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Looking for the topological types for C6H6O2 isomers and for all known nets with the diamond (dia) topology.
Algorithm:
Algorithm:
- Be sure that you have the TTO and TTR collections (see Appendix 3 for details) on your computer and the path TTO in System/TOPOS Parameters/Paths is correct. You may find a frequently updating collection of .tto and .ttr files on the ToposPro official site. All .tto and .ttr files and TTOReprTypes.txt file have to be copied into a separate subdirectories (/TTO within the ToposPro folder by default). In alternative, the path to the TTO and TTR collections can be changed in System/TOPOS Parameters/Paths.
- Find all topologies for all representations of C6H6O2 isomers. For this purpose open the database C6H6O2 from Module 3 and open a Crystal Data, window for the first record. Go to Comment tab and push Representations Topology button. You will find that the topology for the RESORA13 isomer is known in one representation, in which H-bonded molecules are considered as whole; the topology of the resulting 3D single (Z=1) net is cds (also known as 4/6/t4 sphere packing or sqc5 net). For the nomenclature of topologies see Appendix 5.
Pay attention that you need no simplification of the structure and use of the ADS classification procedure. The data on the representation topology are stored in the TTO collection and related to a given structure by its Ref. Code.
- Look for the topologies if other C6H6O2 isomers. Pay attention that in many cases the data on the structures are not contained in the TTO collection; you will get the message
Currently TTO collection contains the data on 3D structures only; not all of them have yet been processed. - Find all known nets with the diamond (dia) topology. For this purpose open TTD Collection window, find the dia topology in TOPOS&RCSR .ttd file and press Examples button. You will get 6023 examples in the bottom list. The specified number of topologies concern the full version of the topological collections. These numbers can be different in the free version of the topological collections, which is included into the ToposPro distribution package. Right-click in the list, select all records, right-click again and save the Ref. Codes. They will be stored in RefCodes.gcd file located in the /TTO folder. Then you may use ToposPro Acquisition Data/Ref. Code filter to find the crystallographic data on the structures (this works only if you have a large database with many structures from CSD). Otherwise you can search CSD with ConQuest program, loading the .gcd list of Ref. Codes (File/Open/Refcode List). You may also save the whole table (Save Table) as a formatted textual file Table.txt located in the /TTO folder, or copy the information in the Clipboard. You may order the table by any column by clicking its header.
The column Occur. contains the numbers of symmetry-inequivalent nets of a given topology stored in the TTO Collection. Such a number can be more than the number of crystal structures because some structures can contain several inequivalent nets of the same topology. A net is bold-selected if it has at least one occurrence. To leave in the list only the nets with occurrence, right-click in the net list and choose Show with Examples. To show all related nets for the selected nets use the item Show Relations. All the relations will appear in the Topological Types Relations list. You may use also the Relations button to show the entire TTR Collection.
