O. A. Blatova

Study of rare-earth π-complexes by means of Voronoi–Dirichlet polyhedra

An investigation of 135 pi-complexes of rare-earth atoms (Ln) was carried out with Voronoi-Dirichlet polyhedra. A novel method for the evaluation of the sizes of polyatomic ligands and steric effects in the structure of organometallic compounds was developed. The dependence of the domain size for Ln atoms on their nature, coordinating number and oxidation state was studied. The reasons for the occurrence of agostic Ln-H contacts were considered with a geometrical-topological analysis.

Analysis of Lanthanide π Complexes in Terms of Voronoi–Dirichlet Polyhedra

The structures of 112 rare-earth π complexes were studied using Voronoi–Dirichlet polyhedra. A new method for identification of chemical bonding between atoms in organometallic compounds was proposed. The dependence of the area of action of a lanthanide atom (Ln) on its nature, coordination number, and oxidation number was investigated. The reasons for the formation of Ln···H aghostic contacts were considered within the framework of the geometric topological method of crystal-chemical analysis employed.

Molecular packings and specific-bonding patterns in sulfonamides

A novel approach to topological analysis of molecular packings and intermolecular bonding patterns is described and tested on the crystal structures of 1463 sulfonamide derivatives taken from the Cambridge Structural Database, as well as three newly synthesized ones. We have revealed strong correlations between the local and overall topological motifs of hydrogen and halogen specific intermolecular bonds; as a rule, a particular local connection type of the molecules provides only one most preferred pattern of intermolecular bonds and vice versa. Molecular packings are found to be almost independent of the existence or absence of specific bonds and in more than 1/3 of cases they obey Kitaigorodskiis model of close packing. The peculiar shapes of the sulfonamide molecules in some cases give rise to a special ‘butterfly’ packing that is topologically less dense than close packings. The correlations found can be used to predict the main peculiarities of molecular crystals with a prospective expert system.

A new set of molecular descriptors.

A new set of criteria for quantitative analysis of molecular interactions is proposed, which is based on the conceptions of atomic and molecular Voronoi-Dirichlet polyhedra. It is shown that the calculation of solid angles of ligands and complexes as a whole allows one to estimate screening effects and the probability of forming intra- and intercomplex non-valent contacts. The set proposed was used to study the influence of steric factors on the stability of complex groups as well as on the presence or absence of agostic contacts in crystal structures of 808 rare-earth pi-complexes.

Analysis of microporous mineral phases with Voronoi-Dirichlet polyhedra

The methods for computer characterization of voids in crystal structures using Voronoi-Dirichlet polyhedra are applied to microporous mineral phases. It is shown that these methods allow an appropriate visualization of interstitial voids, cavities, cages, and channels, which provides an estimate of their geometrical properties, such as size and shape. Some typical minerals are considered to analyse the system of voids, and the methods are found to be an effective tool for predicting the type and positions of interstitial cations.

Analysis of Li+ cation migration paths in oxygen-containing compounds

Novel method for the studying of voids and channels in crystal structures is developed on the basis of the TOPOS structure-topology software. The method is using the Voronoi-Dirichlet crystal space partition. All ternary and quaternary lithium-containing inorganic compounds whose structure has been studied (822 compounds of the LiaXbOz composition and 1349 compounds of the LiaX1bX2cOz composition, where X, X1, and X2 is any chemical element) are analyzed for the first time. The dimensionality of systems of the channels capable of transporting lithium ions is revealed. For all compounds, the migration patterns are constructed, which characterize systems of the conductance channels with the dimensionality 1, 2, and 3; the theoretically calculated coordinates of lithium atom positions in the voids’ centers agree well (accurate within 0.06 nm) with the known structure data. It is found, that 275 compounds have infinite channel system. Of this sampling, 249 compounds (125 structural types) have been described as solid electrolytes; the rest (26 compounds) can be thought of as potential ionic conductors with one-dimensional (6 types), two-dimensional (2 types), or three-dimensional (18 types) conductance.

Chalcogen-Containing π-Complexes of Lanthanides: Crystal-Chemical Analysis and a System of Descriptors for Intermolecular Contacts

A sample comprising 241 π-complexes LnCnHmZk (Z = O, S, Se, Te) was used to analyze the influence of the nature, the oxidation state, and the coordination number of the central atom and the nature of the Z atom on the activity area of the lanthanide (Ln). A new system of criteria based on the concepts of the atomic and molecular Voronoi–Dirichlet polyhedra is proposed for the quantitative analysis of intermolecular contacts. This system was used to analyze the influence of steric factors on the stability of complex groups and the presence or absence of agostic interactions in the structures of 475 complexes LnCnHm, LnCnHmXk (X = F, Cl, Br), and LnCnHmZk.

Packing topology in crystals of proteins and small molecules: a comparison

We compared the topologies of protein and small molecule crystals, which have many common features – both are molecular crystals with intermolecular interactions much weaker than intramolecular interactions. They also have different features – a considerably large fraction of the volume of protein crystals is occupied by liquid water while no room is available to other molecules in small molecule crystals. We analyzed the overall and local topology and performed multilevel topological analyses (with the software package ToposPro) of carefully selected high quality sets of protein and small molecule crystal structures. Given the suboptimal packing of protein crystals, which is due the special shape and size of proteins, it would be reasonable to expect that the topology of protein crystals is different from the topology of small molecule crystals. Surprisingly, we discovered that these two types of crystalline compounds have strikingly similar topologies. This might suggest that molecular crystal formations share symmetry rules independent of molecular dimension.

An analysis of migration paths of Li+ cations in ternary oxygen-containing compounds LipXqOr

A new method was developed for studying voids and channels in crystal structures based on the Voronoi-Dirichlet partition of crystal space, and 822 structurally characterized ternary compounds LipXqOr were analyzed for the first time. For these compounds, the dimensionality was determined and the migration patterns of channel systems capable of providing lithium-ion transport were constructed. The calculated coordinates of lithium atoms in the centers of the voids are consistent (within 0.4 Å) with the known structural data. Among these compounds, 113 compounds have infinite channel systems, 60 compounds (18 structural types, STs) have been described earlier in the literature as solid electrolytes, and 53 compounds (23 STs) can be considered as potential one-, two-, or three-dimensional ionic conductors (13, 3, and 7 STs, respectively).

An analysis of migration paths of Li{sup +} cations in ternary oxygen-containing compounds Li{sup p}X{sup q}O{sup r}

A new method was developed for studying voids and channels in crystal structures based on the Voronoi-Dirichlet partition of crystal space, and 822 structurally characterized ternary compounds LipXqOr were analyzed for the first time. For these compounds, the dimensionality was determined and the migration patterns of channel systems capable of providing lithium-ion transport were constructed. The calculated coordinates of lithium atoms in the centers of the voids are consistent (within 0.4 Å) with the known structural data. Among these compounds, 113 compounds have infinite channel systems, 60 compounds (18 structural types, STs) have been described earlier in the literature as solid electrolytes, and 53 compounds (23 STs) can be considered as potential one-, two-, or three-dimensional ionic conductors (13, 3, and 7 STs, respectively).