Home – Home – Jornals – Journal of Structural Chemistry 2009 number 4

Using MM2 molcular mechanics simulation and MNDO/PM3 semiempirical methods we show that the most probable mechanism of surface modification of alkyl-doped silicon dioxide layers in plasma is the interaction with СН₃ groups. Detachment of the hydrogen atom causes a change in the character of Si-O-Si bonding, which results in an increase in the number of Si-O-Si groups with an angle in a range of 144° to 146°. Subsequent treatment in ammonia plasma leads to pore sealing through the formation of -CH-Si-O-Si-O-Si-O-Si- chains. The mechanism proposed provides a good explanation to FTIR experimental spectra and to changes in the reactivity of porous layers after treatment in helium plasma.

The vaporization enthalpy of polyatomic alcohols with different structures under normal conditions is calculated using a modified Randič method. The vaporization enthalpy of polyatomic alcohols is shown to largely depend on the number of hydrogen bonds formed by alcohols.

Using a hybrid B3LYP density functional method with the 6-31G(d) basis set and the Gaussian-98 program, the geometrical parameters of macrocyclic complexes of Co(II), Ni(II) and Cu(II) with NNSS-coordination of donor centers of the chelate ligand, formed due to template processes in M(II)-hydrozinomethane thiohydrazide-acetone systems, are calculated. Coordinates of atoms, selected bond lengths and angles, and dihedral angles in complexes with MN₂S₂ metal-chelate site are given. It is noted that for all considered M(II) ions the additional six-membered metal cycle, formed because of template stitching, is turned at a considerable angle to two five-membered cycles, and this cycle itself is not planar either.

Heteropoly acid (HPA) H₈(PW₁₁TiO₃₉)₂O·xH₂O (I) is synthesized by three different ways and studied by chemical analysis, potentiometric titration, mass-spectrometry, IR, ³¹P, ¹⁸³W, and ¹⁷O NMR spectroscopy, thermogravimetry, and transmission electron microscopy. Anion I consists of two subparticles of the Keggin structure bridged by Ti-O-Ti. The dimeric anion exists in HPA aqueous solutions at [I] > 0.02 M. At рН > 0.6 it splits to a [PW₁₁TiO₄₀]^5- monomer stable up to рН ~ 6. When heated (150-400)°C, I splits into H₃PW₁₂O₄₀ and, apparently, H₃PW₁₀Ti₂O₃₈ without phase separation. Thermolysis products are soluble and when dissolved in water turn again into I. Complete decomposition of I to oxides occurs at ~450°C.

The molecular dynamics method is used to simulate the structure of liquid chlorobenzene, ortho-chlorotoluene, and their mixtures with concentrations of 0.03 ppm, 0.05 ppm, 0.1 ppm, 0.5 ppm, and 0.95 ppm chlorobenzene. Radial angular distribution functions (RADFs) were found for the distances between benzene ring planes and the angle between them in pure components and solutions. The data obtained from RADFs indicate that in the nearest environment of molecules the parallel orientation of benzene rings is the dominant configuration, while the fraction of perpendicular contacts is relatively small. In a concentration range of 0.03 ppm, 0.05 ppm, and 0.95 ppm chlorobenzene, conglomerates form with structural characteristics close to those of the dissolved substance. At a concentration of 0.1 ppm chlorobenzene, solute molecules start to agglomerate. In a concentration range from 0.15 ppm to 0.9 ppm chlorobenzene, both agglomerates and conglomerates of the same size are present in the mixture. The radial distribution functions of chlorine-chlorine distances calculated in pure components and mixtures indicate the presence of chlorine aggregates. The results obtained are compared with molecular light scattering data.

Structural thermodynamic parameters of aqueous solutions of hexamethylphosphorotriamide are calculated. They are discussed together with previously obtained data on aqueous solutions of disubstituted amides of carboxylic acids. The specific and non-specific components of the total energy of intermolecular interactions are determined. The boundaries of concentration regions with different structural organizations of solutions are found, and the preferential solvation parameters of solution components are estimated.

XRD is used to study the structures of inclusion compounds of diterpenoid 15-ene-steviol with chloroform and 16-S-dihydrosteviol with chloroform and ethyl acetate. In all three cases, the guest-host ratio is 1:2; by means of a branched system of hydrogen bonds, diterpenoid molecules form a three-dimensional associate with helical voids, in which solvent molecules are located. Crystals of all three complexes are isostructural, the ethyl acetate molecule being localized in the corresponding inclusion compound, while solvent molecules are disordered in complexes with chloroform.

Every crystallographic group has finite sets of conical sections (for planar groups) and second order surfaces (for spatial groups). A geometrical method has been suggested on this basis for modeling and studying the cooperative mobility of atoms in symmetric systems. The method was demonstrated for a 21-atomic cluster (point group T-23). It suggests the construction of a variety of regular point systems, interpreted as sequential stages of the cooperative motion of the atoms of the 21-atomic cluster with preserved inner coordinates (bond lengths and angles) in a narrow range of values.

UV spectra of 2-substituted-1-(p-vinylphenyl)cyclopropanes are studied. Based on spectral data, different substituents (-Х) are characterized with respect to their effect on the system of conjugated bonds in the molecule . The cyclopropane ring is found to be a part of the conjugated system of the whole molecule.

The nature of epitaxial intergrowth of black (β) and red (α) modifications of zinc diphosphide is studied. The intergrowth of single crystals is shown to be caused by that the atoms-analogs form almost identical structural motifs in both structures. The black modification grows on the (001) plane of the red one so that its b axis is parallel to the (110) plane of α-ZnP₂.

We have synthesized (±)-diphenyl-4′-chlorophenyl-[(2-hydroxy-1,1-dimethylethyl)amino]methylphospho-nate and studied it by X-ray diffraction.

A principle to design the multi-parameter potentials of hydrogen bonding is proposed and developed. Based on fluctuation theory, they provide the description of temperature evolution of the shape of OH vibrational spectra of liquid water molecules. Approximate solutions expressing the ν_OH frequency and hydrogen bond energy E through the hydrogen bond length and bending (R_O…O, ϕ_H-O…О) and the pair of angles (ϕ_Н-О…О,
χ_-О…О) adjacent to it are found numerically. By their means, spectra are calculated fairly close to experiment in a temperature range up to 200°C. The expressions proposed can be used to quantitatively analyze the networks of hydrogen bonds in computer models of water obtained by Monte-Carlo or molecular dynamics methods.

By means of IR absorption spectra, low temperature ¹Н and ¹⁵N NMR spectra, and quantum chemical calculations we study the structure of complexes with hydrogen bond of molecular and ionic character formed by nitrogen-containing compounds able to be both proton donors and acceptors simultaneously and the interaction specificity in them. Spectroscopic, steric, and thermodynamic characteristics of diphenyltriazene, 3,5-dimethylpyrazole, and diphenylformamidine homoassociates and heterocomplexes of these compounds with carboxylic acids and various proton donating molecules are obtained. Quantum chemical calculations of the structure of complexes and vibrational frequencies in IR spectra are made in the harmonic approximation and with regard to anharmonicity corrections. Calculations taking into account anharmonicity of vibrations are shown to produce the results closest to the experimental data.

The effects of photoirradiation on the conformation state of 4-(4′-dimethylaminostyryl)pyridine N-oxide was studied by spectral (EAS, ¹Н NMR, IR) and thermochemical methods. Trans→cis isomerization was found to proceed in 4-(4′-dimethylaminostyryl)pyridine N-oxide irradiated with light (λ ≤ 400 nm) in chloroform. The conversion of the trans form of 4-(4′-dimethylaminostyryl)pyridine N-oxide to the cis form depends on the time and intensity of irradiation. Maximum conversion was achieved when a photostationary mixture formed with a ratio of components trans:cis = 40:60. Further irradiation of the solutions of 4-(4′-dimethylaminostyryl)pyridine N-oxide in chloroform led to salification with HCl formed during the decomposition of CHCl₃.

Based on the data of the Cambridge Structural Databank, we analyzed the conformations of 139 4-X-C₆H₄-C₆H₄-4′-Y molecules (X, Y = H, F, Cl, Br, I, CH₃, OH, COOH, NH₂, NO₂, CN) and intermolecular contacts formed by these molecules in 95 homo- and heteromolecular crystals. As would be expected, the percent of planar and almost planar molecules (the angle between the planes of the phenyl fragments (ϕ) is 0-5°) in the group was higher (37%) than in biphenyl containing any substituents in the 3,3′,4,4′,5,5′-positions (26%). The percent of almost planar molecules increased considerably when X = OH (48% among molecules having at least one OH group), while equal substituents (X = Y) did not lead to a substantial increase in the relative content of conformers with ϕ in this range. In the given group of crystal structures, the specific intermolecular contacts (hydrogen bonds, Hal…Hal and Hal…N≡C contacts, etc.) often led to the formation of infinite molecular chains or their fragments (trimers and dimers). The structures containing molecules with an NH₂ group typically formed layered (2D) and framework (3D) H associates.

For H bonds stabilized by π-conjugation in carbonylated 1,4-dihydropyridines, an analysis of the structural data of the Cambridge Structural Databank showed that the hydrogen bond was an essential condition for π-conjugation. It was found that π-delocalization possibly correlated with the bioactivity of drugs that were calcium antagonists. In the presence of two carbonyl groups, hydrogen bonds in crystal are predominantly formed by the carbonyl group that is anti-periplanar to the 1,4-dihydropyridine ring.

Systematization of the available literature data on С-F…π, F…Н, and F…F interactions, namely, statistical studies of the geometry of the corresponding contacts were carried out using the Cambridge Structural Database (CSD) and theoretical quantum-chemical estimations of their energies. The most typical supramolecular motifs (finite or infinite) involving the F atom were revealed based on recent X-ray studies of a few dozens of fluoroarenes carried out at the Novosibirsk Institute of Organic Chemistry. Our recent data were summarized. To assess the role of the above interactions, we used topological analysis of electron density distribution in terms of Bader's QTAIM theory. Our DFT/PBE/3z quantum-chemical calculations of the interaction energies of molecular pairs in diazafluorene crystals formed by С-F…π, C-F…Н, and F…F nonvalent short contacts are presented.

The properties of intercalated compounds of graphite fluoride with highly volatile polar guest components were studied by DTA, XRPA, and IR spectroscopy. The role of guest−host and host−host intermolecular interactions in the formation of layered inclusion compounds based on polymer matrices with different degrees of fluorination is shown.

The structural features of packings of similar hard spheres in the vicinity of Bernal density corresponding to space occupancy ~0.64 have been studied. This is maximum density for disordered packings, which give way to crystallization at higher densities. The structure was analyzed using Delaunay simplices. Aggregates of simplices approximating a regular tetrahedron (polytetrahedra) in form have been studied. They have a high local density and various morphologies, but are incompatible with translation symmetry. Percolation analysis of these clusters was carried out. The "critical" nature of structural transformations at Bernal density is related with the appearance of percolation through tetrahedra. The closest disordered packings really have no significant nucleating seeds of crystal structures, as shown by a sensitive seed detection procedure. Their appearance and fast growth are observed after passing through Bernal density. The total fraction of the crystal phase increases monotonically with the density; the fcc and hcp structures appear in different proportions in the packings.

Crystalline solvates of synthetic tetraphenylporphyrin and its pyridinie metallocomplexes (Zn²⁺, Сu²⁺, Ni²⁺, Co²⁺, Mn³⁺, Fe³⁺) have been studied by thermogravimetric analysis. A comparative analysis of our thermochemical data and the literature XRD data was carried out for the pyridine complexes of metallotetraphenylporphyrins. It was found that the energy stability and structural characteristics of the pyridine complexes of metallotetraphenylporphyrins depended on the nature of the central metal ion. The pyridine complexes are stabilized by the direct metal−porphyrin π-dative macrocycle interaction and the increased residual positive charge on the central metal ion. The activation energies of thermal destruction of the pyridine complexes of metallotetraphenylporphyrins vary from 230 kJ·mol^-1 to 330 kJ·mol^-1, which is suggestive of the high kinetic stability of the complexes. For the molecular complexes under study, the limiting stage of destruction was found to be the chemical reaction itself, and the kinetic characteristics demonstrated the compensation effect, indicative of the similar mechanism of thermooxidative destruction of the pyridine complexes of metallotetraphenylporphyrins.

An analysis of the absorption and luminescence spectra and luminescence kinetics showed that in the Eu(DK)₃bpy_17-17 mesogenic adduct, 5,5′-diheptadecyl-2,2′-bipyridine (bpy_17-17) took an active part in the energy transfer to the Eu³⁺ ion. The interligand energy transfer from β-diketonate (DK) ligands was the major mechanism of excitation of bpy_17-17. Importantly, the interligand excitation complex considerably decreased radiation losses during the energy transfer from the absorbing DK ligands to the emitting level of Eu³⁺.

The most widespread procedure for the synthesis of oxyhydrate materials by the sol-gel method is fast alkaline hydrolysis of the soluble salts of heavy metals. Oversaturation of the mother solution during fast hydrolysis provides high dispersity and hence large surface area and availability of the sorption centers of the aggregates being formed. The number and accessibility of sorption centers is also determined by the structure of gel particles. At low hydrolysis rates, there are good possibilities for the structural rearrangements of gel elements, which leads to the formation of ordered supramolecular structures with developed surfaces. The structural characteristics of zirconium gels obtained by fast (5 s), slow (5 days), and ultraslow (5 mos.) alkaline hydrolysis of zirconium oxychloride were determined by derivatography combined with mass and IR spectroscopy (of thermolysis products), X-ray diffraction, IR spectroscopy (xerogels), NMR, electron microscopy, and other methods.

This paper presents the results of our study of molecular librations in liquid ortho-dichlorobenzene (C₆H₄Cl₂) and benzonitrile (C₆H₅CN) at room temperature. We used femtosecond polarization with recording of the optical Kerr effect (OKE). To analyze the libration response, we divided the total OKE signal into the constituent vibrational and rotational responses. Modeling the libration response, we determined the form of the distribution function of libration frequencies and performed qualitative analysis of the peculiarities of the local potentials of molecules.