collision between a photon and a free electron. where . but only in diffraction patterns produced by the interaction between waves and matter. the maximum value of AA (Ah = 0. If a plane wave excites them they become sources of secondary spherical waves which mutually interfere. The phase difference between the wave scattered by 0' in the direction defined by the unit vector s and that scattered by 0 in the same direction is Fig. it causes a variation in wavelength but does not involve a phase relation between the incident and the scattered radiation. Therefore A 0 = .
The modulus of r* can be easily derived from Fig. for obtaining the observed experimental intensity it is sufficient to multiply f by I. From the theory of Fourier transforms we also know that p(r) = lv% F(r*) exp (2nir* . . ) . Equation (3.7a) where Aj is the amplitude of the wave scattered by the jth scatterer.2: r* = 2 sin elil (3.7a) becomes F(r*) = x h exp (2nir* ' I . If these are electrons. 3.2 is the trace of the plane passing through 0 ) we can consider interference as a consequence of specular reflection with respect to these planes.7b) If the scattering centres constitute a continuum. an atom) in terms of intensity I. In our case it is more convenient to express the intensity I scattered by a given object (for example.A. If there are N point scatterers along the path of the .. The wave scattered on the element dr is given.r) dr* = T'[~(r*)]. scattered by a free electron. The ratio I/IeTh is f2. 3.9) . in amplitude and phase. According to the convention stated above eqn (3.The diffraction of Xrays by crystals 1 145 If A is much greater than r there will be no phase difference between the scattered waves and consequently no appreciable interference phenomena will occur. If A is the amplitude of the wave scattered by the material point 0 (its phase is assumed to be zero) the wave scattered by 0' is described by A. If we outline two planes normal to r* passing through 0 and 0' (OQ in Fig. Vice versa.. In this case for expresses the number of electrons. j=1 N (3. Since interatomic bond distances lie between 1 and 4 A no interference effect could be observed by using visiblelight waves.8) where T represents the Fourier transform operator. To give an example. 175) of the density of the elementary scatterers. by p(r) dr exp (2nir* r) and the total amplitude of the scattered wave will be . exp (2nir* r). the element of volume dr will contain a number of electrons equal to p(r) d r where p(r) is their density. F(r*) = 1 v p(r) exp (2nir* r) dr = T[p(r)] (3.. where f is the scattering factor of the object.. p. I.) (3.8) constitutes an important result: the amplitude of the scattered wave can be considered as the Fourier transform (see Appendix 3. . The Thomson formula plays an essential role in all calculations to obtain the absolute values of scattering. incident plane wave we have F(r*) = j=1 x Aj N exp (2nir* . let us imagine a certain number of electrons concentrated at 0' which undergo Thomson scattering.. In crystallography the space of the r* vectors is called reciprocal space. the amplitude of the scattered wave is the Fourier transform of the electron density.6) where 28 is the angle between the direction of incident Xrays and the direction of observation. (3.
33)) as: where Ue(r) = 4nr2pe(r) is the radial distribution of the electron and r* = 2 sin 8/A. a portion of the energy of the incident photon is converted into potential energy of an excited atom (conditions for incoherent scattering). If we assume that p. An atomic electron can be represented by its distribution function pe(r) = 1v(r)l2. In fact both processes are simultaneously present and they are precisely described by modern quantum mechanics.. If.11) gives respectively. etc. the electron conserves its original state the photon conserves entirely its proper energy (conditions for coherent scattering).15 A'. The volume dv contains p. In common practice the scatterers are atomic electrons: they can occupy different energetic states corresponding to a discontinuous set of negative energies and to a continuous band of positive energies. If the electron changes its state. d. For instance. and two 2p electrons in carbon atom. Then.A.. In radial approximation the 2s and 2p electrons have an equivalent distribution.(r) has spherical symmetry (what is in fact justifiable for s electrons. For carbon the Slater formulae give with cl = 10.10) where S is the region of space in which the probability of finding the electron is different from zero.10) can be written (see eqn (3.. Quantummechanical calculations indicate that the processes of coherent and incoherent scattering are simultaneously present and that I. there are two 1s electrons.77 Al..146 1 Carmelo Giacovazzo Therefore. two 2s electrons. can be calculated on the basis of the following observations. c2 = 6. dv electrons and scatters an elementary wave which will interfere with the others emitted from all the elements of volume constituting the electron cloud. Zincoe = + The coherent intensity I. where v ( r ) is the wave function which satisfies the Schrodinger equation. after interaction with the radiation. electrons) then eqn (3. eqn (3. knowledge of the amplitudes of the scattered waves (in modulus and phase) unequivocally defines p(r). 145 the electron scattering factor will be fe(r*) = S pe(r) exp (2nir* r) dr (3. In accordance with p. . Scattering by atomic electrons The processes of Thomson and Compton scattering are an example of waveparticle duality and they seem to be mutually incompatible. less so for p.
In most crystallographic applications the deviations from it. As a consequence of eqn (3. 177 for the transform of a Dirac delta function). whose distribution is very sharp. The pa function is known with considerable accuracy for practically all neutral atoms and ions: for lighter atoms via HartreeFock methods. p. that the centre of the atom is at the origin. are neglected in first approximation. In accordance with eqn (3.(r).3).A. then pa(r) dv = (Cf=. The intensity of the Compton radiation has the same order of magnitude as the radiation scattered coherently. 6 " u a sin (2nrr*) * 2 .3. . 3. f. Generally the function pa(r) does not have spherical symmetry. the scattering of 1s electrons.10) the electron scattering factor is equal to 1 when r * = 0. . dr=C.e. According to the previous paragraph most of radiation scattered at high values of sin O / A is due to electrons of inner shells of the electron cloud (core). pej) dv is the probability of finding an electron in the volume dv. If we assume that pa is spherically symmetric and. Conversely scattering of valence electrons is efficient only at low sin O / A values.3(a) and eqns (3. 3. (b) ScatteRing factors for 1s and 2s electrons. for instance because of covalent bonds.The diffraction of Xrays by crystals 1 147 Equation (3. is more efficient at higher values of r*. 3. . .12) are illustrated in Fig. is called the atomic d r ) scattering factor and will be denoted by fa. Moreover.tq j=1 where Ua(r) = 4m2pa(r) is the radial distribution function for the atom.4(b) fCore and fva.2) or eqn (3. Scattering by atoms Let q.14) the intensity of the radiation coherently scattered from an atom can be obtained by summing the amplitudes relative .4(a) the fa functions for some atoms are shown. qz(r) be the wave functions of Z atomic electrons: then pejdv = I%(r)12dv is the probability of finding the jth electron in the volume dv. at sin O / A = 0 and decreases with increasing sin OIA. 3.3(b). of a nitrogen atom are shown as function of sin O / A . According to the premise of this section the intensity of the Compton radiation of an atomic electron will be lincoe = ZeTh(l f z) where ZeTh is given by eqn (3. The Fourier transform of . 3. In Fig. and for heavier atoms via the ThomasFermi approximation.c. In Fig. we will have fa(r*) = 1 i 2 (b) r* t A'I Fig. can thus be considered the sum of core and valence electron scattering: fa =fcore +fvalence. If every function qj(r) can be considered independent of the others. . equal to Z. . Each curve reaches its maximum value. (a) Radial distribution for I s and 2s electrons of a C atom as defined by Slater functions.13) in Fig. If the distribution of 1s electrons could really be considered pointlike their scattering factor would be constant with varying r* (see Appendix 3. without loss of generality.
4. then we can write Fig. ~ a +0. easily recognizable in crystals composed of light atoms. p. Nevertheless it is appreciable at high values of sin BIA.e. Therefore the description of thermal motion of an atom requires only the knowledge of the timeaverged distribution of its position with respect to that of equilibrium. 181). When we consider the diffraction phenomenon from one crystal the intensity coherently diffracted will be proportional to the square of the vectorial sum of the amplitudes scattered from the single atoms while the intensity of the Compton radiation will be once more the sum of the single intensities. Here we will suppose that the thermal motion of an atom is independent of that of the others. 11720 and Appendix 3. and that pa(r . 186). In accordance with Appendix 3. . where pat(r) is the electron density corresponding to the thermically agitated atom.Since fe = 1 for sin B I A = 0 there is no Compton radiation in. If we suppose that the position of equilibrium is at the origin. that p ( r r ) is the probability of finding the centre of one atom at r'. As a consequence of the very high number of atoms which contribute to diffraction. the electron density is assumed to accompany the nucleus during thermal vibration. (a) Scattering factors for S. pat is the convolution of two . The timescale of a scattering experiment is much longer than periods of thermal vibration of atoms. Notice that the rigid body vibration assumption has been made.148 1 Carmelo Giacovazzo hs to the electrons taken individually: \. 3. If the atoms are disturbed they will tend to return to the positions of minimal energy: they will oscillate around such positions gaining thermal energy.A. The oscillations will modify the electron density function of each atom and consequently their capacity to scatter..r') is the electron density at r when the centre of the atom is at r'. (b) core and valence scattering for nitrogen atom. Their arrangement corresponds to an energy minimum. 0 05 (b) The temperature factor In a crystal structure an atom is bound to others by bond forces of various types. p. Compton scattering can generally be ignored: its presence is detectable as background radiation.=I / The Compton radiation scattered from an electron is incoherent with respect to that scattered from another electron: its intensity is obtained by summing the individual intensities relative to every single electron: sin O/n (4 .the direction of the primary beam. i.B. This is not completely true since the chemical bonds introduce strong correlations between the thermal motions of various atoms (see pp.
19) will be substituted (see Appendix 3. In order to describe graphically a crystal molecule . uT3. the thermal motion of the atom will have spherical symmetry and could be described by a Gaussian function in any system of reference: p ( r r )=p ( r l ) ( ~ J T ) . is known as the DebyeWaller factor. (3.25)) q(r*) = exp ( .20) The six parameters U (five more than the unique parameter U necessary G to characterize the isotropic thermal motion) define the orientation of the thermal ellipsoid with respect to the crystallographic axes and the lengths of the three ellipsoid axes.17) S' the Fourier transform of p(rl). ul3:  q(r*) = exp [2n2(UT1x*' Ug2y*2 U3*3~*22UT2x*y* + 2UT3x*z* + 2Uz3y*z*)]. 186 and 188) by the anisotropic temperature factor (3. Uz3.18) where r r is measured in A and U = (rI2) is the square mean shift of the atom with respect to the position of equilibrium. If assumed isotropic. The function p ( r r ) depends on few parameters. If we assume that the probability p ( r r ) has a threedimensional Gaussian distribution the surfaces of equal probability will be ellipsoids called vibrational or thermal. The consequence of this is to make the electron density of the atom more diffuse and therefore to reduce the capacity for scattering with increasing values of sin 8/A.16 A2) but can also reach 0. centred on the mean position occupied by the atom. it is inversely dependent on atomic mass and on chemical bond forces.The diffraction of Xrays by crystals 1 149 functions and its Fourier transform (see eqn (3. UF2. + + + (3.20 A (B lying between 0.05 and 0.19) The dependence of B on the absolute temperature T has been studied by Debye who obtained a formula valid for materials composed of only one chemical element. The factor B is usually known in the literature as the atomic temperature factor.20 and 3. p ( r l ) is in general anisotropic.38)) is where q(r*) = 1  p ( r r ) exp (2nir* r') dr' . (3.2 ~ ~ U r * ~ ) (8n2u sin2 8/A2) = exp = exp (B sin2 8/A2) where B = 8n2U (A2). and directly dependent on temperature. U12. From Xray diffraction structure analysis it is possible to conclude schematically that the order of value of fi is in many inorganic crystals between 0. Now eqn (3. The corresponding Fourier transform is (see eqn (3. In general an atom will not be free to vibrate equally in all directions.A. pp.20) which represents a vibrational ellipsoid in reciprocal space defined by six parameters UTl.~ " u exp~[(rt2/2U)] ~' (3.B.A.5 81 (B 20 A2) for some organic crystals.
Let pj(r) be the electron density of the jth atom when it is thermically agitated. . (3. The fact that in eqn (3.21).21) The amplitude of the scattered wave is FM(r*)= = = j=l I2 N pj(r .9). If we neglect the effects of redistribution of the outer electrons because of chemical bonds.5 (see Fig. j=l 21 S S j=1 N J. and localized at the origin. Such a model is unsatisfactory if one is interested in the deformation of the electron density consequent to bond formation.D).(r). 3.21) we have neglected the redistribution of the outer electrons leads to negligible errors for FM(r*). the electron density relative to an Natom molecule or to one unit cell containing N atoms is N P M ~= > j=1 C pj(r .5.5).q) exp (2nir* r) dr pj(Rj) exp [2nir* (q + R. and surrounding the space within which the atomic displacement falls within the given ellipsoid with a probability of 0. except in case of small r* and for light atoms. Scattering by a molecule or by a unit cell Fig.150 1 Carmelo Giacovazzo and its thermal motion each atom is usually represented by an ellipsoid. In a real molecule the electron density is generated by superposition of molecular space orbitals V iwith occupation ni: Since pmolecule be decomposed into atomic fragments. centred on the mean position of the atom.)] d ~ . in the previous section indicated by fa. where J. 3. is the electron density of a promolecule. pseudoatoms may become aspherical and carry a net charge). as defined by (3.). a finite set of can appropriately chosen basis functions can be used to represent each jth atomic fragment (see Appendix 3.5). isolated. Then where Ap models the effects of bonding and of molecular environment (in particular. p. in other words.(r*) exp (2nir* q).(r*) is the atomic scattering factor of the jth atom (thermal motion included. of an assembly of spherically averaged free atoms thermically agitated and superimposed on the molecular geometry. By Fourier transform of Ap the deformation scattering is obtained: . where the number of outer electrons represents a consistent fraction of Z. or. If the atom is at position q its electron density will be pj(r .
30).. if the scatterer object is periodic (crystal) we observe a nonzero amplitude only when r* coincides with a reciprocal lattice point: The function F.26) are the Laue conditions.The diffraction of Xrays by crystals 1 151 Since the core deformation scattering is negligible AF practically coincides with deformation scattering of the valence shells. @(r) = 0 outside the crystal.26) are called diffraction directions and relations (3. On the contrary.22) the amplitude of the wave scattered by the whole crystal is where V is the volume of the unit cell and r i = ha* + kb* Ic* is the generic lattice vector of the reciprocal lattice (see pp.. v.35).25) scalarly by a . and (3. (3. etc. In this case we can write + .(r*) can be represented by means of a pseudolattice: each of its points has the position coinciding with the corresponding point of the reciprocal lattice but has a specific 'weight' FM(H)/V. Let us multiply eqn (3.A.. b. p.(r) describes the electron density in the unit cell of an infinite threedimensional crystal. 635).A. c and introduce the definition (3. = ua + vb + wc (with u. molecule. Finiteness of the crystal may be taken into account by introducing the form function @(r): @(r) = 1 inside the crystal. The electron density function for the whole crystal (see Appendix 3.A. w being integers) is the generic lattice vector. Diffraction b y a crystal One threedimensional infinite lattice can be represented (see Appendix 3..) the amplitude of the scattered wave FM(r*) can be nonzero for any value of r*.. If the scatterer object is nonperiodic (atom. For a given node the diffraction intensity I. 174) by the lattice function where 6 is the Dirac delta function and r. will be' function of the square of its weight.5) of r*: we obtain The directions s which satisfy eqns (3. p. Let us suppose that p.A. 183) is the convolution of the L(r) function with pM(r): As a consequence of eqns (3.
: then D(r * . let suppose that the crystal is a parallelepiped with faces Al. We deduce: 1.e.35). 3. The width of a principal maximum in a certain direction is inversely proportional to the dimension of the crystal in that direction.) and it is indicated as: FH = x fi N j=l exp (2nirG . q ) where N is the number of atoms in the unit cell.A. 174). to the volume S2 of the crystal.y *) sin (nA3z*) nx * JCY * nz * (3. If we integrate this function over separate variables. 2.A.24) we notice that. + + A1/2 A2/2 A3/.1 (p.A. it becomes.152 1 Carmelo Giacovazzo and.. k.29) Each of the factors in eqn (3.40) the relation (3.27) becomes = + 1 .A. p. because of the finiteness of the crystals each node of the reciprocal lattice is in practice a spatial domain with dimensions equal to A. In Fig.6 some examples of finite lattices with the corresponding reciprocal lattices are shown.A. If we compare eqns (3. When we consider the diffraction by a crystal the function FM(H)bears the name of structure factor of vectorial index H (or indexes h. the amplitude of the diffracted wave is where D(r*) = S O(r) exp (2nir* r) dr = exp (2nir' .Ad2 . The distribution D is identical for all nodes. A. 3. x FM(H) 53 D (r* . going from an infinite crystal to a finite one. Because of eqn (3.28) and (3.29) is studied in Appendix 3. For example. 1 if we make reference to the components of r. In accordance with .. Thus.A312 exp [2ni(x * x y *y z *z)] dx dy dz.'. 174 D(r*) = sin (nAlx*) sin (nA.A. because of eqn (3.r i ) .Ad2 . i. The maximum value of D(r*) is equal to A. A..A and shown in Fig. the pointlike function corresponding to each node of the reciprocal lattice is substituted by the distribution function D which is nonzero in a domain whose form and dimensions depend on the form and dimensions of the crystal. in accordance with Appendix 3.r) dr and 52 is the volume of the crystal.
30a) the effect of thermal agitation of the atoms we write. (f) a crystal in the form of a parallelepiped (from Kitaigorodskii. Direct and reciprocal lattices for: (a) a onedimensional lattice. If we want to point out in eqn (3. j=1 fi sin 2nHXj.. axis exp 2ni(hxj + kyj + lzj). (3. p. 64 we write FH = where AH= j=1 xf j N exp (2niAxj) = A H iBH N + (3. (1951). (d) a cubic crystal in the form of a sphere. (b) a twodimensional lattice in the form of a rectangle.30a) may be written Fhkl = j=1 xf j imag. F. New York). 3. 149 and Appendix 3. in accordance with p.B N real axis fOj FH = j=1 exp (2niHxj . In the same way I.8 n 2 4sin2 8/A2) Fig. 3. qHis the phase of the structure factor FH. It is cui = 2zHX.The diffraction of Xrays by crystals 1 153 Fig. A.6. In a more explicit form (3.7) FH IFH( (iq.) where qH arctan (BH/A = exp = . (c) a twodimensional lattice in the form of a circle. 3. is the jth positional vector and the transpose matrix of its components with respect to the direct coordinates system is xi = [xi yj zj]. we have indicated the vector as rlT. Consultants Bureau. and the transpose matrix of its components with respect to the reciprocal coordinates system as H = (hkl).31) ' I In different notation (see Fig.HI.30a) j=1 x N f j cos ~ J G H X ~ BH= . The theory o f crystal structure analysis.7. (e) a cubic crystal in the form of a cube. .. (3. 1.30b) According to the notation introduced in Chapter 2. is represented in the Gauss pla_nefor a crystal structure with N = 5.
33) is equivalent to eqn (3.25). The point of view can be further simplified by observing that the family of fictitious lattice planes with indices h' = nh. 3. NOWeqn (3. k. / Fig. an effect of diffraction of nth order due to a reflection from lattice planes H can be interpreted as reflection of first order from the family of fictitious lattice planes H ' = n H.8) the angle between the primary beam and the family of lattice planes with indices h. second order.i s the interplanar spacing. Since the Xrays penetrate deeply in the crystal a large number of lattice planes will reflect the primary beam: the reflected waves will interfere destructively if eqn (3. .154 1 Carmelo Giacovazzo N F = H j=l &. Bragg who considered the diffraction as the consequence of contemporaneous reflections of the Xray beam by various lattice planes belonging to the same family (physically. Indeed. It is easy to see now that eqn (3. Bragg's l a w A qualitatively simple method for obtaining the conditions for diffraction was described in 1912 by W. Equation (3. Let . Put the origin of the reciprocal .8. 3.32) can be written as j / I 0 (3. .32) is the Bragg equation and the angle for which it is verified is the Bragg angle: for n = 1. The reflection and t h e limiting spheres Let us outline (see Fig. The difference in 'path' between the waves scattered in D and B is equal to AB BC = 2d sin 6. Details of the structure factors calculation from a known structural model are given on pp. r* = 2 sin 8/A = lld. from the atoms lying on these planes). k'.. f.33) 2(dH/n)Sin 6 = 2dH.32) is not verified.9. 1 (having no integer common factor larger than unity).14) and (3. Let 8 be (see Fig. exp (2niAXj .2n2AU?H) depending on the type of the thermal motion (isotropic or anisotropic) of the atoms. on the crystal structure. d planes belonging to the family H = (h. L. us note explicitly that the value of FH. 878 and Appendix 2. Reflection of Xrays from two lattice . Reflection and limiting spheres. we obtain reflections (or diffraction effects) of first order. etc. because of eqns (2. 2dHsin 8 = nA. . In practice.9) a sphere of radius l/A in such a way that the primary beam passes along the diameter 10.1. 3. if we consider only the moduli of eqn (3. 2. k' = nk. is the scattering factor of the jth atom considered at rest. 3.. . relative to the same family of lattice planes H.6).sin 8 = where h'.e. in modulus and phase. I' are no longer obliged to have only the unitary factor in common. k I). I' = nl has interplanar spacing d H = dHIn.25) we will have. If it is multiple of A then the two waves combine themselves with maximum positive interference: + Fig. depends on the atomic positions i.
52) A. is the largest period of the unit cell.. If r i > 2/A (then dH< A/2) we will not be able to observe the reflection H. A very high number of lattice points can simultaneously be in contact with the surface of the sphere: for instance. (the smallest period of the reciprocal lattice). Let us give the relevant rules. This condition defines the socalled limiting sphere.30) we write FH A H iBH. The wavelength determines the amount of information available from an experiment.iBH and consequently Q)H + = Q)n (3. In ideal conditions the wavelength should be short enough to leave out of the limiting sphere only the lattice points with diffraction intensities close to zero due to the decrease of atomic scattering factors.05 A: therefore the curvature of the Ewald sphere is small with respect to the planes of the reciprocal lattice. For Xrays and neutrons A . 1 155  Symmetry in reciprocal space There are some relationships among structure factors relative to different indexes H which are originated either from the physics of diffraction and from the crystal symmetry. Therefore: the necessary and sufficient condition for the Bragg equation to be verified for the family of planes (hkl) is that the lattice point defined by the vector ri lies on the surface of the sphere called the reflection or Ewald sphere. = AH. all the points belonging to a plane of the reciprocal lattice passing through 0. then the diameter of the Ewald sphere will be smaller than rg. which coincides with Bragg's equation..(0.The diffraction of Xrays by crystals lattice at 0.34) . Under these conditions no node could intercept the surface of the reflection sphere. Vice versa if A > 2a. Friedel law In accordance with eqn (3. If the primary beam is monochromatic and the crystal casually oriented.. which is comparable with the dimensions of the unit cell (10A): the sphere then has appreciable curvature with respect to the planes of the reciprocal lattice. with centre 0 and radius 2/A: only the lattice points inside the limiting sphere will be able to diffract..Then it will also be: = F. no point of the reciprocal lattice should be in contact with the surface of the Ewald sphere except the (000) point which represents scattering in the direction of the primary beam. AP is the direction of diffracted waves (it makes an angle of 28 with the primary beam): therefore we can suppose that the crystal is at A.. The relation OP=r~=l/dH=IOsin6=2sinB/A holds. When the vector rtT.. It will be seen in Chapter 4 that the experimental techniques aim to bring as many nodes of the reciprocal lattice as possible into contact with the surface of the reflection sphere. where a. That is the reason why we can never obtain diffraction of visible light (wavelength 5000 A) from crystals. In electron diffraction A 0. is on the surface of the sphere then the corresponding direct lattice planes will lie parallely to IP and will make an angle 6 with the primary beam.
jj. = FHexp ( . we have From that the Friedel law is deduced. In this case the Friedel law does not add any additional observable relationship. it is said that the diffraction by itself introduces a centre of symmetry. Let Pl[(x.Since the intensities IHand I. y. z)] be the space group (symmetry equivalent positions are shown in square brackets). By introducing R. in . If the space group is PI [(x. they will show the symmetry of the Laue class I As a further example let P2 [(x.35) into two relations: are From (3. Determination of the Laue class The Laue class of a crystal (see p.~ J T ~ H T ) .36) it is concluded that intensities ZH and I. because of the Friedel law = IFHI holds.35) .! = RXj T are symmetry equivalent. z). The only symmetry operator is the identity. the diffraction intensities from crystals with symmetry P1 and PI will both show a centre of symmetry or. z).36) does not give us any useful result. Then the points r.. Sometimes it is convenient to split eqn (3. other words.156 1 Carmelo Giacovazzo The value of V . although imperfectly. y. usually. ) (2niHT) exp exp ~ J T ~ H ( R X . 17) may be determined by means of the qualitative examination of the diffraction intensities. Anyhow. and its use in eqn (3. We wonder which kind of relationships brings in the reciprocal space the presence of the operator C.35) are described in the following. (x.=l = xfi x fi N exp ( ~ J T ~ H R X . Since these intensities appear to be related by a centre of symmetry.H is opposite to the value of rpH. In conclusion. (2. The most relevant consequences of eqn (3. Z)] we can use R2 in eqn (3. j=1 we can write F".! whose coordinates are related by X.37). Since + F"R exp ( ~ J T ~ H T ) = N . 2)] be the space group. in eqn (3. Effects of symmetry operators in the reciprocal space Let us suppose that the symmetry operator C = (R. and r. = FH.qR equal while their phases are related by eqn (3. according to which the diffraction intensities associated to the vectors H and H of the reciprocal space are equal.y. depend on and IF^^^ respectively. = FH + T) (3.36) and by applying the Friedel law we obtain the following relationship (symmetry equivalent reflections): .36) and consequently obtain F. T) exists in direct space. y.
39) restricts the phase qHto two values.37) to this set we will obtain 2qH= 2nHT + 2nn from which qH XHT = + nn.38) again. The reader will easily verify that the crystals belonging to groups P222.38) would be obtained again only by using matrices R2. Determination of reflections with restricted phase values Let us suppose that for a given set of reflections the relationship HR = H is satisfied.The diffraction of Xrays by crystals 1 157 If the space group was Pm [(x. P2A2. 'centrosymmetric' . in eqn (3.. y.39) Equation (3. FHwill be a real positive number for q. y.z)] where the reflections (hkO). These reflections are called reflections with restricted phase values. For this reason we usually talk in centrosymmetric space groups about the sign of the structure factor instead of about the phase. XHT or X(HT+ 1).10 F is represented in the complex plane for a centrosymmetric structure of six atoms. 4 + z). the contribution of every couple to FHwill have to be real. (Okl). (x.36). ~ 4 P4/m show the intensity . and P2/m 2/m 2/m show intensity symmetry of the 2/m 2/m 2/m Laue class: IFhkrl = I F h d = = IFiid =IFl=IF. Since for each atom at q another symmetry equivalent atom exists at q. z). (3.. By introducing T = T2 in eqn (3. equal to 0. (h01) satisfy the relation HR = H for R = R2. 2). If the space group was P2/m eqn (3. by using R2 and by applying the Friedel law we would obtain eqn (3. If the origin is assumed on the centre T of symmetry then T = 0 and the permitted phase values are 0 and n. In this case every reflection is a restricted phase reflection and will assume the values XHT or ~ ( H + 1).30b). z). We can conclude that the symmetry of the diffraction intensities from crystals belonging to space groups P2. and a negative one for qHequal to n. 4 . ( i + y. H In Fig. Pmm2. R3. This time the Friedel law does not add any additional relationship to those obtained from eqn (3. or less properly. If the space group is centrosymmetric the inversion operator will exist. y. R4 respectively.36). [(x. If we apply (3. As an example of a noncentrosymmetric space group let us examine i . z)]. R3. ( i + x. Then according to eqn (3.IFhill = IFhkil hkl hkll and those belonging to space groups P4. 3.39) we obtain . J . symmetry of the Laue class 4 1 1 1x. Pm and P2/m is that of the Laue class 2/m. (i x.y. and R. .
39) we obtain qok[ = (nk12) + n n : i. ~ 1or )to (3x14. k. q o k l will have phase 0 or n if k is even. { h . { h .O}. (0. k. h. 011 { h . { h . O). h . { h . O. qhko ( n h l 2 ) + nn.. k. 0 . 0. k. h. { h . . 1 (O. for a centrosymmeJric crystal structure with N = 6. k. k. 01. 011. 0 ) (h.1. q h 0 i will have phase 0 or n if 1 is even. ( h . h. 0. O)] All None All { h. 0 ) masks (h. fn12 if 1 is = odd. I ) All ( h . I ) [(h. (0. phase = will fn12 if h is odd. 1 ) All [ { h . 0. I ) All (h. 0 ) .O.O. { h . It is q = ZRHX. By introducing T = T3 in eqn (3. In the same way. I ) All [ ( h . { h .0.I). {h. k. h. I ) .O. [ { h .0). O). O)] (h. The allowed phase values depend Table 3.h. by introducing T = T. Restricted phase reflections for the 32 crystal classes Point group 1 1 m 2 2/m mm2 222 mmm 4 Sets of restricted phase reflections p p p p 4 4/ m 422 42m None All (0.10. (O. k.158 ( Carmelo Giacovazzo imag.e. I } All .k. Thus qhko have phase 0 or n if h is even. F is represented in the Gauss plane . I ) . h. { h . h. h. ~ 4 ) Phase restrictions to ( ~ ~ 154 . 0)l Three principal zones only All (h.e.O. k.k. 0. 0). . k. 0. I ) .O). 0 ) All ( { h . can be found for some space groups. (h. . 111 [(h. 3. 7 ~ 1 4or to ( n / 6 . in eqn (3. 0 ) .O) (O. fA12 if k is odd. { h .O.39) we obtain qhol (n112) + n n : i. k.O).O. 01. k. axis Fig.O) (h. / ) I [(h. h.fi. I ) All { h.O) { h . 7 n / 6 )or .
B. are those described in Table 3. ( 3 . and 6 (and. the projection of a structure in P2. In the space group P4. Conse . the reflections (OkO) with k # 2n are systematically absent. Z ) ] the reflections (OkO) satisfy the condition HR. 4. 3 . and Ccentred. 4 . symmetry operators will exist whose rotational matrix is always the identity while the translational matrix is: + + respectively. = 112. 3. with n integer.2. as well as zones parallel to the axes 2 .35). Systematic absences Let us look for the class of reflections for which HR = H and let us apply eqn (3. only the reflections (001) satisfy the condition HR. j .1 the sets of restricted phase reflections are given for the 32 crystal classes. + z ) .2. y. 2 z ) ] x. 4 . HT. If k is odd. will be systematically absent or extinct. The reader will easily verify that zones orthogonal to axes 2 . Let us give a few examples. Note that the presence of a glide plane imposes conditions for systematic absences to bidimensional reflections. the only condition for systematic absence is I # 4n. If the cell is of type A. glide planes opposite to a. y 1. = 112 the reflections (h01) with 1 # 2n will be systematically absent. b. b. The reader can easily check the data listed in Table 3. In particular. A different point of view may also be used: the existence of reflections with restricted phase is due to the presence of symmetry elements which at least in projection simulate the centre of inversion. as usually said.2. [ ( x . I. 4. In the space group P2. z ) . the reflections belonging to the zone (hkO). y . or c respectively. 1 = 2n for glide planes of type a.35) we obtain: the relation HR = H is satisfied for any reflection. Since HT. along the c axis is centrosymmetric: correspondingly. being insensitive to the z coordinate.2. From this fact the rule follows: reflections for which HR = H and AT is not integer will have diffraction intensity zero or. A cell of type F is simultaneously A. AT3= 114. have restricted phase values. Thus. = H. (hol). HT4= 3114. (JJ. [ ( x . Since HT. of threedimensional type. z ) . y . C. In the space group PC [ ( x . Let us apply now the same considerations to the symmetry operators centring the cell. = H. ( y . P. so the respective conditions for systematic absences must be simultaneously valid. and (hkO) respectively. and c impose conditions on classes (Okl). If we use these operators in eqn (3. For instance. k = 2n. of course. ( x . = H for j = 2. the systematic absences. This relation would be violated for those reflections for which AT is FI not an integer number unless I H = 0 . 6. B. z + +)I the reflections (h01) satisfy the condition HR.The diffraction of Xrays by crystals 1 159 on the translational component of the symmetry element and on its location with respect to the cell origin. z ) . to the corresponding screw axis) have symmetry restricted phases. The conditions will be h = 2n. is semiinteger. In Table 3. 1 + z ) . (2.
) + l(z. The structure factor is then + + + Nl2 Fhkl= j=1 f j exp 2ni(hx.)I.k 1# 3n for reverse absences (h setting) for a hexagonal cell with rhombohedra1 lattice. and 1 are all even or all odd will be present.=I . + kyj + lz. + . k. . z) and (x. Rules for systematic absences may be also derived by using the explicit algebraic form of the structure factor.160 1 Carmelo Giacovazzo Table 3.ky. The same criteria lead us to establish the conditions for systematic k 1# 3n for obverse setting and h . for example. j . Systematic absences Symmetry elements Lattice Set of reflections Conditions none h+k+l=2n h+ k=2n k+l=2n h+l=2n h+ k=2n k+l=2n h+l=2n h+ k+I=3n hk+I=3n hkl i Glideplane 11 ( 0 0 1 ) a b n d b c n d hku Glideplane 11 ( 1 0 0 ) Okl C Glideplane 11 (1 1 0 ) b n d hhl Screwaxis 11 b 2 1 ~ 4 ~ 4 1 ~ 4 ~ Oku quently only the reflections for which h. + NI2 f j exp 2ni[hxj . Suppose. z + 4) will be symmetry equivalent points). y. that the space group contains a cglide plane perpendicular to the b axis (then ( x .2.
Unequivocal determination of the space group Determination of the space group is an important first step in any crystal structure analysis.)] sin 2nky. with few exceptions. p. It is easily seen that Fhol= 0 for 1 odd. be unambiguously identified if their point group is known. The symbols of these groups are printed in bold character in Table 1. p. described in Appendix 3. it is different for centrosymmetric and noncentrosymmetric space groups.). pyroelectricity. 165) and the statistical methods (see Chapter 5. (2) the Laueclass is 2/m (from (3. 322) based on the expectation that the distribution of the intensities is influenced by the presence of symmetry elements and. One way to avoid the Renninger effect is to rotate the crystal about the reflecting plane's normal and repeat measurements. (3) a twofold screw axis along b and a cglide plane normal to b do exist according to systematic absences. Let us add to them the anomalous dispersion effects (see p. Then the space group P2Jc is unequivocally deduced since: (1) the cell has to be primitive (no systematic absences involving threedimensional reflections are observed).38) and systematic absences (OkO) for k = odd and (h01) for I = odd are observed. etc. piezoelectricity. 15) (crystal habit.g. suppose that relations (3. The methods which can give us information about point groups have been schematically described in Chapter 1 (p. One way to produce such forbidden reflections is the Renninger effect. From the qualitative examination of the diffraction intensities (which leads to the identification of the Laue class) and from the analysis of the systematic extinctions 58 space groups are unequivocally determinable (without making any distinction between enantiomorph couples). in accordance with our previous results.B. + Diffraction intensities The theory so far described is called kinematic: basically it calculates interference effects between the elementary waves scattered inside the . Ni2 + Fhkl= 2 x fi exp [2ni(hxj j=l + lz.. in particular.38)). Space groups which are not unequivocally determined could.9.The diffraction of Xrays by crystals 1 161 For 1 even for 1 odd ~ 1 2 j=1 Fhkl= 2 x fi exp [2ni(hxj lz. Sometimes the identification of space group extinctions is disturbed by the presence of one or a few reflections seemingly violating one of the extinction rules (e. As an example.)] cos 2nkyj. 191. which occurs when two or more reciprocal lattice points happen to intersect the reflection sphere simultaneously. only one (hkO) reflection with h k =odd has a meaningful nonzero intensity).
which can be missing (called vacancies). plane defects. which are elastic waves propagating through the crystal and inducing atomic displacements). Only a dynamical effect of particular importance for crystal structure analysis. dislocations). in practice. a single point defect does not produce detectable effects on diffraction maxima but a large number of them.162 1 Carmelo Giacovazzo volume of the crystal. point defects. The interference between the waves only occurs inside every single block. strongly affects diffraction. however. extending along straight or curved lines (e. . or vicarious atoms. line defects. which are convenient to classify into the following groups (see Chapter 9): transient defects.g. whose dimensions satisfy the theoretical conditions of applicability of the kinematic theory. precipitates. having lifetimes measured in microseconds (e. differ by ideal ones also because they may contain a large variety of defects. stacking faults). When agglomerated they can form voids or cracks in a crystal. voids). phonons. the diffracted waves interfere with each other and with the incident beam. thicknesses <10~10~cm) the kinematic theory is a fairly accurate approximation to dynamic theory. as in the case of orderdisorder transitions. Because of the loss of coherence between the waves diffracted from different blocks. Real crystals. the Renninger effect. will be here described (in Appendix 3. inclusions. The theory which takes into account all these phenomena and analyses the wave field set up as a whole is called the dynamic theory of diffraction. 191) in any detail.g. It was initiated by ~wald:[']later on Laue showed that Ewald's theory is equivalent to analysing the propagation of any electromagnetic field through a medium having a periodically varying complex dielectric constant. Dynamic effects develop gradually in a crystal: it may be shown that for sufficiently small thicknesses the incident beam is not weakened considerably. the diffracted intensity from the whole crystal is equal to the sum over the intensities diffracted from every single block. extending along planes or curved surfaces (e. extending throughout small volumes in the crystal (e. For example.B. the diffracted waves are not yet so strong as to give rise to remarkable interference effects with the incident beam and the effects of absorption are negligible. The reader is referred to specialist books or review articles[2331 exhaustive for information. However. small angle boundaries. corresponding equations proved to be valid even for crystals having dimensions of several tenths of a millimetre. Other dynamical interactions will be described on the basis of the kinematical theory properly modified by Darwin and other authors. interstitial. volume defects.g. tilted very slightly to each other for angles of the order of fractions of one minute of arc: each block is separated by faults and cracks from other blocks.51 it can be ideally schematized like a mosaic of crystalline blocks with dimensions of about 10'cm. it neglects two important phenomena: when the incident wave propagates inside the crystal its intensity decreases gradually because a part of its energy is transferred to the scattered beam or it is absorbed. Under these conditions (theoretically. However. The importance of defects with respect to diffraction intensities depend on their nature and on their density. A simplified model of real crystal was proposed by Darwin: [4. p.g. This is due to the real crystal structures. The description of the dynamical theory is out of the scope of this book.
individual dislocations have little effect on diffraction but they may array themselves to form smallangle boundaries separating two relatively perfect regions tilted relative to each other by about one minute of arc (mosaic blocks). According to the above remarks quantity of practical interest is the integrated intensity and not the maximum intensity of the diffraction peak.41) where I. As a consequence (see Fig.11. variations in the orientation of the planes H cause modifications in the orientation of r:). Equivalently.11) the spherical surface of radius 1/31is replaced by a family of spherical surfaces whose efficiency relative to diffraction depends on the distribution of the intensities as a function of the angle divergence and of the wavelength of the incident beam. etc. (a) Incident radiation with nonvanishing divergence. ( b ) Nonmonochromatic incident radiation. Indeed.The diffraction of Xrays by crystals 1 163 or. We can therefore expect that any type of defect which disturbs the crystal periodicity by lattice distortion or substitution or shift of atoms from the equilibrium position will produce some effect on diffracted intensities: among others. 3. In particular. . the incident Xray beam does have an inevitable divergence and an imperfect monochromaticity. it will cause a more rapid statistical decrease of diffraction intensities with sin BIA. they form twodimensional precipitates. clustering along certain planes. is the intensity of the incident beam. According to eqns (3. k1 = e4/(m2c4) takes into account the universal constants existing in eqn (3. Indeed.28) the integrated intensity is given by IH= klk210LPTE (3. the lattice distortions cause variations in the unit cell dimensions and therefore modify the form and volume of the reciprocal lattice points (variations of the spacing dH bring variations in the modulus r i . k2 = 3 1 3 S 2 / ~ 2is a Fig. 3. each node of the reciprocal lattice will have a finite volume and will be in contact with the surface of the reflection sphere for a finite angle interval. defects. because of the finite size of the crystal. its mosaic structure. and lattice distortions.. the same total energy may be measured by integrating the diffracted intensity over a suitable angular range around the ideal Bragg angle.3) and (3. Thus the total diffracted energy during a fixed time is measured.3). On the basis of these premises it is nonsense to affirm that a crystal is in the 'exact' Bragg position for a given family of lattice planes. In addition the surface of the reflection sphere itself has in practice to be substituted by a solid domain. Experimental arrangements normally used to measure diffraction intensities change the orientation of the crystal (see Chapter 4) so as to compel reciprocal lattice points to cross progressively the Ewald sphere while continuously recording the intensity of the diffracted beam. Furthermore.
the beam in the diffracted direction should be related by: Fig. The same consideration holds for waves propagating along the direction of the diffracted beam: the result is that both primary and diffracted beams are weakened because of dynamical effects. a is the diffracted power per unit distance and intensity. 143. 3. If the mosaic blocks are misoriented (as they usually are) then they do not diffract together and shielding of deeper planes is consequently reduced. Reflections affected by secondary extinction can be recognized in the final stages of the crystal structure refinement when for some highintensity reflection JF. Zachariasen's theory has been modified by other author^:[^^] the introduction of an extinction correction parameter in . takes into account the fact that the lattice planes first encountered by the primary beam will reflect a significant fraction of the primary intensity so that deeper planes receive less primary radiation. This phenomenon can be understood intuitively by means of Fig. L is the Lorentz factor and depends on the diffraction technique (Chapter 4. T is the transmission factor and depends on the capacity of the crystal to absorb the Xrays (see Chapter 4. takes into account the loss of intensity due to dynamic effects inside every single block. should be equal to the intensity of the primary beam when to = 0 and I = 0 when t = 0. mainly observable for highintensity reflections at low sin O/h values in sufficiently perfect crystals. A theory describing the mutual transfer of intensity between incident and diffracted beams was proposed by zachariasen.164 1 Carmelo Giacovazzo constant for a given diffraction experiment (Q is the volume of the crystal. called primary extinction. Multiple reflections from a family of lattice planes.12. P is the polarization factor. the unscattered radiation having direction So in Fig. Thus. The sum of the two equations is zero. The equations have to be solved subject to the boundary conditions: I..J < 1 F J . 304). Each scattering causes a phase lag of h/4. It depends on the mosaic structure of the crystal and has two components. defined on p. and t are lengths in the direction of the primary and diffracted beams respectively. The most important one.12. called secondary extinction.. V is the volume of the unit cell). That causes a weakening of the diffracted intensity. At the Bragg angle every incident wave can suffer multiple reflections from different lattice planes: after an odd number of reflections the direction will be the same as the diffracted beam: after an even number of reflections the direction will be the same as the primary beam. 301). The second component of the extinction coefficient.12 is joined by doubly scattered radiation (with much smaller intensity) with a phase lag of n:consequently destructive interference will result. p. A method for inclusion of secondary extinction in leastsquares methods is recalled in Chapter 2. 3. which is the condition for the conservation of energy. 3. 97. where t. p. Secondary extinction is equivalent to an increase of the linear absorption coefficient: thus it is negligible for sufficiently small crystals.[(jl If absorption is neglected the intensity I of the beam in the incident direction and the intensity I of . E is the extinction coefficient. p.
an appreciable influence on the accuracy of the structural parameters included in the refinement. An experimental (often efficient) way to reduce extinction consists of rapid cooling of the crystal by means of immersion in liquid air: this reduces the dimensions of the mosaic grains. The electric field produced by the dipole oscillator at a distance r >>Xohas a magnitude (we neglect the polarization factor and the phase shift due to the travelling in r of the scattered wave) which is w2/(rc2) times its dipole .The diffraction of Xrays by crystals 1 165 leastsquares analysis may or may not have. If the frequency of the primary beam is near to some of these natural frequencies resonance will take place. The scattering under these conditions is called anomalous and can be analytically expressed by substitution of the atomic scattering factor fa defined earlier by a complex quantity Af' and f" are called the real and imaginary dispersion corrections. Indeed prior information on the mosaic structure is not usually available and therefore the corrections which have to be made are not easy to calculate a priori. wo is the natural angular frequency of the vibrating particle. according to circumstances. the electrical susceptibility of a collection of Z uncoupled dipoles is then x = = . Anomalous dispersion It is well known that electrons are bound to the nucleus by forces which depend on the atomic field strength and on the quantum state of the electron. The steadystate solution of the above equations is x(t) = Xoexp (iwt) where If the displacement x(t) is multiplied by e the polarizability moment [ex(t)] of each dipole is obtained. In order to have a simple insight into the problem (a rigorous quantummechanical treatment was carried out by Honl) we recall that the classical differential equation describing the motion of a particle of mass m and charge e in an alternating field intensity Eoiexp (iwt) is where 0 / 2 n is the frequency of the incident wave.w2 + igo which is a complex function of the frequency of the incident radiation. g dxldt expresses a damping force proportional to the velocity. Therefore they have to be considered as oscillators with natural frequencies.m Eoi ZeXo 2e2 1 wi .
542 A). and K. wavelengths. In some special cases ordinary Xray sources can also generate relevant dispersion effects.. For most substances at most Xray wavelengths from conventional sources dispersion corrections are rather small.. Such an energy corresponds to the wavelength A.. ( = 2. the holmium L2 absorption edge (211. 111. Calculated values for CrK.7107 A) are listed in A A the International tables for xray crystallography. Vol.70 3.41 Aft = .(A = 1. From the quantumtheory point of view. . ( = 0.72 Furthermore. An important question is whether Af' and f " vary with diffraction angle.1) suggested by Thomson: n is the phase lag between the scattered and the incident radiation.5444 A): Af = 15. the expression of Ed is not very different from that of a free electron. the frequency wo coincides with that of a photon with just sufficient energy to eject the electron from the atom.5406 A): CuK.o2 igw' rc2 mrc2 + If the electron is unrestrained and undamped then g = wo = 0 and Ed = (E&h = 7 exp (iot) EOi mrc = eL mrc2 Eoiexp [i(ot + n)] which well agrees with eqn (3. when o >> o.09 fl' fu  3. and MoK. Thus it may be expected that a remarkable deviation from Thomson scattering will arise when the primary beam wavelength is close to an absorption edge of the atom being considered. Therefore Thomson scattering is only applicable when o >> w.5368A) very close to CuK.88. For example. the real term is negative when o < wo and positive when o > 01. Since g << o . (A = 1.3905 A) is very close to the CuKBwavelength ( = 1. We define now the scattering factor for an electron as the ratio While the imaginary term is always positive.. so giving rise to A Af'= 11.14. The following dispersion corrections are cal~ulated:[~~1 CuK. Existing theoretical treatments suggest changes of some per cent with sin e/A but no rigorous experimental checks have been made so far: therefore in most of the routine applications Af' and f " are considered to be constant.3922 A). f"~8..(A= 1. holmium has the L3 absorption edge (1. CuK.166 1 Carmelo Giacovazzo moment: 02ex(t) w2e2 exp (iwt) Ed = EOd (iot) = .75..Eoi exp = 08 . radiation: in this case the holmium scattering factor is not the same for K.291 A). = 2nc/wo corresponding to the absorption edge.
Let suppose that a noncentrosymmetric crystal contains N atoms in the unit cell from which P are anomalous scatterers and the remaining Q = N . its intense continuous spectrum may be chosen to high precision in order to provoke exceptionally large anomalous scattering. (b)samarium nearthe ne edge. ~ ~ L edge.indicate that the magnitudes are calculated for the vectors H and . Now we will give only a few elementary ideas about the effects of anomalous dispersion: we postpone the methodological aspects for crystal structure analysis until Chapter 8. ~ .[l21As an example. we plot in Figs. ~ ~ ~ ~ . 3. If synchrotron radiation is used. Several recent works suggest an important role for multiplewavelength methods: the power of such methods depends on the distances between the working points representing f i n the complex plane. Then + where + and . (b) samarium near the L edge.H respectively. . The subscripts P and Q indicate that the structure factors are calculated only with the contribution of P or Q atoms (b) ~ ~ .26A for lanthanum to 1.The diffraction of Xrays by crystals 1 167 Fig. anomalous scattering is an important tool for solving crystal structures (see Chapter 8). 3.14 (a) and (b) the complex scattering factor Af' if" near the L3 edge for gadolinium and samarium respectively.13. Anomalous scattering terms A f ' and P'for: (a) gadolinium near the L3 edge. In Fig.13 we show the anomalous scattering terms Af' and f" for gadolinium and samarium near the L3 absorption edge: spectacular effects as large as 30 electrons/atom could be measured. Since anomalous dispersion may induce substantial variation of the diffracted intensities depending on the wavelength used. Very large effects have been measured["] for rareearth elements in the trivalent state near L3 absorption edges (corresponding wavelengths are of crystallographic interest because edges span from 2. 3.P atoms are normal scatterers.34 A for lutetium).
and F&. respectively: Fb+ = j=1 x f.15(b): from which AZ = 4 (F'JF( cos q.IF(^ and can be easily calculated by means of Fig.168 1 Carmelo Giacovazzo imag axis imag. 3. and F!. The vectors F+ and F. The value of AZ depends on the collinearity of F. IFHI= I F. In Fig. the crystal is constituted of only one chemical element which is the anomalous scatterer. As a last observation it should be mentioned that besides Xray. 3.15(a).e. AZ is a maximum when Fp and FQare approximately at the right angles.15. when anomalous dispersion is present. The Friedel law is satisfied if: the structure is centrosymmetricin this case IF+[and IFI are always equal. the Friedel law is not satisfied in the presence of anomalous dispersion. If they are collinear then (F+I= IF1: but this happens by mere chance. and F. is no longer valid. 3.15(b) F + and (F)* are shown: the latter is the complex conjugate of F. neutron and gammaray anomalous dispersion are also very useful in crystal structure analysis.and they are symmetric with respect to the real axis: The difference AZ = J F + ~ ~ is known as the Bijvoet difference[13] . Neutron anomalous dispersion techniques employ . axis 1 real axis Fig.! P exp 2niHXj. the reflection is centrosymmetric even if the structure is noncentrosymmetric. (b) relation between F. when anomalous dispersion is present. 3. as we can see. (a) Relation between F. I: Furthermore 1 In general.are described in Fig. i.
If in eqn (3.A.k. its 14. z] are the fractional coordinates of the point defined by the vector r. The Fourier synthesis and the phase problem If the structure factors are known in modulus and phase the atomic positions are unequivocally determinable. y.l=2 x = [x. at low velocity (some mm sl).~ J G ~ H + ) X (AH.4 keV resonance corresponds to a wavelength of 0. isotopic e enrichment techniques must be applied in order to provide a sufficiently large resonant scattering. according to eqn (3. towards or away from the crystal (linear Doppler effect). scattering by resonant nuclei (there are no other nuclear scattering contributions) and by electrons can occur simultaneously and interfere with each other. Gammarays are elastically scattered by the electrons of the atoms in the crystal. the intensities of the radiation sources decrease dramatically.45) Vh. 198 for further details). The atomic positions will correspond to the maxima of p(r).4 keV radiation in the decay of the parent isotope j7Co.2 per cent.H exp ( 2 n i ~ x ) exp = (AH+ iBH)eXp ( . An elastic resonant scattering by the nucleus (Mossbauer effect) also occursthe transition involves energies comparable with those employed in conventional Xray diffraction.45) we sum up the contributions of H and H we will have FH (2niHX) + F . The frequency of the incident radiation may be modified by moving the radiation source. This produces a resonance effect in 57Fe (this atom may naturally be present in the crystal or implanted by techniques such as those used for isomorphous replacement) which is superimposed on the various Bragg reflections upon the gamma radiation elastically scattered by all the atoms in the crystal. Since both the processes are coherent. An ideal nucleus for gammaray resonance is j7Fe. (3. Indeed.16) the electron density is the inverse Fourier transform of F(r*): p(r) = = F(r*) exp (2nir* 1 r) dr* Fhklexp [2ni(hx + ky + lz)]. This is the most severe drawback for the use of gamma rays: relatively large signals are produced by relatively very weak radiation sources. A widely used experimental setup includes a radioactive source which emits the 14. Conversely.iBH)eXp ( ~ G ~ H X ) = 2[AHcos 2 n ~ + BHsin 2nHXI x . The anomalous scattering amplitudes increase dramatically in going from Xray to neutron to gammaray.The diffraction of Xrays by crystals 1 169 nuclear isotopes with resonances in the range of thermalneutron energies (see p. iron atoms included.86 A. Since 5 7 ~ has a natural abundance of about 2.
71.. to several tens of thousands for macromolecules. the temperature of the experiment. even if p(r) is positive everywhere..5 A in inorganic crystals. p. There.16.47) is qualitatively represented in Fig. Fig. the radiation used (the resolution improves when we pass from electrons to Xrays and neutrons). @(r*)= 0 outside this sphere.16.A. 0.In the second step the diffracted beams are focused by means of lenses. the chemical stability under the experimental conditions of temperature and pressure. 3. Because of the limit of natural resolution or of an artificially introduced limit (for instance in order to save time and calculations) the electron density function will be affected by errors of termination of series. In particular. The righthand side of (3.46) varies from several tens or hundreds. and by interfering with each other they create the image of the object.46)). = 1/(2dmin). Since the reflections at high values of sin B/A.5 A in organic crystals..35) we have If r * is the radius of the available reflection sphere.46) can be interpreted as the second step in the process of formation of an image in optics. (a) Electron density p ( r ) . The effect of the convolution (3. The number of reflections used in practice in eqn (3. Roughly speaking. for unit cells of small dimensions. 3.. are no physical focusing lenses for Xrays but they can be substituted by a mathematical lens (exactly.46) is obtained. can reach the limit of 0. The mathematical operation represented by the synthesis (3. according to Appendix 3.46) is explicitly real and is a sum over a half of the available reflections. cos 2n(hx + ky + l z ) + Bhklsin 2n(hx + ky + lz)] (3. Because of the decrease of the atomic scattering factors the diffraction intensities (and consequently IFH\)weaken 'on average' with the increase of sin B/A. pl(r) can be negative in more or less extended regions: the atomic peaks can be broad and surrounded by a series of negative and positive ripples of gradually decreasing amplitude. T[@(r*)] is a function with a maximum at r = 0 and the subsidiary maxima of weight decreasing with l/rL. for Xrays dm.A. and 1. The first step consists of the scattering of the incident radiation which gives rise to the diffracted rays with amplitudes FH. and can be considered zero for values above a given (sin B/A). . give the fine details of the structure (small variations of the atomic coordinates can produce big changes in highangle structure factors) the quantity dm. According to eqn (3. 181.. is adopted as a measure of the natural resolution of the diffraction experiment. The effect can be mathematically evaluated by calculating the function pr(r) available via the function @(r*) is the form function: @(r*)= 1 inside the available reflection sphere. (b) electron density obtained via a Fourier synthesis with series termination errors.170 ( Carmelo Giacovazzo from which x [A. dmin depends on different factors such as: the chemical composition of the crystal (heavy atoms are good scatterers even at high values of sin B/A).03 A in protein crystals. by Fourier synthesis (3.
let P2/m be the space group with a = 7. Different algorithms are used to make calculations faster. dmin= 0.41). If the grid is too coarse the interpolation between grid points to find the maximum of the electron density may be uncertain. but there are methods we can successfully apply (see Chapters 5 and 8). for V = 1000 A3./(tm) where z is the centring order of the cell and m the multiplicity factor of the Laue class (this is not strictly exact as the multiplicity factor refers to general reflections of type (hkl) and may be different and less than m for certain zones of reflections). The number of independent reflections to be measured is roughly N. it will be sufficient to sample p upon the grid points lying inside the asymmetric unit for reconstructing the whole content of the cell. 8890.A general solution to the problem has not been found. are rather large: for instance. if the grid is too fine a great deal of computing may be unnecessary. according to F I eqn (3.The diffraction of Xrays by crystals 1 171 In order to reveal the atomic positions. Furthermore. Very often the volume of the unit cell is much larger than 103A3 (V > lo6hi3 is not infrequent for macromolecules). only the moduli I H can be obtained from diffraction intensities because the corresponding phase information is lost.8 A . it is not possible to apply eqn (3.   Modulated crystal structures So far our attention has been devoted to condensedmatter systems with perfect threedimensional space group symmetry. A = 0. For instance. In absence of symmetry. This is the socalled crystallographic phase problem: how to identify the atomic positions starting only from the moduli IFH(. If symmetry is present the amount of calculation is smaller. and Appendix 2.25 A.. b = 16. pr(r) is sampled upon a threedimensional grid whose spacings along each of the unitcell axes have to be fixed with some care. The most convenient are the BeeversLipson technique and the fast Fourier transform algorithm by Cooley and Tookey (see Chapter 2. pp.1 A and /3 = 93'. In recent years numerous systems have been found which can be considered as perfect crystals with periodic distortion (from some basic structure) of the atomic positions (displacive modulation) and/or of the occupation probability of atoms . In practical cases N.20. and N. The number of grid points lying inside the asymmetric unit (114 of the unit cell) is now 33 x 33 x 17 = 18 513. Unfortunately./2 independent) reflections and the number of grid points is Np = v / h 3 where A is the grid spacing (say 0. the calculation of p is a fairly arduous task involving timeconsuming procedures. we have N.2 A and c = 8. Indeed. If we divide a and c into 33 and b into 66 intervals the grid spacing will have a sufficient and almost identical resolution in all three directions. there are measurable (only N.1).47) only on the basis of information obtained directly from Xray diffraction. at a resolution dm.8 A. 8180 and Np 64 000.4 A in the three directions). Thus even with the use of highspeed computers.
2nK m m u . sin [2nK . To the last exponential term in (3. (r* . sin [2nK (r? + ru) . ..@. (r.17) is the Bessel function of the first kind of order m. The Bessel functions J. K is the modulation vector.) x exp {2nir* . Jm(see Fig.48) reduces to fi(r*) exp (2nir* r y ) x exp (2nir* ru) x .172 1 Carmelo Giacovazzo (density modulation).I) u =fi(r*) exp (2nir* r ? ) x exp (2nir* r.)]}J.) x exp {im(@. generally weak.48) .. If satellite reflections can be labelled by rational indices in terms of the reciprocal lattice L* of the basic structure.2 n K . depending on the temperature. which may be expressed in the reciprocal space by K = k. In such a case the main and the satellite reflections are called substructure and superstructure reflections respectively (see page 80).. (ry + ru) .g. + where ry is now the average position of the jth atom. The presence of periodic distortions is revealed from the existence of the socalled satellite reflections..g..(z). 3.mK)].(z) may be applied. In these cases we have to admit that satellite reflections can assume nonrational indices. are its displacement wave amplitude and phase respectively.(z) = (l)"Jm(z). ry)}x exp [2niru . sin [2nK .n = 0.[76] In a perfect crystal the jth atom in the unit cell defined by the lattice vector r.(2nr* . + ru + g.@.) =fi(r*) exp (2nir* r y ) x J_. In order to prove the existence of satellite reflections we briefly examine the simple case of a onedimensionally displacively modulated structure when the displacement vector field is a harmonic function.I) (3.48) the Jacobi expansion exp (iz sin a ) = m=m x +m exp (ima)J. and gj and 4.17.I. + r. In a harmonically modulated crystal it will be + r U = ry ..2. which are regularly distributed around the socalled main reflections.1.@. 3.c*. Then (3. where fi(r*) is the usual atomic scattering factor.g. = ua + vb + wc is located at r.. The contribution of the jth atom to the structure factor is now given by + fi(r*)C exp 2nir* {ry U + ru + g.a* k2b* k. then the distortion periods are commensurate with the translation periods of the basic structure and a new lattice Lr* can be introduced which contains L*. For some crystals the positions of the satellite reflections vary continuously with respect to L*. that the periodic distortions are incommensurable with the translation periods of the basic lattice. or also. The result is the socalled incommensurately modulated structure (IMS). satisfying J. (r? + ru) .3. x exp {im[@. = ry ru.(2nr* Fig. u .
The diffraction of Xrays by crystals 1 173 Provided the number of cells in the crystal is large enough the sum over u leads to (1/V) 6 ( H .20). We also see that four indices are now needed for the identification of a diffraction effect. ( 2 n ~ 'gj)(l)m exp X . We will show in Appendix 3.4) satisfies the properties . and that the symmetry group of an IMS cannot be a threedimensional space group. It easily seen that (3.) exp (im@j). n) may then be written as + N = j=l A(H1) (2nir* r y ) ~ . 6(rro) d r = 1 (3.A.A. The structure factor of the reflections H' = (h. Consequently the reflections occur for r* = H' = H + mK: for m = O we have main reflections (H' = H). then 6 (r . According to Fig. 6 = w for r = r o .rO)= 6 (X .r* + mK) where H = ha* kb* + lc*. Appendices 3. (3.yo) 6 (2 . The above results also suggest that the reciprocal lattice of an IMS is aperiodic in the threedimensional space. The above formalism may be extended to onedimensionally density modulated structures and also to multidimensional (harmonic or not) modulations. (3.2) 6(x xo) may be considered as the limit of different analytical functions.A Mathematical background The Dirac delta function In a threedimensional space the Dirac delta function 6(r .ro) has the following properties 6 = 0 for r f ro.A.17 the average intensity of satellite reflections rapidly decreases with m. if ro = xoa + yob + zoc. exp (2niK r. for m # 0 satellites are defined. k.x0) 6 (y .49). 3. Thus the symmetry in the threedimensional space can also be a poor residue of the full symmetry in the higherdimensional space. as the limit for a + 0 of the Gaussian function Of particular usefulness will be the relation where x* is a real variable. 1. It is easily seen that.E (main references will also be given) that such a reciprocal lattice may be transformed into a periodic lattice provided a higherdimensional space is taken into consideration. For example.1) where S indicates the integration space. Thus the delta function corresponds to an infinitely sharp line of unit weight located at ro.
) where x. Consequently The lattice function L Delta functions can be used to represent lattice functions.7) are both vanishing.4) becomes d(r . and has decreasing subsidiary maxima with increasing x : the value of its integral from w to + w is unitary for any value of g.A.x O ) ] / [ n (. 3.xo)]dx * = lim sin [2ng(x .A.A.ro) =f (r0) .=o(r 6 ( x . The function Y = (sin 2 n g x ) / ( n x )is plotted for g = 1. L ( x ) vanishes everywhere except at .A. = nu and n is an integer value. g sin [2ng(x .1). Clearly Y ( . in a onedimensional space a lattice with period a may be represented by +m L(x) = .x ) = Y ( x ) .xO)] n(xxo) ' The function sin [2ng(x .6) where S* indicates the r* space.xO)]satisfies all the properties of a delta function.7) f ( r ) .A.ro)= 6(ro. 3.and righthand members of (3. Therefore the limit for g+ w of sin [2ng(x. In a threedimensional space (3.l. oscillates with period l / g .xo)] n(xx0) .1): indeed its righthand side may be written as exp [2nix* ( x . for r = ro both are infinite.xO)]I[n(x xO)]takes the maximum value 2g at x = x o (see Fig. Indeed.A.A.3.xo) = lim . From (3.A.ro). x Consequently we can also write: 6 ( x . for r # ro.x. (3. left.r ) (3.174 1 Carmelo Giacovazzo Fig.7) is derived.* exp [2nirS ( r . For example.ro)]dr* (3.4 ) = I. Two important properties of the delta function are: 6 ( r .
reduces to h p(r') d(rf .A. z) plane.16) Because of (3.6). (3. w are integer values. while we could conventionally say that r is a vector in 'direct space'.2. c may be represented by where r. (3. We show now that p(r) = i* F(r*) exp (2nir' .15) and (3. (3. in turn. v.15) The vector r* may be considered as a vector in 'Fourier transform space'.16) may be written as F(r*) = T[P(~)]. p(r) = T'[F(r*)] (3.The diffraction of Xrays by crystals 1 175 the points nu. Accordingly.)..A.15) the righthand side of (3. in a threedimensional space: (1) a periodic array of points along the z axis with positions z. Obviously TlT[p(r)l= p(r) .=m C +m S(z . Analogously a threedimensional lattice defined by unit vectors a.16) becomes p(r') (l* exp [ 2 d r * (r' . . (3. which.17) (3.14) The Fourier transform The Fourier transform of the function p(r) is given (for practical reasons we follow the convention of including 2n in the exponent) by r p(r) exp (2nir* r) dr.A.A. Relations (3. b. = nc may be represented as += f'~(r> w ) ~ ( Y I = .r) dr' = p(r). parallel to x and separated by c may be represented by (3) a series of planes parallel to the (x.A. = ua ub wc and u.r)] dr*) dr'.r) dr*.A.18) respectively: we will also say that p is the inverse transform of F.12) n=m + + C (2) a series of lines in the (x.. y) plane and separated by c is represented by P3(r) = .A..A..A.z.A. because of (3.A.).
so that F(r*) is pure imaginary (then A(r*) = 0). If p(r) is symmetric with respect to the origin. because of (3. r)] dr = A(r*) . 17) and (3. or.176 1 Carmelo Giacovazzo but ?T[p(r)l = T[F(r*)I = ~ ( .A.21) it will result F(r*) = FV(r*).2(a)) 2.A. say p(r) = p(r). p(r) exp [2ni(r* . It should be noted that the larger the 'width' of p(x). 3. Some examples of Fourier transform In a onedimensional space (3. 1.2 ~ c ~ a ~ x * ~ ) . Gaussian function : Since +m exp [$hu2 then + itu] du = (3. Its Fourier transform is the Cauchy function (see Fig. Exponential function : p(x) = exp (g Ix 1). if F(r*) = F(r*) then p(r) is symmetric with respect to the origin. 3. Vice versa. in other words. it may be concluded that where F(r*) is the complex conjugate of F(r*). the smaller is that of F(x*) (see Fig. S I. Since 1 1 S p(r) cos (2nir* r) dr p(r) sin (2nir* r) dr .25) T[p(x)] = F(x*) = exp ( .15) becomes Let us consider some examples for p(x).4 F(r*) is a complex function: by denoting A(r*) = B(r*) = then We calculate now the Fourier transform of p(r).A.iB(r*). F(r*) will be a real function (B(r*) = 0).A.2(b)) .A. P(r) exp (2nir' r) dr = I. If p(r) = p(r) then F(r*) = FW(r*).A.
6(x .sin [n(2n .2(c)) +m F(x*) = . 3.nu).E. 3. 3. 3.1. 1 2 sin (nax *) = 2 2 cos (2nnax *) sin (nax *) sin . If p(x) = 6(x . 4. sin (2ngx *) nx * for g < x < g. Examples of Fourier transform. Then (see Fig.A. [n(2n + l)ax*] . Rectangular aperture: p(x) = c Then ~ ( x *= cly exp (2nix*x) dx = c ) which is plotted in Fig.The diffraction of Xrays by crystals 1 177 Fig.=. where represents a set of N = 2p + 1 equally spaced delta functions.CD 6(x) exp (2nix*x) dx = 1.A. Then T[pp(x)] = n=p pp x P P exp (2ninax*) = n=p l cos (2nnax*)  2 sin (nax *) .a ) then F(x*) = exp (2niax*). Onedimensional finite lattice: pp = C. 5.l)ax*] .A. otherwise p(x) = 0.2. Dirac delta function: p(x) = 6(x).
178
1
Carmelo Giacovazzo

1 {sin [n(2p + l)ax*] sin [ n ( 2 p  l)ax*] 2 sin (nax *)
+ sin [n(2p  l)ax*] sin [n(2p  3)ax*]
+ sin [n(2p + l)ax*] sin [n(2p  l ) a x * ] )  sin [(2p + 1)nax*I  sin Nnax * sin nu* sin m x *
'
The function sin N n y f(y)== is plotted in Fig. 3.A.3 for N = 6 , 7. When y = h ( h is an integer value) numerator and denominator of the righthand member of (3.A.27) both vanish. Then the value of f ( y ) (as determined from its limit for y +h ) is equal to N if N is odd; if N is even, then f ( y ) is equal to N if h is even, to N if h is odd. Between each pair of main maxima there are N  2 subsidiary peaks. Each main peak has width equal to 2 / N ( 1 / N is that of the subsidiary peaks), therefore it becomes sharper as N increases. Furthermore the ratio between the amplitude of a main peak with respect that of a subsidiary one increases with N. What we noted for f ( y ) may be easily applied to (3.A.26), whose principal maxima are at x* = hla. 6. Onedimensional infinite lattice :
According to 5 above the Fourier transform of p will be F ( x * ) = lim
N=
sin Nnax * sin nax* '
The function F ( x * ) will present infinitely sharp lines at x* = h l a of weight l l a . Indeed
I&
+&
sin N m x * 1 &*=lim sin nax * a
E',
I&
+'sin N n y sin n y dye
Whichever the value of
when N+m the value of the integral is unity.
Fig. 3.A.3. The function f ( y ) = s i n N n y l s i n n y for N = 6,7.
The diffraction of Xrays by crystals
1
179
Consequently we could write
or, in words, the Fourier transform of a onedimensional lattice with period a is a onedimensional lattice with period l l a represented by delta functions with weight l/a.
7. Threedimensionalfinite lattice:
Its Fourier transform is F(r*) =
=
u=p1
x x x
P1
P2
P3
exp (2nir* ru,u,w)
.
u=p2
w=p3
9
exp (2niur' a )
. .x
P2
exp (2nivr' b)
.
2
P3
exp (2niwr*
.e)
 sin Nina . r* sin N2nb r* sin N3nc. r* sin n a . r* sin n b r* sin JGC r* '
where Nl = (2p1 1), N2 = (2p2 I), N3 = (2p3 + 1). In accordance with point 5, each of the terms in the righthand side of (3.A.29) is maximum when r* satisfies with integer values of h, k, 1. It is easily seen that the solution of the above three equations is given by r =ha* : where
+
+
+ kb* + lc*,
and V = a b A c. The vectors a*, b*, c* are nothing else but the basic vectors of the reciprocal lattice defined in 3 2.3. When Nl, N2, N3 are sufficiently large then F(r*) has appreciable values only in the reciprocal lattice points defined by the triple of integers H = (h, k, 1).
8. Threedimensional infinite lattice:
Its Fourier transform is the limit of (3.A.29) for Nl, N2, N3 tending to infinity: F(r*) = lim
N,,N~, N+
sinNlna . r * sinN2nb . r * sinN3ncar* sin n a . r* sin n b r* sin JGC r* '
.
According to points 6 and 7 F(r*) represents a threedimensional lattice by an array of delta functions the weight of which may be calculated by
180
1
Carmelo Giacovazzo integrating F(r*) on a domain dV* about a specific lattice point H. Since dV* = d h a * . dkb* ~ d l c = V* d h d k d l * because of the point 6 ~ ( r *d)v * = V* lim
N,.N~.NP=
I ',
'l
sin N,nh sin nh sin N2nk ,, sin nk
E2
x dhl
dkkl_3
E3
sin N,nl d l = V * = 1 v sin n~
arises. In conclusion, the Fourier transform of a lattice in direct space (represented by the function L(r)) is the function L(r*)IV:
which represents a lattice again (called the reciprocal lattice) in the Fourier transform space.
9. Fourier transform of a onedimensional periodic array of points along the z axis, as defined by (3.A.12). Then
10. Fourier transform of a lattice plane lying on the plane z = 0 and with translation constants a and b. Then p(r) = b(x  nu) 6(y  nb) S(z) and
Fourier transform of spherically symmmetric functions
If p(r) is spherically symmetric we can represent r and r* in spherical polar coordinates (r, 0, cp) and (r*, %*, cp*) defined by (see Fig. 3.A.4)
. .
/ '
,I.
x = r sin p, cos 8
y = r sin g, sin 8
z = r cos p,
y *
with r > 0, 0 < cp 6 n, 0 s 8 < 2n. Analogous transformations could be written for r*. Without loss of generality we can choose z along the r* direction: then r r* = rr* cos cp. Furthermore, for each point with coordinates (r, 8, cp) another point will exist, equivalent to the first, with coordinates (r, n + 8, n  cp). The contribution of both the points to the integral (3.A.15) will be exp (2nirr* cos cp) exp [2nirr* cos ( n  p,)] = 2 cos (2nrr * cos 9). Thus (3 .A.15) reduces to
+
3~
n
2n
Fig. 3.A.4. Polar and Cartesian coordinates.
F
r
)
p(r)cos(2nrr*coscp)r2sincpdrdp,d%
The diffraction of Xrays by crystals
1
181
where r2 sin rp is the Jacobian of the transformation (from Cartesian to polar coordinates) Integration over rp and 8 gives F(r*) =
1
m
4nr2p(r)
0
sin 2nrr * dr = 2nrr *
Q U(r) sin 2nrr* dr 2nrr *
(3.A.33)
where U(r) = 4nr2p(r) is the radial distribution function. Thus F(r*) is also spherically symmetric and its value at r* = 0 is given by F(0) =
0
U(r) dr.
As an example, let p(r) be a spherically symmetric function equal to 1 for r S R and vanishing elsewhere. Its Fourier transform F(r*) =
6
2
4s2
sin 2nrr* 2nrr *
r sin 2nrr* dr = $ n ~ ~ r p ( y )
where rp(y) = 3(sin y  y cos y)Iy3 and y = 2nr*R. The function q ( y ) is plotted in Fig. 3.A.5. The main maximum occurs at y = 0. Intensities of the subsidiary maxima decrease when y increases. The distance between consecutive maxima is inversely related to R.
Fig.3.A.5. Thefunction p,y ,=B(sin y ycos y ) / y 3 is plotted as a function of y = 2nr'R.
+
Convolutions
The convolution (or folding) of two functions p(r) and g(r) (it will be denoted by p(r) *g(r)) is defined by the integral
where S is the r space. Note that in (3.A.34) the integrand is a function of both u and r while the integral is only a function of u. The relation between p(r) and g(r) is symmetrical in forming their convolution. That may be proved first by replacing in (3.A.34) r by R = u  r and after R by r: then Convoluting two functions very often has the effect of 'broadening' the one by the other. As an example, the convolution of two Gaussian functions N(a,, al) and N(a,, a;?)is the Gaussian function N((a: 0;)ll2, a , a,). The convolution operation appears in many scientific areas, and is involved in the interpretation of most experimental measurements. For example, when the intensity of a spectral line is measured by scanning it with a detector having a finite slit as input aperture, or when a beam of light passes through a groundglass screen and is broadened out into a diffuse beam. Suppose in the second example that p(8) is the angular distribution of the incident beam and g(B) is the angular distribution which could be obtained if the incident beam was perfectly collimated. For any given p(8) the angular distribution of the transmitted beam is given by:
+
+
182
( Carmelo Giacovazzo
That may be explained by observing that the component of the transmitted beam emerging at angle 0 due to the light component incident at angle 8 ' (and therefore deviated through the angle 8  8') has intensity p(01)g(8 0'). If interference effects are absent the total intensity in the direction 0 is the integral of p(O1)g(8  8') over all values of 0'. A very important theorem for crystallographers is the following: T [ P ( ~* g(r)l = T[p(r)l T[g(r)l. ) The lefthand side of (3.A.35) may be written p(r)g(u  r) exp [2ni(u r*)] dr du where r and u vary in S and S" respectively. Denoting u = r T[p(r) * g(r)] =
=
(3.A.35)
(3.A.36)
+ r' gives
11 I,
S'
p(r)g(rt)exp [2ni(r
+ r') . r*] dr dr'
S
p(r) exp [2ni(r. r*)] d r l g(rt) exp [2ni(rt r)] dr'
S'
.
In an analogous way the reader will prove that
If g(r) = p(r) (3. A.34) will represent the autoconvolution of p(r) with itself inverted with respect to the origin: in crystallography it has a special significance, the 'Patterson function', and will be denoted by P(u). It is
the transform of which, according to (3.A.3.9, is given by T[P(u)] = [A(r*) iB(r*)][A(r*) iB(r*)] = (F(r*)I2. (3.A.39) It is now easily seen that the Fourier transform of an autoconvolution is always a real function: therefore, in accordance with the conclusions of p. 176, P(u) will always be centrosymmetric even if p(r) is not.
+
Convolutions involving delta functions
Because of (3.A.8) and (3.A.34)
If r and u are assumed to belong to the same space, choosing the same coordinate system transforms the above relation onto 6 (r  ro)* p (r) = p (r  ro). (3.A.40) We see that the convolution of p(r) with 6(r  r,) is equivalent to a shift of the origin by r , (see Fig. 3.A.6(a)). Suppose now that f (x) is a function defined between 0 and a. Because of (3.A.10)
The diffraction of Xrays by crystals
1
183
~(x,Y)
w
0
0
0
0
0
0
Fig. 3.A.6. Convolutions of the function fwith: (a)the Dirac 6 ( x  a ) delta function; (b) a onedimensional lattice. In (c) the convolution of the function f(x, y ) with a twodimensional lattice is shown.
where p(x) is a periodic function defined between a and +w, equal to f(x) for 0 s x s a and with period a. Indeed each term in the summation corresponds to a function equal to f(x) but shifted by na (see Fig. 3.A.6(b)). It may be concluded that each function p(x), periodic with period a, may be considered as the convolution of the function f (x) = p(x) defined between 0 and a, with an array of delta functions located at the lattice point positions. This result may be generalized to a threedimensional space. Indeed
where: f (r) is a function defined for 0 s ' x s a, 0 s y s b, 0 s z s c; p(r) is a function defined for x, y, z between w and + w , periodic with periods a, b, c, and equal to f ( r ) when O s x s a , O S y s b , O s z s c . In conclusion, a threedimensional periodic function p(r) may be considered as the convolution of a function defined in an elementary cell with a threedimensional lattice, this last represented by the lattice function L.
Some properties of convolutions
Let p(x) and g(x) be two onedimensional distributions defined in the interval (a,+w) and C(u) their convolution. Consider the characteristic equation of C(u): += +m +m p(x)g(u  x) exp (itu) dx du. C(U)exp (itu) du =
L (L
)
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Carmelo Giacovazzo
Table 3.A.1. Properties of distributions under the convolution operation
Changing the variable u into q = u  x gives
+rn +"
C(u) exp (iru) du =
p(x) exp (itx) dxlm g(q) exp (itq) dq (3.A.42)
which implies that the characteristic function of a distribution obtained by convolution is equal to the product of the characteristic functions of the constituent distributions. From (3.A.42) several properties of great import follow. Setting t = 0 in (3.A.42) gives
where A represents the area under the distribution. Taking the derivative of (3.A.42) with respect to t and setting t = 0 yields
Thus, the mean of the convolution is equal to the sum of the means of the constituent distributions. By extending the procedure Table 3.A.1 may be obtained. The following notation has been used:
are the central moments of order p for the convolution distribution (similar expression can be derived for the constituent distributions). Accordingly po= 1, 111 = 0, p, coincides with the variance a', while yl = p3/a3 and y,= [(p4/a4) 31 are the skewness and the excess parameters for any distribution.
Deconvolution of spectra
Often it occurs that an experimentally measured function C may be considered as the convolution of the functions p and g. If p is known in advance then it may be of some interest to obtain g. That frequently occurs in spectroscopy or in powder diffraction, where a spectrum is often constituted by overlapping peaks and it is wanted to deconvolute from such a spectrum a given lineshape function. Effects of such selfdeconvolution
The diffraction of Xrays by crystals
1
185
are:['"16] the component lines are more clearly distinguished, their location, area, etc. are more correctly defined, the signal to noise ratio is increased. Let us consider C as the convolution of the lineshape function p and of the ideal spectrum g. Then p may be decon~oluted[l~~ C by taking the from Fourier transform of
and by calculating T k l = T[C]/Tbl. (3.A.43) g is finally obtained as inverse Fourier transform of the righthand side of (3.A.43):
An example of what can be achieved is shown in Fig. 3.A.7. In (a) a diffractogram of quartz measured between 67" and 69" is shown, in (b) a possible Fourier selfdeconvoluted spectrum is drawn. The widths of deconvoluted lines are narrower, peak centroids shift as a result of changes in degree of overlap: since integrated intensities of peaks are retained (see p. 184) more careful estimates of integrated intensities of single peaks may now be accomplished. The practical use of (3.A.44) is not always straightforward.[183191 The limited instrumental resolution and the random errors 'associated with experimental data are a difficult problem. In particular, random errors are usually amplified by the process so that the righthand side of (3.A.44) could coincide with a function g' substantially different from g. Filtering operations or supplementary considerations are then introduced to reduce spurious features.
28
Fig. 3.A.7.
3.B Scattering and related topics
Compton scattering
A photon of energy hv (v = CIA) moving along the direction so is scattered by a completely free electron located in 0 , initially at rest. Let s be the direction of the scattered photon, 28 the scattering angle, hv' = hc/(A dA) its energy and mv2/2 the recoil electron energy. Conservation of energy (neglecting any relativistic effect) requires
+
which may be approximated to
 dA = $mu2
hc A2
Conservation of momentum requires
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Carmelo Giacovazzo
which, on assuming A + d = A may be reduced to A ,
h imv =  sin 8. A
(3.B.3)
Finally, v may be eliminated from (3.B.1) and (3.B.3) so as to obtain
The anisotropic temperature factor
Thermal agitation will cause the atoms to fluctuate about their equilibrium positions. Let us suppose that the force field around an atom located at the origin of the coordinate system (its equilibrium position) is anisotropic and harmonic. Then the meansquare vibrational amplitude is different for different directions and equal in the two ways of the same direction. In any rectilinear coordinate system defined by A = [a, b, c] let p ( r l ) be the probability of finding the atomic centre moved in r t = x t a + y l b + z'c = X'A. In general det p(xl, y', z t ) = ( 2 ~ r )  ~ / ~ (U)1'2 exp [~(X'U'x')], (3.B.5) where U is the variancecovariance matrix (it represents a symmetrical tensor)
u=
The Fourier transform of p(X1) gives
i
(x'" (xtyt) (xtzt) (x'y') ( y f 2 ) (y'z') = ( x t X ' ) . (xtzt) (ytz') (zt2)
1
X*~ q(X*) = exp (2n2X*u*x*) = exp [  ~ ? G ~ ( U T ~2U&.x*y*+ . . .)I = exp (X*/3X*) = exp  ( p , , ~ + ~ * 2P12x*y*+ . . .)I where U* is the variancecovariance matrix expressed in reciprocal coordinates and
+
Usually crystallographic leastsquares calculations (see p. 94) provide estimates of the tensor fi from which U* is easily derived via eqn (3.8.6). Then the atomic scattering factor, calculated for r* = r & and corrected for thermal motion is (see p. 153)
fo exp (HPH) =fo exp [2n2(Au*H)]
where fo refers to the atom at rest. In order to obtain U from U* we only need to apply eqn (2.28). We obtain U = GU*G from which In accordance with a well known property of tensors, the meansquares vibrational amplitude (u2) in the direction defined by the unit vector n = NA = N*A*, is given by (u2)(,) = NUN = N*u*N*. (3.B.8)
The diffraction of Xrays by crystals Let us now express n as a ratio between a vector r = XA = X*A* parallel to n and its modulus: n = rlr. Then eqn (3.B.8) may be written as
1
187
or also
From (3.B.9) the following relations arise:
The following exercises may be useful to clarify some aspects of the subject: Calculate the Pijs corresponding to the isotropic temperature factor Biso defined by (3.19). If in (3.19) sin2 8/A2= r*'/4 = 1/(4dh) is replaced by (2.17b) then
$ = BisoG /4 *
is obtained. If $ is the anisotropic tensor in the coordinate system A, calculate its expression in A' = MA. According to (2.A. 15) $' = (M)~$M,. If $ is the thermal tensor of a given atom, calculate the tensor $' of the atom referred to the first one by the symmetry operation C = (R, T). In accordance with (2.A. 16) $' = R$R. Calculate the principal axes of the ellipsoid describing the anisotropic temperature factor $ and their orientations with respect to the crystallographic axes. See p. 76. Calculate the isotropic temperature factor equivalent[201 to a given anisotropic temperature factor (often the anisotropic parameters are deposited and equivalent isotropic are published). The equivalent isotropic motion is defined as that one which gives rise to the same value ) ~ of (u2): in our case ( u ~= () u ' ~ ~ ~ ~ . ~ ~ ~ Let us suppose that eigenvalues A,, A,, and A3 of the anisotropic tensor $ have been calculated. Then, according to (2.38b) we can write (u2)aniso=
1
$(A1 + A2 + A3)
(3.B.lOa)
while, for an isotropic motion (see eqn (3.19))
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Carmelo Giacovazzo
Isotropic and anisotropic motion will be then equivalent if Let us now observe that, under a transformation of axes, the matrix $G transforms, because of eqns (2.E.8) and (2.21), according to in other words, PG transforms in the same way as a rotation matrix of a symmetry operator (see eqn (2.E.1)). Therefore the trace of $G is invariant under the transformation and, according to p. 75, it is constantly equal to A, + A, A,. At the end we can replace eqn (3.B.lOb) by the most simple equation
+
1 1 (u2)equiv = 2 Tr (PO) = 6~ i,j The reader will easily derive from (3.B.lOd) specific formulae for specific crystallographic systems: e.g. for cubic, tetragonal, and orthorhombic systems (u2)equiv= (Plla2+ P22b2 + P 3 3 ~ ~ ) 1 ( 6 ~ d ~ ) , for hexagonal and trigonal systems (hexagonal setting) etc. Readers are referred to Schomaker and ~ a r s h [ ~ l ] the estimated for standard deviation of (u2) In reports of crystal structure determination thermal motion is usually presented in direct space by means of a probability ellipsoid. Each ellipsoid is centred on the mean position of the atom: the surface has constant probability density obtained, in accordance with eqn (3.B.9, on assuming
jpulx'= ~2
where C is a chosen constant. The probability P that a thermal displacement falls within the ellipsoids may be calculated as P(c)=~
ellipsoid
p(X')dXr.
The most often used value is C = 1.5282: then[''] the ellipsoid encloses 50 per cent of the trivariate Gaussian probability density.
Symmetry restrictions on the anisotropic temperature factors
Coefficients Pii as provided by crystallographic leastsquares procedures (see p. 94) are affected by various error sources: for example, experimental errors on diffraction intensity measurements, inadequacy of the atomic scattering model, wrong or unapplied absorption correction (see Chapter 4), existence of nonharmonic force fields around the atoms, etc. Thus the thermal parameters estimated by least squares could be physically unrealistic; for example the variancecovariance matrix U should not result positivedefinite. Necessary and sufficient conditions for positiveness are (det U) > 0; Uii > 0; and UiiUi,> 0 for i, j = 1, 2, 3.
The diffraction of Xrays by crystals
1
189
If the above conditions are violated then atomic vibrations could be described by imaginary ellipsoids or by paraboloids or by hyperboloids, with the obvious meaning that experimental data are not of sufficient accuracy to justify the use of anisotropic temperature factors. If an atom lies on a special site of a space group the components of the thermal tensor are restricted according to the site symmetry. Indeed the thermal ellipsoids must remain invariant after application of the n symmetry operations which leave invariant the site. In accordance with point 3 in the previous section the relations arise, from which the $ restrictions can be derived. Such restrictions can also be obtained in an easier way by using Wigner's theorem according to which the symmetry of the $ restrictions is displayed by the matrix
Since no atomic position is left invariant after the application of glide planes or screw axes, only point symmetries have to be taken into account. Furthermore, ellipsoids are centrosymmetric, thus no additional $ restriction arises if an inversion centre is added to the site symmetry, or if a mirror plane is replaced by a twofold axis perpendicular to the plane. Thus it is not difficult to understand that ellipsoid symmetry is one of the following three cases: (1) spherical symmetry, for atomic sites with symmetry 23 and its supergroups; (2) ellipsoid of revolution, for site symmetries 3, 4, 4, and 'noncubic' supergroups; (3) general ellipsoid. For site symmetry 222 and its orthorhombic supergroups the orientations of the ellipsoid axes is fixed by symmetry; for site symmetry 2, m, or 2/m only the orientation of one ellipsoid axis is fixed by symmetry. In Table 3.B.1 all the conventional special positions are collected in seven b l o ~ k s . [ ~ ~ , ~block shows the possible point groups to which each site Each ~ ] may belong, the 'minimal' site symmetry characterizing each position and a crossreference number identifying the type of $ restrictions described in Table 3.B.2. The letter h, when present, warns that an hexagonal setting is involved and the letter w suggests that the rule holds for hexagonal and nonhexagonal settings. To make Table 3.B.1 clearer we note that all the special positions in the first block belong to one of the point groups m3m, 43m, 432, m3, 23. According to previous observations, we now neglect whether symmetry axes are proper or improper; thus the 'minimal' symmetry 311111 210011 associated with the sites. Conversely, under the same is i Z[lool or 2[ooll2 k 0 ~ ~ l convention, all sites with symmetry 2[,,] 211001 or 2[rn11 or ?[,ll 211001 2[,,] 2[loo1 all represented in block five of Table 3.B.1 by or are the site with 'minimal' symmetry 2[,,] 2[1001 To make Table 3.B.2 clearer we observe that case No. 23 may be rewritten as: P11, P33 = P22' P121 P13 = P121 P23.
190
1
Carmelo Giacovazzo
Table 3.B.1. Site symmetry table giving key for the 29 types of symmetry prestrictions m3m, 43m, 432, rn3,23
3[1111 2 [ ~ ~ 1 1
2/m, m, 2 l W2001]
0101 1001
6/mmm, 6m2, 6mm, 622, 6/m, 6, 6, 3m, 32, 3, 3 W h 310011 9 w 4/mmrn, 42m, 4mm, 422 4ffr~4,4 1 4l001
4[~1~1
411~~1
0
1
21iio1
101,
I
20111
2 h 3 Il h 4 tl 5 6 7 8 10 11 12 13 14 15
2
0
1001 2210] 1201
0101
I6 17 18 19 20 21 22 23 24 25 26 27 28
3rn, 3m, 32, 3, 3
%iil
3[iii1 3[1i11 3[iii1 rnrnrn, rnm2, 222 2[00,1 2[1001 w 2[001, 2[1101 2 0 0 2[1011 111 2~001 ~[OIII h 2100111 0 1 210 h ~ [ O O ~ I 210101
i, 1
1 29
Table 3.B.2. Symmetry firestrictions.
Crossreference No.
Pi1
P22
P33
Pi2
Pi3
P23
Crossreference No.
Pi1
Pz,
P33
Pi2
Pi3
P, 2
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
A A A A A A A A A A A A A A A
A C A B A A A D A A A A A C A B C A C B A B B B C B C
A A B B A
O 0 O 0 O 0 O 0 D D  D D D D D / 2 0 O 0 D 0 O E O 0 B/2 0 A/2 0
16 17 18 19 20 21 D D 22 D 2 3 0 24 0 25 0 26 0 27 F 28 29 0 0
0 0 0 0 D
A A A A A A A A A A A A A A
B B B A A B B B B B B B B B
C C C C C A A B B C C C C C
D O O D D D D D D B/2 A/2 B/2 A/2 D
0 0 E 0 0 F E E E E E D E D D F D F F/2 F 0 F E 0 E E/2 E F
First ~ i p s c o m b [investigated the possibility of using multiple diffraction ~~] intensities for phase determination. . In spite of many subsequent investigations.1. As already noted. the threebeam diffraction effect can be treated in accordance with dynamic diffraction theory and used for the experimental solution of the phase problem. Renninger effect described in: (a) reciprocal space.l(a)). 3. only in more recent years[2s301has it become clear that dynamical theory applied to threebeam diffraction is a powerful tool for the experimental solution of the phase problem even for common (say imperfect) crystals. On the other hand.12) sets up that the diffracted beam Hz can act as an incident beam for the reflection H1 .8. to the beam diffracted in direction sl by lattice planes H1 a twicereflected beam overlaps.25) it will have to be By subtracting the second equation from the first we obtain (sl .HI. 3. it can be the reason for apparent violation of the systematic extinctions (but the shape of their diffraction peaks is different from that of the normal reflections and therefore easily recognizable).B. 3. In the same way the beam diffracted in direction s2 from the planes Hz will overlap with a twicereflected beam. the multiple diffraction (Renninger) effect can be considered as a disturbance. (3. when diffraction data are collected for crystal structure solution.B.l(b)). and a short account is given here. first from the planes H1 and then from the planes Hz . Therefore.B. but conclusive results were not obtained. first from the planes Hz and then from the planes HI . The reader is referred to a recent book[311 a review of the various contributions and a description of the for Fig. General solutions for the threebeam case are now available which provide a satisfactory interpretation of experimental results.s2)lA = r& . In general.B.The diffraction of Xrays by crystals 1 191 The Renninger effect and experimental phase determination by means of multiple diffraction experiments Let us suppose that the two nodes HI and Hz are simultaneously at the surface of the reflection sphere: according to eqn (3. (b)direct space.Hz (see Fig.HZ which is thus in the diffraction position (see Fig. This point of view is extremely promising.12) Equation (3.r& = r&H2.
is the amplitude of the Umweg wave defined by D =RW)FH~FH. 3.14) may be used to interpret the main features of typical qscan profiles (we assume that r.3) where the Ds are the amplitudes of the excited wavefields in the crystal (the intensities are given by 1= 1 D 12). 0: for <<O it is @j+ A($) = 0. . interfering waves are Fig. In eqn (3. is inside the Ewald sphere.H~. it is between n/2 and n when it is outside.  6 . crosses the Ewald sphere from inside (. The integrated : 3scan profile may be approximately calculated (except for a range very close to the threebeam setting) according to (see Fig.. u Ciare suitable parameters.2.13) and (3. Typical resonance curves for IR(q)1 and A(q) are given in Fig.(3)is monitored while the crystal is rotated about the vector r. . scatterings produces a wave whose intensity depends on the triplet invariant phase Without anomalous dispersion effects it is equal to Such an intensity can be measured by a qscan experiment (see Fig. lR(+)l and A(3) are the modulus and phase of the complex resonance[331 term R ( q ) = )R(q)l exp (iA(+)] which governs the amplitude and the resonance phase shift of the Umweg wave.8.H. and scanned through the threebeam position. (b) reciprocal space.. 3 < 0) to outside ( 3 > 0)). is the twobeam amplitude of the reflection HI.B.4.8.[^^] The interference between the wave directly diffracted from H1 planes (primary reflection) and the 'Renninger Umweg wave' generated from Hz and HI . 3.3.B. Diagram of the interference between the unperturbed twobeam amplitude Do and the Umweg resonance term D.scan (b) Ewald sphere theoretical background: here a short account of the results is given in accordance with Hummer and ill^.B. IR(q)I is highest near the threebeam position.B. 3. 3.192 1 Carmelo Giacovazzo Detector I Fig. Equation (3.2): the integrated intensity IH. 3. 13) DL. *scan experiment described in: (a) direct space. D.B. Suppose Q. A(q) varies from zero to n when 3 is scanned through the threebeam position: it is less than n/2 when H.B.
( large then the intensity of HI is is increased at the cost of the H2 reflection intensity. that is a strong depletion of the HI intensity.8. 3. which contain the phase information. Some concluding remarks may be useful: 1. A(3)) = 1. The result is the socalled aufhellung effect. This loss of intensity is not compensated by the scattering power from H2 into H1 reflection. Since dynamical threebeam interaction has a very small angular in .5. When we get near the threebeam position ID. Then profiles can be separated into two parts: the symmetric AI curve. 3.If IFH2[ small and are is IFHZHII is large enough (or vice versa as the influence of (FH21 IFH2H11 and is symmetric) then intensity is removed from the H1 reflection and coupled into the H. Therefore one is able to define ideal profiles that satisfy the condition +  +  .[~~] A special sixcircle d i f f r a ~ t o m e t e rproved to be useful: ~~~] two circles (8. 0. If a. If IFH. This effect is called umweganregung by ~ e n n i n g e r . have been recently secured[341 are shown in Fig. 3.The diffraction of Xrays by crystals 1 193 essentially in phase. the ideal 3scan profiles. the 3 scan is performed by rotating only about the axis: the detector circles (8.B. When the vector H1 is aligned into the T) axis. A(3)) 1.0 v  out Fig.5 are marked by the condition AZ(tp)lG1= 1. = n/2 an increase in intensity will occur about 3 0. I & ( 3 ) and I&(+) are the qscan profiles for the positive ( + a 3 ) and the negative triplet phase (a3) respectively. Ideal 3scan profiles can only be obtained if the dominant process in he threebeam interaction is due to the interference effect. IHl(v) for a given a3is equal to IH1(3) for the phase (180 . reflection via the coupling Hz. For larger values of 3 ZH1(3) I$.(qj)l rapidly increases while A(3) approaches 7612: then the intensity ZHl(3)>GI.B. and . 3. Y) for the detector and four circles for the crystal motion (see Fig.a . f7612. That occurs when IFH21 and IFHlH21 about twice as strong as IFHl/. 7612 the qscan profile will show a nearly symmetrical decrease of the intensity about I$ 0. +45" (or Q3= 45') should present characteristics between those for a.HI. Therefore 3scan profiles for Q3 and (180 .6).Iis very small and IFH. The type of asymmetry is reversed for triplet phase a3 180". where cos ( a .a 3 . A 3 ) is negative: then ZH1(3)drops will approach below the twobeam value G I . 2. Schematic drawings for the amplitude of the resonance term Rand for its phase factor in function of tp.14). Exact 3scan can be difficult for conventional fourcircle diffra~tometers. Profiles for other quadrants can be obtained by observing that. According to this method. but R ( 3 ) = 0. which represents the phaseindependent umweganregung or aufhellung effect. expected profiles for a. according to (3.B. = It is easy now to foresee that for triplet phases with a. kn14. Y) may be moved to observe the reflections H1or H2. . = 0 and for Q3= 90" (or a3 90"). n. [ ~ ~ ] Unweganregung and aufhellung effects can be evaluated[361 comparing by the 3scan profiles for 0. Thus the ideal profiles shown in Fig. Then IH1(3) =I&. ) are related by a mirror line through 3 = 0.Q3). +    in . Ideal qscan and profiles for a. Just after scanning through the threebeam position IR(q)( is still large but cos ( a .0 v out AI(3) = Gl where AI(3) is defined as AI(3) = m i 1 ( 3 ) + G1(3)). where cos ( a . tp is assumed to be zero at the ideal threebeam position.B.4.
.
(c) Inelastic scatteringelectrons of the primary beam interact with atomic electrons. The following relation is valid: Two energetical intervals are commonly used: we will talk about highenergy diffraction (HEED) when V 50120kV (with the advent of highvoltage electron microscopes this range needs to be extended to 1MeV) and A =0.The diffraction of Xrays by crystals 1 195 range. and lowenergy diffraction (LEED) when V = 10300V and A=41 A. Nonconventional sixcircle diffractometer. 3. Electrons are accelerated through a potential difference of V volts.1". 5. Electrons are strongly absorbed by matter and therefore ediffraction in transmission is applicable to very thin layers of matter (10p7105 cm). 3. half an hour when synchrotron radiation is used. It is safe to calculate in advance the most suitable 1 . If polarized radiation is used. The absolute configuration of a noncentrosymmetric structure may be determined by accurately measuring one (or more) triplet phase. or in a heated pointed filament of 12 pm size (see Chapter 9). (b) elastic scatteringthe electrons are scattered by the Coulombic potential due to the nucleus. Electron diffraction The diffraction of electrons (ediffraction) was demonstrated by Davisson and Germer in 1927.. angles for each 1 reflection HI and choose for measurements threebeam cases which are separated from all the others by an angular distance greater than 0. some hours for less intense sources). 6. FH2.6. Finding three beam points is not very easy for large structures (more than three reciprocal lattice points can simultaneously lie on the Ewald sphere). no loss of energy occurs: such a scattering is the most important in electron microscopy. The electron beam is produced in an electron gun by a 'hairpin' filament with diameter of about 10 pm. The scattering is caused by the interaction of the electrons with the electrostatic field q(r) of the atoms.8. both the divergence and the spectral width of the primary beam should be small enough.05 A. But also properly modified Xray equipments based on rotatinganode generators can play an important role. 4. Measuring with the necessary statistical accuracy a single 3scan profile is a timeconsuming process (say. Thus the interaction of electrons with matter may be divided into three processes: (a) no interactionthe electron passes straight through the specimen. the have polarization factor may be exploited to attain such a rule. As a rule. but also divergence of 106rad may be achieved for special purposes. Since the proton mass is much larger than that of electron. the qscan profile is usually obtained as the sum of many fast scans. Fig. Synchrotron radiation seems therefore the most suitable source for qscan experiments. Electromagnetic lenses restrict divergence to or lop4 rad. more reliable phase estimates can be obtained if FH. In order to avoid the influence of longrange intensity variations. FH1H2 comparable magnitudes. and are scattered having suffered a loss of energy. q(r) is the sum of the field caused by the nucleus and the field caused by the electron cloud. having a value near fnI2. In a microscope such electrons are focused at .
8. 146). we observe that: 1. is indeterminate.B. fa..B. While the nucleus with the charge Ze can be considered as a point. is in electrons and f.15) with the atomic scattering factor for the Xrays. sin @/A Fig.p e w ) where p. Let us introduce into Poisson's equation the inverse Fourier transform v2(] fae(r*)exp (2nir* . is the electron density function (as defined for Xray scattering). . The curves fa.7).r) dr* r) dr*. (3) neutrons. 3 and 4) : where fa.3) to the atomic number Z than fa. in (fte occurs in the first Born approximation for electron scattering by atoms). as for Xrays (see p. 3. I + I 2nir*12fae(r*) exp (2nir' we obtain the Mott formula fae(r*)= nl(Z fax(r*))lr*'. the electrons occupy a finite volume: therefore. but a sensible value may be obtained by the boundary condition It is still preferred to tabulate (see International tables for xray crystallography.(r) is the charge density due to the atomic nucleus and p... q(r) is related to the electron density by Poisson's equation V"@) = 4nbn(r) . Vols.r) dr* . (on the average fae(0) ~ 2 " ~ Therefore the positions of the ). 2. r) dr*) = 4n fax(r*)exp (2niP I . and that for electrons.B. Typical scattering curves for: ( I ) electrons. the escattering will have a geometric component which will take into account the distribution of the electrons around the nucleus. f. 3. are less sensitive (see Table 3. Consequently diffraction effects are easily detected even from volumes much smaller than those required for Xrays (in practice.4n Z exp (2nir* Since the lefthand side is equal to I . starting from thicknesses of 100 A for simple structures constituted of heavy atoms). If we compare numerically eqn (3. (2) Xrays.7.196 1 Carmelo Giacovazzo different positions and produce an effect called chromatic aberration (causing blurring of the image). By supposing a spherical symmetry a simple relation may be obtained between the atomic scattering factor for Xrays. escattering is much more efficient than Xscattering (see Fig. For sin 8 / A 0 the value of fa.
The function q ( r ) terminates at . The electrons can exist in two spin states and therefore can be polarized. one might think it would be easy to obtain resolved images of the atoms (in some cases they have been effectively obtained). Some atomic scattering amplitudes for electrons at sin 811 = 0 based on the rest mass of the electron (for and electrons of velocity v multiply fa. Besides. nucleation of new phases. by [ I . HEED microscopy is particularly favourable for studying superstructures.B. catalysis. The aberrations of magnetic lenses. Usually internal fields of crystal structures are not strong enough to do that. With A = 0. hydrogen atoms in an organic compound) may be more easily determined by ediffraction.g.( v / c ) ~ ] . 3. particularly the spherical aberration are the principal obstacle: electrons widely scattered are focused at positions different from those to which are focused electrons travelling close to the lens axis. the atomic positions can be fixed by means of the threedimensional Fourier synthesis whose maxima correspond to the positions of the atomic nuclei. LEED techniques are commonly used for studying crystal surfaces (electrons can penetrate into a crystal only for a very small thickness). or transformed into images by means of adequate electronic optics. In HEED techniques diffraction angles are very small. As for Xrays.The diffraction of Xrays by crystals Table 3. There are a lot of reflections having 20 between 0" and 2". the radius of the Ewald sphere is very large and its surface is in practice reduced to a plane: thus. orderdisorder phenomena." ~ ) . and generally the real structure of crystals. all the nodes of a reciprocal plane can simultaneously be in Bragg position.05 A. Under these conditions sin 8 in the Bragg law can be approximated by 0. Because of these characteristics. or collected on a photographic plate for measuring the intensities. Tens or hundreds diffracted beams can be simultaneously observed on a fluorescent screen. The result is that a point object is spread over a length Ar in the image plane. 4. grain boundaries. oxidation. etc. nuclear scattering for neutrons for specific nuclei Element fte(0) (lo' cm) Specific 1 197 b (lo'' cm) light atoms in presence of heavy atoms (e. The theoretical resolution of an electron microscope is approximately 2 A at 100 kV and less than 2 at higher potentials.3. in order to study processes of electronic and ionic emission.
4 ys): heatremoval is then easy and high fluxes are allowed (higher than those produced by reactors). is created which decays by reemitting the neutron. Interpretation of the spectra is not easy because of multiple scattering of the electrons. Water. Cu. They produce fast neutrons whose energy is reduced by collisions in a moderator of heavy water or graphite.9132 nuclear magnetons. transition elements). polyethylene.B. or liquid methane are frequently used: the choice is determined by the scattering experiment.8(a)). it is possible to have negative scattering factors for some nuclei (for instance. Highenergy neutrons are slowed down to thermal energies by appropriate moderators. 3. (a) Spectrum from a nuclear reactor. (b) A schematic timedependence of two pulses of neutrons leaving the moderator with different energies (A. of several orders of magnitude less than the wavelength associated with the incident neutrons. A next pulse starts when the number of neutrons (N.B. So retarded neutrons are called thermal and their speed obeys a Maxwell distribution: the corresponding spectrum is white (see Fig.8.0. 5 5 ~ n )for them the scattering is out of phase by 180" with respect to the : Fig.7). i.).Ab'. 3. By convention. Highenergy protons (1 GeV). 62Ni. The neutronatom interaction comprises interaction with the nucleus and interaction of the magnetic momentum associated with the spin of the neutron with the magnetic momentum of the atom. During the thermalization process neutrons undergo a large number of collisions which cause pulse broadening. Additional information is provided by means of Auger spectroscopy of scattered electrons.e. 'H. Its wave properties were shown in 1936 by Halban and Preiswerk and by Mitchell and Powers. the scattering amplitude is assumed positive where there is a phase change of 180" between incident and scattered waves: it has the dimension of length and is measured in units of 1012 cm. 3.8(c): high intensities at short wavelength (A < 1A) is a very significant characteristic of pulsed neutron sources. Neutron scattering A neutron is a heavy particle with spin 4 and magnetic moment of 1. strike a target such as uranium or tungsten releasing several tens of neutrons per proton (25 neutrons for 238U). in short pulses at the appropriate pulse frequency. Zn. The width of the pulse leaving the moderator is roughly proportional to the wavelength (see Fig. The shaded wavelengths are selected by a monochromator. Neutrons can also be produced in a pulsed manner by spallation. Neutron diffraction experiments (ndiffraction) require high fluxes provided nowadays by modern reactors. nucleus + neutron. When the neutron is very close to the nucleus a metastable system. 3.B.The pulsed neutron flux is only present for a very short time (the burst lasts around 0. Since Ab' can be greater than b. This effect mainly occurs for atoms with incompletely occupied outer electron shells (for instance. Pb) selects the desired wavelength A.B.198 1 Carmelo Giacovazzo the crystal surface: thus in principle the structure of outer layers can be different from that of internal layers. (c) Neutron flux distribution on a pulsed neutron machine. 48Ti. > A. 3. The neutronnucleus interaction is governed by very short range nuclear forces (10l3 cm).) is small enough. Since the nuclear radius is of the order 10l5 cm. . at a repetition rate between 24 Hz and 50 Hz. the nucleus will behave like a point and its scattering factor bo will be isotropic and not dependent on sin B/A (see Fig. A characteristic neutron spectrum is shown in Fig.8(b)) so that the fractional wavelength resolution is nearly constant. liquid hydrogen. For appropriate energy a resonance effect can occur: then the scattering factor assumes the form b = bo . A monochromator (usually single crystals of Ge.
54Sfmag (10l2 cm)  where y is the neutron magnetic moment in nuclear magnetons. for which I = 4.(w+b+ Wb)'I which contributes to a uniform background with no diffraction effects. According to quantum mechanics. then it can be combined with the neutron spin in a parallel or in an antiparallel fashion yielding the total spin of either J = I 4 or J = I . If I is the angular momentum. Interaction occurs in a finite domain around the nucleus: therefore. Let us consider the case of identical atoms with all spins parallel (ferromagnetic materials) and spins alternating parallel and antiparallel (antiferromagnetic materials). there are 2J 1 orientations in space compatible with one spin of value J.wnbE . b 0. and corresponding scattering factors b+ and b.will be the coherent scattered amplitude. magnetic scattering will decline with sin6lA. 1659 for a more extensive treatment of anomalous scattering). This is particularly important for hydrogen. one chemical element exists in a crystal structure in different isotopic forms which are randomly distributed over all sites occupied by the element.25. p is of the same order as nuclear scattering.4. S the electron spin quantum of the scattering atom. with square amplitude given by [(w+b: + Wb:) . w+ = [2(I + 4) 1]/[2(2I+ I)] = (I + 1)/(2I 1) corresponds to states of parallel spins while the other one. . b+ 1. w.75. A few nuclei also present an imaginary wavelengthdependent term Ab" (see pp. fmag the atomic scattering form factor given by the Fourier transform of the distribution of electrons having unpaired spin and normalized so as to be fmag = 1 for 6 = 0. In conclusion.The diffraction of Xrays by crystals 1 199 nuclei with b > 0.39. Incoherent scattering will also occur. w. One fraction of these.= I/(2I I). Atoms which possess a magnetic momentum because of the presence of unpaired electrons interact with the magnetic momentum of the neutron giving additional neutron scattering.and scattering amplitudes b+ and b. Then b = w+b+ wb. :1 F F + sin2 cv I FmagI2 where a is the angle between the unit vector in the direction of the spin . If wn is the relative abundance of the nth isotope then the effective scattering factor will be b = C wnbn and the total diffuse background scattered intensity will be 1. Nuclear and magnetic scattering are additive for unpolarized neutron beams: then I 1' = I .04 x 10l2 cm.b2. The magnetic scattering amplitude of each atom is given by + + + + + + + + + +    p = (e2ySfmaglmc2) 0. as for Xrays and electrons. In general. and most of the scattering is incoherent background. corresponds to states of antiparallel spins.= 0. This disorder generates a pervasive coherent and incoherent background in the diffraction spectrum.i) 1 = 2(2I+ 1) 1 1 possible states. Then w+ = 0.7 x 10l2 cm. The angular momentum of the nucleus is another factor which influences the capacity of scattering. b. The scattering factor of the element will be a weighted average over various states of spin of every isotope and over various isotopes. c the velocity of light. The compound nucleus will then have [2(I+ 4) 1 [2(I .4. e and m are the charge and the mass of the electron. a single isotope with I > 0 can be described as a random mixture of nuclei with atomic fractions w+ and w.
f. scattering lo' cm for electrons. give the spin density distribution of the magnetic atoms. F and Fig. Fourier syntheses with coefficients F. The interaction of neutrons with the matter is weaker than that of Xrays or electrons (see Table 3. The b values vary nonmonotonically with the atomic numbe.. Magnetic symmetry can be described by means of space groups of antisymmetry or by means of colour groups (see Appendix l . b.36.B. 4.96..F. Thus reflections with high values of sin 8lA can be collected giving atomic positions and thermal parameters with accuracy higher than from Xrays..g. b. Therefore high neutron fluxes and crystals with dimensions of several millimetres are needed for measuring appreciable scattered intensities. Monochromatic beams of polarized neutrons are easily obtained from unpolarized beams by using suitable singlecrystal monochromators (for example.. = 0. gives the positions of the nuclei (they do not necessarily coincide with the atomic positions found by Xray diffraction). b. = 0. Since b does not depend on sin 8/A nuclear scattering decreases only because of the temperature effect. the peak is negative too. fa. (10121011) cm for Xrays. In many cases X. The peak heights are proportional to the b values of the corresponding nuclei: if b is negative. This allows us to distinguish between atoms having very close values of Z (but very different values of b : e. .3). For the multidomain samples it will be necessary to average over the various spin orientations. Neutrons are particularly useful for localizing hydrogen atoms. 1. The threedimensional Fourier synthesis with coefficients F. For ferromagnetic and ferrimagnetic samples external fields for orienting the spins can be applied so as to obtain sin2 a = 0 or sin2 a = 1. Usually they are partially or completely substituted by deuterium with a value b > 0 and with negligible incoherent scattering. either constructive or destructive interference between nuclear and magnetic scattering amplitudes can occur. Among the most important characteristics and applications of neutron diffraction we quote: 1.25) and to localize the positions of light atoms in the presence of heavy atoms. Z: isotopes of the same element can have very different values of b. 10l2 cm for neutrons..200 / Carmelo Giacovazzo orientation in the sample and the vector r * .. In other cases the magnetic structure has a cell which is a multiple of the chemical cell causing additional purely magnetic reflections. For a given polarization. Generally speaking. Thus the technique may detect a weak magnetic scattering even when it is accompanied by a strong nuclear scattering. 3. For a sample containing a single magnetic domain sin2 a is equal for all atoms.2(b)) associated with classical threedimensional space groups. Measurements of IFI2 for both cases separate magnetic from nuclear scattering and allow the study of magnetic structures.    2. amplitudes are fa. Sometimes the magnetic cell coincides with the 'chemical' cell so that the magnetic contribution to the intensities is added to nuclear contribution.. a CoFe alloy). = 0.and ndiffraction experiments are both performed in such a way that accurate maps of the electron density can be obtained.
Here L. No attempt will be made to deal exhaustively with the great amount of work made in the field: only the basic principles of the phenomena will be described. is the flight path from moderator to sample and L2 is that from sample to detector. At spallation neutron sources.555LdHsin O0 where L is measured in meters. In addition the equations suggest that resolution improves with increasing flight path.The diffraction of Xrays by crystals ( 201 5. Iiquids. and amorphous solids Introduction In this appendix we will describe the scattering of Xrays from gases. = 2dHsinOH. Then + tH= 505. intensities are measured by moving a detector to different scattering angles OH chosen according to Bragg's law A. Thus time of flight depends linearly on both the flight path and on the wavelength. even if the source is on for brief pulses the full spectrum may be used (in monochromatic techniques coupled with a reactor the source is on all the time but a small portion of the spectrum is used). For further information the reader is referred to specialist papers on the subject or to some enlightening books.1 eV. and amorphous solids. From de Broglie's relation mu = h/A (m and v are mass and velocity of the neutron respectively) the following relation arises: mv = m(Llt) = hlA. 3. the discrimination among neutrons with different wavelengths may be accomplished by their time of arrival at the detector (time of flight): thus diffraction effects can be measured at a fixed scattering angle $0: AH = 2dHsin OO. Area detectors (see Chapter 4) are the best choice for timeofflight techniques. The energy of a neutron with wavelength of 1A is of the order of 0. t in ys.. In diffraction techniques using monochromatic radiation. where the neutron beam is pulsed. A and dH in A. which is comparable with the energy of the modes of thermal vibration of the crystal.[3w1] First ~ e b y e [ ~(but see also ~ h r e n f e s t ~realized that no arrangement of '] ~~]) molecules of finite size could be considered completely random. Indeed. 6. According to . The most random array which can be imagined is that of a monoatomic gas: but even in this case the finite size of the atoms prevents their approaching one another within a distance smaller than a given threshold. L.C Scattering of Xray by gases. Some additional information about neutron diffraction experiments with pulsed neutron sources should be useful. This causes inelastic scattering but also allows for the possibility of studying energy changes with good accuracy. where L = L. liquids.
C.2) The product @(r) @(r + u) is always vanishing except when both the points .C. Diffraction from a finite statistically homogeneous object Usually the motion of atoms or molecules in gases and liquids is extremely rapid compared with the duration of a diffraction experiment. two types of effects could be found on the diffraction patterns: (1) the effects due to the more or less fixed spatial arrangements of the atoms in the molecules (even if molecules have random positions and orientations).1) over all the atoms in the assemblage the total incoherent scattering is obtained. for monoatomic gases external interference effects are dominant. is usually collected. In the following sections some formulae will be developed which refer to the coherent scattered radiation. Such a function has to be subtracted from the total scattering pattern: only after that can the coherently scattered intensity be used to deduce structural parameters. for which trying to calculate the atomic positions has no practical meaning while it is possible to estimate interatomic distances (on which diffraction intensities depend). Indeed.202 1 Carmelo Giacovazzo Debye. in experiments the total. A similar conclusion holds for amorphous materials. which is a smooth function slowly increasing with sin B l A . while for polyatomic gases internal interference effects are not negligible. The relative importance of the two types of effects is a matter of degree. say both coherent and incoherent radiation. Again in liquids (or amorphous solids) the existence of average interatomic distances produces well marked external interference effects: if the liquid is composed of groups of atoms the internal interference effects are again not neglibible. If we sum (3.27) and the Patterson function becomes P(u) = I R p d r ) p d r + u)@(r)@(r+ u) dr. According to the discussion on p. (3. In accordance with eqn (3. called 'external interference effects'. in the case of amorphous bodies the incoherent radiation may be an important fraction of the total radiation. However. called 'internal interference effects'. Suppose that the object we want to investigate is finite and statistically homogeneous. (2) the effects due to the mutual configuration of the molecules. In these conditions the phase value of F(r*) has no practical interest while its modulus can provide useful information on the statistical distribution of the atoms. the incoherent intensity relative to one atom is given by k where k varies over the individual electrons of the atom. Indeed the measured diffraction intensity is the weighted sum of contributions arising from the various configurations of the atoms. 147. which may be not arbitrary since it is conditioned by their dimensions and their packing. of volume a.
C. The space + domain in which this condition is verified is a function of u and will be denoted by Qv(u). say w = 1/52.A.A. the smaller the A domain).~ . Accordingly + ' \ \ \ +. that Rv(u) is the volume which belongs to the object and to the object shifted by u.4) Fig.C.(u) is the Patterson function for the unit volume.C. The dashed area has volume Rv(u) For homogeneous objects (3. From (3.C. according to (3. Thetypicalform ~'~ diffracting object. It is readily seen from Fig.2 for a onedimensional example). and (3. as a .9) it is easily deduced that 1D(r*)12rapidly decreases with (r*l. 1D(r*)l2 is centrosymmetric: its maximum value is 1 D (0).2. + (3. together with its approximate dimension rz ( 1 / ~ )= l/ro.37).6) j Qv(u) exp (2nir" u) du = ID(r*)12 (3. (D(r*)I2 f repeats itself around each lattice point: the larger is 52. v(u) is centrosymmetric (v(u) = v(u)). 3.A. Then an approximate estimate of the domain volume is obtained.C. 3. where ro is the average dimension of the Fig. Furthermore.1.27) D (0) = 52 so that Furthermore.6) Q* ID(r*)l2dr* = L Pv(u) d u b *exp (2nir* u) dr* .   r* of . 3.C. D ( r X .C.21) is T[Qv(u)] = so that Since @(r) is real. it decreases with increasing u and takes its maximum for u = 0 (v(0) = 1).C.C. Replace in (3.1' According to (3. according to eqns (3. (3.1.C.37) The Fourier transform of Qv(u).9) the decreasing function ID(r*)I2 by a constant which is equal to its maximum value 52' in a volume w defined by S2'w = 52 (see Fig. According to (3.3.3) may be written as where P.8) and (3. and is appreciably different from zero in a domain near the origin NU of the reciprocal space (when the diffracting object is a crystal.The diffraction of Xrays by crystals 1 \ 203 I r and r u are inside the object: in this case @(r)@(r u) = 1. function of r*.C.C.4). & I I I I 1 where RY(U) = I" @(r)@(r u) d r = @(r)* @(r). where 0 6 v(u) 6 1.
C. Equations (3. Let us define P(r) = Pa(r) * qa(r) where pa(r) is the electron density relative to one atom and qa(r) is the probability of finding an atom in r. On assuming the origin on an atomic site. In general p(u) is not easily found.C.11) where P.7) may be written in terms of autocorrelation functions of atomic density rather than of electron density.C. according to (3. Figure 3. and Nl is the number of atoms contained in the unit volume (of course fluctuations from this value are possible due to thermal motion or to structural features of amorphous solids). 2roeo= A from which   For Cu K. Diffraction from a finite statistically homogeneous object with equal atoms Suppose that the object is composed of N atoms of a single type. (2Ir:) 8.(u) is just the autocorrelation function of the atomic density. In general we could write where p(u) is a distribution function defining the configuration of the atoms. Then. Then v. radiation and an object with ro = 0.1 pm it is 8.5) Pa(u) = Qv(u)Pal(u) and (3.*) sin 8. C. A very simple model for which p(u) may be rigorously calculated was proposed by Zernicke and ~ r i n s : [it concerns ~~] the onedimensional arrangement on a segment of length L of N rigid spherical particles of diameter d.0.C. only for a completely random atomic distribution.1 pm constitutes the upper limit for the dimension of the object. Let Pal(u) be the function Pa(u) calculated for the unit volume. where 1 = LIN is the average length allotted to each particle. = 4. Then P(u) = Pa(r) * Pa(r) and IF(r*)I" * qa(r) * qa(r) T[P(u)] = f '(r*) T[Pa(u)] .C.204 ( Carmelo Giacovazzo In terms of diffraction angles the width of the diffraction peak near the origin of the reciprocal space may be obtained from the Bragg relation (2/r. At very small concentrations (quasizero volume particles which do not exert any influence on each other) p(u) . (3. It is easily seen that always p(u) = 0 when u < d (the spheres are impenetrable).3 shows p(u) as a function of four values of the particle concentration dll. the probability of finding a second atom in the volume dv at the extremity of the vector u is dp(u) = dvlv. = l/Nl is the average volume available for each atom.4 x On assuming that diffraction around the central peak may be observed down to 8 = low3. 11) becomes Let us now express Pal(u) in a more convenient form.5) and (3.
Indeed. integrating z(u) on the unit volume gives from (3.C. The distribution p ( u ) for onedimensional arrangements of objects of length d as a function of the compactness. Oscillations of p(u) are larger for higher concentrations. 3. is similar to the atomic distribution of the perfect gas. 12) the relation follows. and amorphous solids.C.C. Write now (3. liquids. Let us now denote by z(u) the probability of finding an atom in the element of volume dv located at the extremity of the vector u from an atom located at the origin.14) by emphasizing the oscillating part of p(u): .The diffraction of Xrays by crystals 1 205 (d) v= Fig. For higher concentrations the model represents distributions similar to those found in real gases.3. while p(u) 1 at long distances. Then  It may be noted that l / v l is not only the asymptotic value of z(u) but also its mean value. p(u) will oscillate about unity at short distances from the origin. When dl1 becomes maximum the close packing of the particles gives rise to a perfect lattice of period d: then very sharp maxima of p(u) will occur at u = nd (full shortrange and longrange order).
1] (which in disorder structures is a function slowly varying with r*). According to (3. 181. C. most liquids.l]) * lD(r*)12. and in finely dispersed crystal powders) the function I E ( ~ * and p(u) will also be isotropic. It is detectable only at very small angles and it is distinguishable from the primary beam (see the previous section) provided the diffracting object is very small (say. The function ID(r*)I2 can be considered very broad with' respect to the Dirac delta function but very sharp with respect to T[p(u) . Such a distribution may be determined by inversion of (3.A. <l pm).1 exp (2niu r*) du 1 The first term in (3. 16) becomes (Nl = NlQ) N F(r*)12= f2(r*)60* v1 N ~(r*)~'+ f2(r*)(l 1 + T[p(u) Vl . Thus the atoms: if this is perfectly uniform p(u) = 1 and I E ( ~ * ) [ ~ = variations of IE(r*)I2about its average contain information about the atomic distribution in the object.9) the integral of the ID(r*)I2 peak is Q: therefore In terms of the normalized intensity I ~ ( r * ) l 'eqn (3. Then using )[~ results in Appendix 3.206 1 Carmelo Giacovazzo Then the Fourier transform of z(u) is and (3. 19): which is the most general formula describing the diffraction from a statistically homogeneous object composed of atoms of one kind.C.C. We will discuss such a peak on p. in gases.C. p. for example. 213.19) corresponds to the peak at the origin of the reciprocal space.C. The second term depends exclusively on the statistical distribution of the 1.18) becomes [p(u) . Diffraction from an isotropic statistically homogeneous object If the diffracting object is statistically homogeneous and isotropic (that occurs. It does not depend on the internal structure of the object but only on its external shape. and neglecting the first term on the .
(3. The Debye formula A simple way to describe diffraction from an isotropic statistically homogeneous object composed by a collection of N identical groups of atoms with known geometry but random orientation and position was proposed by Debye.C.21) and (3.C.= .C.C.C.23) .22) also hold when the object is made by particles constituted by groups of atoms: then v. .l)(sin 2nr*u) dr*.q. Then N and Since the observed intensity will be the average with respect to all the possible mutual configurations of the atomic groups ~ where u ~ . is the average volume available for each particle..1) is the radial atomic distribution function: the product of such a distribution for du gives the number of atoms situated at a distance between u and u + du from the atom assumed to be at the origin. Inverting (3. Let 4 (r*) = C J(r*) exp (2zir* 5 ) ]=I P be the structure factor of the nth group of atoms (each group composed of p atoms).ql .21) gives U r*(I~(r*)l'. Equations (3.The diffraction of Xrays by crystals 1 207 righthand side of eqn (3.C.22) shows that from diffraction experiments the average number of neighbouring atoms can be deduced as a function of the distance from a given atom chosen to be at the origin.22) Equation (3. 180 we obtain sin 2nr * uii sin 2nr*uii 2nr*uij ) (3. In accordance with p.19) give sin 2nr * u du 2nr*u where 4nu2(p(u) .C.
28) is obtained. to IF(r*)12= ~ f ' ( r * ) .C.) (3.C. It is easily seen that Debye maxima will correspond to those provided by (3.C. in terms of IF(r*)I2.23) becomes For a tetrahedral molecule (i. . Therefore p(u) = 1.615/(sin (3. In particular. the interatomic distance x = 0. Diffraction by gases For a perfect gas (consisting of identical atoms with negligible volume and exercising no action on each other) any atom can occupy any position with the same probability.C. 174.C.27). In favourable conditions estimates for interatomic distances can be readily obtained from the intensity diffraction pattern. It is easily seen that the maxima in the IE(r*)I2 curve will coincide with those given by (3. in other terms. sin 2nr * uij 2xr*uij where Y = f /N(Cf=l (f?)"'. SiC1.21).5m) but maxima will become weak and ill defined.C. (3. from the first maximum located in (sin O/A).e.[433451 According to p.208 ( Carmelo Giacovazzo In terms of normalized intensity (3. In order to give some examples. for a molecule composed of two atoms at distance 1 (3.23) becomes (1E(r*)I2) = 1 + i+j=l 5 YiY.21) reduces to I ~ ( r * ) l ' =1 or.14) reduces to and (3.C.23) becomes where 1 is the edge of the tetrahedron and d its radius. when The position of the mth maximum for large values of m will approach more and more closely to x sin B/A = (0.C. the value of the interference term sin2nr*x/(2nr*x) is unity for r* = 0 and becomes zero for r*x = n/2: subsidiary maxima occur when or.125 + 0.
for which supplementary considerations are needed (see p. A typical diffraction pattern provided by chlorine diatomic molecules is shown in Fig.C. For C > 118 (e.5 (curve (a)).C. As soon as r* by is out of the peak at the origin the value of IF(r*)I2 is equal to ~ f ' . and peaks can be measured at greater values of sin 81A. Schematic diagram of the diffraction pattern for the diatomic molecule C.C. where v o = 4 ~ ~ ( d / 2 ) is /the volume of one atom.C.18)). where y = 2nr*d. highly stabilized. 3.C. If the gas is a mixture of perfect monoatomic gases the scattering is practically given by If the gas is composed of identical molecules formed by atoms with negligible volume and arranged as in a perfect gas then features will appear in the scattering curve which are influenced by the molecular structure. 212). I. Since electron scattering is much more intense than Xray scattering (see p. usually ] a sample injection system.21) becomes I sin 011 Fig. 3. Schematic diagram of the scattered intensity from a monoatomic gas. Then (3.5. are between 30 and 80 kV.C. Since atoms are impenetrable. by S2/N in (3. 3. where d is the atomic diameter. which is not acceptable: for such cases the diffraction by gases closely resembles that by liquids or amorphous solids. C is the concentration ~ 3 factor (ratio between the effective volume occupied by the atoms and the gas volume) and (see p. an atomic distribution function p(u) such as that described in Fig. ~ ~consists of an electron gun. The maxima in the experimental curve are not well defined (they are represented by roughly horizontal portions of the curve) because of the continuous decay o f f with sin @/A. In order to compensate the fast decay of the scattered intensity with sin @/A a rotating sector is introduced into the path of the scattered electrons: it is a metallic disc designed in such a way that the intensity reaching the photographic plate is larger at larger scattering angles. 3. For real gases the intrinsic volume of the atoms is no longer negligible.4.4. Since q(0) = 1 it is IE(0)I2= 1 . Very small quantities of gas can be used with shorter exposure times. For r* = 0 the value of ( ~ ( r * )is ~ l ~~f (replace JD(r*)I2 1D(0)1' = Q2 and v. 195) electron diffraction is preferable for gases. with exposure times of a few minutes. 3. In these conditions the diffraction pattern will emphasize highangle interference effects. the observed intensity is of type described in Fig. for highpressure gases) IE(O)(' < 0.The diffraction of Xrays by crystals ( 209 If the central peak is also taken into consideration.g. 181) q ( y ) = 3 (sin y .8C: thus the asymptotic value of JE(r*)I2 for r * 0 is smaller than unity by a quantity proportional to C. + .3(a) may be chosen. whose intensity will now be Fig. Typical electron accelerating voltages. Gas electron diffraction a p p a r a t ~ s [ ~ ~ .C. The maxima should be better emphasized by plotting JE(r*)I2 (curve (b)). and the detector: the last is often a photographic plate.y cos y)ly3.
3.210 1 Carmelo Giacovazzo Fig.C. Electron diffraction patterns from C. 3. 3. were refined by a leastsquares process applied to molecular intensities: the good final agreement may be deduced from the small differences between the E and T curves. two camera di~tances). the molecular structure of C6H5NO2 in the planar and orthogonal conformation. The corresponding radial distribution curve p ( u ) is shown in Fig. the scattering optical density distribution is converted into electron distribution.Ib)lZb. . Zb is the background intensity. is the total observed radiation. in combination with ab initio molecular orbital calculations and Xray singlecrystal structure analysis of several derivatives.C.8: the positions of the most important distances are marked by vertical bars whose height is proportional to the weight of the distances. while a local mm2 symmetry was assumed for the benzene ring and the nitro group). gas (working temperature about 353 K. 3.C.H.6 the onedimensional spectrum in Fig. . I.'~'' sufficient to be measured by a microphotometer. of In Fig. The experiment was made in order to determine.6. The geometrical parameters of the theoretical model (the molecule as a whole was supposed to have a binary symmetry.C.NO2 are shown (corresponding to two different positions of the plate). s = 4n sin 8/A. together with vibration amplitudes.NO.7 may be derived.6 two gasphase electron diffraction patterns[481 nitrobenzene C6H. From data in Fig.C. After the background elimination. In the figure the curve sM(s) is given where M(s) = (I. 3.
The diffraction of Xrays by crystals
1
211
I
I
I
I
I
!
I
I
0
5
10
fb
20
s (Am'
2 5
3 0
35
Fig. 3.C.7. Molecular intensity curves (E, experimental; T, theoretical) for CH O , ,N , (gas electron diffraction, two camera distances). Also shown are the difference
A  3  v
  V
V
A n V
v


v I
I
I
I
I
I
I
I
0
1
2
r(A)
4
5
6
7
Fig. 3.C.8. Radial distribution curves for CH ,, NO, (E, experimental; T, theoretical). Also shown is the difference curve (ET).'~'
212
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Carmelo Giacovazzo
Diffraction by liquids and amorphous bodies
In liquids or amorphous bodies each molecule may be considered in contact with a certain number of neighbours. Thus both internal and external interference effects will dominate the diffraction pattern. Let us first consider an atomic liquid: if atoms are assumed to be hard spheres which do not exert any force on each other the distribution p(u) may be cal~ulated.[~~1 In Fig. 3.C.9(a) p(u) is plotted for two values of the concentration parameter C (ratio between the effective volume occupied by the spheres and the total volume of the liquid). The corresponding I E(r*)I2 functions may be derived by application of (3.C.21) and are shown in Fig. 3.C.9(b). Their main features are: (1) for small values of r* it is 1 E(r*)I2 < 1; (2) a large maximum occurs at about r* =0.95/d. Its intensity increases with C while its position does not vary; (3) for lage values of r* 1E(r*)I2 tends to unity as for perfect gases. In spite of the purely geometrical nature of the model the diffraction pattern of monoatomic liquids closely satisfies the model predictions. In Fig. 3.C.10 the IE(r*)I2 curve of liquid mercury is shown: its Fourier transform (eqn (3.C.22)) shows a maximum a little over 3 A. A further example concerns the diffraction pattern of water. As it is well known, the molecules are strongly polar and Vshaped with 0  H distances 1/d r* of about 1 A, and nearly tetrahedral HOH angles (109"). For our purposes, (b) they may be geometrically represented by spheres of about 2.8 A diameter. Fig. 3.12.9. (a) Distribution functions P ( u )for hard spheres of diameter dfor two values of the The water scattering curves[s01 at 1.5 "C and 83 "C are shown in Fig. curves concentration parameter C. (b) I E ( ~ * ) I ~ 3.C.ll(a); the corresponding radial distribution curves are given in Fig. corresponding to the two distribution shown in (a). 3.C.ll(b). The main maximum for the radial distribution occurs at a radius of about 2.8 A while a second broader maximum occurs at about 4.5 A, nearly vanishing at high temperature. Such results suggested to Bernal and ~ o w l e r [ ~that the arrangement of H 2 0 molecules in water may be l] described as a brokendown ice structure in which each molecule tries to bind four neighbours: since bonds are continually breaking and reforming at any instant each molecule is bonded to fewer than four neighbours. As a last example, examine now Fig. 3.C.12, where the diffraction patterns by vitreous silica, a cristobalite crystal powder, and silica gel are shown. The main maxima of all the three curves nearly overlap: but cristobalite shows numerous sharp maxima while only one maximum occurs in vitreous silica. Furthermore, vitreous silica intensity decreases with sin 8/A as we have just seen for liquids, while silica gel shows increasing intensity toward small sin OlA. The radial distribution function for vitreous shows a first peak at r = 1.62 A and a second one, at 2.65 A: that indicates that the tetrahedral coordination in the crystalline state persists in the vitreous state (but here the orientations of the tetrahedral groups are randomly distributed). The vitreous state is essentially homogeneous (diffraction intensity decreases at small sin $/A as for liquids) while silica gel  is made from very small discrete particles (10100 A) with voids among 0.5 1 2 r * them (diffraction intensity increases at small scattering angles: see the next section). Fig. 3.C.10. I E ( ~ * ) / ' curves for liquid mercury.
The diffraction of Xrays by crystals
1
213
Smallangle scattering
Smallangle scattering is a technique for studying structural features or inhomogeneities of colloidal dimensions.[401 For wavelengths of about 1A the typical angular domain of the technique ranges up to one or two degrees. We have already seen (p. 204) that when diffraction occurs from a finite statistically homogeneous object of volume S2 a central peak in the intensity curve may be measured which becomes broader as the object size decreases, and does not depend on the internal structure of the object. Its intensity distribution varies according to (3.C.18):
Since diffraction is considered at very small angles f (r*) will coincide with the number of electrons per atom. Thus the above equation reduces to
We consider now a system constituted by N particles with electron density p randomly dispersed in a homogeneous medium of electron density po (solvent). Particles are supposed to be separated from each other widely enough, thus they will generate independent contributions to the diffracted intensity. The system may also be thought of as a medium of constant p, and macroscopic volume S2 to which N particles are summed with density Ap = p  p,. If S2 is sufficiently large the central peak due to the homogeneous medium is totally unobservable, while the observed intensity distribution may be ascribed to electron inhomogeneties only. In this case the mean scattering power for particle is
where IDP(r*)l2is the average value of )DP(r*)l2 over all the possible particle orientations. Different shapes of particles will give rise to different shapes of the scattering function in reciprocal space: ideal scattering intensities can therefore be calculated for spherical, cylindrical, flat, ellipsoidal, etc., particles. The results are all rather similar, particularly in the central range, but remarkable differences occur at larger angles. It may then be expected that in the central part a universal approximation for all particle shapes must exist Let us assume the origin 0 in the centre of gravity of a particle of volume
Fig. 3.C.11. (a) 1 f ( r * ) l 2water scattering curves at 1 .5"C and 83 "C; (b) the corresponding distributions 4nu2p(u).
Sil~ca Gel
I
.
Vit. SIO,
 #   '
.......
..
.
... .. .. .. . . :: :: .; .. . . . .. . ..., :.: ,. . .. . . . ... ... ... .. . .
.
.
. : :
:.
.
.. Fig. 3.C.12. Diffraction patterns for silica gel, vitreous SiO,, and for cristobalite.
.
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Carmelo Giacovazzo
up and let us estimate Dp(r*)=
l
exp (2nir* r) dv.
(3.C.32)
At very small angles we can expand the exponential function in (3.C.32) in power series: it will suffice to expand cos 2nr* . r according to cos 0 1 0'12. In Cartesian coordinates cos 2nr* r = 1 

.
+ y2P2+ z2y2)2,
where a; p, y stand for the cosines between r* and Cartesian axes. When integration is performed the contribution of mixed products vanishes by hypothesis (the centre of gravity has been located at the origin) and we have Dp(r*) = v,  2n2r*2
((u21
x2 dx
+ 82j dy + y2
y21
z2 dr).
Since we are interested to calculate IDP(r*)l2, say the average of IDP(r*)l2 over all particle orientations, we have to rotate Cartesian axes about the origin. We can then replace (u2, P2, y2 by ( a 2 ) = ( p 2 ) = (y2) = 5 SO as to obtain
where r2 stands for (x2+ y2 + z2) and R = ( l v ) ( r2 du)
UP
is the radius of gyration (= the mean square distance) of the particle with respect to its centre of gravity. According to (3.C.31) the scattering power per particle will be
where n, = ( p  p,)vp. By taking the logarithm to the base 10
is obtained. If lg ~ ~ , ( r * ) l ' plotted against ( 2 0 ) ~ curve will be obtained is a which, at small values of 0, is close to a straight line with slope (u = 5.715R;lA2, from which the gyration radius R, = 0.418~is obtained.
The diffraction of Xrays by crystals
1
215
In Fig. 3.C.13 the Guinier plot for a lowconcentration solution of haemocyanin from Astacus leptodactylus is shown.[54] The reader will easily derive from the figure (CuK, radiation used) a gyration radius of R,= 62 A. The radius of gyration is connected to the geometrical parameters of some simple homogeneous bodies in the following way:[s5] sphere of radius r:
%
,
I
1 2 3 4 5 6
10512tv2
R i = 3r2/5;
hollow sphere (limiting radii r, and r2):
Fig. 3.C.13. A Guinier plot.
ellipsoid (semiaxes a, b, c):
~ 2=, (a2 + b2 + c2)/5;
prism with edge lengths a, b, c:
R: = (a2 + b2 + c2)/12;
elliptic cylinder (height h ; .semiaxes a, b): hollow cylinder (height h, radii r,, r2): Other important parameters can be evaluated directly from the scattering data: among others the molecular weight (from the scattering intensity at zero anglesrs6]),the total surface of the particles for unit mass (from the region where the smallangle scattering tends to zero[s73s8]), the volume and of the particle. This latter may be obtained by integrating (3.C.31) over all the reciprocal space (by extrapolation of r*2~ ~ , ( r *at lvery small r*): ) ~
According to (3.C.9) the above relation reduces to from which up may be derived. So far we have considered particles dispersed in a homogeneous solvent and widely separated from each other. If the concentration of the particles increases the mutual interference will enter into play and the scattered intensity is no longer the sum of the individual particle scatterings. As described in on p. 206 a probability function p(u) can be introduced: then 4m2p(u) du will represent the number of particles with distance u lying in the interval (u, u du) from a particle at the origin. Then the scattering power per particle will be (see eqn (3.C.21))
+
2 " 1 ( r * ) = ( ~ ~ ( r * ) ~ ) u[p(u)  1 sin (2nr*u) du (l+ r*v1 0 where (IFp(r*)12)is the squared modulus of the structure factor of a particle
216
1
Carmelo Giacovazzo
averaged over all orientations. From the above equation the function p ( u ) may be derived by inverse Fourier transform.
3.D About electron density mapping
The accurate determination of charge density distribution is of basic importance in several scientific areas. For example, for the study of (1) electronic structure of metals and alloys;
(2) metalligand interaction;
(3) variation of solid state properties (i.e. conductivity) with temperature. Spatial partitioning of charge density can also answer some specific questions, such as the location of lonepair maxima, the net charge of a particular atom, the excess charge accumulated in a covalent bond, and so on. Such results can be attained only if the selection of the compounds, the process of measuring diffraction data, and their subsequent treatment is carried out with great care. Among the various desiderata we mention the following. 1. Compounds with a small valencetocore ratio are less suitable to charge density studies. If we assume that the number of valence electrons per unit volume is approximately constant for different compounds, the valencetocore ratio is fixed by the number of core electrons per unit volume. Stevens and ~ o ~ ~ e introduced the criterion n s [ ~ ~ ]
1
core
as a possible criterion to estimate the suitability of a system for charge density studies (V is the volume of the unit cell). S varies from 35 for the firstrowatom organic crystals to 0.10.3 for metals and alloys. Crystals with S < 1 require extremely precise diffraction data and careful work. 2. Centrosymmetrical crystals are often preferred (in acentric crystals the phases of the structure factors cannot be uniquely determined).
3. Collection of diffraction data has to be carried out at low temperature. Then thermal diffuse scattering can be neglected (a posteriori corrections are seldom accurate), high resolution data become available (then accurate structural parameters can be calculated), and electron charge density can be easily deconvoluted from the atomic thermal vibrations.
4. Sophisticated measuring programmes should be used, in order to perform optimal scanning mode and profile analysis, decide differentiated measuring times (in order to obtain a set of structure factors with equal variance), prevent multiple scattering, and perform careful correction for extinction, absorption, anomalous dispersion, etc.
5. When possible, neutron data should also be collected in order to obtain nuclear positional and thermal parameters which are unbiased by asphericity in the atomic charge density.
218
1
Carmelo Giacovazzo
Yq,, = 3 sin2 6 cos 241 = 3(s:  s:) Y;,, = 6 sin2 6 sin @ cos @ = 6sxsy Yq,, = 3 sin 6 cos 6 cos 4 = 3sxs, Y;,, = 3 sin 6 cos 6 sin 4 = 3sys, Y;,, = 6 cos2 6  2 = 6s;  2 Y',,, = 15 sin3 6 cos 341 = 15(s:  3s,2)sx Y;,, = 15 sin3 6 sin 341 = (45s:  1 5 s ; ) ~ ~
1
quadrupoles.
Y;,, = 15 sin2 6 cos 6 cos 241 = 15($  s;)s, Y:, = 30 sin2 6 cos 8 sin cos @ = 30s,sys, Yg,,= 1.5 sin 6(5cos2 6  1)cos @ = 1.5(5s; l)s,
$ J
Y:,, = 1.5 sin 6(5 cos2 6  1) sin @ = 1.5(5s:  l)sy Y;,, = 10 cos3 6  6 cos 6 = (10s;  6)s,
In Fig. 3.D.1 some electron density plots in special sections of direct space are shown.[611 In most organic molecules the expansion (3.D.2) may be stopped at octapoles: then the deformation charge density is described by a linear combination of 16 terms, for which 16 population parameters have to be estimated. In some formulations[621the freeatom valence shell is modified by an expansioncontraction radial parametrization in order to take into account the fact that an atom will expand or contract when it becomes more negative or more positive. Such a feature may be incorporated into a perturbed valence density p:,,ence(r) given by is, where pvaIence as in eqn (3.D.1), the freeatom ground state density, PValenc,the valence shell population, and k3 is a normalization factor. If is k > 1 the atom is contracted relative to the free one [indeed p l ( r ) is proportional to p(kr) with kr > r]. The atomic scattering amplitude has the same type of multipole expansion as the atomic charge density. By Fourier transformation of (3.D.2) one obtains
I
octapoles.
where 6*,
#* are angular components of the Bragg vector,
and ji(x) is the spherical Bessel function of order 1. From (3.D.3) the calculated structure factors Fcalc easily obtained. are Then (full or blockdiagonal) leastsquares refinement can be carried out: as well as the usual positional and thermal parameters for each atom, the population parameters of the deformation terms may also be refined. Such a formalism should improve (with respect to traditional crystallographic refinements) the agreement between observed and calculated structure factors.
220
1
Carmelo Giacovazzo Suitable Fourier syntheses can be calculated and analysed in order to reveal the effects of interatomic bonding on the charge clouds. Fourier maps of large usefulness are 1 Ap(r) = y where
x
H
( 4 ( H )  F2(H)) exp (2niH. r)
6 = F c a ~ cmultipole, F2 = F c a ~ cfree atoms. AP is then the deformation map, , ,
i.e. the difference between the atomic densities represented by spherical harmonics and those represented by free atoms;
F' = Fobs,F2 = Fcalc, rnultipole Ap is then the residual density, e.g. the part
of electron density not accounted for by the multipole model;
4 = Fobs, F2 = Fcalc, atoms, free under the condition that F2 is calculated
with parameters from highorder (HO) refinement (highorder reflections are unaffected by chemical deformation of valence orbitals and locate atoms carefully). Ap is then denoted as a (X  XHO)deformation map;
Fl = Fobs, = Fcalc, atoms, F2 free with fi calculated as in (3) but for core electrons only. Ap is the (X  X,,) valence map;
F calculated with parameters from 2 neutrons or a joint highorder Xray and neutron data. Then Ap is the X  N or X  (XHO N) deformation map;
4= Fobs, F2= Fcalc, atoms,with free
+
4 = Fobs, = Fca~c,~reeatorns, F2 calculated as in (5) from core with electrons only. Ap is then a X  (XHO N) valence map.
+
The estimation of the charge density model obtained at the end of calculations is different according to whether least squares or Fourier methods have been used[671.However, direct and reciprocal fitting are nearly equivalent: indeed, if we assume in (3.D.4) that Fl = Fobs,F2= Fcalc, AF = Fobs(H) Fcalc(H),and we calchlated the difference Patterson 1 Ap(r)Ap(r + u) dr =  I A F cos~ ~ 2nH u, V H then for u = 0 we obtained
I
x
Thus leastsquares parameters which give the best fit between observed and calculated structure factors are expected to give rise to the lowest variance in Ap. Direct evaluation of atomic or molecular charges, of dipoles and higher moments, etc, can be obtained from the estimated population parameters or directly from the electron d e n ~ i t y . [ For ,example, the net charge on atom ~~ ~~] j is
The diffraction of Xrays by crystals
1
221
when the integration is made over the (not always easily defined) atomic volume. Also, the dipole moment of a molecule may be calculated as
where the integration is over the molecular volume.
3.E Modulated structures and quasicrystals
Embedding of modulated structures in higherdimensional space
In Chapter 3, pp. 1713, it has been suggested that incommensurately modulated structures (IMS) can be better described in higherdimensional spaces. From now on S, and L, will denote ndimensional space and lattice respectively, while S and L,* will be their reciprocals. We will show that X the reciprocal lattice L: of an IMS, even if aperiodic in ST, may be transformed into a (3 d)dimensional periodic lattice (say LT+d) by embedding the IMS in a metrical (3 + d)dimensional space S3+,. Let us suppose that the reciprocal vector H of a main or of a satellite reflection may be written in S as :
+
where and kf, k:, k: are the a * , b*, c* components of Ki. One of them should be irrational for incommensurate modulation. Since (3 + d) indices hi are necessary to label a single diffraction effect, we will speak of ddimensional periodic modulation or of ddimensional modulated structure. In Fig. 3.E.1 a section of the threedimensional diffraction pattern of a onedimensional modulated structure is sketched. The main reflections are marked by the largest spots. with basis vectors A L:+d lattice may now be
bl = a * , b2 = b*, b3 = c*, b3+i= Ki
+ ei
(i = 1, . . . , d) (3.E.2)
Fig. 3.E.l. Onedimensional modulated structure: sketch of a section of the threedimensional diffraction pattern, showing main and satellite reflections.
where the eis are unit vectors perpendicular to S g Then in S:+, a reciprocal vector may be written as
0W W
a*
ns
Q
M W W
v
a
w
L ,
According to hypotheses, H is the projection of H' in ST. Consequently the whole threedimensional diffraction pattern LT is the projection in ST of a (3 d)dimensional reciprocal lattice L,*+,. In Fig. 3.E.2 such a projection is shown schematically for a onedimensional modulation: Sz is represented by a horizontal line, el is a unit vector perpendicular to ST, main and satellite reflections are labelled by M and W respectively. In S3+dthe (3 d)dimensional direct lattice L3+dis defined by the set of
el
0
0
+
+
Fig. 3.E.2. From SX to S Main and satellite : . reflections are denoted by M and W respectively.
222
1
Carmelo Giacovazzo
vectors ai reciprocal to bi according to the conditions ai . bj = 4,. have We
where a, b, c are reciprocal to a * , b * , c * . The reciprocity condition is easily verified: for example,
If a position is defined in S3 by it will be defined in S3+, by
where Indeed, the first three coordinates in S3 and in S3+dcoincide, owing to the fact that L3 is the projection of L3+, along ei; any point r in S3 satisfies the relations
In accordance with (3.E.3)
so that
x3+,
= k{xl
+ k h 2 + k&x3
is obtained, which coincides with (3.E.4). If in S3+, the new coordinates
The diffraction of Xrays by crystals
1
223
are introduced, it may be concluded that S3 is defined by tj=O for j = l ,
. . . , d.
The electron density p ' in S3+dis periodic in (3 be calculated in the usual way: p(xl,
+ d)dimensions and may
j=1
. . . , ~ 3 + d= )
1
2
FH, exp
hl,...,h~+,~
where V is the volume of the unit cell in S3. According to reciprocity rule (the Fourier transform of a projection corresponds to a section and vice versa) the electron density distribution p in S3 is the section of p ' with S3. Therefore in S3+dthe shape of the atoms is a hypersurface which extends in the extra dimensions. In Fig. 3.E.3, a schematic representation of p ' for a onedimensional modulation is described. A scattering formalism for a large variety of modulated structures is now a ~ a i l a b l e : [ ~ substitutional and/or displacive modulations of each of the ~~~I atoms in the crystal may be taken into account, together with the translational or rotational displacement of a molecule or one of its segments in molecular crystals.
Quasicrystals
In a famous paper by Shechtman, Blech, Gratias, and cahn17'] electron diffraction patterns of a rapidly solidified A1Mn alloy were shown which suprisingly displayed fivefold symmetry. Sharpness of the spots suggested longrange translational order, but the presence of the fivefold symmetry violated the sacred rules of crystallography. In particular, by rotation of the specimen, fivefold axes (in six directions), threefold axes (in 10 directions) and twofold axes (in 15 directions) could be revealed: the subsequent ascertainment of the existence of an inversion centre fixed, for this AlMn phase, the icosahedral point group m55. Somewhat later a large number of alloys with 'forbidden' symmetries were found: such kinds of materials (providing electron diffraction patterns displaying sharp peaks and forbidden symmetry such as icosahedral, octogonal, decagonal, dodecagonal, etc.) are called quasicrystals. A huge amount of theoretical and experimental publications are now available: for a more comprehensive treatment of the subject and for relevant literature the reader is referred to three excellent review~.[~+'~] A useful premise to quasicrystals (as well as to the IMSs) is the definition of quasiperiodic functions. It is well known that a periodic function f (x) =f (x 1) may be uniformly approximated by finite sums of functions exp (2ninx). Accordingly, in a p dimensional space
Fig. 3.E.3. Schematic representation of the density p' i n S,. S, is the horizontal line: its bulging parts represent real atoms. (a) Perfect crystal; (b)density modulation; (c) displacive modulation.
+
f '(XI, . . . , x,)
=
nl,
..., np
q(nl, . . . , n,) exp (2ni(nlxl + . . . + n,x,)
is a periodic function. However, its 'projection' on onedimensional space
f (x) =
nl,
C ...,
q h ,
. . . , n,)
exp (2ni(nlv1 + . . .
+ npvP)x)
(3.E.6)
np
obtained by fixing in f ' xj to v,x is not periodic if some of the vjs are irrational. Functions which may be uniformly approximated by finite sums
6(x nu). 5a can be associated. 9. The existence of delta peaks may be demonstrated by examining periodic approximations off (x). 7. first line) but the diffraction pattern will display delta peaks owing to the fact that the order is perfectly maintained at long distances. Here. 10.5(a). . Fig. is not periodic. 1. 3. x. It is easily seen from Fig. = n ( 3 .z) . Since a and az/2 are incommensurate numbers the structure is not periodic (see Fig.472.( z . giving rise to a nonperiodic pattern (the numerical sequence is 0. 2.4. . An aperiodic longrange ordered structure and its periodic approximants.4. (Fibonacci sequence). a square lattice with a unit cell with edge length (1 + z2)'I2 is drawn.v2x2 . All the lattice points contained in a band parallel to such a direction and with width (1 z) are projected on it (stripprojection method). sin 2nx1 A2 sin 2ncux.224 1 Carmelo Giacovazzo of functions exp [2ni(n. 0 I 0 *o* o* '63 . 3. 2. .854.E. schematically represented by C. 3.). 3.472.618.rnaz12). . z = 2 cos (1615) = (1 + f i ) / 2 = 1. small solid circles represented by C G(x .854. 0 I 0 *o o* 5a 0. If we assume X. 5. 1. The chain may also be written + x. etc. is the golden mean.4 that better periodic approximations of the aperiodic sequence can be obtained by higher order approximants. 6.v..618034. In Fig. An irrational direction is drawn..E. We take three simple examples. + n.236. Let f '(x. = ax1 where cu is an irrational number then + f (x) = A. .x)] are quasiperiodic functions. and a periodic sequence of . n and m are any integers. at an angle of arctan(l1z) with the cell edge. in the sequence SLSLLSLSLLSLLSLS. 3.v1x + n.1) frac(nz).E. 3. a. All intervals in the projection will have length either 1 or z (L and S respectively). f (x) is the superposition of a periodic sequence of large open circles.E.) = A 1 sin 2nx1 + A 2 sin 2nx2. Since + successive approximations to t are to which periodic structures of increasing periods a12.618. 3a.
(b)The Fibonacci sequence results from a cut of the disconnected 'line atoms' of the twodimensional crystal with the real space S.. Since there is a weighted average lattice with constant a = (3 . 3.z) the sequence may be considered as a modulated structure with modulation factor g(x) = ( t .=(z.5. z) (see Fig.The diffraction of Xrays by crystals 1 225 Fig.1) frac (x).ES(b)): then the reciprocal average lattice is also square with basis vectors In order to obtain the quasiperiodic onedimensional sequence on S1 (see . where frac (x) is the fractional part of x. The procedure for embedding a onedimensional aperiodic sequence in a twodimensional space may be performed in accordance with the previous section. (a) Projection of a band i n a twodimensional lattice t o obtain a nonperiodic ordered sequence (Fibonacci sequence). which may be embedded in a twodimensional space.E. For the last example we can choose al . 3. The above three examples suggest that aperiodic sequences in one dimension can be obtained by projection of periodic sequences in two dimensions. 1) and az = (1.
Clarendon. H.. 0. Phizackerley. 125. Dynamical scattering of xrays in crystals. G. Acta Crystallographica. J. Springer. D. Acta Crystallographica. Laue. . ~ a c k a y [ first ] ~~ showed that their Fourier transform satisfies a fivefold symmetry. 6. 12. S. in which a lattice with translational periodicity is obtained is determined by the number of n rationally independent reciprocal basis vectors which are necessary to index the diffraction pattern.^^] TWOexamples are shown in Fig. 519. K. 3.6.[^^. Ergebnisse der exakten Naturwissenschaften. J. Thus the real onedimensional quasicrystal results from a cut of the disconnected 'line atoms' of the twodimensional crystal with the physical space S. (1949). P. Twomey. W. W. and Templeton. 15. P. Chapuis. Darwin. Ewald. (1914). C. (1978). (1980). Journal of the Association for Computing Machinery. Annalen der Physik. Philosophical Magazine. and noncrystallographic point symmetry. 558. (1967). P. 23. J. A. 13. K. H. Proceedings of the K. 10. 54. Brewster. 153. The pattern shows a fivefold rotation point. V. Templeton.. P. References 1. (a) A twodimensional quasilattice showing one fivefold rotation point (plane symmetry 5mm). 43.E.. 453.5(b)) one has to attach parallel line elements in the lattice vertices. In Computational crystallography. Templeton. Becker. 10. Well known twodimensional examples of quasiperiodic structures are Penrose ti ling^. and Robertson. The procedure may be generalized to the ndimensional case: the dimension of the space S. P. C. L. The real aperiodic crystal is again the cut (in the direct space) of the ndimensional crystal with the physical space. 274. While the latter show main and satellite reflections. 74. D. Acta Crystallographica. 27. the quasicrystals show one kind of reflection only. P. Phillips.. 800.226 1 Carmelo Giacovazzo again Fig. M. (1917). The characteristics of the quasicrystals do not coincide with those of the incommensurately modulated structures. 129. Fig. H..E. no average structure. Kennett. 3. decagonal. G. 856. N. Octagonal. pp. G. R.6: in (a) tiling of the plane is achieved by putting together two rhombic units in accordance with some matching rules (without them the plane should be covered in a periodic way).. 14. 0. Phillips. A38. 2. Basic oblate and prolate rhombi with their matching rules are shown: similarly arrowed edges must fit. P. 315. and crystallographic point symmetry. von (1931). 7. Acta Crystallographica. J. (1963). Darwin. 133. L.E.97. 8. (b) Penrose tiling with kites and darts (it does not show fivefold symmetry). 3. Berlin. 313. Kato. Becker. K. 11. Prestwich. 4. Nederlandse Akademie van Wetenschappen. The threedimensional icosahedral lattice mentioned at the beginning of this section may be embedded in a sixdimensional space. Templeton. Oxford. an average structure. all of them can be embedded in a periodic fivedimensional space. Journal of the Association for Computing Machinery. L. 5. Philosophical Magazine. and Coppens. Bijvoet. A32. (1985).. M. (1974). J. Acta Crystallographica. (1922). 9 . In (b) 'kites' and 'darts' are used: no pentagonal symmetry is shown.. 10. and Hodgson. (1962). (1982). D. 9. (1978). 2. 84. K. Nuclear Instruments and Methods.. B52. M. 4629. A36. (1982). A41.. (1976). C. and dodecagonal twodimensional quasicrystals are also known. 16. Acta Crystallographica. Zachariasen. Pinsker. and Hodgson. 3. T. A30. G.
Renninger. Zeitschrift fur Physik. and Fowler. 46. Krutter. R. 147. J. 30. (1933). Schultz. Structural Chemistry. 43. E. B. A. D. 41. H. special periodic report. (1974). H. Journal of Chemical Physics. In International tables for xray crystallography. Powder Diffraction. 271. Annalen der Physik. D. H. C. 54. H. and Kratky. Yoder. (1984). M. Hummer. (1980).. and Prins. 41. Acta Crystallographica. H. 4 (ed. 2. H . J. (1986). San Francisco. Freeman. 809. (1915). P. Ehrenfest. and Bondza. J. M. and Bacchi S. and Warren. and Collella.. D. 39. S. 12. C. Mantsch.. (1989). W. J. (1915). (1982). 11. G. Pilz. 141. 1578. Direct analysis of diffraction matter. 25. W. L. 50. 38. 33. 3 (ed. Acta Crystallographica. Acta Crystallographica. Glatter. Academic. (1977). 130. 202. S.. Small angle xray scattering. Sim and L. IV. and Billy. E. 760. Peterse. R. A45. (1962). G. 29. and Cameron. Sutton). J. Applied Spectroscopy. Sim and L.. . (1975). Schomaker. (1989). A. Sutton). and Thorkildsen. G. Acta Crystallographica. Morgan. Weckert. Series A. K. (1937). 42. C. Moffatt. Colella. (1939). D. London. 130. Mo. Hummer. A42. and Clark. K. Chapman. Debye. 42. and Morningstar. Hoyaerts. L. A42. (1966). K. (1981). Acta Crystallographica. and Levy. A.. I. Amsterdam. Acta Chemica Scandinavica. P. Annalen der Physik. Wiedemann. I. 17. Physics Review Letters. Maun. B.. 0 . Hauback. 24. (1955). Portalone. 39. Chang. Acta Crystallographica. 0. and Marsh. E. 819. Hosemann. H. European Journal of Biochemistry. 106. K. 37. The Chemical Society. 36. Hildebrandt. 127. G. B. 21. 32. K. E.. Bernal.. (1951). Journal of Chemical Physics. 3.. 47. (1988). (1990). E. 18. R. Journal of Applied Crystallography. pp. 44.. and Hummer. 46. (1949). L. 666. 22. Guinier. A38. Fournet. 1. Toraya. K. A30.. 1132. and Palm. B. 49. Journal of the American Ceramic Society. K. Acta Crystallographica. Domenicano. 48.. (1976). Multiple diffraction of xrays in crystals.. Acta Crystallographica. A46. and Witters. Johnson. No. J. P. and Fournet. H. George. 31. R. Lipscomb. Wiley. A. Acta Crystallographica. Guinier. Juretscke. R. E. 52. 21. 27. 777. 12. 51. Molecular structure by diffraction methods. 184. 121.. A. (1938). 3. G. Kauppinen. R. W. W.. G. (1984). P. Colapietro. (1952).. Physics Review Letters.. 105. (1917). 26. K. G. (1927) Zeitschrift fur Physik. (1936). Guinier. Goral. (1988). 35. A. H . M. 841. H.The diffraction of Xrays by crystals 17. 28. E. Weckert. F. 539. 107. (1963). Warren. Hamilton.. B.. Chang. G. A. Vol. Berlin. L. New York. A39. Post. Unnam. No. R. 6. K. 23. R. A38. 193. 519. J. and Bock. M. 34. and Alder. I. 182. (1959). E. Zernicke. F.. V. 54. (1983). and Billy. 609. ( 227 . (1987). Ewald. 127. special perodic report. Birmingham. 20. 53. 0. 85. Hargittay. 40. J. H. 1. (1982). The Chemical Society. A. Transactions of the Faraday Society. Xray diffraction. R. 516. A. Proceedings of the Amsterdam Akademie. E. (1981). K. Acta Crystallographica. 515. 19.. N. 192. N. Kirkwood. NorthHolland. R. Hummer. 19. Smallangle scattering of xrays. 2. Journal of Chemical Physics. 20. Molecular structure by diffraction methods. (1974). G. I. 45. P. 161. Springer. H. Oberhammer. 413. D . Lontie. 31136.. (1982). J. Kynock Press. Acta Crystallographica. 35. Annales d e Physique. C. 387.. 46.
. 85. 81. Physical Review Letters. 56. de Wolff. V. P. A. and Becker. D. 67. . Acta Crystallographica. Petricek. 408. (1951). Acta Crystallographica. Hirshfeld.. 261. 62. Ruble. (ed. J. 71. Luzzati. 939. (1975). 87. Stevens. Acta Crystallographica. B. (1977). Scientijic American. B38. A. Janner. 399. Israel Journal of Chemistry. W. 74. and Craven. Mackay. Shechtman. P. P. (1960). A 4 4 1051. 73. R.. (1953). Coppens. P. F. 58. 86. 13. P. F. Acta Crystallographica. 83. A41. (1988). J. 75. 168. Israel Journal of Chemistry. 53. Janner. A38. A. 609. A. 35. A . L. M. Acta Crystallographica. 19. and Pople. 478. 66. Gratias. Janssen. (1976). (1969). (1974). W. Acta Crystallographica. and Janssen. 70. M. M. 777. 198. Janot. H. 16. Springer. Physical Review Letters. 18. G. (1984). Gardner. Acta Crystallographica. D. Israel Journal of Chemistry. L. 57. Mittelbach.228 ( Carmelo Giacovazzo 55. 0. A114. 51. Vol. (1978). R. J. 60. M. Janner. 83. Penrose. (1988). 80. Hehre. Acta Crystallographica. 76. J. and Coppens. Stewart. (1977). (1982). P. Epstein. Hirshfeld. I. 4430. 61.. (1980). Acta Crystallographica. Acta Crystallographica. Physica. 643. 68. A. (1982). (1974). (1976). P. Coppens. Janssen. J. R. 110. 915. Stewart. Blech. K. D. 190.. A36. Zeitschrift fur Kristallographie. 77. (1977). Yamamoto. Journal of Chemical Physics. 115. Petricek... 2688. 565. Physical Review. and Janner. 10. and Porod. T. (1964). (1980). 78. de Wolff. 55. K. 64. T. and Cahn. A37. W. Acta Crystallographica. T. Journal of Physics F : Metal Physics. 16. T. 11. 65. 69.. and Katz. 1409. Berlin. A.. Acta Crystallographica. KurkiSuonio. Stuart). Janssen. 58. and Janssen. KolloidZeitschrift 124. In Die Physik der Hochpolymere. R. T. and Coppens. Physical Review Letters. M. (1986). F. and Dubois. Rees. 79. (1990). Porod. 180. Bulletin of the Institute of Applied Mathematics. (1971). A 3 4 909. (1977). A32. (1982). P. V. Acta Crystallographica. (1973). M. E. (1981). V. (1985). A36. 63. F. (1985). 2657.. 179. 84. 53. 2303. 236. (1988). and Janssen. A32. 625. A42. Acta Crystallographica. Journal of Chemical Physics. A. P. 16. Acta Physica Austriaca. 82. B15. 59. Stewart. Hansen. Kratky. A30. 769.. Ch. A. N. G. 54. T. 1951. 266. R. B. J. L. B27. Physics Reports. Duneau. 72. Steurer. (1977). 98. and Coppens. F.
The ultimate goal of extracting structure factor amplitudes from diffracted intensities requires the application of a series of correction factors. Xray sources Conventional generators All the standard laboratory sources normally used for Xray diffraction experiments generate radiation using the same physical principles but can vary substantially in their construction details. Although. we will concentrate our attention on Xray diffraction. as seen in Appendix 3. This process. only a discrete number of possible wavelengths can be selected for experimental use. The specimens that will receive our attention are single crystals and polycrystalline materials. M O N A C O Introduction This chapter discusses the experimental methods used to study the diffraction of Xrays by crystalline materials. Most of the electrons do not lose their . 195 and 198). is discussed in the final section of the chapter. The two types of conventional generators that are used in conjunction with the data recording devices discussed on pp. electrons and neutrons are also diffracted by crystals.Experimental methods in Xray crystallography H U G O L. Most of the techniques used for diffraction data collection require monochromatic radiation. 245 and 287 are sealedtube and rotatinganode generators. strikes a metal target and is therefore rapidly decelerated by collision with the metal atoms. Due to the way in which radiation is produced in the conventional generators. We discuss the methods used to record the diffraction pattern and to measure the intensities of the Xrays scattered by these two types of specimen in separate sections. We begin discussing how Xrays are produced and how one can define the beam of radiation that will interact with the crystalline sample. called data reduction. The origin of Xrays in the conventional sources Xrays are produced when a beam of electrons. that is aggregates of a very large number of very small crystals.B (pp. This limited choice and the difference in intensity are two of the major differences between this type of radiation and that generated by synchrotrons. accelerated by a high voltage.
4. This equation shows that there is a minimum value for the wavelength of the Xrays that can be obtained by this process which is a function of the voltage accelerating the electrons. The intensity maximum is found at a wavelength which is approximately 1. Figure 4. e is the charge of the electron.5 times Amin. and M orbitals. The electrons with an energy above the threshold potential are capable of ionizing the target atoms by ejecting an electron from one of the inner shells. Monaco energy in a single collision but do it gradually through multiple events. 0 0. Total conversion of the electron energy into radiation is not a highly probable event and therefore the radiation of the highest intensity is obtained at a somewhat longer wavelength.6 0. a quantity which is proportional to the areas under the curves. Characteristic spectrum of copper superimposed on the white radiation spectrum. and Kg lines. The result is the production of a continuous spectrum of Xrays called white radiation. and n a constant with a value of about 2.2 A 0. The characteristic spectrum of copper is shown in Fig.5 1. When the energy of the electrons striking the target is higher than a certain threshold value.1 shows some continuous Xray spectra as a function of the accelerating voltage.1. 2. 4. can be calculated using the equation where A is a proportionality constant.5 2.230 1 Hugo L. emit the energy difference as a characteristic Xray photon whose wavelength depends on the difference in energy between the two levels involved. a measure of the number of electrons which are generating Xrays. Xray white radiation spectra as a function of the accelerating voltage. the energy of an Xray photon is Emax hvma. If all of the energy carried by an electron is transformed into radiation. discontinuous and with very sharp lines.8 1. i the electrical current. 4. vmaxthe photon frequency and the subscript max indicates that this is the maximum possible energy. L. and M and correspond to transitions from higher energy orbitals to the K.= eV = where h is Planck's constant. If we substitute the frequency in terms of the wavelength and where the potential V has to be measured in volts and the minimum wavelength is obtained in angstroms. The total Xray intensity generated per second in this way. This second spectrum is called the characteristic spectrum because its peaks are found at precisely defined wavelengths which depend on the material constituting the target.0 ~avelength(i) Fig. and V the accelerating potential.2 0.0 Wavelength (ii) Fig.2. V the accelerating potential. since the new level has a lower energy. When that happens another electron from a higher atomic energy level can move in to fill the vacancy created and.2. 0. appears superimposed on the white radiation curves just described. . Notice that as the voltage is increased both the minimum wavelength and the position of the intensity maximum shift to the left. L.0 1. a second type of spectrum.4 0. Notice the ratio of the relative intensities of the K. Z is the atomic number of the target. that is to the orbitals of principal quantum numbers n = 1. The characteristic lines of this type of spectrum are called K.
Thus. line is actually split into a doublet. not easily separable.2 has a scale on the abscissa which cannot show it. Xray radiation corresponding to all the possible energy differences is not observed because some energy transitions are forbidden by the selection rules. the line is called P. although Fig.if they are separated by another shell. line is approximately twice as intense as the K. by Moseley's law Y = C(Z . i the electrical current. When the two orbitals involved in the transition are adjacent the line is called a.. Both are doublets of slightly different wavelengths as pointed out before. for this reason. The characteristic frequency is higher the higher the atomic number and so the Mo K..3) where the constant C depends on the atomic energy levels involved in the transition and the constant a takes into account the interactions with other electrons.5418 A and the Mo K.Experimental methods in Xray crystallography 1 231 and 3. The K. Z. line is about 90 times more intense than the white radiation of equal wavelength (I. It can be shown[21 that the ratio zK/zwis a maximum if the accelerating potential is chosen to be V = 4VK.. The Xray photon energy is the difference between these two energy levels. in a plot of Y " ~as a function of 2 for a given transition the points corresponding to different target elements lie in a straight line and different lines are obtained for the K. a quantity which is proportional to the energy required to remove a K electron from the target atom.['1 Here. the a and /3 lines are actually split into multiple lines that are very close to one another because the difference between these energy levels is small. Thus. radiation and therefore require the elimination of the Kg component of the spectrum which is always present.VK)'.I)..' (4. the Cu K. line. 241.4) where B is a constant... of very similar wavelengths and which are. If this condition is fulfilled. 4. K../KB depends on Z but it averages 5 (see ~ieck'']). line is produced by a copper target in which the atoms lost an electron in the orbital of n = 1 and the vacancy was filled by an electron of the orbital n = 2. line and the ratio K. line ( 2 = 29).The data collection methods that use monochromatic radiation discussed later all use K. the Cu K. lines. line ( 2 = 42) has a higher frequency and therefore a higher energy than the Cu K.a)2 (4. transitions. The frequency of the characteristic line corresponding to a given transition is related to the atomic number of the element that gave rise to it. A full list of the wavelengths of the characteristic lines of the elements which are used in Xray diffraction studies can be found in the International tables for xray crystallography. Sealedtube and rotatinganode generators A conventional generator consists of a highvoltage power supply with electronic controls.. Thus. 12 = 1. connected to either a sealed tube or to the cathode of a . we will just point out that the two most frequently used lines are the Cu K. Since for every principal quantum number n there are n energy levels corresponding to the possible values of the quantum number 1 (from 0 to n .). Still. the Km1 and K. and VK the excitation potential of the K series. KB1. The methods used to achieve this are discussed on p. line. The intensity of a characteristic K line can be calculated using the equation: ZK = Bi(V . the K. 12 = 0.7107 A. etc.
can be estimated from the considerations of the previous paragraphs and taking an excitation voltage given by ~ i e c k . when one looks at the focused electron beam on the target. Figure 4. The Xrays generated come out of the tube through four beryllium windows: the two that are shown in the figure.232 1 Hugo L.3(b) is a sketch of a rotating anode chamber showing the two Xray windows used for singlecrystal work. that are found in the direction of the longest axis of the rectangular focus. The process of Xray production discussed in the previous section is highly inefficient: only about 0. the focusing cup. a small square focus with a side equal to the smallest rectangle side. keeping. it therefore becomes necessary to cool it. the others may be used when a linear focus is needed. line of a wavelength which is adequate for the diffraction experiment to be performed. water has to be circulated to cool the anode as is done in the case of a sealed tube. For molybdenum even higher voltages are required.3(a). The system is therefore mechanically much more complicated than a tube and it requires a fairly frequent and demanding maintenance work. It consists of a cathode with a filament that emits the electrons that are accelerated under vacuum by the high voltage applied and hit the fixed anode made of the metal whose characteristic spectrum has a K. rotatinganode generator. Monaco FIL WATER CATHODE FOCUSING \ CUP I I FILAMENT WATER 1 1 R OA A TSO N TXI I Fig. At the same time. the rest being dissipated as heat. in the direction of the longest side of the rectangle one can see. ' ' ] This value for the copper K energy level is 8. placed with its longest axis parallel to the direction of the windows. by choosing the appropriate angle. (a) A sealed Xray tube.3. In order to avoid melting of the target. 4. The first two windows are used for singlecrystal work. 4. Just how high the voltage to be applied must be. which is done by circulating cold water as shown in the figure. The high vacuum is necessary because the presence of gas molecules in the tube decreases the efficiency of the Xray generating process by collisions with the electrons in the beam.981 kV so if one wishes to apply a voltage of 4 times V. In the second case there must also be a way of making. The path followed by the water that cools the anode is not shown in the figure. This area is always chosen to be rectangular with the sides in a ratio of at least six to one. The sketch of a sealed Xray tube is shown in Fig. which determines the surface that produces Xrays. (b)Sketch of a rotatinganode chamber. and another two in a direction perpendicular to it. The problem of heat dissipation also dictates the choice of the focal area of the beam of electrons on the anode. the chamber has to be kept under vacuum for the reasons stated before. and monitoring the high vacuum required for Xray generation. and of course the anode has to be rotated at a certain speed. It is the efficiency of the cooling system that ultimately determines the maximum power that can be applied to the tube. In this way. about 36 kV have to be applied. used to focus the electron beam on the target. and the anode which rotates about an axis parallel to the direction of the windows. the real area that dissipates heat is several times that of a square of that size.4 is a photograph of a modern rotating anode Xray generator.1 per cent of the power applied is transformed into Xrays. the target area seen by the electron beam is continuously renovated because the anode is rotated. In a rotatinganode generator. Figure 4. In this way. In rotatinganode generators. much higher powers per unit of focal area can be applied to the unit and consequently higher Xray intensities can be produced. the filament. ~ h i l l i p s ' ~ ] gives a detailed discussion of the advantages of . The anode is cylindrical and rotates about the axis shown.
4. the diffracted beams will be more separated on the detector if a longer wavelength is used. Choice of the type of radiation As discussed above. Thus. 155 that there is a limiting sphere of radius .) rotatinganode generators together with an exhaustive description of the practical problems encountered in their operation. (Photograph courtesy of Enraf Nonius. their K. We saw on p. the K.5 and 0. As will be seen later.7A respectively. Another consideration is the maximum resolution of the reflections that will be recorded. Thus. for a given crystaltodetector distance and unit cell. copper is used for macromolecular work in which one usually was large unit cell parameters and for the structure determination of organic molecules. lines are those of highest intensity and therefore they are the ones that are normally used for standard Xray diffraction work. which do not contain atoms that absorb this radiation strongly.4.Experimental methods in Xray crystallography 1 233 Fig. Absorption of the radiation by the sample is therefore also a primary consideration in the selection of the wavelength to be used. in practice. Two of these metals are most frequently used: copper and molybdenum. A rotatinganode Xray generator. the choice of the wavelength of the Xrays generated by conventional equipment is limited to the values of the characteristic K. lines of the metals commonly used as targets. transitions generate radiation with a wavelength of about 1.
the spectrum extends into higher energy regions covering the Xray range. as we will see. often circular or elliptical. This sphere obviously has a different size for the two types of radiation discussed and therefore molybdenum radiation may be required to record data to a resolution not accessible to copper radiation. radiation is emitted in a very narrow cone parallel to the instantaneous velocity. 2. Finally we mention the detection efficiency of the method that will be used to record the diffracted intensities. Figure 4. the Xrays they produce are in many ways much better than those generated by conventional sources. From the extensive literature that exists in this ever expanding field we recommend two very elementary description^. 4. On the other hand.[~] possible Xrays. The electrons or positrons are accelerated in the linear accelerator (linac) and then in the booster t o be finally injected into the storage ring where they are kept circulating for periods of several hours. However. If the velocity is like that of the electrons moving in an antenna.[^^'] an introductory textbook. electrons. In these installations either electrons or positrons are accelerated at relativistic velocities along orbits of very large radii. their use has grown steadily in the crystallographic community.5. by necessity. . An additional consequence of relativistic effects is a distortion of the angular distribution of the radiation. and so the radiation is generated in cones tangent to the path followed by the particles (see for example chapter 1 of ~ o c h [ ~ ] ) . When the charged particles move at velocities approaching that of light. Outline of a typical synchrotron radiation facility. Fig. not shown i n the figure. since. volume 3 of the series is totally devoted to Xray methods. very complex and those that produce suitable Xrays are limited. the 6 GeV storage ring to be built in the USA[~] the European and Synchrotron Radiation ~ a c i l i t ~ designed specifically to produce the best . several metres or even hundreds of metres.[g]In this last treatise chapters 1. These sources are. Film is a better detector for copper than for molybdenum radiation and some area detectors have been optimized for use with copper radiation.234 1 Hugo L. as well as other types of electromagnetic radiation. Notice the scale at the bottom of the picture corresponding t o 050 m . The beam lines. Synchrotron radiation Xrays. and 11 of volume 1 are specially relevant to our discussion. emission takes place in the radiofrequency range but when the charged particles. Among those. radiation which explains why this type of radiation is so widely used for smallmolecule singlecrystal Xray diffraction work.5 shows the essential elements of a synchrotron radiation source. diffractometer counters have a very high counting efficiency for the Mo K.['] and a more advanced treatise in several volumes. move with a speed approaching that of light. As a result. located mainly in the United States and Europe. promise to be of special importance is the development of this field. or positrons. Monaco 2 / A that limits the volume of reciprocal space accessible to diffraction experiments. more beam time has been made available to crystallographers and more synchrotron sources are planned for construction in different countries. Generation of Xrays in a synchrotron radiation source It is well known that charged particles moving under the influence of an accelerating field emit electromagnetic radiation. are tangential t o the particle trajectory. In a synchrotron source the charged particles are made to move in closed trajectories. can also be generated by sources known as synchrotron radiation facilities. The energy of this radiation is dependent on the velocity of the particle.
It can be shown that the flux of radiation normalized to the ring current generated by . 6 ~ ~ ~ i (4. The total power can be shown to be equal to[8391 P. c the speed of light. the particles must be accelerated. first by a linear accelerator and then by a booster as shown in the figure. are tangential to the storage ring. The radiation emitted at a modern storage ring comes from two sources: the bending magnets and the insertion devices.Experimental methods in Xray crystallography 1 235 Notice the scale at the bottom which gives an idea of the size of this type of facility. The first is the radiation we have discussed so far. The beam lines. a toroidal cavity in which the charged particles are kept circulating under vacuum. not shown in the figure. and R the bending radius of the orbit. the current i in amperes and the power is obtained in kW. A more exact relationship between these two parameters is given in reference [lo]. E the energy of the particle. the second is generated by special devices called wigglers and undulators which are briefly discussed below. The power is thus seen to be directly proportional to the current in the storage ring.. Prior to injection into the storage ring. the magnetic field B in tesla. An extremely high vacuum is required or else the particles are lost by collision with the atoms present in the cavity. mo its mass at rest.7) where the energy of the particles is measured in GeV. The other two elements that are essential to the operation of the ring are the socalled lattice. for example. the ratio of the total energy to the rest energy of the particle. = 2 6 . This equation explains why highenergy particles are required and also why only electrons or positrons are used. An important property of the radiation generated by bending magnets is its wide spectral distribution which can be described quantitatively in terms of the spectral flux N which is the number of photons emitted per unit time interval into a relative band width AA/A into an angle element d e in the plane of the electron orbit and integrated in the vertical plane. that is the set of magnets which force the particles to follow a closed trajectory as well as performing other functions. The basic element of the installation from which radiation is generated is the storage ring. The quantity y. is of considerable importance since it is approximately related to the opening angle of the cone of radiation by where AI+!J is the emission angle in radians.. It can be shown that a charged particle moving along a circular orbit emits as electromagnetic radiation the following power[8*9] where P is the energy emitted per unit time. The total power emitted by the ring is the power emitted by a particle in one revolution multiplied by the number of particles and divided by the time it takes them to complete a revolution. and the radiofrequency cavity system which restores to the particles the energy they lose as synchrotron radiation. e is the particle charge. The power emitted by heavier particles such as protons is too low to be of significant importance.
. notice their position relative t o the maxima...0 Gev. A. France) (1. is measured in keV and A. Italy) (1."") PHOTON ENERGY ( K e V ) .1. (Figure taken from ~aterlik.5 GeV.8) where the factor Gl(y) is an energydependent function that can be found tabulated for example in the book by ~ a r ~ a r i t o n d o . E. A. 105 mA). It can be shown that ideally the wavelength used at a synchrotron source should fall in the range 0. taken from the literature. and other relevant parameters for the WAVELENGTH (A) 124 'I 12. 565 mA).25ACto 4.0Ac. A widely used parameter related to the critical photon energy is the critical wavelength A. France) (5.6 taken from ~aterlik. As can be seen in the figure although it does not correspond to the maximum flux it is close enough to give a good idea of the position of this maximum.4 I 124 0 12 I I I 1 Fig. is the critical energy associated with a magnetic field B which in keV is given by where E is measured in GeV and R. 4. The critical wavelengths are indicated by arrows. 250 mA). energy of the Cu K line corresponds to about 8 keV and that of the M o K. e = DORIS (Hamburg. Monaco bending magnets is equal toLs1 N(hv) = 1.' (0. d = NSLS (Brookhaven. HOR = horizontal plane.["] The critical wavelength. [ ~ ] variable y is The defined as follows where E. f = ESRF (Grenoble.4/Ac (4.0 GeV. An alternative expression for E .6.1% band width) (4. the radius of the bending magnet in metres.11) where E.236 1 Hugo L.8 GeV. is useful as an indicator of the suitability of a source for Xray experiments. is with B measured in tesla. 685 mA). = hv.5 GeV. USA) (2. a =ADONE (Frascati. Recall that the photon .0 GeV. b = DCI (Orsay.15] gives E. line t o about 17 keV. 4. 100 mA). 500 mA). Germany) (5. = he/& = 12. c = SRS (Daresbury. Table 4. The spectra of total emitted flux for several synchrotron radiation sources is shown in Fig. Spectral distribution of several storage rings.256 x lo7 y Gl(y) photons s' mradI m ~ . UK) (2. in A.
E. Japan Moscow. E. Japan Moscow.1. USA Okazaki. Italy Group Ill. Germany Stanford. USSR Tsukuba. China Orsay. USSR Stanford. E. Japan synchrotron sources in operation in 1987. Germany Tsukuba. USA Hamburg. Group IV.) Emittance ( x 10' m rad) Insertion (devices) Group I. 230 keV DCI SRS Vepp3 Photon Factory NSLS Bonn Siberia II BEPC Elsa Arus Spear Doris II Tristan ACC Orsay. Germany Moscow. USSR Washington. : 30 keV CESR Vepp4 Petra PEP Tristan Ithaca.Experimental methods in Xray crystallography Table 4. Germany Tsukuba. Japan Orsay. Sweden Berlin.062 keV Sor ring Siberia I Max COSY Teras ACO NSLS UV SOR Fian C60 Vepp2M Hesyrl Superaco SPRL Bessy Aladdin INSES Pakhara Sirius Adone Tokyo. The full width at half maximum of the beam can then . USSR Novosibirsk. E.. France Daresbury. USA Wisconsin. USA Berlin. s 0. USSR Beijing. Japan . Japan Brookhaven. USSR Tomsk. in the horizontal and o. the number of photons is multiplied by the energy of a photon hv. in the vertical plane. 0. i. If the spectral flux is transformed into power. France Stanford. Germany Wisconsin. USA Tsukuba.e. UK Novosibirsk.06 keV N100 Surf II Tantalus I Karkhov.J. France Brookhaven. China Bonn. USA Group II. The charged particle beam in the storage ring has a Gaussian profile characterized by the parameter ox. Relevant parameters of the Synchrotron Radiation Sources i n operation in 1987 (taken from reference 5) Name Location E(GeV) R(m) i(mA) EAkeV) 1 237 1. USSR Frascati. Other parameters of interest are the source size and the divergence of the irradiated beam. USSR Hefei.I. USSR Lund. USSR Hamburg. USA Novosibirsk. USA Tokyo. it can be shown that half the total power is irradiated below and half above the critical value A. USA Bonn. Germany Erevan. Japan Moscow.
vary along the orbit their variations are correlated and it is thus useful to define another parameter...'~] defined as the number of photons emitted per unit area of the source at point x. and a. A radiation spectrum quite different from that produced by bending magnets can be obtained by the use of insertion devices..1 per cent relative band width per unit solid angle dS2 and unit time in the direction defined by the angles 3 (defined by the instantaneous velocity of the charged particle and the projection of the direction of observation onto the vertical plane) and 19 (defined by the projection onto the horizontal plane instead). These are a series of periodically spaced magnets of alternating polarity which are inserted in a straight region of the ring and which do not alter the ideal closed orbit of the particles in the storage ring. The emittances of the synchrotron sources in operation in 1987 are also shown in Table 4. z over a 0. Monaco be calculated as 2. a. which is the brightness for x = z = q = 0 it is obvious that From this equation it can be seen that the brightness can be increased by increasing the flux or by decreasing the as. If one defines the central brightness b. which is often used to compare the potential performance of two sources. It can be shown that chapter the spectral brightness b is equal to (see ~ a r ~ a r i t o n d o [ ~ ] 2) where N is the spectral flux.350 and the source area F is estimated as Similarly the angular distribution is characterized by the parameters ox. Decreasing the a s can be accomplished by reducing the emittance of the storage ring (eqn (4. According to their characteristics they are called wigglers or undulators. is the spectral brightness. which at special symmetry positions is found to be The emittance is instead a constant along the charged particle path and it is thus another important parameter characteristic of an installation.. The parameter that has to be examined to determine whether an insertion device is a wiggler or an undulator is the K parameter . the emittance.238 1 Hugo L. and the solid angle of emission is then estimated as Although a.12)). The emittance of a ring is thus a fundamental parameter to be taken into account in comparing the expected performance from two different sources.. also called spectral brillian~e.1. Most insertion devices create a sinusoidal magnetic field which forces the charged particles to oscillate around the mean orbit. and a. Another useful function. a.
resulting from the small crosssection of the charged particle beam and the high degree of collimation of the radiation. If the parameter K << 1 the device is called an undulator and interference occurs between radiation which is emitted by the same electron at different points in its path through the device. [ ' ~ ] Fig. is related to the magnetic field of the device Bo.[ll]). The possibility of selecting the wavelength for Xray diffraction work has not been fully exploited although it is clear that it has farreaching consequences. to higher values and to increase the intensity of the radiation by a factor proportional to the number of periods of the magnetic array. 8 the angle of observation and a which. as we have seen. The intensity which is produced by an undulator with N poles at 8 = 0 is amplified by a factor proportional to N2. As is evident from this equation. As a result.7. It can be used for example to solve the phase problem in macromolecular work (see Chapter 8.Experimental methods in Xray crystallography 1 239 where a is the maximum deflection angle of the electron or positron trajectory. 233 that in practice only the characteristic lines of copper and molybdenum are sufficiently intense for use in crystallographic Xray work and thus with conventional sources one is limited to only a discrete number of possible wavelengths. Furthermore. a .[12] Probably the best known property of synchrotron radiation is its high brightness. K becomes the ratio between the maximum deflection angle of the electron trajectory along the insertion device. and AI). 4. The effect of a wiggler on the emitted spectrum is to shift the critical energy E.[lo] Comparison of synchrotron and conventionally generated Xrays We have seen on p. crystal absorption and radiation damage (see pp. The spectrum emitted is very wide and in fact extends in both directions far beyond the range spanned by the Cu K. No interference effects are observed and so the emitted spectrum is qualitatively very similar to that obtained from bending magnets. 4. is the period of the magnetic array measured in centimetres. the wavelength of the peaks can be shifted by changing the parameters that appear in parentheses. radiation is emitted as a series of relatively sharp peaks whose wavelengths are given by the equation[l01 where 8 is the angle at which radiation is emitted and j is the harmonic number. ~ ~ ] In . taken from ~ i s e n b e r g e r . Bo is the oscillating magnetic field measured in tesla and A. and Mo K. lines. p. A detailed comparison of the brightness and other properties of Xrays produced by synchrotron sources and sealedtube and rotatinganode generators can be found in ~ o n s e . 304 and 308) are wavelength dependent and thus can be minimized by optimixing the Xray wavelength used. Synchrotron radiation does not have this limitation as should be clear from Fig. Recalling that l l y is approximately equal to the natural opening angle AI).6. 544) by measuring anomalous dispersion effects (see for example Hendrikson et al. When the parameter K >> 1 the device is called a wiggler.
As a result. As a result diffracted intensities have to be corrected for this polarization effect in different ways as we will see later (p. can be lo5 times more intense than that from a rotatinganode generator. Monaco Fig.7. pulses of radiation are emitted at . produced at a given point in the orbit as a flash when a bunch passes through that point. An important property of synchrotron radiation is that it is completely linearly polarized in the plane of the orbit of the charged particles and elliptically above and below this plane. B = rotating. as we have seen. In the figure one can see that radiation from bending magnets. ' ~ ' ) 1900 1940 1980 Year the brightness of Xray sources is plotted as a function of the year in which they became available. are the least intense of the possible synchrotron sources. 4. 303). The brightness of xray sources as a function of the year in which they became available. F = 6 GeV source with undulator. We mentioned before that the energy emitted by the moving charged particles is replenished by a radiofrequency cavity. Thus. synchrotron radiation has a well defined time structure. D = Brookhaven National Synchrotron Light Source (NSLS) bending magnet. that is. synchrotron radiation is. Only the particles with an adequate phase relation with respect to the radiofrequency field can keep a stable orbit and they end up gathered in bunches which have a length that is dependent on the radio frequency used. (Figure taken from ~ i s e n b e r ~ e r . E = SSRL 54 pole wiggler. anode generator. which. The number of bunches of charged particles circulating around the orbit is an integer and can be regulated by varying the parameters of operation.[141 sample of such a small size can only be treated as a polycrystalline material with a conventional source. C = Stanford Synchrotron Radiation Laboratory (SSRL) bending magnet. The points correspond to the following sources: A = Xray tube. and permits singlecrystal A work with specimens that can be only a few pm3 in volume.[g1Xrays generated from conventional sources are totally nonpolarized. produces higherresolution data. As a result.240 1 Hugo L. in fact. data collection at a synchrotron source is faster.
Since p depends on the density of the material. All of the data collection methods discussed later require that a narrow pencil of Xrays strike the specimen under examination and. Filters One way to select a wavelength interval out of the spectrum generated by the source is by filtering the radiation through a material that selectively absorbs the unwanted radiation while letting through most of the photons of the wavelength that will be used for the diffraction experiment. Here we discuss the methods used to select a narrow wavelength out of the spectrum generated by the source and how to define a narrow parallel beam of Xrays to be used for diffraction experiments in conjunction with the data collection devices discussed later. has received so far very little attention in Xray diffraction work. the incident intensity. For example the European Synchrotron Radiation Facility is planned to produce pulses lasting from 65 to 140 ps and the pulses will be separated by a minimum of 3 ns.e. the thickness of the filter. x the distance travelled by the Xrays in the material. and p is the linear absorption coefficient which depends on the substance.e. This equation shows why harder Xrays. for nickel is shown in Fig. I. the continuous parts of the curve follow approximately the equation pm = kz3A3 (4. collimation. and the wavelength of the Xrays. as a function of the wavelength for different materials used as filters can be found in Koch and ~ a c ~ i l l a v r ~ . the wavelength of this radiation spans a very wide continuous spectrum. Ideally the radiation should consist of photons of only a single wavelength. Monochromatization. If the filter is a pure element. of clear importance in timeresolved studies. i. In the figure it can be seen that the curve of pm versus A. and that although synchrotron sources emit a spatially confined narrow beam. called the absorption edge. a characteristic of the substance that depends only on the wavelength considered. most of them also require that the energy of the radiation be limited to a wavelength band as narrow as possible.['] This property of synchrotron radiation. and focusing of Xrays We have seen that conventional Xray sources generate the discrete lines of the characteristic spectrum of the anode superimposed on the white radiation continuum and that radiation is emitted in every possible direction. The absorption of Xrays by a material follows Beer's law: where I is the transmitted intensity. the mass absorption coefficient.17) where k is a constant with different values for the two branches of the curve and Z is the atomic number of the element.Experimental methods in Xray crystallography 1 241 perfectly defined time intervals. in addition. are absorbed less than those . [ ~ ' plot of pm versus A. its density. Complete tables of p . the quantity that is usually tabulated is pm = p l p . i. Xrays with a shorter wavelength. shows two continuous branches separated by a sharp discontinuity. 4..8 and a ~ along with the radiation spectrum generated by a copper anode.
Thus. when this energy is reached massive absorption of radiation occurs with photoionization of the filter and production of fluorescent radiation. Roberts and parrish[16' give a table of the appropriate filter thicknesses necessary to produce K.8. and Kg peaks. and the Kg peaks depend not only on the absorption coefficient of the filter but also on its thickness. Since copper has Z = 29 and nickel Z = 28 there is a difference of one between the atomic numbers of the target anode used to generate the Xrays and the filter with an absorption edge falling in between its K. Figure 4. of the mass absorption coefficient p as a function of the wavelength for nickel. WHITE RADIATION with a longer wavelength. and the Kg peaks of the anode that has been used to generate the Xrays. A variation of the simple filter technique is the Ross balancedfilter method. 4./KB ratios of 100 and 500 for different elements used as targets and filters. The continuous line is the Xray spectrum generated by a copper anode. the unavoidable Kg peak. peak lost by filtering which can vary between about 40 and 70 per cent. peak that will be used for the experiment. Similarly to the displacement of the position of the characteristic lines with Z.8 shows that a nickel filter has its absorption edge at the wavelength necessary to very strongly absorb the copper Kg peak. The broken line represents the variation .e. the unwanted radiation of highest intensity. A common single filter is chosen so that its absorption edge falls in between the K. This is generally true for every element with Z s 70 and for the elements of the second long row of the periodic table it is also true that both the elements of Z . The same table gives also the percentage of K. Notice that the absorption edge of nickel falls in between the K. and the KB characteristic lines of copper. i. Thus both Nb ( Z = 41) and Zr (2 = 40) can be used as filters for Mo (2 = 42) radiation. absorption edges move to shorter wavelength as the atomic number of the element increases.[16]In this method two filters are used: one with its absorption edge at slightly shorter and the other at slightly longer wavelength than the K.242 1 Hugo L. .2 can be used to absorb the Kg peak of the anode with atomic number Z. In this way. The presence of the absorption edge in the curve is explained by the fact that the photons at the edge have the wavelength corresponding to the energy necessary to eject an electron from the K orbital of the atoms of the filter. The relative intensities of the K. can be greatly attenuated without reducing too much the intensity of the K.1 and Z . Monaco Fig.
which determines the divergence of the diffracted beam and the resolution of the crystal.Experimental methods in Xray crystallography 1 243 peak selected. The simplest type of crystal monochromator consists of a single crystal with one face parallel to a major set of crystal planes mounted so that its orientation with respect to the Xray beam can be properly adjusted. Crystal monochromators An alternative and more selective way to produce a beam of Xrays with a narrow wavelength distribution is by using a singlecrystal monochromator. Thus. Roberts and parrish[16]give a table with the important properties of crystals commonly used as monochromators. diffracted beams are observed at scattering angles 13that depend on the wavelength of the radiation A. 303). crystal monochromators can be used to focus the Xray beam in a very small area. (3) the presence of one or more strong diffracted intensities that can be chosen so that the intensity loss of the beam. the . The most important properties of a crystal monochromator are: (1) the crystal used must be mechanically strong and should be stable in the Xray beam. and (4) the mosaicity of the crystal. should be mall.[lglThe curvature of the surface can be produced by simply bending the crystal.^^] The reflection chosen should also have a scattering angle as small as possible in order to minimize the loss of intensity due to the polarization factor (see p. In a variation of this simple type of flat monochromator. The thickness of the filters is chosen so that the radiation is absorbed to the same extent except in the interval in between the two absorption edges. A further variation consists of not only bending the crystal but also in grinding its surface so that the radius of curvature of the diffracting planes of the crystal is different from that of its surface. selecting a given diffraction angle 8 is equivalent to choosing a particular wavelength out of the spectrum incident on the crystal. In this way. in which case the diffracting planes should ideally be tangential to the curved surface. With this technique two measurements are made with either one of the two filters in position and the measured intensity is then taken to be the difference between the two values obtained. may be reduced as much as possible. which is always appreciable. The advantage of this type of monochromator is that it does not suffer from some optical aberrations present in singly bent crystals.[161 Curved crystal monochromators are frequently used to select the wavelength of synchrotron radiation. In addition to the requirements stated before.32) shows that when radiation of different wavelengths impinges upon a crystal. (2) the interplanar distance should be in the appropriate range to allow the selection of the desired wavelength at a reasonable scattering angle. the reflected radiation will concentrate on the other focus of the ellipse. the crystal surface is cut so that it forms an angle with the set of planes that diffract the radiation. the diffracted beam has a smaller width and as a result more photons are concentrated in a smaller cross section of the bearn.['^.[l6] By properly curving their surface. If the monochromator is bent in the shape of a cylinder of elliptical section with the source in one of the foci. Bragg's equation (3.
5 mm we can get an estimate for the maximum divergence y y = 2 x 0. y. S. and S are the two . although slits can be used instead in which case square or rectangular beams can be defined.5150 = 2 x lop2radians. Collimators The function of collimators is to define a narrow cylindrical beam of Xrays that ideally should be as parallel as possible. L Crystal monochromators are more selective than filters '~] and. If we substitute in this equation d and 1 for two reasonable values: 50 and 0.. I I Id I I  . in the case of conventional generators.9. These apertures are commonly circular. 4. when viewed at the appropriate takeoff angle is seen as a square. Cylindrical beam pinhole collimators are typically used with conventional sources to define a beam of radiation that is monochromatized by either a filter or a crystal monochromator. It consists of a cylinder with two apertures defining the beam and a third guard aperture which does not affect the beam size defined by the other two but eliminates the radiation scattered by the defining aperture furthest from the Xray source. ~ u x l e ~ [ ~more recently Arndt and sweet[l7Ihave extensively discussed and ~ ] the conditions that can be varied in order to optimize collimation.244 I Hugo L. can be calculated as shown in the figure as dl2 tan y/2 = = dl1 112 and since the angle is very small where y is calculated in radians. 4. The Fig. A discussion of this type of crystal monochromator can be found in ~ a r ~ a r i t o n d o . are capable of resolving the Kal and K. of d. and have a diameter . in addition to the parallel Xrays.[lsl Another type of monochromator of wide application in synchrotron sources is the doublecrystal monochromator in which the incident Xray beam is diffracted twice by two similar crystals. Such collimators never produce an ideally parallel Xray beam but. Monaco crystals should have in this case a very small thermal expansion and a large thermal conductivity because the power applied is much larger than in the case of conventional sources.9. If 1 is the distance between the two defining apertures S1 and S2 and d is the diameter of the collimator the maximum angle of divergence of the beam. apertures defining the beam which are separated by the distance I. S is the guard aperture. A simple pinhole collimator is shown sketched in Fig. doublet which cannot be separated by any filtering method. A conventional Xray source. This type of monochromator can be constructed with different geometries designed to improve the resolution and/or to keep the Xray beam in the original direction. Pinhole collimator showing the angle of greatest divergence y. they also produce convergent and divergent Xrays as shown in the figure.
very small: 14' for glass and 23' for nickel mirrors. 63). and the crystal to detector distance. the reflected radiation will converge to the other focus of the ellipse and a very intense Xray beam will be obtained at that point. Depending also on the reflection to reflection resolution necessary for the experiment. also called Ewald sphere. the crystal to focus distance. radiation. radiation. for the Cu K. which is a function of the wavelength A and can be calculated by the equation[17. depend on the reflecting material as shown by the equation given above and they are. A table of this property and other parameters of interest of mirrors can be found in witz. that is constituted by several small flat pieces which are easier to produce than large curved single mirrors. will not be reflected and therefore they will be eliminated from the beam.[211 This doublemirror system has been used for Xray diffraction work on virus crystals which. Data collection techniques for single crystals We saw in Chapter 3 (p. p the density. in particular the fairly intense Kp peak. by properiy choosing the glancing angle of the Xrays on the mirror the radiation can be partially monochromatized. If the angle of incidence is chosen to be within ten per cent of 8.[221 Mirrors are also very extensively used in the beamlines of synchrotrons. magnification or demagnification of the source. and change in the polarization of the radiation. calculated for a wavelength corresponding to the Cu K. ideally in the shape of an elliptical cylinder with the source in one focus. different conditions are found which maximize the signal to noise ratio given the restrictions imposed by the experiment. Thus. In addition to focusing and partial monochromatization they perform several other functions: splitting of a beam into two. was . This principle is used in the design of a very powerful device that is used to focus and partially monochromatize an Xray beam and which uses two curved mirrors with perpendicular axes of curvature. 155) that the condition for Xray diffraction to occur in a crystal is that the scattering vector r* should coincide with a node of the reciprocal lattice associated to the crystalline lattice defined in Chapter 2 (p. The values of the critical angles 8.[l8I The function to be performed determines their geometry and so their surface can be flat or curved and the mirror can be bent or segmented. and A the atomic weight of the reflecting material.[lgl If the reflecting surface of the mirror is curved. the Xrays having a wavelength shorter than the corresponding A. pose particularly serious problems for the spatial separation of the very close diffracted beams. The sphere of reflection.191 where Z is the atomic number. Mirrors Xrays can be reflected by mirrors when the angle of incidence is smaller than a certain critical angle 8.Experimental methods in Xray crystallography 1 245 variables that can be adjusted are the crystal and Xray focus size. in general. having very large unit cell parameters.
A. i. and it was with it that diffraction from crystals was discovered. 4. The Laue method... We saw that the characteristics of the crystal and the conditions of the experiment cause these nodes of reciprocal space to have a volume. We will make use of all these concepts in our discussion of the data collection devices that will follow. the practical applications of the method are rather limited. In addition. and also because the diffraction pattern produced is rather difficult Fig. If the scattering experiment is performed with radiation of a single wavelength there will be a single Ewald sphere of radius 1/A and the probability that a stationary reciprocal lattice node may by chance be on its surface will be fairly low. specimen is hit with radiation of a wavelength in the interval between A.251 is for this It reason. so that all the nodes from which one wishes to measure the diffraction cross the Ewald sphere completely... In the Laue method. A stationary specimen is irradiated with Xrays covering the . .[24. The shaded wavelength interval A. diffraction from only a crosssection of the node is not acceptable since it is the entire volume that should give rise to the diffracted intensity from which the structure factor amplitude is to be derived. If the white radiation spectrum resulting from a conventional generator is used to produce Laue diffraction. 155) and it was shown that diffraction is observed whenever a reciprocal lattice node lies on this sphere. and A.10. 4.e. the crystal. 163. the second method is to move thc reciprocal lattice nodes. Monaco defined (on p. The first method is historically the oldest. to have a series of Ewald spheres corresponding to different wavelengths. one needs all of the diffracted intensities that can be measured corresponding to the nodes found within a sphere of radius D* = l/R. Broadly speaking there are two ways to tackle these problems: the first is to use polychromatic radiation...10.. Furthermore. and as pointed out on p. in order to solve a structure. the shaded area represents the volume of reciprocal space containing all the nodes that will produce diffraction when the stationary . it is called the Laue method.e..246 1 Hugo L. i. the inverse of the resolution of the structure..[23] In Fig. area represents the volume of reciprocal space that produces diffraction. different crosssections of a node are excited by radiation of slightly different wavelengths and the result is an intensity integrated over the wavelength rather than over the volume sweeping through a single Ewald sphere. The direction of the diffracted beam is determined by the vector joining the centre of the Ewald sphere and the reciprocal lattice node lying on its surface.
L3'] All the other data collection methods discussed in this chapter use monochromatic radiation and therefore require a more or less complicated mechanism to move the crystal as the diffracted radiation is measured. The use of the Laue method with synchrotron radiati~n"~] provides an extremely fast and efficient method to record diffraction data. Figure 4.12 shows a rotatingcrystal photograph. has nowadays been largely superseded by other data collection methods.11(a) and (b). 4. Recall that the radius of the Ewald sphere is A'. the circles will project undistorted onto the film and when the film is unrolled they will appear as straight lines (layer lines) that contain the diffraction spots. From it one can calculate quite easily the spacing between the equidistant planes of reciprocal space and then use this value to compute one of the unit cell parameters of the crystal. since for many years it was the standard instrument used to quantitatively measure diffracted intensities. Such points all lie on equidistant circles of decreasing radii as we move away from the centre of the Ewald sphere.Experimental methods in Xray crystallography 1 247 to interpret. The Weissenberg camera Although the Weissenberg ame era. that the method fell into disuse until the advent of synchrotron radiation and the development of very powerful computers. The cylindrical film rotation camera The simplest way to produce a regular motion of the reciprocal lattice is to rotate the crystal about a direct lattice axis oriented normal to the incident beam direction: then.11(c).11(c). 4. is the radius of the cylindrical cassette and dH is the constant distance between two consecutive reciprocal lattice planes in the family then tan an= df/rf and ndH sin an= 7 A as shown in Fig. it is still used for spacegroup and unit cell determination of smallmolecule crystals. 4. Whenever a reciprocal lattice point intersects the Ewald sphere a diffracted beam passes through the point as shown in Figs. 126. there is a family of equidistant reciprocal lattice planes perpendicular to this axis of rotation. If the distance on the film between the layer line corresponding to the nth reciprocal lattice plane and the 0 layer line is df. If a cylindrical cassette containing a piece of film is placed so that the cylinder axis coincides with the crystal rotation axis. The applications are already important in the field of smallmolecule~27~281well as macromolecular as crystallography[29~301 where it has opened up the possibility of performing timeresolved studies in the crystalline state. as shown in Fig. Currently. r. historically it has played a central role. as seen on p.[^'^^] introduced in 1924. . that is for the preliminary characterization of crystals whose diffracted intensities are then measured with the diffractometer.
This is because all the reciprocal lattice points present in one plane are projected by this geometry on to one layer line and thus the information concerning the other two indices is not easy to extract. 1 dH==sintanP1. which is essentially a cylindrical film rotation camera with two differences. nh nh df r f Using this value. The cylindrical film rotation method. This difficulty can be overcome by the use of the Weissenberg camera. Zerolevel Weissenberg photographs Although in a rotation photograph the index corresponding to each layer line is trivial to assign. The intersections of the reciprocal lattice planes and the Ewald sphere produce on the film a series of parallel lines. .11. Incidentally. notice that because of this relationship equally spaced planes in reciprocal space do not produce equally spaced layer lines on the film. the unit cell parameter corresponding to the real axis coincident with the rotation axis can be calculated. The rotation axis is horizontal and is found i n the plane of the figure. Monaco rotation axis Fig.248 ( Hugo L. 4. the method cannot be used to easily map the reciprocal lattice. (a) The intersection of a family of equidistant reciprocal lattice planes and the Ewald sphere. The circles shown i n (a) are now projected as parallel vertical lines. Thus the interplanar spacing in reciprocal space is sin a. The points lying on the circles represented will produce diffraction. (c) A cylindrical film is placed with its axis coincident with the rotation axis. (b) Projection i n the direction of the incident Xray beam..
a single reciprocal lattice plane is mapped on to the film plane. spots belonging to the same reciprocal lattice plane that cross the Ewald sphere at different times and which would end up recorded on the same layer line are recorded instead in different positions on the film. A typical rotation photograph showing a family of parallel lines due to the set of parallel reciprocal lattice planes. is again the cylindrical cassette radius one can write . crystal rotation and film translation along the cylinder axis are coupled. Figure 4.13(b) the reciprocal lattice point P is crossing the Ewald sphere and therefore it is in diffracting position. The first is the use of a layer line screen that blocks all the diffracted radiation with the exception of that due to one selected reciprocal lattice plane at a time. 4.Experimental methods in Xray crystallography ( 249 Fig. Notice that the lines are not equally spaced. In this representation the origin of reciprocal space is found at point 0. the first is proportional to the angle 2 8 as can be seen in the same figure. 4. In Fig. The second difference is the coupling of the rotation motion to a displacement of the film along the cylinder axis. the intersection of the incident Xray beam with the Ewald sphere.12. as already pointed out. shown on the unrolled film on the right. the second is proportional to the rotation angle o since. The line tangent to this point has one index equal to zero and corresponds to one of the reciprocal lattice axes. Thus.13(a) shows the Ewald sphere projected on to a reciprocal lattice plane that would produce one layer line in a normal cylindrical film rotation camera. are x and z . Its coordinates. The view is in the direction of the rotation axis and each of the lines represented corresponds to a reciprocal lattice row of a given index. In this way. If r.
(a) When a layer line screen selects the zerolevel plane. 4. film film and Normally rf is chosen so that C1has the value of 2" mml. Zerolevel Weissenberg method. for this particular level. (b) When the crystal is rotated an angle w = Othe point P belonging to one of the reciprocal lattice axes is in diffracting position. 8 is equal to w because the sides of the two angles are perpendicular and one can write . Thus measuring the x coordinate of a reflection in millimetres one can automatically calculate the corresponding value of 20.13. Monaco film Fig. the two angles w and 20 can be measured on the film on the same scale. Thus. Figure 4. Its coordinates on the film are xand z. a series of equidistant lines will contain all the reciprocal lattice nodes that can produce diffraction on the film.13(b) shows that a normal to the zerolevel reciprocal lattice row passing through A bisects the angle 28.250 1 Hugo L. The coupling parameters of the film movement to the crystal rotation are chosen so that the constant C2 in is also made equal to 2 and thus.
When w equals 180" the zerolevel line is found again tangent to the Ewald sphere but it has been flipped over. .Experimental methods in Xray crystallography 1 251 and x = 2C2zlC. Notice that after a 180" rotation the pattern is perfectly symmetrical about the point where w = 90" on the projection of the rotation axis onto the film plane. When the angle o reaches the value of 90" the zerolevel line will be found in the direction of the Xray beam and the line traced by the spots will have reached the point where the film is cut to let the Xrays through. Thus the reciprocal lattice axis passing through 0 will produce on the film a series of spots that will be found on a straight line which will normally have a slope of 2. Fig. The spots recorded after that will change the sign of the only index which is varying along the line. (b) After a rotation of 180" plus the w of (a)the film shows this pattern. which is the equation of a straight line of slope 2 if the two constants C . Figure 4. that is they will begin to be recorded on the bottom half of the film. and CZare chosen to be equal. Immediately thereafter the spots will be recorded on the other side of the film interruption.14.14 shows the Ewald construction and the film appearance at the beginning of the rotation cycle and after a rotation angle of slightly more than 180". 4. (a) Five reciprocal lattice nodes have crossed the Ewald sphere and produced the five spots lying on a straight line on the film.
one for each of the two reciprocal lattice axes found in the plane that is being examined.18(b) shows the solution which is adopted to circumvent this problem.252 1 Hugo L. Each of the layer lines that do not pass through 0 will produce a curve similar to the one shown in the figure and therefore the film will show a family of nonintersecting curves or festoons that will be found on both sides of the line crossing the centre of the film.15. After the plane axes and the festoons have been identified. Figure 4. reciprocal lattice axes are identified in the photograph by the straight lines they produce and the angle between them is simply the o value that separates the lines on the film. Upperlevel Weissenberg photographs Figure 4.16 is a picture of the camera and Fig.18(a). one from each of the two families found on the film. it is not difficult to index a photograph like this by inspection. Monaco Fig. It is instead a curve of the type shown on the righthand side of Fig. Figure 4. at increasing distances from the centre. film If the second reciprocal lattice axis. shows that for a nonzerolevel photograph there is an area of the reciprocal lattice plane that cannot cross the Ewald sphere. This area becomes larger the further the plane is from the zero level. forms with this axis an angle of a*.17 is a typical zerolevel Weissenberg photograph. a projection of the Ewald sphere on to the plane defined by the incident Xray beam and a normal rotation axis.15. The rotation axis is no longer chosen to be normal to the Xray . On every film there will be two festoon families. 4. All noncentral reflections are found at the intersections of two festoons. Each festoon corresponds to one reciprocal space line and therefore the reflections found on it will have one index in common.when o equals a* this second axis will be found tangent to the sphere of reflection and after that will begin to produce a second straight line parallel to that traced by the first axis and separated from it a distance w = a*. 4. which has to be found in the plane selected for recording.15 shows that for reciprocal lattice lines not passing through the origin of reciprocal space.Thus. 8 is not equal to o and therefore the relationship between x and z is no longer the equation of a straight line. Figure 4. 4. For noncentral reciprocal lattice lines 28 is not equal to 2w and the plot of xversus zis not a straight line but the curve shown in the figure.
17. (Photograph courtesy of Enraf Nonius.Experimental methods in Xray crystallography 1 253 Fig. A modern Weissenberg camera. 4.16. . 4.) Fig. Notice the straight lines of points produced by the zerolevel lines and the festoons due to the nonzerolevel lines. Zerolevel Weissenberg photograph.
20 shows the film with the projections of the intersection of the reciprocal lattice plane and the Ewald sphere in four situations. A detailed description of this method is found in ~ u e r ~ e r .19(b) which shows on the righthand side the projection of this circle onto the film. the precession angle. 4. This projection is also a circle because the film is always parallel to the reciprocal lattice plane and the distance between the two planes is constant. is still a very popular instrument. it is instead tilted so that its intersection with the reciprocal lattice plane falls on the Ewald sphere.19(a). 4. This is so because the distance between the spots on the film is simply a reciprocal lattice distance scaled by the Xray wavelength and the crystal to film distance. All the reciprocal lattice points which fall on this circle produce a diffracted beam that will be recorded on the film. The precession camera The precession camera. These situations are Fig. After a full cycle has been completed we are back to the situation represented in Fig. At the same time the film that will collect the reflections is made to move in the same way so that it is always parallel to the reciprocal lattice plane that will be photographed and keeps with it a constant distance. introduced by Martin Buerger in 1942. In the precession camera the crystal is rotated in such a way that the normal to the plane family precesses about the Xray beam. Figure 4.18(b)) and the method is called the equiinclination method. 4. in other words it revolves about the beam keeping a constant angle p. the angle made by the incident and diffracted Xrays with a normal to the rotation axis going through the centre of the Ewald sphere are equal (see Fig. 4.254 1 Hugo L. 4. This situation is represented in Fig.18.19(b) and (c). 4. upperlevel Weissenberg photographs are seldom recorded. Upperlevel Weissenberg photographs. . it intersects the sphere defining with it a circle.19(c). it shows very clearly the reciprocal lattice plane symmetry. there will be a blind area for upperlevel planes. As a consequence.[35]A precession photograph is quite easily indexed by inspection. especially among macromolecular crystallographers. and can be used to quickly and easily calculate the unit cell parameters. (b) The equiinclination method. 4. When the precession angle p is different from 0 . that is to say with a family of reciprocal lattice planes perpendicular to the beam as shown in Fig. two are those shown in Figs.19(b). This figure shows the zerolevel reciprocal lattice plane tangent to the Ewald sphere at the point 0. When the normal to the reciprocal lattice planes has described half of its revolution movement about the Xray beam we find the situation shown in Fig. (a) If the incident Xray beam is normal to the rotation axis. the other two correspond to the positions in which the projection of the normal on to the plane of the figure coincides with the Xray beam. During this revolution the normal to the planes describes a cone whose axis is the Xray beam. Monaco r o t a t o n axis beam. ' ~ ~ ] Since the main uses of the Weissenberg camera are nowadays spacegroup and unit cell parameter determination and no longer quantitative intensity measurements. because it produces an undistorted picture of a reciprocal lattice plane. rotation GIs/ diffracted beam The precession motion In the precession method a crystal is first oriented with one of its axes parallel to the Xray beam. the zerolevel reciprocal lattice plane is no longer tangent to the Ewald sphere.
Since the precession . Precession motion. On the righthand side we view the f ~ l m the direction in of the normal to the planes. (4. 4. When a full revolution has been completed the intersection of the reciprocal lattice plane and the Ewald sphere has described a circle whose radius is the diameter of the intersection and equal to 2 sin plA.19(b) and (c) if we imagine that we are viewing the Ewald sphere not from a side but from the top or the bottom.19. After half (c) a precession cycle we find the situation shown here. The circle on the film has now moved from above to below the film origin. (a) The crystal is first or~ented with a family of reciprocal lattice planes perpendicular to the Xray beam.. The intersection of the zerolevel plane with the Ewald sphere projects onto the parallel film as a circle centred on N. and tangent to the film centere 0.Experimental methods in Xray crystallography 1 255 FILM E w a l d sphere (b) I F I LM I Xrays Ewald sphere FILM (c ) Fig. described by the same Figs 4. (b) The normal to the reciprocal lattice planes forms an angle y with the Xray beam.22) All the points in the reciprocal lattice plane which are found within this radius have passed through the Ewald sphere and therefore have produced a diffracted beam which has been recorded on the film.
19(a). moving each time in opposite directions. the screen also moves in such a way that it is always parallel to the film and therefore parallel to the reciprocal lattice planes. In fact.21. Movement of the projection of the intersection of the reciprocal lattice plane and the Ewald sphere onto the film as one precession cycle is completed. the movement of crystal. In Fig.19(b) and (c) we have shown the precession motion indicating only a zerolevel reciprocal lattice plane. As the crystal and the film move. Fig.256 1 Hugo L. Isolating a zerolevel reciprocal lattice plane In Figs.19(c) it is outside. 4. as can be easily understood reconsidering Fig.and firstlevel reciprocal lattice planes and the screen used to stop the beams diffracted from the first level. film and screen are always coupled to satisfy this condition. the diffracted beams originating from all the other planes have to be stopped using a layer line screen. 4. 4. the maximum radius of this circle is normally A'. When a full cycle has been completed and we are back to the situation shown in Fig. in Fig.19(b) the reciprocal lattice point R is inside the Ewald sphere. Only four extreme situations are represented. depends on the radius of the annulus. the annular radius Fig. The position of the screen.20. screen \ \ \ \ .21 shows the cones generated by the zero. 4. The screen is set at a distance from the crystal s so that only the diffracted beams originated from the zero level are let through and therefore produce a signal on the film. Monaco angle is usually not larger than 30°. 4. Diffraction cones generated by the zero and first reciprocal lanice planes. that is the crystal to screen distance. 4. it is a family of reciprocal lattice planes that always intersects the Ewald sphere generating a set of concentric circles of variable radii. every reciprocal lattice point that will produce a signal crosses the Ewald sphere twice. 4.19(b). Thus in a full precession cycle. In the precession camera. The screen is simply a metal plate with an annular aperture that will let through only the diffracted radiation coming from the selected reciprocal lattice plane. the point is again inside the Ewald sphere. The circle defined by the projection will contain all the reflections collected by the camera. In order to record only the zerolevel plane. Figure 4. If s is the crystal to screen distance and r.
22.22. . In order to produce an undistorted photograph of the reciprocal lattice plane. the film centre has to be' moved forward from 0: to 0:. 4.21. Upperlevel precession geometry. and Al the radius of the Ewald sphere. From the construction in Fig.Experimental methods in Xray crystallography ( 257 and as shown in Fig. The upper level origin 0. f is the crystal to film distance. is the new centre of the film that will permit the collection of an undistorted upper level. 0. 4. 4.23 is the construction used to calculate the crystal to screen distance for an upperlevel precession photograph. Upperlevel precession photographs Let us consider an upperlevel reciprocal lattice plane whose normal forms a precession angle p with the direction of the Xray beam as shown in Fig. In this case we can write cot v = s / r S Also the distance between the upperlevel layer and the zerolevel plane is nd* = l/A(cos p .cos v).22 we can write Dlnd* =flA' where D is the distance the film has to be moved forward. nd* is the distance between the upper and the zerolevel plane. Fig. Figure 4. f i s the crystal to film distance. nd* the distance between the upperlevel plane and the zerolevel plane. Thus we can calculate D for any upperlevel plane and crystal to film distance. 4. represented in the figure lies a distance nd* from the intersection of the Xray beam with the Ewald sphere.
22 rb = l/A(sin v . The projection of this area onto the plane of the figure is the line that goes from the point 0.nd*A and finally s = r. we notice that if n is made equal to 0 this equation reduces to (4. (4.nd*A) (4.26) where f is the crystal to film distance.258 1 Hugo L.25) which can be used to calculate the crystal to screen distance for any upperlevel precession photograph. If r is the maximum radius and f the crystal to film distance . rM/f = (sin v r . is rBla = f /Ap1 from which rB= f (sin v . 4. the expression derived for a zerolevel precession photograph.23). rb. Setting the layer line screen to select an upperlevel plane.27) Fig. + sin p)(l/A)/AI = f (sin v + sin p). 4. rB. We can use Fig. The blind region circle has a radius. 4. Monaco Thus cos v = cos p . cot cos'(cos p .sin p). that can be calculated from Fig.23. 4.sin p) (4. Reexamining Fig. to Q. Incidentally. we notice that there is an area of the reciprocal lattice plane that will never pass through the Ewald sphere. . On the film the radius of the blind region.23 to calculate the radius of the limiting circle for any upper level.22..
Experimental methods in Xray crystallography 1 259 Calculating unit cell parameters from a precession photograph Figure 4. i.25 is an h01 zone. if possible using one of the many optical devices available to improve the quality of the measurement.24 is a picture of a precession camera and Fig. and the distance between two consecutive reflections along the two axes.25 a zerolevel precession photograph of a protein crystal that belongs to the space group P3221. 4. The precession camera. 4.e. the crystal to film distance. the distance between several spots.) . The precision of the parameter determination. as shown in Fig.e. i. the axes shown are a* and c * . In order to determine the unit cell parameters one has to know the wavelength of the Xray radiation.26 and a* = df lhf (4. If df is the distance between two spots on the film.28) where f is the crystal to film distance and a* the reciprocal lattice parameter from which the unit cell parameter can be easily calculated. As a result. indexing of the photographs is easy but the drawback in both cases is that most of the diffracted radiation is not recorded and therefore it Fig.24. 4. The rotation (oscillation) method in macromolecular crystallography In our discussion of the Weissenberg and precession cameras we have seen that in both methods only one reciprocal lattice plane is recorded per film. Figure 4. can be increased if a larger distance is measured. (Photog1 courtesy of Huber Diffraktionstechnik.
4. From this picture it is quite easy t o calculate the t w o unit cell parameters as described i n the text. that is if the intensity of the reflections does not change as the crystal is exposed to the Xray. 4.260 ( Hugo L. is wasted. be explored one layer at a time.25. as is the case of macromolecular crystals. . Monaco Fig. in theory. with sufficient time available all the reciprocal lattice region of interest can. If the crystals do not decay in time. Determining the unit cell parameters from a precession photograph. both the precession and Weissenberg methods are extremely inefficient. Zerolevel precession photograph of a protein crystal showing the t w o reciprocal lattice axes. But if radiation damage is a problem. this is not too a serious a problem. For I Fig. Notice the holes punched on the picture used to roughly define its centre during densitometry.26.
This situation was changed by the introduction of computercontrolled microdensitometers which assured that films could be conveniently scanned and reliable intensities could be extracted from them. The flatfilm rotation method had been used since the very beginning of Xray crystallography[36]but it had been abandoned due to the difficulties in indexing and quantitatively measuring the reflection intensities on the film. the two circles that result from the intersection of the Ewald sphere at the beginning and end of the rotation range and each reciprocal lattice plane. that is it is moved back and forth. Although in the early days of protein crystallography this was the way that data were collected. Geometry of the rotation method In the rotation method a crystal is made to rotate or oscillate. The film is placed flat and normal to the Xray beam. 4. the recording of a complete data set of a protein crystal with the precession camera usually requires one crystal per photograph.27). method for macromolecular crystal data collection.27. A pair of lunes is shown on the righthand side. one crystal per reciprocal lattice plane. through a small angle about one axis perpendicular to the Xray beam and the diffracted intensities are recorded on a flat film (that can also be Vshaped) contained in a casette perpendicular to the incident Xrays (see Fig. When the crystal is rotated a small angle A@. the ArndtWonacott ame era.Experimental methods in Xray crystallography 1 261 example. The motion is shown leaving the reciprocal lattice planes fixed and rotating the Ewald sphere about the point 0. i. An asymmetric unit of reciprocal space is covered by successively exposing different cassettes.e. we saw that reciprocal lattice planes perpendicular to the rotation axis generate a series of layer lines on a cylindrical film. 4.[^'. and in a relatively short time the rotation method became one of the major. The rotation motion. In describing a crystal rotation. When we discussed the Weissenberg camera. the search for a more efficient way to record diffracted intensities led in the early 1970s to the reintroduction of the screenless flatfilm rotation (oscillation) method for macromolecular data collection. if not the major. and therefore often preferred. Small rotation angles are required to avoid reflection overlap on the film. the intersections of the Ewald sphere with each reciprocal lattice plane define two lunes per plane.27. After the spindle has rotated an angle A@. A new type of flatfilm rotation camera with eight cassettes that are used for successive exposures. it is easier. Let us now see what happens if we have a flat film perpendicular to the Xray beam as shown in Fig.^*] was built. to leave the reciprocal lattice fixed and move instead the Ewald sphere. 4. During the rotation of the crystal it is kept stationary. define two crescentshaped lunes Fig. .
x .29) the is the maximum allowed rotation range in radians. f~lm I I Fig. ..28. 4. 4. These have to be properly identified and dealt with during film processing. The missing parts of reflections A will be found on the previous rotation photograph and those of spots B on the following one. Since nodes in reciprocal space have a volume.29. Ir*IIR&. Projection of the intersections of the Ewald sphere and three reciprocal lattice planes on the film. Thus.28 we notice that the area of reciprocal space that crosses the Ewald sphere becomes a series of points along the projection of the rotation axis. ~ o n a c o t t [has ] ~ ~ examined the factors that limit the maximum rotation range allowed without having reflection overlap from different reciprocal lattice planes on the film. In one case the missing part of the reflection has been recorded in the previous film. Monaco r o t at ion axis Fig. The spots labelled A are recorded at one end of the rotation range and those labelled B at the other end. Thus a rotation photograph contains reflections coming from all the reciprocal layers that intersect the Ewald sphere as shown in Fig. a substantial number of reflections on a rotation film are partially recorded reflections.262 / Hugo L. The idealized shape of partially recorded reflections.A (4. One of the reasons why the rotation methud has been so successful is that it has been found that reflections partially recorded on different films can be added together[381 yield a reliable value to for the total diffracted intensity. which is different if they are recorded at the beginning or the end of the rotation range. Reexamining Fig.29 shows the idealized shape of the partially recorded reflections. a reflection is not completely recorded on the film until the entire volume has passed through the Ewald sphere. Any reflection whose reciprocal lattice node has not completely passed through the Ewald sphere is called a partially recorded reflection or.28. no matter how small their reflecting range. Figure 4. The expression for the maximum rotation range 1s: A@rnax where A@. 4. Since the rotation range in macromolecular crystallography is usually quite small. 4. as we will see. The reflections contained in each of the lune pairs come from the same reciprocal lattice plane and therefore have one index in common. regardless of the percentage of the volume that has passed through the sphere of reflection. more improperly.. reflections found along this line will always be partially recorded.. that contain all the reciprocal lattice points that will produce diffraction on the flat film perpendicular to the Xray beam. R:. in the other it will be recorded on the next. half spot. The innermost pair of lunes corresponds to the plane with index one because the plane with index zero is tangential to the Ewald sphere.
0 A resolution. As an example let us calculate A@.72 per cent but it increases to 4.4" A@.30.. From the figure it should be evident that even if the rotation axis has no symmetry it is never necessary to rotate a crystal much more than 180" in order to collect all of reciprocal space with the exception of the blind region. A plot of the percentage of reciprocal space which cannot be measured in a rotation experiment as a function of the resolution desired has been calculated by ~ o n a c o t t . The volume which has not been covered by a 180" rotation has been dotted in Fig.51100 x 57. represented by a 360" rotation of the Ewald sphere about the rotation axis. [ For Idata of up to 5 A resolution. the crystal has to be rotated about a different axis. not represented in the figure. From the figure it should also be clear that. Figure 4.. From the figure it should be apparent that the volume of the blind region increases with the resolution of the data to be collected. 4. and A is the reflecting range of the crystal. r* is the pertinent reciprocal lattice vector.3 to convert radians into degrees. In order to record the data generated by the reciprocal lattice nodes present in the blind region. it is ~~ only 0. will cover the volume of reciprocal space limited by the toroid generated by the rotation of the sphere but will leave out the shaded volume shown projected onto the plane of the figure.. The shaded reaion represents the volume of reciprocal space inaccessibleto the rotation movement. A limiting sphere of smaller radius represents the maximum resolution of the data that will be collected in the rotation experiment.3 . for a maximum resolution of 2.0.4 = 1" where we have multiplied by 57.31(c) and its size depends on the resolution desired as shown in the same figure. a blind zone inaccessible to the rotation geometry. in rotation axis film / Fig. 6 2.Experimental methods in Xray crystallography 1 263 maximum resolution in reciprocal space of the data that will be collected.58 per cent for 2.5 A when the relevant reciprocal lattice vector is 1/100 A and A is 0. The maximum rotation range of the crystal. 4. In Fig.30 the Ewald sphere is represented projected onto the plane determined by the Xray beam and the crystal rotation axis.31 shows the total volume of reciprocal space swept out as the crystal is rotated a total angle of 30°. and 180". Rotation geometry showing the Ewald sphere projected on to the plane defined by the Xray beam and the rotation axis. 90°. 4.  . A limiting sphere centred o n 0 shows the resolution desired or attainable.
not the only consideration in the choice of the rotation axis.31. In each case a limiting sphere corresponding t o a chosen resolution defines the volume of reciprocal space of interest. a 30" total rotation range will suffice to cover a reciprocal space asymmetric unit in which the only missing volume will be the blind region. which is equally important.264 1 Hugo L. order to minimize the total rotation range. which in this way does not become a limiting factor in the choice of the maximum . Thus if a hexagonal crystal is rotated about the c axis. Volume of reciprocal space explored by a total rotation range of 30" (a). We have seen that the maximum rotation interval per photograph is dependent on the unit cell parameters. 4. one would like to rotate about the axis with the largest unit cell parameter.rays limltlng sphere for a g l v e n r e s o l u t on Ewald sphere ' Fig. it is desirable to rotate the crystal about the crystallographic axis of highest symmetry. however. 90"(b). Symmetry is. Another factor. is the size of the unit cell parameters. Monaco X . and 180" (c). Ideally.
four different sets of coordinate systems have to be introduced. 4. If at the beginning of the rotation experiment the crystal and laboratory coordinate systems coincide. In this new coordinate system.Experimental methods in Xray crystallography ( 265 Fig. 2. and c* and the angles a*. reciprocal lattice with its unit vectors a * . where a%is the projection of a* onto the xo axis. The origin of the film system at the intersection of the Xray beam with the film. r* = ha* + kb* +LC*. rotation range per photograph. Calculation of the film coordinates for a reflection In order to calculate the film coordinates for a reflection.* + kb: + LC. there may be practical reasons that partially or totally limit the freedom of choice of the rotation axis. b*.32). the coordinates of a point in the . The origin of crystal and laboratory systems is at the intersection of the Xray beam with the Ewald sphere. after the crystal has rotated a certain angle @.. etc. and film coordinate systems. An example is crystal morphology.) can be calculated as follows xo = ha: yo = ha: z0 = ha: + kb: + lc: + kb: + LC. The third coordinate system is the laboratory orthogonal coordinate system which remains fixed as the crystal is rotated. yo. A crystal shaped as a very thin plate with its highest symmetry axis perpendicular to the plate cannot be easily mounted with that axis parallel to the spindle. (x.32. In this coordinate system. The second coordinate system in an orthogonal system called the crystal coordinate system which is linked to the crystal. the coordinates of a reciprocal lattice point. b*. Still. and c* and differs from it in that it is always orthogonal (see Fig. that is it rotates just as a*. laboratory. The first is the crystallographic P*. This system is defined so that z is parallel to the rotation axis and x is parallel to the Xray beam but points in the opposite direction. a reciprocal lattice point is specified by the vector r* (see p. and y*. The crystal. 4. 65).
since xo. 4.1391 Once @ for a reflection is known its coordinates in the laboratory system and its position on the film can be calculated in the way that has been outlined.32 shows the relationship between the crystal.32.Apl cos @)2+ (yo .33 shows that P is on the Ewald sphere when the centre of the sphere has moved from A to A' that is from (Ap'.33. Monaco laboratory system will be as can be seen in Fig. The crystal coordinate system is only shown before the rotation. the reflection coordinates in the laboratory system. and z. can be calculated. Let us consider the reciprocal lattice point P which crosses the Ewald sphere at a rotation angle @. A' sin @. The fourth coordinate system is the projection of the laboratory coordinate system on to the film plane.AI sin and + 2. yo. When the crystal rotates an angle Q.) (4. 4. Figure 4. film .266 1 Hugo L. Since P lies on the Ewald sphere. y. are only functions of the reflection indices and the unit cell parameters. and film coordinate systems. = A2 + 2. In order to convert from the laboratory to the film coordinate system we only need to know the crystal to film distance. x. point P lies on the surface of the Ewald sphere and the centre of the sphere has moved from A to A'. laboratory. and 2. that is when it is coincident with the laboratory system. 0). Figure 4. its coordinates must satisfy the equation of a sphere (xo . 0. Xrays Fig. Thus we can calculate the film coordinates for a reflection if we know the angle Q. 0) to (A' cos @. at which this reflection crossed the Ewald sphere.32) xo cos @ +yo sin cP = ~A(x:+ y: which can be solved to find the value of @. If the angle @ at which a given reciprocal lattice point crosses the Ewald sphere is known.
4. we The picture is the second of a series collected with the c* axis mounted on the spindle.35 can be indexed.35 is a rotation photograph of a protein crystal. space group P212121. with the possibility to expose only one cassette at a time.[371 There are other commercial versions of rotation cameras. Partially recorded reflections can be identified by examining the spot shape (see Fig.) .34 is a photograph of an ArndtWonacott rotation camera. (Photograph courtesy of Enraf Nonius. more easily when the spot shape is not very regular as in this case.[401 will briefly discuss how Fig. which are very demanding on the operator unless very long exposure times per film are used. Partially recorded reflections are those that appear recorded on more than one film. Although a knowledge of the crystal setting and indexing of one or more rotation pictures is not essential to process the data.1. 4. the unit cell parameters are a = 46. The ArndtWonacott rotation camera. 4.and it was mounted with the c* axis on the spindle.1. Figure 4. When data collection with the rotation method is started on a protein crystal. and c = 76.35 is orthorhombic.29) or. some of which.5 cm and A@ is in this case 3". the space group has already been determined using the precession method and the unit cell parameters are known. b = 49. Fig.1 A.Experimental methods in Xray crystallography 1 267 Indexing a rotation photograph Figure 4. the choice of the rotation axis was dictated only by the size of the unit cell parameters. Since in this case there is no higher symmetry axis. It was exposed at a crystal to film distance of 7.34. 4. The crystal that produced Fig. Also precession photographs of the zerolevel projections and some upper levels are usually available. by placing the photograph on top of the previous and the following one.
then indexing is done simply by counting spots. for the smallest circle it is 0 and for the concentric lunes it is successively 1. 4. 2. (compare with Fig. Monaco Fig.35 we can see the small circle closer to the beam stop that corresponds to the h01 plane. Rotation photograph of a protein crystal.268 ( Hugo L. The first index h is the most difficult to determine but the position of the c* axis. 4. its intersection with a * can be found by locating a * . This is currently done using an instrument called a . which corresponds to h = 0 can be found looking at the picture exposed before Fig. the first step is the extraction of the relative integrated intensities from the film. These charts are nowadays not very widely used.28).35 which shows symmetry about the rotation axis. In fact in Fig. For a discussion of the indexing procedure see text. The k index of the reflections is the easiest to identify. here we are aided by systematic extinctions. etc. 4. in order to be able to quantitatively use the data recorded with these methods. Densitometry The data collection cameras that we have seen in this chapter normally use film as a detector for the radiation diffracted by the crystals. 4.35.35 was exposed with the Xrays in approximately the direction of the b axis. 3. The axis of symmetry is the c* axis. In Chapter 3 (p. The c* axis is horizontal because it coincides with the rotation axis. 161) we have seen that the quantity that is proportional to the structure factor amplitude is the integrated intensity of the diffracted Xrays. In order to find h and I we have to find the c* and a * axes on the film. 4. Notice the fiducial marks that are used to determine the centre of the film during densitometry. ~ e r n a l ' proposed the use of specially designed charts to more easily ~~] index rotation photographs. The rotation picture recorded before the one shown in Fig. Therefore.
called pixels.. is the incident light intensity. 4. ./I. There is a relationship between optical density and number of Xray photons striking the film that we will explore more carefully in the next section but which can be assumed.5 x 12.36 shows the computer output from a scanning program with a Fig. for the time being.0. The total optical density of a spot on a film is the sum of the optical density of a certain number of squares. D= DB. The optical densities from 0 to 2 correspond to numbers that range from 0 to 9 in the figure. and D is the optical density.um2 and are therefore called microdensitometers. Modern instruments are capable of measuring optical densities of very small areas. (4. covering the spot area minus the same number of terms with an optical density equal to that of the film background.Experimental methods in Xray crystallography 1 269 densitometer or film scanner. Optical density and integrated intensity The quantity that is measured by the densitometer is the optical density of the spots produced by the diffracted beams on the film. CD~C spot area Figure 4. as small as 12. The optical density of the spots is determined by shining visible light on the film and measuring the ratio of the intensity transmitted to that of incident light and it is defined as D = log I. to be linear up to Xray optical densities of at least 1.36. the transmitted light intensity.33) where I. hence the name densitometry applied to the procedure followed to measure the relative diffracted intensities on film. Computer output showing a reflection recorded on film and scanned with a 25 pm raster. I.5 .
Solving the differential equation n = no[l . This last effect is called the Wooster effect. the number of excited particles will increase by dn and where (no . = and D =fn12. will correspond to n = n.. in the expression of n as a function of E. = 2. the fraction of light transmitted. [421 If the film contains a number of excitable particles no per unit area and n have been excited by the Xrays. If. we substitute . is the fraction of particles that have not been excited. f is the surface covered by a grain. The maximum optical density that can be measured.[411 Film as an Xray detector When an Xray photon strikes a film. it excites a silver halide particle which. although normally these numbers do not range from 0 to 9 but from 0 to 255. Here we will follow Vonk and Pijpers in their derivation of a relationship between the number of photons striking the film and the optical density they produce. and rn is the number of particles excited per photon. as d E photons strike the film. On the other hand.. when the optical density is measured. the optical density should not vary significantly within the sampling area. The sampling area has to be chosen bearing in mind that because of film graininess statistically more significant results are obtained with larger areas.3 log ItlIo fnlK. As more and more particles are excited on the film. Solving the differential equation we obtain ItlIo exp (fnlK). This last interval was chosen to make the spot representation clearer. normally taken to be equal to 1. Monaco diffraction spot in which the optical densities from 0 to 2 correspond to numbers that range from 0 to 9.3K. will decrease..n)ln.exp (maElno)] using as boundary conditions n = 0 for E = 0 and n = no for very large values of E. will produce a black silver grain on the film. and dn the increment in excited particles as before. Assuming that the fraction of light transmitted by the film is proportional to the area that has not been excited one can obtain dIt/Io= fIt dnlIoK where It/Io is proportional to the unexcited area. K is the proportionality constant. Dm.270 1 Hugo L. a is the fraction of radiation absorbed by excited and unexcited particles. otherwise one is averaging transmitted light rather than optical density and the final optical density will be in error because of the logarithmic relationship between the two quantities. when the film is developed.
e. and depending on the instrument can be as high as 12 revolutions per second.35 would have to be 1. cathode ray tube and flatbed microden~itometer. A beam of visible light is passed .. is proportional to exposure time when a film is exposed to successively higher Xray doses by increasing the time that it is hit by a constant Xray beam.[~~~ The first kind is by far the most widely used by Xrays crystallographers and it is for that reason that it will be briefly described here. like for example those used for diffractometers. the statistics of counting rates can be analysed theoretically by a Poisson distribution. If film were an ideal Poisson detector the factor 1.. (4.. The ratio D I E is called the film speed at density D.3K.Experimental methods in Xray crystallography 1 271 n and no in terms of D and Dm. representing the optical density of the film when all the silver halide granules on it have been excited.. and the function in parentheses shows how this value decreases as exposure progresses.35 than the equivalent parameter in more ideal Poisson detectors. is usually well beyond the optical density range that can be measured with the densitometer . that is the number of photons exciting the film. This equation can be simplified[421 two successive series expansions to by D I E = So(1. So is the initial speed. If aDis the standard deviation where ND is the total number of quanta producing the optical density D. Arndt et have derived a simple approximate expression for the fractional standard deviation of an optical density measurement on film. [491 In a rotatingdrum scanner. Rotatingdrum densitometers have been described by brah hams son[^^] and ~ u o n g [ ~and their performance in the scanning of precession photo'] graphs has been analysed by Nockolds and ~ r e t s i n g e r [and ]by Matthews ~~ et a1. Some typical values have been determined by Vonk and ~ i j ~ e r s [ ~ more recently by ~ l d e r [for~ ] widely used and ~ ] ~ very types of Xray film.D /2Dmax). The parameter Dm. Thus the fractional standard deviation of film is higher by a factor of 1. All radiation counters are assumed to be approximately Poissonian detectors.35) From this equation we see that for large values of Dm. i. This equation shows that the fractional standard deviation is not dependent on the film speed. Microdensitometers There are currently three different types of microdensitometers in use: the rotatingdrum. we obtain where So = mafI2. is characteristic of the film and can be determined plotting D I E as a function of D. the film is mounted on a cylindrical drum that has a rectangular aperture for the film and which rotates about the cylinder axis.0 instead.. The rotation speed is variable. The exposure E. and small optical densities the relationship between optical density and exposure is linear. The value of Dm.
those reflections which are too strong to be measured on the first film will normally fall within measuring range on the second or third. We will briefly discuss how these two limitations are handled experimentally. The optical density values thus measured can be stored on magnetic tape or directly in the computer connected to the densitometer.1) can be made to correspond to an optical density of either 2 or 3. A is arbitrarily set to one and B is determined from the scaling factor between successive films in the pack. source and detector will be advanced 100 ym and another strip will be read until the entire film is covered by 100 x 100 ym pixels. The nonlinearity of the film response can be handled by constructing experimentally a table that relates an optical density produced by the scanner to a given exposure.35)) show that there is a maximum value of optical density that can be measured for a given type of film and that the optical density is a linear function of the exposure only for relatively low values of D. After the integrated intensities have been calculated. Monaco through the film and its intensity is measured by a detector. There are two strategies used by computer programs in processing densitometer data. The problem of a limited dynamic range of the film.34) and (4. all the films in the pack can be scaled together. 50. Since a substantial fraction of the radiation is absorbed by the Xray film. 100. Source and detector are stationary during one revolution of the drum and are automatically stepped along the cylinder axis until the entire film is covered. An alternative approach proposed by Matthews et a1. The equations relating optical density on the film to the total number of photons that have caused it ((4.272 1 Hugo L. or 200 ym or more and the transmitted light is measured at intervals equal to these values. Both strategies have their advantages and disadvantages and have been used extensively to scan all types of diffraction films. After that.[49]is to assume a parabolic relationship between integrated intensity and optical density. In the second approach. the instrument gives an optical density of 0. 25. where A and B are two constants. integrated intensities are obtained online as scanning of the film proceeds. The incident light intensity I.5.[48. can be solved by placing more than one film in the cassette that records the Xray diffraction pattern. The raster size is variable. The maximum integer reading of 255(2'. the entire film is In read as described above and the data are stored for subsequent computer processing to obtain the integrated intensities. The instrument is interfaced to a computer and the process is totally computer controlled. of a limited optical density range that can be measured. In . i.e. is measured as the beam goes through air..491 the first. Thus if a raster size of say 100 ym has been chosen a strip 100 ym wide will be read in one revolution at 100pm intervals. Since one is interested in relative integrated intensities. When the light beam goes through air. In this experiment the exposure times are proportional to the number of photons hitting the Xray film. it can be 12. the table can be constructed by exposing the film to the same Xray beam during different times and measuring the optical density of the spots under the conditions that will be used for data scanning.
Thus. Both the molecular excitation of the fluorescent material and the gas ionization in the counter detector are events that can be triggered by the arrival of only one photon. Modern diffractometers use the equatorial geometry in which the diffracted beams are always measured in a horizontal plane defined by the incident . The singlecrystal diffractometer An alternative to the data collection methods using film that we have described so far is the singlecrystal d i f f r a c t ~ m e t e r . Its most important advantage is better precision since film has a much higher level of background. a limitation that is not very important for nondemanding crystals but can become very severe if radiation damage of the sample is a problem. the estimated standard deviation is 0=~ 1 ' 2 where N is the number of counts. The fractional standard deviation is thus = ~ 1 / 2 /N1'2. a goniostat that orients the crystal so that a chosen Xray diffracted beam can be received by the detector. using the technique called profile fitting. ~ ~ ] Nowadays. The detector is usually of the scintillation counter type in which Xrays excite a fluorescent material and thus generate visible light which is measured in an appropriate way. For such a distribution. smaller estimated standard deviations can be ~ b t a i n e d . Xenon filled proportional counter detectors are also used. 281. ~ this that is a model intensity distribution in two dimensions is determined by averaging the measured profiles of a certain number of reflections on the film. particularly with Cu K. [ ~ ~ . This type of Xray detector will be further discussed on p. Its only disadvantage is that it measures one reflection at a time. and a computer that controls goniostat and detector movements and performs the mathematical operations required to position the crystal and detector in the desired orientations. It is then assumed that all the reflections have this standard profile and the measured data are fitted to it. DWractometer geometry A singlecrystal diffractometer consists of an Xray source. Although the simplest approach to determine the integrated intensity is to simply subtract the background from the area covering the spot. diffractometer measurements can be said to be intrinsically more precise than those obtained from film methods. radiation. = ~ We saw on p. that almost all of the data required to solve small molecule structures are collected and the diffractometer can also be used in macromolecular crystallography. an Xray detector.35.In ~ ~ ] method. 271 that for film methods the fractional standard deviation is larger by a factor of 1. the different intensity values obtained follow a Poisson distribution. It can be shown experimentally[s3]that if an Xray beam is measured several times with a diffractometer detector. a model profile for the reflection is constructed. it is with this instrument.Experimental methods in Xray crystallography 1 273 this second approach the nonlinearity of the film response is handled in the film scaling procedure.
In general. 4. The fourcircle diffractometer. The detector moves independently and forms an angle 20 with the incident Xray beam. rotations coincide. 4. If we x Fig. the o circle. w is 0 when the x circle is perpendicular to the incident Xray beam. The four circles of the diffractometer are thus the Q.38. x tor Fig. 4. In the figure. Rotation of the cradle about the main axis defines the angle o. . rotating about the instrument main axis. The angle 28 is 0 when the detector is positioned in the direction of the incident Xray beam. The x circle carries the goniometer head with the crystal and together with it constitutes the Eulerian cradle. In order to observe diffraction. The most widely used type of goniostat uses the Eulerian cradle which gives rise to the fourcircle diffractometer shown schematically in Fig. only two rotations are required to bring a reciprocal lattice node to the intersection of the Ewald sphere and the equatorial plane.37. is arbitrary and can be defined with respect to the crystal orientation.37. The detector can only move on this plane and it forms an angle 28 with the incident beam as shown in Fig.38. defined by the rotation of the cradle. Monaco Xrays and the rotation of the detector about an axis passing through the crystal. At the same time. and the zero position of Q. 4. and the 28 circle described by the rotation of the detector about the main axis. and x circles about which the crystal can be rotated. The diffractometer equatorial geometry. The instrument has a main axis that is normal to the equatorial plane and therefore to the incident and diffracted Xray beams and passes through the crystal. Both the 28 and o rotations are about the main axis but the first moves the detector and the second the cradle.274 ( Hugo L. The angle x is defined by the spindle of the goniometer head and the main instrument axis. If the angle x is 0 the o and Q. defines a plane that contains the incident beam. In a threecircle diffractometer the degree of freedom that is missing is the rotation o. is 0 if the spindle axis is parallel to the main axis. in other words the cradle is fixed with its x plane perpendicular to the incident Xray beam.rotation about the spindle axis of the goniometer head defines the angle Q. The cradle is constituted by the circle which carries the goniometer head with the crystal. all the reciprocal lattice nodes are brought in turn to some point on the circle defined by the intersection of the sphere of reflection and the equatorial plane. The cradle can rotate about the main instrument axis describing the angle w . the detector is moved to the appropriate 28 angle so that it can receive the diffracted beam. point P is in diffracting position because it is on the Ewald sphere and produces a scattered beam that can be detected because it is on the equatorial plane. in exactly the same way as in the rotation camera. Reflections will always be measured on this plane. The detector.
39(a) which is a projection looking down the instrument main axis. the x axis. perpendicular to the plane. which forms an angle of 50" with the main instrument axis as shown in Fig. The reciprocal lattice vector r* lies in the x plane and the x axis bisects the angle formed by the incident and diffracted beam. 4.40. 4. It is for this reason that. is the kappa goniostat. 4.Experimen$al methods in Xray crystallography 1 275 Fig. the socalled bisecting geometry arrangement is chosen in which the x plane is moved so that it is made to contain the vector r*.41. bisects the angle formed by the incident and scattered Xrays as shown in Fig. 4. However. The advantage of this system is that it is less cumbersome than the Eulerian cradle and thus x Fig. a rotation about @ or w can bring the reciprocal lattice node on the Ewald sphere as shown in Fig. efc. (a) The crystal can be first rotated about @ until the node lies on the sphere. . 4. collimator. (b) A x rotation brings the point on the sphere of reflection to the equatorial plane where it can be measured. An alternative to the Eulerian cradle. the extra degree of freedom provided by the w circle can prove very valuable. the direction of the scattered beam thus defined may be such that detection may be difficult or even impossible because of the interference of the x circle. In this type of geometry the x circle does not exist and the goniometer head carrying the crystal is mounted on an arm that can rotate about an axis. start with x = 0.40. Quite often.39. Under these conditions. that is used in a widely diffused instrument.39(b). although in principle rotation of the crystal about two axes plus the detector movement are sufficient to satisfy the diffraction condition. the K axis. Bringing a reciprocal lattice node to the intersection of the Ewald sphere and the equatorial plane. Then. Measurement of the scattered beam can then be accomplished by placing the detector at the appropriate 28 angle. The bisecting geometry arrangement. 4. it can be brought to the equatorial plane by a rotation about the x axis as shown in Fig.
b. points towards the Xray source for 28 = 0. bG. w. A second orthonormal coordinate system. Its basis uectors are called aG.cos cD sin w cos x sin x sin w sin n p x cos w cos x Let be the coordinate matrix of the vector r* with respect to the reciprocal coordinate system Fig. 4. bD. where (see p. When one or more of the diffractometer angles differ from 0 the two coordinate systems are related by a rotation matrix F such that Fig. and CG and it is coincident with the diffraction system when all the diffractometer angles are equal to 0. .41. A. and 28 for which scattering will be observed for a given reflection of a crystal. it is necessary to determine the crystal orientation with respect to the Eulerian cradle. the crystal coordinate system. X . ..42. a and b are the t w o basis vectors that are . The diffraction orthonormal system as seen in the projection on t o the equatorial plane. cD such that a. Let us define the diffraction orthonormal coordinate system. Accordingly. the vector cD is normal to the figure plane and points away from the observer. is defined. with respect to the goniometer head and therefore relative to the crystal. and cD form a righthanded system. The K geometry goniostat. Monaco 9 rotations that would cause collisions or would produce diffracted beams that would be blocked by the x circle in the conventional fourcircle diffractometer are still practicable. In this section we follow the International tables for xray crystallography. found o n t h i s plane.sin cD sin w cos x sin cD cos w . in Fig. and bD are both in the equatorial plane. AD.42. 4.. bD is parallel to the diffraction vector for positive values of 28 and cD is parallel to the instrument main axis and has a direction such that the three unitary vectors a D . 265 for the rotation method. 72) cos cD cos co . Determination of the crystal orientation and unit cell parameters: the orientation matrix Before one can predict the values of the angles cP.[54] and define several coordinate systems similarly to what was done on p. with basis vectors a D . 4. a.276 1 Hugo L.
and HJ. sin o cos Q. 66) XG = UH or H = (u)'x. If the angles w.40) where U is the transposed orientation matrix. p.cosx sinx ( ) . Q. Hz. then as was pointed out the diffraction vector r* is in the x plane.42). and XG3can . Then. 4. X. and o that will bring the node to a position that satisfies the diffraction condition.37) If the bisecting geometry arrangement was chosen. are measured.38) the values of the angles Q. cos x XG= lr*J cosQ. and Q.. then the vector coordinates in the diffraction system are and its coordinates in the crystal system AG cos @ sin o + sin Q. (4..Experimental methods in Xray crystallography and let 1 277 be the coordinate matrices of r* with respect to the systems AG and AD respectively. 66 and since (F)' = F XG = FXD. How do we then calculate the coordinates of a reciprocal lattice node in the fixed crystal system? In order to do this we need to introduce the orientation matrix U defined by and (see. and w corresponding to the diffraction condition of three general reflections. X. according to p. (4. in other words w is 0 and the vector coordinates in the crystal fixed system are: sin Q. XG2. the coordinates of the three reciprocal lattice points in the fixed crystal system. remembering the way in which the diffraction coordinate system AD was defined (see Fig. Let us now see how the orientation matrix can be determined in the general case in which the crystal unit cell parameters are unknown. HI.. X. XG1. If the angles X . Thus if we know the orientation matrix we can calculate the fixed crystal coordinates of any reciprocal lattice node and therefore we can determine the Q.38) Thus if we know the coordinates of a reciprocal lattice node in the fixed crystal system we can determine without any ambiguity from eqn (4. and w values for which diffraction will be observed for the node. are such that the diffraction condition is satisfied. cos o cos x sin Q. cos o cos x sin x cos o + (4.
68). If the unit cell parameters are known the angles corresponding to only two reflections are sufficient to calculate u. Multiplying both sides of the first eqn (4.38)). HA* = W A G = X ~ U .28 scan. 2.43).42) can be written in the more compact form Recalling eqn (4. [ ~ they In the o scan the detector is left stationary while the crystal and thus the chosen reciprocal lattice node is made to cross the Ewald sphere by a . the orientation matrix from (4.['~] In the more general case we have discussed. 1.~ U A ~ (4. Since HM and XM are known.40) we obtain = XGAG. There are basically two scanning modes that are very widely used (but see also ~ ~ c k o f f and ~ ] ) are called the o scan and the 28 or o .15) and from it one can determine the unit cell parameters of the crystal. U = H ~ l x.41) Now we can write for the three reflections. Measurement of the integrated intensities In order to obtain the integrated intensity of a reflection. the orientation matrix yields also the unit cell parameters of the crystal A* = UAG and since AG is orthonormal (see Chapter 2. ~ . Monaco be calculated since they depend only on the angles and the magnitude of the vectors Ir*l (eqn (4.39) and finally. Now the matrix A*A* is nothing else than the metric matrix G* of the reciprocal lattice defined by (2. and 3 HIA* = X G l ~ G If one defines the matrices Equation (4.278 1 Hugo L. the entire volume of the node must be made to sweep through the Ewald sphere while the detector counts the diffracted photons. p. one can calculate U.39) by H and introducing the second eqn (4.
The advantages and disadvantages of these two scanning modes are extensively "I discussed by ~ y c k o f.43(a). (b) The w2%scanning mode. 4. From the figure it can be seen that the section of the reciprocal lattice node sampled lies on an arc passing through the node and centred at the origin of the reciprocal lattice.26 scanning mode the crystal is moved in the same way but the detector follows the o rotation at twice the angular speed of the crystal so that in the end A26 = 2Ao. This type of scanning mode is illustrated in Fig. 4. . This scanning mode is illustrated in Fig.Experimental methods in Xray crystallography 1 279 rotation of A o about the main axis. Diffractometer scanning modes.43. In this case. the section of the node sampled lies in the direction of the vector r*. 4. In the 26 or 0 .43(b).[f The simplest way to obtain the net integrated intensity is by using the Fig. (a) The w scanning mode.
[551In this method peak profiles are fitted to a shape that was previously determined and is periodically updated as data collection proceeds. If step scans are made. [The ]criterion used is the ~~ function a l l .) 1 . In this simple case. Once the appropriate A and Xray source operating conditions have been chosen. This method requires an accurate definition of the scanning width Am. which becomes a minimum when the appropriate width is found. profile analysis of the peaks further improves the quality of the data.44. the standard deviation of the measured intensity can be estimated by where I. 4. Monaco socalled backgroundpeakbackground (BPB) method in which the integrated intensity of the reflection is calculated by simply subtracting the background resulting from the average of measurements to the left and to the right of the peak from the total peak counts. The recording of the complete reflection profile by carrying out step scans is clearly a more sophisticated alternative but it is much more demanding in terms of data storage space.44 is a photograph of a modern fourcirclediffractometer. Figure 4. The problem of defining the peak width in a stepscanmeasured reflection is discussed by Lehmann and ~ a r s e n . (Photograph courtesy of Siemens Analytical Xray Instruments. the main steps that have to be taken in order to record a data set Fig. calculated for all possible peak widths.280 1 Hugo L. A modern fourcircle diffractometer. is the intensity of the peak and IB that of the background.
Start data collection. at this point one is in a position to determine very accurate unit cell parameters by using an adequate number of Friedel pairs (see p. 2. 3. 5. from the drawback that it collects only one reflection at a time. 259). remember that an absorption correction is essential. If possible. range. When data have to be collected from macromolecular crystals which have very large unit cells and which therefore require the recording of many reflections and which in addition have. 6. Check for systematic absences. the diffractometer is an inadequate data collection device. Using the results of (4) find reflections at high 20 values that will yield a better orientation matrix and more precise unit cell parameters. the first is that. 8. transform the unit cell that has been found into another of higher symmetry. Select a subset of the reflections to periodically check the orientation of the crystal and another to monitor radiation damage (see p. 155) at high 2 8 values and leastsquare refinement methods (p. in which order and 20 range. as we said in the previous section. Decide which reflections will be collected (one or more asymmetric units). On the other hand. 306). 90). If at this point one suspects that a better crystal is available. If required. 7. This is due to two main reasons. 10. the diffractometer is the ideal data collection instrument for smallmolecule crystals but it suffers. before removing the crystal. determine a preliminary orientation matrix and the unit cell parameters. a more or less serious radiation decay problem. Control the quality of the crystal by examining the profile of some reflections. that is with the reflections recorded on film and with a choice of the rotation range A@ made in order to minimize the number of films exposed and the fraction of partially recorded reflections. the rotation method described earlier (p. as we have seen. the second is that during the . Choose the scan mode. it is wise to select it and repeat steps (1) through (3). Once a satisfactory number of reflections has been found. Search for the reflections that will be used to determine the orientation matrix and unit cell parameters of the crystal. film is a poorer detector than diffractometer counters.Experimental methods in Xray crystallography 1 281 from a crystal with a diffractometer can be summarized by the following checklist: 1. 9. 4. and most probably record the data necessary for an empirical absorption correction (see p. and speed by examining an adequate * number of reflections carefully. 11.When data collection is finished. 308). Area detectors Due to its high precision. Mount the goniometer head with the specimen and centre the crystal optically. has an intrinsically lower precision. At this stage it is easier to look for reflections at fairly low 28 values. in general.
wavelength has enough energy to induce on average the formation of 320 ion pairs. Monaco film exposure the signal is recorded by the film only during a fraction of the total exposure time. However. Typically A is no more than a few tenths of a degree whereas A@ can be one degree or more. which is the main advantage of the rotation method. Multiwire proportional counters are gas filled chambers that contain three parallel planar electrodes. The free electrons and the positive ions move in opposite directions.[601 Principles of operation of area detectors The most common area detectors types that are currently used in macromolecular work and that include the current commercially available instruments belong to two groups: multiwire proportional counters and television area detectors. which is based on entirely different physical principles and.[61. The anode and at least one of the cathodes are arrays of parallel wires which are perpendicular among them. ~ ~ ~ ] ) . in most cases. There are many reasons why this is not done when working with film but this is instead perfectly feasible when the detection is done by the devices called area detectors or Xray positionsensitive detectors. has not yet been as thoroughly tested as the other two groups.621 gas filling the chamber is The usually a xenoncarbon dioxide mixture (see also Mokulskaya et u I . it should be pointed out that the devices that are currently available commercially have been optimized for the detection of copper radiation 2nd are. because it is more recent.282 1 Hugo L. the former in the direction of the anode where they produce an ionization avalanche with the formation of several orders of magnitude of new ion pairs. It has been calculatedf621 that an Xray photon of the Cu K. in the rotation method the signal is recorded on the film during a time equal to tAlA@ where t is the total exposure time whereas the background is recorded instead during the total time t.[621 These ion pairs move again in opposite directions under the influence of the electric field and in so doing generate the electrical signal which is measured in the detector and which is localized in the region . and although they have not yet found many important applications in smallmolecule crystallography they will probably turn out to be very useful in cases when radiation damage is a problem. so that A is spanned by several rotation photographs. and then measure the integrated intensities only on those films in which the reflection is found. If the reflecting range of a reflection of the crystal is A and the rotation range selected A@ this fraction is A/A@. We will briefly discuss the Xray detection mechanisms of these three types of detector.[579581 One could. In other words. Area detectors are thus probably the best choice for the data collection of macromolecules. in principle. an anode sandwiched in between two cathodes. improve this situation by simply reducing A@. less efficient in the detection of the higherenergy molybdenum radiation which is very often used in smallmolecule work.[591 Area detectors were designed to combine the photon counting efficiency of the diffractometer with the ability to record a large fraction of the reflections which simultaneously cross the Ewald sphere. To these two groups there has been a recent addition: the imaging plate. When an Xray photon is absorbed by a Xe molecule an inner shell electron is emitted with a kinetic energy that is most of the energy of the absorbed photon and which is sufficient to produce the ionization of many more molecules.
An electronic transition in these ions generates the luminescence with an intensity proportional to that of the original The storage phosphor is read by an image reader which releases the stored information by means of the laser and collects the emitted radiation and channels it into a photomultiplier tube which converts the radiation into an electrical signal. The light thus generated has a wavelength of 390 nm and is irradiated from the plate areas which were previously hit by the Xray photons. This enhancement is achieved by an image intensifier in which the photons produced by the first phosphor generate a certain number of electrons from a photocathode which are then accelerated and strike a second phosphor that is optically coupled to the camera. The imaging plate is essentially a storage phosphor. In television area detectors the Xray radiation is converted into visible light by a fluorescent phosphor. a certain number of these images have to be added before the statistics become satisfactory.[71 The area detector phosphor. is either polycrystalline gadolinium oxysulphide or zinc sulphide and it produces between 250 and 500 visible photons per Xray photon. The function of the carbon dioxide molecules is to absorb the ultraviolet photons which are generated in the avalanche process and which could produce the photoemission of electrons and thus start the whole process in another region of the counter. The plate can be used repeatedly. that is the fluorescent material that transforms Xrays into visible light. after suitable intensification. Since the photons arriving in 40 ms.[~~] The television camera tube consists of a photoemissive cathode with an intensifier that accelerates the electrons generated by the light producing a charge image which is scanned by an electron beam used to measure the signal. These visible photons.[''] . This phenomenon is called photostimulated luminescence. which is the period necessary to scan the image. the sensitivity of the camera is not enough to measure them and so an increase in the signal is required to make it detectable. are detected by the photocathode of a standard highsensitivity television camera tube which is linked to a computer. since exposure to visible radiation restores it to its initial condition. The photostimulable material covering the plate is Ba F Br:Eu2+ crystals.Experimental methods in Xray crystallography 1 283 where the initial photon hit the counter. The photon gain of these intensifiers is of the order of either 100 or 1000. it has been found that the photostimulated luminescence is reduced to one half of its initial value after approximately ten hours. are not enough to give good counting statistics. This means that the Xray photons produce on the plate a latent image that is then excited by stimulation with a HeNe laser producing light at 633 nm.[661In spite of this gain in photon numbers. The two other elements of the detection system are an image processor and an image writer that can be used to imprint the plate image onto photographic film to produce a permanent The characteristics of the image reader turn out to be crucial for the performance of the entire system and the best precision could not be obtained until an adequate readout instrument was built. Subsequent excitation of these centres by the laser liberates again these electrons that return to the Eu3+ ions which thus become excited Eu2+ ions. When the plate is hit by Xray photons some of the Eu2+ ions are ionized to Eu3+ ions and the electrons that are freed are trapped in Br vacancies introduced in the crystal that are called F centres.[681 The radiation energy of the Xray photons can be stored by the phosphor for fairly long periods.
= A12 sin = A/2 sin 8. limits the resolution of the data to be collected. or another type of threecircle diffractometer or a K goniostat. Monaco The performance of the three types of detector mentioned here has been analysed in several of the references given in this section and in particular by ~ r n d t . as shown in Fig. it can be moved back and forth providing another degree of freedomthe crystal to detector distance D.. 4. Multiwire proportional counters and television detectors use either a modified rotation (oscillation) camera with a vertical spindle. a Eulerian cradle. Figure 4. R.46. [Multiwire proportional counters and television detectors are ~~] already fairly widely spread in many laboratories and the data they have produced have been used to solve several new protein structure^. the data collection system requires some means of orienting and moving the crystal. The detector is mounted on a horizontal arm and can be moved about an axis passing through the crystal in a way totally analogous to a standard diffractometer counter and. Data collection with an area detector In addition to the area detector... Fig.[741 can write Bragg's "aw as follows: R... and.284 1 Hugo L. (Photograph courtesy of Enraf A television area detector with a K . 4 gonic Nonil ..^^^^^] The special characteristic of the imaging plate is its very wide dynamic range which appears to make it the ideal detector to be used with the very intense synchrotron radiation. Om. in addition.45 is a photograph of a television area detector which uses a K goniostat. Following we Xuong et a1. The angle formed by the Xray beam and a normal to the centre of the detector is called 8.
.. crystal to detector distance D. the angle 8 and the .tan'(a12D) where a is the detector width. and the unit cell parameters of the crystal.. is the longest unit cell parameter of the crystal measured in ingstroms..[73] the crystal to detector distance for one type of multiwire proportional counter is calculated in centimetres. and emin defined are in the figure and are a function of the detector size. differ in their construction details. . is the maximum and R. the minimum resolution of the reflections that can be measured by the detector in the position corresponding to the selected values of 8. the crystal to detector distance. The angles &. From the figure it can be seen that 28. D must be selected according to the characteristics of the detector...45) can be used to calculate the value of 8. The equivalent equation for another type of multiwire proportional counter[741 is: Thus...Experimental methods in Xray crystallography 1 285 detector Fig. The volume of reciprocal space accessible is limited by the two spheres of radii l/R.. data from the same crystal would have to be collected at very different Ds by the two detectors which. Once D has been . the wavelength of the radiation. . = 8. radiation by the following equation: where a. 4. to be selected for data collection to a particular resolution once that D.. where R. Projection of the Ewald sphere and the area detector on to the plane defined by the incident Xray beam and a normal to the detector passing through the crystal. although based on the same general principles. and l/Rmi. and D. for Cu K. Equations (4. 28.46.. + tan' (a/2D) = 8. which in turn are a function of Dand 8. The first two parameters do not normally change for different experiments performed at a given installation and therefore D can usually be calculated with a very simple formula in which the only variable is the maximum unit cell parameter of the crystal. has been chosen. For example in Howard et a1.
the rotation range. and @. The first is that the detector is not always perpendicular to the Xray beam but can form with it an angle 8. one can calculate the 8. 278). as pointed out before. the rotation angle at which the node crosses the Ewald sphere for all the reflections to be collected can be predicted[761 (see also p. and.[762771 crystal is also rotated the about an axis but the frame is recorded with the crystal held stationary. Monaco determined. Many of the considerations discussed earlier (p. knowing the detector width a. and y. In addition to the detection method there are basically two fundamental differences between the two techniques. the spatial resolution of the detector are expressed by the number and size of the pixels. of the reciprocal lattice nodes to a given resolution and.[733751 pointed AS out before this strategy improves the signal to noise ratio since reflections are integrated only in the frames in which they appear. in general.286 1 Hugo L. a full data set collected with an area detector contains a very large fraction. in general. since the crystal orientation can be obtained automatically by efficient computer programs. In most cases the crystal is more or less accurately aligned before data collection can begin so that x. The second major difference is in the choice of A@. Obviously this fact has to be taken into account in the prediction of the detector coordinates of the reflections collected. [ ~ ~ ~ ) . It is worth noticing that these strategies of data collection are the only ones described so far that truly sample the entire volume of a reciprocal lattice node. 259) are thus applicable to this technique in which data are collected in a series of consecutive rotation (oscillation) frames. Each of the electronic pictures generated by the detector is called a frame and the individual elements of the picture are called pixels.The A@ between frames is of the order of 0. In both cases the detector does not move while data collection proceeds. The camera or the goniostat and the detector are controlled by a computer which is. whereas with the diffractometer one looks at a reflection profile on a single plane that can be chosen to cut the node volume in different ways as seen earlier (p. With film methods what one sees is a projection of the entire volume on to the film plane.01" in order to better scan reflections that in some cases can be very sharp. However. the space between reflections. required to collect data to the resolution desired. Two methods have been proposed to make the reciprocal lattice nodes of the crystal cross the Ewald sphere: the rotation (oscillation) method and the stationary picture method. In the first method the crystal is rotated about an axis which is often the vertical axis in pretty much the same way as when film is used. connected to another computer which receives from it the frames that are then used to calculate the integrated intensities (see for example Blum et u Z . Thus. the coordinates of a reflection on the detector.[78]it is also possible not to orient the crystal .. a possibility that ought to further improve their quality. area detector data are the only ones that can be profile fitted in three dimensions. if not all.06" and subframes are sampled at distances of 0.[771This second data collection strategy is less widely used than the rotation (oscillation) method. In the electronic stationary picture method. The reflection intensity is thus extracted from a series of still electronic pictures at slightly different values of a.. which in this case is selected so that each reflection appears in several frames. 265). The reflection size on the picture.
in this case. give rise to a series of concentric rings. these circles and the sample define a series of concentric cones with apex in A.[731A strategy that can be used to cover a section of reciprocal space with an area detector. In this case. Rotation of the specimen is a standard practice in data recording of polycrystalline materials. the cones will generate concentric arcs. fa) If the specimen is an aggregate of randomly oriented crystallites. In this last case one only measures the radius of the cone and the diffracted intensity at a single position. diffraction is observed when the scattering vectors lie at the intersection of the Ewald sphere and a series of concentric spheres centred at the reciprocal lattice origin. which are segments of the rings. Exceptions Fig. It may even present spots corresponding to single reciprocal lattice nodes. The parameters reported are 28. If the orientation of the crystallite in the specimen is not perfectly random. rather than having one point on the Ewald sphere. we now have a series of circles. The entire surface of these cones gives rise to diffraction. A simple way to record the diffraction pattern of a polycrystalline material is by placing a film perpendicular to the incident Xray beam. and the relative intensity of the radiation along any direction on the cone. that is to simply record the position and the intensity of the diffracted radiation on any plane that contains the incident Xray beam. These orientations define a sphere of radius r*. thus generating a more homogeneous diffraction pattern. is discussed by Xuong et al. with these specimens. If the sample can be considered perfectly isotropic this single measurement is sufficient to completely characterize the diffraction pattern. the pattern obtained will not be isotropic. The result is equivalent to having a sample with many more possible crystallite orientations and therefore closer to isotropy. the distances from the singlecrystal reciprocal lattice nodes to the origin of reciprocal space. on the strip. In that case the powder sample can be appropriately rotated so that each crystallite adopts many different orientations in the course of data collection. Figure 4. The diffraction cones will.Experimental methods in Xray crystallography 1 287 before data collection begins and find the orientation afterwards. (b) The intersection of the sphere of radius r* with the Ewald sphere is a clrcle that together w ~ t h point A defines a diffraction cone of all the possible directions in which diffraction is observed. which together with the position of the sample A fixes the direction of the diffracted beam. Thus. . a narrow strip of film can be placed on a cylinder centred at the sample. during frame processing. A final possibility is to reduce the strip to a line. The most remarkable difference with the singlecrystal case is that we must now think of the scattering vectors not as lying on discrete nodes of reciprocal space but on the surfaces of spheres whose radii are the reciprocal lattice vectors r&. In strict analogy with the singlecrystal case.47.47 shows the effect that this random orientation has on the diffraction of a specimen assumed to contain only one reciprocal lattice node. So. 4. Alternatively. which is obviously applicable when the crystal orientation is known before data collection begins.[741 Data collection techniques for polycrystalline materials Xray diffraction of polycrystalline materials An ideal polycrystalline material or powder is an ensemble of a very large number of randomly oriented crystallites. the vector r* is found in all the possible orientations with respect to the Xray beam. that is the angle made by any vector with origin in A and lying on the diffraction cone surface and the incident Xray beam.
The methods which use them are the most widely diffused in . Another important feature which distinguishes powder diffraction is that the intensity of the diffracted radiation on the cone surfaces can arise from the contributions of more than one singlecrystal reciprocal lattice node. In the figure it can be seen that the diffraction due to the sphere of radius rT can be measured at many different values of the angle 28. radiation of adequate intensity in a rather extended energy interval. In this case. and we have only one possibility if we want to measure the diffraction that arises from the sphere of radius r:: to have some means of detecting radiation at an angle 28. When the diffraction experiment is performed with monochromatic radiation.. measured along any direction on the cone surface. that is when there only a single Ewald sphere. however. one for each wavelength. For the remainder of this chapter we will assume that we are dealing with monochromatic Xrays. there will be diffraction produced by radiation of different wavelengths. 28. there is only one diffraction cone corresponding to each sphere of a given radius rT in reciprocal space. Figure 4. are the cases in which the preferred orientations and other properties of the crystallites need to be studied. For different acceptable choices of 28.[791 Just like the Laue method they are best practised with a synchrotron source which can furnish. possible to shine on the specimen Xrays with a wavelength variable within a certain range. The four reciprocal lattice nodes represented in the figure are found at the same distance from the origin of reciprocal space 0 and therefore they will all contribute t o the intensity of the line of the cone corresponding to the distance r r . It is.49 shows the Ewald spheres corresponding to the two values limiting the wavelength interval of the radiation used. In other words. etc. The experiment is exactly equivalent to the Laue method used for single crystals. with the incident Xray beam. 4. A powder diffraction maximum.48 shows in projection that this can happen both as a result of chance and crystal symmetry. and each will generate a diffraction cone with a given sphere of radius rT. They obviously require a detector that will discriminate the energy of the arriving scattered radiation and have some advantages that make them the best choice in certain situations.288 1 Hugo L. the angle 201 corresponds unambiguously to the sphere of radius rT. The methods which use polychromatic incident radiation and analyse the energy or wavelength of the scattered radiation at a fixed scattering angle are called energy dispersive methods in powder diffraction.48. there will be many Ewald spheres. Figure 4. Monaco Fig. as we have seen. is thus said to have a certain multiplicity that will be higher the higher the symmetry of the crystallites under examination. to that of radius r t ..
If the powder diffraction at very high 28 angles needs to be studied.50 shows the sample and Xray beam and the position of the film in the transmission and backreflection cameras.e. The cameras that use this geometry are called backreflection cameras. In this case the problem is the opposite. Although these cameras offer the advantage of recording the entire circle resulting from the projection of the diffraction cone onto the film plane. they suffer from a serious disadvantage: they are limited to maximum 28 values which for the standard specimen to film distances and film sizes are about 45". In the DebyeScherrer camera. 4. standard laboratories. Figure 4. higher than a minimum value can be recorded. tacitly assuming that the specimen was positioned in between the source and the film.51(b) shows the appearance of the strip after recording a typical diffraction pattern. The cameras that use this geometry are called transmission cameras and in them the film is usually kept stationary during data collection.Experimental methods in Xray crystallography 1 289 Fig.[s0. From the rich literature that covers the diffraction of polycrystalline materials in depth we recommend two books.51(a) is a photograph of the camera and Fig. Figure 4.811 Cameras used for polycrystalline materials We have already mentioned that a very simple way to record the diffraction pattern generated by a powder is by simply placing a film perpendicular to the Xray beam. As seen in the figure. the recording film is a strip which is placed on a cylindrical drum centred on the sample. 4.[82]probably the most popular diffraction camera for powders. the . The two Ewald spheres limiting the wavelength range of the polychromatic radiation used define with the sphere of radius r: two limiting diffraction cones. The shaded region in the figure shows the range of 0 values that can be used to measure the diffraction in an energy dispersive experiment. It should be clear from our discussion that they are useful only in those cases in which the diffraction pattern of the polycrystalline material needs to be recorded at fairly low or rather high 2 8 values. All the cones in between correspond to r: for different wavelengths. the flat film can still be placed perpendicular to the Xray beam but in between the source and the specimen instead.49. i. A geometry which allows the recording of the diffraction pattern of a polycrystalline material at both high and low 28 values is that used by the DebyeScherrer camera. only the diffraction at 28.
(b) Sketch of a diffraction pattern recorded with the DebyeScherrer camera using the Straumanis method of film mounting. 4.51. Monaco Fig. Notice the doublets at high diffraction angles.50. Position of the specimen and the film in transmission (T) and back reflection (BR) cameras. Fig. 8 = o0 (b) @=90° .290 1 Hugo L. 4. (a) The DebyeScherrer camera.
the presence of double lines centred on one of the punched holes serves to unambiguously identify it as that corresponding to the collimator making it unnecessary to mark the strip.51(b). sin 8 = A . Since.8009" for 8 = 80" instead. Thus. and R i s the radius of the camera. They correspond to the K. S a n d S' are the distances between the symmetrical arches corresponding t o one diffraction cone. One of the two holes is then used for the collimator and the other for the beam trap. An important advantage of this method of film mounting is that the positions 8 = 0" and 8 = 90" can be very precisely determined by taking the averages of the arch positions corresponding to several diffraction cones on the film. That the doublets correspond to high 2 8 values can be seen by differentiating Bragg's law: 2d. In the socalled Straumanis method of film mounting two holes are punched in the film strip positioned at about one quarter and three quarters of the total film length.5418. As seen in Fig. in most cases the diffraction pattern is isotropic. punching a hole for the other. A8 = 0. for both high and low values of 28. Projection of the drum of the DebyeScherrer camera on t o its axis. The advantage of the Straumanis method of film mounting is that it provides accurate measurements for the positions of the arches that will then be translated into Bragg spacings.46) In the case of Cu K. as we have seen. if we take il = 1. if S is the distance between the arches due to a diffraction cone and R is the radius of the cylinder SI2nR = 48/360° for the arches centred on the beam trap ( 8 = 0") and S1/2nR = (360" .52. a third alternative is usually preferred. 2dHcos 8 d 8 = dil. '\ S' XRAYS  Fig. and one is therefore only interested in the position of the arches and their relative intensities. this limitation is not very severe.0038 A. one can easily calculate the corresponding 8 values since as seen in Fig.48)/360° for those centred on the collimator ( 8 = 90"). the doublet is separated by 0. The big advantage of the camera is that it records the entire pattern generated at all possible values of 28. radiation. It is the diffraction pattern recorded that tells us which hole corresponds to 8 =90°. 4. and both ways of mounting the film have been used. Although one can place the film so that the cut in the cylindrical surface is made to coincide with the collimator or beam trap. From the position of the symmetrical arches. In addition to the cylinder that holds the film strip in place. the main body of the camera has a collimator that serves to define the incident Xray beam and a beam trap that stops it after it has travelled through the specimen. lines of conventional generators which are normally not resolved by Xray filters but are clearly separated after diffraction by powder samples at high 2 8 values. the arches centred on one of the two holes punched are present as doublets. 4.52. its main disadvantage is that it does not record the entire projection of the diffraction cone but only a segment. dH. il(sin cos 8 A8 = Ail.. and A8 = AI tan 8 Ail. .Experimental methods in Xray crystallography 1 291 pattern shows a series of arches resulting from the projection of the diffraction cones on to the cylindrical surface. and K. The specimen is in the centre of the circle. (4.0240" for 8 = 10" and A8 = 0. 4..
. Parafocusing cameras offer the advantage of producing very sharp diffraction lines in times comparable with those required for standard exposures in the DebyeScherrer camera.6mm. 4. can be broadly classified into two groups: the Seemannand the ~ u i n i e r [ ' ~ ] types. d H . This range depends on the details of camera construction but one can roughly say. can be easily calculated by simple application of Bragg's law. of which there are many variants used for different applications.53(b) for the Guinier geometry. In the DebyeScherrer camera the sample is usually present in the form of a small cylinder placed in coincidence with the camera axis and it is slowly rotated about this axis during data collection in order to minimize the effect of the possible preferred orientation of the crystallites. the corresponding interplanar spacings. 243. 4. the diffracted radiation will converge in both cases on the parafocusing circle of the camera thus producing a very narrow line on the film. As seen in the figure. both cameras restrict the range of 26 that can be recorded. The DebyeScherrer camera produces rather broad diffraction lines which for some applications may be a serious drawback since some of the lines on the pattern may be found overlapping on the film. A camera that has a larger cylindrical radius will resolve the diffraction lines better since for a given A 0 there will be a larger corresponding AS. After the 0 values of a given diffraction cone have been determined. a simple relationship will exist between the distance S measured in millimeters and the scattering angle 8 measured in degrees.292 1 Hugo L. The price to be paid is longer exposure times and higher levels of background. The convergent beam necessary for the Guinier camera can be produced by a bent or bent and ground crystal monochromator of the type we have discussed on p. since the diffracted Xrays must travel a longer path which is normally through air which with its scattering raises the background level.53(a) for the SeemannBohlin and in Fig. Since an arc of a circle subtends equal angles at every point on the circle. Two values of R that have been very extensively used are 57. that SeemanBohlin cameras record the diffraction lines only above a certain minimum value of 26 whereas Guinier cameras do it up to a certain maximum value. If one attempts to separate the lines by using a collimator of smaller diameter or a camera of larger radius the exposure time may become unacceptably long. It is for those cases that the focusing or parafocusing cameras have been devised. Parafocusing cameras. and from the figure it should be appreciated.26mm and 114. Monaco From the first equation we find that If the radius of the camera is chosen so that its value in millimetres is an exact multiple of l80/1d. The principle on which parafocusing cameras is based is shown in Fig. In both cases the sample is ideally an arc of a circle which is irradiated by reflection by a divergent beam in the case of the SeemannBohlin camera and by transmission by a convergent beam in the case of the Guinier camera.
Just as in the case of single crystals. and relative intensity of the diffraction pattern produced by a polycrystalline material are called powder diffractometers. (a) The SeemanBohlin parafocusing geometry. In the Gandolfi camera[861 crystal the is mounted on a spindle inclined at 45' with respect to the camera axis and is rotated about both this and the camera axis. The final result is a diffraction pattern that closely resembles that produced by a true polycrystalline material. Diffractometers used for polycrystalline materials The powder cameras described in the previous section all use film to record the intensity of the diffracted Xrays. The instruments that use this type of detector to measure the position. Notice the different way in which the t w o geometries restrict the 20 range available for measurements. If necessary the crystal can be mounted in more than one orientation during a single exposure. .53. (b) The Guinier parafocusing geometry. an alternative to this measuring method is offered by quantum counter detectors. 4. the effect of the crystal motion will be that of randomizing its orientation as exposure proceeds.Experimental methods in Xray crystallography \ DIFFRACTED J BEAM 1 293 INCIDENT BEAM CRYSTAL MONOCHROMATOR DIFFRACTED BEAM Fig. If after a complete revolution about one of the axes there has not been an integral number of rotations about the other. that is Bragg angle. The final type of camera that we wish to mention here is a modification of the DebyeScherrer camera that can be used to produce a powder pattern when the specimen is a single crystal.
as measured in the plane on which the detector is moving. although gas ionization counters are also used. Fig. in this way of recording the data lies the only weakness of the diffractometer when compared with the diffraction cameras that simultaneously record all the reflections in the accessible 26 range.) . in other words. the sample may also be rotated about an axis which is found in the plane in which the detector moves in those cases in which the preferred orientation of the crystallites in the specimen is a problem. its relative intensity is recorded as a function of 28. When a diffraction line is found by the detector. and which is normally in the vertical position. courtesy of Philips Analytical. For most applications. tracing a circle centred on the specimen. The detector simply moves. the powder diffractometer is simpler than the singlecrystal diffractometers we have described. this limitation is not very severe in the case of polycrystalline materials and is more than counterbalanced by the greater precision offered by these instruments. As we have seen before.54 is a photograph of a powder diffractometer and Fig. only one way of scanning a reflectionby varying the angle 28 that the detector makes with the incident Xray beam. Since the 26 angle and relative intensity of an isotropic diffraction cone can be measured in any plane that passes through the cone apex and bisects a projection of the cone. to increasingly higher values of 26. the measuring strategy is the same as that of the singlecrystal diffractorneter: the relative intensity and 26 angle of each diffraction cone generated by the polycrystalline material are measured one at a time. Each of the peaks in the figure fully describes one of the diffraction cones of the specimen. A.294 1 Hugo L. 4.54. As in the case of the other recording methods described. 4. powder diffractorneter.55 shows a typical output record of a powder diffractometer in which the variable in ordinates is the number of counts measured plotted by the diffractometer as a function of the scattering angle 26. Figure 4. Monaco Powder diffractometers are thus characterized by a counter which is no different from those used for singlecrystal work: it is normally of the scintillation type. Whatever the detector. There is. in a plane that contains the incident Xray beam.
r. if the source is at a distance r from the specimen. As we have seen. the parafocusing effect is produced on a circle of radius r to which the specimen is tangent (in the SeemannBohlin arrangement the specimen is an arc of the circle). The most widely used parafocusing geometry is that found in the instrument called the BraggBrentano powder diffra~tometer. the radius of the goniometer circle. As seen in the figure the triangle SOD is isosceles since two of its sides are the distance r. This equation shows why if R . A characteristic that distinguishels the modern powder diffractometer is the use of a parafocusing arrangement that improves the intensity and resolution of the diffraction maxima. This goal is achieved by moving the flat specimen so that it is tangent to focusing circles of variable radii for different values of 26 but which produce the focusing effect at the constant distance from the specimen R. In which is flat. 4. it is obviously necessary to ensure that the parafocusing effect is also produced at a constant distance from the sample. Notice at higher 2Bvalues the separation of the peaks .[~'] the BraggBrentano diffractometer the specimen.Experimental methods in Xray crystallography counts 1 295 0 20 Fig. is irradiated by a divergent beam and so in a sense this geometry can be considered a modified version of the SeemannBohlin arrangement discussed before.. In practice. into doublets corresponding t o the K. and K lines. the radius of the focusing circle must vary with the scattering angle of the diffracted radiation 26. A normal drawn from 0 to the other side R defines with each of the sides r an angle equal to 6 and we can then write sin 6 = $ Rl r and r = R 12 sin 6. . Diffraction pattern of a polycrystalline material recorded with a diffractometer. Figure 4. the useful interval in which the instrument can be used.56 shows the parafocusing geometry of the BraggBrentano diffractorneter.55. Since in the BraggBrentano diffractometer we have the additional constraint that the detector moves around the sample keeping a constant distance R .. is a constant. the parafocusing geometry of the BraggBrentano diffractometer can be maintained by rotating the sample S in a range spanning from a few degrees to about 160°.
in general. it results. Xrays are made to travel both before reaching the sample and after diffraction through a series of metal plates parallel to the plane where divergence is allowed. which may be an essential requirement in some types of application. the angle 28 made by the detector and the incident Xray beam is slowly incremented by small A28 and the number of counts is measured and recorded. like for example in crystallite size or and strain measurements or if the data are going to be used for Rietveld refinement. Modern powder diffractometers can be used with equal ease in both the continuous and stepscanning modes. In order to ensure that this is truly so and that no important divergence occurs out of that plane. it has been tacitly assumed that divergence of the Xray beam can only take place in the plane of the figures. Although this operation mode requires more time and computer memory. . In the stepscanning mode. These plates are called Soller slits and they are an essential part of the optics of the powder diffractometer. adequate for most standard applications. The first mode of operation is faster and. in a much more accurate diffraction line profile. in the end. This makes it possible to use more than one detector (or a curved positionsensitive detector) to simultaneously record several diffraction maxima. Monaco DETECTOR Fig.296 1 Hugo L. instruments that use the SeemannBohlin parafocusing geometry have also been designed and marketed. Probably the most serious limitation of this geometry is that it excludes the value of 28 = 0" and so the instrument requires calibration using the known 28 position of the maxima of samples used as standards. With this geometry the specimen does not have to be moved since it is assumed to be constantly an arc of the focusing circle but the specimen to detector distance requires adjusting as the scattering angle 28 varies. 4. Although less widespread than the BraggBrentano diffractometers. Parafocusing geometry of the BraggBrentano diffractometer.[889891 Their main advantage stems from the fact that in this arrangement all the reflections focus on a circle of fixed radius.56. In our discussion of the parafocusing geometry.
Thus.57. and also of the compilation of a file containing the diffraction patterns of a number of known crystalline materials sufficiently large to give a reasonable probability that an unknown would be found among the standards present in the This original file has since been expanded to such an extent that in 1986 it included data for more than 44 000 crystalline phases. 4. Figure 4. A C U N ~ ~ positionsensitive detector used for powder diffraction work.[941 The file is currently known as the Powder Diffraction File (PDF) and it is updated and distributed by an international organization called the . in a sense curved positionsensitive detectors are the equivalent of the area detectors used in singlecrystal work adapted for use with polycrystalline materials.) Curved positionsensitive detectors based on the same principles discussed on p. They offer~ advantage of combining the high precision of the ~ ~ ~ ' the diffractometer with the possibility of simultaneously recording the entire diffraction pattern generated by a polycrystalline material. (Photograph courtesy of INEL. These type of detector are curved gas filled chambers with a metal grid in the position of the cathode and either a curved wire or a blade which functions as the anode.Experimental methods in Xray crystallography 1 297 Fig. The simultaneous recording of the entire diffraction pattern offers the possibility of following processes in which the relative intensities of the Bragg peaks varies in time as the experiment proceeds. 282 have also been devised for use in powder diffraction ~ o r k . which may be one of the several in which the material may crystallize. Uses of powder diffraction Probably the best known and most widely used application of powder diffraction is as an analytical tool for both qualitative and quantitative analysis of crystalline materials.57 is a photograph of a curved positionsensitive detector used for powder diffraction work. From our discussion it should be evident that the Bragg spacings dH and relative intensities of the diffraction cones generated by a given polycrystalline material are a function not only of the substance under investigation but also of its crystalline form. Powder diffraction became a widely used technique for the identification of polycrystalline unknowns in the 1930s as a result of both the clear definition of the minimum number of parameters required to preliminarily identify a specimen as a member of a more or less restricted group of substances. in other words they are curved linear detectors.
22 35 2. Trondheim (1969) is stable below 770°C. Figure 4. This task can be accomplished using both manual[951 computer method^[^^. Universitetet i Trondheia.5418 Filter Ni Dia. Alexander and K l ~ g [ have] derived the equation that relates the intensity of a given ~~ . In particular it may not always be possible to unambiguously index the lines present in a pattern and therefore the Miller indices corresponding to a given Bragg spacing may not be available in the file. 2 262330 . Due to absorption effects of these specimens the assumption of a direct proportionality between the intensities measured and the amount of a given crystalline phase present in the sample is not possible. FORM M . Scand. Ibid.298 1 Hugo L. The quantitative analysis of the different crystalline phases present in an unknown is another important application of powder diffraction.55 100 2. Cut off I/I Diffractomter I / I c o r .58. 8 BaFz with A1F3.575 co S... Orthothabic ao  5.53 Ref.P. Not all of the cards contain all of the information shown in the figure. CuKo A 1. formed at 50 1. The information contained in the card should be readily interpretable. nwS mP 'V Color sign  Hovedfagsarbeide for den Matematisk Naturvitenskapelige Embetseksamen. 019 028 134 223 036 119 029 D 4.58 is a reproduction of a card in the PDF. The simultaneous identification of more than one component in a sample is also possible using the method described above but clearly with a degree of difficulty that increases with the complexity of the diffraction pattern generated.G 19.96 20 B&lFS (aphrse) Barium N u m i n m Fluoride hkl I Rad. International Centre for Diffraction Data. Using the information contained in the PDF it is often possible to match the diffraction pattern of an unknown to that of one of the known substances present in the file. 4. Monaco 2558 d 1/1 2559 J 3. (1972) Sy s.C. Ref.156 + a p bo 7.D. Notice that the relative intensities are expressed as percentages of the strongest line which is arbitrarily assigned an intensity equal to 100.^^] with a current tendency in favour of and the latter. Schultz et al. Acto Chea.2 1 Fig.34 30 4. p&der diffraction data file. Joint Committee for Powder Diffraction Standards (JCPDS).64 A Y Z Dx c Ref.S. Re~roductionof a card of the J.
and . the determination of x l requires the addition of an internal standard.Experimental methods in Xray crystallography 1 299 diffraction line due to a component to its weight fraction in the sample for the case of a flat polycrystalline specimen. and pM the mass absorption coefficient of the matrix. In this case eqn (4. pi is not equal to pM but there are only two components in the sample. pi its density. In the first case the mass absorption coefficient of component i is identical to that of the matrix. 241). is not a linear function of x l . Plots of the ratio IHI/fi1 a function of x 1 can then be either calculated using the tabulated values of . KH. For this case it can be shown that1''] . 1 and 2.ul and p2 or determined experimentally from the intensities measured from samples of known composition.uM and there are more than two components. If the sample is a uniform mixture of n components and extinction and microabsorption effects can be neglected. This not very frequent case arises when the specimen is a mixture of different crystalline forms of the same compound. that is of all the other components in the sample with the exclusion of component i. is the intensity of a given diffraction maximum H due to component i. pi is its mass absorption coefficient (defined on p. These curves can then be used to determine x l for an unknown specimen. This equation can be specifically applied to three different cases. as so in this case I. whose identity (and therefore their mass absorption coefficients) is known.is a proportionality constant which depends on the component and the diffraction line. it can be shown thatrg8] where IH. xi is the weight fraction of component i in the sample. In the general case in which pi is not equal to . In the second case. In this case the intensity of line H due to component 1 is If I is the intensity of the same line for the pure component 1 : .48) reduces to that is there is a direct proportionality between the intensity of a line H due to component i and the weight fraction of i in the unknown.
In this case the precision of the measurement depends on the 8 angle of the diffraction maximum used in the determination as can be seen rewriting Bragg7slaw and differentiating 2ddH = A csc 8 cot 8 d 8 whence Therefore for a given precision in the angular measurement 8 the relative error in the measurement of d. It can be shown that where xi and x f are the weight fractions of the i component and the flushing agent./IKS as a function of xi can then be used to determine xi for an unknown. normally corundum (aA1.03). Alternative equations can be derived when the quantitative analysis is done in the presence of a socalled 'flushing which can be any pure crystalline compound added to the specimen. Ii and If their diffracted intensities and the two constants ki and kf their intensities relative to that of a reference substance. that is if its crystallites do not easily adopt a random orientation.[104] . 112) and the experimental conditions selected for the experiment. information about the preferred orientation of the sample constituents can be obtained by studying the entire diffraction ring in two dimensions. If the polycrystalline material has texture.[loo] Another common application of powder diffraction is in the determination of the unit cell parameters of a crystalline phase that can only be. In order to carry out such an analysis. of the ratio IH. A careful analysis of the profiles of the diffraction maxima of a polycrystalline material can give information on the distribution of sizes of the crystallites and on the presence of lattice strains. obtained as microcrystals. experimentally determined. In this case. The final application of powder diffraction that will be mentioned here is the Rietveld method used for the solution of a crystal structure with a limited number of parameter^['^^^^^] and for quantitative phase analysis. the intensity of a ring corresponding to a given diffraction cone will not be homogeneous. Monaco The linear plots. decreases for larger values of 8. it is essential to previously extract the pure diffraction profile from the experimentally determined profiles that are influenced by the instrument used (see p.300 / Hugo L. Many other theoretical methods that try to avoid the use of an internal standard have been proposed and have had a more or less limited amount of success. this equation reduces to where the constant kiis readily available for many substances. If the flushing agent is chosen to be corundum.
P. the other three factors. we will also discuss the problem of radiation damage of the crystals which is usually handled before the other corrections are applied. is that of scaling partial data sets originating from different crystals which when merged will produce the final total set of relative integrated intensities. Depending on the method used to record the reflection intensity and on the position of the reciprocal lattice node. In data reduction the different reflection dependent parameters present in eqn (3. Another problem that is often encountered. Data reduction In Chapter 3 we saw that in the relationship between integrated intensity and the square of the structure factor amplitude there are several factors that vary from reflection to reflection. the intensity of the corresponding reflection will be proportionally higher. the extinction coefficient which was discussed on pp.Experimental methods in Xray crystallography 1 301 We have already seen in Chapter 2 that in the Rietveld method of refinement the entire diffraction profile of a peak is calculated using a starting model for the unit cell content and the model is then refined by comparing point by point the calculated and measured diffraction profiles. cross the sphere of reflection. the times required for different nodes to cross the Ewald sphere are different. polarization. Lorentz. The corrections applied are called. that always have a nonnegligible volume. however. We discuss this problem briefly at the end of the chapter. This method of crystal structure determination has already permitted the solution of structures of moderate complexity and which could not be solved before by the conventional singlecrystal methods because the substances yielded crystals of inadequate size. This. 97 and 164 and will concentrate on L. Here we will neglect E. If a node is in diffracting position for a longer time. We will derive the form of the Lorentz factor in a very simple case and then show the form it takes in a more complicated situation.41) are taken into account by multiplying the relative intensities by suitable correction factors. In addition. The time a node is in diffracting position is dependent on two factors: the position of the node and the velocity with which it sweeps through the sphere of reflection. This factor would not be important if the method used to record the integrated intensities ensured that every reciprocal lattice node were in a diffracting position for exactly the same time. Lorentz correction We have seen that diffraction arises whenever reciprocal lattice nodes. as it would affect every reflection in the same way and in the end it would simply scale all the intensities by the same factor. . as we have seen. especially in the case of macromolecular crystal data sets. In order to calculate the relative structure factor amplitudes to be used in the solution of the crystal structures as described in Chapter 5 one needs first to take these effects into account. The Lorentz correction simply takes this factor into account. is not the case. and absorption corrections respectively. and T. The procedure followed to extract relative structure factor amplitudes from raw integrated intensities is called data reduction.
302 1 Hugo L. Figure 4. 4. This is for example the case of a zerolevel rotation or Weissenberg photograph or of the equatorial reflections measured with a diffractometer. If the axis of rotation makes an angle 90"p with the incident Xray beam . Vn = (wlA)2 sin 8 cos 8.51) which is the simplest possible form that can be taken by the Lorentz factor. 4. and therefore the reciprocal lattice.59. is assumed to be rotated if n at a constant angular velocity o . In a more general case one has to compute Vn according to the geometry 'of the diffraction experiment and then apply the standard equation we have seen. and L = (2 sin 8 cos 8)' = (sin 28)'. Lorentz correction for a crystal rotated about an axis normal to the plane defined by the incident and scattered Xray beams. Substituting Ir*l in terms of Bragg's law Ir*l = l l d = 2 sin BlA. (4. the Lorentz factor can be defined as follows which is indeed proportional to the time during which diffraction takes place for a given reciprocal lattice node. Monaco AXIS Fig. The linear velocity of the point P is and its component along the radius of the Ewald sphere Vn= Ir*l w cos 8 since 8 is the angle formed by the linear velocity V and the radius of the sphere of reflection passing through the point P as shown in Fig. The crystal.59. V is the linear velocity component of the reciprocal lattice node along the radius of the sphere of reflection.59 shows the Ewald sphere for a diffraction experiment in which the crystal is rotated about an axis which is normal to the plane defined by the incident and the diffracted beams.
i. although in practice this variation is less substantial.[lo8] When the original Xray beam.5 depending on the scattering angle. which in this simple case was shown to be equal to where 6 is the Bragg angle of the reflection considered and the diffracting crystal was tacitly assumed to be ideally mosaic. and 28. the monochromated beam.52) where y is the projection on to the zero layer of the angle 28 between the incident and the diffracted beam. the diffracted intensity is affected by a factor. For a data set collected with CuK. the angle of the reflection of the monochromator crystal which was used to select the wavelength. radiation between 508. Notice that in theory this factor can have values ranging between 1. In this situation the projection onto the zero level of 28.e.1081 where 8 is the Bragg angle of the reflection produced by the specimen and 6. The angle p is the angle between the projection of the normal to the reflecting plane on to a plane perpendicular to the incident monochromatized Xrays and the plane of incidence. y. resolution it varies between Pso= 0.51).0 and 0.7470. If the crystal is assumed to be a perfectly mosaic crystal it is equal to . that is when the radiation is produced by a conventional source and monochromatized using an appropriate filter.9995 and P2 = 0. ~ i ~ s odiscusses~ ~ form of the L factor for the different experimenn [ ~ the ~ tal arrangements which are used in data collection and gives tables of the values of L as a function of the parameters which can be selected. The more general form of the polarization correction for an incident beam monochromatized with a crystal is[17. called the polarization factor. Polarization correction The polarization correction depends on the state of polarization of the incident Xray beam and on the scattering angle of the diffracted beam. and the scattered beam all lie in the same plane this angle is equal to 0 and the polarization factor takes the simpler form The exponent n depends on the characteristics of the monochromating crystal. This simple expression for the polarization correction can be applied whenever the incident Xrays are not polarized.52) reduces to eqn (4. is identical to 28 and the expression for L given by eqn (4.Experimental methods in Xray crystallography 1 303 and the point P is not on a zerolevel layer but rather on the nth layer with a diffraction cone with a semiangle equal to 90Yit can be shown that[10s21061 L = (cos p cos Y sin y)l (4. If the rotation axis is normal to the Xray beam and the reflection is on a zerolevel p = 0 and Y = 0. In Chapter 3 we have seen that when a totally nonpolarized beam is diffracted by a crystal.
[112] where the angle p is defined as above and Here EL is the amplitude of the optical field in the plane of incidence of the Xrays and Ek is the component perpendicular to it. R.60 shows that. In this expression for the polarization correction. The second method is by calculating it theoretically on the basis of the characteristics of the source and of the crystal used to monochromatize the radiation. the transmission factor T is related to the absorption of the incident and diffracted Xray beams by the crystal. the linear absorption coefficient. the LP correction. 241 where it was pointed out that according to Beer's law. the form of the polarization correction changes again. with respect to what it would be without absorption by the factor Fig. In eqn (3. as can be seen in the picture for points 0 . in this case. which is valid for every point in the crystal. 4. This can be done in two ways. that we . Equation (4. the constant K2 included 8. the path of the incident and scattered beams i n the crystal depends on the position of the scattering point within the crystal. The path lengths are dependent. as we have seen. For a given scattering angle 29. that is on the reflection considered. The polarization correction is frequently grouped with the Lorentz correction in a single factor. and on the incident and scattering angle. An expression for the polarizaton correction to be used with synchrotron radiation has been derived by Kahn et a1. The intensity of the diffracted Xrays is thus reduced. one is by measuring the polalrization ratio of the beam that will strike the specimen. and T. c' Absorption corrections As pointed out in Chapter 3. the problem is to obtain an accurate value for the parameter which depends on the setup of the facility used. the crystal volume. Real monochromator crystals are usually an intermediate between these two extreme cases and one should ideally examine the monochromator used to decide the appropriate form of the polarization correction that should be used in the specific case.60. this path can be very different for different points in the crystal. on the location of the point scattering the Xrays. absorption reduces the intensity of an Xray beam travelling through a given material by an amount which depends on the material and the length of the path travelled by the radiation in it.55) can be used to calculate a very rough estimate of the optimum crystal size for a given compound of linear absorption coefficient y.304 1 Hugo L. Figure 4. Here x is the total path length and y is. for a given scattered beam. whereas if it is assumed to be an ideal crystal it is equal to 1.41). We have briefly discussed the absorption of Xrays on p. of the crystal.[105"111] If the radiation striking the crystal monochromator is the totally polarized synchrotron radiation. Monaco 2.
can be found in the International tables for xray crystallography. Hence I o a x 3 and I m x 3 e . p. Spheres or cylinders are. however. one simply has to integrate eqn (4. i. the diffracted intensity after absorption and x = 3 / p .e. In order to get T. In any case it is always instructive to calculate the value of p for the crystal being examined in order to get an indication of the severity of the absorption problem. An analytical evaluation of T according to eqn (4.56) would be. Mechanical devices exist that can be used to accomplish this.[l14] . not very good approximations for the shape of most real crystals so that if one wants to assume that the specimen under study is a cylinder or a sphere. is its mass absorption coefficient. the ideal method to use in order to take care of the absorption correction. it is usually necessary to grind it into that shape. for a given wavelength. p can be calculated by the following equation: where gi is the mass fraction of element i present in the unit cell.Experimental methods in Xray crystallography ( 305 will take to be proportional to x3. R being the sphere or cylinder radius and 8 the scattering angle. Since we want to maximize I. No structural knowledge is required.55) over the total crystal volume. Numerical evaluations have been obtained in the case of spheres or cylinders. and p is the crystal density. only the values of the mass absorption coefficients of the elements which. The linear absorption coefficient for the crystal can be calculated from the mass absorption coefficients of the atoms present in the unit cell. one would get a different value of T for every reflection measured. This explains why absorption corrections become more important for heavyelement crystals and for radiation of longer wavelengths.~ . If instead of writing x we decompose the path into p the incident or primary beam path and q the diffracted or secondary beam path the transmission factor T can be written as follows: where the integration is over the entire crystal volume V. Recall that p i is a function of the atomic number of the element and of the wavelength of the radiation used: it is smaller for lower atomic numbers and for shorter wavelengths. they can be found in ~ i p s o n [ " ~ ] where T is given as a function of pR and 8. The problem is that the integral in eqn (4. in theory. From the values of p . the transmission factor for an entire crystal. as we have seen. Sometimes all it takes is a change from copper to molybdenum radiation to sufficiently reduce the absorption problem in a given crystal structure determination. The result would depend on the beam path in the crystal which is a function of the reflection considered.56) cannot be calculated analytically even in the case of the simplest crystal shapes.
there are many cases in which analytical methods cannot be applied. 4. that is the point is in the equatorial plane and on the Ewald sphere. 4. however. In this method. to obtain. it must be mounted inside a capillary and bathed in its mother liquor. In practice what is done is to bring the @ rotation axis to a direction coincident with that of vector r* which requires the choice of a reflection with a x value of 90" (see p. [ " ~ ] Here we will only briefly discuss one of them. In the method of North et al. The experimental absorption correction methods are reviewed by ~ a r t e l s . Such a rotation is called an azimuthal or qscan. 274)..40 for example we have point P in the diffracting position. an accurate description of the crystal shape and size is very difficult. In many cases.. mainly because they are quite easy to implement. Monaco This approach is. The contribution AT can be calculated analytically and it depends on the values of px at each vertex of the tetrahedron and on v=. Then the azimuthal angle I is equivalent to the diffractometer angle @ and a @scan produces a # curve similar to that shown in Fig. Clearly. it is for these situations that empirical absorption correction methods have been proposed. An analytical method that can be used to calculate T for any polyhedral crystal was proposed by de Meulenaer and ~ o m ~ a .61. If the crystal is rotated about the vector r* the point P will still remain in the diffracting position and the variations in intensity observed may be attributed to absorption effects. the calculations are performed by a computer program which requires a precise knowledge of the crystal shape which is input as the equations of the planes defining the faces of the crystal.(@) is the maximum intensity observed as @ is varied over the 360" range. The total transmission factor is then calculated as where AT is the contribution to the transmission factor of each tetrahedron and VT its volume. the transmission factor for a given reflection is given by the mean T(H) = t ( T ( @ i n c ) + T(@reJ) (4.306 1 Hugo L.61. not always possible since there are many crystals that will not survive the very harsh treatment required to shape them into an ideal form. both of which absorb the Xrays differently from the crystal. In Fig. Thus. if not impossible. Furthermore. This~method divides [" ~ an arbitrary crystal volume into smaller polyhedra that are ultimately subdivided into tetrahedra. the transmission factor T at @ and 4. and as seen in Fig. the very widely used method of North et a1. which attempt to measure T experimentally are currently the most widely used. 4.58) . + 180" must be identical since the only difference between these two positions is that the crystal has been flipped over. in this method.[1171 The method is designed to correct intensities measured with the diffractometer and the crystal is therefore assumed to be totally bathed by the incident Xray beam. if one is dealing with a protein crystal. These methods. The relative transmission factor for a given value of @ is then given by T = I(@)IZrnax(@) where I.
00 80. by examining the differences in intensity observed for symmetry equivalent reflections is presented by Takusaga~a[1221 discusses together absorption and radiation damage correcwho tions for data collected with an area detector. The plot can be used to apply an empirical absorption correction as described in the text.00 @ZY Fig. together with other factors.1211 They have the disadvantage that they require several qscans.70)) that should obviously decrease after the absorption correction is applied. much more experimental work to obtain a result that does not always justify it.e. A discussion of the applicability of this assumption can be found in Kopfmann and ~ u b e r . define the orientations of the crystal in which the where Q and .[lZ3] Whatever the absorption correction used. An example of the way in which absorption correction effects can be taken into account.00 240.00 160.61. and in spite of the fact that so many different methods to determine T have been proposed. From the differences between the calculated and measured structure factors it is then possible to calculate correction curves that can be applied to the raw data. the redundancy in the data set can be used to check whether the correction has improved the data or not. for a reflection chosen with a x value close to 90". [ " ~If the transmission curves are measured for symmetry] equivalent reflections this assumption is not necessary. incident and reflected beams for the H reflection coincide with or lie in the same plane as the incident Xray beam.Experimental methods in Xray crystallography 1 307 0.00 I20.[1191 Other methods that calculate transmission curves based on the differences observed in symmetryequivalent reflections have been proposed.00 40. Although.90 0. A final possibility is to take care of the absorption effects after a preliminary structure has been solved using the uncorrected data. absorption still remains one of the .00 ANGLE 200.[120.00 320. Relative transmission factor plotted as a function of the scanning angle @ = y. This is normally done by calculating an R factor (see eqn (4. as we have seen.00 280. 4. An underlying assumption of this method is that the total transmission is the product of the transmission of the primary and the secondary beams. the theory of Xray absorption by crystals is very well established. i.
A combination of these factors is. Radiation damage corrections So far we have tacitly assumed that as data collection proceeds the integrated intensities measured do not change with time. although it is also possible for the rotation and the areadetector methods as well. of course. this is very seldom the case since crystal decomposition triggered by exposure to Xrays is not at all an uncommon occurrence.62. Figure 4. about 20 per cent during an exposure time of less than two days. as a function of data collection time. after exposure.308 ( Hugo L. some integrated intensities will be higher. Unfortunately. Radiation damage is evidenced by monitoring the intensity. if not the most serious. possible. EXPOSURE I HRSI . This type of monitoring is usually done when data are collected with the diffractometer. of a certain number of reflections. or at least that they do not change significantly. on the average. 4. it is known to be substantial in the case of macromolecular crystals. Fig. which can either increase or decrease the intensities. Radiation damage can vary remarkably with the specimen considered. Typical behaviour of the relative intensities of three reflections of a protein crystal monitored with a diffractometer at different times after exposure begins. ideally sampling as large as possible a region of reciprocal space. for example due to free radicals generated by the radiation.[1241 The causes that lead to the changes in intensity as a crystal is exposed to higher and higher Xray doses have been listed by ~ b r a h a r n s . exposure to radiation can increase its mosaicity thereby reducing extinction effects. Another effect is chemical damage. source of error in the experimental determination of relative integrated intensities. [ ' ~ ~the If ] specimen can be considered to be close to an ideal crystal. which explains the difficulties encountered in proposing a satisfactory model for this phenomenon and the scarcity of research papers dealing with this subject. there is in real crystals a loss of short. Monaco most serious. but it is also present in many smallmolecule crystals as a survey conducted in 1971 has shown. More often.62 is a plot of the values measured for three reflections of a protein crystal that decayed.and longrange order that produces instead a decrease in the measured intensities. The result will be that.
not only of the time after data collection started but also of the scattering angle of the reflection 6.[1251 Sometimes. This correction factor is a function. the value of n that best fits the data measured. Sn is the If. and a. of the monitored reflections can be used to correct all the data collected. a correction based on just a few monitored reflections may not be acceptable. one can define Sn as the following function of exposure time: and then determine the constants a. The problem of intensity variations due to radiation damage was perceived quite early on in protein crystallography. R(t. S = sin 6/12.. The first model that attempted to explain them in the case of myoglobin was proposed by Blake and Phillips in 1962. a disordered fraction A2 that scatters predominantly at low values of 6. The variation of the intensities as a function of time is then governed by the equation where D is a disorder parameter. i. the value that should be used to extract the relative structure factor amplitudes. A scheme that attempts to overcome this difficulty has been proposed by 1bers. and the quantities Al(t) and . i. for example by fitting the intensities of each monitored reflection to a polynomial of the form[125] where t is the exposure time and n is a number that ranges from 1 to 7.e.Experimental methods in Xray crystallography 1 309 The radiation damage correction factor. The value of R can be estimated without resorting to any particular model for the radiation damage process.[12'] The model describes the diffraction pattern from the irradiated crystal as due to three different components: an undamaged fraction A.] (see Chapter 5) in scale with the observed amplitude (FoI. scale factor for the nth reflection measured at time t that brings the calculated structure factor amplitude IF. anisotropy can be readily taken into account. If a general trend for the different standard reflections is identified. The discrepancy index is then calculated for each standard reflection as a function of n and used to decide the best form of the polynomial to be used. then the same form of the polynominal can be adopted and a weighted average of the coefficients A.[lZ6] after the structure has been solved. and a totally amorphous fraction A3 that no longer scatters coherently. In the simple case in which the decay is found to be linear. 6). if the best n turns out to be equal to 1. is defined as follows that is it is the inverse of the factor by which the intensity measured at time t has to be multiplied to yield the intensity corrected at time zero.e. by leastsquares refinement along with the other structural parameters (see Chapter 5).
it improves the signaltonoise ratio of the diffracted peaks.. by reducing the thermal diffuse scattering. [ ' ~ ~ ]their model another state. anisotropy is also taken into account. Even a modest decrease to say 4 "C has already important beneficial effects on most crystals but the best results are obtained when working at liquid nitrogen or. and has also tested the validity of the different possible assumptions in the case of myoglobin. A. if radiation damage has made it necessary to stop data collection at a certain stage before the set was completed. with a In dosedependent rate of formation is introduced. His conclusion is that for moderate radiation damage all the rate models work satisfactorily whereas for severe cases none do.D we have already seen that precise electron density determinations of small molecule crystals require that the data be collected at low temperature. will be held strictly constant throughout the data collection process. before these sets can be merged together into a single one it is' necessary to scale them by applying the appropriate relative scale factors. take for example film developing and fixing times. and A. In Appendix 3. Monaco A2(t) can be calculated by making different simplifying assumptions for the rate processes involved. For example data collection on films with the rotation method requires scaling as there is no way to ensure that all the data collection parameters. each measured under more or less different conditions.. In working at low temperature decreases the intensity losses due to thermal vibrations and thereby improves the resolution of the diffraction pattern and. Hendricks~n['~~] proposed a general method has that considers all the possible paths between A.310 1 Hugo L. even better.[131. In order to determine the relative scale factors to be applied to the subsets. Relative scaling of partial data subsets is done on the basis of the reflections which these subsets have in common. or they may also come from the same crystal. The molecules in this state are thought to be only superficially perturbed... A refinement of the Blake and Phillips model has been recently proposed by Sygusch and ~ l l a i r e . 8) as a function of a certain number of parameters that can be determined from the variation of I ( t ) as a function of t for the monitored reflections. it is first necessary to . Relative scaling If the final total data set of relative integrated intensities has not been collected under strictly constant conditions but results from merging a certain number of subsets. The subsets may be derived from different crystals. In addition. The usefulness of all the models proposed is that they furnish a form for the variation of R(t. liquid helium temperatures. A. The parameters so determined can then be used to calculate a correction factor for each reflection present in the data set collected.1321 addition to greatly reducing radiation damage. Although the experimental problems posed in this case are more difficult to solve. that is the background radiation resulting from the correlated atomic displacements in the lattice. An efficient way to minimize radiation damage and therefore to make the application of a correction less significant is by collecting the data at low temperature. low temperature data collection is a well established technique for small molecule crystals['301and shows great promise in macromolecular work as we11.
An alternative way of solving the equations of Hamilton et al. ..e. Ki the relative scale factor to be applied and VH.[1331is currently the most widely used. the ith observation of reflection H. L and then approximates q by the Taylor expansion: In the special simple case in which the weights can be written as the product of a term which depends on the reflection and another which depends on the subset an exact solution for this problem has been found. that of Hamilton et a1. In this method one defines is where IH.the weight of the ith observation of reflection H. Among the different criteria proposed. one of them is arbitrarily set equal to zero. It can be shown that this condition can be stated in the equivalent Now if one defines the relative scale factors are chosen so that the quantity I/J is a minimum and therefore the condition from which the best value for the intensity of reflection H. 94). the best values for these parameters are determined using the iterative nonlinear leastsquares procedure described in Chapter 2 (p. i. that is for each iteration qH. I. approximated by is Given that the AGl(i)s are not independent. .Experimental methods in Xray crystallography 1 311 define the conditions on the data that the scale factors ought to satisfy. [ ' ~ ~their formulation one sets in turn all In ] the derivatives of q with respect to the Gis to zero. is found is and IH is Since in this formulation the residual is not linear in the Gis. 1 is the subset in which the ith reflection is present. and then the other Gls are corrected until convergence is achieved. that is one GI is made constant. 6q/6G1= 0 for 1 = 1 .[1341 is useful It in scaling the different films present in a pack which have in common many . was proposed by Fox and ~ o l m e s .
A Determination of the number of molecules in the unit cell of a crystal One of the first fundamental parameters required in a crystal structure determination is the number of molecules present in the unit cell of the crystal. In both cases the number of molecules present in the unit cell is a function of the crystal density. the molecular weight of the substance under investigation. 538). Another alternative procedure that avoids the use of iterations to determine the scale factors has been proposed by ~ a ewho defines the ~ [ ~ ~ ~ residual (4.61) N (4. If we can assume that the only species present in the crystal is the .!IH. and the unit cell volume. When merging together different subsets of data into a final data set.68) A". is used. = log KIIH.70) where I(H)i is the ith measurement of reflection H... Appendix 4.. (Z(H)) is its mean value and the summation extends over all the reflections measured more than once in the set.312 1 Hugo L.log K. and minimizes the quantity where the subscripts i and j refer to different subsets. In the cases in which R is calculated using independent reflections which ought to have equal intensities for symmetry reasons. A very widely used definition for this parameter in terms of the intensities is that given by eqn (4. If the number of data points is large there is very little difference in the relative scale factors found by this method and the classical solution of Hamilton et al. Smallmolecule crystals do not usually contain important amounts of solvent and/or other substances whereas in macromolecular crystals a substantial fraction of the unit cell volume is occupied by solvent (see Chapter 8. Monaco reflections and differ only in those which are outside the dynamic range of each film.. it is customary to calculate a reliability index for the set that can be defined either in terms of the structure factor amplitudes or of the intensities. the notation R. p.
using (4.Experimental methods in Xray crystallography 1 313 compound under investigation. From this equation we can obtain The mass of the unit cell is where V is the unit cell volume and p.wm.m. and N is Avogadro's number.A.[1371 In a macromolecular crystal (see Chapter 8.).2).2) can be used to calculate a more accurate molecular weight. a precise molecular weight can be used to yield an accurate density for the crystal using the integer closest to the n determined experimentally. Alternatively. the mass of the protein in the unit cell. n. M. s is the mass of salt per unit mass of solvent.[136] If the molecular weight of the compound is known. The density of the crystal is Equation (4.A. Measuring the density of a smallmolecule crystal usually poses no serious problem. 536) there is water which is eliminated when the crystal is dried and water which remains bound to the macromolecule and there is also salt dissolved in the solvent. the molecular weight .1) can also be written where the unit cell volume has to be measured in A3 and the density in g cmP3.2) We will briefly discuss one of them. In the case of protein crystals. the situation is not so simple and there are several alternative equations that are equivalent to (4. the number of molecules in the unit cell. can be easily calculated. is the crystal density. the total mass of the unit cell of the crystal is m = m. then. if the density measurement is very reliable and the molecular weight is not. The mass of the protein in the unit cell is where n is the number of molecules in the unit cell. its mass in the unit cell is where n is the number of molecules in the unit cell. and w is the solvent not accessible to the salt because it is strongly bound to the macromolecule.A. eqn (4. There are several methods available and the measurements can be done with high precision. p. the molecular weight of the substance. . + dm + um. + s(m .A. M. Since n has to be an integer. u is the fraction of liquid which remains in the crystal. where m is the total mass of the unit cell and m. If d is the fractional loss of mass when the crystal is dried.
W. pp. (1985). Bienenstock. 2. Amsterdam. R. B. Scientific American. New York. w. Vol. (1988). U. MacGillavry and G. 157200. and Parrish. pp. J. Birmingham. P. Timasheff). (1984). H. Rieck). M. H. 68793. Grenoble. Oxford University Press. H. H. 4858. 30016. D.s . Science. Tanner and D. C.A. pp. 17.A.. and Sweet. N. Bonse. pp. Roberts. H. 111. Phizackerley. Arndt. W. D. D. (1962).A. Physics Today. (1977).2) but in this case determining the crystal density is a much more serious experimental problern. 1 . Modern xray analysis o n single crystals. Monaco of the protein. Winick. MacGillavry and G. ESRF (1987).s n = 0. and Merritt. and Schulz. New York. Stuhrmann). W. 7281. (1962). A. U. Birmingham. E.3) has been derived by ~ a t t h e w s . Plenum. Ch. G. Berlin. Foundation Phase Report. 1099101. ESRF. G. 36. Vol. Function and Genetics.d . Academic. In Methods in enzymology. B. and S. New York. An alternative to eqn (4. (ed. Thus n=NVp. E. In Characterization of crystal defects by xray methods (ed. Luger.s Mp l + u . Kynock. B. Vol. (ed. W.) (1983). H. s. G. C. Academic. Rieck). pp. In International tables for xray crystallography. MacGillavry and G. the first two parameters are usually not determined. (1980). Euler. W.3) can be used in much the same way as eqn (4. 5972. Bowen). 7788. (1962)..S W ' (4. and MacGillavry. H. H.3) Equation (4. In International tables for xray crystallography. 111. 17. Birmingham. 11819. W. Kynock. Journal of Applied Crystallography. H. Rieck). (1988).. Phillips.s . 1 . Handbook o n synchrotron radiation. Hirs. Koch. (1988).s w Vp. (1980). Margaritondo. North Holland.602 Mp 1 + u . 16. References Rieck. Hendrickson. " Another ~~] approach to determine n for macromolecular crystals is discussed in Chapter 8 (p.314 1 Hugo L. Koch. In Uses of Synchrotron Radiation in Biology (ed. Rieck. Orlando. 298319. In International tables for xray crystallography. s is the quantity most easily measured and d is quite difficult to determine and requires the use of several crystals for better precission. Materlik. K. Vol. W. 231. Proteins : Structure. Wyckoff. A. (1986). H. C. 114. Eisenberger. Kynock. pp. Arndt. P. C. E. Acta Crystallographica A44. P.. (1983). (ed.. A. R. 4. C. W. and N is Avogadro's number. (ed. H. C.[l3'] In addition. Walter de Gruyter. 121. L. 257. and Winick. I11 (ed. 538).A. D. 7388. one needs to know u. W. B. U. Smith. K. Introduction to synchrotron radiation. (1987). In The Rotation Method in . and d .d . (1982). they are instead estimated from the average of known protein crystals.
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more than one set of positional vectors r may correspond to the same set of intensities. we must somehow derive the missing information. . It is noteworthy that. With this notation no ambiguity should arise between. In this chapter we shall analyse the most important methods commonly used to solve the phase problem. where generally lower case letters indicate the general reciprocal vectors as well as the matrix of their components. because from the experimental data only the magnitudes. the scalar product of the reciprocal vectors h by the direct position vector r. the number of which is equal to the number of observed reflections. but not the phases. As already observed in Chapter 3 (p. as in the case of other physical experiments (cf. while the atomic position vectors r are unknown. indicated by hR (the transpose sign is usually omitted). even though the number of relationships greatly exceeds the number of unknowns (there may be up to 100 reflections per atom). The problem must in principle have a solution (even if not necessarily unique). p.Solution and refinement of crystal structures Introduction The goal of a structural analysis is to obtain the distribution of atomic electron density in the unit cell (in practice the atomic positions) starting from the diffraction data. these are called homometric t Throughout this chapter the convention of using capital letters for the I x 3 matrix of the reciprocal lattice indices will not be followed. the intensities only depend on the interatomic vectors. the terms f and h are known quantities. of the structure factors may be obtained. 169) it is not possible to reach this goal in a unique and automatic way. in order to compute the electron density by means of eqn (3. Chapter 1. which may be expressed as? In these relationships. and the product of the indices matrix h by the rotation matrix R of a symmetry operator. for instance. Indeed. Therefore. . in order to conform with the notation generally used in the literature on Patterson and direct methods.1) is not unique. indicated by h r. 17). since the measured intensities are proportional to the squares of the structure factors. which are independent of the arbitrarily chosen reference system. It is theoretically possible that the solution of equations such as (5. Unfortunately these unknowns appear as argument of trigonometric functions and the solution of systems of nonlinear equations can not be obtained in any analytical way.45).
and skill and can only be used with simple structures.83 for centrosymStructural metric structures and 0./. Before considering the different methods employed to define an initial model. then the initial model will be incomplete and the index R will not decrease below 0. 5 if centrosymmetric or 0. in practice the constraint that the solution must obey stereochemical rules makes it extremely unlikely that more than one homometric set is chemically acceptable.['] Nevertheless. From the M positional vectors of the model the structure factors may be computed. the methods based on Only the use of the Patterson function and the socalled direct methods will be considered here. It may also happen that the postulated model contains errors which can not be corrected by the following refinement. constituting the so called initial structural model. it is therefore necessary to establish the criteria which allow us to assess its correctness.25. obtained directly from the intensities. mainly used in solving biological macromolecular structures. if the presence of these molecules in the cell is overlooked. the R value for totally random atomic positions has been statistically evaluated to be 0.320 ( Davide Viterbo sets. ingenuity.] on the same scale of IF:[. The possibility of solving a system of nonlinear equations relies on that of obtaining a first approximate solution. obtained as K = C h JF. In the case of equal atom structures. The most common parameter used to express this agreement is the R index (also called agreement index or residual) where K is a scale factor bringing IF. They are seldom used today and for this reason they will not be treated (for a comprehensive account the reader is referred to Lipson and ~ o c h r a n [ ~ I ) . will indicate a correct model.[21 models yielding values of the R index lower than these extreme values may be considered as plausible initial guesses to start the refinement process. We will consider the behaviour of the R index in some more detail in the paragraph on structure refinement.IF. In general a model with R G 0 . unless the positions of the solvent molecules are taken into account.4 if noncentrosymmetric will be a good starting point."J/C. A quite frequent case is represented by crystals containing one or more solvent molecules. will be dealt with in Chapter 8. the first crystal structures were solved by trial and error methods.59 for noncentrosymmetric structures. while those using isomorphous replacement and anomalous dispersion. . A good agreement between the IFils and the observed moduli IF. Historically."(. This can then be refined until the best agreement with the experimental data is achieved. and therefore it does not converge to the correct solution.150. These methods require a great effort. consisting in a systematic trial of all structural hypotheses compatible with the known physical and chemical properties of the considered crystal.
Their form depends on whether or not the crystal possesses an inversion center (centric distribution or acentric distribution respectively). 2. The derivation of the theoretical probability distributions of structure factor amplitudes is given in Appendix 5. but it will decrease for increasing values of sin 8/A. which will be seen to be useful quantities. For the two cases we have Pi(lF1) = fi exp(JGZ IFI2/2I) (centric). a short digression will be necessary to describe some important results derivable from a statistical analysis of the observed intensities. It also allows us to obtain an estimate both of the scale factor by which one has to multiply the measured data to scale them to their absolute value. especially in connection with the use of direct methods. They are derived[4351 under the hypothesis that the atomic positions are random variables with uniform distribution throughout the unit cell (i. This is a problem in the practical use of distributions (5. we have .5) 2I1 F PI([FI) = exp(I FI2/2) where E and E is a factor (defined in Appendix 5. In order to overcome this problem the unitary structure factors and the normalized structure factors are introduced. will not have a constant value in all the reciprocal space. and of the temperature factor. In the same way by which (IF[') was defined.Solution and refinement of crystal structures Before entering into the discussion of these methods. being a function of the atomic scattering factors.5). 1 321 Statistical analysis of structure factor amplitudes The statistical analysis of the observed structure factor moduli gives very useful indications on the presence or not of those symmetry elements which do not give rise to systematic absences. Finally it is a basic step in the calculation of unitary and normalized structure factors.4) and (5. (5.A. all points in the cell have the same probability of hosting an atom). (acentric).A) depending on the specific symmetry of the weighted reciprocal lattice.4) (5.e.
1 and may be compared with the lEi corresponding experimental values to verify whether the structure is centrosymmetric or not. but in general the values of IFhI:.1. 5. The comparison of the distribution of the observed amplitudes with the theoretical distributions of Fig.322 1 Davide Viterbo and in the case of all equal atoms Z = 1/N. when expressed in terms of normalized structure factors. B is the overall isotropic temperature factor. derive Both U and E are independent of the scattering angle 8 and correspond to idealized point atom structures. From (5. Table 5. with respect to the acentric one.7) we can immediately . we may write (Fhl:bs K t I O F ~ ~ ' exp (2~s') = (5.1 will allow us to establish the presence or not of the inversion centre in the crystal under consideration. Some of .. I°Fhl is the structure amplitude in absolute scale for atoms at rest.10) and acentric (5. Theoretical values of some functions of \El obtained from the centric (5.11) distributions and their comparison with the corresponding experimental values for the AZOS structure Theoretical Centrosymmetric Noncentrosymmetric Experimental for AZOS . showing a maximum corresponding to intermediate values of the intensities. 5. and s = sin OIL.these values are reported in Table 5. Assuming that the thermal motion is isotropic and equal for all the atoms.3)) is the scale factor. The centric and acentric distributions. The two curves are quite different. So far we have implicitly assumed that the observed structure factor moduli are on an absolute scale. obtained from the intensities Ihthrough eqn (3.41)..1.12) where K' (reciprocal of the scale factor used in eqn (5. are on a relative scale. They are represented in the curves of Fig. become Fig. the centric distribution foresees a higher percentage of reflections with extreme intensity (weak and strong reflections). From the distributions it is possible to derive the theoretical mean values of several functions of I El or the theoretical percentage of I El > t. Probability distributions of a normalized structure amplitude for centrosymmetric (centric) and for noncentrosymmetric (acentric) structures. which are completely independent of the structure complexity. 5.1.
The intercept of the line on the vertical axis will give us In K' and its slope the value of 2B. the presence of structural m. assumed in deriving (5.[~~ hereinafter).2 is an example of such Wilson plot for a typical small organic AZOS structure (pcarboxyphenylazoxycyanidedimethyl su~phoxide.14) tells us that a linear relation will exist between In ( ( I F ~ ~ J ~ ) ~ / & (s2) and that a plot of these values obtained from the and ) experimental data can be interpolated by the best straight line passing through them. in fact. The average value of both sides of (5.2.5). Figure 5.Solution and refinement of crystal structures 1 323 Using the results of the statistical analysis of the intensities. exp ( . such that within this range the decrease of the f s with s may be neglected. .2. The main reason for the deviations of the experimental points from the straight line is the breakdown of the condition of equiprobability of all atomic positions. are given in Table 5. 5.12) will be (JFobsJ2)s ' ( I o F J exp~ . Fig.13) from which where (s2) is the mean value of sin2 O/A2 in the considered interval and is computed using the tabulated values of the atomic scattering factors for atoms at rest for s = Dividing the reciprocal lattice into several intervals of s. Wilson plot of AZOS together with the formula of the compound. obtained from 1908 observed reflections. (5.4) and (5. ~ i l s o n [ ~ ] proposed a method to derive the values of K' and B.2 ~ (s2)) (5.2 ~ =K ~) ( (s2)) = K' C.14). Let us consider a set of observed intensities falling within a restricted range of s. the numerical values of the terms appearing in eqn (5.
2.60 A2 and K' = 2.2 73.72.0327 0. the Patterson function is always centrosymmetric even when p(r) is not. i.1309 0.e.2946 0. According to (3.2619 0. This is in agreement with the deductions of p.1964 0.00000.5298 0.8209 2.2.6986 1.7 507.0655 0.22920.7922 0.7 ( I F I ~ ) . 5.1964 0.2879 0.06550.0982 0.13090.9 1322. 0.8044 0.I 1.5310 0. obtained by leastsquare fitting.4529 0.0277 0.2619 0.1378 1 2 3 4 5 6 7 8 9 10 82 124 156 182 210 231 248 269 272 134 regularities. The normalized structure factors can then be calculated by means of the relation \ K' exp (2Bs2)s Of? The last column in Table 5. Since IFh/ lFphl.4 392.2 420.A.2177 0.16) We have shown (see (3.2451 1.1619 0 1267 .26190. Numerical values of the different terms in eqn (5. U)dr* = 1 V IF.2292 0.05. 0 1 179 .3110 (lF21).2292 0.9 410. such as the phenyl hexagon in AZOS. / ~ .5 821.3 Xs 2199. has a slope of 9.9 1020.1637 0.0663 2.0273 0. (s2) 0. which confirm the presence of an inversion centre.1309 0.29460.14) employed to obtain the Wilson plot of AZOS shown in Fig./a).3 646.1637 0.324 1 Davide Viterbo Table 5.2 Interval ~imitss' 0.0 52. 182) the Patterson function was defined as the selfconvolution of the electron density p(r). In [(IFI):/~.)^ exp (2nih h ' u).8 450.8 234. is in contrast with this assumption.3274 0.A (p.03270. From these values we can derive that B = 4. we may write = 1 P(u) = V cos 2nh u h and then P(u) = P(u).4 146.1.2946 0.0655 0. 3736. The broken line in Fig.4166 0. The Patterson function and its use In Appendix 3. .2 292.0982 0.~ [ l ~ ( r * ) l ~IF(r * )I exp (2nir* = ] v* .09820.39)) that the Fourier transform of P(u) is IF(r*)I2 l~ (in symbols I ~ ( r * )= T[P(u)]) and vice versa P(u) = ~ .6329 0.0 46.A.5 562. 5.8 1359.20 and an intercept of 0.8756 .1 gives the experimental values of several statistical indicators based on the IEl values of AZOS (space group P2.3274 Reflect[on no.19640.38) we have P(u) = p(r) * p(r) = j p(r)p(r + u) d r V (5.16370.9 791.
and in 5. The Patterson function will have the same periodicity as the electron density and therefore the size of the unit cell will be identical. This higher density of peaks becomes a more serious problem for real structures with nonpointlike atoms.3). This condition is verified only when the vector u coincides with an interatomic vector (in Fig. 5.16) then becomes a summation over the n points. 5.16). Let us.3(d) the case of a vector u coinciding with two parallel interatomic vectors of equal length is illustrated.3(a) u coincides with the vector 24). 5.Solution and refinement of crystal structures 1 325 176 concerning the centrosymmetric nature of all functions with real Fourier transform.4(a) a set of N = 5 points is represented.)p(r. Since 1 ~ ~ 1 depend on the interatomic vectors [cf. and In order to derive P(u). for simplicity. all the atoms of the original structure p(r.) are shifted by a fixed vector u to obtain the corresponding p(r. In the first case the value of P(u) will be proportional to the product of the weights of the two superposed atoms. while for a general u (Fig. it will be P ( u .3 a higher weight has been given to atom 1 (heavier atom) and in 5.~)) ) both being single Patterson peaks. P(u) = 2 x ( 6 6)=72. we will then have: P(u2. with reference to Fig.4(c) the same set of vectors. while the remaining N(N . 5. for instance. 5. In Fig. given N atoms in the cell they will give rise to N' peaks in P(u). multiplied by the multiplicity of the same vector. Let us. after they have been translated to a common origin. This can be verified starting from the definition (5. in the second P(u) = 0.1) are distributed over the cell. where in 5. 5. .4)= 6 x 6 = 36.1)] we ' may expect that also P(u) will contain information on these quantities.4(b) the corresponding distribution of interatomic vectors. 5. two terms will contribute to the summation in (5.~) and it is said to have a multiplicity of two. + . suppose we have an idealized structure made up of n point atoms with an associated weight equal to their atomic number (Fig. N of which will superpose on a single peak at the origin (they correspond to the N zero distances of each atom with itself). In fact the Patterson peaks are wider than the maxima in an electron density map. while in 5. The integral in (5.3) coincides with an atom of the original structure. suppose that atom 1 is a sulphur and the others are carbons. as each corresponds to only one interatomic vector. + u).3(d). are shown.3(b)) all point of the translated image fall into regions where p(r) is zero. P ( q 4 ) = 6 x 16 = 96 and. the height of each peak will be proportional to the product of the atomic numbers of the atoms connected by the vector u. Finally in 5. that is when a point in the translated structure (broken lines in Fig. the last corresponds to the distribution of peaks in the Patterson function. This concept can be further clarified by considering Fig. ~ From what we have seen so far it follows that the Patterson function will have maxima corresponding to all possible interatomic vectors within the unit cell. + u) #O.4. the products will be nonzero only when p(r. eqn (5. As illustrated in the onedimensional example of Fig. ~> P(uZ. u) are performed and finally all these contributions are summed. the number of peaks in the Patterson function is much greater than that in p(r).18) and P(u) becomes twice as large as P(u'.3(c) the case of a vector u coinciding with the distance 14 is represented. On the other hand. then the products p(r.
5. It is also possible to eliminate the origin peak.4.17) will be . consisting in computing the Patterson function with coefficients IEhI2 or better IFhEh(. For these reasons the Patterson map of a structure.The (l$EhI coefficients are more convenient. Fig. because of the nonzero width of the peaks in p ( x ) . (c) Patterson function obtained by translating all vectors in (b) to a common origin.1)). 3. in which each atom has a weight equal to its atomic number: (a) two images separated by a vector coinciding with the interatomic vector between atoms 2 and 4 of equal weight. 5. To overcome this problem it is convenient to employ a sharpening procedure.3. (b) two images separated by a vector not coinciding with any interatomic vector. because oversharpening is sensitive to the series truncation errors (cf. Schemes for the construction of the Patterson function of a pointatom structure. 5.e. the Patterson peaks will have a width twice as large. may appear as an almost featureless distribution of vector density.5. 7.16) and may produce spurious peaks or a downscaling of correct peaks in the map. (d) two images separated by a vector coinciding with the two parallel interatomic vectors of equal length between atoms 4. (c) two images separated by a vector coinciding with the interatomic vector between atoms 1 and 4 of different weight. (a) Scheme of a molecule formed by five point atoms. (c) Fig. 8 and 6.In fact the normalized structure factors correspond to a pointatom structure with no decrease of the atomic scattering factor with increasing sin 8/A. which may obscure some short vectors. the coefficient in the series (5. by subtracting from the coefficients the terms corresponding to the interaction of each atom with itself (i. (b) corresponding representation of all possible interatomic vectors. with even a moderate number of atoms. the first term in the righthand side of (5.326 1 Davide Viterbo Fig.
these will correspond to multiple peaks. significantly higher than that of the other lighter atoms. The following considerations apply: 1.5.e. 5. of the 230 space groups. . The structure contains a limited number of heavy atoms (i. of course. The molecular geometry is such that it will give rise to several interatomic vectors with almost the same length and direction (e. systems with condensed aromatic rings).g. Before illustrating the methods for interpreting the Patterson function. the 1 ~ ~ must sbe in an absolute scale. giving rise to three types of peaks:  Vectors Height ZpZp very high Z ~ intermediate Z ~ ZIZIvery low heavy atomheavy atom heavy atomlight atom light atomlight atom 2. the symmetry elements in the crystal will be translated in the Patterson function so that they will all pass through the origin and at the same time they will lose their translational components. we can infer that the map will have prominent maxima when: 1. From the previous considerations about the height of the Patterson peaks. By applying these rules it can be seen that.Solution and refinement of crystal structures 1 327 where. with an atomic number Z. Illustration of the widening of a Patterson maximum with respect to the electron density maxima contributing to it. let us first analyse how the symmetry of the crystal is reflected into the vector map.6 shows 1~ the comparison between a normal and a sharpened Patterson section. Since all vectors are translated to a common origin. only 24 have a symmetry compatible with Fig. ZI). Figure 5.
with equivalent positions: x. u.O. 5. 4 . . The presence or lack of Harker lines or sections may also give valuable indications on the space group symmetry when this is not uniquely defined. y. . 0 . the term F i computed by relation (5. . . in fact. u. . c b glide I to a c .O. 0. 4 4. 0.2) with the contribution of the M heavy atoms in the unit cell. axis 11 to a. for instance.O. P2. Pna2..3. Z. Harker lines and sections relative to the most common symmetry elements Fig.22). as illustrated in Fig. 0 i v. w u. 4. . 2 axis 1) to a. v.O. 0. with one or two constant components. for instance. The peaks due to the vectors between these atoms will dominate the map and it is therefore usually quite an easy task to derive the positions of the heavy atoms. p i ) Primitive monoclinic (P2. . 0. 0. u. c 2.y 4. 0.7. z and 2. w u. 2.7.0.b. b . 2. . In fact + In the space group P2. . . The heavy atom method The procedures for the interpretation of the Patterson function are greatly simplified when the structure contains a limited number of heavy atoms. y. . c glide 1 to a.v. c mmirrorI. we have: Crystal space group Triclinic (PI.2y. between equivalent atoms related by symmetry elements other than the inversion centre. The symmetry operators present in the crystal leave a trace in the Patterson function. the space group P2. 22). Then. Pbca . . the resultant of the contributions of the two heavy atoms is quite close t o F. u. w . the equivalent positions x. . $. 4. v. 0) and (0.2.c a glide I to b. called ~ a r k e r [lines and sections. b.w v. 4) respectively. w .. will have vectors between equivalent atoms located on a Harker section with coordinates (2x. 4. These are produced by vectors. w . The Harker lines and sections corresponding to some of the most common symmetry elements are listed in Table 5. y. w . In a similar way it can be seen that the space groups Pm and PC give rise to Harker lines with coordinates (O.. Thus. and f.) and six light atoms contribute t o the structure factor F. P2. . consisting of particular clusterings of vector maxima ~] on specific lines or planes of the map. v. 0.2.. 0 ./c) Centred monoclinic (C2. Thus. generally represents the predominant contribution to the structure factor.O. . v.toa. One may then assume that the phase @iof lFtl is a good approximation of the true phase of Fh and compute an electron density map using as Table 5.328 1 Davide Viterbo the Patterson function. 4.3. . . if the atoms have a sufficiently high atomic number. the information about their coordinates represents a good initial model. Z give rise to maxima on the Harker section at (2x. Argand diagram i n which t w o heavy atoms (with atomic scattering factors f. 5. . . u. Cc.2y. C2/c) Primitive orthorhombic (P2. b. $. .) Patterson group pi P2/m C2/m Pmmm 2.
1.20) will be 0. Br. as described in Chapter 2. As we have seen. but in general it is necessary to operate in more than one cycle by the socalled method of Fourier synthesis recycling. Supposing that the data measured for the three derivatives are equally good.H3. Let as now consider some examples. . From its position one may easily derive the x and z coordinates of the heavy atom. where X is a halogen considered as a heavy atom. the chlorine compound will be difficult to solve.20) become less than 1. but one has also to consider that their contribution to the diffracted amplitudes may became so dominant that the observed data will be almost unaffected by the contribution of the remaining light atoms. 5618 for X = C1. Each cycle requires the calculation of the structure factors from the coordinates of the known atoms.21. Space group PI. Space group P2. the y coordinate may be arbitrarily assigned in order to fix the origin along the twofold screw axis. 2450. In order to find the positions of the heavy atoms it is necessary to locate them with respect to the symmetry elements and to the conventional origin of the unit cell. (twofold screw axis parallel to b). then. while with iodine it will be very easy to solve the structure but its accuracy will be further reduced. contribute) with the corresponding calculated phases $ The map will not only reveal the heavy atoms but also other atoms of the structure. From the previous considerations one may get the impression that it would be advantageous to have compounds containing atoms of high atomic number.I . I respectively and the ratios (5. has component u = 2x. 2. v = 2y. If the initial model is correct. each cycle will reveal new atoms until the structure is completed. but during the refinement a more robust way of fixing the origin should be used. 2. The definition of the final structure will then be rather inaccurate. In the most favourable cases the structure may be completed from the first electron density map.Solution and refinement of crystal structures 1 329 coefficients the observed amplitudes (to which all atoms in the structure will . As an example let us consider a hypothetical organic compound of formula C3.90. assuming for the moment that the asymmetric unit only contains one heavy atom. 22. the vector between equivalent heavy atoms gives rise to a peak on the Harker section at 2x. = 578. their phases will then be used to compute a new electron density map. but at the same time the accuracy of the refined positions of the light atoms will increase.07 respectively. 0.04X. supposing that there are two molecules in the cell. C 2: = 2708 and C 2. once it has been localized on the map it will immediately give the heavy atom coordinates with respect to the origin chosen on the inversion centre. w = 22. p. The vector between equivalent atoms related by the inversion centre. with bromine the solution should be quite easy with still a reasonable accuracy of the final structure.0. 107. i. but the refined structure will be quite accurate. then the interpretation of the Patterson function and the process of completing the structure become more and more difficult.? Let us t This is correct in the process of finding a starting model formed by a heavy atom. It has been demonstrated empirically that the best ratio between heavy and light atoms is that for which As the values of the ratio (5.
Space group P2Jc.4 .1249. The final coordinates of the sulphur in the refined structure are: x = 0.21100.2y.20) is 0. 2y. v = 2y = 0. 22. This may become easier when atomic groups of known stereochemistry or one or more atoms of intermediate atomic number (from Na to Cl) are present. computed with the signs derived from the contribution of the S atoms only.097 A from the original position).8(b)). =a 3.22 = 26. C 9 H s ~ 2 0 4 ~ [ s 1 The heavy atom is the sulphur and the value of the ratio (5. w = 4 . In Fig. showing both the true structure and its mirror image (enantiomorph). In Fig.8(a) the highest peak is at u = 2x = 62.8(b) there is a large peak centred at v = 4 . The highermelting isomer of methyl(pheny1sulphonyl)furoxan[81 crystallizes in this common noncentrosymmetric space group. which are related by an inversion centre (this is true for any makes it more obvious).20). Space group P212121. 5. Finally the inversion centre will produce a vector between equivalent heavy atoms of components 2x. the electron density map. 2.115. 5.384.2/100 and therefore y = 0. The structure value of y. The coordinates of the S atom found in this way are confirmed by the presence of a fairly large peak at position u = 2x = 0.124. This very common space group will be illustrated by means of the structure of the lowermelting isomer of methyl(phenylsulphonyl)furoxan. w = 22 = 0.22 (Fig. z and R. a. It may be quite difficult to unravel one image from the other. 4. 4 .91100 and then: x = 0. 2 = 0. 5. z = 0. The general equivalent positions are: The twofold screw axis gives rise to a Harker section of type %.230. a sufficient number of light atoms. all belonging to the same image.330 1 Davide Viterbo assume y = i. y = 0. 4. we $.8(a)).37. but the choice y factors computed with the contribution of the heavy atoms only will then be real quantities and the map obtained with the corresponding phases will be centrosymmetric.i (Fig. Despite the low value of the ratio (5. should be localized in order to break down the centrosymmetric nature of the subsequent Fourier syntheses.2y = 25. allowed the localization of all the other nonhydrogen atoms.245.189. . will then have two equivalent heavy atoms at positions x. 5.1143 (shifted by only 0. while the glide plane generates a Harker line at 0.2880.
8. v . Methyl(phenylsulphonyl)furoxan LMI: (a) Harker section u. 5. $.Solution and refinement of crystal structures 1 331 Fig. (b) Harker line 0. . i. w.
2x = 38. v = 2y = 0/100 (in agreement with the first section) and then x = 0. The largest peak at 50 and 6. 22. . giving y = 0. 4.2y.2x. 5. is not the highest peak but the fourth highest. Methyl~phenylsulphonyl)furoxan M I : H (a) Harker section v. i. the second and third peaks are . In the first the highest peak is positioned at v = $ . b. 4 . w.9(a. f . v.81100 and w = 4 . 2x.033.22 = 43.6 is in common with the first section. because of the special value of y = 0. w. (b)Harker section u. 5.059 and y = 0. In the second the highest peak is at u = .332 ( Davide Viterbo 24 L 28 1 I I 2133 $ 1 I I I I I J ' (b) Fig.2/100. confirming the coordinates derived from the first two sections.2y = 501100.2/100.9. w = 22 = 6.22 (Fig.61100. c)). 4 .0. (c) Harker section u. The general equivalent positions are The three mutually perpendicular twofold screw axes give rise to three Harker sections of the type 4.0 and 2 = 0. 4. In the third section the peak at u = 2x = 11. 2y. :.
(co). y = 0. The values of the function are on an arbitrary scale and can be scaled to their . (Continued) probably due to an accidental superposition of several vectors connecting lighter atoms.0589. z = 0. Let us now consider the case of a compound with more than one heavy atom.Solution and refinement of crystal structures 1 333 23 27 I I I I I I 1 (d Fig.0094. 5..[~~ in crystallizing the space group p i with Z = 2.).(Noc~H~)(Nc~H. In Table 5.0343 (shifted by 0. computed with the phases due to the contribution of the S atoms only.4 the coordinates of the highest peaks in the Patterson map are listed in decreasing order of height.0162 A from the original position). revealed the whole molecule (excluding hydrogens) and the coordinates of the S in the final refined structure are x = 0. such as the complex F~. Also in this case the Fourier map.9.
180 0.405 0.450 .645 0..List of the highest Patterson peaks of the complex Fe.070 0. In fact in this way we wouldn't be sure that the other three Fe atoms are referred to the same origin as the first.300. v 2 = 1.290 0. 2y.(CO)11(NOC2H.380 0.420 0.000 0.Fe(1) the coordinates of Fe(1) are simply obtained by dividing its components by two. Fe coordmates obtained from this interpretation Peak Origin 1 2 3 4 5 6 7 8 9 10 11 12 13 u v 0 0. For instance.Fe(2) and Fe(1) Fe(2) in the Patterson.400 0. we may therefore assume that maxima 10.1 10 0.810 0.645 will give x2 = 0.490 0. the height of a single FeFe peak is Z. 12.570 0.275 0. 11. In our case it will be the last position. 13 to obtain the coordinates of the other Fe atoms. also taking into account the periodic nature of the Patterson function.Fe(2) and Fe(1) Fe(2) respectively. z2 = 0.)(NC2H5) and their interpretation in terms of vectors between Fe atoms.080 0. = 676 in absolute scale and about 30 in the relative scale. If we choose peak 10 as Fe(1) .820 0.822.260 0.710 0.4.360 0.380. in fact u2 = 1.700 0.075 0.1 10 0. Indeed in the space group PI there are eight different positions of the inversion centre where the origin may be chosen.690. Peak 3 and peak 5 may then be interpreted as Fe(1) . In order to resolve this ambiguity the peaks corresponding to vectors between nonequivalent Fe atoms should be used.245 0.430 0.334 ( Davide Viterbo absolute value by multiplying by the ratio C j Z?/P(O 0 0) = 82401364 = 22.470 0.135 H 364 144 138 120 72 65 65 63 59 55 38 33 30 27 Interpretation 0 0.195 0. y2 = 0.6.0 along the three axes to obtain the values listed in the bottom + + Table 5. w2 = 1. we must consider the eight combinations: giving for Fe(2) the coordinates referred to the eight possible origins: Only one of these positions will account for the vectors Fe(1) .760 0. The vectors between equivalent atoms linked by an inversion centre have components 2x.480 0.285 0.485 0.650. and 13 are of this type. Once this has been done.560 0.420 0.300 0. 22 and correspond to single peaks.400 0. 12. for peak 11. after these Fe(2) coordinates have been translated by 1.165 w 0 0. we are not allowed to simply divide by two the components of peaks 11.020 0.455 0.
Two pictorial examples of how positivity restricts the possible values of the phases are described in the Appendix 5. p(r) 3 0 (positivity). while the second wiIl be negative or zero and therefore physically unacceptable. in the form of inequalities. while a more formal explanation will be given later. 36575) is done by means of two reliability indices (or figures of merit): an Rfactor based on E values (RE) and R(Patt) which measures the agreement between the observed and predicted (from the atomic numbers) Patterson values. the first mathematical relationships capable of giving phase information were obtained.C. They are the so called vector and superposition methods which are described in some detail in Appendix 5. 1 335 Advanced Patterson methods Procedures for the automatic determination of positions of heavy atoms from the Patterson function.~1~161 procedure The implemented within the SHELXS86 computer program[lOlwill be briefly described.Solution and refinement of crystal structures part of Table 5. which may be applied also in the absence of heavy atoms. i. in the case of Xray diffraction. Several possible solutions are given and the selection of the 'best' solution to be further processed (by the methods described on pp. Because of their limited practical interest.[191 1953 Hauptman and Karle['O1 established the basic concepts In and the probabilistic foundations of direct methods. first with all signs correct and then with all signs reversed: the first map will be everywhere positive or zero. With a similar procedure we may deduce the coordinates of the remaining two Fe atoms listed in the table. by Harker and as per['^] in 1948 and then further developed by Karle and ~ a u p t m a n [ ' ~ l and by other authors. two important properties of the electron density function should be considered: (1) it is everywhere positive. The relation between positivity and phase values may be simply understood by just imagining the computation of p(r) of a centrosymmetric structure as a Fourier series. Direct methods Introduction With the term direct methods are indicated those methods which try to derive the structure factor phases directly from the observed amplitudes through mathematical relationships. Historically. it is possible to relate these two quantities. they will not be treated here and the reader is referred to more specialized textbooks. the great power of these methods in solving complex crystal structures had its highest recogni . In general the phase and the amplitude of a wave are independent quantities and in order to understand how. (2) it is composed of discrete atoms (atomicity). We finally mention that there are other methods for interpreting the Patterson function.B.e.4. The list of the highest peaks in the Patterson map is analysed in terms of Harker and cross peaks. have been developed both for small molecule^[^^^^] and for biological macromolecules.
because of the convolution theorem. 5.10. we obtain . (5. The Fourier transform of p2(r) is ( l / V ) G h and. was able to derive a Also in 1953 ~ayre. Hauptman and the physicist J.24) by F. the convolution integral (3.A..21) We can also define the structure factor corresponding to p2(r) N Gh = gh j=1 exp ( 2 n i h q ) (5. Since Fh is a discrete function defined only at the nodes of the reciprocal lattice. .23) becomes Oh Fh = y c FkFhk.21) and (5.336 ( Davide Viterbo Fig.22) we also have F = (fhlgh)Gh = OhGh. k which is Sayre's equation. We have seen that the Fourier transform of p ( r ) is ( 1 I V ) f i and for the case of all equal atoms N Fh =fh j=1 exp ( 2 n i h q ) . He considered that for a structure formed by well resolved and almost equal atoms.34) becomes a summation From the ratio of (5.22) where gh is the scattering factor of the 'squared' atom. tion in the Nobel Prize for Chemistry conferred in 1985 on the mathematician H. the two functions p ( r ) and p2(r) are quite similar and show maxima at the same positions. h and (5. 5. it will correspond to the convolution product ( l / V ) F h * ( l / V ) F h . Comparison between p ( x ) and p 2 ( x ) for a onedimensional structure with equal and well resolved atoms. A onedimensional example is illustrated in Fig.['~] very important relation. using the atomicity condition. Multiplying both sides of (5. valid for both centrosymmetric and noncentrosymmetric structures.10. Karle.
has proved to be the most important approach for the practical use of direct methods. Structure invariants and semiinvariants As already mentioned.C. On the whole.[203221 The most general s.Solution and refinement of crystal structures 1 337 For large values of IFhJthe lefthand side will be large.26) and (5. The structure factor of index h. which is zero because of condition (5. = 2nh ro.26) which for centrosymmetric structures becomes where S(h) stands for the sign of reflection h and the symbol = stays for 'probably equal'. if IFkl and IFhkl also have large values.i. will be N FA = x fi '. 4 1 the modulus remains unchanged while the phase changes by Aq. The variation of the phase of the product (5.29). due to the same origin shift. the use of probability techniques to obtain relationships between phases and magnitudes. We will therefore describe in more detail these methods and the procedures employed for their practical applications. It is therefore likely that the largest terms in the sum on the right will also be real and positive. . We note that (5. These last quantities are independent of the chosen reference system. Relations (5. it will be @hk= 9)h+ 9)k+ 9)hkzO (5.i.2nh ro].28). exp (2nih (5 . is represented by the product when Let us show that its value does not change when the origin is moved by a general vector ro. the goal of direct methods is that of obtaining the phases directly from the observed amplitudes. Since their value depends only on the structure.).27) coincides with the indication obtained in Appendix 5. and positive. referred to the new origin. will be . they are called structure invariants (s. From the observed amplitudes we can only obtain informations on single phases or linear combinations of phases which are independent of the choice of origin (the other features of the reference system being already defined by the choice of the space group). while in general the phases depend on it. real.rO)) . It follows that.27) are expressed in a probabilistic form and indicate the necessity of applying probability methods to estimate their reliability. = Fh exp {2nih rO) = 1 exp [i(qh .
A basic property of a S. + Vhkl called quartet . Alternatively.S.i. its importance has been recognized in recent years. its phase is j=1 N always zero. Because of (3. g.32) + q is independent of any choice of origin. 5.O. however. The permissible origins are on the eight inversion centres present in the cell.31) we can derive that the phase of g . with phase qh + qk+ called triplet invariant. H . Considering that the practical use of these relations is still under discussion. etc.32) may be written as (5. i.Fhkl with phase g. 4 ..C. and T will depend on it. . since is a s. which does not contain any phase information.17).Q ) ~ + Q ~ is a s. For instance in P?. in a given space group possessing the symmetry operator C = (R. ~ ~ ] are single phases or linear combinations of phases which are invariant with respect to a shift of origin. sextet. Fig. relation (5.S. 5.0). The origin is conveniently chosen on the inversion centres and then T = (0. by adding one or more pairs of symmetryequivalent phases. For instance. can now be related to a S. any one of them. chosen as origin.. while (p. will always give T = (O. 3. Structure semiinvariants ( S ..338 1 Davide Viterbo The simplest structure invariants are: 1.37). F h R h= IFhI2. FhFkF. . changes by Ag..i.FkFh. Fooo= C Zigiving the number of electrons in the unit cell. by applying (5. if it is possible to find a reflection h such that V = T H . It is easy to see that Ag..0. = 2n2h ro when the origin is shifted of a vector ro.h hR = 0. provided that the position of the origin is restricted to those points in the cell which possess the same point symmetry (the socalled 'permissible origins').h + qk+ g. With a simple extension it is possible to define quintet. 0).is its capability of being transformed into a s.S. = 0 (or 2nm) when the components of ro are 0 or 1 as happens for the eight inversion centres in (cf.e.S. S . invariants. F. The qualitative example relative to the sign of F.i. we shall see that these invariants play a primary role in the procedures which will be described later. is a S. .33) holds and therefore the value of y H will not change if we move the origin within those points which maintain the vectors T unchanged (identical point symmetry). invariant. the dependence is such that (5. ) [ ~ ~ . the phase qHis a S. we will just mention here that complex probabilistic formulae have been derived to allow the estimation of these higher invariants. T). 2. described in Appendix 5..
s. because is a s. and Ch = 0 mod (2. In general we may write C h = 0 mod o. exp [2ni(h .Solution and refinement of crystal structures As another example.k) .18).i.. with integer components.0.k have similar sip B I A values and therefore the variation of the atomic scattering factors with the indices can be overlooked. exp [2nik q. where o.C.. Thus. in PI if C h = 2H (i. if the three components of the sum vector are all even). . then q = Q)2h. 5.k) . one can refer to special tables (see. for any value of k. which is a s. the vector C h is called the semjinvariant vector. 2L).s.I2. Fig.S. in P2.2) (meaning that each of the three components of the vector Ch gives a zero rest when divided by 2).0. f. In (5. 0.] x i3 fi.21 . (q.. The two examples given above refer to single phases and are therefore onephase semiinvariants. When the origin is chosen on a twofold screw axis.[23] Before considering probability methods. called semiinvariant modulus. .1)) IFh. The same process may be carried out automatically on a computer following an algebraic approach.q. In order to identify which phases or combinations of phases are s.. let us consider.exp {2ni[(h .] For simplicity let us assume that reflections h. (5. A compact way to indicate these two conditions is: Ch = 0 mod(2. for example.e.] x i2 fj. let us use the positivity property of the electron density function to obtain an indication on the value of triplet invariants.21. ~ i a c o v a z z o [ ~in ]which the ~ ) space groups are classified in such a way that those belonging to the same class have the same permissible origins.ql)l>. while the second must be zero). q. is a vector.0. the combination C $h is a S.nk. the phase q2h. ilh which is proportional to (cf.2. The development of the product FhFkFhk gives FhFkFhk = 1 339 z il fjl exp [2nih . and h . The permissible origins are located on any of the fqur screw axes present in the unit cell (cf.s. k. We can generalize what we have seen so far to the case of the linear combinations of more phases.2) (with the same meaning as before for the first and third components.36) we can separate the terms: 2) I I 2 fifj. it is a s. in space group P2. if C h = (2H.
but being a sum of positive and negative quantities. It is also important to point out that the use of normalized structure factors.D. ' is ~ ] ~ given by (cf. it will on average be small. when IFh/.9) the terms (2).37). which is proportional to IF..k) = + .)^ . . here we will just consider the main results. This deduction is in agreement with (5.27).2 f. Recalling equation (5. which are the Fourier transform of the electron density around each atom. . In Appendix 5. which shows that the value of the triplet does not depend on the diffraction angle. The last term R is the only complex term.D the probability formulae for triplet invariants are derived. If the electron density is positive. 3212.q. derived from Sayre's equation. and (4) are proportional to lFh12 (lF12)) IFkI2 ( 1 ~ 1 ~and )) .)]} = R.37) In the case of a centrosymmetric structure this relation implies that. S(h)Sfk)S(h .( 1 ~ )respectively and for large values of I 1 ~ ) F they will be large and positive. For a noncentrosymmetric structure the distribution associated to (5. i + [k . (q. from now on we will use the normalized structure factors. where the scattering power is higher.A. corresponding to a pointatom structure. C ~ R i + (5. R may be considered as a 'noise' term. Probability methods For the same reasons considered on pp.340 1 Davide Viterbo which is proportional to IFk12 i f. implicitly corresponds to a sharpening of the atomicity assumption for the electron density. both the positive terms and the noise term R are larger.17)) where: (1) for equal atoms Ghk = ( 2 / @ ) IEhEkEhkl. and that they decrease by comparable amounts as the diffraction angle increases. then the product of the three signs of the structure factors. IFk[. will also be positive and the summation in (1) will then be positive. (5. The use of normalized amplitudes is also suggested by (5.26). the atomic scattering factors.C. and with the pictorial derivation given in Appendix 5. derived by ~ o c h r a n . (3). and IFhkl are large. For large values of the structure amplitudes we can then write FhFkFhk= fj + K { J F ~ +' IF^^^+ IFhk12 ~ ( I F I ~ ) } 3 0 .. Indeed we may note that at low sin 8/A.
with j = 1.39). given by (5.e.11 for different values of Ghk. 5. r. then the total probability distribution for qh is given by the product of the r distributions of the form (5. for .38) different values of the parameter G.. as it is shown in Fig. The exponent of (5. being the atomic number of the jth atom.11. all defining the same phase qh through triplet relations such as (5.38).40).41) may be developed as where ah= [ iG. qh= qk+ qh. i. where A is a normalization factor.38) L is j=1 a normalization term depending on Ghk only.Solution and refinement of crystal structures 1 341 Fig. .]I . i. its trend is Mises distribution[251 very similar to that of a Gaussian. . 2. which are assumed to be independent of one another. All curves have a maximum at Qhk= 0. The variance of the relation will therefore decrease as Ghkincreases. 5. cos oj ( j=1 TI1" . . qhpk1 known (with associated amplitudes I Ekjl and I Eh. N (5. P(Qhk) is a socalled von and Ghk is its concentration parameter.39b) with on= C 27. In (5. and their width around the most probable value narrows as Ghk increases. are If more than one pair of phases qkj. 2.e.). . Trends of the probability distributions (5. (2) for nonequal atoms Ghk= 2 0 ~ 0 2 ~ ' ~ IEhEkEhkl.
[271 we shall see later.+ qh+.) = Ph f 50". we obtain 0 t 2 0 4 8 12 Gora Fig.48). then the absolute value of the tanh argument may become rather large and P f approaches the extreme values 1 or 0. cos LC)~ r plane. while for a..D) P = 4 + $ tanh[(~. With a procedure similar to that described in Appendix 5. sin Ph = H Fig. In the case of centrosymmetric structures the probability that the sign relationship (5.42) to (5.of . when several terms. ( q h ) = Ph It 19". sin m.. (5.12. which are statistically the most effective in determining the value of the given s. Not only it has been possible to improve the estimate of triplets.i.44) become immediately clear. given "appropriate" sets of normalized structure factor moduli. 5.27) is true.46) the product of the different probabilities P(Eh) (given by (5. all with the same sign. 1 6 Figure 5. contribute to the summation. but also to derive reliable estimates of other phase relationships. In the past 1015 years probability methods have seen new important developments. Finally eqn (5. i. For instance we may deduce that for ah= 2. and mi = qk. the angle between each vector and the real axis is an indication of a probable value of qh. this formula plays an important as role in the phase determination process. ' When several relations for the same S(h) exist (5. ' .14 shows the trend of (5. o. Trend of the standard deviation. 5. Equation (5. At the basis of the new approaches stands the following principle: 'It is possible to obtain a good estimate of s. it can be seen that AH = a. (9.19)) should be considered.D. both s. of the combination of five triplets of type (5. = Ghk.44) are easily understood when the r relationships of type (5.45) as a function of n. (5.s.12 the case with r = 5 is illustrated.40) are plotted on an Argand diagram as vectors of modulus Gi and phase mi.41) becomes which still is a von Mises distribution with a maximum for qh= Ph and a variance[261 depending on ah as shown in Fig.13. sin c+) '=I (C G. = 10.42). and relations (5. r OH = ahcos Ph = 2 G.i.a. Vector representation.44) gives the most probable value of qh and is known as the tangent formula.s. is given byCz8] (Appendix 5. in the complex C G. the distribution (5. or s. Equations (5. 5.43). defined by (5. and s. 5. cos j=1 I 1 with G. or s.40) involving the same reflection h.D.~"IEhEkEhkl)]..43). it can be seen that.342 1 Davide Viterbo and tan ph = t (iG.13.s. In Fig.
. (Ell. we will have TI 0 and G = 0 Then.50) could be considered = ql as the sum of two triplets.[331 concept the +  +  +  . Cochran's formula[24]for triplets. then Q n (since cos Q = 1.(. JEk+ll. The first task will then be to identify these moduli. in fact it may be seen as P(@hk I IEhl.I. and that Q also depends on JE. \E. derived by ~ i m e r s k a . ~ 7 . these are called negative quartets). Given their set {JEl). derived in Appendix 5. when the cross magnitudes have very small values. then the indication Q = 0 is strengthened. .~~] (quartets): Q = Q7h + Q7k + TI + Q7hkP (5.D. 5. indicated as the phasing magnitudes.s.qh+.14. and confirmed Schenk's empirical findings.+.I is large. and + qh+&.49) where @ is any phase relationship we want to estimate and the vertical bar after it stands for: 'given all magnitudes in {\El)'.i.51) Because of the 1/N factor any reasonably sized structure will have very small B values. with a variance depending on ~~] = (2/N) IEhEkElEh+k+lI .If the last three moduli are also large. such as TI = ~ 7 . and rank them according to their effectiveness in estimating s.the second task will be to derive the probability distribution P(@ I {IEI)) (5. In a similar way we can see that the same quartet can be written as the sum of two other pairs of triplets. given the seven basis and cross magnitudes. [indicates that Q = 0. Later ~auptrnan[~'] derived the probability distribution of Q. We can then say that the quartet not only depends on the four basis magnitudes IEhI. (5. is a trivial example of such conditional distribution. He then formulated the neighbourhood principle. Empirically it was also found that. ~.I and IEk+.+. IE. given the four associated magnitudes. IEkl.51). IEh+lI. Schenk pointed out that quartet (5. Trend of P+ = $ + f tanh ( x ) (cf.Solution and refinement of crystal structures 1 343 Fig. or s.I.I. and for this reason quartets estimated in this way can not be used in practice.50) Their distribution. (5. IEhkl). and therefore Q = TI T.+. 0 with a strengthened reliability with respect to that indicated by (5. if also I Eh+. ~ c h e n k [ ~extended this principle to the case of fourphase s.i. but also on the three cross magnitudes (Eh+.48)) as a function of x.
344 1 Davide Viterbo of neighbourhoods being very close to that of phasing magnitudes. = (R. the second has h2 even and phase 0. then the quartet is equivalent to Q [Q' . T. then T = fn/2. which is a function only of the symmetry operators. i ) . This definition will be clarified through some examples. in contrast with the indication T 0 given by (5. The general use of the spacegroup symmetry in estimating triplets has been described by ~ i a c o v a z z o . The importance of taking the spacegroup symmetry into account is first illustrated by the case of a special triplet in the space group P2.]. 4. R. R2 = (7.12) will give a null vector. i ) . The symmetry operators in P212121 are: R. a significant advantage is obtained by considering also Q'.Q = 2n(h + k)T.50). if.). which leaves some special reflections unchanged ( H = HR. differing from by a constant angle. even. as it gives precise general rules for identifying the phasing magnitudes.g.i.in the most common space groups. forming the first representation of the triplet. n .i.O). ~ a t e r [ ~ ~ he also gave rules for deriving the neighbourhoods of the main s. at the same time.+rland IEkRS+. The first representation of a s. besides the identity. a completely general use of the spacegroup symmetry. = (0. T. n . 5.) and if one of the cross reflection (e.39a) should be replaced by l / m P .38) when the three normalized amplitudes are large. R.i. On the other hand.. T. I . [ ~ ' ~ also showed that for nonprimitive cells the l l f i who factor in (5. 1. allowing. is odd and k.i. Since the larger the number of phasing magnitudes the better the estimate of the s. h + k) is of this special type. all the others being zero).. T. The set of all basis and cross magnitudes which appear in the first representation forms the first shell of phasing magnitudes (first phasing shell).: if the first reflection has kl even and I .2. T and T'.I. As we have seen. this case the first representation is formed by Q and In Q ' and the first phasing shell contains nine magnitudes. = (1. = (T. i .0.0). = I. and the third has consequently phase f n/2. . 1). = (0. but with two new cross terms IEhR.2. and when no special symmetry conditions exist. and a triplet equivalent to T may be written as  because 1. have the same G but opposite phase and their combination in a phase diagram (similar to that of Fig. Q in general depends on seven magnitudes. is the number of atoms in the primitive cell. there is an other symmetry operator C. Let us now consider the example of a quartet such as (5. 1) (only the diagonal elements are indicated. the first representation is formed just by Q and the seven magnitudes form the first phasing shell. which does not contradict the expected restricted value T = f n / 2 . where N. = (1. and of some S. is formed by the invariant itself plus all symmetry equivalent s.0. 4). odd and restricted phase 0. T3 = (4.S. 4. The representation theory proposed by Giacovazzo[35~361a generalizais tion and a systematization of the previous ideas.
the estimate of q. ?). If M vectors H are selected (80100 reflections with largest IEHI). The probability that EZhis positive was derived by Cochran and ~ o o l f s o nand ~ ~ [ ~ is given by which is greater than 4 when (EhI> 1 and approaches 1 as IEZhJ and lEhl increase.i.. for which R.32).34). The collection of all s. q .211 and {IEh.I). and an equivalent quartet may be set up with two new cross terms. Let us now consider a few examples regarding onephase s. IEh+kl. Its second representation is defined as the set of all special quintets of type where H is any reciprocal lattice vector for which IEHI is large.21 is given by the set of triplets (5. 1). As an example of second representation of a s.Solution and refinement of crystal structures 1 345 A numerical example will further clarify the above ideas. Let us now consider a general nphase s. Ci and Cj forms the first representation of @ and the first phasing shell will contain all the associated basis and cross magnitudes. but the quintet will depend on four basis magnitudes JE. then the second representation will be formed by M quintets and the second phasing shell will contain 10 x M magnitudes. = ( I . in P?.s. in the space group P2. let us consider the quartet Q = q 1 5 3 + 4)&1 + (PzI2 + Q)ji6 (C~OSS: 365. h r indicates a reflection equivalent to h.S. . (EHl and on six cross terms IEh*Hl. 1.0. In general (the few exceptions are beyond our scope) it is possible to find a phase qHand two symmetry operators Ci and Cj such that is a structure invariant./c.s.55) reduces to (5. the first representation of the s.s.i.l() with j assuming all possible values of the index k within the set of measured reflections. Since the term added to T is null. 643) 504. the S. ?. obtained by varying H . ?. gives at the same time the value of @. IEkl.s. IEk+nl. = I. may be represented by the triplet (5. R.j. Since q1 differs from @ by a constant term depending only on the symmetry operators.I.35) and the probability formula will be a function of all the magnitudes in the first phasing shell: IE2h.rt and the probability formula will be of the tanh type. In P2. let us consider the case of a triplet T.0. which alone will form its first representation with the corresponding phasing shell including the two magnitudes lEzhl and IEhl. Similarly in the space group P2. for which (5. onephase s. IEh+kfHI. q2. then C = T. R3 = (I. q2h. are special reflections with phase restricted to 0 or . R4= (1. we . As we have seen. The first cross reflection is such that (504)R4= (504).
.s. In space group P212121let us consider the s. such as (5. The term (l)k=exp(nk) corresponds to the constant angle nk and is obtained by applying (3.312 IE2h.o. +. With an extension similar to that used to derive (5.58) and.S.i.S. @ = q4O6) for which the first representation (5.by the first (3) triplets by the second representation (PI0 (4) quartets by the first r e p r e s e n t a t i ~ n . from the observed magnitudes. lEql and the four cross terms IEH+. in noncentrosymmetric space groups. which will not be reported. For this reason all probability formulae.= < Formulae (5. and S.e. . for each quintet.I)) k (5.38).O. Once the phasing magnitudes have been identified it becomes possible to derive the appropriate probability distribution (5. 0.[3w11 (2) twophase S. IEhRfql. by the second representation. Fixing the origin and the enantiomorph In the previous sections we have seen how it is possible to derive the values of s.s. The second representation of a S.I for each triplet (5.0. So far formulae have been derived for estimating: (1) onephase s. then P+(E2h. and s.I. the same will apply to s.I2 . and they were known as the C formulae[201.21\ C (l)*(IEhk. only define the cosine (i. since all the phases change their sign in going from one form to the other. then P+(E2h.35). the concentration parameter G or the tanh argument are now substituted by more complex functions of the considered phasing magnitudes. [ ~ ~ . will also be illustrated by means of an example.48).s. with variable k index.346 1 Davide Viterbo then have P+(EZh. in fact.. In order to pass from these values to those of the individual phases it will be necessary to fix the origin.57) where the sum is over all values of k. When all major express the phase relation between qhkl terms in the sum have k even. 0. and. the second representation is defined as the set of quintets with q varying over all reflections with IE.U)= 1 + tanh : ( :030.I large. 21) = > when they have k odd. Only their practical use will be illustrated in the following sections.i. The second phasing shell will include IEHI = IE4.21) .55) reduces to the set of triplets +.49). it will be necessary to choose between the two enantiomorphic forms compatible with the observed amplitudes. the derived probability distributions for noncentrosymmetric structures have the form of a von Mises function as (5.21) $ and S(2h.o.53).56) and (5.38) and for centrosymmetric structures the tanh form of (5.57) and those for some other space groups were derived long before the concept of representation was introduced.S.37) to and qgki in (5.21)$ and S(2h. ~ ~ I In most cases.I. a term IEhI = IE2.
60) will change and Ah. 5. Z3 = 1 and C 2. The choice of the space group with the corresponding set of symmetry operators already imposes some restrictions on the points where the origin may be localized.i. ql = 0".7. Indeed. The phase determination process can then be summarized as shown in the flowdiagram of Fig. .In order to obtain all phases referred to one form it will be necessary to fix the enantiomorph. (b) values of the phase ra. Xo h2 .q). We will then have to choose the origin among the permissible ones and this may be performed by fixing the value of a limited number of suitable phases. In order to show how this is possible.60) When the origin is shifted so that Xo varies from zero to the identity period a.16(c) the variation of q2 with X. 4 4 68 Fig. and only the phase qh will depend on X. will follow these changes. = 6). only the sites with the same point symmetry will be suitable and represent the socalled permissible origins. while all phases will change their sign ( q + 360 .26 170 292 2i6 374 3b8t40 I 85 131 177 (c) 29 9 223 3 k 5 it I 92 . 5.Xo). will be / Estimate i s . (5. = 3. and S. sin 2nh(x. and s. 8 . 5. = 0". then the origin is uniquely defined by fixing q.16. for different origin positions.l5. 5.. referred to an origin at Xo.S. Flow diagram of the phase determination process by direct methods.16(a)) formed by three atoms of different atomic numbers ( 2 . Figure 5. is also shown: it can be seen that q2goes to zero at two points. The unitary structure factor for this structure. while at Xo = 0. 4 5 ' I Us 0 . (a) Onedimensional structure made of three nonequal atoms. 3 (i/6) j=1 Z.s!s I I I I I O r i g i n (and e n a n t i o m o r p h ) definition Fig. the trigonometric terms in (5. A change of enantiomorph is achieved by inverting the direction of the x axis. 5 . Z 2 = 2. Xo = 0.Solution and refinement of crystal structures 1 347 the absolute value) of the s.16(b) illustrates this variation in the case h = 1: we can see that at Xo = 0. q1= 109". . . The modulus JUhl does not depend on the position of the origin. and therefore Uh.15. In Fig. Bh. let us first consider a onedimensional structure (Fig. (c) corresponding values of the phase p. Since there is only one value of Xo for which q1= 0°. again 1 Uhl will not change.
any three noncoplanar vectors will define a primitive cell if HI Hz A H3= V* = a* b* A c* = volume of the reciprocal cell.348 1 Davide Viterbo and Xo = 0. nH2.. i.. Fixing q. Position of the eight distinct inversion centres in a P I unit cell. m. (OlO). in which any point of the unit cell is a permissible origin and therefore no semiinvariants which are not at the same time invariants exist. they will lie on the intersection lines between the two sets of planes.17). ?Z The three vectors will then form a primitive cell if A= (1 1: :I h2 k2 1 = f l . for + . by fixing qh= 0°. 2 (5. 5. the origin is restricted to h possible positions. It can then be seen that the enantiomorph can be chosen by restricting the value of q. We will first consider the space group PI. It should finally be observed that at X o = 0. = 0" we will restrict the possible origins to lie on planes parallel to the crystallographic planes of indices HI. (or in general of another phase q h ) within the interval 0n (or. but only restricts its possible position to two points. numbered as i n Table 5.... we can uniquely fix the origin along the x axis by fixing the phase of the (100) reflection and thus restricting the possible origins to lie on planes parallel to (100). in general. In the space group PI the permissible origins lie on the eight distinct inversion centres in the unit cell (Fig. In analogy with the onedimensional case. 5. Finally. Similarly the origin may be fixed in the other two directions by fixing the phases q. .61) and developing the mixed product we can easily obtain . The number of such points within the unit cell is given by the value of A and only when the primitivity condition (5.63) Fig. When the origin is shifted.17. corresponding t o the positions of the permissible origins. = 0°. and a change of enantiomorph will give q2= 45".63) is obeyed. the possible origins will be at the same time restricted to lie on planes parallel to the planes Hz. at a distance a12 from each other. the three phases will fix the origin in a unique way. Using (5. = O" does not define the origin uniquely... crystallographic planes. Let us now generalize to three dimensions the procedure just described to fix the origin in one dimension. .76. The three reflections (loo). n2n).e. but in a triclinic lattice there are infinite ways in which a primitive cell may be chosen. By fixing q. Indeed. and q.5. = O" (with H # mH.. and (001) define a primitive cell in the reciprocal lattice. n positive or negative integers) the origin will be further restricted to be at the intersection points of the above lines with the planes parallel to the H.7 (position for which q1= 0") q2= 315". If we also fix q. by fixing q. as in our case.
n. 0) or (0. for instance.17 Origin Parity 1 349 instance.s. we restrict the possible origins to lie on four points (in Table 5. The choice of the twofold screw ) axis corresponds to that of one of the four inversion centers on the projection along y . then it can be fixed by fixing the phase of a reflection with an appropriate parity. y. e. when the origin is placed at the different inversion centers in the P1 cell of Fig. If along a given direction the origin is restricted on points separated by 4. but it must also be different from ugu (for which both origins 1 and 3 have a + sign). O). Similar procedures may be devised for the other space groups. (Fig. the permissible origins are all the points on the four 21 axes at (0. .y.O. The above rules given for PI are also valid for all primitive centrosymmetric space groups with symmetry not higher than orthorhombic. O n the other hand..5 these are the origins 1. y. a phase quo. in space group P2.0. The phases q. the phase cpH of the reflection H = (hkl) will change by nh. i). 4. (0. When the origin can be shifted in a continuous way along an axis. with the b axis parallel to the twofold screw axis.18). (4. ugg. are S. and a n value if the origin is on the other two screw axes.18. 5. 0). for instance. ($. e. In order to fix uniquely the origin.Solution and refinement of crystal structures Table 5. from (O. 5.S. with reference to Table 5. by imposing that its sign must be . i). 0). 3. will have. If we consider a reflection of different parity.5. y. k. a zero value if the origin is chosen at (0. Projection along the y axis of a P2. y. Sign variations for the reflections divided into parity groups. by fixing the sign to be + . 5. or 1 (cf. ggu. 7). in fact the combination ggu ugg ugu = ggg is a s. y. the projection reflections h01 have restricted phases 0. We will. 0" the = + + + Fig. In order to further reduce the ambiguity we will have to fix the sign of a reflection of different parity (not ggg).5).. Its parity should not only be different from that of the two already chosen. the possible origins are restricted to points 1 and 3. 5. 0) to (i. and indeed the (gOg) crystallographic planes pass through all permissible origins. it is possible to fix it by using a reflection the phase of which only takes unique values within the corresponding unit period. By fixing quo. Table 5.g. Reflections of type ggg are structure semiinvariants and may not be used to distinguish among the possible origins. cell with the twofold screw axis parallel t o b. we will have to fix the sign of a third different reflection.. Any change of origin among the eight permissible ones will have an effect on the sign of a reflection H which will depend on the parity of the three components h.g. choose uug.5. this is equivalent to saying that the sign of the reflection will change or not depending on whether h is odd (u for ungerade in German) or even (g for gerade). Thus.
Let us for instance.. (hol). i). Therefore. = n / 2 we fix the enantiomorph. axes. within the interval 0n. and (hkO). will depend on the value chosen for q....350 1 Davide Viterbo origins are restricted on the first two 2. is even or odd (cf. S n and.. and qZl3 form a triplet invariant with qjil By restricting 0 S vji1 G n also 0 G Q.is fixed to be zero.2. with value restricted to f n/2. we have always used three phases to fix the origin. By choosing q. + Vu. A second phase of type qgoU (or q~. In the examples considered so far.) will assume a zero value at (0. we will have to fix a phase of type q. and guu reflections are systematically absent and the origin is fixed by fixing the phases or the signs of two reflections belonging to the other four parity groups. are S. n or k n / 2 depending on whether the index following the zero. Suppose that the origin has been fixed using reflections of type: uOg (with phase 0.. in this space group.S. Going from one enantiomorph form to the other will change the sign of all individual phases and. n ) .S. in a cyclic way. Unfortunately the most probable value of Q. In the centred space groups some of the permissible origins are related by translational symmetry and are indistinguishable. in a Ccentred lattice all ugg. or S. the sign of all linear combinations of phases. Since all linear combinations of phases for which the sum of the indices is ggg. 0) and a n value at (0. Suppose that the two have been assigned zero value to fix the origin. n ) and Ouu ( f n/2). In = " order to fix uniquely the origin along the y axis. at the same time. in which the permissible origins are located at the eight points midway between the three orthogonal. if its value is sufficiently far from the extreme values zero or n. y..this choice will fix the enantiomorph. nonintersecting 21 axes. and this is true for all primitive space groups up to the orthorhombic system. It is therefore possible to apply the rules derived for the space group PI: the origin may be fixed by fixing the phases of three zone reflections belonging to three linearly independent parity groups (not ggg). the choice of one of the two values allows an unambiguous choice of the enantiomorph. Let us finally consider the very common space group P2.2.o = fn / 2 is a twophase s...S. . For this reason the number of phases needed to fix the origin is reduced...i. The origin may be fixed in a simple way by using reflections belonging to the three principal zones (Okl). gug. as. For instance Vuo. Chapter 3 . as a consequence. y. for instance.2. as will be shown by the following example. and by fixing qgoU0 the origins are restricted to lie on the first screw axis. then the sign of the s. These reflections have phases restricted to two values: 0. consider the space group P21. ugu. This problem does not arise in the space group P2. is zero and in this space group it may be difficult to properly fix the enantiomorph by restricting the phase of one reflection. guO (0. pp. is reduced the number of allowed parity groups. it is possible to set up S. they phases q.. the most general way of fixing the enantiomorph will be that of restricting a suitable s.s. 1578). because the (hll) planes intersect the y axis only once within the period b.2..s. Thus. if quo.
or S. which unfortunately are not easy to obtain. In general this third reflection will not be in the considered independent portion of reciprocal lattice. If all the indices are reconducted within the same independent portion of the reciprocal lattice. and it can be expressed as fHR.Solution and refinement of crystal structures 1 351 For a complete and general theoretical treatment of the procedures for fixing the origin and the enantiomorph in all space groups. Chapter 3. if also the JEl value of reflection h f kR. In some cases a more detailed statistical analysis is carried out in order to reveal the presence of pseudotranslational symmetry (cf.541 examples of the use of this information will be given later. Setting up phase relationships We will focus our attention on triplets. being similar. the set of all relationships obtained in this way is often called the C P listing. For each reflection h all pairs of reflections k and Rk with large IEl must be found. The triplet search must take into account the reciprocal lattice symmetry and the relations between the phases of equivalent reflections. In general the availability of a certain number of experimental tripletphase values.E). would be of great help in solving a structure by direct methods.['^. the values of the normalized structure factors are first calculated. and at the same time the absolute configuration (see later). each reflection h will have to be combined with all vectors fkRi. is large then the triplet is retained.The minimum IEI value is chosen in such a way that the number of reflections employed is approximately equal to ten times the number of atoms in the asymmetric unit and usually lies between 1. Appendix 5. The phase relationship will then become . by multiple diffraction experiments (cf. obtained by varying R. Phase determination procedures We will first describe some of the steps which are common to all direct methods practical procedures. p. Since the most important relations are those estimated with the highest reliability. is represented by the experimental measurement of some triplet phases with value close to fn/2.S.2 and 1.6. we will only set up triplets relating reflections with large JEl.15). such as the existence of pseudotranslational symmetry or the coordinates of a previously located fragment. 3234 and using equation (5.[53.^^] A very effective way of defining the enantiomorph. Normalization By the method described on p. 191). over all rotation matrices of the space group not related by an inversion centre.. the reader is addressed to more specialized textbook^.i. Most computer programs will supply a list of reflections sorted in decreasing order of JEl and perform a statistical analysis of the normalized amplitudes as shown earlier. the procedures for setting up other s.[4s521 Some of the most recent programs allow one to introduce the available a priori information.
64) reduces to + and in (5. the accuracy of which will increase with increasing G. a . but it can be estimated a priori by . A 9 = 2n(kTi HT. the poor determination of some phases by few lowreliability relationships.43) is a measure of the reliability with which a phase cph may be determined combining several phase relations. Given the phases in the starting set. with the sign indicated by (5. Since at the beginning the phases are where Qz.46) or the corresponding value from the second representation. n.66). the weak links in the chain. as defined by (5..q h p k l Z . Two methods are used to define the values of the extra unknown phases necessary to start up the process. Definition of an optimum starting set of phases From (5. all other phases are determined one after the other in a chain process.64) or (5.[s71 We have seen that a. = ( q h ). while G represents the tanh argument in (5. nk. not known.12 is rotated by an angle Ph = ( G h ) in such a way that it falls on the real axis. i. as much as possible.qkl.65) the signs are of no use. ~ unknown starting phases are directly assigned permuted numerical values. An optimal starting set of phases can be defined by means of the convergence procedure. For centrosymmetric structures (5. The choice of the reflections in the starting set is therefore very important and the best starting set will be that allowing one to eliminate. in general they will not be sufficient to start up the phase determination process. represent the sequential numbers of the corresponding reflections in the sorted list. It is necessary to start with a larger number of phases.352 1 Davide Viterbo Most computer programs store triplet relations in the form where n h . given the two phases or signs in the righthand side we can derive an estimate of the lefthand side phase.) and G is either defined by (5.can not be computed. it is more suitable for centrosymmetric structures as we shall see later through an example. it can be seen that Qhk1.S. Even if these are chosen among the reflections involved in large numbers of triplets. Fig. With the symbolic addition[ss2261 method these phases are assigned a symbolic value and all other phases are determined as combinations of these symbols.39) or it is the parameter obtained by means of the second representation. for this reason it is more widely used and will be described in more detail. This method is easier to automate and can more readily incorporate some of the most recent developments in direct methods. With the m ~ l t i s o l u t i o n [ ~ ~ ~ ~ ~the method. 5. 5. If the vector representing ahin Fig. (usually fewer than five) is available.64). We have seen that the origin may be fixed by assigning an arbitrary value to up to three phases. and the problem is not overcome even when a limited number of reliably estimated onephase S.19 is obtained.e.
it may be seen that the ratio tends asymptotically to 1. all phase relationships contributing to it are eliminated and the (a. ( G ) . cos 9) d6. Fig. 5. or another reflection already included in the starting set. using the G values only. 5. the reflection which is less related to the remaining reflections is eliminated.67) with its expected value.19. The estimated value (cu. ) = 6 2 " 1 and it can be computed for each reflection. I .Solution and refinement of crystal structures 1 353 I Fig. at the same time.of the modified Bessel functions of first and zero order. The convergence process is a step process in which.20 illustrates the trend of (5. as a function of G. defined as Il(Gj) .) is (temporarily) eliminated. Trend of the ratio.12 rotated by an angle Ph = (v. Figure 5.68) as a function of G . the process must converge towards the group of reflections which are most strongly interrelated and are therefore the most effective in starting the phase determination process. substituting each cos Qj in (5.) is then given by (COS .S.Dl(Gj) (5. ..) values of the other reflections involved in these relations are updated. exp (G. provided it is not an accepted onephase S. When a reflection is eliminated.0 as G increases.. Since.) in order t o bring the vector ah on t o the real axis.20. at each step. 5.68) cos 6. ( G ) / I . the reflection with minimum (a. before any phase information has been obtained. =Io(G. at each step.) where Io(x) and Il(x) are modified Bessel functions of zero and first order. These functions and their ratio are readily available[581and Fig.
is reduced to zero (or to a very low value).21 illustrates the convergence procedure. By putting this reflection into the starting set. t Fig. the reflection is not removed but kept in the starting set as an originfixing reflection. a reflection is eliminated with an (a.21. The flow diagram of Fig.). if not. each time adding a new reflection into the starting set. w i t h smallest <d> Yes t + [ defined without /canorigin\ be \this reflect ion?/ N7 data.) . update all c ds f o r origin d e f i n i t i o n . 5.69) a weight depending on (ct. . 5. The convergence process is repeated several times. on the other hand it is an essential link between these last reflections and those previously eliminated. we assign a value to its phase and in this way we insert the missing link (or replace the weak link) in the chain process.) and (a. If.[591 Calculate <a)for all reflections A  Find reflect~on.which. in the final steps. not already i n t h e startina set . the remaining ones are analysed to check if it is still possible to fix the origin. Flow diagram of the convergence procedure. than this reflection is not (or is only poorly) connected with the remaining few reflections. ref Iections A reflections t o Yes r / reflection w i t h small~st c d > at t i m e of elimination I goes into starting set.. until the desired number of startingset reflections has been reached...354 1 Davide Viterbo Before eliminating a reflection. The procedure may be further improved by assigning to each contributor to the summation in (5. at the elimination moment.
NTREST. R. In practice it has been found that often for the correct set of phases A > A . This function differs from the will correspond to a minimum previous foms because it is not a selfconsistency figure among the determined reflections only.71) it should be minimum for the correct set of phases. NQUEST: these four functions have the same functional form: . SS2FOM. the phases of which have been determined. called figures of merit (fom). Since [Ell= 0. It is defined as for a correct structure A should be close to the theoretically estimated A. which allow an a priori estimate of the goodness of each phase set. The inner summation at the numerator corresponds to Sayre's equation (5. fom: this is a measure of how much triplets deviate from their expected statistical behavior and is defined as ~ c = e lo0(z h  (ah)~)be. MABS (absolute fom) represents a measure of the internal consistency of the employed triplet relationships in estimating the phases.Solution and refinement of crystal structures 1 355 Figures of merit As we shall see.SSlFOM. the phase determination process usually leads to more than one solution.3 indicate a promising phase set. tpo fom: this is defined as where the outer summations are over a certain number (50150) of reflections with lowest lEll value. Given several sets of phases it would be rather time consuming to compute and interpret all the corresponding electron density maps to see which yield the correct structure. and MABS values between 0. The tripletgenerating routine will have to set up also the relationships ( q Otriplets) linking each of these 1 reflections with pairs of reflections k and 1 .0. Several functions have been proposed[60]and we will analyse those most commonly used.24) (written here in terms of normalized structure factors) relative to each reflection 1. vo 4.k with large (El. but it establishes the coherence of the obtained phases with some weak reflections not used for their determination. It is instead easier to compute some appropriate functions. the large terms in the summation must tend to cancel each other out and the correct set of phases value. and MABS = 1. (5.9 and 1.
are mainly of two types ..43) and P(a. but the expected values of other appropriate functions of a.0. as shown in (5.0...72).s. are finally combined to give CPHASE = TI + T2+ T3+ T4 Bl+BZ+B3+B4' A better understanding of the statistical meaning of the MABS. and r running over all estimated relationships of each type.0 and 1. derived by Cascarano et a1. maximizes their values. j = 3 for negative triplets.68). By a similar method.356 1 Davide Viterbo with j = 1 for onephase s. may also be derived and used as foms.) of a.s. In fact the reflections with large ( E l . Once the different foms have been calculated for each phase set it is useful to derive a combined figure of merit.[60] which also allowed the derivation of some new effective functions.) it is possible to derive various theoretical moments. j = 2 for twophase s. 322 we saw how the expectation values in Table 5. CFOM. D. values. are related to moments of P(ah).[611 On p. Different ways of combining the individual foms have been used.11). for which phases are determined. R. Similarly for the other three functions. while CFOM << 1. from P(ah) and P(a. A correct set of phases should lead to CFOM==1. defined in (5.1 could be obtained from the distributions (5.10) and (5. The correct set of phases should give rise to the largest number of negative cos Q. < 0.).[601 which each function is introduced with a properly estimated weight in and the resulting combined fom is normalized to fall between 1. thus maximizing NQUEST. The four foms based on phase relationships. which may then be compared with the corresponding 'experimental' values computed using the different sets of phases.0) by means of their first representation and Q. E rather than F.(lGjrl) is the expected value of cosQjr. MABS and R. and qofoms was recently achieved by a more rigorous probabilistic approach.0 should indicate a wrong solutioa. The electron density map(s) corresponding to the most promising phase set(s) (with highest CFOM) will be calculated first. For instance in the case of negative quartets (5. Electron density maps (Emaps) In the calculation of the electron density maps it is more convenient to use as coefficients of the Fourier series. a good agreement between the estimated (through the Gj values) and the calculated cos Qj values. its capability of discriminating the correct set of phases will in general be higher than that of the individual functions. while qo is related to a moment of P(a. a more objective procedure is described by Cascarano et a1. At the basis of this approach is the use of the probability distributions P(ah) of ah defined in (5. and a. are the values of the individual quartets computed with the determined phases.73) becomes where the summation is extended to all quartets estimated to be negative (G. j = 4 for negative quartets respectively.
labelled by their sequential numbers. may then be represented in projection directly on the lineprinter output. 5. The peaks of each fragment.6.6): some lowangle reflections (small indices) with very large IF( and several highangle (large indices) ones with relatively small (F1. h k I E 1 357 No. For most structures it then becomes possible to go from the diffraction intensities to the refined molecular picture without human intervention. h k I E (this may be verified in Table 5.[621to this aim the map interpretation procedure has been improved and the peaks are assigned an atomic symbol. also for the limited number of terms in the Fourier summations.22 and 5. This list may then be analysed in terms of distances and angles among the peaks. The contribution of these small IF( to the electron density would be obscured by that of the lowangle reflections. with the hope that another statistically less favoured phase set will yield the correct structure.Solution and refinement of crystal structures Table 5. and by using the (El this problem is overcome and the resolution of the maps is improved. Unfortunately the phase set with the highest CFOM does not always yield an Emap interpretable in terms of a chemically plausible structure. peaks related by a sensible chemical geometry may be selected and labelled as a possible molecular fragment. AZOS: list of the 50 reflections with largest IEl value No. Figs. On the other hand. In these cases it will be necessary to compute some other Emaps. Recently an automatic link between the Emap output and a structure refinement program has been established. the Emaps often show spurious peaks.23). . The programs for the calculation of the electron density maps usually also perform an automatic peak search and supply a list of maxima sorted in decreasing order of height. where it will be easy to reconstruct the image of the molecular fragment by connecting the peaks related by possible chemical bonds (cf.
The sign expansion procedure may be followed in detail in Table 5..~"0. At step (17) a new symbol d must be introduced in order to define new signs. Also some contradictory indications are obtained. 10 signs are not defined with only four symbols. is clearly contradictory with respect to the others and it will be neglected. No indication is obtained about symbol d.6 are confirmed several times and new indications that a = . the 50 reflections with largest IEJvalue are listed in Table 5. the convergence procedure defines the following starting set of signs: No. the ~ minimum tanh argument being 0. it should be supposed that a wrong choice has been made at some previous step and the procedure should be reconsidered from the beginning. at step (20) we have two different. the Emaps often only show a partial image of the structure.. .. We may now illustrate the most common phase determination procedures. symbolic indications for the sign of the same reflection and their comparison suggests that symbols b and c correspond to the same sign. At this point it is not convenient to introduce new symbols. only two are consistent with the previous indications: and . In our case this did not happen and it has been possible to define the signs of all reflections ++ +++ + . 323).46) or (5. which will then have to be completed. for instance. S(165) has seven contributions: .and b = + (in agreement with a = .b ) are obtained.6. with 40 signs already defined. .141 x ( 2 . h k 1 Sign Parity gug uug ggu Originfixing reflections Other reflections with symbolic sign 3 8 16 1 2 12 0 1 1 1 10 4 4 0 1 6 0 8 6 2 2 1 2 4 4 + + a b c + In the unit cell there are four molecules of row formula C10HllN304S and o~o. Symbolic addition method This method will be illustrated through an example. Similarly at step (22) we have the indication that a and b represent opposite signs.522. ab. The probability of the individual sign relations will decrease. several other indications about the values of the symbols are obtained: the indications b = c and a = .358 1 Davide Viterbo Besides. As the sign determination is carried out. with very low probability.95. Not all the signs of the first 50 reflections are determined.7. but rather to use other reflections with smaller [ E l . ab. The first six indications confirm the relation a = 6. ab. The probability with which a sign is determined is given by = (5. but not contradictory. .47) relating these reflections. 2 1 ) = 1. For AZOS 200 reflections with (El Z.61 were used. but. while the seventh.141.48) and it can be seen that it is never less than 0. We will use the same AZOS structure employed earlier (p. Out of the 24 = 16 possible sign combinations. we will have several multiple indications. in the case of complex structures.. When using all sign relations of type (5. If the determination of one or more signs turns out to have several contradictory indications of similar probability.1.
b c . Step by step illustration of the symbolic addition procedure for the 50 of Table 5.7.b .Solution and refinement of crystal structures Table 5. abcd is chosen + Confirm b = c Indication that ab = or a = .6 Step Relation Sign Comments and indications 1 359 abc a b c symbol a cancels out a b c abc abc introduced because fewer than half the signs have been determined a a b c a b c .b c  d d d d d d Two different indications implying that bc = or b = c.
enantiomorph fixing reflections. besides the origin and.44). also a limited number of other phases necessary to initiate the phase expansion process by means of the tangent formula (5.7.[^^@] but. 0. and I/JO foms indicate that the set with d = .22(a)) and a dimethylsulphoxide group (5. instead of using symbols.360 1 Davide Viterbo Table 5.g. The values of the MABS. indeed. defined by the convergence procedure. SO far. the most striking results[651have been obtained by I. 5. Fig. .is more reliable and. All restricted phases are assigned the values defined by the spacegroup symmetry.. f37~14. the corresponding Emap shows the two fragments interpreted in Fig. has also been automated into a number of computer programs. When the most probable values are substituted for the symbols. 5.One of these will be correct within 45". The symbolic addition method.22. Karle using a careful manual procedure proposed in 1 9 6 6 . when needed. R. and J. ~ ' ~ ~ Multisolution methods The basic idea of these methods is that of assigning approximate numerical values to the starting phases. two sets of signs are obtained for AZOS and the corresponding electron density maps may be computed.22(b)). (Continued) Step Relation Sign Comments and indications a a a a a a bcd b c d bcd bc bc bc + + + + + + a a a   bc Again b = c confirmed a a a a bcd bcd b c d b c d b b using four symbols. we may tentatively give them the four quadrant values: fn/4. AZOS: representation and interpretation of the Emap computed with the best sign set obtained by application of the symbolic addition procedure. the most general of which is SIMP EL. both for centrosymmetric and for noncentrosymmetric structures. The starting set. will include.22 in terms of a pcarboxyphenylazoxycyano group (5. e. n . It has been found empirically that initial errors of 4050" usually do not spoil structure solutions. or fn/2. The structure obtained in this way will then be refined with the procedures described in the next paragraph. If these are general phases with values anywhere between 0 and 2n.
the use of the SIR (semiinvariant representation) program. as a result the determined phases are completely wrong. estimated by means of the second representation has a sufficiently high tanh argument to be accepted and these indications are only used to compute SSlFOM. the total number of combinations of numerical values to be developed by the tangent formula.723 selected for phase determination.[~~] C39H49N013. which allow a considerable reduction of the number of combinations with a minimum increase in the phase error. to which a few onephase s. estimated by the El formulae may be added. Its structural formula is Normalized structure factors are computed by the normalization routine and 362 reflections with JE1> 1. Appendix 5. We will follow in detail the solution of the structure of the antibiotic 21acetoxy11(R)rifamicinol (RIFOL).s. it may also happen that simpler structures can not be solved. will be This number grows very rapidly with increasing ng and ns and only by limiting the number of startingset reflections it is possible to maintain the computing time within reasonable limits. None of the 17 onephase s. some triplets with an actual value quite far from zero are used.[671 this program is based on the multisolution strategy strengthened by the use of all phase relationships for which a reliable estimate may be obtained by means of the representation method.Solution and refinement of crystal structures 1 361 If ng and ns are the numbers of general and special reflections in the starting set.H20.s. 326 twophase s. are . because of the rather crude probabilistic estimate of triplets. it may happen that at some stage of the 'chain' phaseexpansion process.[~~] mainly are based on the use of triplets estimated by Cochran's formula. which crystallizes in the space group P2. Although more complex structures have also been solved. the noncentrosymmetric space group is confirmed by the statistical analysis and no pseudotranslational symmetry (cf.E) is detected. In fact. with Z = 2. With these programs it is possible to solve structures with up to 6070 atoms in the asymmetric unit. while in the following we will describe.CH30H. through a practical example. This limit can be greatly reduced by using the so called magic integers (described in the Appendix 5. such as MULTAN.s.G the most promising developments of the multisolution techniques are outlined. Most multisolution computer programs.F). In Appendix 5. In the recent years several new developments have been proposed in order to overcome these problems and to make direct methods capable of solving increasingly more complex structures.
s.6 are actively used in the phase determination procedure.S. Table 5.F. are accepted.S. R may also be negative and for some triplets a negative G' value may be obtained. but a passive use to compute an effective fom proved to be very useful. The convergence procedure is carried out using positive triplets and twophase S. enantiomorph fixed by the magic integer procedure). Finally also 1009 negative quartets are estimated by their first representation and the most reliable 500 are used to compute NQUEST. For RIFOL 2280 positive triplets estimated with G ' a 0. while 129 with J G J >0.39) and R is a function of all the magnitudes in the second phasing shell.8. It may be noticed that the origin is fixed following the rules given earlier (p. estimated with a reliability depending on the concentration parameter G. indicating that their expected value is n. to be used in the calculation of the corresponding fom. these are treated as known phases and directly included in the starting set. we have where S2 is the value of the S. while 141 negatively estimated triplets are employed to compute the NTREST fom. Besides. allows their elimination from the phase determination process. Appendix 5. The contribution of (5. Triplet invariants relating the 362 strongest reflections are set up and estimated by means of their second representation (PI0 formula).with k.362 / Davide Viterbo estimated using their first representation. all of them are used to compute SS2FOM. The reliability of the negative estimates is in general too small for an active use of negative triplets in the phase determination process. triplets relating the 100 weakest reflections with # the considered 362 strongest reflections are generated. are treated in the same way as triplets.8. For RIFOL the convergence procedure defines the starting set reported in Table 5. the capability of the PI0 formula of sampling out most triplets with a value far from zero.S.[4s1The concentration parameter of the von Mises distribution is given by where G is the Cochran parameter defined by (5. When also some onephase s.77) to (a.)will be given by G .6 are actively used.s. At the same time 1399 I . D. RIFOL: starting set of phases defined by the convergence procedure Type Origin Code h k 0 0 1 Phase 5 5 15 2 4 6 Permuted 18 6 72 10 149 3 25 1 17 8 Total number of permutations 24 4 4 1 2 4 .(G).. 349) for the space group P2. All permuted phases are general and are expressed in terms of magic integers. which then becomes more stable. In fact for each reflection h forming a S. Twophase s. giving rise to 24 phase permutations (cf.
it will be used to define the following reflections with its corresponding a value.26 7.37 4 72 17 5 4 17 5 7 15 99 24 99 31 25 188 72 0 x x 0 6.71 6. (if any) are assigned their G values. The remaining reflections are then determined by a similar chain process.88 3. + Table 5. the phase determination process should therefore be carried out in an order inverse to that of elimination. Starting from the eight reflections in the starting set. In Table 5. At this point different foms are computed. the phase extension is carried out following the order indicated by the convergence procedure. When a sufficiently large number (60100) of phases has been determined.01 9.40 x 0 0 0 .94 6. + S ~ ~ ) Bh S .S.S.15 3.00 8.)+C G s ~ C O S ( Q ) ~ .Solution and refinement of crystal structures In the SIR program a weighted tangent formula is used. + * tan qh= S C Gtwcos(qk.10 6.78 6. for instance the phase of reflection 24 can now be determined using all relations involving 24 and two other reflections among the 60100 determined ones. onephase S.92 7.28 6.9 the final part of the inverted convergence map (divergence map) of RIFOL is reported and with its aid we can follow the phase determination process. RIFOL: divergence map illustrating the phase determination path starting from the set of reflections in Table 5. It is in fact possible to redetermine the initial phases with a greater number of contributors to the sums in (5. the reflections eliminated at the end are those best related to the starting set.75 7.69 7.+qhk. As we have seen.S. while the sums over s refer to twophase S. i.80 10. one should proceed to their refinement.47 10. with 24 (written as a triplet but with an asterisk instead of the third code number) and is related by a triplet to the starting set.Th (5.22 * 0 0 7 9 3 0 5 4 17 72 40 25 25 72 188 15 40 17 x x 0 x 0 0 0 0 0 0 8.35 5.72 6.8 Code 24 99 40 188 31 13 135 7 44 37 h 4 8 2 4 3 3 7 k 1 1 5 5 1 2 6 I 17 19 14 13 1 17 12 19 5 14 (a) Contributors 4 24 4 4 15 24 15 13 31 5 7 5 15 8.78) where the summations over t extend to all triplets linking qh to two other known or previously determined phases.78) will have one term.29 4.65)).60 6. The weight attributed to each relation is calculated from the a = ( T ~ B')"~ values of the reflections contributing to At the beginning the originfixing reflections and the restricted permuted phases are given a = 100. The second reflection no.26 8.) C Gs% sin ( ~ k+ S2s) .50 13.46 8.78). each summation in (5.9.72 11. while the general phases represented by magic integers are given an a value which depends on the root mean square deviation of the representation. 99 forms a twophase S.41 11. Reflection 24 is the first to be determined by a single triplet relation (written in the form of (5. The tangent refinement process is repeated until selfconsistency and then the remaining phases are determined and refined.e. 1 363 C Gtw sin ( ~ k+ ~7hk.42 5.02 4.09 5.
457 0.054 . The first set with the highest .683 0.049 1. RIFOL: representation and interpretation of the Emap computed with the first and best set of phases i n Table 5.517 0. 5.401 0.056 1. RIFOL: list of the ten best sets of phases with their relative figures of merit Set MABS ALCOMB Figures of merit PSCOMB CPHASE CFOM 1 2 3 4 5 6 7 8 9 10 1.422 0.435 0.479 0. ALCOMB and PSCOMB are combinkions of functions based on a and qo respectively.925 0.431 0. only part of the molecule can be located.885 0. This step may become quite demanding of computer time when the number of phase permutations is increased.440 0.885 0.093 1.052 1.495 0.501 0.10.502 0.388 0.383 0.554 0.567 0.426 0.431 0. 0.91 1 0.432 0.624 0.878 0.495 Fig.032 1.496 0.23.090 1. Table 5.10 gives the list of the 10 best sets output by SIR in decreasing order of c F ~ M .921 0. The complete tangent procedure is repeated for each of the 24 permutations of the phases in the starting set.539 0.538 0.843 0.566 0.601 0.431 0.920 0.016 1.554 0.500 0.429 0.044 1.533 0.348 0.10.364 1 Davide Viterbo Table 5.051 1.
i. p represents the fraction of scattering matter in the fragment and is forced within the interval 0. The structure factors for the known fragment are calculated and appropriate pseudonormalized structure factors for the known and unknown part of the structure are obtained.24. but computed with the pseudonormalized structure factors. RIFOL: final structure. 2.. 5. Completing and refining the structure The structural models obtained both by Patterson and direct methods are often incomplete (in the sense that not all atoms have been localized) and in all cases they only represent a crude first approximation of the real structure. defined according to the criteria / Carbon 0 Oxygen 0 E l a p 1 1 and I J % ~ ( p = ErnZrn/C. If the fragment is a sufficiently good initial model the procedure should yield an Emap showing a larger fragment and further recycling should lead to the complete structure. without solvent molecules. with initial phases obtained from the partial structure. the difference structure factors are used in a weighted tangentformula procedure. The procedure was also tested on the RIFOL structure. 5. using (5. The final refined structure is shown in Fig. 329) in connection with the problem of locating the light atoms when the initial . on the basis of the estimated a s computed by these formulae.( and phase qi. 5. Other procedures for completing a partial structure have been proposed and among them we recall the DIRDIF procedure.) G 1. are used to select the correct solution. 5. but the structure can be easily completed by the methods described in the next paragraph. and q O . Not all atoms are found in the map (solvent molecules plus eight atoms are missing. related to R.'~] been has implemented. The first and simplest procedure was proposed by ~ a r l e [and is ~~] known as Karle recycling.e. a convergence procedure will define the best starting set of phases. In SIR a new probabilistic meth~d['~. Phase expansion and refinement is performed by means of a new weighted tangent formula.24 the complete structure was recovered.65. the fragment outlined by the broken line can yield the complete molecule when input as a partial structure. which may be interpreted in terms of the RIFOL structure as indicated by the connected circled maxima. The method of Fourier recycling was outlined earlier (p. which will include both permuted phases and phases calculated from the partial structure.250. The most accurate phases.23.[70]which is based on difference structure factors. and two specific foms. structure factors corresponding to the unknown part of the structure. two to close the macrocycle and the others in the side chains).Solution and refinement of crystal structures 1 365 CFOM yields the Emap shown in Fig.5 are then used as starting set in a tangentformula extension and refinement process. i. These are then used in the new probabilistic formulae for the estimation of s.24. Fig. Partial structure recycling It may happen that in the best Emap only a small molecular fragment can be recognized and in this case direct methods can be used to complete the structure.2). starting from the eightatom fragment (11 per cent of the total number of electrons) surrounded by a broken line in Fig. With the coordinates of the fragment the corresponding structure factors are computed in modulus IF.
As a consequence a light atom close to a heavy atom may be obscured by its ripples. illustrated in the Argand diagram of Fig. The Fourier cycles not only allow the location of the new atoms but also the improvement of the positions of the model atoms.16). the method can still be applied but the Fourier coefficients should be corrected by appropriate statistical weights. will hold better the better is the initial model.2) 1 pc(r) = V F i exp (2nih h r) will show maxima at the positions of the atoms of the given model.81) should be computed. = cpi. Difference Fourier method Another convenient way of completing and refining a structural model is the difference Fourier synthesis method.(r) = V Fi exp (2nih h . Since the number of " (IFgI . Mustration of the approximation %truez vh.H. C If in the model an atom is missing... the size of which incieases with increasing peak height.IFiI) exp (2nih h .pc(r) = . ( F i . this approximation.. then p. are not known and we have to assume cp. A Fourier series having as coefficients the ( F a s computed using eqn (5.) 1 p. The derivation of these weights is given in Appendix 5. Unfortunately the values of cp. such as those proposed by ~ i m [ ' l . the difference series 1 Ap(r) = p.(r) . Indeed. while a z FI series with coefficients F = I z exp (icp.80) will show some ripples around each peak (see Fig. An important property of the difference syntheses is that they are almost unaffected by series truncation errors..81) then becomes Ap(r) = 1 D Fig.(r) will show a maximum.79) and (5. r) represents the true structure.25. The same method can be used to complete a molecular fragment when all atoms have approximately the same weight. .. For very small fragments the direct method procedures mentioned at the end of the last paragraph are usually easier to apply. If 5060 per cent of the electron density has been located with sufficient accuracy it is quite easy to complete the structure.r) . the Fourier maps computed by means of (5. 5. where some other procedures for completing a partial model will also be described. because of the limited number of observations.366 / Davide Viterbo model is formed by one or more heavy atoms. 3.. In order to see how much the initial model deviates from the real structure. taking into account the different contribution of the known atoms to the different structure factors.. If the initial model only contains a smaller percentage of the electron density.F i ) exp (2nih (5.(r) will be zero at the corresponding position.25. ~ ~ ] . while p. The difference synthesis will also show a peak at the same position but it will be almost zero at the positions of the model atoms (if these are correct) where PO@> = pc(r).. Equation (5. 5.r + icpi).
3. As we have seen in Chapter 3 (p. Fig. In Fig.Solution and refinement of crystal structures 1 367 terms in the two series (5. then Ap will show a small positive maximum surrounded by a negative ring. their height is usually smaller than that corresponding to the atomic number of the missing atom. because of the thermal motion the electron density function around each atomic nucleus becomes wider. maximum has an ellipsoidal distribution). when the errors are not too large. in the Ap map the latter will be close to a negative minimum. 5. too high a thermal motion has been assumed for one atom of the model. is illustrated in Fig. for the atom of the model it is assumed: (a) too small an isotropic motion. the line joining the two positive lobes represents the direction of largest thermal motion. 5. Finally.82). Chapter 2.26. Several computer programs have been implemented to carry out the crystallographic leastsquares refinement. The qualitative indications obtained in this . The lack of truncation errors allows the correct localization of light atoms even when the model contains much heavier atoms.27(b) together with the corresponding difference synthesis showing two positive maxima and two negative minima.27.27(a) the case in which the thermal motion has been neglected or underestimated in the model is represented. and later in this section). 90108. (b) an isotropic motion when an anisotropic model should be assumed.28). its wrong position in the model. allow the localization of hydrogen atoms (with only one electron they contribute very little to the Xray diffraction) even in the presence of medium size atoms (cf. 5. Leastsquares method By far the most widely used method of structure refinement is the leastsquares method. will appear. and in the difference synthesis a negative depression. 5. density will therefore have a smaller and wider peak with respect to p. Let us now see how the different types of errors in the model are reflected in a difference synthesis. The theory and the computing procedures have been described in Chapter 2. 1. on the other hand. If p. 5. Position error of a model atom (top) and corresponding difference synthesis (bottom).way allow one to recognize those atoms for which it is more important to carry out the leastsquares refinement varying the six parameters of the anisotropic thermal motion (cf. If. . We have already seen that they appear as positive maxima. usually they are integrated within complete crystallographic packages such Fig. Appendix 3. but in general. Thermal parameter errors and their effect on the difference syntheses. Position errors. 148).B). but. Missing atoms. 5. 2. pp. the truncation errors will also be approximately the same and will cancel out in the difference (5. the case in which an isotropic thermal motion has been assumed in the model (the p. it is easier to correct the position errors by the leastsquares methods (cf.26.80) is the same. For this reason. 90108. surrounded by a positive ring. Errors in the thermal parameters. pp. Their effect is shown in Fig. because of the approximation made for the phases. maximum has a spherical distribution) while the real motion is anisotropic (the p. difference Fourier series. Fig. gives the correct position of the atom and p.. It is possible to have a quantitative estimate of the shifts to be applied. computed when the model has been corrected for most other important errors. while the correct position will be towards the neighbouring positive maximum along the maximum gradient line. The p.79) and (5.
94) the refinement must be repeated in several cycles until convergence. For AZOP the refinement was performed using 1176 observed reflections by means of the system of programs SHELX. the known atomic positions are also shown linked by their chemical bonds. Z = 2). [ ~N ] C V A X .['O1 the first four cycles were carried out varying the overall scale factor and the three coordinates plus the isotropic thermal parameter of each atom. In the next step the 1 refinement is carried out varying for each atom the six components of the anisotropic thermal parameter as described on pp. the total number of varied parameters is 1 4 x 1 = 45 and the R factor reduces to 0. Four anisotropic refinement cycles were performed with 1 9 x 11= 100 varied parameters and at convergence R = 0. and the hydrogen atoms are clearly seen as maxima in the map. The structure factors computed with this model. Figure 5. Here we will illustrate the practical application to the refinement of the fairly small structure of 2a~oxycyanopyridine[~~] (AZOP. The coordinates of the four hydrogen atoms derived from the map are then introduced in the refinement process with appropriate isotropic temperature factors. 5. as SHELX. As we have seen in Chapter 2 (p. AZOP: structural formula and projection on the mean plane of the molecule of the difference map computed when R = 0. but this usually can not be done in a straightforward way. C6H4N40.28 shows a projection of the map onto the mean plane of the AZOP molecule.368 1 Davide Viterbo Fig.space group PI.28) were obtained.28.078. Fig.[67]from the best Emap the coordinates of all the 11 nonhydrogen atoms of the molecule (cf. ~ CRYSTALS[~'] and those commer~R ~~] cially available together with most singlecrystal diffractometers. a sufficiently low value to indicate the correctness of the model.34. In fact the contribution of the + + .05 A'). 5. assuming an isotropic temperature factor equal for all atoms ( U = 0.078 (the scheme of the molecule is added to the map for reference).148. 1868. The structure was solved using the SIR program. yield a residual R = 0.['~]X T A L . At this point we may assume that the model formed by the heavier atoms is sufficiently well refined and we can compute a difference Fourier synthesis in order to localize the hydrogen atoms.
because of the errors in the experimental data. but following the indications of Chapter 2 (p. As we have seen in Chapter 2 (p.Solution and refinement of crystal structures 1 369 hydrogen atoms to the observed amplitudes is very small and rapidly decreasing with increasing sin 8/12.052 with q = 0. 271 and 280). 106) it is possible to impose some geometrical restraints during the leastsquares refinement. Up to this step all observations were given the same unitary weight.02A. In Chapter 2 we also saw how it is possible to express the weights in terms of a polynomial in IFo[. Four cycles of refinement varying 100 3 x 4 + 1= 113 parameters converged to R = 0. The weighted R factor C wiA4 . Since this is not the only error affecting our observations. for 1 FolG 4Fmin + > w = 1 6 ~ i ~ ~ / l ~ ~ 1 ~ for IFo[ 4Fmi. in lFol or sin 6/12 intervals).. for each I o the corresponding estimated standard deviation a(Fo) due to counting errors may be derived (cf. the refinement shifts them into stereochemically incompatible positions (e. For AZOP the intensities were measured with an automatic Fl diffractometer using a scintillation counter. values which are too high and tend to cancel out the H atoms or too small for H linked to atom with significant thermal motion).98f 0. it is necessary to modify the weights introducing an FI empirical dependence on I o itself. It is recommended that these positions are checked against those obtained from a difference Fourier synthesis. 1012). in order to get meaningful values of the estimated standard deviations of the varied parameters. pp. = 2Fmin and a. as initial guesses. The weighting function available in the SHELX program is 1 where q is an adjustable parameter chosen in such a way that the (w AF. where Fminis close to the minimum observed amplitude. In addition a common isotropic thermal parameter was assumed for all four H atoms. = 2/Fm. bond distances which are too short or too long) with abnormal temperature factors (e.84) afforded a final R value of 0. the observational equations should be properly weighted.g. Their refinement may then be carried out as described above. Cruick~hank[~*I proposed the scheme Later with a.g. Chapter 4. in our example we have imposed that the CH distances should remain within 0.g.055. which was varied as a single parameter. Several weighting functions have been proposed and the first scheme suggested by ~ u g h e s [was ] ~~ w = constant = 1/16Fk.) values remain constant when the reflections are grouped in different ways (e. The last four cycles with the weighting function (5.. A frequently used alternative procedure for locating the H atoms consists in calculating their positions on the basis of the most common stereochemical rules. the accuracy of their localization is therefore quite low and often.0007.
the errors in the model are negligible in comparison with the errors in the data and there are no significant systematic errors. we should expect R values in the range 0. Equation (5. No such correlation was found for AZOP. 97) and have J . How low should the final R factor be in order to have good confidence in the quality of the refined model? The answer to this question is not straightforward.370 1 Davide Viterbo and the goodnessoffit measure (also called standard deviation of an observation of unit weight) GofF = nm are also computed.07. The final R value will also depend on the selection of reflections used during the refinement. because it depends on the type and complexity of the structure and on the quality of the experimental data. 568). It is also important to check for possible correlations between parameters during the leastsquares refinement.006A for nonhydrogen atoms. and. p.86) is nothing but the quantity defined in (2. For AZOP R. The quality of the model should then also be assessed by looking at the standard deviations of the atomic parameters or at those of the derived geometrical quantities.5.504. It is in fact common practice to discard the very . In the case of AZOP three such reflections were eliminated. In these cases the final model may still contain some fairly large errors. such as bond distances. the correlation coefficient Pij = COV (PiPj) ~ ' ( ~ i ) ~ ~ ( ~ j > which is close to zero if the correlation is negligible and close to 1 for large correlation. which should be less than 0. In Chapter 2 we saw that the leastsquares procedure gives the variancecovariance matrix of the derived parameters (eqn (2. at convergence the R value may be in the range 0. Chapter 8. systematically smaller than IF. Most programs compute the correlation matrix and output the offdiagonal elements which are greater than 0. with intensities collected at room temperature on a diffractometer. some leastsquares FJ programs allow an empirical correction of this effect but it is common practice to simply discard these few reflections from the refinement.(. for each term in the matrix.054 and Go= = 1. It is therefore straightforward to calculate. p. for small or medium size structures giving good quality crystals (as it is usually the case for most organic or organometallic compounds). In the final stages of the refinement one should check whether some intense lowangle reflections are affected by secondary extinction (cf.250.15 for large molecules and up to 0.080. Nevertheless.30 for macromolecules solved at low or medium resolution.030. Usually as the complexity of the structure increases the quality af the crystals and of the diffraction data decreases. = 0.56)). For very accurate lowtemperature measurements these values may be further reduced. which may often be corrected by applying stereochemical or energy constraints (cf.58) and GofF should be close to unity if the weights of the observations have been correctly assessed.
Since the I$ value is less sensitive to the position of the light atoms. other agreement indices have been proposed. R becomes a rather weak guide. The only valid check of the indication given by the R value is the convergence of the svbsequent Process of completing and refining the model. Chapter 2. Among them we recall the weighted residual proposed by ~ a m i l t o n [ ~ ~ ~ already considered in Chapter 2 (p. For instance this test may be used for determining the absolute configuration of optically active molecules from the effect of anomalous dispersion. As an example of the weakness of the R index. in most cases.[80]On the other hand. the intensities. 103). @some ~I caution is necessary. the refinement of a . is certainly a better one. such as Pt. but too high a cutoff value will considerably reduce the number of observations and the leastsquares refinement will yield higher standard deviations (cf. only for very accurate structural analyses would the latter procedure reveal significant changes in the final model. Nevertheless the second model. Of course the higher is n the lower will be R. with a smaller average position error and a uniform distribution of errors over all atoms. of which are measured by diffractometer . let US consider the case of a structure containing one heavy atom.[811 In following the convergence of our refinement we have mainly used the R factor defined in (5. 1024). When the choice between a centrosymmetric and a noncentrosymmetric space group is ambiguous or when the structure shows pseudotranslational symmetry. and a more rigorous procedure requires the use of all data with proper weights["] and a prior statistical treatment of weak reflections to account also for negative measurements. Ir. N. Although the R index is the most widely used criterion to assess the goodness of a structural model.[831although. as pointed out by ~ o g e r s . When the model is an incomplete representation of the molecule. its indications should be regarded with some caution. pp. There is no theoretical justification for discarding weak reflections.3). where it was shown that the ratio of the residuals R. the inclusion of weak reflections becomes essential.Solution and refinement of crystal structures 1 371 weak reflections. As mentioned in the introduction of this chapter. Os. while IFiI only depends on the limited number of parameters defining the incomplete model). and a certain number of lighter atoms (C.(l)lR&(2) obtained from two refinements of different models may be used for testing the significance of the difference between the two models. or Cd. usually with 2 G n G 3 (for AZOP n = 2 was used to select the 'observed' are omitted. as it measures the agreement between quantities which depend on largely different numbers of parameters (IF:] depends on all atomic parameters. 0 ) . some of which are statistically more appropriate to assess the significance of small changes in the final refinement stages. ~ ( 1 )reflections with I s na(Z). I. a model with the heavy atom correctly placed and the light atoms quite inaccurately localized will give a lower R value than a model with a small error in the position of the heavy atom and an almost correct position of the light atoms. with large estimated standard deviations.
PC instead of P2. The correct solution was only obtained after estimating the triplet invariants by their second representation. and (ii) those for which the reported space group lacks a centre of symmetry. Two types of structures can be considered: (i) those for which the reported space group has a lower Laue symmetry than that of the actual structure./c.e. as half of the refined parameters have a linear relation (the overlooked inversion operation) with the other half. which is instead present. It may happen that the structural model obtained by direct or Patterson methods is constituted by a correctly oriented molecule. and a wrong choice is more frequent than one might think. the initial attempts at solving the structure by direct methods gave correctly oriented molecules. 1.25. Wrong space group. This is a direct consequence of the nonlinear nature of the problem. The solution will give two molecules related by an inversion centre in a general position. may be recognized because they usually lead to abnormal values of some bond distances and angles or of the thermal parameters. Cc instead of C2/c. which. An interesting analysis of such errors is given by Marsh and ~ e r b s t e i n [ who ~noted that a ~~ ~~] relatively large number of structures has been reported with space group of unnecessarily low symmetry. . implies the presence of several local minima in the function to be minimized. 161). instead ~~) of Cmcm (several examples are given by Marsh and ~ e r b s t e i n [ ' ~ ~ 'They. For the first type the correct space group may often be found using geometrical consideration^[^^^^^^ such as those implemented in the computer programs NEWLAT['~] or LEPAGE. the refinement by leastsquares should in theory yield a singular matrix (cf. An alternative way. 2. Cmc2. would be to try to solve the structure in the lower symmetry group P I . As explained in Chapter 3 (p. p. after translating one of the two molecules in such a way that it is referred to the inversion centre at the origin (i. In most cases the entire molecule is shifted by a vector corresponding to a large Patterson peak due to several superposing interatomic vectors. which is often successful when applied to structures belonging to the space group PI. which are adjusted when the refinement is carried out in the correct space group. are particularly disturbing. 93). the structure can be refined in PI. Two types of errors. this can be located by inspection and then. C2 or Cm instead of C2/m.B . When these methods fail one can try to find the correct position by the Patterson method described in Appendix 5. Chapter 2. 100). The most common errors occur for the following space groups: P1 instead of PI. in practice this relation may not be exact. but in any case the solution of the normal equations will be very unstable with large errors in the atomic parameters and large values of their estimated standard deviations.[~'] For the second type. the determination of the space group from the diffraction data is not unique. but its position with respect to the symmetry elements is incorrect. the general coordinates of the inversion centre are subtracted from all atomic coordinates). Pna2. instead of Pnam. Incorrectly positioned molecule. An example is given by the AZOP structure. which occur quite often.372 1 Davide Viterbo structural model will not converge if the model is affected by large errors. shifted from the correct position and their refinement would not converge to an R value lower than 0. as observed in Chapter 2 (p.
We saw on p. No distinction can be made between dynamic and static disorder and the case of a molecular fragment oscillating between two positions in all unit cells is indistinguishable from that in which half of the cells have the fragment in one position and half in the other. is the substitutional disorder where the same site is occupied by different types of atoms in different cells. i.and spaceaveraged contents of the unit cell and the result of a diffraction analysis is this averaged contents. it is referred to as static disorder and in this case the average contents of the unit cell is obtained by averaging over the space. 85). cf. p. An example of such dynamic disorder in the cis form of the complex [ ( q 5 C 5 ~ 5 ) 2 ~ e 2 ( C 0 ) 2 ( ~ 2 . An important example of this type of disorder. Often merohedral twinning is not recognized and then in most cases the structure fails to be solved. On the other hand if the movement is stepwise between two or more energy minima. 837. it is impossible to refine the model to an acceptable R value because of the systematic errors on the observed amplitudes.C been] recently described. Two important effects may cause a lack of convergence in the refinement process: twinning and disorder. which may be interpreted in terms of different rates of stepwise rotation around their fivefold axes. over the different unit cells. depending on the fraction of each species. two positions in the cell. 148 that. then the same atomic species are located in both possible positions with an occupation factor depending on the 'population' of each position (the term population will be associated with the fraction of time spent in the given position in the case of dynamic disorder and with the fraction of cells having atoms in that position in the case of static disorder). because of the thermal motion. 87). the total electron density will be divided between the positions of the minima. But larger movements are sometimes possible in crystals.[921 has 0 ) 2 the two independent cyclopentadienyl rings show different thermal motions. say. This will be more difficult when all reflections from the two individuals superpose exactly (merohedral twins. atoms oscillate around an equilibrium position and we may say that they are affected by a small dynamic disorder.Solution and refinement of crystal structures 1 373 A critical view (possibly a bit too pessimistic) of the accuracy of the reported structure determinations has been presented by ones[^'] and the reading of his paper is highly recommended. This hypothesis was confirmed by a recent solidstate NMR Another type of disorder may occur in crystals. then only an average structure is obtained with abnormal thermal motion and the refinement will not converge. the diffraction intensities of a twinned crystal must be carefully analysed in order to separate the contributions from the different individuals forming the twin.e. even when a solution is found. When the disorder is between. which is common in minerals and alloys. Diffraction experiments will just show a timeaveraged situation and if the movement is continuous the electron density will be smeared out. In the case of substitutional disorder the different atomic species are introduced with the same coordinates but with different occupation factors (cf. Real crystals deviate from the ideal picture of a periodical perfect repetition of a unit cell. giving rise to a real dynamic disorder. p. The structure factors depend only on the time. If a disordered structure is refined without taking into account the disorder. As we saw on p. if this is not .
I2 . when the first ratio is greater than 1. t In a normal Xray experiment. thus (+)tartaric acid corresponds to 7a. 489) that for compounds containing asymmetric carbon atoms. The two optical isomers differ in hand and may be related either by an inversion or by a reflection operation (inverse congruence). the two enantiomers are indistinguishable. and anomalous dispersion is only large for heavier atoms near their absorption edges. a onebyone comparison of the two ratios indicates that the wrong configuration has been chosen if. it is essential to apply a proper absorption correction to the diffraction data. The ratios IF". When one or more anomalous scatterers are present. Fisher proposed to assume as reference that ( )glyceraldehyde corresponds to the configuration 5a shown in the table on p. with no anomalous dispersion. radiation by Rb). because of Friedel's law.I should be measured and compared with the ~ computed values.. as they give rise to the same diffraction pattern. Since the Bijvoet["] differences 1 ~ ~ 1IF.J/JF?.374 1 Davide Viterbo known one may initially assume an occupation factor of 0. Fortunately the first determination of the absolute configuration of NaRb(+)tartrate[941by the method described below (using the anomalous scattering of the Zr K. We shall see in Chapter 7 (p. and van ~ o m r n e l . then both IFhI and IF. 545) that the method is also applied in macromolecular crystallography. isomers of opposite chirality (enantiomers) are possible and that their solutions rotate the plane of polarized light in opposite directions. proved that the assumption was correct. such as Pna2. when the anomalous dispersion effect is present. 168) it was shown that. Since this is an arbitrary assumption there was only a 50 per cent chance of it being correct. such as q u a r t z The term 'absolute structure' has been recently proposed and discussed$'~" .5 and than refine the factor to convergence (the occupation factor is highly correlated to the temperature factor and some caution should be used in the leastsquares refinement). Since then the anomalous dispersion method has been used to determine the absolute configuration of a large number of molecules and it will be shown in Chapter 8 (p. as it does not apply to the case of noncentrosymmetric but achiral space groups (polar groups with reflection symmetry operations. /IF?. Absolute configuration In Chapter 3 (p. By simple chemical methods it is not possible to decide which of the two configurations corresponds to the isomer rotating the plane of the light to the right (( )rotamer).\ and IF. the second is less than 1 and + + i We should note that the term 'absolute configuration' is not always correct in describing crystal structures. In order to illustrate how the absolute configuration may be determined it is instructive to consider the procedure originally used by Bijvoet.) o r to that of achiral molecules (without asymmetric centres) crystallizing in noncentrosymmetric space roups. Friedel's law is no longer satisfied. ~ ~ ~ ~ which gives reliable results only when the anomalous dispersion effect is sufficiently large and for this reason it is no longer used.1 are tabulated for a limited number of reflections with large Bijvoet differences. Only when disorder is treated in a proper way will the refinement converge to an acceptably low R value. Peerderman.are rather small. 487 and to establish the configuration of all other chiral molecules in a relative way with respect to this convention.
A Structure factor probability distributions We will use the central limit theorem stating that. then the correct enantiomer is obtained by &anging the sign of all atomic coordinates. If this is the case.(xj)2. and approaches 1 if they are inverted one with respect to another. all q values will be equally probable and (cos 2nh q ) = 0. 97) in which the structure factor is written as IF(h. each with mean value (xi) and variance (ui2. hence The variance of xj is defined as a. i. N).A.1) Whatever the distributions of the variables xj are (they may be all different). When the anomalous dispersion effect is small all the reflections should be used and efficient methods have been proposed by and in the latter an absolutestructure or chirality parameter x is refined in a leastsquares process (cf. = (x. (x) = j=1 x N (xi) and a2= j=1 x 4.4) Assuming a random distribution of the atomic coordinates. given N independent random variables x. (5. ( j = 1.) .x) IFhI2 x IF.A. their sum X = i=l N C xj has a mean value equal to the sum of the individual mean values and a variance equal to the sum of the variances. x)I2 = (1 . provided that N is sufficiently large. .89) where x is close to zero when the model and the crystal are in the same chirality. p.Solution and refinement of crystal structures 1 375 vice versa. Appendices 5.I2 + (5.e. the sum X will have a normal probability distribution For a centrosymmetric structure the structure factor may be written as where the sum is extended to the independent atoms only so that Fh can be considered as the sum of N/2 independent random variables xj = 2fi cos 2nh q with mean value (xi) = 24 (cos 2nh q ) . N (5.
(5.A. 02. (cos28) = 4.A. 13) Equation (5.A. The approximate character of (5. and thus (5.A.A.A ~ / x ) . A.. B) dA d B = P(A)P(B) dA dB = exp ( .e. exp 0. Because of the central limit theorem.376 ( Davide Viterbo Because of (5.( .exp (.14) over g.A.7) given that. in modulus and phase). If the structure factor is expressed in polar coordinates (i. VzZ F has the same probability of being positive or negative and the probability Pi(lF() that its modulus has a given value is given by Pi(l FI) = 2Pi(F). 1 = 1 For a noncentrosymmetric structure F = A h + iBh and.13) represents the probability that the structure factor F lies within a region of the complex plane of area dS = dA dB. in analogy with h the derivation of (5.5) the second term is zero and cy7 = 4f7(cos22xh . then F dS = I 1 dlFJdg.) = 2f7 (5.A. we have ( A ) = 0.12) The joint probability that A lies between A and A dA and at the same time B lies between B and B + d B is given by the product of the two distributions (5.8) to (5.5) is immediately derived.F2/2X). and 1 P(A) = .A.10). while Pi(lFI) has a Gaussian shape F and goes to zero only at k ~ .11) we can see that also for noncentrosymmetric structures Z = ((FI2).A.In deriving the value of (1~1') we did not consider the effects due to the presence of . From (5. and + F The distribution of the amplitude I 1 alone is obtained by integrating (5.4) is clearly indicated by the observation that the maximum value of I 1 is C f.( A ~+ B2)/z) dA dB.B2/Z).11) m 1 P(B) = exp m (.10) gives eqn (5.4). Jx c (5. for a randomly variable angle 8.A. = 4X (5. N = 4X ( B ) = 0.A. I. the mean value of F will be h and its variance Finally the distribution function of F is given by L Pi(F) = . 12) 1 P(A. substitution of (5.
[991 We note that the calculation of the ratio of the average observed intensity for specific classes of reflections over that of the general reflections. Space group Pm: in the projection on the plane rn the t w o related molecules superpose. consider the effects due to the presence of a mirror plane. other symmetry elements besides the inversion centre.1.A.9) is generalized to where E will be equal to 1 for the general reflections and greater than 1 for certain classes of reflections which are influenced by the presence of symmetry elements. Patterson vector methods We will consider here the socalled vector methods[1001 which allow a systematic use of the information contained in the Patterson function also when no heavy atoms are present. The Fourier coefficients FhOI relative to this projection will have a distribution corresponding to a structure of N / 2 atoms with scattering power 26 and then The mean intensity of the h01 reflections will be twice that of the general reflections hkl. computing the ratio ( IFhOl1')/(I ~ ~ ~which 1 ~ be) close to 2 for Pm and close to 1 for P2. all atoms related by the m plane are superimposed. In Fig. 5. The Patterson function can be considered as formed by the superposition of N images of the crystal structure displaced one with respect to the other by the amount required to bring to the origin each atom in the unit cell.Solution and refinement of crystal structures 1 377 I " Fig. For instance we can distinguish between the space groups Pm and P2 by ~ will . for instance. each with double weight. The values of E and the relative reflection classes for the different symmetry elements are tabulated in the International Tables. Let us.1 we can see that on the projection along the b axis. 5. 5. . the projection of the electron density on the ac plane will only contain half of the peaks. by considering the space group Pm (m perpendicular to the b axis).A.A. thus in Pm E = 2 for the h01 reflections. (5. can be used as an indicator of the presence of some symmetry elements. In order to take into account the symmetry element effects.B.
8.B. the peaks referred t o the central origin are interpreted as the superposition of five images and the peak numbers refer to the atoms linked by the corresponding vector.4(a). It can be easilj seen that the same map can also be interpreted in terms of five displaced images of the enantiomeric structure.4(a).1.l(b) illustrates how the Patterson map oj Fig.B. (a) Four unit cells of the fiveatom structure of Fig. 5. as we shall see. these are the socalled superposition methods. 5. the two maps are thus separated b) an interatomic vector. Let us first consider the vector superposition in which one Patterson mar is superposed on an other in such a way that the origin of the seconc coincides with a given vector of the first. Figure 5. 5. The set of coincident peaks will reveal one or more Fig. (b)four cells of the Patterson map in which the peaks indicated by r e f e r to the central origin and those indicated by 0to the other origins.378 1 Davide Viterbo Each image represents the ends of all the vectors from the atom at the origin to all the others.l(a). the proposed methods may be difficult to apply in practice. 5. repeated in Fig. 5. It is in theory rather simple[1011 extract one image of the structure from to the overlapping set.4(c) can be interpreted in terms of five displaced images of the fiveatom structure of Fig. but. .
2 . . . Unfortunately. When more than one image is revealed.3.B.8. 5. In practice we have a continuous Patterson function in which the peaks of finite width overlap.2 after the first superposition are indeed I(l) and I(2). . . 5. the correct . . . A further problem arising with vector superpositions is that the obtained image is not referred to the true origin of the cell as it is apparent from Fig. In particular. I(3).8. 5. also in a sharpened map. 5.B. while single peaks are not resolved from the background. 5. 3 . indicated by the second arrow (only one image is shown). 5. N in the unit cell.2).2. . . this simple method is only applicable in the ideal case of a Patterson function corresponding to a point atom structure. the structure plus its inverse are obtained for a noncentrosymmetric structure (Fig. In fact. 11(1)= 1(2) and Ir(2) = I(l) (I(n) is the enantiomer of I(n)) as illustrated in Fig.e. 5. In general I1(n) will not coincide with any image I(1). . . I(3). indicated by the first arrow (two enantiomorphic images of the molecule are shown). 5. +are the coinciding peaks after a second superposition on peak 13.1 is superposed on peak 12 of the present map.2. .B. not at the origin. for reasonably sized molecules with no heavy atoms.8. Patterson superpositions: are the Patterson peaks as in Fig.2. . N in turn at the origin. . for a centrosymmetric structure only one image is obtained. iteration of the superposition process on different peaks will eventually yield a single image.B. if the structure contains atoms 1 .N in turn. only the peaks with high multiplicity appear. . 2 . . i. . .\@ \ \ Fig. I(2). .Solution and refinement of crystal structures 1 379 0 0 images of the structure. where superposition of the double image on a new peak reveals one image only.B. . but at the end of the vector 12.1. 3 . I(2).I(N) obtained by placing atoms 1 . 3 . the Patterson map P will be the superposition of the images I(l). .1 and then perform the above superpositions. O are the coinciding peaks when the origin of the identical map of Fig. the two images left in Fig. After translation by a vector 12 the new function will be where the different images are obtained by placing atoms 1 . because of the choice of the translation 12. 2 .B. The reader is advised t o reproduce on transparent sheets three copies of Fig. This is illustrated in Fig. I(N) unless n = 1 or 2.8. if the superposition is on a single peak. . 5.4(c)). If the superposition is on a multiple peak the number of images obtained is multiplied by the multiplicity of the peak (Fig. 5. Thus superposition on any recognizable peak will give multiple images and several superpositions will be necessary to reveal a single image of the structure. The basic principle of the method may be understood by considering that.
DIUS the imaae ~ ' ( i ) its atom 1 i n peak 21 (enantiomorph). 10~ationof the structure with respect to the symmetry elements can be obtained by the described later. plus the image with its atom on peak 21 (enantiomorph). but not their orientation and position.3.1) .380 1 Davide Viterbo Fig. In order to carry out any superposition process it is necessary to evaluate the degree of coincidence between the peaks of the superposing maps. 5. (b) image l(2) and its enantiomorph 1(2) with their atom 2 at the origin. (a) Image l(1) and its enantiomorph 1(1) with their atom 1 at the origin.B. (c) image . (3) both orientation and position are known.B. The shadowed images 1U) in (a) and 1(2) in (b) are found in the superposition on peak 12 of Fig. 5. they are identical to 11(2) in (d) and l'(1) in (c) respectively.[100] three such functions have been proposed: 1. (d) image l'(2) with its atom 2 on peak 12.u ) (5. 5.2.8. especially when some structural information is available. This is done by means of the socalled imageseeking functions. Information of the first type is often available from known bond lengths and angles or from the Cambridge Structural ~atabase. Despite these problems.[''~] we shall see how and it can be exploited.l(b)). The product function ( r )= P ( r ) X P ( r . (2) the orientation is also known. but not the position.I ' ( l ) with its atom 1 on with peak 12 (Fig.8. superposition methods can still be applied in practice. This can be of three types: ( 1 ) the stereochemistry of one or more rigid molecular fragments is known.
.u) (5.B.Solution and refinement of crystal structures 1 381 which takes very high values when coincidences occur. with their origin at the position of atoms 1 and 1' (related by an inversion centre) respectively. Images 1(1) and I(1') coincide and reveal the structure properly placed with respect to the origin.B. 1. Starting from the known molecular fragment (atomic model) it is possible to build up the corresponding vector map (vector model). An example of this atomic superposition is shown in Fig. If the ratio (5. Let us first consider how the superposition method can be conveniently applied when the location of one or more atoms (both independent and related by symmetry) in the cell is known. In this case Patterson maps with their origin at the sites of the known atoms are superposed. This model map is superposed on the Patterson function with its origin coinciding with that of the Patterson function and then rotated in all possible orientations. For each orientation the match between the ends of the m vectors of the model and the Patterson peaks is evaluated by means of functions similar to those considered above. Determination of the orientation. 328.20) is very low.u)} (5. are superposed.3) which is also sensitive to the errors on u but has the advantage of a low background noise. Atomic superposition can be used when the crystal contains a heavy atom. Their form is now: (a) product function where P(uj) are the values of the Patterson function at the ends of the vectors. The sum function E (r) = P(r) + P ( r .2) which is less sensitive to the errors on u. the straightforward application of the Fourier recycling procedure may be inefficient and atomic superposition may be a convenient alternative. 5. The minimum function M(r) = min {P(r). It is convenient to divide the process of locating a fragment of known stereochemistry into two steps: determination of the orientation and determination of the position with respect to the symmetry elements. Atomic superposition in this case is facilitated by the fact that the coinciding images are made up of vectors between heavy and light atoms which are well resolved over the background of vectors among light atoms. but can often produce spurious peaks and in general a high background noise. 2. We can now describe one of the procedures[10~106] proposed to solve the Patterson function when the stereochemistry of part of the molecule is known.4(d) in which two maps. the position of which has been determined by the method described on p. but is subject to considerable background noise and is very sensitive to small errors in the value of the vector u used for the superposition. 3. P(r .B.
C are single and 3 double peaks of the Patterson function with its origin on atom 1. shifted from the correct origin at the inversion centre. (b) corresponding Patterson map.8.382 1 Davide Viterbo Fig. (a) Centrosymmetric threeatom structure. (d) Atomic superposition: are the known positions of the related atoms 1 and 1'. while superposition o n the single peak 25 gives the fullline image only. x . 5. + 9 . (c) vector superposition on the double peak 23 45 gives the t w o images in full and broken lines. 0.4. O are single and double peaks of the Patterson function with its origin on atom 1'. are the overlapping peaks showing the structure referred t o the correct origin.
. Determination of the position with respect to the symmetry elements.5).6). (b) when the symmetry element is an axis the search is a twodimensional one on the plane orthogonal to the axis. when the absolute minimum is assumed. such as the rotation function. where n is usually equal to 1020 per cent of the total number of vectors. The correct orientation will correspond to large values of the functions (5. the location of the fragment can be determined by systematically translating it in all possible positions within the asymmetric part of the unit cell and then by generating. To overcame this problem it is preferable to use the mean of the n smallest values ( M ) . The described procedure operates in the Patterson space. usually operating in the reciprocal space. small errors in the model may produce small values of M even for a correct orientation.B. and x (cf. [lo'] The orientation of the model can be varied following the same Eulerian scheme (a detailed description is given by Stout and ~ e n s e n [ ' ~ ~ ] ) in used most diffractometers to define the position of the reciprocal lattice vectors in terms of the three angles 8. especially and . considering that: (a) when the symmetry element is a plane the search is performed only along the direction orthogonal to the plane. 72 and 2746). 2. for each position. but. This function is the most sensitive and is usually preferred. Each vector set obtained in this way is compared with the Patterson function and the fit is evaluated by means of one of the functions used in the orientational search. P(uJ . (5. . Once a likely orientation has been defined. (c) when the symmetry element is an inversion centre the search is three dimensional.Solution and refinement of crystal structures (b) sum function 1 383 (c) minimum function M = min {P(ul). Normally the search of the position of a fragment with respect to the different symmetry elements is carried out separately for each symmetry element. all the vectors between the atoms of the fragment and those of the symmetryrelated fragments. They can be further improved by shifting the atoms of the model in such a way that a better fit of the set of interatomic vectors on the maxima in the Patterson function is obtained.B . and (5.B. but other methods.[1091 have been proposed[1101131 successfully applied. pp. P(u. q. .)).4). The number of orientations to be examined can be quite large and the symmetry of the Patterson function and that of the vector model can reduce the range of the rotational search. Because of the errors in the model the orientation and position are determined by the above method only in an approximate way.
Their contributions to the electron the amplitudes IFhJ density function p(x) = (lla) h Fh cos 2nhx Fig.2.k are shown as full lines. As a second example we shall consider the projection of a centrosymmetric structure for which the amplitudes I FhI. S(h . curve 2 the term . IFk!.r. positive). B. Patterson orientation search routines have been incorporated into direct methods programs. C.k) r contributing to the electron density function p(r). 5. 5. lFklcos 2nk r.   + + + + + + . Onedimensional centrosymmetric structure with IFh/ and lFZhllarge: curve 1 shows the trend of IFh[cos Pnhx. and IFh. whatever the sign of I Fh1.1. negative). p.C. They are at the basis of the socalled molecular replacement methods.C.[lolIn both these cases the correct position of the oriented fragment is found by direct methods.2. while the dotted lines are located half way. if F is positive. 4 h and curve 3 the term +IF.[701 Another example is the PATSEE routine[116] incorporated into the SHELXS86 system.\ cos2n2hx ( 4 . the sign of IF. C. instead of fitting the vector model. 5. I FkI.["~] Recently. if negative. 553).rand IFh_klcos2n(h.I FhI cos 2nhx ( F . and D in Fig. curve 2 that of IFh/ cos Pnhx. if 1 Fhl and IF. 5.[ are large.C. It follows that the possible maxima of the electron density will be restricted to the regions indicated by A. and cos 2nh . 5. 1 is more likely positive. if positive. where curve 1 shows the term + 1 1 cos 2nhx (Fh positive). and IFh*/ large: the full lines represent the maxima of lFhl cos 2nh. If I Fhl. If we associate to the full lines the maxima of the terms IFhlcos2nh r. .I cos 2n(h . For each region the signs S(h). .C. F would then contribute to the electron density in the region indicated by the letter A.k).. k hk 1 1 1 I Fig.2 the traces of the three families of planes h. the hatched regions A.the broken lines the corresponding minima. and curve 3 that of F cos 2 ~ 2 h x the hatched regions A and B are I. the same applies to the other two terms. Chapter 8. will contribute to both regions only with a positive sign. B. r = 1 if it is negative. k. This argument can be generalized to three dimensions.C. In Fig. and h . 5. A highly automated routine has been built into the DIRDIF system. and in the region B. the corresponding terms must add up to give a preponderant contribution to p ( r ) . S(k). IFkl. IFkIcos2nk. those in which a high value of the electron density is indicated. r. will be large and are illustrated in Fig. a fit is searched for between the structure amplitudes calculated for the model and the observed ones.[l14]For each orientation or position of the model fragment.1. I are large.C Two examples of deriving phase information from positivity Let us first consider a centrosymmetric onedimensional structure for which and IF2hlare large. Threedimensional centrosymmetric structure with IFhl.. It follows that. where the above conditions are satisfied for all three terms at the same time. . then the dotted lines will represent the corresponding minima. This will happen when h cos 2nh r = +1. with p(x) everywhere positive.k) of the three structure factors are Region S(h) S(k) S(h .. in both cases F.k) is always positive. I Fhklare large.384 1 Davide Viterbo in protein crystallography (cf. IFh. A procedure combining direct and reciprocal space searches has been recently described by Rius and ~iravitlles.k) A B C D In all cases the product S(h)S(k)S(h .. D are those in which high values of the electron density are more likely.
=1 2n(h . N . we have (5.2) For the real and imaginary components of Eh = A h + iBh we have Similarly to (5. we can derive Ah =  2 cos [C. Then.k) q]).(h . Eh will have a normal distribution with mean and variance 4=. q] Under the assumption that all points in the unit cell have equal probability of housing an atom.4) Under the assumption that Ek has a fixed value (i. = l x 1 exp (2nih q) =  x mi4 exp (2nik .3) Supposing that the two exponential terms in the middle formula in (5 . l ) are independent.( 4 ) ' ) . because of the central limit theorem. Thus also the terms g.( ( E ).k) .e. we can write[ll'] With the same assumption for Eh.(k)S.q = mi=l 1 .D Probability formulae for triplet invariants For a structure with N equal atoms in a P I unit cell.. the normalized structure factor of index h can be written as the sum of N independent terms 1 Eh =  f i . which are functions of q.S. the atomic position vectors q will form a set of independent random variables..D. I).D .Solution and refinement of crystal structures 1 385 5. both its modulus and phase are known).k)] m. will be random variables.D.(k)C.(h .D. (5. (5.D.k + k) .) = (exp (2nik q)) (exp [2ni(h .5 ) exp [2ni(h .D .4) becomes and substituting in (5 .=I 2 1 (5.k) .
(k) = cos 2nk q Bh = and S.D.q k . (5. Ek. as they are of ~ order 1/N2 [cf. then dS = IEhI dlEhl d q h and As lEhl is known.10) where the terms (Ah)2/Nand ( B h ) 2 /have been neglected. are known dQhk= d q h and the distribution of qh is . The probability that Ah lies in the interval between Ah and Ah dAh and at the same time Bh lies in the interval between Bh and Bh dBh. EhPk)can be expressed as the product of the separate distributions of Ah and Bh.386 1 Davide Viterbo where C.Thk.14) by its integral with respect to qh[118] where and Qhk = Q)h . Bhl Ek. Eh.). = I x Pi.8)] and become very small for any reasonable N.) = exp 1 n {[(Ah .k)] =  fl.(Ah))2+ (Bh .(k) = sin 2nk 5.13) which gives the probability that Eh lies within an area of surface dS = dAh dBh in the complex plane. simply indicated as P(qh).(Bh))2]) (5. eqns (5.D.=I 1 [S.D.D.k) + Cj(k)Sj(h . Bh I Eh. we are interested in the conditional probability P ( q h I IEhI.(k)Cj(h . Similarly x fl 1 . which can be obtained by dividing (5. The conditional probability density function P(Ah. When expressing Eh in polar coordinates (modulus and phase). is therefore given by + + P(Ah. Since qk and qh. Eh.
15) isr5'] L = 2n&(Ghk). they will identify a supergroup (see Appendix l. ~ u e r g e r [ ' ~suggested that such structures should be treated as ~.19) we consider the two cases S(h) = S(k)S(h . i.(r) is repeated by a pseudotranslation (in the sense that it does not necessarily correspond to a crystallographic translation) u.k) = .22) + and P+< i (and P.D.exp x + exp (x) = tanh (x) 1. k ~ h . EhI (5. say p. . D.k (5.where &(x) is the modified Bessel function of zero order.(r) = p. The function (5.Solution and refinement of crystal structures 1 387 equivalent to that of Qhk. we have and p+= 1 exp x = tanh x 1+ exp (2x) .19) Indicating by P+ or P. An important type of pseudosymmetry is the pseudotranslational symmetry occurring when a nonnegligible amount of the electron density. in the special case in which these atoms exactly satisfy a higher symmetry. the probability that E.2 (E.k) (with probability P + ) and S(h) = S(k)S(h .46). where P + is always greater than i .38). p.D.[281 applying the centrallimit theorem to By we obtain 1 exp . In a similar way it is possible to derive the probability formulae for centrosymmetric structures. If in (5.14.k) = 5. P+> 4 if S(k)S(h . We can finally writeLz4] which is equal to the Cochran distribution (5. 5.E) of the space group to which the whole structure belongs..22) is illustrated in Fig.P + exp (x) + exp x + exp (x) + and finally P+ = 4 + f tanh 1 (* EkEh.(r u).e.) .k) (with probability P) we obtain eqn (5.respectively.E Pseudotranslational symmetry We will say that a structure possesses pseudosymmetry when a nonnegligible part of the atoms approximately satisfy a higher symmetry than that of the whole structure.~ 1 [ )'Im .~'~~ + .D.D. The value of the integral at the denominator of (5. has a positive or negative sign. It can be noted that.> 1) if S(k)S(h .
388 ( Davide Viterbo the sum of a substructure. while the light atoms occupy general unrelated positions: the heavy atoms form the substructure and the light atoms the complement structure. in Fig.E. the value x = 0. p.l(a). 5. For the structure of Fig. cp.766 (Fig.E. In Fig. it is always possible to find a value of x (0 < x < 1) for which the three equations (5.. 5.F. cp2 = 3. in which two similar but not equal atoms are related by a vector u = a / 3 . Statistical methods for ideiltifying the type of pseudotranslational symmetry and the related sub. expressed for convenience in cycles (0 6 cp < 1) l~~ instead of degrees. cp2 = 4x mod (I).e. [49.064 with an error of 0. Finally.E. 5.136 cycles (49"). Let us consider the example given by ~ o o l f s o n . = 0.2.E. .F Magic integers I (c) Fig.830mod (1) = 0.130 cycles (47"). = 3.l(b) the case in which the pseudotranslation is only approximately obeyed.51.002 cycles (lo). by using the three integers 3. 5. according to p. Because of the presence of pseudotranslational symmetry.F. (I E.P P W . [Three~phases. imposing certain relations between subsets of atomic positions. the substructure reflections will have h = 3n.2) are approximately satisfied. = 5x mod (1). cp. 5. .(r) and the complement structure. Id slightly different heavy atoms related by a pseudotranslation vector u = e/3.1201 + + + 5. u = a12 b/2. 147.1). + Magic integers were first introduced by White and W o o l f s ~ n and~allow [~ ~~ one to represent several phases in terms of only one variable. .F. For instance.l(c) another example of pseudotranslational symmetry is shown. when the reflections are grouped in different ways. 0360").and superstructure reflections have been recently proposed.1) will give: cp. the reflections with h k = 2n + 1 would be systematically absent. (a) Heavy atoms exactly related by a pseudotranslation vector u = a/2 + b/2. If the structure only contained the heavy atoms. A twodimensional example of pseudotranslational symmetry is shown in Fig. . We will now see that. 5 in (5. the assumption that the atomic coordinates are independent random variables is violated.7. is shown.064 mod (1) = 0. 160. are considered. In the reciprocal space this is revealed by a nonuniform value of the averaged normalized intensity. where the two heavy atoms 1 and 1' are related by a centring translation. 5.298 mod (1) = 0. = 2.2) where mod(1) indicates that the phases are always taken within the interval 01 cycles (i. through of the type cpi = mix (5. if cpl = 0.(r) = P(F) .830 with an error of 0.1. we will have 91= 3x mod (11. cp. ~ . (b) heavy atoms approximately related by a ~seudotranslation vector u = a12 b12: .3.F.E. the unit cell would be centred and.298 with an error of 0.l(a). As we have seen. which will therefore be systematically weaker than the reflections with h k = 2n (substructure reflections) to which both heavy and light atoms contribute. only the light atoms will contribute to these reflections (superstructure reflections). p. (5. = 0. 4. whatever the value of the three phases.F. the reflections have to be divided into the set of substructure reflections with high mean intensity and the set of superstructure reflections with low mean intensity.1) where the mi are the magic integers. 12).
2. A comparison between the use of quadrant permutations and that of magicinteger permutations is shown in Table 5. ~ a i n [ ~ ~ ~ . . . . increases as n increases and. . .5 should be explored). ~ ~ ~ ~ described the theory of magic integers and gave some rules for selecting those sequences which minimize the mean square deviations (Aq2) of the represented phases. gives the . . = 2x mod (1) and q2= 3x mod (1) (Fig. This comparison may be better illustrated by considering the case n = 2.~..1) and x is explored at regular intervals in the range 01 (if the enantiomorph has to be fixed. . slightly higher (Aq). Magic integer sequences based on the geometric progression with common ratio r = 2 (top) and on the Fibonacci series (bottom).F. the lines q . . m3 . the value of x which best satisfies (5.2) as a function x.~. 4. will give rise to the magic integers listed in the top part of Table 5. are those for which 2m1 = m.1.1. . p.1.1... The optimal sequences also have the advantage that the errors are equally distributed among the represented phases. . m.F. it is preferable to use magic integers based on Fibonacci series. .618. mnPl2 mn2.F..F. Ax is therefore a function of n and of the m.2). at the cost of . root mean square error of the phases represented with the different magicinteger sequences.. The choice of regular + Table 5.F. 4. 13. So far we have used the sequence of three magic integers 3. 5. .. Table 5. In several multisolution programs the general phases in the starting set are expressed in the form (5. . .. It turns out that the optimal sequences m. The value of the interval Ax is chosen in such a way that the mean variation of the phases from one value of x to the other is of the same order of magnitude of the corresponding (Aq). From . 2.F. . q2).F. 5. number 1. 3.m1 form a geometric progression of integer numbers with common ratio r 3 1. 16. (Aq). + 1 and the differences m.. . with the help of Fig. An integer progression with common ratio less than 2 is the socalled Fibonacci series 1. 1. 8. .F.1 it may be seen that (Aq). is the root mean square error of the phases represented by each sequence n Sequence (AQJ)~. In order to keep the number of explored x values (each value corresponding to a trial starting set of phases) within reasonable limits.F. 2. . 5. . but other longer or shorter sequences of different integers may be used.1.2(a)). where the column headed (Aq). For r = 2 the progression 1.Solution and refinement of crystal structures 1 389 The reader may assign any three values to the phases and find by trial and o 766 error. where each term is defined as the Fig. for which it is possible to draw in the plane ( q l . The accuracy with which phases can be represented by magic integers depends on the values of the integers and on the length of the sequence. 5. m2. m2 . . The corresponding magicinteger sequences are listed in the bottom part of Table 5.m2. 5.. only the interval 00. Representaton o f t h e three phases In sum of the two preceding ones (F.l.m. 8.F. . values and it is smaller the larger are the integers. = Fnl Fn2) and r tends to the golden eqns (5. for a given n it is lower when the integers are larger (r = 2).F.
i. as the first phases will be determined by few relationships. starting with a fairly large set of phases (more than 4050 phases). At the basis of all recent developments of the multisolution techniques lies the empirical observation that it is possible to solve structures.The new phases obtained in this way are called secondary phases. The starting set of phases will therefore include the originfixing phases. + + .2. This corresponds to a more efficient way of sampling the phase space than that shown in Fig.. called primary phases. while the accuracy of phase representation is kept within acceptable limits. The first factor will make the initial steps of phase expansion very critical. if then q s =(ml m. 5.["^] A limited number of phases (normally 1015). = 3x: the p triangles indicate the 12 regularly spaced points.. With a Fig..G New multisolution techniques In the multisolution process described on p.e. q2): (a) Lines q. giving rise to the same number of phase permutations. For instance. Those using magic integers are at the basis of the computer programs MAGIC['^^] and MAG EX. 360 there are two main limitations: the restricted number of startingset phases and the 'chain' character of the phase expansion process by means of the tangent formula. Illustration of two phases in the plane (q. along these lines. the use of magic integers allows an increase in the starting set of phases without a great decrease in accuracy..390 1 Davide Viterbo Table 5."I.)x n.F. intervals along x. The different methods proposed differ in the way in which the large initial set of phases is set up. f 3n/4) and the permutations obtained with magic integers based on the Fibonacci series. obtained by quadrant permutation.. gives rise to a closepacked hexagonal disposition of points in the phase space. even though these might be very inaccurate. Quadrant No. Comparison between quadrant permutations (f n/4. This is also true for n > 2 and it may be concluded that the use of magic integers allows a considerable reduction in the number of trial permutations. This is set up using all triplets relating the phases in the starting set. the primary and secondary phases. are expressed as qpi mix. and their number can be up to 6070. The selection of the x values to be tried is done by means of the qmap. with intervals of the order of (Aq).. permutations Magic integers No. permutations (AV)~. while the second factor will amplify the first effect in the following steps. 5. it will be possible to express also the phase of the third reflection as a combination of magic integers.2.S.F.F. (b)The triangles indicate the 16 points corresponding to quadrant permutation. 5. As we have seen.. = 2xand r .2(b). If two of these = phases enter in a triplet with sufficiently large G.
a triplet may be written in terms of independent reflections as where b is a constant angle depending only on the symmetry operators of the space group. (5.2) we substitute the primary and secondary phases expressed in terms of magic integers. The leastsquares procedure may now be carried out and new values of the phases obtained. the values obtained in this way will in general not be integer and will be approximated to the nearest integer. To obtain the correct phase values it is necessary to know the values of the righthand terms of relations such as (5.G. Each set is then refined by a leastsquares procedure assuming as observational equations all triplet relations of type (5.G. needs an important warning.G.4) @ ( x ) is a onedimensional Fourier series and can be easily calculated at regular intervals of x of the order of 1/(4Mm. with respect to the tangent formula. cos (M. are selected to obtain the same number of sets of numerical values of the phases. The first proposed random procedure is at the basis of the program. zero. is that all phases are refined at the same time. The condition that all NR relationships of type (5. these in turn will yield new estimates of the ns and the process is repeated until convergence.2). Some 100 best interrelated phases (selected by means of the convergence procedure) form the starting set and are assigned several sets of random values. we will obtain where M is a combination of integers and B = b +other constant terms appearing in the definition of secondary phases. We must have some prior estimate of the n values. but in our case. in another way. or. the cost is a longer computing time. Some 100 x values.64).G. The use of a leastsquares procedure in the case of cyclic variables defined modulo 2n.2) not reduced modulo 2n.x + B. If in (5. corresponding to the highest values of @@). we must know n in the equation CD = 2nn (n positive. after this refinement.. An extreme radicalization of the basic idea of enlarging the starting set by allowing larger phase errors.Solution and refinement of crystal structures 1 391 procedure similar to that used in deriving relation (5.). Each phase set. the cyclic nature of the variables introduces the new unknowns n. The @mapis thus obtained and its maxima indicate the best values of x.3) among the startingset phases should be as close to zero as possible (or cos CD = +1) may be expressed as NR @(x)= r=l G.) = max. The advantage of this refinement procedure.G. It may be interesting to note that this is another way in which the 'phase problem' shows up: it is generally possible to solve an overdetermined system of some thousands linear equations in terms of some hundreds of unknowns. the number of which is equal to the number of observational equations. which are then further refined and expanded. or negative integer). and this may be obtained from the starting random values of the phases.[1271 starting phases are now assigned random values between 0 The and 360" and then refined with different techniques. is expanded by the tangent formula and . is the random approach to the phase problem.
are directly refined by a carefully weighted tangent formula. The success of this and other random methods implies that.392 1 Davide Viterbo tested by some figures of merit. All the described random procedures have proved very successful in solving rather complex crystal structures. the value which maximizes (or minimizes) a selected function of the parameters is taken as a better value for this parameter and is used in the subsequent calculations with the next parameters. Applications of this method have shown that it is possible to hit the correct solution starting with a limited number (around 100) of random phase sets.nAuj to u9 nAu.6) and A large value of F is in agreement with the most probable value of the triplets.G. The advantage of the parametershift method is its ability to jump away from a local extremum. if N (=loo) is the number of starting phases. the probability of getting the correct solution decreases as the structural complexity increases. in 2n steps of Aui.['^'] In the first the initial random phases are refined by parameter shift. Finally we mention an alternative random procedure[1341which has . Its derivation is too long to be reported here and we will just mention that it also includes quartet invariants.25. has been implemented within the SHELXS86['01 program.24) expressed in terms of normalized structure factors. only shows a limited number of minima. are accepted. Also in this case a limited number of trials (50200. More recently two new random procedures have been incorporated into the computer programs X M Y [ ~and ~ . A similar random start procedure. ~ ~ ~ ~ ~ SAY TAN. A more straightforward procedure is applied in the RANT AN['^^] program in which the random starting sets of phases. in which the refinement is carried out. In the XMY procedure the function which is maximized is + where Xh = C k IEhEkEhkl COS (9)h + 9)k + qhk) (5.[1331 By this method all parameters are supposed independent so that each of them can be varied systematically from uy . The initial random phases are assigned a weight w = 0. including all reflections with large (El values.25 and at each cycle only the phases determined with a sufficiently high ah value. it will be sufficient'to start from a limited number of random points in this space to converge to the minimum corresponding to the correct solution. depending on the structural complexity) is capable of yielding the correct structure. then the Ndimensional space. In SAYTAN random phases are refined by means of a modified tangent formula derived from Sayre's equation (5. 1) > 0. The process is continued until selfconsistency. so that wh =: min (0. 2ah. but with a different strategy.
H. . then (sin a ) = 0 and (5. on the other hand. but in the righthand side of (5. In the MESS approach. the starting phases are derived from triplets perturbed by random shifts A@ obeying a von Mises distribution. and FQ is the contribution of the Q unknown atoms. 5 . In order to derive (cos a ) we must first know the probability distribution of c?.1.H Procedures for completing a partial model Weights for Fourier syntheses Given the positions of some atoms. Vector representation i n the complex plane of the structure factor as a sum of t w o components. 2) becomes indicating that the 'best' Fourier synthesis is obtained by weighting the IFNI factors by w = (cos a ) .H.. When phases are generated at random they are in general inconsistent with positivity and atomicity of the electron density. let where FN is the structure factor of the complete structure.e. H. what weights should be given to the coefficients in order to obtain the 'best' Fourier map revealing the remainder of the structure? This problem was first tackled by ~ i m [ ~ ' . ~1 . + B2Q)lCQ] (5.1.H. a .9. and only the refinement process will make them comply with these conditions. since a can equally have positive and negative values. Also in this case the number of trials necessary to get the solution is comparatively small and the procedure proved successful in solving several complex structures. 5.4) where CQ = C.2) a is unknown and the best estimate of FQ is obtained by replacing exp (ia) by its expected value (exp (ia)) = (cos a ) + i(sin a ) = (COS ) .A. f: is a summation over the unknown atoms. With reference to Fig.s. 5.s. we have seen that these two conditions are at the basis of the probability formulae for triplets or other i. these phases will then comply with positivity and atomicity.. where a = qN.13) becomes + 1 P(AQ. i. Ideally we should compute a Fourier synthesis with FQas coefficients.H.. ' ~ ] .Solution and refinement of crystal structures 1 393 recently been incorporated in the SIR program[671 and is indicated with the name MESS.we have A$ + B ~ Q = IFQI2 IFNI2 = + . Fp is the contribution of the P known atoms. From the triangle in Fig.5) Fig.(A. or s.2 lFNlIFPIcos a (5.H. For FQ= AQ iBQ the probability distribution (5. BQ) = exp JGCQ [ . 5.
1) .8) Finally P(a) = exp (X cos a) 2"Io(X) .394 1 Davide Viterbo The only unknown term is a and (5.H.H. positions of heavy atoms) can be initially determined.7) where X = 2 lFN( IFpIICQand K is a normalizing constant given by (see eqns (5.13) Syntheses for completing a partial model We have seen that often only part of the structure (e.H. (5.H.H.17)) K= $ exp (X cos a ) da = 2nIo(X). For this purpose Ramachandran and Raman[136] proposed several types of Fourier syntheses[13721381 different coefficients. this information can then be combined with the Patterson function to define the rest of the structure.D.3) becomes dm=. P ( a ) = (1/K) exp (X cos a ) .e.H. 1 complex conjugate of Fp) where the terms have the same meaning as in (5. ~ . Among them we will recall the a with and the /3 syntheses. (5.15) and (5.g. i. (5. with coefficients a synthesis /3 synthesis IF~(~F~ 1 ~ ~ 1 ~(F. 10) When this weight is used in Fourier recycling.6) is essentially a probability distribution of a . Recalling eqn (5.H. we may now derive w = (cos a ) = and (5 . then IFN( (Fobs( = and the employed coefficients are Similarly ~ o o l f s o n [derived that for centrosymmetric structures '~~~ FP+ (FQ)= IFobsl tanh (X12)Sp where Sp is the sign of Fp."(X) Io(X) ' (5.D.68).
H. for noncentrosymmetric structures. F. . to reveal the known P atoms and the unknown Q atoms respectively. considering that IF~12 = ((FP + F~)(F.) = Fp + FQ FT. it contains fewer background peaks than the /3 synthesis and is more effective in suppressing the peaks corresponding to wrong atoms in the initial model.H. and 4 contributes mainly to the background.20) The new synthesis is referred to as the 2F.) (5. synthesis. By illuminating the .~ r e n d t [ ' ~ lThe ]).H. 5. contributes to the background and the desired Q peaks. proposed by Tollin et between the a synthesis and the optical image synthesis by holography (see any optics textbook such as ~ e y e r . A similar development for the coefficients of the /3 synthesis yields to I F ~ ( ~= Fp~ FQ+ F$ exp 2iqp / F I +IFQ~~/F~ (5. and the second to the desired unknown part.16) where the first two terms contribute.1). while the last two terms contribute mainly to the background. contribute to the background and the P peaks. In order to give the P and the Q peaks the same weight. From (5.12) are obtained as where the last two terms mainly contribute to the background.5) the expected value may be derived and. the Patterson coefficients IFNI2 become and those of the a synthesis where 4 and F.H.2. (5.H.12) (also called weighted y' synthesis). An advantage of the /3 over the a synthesis is that it gives the electron density map when Fp = FN. as in the case of the /3 synthesis. the first term contributes to the known part of the structure.H.IFPI) exp (iq. but only with half weight. The waves scattered by the object Q interfere with those from a coherent point source P and the fringe pattern is recorded on a photographic plate to form a hologram (H).F. it has been shown that.exp (2iqp) + + {JFQ12 (lFQ12))lFg. the coefficients of the y' synthesis should be altered to (2 IFNl (cos a) . principle of holography is illustrated in Fig. with equal weight. + F.18) the coefficients (5.H.H. Let us conclude this paragraph with a comparison. The intensity pattern on the hologram will depend on the phase relationships between the interfering waves from P and Q. ~ a i n [ l compared the P synthesis with the synthesis computed with ~~] coefficients (5.Solution and refinement of crystal structures ( 395 Considering (5.
H. When the hologram is illuminated by a light from the source P. If t. Scheme of the formation of a hologram.23). 5 ' (b) IMAGE RECONSTRUCT ION hologram with light identical to that from P.H. = T. exp (2xias) + 1 T. the resulting modulated function will be IT. exp (5.396 ( Davide Viterbo n laser (a) RECORDING mirror 'reference beam image / .21) where a is the separation between t.(x) and t Q ( x )are the functions describing the source P and the object Q.H. In the case of a partially known . the image of the object Q may be reconstructed. 1 T . Comparison with (5.2.(x) and tQ(x).H. The intensity at s on H will then be where the s dependence has been omitted.H.15) shows that the four terms of the a synthesis coefficients are formally similar to those in (5. 5. the corresponding scattered amplitudes will be their Fourier transforms TP(s) and TQ(s).23) Its Fourier transform will be the combination of the transforms of the four different terms and will show the image of the object Q. [ ~ T. laser Fig.(^ + + T $ T .~~TQ ( h i a s ) . IT. The amplitude at a point s on the hologram will be A ( s ) = Tp(s)+ TQ(s)exp (2nias) (5.
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the ionic model. is related to the energy of thg electron. . (s = fi). d. we shall see how it is possible to rationalize some atomic structures in terms of the energetics of crystal formation. The closepacking model of spheres is examined closely and used as a helpful tool to describe many structures. attractive for its simplicity. (2) 1. The structure of the atom Atoms with a single electron We know from quantum that the motion of the electro~ (e) in a hydrogen atom can be described by means of the wave function Y(x. or orbital. . 1. 3. f. expresses the angular momentum h/2n) (where h is Plank's constant) of the path ~f module (= the electron and determines the form of its orbital: orbitals are indicated by the letters s. the azimuthal quantum number. (1 s m S +1) represents the angular momentum component in the direction of the magnetic field and characterizes the orientation of the orbital. .Ionic crystals FERNANDO SCORDARI Introduction This chapter deals with a class of natural and synthetic compounds that. The electron can assume different states of energy. Finally we see how the concepts and principles illustrated previously are very useful for the systemization of several ionic structures with different degrees of complexity.1 . n . y. (4) s. can be treated as being composed of oppositely charged spheres. will be used even if departure from the predictions are common particularly when bonds have quite prevalent covalent character. at least to a first approximation. To this end. z)I2 dv expresses the probabjlity of finding the electron in a given element of volume. p. We start by illustrating some important chemical and physical concepts that are later on applied to the organization of ionic crystals. the magnetic quantum number. 1. dv. g . 2. the spin quantum number. . and can have any positive integral value from 1 to w. and that IY(x. 4 . determines the way in which the electron spins. . y. the principal quantum number. v m (3) m. and correspond respectively to 1 = 0 . m. z). . each distinguished by four quantum numbers n. For instance. s: (1) n.
These configurations allow us to estimate the magnitude of the v vector that is proportional to the probability (summed over all distances) that the electron will be found in that direction. 6.. (6.. This exploits the Pauli principle and a scale of the relative energy of the orbitals. ~ isr )known as the radial probability function. r. and 3d. &&% r (4) .1) While R. Fig. Therefore two electrons belonging to the same orbital. must spin in opposite ways. 2s. . occurring before the main maximum. Relationship between the orthogonal coordinates x y zand the spherical coordinates . v. It is = ( represented in Fig.1) Y(x. The spatial shapes of the angular probability functions are illustrated in Fig.2 for orbitals Is. (as shown in Fig. produces some important effects. z ) can be resolved into the products of three functions with separate variables: Y(r. or gradual building up of atoms.3. the same. 6. Let us examine now the angular part of Y(r. The probability of finding the electron in a spherical shell of volume 4nr2 dr.. 3s.1. ~ ( 6 ) @ r n ( ~ ) .(r) dr. and 3d for the hydrogen atom. as defined by the first three quantum numbers. q ) = R n . and s. 6. 6.2) whereby we can deduce that the ionization energy required by the 3s electron is greater than that required by the 3p electron. l ( r ) e 1 . The Pauli principle can be synthesized as follows: in an atom no two electrons exist which have all four quantum numbers. 1. 3p. For example when the electron is located in the 3s orbital it is more penetrating than that when it is in the 3p. Radial probability functions for orbitals 1s: 2% 2p. m. 8.404 ( Fernando Scordari Using the spherical coordinates r. is 4nr2R. q (see Fig. 3% 3p. y. 2p. 8 and @ take different algebraic forms according to the quantum numbers with which they are associated. The presence of secondary maxima. 6 . n. \ X Fig. 6.. 6 . The functions R.(r) gives the probability of finding the electron at a certain distance from the nucleus. 6.2. 6. Atoms with more than one electron The basic configuration of the electrons of an atom can easily be deduced by means of the aufbau principle. the form and the orientation of its orbital are determined by 8 and @. at a distance of r from the nucleus. q ) . The function Dnal(r) 4 ? ~ r ~ R .
6. Relative energy of various orbitals versus the atomic number Z. P. 6.4). though not always reliable (see Fig. and (c) dx2.2.. (b) P P.3. 6.Ionic crystals 1 405 dXby2 d ~2 d x ~ ~ X Z dyz Fig.. . orbitals.. dr2. I (d The energy of the orbitals for various neutral atoms increases in the following order: This experimental scale. Fig. dVr dxrl dyz .4. Angular probability functions for: (a) s.
Such variations in electrons attraction can be evaluated by means of: ionization energy (IE).1 by a broken line. and so on. have their external electrons in orbitals (n . indicate the increasing quantities of energy necessary to free electrons 1. etc. Elements whose valence electrons are in the s orbitals belong to groups IA or IIA: alkaline metals have only one valence electron in their s orbital. taking into account its electron configuration. while alkalineearth metals have two.406 1 Fernando Scordari nevertheless constitutes a good guide for the building up of atomic structures and especially for the location of valence electrons. The influence which the nuclear charge has on the external electrons varies according to which orbitals they occupy and to what degree they are shielded by the electrons closer to the nucleus (see p. Interactions between ions Notes on chemical bonds A knowledge of the structure of an atom allows reasonable predictions to be made about interactions between adjacent atoms. taking into account its chemical behaviour similar to that of the other noble gases. The relative energy of the orbitals versus Z is shown in Fig.4. Those elements whose valence electrons are in the p orbitals belong to groups I11 to VIIIA. 2. exactly as predicted by the energy scale. Such elements are known as posttransition metals and nonmetals. electronic affinity (EA). First. 6. Following the aufbau principle the orbitals are filled gradually as shown below: Chemical element Orbital n I m s Electrons On the same principle. The elements in groups from IB to VIIIB.2) the last orbital s(n). second energy of ionization. 419). At this point it will be useful to recall certain general concepts of chemistry. The closer the electron is to the nucleus the greater the energy required.l)d which immediately precede the last orbital ns. and are separated roughly in the Table 6. Helium (in the hatched square) can be placed either in group IIA. For example the outermost electrons of Rb and Sr occupy the 5s orbital rather than the 4d. In accordance with recent thermodynamic conventions endothermic .1. or in group VIIIA. Finally there are the lanthanides and actinides which are characterized by a gradual filling of the f orbitals preceding by two places (n . known as transition metals. the entire periodic table can be obtained in the same way. electronegativity (EN). I E is the energy needed to remove an electron from the orbital of an atom to an infinite distance. as illustrated in Table 6.
Nobel gases. t . "The stair step running from boron to astatine. T h e p e r i o d i c t a b l e of e l e m e n t s a n d c o n f i g u r a t i o n s of i n t e r n a l e l e c t r o n s ( f i r s t c o l u m n ) a n d v a l e n c e e l e c t r o n s ( f i r s t r o w ) .Table 1. bTran~ition metals. with t h e m o s t i m p o r t a n t u n d e r l i n e d nner !lectronc 0 2 1 0 1 8 16 i4 16 "Light metals. divides nonmetals from posttransition metals. T h e o x i d a t i o n s t a t e s in c o m p o u n d s a r e g i v e n in t h e u p p e r p a r t of t h e cases.
E. unlike IE and EA..93 0.35 1. Partial series of the electronegativity of elements i n accordance with Sander~on[~' Element EN H He Li Be B C N Element EN V2 Cr2+ Mn2+ Fe Co2+ Ni2+ Cu Zn2+ Ga3+ Ge4+ As3+ Se Br Kr Rb Sr Y zr2+ Nb Mo Tc Ru + Element Rh Pb Ag Cd In Sn2+ Sn4+ Sb Te I Xe Cs Ba La Ce Pr Nd Prn Sm Eu Gd Tb EN 1.46 3.04 1.96 0. while exothermic energy (given off by the atom) is marked negative.24 1.33 1.92 1.88 2.19 1. (2) weak bonds with energy E.2.31 2. ~ ] to define E N have led to various electronegativity series. Type (1) bonds are due to direct interaction between the outermost .94 0.OO 1.94 Element DY Ho Er Trn Yb Lu Hf Ta W Re 0s Ir Pt Au Hg TI+ EN 0.94 0.94 0.13 1.36 1.57 1.96 0.53 2. as the addition of the first electron has brought the atom to a sort of 'saturation' level. R.96 3.). in correspondence to R = R e .98 1. the E N cannot be an invariable value for each element.96 0. It is difficult to evaluate this property.38 0. is indicated by E.17 0.94 0.98 1.70 1.33 1.36 1.66 3. and E. as opposed to the energy they would possess at an infinite distance.06 1. The minimum of this function. E.70 0.69 0. The acquisition of a first electron by nonmetallic atoms involves the giving off of energy.92 0.44 1.12 1.19 2.74 1. E A is the energy given off when an electron is added to the valence shell of an atom. EN expresses the property of an atom to attract electrons to itself when it combines. > 90 kcal moll. < 35 kcal mol'.93 3. The semiempirical series adopted here is that of ~ a n d e r s o n . Since the vast majority of elements can form large numbers of combinations. [illustrated in ~] Table 6.96 1.47 2.13 1.72 1.92 0.75 1.73 1..61 2.02 2.72 1.96 0.42 1. since.01  2. Two atoms or ions are influenced by two forces: attraction (Fa) and repulsion (F. the acquisition of a further electron is an endothermic process.96 0.94 0. The various methods u ~ e d [ ~ . The algebraic sum of their relative energies. However.31 0 F Ne Na Mg Al Si P S CI Ar K Ca Sc ~i'+ 0.86 2.40 TI^+ Pb2+ Pb4+ energy (absorbed by the atom) is marked positive.10 2.24 1.09 1. it depends also on the nature and number of the atoms with which it bonds.58 2.92 0.96 0.47 1.14 1.28 3.50 2.34 2.74 2.86 1. is the bond length in correspondence with which the forces of attraction and repulsion are balanced.2.76 2.47 1. The bonds can be divided orientationally into two categories: (1) strong bonds with energy E.26 1.93 0.92 0.54 1.61 1. represents the energy gain of a couple of ions in 'contact'.408 1 Fernando Scordari Table 6.63 0.16 2.88 1.85 1.92 4.
2) Using Table 6. then the bond is referred to as an ionic bond (e.. forces like van der Waals forces or hydrogen bond. What conditions must be satisfied in order that a combination of ions may be considered stable? 2. an NaCl crystal). The various types of bonds which form between the atoms play an important role in determining geometrically the structural pattern and the physicochemical properties which characterize a crystalline substance.2 for NaC1. The further apart two elements are in a given period.e. molecular crystals.exp [O.lonic crystals 1 409 orbital electrons. What are the configurations that such combinations give rise to? The energy associated with a given ions' disposition will be analysed . finite.ENy). Finally. an H.~~(AEN.g. in accordance with ~ a u l i n ~ ID~can be estimated by means of the following . In nonmolecular crystals the protagonists are atoms or ions (simple or complex) which are held together by more or less localized bonds. and LiF the following values for ID can be obtained: 0. then the bond is known as metallic (e. crystalline Na). essentially electrostatic. hydrated salts.)~]. by Coulomb interactions.['] Van der Waals forces are present in all compounds: together with hydrogen bonds they play a primary role in molecular crystal structure (see Chapter 7). etc. The degree of ionicity of a bond (ID) can be evaluated if the difference in electronegativity between two atoms involves (X and Y) is known. in particular ionic crystals. If the bond between them is simple. This chapter will deal with nonmolecular crystals. atomic aggregates can be found.[ ] equation: (6. The following questions will be considered: 1. the greater is the difference in electronegativity between them. more or less complex. instead. In molecular crystals. Hydrogen bonds are fundamental for the cohesion of many compounds like proteins. then. molecules. lonic crystals The periodic table (Table 6. Type (2) bonds are due to weaker. giving origin to high concentrations and impoverishments in comparison with the original electronic densities. 0. the outermost electrons tend to be transferred from one atom to the other. 0. KC1.2 show that the E N of elements varies with a certain regularity.90.g. If the bond electrons tend to be concentrated in the region between the atoms. and in limited cases of maximum polarization. molecule). if the bond electrons belong to the whole crystal. (AENxy = ENx . i. In fact it increases much more from left to right (along the periods) than from bottom to top (along the groups). and the more markedly ionic are the bonds of the compounds they form together. then the bond is termed covalent (e.77. ID = 1 .g. Most compounds are characterized by bonds of an intermediate nature which are referred to as heteropolar covalent bonds. If. within which considerably stronger covalent bonds are formed than the van der Waals bonds which are formed between the molecules (see Chapter 7).80.1) and Table 6.
then the stability of a structure can be calculated by means of UL. p+p+) and on the repulsion between fully occupied orbitals at any attempt to superimpose them (Pauli's principle)). being about 80 per cent of the entire potential energy. provided that the groups of atoms associated mainly by covalent bonds are considered as single ions.TS + PV. i. compounds with prevalently ionic bonds are to be found amongst combinations of alkaline metals. is not negligible when transition metals are present in the structure. thus free energy takes the form: where F is Helmholtz's free energy. due to the prevailing short radius forces (such forces depend both on the repulsion of the charges (ee. E . the percentage of energy due to van der Waals forces depends on momentary interactions between induced dipoles.. E. This type of force is always present.e. Lattice energy: the contributions of attractive and repulsive terms With reference to Table 6. as we shall see. E. and S is the entropy. can be estimated experimentally using the BornHaber cycle.. while the atomic building of some typical structures will be analysed in order to answer the second.. since the barycentre of the positive nucleus does not correspond to the barycentre of the negative charges. The lower the AEN between the ions combined. Thus momentary dipoles are formed which interact electrostatically with other induced dipoles. energy due to van der Waals forces.410 1 Fernando Scordari briefly in order to answer the first question. Ev is the dynamic term which expresses the vibration energy of the mobile ions oscillating around the equilibrium positions. E . known also as cohesion energy. (6. energy due to covalent bonds. having a charge equal to that of the whole group. E. Chapter 7 should be consulted for an analysis of the other terms of particular importance for molecular crystals. Gibb's free energy. If the temperature is not very high and the structure is well ordered. alkalineearth metals . due to thermal agitation. which. 411). is about 1015 per cent...4) UL is the static term. if for Ev and TS << UL. is the sum of two terms: E = UL + Ev. T is the absolute temperature. E is the internal energy of the crystal. energy due to crystal field stabilization. UL can be calculated not only for ionic crystals but also for partially ionic crystals (crystals in which there are prevalently covalent bonds as well as prevalently ionic bonds). also known as lattice energy. U is the sum of various values: electrostatic attraction energy E. is definitely the dominant term. due to . Finally. indicates the stability of a crystalline structure. and expresses the potential energy of the immobile ions in the equilibrium positions. the more substantial is the percentage of energy due to covalent bonds.. G = E . F = UL results. E. The term P V (pressure x volume) can be omitted if the pressure is not high. This section will deal only with the first three contributions: E. (see p. etc.1. repulsion energy. the prevailing long radius forces. E. while E .
they are mutually attracted by a force from which the potential electrostatic energy of the charges can be derived: 1 411 In accordance with Born.8) where b and p are empirical parameters. then the total IE is the sum of the partial I E S . +zle.9) gives: . Substituting (6. Born's exponent. At a distance of R from each other.Ionic crystals (groups I. IIA). Alternatively the repulsion energy can be expressed as follows: E. part of group IIIA. can be defined as the energy necessary at absolute zero to break down a mol of crystal into its ionic components.11) in (6. by means of compressibility measures. which can be determined. = b exp (RIP) (6. The formation of an ionic bond can be considered as having two distinct phases in origin: (1) a positive ion or cation forms in the following way: (2) a negative ion or anion forms in the following way: If ionization takes place by means of the taking off of more than one electron. [ ~ . the repulsion energy is given by: where B is a constant of proportionality. n. like n. and nonmetals (groups VI and VIIA). is obtained as follows: hence: Re is the equilibrium distance between two ions. transition metals with low oxidation numbers. is a value linked to the type of ions which form the crystal and variesM from 5 to 12. The total potential energy E for a couple of ions is given by: The minimum of the function E. carrying them to an infinite distance. let us consider two opposite charges supposedly concentrated in a single point. ~ ] For example. z2e (e being the charge or an electron). energy of a crystal. Lattice energy. or rather the U.
'Touching' cations and anions alternating i n a row.12) not only in the number of the interactions N.39 z .10) we found B = 1. ~ a d e l u n g ' s [ ~ ~ ~ ] constant expresses the geometric characteristics of the lattice. = +2zlz2e2/(2~).. in terms of atoms. ~ ~ e ~ ~ " . = 2B/Rn + 2B/(2R)" + 2B/(3R)" + .  Let us calculate the potential energy in the case of a row of N couples of ions of opposite charges.16) becomes: AMvalues for some important lattice types are given in Table 6. = 2z1z2e2/R and E . Fig. is given by: Using the same procedure we will also obtain: E .5. positioned as illustrated in Fig. .9) takes the form: Following the same procedure used in (6. (6. 6. 6. For the two anions on either side of the reference cation (heavily marked circle) and for the two cations immediately outside them. the potential energy will be respectively: E. just equal to the couples of opposite charged ions.15) and observing that the electrostatic ~/2n.Replacing B in (6. . If No (Avogadro's number) is the number of couples of ions contained in a mol. its potential energy can be calculated as .. interactions between each ion and all the others are N .15) will be: Equation (6. (6. but also in the constant 1. (6. 2B/Rn.. @ @ @ @ @ @ @ @ @ %1 . Taking into account all the ions around the marked cation the total E .16) differs from (6.5.14) Thence in the case of a row of ions (6. of a cell which is repeated many times in space.39.412 ( Fernando Scordari . Since a crystal is the content.5: more generally it depends on the type of threedimensional lattice which the ions form. This constant derives from the positions of the ions considered in Fig..3. 6.. and will be indicated here as AM.
. the coefficient . The electrostatic potential.) Anatase (TiO.) 1 413 AM. compounds Structure CsCl Halite (NaCI) Zinc blende (ZnS) Wurtzite (ZnS) Fluorite (CaF. for A . b. using the BornHaber cycle.18) E L is the potential energy of an elementary cell. 6. but not on the number or nature of the intermediate stages of the reaction.3.O) Rutile (TiO. The BornHaber cycle allows the enthalpy or heat of formation AHf of an ionic crystal to be measured. and introduce qEl M(g)+X(g) FHEI  M?g)+x(. .814 X lop8cm. starting from the elements.x. . Sketch of the BornHaber cycle. = x. If in (6.6.17) we = insert the values A . Interpreting the principle of conservation of energy in thermodynamic terms. For example. This term is in practice evaluated by means of particular series.derives from the fact that every couple of ions is included twice in the calculation of (6. represented by the first term of (6. A scheme of the cycle is shown in Fig. are the interatomic vectors between the i and j ions of the cell. some Coordination number follows: (if i = j.18). such as an optimized Ewald's series. diminishes gradually over long distances. (6. AHIE 118.Ionic crystals Table 6. AHIEand AHEA respectively the ionization energies of the metal in its gaseous state and the electronic affinity. Re = 2. that is to say: AHf = AHM AHx + + AHIE+ AHEA+ UL AHM+AHx where AHMand AHx are respectively the sublimation energy of a metallic crystal (M(. N is the number of ions contained in the cell. Madelung constants.6.) and the dissociation energy of the molecule X2 in its gaseous are state (X2(. = 1.74745. and p is the hardness parameter due to its repulsive forces. depends on the point of arrival and of departure.J.) Cuprite (Cu. n = 9. x . 6.2 kcal mol' has been determined.4 kcal mol'.[71 which accelerate their convergence. I # 0). is the repulsion coefficient between the i and j ions. the Hess' law states that AH. = AHEA 83. Born and Haber applied the Hess' law to ionic crystals. 1 is a generic lattice vector. AHx = 29.)  Fig.186.18). for NaCl an enthalpy equal to = 98.3 kcal mol' then UL= .5. zl and z2 are the number of their charges expressed in terms of electrons. Knowing that AHM= 24.
then the two subgroups of the d orbitals. the e. The e. whose lobes are orientated along their Cartesian axes. The first encompasses the three orbitals.. As a result.. dyz). we obtain: = . the conversion factor ergs . The agreement between experimental data and the results of the calculations is particularly good in this case. which is very close to the value obtained from experimental data...2. when all the d orbitals are filled. dX2. If the cation is isolated. dxz. It follows the barycentre principle: the algebraic sum of the energies of the d orbital electrons. 6.[''~] This theory manages to interpret qualitatively. 6.7(c)). Let us analyse two cases: (1) a transition metal in an octahedral coordination. d. will have different energy values..(dxy. The limitations of the CFT are in its presuppositions. If. a series of experimental data.3). although the method tends generally to underestimate the value of UL: in particular the estimate is at least 10 kcal mol' below the experimental value for halogen compounds. (2) a transition metal in a tetrahedral coordination.7(b)). and in particular those having incomplete d orbitals. which are too low compared with observed values. and d. distributed symmetrically at equal distances from the d orbitals (spherical field conditions). In order to explain this discrepancy.kcal. however. the d orbitals all have the same energy (degenerate orbitals). positioned at the vertices of an octahedron and orientated in relation to the orbitals as shown in Fig. d.8(a).. and for this reason the electrons prefer the latter. since it presupposes that between metal ions and ligands interactions of an electrostatic nature only develop. which are in an intermediate position. Lattice energy: CFSE contribution The Born theory often gives UL values for transition metals... whose lobes are orientated along the diagonals of their Cartesian axes. orbitals (shaded) point towards the ligands and are nearer to them than are the t2. is equal . orbitals (white).2 and d. dZ2)and t2. is indicated by A. (Fig. To understand the type of action that the ligands have on the d orbitals of the metal ions. They will have the effect of increasing the energy of the d orbitals. The five d orbitals can be divided into two distinct subgroups on the basis of their orientation. The second group encompasses the two orbitals. orbitals. orbitals have a higher energy value than the t.183. For case (1) we will consider a cation which has all five d orbitals empty. known as crystal field splitting. Bethe and Vleck formulated a theory known as the crystal field theory (cFT).2. while the ligands are considered as point charges.414 1 Fernando Scordari . 6.charges surround the cation. eg(dX2. 6. their spatial geometry must be borne in mind (see Fig. which will remain degenerate (Fig.. with conceptual simplicity. and t. The difference in energy between the e. we imagine that six q. Let us now suppose that the cation is surrounded by pointlike negative charges q.3 kcal molI.
orbital reduces the metal's stability by 0. @.'. y I I Fig. since E. on 1/~.7.6Ao. and (b) a tetrahedral crystal field. on the symmetry of the metal ionligands. while every one that fills an e.6A0 if it belongs to an e. orbitals stabilizes the metal by 0. 6. are not shown.8.!' metal ion in s p h e r i c a l field'.4Ao less than E. ranges between 20 and 90 kcal mol' and depends: on the cation charge (it increases as the charge does). 1 metal i o n in t e t r a h e d r a l field 1 metal ion i n o c t a h e d r a l field 0 00000000~'~E~ 0 metal ion free to that obtained when the cation is in spherical field conditions.< Br. orbital) is known as the crystal field stabilization energy (CFSE) . It might seem. . A.4Ao. (b) Fig. For clarity's sake two of the three orbitals.4Ao if the electron belongs to a t2. and octahedral fields. Moreover.... orbital has an energy value which is 0. a transition metal in (a) an octahedral crystal field.. 0 0 0 0' E f! s. orbital. that the free cation is energetically more stable than the complex.. In order that the d configuration in an octahedral field should have the same energy as that in a spherical field. 6.. (6. and an e.. . f The value obtained from the algebraic sum C i( xi)Ao of all the electrons of d orbitals (x = 0. They are oriented at an angle of 45" to the x axis.< OH.. it is necessary that: 6(Es. > Ei. every electron which occupies one of the t.['1 on the nature of the ligands (some of which in order of increasing stabilization are: I. judging by Fig.6Ao. Orientation of the orbitals e and .Ionic crystals 1 415 I I . orbital. In reality the bond energy (disassociation energy of a pair of touching ions separated into two atoms) is more than enough to compensate for the increase in the energy of the d orbitals. and X + Y = A.o t0 At I '\OO0 0 0 0 .Y) + 4(Esf+ X) = lOE. .20) The solution which satisfies (6. When the cation is in an octahedral field the energies are indicated respectively by X and Y for a t2.t and t . the absolute energy of a d orbital of the cation in spherical field condition. spectrochemical series). or +0. on the type of d orbital involved (it increases substantially from the 3d orbitals to the 5d orbitals). or to be more precise. < F. . in the planes x y and xz respectively. LY= 0.20) is: X = 0..7.t of .< NO. tetrahedral. Let us indicate Ei the absolute energy of a d orbital of the cation when isolated and E.< s' < C1.4Ao. Energy levels relative to the d orbitals in spherical. Thus.< H 2 0 < NO. an electron which occupies a t2. 6. on the distance (R) between the metal ion and ligands.
8 1.6+ P 2. forming a highspin complex (four electrons which spin in the same way give a very paramagnetic compound). in a tetrahedral coordination the three t2 orbitals have more energy than the two e orbitals (Fig.8(b) shows four ligands at the vertices of a tetrahedron.4 shows the CFSE relative to high. or it may associate with another electron already in a t2. and is inferior to the Ao(A. > P. orbital.8+2P 1.lA.416 1 Fernando Scordari Let us now analyse how the electrons are positioned in the d orbitals. orbital. The fourth electron has two possibilities: it may occupy an e. (2) to compensate the exchange energy which is lost when Hund's first rule is violated. orbitals.2 0.2 1. e. Lowspin configuration t. The first three electrons occupy the three t. P. Figure 6.6+4P 0.4 1.. If the A.6 0.0 0. CFSE(A.O+5P 0 1 2 3 4 5 6 7 8 9 10 0 1 .4+P 0. which we shall call tZ.and lowspin configurations. .7(a)).) 0. If the A.2+3P 0. for octahedral sites. orbital. then the fourth electron will go to fill a t2.8+3P 1.0 0. in its fundamental state. The three d orbitals. then the fourth electron will go to fill an e. 6. = 419) for two reasons: (1) because there is no direct interaction between the ligands and the d Table 6. The crystal field separation value is indicated by A. Two factors influence the fourth electron and decide which tendency will prevail: the A.6+4P O. are nearer to the ligand than are the other two e orbitals. unlike an octahedral coordination. We will now examine the case of a transition metal in a tetrahedral configuration. and the pairing energy.0+ 5P e. Table 6.8 1.4. The latter can be defined as the energy necessary: (1) to overcome the repulsion which exists between two electrons which occupy the same orbital.i2+v3+ 2 3 v2+cr3+Mn4+ 3 cr2+~n3+ 3 ~n'+Fe~' ~ e ' + ~ o ~ + N i ~4 + 5 co2+Ni3+ 6 Ni2+ 6 cu2+ 2n2+~a3+Ge4+ 6 ca2+sc3+Ti4+ 1 2 2 2 2 3 4 0 1 2 3 4 5 6 6 6 6 6 + + 1 2 3 4 .0 0. CFSE (A. in accordance with the Hund's first rule. CFSE for transition metals of the first series i n octahedral configurations Number of d electrons Ion Highspin configuration t.2+3P 0. follows the maximum multiplicity principle: in a partially filled orbital the number of electrons having the same spin orbital is maximum).4 0.) 0..0 2P 3P 2. thus further stabilizing the complex. < P. or maximum multiplicity principle (an atom. forming a lowspin complex (two electrons which spin in opposite direction plus two electrons which spin in the same way give a compound which is not very paramagnetic). which spins in the opposite direction. This implies that.4 0. orbital.
e. OSSE (i. If the CFSEs of Table 6. high spin OSSE high spin CFSE.Ionic crystals 1 417 orbitals of the metal ion.6). For the ions involved see Table 6. easily computed with the aid of Table 6. Table 6.4 Number of d electrons CFSE. the CFSE favours octahedral complexes. At this point it will be useful to list the factors. CFSE for transition metals of the first series in tetrahedral configurations. 425). .5). both because A = (9/4)A. and the octahedral site stabilization energy. but also to resolve certain problems without recourse to Xray techniques. the position of the ligand in the spectrochemical series (see p.6. Table 6.4 and 6. OSSE for transition metals of the first series. which are at times mutually opposed. can be calculated in A units (see . Table 4.5. Amongst the numerous applications of lattice energy calculations. octahedral if on the right: a high ligand charge favours octahedral coordination. tetrahedral complexes have only highspin configurations.) Applications of lattice energy calculations Lattice energy calculations make it possible not only to rationalize a series of observations arising from structural analyses. CFSE(A.5 are multiplied by the scale factor 419.5 shows the CFSE relative to highspin configurations for tetrahedral sites. For the ions involved see Table 6. they can be compared with the CFSE of Table 6. This explains why. increasing the number of electrons in tZgorbitals. (2) because there are four ligands instead of six. which govern cation coordination: voluminous ligands favour tetrahedral coordination (see p. A.4 Number of d electrons e Highspin configuration t. the difference between the CFSEs concerning octahedral and tetrahedral sites).. Tables 6. as experience has demonstrated. which in turn favours the formation of lowspin complexes. and because the CFSE of tetrahedral complexes is generally less than those of octahedral complexes (cf. 415) favours tetrahedral coordination if on the left.4. because it increases Ao. unit CFSE. low spin OSSE low spin .
and silicates. Na+. borates. (5) the determination of charge distribution in complex ions. 444).418 1 Fernando Scordari various automatic programmes. M(1) and M(2) respectively. then the cations with smaller charges will prefer the M(l) site. Fe3+. Ionic radius An important factor which influences the geometry of the structure of ionic compounds is the socalled ionic radius. moving the atoms in all possible directions. has Mg2+ in M(l) and Ca2+ in M(2). If.0) and on the mirror plane.76 = re(Sc3+)= 0. phosphates. just as the actual structure shows them to be. It expresses the 'dimensions' of an . the concentration of A13+ in a particular tetrahedral site determines the site which the Na+ will occupy. at the centre (0. etc. where re(Li+) = 0. ~ e c e n t l ~ . [ ' ~ ] starting from the ideal structure of olivine. was calculated for 16 isostructural compounds with olivine.) at high temperatures. = monticellite.0.). c a 2 + . it has been noticed that the compact regular layers of oxygen atoms used as input in the calculations are deformed in the process of potential energy minimization. can be described as a distorted hexagonal closestpacked system of oxygen atoms (see p. (2) the effect of the distribution of certain cations in certain sites on the position of others. (4) solutions to structural problems.745 A. (3) structural predictions. The determination of the structure of an inorganic crystal by means only of calculations of potential energy has serious practical drawbacks if suitable crystallochemical information is lacking initially.[1s1 The structure of olivine. It would be necessary to do an enormous number of trials.) Pbnm. In accordance with the calculation.g.0. U.[161Here too the calculations agree with the experimental data. (7) the effects of temperature and pressure on structures Let us examine some examples in more detail. instead. the compound MgCa[Si04]. In silicates with an olivinetype structure these cations may be monovalent.Fez+.0. where r e ( ~ g 2 + ) 0. The six coordinated cations occupy two sites which are not crystallographically equivalent. Potential energy calculations indicate that if the ionic radii of the cations are comparable.O. then the cation with the greater volume will prefer the M(2) site. the ionic radii are of quite different sizes. the compound Li+Sc3+[Si04]is found to have Li+ in M(l) and Sc3+ in M(2). including certain berylites. M ~ ' + .00 A. Moreover.[72132141 the following: are (1) the distribution of cations in different sites. or trivalent (Li+. that is to say. (6) the estimation of the elastic constants of stable minerals subjected to very high pressures.72 # re(Ca2+)= 1. if their precise positions are not known initially.0. Another example is the influence of the Al/Si distribution on the sites occupied by Na+ in albite (AlSi. space group (s. bivalent.
95 and re(F) = 1. while S indicates a screening effect which depends on the distance of the electrons from the nucleus and on which orbital they occupy.32 A. which agree perfectly with the ionic radii quoted by ~auling. Use the multiplication coefficients 0. re(Na+) = 0. data derived from structural determination by means of Xray techniques suggest that d M x (the interionic distance between a cation M and an anion X) is the sum of the two 'radii' characteristic of the two adjacent ions. ~] characterized by pairs of isoelectronic ions such as NaF. use the coefficients 0. It is preferable to use 0. but very little from the most electronegative atom to the anion.7. for the compound NaF: and.30 to 0. (n . because the latter are nearer to the nucleus. and it is known that d M x = 2. Cations are generally smaller than anions. For example. certain principles suggested by Slater are followed: 1.S. 3.2). in accordance with ~ a u l i n ~ . respectively. are merely conventional terms. Group the electrons as follows: 2.g.(K) = 2. or for those which belong to the next group to the left. ro(Li+)= 0. The average radius of the outermost occupied orbital varies considerably from the least electronegative atom to the cation.since the ionic radius is inversely [~] proportional to Z. for electrons which belong to the same group. 6. 6.162. Various ionic radius systems have been proposed.35 in the case of groups (Is). 2p orbital electrons are better shielded than the 2s orbital electrons. we can obtain: By resolving the system (6.586. receive from them. amongst the most accurate. RbBr.186 A and r.2). e. These systems show that: 1. (n .. 'atomic radius'. This effect can be explained on the basis of the radial distribution curves (Fig.35 and 1. and calculated their effective charge Z.85 for electrons belonging to the groups (ns.36 A can be obtained. With this aim. which show how s orbital electrons provide better shielding for electrons of other orbitals than they. For example. ro(Li) = 1. The problem which needs solving is how to divide d M x between the anion and the cation.2)p) or to any preceding group.[~I This procedure can be extended to analogous isoelectronic compounds..35 and 0.2)s. = Z . CsI. KC1. Nevertheless. In order to evaluate S. Z expresses the formal charge..[(r) = 0 (Fig.Ionic crystals 1 419 ion considered as a rigid sphere. ro(K+)= .1)p) respectively and 1 for those belonging to the group ((n . does not exist. thanks to the large number of structures examined. ~ a u l i n g [considered certain alkaline halides.l)s. np) and ((n . in turn. If the electrons belong to groups (nd) or (nf). are those which have appeared Effective ionic radii extracted from Shannon's original work[lglare given in Table 6.21). when D. Since a finite value of r.. and thus also 'ionic radius'.
Effective ionic radii ( r e ) versus coordination number (CN) according to Shannon[lgl Ion CN Spin re Ion CN Spin re Ion CN Spin re .420 1 Fernando Scordari Table 6.7.
Ionic crystals Table 6.7. (Continued) Ion CN Spin re 1 421 Ion CN Spin re Ion CN Spin re Ion CN Spin re Na' Na' Nb3+ Nb4+ Nb5+ ~ d ~ + Nd3+ Ni2+ Ni3+ Ni4+ yo2+ Np2+ NP3+ NP4+ Np5+ NP6+ Np7' o2 OH os4+ os5+ os6+ os6+ os7+ os8+ p3 p5+ + pa3+ pa4+ pa5+ pb2+ .
while for Li and Cs they are 1.742 A and ro(Br) = 0..10.15) can be rewritten as: E = . In the anions the added electron increases the radius by a few per cent. while an increase in Z. r. dEldR = 0. ro(C1) = 0.13)).5 and eqn (6. 6. while (6. For R = Re. Thus an increase in n tends to increase the atomic volume (the most probable radius increases with n.2. .which act on the atomic radius producing contrasting effects. tends to contract orbitals. The lattice energy allows this trend to be quantified approximately. which is defined below. 4.869 A.AMzlz2e2 CNB +. hardly countered at all by the effects of Z. which is not countered by n (which is constant). see Fig. see Fig.. the Z. induces a notable increase in the atomic volumes from Li to Cs. Since the anion radii remain more or less the same. from which we can work out: Let us suppose that ions of opposite charges can crystallize just as well into a CsCl type structure as an NaCl (halite) or ZnS (wurtzite) one. 3.25) shows that those of a ZnS type lattice (R3) are smaller than it by =4 per cent. The dimensions of the atoms decrease along the period (with n a constant).) are 2.422 1 Fernando Scordari 0. For example.(Br) = 0. In the first case the sharp increase in Z.39) and CN. The ionic radius varies with the coordination number (CN). which in turn increases the effective ionic radius re of the ion of the opposite charge (the cation). e. There is a close relationship between ionic radius and spin state in transition metals.3 per cent greater than those of an NaCl type lattice (R2).R" R where AM is Madelung's constant (which has taken the place of 1. calculated with Slater's principles for Na and C1 are respectively 2. 6. and increases sharply along the group from top to bottom (with n a variable). In the second case the regular increase in n.g. Obviously this also follows for the ionic radius.851. The ionic radius depends on the electronic spin state.20 and 6. ro(C1) = 0. This occurs because the dimensions of an atom depend both on n and on Zeff.. induces a decrease in the dimensions from Na to C1. Assuming that the intermediate value n = 9. 2.2).592 A. we obtain: The result of (6. that is the two anions coordinated by the cation. (6.725 A.3 and 2.. is the coordination number (which has taken the place of the number 2. Note that the repulsion forces increases with the CN. the alkaline metals having the largest dimensions.24) indicates that the interionic distances of a CsCl type lattice (R. the variations occur almost entirely in the cation radius... In fact.
415. then the first six electrons tend to occupy the lower energy level orbitals. have coinciding barycentres of their positive and negative charges. and the coordination polyhedra which the ligands form around the transition metal. the open circles refer t o highspin configuration.7). (b) the dimensions of the anion and its charge. The full circles refer t o lowspin configuration. (c) the deviation of the electronic configuration from that of a noble gas. (b) =trivalent.9). 6. or covalent bonding. These differences in turn affect the ionic radii of the transition metals which have from four to seven electrons in their d orbitals. Two ions of opposite charges. Dependence of the effective ionic radii on the spin state in transition metals of the 1st series: (a) = bivalent. and A. is high. while if A. which is greater in the anion. is low they occupy both energy levels (Fig. and therefore a certain degree of polarization. If. In accordance with ~ajan. A.['O]the polarization depends on: (a) the dimensions of the cation and its charge. for example. Fig. 5. if they are far enough apart. Combination requires a sort of participation on the part of the electronic charge. depend on the type of ligands. The ionic radius is influenced by polarization. 6. electrons with high spin have a larger radius than those with low spin (Fig. 6. .9. To be more precise. When the ions are brought together a distortion of the electronic charge known as polarization.Ionic crystals 1 423 as explained on p. takes place. A.
forces are acting. It follows that the polarizability of halogens varies according to the scale: I. Maximum filling principle The lattice energy of No pairs of ions can be expressed as the sum of the potential energy contributions (uij) relative to all the possible pairs whose components are distant rij: 1 'No UL=uij(ri. whilst reducing their distances to a minimum'. . 0 = Z / r .> C1. and d type electrons. are particularly easily polarized.) (with i # j).26) The lattice energy is minimal if the total potential energy is minimal. the equilibrium distance is as high as possible. we can hope to: (1) predict the most probable arrangement of the anions which surround the cation (coordination polyhedra). or almost central.and p3. that for alkaline metals the polarization power increases according to the following scale: Li+ > Nai > K+ > Rbf > Cs+ (ionic potential. 2 i. the weaker are their bonds. this occurs when: (1) the interatomic distances are as close as possible to the equilibrium distances (R. (2) the number of ions at. by means of a simple geometric rule (radius ratio rule). Moreover. These conditions are general and apply to crystals having simple structural units. By supposing that the ions behave as if they were rigid spheres on which central. or very nearly at. Anions with a high negative charge. (2) describe certain atomic building by means of dense mechanical models based on rigid spheres of equal radius (closest packings).).> Br.424 1 Fernando Scordari This means. increases from right to left). p. or complex units connected to similar units by central or near central forces of attraction.'+ it polarizes more than Mg2+ one extra contiguous anion: this effect is even more noticeable between Cu+ and Naf. such as As3.j=1 2 (6. Therefore.> F. it has been shown above how the different peripheral electrons are shielded by the s. analogously with that of haicogens. although ~ i ' +has approximately the same ionic radius as Mg. The maximum filling principle can be expressed as follows: 'Simple (atoms or ions) or complex (groups of atoms or ions) structural units on which central or near central attractive forces act tend to increase contact with each other to the maximum. Regarding the anions. for example. due both to the greater distance from the nucleus and to the increasing shield effect. the greater the dimensions of their outermost electrons.
[ ~ ~ ] The term coordination is used to refer to the atoms or ions which surround a central atom or ion. Sometimes the first coordination shell is not easily distinguished from the second. The coordination number of each polyhedron is indicated below it. (6) pentagonal bipyramid. + Radius ratio rule If the ions are considered as behaving like rigid spheres. and so on. versus p. They can be found in structures as isolated polyhedra. (2) trigonal bipyramid.e. from their average. ratios. (13) pentagonododecahedron. and/or connected to polyhedra of the same or another type. (7) trigonal dodecahedron.225 cations and anions are no longer adjacent in tetrahedral coordination. (12) rhombododecahedron. (9) threecap trigonal prism. with CN = 6.10..tetrahedra in silicate melts. (1) tetragonal pyramid. (5) sevenvertex polyhedron. i.3./r. if only a little. Figure 6. < 0. e. for CsCl. . 6.g. (8) twocap trigonal prism.Ionic crystals 1 425 Coordination polyhedra It is sometimes convenient to illustrate crystal structures by means of coordination polyhedra.155 S p.e. (3) trigonal prism. From Fig. Figure 6.11 shows some of the most common regular geometrical dispositions and their relative p. to the number of bonds formed by an atom. otherwise the dMx vary. at a tangent to the first nearest neighbours. (4) onecap trigonal prism.g. The coordination number (CN) is equal to the number of the first nearest neighbours. since for p. If it is not otherwise specified below. < 0. (11) truncated tetrahedron.. NaC1. The Xs at a tangent to M are known as the first nearest neighbours of M and constitute the first coordination shell. that within the range 0. which for the three Fig. but also allows their stoichiometry to be deduced. = (r.). The p.g. it may be assumed that the central ion is the cation (M) surrounded by the anions (XI. octahedra where 1< n < 1. and form the second coordination shell. are known as the second nearest neighbours of M. in order to underline the geometrical relationships which characterize structural frameworks. Often such polyhedra continue to exist beyond the crystal state as definite physicochemical realities. 6. the results obtained by geometrical methods must be integrated with further energetic considerations. [siO4I4. and ZnS type structures having the following ratios: This formalism not only indicates the coordination number around each ion.10 and 6. (14) truncated octahedron.11. for example.(SO4). values for a given anion increases as rM. all the centres of X. (10) icosahedron. in aqueous solution of iron s ~ l ~ h a t e . The coordination polyhedron of M can be obtained by 'joining the dots'.12 shows the trend of U. an attempt can be made to predict by geometrical means which coordinations will be preferred. and thus the number of contacts also increase. M in 3. e. thus it is no longer possible. Some of the possible coordination polyhedra are shown in Figs. In such cases the uncertainty is expressed by attributing two numbers to the CN. 6. e.225 a triangular coordination is stable. i. The distances dMx are all equal when M occupies certain symmetrical positions. 6 2. The parameter used for this purpose is p. However. The next Xs. or Fe(H20). Some coordination polyhedra.11 it can be deduced.
Cuboctahedron Fig. m 1= (AD .F G ) / 2 AH' = r X g . and the procedure followed to calculate and p. O'C = r X G (00')' = ( A O ) 2 .11. D / C ~ B A Octahedron Square antiprism or Thomson's cube A B = 2 r x . 00' = = / 2 . A O = r M + r X . name. .AH = r x m .426 1 Fernando Scordari Anions Polyhedron Relationships between rM and rx Dumbbell B A H Triangle C Tetrahedron B Square .( G + 2 ) / 2 = 0 + (m)' + Cube Hexagonal cuboc. 6. At the side of each polyhedron there is its coordination number.. Other very common coordination polyhedra. (rM/rX)' 2rM/rx.
12 it results that: (1) the UL trends are characterized by three discontinuity points in correspondence to the values p..12. Accurate studies[221 determine p(r) to have shown. however. and an NaCl type when 0.17). However. values for CsCI. since Re < R:. = 0. while in (a) and in (c) the same polyhedron for a larger cation (M' > M) and for a smaller one ( M < M) are illustrated respectively. is obviously a gross simplification of the physical reality. (2) the UL trends favour a CsCl type structure when p.71.41).12.414.32 instead of 0. if the ionic radii r.732. > 0. Such compounds with an MX stoichiometry should have structures with a CN = 8. Thus Re has the same value in both configurations (b) and (c). in accordance with the UL(NaC1) trend of Fig. and ZnS type structures are lower than those predicted by geometrical means. 6. The reasons why these discontinuities exist become clearer on observing Fig.32. = 0. for p. U.71 > p. From the point of view of the energy.32 < p. The difference is most accentuated i n the range between an NaCl and a ZnS type structure (0. since the anions already adjacent in (b) cannot come any closer together.e. In accordance with (6.13. From Fig: 6. there is another cation M"' < M so that p.732). and (c) illustrate the changing relationships between equal anions (white circles) in an octahedron. as the cations vary i n size (broken circles).32. > 0. UL does not vary in the range 0. < 0.71. NaCI. between configurations (b) and (c). Despite this. alkalineearth metal oxides are the compounds to which a mechanical atomic model is most easily applied. 6. and also spherical. values a little below the discontinuity point (p. i. In (b) an octahedron of M(X). (3) the UL(NaCl) curve is closer to that of the UL(CsC1) than to that of the UL(ZnS). composition is shown. Alkaline halides and. < 0. (b) (4 Applications of the concept of ionic radius To assume that an atom is rigid. < 0. 6. Configuration (c) becomes unstable and could evolve into configuration (d) if pe < 0.414. the value of UL(NaC1) decreases gradually from configuration (a) to configuration (b). to a lesser extent.Ionic crystals 1 427 compounds in question is M:X = 1:1. for example. the minimum p. Configuration (d) is preferred to (c) if. 0. In the same way. an NaCl type structure is likely to be preferred to a CsCl type when p. pattern versus p. 6. Fig. .32.13. 0. (a). PO @ L3 ...(M) Fig. the concept of ionic radius often produces satisfactory results. (b).225. that is to say. that in MgO the electronic cloud of the oxygen only partially wraps the cation: therefore the terms sphere and ionic radius lose any meaning.
435). 'Average' ionic radii for a CN = 6 are used. the metaloxygen distances. but also those between ions of similar charge in the CN function.67. type have been obtained by plotting the average quantum number n (which indicates roughly the dimensions of the ions) on the y axis and the electronegativity difference. (e) A12Mg0. which is contrary to the experimental data. NaCl type configurations are stable for 0. These fields conform t o the following structure types: (a) 0K2S04. and one. for example.e. Improvements in structural predictions can be obtained by considering not only geometrical factors but also chemical factors. (spinel). = 0.32. 422). i. The dimensions of the cation depend on the CN (see p. and M:X = 8:8 in the lower field C (p. (f) Sr2Pb04. in accordance with both the radii ratio: (p.41 G p. Such a diagram makes it possible to work out the field in which a certain A. p. such compounds are governed by the cation coordination number (since the cation is generally smaller than the anion) and the stoichiometry. So according to as so. Fig. Three fields are shown (T.41.53 and the stoichiometry indicate a compound Na+:Cl. 6.) and tetrahedral (r. The on prediction is improved if p. 6. CsC1. C).12.(A) and r. [ ~ ~ I 'fields of stability' for the most important structures of The A2B04 composition are shown.AEN is used instead of AEN. in accordance with the results of structural analysis. 6. 6. is constituted by M:X = 6:6 structures and can be explained by considering not only the interactions between ions of opposite charge. rx = 1. (i) A12Ba04. < 0. structure prevails. M:X = 6:6 in the intermediate field 0 (0. Considering Fig.(X) are more or less the same. The first anomaly involves the T field.14 a broken line is shown for p. The diamonds and squares show the type of coordination polyhedron on which the real halide structures are based: octahedra and cubes respectively. Finally using effective mean ionic radii. = 0. (b) Na2S04(thenardite). (g) K2NiF4. = 1. and the geometric relationships between the coordination polyhedra (see p. shows that almost all the structures are of M:X = 6:6 type. as deduced by ~ h i l l i p s . several have found quantitative relations between crystallographic and compositional parameters in garnets. can crystallize in either type of coordination. Also for NaCl both the p. 6. Fe). However. 6.32) shows the reduced T field according t o the energy indications of Fig. The broken line (p.) coordinations.12. CsBr (r. delimited by t w o unbroken lines (p.= 6:6. Experimental data.X. and the cell . such as polarization. (olivine). they represent stability areas for the alkaline halides.15. > 0. = 0.32 < p. Therefore ambiguity remains as to the ionic radius dimensions when the structure (and thus the CN) is not known.[^^] it is possible to calculate the oxygen fractional coordinates.0. = 0. and r. C.(B) the stability fields for A2B04 structures are shown. even if some borderline cases may be contrary to the general trend. The incongruence between the observed structure M:X = 6:6 and the predicted structure M:X = 4:4 by the radius ratio rule is only apparent. two are of M:X = 8:8 type (CsI.85) and the stoichiometry (M:X = 1:l). 6. In accordance with geometrical criteria.BO. The other anomaly involving the lower field. Graphs for compositions of M. (h) FeJaO.428 1 Fernando Scordari LI + Na" K+ RbiCs' Fig.14.= 4:4 would gain potential energy and would therefore seem likely to be preferred. < 0.15. if re(IVLi+)were used for LiI.12. Otherwise. The rule of the radius ratio predicts M:X = 4:4 structures in the higher field T (p. The configuration Li+:I.27 would be found to be the right value. CsBr). AEN (which indicates the degree of polarization of the bond).= 8:8. 0.41).41). on the other hand. (c) (Mg..73.96 A) forms a compound Cs': Br.73). Let us compare the theoretical data with the experimental data for the halides.73). = 0. SiO. Another example can be illustrated by means of Fig. (d) Be2Si04 (phenakite).[241 the x axis. < 0. = 0. which corresponds to the point of intersection of the NaCl and ZnS curves in Fig. Taking into account ionic radii r. the values observed. The diagram was obtained empirically on the basis of about 130 structures using the effective radii of the cations in octahedra1 (r. In Fig.
one third of each of which belongs to it. MX. which are all alike from a physical point of view. 6. etc. it should be borne in mind that in the common structures. Let us denote by packing coefficient (ci) the ratio: ci = C (VaIVc) (6. so a total of two holes can be associated with each sphere. some compounds of the type MX. or groups of either. Spheres belonging to the next layer may correspond to the b or the c holes of layer A. take on structures which can be described by means of closest packings of rigid spheres of equal radius. and (OH) are the number of OH groups present in the formula unit (f. For discussion of the concept of ci see Appendix 6. atoms. Such holes.27) where C V is the volume of the atoms or anions contained in the a elementary cell of volume Vc. are indicated by b (white) and c (black). every sphere is surrounded by six holes.u. Hexagonal closest packing (HCP) and cubic closest packing (CCP) satisfy this requirement. known as a hole. This layer has the following characteristics: every sphere is in contact with another six spheres. r(Y)..Ionic crystals 1 429 edge of oxide garnets and hydrogarnets as follows: where r(X). and others with a more complex stoichiometry. replace rigid spheres forming the socalled closestpacking structures.A. 6. The basis of the HCP and CCP dispositions is a layer of spheres (layer A) packed as closely as possible similar to that illustrated in Fig.16. According to the maximum filling principle. When analysing their characteristics. and r(Z) are the mean ionic radii respectively of cations 8. and are thus said to belong to . ions. and 4 coordinated. between every three spheres there is a space. ci + max.) of garnets: Closest packings Most metals.
type sequence. and triangles. tetrahedral. illustrated in Fig. where n is a whole positive number including zero and h is a vector perpendicular to the compact layer of a module h (which is equal to the distance between two successive compact layers). The two characteristic sequences which represent HCP and CCP and their orientation with respect to the compact layers. type sequence. Fig. . The HCP cell is projected in the direction [OOl] 11 h. while on the right is shown the symmetry of a pair of layers AB (3m). and triangular. are illustrated in Fig. A compact layer of spheres characterized by triangular cavities indicated by white spaces (b) and black spaces (c). . The other three can be traced by joining the centres of the spheres which correspond to the three possible holes of the closest packings: octahedral. . 6. . 6.17. 6. while the CCP cell is projected in the direction [ I l l ] 11 h. in general a sphere may correspond to any of three possible holes: a (for layer A) belonging to site (Oa. octahedra. An HCP cell contans two spheres (that of a simple hexagonal cell contains one). + Oa2+ nh) b to site ((2/3)a. 6.16. and c to site ((1/3)al + (2/3)a2 + nh). With reference to a hexagonal mesh of sides a. a CCP cell contains four.430 1 Fernando Scordari Fig. At the top of the sketch on the left is shown the symmetry of the layer A (6m). An ABAB. . HCP is characterized by an ABAB . sequence determines a compact cubic cell (bottom). . It is possible to identify four types of polyhedra in both packings: cuboctahedra. as does a facecentred cubic (FCC) lattice (for this reason it is possible to use FCC or CCP with the same meaning). while CCP is characterized by an ABCABC .. sequence of layers determines a compact hexagonal cell (top). . tetrahedra. layer B or layer C. . and a2. while an ABCABC .17. The first. can be traced by joining the centres of the 12 spheres around a central sphere of equal radius.11. + (1/3)a2+ nh).
. CCP has (Fig. therefore. HCP has all the octahedra and half of the tetrahedra sharing faces with polyhedra of the same type. The first is q (6. share edges. compared with that of the oxygen atoms. (2) eight tetrahedral holes. that they can occupy tetrahedral or octahedral holes. It contributes to the formation of: (1) six octahedral holes ( 0 ) three of which are shown in the figure. these are the differences which concern us most here. Supposing that the sequence is an ABAB . 6. as are two layers of tetrahedral holes (TL). Four spheres are needed to form each tetrahedral hole. 3. consequently a double layer of spheres has the following characteristics in both HCP and CCP: 1. obviously there is a ratio of one hole to each sphere. for example.74 both for HCP and CCP. are in correspondence with the three spheres marked with a thick T and one of which is in correspondence with the sphere marked S and three of the spheres marked with the same T. Let us examine. Octahedra and tetrahedra which share faces. .18. There are two coefficients which characterize closest packings.32). (top right) and tetrahedral. The differences between HCP and CCP are in the geometric elements shared by the polyhedra in the direction perpendicular to the layers. differently orientated (TL."~". Octahedra which share edges. Fig. while each sphere helps to form eight tetrahedral holes. the other three can be obtained by a symmetry plane m which passes through A. 6. which has a value of 0. In Fig. the other half of the tetrahedra sharing vertices.Ionic crystals 1 431 Many cations have a radius of just the right size. 0. 6. type. the other four can be obtained by a symmetry plane m which passes through A. A layer of octahedral holes (OL) is enclosed by two layers of spheres. .).19. and finally the octahedra which share edges. The tetrahedral (black triangles) and octahedral (white diamonds) holes of a CCP are shown. above and below A). 6. It is easily found. Such differences are very important for certain ~toichiometries[~~]we shall see below. Octahedral. (bottom right) holes with relative coordination polyhedra &a& out from t w o fo~~o~in~compact~a~e~~. these two types of holes more closely in order to find out what is their quantitative ratio to the spheres. since they affect the as stability of the structure and thus which type of packing is preferred.27). 6. An FCC cell. It follows that.:~~~~~$~~ of that of the tetrahedral holes. Instead. so there is a ratio of two tetrahedral holes to each sphere.18 a layer A (black spheres) and a layer B (white spheres) are shown. This situation is common both to HCP and CCP. three of which. . shown in the figure. a sphere marked S (belonging to layer A and not visible in the figure) is surrounded by a total of 12 spheres (six of A and six of two B layers. T.19) all the octahedra sharing faces with half of the tetrahedra. remembering that an elementary HCP cell contains two spheres . and TL. Fig. as do half of the tetrahedra. and finally the octahedra and tetrahedra sharing vertices and edges. Note that the number ~~~~~[~~j:~:". the other half of the tetrahedra sharing vertices. in CCP the octahedra share edges only. Since six spheres are needed to form an octahedral hole and every sphere helps to form six holes. Tetrahedra which. through they are orientated in different directions (see Fig. while in HCP the octahedra share faces in the direction perpendicular to the OL and edges parallel to the OL. 2.
21. distorted to a greater or lesser degree. 6. where p . = 4v. A BCC cell. = 0.Pb3mc. = 0. ~ 3 m 1 . The minimum symmetry content common to all closest packings is P3ml.150 (Fig. HCP and CCP. h = ~ 9 6 1 3h / D = q 6 / 3 = = . HH'= : l / 3 ( B H 1 ) DV3/6.e. is the maximum dimension of the crystal perpendicular to the closestpacked layers which the sequence can reach when the structure is completely disordered.70 and CN = 10.[301the second is to obtain them by means of combinatorial analysis. nh. Fig.16 shows the symmetry of a closestpacked layer (6mm) and of a pair of such layers (3m).432 1 Fernando Scordari Fig.For HCP and CCP the space groups are . will be in the range .189(D/2)3 from which c.72 and CN = 11. The central sphere is surrounded by eight spheres at a distance of D and six more distant spheres at 1. the BCT (bodycentred tetragonal). = 0.68 and 8 6 spheres of the same type coordinated around a central sphere. while a CCP one contains four (Fig. but for n = 20 the number of possible packing rises to 4625. for n = 6 there are two: ABCACBA and ABABACA. These are the PTP (primitive tetragonal packed). 1. ~ g m ~ m 3 m .E. + . 6. 0. 6.20) it follows that h l D = 0. The other parameter is the ratio hlD. The volume of a sphere is V = 4. have 12 spheres all at the same distance from the central sphere. therefore colD = 1. the third (taken on by several structures) has c. The repetition period.20. When real structures are considered the symmetry may be reduced. Combinations of HCP and CCP can create an indefinite number of closestpacking structures.8165.[311 Figure 6.1). The centres of the three spheres marked A and the centre of the sphere marked B together form a trigonalpyamid. One of the following ways can be chosen to derive the possible packings: the first is to count all the possible sequences once having generated them.150 ( 2 0 = 1V3.. the side of an . 6. 6./mmc. co = 2h.74.8165.17). ./a3 = 0. but also to the distortions which the cations produce in the lattice. For example. respectively: P63/mmc and ~ m 3 m . and the BCC (bodycentred cubic). As n increases. It canbe deduced from this t h a ~ BH' = D V 3 / 2 . there is only one possible packing for n =4: ABACA. where / i s the side of the cell). Other symmetries are represented by all those space groups which can have as a subgroup P3ml (see also Fig. 2h S nh ~ p . eight at a distance of D and six at a distance of 1. in "~ HCP. the second (not found in the known structures) has c. the number of possible sequence combinations grows very rapidly. on the other hand. due not only to the arrangement of the cations which occupy the various holes. R3m. The first has c. Since h = [ ( ~ V ' 3 / 2 ) ~ ( ~ f i / 6 ) ~ ](see Fig.~ 6 m 2 . elementary CCP cell will be a. For example. Therefore.63.21). = ~ j 6 where D is the diameter of a sphere. There are other close packings characterized by spheres with fewer next neighbours. For example. i. P6. some structures belonging to systems different from those just examined can be described as closest packings.
above all the largest ones with the lowest valence (formal charge). It follows that the lowest coordination expected for Na+ (which taking into account the oxygen has p.[321 In structures of a certain complexity. thus making the structure less stable than if the distances are very close to Re.+ ICl).71) is 6.=0. Too many anions would increase the cationanion distance. are the first to take on higherenergy coordinations. In such cases some cations. + Pauling's second rule Known as the valence sum rule. introducing the concept of the ionic radius.half of which is it substituted by AP+. this rule means that the electrostatic balance is satisfied by the cations belonging to the primary coordination. compatible with the equilibrium conditions imposed by the minimum potential energy. followed by smaller highervalence cations which tend to form more rigid coordinations. The general principle of the minimization of potential energy can be applied to such compounds.)'. rule can be sumThe marized as: v=& (6. Na8C12[Si6A16024]. then we can define the electrostatic bond strength as si = V~/(CN. (C0. vi and (CN. the cationanion distances do not depend only on the ionic radii of the cation and anion involved. 4. has its usual CN.. while Si4+. but also on the average radius of each of the other cations. However. and vice versa. are respectively the valence and the coordination number of the ith cation.Ionic crystals 1 433 Pauling's rules Ionic bonds play an important role in the building up of structures for the vast majority of minerals. In fact. The distance between the cation and the anion is determined by the sum of the radii. . can be seen as large negative ions bonded to the cations by essentially ionic interactions. The optimum distance is the sum of the ionic radii: rM r. (SO4)'. has CN = 4 (302.e. but in sodalite. while the coordination number of the cation is determined by the radius ratio. surround the cation. which have prevalently covalent bonds internally. A coordination polyhedron is formed around each cation. The maximum number of anions.28) i where i is extended to all the cations coordinated by the anion in question. The Pauling rules are derived from this principle. i.).)~. If V is the valence of an anion. even the groups (Si04)4. Pauling's first rule This rule synthesises the geometric relationships which tend to be established between cations and anions in a stable structure. this rule analyses the electrostatic balance: The valence of an anion in a stable ionic structure tends to compensate the strengths of the electrostatic bonds which reach it from the cations situated at the centres of the polyhedra of which the anion is a vertice. In practice. it can happen that not all the cations have optimum CN and dMx distances.
from a given Na+ is .. 116.[361 Calculated bond valences can be used through (6. A13+.P5+. Brown and ~ h a n n o n [proposed the following equation: ~~] where so. In order to calculate the strength of each electrostatic bond. the parameter R1 represents the expected bond length when the valence is assumed to be one. Amongst the various applications of this method[351it is often used by crystallographers to distinguish 0'.g.28) to calculate experimental atomic valence and so the oxidation state of an . this simple model needs to be modified slightly.is surrounded by three ~ i ~then: which is exactly the opposite of the oxygen valence.and H 2 0 in some complex mineral structures. The agreement between the experimental and the theoretical valence is very good. and N are empirical constants. This means that each oxygen receives 416 of the + . Mg2+. or certain bonds have been overlooked. sb3+). generally the difference does not exceed 5 per cent. or more correctly the bond valence (s). Since very 0'.622 A and N = 4. For so = 1. Each ~ i cation coordinates six 02and around each oxygen ~ + there are three Ti4+. s can be determined. Si4+ in place of A13+ or vice versa). Since there are 6 Na+ surrounding each C1.434 1 Fernando Scordari For highsymmetry. The experimental bond valence can be obtained by applying (6.) which is characterized by strongly distorted Ti06 octahedra. and N for each cation[341 and the bond distance R. Ti02 (space group P42mnm) whose structure is based on slightly distorted Ti06 octahedra. all equidistant from it follows: The same procedure can be applied as a rough guide to rutile.g. For example. Ro. or the wrong atoms have been ascribed to certain sites (e. In such as a case (6. (2) the structure has not been interpreted properly. In structures with irregular polyhedra. For example Na+. If the agreement is not satisfactory for an ionic structure it can be ascribed to the following: (1) the structure has not been correctly determined. simple ionic structures it is possible to give a single value to the bond strengths and to find the valence of a given ion by multiplying the bond strength i times. Ro = R. (3) The cations have stereochemically active lonepair electrons (e. Si4+.30). which can be deduced from the structure.from (OH).290.29) becomes: By inserting the correct values for R. for NaCl (space group ~ m 3 m ) the bond strength which reaches a given C1. and s6+ have values of R1 = 1. like brookite (a polymorph of the compound TiO. valence of titanium.
0(.22.98. In order for the potential energy to be minimal it is necessary that: (1) the distances between the cations should be as great as possible.. This effect is accentuated where there are cations with high valence and low coordination number. (2) the cations should be shielded as much as possible from each other.29.=2.85. 4. like [PO4I3.=4. compatible with the existence of the structure itself. %. for any given pair of polyhedra. The sketch at the bottom shows the different shielding effects produced by three or four anions together on the underlying cation. from a qualitative point of view.14. .=3. and above all two tetrahedra which share a face. Geometrical relationships between some regular polyhedra. and least likely when a face is shared.96.. of faces between coordination polyhedra reduces the stability of a structure. do.96. in particular. = 1. = 2. they hardly ever share edges and never share faces.80A.43. 6.=2.40 A.Ionic crystals 1 435 Pauling's third rule This summarizes. Figure 6. the following intercation distances can be calculated: = 3.are found either isolated or sharing vertices. The least probable of all the configurations are two tetrahedra which share an edge.=1.22 illustrates the distances between cations for certain regular polyhedra. =3. 4. d. d. Considering the oxygens as touching rigid spheres with a radius of re = 1. when they share an edge than when they share only a vertice. As can be seen. dc. even the likelihood Fig. the influence that the fact that the coordination polyhedra share geometric elements has on the potential energy and thus on the stability of the structure: The sharing of sides and.80. For tetrahedra containing cations with a higher charge. the fulfilment of conditions (1) and (2) are less likely. This explains why in silicates the tetrahedra [SiO4I4.
NaC1. so much so that in the case of group having yet higher cation charges. as predicted by the third Pauling rule. Structures like CsCl are only possible if the anions are large enough to keep the cations far enough apart. This rule summarizes the common observation that most of the nonfluid substances that surround us are crystalline and not amorphous. Ideal a n d defect structures The preceding paragraphs have dealt mainly with the principles which underlie the structural building of ionic compounds. while in the case of HCP they share faces.22. The structural differences concern mainly the way in which the TiO. in accordance with the indications of Fig.436 1 Fernando Scordari that they will share vertices is reduced.. ionic compounds with an MX stoichiometry (see p. three. CaO.However.). and so no further comment is necessary: In a crystal containing various cations. Pauling's fifth rule The fifth rule. It should be remembered here that. having considerable differences for instance with regard to volume and chemical properties. 437) crystallize not with an HCP lattice.24 A and 4. MgO. On the basis of what has been said.g. Source applications of these rules together with symmetry and other crystallochemica1parameters are given in Appendix 6. those with high valence and a low coordination number tend not to allow the coordination polyhedra which they form to share any features. CsBr. the question of how to realize the ~ [ ~ ~ be relative stability of certain ~ i 0 polymorphs can ~ understood. In rutile. known also as the parsimony principle. Pauling's fourth rule The fourth rule is an obvious corollary of the third. in octahedral coordinations the shielding of the two cations is more accentuated. while anatase is the least stable. and four edges with a similar number of other octahedra. This explains why numerous halites tend to keep the NaCl structure rather than that of the CsCl.B. brookite. the distance between two cations for CsF is 4. and anatase. Figure 6. 6. The structural stability of brookite is less than that of rutile. favoured by p.92 A for CsCl). CsI (in the NaCl structure type. as can be observed in the case of CsC1. brookite. that it is almost nil. This means that the number of structural units. each octahedron shares respectively two. but with a CCP lattice (e. octahedra are linked to one another. .22 shows that do. = dCf.I2. etc. This compound has three polymorphic modifications: rutile. and anatase. like [S0. tends to be low for any given substances. This is because the energy levels involved in the formation of the two packings seen along h is different: in the case of CCP the octahedra MX6 share edges. states that: The number of essentially different constituents in a crystal tends to be small.
. From the point of view of symmetry. the packing definitely preferred by MX compounds is CCP.:). those structures in which it is possible to single out an elementary cell 100 per cent representative of all the cells that make up the crystal. the space group ~ d 3 m adopted both by the spinel and by the magnetite.0. which. atomic configurations. i. will now be examined. can be rationalized from its crystallochemical formula in the following way: ~ e ~ + ( ~ e e. Therefore the structure of magnetite can be represented by a particular cell of statistical significance having its tetrahedral sites occupied by Fe3+ and its octahedral sites occupied by 0.. will be analysed briefly. apart from taking into account the stoichiometry. . 00. In such cases the compound is better defined by a crystallochemical formula. or at least not very complex.O4 which substitutes the less explanatory stoichiometric formula Fe304. . It can be seen from the stoichiometry of these compounds that all the octahedra are occupied and that therefore an HCPbased structure is decidedly less probable than a CCPbased structure. 1 437 MX structures As predicted by the third Pauling rule. the composition of a nonstoichiometric magnetite Fe. while A13+ occupies the octahedral ones.5 Fe3+.e. the octahedra share edges and faces. will be considered briefly from the point of view of their classification. This structural peculiarity is evident from the crystallochemical formula Fe3+ (Fe::. defined on the basis of their stoichiometry. For example.with the necessary abandoning of 5 per cent of the octahedral sites and the formation of gaps (represented by the square). in fact. IG the next section some classes of simple structures. while in the second the octahedra only share edges.Ionic crystals Some simple. and HCP is never adopted. Moreover. represents in the first case true symmetry and in the second statistical symmetry.)204. The nonexistence of hexaognal packing in the structures of MX compounds can be best explained with help of Fig.23. 6. 442) and adopts the following ideal structure: Mg2+ occupies only the tetrahedral sites. In the first case. Particular attention will be given to ideal structures. included amongst the ionic compounds by tradition.O. Thus the representative cell is a statistical cell which expresses the probability that a certain site will be occupied by a given atom. the compound MgA1204 (spinel) parent of the spinels. The silicates. 442) in which Fe2+ occupies only octahedral sites. In such cases all the crystallographic sites which are symmetrically equivalent (including the translation) must be occupied by the same chemical species and the resulting compound is defined as an ideal chemical formula. considers also the percentage of presences (occupancy) of a certain chemical element in a given crystallographic site. while BCC is rare. In defect structures the relative positions of the atoms are not regular throughout the crystal.5 Fe2+ and 0. is a normal spinel (see p. characterized at most by few dozen atoms per elementary cell. The compound Fe304 (magnetite) is instead an inverse spinel (see p. while Fe3+ occupies half tetrahedral sites and half octahedral ones.In fact the reason why it is not F: & stoichiometric becomes clear immediately: it is due to the substitution of Fe2+ by Fe3+. Fe.
and carobbite (KF).23(a)) to give a regular one positiveone negative ion pattern (Fig.). space group Fm3m. 6. 6. other examples are: periclase (MgO). A representation of the structure of fluorite. 6. cubic. Such a succession of layers gives rise to a cubic structure like that of NaCl. > 0. is illustrated.25(b). space group Fm3m. sylvine (KCl). The elementary cell (dotted lines) consists of four such polyhedra occupied by calcium and four similar empty polyhedra. In (c) the structure of NaCI. is shown in Fig. while Fig. The tetragonal structure of rutile. CaF. of which only a few are illustated here..438 1 Fernando Scordari Fig. 112. 6. and consequently the cations are further apart and better shielded (see Fig.73) at 112.23.g.. while each anion F. Such effects are considerably attenuated if alternate rows are translated a distance of R/2 in the direction of the arrows (Fig. bunsenite (NiO). Figure 6.similar to BCC.(p. 6.= 8:4).24. Some alkaline halides also crystallize naturally: villiaumite (NaF).ions with all the octahedral sites filled by Na+. 6. 112.).24. wustite (FeO). 6. 427). manganosite (MnO).25 illustrates a layer of octahedra (OL) seen (a) perpendicular to and (b) parallel to its extension. together with the geometrical relationships between them.23(a) is not stable due to the strength with which like charges repel each other. the white are Ca2+ OFFig. Apart from the halides previously mentioned (see p. Due to the alternate filling of these sites the cubes share edges instead of faces. Various compounds such as SrCl. Each cation Ca2+ is surrounded by eight F.positioned at the vertices of a cube.. < 0. The successive translation (equal to R) of a third layer brings us back to the initial configuration.22). halite (NaCl). The ratio M:X = 6:3 is favoured when p. which is why MX compounds almost always adopt CCP type packings. in substitution of F. By moving alternate rows in the direction of the arrows a distance of R / 2 . In the figure the cubic coordination polyhedra of the ca2+ (black circles) are outlined. have a CaF. 6.73 allowing the formation of structures similar to that of rutile (TiO. type structure. read 'are substituted by'). This tendency is strengthened if the cations are bivalent.23(b)). 6. The structure adopts a quasiclosest packing of F. with half of the sites at the centre of the cube empty and half occupied by Ca2+ alternately.is surrounded by four Ca2+ positioned at the vertices of a tdtrahedron (Ca2+:F. can be described as HCP. or in other words. Fluorite (CaF. The black octahedral are occupied. In (a) an unstable layer of cations (white spheres) and anions (black spheres) of equal radius R / 2 . and lime (CaO)./mnm. BaCl.X structures Such compounds present a wide range of structures.26(a) shows a packing of OL layers of the type shown in Fig. A compact layer like that shown in Fig. or halite is shown. In order that a succession of layers of the same type (along the perpendicular to the layer examined) should be stable it is necessary that a second layer be translated by R. 2Ca2+ t K+ + ~ a ~ 3Ca2+ + 2K+ + U4+ (for + + . etc. the stable layer illustrated in (b) is obtained. and others with more complex formulae in which some cations are substituted by other cations e. . MX2 and M. space group P4. a CCP of C1.
or if instead 3Ti4++ ~ g . pyrolusite (MnO. An octahedral layer (OL) obtained by combining t w o compact layers of spheres of equal radius. if 3 ~ i .26. Minerals with a brucite type structure include: portlandite (Ca(OH). seen parallel t o their extension.g. 6. (on the left). 6. In (b) the distorted closest packing is shown. 6. +2Sb5+ bystromite (MgSb206) is formed.. 6. 6. nibrucite (Mg4NiO(OH). rather than to occupy all the octahedra of OLA and none of OLB.). and their . A TiO. This is in agreemwnt with p. Another group of minerals with brucitic layers. in (b) parallel t o its extension. space group ~ 3 mwhich conform to .). while in (c) the rows of occupied octahedra are outlined. an antifluorite + Fig. with the corresponding sequence of octahedral layers OLAOLBOLAOLB. This is because in the first case the octahedra are linked by (six) vertices and (two) edges. Figure 6. It is more advantageous from the point of view of energy to fill every other octahedron of each row.Ionic crystals 1 439 empty. Fig. and with the stoichiometry of rutile which predicts that half of the octahedral holes will be occupied.). of brucite (Mg(OH). In (a) it is seen perpendicular t o its extension.. It is also common amongst more complex compounds in which the Ti4+ is substituted by cations with a . CCP is: chlormagnesite (MgCl.). lawrencite (FeCl. Another structure typical of compounds with a ratio of M:X = 6:3 is that .26(a)). The occupation of the holes occurs in such a way that the octahedra share edges and vertices. as is illustrated in Fig.25. in which the octahedra share edges only. type structure is certainly one of the most common among strongly ionic binary compounds such as fluorides and oxides. This feature means that HCP is preferred to CCP. then similar radius: e. with Si4+hexacoordinated. the second involves all the octahedra of alternate octahedral layers being occupied (e.26(b) shows a structure of rutile obtained by the distortion of the ideal HCP as seen in Fig. extension along the axis c i n the structure of rutile TiO. There are two possible ways for half of the octahedral HCP holes to be occupied without the octahedra sharing faces: the first has already been illustrated for rutile. scacchite (MnCI.@]they are known as 'brucitic layers'. Minerals with a structure like that of rutile include: sellaite (MgF.).). A OLB OLA OLB B A B A OLA . OLA occupied entirely and OLB left completely free in Fig.g. pyrochroite (Mn(OH). In (a) (on the right) a sequence of ideal compact layers ABAB. never faces. stishovite (SiO..26(a). cassiterite (SnO. .).): trigonal with space group ~ 3 m l It has a layered structure which can be described by means of HCP. If the cationanion positions of fluorite are inverted. The rows of black octahedra (perpendicular to the sheet) are occupied.dipoles which link together the fully occupied octahedral layer.). as happens in rutile. . while the white ones are empty. The layered structure of rutile is due to the permanent OH.) a highpressure compound.). + 2 ~ a ~ + tapiolite (FeTa206) is ~ ~ + formed. Brucite is an example of the second type. but in the second by (six) edges only.26(c).+ e .
whose structure is based on the same type of layer. Fig. but also why the structure is stable. An HCP type packing.27(b)). only one third of their octahedral holes are occupied. and then to divide it into (OH).. have MX. alternating with empty octahedral layers results[391 (bayerite.O. as seen in the compounds Li20. characterized by a bayeritetype layer (Fig.. are rhombohedra1 with space group R ~ C Their structures are . 1 indicates the mesh of bayerite. are related by a plane of symmetry m which passes through the empty layer. stoichiometry: they are both monoclinic with space groups C2/m and P2.groups indicates that their structure is layered like that of brucite. which overlies another layer of octahedra twothirds occupied (Fig. ANOH).27(c)).27(a)).+. two occupied octahedral layers.27(a)). 6. Both corundum (aA1203) and haematite (aFe203)have an M:X = 6:4 ratio. the substitution of 3 ~ g 4 2A13+ 0. OLA OLB 1 I  C I OLB I . 6. so the same orientation of the layers recurs every other full layer (Fig. like that shown in Fig. two polymorphic modifications of the compound Al(OH). with partially occupied. 6.. R. Such a structure can be described as a CCP having all its tetrahedral holes occupied by