Manual 


ToposPro practical manual
Version 5.0 (release 1.1.4) V.A. Blatov & D.M. Proserpio
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1. Working with DBMS (DataBase Management System). General crystallographic information.

1.1 Standard operations to work with ToposPro databases.
Tools: commands from menu sections Compound, DataBase and Window.

Сreating a new database from CIF, SHELX or Systre formats.

Copying, moving, deleting and undeleting database records.

1.2 Viewing, editing and creating database records.
Tools: Crystal Data window.

Viewing and editing crystallographic information.

2. Data filtering. Working with the program AutoCN. Computing and editing an adjacency matrix. Inorganic, organic, metal-organic frameworks and artificial nets.

2.1 Searching for compounds in a database. Computing and saving an adjacency matrix containing the information on valence and non-valence bonding in the crystal structure. Automated storing coordination numbers of atoms in the database.
Tools: DBMS filters, the program AutoCN

Filtering different modifications of lithium sulfate including hydrates, computing and saving adjacency matrices for them.

2.2 Looking through and editing adjacency matrix.
Tools: Crystal Data window.

Determining typical interatomic distances for hydrogen bonds in a lithium sulfate hydrate. Removing all van der Waals contacts from the adjacency matrix.

2.3 Building the adjacency matrix for an artificial net.
Tools: the program AutoCN, Crystal Data window.

Building the adjacency matrix for the vab net. Producing subnets for the nbo net.

Appendix 1. Details of the AutoCN algorithms.

3. Working with the program IsoCryst. Visualizing crystal structures. Geometrical and topological analysis.

3.1 Drawing an image of a crystal structure, performing standard geometrical calculations, analysis of the system of chemical bonds.
Tools: The programs AutoCN and IsoCryst, Crystal Data window.

Analysis of the crystal structure of β-UO2SO4

Analysis of a hydroquinone polymorph

3.2 Search for a given finite fragment in the net.
Tools: The program IsoCryst, DBMS filters.

Search for hydroquinone polymorphs.

3.3 Analyzing interpenetrated arrays.
Tools: The program IsoCryst.

Analysis of an interpenetrated hydroquinone polymorph.

3.4 Determining molecular coordination numbers, analysis of molecular packing and intermolecular bonds.
Tools: The programs AutoCN and IsoCryst.

Analysis of α-S8 crystal structure.

4. Working with the program ADS. Simplification of crystal structures.

4.1 Standard methods to simplify valence-bonded, hydrogen-bonded and specific-bonded structures.
Tools: The programs ADS, AutoCN and IsoCryst, Crystal Data window

Simplification of CaCO3 polymorphs.

Simplification of the H2S crystal structure.

Simplification of the crystal structure of SAKNAU, 4,4'-bipyridinium tetracyano-platinum.

Simplification of the crystal structure of ACOKIM, 4-iodo-2,3,5,6-fluoro-benzonitrile.

4.2 Special methods of simplifications. Constructing edge and ring nets. Simplification of nets with synthons. The cluster and skeleton simplification modes. Hopf ring nets. Augmented nets.
Tools: The programs ADS, AutoCN and IsoCryst, Crystal Data window, Simplify Adjacency Matrix procedure

Edge-net simplification of the crystal structure of SAYNAI, 3-(chloroacetamido)pyrazole.

Ring-net simplification of the crystal structure of XEHKIE, 2,3,5,6-tetrachloro-trans-1,4-diethynylcyclohexa-2,5-diene-1,4-diol.

Cluster simplification of the crystal structure of NAPFUG, a Metal-Organic Framework Zn4O(NBT)2, H3NBT= 4,4′,4′′-nitrilotrisbenzoic acid.

Skeleton simplification of the crystal structure of ACUCIK, (5-[2-(3-pyridyl)ethenyl)thiophene-2-carboxylato)2Zn.

Building Hopf ring net for the crystal structure of GULBAR, [Zn(atz)(isonic)]·0.5Hisonic, atz =5-amino-tetrazolate, Hisonic=isonicotinic acid.

Generate the augmented version of a given net. Open the idealnets database available in the root folder. This database contain all RCSR nets and some more sphere packings. It is quite useful when you want to examine a given net in its maximum symmetry embedding. Let’s build gsi-a from gsi.

Appendix 2. The concept of “underlying net” and crystal structure representation. Methods of simplification.

5. Working with the program ADS, TTD, TTO, and TTR collections. Identification and taxonomy of nets. Different structure representations.

6. Working with the program ADS. Searching for and analyzing entanglements.

7. Working with the program ADS. Computing and analyzing natural tilings.

8. Working with the program Dirichlet. Constructing Dirichlet domains and computing their characteristics.

8.1. Constructing and drawing atomic and molecular Dirichlet domains (Voronoi-Dirichlet polyhedra, VDP).
Tools: The programs AutoCN, Dirichlet, ADS and IsoCryst.

Determination of coordination numbers and oxidation state of uranium atoms in β-U3O8.

Constructing molecular Voronoi-Dirichlet polyhedra for benzene molecules and estimating their sizes.

8.2. Computing and analyzing migration maps for solid electrolytes.
Tools: The programs Dirichlet, IsoCryst and ADS, Crystal Data window.

Computing and analyzing the migration map in α-AgI.

Computing and analyzing the migration map in β-alumina, Na2O(Al2O3)11.

9. Working with large groups of structures. Data filtering.

9.1. Working with DBMS filters. Searching for a given finite fragment.
Tools: The programs AutoCN and IsoCryst, DBMS filters.

Searching for the Bergman clusters in Cu-containing intermetallides.

9.2. Simplification and taxonomy of nets. Tools: The programs AutoCN and ADS, Microsoft Excel.

Classification of single 3-periodic nets in Cu-compounds by topological types.

10. Searching for topological relations between nets.

Searching for topological relations between nets and working with net relation graph.
Tools: The programs ADS and IsoTest, the TTD collection, Generate Representations procedure, DBMS filters, net relation graph tools.

Searching for all three-periodic uninodal subnets of diamond (dia) and lonsdaleite (lon) topological types. Searching for the shortest transformation paths between dia and lon.

11. Searching for building units. The Nanoclustering procedure.

Searching for building units and the corresponding underlying net.
Tools: The Nanoclustering procedure, the programs ADS, the TTD collection.

Searching for building units and the underlying net in the crystal structure of Cu5Zn8.

Searching for building units and the corresponding underlying net.
Tools: The Nanoclustering procedure, the programs ADS and IsoTest, the TTD collection, the Distribution procedure.

Searching for building units and the underlying net in the crystal structures of ZrZn22 and NaCd2.

12. Analysis of coordination compounds.

12.1. Analysis of chemical composition and coordination types of ligands.
Tools: the programs AutoCN, ADS, Topology/Ligands filter.

Searching for all structures containing/not containing ligands with sulfur atoms.

Searching for all structures containing ligands of a specified composition and/or coordination type.

Searching for the structures containing only a given number of kinds of ligand.

12.2. Analysis of chemical composition, topology and dimensionality of complex groups.
Tools: The program ADS, Topology/Ligands filter, Compound/Distribution procedure.

Searching for the structures containing complex groups of a specified local topology.

Searching for the structures containing complex groups of a specified dimensionality and composition.

13. Analysis of polynuclear coordination clusters.

Classification of metal skeletons in polynuclear coordination clusters.
Tools: The programs AutoCN, ADS, Modify Adjacency matrix procedure.

Separating and classifying metal skeleton in BEQXEB, [Mn84O72(O2CMe)78(OMe)24(MeOH)12 (H2O)42(OH)6]·xH2O·yCHCl3.

Appendix 9. ToposPro Parameters.



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