Introduction and a Short Dictionary of Network Terminology1
Chapter 1...... 1
Introduction and a short dictionary of network terminology1
1.1. Who is this book written for?...2
1.2. Nomenclature used in this book.2
1.3. Why did we write this book?...4
1.3.1. Some history...... 4
1.3.2. A rapid expansion...... 4
1.3.3. Problems with names and nomenclature5
1.3.4. What this book is and is not.6
1.3.5. The contents of the book...6
1.4. Some words, their origin and current usage8
1.4.1. Tectons and building blocks.9
1.4.2. Nets of coordination polymers and metal-organic frameworks10
1.4.3. Crystal engineering and reticular chemistry11
1.4.4. Supramolecular self assembly using synthons and secondary building units 12
1.4.5. Glossary of terms...... 14
Chapter 2...... 19
Why bother with nets ?...... 19
2.1. Possible impact on society....19
2.2. A fruitful way of looking at molecular crystals with strong, directed intermolecular bonding 21
2.2.1. The analysis of a crystal structure21
2.2.2. Three reasons for the net approach23
2.2.3. Seeing the structure in all these structures24
2.3. Synthetic targets for molecular nets: magnetism, chiral channels, gas storage and more 25
2.3.1. Intrinsic properties of 3D-nets
...... 25
2.3.2. Applications...... 26
2.4. Patents related to molecular 3D-nets32
Chapter 3...... 39
What is a net?...... 39
3.1. Definitions...... 40
3.2. Short survey of network interactions42
3.2.1. Covalent bonds...... 42
3.2.2. Coordinative bonds.....43
3.2.3. “Normal” hydrogen bonds.45
3.2.4. “Weak” hydrogen bonds..47
and interactions.49
3.2.6. Phenyl “embraces”.....50
3.2.7. Metal-metal bonds and interactions50
3.3. How to assign nodes...... 51
3.4. Interpenetration...... 53
3.4.1. “Nature abhors a vacuum”53
Chapter 4...... 57
Naming the nets and finding them..57
4.1. A state of some concern, but with a solution?57
4.2. Nomenclature...... 58
4.2.1. Nomenclature according to Wells60
4.2.2. Schläfli symbol...... 60
4.2.3. Rings and circuits...... 61
4.2.4. Extended Schläfli or vertex symbols63
4.2.5. Zeolite-like abbreviations.64
4.2.6. Some notes on notation...67
4.2.7. Fischer symbol...... 68
4.2.8. Graph set theory...... 68
4.3. Examples...... 69
4.3.1. Diamond net...... 69
4.3.2. CdSO4 net...... 72
4.4. Searching the literature...... 73
4.4.1. Using words...... 73
4.4.2. Searching the Cambridge Structural Database75
4.5. Recommendations...... 76
4.6. A few words about Alexander F. Wells77
Chapter 5...... 81
The most common 3D-nets...... 81
5.1. Requirements for a 3D-net....82
5.2. The most common 3D-nets...83
5.2.1. The103-srs or (10,3)-a net, also known as the SrSi2 net84
5.2.2. The 103-ths or (10,3)-b net, also called the ThSi2-net86
5.2.3. The 66-dia or diamond net.87
5.2.4. The 64.82-nbo or NbO net with square planar coordination89
5.2.5. The 65.8-cds or cadmium sulphate net with square planar coordination 90
5.2.6. The platinum sulphide, (42.84)(42.84)-pts net, a square and a tetrahedron 92
5.2.7. The 46.64-bnn, or boron nitride net93
5.2.8. The 412.63-pcu net with octahedral nodes94
Chapter 6...... 99
Three-connected nets...... 99
6.1. Some remarks concerning the building blocks99
6.1.1. Link lengths and angles...99
6.1.2. Torsion angles, between consecutive nodes101
6.1.3. The net and the tecton...102
6.2. Uninodal three-connected nets102
6.2.1. The 123-twt net...... 102
6.2.2. The (10,3)-c 103-bto net..103
6.2.3. The (10,3)-d or 103-utp net 105
6.2.4. Other uninodal (10,3)-nets106
6.2.5. The (8,3)-a and (8,3)-b nets (83-eta and 83-etb)108
6.2.6. The (8210)-a, LiGe or 82.10-lig net110
6.2.7. The 4.142-dia-f net.....110
6.2.8. The 4.142-dia-g net.....111
6.2.9. The 4.8.10-lvt-a net.....112
6.3. Binodal three-connected nets.114
6.3.1. The (6.102)(62.10)-nof net114
6.3.2. The (83)(83)-noj net....115
6.3.3. The (103)(6.102)3-noh net116
6.3.4. The (82.10)(82.10)-nod or (8210)-b net117
6.3.5. The (6.122)(6.102)2-nob net 118
6.3.6. Two uniform binodal nets: (9,3)-a: (93)(93)-nta and (9,3)-b: (93)(93)2-ntb 119
6.4. Trinodal three-connected nets.120
6.4.1. The (4.122)(4.122)(4.122)-mot-a net120
6.4.2. The (72.8)2(72.8)(7.123)-noe net121
6.4.3. (4.122)(4.122)2(123)2-“net 10”
...... 122
6.5. Multinodal three-connected nets 123
6.5.1. The (83)(83)(82.10)(82.10)
(83)(83)-nos net, a hexanodal net123
6.6. Summary of three-connected nets
...... 123
Chapter 7...... 127
Four-connected nets...... 127
7.1. Uninodal tetrahedral nets....127
7.1.1. The SrAl2 or 42.63.8-sra net.
...... 127
7.1.2. The sodalite or 42.64-sod net
...... 129
7.1.3. The quartz or 66.82-qtz net130
7.1.4. The CrB4 or 4.65-crb net.132
7.1.5. The gismondine or 43.83-gis net133
7.1.6. The lonsdaleite or 66-lon net.
...... 134
7.1.7. The Irish ladder or 42.63.8-irl net135
7.1.8. The polycubane or 43.83-pcb net136
7.1.9. The 42.63.8-pcl net.....137
7.1.10. 66-neb, 54.62-unh, 4.65-cag, 66-gsi, 66-mmt, and 4.64.8-zni138
7.2. Uninodal nets with “square planar” nodes139
7.2.1. The 42.84-lvt net...... 139
7.2.2. The 86-tcb net...... 140
7.3. Nets with both tetrahedral and square planar nodes141
7.3.1. The twisted pts or (4.63.82)2(42.62.82)(62.84)-ptt net142
7.3.2. The or (42.62.82)2(4.64.8)-mog net143
7.3.3. The(43.63)4(64.102)-asv net 144
Chapter 8...... 149
Nets with both three- and four-connected nodes149
8.1. Alternating nets with stoichiometry (3-conn)4(4-conn)3 (ns3/ns4 = 4/3)150
8.1.1. Boracite, (63)4(62.84)3-bor and twisted boracite (63)4(62.82.102)3-tbo
...... 150
8.1.2. The Pt3O4 or (83)4(86)3-pto net
...... 152
8.1.3. The C3N4 or (83)4(86)3-ctn net
...... 153
8.1.4. Other alternating nets with stoichiometry (3-conn)4(4-conn)3154
8.2. Nets with 1:1 stoichiometery (ns3/ns4 = 1)155
8.2.1. The InS or (63)(65.8)-ins net
...... 155
8.2.2. The (4.82)(4.85)-dmc net.156
8.3. Nets with 1:2 stoichiometery (ns3/ns4 = 1/2)157
8.3.1. The (5.82)(4.52.6.7.8)2-dme net157
8.3.2. A (6.82)(64.8.10)2-net...158
8.4. Nets with 4:1 stoichiometery (ns3/ns4 = 4)158
8.4.1. The (62.10)4(64.102)-jph net
...... 159
8.4.2. The (103)4(106)-dmf net.160
8.5. Nets with 2:1 stoichiometery (ns3/ns4 = 2)161
8.5.1. The (83)(86)2-tfa net based on tetrahedral nodes161
8.5.2. The (83)(85.12)2-tfc net based on square planar four connected nodes 161
8.6. Summary of three- and four-connected nets162
Chapter 9...... 165
Nets with higher connectivity than four
...... 165
9.1. Five connected nets...... 165
9.1.1. The 44.66-sqp net...... 165
9.1.2. The 44.66-nov net...... 166
9.1.3. The 46.64-bcu-l net.....168
9.1.4. The 34.42.84-cab net and other five-connected nets with cubic symmetry 168
9.2. Six-connected nets...... 169
9.2.1. The NiAs or the (412)(49.66)-nia net169
9.2.2. The 48.54.63-bsn net....170
9.2.3. The 49.66-acs net...... 171
9.2.4. The 48.53.64-smn net...172
9.3. Seven-connected nets...... 173
9.3.1. The 416.54.62-wfq net...173
9.4. Eight-connected nets...... 174
9.4.1. The CsCl or 424.64-bcu net 175
9.4.2. A 33.415.58.62 net.....175
9.5. Nets with three- and five-connected nodes176
9.5.1. The stacked hexagonal layer net, or (63)(69.8)-hms net176
9.5.2. The graphite or (63)(69.8)-gra net177
9.5.3. The (4.82)(4.56.6.82)-mcf-d net178
9.6. Nets with three- and six-connected nodes178
9.6.1. The rutile or (4.62)(42.610.83)-rtl net178
9.6.2. The pyrite or (63)(612.83)-pyr net179
9.6.3. The (4.62)(42.610.82)-sit net
...... 182
9.7. Nets with four- and six-connected nodes183
9.7.1. Tetrahedrons and octahedrons; the corundum or (43.63)3(46.69)2-cor net 183
9.7.2. Square planar and octahedral nodes, the (44.62)(48.67)-fsg net184
9.7.3. Tetrahedrons and octahedrons, another (44.62)(48.66.8) net185
9.7.4. Tetrahedrons and octahedrons; the (43.63)(46.66.83)-fsh net185
9.8. Nets with four- and eight-connected nodes185
9.8.1. The fluorite or flu net...185
9.9. Summary of higher connected nets
...... 187
Chapter 10...... 191
Some mathematics related to 3D-nets
...... 191
10.1. Nets, Polyhedra and Topology192
10.1.1. Definitions...... 192
10.1.2. The Platonic bodies and the (n,p) relation to dimensionality192
10.1.3. A few words on topology195
10.2. Genus, Tilings and Nets....197
10.2.1. A classification of nets in terms of their genus197
10.2.2. Comparison to Wells Zt classification199
10.2.3. Nets as tilings and the concept of transitivity202
10.2.4. The analysis of the voids as the dual of a net204
10.2.5. The pqrs to srqp relation of dual nets206
10.3. Glossary...... 207
Chapter 11...... 211
Interpenetration - strategies and nomenclature211
11.1. What is interpenetration....211
11.2. Strategies to control interpenetration212
11.2.1. Density of nets...... 212
11.2.2. Lengths and thickness of links, size of counter ion213
11.2.3. Analysis of the voids within a net215
11.2.4. Specially designed ligands 217
11.3. Nomenclature...... 217
Chapter 12...... 227
3D-nets as specific synthetic targets – Crystal Engineering227
12.1. Choice of interaction (hydrogen bonds, coordinative bonds etc)227
12.1.1. Covalent bonds...... 227
12.1.2. Metal-ligand bonds (coordination bonds)227
12.1.3. Hydrogen bonds...... 228
12.1.4. Connecting the building blocks230
12.2. Reaction conditions...... 231
12.2.1. Solvents and concentrations
...... 231
12.2.2. Templating agents.....231
12.2.3. Methods of crystallization232
12.2.4. Hydrothermal or solvothermal methods233
12.2.5. Grinding and kneading, mechanochemical methods234
12.3. Synthesis of chiral, porous, 3D nets235
12.3.1. Intrinsic chiral nets and induced chiral nets235
12.3.2. Interpenetration...... 237
12.3.3. Some chiral nets other than srs238
12.4. Some notes on polymorphism and supramolecular isomerism239
12.5. Specific properties of nets and their analysis241
Chapter 13...... 245
Computational tools...... 245
13.1. Regular visualisation tools for net discovery and analysis245
13.1.1. Mercury...... 246
13.1.2. Diamond...... 248
13.1.3. Crystal Maker...... 251
13.1.4. RPluto...... 251
13.2. Software packages that can search for a nets251
13.2.1. OLEX...... 251
13.2.2. TOPOS...... 254
Appendix A...... 257
Ideal nets...... 257
Appendix B...... 271
Stereo drawings...... 271