Variational method for calculating the anharmonic vibrations of polyatomic molecules using a combined morse-anharmonic basis taking into account the fragmentary structure of molecules

A method of variational solution of anharmonic vibration problems using a mixed Morse—anharmonic basis is proposed. The basis functions are the products of the Morse oscillator eigenfunctions for vibrations of peripheral bonds, the harmonic oscillator eigenfunctions for almost harmonic skeletal and deformation vibrations, and the anharmonic basis functions for essentially anharmonic skeletal and deformation vibrations. The anharmonic basis wave functions are taken as a linear combination of the Morse and harmonic oscillator eigenfunctions. The introduction of the combined Morse—anharmonic functions allows one to factorize the solution of a problem into a series of individual blocks according to the fragmentary structure of molecules. Volgograd Pedagogical University. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 231–238, March–April, 1995. Translated by I. Izvekova     

Method of computer-aided determination of the type of normal vibrations of polyatomic molecules

Correct assignment of calculated and experimental frequencies, as well as corservation of the initial assignment in case of a random coincidence of two frequencies during the solution of an inverse spectral problem, are important problems in spectroscopy of polyatomic molecules. Vibrations are classified according to their form, which is thought to be a more reliable basis for assignment than frequency. We offer a PC program to determine the type of vibrations according to their form (obtained by solving a direct vibrational problem) in a given system of vibrational basis set functions. Optimization of systems of basis set functions for molecules with six-membered rings is discussed. L. Ya. Karpov Physicochemical Scientific Research Institute. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 298–303, March–April, 1995. Translated by L. Smolina     

Force fields of halide-substituted methane derivatives

The paper describes methods for determining the force fields of large sets of molecules which share the common property that in their constituent groups of molecules the equivalent force constants always change monotonically with the properties of substituent atoms belonging to the same subgroup of the periodic table. The force fields of the CH_4−nX_n (n=0–4, X=F, Cl, Br, I) molecules of the methane series are obtained. The applications of these force fields are discussed. In particular, they can serve as a basis for a data bank of the force fields of fragments suitable for constructing the force fields of more complex molecules. Russian Scientific Center “Applied Chemistry”, St. Petersburg. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 2, pp. 250–256, March–April, 1996. Translated by I. Izvekova     

Complementarity and justification in science,or comments on some fundamental concepts and problems in the theory and methods of structure and property investigations of complex molecules and molecular systems

Major problems in using some key notions of the theory of structure, such as bond length and potential function parameters, are discussed on the basis of the general complementarity principle formulated by Bohr. It is shown that the use of this principle and model representations, indispensable in microworld studies, inevitably involves subjectivism arising in the solution of inverse problems, and leads to the violation of the requirement of reason. Vernadskii Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences Translated fromZhurnal Strukturnoi Khimii, Vol. 35, No. 4, pp. 123–134, July–August, 1994. Translated by O. Kharlamova     

Data selection for structure generation in structure elucidation systems using molecular spectroscopy databases

Data selection techniques are considered for structure generation in structure elucidation systems using molecular spectroscopy databases. The starting data are sets of microfragments and connected structural fragments obtained from computer-aided analysis of mass, IR, and NMR spectra. Selection of fragments that do not isomorphically fit in larger fragments mostly leads to correct results with fewer output structures anddemands less computer time. Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 35, No. 2, pp. 46–53, March–April, 1994. Translated by L. Smolina     

Experimental structural and conformational studies of carbonyl molecules in the ground and lower excited states

Experimental data (obtained by the authors and taken from the literature) on the structure and conformations of carbonyl molecules in the ground and lower excited electronic states are presented. The structure of carbonyl fragments, the orientation of substituent groups, the energy of the molecules in excited states, and the potential functions of the internal rotation and inversion are considered. The structural similarities of the molecules are discussed. M. V. Lomonosov Moscow State University, Chemical Faculty. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 269–285, March–April, 1995. Translated by I. Izvekova     

X-ray fluorescent and EXAFS studies of the electronic and spatial structure of dialkyl sulfides and their PdCl2 complexes in extraction systems

SK_α, SK_β, ClK_β, ClK_β, and PdL_β2 X-ray fluorescent and PdK EXAFS spectra were obtained for some organic solutions of dialkyl sulfide complexes with palladium chloride. Solvent effects on the electronic and spatial structure of complexes in solution are discussed. In the benzene solution of [PdCl₂2(C₆H₁₃)₂S], complex molecules interact with solvent molecules along a coordinate that is perpendicular to the plane of the complex molecule. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurmal Strukturnoi Khimii, Vol. 35, No. 4, pp. 105c111, July–August, 1994. Translated by L. Smolina     

Molecular dynamic study of stabilization of the Cl−−Cl− anion pair in steam

This paper studies the formation of a stable anion pair as a result of cluster interactions with water molecules (the number of molecules n=4, 6, 8, and 14). The hydration shells of the clusters obtained in a preliminary calculation are destructed to form closed chains of properly oriented water molecules in the space between the anions. The type of the resulting structure depends on the number of shared water molecules. The character of stabilization of the anion pair, determined by calculating different energy terms, also changes as n increases. The cyclic structures obtained in the region of the anion pair differ considerably from the structure of isolated Cl⁻ (H₂O)_n clusters and that of the aqueous solution of NaCl. The capture of water molecules by the anion pair is manifested in the nucleation of industrial steam. Institute of Thermal Physics, Ural Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 2, pp. 289–298, March–April, 1996. Translated by L. Smolina     

Topological analysis of the structure-mesomorphous property ralationship

The use of topological indices to reveal the relationship between molecular structure and mesomorphous properties is discussed. Mathematical models for classification of mesophase types are proposed. The effect of molecular structure and attractive ability on phase transition temperatures is described. Examples of using correlation equations to predict the properties of 2,5-disubstituted 1,3-dioxanes are given. A. V. Bogatskii Physicochemical Institute, Ukrainian Academy of Sciences. Translated fromZhurnal Struktumoi Khimii, Vol. 35, No. 4, pp. 53–60, July–August, 1994. Translated by L. Smolina     

Parametric method in the theory of the vibronic spectra of complex molecules. Absorption spectrum of decapentaene

The absorption spectra of decapentaene are analyzed and calculated using the available efficient methods of calculating the matric elements of the vibronic problem, a new parametric method for determining the potential surfaces of excited molecules, and a fragmentation approach to the design of molecular models. Good agreement for the fine vibrational structure of the calculated and experimental spectra (differences between the main band frequencies and intensities less than 20 cm⁻¹ and 10%, respectively) is obtained without correcting the parameters of the method. The mechanisms of excitation-induced structural changes in linear polyenes and the effect of bond angle changes on the vibrational structure of the spectrum are revealed. A new interpretation of the absorption spectrum of decapentaene in an argon matrix is proposed [J. Mol. Spectrosc.,114, 54–59 (1985)]. It is shown that the parametric method allows quantitative prediction of fine structure for the vibronic spectra of complex molecules. K. A. Timiryazev Moscow Agricultural Academy. Translated fromZhurnal Strukturmoi Khimii, Vol. 37, No. 6, pp. 1031–1039, November–December, 1996. Translated by I. Izvekova     

Band shape in vibrational spectra and interactions of polar molecules in liquids

The structure and shape of bands in the Raman vibrational spectra of polar molecules in liquids are analyzed. The possibility of using these data to examine interactions of molecules as well as their vibrational and orientational dynamics is shown. Translated from Zhumal Struktumoi Khimii, Vol. 38, No. 2, pp. 270–281, March–April, 1997.     

Structural transition to electrolyte-water solvent and changes in the molecular dynamics of water and properties of solutions

A model of concentration transition “ions and complexes in a water structure → ionic and ionicaqueous clusters → polymer structures of salt and crystal hydrate melts” is suggested. The appearance of cluster nanostructures outside the first zone of a waterlike structure is regarded as a general characteristic of solutions. The characteristics of solutions, phase equilibria, and salts of complex composition are interpreted based on this model. Investigation of the complex dielectric constant of electrolytic solutions in the SHF and EHF bands (7–119 GHz) at high concentrations showed that there are two dispersion regions in which the relaxation times differ by a factor of 5–10. Relaxation processes are separated, the numbers of molecules in hydration shells are calculated, and relaxation times are determined for bulky tetrahedral water with hydration shells of ions, for clusters, and for ionicaqueous polymer chains. It is shown that the two structure subsystems of water molecules in concentrated solutions may be described using the limited rotator/generalized diffusion molecular model. Translated fromZhumal Strukturnoi Khimii, Vol. 39, No. 5, pp. 851–863, September–October, 1998.     

Stereochemical analysis by simplex representation of molecules

Stereoanalysis of molecules by partitioning a spatial structure into a system of simplices is described in detail. Potentialities of simplex representation of molecules in defining stereochemistry are demonstrated for chiral structures of various complexity and planar unsaturated molecules (“two-dimensional stereochemistry”). A concept of “stereochemical charge” is introduced. A. V. Bogatskii Physicochemical Institute, Ukrainian Academy of Sciences. Odessa State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 3, pp. 553–558, May–June, 1998.     

Vibrational spectra and the structure of long-chain aliphatic compounds

Polymorphism and the structure of mesomorphous states of long-chain aliphatic compounds (LAC) have been studied by vibrational spectroscopy (theory, experiment) using calorimetry, polarizing microscopy (PM), and X-ray diffraction (XRD) analysis as auxiliary methods. LAC are represented by homologous series of alkyl- and alkoxybenzoic acids, alkylcyclohexanecarboxylic acids, their completely or partially fluoroalkyl-substituted analogs, and 4-cyano-4′-(n-alkoxy)biphenyls. The studies were performed at 77–500 K. IR absorption and Raman spectra were measured at 30–4000 cm⁻¹. The compounds are characterized by conformational polymorphism. The molecules and their H-complexes undergo structural rearrangements during phase and conformational transitions. In the course of the rearrangements, alkyl and fluoroalkyl radicals (AR and FAR) are twisted, and carboxyl groups are disordered. The rearrangements dictate the structure of mesophases, which are mostly formed of H-complexes consisting of dimers, monomers, and open associates. N. G. Chernyshevskii Saratov State University. Institute of Physics, Ukrainian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 338–344, March–April, 1995. Translated by L. Smolina     

Estimation of the densities of solutions using the geometrical parameters of their component molecules

A new model based on certain physical concepts of interatomic interactions is proposed for simulating the volume characteristics of molecules that allow reliable estimations of the densities of substances and solutions. The model is used to calculate the solution densities for six substances within wide concentration ranges. Chelyabinsk State University. Translated fromZhurmal Strukturnoi Khimii, Vol. 36, No. 5, pp. 823–827, September–October, 1995. Translated by I. Izvekova     

Spatial localization and dynamics of water molecules with good tetrahedral surroundings

The local structure of the molecular- dynamic model of water (729 particles at 300 K) is analyzed by isolating molecules whose surroundings differ slightly in configuration from a regular tetrahedron. These molecules are not randomly distributed in space but form nanometer clusters having a fractal structure. In these clusters, molecules are less mobile than the model molecules in general;their self- correlation function of rate and the density of vibrational states also differ from the average characteristics of the system. Translated fromZhumal Strukturnoi Khimii, Vol. 38, No. 4, pp. 713–722, July–August, 1997.     

Complete sets of structure fragments for interpreting IR spectra using IR databases

This paper studies the possibility of revealing various fragments (not given beforehand) in a structure by analyzing the structures selected from the database as a result of a retrieval by the IR spectrum of the compound; the fragments range from those with two nodes (e.g., C=O, C=C) to those with some limited number of connected nodes. It is shown that complete fragment sets reflecting the composition of the selected compound (fragment compositions) contain the information about the set of bonded fragments of the compound. Various factors affecting analysis of the compiled list of fragments are considered using a particular example. Different techniques for revealing structural information are discussed. Scientific and Technical Center of Chemical Informatics, Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 2, pp. 368–378, March–April, 1996. Translated by L. Smolina     

Secondary structure of crystals

Published experimental data on the dependence of the properties of crystal substances on crystal size are discussed. The dependence is of the same form for different properties and different crystal substances. When the crystal diminishes in size, its properties remain constant until the size decreases to 10⁻⁵–10⁻⁶ cm; smaller crystals considerably change their properties. It is shown that the currently available experimental data are sufficient to substantiate the notion of an “elementary unit of a solid crystal” (“crystal quantum”). The elementary unit of a crystal is regarded as a basis for the secondary structure (macrostructure) of a solid and an elementary carrier of its “crystal” properties. Due to this notion, we can interpret the vast experimental material on the real structures and properties of solids from a single viewpoint. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 4, pp. 724–730, July–August, 1995. Translated by L. Smolina