P. G.

Russia (Chairman), USA India The Netherlands UK USA UK

IUCr Monographs on Crystallography Accurate molecular structures: their determination and importance editors 2 P. P. Ewald and his dynamical theory of X-ray diffraction editors Electron diffraction techniques, Volume 1 editor Electron diffraction techniques, Volume editor The Rietveld method editor Introduction to crystallographic statistics Crystallographic instrumentation Direct phasing in crystallography: fundamentals and applications The weak hydrogen bond in structural chemistry and biology 10 Defect and microstructure analysis by 11 Dynamical theory of X-ray 12 diffraction diffraction

The chemical bond in inorganic chemistry

IUCr Texts on Crystallography 1 The solid state: from superconductors to superalloys translated by Fundamentals of crystallography editor X-Ray charge densities and chemical bonding The basics of crystallography and diffraction, second edition IUCr Crystallographic Symposia Patterson and Pattersons: fifty years of the Patterson function editors 2 Molecular structure: chemical reactivity and biological activity editors Crystallographic computing 4: techniques and new technologies editors Organic crystal chemistry editors Crystallographic computing 5: from chemistry to biology editors Crystallographic computing 6: a window on modern crystallography editors 1 Correlations, transformations, and interactions in organic crystal chemistry editors

BROWN
Department of Physics and Astronomy McMaster University Hamilton Ontario

OXFORD

Preface

11 April 2001

Contents

R0

a priori

Historical introduction

1.1

Introduction

a posteriori

1.2

Chemical bonds

HISTORICAL INTRODUCTION

Fig.

et al. et al.

MODEL

1.3

The ionic model

ionic model

U,

1.4

Quantum mechanics

et al.

et al.

1.5

The symmetry model

et al.

1.6

Topological models

1.7

Pauling's electrostatic valence model

s=

The rule of parsimony.

bond valence

bond valence model

et al. et al.

The ionic bond

2.1

Introduction

et al.

BOND

Crystal energy and the Coulomb field

UyfeTmi,

Eh E h

Ei<mono, Qh

r Q{ E^mono

Qt.

Qt.

et al.

E^oclii E^oclii EitTnono

EitTnono

i, Ei<mu\t E^mono

Qt . U\oca\

How are the atom fragments chosen?

BOND

Q{, Qt Q{.

Every part of the electron density of the crystal must belong to at least one atom.

The partitioning must ensure an appropriate assignment of charges, Qf. Qh Qt Vt. Consistent with the above constraints, the partitioning should be chosen so as to minimize Emu\t. Emu\t

et al.

Vt.

2.4

The Madelung field of a crystal

et al.

Q{ Qt.
2

BOND

Fig. {(x,y,z);x + y = I } . et al.

Fig. et al.

Cy, Py,

qt

Py,

Qf

qt.

Ptj

Cy

Cy. Cy Qf a priori, Cy. Cy

Cy,

Cy Cy

Bond networks and bond graphs

a network consists of an array of nodes which are connected by links. valences the fluxes

Na

Na connectivity

adjacency matrix,

Table 2.1

Bl Bl B2 HI H2 H3 H4 H5 H6

B2

HI

H2

H3

H4

H5

H6

0 0 1 1 1 0

0 0

1 1 1 1

0 0

1 1 0 0 0 0 0 0

1 1 0 0 0 0 0 0

1 0 0 0 0 0 0 0

0 1 0 0 0 0 0 0

1 0 0 0 0 0 0 0

0 1 0 0 0 0 0 0

BOND

Fig. 2.4.

Fig. 2.6.

2.6

Coordination number

Definition of coordination number. The coordination number of an ion is the number of ions to which it is linked by electrostatic flux.

et al. tertiary bonds,5

secondary bond was tertiary bond

THE

BOND

Fig.

et al.

Conclusions

The chemical bonding can be completely described in terms of localized bonds between neighbouring atoms.

The bonds have a cation at one end and an anion at the other.

3
The bond valence model

3.1

Experimental bond valences and bond lengths

Ctj,

bond strength,

E X P E R I M E N T A L B O N D VALENCES AND B O N D LENGTHS

Fig. 3.1. et al.

experimental bond valence, S.

Rtj R0, B, B RQ, B

j,

Sy

28

THE BOND

MODEL

valence sum rule, (Vf

Qf Sy,

Vj)

et al.

RQ, B,

3.2

Empirical network equations

Sy valence sum rule loop, network equations. equal valence, rule,

theoretical bond valences s. S, s,

unstrained structures, S. strained structures

(3-

Table 3.1 S, s S s-S

s, R,

Qh Vt, sy,

for unstrained structures at equilibrium all bonds have the same bond capacitance. R0 B,

et al.

THE BOND

MODEL

31

Vi sy

the bond valence model cannot distinguish between ionic and covalent bonding.

The bond valence model

Principle of maximum symmetry,

THE BOND

MODEL

Rule 3.1 As far as allowed by the chemical and geometric constraints, all atoms and all bonds in a compound will be chemically and geometrically indistinguishable.

Rule The breaking of symmetry is always the consequence of an identifiable chemical or spatial constraint.

Rule The sum of the valences of all the bonds formed by an ion is equal to the valence of the ion.

Condition 3.1. The stoichiometry must obey the electroneutrality principle, namely that the sum of all the atomic valences (formal ionic charges), having regard to their sign, is zero. Condition The bond graph must be bipartite as described in Section 3.5, i.e. all of the bonds must connect a cation, e.g. Na+, to an anion, e.g. Cl~.

loop,

equal valence rule.

Rule 3.4 The sum of bond valences around any loop in the bond network, having regard to the direction of the bond, is zero.

The valence of each atom is distributed as uniformly as possible among the bonds that it forms.

Rule Increasing the bond valence between two ions reduces the distance between them as shown in Fig. 3.1.

3.4

The distortion theorem

Rule 3.6 For any ion, lengthening some of its bonds and shortening others, keeping the bond valence sum the same, will always increase the average bond length. AR,

34

THE BOND

MODEL

AR

Rule 3.6a For any ion, lengthening some of its bonds and shortening others, keeping the average bond length the same, will always increase the valence sum.

Rule If an ion is placed in an environment in which the average bond length is too long, i.e. in a cavity which is too large for the ion, the environment will distort in such a way as to increase the lengths of some bonds and decrease the lengths of others in order to raise the bond valence sum to the expected value.

3.5

Bond networks with non-bipartite graphs

BOND N E T W O R K S WITH N O N - B I P A R T I T E G R A P H S

35

Fig. 3.3.

36

THE BOND

MODEL

Fig. 3.4.

CF3CO^ C\+ C4+Q\~]~

Fig.

Fig. 3.6.

38

THE BOND

MODEL

(T TT a

et al.

et al.

4
Anion and cation bonding strengths

4.1

Bond graphs and coordination number

Rule 4.1 A bond exists between a cation and an anion if its experimental bond valence is larger than 0.04 the cation valence.

BONDING STRENGTHS

ideal coordination numbers

BONDING STRENGTH

Fig. 4.1.

4.2

Anion bonding strength

anion bonding strength, sa,

P-O

BONDING STRENGTHS

maximum and minimum anion bonding strengths.

BONDING STRENGTH

47

pKa,

pK^

strong

Lewis base strength. weak anions

4.3

Cation bonding strength cation bonding strengths, sc, vc

Fig. 4.3.

pKa.

BONDING STRENGTHS

strong

weak cation Lewis acid

strength.

Fig. 4.4.

Fig. 4.5.

4.4

The valence matching principle

Valence matching principle, Rule The most stable compounds are formed between cations and anions that have the same bonding strength.

(sa =

(sc = (sc =

(sc=

BONDING STRENGTHS

4.5

Hard and soft acids and bases

hard

soft,

A P P L I C A T I O N S OF THE

MATCHING PRINCIPLE

4.6

Applications of the valence matching principle

Fig. 4.6. sc/sa

BONDING STRENGTHS

s^Sn

Liquids

5.1

Introduction

The cation and anion bonding strength of water

Fig. 5.1.

sjsa sc/sa sjsa

(sc =

Reactions of cations with water

et al.

et al.

n, n.

5.4

Reactions of unions with water

Fig. 5.4.

PO^~

PO34~

(sc =

pK^,

Aqueous solubility

Mg(H2O)6SO4

CO\ CG>\ +

Fig.

(sc Sg)

A=

5.6

Aqueous solutions of soft ions

(sc =

Non-aqueous solutions and melts

(sc = Q.Q6

Fig. 5.6.

like weak

Cation coordination number

6.1

Introduction

ab initio

mutatis mutandis,

6.2

Anion-anion repulsion

Fig. 6.1.

Fig.

a.

Table 6.1

et al.

Fig. 6.3.

a,

s'',

COORDINATION

RQ =

b= s'.

s' <

Fig. 6.4.

s'

THE S T R E N G T H OF THE

6.3

The strength of the unions

Coordination number rule. Rule 6.1 The total number of bonds formed by all the cations in a compound equals the total number of bonds formed by all the anions.

6.4

Other factors

Rm[n

COORDINATION

6.5

Applying the different effects

APPLYING THE DIFFERENT EFFECTS

73

74

COORDINATION

Fig. 6.5.

Hydrogen bonds

7.1

Introduction

(sr =

Rmin

et al.

I995a,b,

The role of anion-anion repulsion

THE ROLE

77

s'

Fig.

s',

s'', Sh,

Rm[n s'

Sh Sh Sh. S^ s1', Rmin s' >

Sh Rmin s' > Rmin. Sh

s'.

Rmin. Sh, s', Sh s'

Fig. S^ <

Sh,

ROO S^>Q.4vu, S^>Q.2vu,

The normal hydrogen bond normal hydrogen bond

STRONG H Y D R O G E N BONDS

Strong hydrogen bonds

Strong hydrogen bonds

ROO

HYDROGEN BONDS

83

Fig. 7.6.

Weak hydrogen bonds

Rmin,

(Sh <

7.6

The structural chemistry of the hydrogen ion

Other types of hydrogen bond

et al.

S^

(pK^)

et al.

7.8

Assigning experimental bond valences to hydrogen bonds

et al.

of Sh

Sh

(S <

Electronically distorted structures

8.1

The origins of electronic distortions

Madelung field. Coulomb field.1

lone-pair cations,

Fig. 8.1.

et al.

8.2

Non-bonding valence-shell electrons

lone pairs

et al.

Fig. 8.4.

V,

D.

Table 8.1 Sp

Rmin. NC>3~,

r, 6)

r D.

9, 9.

al.

et al.

8.3

Transition metals

TRANSITION

8.3.1

Jahn- Teller distorted cations

Fig. 8.6.

dx2_y2

dx2_y2

x-y

8.3.2

Transition-metal cations with empty or near-empty d shells

TRANSITION

et al.

et al.

Fig. 8.9.

TRANSITION

Fig. 8.10.

Table

8.4 Conclusions

Physical properties of bonds

9.1

Introduction

9.2

Bond lengths and bond angles

R0, B

q, V, k

<j), S,

R0

Bln(k).

R0 k

BOND LENGTHS AND BOND

RQ.1 k k

RQ, RQ TT R0 RQ

TT

TT TT RQ TT et al. RQ et al.

k k

et al.

Si

x = [(Si + S2)/2V] S2, V/4, V (S =

BOND L E N G T H S AND BOND

9.3

Bond force constants and thermal vibrations

Fig. 9.1.

G, S.

S>
1 1

b,
1

a= A,

b= G,

(A2),

Fig. 9.2.

T,

k A. (A2} U, (A2) U

(A2) et al.

(A2), U,

(A2)

d(A2)/dT dUuncoi/dT

THERMAL

Fig. 9.3.

9.4

Thermal expansion

et al.

R&.

114

PHYSICAL P R O P E R T I E S OF BONDS

R'

(R)

(R) SR S',

Re

SR/B SR S' Re.

SR/B

(R) Re = AR AR

(SR2), (SR2) (A2)

B = 37

Fig. 9.4.

G Rp

pS, p R S

et al.

(A*),

R,

Fig. 9.5.

R',

(A2)/2R.

Gt

Fig. 9.6.

9.5

The variation of R0 with temperature

RQ,

AR.

R + AR R0

R%, T,

T S

dR/dT

Solids

10

Space and space groups

10.1 Introduction

SPACE AND SPACE G R O U P S

10.2 The crystal lattice and translational symmetry

R(l, m, n), b, c

m, n)

unit cell

R(l, m, n) R(l,m,ri)

THE CRYSTAL

SYMMETRY

Fig. 10.1.

Fig. 10.2.

124

SPACE AND SPACE G R O U P S

Fig. 10.3.

Fig. 10.4.

10.3 Space groups

asymmetric unit

G, space group.

x, y, z

x, y, z.

p/n

ri)

G, ofmG R, mG mG =

10.4 Special positions mG

Fig.

CO\

mG = ofmG/2 =

non-translational unit.

mN, mG,

Fig. 10.6. nis mwT). ms mw (ms 2, ms6, mw ms3, mwT), ms 2, mw mw

mN.

mN S W, mw S S mw\& S, ms, W* S= N,

Rule 10.1. In a given space group, all the Wyckoff positions with the same multiplicity, mw, have site symmetries of the same order, ms.

Fig. 10.7.

m s,

Rule 10.2. The order of the site symmetry of any Wyckoff position is in inverse proportion to its multiplicity. S, mw,

10.5

Matching the special positions to the chemistry his fundamental law of crystal chemistry

Rule 10.3. Since all the atoms in the chemical formula must exist on one or other of the Wyckoff positions of a crystal, the multiplicity of an occupied Wyckoff position must correspond to the frequency with which the corresponding atom appears in the chemical formula, and the site symmetry of the Wyckoff position must correspond to a possible symmetry of the atom's bonded environment.

spectrum

mN,

10.6 The symmetry of bonded neighbours

inter alia

ms = 4%, ms = 24). (D^k) ms= ms=8)

ms =

ms=6.

Table 10.1

m3

m+12

Table 10.2

m6 26

10.7

Summary

Modelling inorganic structures

11.1

The problem of a priori modelling

topology

structure, geometry, relative

stability.

THE T O P O L O G Y

135

11.2 Determining the topology

Principle of electroneutrality

Rule 11.1 Since the sum of all atomic valences is zero, the sum of the atomic valences of the cations is equal to the sum of the atomic valences of the anions. Coordination number rule Rule 6.1 Since each bond starts on a cation and ends on an anion, the sum of the coordination numbers of the cations equals the sum of the coordination numbers of the anions, and both are equal to the total number of bonds in the formula unit.

Rule 11.2 The ratio of the average coordination number of the cations, (Na), to the average coordination number of the anions, (Nx), is the same as the ratio of the number of anions, x, to the number of cations, a.

Rule 11.3 Compounds that have a high anion content will stabilize high cation coordination numbers. Principle of maximum symmetry

Rule 3.1 As far as allowed by chemical and geometric constraints, all atoms and all bonds in a compound will be chemically and geometrically indistinguishable. Principle of close packing Rule 11.4 Like ions tend to lie on close packed lattices, since this arrangement minimizes their repulsive energy when they are confined to a fixed volume.

Shubnikov's fundamental law of crystal chemistry Rule 10.3 Atoms will occupy Wyckoff positions in the crystal that are compatible in both multiplicity and symmetry with the bond graph.

11.2.1 Space-based approaches

THE TOPOLOGY

Random structure approaches

et al.

et al.

Lattice models

T H E TOPOLOGY

139

Fig.

HCP FCC

et al.

et al.

11.2.2 Chemistry-based approaches

THE T O P O L O G Y

141

Rule 11.5 When generating a chemical structure, the strongest bonds are formed first, followed by the others in decreasing order of their valence.

a priori

Creating the bond graph

THE TOPOLOGY

143

Fig. 11.2.

Fig. 11.3.

THE T O P O L O G Y

145

Sy

Sy

Fundamental building blocks

Fig. 11.4.

THE T O P O L O G Y

147

OPb64+.

et al.

et al.

Polyhedral linkage

Fig. 11.5.

Fig. 11.6.

THE T O P O L O G Y

149

et al.

Fig. 11.7.

THE T O P O L O G Y

151

The space group method

ms = ms=

ms= ms = ms=

ms =

V2

ms =

P4i23,

'a).

Weakly bonded structures

a priori

11.2.3

Valence maps

Fig. 11.8.

pt pt

THE TOPOLOGY

159

Fig. 11.9.

in ph pt c

pf

et al.

Fig. 11.10.

11.3 Refining the geometry

et al.

et al.

et al.

et al.

11.4 Modelling defect structures

et al.

et al.

11.5 Modelling glasses

al.

11.6 Summary

Lattice-induced strain

12.1 The origins of lattice-induced strain

Fig. 12.1.

Fig. 12.2. et al.

lattice-induced strains

12.2 Structures with lattice-induced strain

bond strain index et al. S s cr3

global instability index et al.

Gil

Gil

Gil

et al.

et al.

Fig. 12.4.

I992a).

12.3 Relaxation of lattice-induced strain

12.3.1

Relaxation of the geometry

(S=

(S =

12.3.2

Relaxation by defects

Fig. 12.5.

et al. 12.3.3 Electronic relaxation

8.

12.3.4

Relaxation of symmetrydisplacive phase transitions

12.3.5

Changing the bond graphreconstructive phase transitions

Fig. 12.6.

12.4 Incommensurate structures

et al.

RQ = 2l4pm

STRUCTURES

175

Fig. 12.8. et al.

Fig. 12.9.

et al. et al.

et al.

et al.

et al.

12.5

Summary

13

Applications

13.1 Introduction

13.2 Crystallography

13.2.1

Structure solution ab initio,

ab initio et al.

et al.

(p\

V\ V\ V2 S,

YiS\

^S2

andp2,

p i.

et al.

et al.

et al.

p\

et al.

et al.

et al.

13.2.2

Analysis of crystal structures

primae facie

et al.

bond valences (vu)

S
0.30
0.28, 0.27 0.26, 0.25

bond valence sums (vu)

Sum

1.54 1.48 1.49 1.49

0.15

1.99
2.07 2.00 0.03 2.08 2.04

0.04

0.24

0.31
Sum

(0.76)
6.00

(0.82), 0.15 (1.00)

1.05

1.12

(1.00)

13.3 Physics

13.3.1

Perovskite-related solids

Fig. 13.1.

13.3.2

Electrical properties

et al.

APPLICATIONS

Fig. 13.2.

V(O) =

et al.

et al.

13.3.3

Magnetic properties

Fig. 13.3. et al.

et al.

13.3.4

Grain boundaries

et al.

et al.

et al. et al.

et al.

13.4 Mineralogy

et al.

13.4.1 Soil chemistry

et al.

et al.

et al.

et al. (I997a,b,c)

et al. (1997 a,b)

et al.

et al.

13.4.2

Zeolites

CHEMISTRY

197

13.4.3

Glasses

et al.

13.5

Chemistry

et al.

13.5.1

Nuclear magnetic resonance

et al. et al.

fy

M et al.

et al. NMR NMR

et al.

13.5.2

Transition-metal complexes

et al. et al.

TT

TT

et al.

et al.

et al.

13.5.3

Heterogeneous catalysis

s,

E:

CHEMISTRY

201

et al.

et al. 13.5.4 Esterification and hydrolysis

Fig. 13.4.

Table 13.3

Fig. 13.5.

BIOLOGY

203

13.6 Biology

13.6.1

Enzymes

et al.

et al.

et al.

et al.

et al.

et al.

et al.

et al.

13.6.2

Calcium and sodium binding by proteins

BIOLOGY

205

et al.

et al. et al. (cis-

13.7 Databases

et al.

et al. et al.

et al.

14

Chemical implications of the bond valence model

14.1 Why is the bond valence model so robust?

14.1.1

The attractive force

WHY IS THE BOND

M O D E L SO R O B U S T ?

209

14.1.2

The repulsive force

R0

TT TT

RQ

TT

14.2 Two-body potential models

14.3 The properties of the bond graph

ELECTRON-PAIR MODEL

211

14.4 The Lewis electron-pair model

Fig. 14.1.

WHY ARE

FROM

et al.

14.5 Why are cations different from anions?

Fig. 14.2.

14.6

Orbital models

ad hoc

PO^"

14.7 Electron density models

et al.

et al.

a, b, c

Fig. 14.3.

et al. et al.

14.8

The topology of the Madelung field

14.9

Conclusions

et al. et al.

Bond valence parameters

Al.l Introduction

et al. S S= R

A1.2 Determination of bond valence parameters

Table Al.l

B(pm)

o2 o2 o2F-

o2cr o2 o2-

(Continued)

R Q,

N,

S, s,

B B N) RQ.

R0

RQ

B B RQ. R0

N), N),

B B
1

RQ RQ

i. RQi, RQ
B

228

APPENDIX 1

RQi B Rw Rw B RQi RQ

R0. RQ. B RQ.

(R) et al. RQi

RQ

b RQ RQ

BOND

PARAMETERS

229

RQ R0 R0

rt

ct

Cj

RQ RQi et al. R00, R0^, R00 Ros R0^.

RQ I999a,b; I997a,b,c; et al.

R0 RQ et al. et al. R0 R0

230

APPENDIX 1

RQ et al.

et al. B et al.'s

RQ

B,

A1.3 Other bond valence expressions

rc,

a, b, c,

BOND

PARAMETERS

231

S g,

S=0 R e= e/(l +g).

e/c. e= et al.

et al.

a (=

RI

av

232

APPENDIX 1

SQ,

Space group spectra

mw,

Table A2.1

Table

Table A2.3

234

APPENDIX 2

Table A2.4

Table

(Continued)

111

236

APPENDIX 2

Table

Table

(Continued)

238

APPENDIX 2

Table A2.9 (Continued) 1 1

2,1

*
2,1 2,1 2,1 2,1

* *

* *

12,2,2,

2,1

Table A2.10

P2l

Appendix 3 Solution of the network equations

N&+1

Nb Nb Nb s. M:

s NA +

et al.

Vjv V v

a, b, c, d, e,

242

APPENDIX 3

d=\-a, e=l-2b.

c= Ib, f=(lb-\}/2.

b = 1/21 =

f=

c = 5/27 = 0.18vu, 11/27 = 0.41 vu,

e = 13/27 = 0.48 vu,

a = 21/54 = 0.39 vu, d = 33/54 = 0.61 vu.

Appendix 4 Cation and anion bonding strengths

Table A4.1 (Continued)

Table A4.2

Table A4.3

Appendix 5 References to the ICSD and the CSD

Table A5.1 et al.

Acta Cryst. Acta Cryst. Acta Cryst. Acta Cryst.

Can. J. Chem. Solid State Chem. Zeit. Kristallogr.

Proc. Japan. Acad. Acta Cryst. C. R. Acad. Sci. Inorg. Chem. Mater. Res. Bull. Amer. Miner. Zeit. Kristallogr.

Acta Cryst. Acta Cryst. Ferroelectrics

Table A5.1

(Continued}

Acta Cryst. 11, Acta Cryst. 18, Acta Cryst. 18,

Dokl. Akad. Nauk SSSR239, Zeit. Anorg. Allgem. Chem. Ann. Acad. Sci. Fenn. Ser. A6 Physica 313, Nature

Acta Cryst. 26, Zeit. Anorg. Allgem. Chem. 480, Solid State Chem. Acta Cryst. B26, Amer. Miner. 60, Zeit. Kristallogr. 90,

Acta Cryst. Acta Cryst. Acta Cryst.

Amer. Chem. Soc. C. R. Acad. Sci.

et al. 226,

Physica Statu Solidi

Table A5.1 (Continued)

Acta Cryst. Naturwissenschaften

Acta Cryst. Ark. Kemi. Zeit. Kristallogr. Norsk Geol. Tijdskr. Chem. Phys. Ark. Kemi. Australian J. Chem. Acta Cryst. Kobutsugaku ZasshilS, Acta Cryst.

Acta Cryst. Zeit. Electrochem. Zeit. Electrochem. Adv. X-ray Anal. Chem. Phys.

Acta Cryst. Zeit. Kristallogr.

Table A5.1

(Continued}

Phys Rev. B Solid State Chem. Zeit. Kristallogr.

Phys. Rev.

Miner. J. (Japan)

Acta Cryst. Phys. Stat. Solidi

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Amer.Miner.

Solid State Chem.

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Acta Cryst. Mat. Res. Bull.

Table A5.1 (Continued)

Physica C

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Amer. Chem. Soc. 109,

252

APPENDIX 5

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List of symbols
B Na Nb R R0 r s s' S V f

Index

see

see

see also see see see see also

see see also

see also

(cont.):

see also see also

see

see

see

Cr(H2O)l+

see

see also see also

see see

see see also

see (A3B2(XO4)3) see

see also see

see also

see

see

see

(cont.): see

see see

see also

see

see see see

see also

see see see see (A2MN2O1) 111

see also

see

see

see also

see also

see

see also see see

see

(cont.): see also

see also

see

see see