Chemistry Reference
In-Depth Information
2.3 Computer Tools to Study Periodic Graphs
Although the concept of a periodic graph began as far back as the classic series of
1990s. Now there are the following crystallochemical program packages that are
based on the periodic-graph approach and distributed free of charge:
isomorphism by comparing their adjacency matrices;
3dt
(
3D tiler
) works with 3D space
tilings based on periodic nets [
34
].
of crystal structures; it includes the procedures to build various structure representations,
underlying and packing nets.
Gavrog Systre and TOPOS were used to create a new type of electronic
databases that can be called
crystallochemical
since they describe the topology of
periodic nets as contrasted to
crystallographic
databases like the Cambridge Struc-
tural Database or Inorganic Crystal Structure Database that contain the information
on atomic positions, perhaps on some bonds, but not on the overall topology of
crystal structures. Currently, the following free crystallochemical databases are
available:
chemistry and selected by hand. Most of them were revealed as underlying nets in crystal
structures, and the remaining nets can be useful for crystal design. The three-letter nomen-
clature for net topologies used in this chapter was originally elaborated for RCSR.
mathematical procedures. Although the epinets do not originate in crystal structures,
some of them have been found out as underlying nets. The epinets are denoted by
sqc
XXX
symbols where XXX is an ordinal number, for instance,
sqc
1964.
contains the information on topological indices of more than 71,000 topological types
including RCSR and EPINET, while the TTO collection links the data on underlying nets
with the structural data stored in crystallographic databases.
Below we use the periodic-graph approach together with the TOPOS program
package and TTD collection to perform the systematic analysis of topology of
cation arrays in inorganic oxoacid salts and to reveal the relations in their structure
organization.
1
Generation, Analysis and Visualization of Reticular Ornaments using Gavrog
;
http://www.
2
