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Index
Topology dictionary (topoCIF) version 0.9.6
Category TOPOL
Name:
'TOPOL'
Parent category:
TOPOLOGY
Definition:
The TOPOL category covers data on connectivity
between atoms and structural groups and the
related structural properties as calculated from
the ATOM, CELL and SPACE_GROUP data.
Examples:
Example 1 - Connectivity of the diamond crystal structure.
All atoms coincide with the nodes and all bonds coincide
with the edges, so the atomic network coincides with the
underlying net.
loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z
2 1/4-x,1/4-y,z
# - - - - data truncated for brevity - - - -
13 -y,-x,-z
# - - - - data truncated for brevity - - - -
192 3/4-z,1/2+y,1/4-x
loop_
_atom_site.label
_atom_site.fract_x
_atom_site.fract_y
_atom_site.fract_z
C1 0.12500 0.12500 0.12500
loop_
_topol_net.id
_topol_net.overall_topology_RCSR
1 dia
loop_
_topol_node.id
_topol_node.net_id
1 1
loop_
_topol_link.id
_topol_link.node_id_1
_topol_link.node_id_2
_topol_link.symop_id_1
_topol_link.translation_1
_topol_link.symop_id_2
_topol_link.translation_2
_topol_link.distance
_topol_link.Voronoi_solid_angle
_topol_link.type
_topol_link.order
_topol_link.multiplicity
1 1 1 1 [0 0 0] 13 [0 0 0] 1.5446 22.04 v 1 16
loop_
_topol_atom.id
_topol_atom.node_id
_topol_atom.atom_label
_topol_atom.element_symbol
1 1 C1 C
|
Example 2 - Connectivity of atomic and underlying nets for an
interpenetrating array of two LiCo(CO)4 networks. The atomic net
consists of Li, C, O, and Co atoms, while the underlying net is built
from three kinds of nodes: Li and Co atoms and carbonyl (CO) ligand;
the nodes are labeled as ZA1, ZC1, and ZB1, respectively. Two
possible variants are shown: the coordinates of ZA1 are specified by
a reference to the Li1 atom, while the coordinates of ZC1 are specified
explicitly. Both atomic and underlying nets are described in the
TOPOL_NET section.
loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z
2 -x,-y,z
3 x,-y,-z
# - - - - data truncated for brevity - - - -
24 -z,y,-x
loop_
_atom_site.label
_atom_site.fract_x
_atom_site.fract_y
_atom_site.fract_z
Li1 0.00000 0.00000 0.00000
C1 0.31850 0.31850 0.31850
O1 0.19920 0.19920 0.19920
Co1 0.50000 0.50000 0.50000
loop_
_topol_net.id
_topol_net.label
_topol_net.z_number
_topol_net.special_details
_topol_net.overall_topology_TOPOS
1 Net_1 2 'Atomic network' 'Unknown'
2 Net_2 2 'Underlying net with carbonyl ligands as nodes' '2,4T3'
loop_
_topol_node.id
_topol_node.label
_topol_node.net_id
_topol_node.fract_x
_topol_node.fract_y
_topol_node.fract_z
1 Li1 1 . . . # Li
2 C1 1 . . . # C
3 O1 1 . . . # O
4 Co1 1 . . . # Co
5 ZA1 2 . . . # Li
6 ZB1 2 0.25036 0.25036 0.25036 # (CO)
7 ZC1 2 . . . # Co
loop_
_topol_link.id
_topol_link.node_id_1
_topol_link.node_id_2
_topol_link.distance
_topol_link.type
1 1 3 1.9121 v # Li1-O1
2 2 3 1.1452 v # C1-O1
3 2 4 1.7422 v # C1-Co1
4 5 6 2.4032 gl # Li1-(CO)
5 6 7 2.3963 gl # (CO)-Co
loop_
_topol_atom.id
_topol_atom.node_id
_topol_atom.atom_label
_topol_atom.element_symbol
1 1 Li1 Li
2 2 C1 C
3 3 O1 O
4 4 Co1 Co
5 5 Li1 Li
6 6 C1 C
7 6 O1 O
8 7 Co1 Co
|
Example 3 - Connectivity of an underlying net of the calcite
(CaCO3) crystal structure. The nodes of the underlying
net correspond to Ca atoms and carbonate (CO3) groups.
loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z
2 -y,x-y,z
# - - - - data truncated for brevity - - - -
13 2/3+x,1/3+y,1/3+z
# - - - - data truncated for brevity - - - -
36 1/3-y,2/3-x,1/6+z
loop_
_atom_site.label
_atom_site.fract_x
_atom_site.fract_y
_atom_site.fract_z
C1 0.00000 0.00000 0.25000
O1 0.25930 0.00000 0.25000
Ca1 0.00000 0.00000 0.00000
loop_
_topol_net.id
_topol_net.overall_topology_RCSR
1 pcu-b
loop_
_topol_node.id
_topol_node.label
1 ZA1 # CO3
2 ZB1 # Ca
loop_
_topol_link.id
_topol_link.node_id_1
_topol_link.node_id_2
_topol_link.symop_id_2
_topol_link.translation_2
_topol_link.distance
_topol_link.type
1 1 2 20 [-1 -1 0] 3.2122 gl # (CO3)-Ca
loop_
_topol_atom.id
_topol_atom.node_id
_topol_atom.atom_label
_topol_atom.element_symbol
_topol_atom.symop_id
1 1 C1 C 1
2 1 O1 O 2
3 1 O1 O 2
4 1 O1 O 3
5 2 Ca1 Ca 1
|
Example 4 - Connectivity of an underlying net of the cuprite (Cu2O)
crystal structure. Oxygen atoms coincide with the nodes,
while copper atoms represent the edges. There are two
interpenetrating networks of the diamond topology.
loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z
2 1/2-x,1/2-y,z
# - - - - data truncated for brevity - - - -
20 -z,1/2+y,1/2+x
# - - - - data truncated for brevity - - - -
48 1/2-z,y,1/2-x
loop_
_atom_site.label
_atom_site.fract_x
_atom_site.fract_y
_atom_site.fract_z
O1 0.25000 0.25000 0.25000
Cu1 0.00000 0.00000 0.00000
loop_
_topol_net.id
_topol_net.z_number
_topol_net.overall_topology_RCSR
1 2 'dia'
loop_
_topol_node.id
_topol_node.net_id
1 1
loop_
_topol_link.id
_topol_link.node_id_1
_topol_link.node_id_2
_topol_link.symop_id_2
_topol_link.type
1 1 1 13 gl
loop_
_topol_atom.id
_topol_atom.node_id
_topol_atom.link_id
_topol_atom.atom_label
_topol_atom.element_symbol
1 1 . O1 O
2 . 1 Cu1 Cu
|
Example 5 - MOF-5 (multiple nets; two polyatomic nodes and a molecular linker).
loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z
2 -x,-y,z
# - - - - data truncated for brevity - - - -
5 z,x,y
# - - - - data truncated for brevity - - - -
26 x,y,-z
# - - - - data truncated for brevity - - - -
37 y,x,z
# - - - - data truncated for brevity - - - -
192 1/2-z,1/2+y,-x
loop_
_atom_site.label
_atom_site.fract_x
_atom_site.fract_y
_atom_site.fract_z
H1 0.30590 0.19410 0.04520
C1 0.25000 0.25000 0.11050
C2 0.28310 0.21690 0.02630
C3 0.25000 0.25000 0.05380
O1 .25000 0.25000 0.25000
O2 0.28180 0.21820 0.13390
Zn1 0.29350 0.20650 0.20650
loop_
_topol_net.id
_topol_net.label
_topol_net.special_details
_topol_net.overall_topology_TOPOS
1 Net_1 'Atomic network' 'Unknown'
2 Net_2 'Underlying net with zinc tetranuclear complex groups as nodes and benzene rings as links (cluster representation)' 'pcu'
3 Net_3 'Underlying net with zinc, oxygen and benzenedicarboxylato ligands as 4-coordinate nodes (standard representation)' 'fff'
loop_
_topol_node.id
_topol_node.net_id
1 1 # H1
2 1 # C1
3 1 # C2
4 1 # C3
5 1 # O1
6 1 # O2
7 1 # Zn1
8 2 # C6O13Zn4
9 3 # C8H4O4
10 3 # O1
11 3 # Zn1
loop_
_topol_link.id
_topol_link.node_id_1
_topol_link.node_id_2
_topol_link.symop_id_2
_topol_link.distance
_topol_link.type
1 1 3 . 0.9594 v # H1-C2
2 2 6 37 1.3013 v # C1-O2
3 2 4 . 1.4554 ar # C1-C3
4 3 3 26 1.3502 ar # C2-C2
5 3 4 . 1.3936 ar # C2-C3
6 5 7 . 1.9340 v # O1-Zn1
7 6 7 . 1.9114 v # O2-Zn1
8 8 8 26 12.8345 gl # (C6O13Zn4)-(C6H4)-(C6O13Zn4)
9 9 11 5 5.5309 gl # (C8H4O4)-Zn1
10 10 11 . 1.9340 v # O1-Zn1
loop_
_topol_atom.id
_topol_atom.atom_label
_topol_atom.node_id
_topol_atom.link_id
_topol_atom.symop_id
_topol_atom.element_symbol
1 H1 1 . 1 H
2 C1 2 . 1 C
3 C2 3 . 1 C
4 C3 4 . 1 C
5 O1 5 . 1 O
6 O2 6 . 1 O
7 Zn1 7 . 1 Zn
10 C1 8 . 1 C
11 C1 8 . 55 C
12 O2 8 . 55 O
13 O2 8 . 80 O
14 O2 8 . 6 O
15 O2 8 . 59 O
16 O2 8 . 42 O
17 O2 8 . 78 O
18 C1 8 . 78 C
19 C1 8 . 5 C
20 Zn1 8 . 6 Zn
21 Zn1 8 . 55 Zn
22 C1 8 . 69 C
23 C1 8 . 6 C
24 O2 8 . 41 O
25 O2 8 . 69 O
26 O1 8 . 1 O
27 O2 8 . 5 O
28 O2 8 . 82 O
29 Zn1 8 . 5 Zn
30 Zn1 8 . 1 Zn
31 O2 8 . 1 O
32 O2 8 . 37 O
33 O2 9 . 14 O
34 O2 9 . 26 O
35 O2 9 . 1 O
36 O2 9 . 37 O
37 C1 9 . 14 C
38 C3 9 8 14 C
39 C2 9 8 14 C
40 H1 9 8 14 H
41 C2 9 8 37 C
42 H1 9 8 37 H
43 C2 9 8 26 C
44 H1 9 8 26 H
45 C2 9 8 1 C
46 H1 9 8 1 H
47 C3 9 8 1 C
48 C1 9 . 1 C
49 O1 10 . 1 O
50 Zn1 11 . 1 Zn
|
Example 6 - Cyanamide (simple atomic network example with hydrogen bonding).
loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z
2 1/2-x,-y,1/2+z
3 1/2+x,1/2-y,-z
4 -x,1/2+y,1/2-z
5 -x,-y,-z
6 1/2+x,y,1/2-z
7 1/2-x,1/2+y,z
8 x,1/2-y,1/2+z
loop_
_atom_site.label
_atom_site.fract_x
_atom_site.fract_y
_atom_site.fract_z
H1 0.19700 0.11100 0.02200
H2 0.05900 0.26600 0.08700
C1 0.14120 0.08370 0.23120
N1 0.14590 0.16990 0.10179
N2 0.14010 0.01250 0.34609
loop_
_topol_node.id
1 2 3 4 5
loop_
_topol_link.id
_topol_link.node_id_1
_topol_link.node_id_2
_topol_link.distance
_topol_link.symop_id_2
_topol_link.translation_2_x
_topol_link.translation_2_y
_topol_link.translation_2_z
_topol_link.type
_topol_link.order
1 1 4 0.8988 1 0 0 0 v 1 # H1-N1
2 1 5 2.1228 2 0 0 -1 hb ? # H1-N2
3 2 4 0.8826 1 0 0 0 v 1 # H2-N1
4 2 5 2.2152 4 0 0 0 hb ? # H2-N2
5 3 5 1.1520 1 0 0 0 v 3 # C1-N2
6 3 4 1.3148 1 0 0 0 v 1 # C1-N1
loop_
_topol_atom.id
_topol_atom.atom_label
_topol_atom.node_id
_topol_atom.element_symbol
1 H1 1 H
2 H2 2 H
3 C1 3 C
4 N1 4 N
5 N2 5 N
|
Example 7 - FAU zeolite tiling example.
loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z
2 1/4-x,1/4-y,z
# - - - - data truncated for brevity - - - -
13 -y,-x,-z
# - - - - data truncated for brevity - - - -
41 x,z,y
42 z,y,x
# - - - - data truncated for brevity - - - -
47 x,1/4-z,1/4-y
# - - - - data truncated for brevity - - - -
192 3/4-z,1/2+y,1/4-x
loop_
_atom_site.label
_atom_site.fract_x
_atom_site.fract_y
_atom_site.fract_z
Si1 0.94690 0.12510 0.03640
loop_
_topol_net.id
_topol_net.overall_topology_iza
1 FAU
loop_
_topol_node.id
_topol_node.net_id
_topol_node.label
1 1 Si
loop_
_topol_link.id
_topol_link.node_id_1
_topol_link.node_id_2
_topol_link.distance
_topol_link.symop_id_2
_topol_link.translation_2
_topol_link.type
1 1 1 3.0470 47 [0 0 0] gl
2 1 1 3.0473 13 [1 1 0] gl
3 1 1 3.0539 41 [0 0 0] gl
4 1 1 3.0814 42 [1 0 -1] gl
loop_
_topol_atom.id
_topol_atom.node_id
_topol_atom.atom_label
_topol_atom.element_symbol
1 1 Si1 Si
loop_
_topol_tiling.id
_topol_tiling.net_id
_topol_tiling.signature
_topol_tiling.vertices
_topol_tiling.edges
_topol_tiling.faces
_topol_tiling.tiles
_topol_tiling.d_size
1 1 '2[4^6.6^2]+[4^6.6^8]+[4^18.6^4.12^4]' 1 4 5 3 24
|
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