Local Coordination versus Overall Topology in Crystal Structures: Deriving Knowledge from Crystallographic Databases

Abstract

We propose three independent methods for determining geometrical shape and topological type of local atomic environment in crystals that is represented as a coordination figure. The methods are based on comparison of the edge graphs of the simplified Voronoi polyhedra, maximizing volume of intersection of polyhedra, and comparison of angular fingerprints of polyhedra. We implemented the methods to the program package ToposPro and tested them on 9642 crystal structures of five-coordinated copper and zinc complexes. The methods showed good selectivity and coincidence. We discuss correlations of the coordination figure type with other structure descriptors and perspectives to use the obtained results in knowledge databases.

Topological study of diverse hydrogen-bonded patterns found in a system of a nickel(II) complex and the sulfate anion

“…Additionally, a recent inclusion in the ToposPro package was applied to evaluate the coordination modes of both the complex cation and the sulfate anion. This algorithm compares the similarity of the coordination figure of an atom or a molecule to some idealized coordination figures on the basis of comparison of angular fingerprints of coordination polyhedra (Shevchenko et al, 2017). In these calculations, parameters and (as defined in Shevchenko's paper) were given values of 18 and 9 , respectively.…”

Using crystallography, topology and graph set analysis for the description of the hydrogen bond network of triamterene: a rational approach to solid form selection

“…In a recent paper by Shevchenko et al [ 22 ] it is recognised that the coordination sphere significantly affects the topology of the crystal as a whole. A further paper by Zolotarev et al [ 23 ] shows how a study of topology can be incorporated into the prediction of possible crystal forms.…”

Design and synthesis of coordination polymers with Cu(ii) and heterocyclic N-oxides

“…The underlying net can be automatically constructed by the ToposPro program package and assigned to a topological type from the TTD collection. [31][32][33][34][35][36][37][38] These characteristics and relations compose the knowledge base for coordination compounds and enable the prediction of topologies and geometries of new structures constructed from topologically similar SBUs which is a goal of reticular chemistry. [39][40][41][42][43][44][45] Therefore, we used ToposPro in screening the Cambridge Structural Database (CSD) for CuIJI,II) (mainly CuIJII)) coordination compounds with heterocyclic ligands containing N-oxide groups (O←NC 2 ), which enables us to make their topological analysis and use the topological relations in the design of new coordination networks with 1-hydroxoimidazole-3-oxides as ligands and CuIJII) as the coordination center.…”