Werner Massa

Crystal Structure Determination

Springer-Verlag Berlin Heidelberg GmbH
Werner Massa

CrystalStructure
Determination
Translated into English by Robert O. Gould
Second Completely Updated Edition

With 107 Figures and 13 Tables

i Springer
AUTHOR TRANSLATOR

Professor Dr. Werner Massa Dr. Robert O. Gould

University of Marburg University of Edinburgh
Department of Chemistry Structural Biochemistry Unit,
Hans-Meerwein -Straße Michael Swann Building
35043 Marburg Mayfield Road
Germany Edinburgh EH9 3JR
E-mail: massa@chemie.uni-marburg.de UK
E-mail: gould@ed.ac.uk

The book was originally published in German under the title "Kristallstrukturbestimmung;'
3. Auflage. © B. G. Teubner GmbH, Stuttgart/LeipziglWiesbaden, 2002.
1'1 English Edition Springer-Verlag 1999

ISBN 978-3-642-05841-7 ISBN 978-3-662-06431-3 (eBook)

DOI 10.1007/978-3-662-06431-3

Library of Congress Cataloging-in-Publication Data Applied For

A catalog record for this book is available from the Library of Congress. Bibliographie information
published by Die Deutsche Bibliothek.
Die Deutsche Bibliothek lists this publication in Die Deutsche Nationalbibliographie; detailed bib-
liographie data is available in the Internet at <http://dnb.ddb.de>.
This work is subject to copyright. All rights reserved, whether the whole or part of the material is
concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitations, broad-
casting, reproduction on mierofilm or in any other way, and storage in data banks. Duplieation of
this publication or parts thereof is permitted only under the provisions of the German Copyright
Law of September 9, 1965, in its current version, and permission for use must always be obtained
from Springer-Verlag Berlin Heidelberg GmbH.
Violations are liable for prosecution under the German Copyright Law.
springeronline.com
© Springer-Verlag Berlin Heidelberg 2004
Originally published by Springer-Verlag Berlin Heidelberg New York in 2004
Softcover reprint of the hardcover 2nd edition 2004

The use of general descriptive names, registered names, trademarks, etc. in this publication does
not imply, even in the absence of a specific statement, that such names are exempt from the relevant
protective laws and regulations and therefore free for general use.
Cover design: Erieh Kirchner, Heidelberg
Typesetting: Hilmar Schlegel, Berlin
Printed on acid free paper 32/3141/LT-5 4 3 2 1 0
Preface to the Second English Edition

The second English edition is largely based on the tbird German edition of tbe Teub-
ner Studienbuch "Kristallstrukturbestimmung:' which appeared in 2002. In particu-
lar, Chapter 7, dealing witb experimental metbods, has been extensively rewritten. In
view of tbe huge recent advances in tbe use of area detector systems for single-crys-
tal data collection, tbeir description has replaced much of the material on "classic"
metbods. Similarly, tbe practical example (Chapter 15) now describes area-collector
metbods more fully. Among many otber cases, tbe sections on Rietveld refinement,
macromolecular crystallography and uses of databases have been updated. I am grate-
ful to my colleague R. O. Gould for continuing his excellent translation of tbe first
edition, and for tbe friendly and careful collaboration in achieving many large and
small improvements.

Werner Massa Marburg, November 2003

Preface to the First German Edition

Crystal structure analysis using X-rays has undergone an expansion of avalanche

proportions in tbe last twenty years, tbanks to tbe development of rapid and auto-
matic means of data collection and tbe enormous growtb of tbe computer hardware
and software for carrying out tbe necessary calculations. Because of its wide appli-
cability and its precision, it has become one of tbe most important tools in botb
organic and inorganic chemical research. Despite tbe fact tbat crystallography plays
a very minor role in most undergraduate study, many students have found that in
tbe course of graduate or even undergraduate research, they need to undertake a
crystal structure determination themselves, or at least to become competent to inter-
pret crystallographic results. Thanks to ever improving program systems, tbe many
complex steps of a structure analysis are certainly becoming less and less difficult for
tbe beginner to master. Nonetbeless, regarding tbe process simplyas a "black box" is
fraught witb danger.
This book is aimed at tbose students of chemistry and related subjects who wish
to take a look into tbe black box before tbey step into its territory, or who simply wish
to learn more of tbe fundamentals, tbe opportunities and the risks of tbe metbod. In
view of tbe well-known fact tbat tbe likelihood a book will actually be read is inversely
proportional to its number of pages, fundamentals of tbe metbod are treated here as
briefly and as intuitively as possible. It seems more important tbat chemists should
have a grasp of tbe basic principles and tbeir application to a problem, tban tbat tbey
be in a position to understand fully tbe complex matbematical formalisms employed
by tbe computer programs.
On tbe otber hand, some aspects of the subject, which bear direcdy on tbe quality
of a structure determination, are wortb fuller treatment. These include discussion of
a number of significant errors and the recognition and treatment of disorder and
VI

twinning. Most important crystallographic literature is available in English, but a few

references in other languages, principally German, have been included.
This book is based in part on lectures and on a seminar at the University of
Marburg. Consciously or unconsciously, many colleagues have made their contribu-
tions. I am particularly grateful to Professor D. Babel for many helpful suggestions
and a critical reading of the manuscript. I thank Dr. K. Harms for proofreading the
manuscript and Mr. C. Frommen for considerable assistance with the production
of camera-ready copy using the ~TPC program. Finally, I acknowledge the help of
my wife Hedwig and my children for all their assistance and patience during the
preparation of this book.

Werner Massa Marburg, April 1994

Contents

1 Introduction 1

2 Crystal Lattices 3
2.1 The Lattice . . . . . . . . 3
2.1.1 The Unit Cell 4
2.1.2 Atom Parameters . 5
2.1.3 The Seven Crystal Systems . 6
2.2 The Fourteen Bravais Lattices . . . 7
2.2.1 The Hexagonal, Trigonal and Rhombohedral Systems 8
2.2.2 The Reduced Cell . . . . . . . . . . . . . . . . . . 9

3 The Geometry of X-Ray Diffraction 13

3.1 X-Rays . . . . . . . . . . . . . . . . . . . 13
3.2 Interference by a One-Dimensional Lattice . 16
3.3 The Laue Equations . . . . . 18
3.4 Lattice Planes and hkl-Indices 20
3.5 The Bragg Equation . . . . . 22
3.6 Higher Orders of Diffraction . 23
3.7 The Quadratic Form of the Bragg Equation 23

4 The Reciprocal Lattice 27

4.1 From the Direct to the Reciprocal Lattice 27
4.2 The Ewald Construction . . . . . . . . . 30

5 Structure Factors 33
5.1 Atom Formfactors . . . . . 33
5.2 Atom Displacement Factors 35
5.3 Structure Factors . . . . . . 37

6 Crystal Symmetry 41
6.1 Simple Symmetry Elements . . . . . . . . . 41
6.1.1 Coupling of Symmetry Elements. . . 42
6.1.2 Combination of Symmetry Elements. 44
6.2 Symmetry Directions. . . . . . . . . . . . . 44
VIII CONTENTS

6.3 Symmetry Elements Involving Translation . . . . . . . . . . . .. 46

6.3.1 Combination of Translation with Other Symmetry Elements 46
6.3.2 Coupling of Translation with Other Symmetry Elements.. 46
6.4 The 230 Space Groups . . . . . . . . . . . . . . . . . . . . . .. 52
6.4.1 Space-group Notation in International Tables for Crystallo-
graphy . . . . . . . . . . . . . . . . 52
6.4.2 Centrosymmetric Crystal Structures . 55
6.4.3 The Asymmetric Unit . . . . . 56
6.4.4 Space Group Types. . . . . . . 57
6.4.5 Group-Subgroup Relationships 57
6.5 Visible Effects of Symmetry . . . . . . 58
6.5.1 Microscopic Structure . . . . . 58
6.5.2 Macroscopic Properties and Crystal Classes 59
6.5.3 Symmetry of the Lattice . . . . . . . . . . 59
6.5.4 Symmetry of the Diffraction Pattern - The Laue Groups 59
6.6 Determination of the Space Group . . . . 61
6.6.1 Determination of the Laue Group 61
6.6.2 Systematic Absences 62
6.7 Transformations ..... 65

7 Experimental Methods 67
7.1 Growth, Choice and Mounting of a Single Crystal 67
7.2 Measuring the Diffraction Pattern of Single Crystals 71
7.2.1 Film Methods . . . . . . . . . . . . . 71
7.2.2 The Four-circle (serial) Diffractometer . 74
7.2.3 Reßection profile and scan type 78
7.3 Area Detector Systems 81
7.4 Data Reduction . . . . . . . . 86
7.4.1 Lp correction 86
7.4.2 Standard Uncertainty 87
7.4.3 Absorption Correction . 89
7.5 Other Diffraction Methods . 91
7.5.1 Neutron Scattering . 91
7.5.2 Electron Scattering 92

8 Structure Solution 93
8.1 Fourier Transforms . . . . . . . . . . 93
8.2 Patterson Methods . . . . . . . . . . 95
8.2.1 Symmetry in Patterson Space 97
8.2.2 Structure Solution Using Harker Peaks . 97
8.2.3 Patterson shift methods . . 99
8.3 Direct Methods . . . . . . . . . . . . 100
8.3.1 Harker-Kasper Inequalities .. 100
8.3.2 Normalized Structure Factors 101
8.3.3 The Sayre Equation . . . . . 102
 IX

8.3.4 The Triplet Relationship . . . . . 103

8.3.5 Origin Fixation . . . . . . . . . 105
8.3.6 Strategies of Phase Determination 106

9 Structure Refinement 111

9.1 The Method of Least Squares . . . . . . . 111
9.1.1 Refinement Based on Fo or F; Data 115
9.2 Weights.......... 116
9.3 Crystallographic R-Values . . . . . . . . . 118
9.4 Refinement Techniques . . . . . . . . . . 119
9.4.1 Location and Treatment of Hydrogen Atoms. 120
9.4.2 Restricted Refinement . 121
9.4.3 Damping . . . . . . . . . 122
9.4.4 Symmetry Restrictions 122
9.4.5 Residual Electron Density 123
9.5 Rietveld Refinement . . . . . . . 124

10 Additional Topics 127

10.1 Disorder . . . . . . . . . . . . . . . . . . . 127
10.1.1 Site Occupancy Disorder . . . . . . . 127
10.1.2 Positional and Orientational Disorder 128
10.1.3 One- and Two-Dimensional Disorder 130
10.1.4 Modulated Structures . . . . . . . . 131
10.1.5 Quasicrystals............. 131
10.2 Anomalous Dispersion and "Absolute Structure" . 132
10.2.1 Chiral and Polar Space Groups . 137
10.3 Extinction . . . . . . 139
10.4 The Renninger Effect . . . . . . . 141
10.5 The A/2-Effect . . . . . . . . . . 142
10.6 Thermal Diffuse Scattering (TDS) 143

11 Errors and Pitfalls 145

11.1 Wrong Atom-Types. . . . . . . . . . . . . 145
11.2 Twinning.................. 146
11.2.1 Classification by the Twin-Element . 147
11.2.2 Classification According to Macroscopic Appearance 147
11.2.3 Classification According to Origin . . . . . . . . . . 148
11.2.4 Diffraction Patterns of Twinned Crystals and their Interpre-
tation . . . . . . . . 149
11.2.5 Twinning or Disorder? 155
11.3 False Unit Cells. . . 155
11.4 Space Group Errors . . . . . 156
11.5 Misplaced Origins . . . . . . 158
11.6 Poor Atom Displacement Parameters. 159
X CONTENTS

12 Interpretation and Presentation of Results 161

12.1 Bond Lengths and Bond Angles .. 161
12.2 Best Planes and Torsion Angles. . . 162
12.3 Structural Geometry and Symmetry 163
12.4 Structural Diagrams 165
12.5 Electron Density . . . . ...... 169

13 Crystallographic Databases 171

13.1 The Inorganic Crystal Structure Database (ICSD) 171
13.2 The Cambridge Structural Database (CSD) ... 171
13.3 The Metals Crystallographic Data File (CRYST-MET) 175
13.4 Other Collections of Crystal Structure Data 175
13.5 Deposition of Structural Data in Data Bases 175
13.6 Crystallography on the Internet ..... 176

14 Outline of a Crystal Structure Determination 177

15 Worked Example of a Structure Determination 181

Bibliography 199

Index 205
 XI

Commonly used Symbols

a, b, C lattice constants OT symbols for axial glide planes
a*, b*, c* reciprocallattice constants
A Angström unit (= 10- 10 m)
B Debye-Waller Factor (= 8:rr 2 U)
d lattice-plane spacing OT symbol for diamond glide plane
d* scattering vector in reciprocal space
E normalized structure factor
f atomic scattering factor (formfactor)
Fe calculated structure factor
Fo observed structure factor
FOM figure of merit
hkl Miller indices
I reflection intensity
L Lorentz factor
Mr mass of a mole
n order of diffraction OT symbol for diagonal glide plane
p polarization factor
R conventional residual, calculated from Fo-data
SH sign of a structure factor
TDS thermal diffuse scattering
U atomic displacement factor (= B/8:rr 2 ) OT unitary structure factor
w weight of a structure factor
wR weighted residual, calculated from Fo-data
wR 2 F;
weighted residual, calculated from -data
x,y,z atomic coordinates
Z number of formula units per unit cell

a,ß,y unit cell angles

L1 path difference for interference OT other differences
/),.f', !l.f" components of anomalous scattering
e extinction coefficient
f} scattering angle
A X-ray wavelength
t-t absorption coefficient OT various angles
Q density
a standard error
(/) phase angle of a structure factor