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Fundamentals of Crystallography

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Crystallography

C. GIACOVAZZO, H. L MONACO, D. VITERBO

F. SCORDARI, G. GILLI, G. ZANOTTI, M. CATTI

Edited by

C. GIACOVAZZO

Dipartimento Geomineralogico, University of Bari, Italy

and Istituto di Ricerca per lo Sviluppo delle Metodologie

Cristallografiche,

CNR, Bari, Italy

OXFORD UNIVERSITY PRESS

1992

Contents

List of contributors

1

Symmetry in crystals

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 rotorefiection

Refiection 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: L A The isometric

transformations

l.B Some combinations of

movements

l.C Wigner-Seitz cells

xiii

rotation matrices

l.E Symmetry groups

l.F Symmetry

generalization

1

3

3

5

5

5

6

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11

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22

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35

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41

References

43

45

55

60

Crystallographic Computing

Carmelo Giacovazzo

61

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

Coincidence-site 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

Non-linear (unconstrained) least Squares

61

61

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68

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73

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74

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80

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93

viii

Contents

Least-squares 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

variance-covariance

matrix M^

2.H Derivation of the

unbiased estimate of

Mx

2.1 The FFT algorithm and

its crystallographic

applications

2.J Examples of twin laws

References

Carmelo Giacovazzo

94

98

104

108

109

109

112

117

120

122

124

125

127

127

128

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131

131

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 X-rays by

gases, liquids, and

amorphous solids

3.D About electron density

mapping

3.E Modulated structures

and quasicrystals

References

131

133

137

crystallography

Hugo L. Monaco

141

X-ray sources

Conventional generators

Synchrotron radiation

141

142

144

144

146

147

148

150

151

154

154

155

155

Contents

Monochromatization, collimation, and

focusing of X-rays

Data collection techniques for Single

crystals

The Weissenberg camera

The precession camera

The rotation (oscillation) method in

macromolecular crystallography

Densitometry

The single-crystal diffractometer

Area detectors

Data collection techniques for

polycrystalline materials

X-ray 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

Solution and refinement of crystal

structures

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 semi-invariants

Probability methods

Fixing the origin and the enantiomorph

241

245

247

254

259

268

273

281

287

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293

297

301

301

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304

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319

319

321

324

328

335

335

335

337

340

346

Completing and refining the structure

Difference Fourier method

Least-squares method

Absolute config uration

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

ix

351

365

366

367

374

375

377

384

385

387

388

390

393

397

lonic crystals

Fernando Scordari

403

Atoms with a Single electron

Atoms with more than one electron

Interactions between ions

Notes on chemical bonds

lonic crystals

Lattice energy: the contributions of

attractive and repulsive terms

Lattice energy: CFSE contribution

Applications of lattice energy

calculations

lonic radius

Maximum Alling principle

Coordination polyhedra

Radius ratio rule

Applications of the concept of ionic

radius

403

403

404

406

406

409

410

414

417

418

424

425

425

427

x I 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 2 and M2X structures

MX 3 and M 2 X 3 structures

A m BX p 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

429

433

433

433

435

436

436

436

437

438

440

441

445

447

453

Gastone Gilli

465

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

atom-atom 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

465

467

468

468

453

456

459

463

473

478

480

482

483

484

484

486

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 three-centre-four-electron linear

Systems

Nucleophilic addition to organometallic

Compounds

Nucleophilic addition to the carbonyl

group

A case of conformational rearrangement

Resonance assisted hydrogen bonding

(RAHB)

References

Protein crystallography

Giuseppe Zanotti

Introduction

Protein crystals

Principles of protein crystallization

The solvent content of protein crystals

Preparation of isomorphous heavy-atom

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 I xi

Parameters

Picking up minor heavy-atom sites:

the difference-Fourier synthesis

A third approach to the resolution of

the phase ambiguity: real-space 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 conjugate-gradient

algorithm

8.D Conventions and

symbols for amino

acids and peptides

594

Michele Catti

599

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

X-ray topography of dislocations

Energy of a dislocation

Motion and interaction of dislocations

Partial dislocations

Small-angle grain boundaries

Point defects

Thermal distribution of defects

Diffusion

Ionic conductivity

Appendix: 9.A Properties of second-rank

tensors

Further reading

Index

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