E. V. Bartashevich

Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test

The results of the fifth blind test of crystal structure prediction, which show important success with more challenging large and flexible molecules, are presented and discussed.

Atomic dipole polarization in charge-transfer complexes with halogen bonding

The polarization effects associated with halogen bonding for the series of charge-transfer complexes D(m)···X-Y, where donor molecules D(m) = NH(3), H(2)O, H(2)S, C(2)H(4), CO and X-Y = Cl(2), ClF, Br(2), BrCl, ICl, I(2), are characterized in terms of the quantum theory of atoms in molecules using the B3LYP/6-311** Kohn-Sham wave functions. We study the electrostatic potential features of separate donor and acceptor molecules, the change in atomic charges as well as the atomic electric dipole moments and their components, and the intra-atomic electron density dipole polarization and the bonding dipole moments resulting from the electron density redistribution between the molecules in the charge-transfer complexes. The equation linking the most negative electrostatic potential values in the donor molecules and the most positive values in dihalogen molecules with the stretching force constants was found using two-factor regression. It is demonstrated that the dipole polarization of the acceptor atom mirrors the strength of halogen bonding in complexes in a series of different donors and acceptors. An exponential relationship between the magnitude of the total atomic electric dipole moment of the acceptor atom and the intermolecular stretching force constant is established for weakly bounded complexes.

Interplay between non-covalent interactions in complexes and crystals with halogen bonds

Studies on the structure and properties of complexes and crystals with halogen bonding accompanied by different secondary non-covalent interactions are summarized. The signs of halogen bonding are systematized and modern methods and approaches used to provide clear and reproducible estimates of the strength of halogen bonds are analyzed. The halogen bond strength values are compared with the strength of the other non-covalent interactions. The contradictions in the interpretation of the results from different studies of the strength of halogen bond are discussed. The bibliography includes 249 references.

Complex structure tri- and polyiodides of iodocyclization products of 2-allylthioquinoline

Iodocyclization products of 2-allylthioquinoline are obtained in the form of polyiodides with different stoichiometric compositions. X-ray crystallography data are analyzed for two different crystal structures of 1-iodomethyl-1,2-dihydro[1,3]thiazolo[3,2-a]quinolinium polyiodides: triiodide C12H11INS+I3− and complex polyiodide 2(C12H11INS+I3−)·I2. A comparison is made of the nonbonding interactions of dihydrothiazoloquinolinium with atoms of the triiodide anion and complex polyiodide to show the crystal structure features attributed to the participation of molecular iodine.

Raman spectroscopy study of new thia- and oxazinoquinolinium triodides

A number of new solid polyiodides of thia- and oxa-zinoquinolinium derivatives have been characterized using a combined approach of Raman spectroscopy and periodic 3D calculations of the Raman intensities. Various cation–anion ratios, including tri- and polyiodides of the complex structure [I3⋯I2]−, have been studied. For the oriented single crystal containing the [I3⋯I2]− fragments, the polarized Raman spectra and the angular dependency of the band intensities on crystal rotation have been obtained. These techniques have allowed us to get new information on the spatial organization of the intermolecular interactions of iodine in polyiodide-anion chains. They have also shown perspectives on the geometrical characterization of complex polyiodides using Raman spectroscopy.

Theoretical estimation of the possibility of formation of oxadiazocines in the nucleophilic addition of resorcinol to pyrimidines and synthesis of new azoloannelated benzooxadiazocines

A method was proposed for estimating the possibility of cyclization of adducts of resorcinol with pyrimidines to form oxadiazocines based on the conformational criterion and analysis of charges on the C(5) atom of the pyrimidine ring and on the H atom of the hydroxy group of the resulting adducts. A series of new derivatives of 4,5-dihydro-11H-5,11-methanobenzo[g]azolo[1,3,5]oxadiazocines were synthesized.

Nontypical iodine-halogen bonds in the crystal structure of (3E)-8-chloro-3-iodomethylidene-2,3-dihydro-1,4-oxazino[2,3,4-ij]quinolin-4-ium triiodide.

Two kinds of iodine-iodine halogen bonds are the focus of our attention in the crystal structure of the title salt, C12H8ClINO(+)·I3(-), described by X-ray diffraction. The first kind is a halogen bond, reinforced by charges, between the I atom of the heterocyclic cation and the triiodide anion. The second kind is the rare case of a halogen bond between the terminal atoms of neighbouring triiodide anions. The influence of relatively weakly bound iodine inside an asymmetric triiodide anion on the thermal and Raman spectroscopic properties has been demonstrated.

Theoretical investigation of the antituberculosis activity of compounds of the dihydropyrimidine series

An analysis of the tuberculostatic activity of dihydropyrimidine derivatives has been carried out using the 3D QSAR algorithm BiS/MC. Conformers responsible for the biological action of these compounds have been found and their complexes with receptors have been modeled. It is shown that oxygen atoms of the podand chain or ether group of most biologically active compounds interact with postiviely charged atoms of the receptor. Pharmacophore and antipharmacophore fragments have been identified. The relationship of the tuberculostatic activity and characteristics of the receptor-ligand complexes have been established (correlation coefficient, 0.99). The results can be used for directed synthesis of effective antituberculosis agents and for predicting the tuberculostatic activity of new compounds.

A Method for Multiconformational Modeling of the Three‐Dimensional Shape of a Molecule

A method for multiconformational modeling of the three‐dimensional shape of a molecule is proposed that includes search for conformers, their optimum superposition, and analysis of spatial features of the resulting structure. The method allows one to determine features of various molecular conformations of compounds under study, to assess the contributions of conformers to particular properties of the substance, to evaluate the space occupied by the molecule, and to compare the average size of the multiconformational model of the molecule with the sizes of the most stable conformations. The potentials of the model are illustrated by density calculations for 137 organic liquids.

Genetic Algorithm for Predicting Structures and Properties of Molecular Aggregates in Organic Substances

A genetic algorithm for predicting the structures and properties of molecular aggregates in organic substances is proposed. It has been used for modeling the most probable dimers and trimers existing in 137 organic liquids. It has been shown that the geometric and energetic features of modeled aggregates agree with known data. The energy of aggregation correlates with the enthalpy of evaporation of substances. The dependence of the energetic and geometric features of aggregates on the chemical nature of their constituent molecules is discussed.