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About ToposPro
ToposPro is a program package for comprehensive analysis of geometrical and topological properties of periodic structures (crystals, networks, tilings). ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters. Two main principles characterize the ToposPro philosophy:
Objectivity: processing crystallographic data should be as much independent of a human as possible; the crystal structures of any chemical nature and complexity should be analyzed with universal algorithms. This principle declares an alternative to traditional visual crystallochemical analysis: a crystal structure should be treated with formal computer procedures, the structure images should be used only to illustrate the results, not as a source for conclusions. For example, when exploring microporous structures, a researcher should consider in the same scheme inorganic zeolites built with ion-covalent bonding, metal-organic coordination frameworks, or supramolecular architectures assembled with H-bond, specific, or van der Walls contacts. Moreover, the cages and channels in such structures should be separated with a universal algorithm, not with the motto: “I see it in that way”.
Completeness: all available data should be considered while searching for or checking new regularities. The situation is inadmissible when one draws the conclusions after analyzing only few compounds, ignoring hundreds or thousands of crystal structure determinations related to the problem under consideration. To apply this principle one has to implement new computer methods for crystallochemical analysis of large amounts of diverse crystallographic data in an automated mode.
The first principle is provided in ToposPro with a set of applied programs, unique algorithms and methods of crystallochemical analysis. The second principle is realized as the ToposPro database management system (DBMS) that supports various kinds of crystallographic databases and allows the researcher to compose his own data samples for a subsequent computer analysis. DBMS is integrated to the applied programs with a user-friendly interface. All ToposPro methods can be subdivided into two groups: geometrical and topological. The first group is realized in the programs DiAn and IsoCryst and covers routine geometrical calculations (distances, angles, RMS planes, etc.) as well as visualization of crystal structures. The second group includes a number of procedures for studying the connectivity properties of the whole crystal space; they gave origin to the name TOPOS thus declaring the main destination of the package. Most of the topological procedures are gathered in the programs AutoCN and ADS. One more set of methods, being formally geometrical, connects these two groups together. These are the methods of the program Dirichlet intended for construction of the Voronoi partition of the crystal space. They were described in detail in a special review and require merely the initial crystallographic data to restore the crystal space connectivity. The crystal space is represented as a union of convex polyhedral atomic domains, and any face of any domain is shared between strictly two domains. Thus, any Voronoi polyhedron face corresponds to an atomic contact to be classified as valence, non-valence (H bond, specific, or van der Waals), or not bonding according to additional geometrical criteria. Having the crystal space connected in this way we can apply the ToposPro topological methods.
Classes of crystal structures and chemical compounds, for which ToposPro is designed to work:
ionic and covalent inorganics
intermetallics
organic and other molecular crystals
metal-organic, coordination polymers
solid electrolytes
microporous structures
nanoclusters
Crystallochemical tasks that can be solved with ToposPro
topological classification and identification of periodic and molecular structures
search for occurrence of topological motifs in crystal structures
analysis of molecular packings
topological analysis of systems of intermolecular hydrogen and/or halogen bonds
search for relations and transformations between different topological motifs
separation of and search for structural building units (molecules, ligands, cages, clusters, complex groups) in crystal structures
simplification of the structure topology for the subsequent classification
subdivision of the crystal space with Voronoi polyhedral
construction of tilings
search for migration paths in solid electrolytes
Certificate
ToposPro is a program package for comprehensive analysis of geometrical and topological properties of periodic structures (crystals, networks, tilings). ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters. Two main principles characterize the ToposPro philosophy:
Objectivity: processing crystallographic data should be as much independent of a human as possible; the crystal structures of any chemical nature and complexity should be analyzed with universal algorithms. This principle declares an alternative to traditional visual crystallochemical analysis: a crystal structure should be treated with formal computer procedures, the structure images should be used only to illustrate the results, not as a source for conclusions. For example, when exploring microporous structures, a researcher should consider in the same scheme inorganic zeolites built with ion-covalent bonding, metal-organic coordination frameworks, or supramolecular architectures assembled with H-bond, specific, or van der Walls contacts. Moreover, the cages and channels in such structures should be separated with a universal algorithm, not with the motto: “I see it in that way”.
Completeness: all available data should be considered while searching for or checking new regularities. The situation is inadmissible when one draws the conclusions after analyzing only few compounds, ignoring hundreds or thousands of crystal structure determinations related to the problem under consideration. To apply this principle one has to implement new computer methods for crystallochemical analysis of large amounts of diverse crystallographic data in an automated mode.
The first principle is provided in ToposPro with a set of applied programs, unique algorithms and methods of crystallochemical analysis. The second principle is realized as the ToposPro database management system (DBMS) that supports various kinds of crystallographic databases and allows the researcher to compose his own data samples for a subsequent computer analysis. DBMS is integrated to the applied programs with a user-friendly interface. All ToposPro methods can be subdivided into two groups: geometrical and topological. The first group is realized in the programs DiAn and IsoCryst and covers routine geometrical calculations (distances, angles, RMS planes, etc.) as well as visualization of crystal structures. The second group includes a number of procedures for studying the connectivity properties of the whole crystal space; they gave origin to the name TOPOS thus declaring the main destination of the package. Most of the topological procedures are gathered in the programs AutoCN and ADS. One more set of methods, being formally geometrical, connects these two groups together. These are the methods of the program Dirichlet intended for construction of the Voronoi partition of the crystal space. They were described in detail in a special review and require merely the initial crystallographic data to restore the crystal space connectivity. The crystal space is represented as a union of convex polyhedral atomic domains, and any face of any domain is shared between strictly two domains. Thus, any Voronoi polyhedron face corresponds to an atomic contact to be classified as valence, non-valence (H bond, specific, or van der Waals), or not bonding according to additional geometrical criteria. Having the crystal space connected in this way we can apply the ToposPro topological methods.
Classes of crystal structures and chemical compounds, for which ToposPro is designed to work:
Crystallochemical tasks that can be solved with ToposPro
Certificate
