Home – Home – Jornals – Journal of Structural Chemistry 2016 number 1

Within density functional theory with regard to the dispersion interaction the crystal structure parameters of hydrogen azide are determined. The pressure effect on its structural and electronic properties is studied in the range of 0-10 GPa. By means of the Vinet equation of state the bulk modulus of compression is found to be 9.26 GPa. It is shown that with an increase in the pressure molecules approach each other in molecular layers and this is accompanied by an increase in the total electron density contours, which means the principal possibility for polymerization. The external pressure of 10 GPa leads to the broadening of the upper valence energy bands and a decrease in the band gap from 6.14 eV to 5.51 eV.

Three possible models of the ordered arrangement of B, C, and N atoms in chalcopyrite sublattices are considered. Crystal lattice parameters are obtained from the first principles, band spectra are calculated, and the role of B, C, and N atoms in the formation of chemical bonds and the valence band in the B₂CN, BC₂N, and BCN₂ crystals is revealed.

Electronic characteristics of trHbN hemoglobin whose composition contains the (ONOO) group with the structure close to the structure of 1) peroxynitrite and 2) a nitrate anion in the gas phase are calculated. Electron correlation is considered by the multiconfigurational self-consistent field (MCSCF) method during the optimization of the geometry of the whole structure. Localized molecular orbitals (MOs) are used as starting ones. In the wave function of the MCSCF method two complete active subspaces (CASs) are set. These are the subspace of iron atom 3 d orbitals and the subspace describing chemical bonds in peroxynitrite (bonding and antibonding MOs plus the orbital of one lone pair on the O₂ moiety. The composition of the system involves two water molecules. The peroxynitrite structure is considered in two different spin states that correspond to the singlet and triplet states of this anion in the gas phase where the vibrational spectrum is characterized by frequencies of about (70-30) cm^-1. The protective reaction of the active center of the tubercule bacillus is discussed.

The geometric parameters of the molecular structures of 4-monoiododipyrrine, 4,4′- and 5,5′-dibromodipyrrine complexes with zinc(II) and boron(III) of the composition [ZnL₂] and [BF₂L] respectively are determined at the M06 and B3LYP levels of density functional theory with the Def2-SVP basis set. The lengths of Zn-N, B-N, and B-F coordination bonds, N-X-N, F-B-F, C-C-C bond angles, the dihedral angles between the planes of pyrrole rings in the dipyrrine ligand, dipyrrine planes in [ZnL₂], dipyrrine core and the plane passing through the atoms of the BF₂ group are optimized. The effect of structural factors on the geometric parameters and the widths of the HOMO-LUMO energy gap in halogen substituted dipyrrinates is analyzed.

The geometrical structures, relative electronic and magnetic properties of small Al _n Co^- (1 £ n £ 9) clusters are systematically investigated within the framework of density functional theory at the BPW91 level. The single Co doping can dramatically affect the ground state geometries of the clusters. At the same time, the resulting geometries show that the lowest energy Al _n Co^- clusters prefer to be three dimensional structures. Here, the relative stabilities are investigated in terms of the calculated average binding energies, fragmentation energies, and second-order energy differences. Moreover, the result of the highest occupied-lowest unoccupied molecular orbital energy gaps indicates that Al₆Co^- clusters have the highest chemical stability for Al _n Co^- (1 £ n £ 9) clusters. Furthermore, the natural population analysis reveals that the charges in Al _n Co^- clusters transfer from the Al frames to the Co atom. Additionally, the analyses of the local and total magnetic moments of the Al _n Co^- clusters show that the magnetic effect mainly comes from the Co atom.

The reaction mechanism of the N-N bond cleavage in Ta(IV) hydrazido and hydrazidium complexes is studied using density functional theory. The N-N bond cleavage in Ta(IV) hydrazidium generates formal Ta(IV) nitridyl. The N-N bond cleavage in Ta(V) hydrazido gives terminal Ta(V) nitrido species. In the tetrahydrofuran solvent, terminal Ta(V) nitrido dimerizes through a one-step direct pathway leading to the [Ta(V),Ta(V)] bis(m-nitrido) product. Two Ta-N bonds form simultaneously between the Ta center of one molecule and the terminal N atom of another. In the toluene solvent, there are two pathways of H atom abstraction and protonation producing mononuclear Ta(V) parent imide. The former consists of three steps originated from formal Ta(IV) nitridyl. The latter is unfavorable with terminal Ta(V) nitrido as the precursor.

We present density functional calculations of O₂ and CO adsorption on an AlAu₆ cluster. It is found that in the AlAu₆ cluster the active sites would be first occupied by coming O₂ rather than CO due to a more negative binding energy of the former. Furthermore, the catalytic mechanisms of CO oxidation in AlAu₆ clusters, which are based on a single CO molecule and double CO molecules, are discussed. This investigation reveals that the reaction of a single CO molecule with the AlAu₆O₂ complex has the lowest activation barrier (0.27 eV), which is 0.51 eV lower than that of the pure cluster. For the AlAu₆O₂(CO)₂ complex, due to the structural distortion of the AlAu₆ cluster, the activation barrier of the determination rate is higher by 0.53 eV than that of the AlAu₆O₂CO complex, which shows that the cooperation effect of the second CO molecule can go against CO oxidation. For the Al@Au₆O₂(CO)₂ complex, the activation barrier of the determination rate is lower by 0.07 eV than the path of one CO molecule, which demonstrates that the cooperation effect of the second CO molecule can prompt CO oxidation.

Density functional theory (DFT) levels are employed to calculate the vibrational frequencies and geometrical data of b-diketones. We evaluate the relative performance of the different levels by comparing theoretical results to experimental values. The applied DFT levels in this work are B3LYP, BLYP, B3P86, B3PW91, BPW91, G96LYP, BP86, and G96PW91 with the standard 6-31G, 6-31G*, 6-31G**, 6-31+G**, 6-31++G**, 6-311G**, 6-311++G** basis sets. The best results are obtained at the B3LYP, B3PW91, and B3P86 levels.

The molecular structure of 1,3-dimethyluracil (C₆H₈N₂O₂; 1,3-DMU) is studied theoretically and experimentally using Gaussian 98 calculations and different spectroscopic techniques. The vibrational spectrum for 1,3-DMU in the solid phase is recorded in the IR range 4000-400 cm^-1. Initially, in order to get the most stable structure, twelve structures were proposed for the titled compound as a result of the internal rotation of CH₃ around C-N bonds and keto-enol tautomerism. The single point energy and frequency calculations are obtained by MP2 (Full) and DFT/B3LYP methods with the 6-31G( d ) basis set using the Gaussian 98 computation package. After the complete relaxation of twelve isolated isomers, the ( diketo ) tautomer was the only favored structure owing to its low energy relative to the other isomers and the prediction of real frequencies. This interpretation is supported by the recorded infrared spectrum that shows the presence of only the diketo tautomer. Aided by the normal coordinate analysis and potential energy distributions, a confident vibrational assignment of the fundamental frequencies is calculated. The results are discussed herein and compared with similar molecules whenever possible.

An in situ comparative study of the reduction of Co-containing catalysts for the Fischer-Tropsch process in hydrogen and supercritical (SC) isopropanol is performed by ferromagnetic resonance (FMR) spectroscopy. According to the FMR data, the reduction of cobalt-containing oxide particles to metal in hydrogen starts at temperatures of ~360°C, which is substantially lower than a temperature of the formation of metal particles of the active phase according to powder X-ray diffraction and differential thermogravimetry data ( Т ~ 450°C). In SC isopropanol, the reduction to Co metal occurs at lower temperatures ( T ~ 245°C) as compared with the reduction temperature for these catalysts in hydrogen. It is shown that the reduction in SC isopropanol can lead to the formation of superparamagnetic Co nanoparticles with a narrow particle size distribution.

By mass spectrometry it is found that naphthalene, 1-naphthalenesulfonyl chloride, 2-naphthalenesulfonyl fluoride, 2-naphthalenesulfonyl chloride, 1,5-naphthalenedisulfonyl chloride, 1-naphthalenesulfonamide, and 2-naphthalenesulfonamide evaporate congruently on heating and their saturated vapor is presented by the corresponding monomeric molecular forms. The relationship is established between the character of the fragmentation of molecules during electron ionization and the specific features of their geometric and electronic structures.

The structure and stability of hydrate shells of singly charged sodium and chlorine ions are studied by computer simulations under the conditions of nanoscopic flat pores with the use of the previously proposed detailed force field model containing polarization interactions, transferring charge effects as well as many-body interactions of covalent type. It is found that the effect of ousting a monatomic ion from its hydration shell, which has previously been observed by independent authors in bulk vapor, is also reproduced persistently in nanoscopic pores. Whereas the ousting of the ion from its hydration shell in bulk vapor is accompanied by the loss of thermodynamic stability of the system and at sufficiently high vapor pressure causes avalanche-like condensation, under the conditions of a nanoscopic pore the thermodynamic stability is retained. The obtained data show that the ousting of the ion from its hydration shell is a universal phenomenon covering the majority, if not all, of monatomic and, possibly, some of molecular ions.

An X-ray diffraction study is performed of the structure of Al-Ge melts containing 0 at.%, 10 at.%, 20 at.%, 30.3 at.%, 40 at.%, 50 at.%, 60 at.%, 70 at.%, 80 at.%, and 100 at.% Ge near the liquidus line at 1273 K. The melts containing 40 at.%, 70 at.%, and 80 at.% Ge are studied in the temperature range up to 1823 K. The structural factor (SF) curves of the melts have a shoulder on the high-angle side of the first maximum at contents above 20 at.% Ge; the position of the shoulder coincides with that on the SF curve of liquid germanium. An increase in temperature leads to gradual smoothening of the shoulder because of the increase in the structural homogeneity of the melts, which is attributed to the metallization of the residual covalent bonds between germanium atoms. The structure of the melts is found to be microheterogeneous for germanium contents above 20 at.%, which is due to the coexistence of microclusters of liquid germanium and those of the melt with 20 at.% Ge, which provides a satisfactory description of the experimental SF curves in the concentration range 20-100 at.% Ge at temperatures near the liquidus line.

The method of molecular dynamics is used to investigate the effect of monohydric alcohols on the formation of the local structure of ionic liquids based on the dimethylimidazolium cation at T = 400 K. The intermolecular interaction energies are analyzed to find that the increase in the length of the alkyl chain in the alcohol molecule reduces the influence of the solute molecule on the formation of the local structure of the dmim⁺/Cl^--solute molecule systems. An analysis of the radial distribution function shows that the change in the structure and physical characteristics of the solute molecule does not affect the interaction between the hydroxyl group proton of the alcohol molecule and the ionic liquid anions, whose interactions form the hydrogen bond H^alcohol…Cl^- with a length of 2.3 Å.

Thermodynamic characteristics are calculated for aqueous diamine solutions prepared by substituting an amino group for the hydroxyl group of amino alcohols. Patterns are revealed in the change of the structural properties of the mixtures. The correlation between the entropy and enthalpy characteristics of the water-diamine systems and the excess packing coefficients suggests that the universal interactions determine the structural and energy properties of aqueous solutions of the studied diamines. The form of the concentration dependences of the structural and thermodynamic characteristics in the studied systems is found to be symbatic with the data for the mixtures of water with aprotic amides. The reasons for this are discussed by comparing the results with our previously published data for aqueous solutions of aprotic amides.

A method is proposed for determining the hydration number of an individual ion within the approach (V. P. Korolev, J. Struct. Chem. , 55, No. 3, 463 (2014)). In an infinitely dilute solution, the hydration numbers of ions are given by the formulas NH₄⁺(H₂O)₂, Cl^-(H₂O)₄, and NO₃^-(H₂O)₇. The structure of aqueous complexes is discussed, and a structurally relevant parameter, i.e., the density of water of hydration, is determined. Salt concentration dependences are derived for the hydration number and apparent volume of NH₄⁺, Cl^-, and NO₃^- ions. The density of the cationic (Н₂О-NH₄⁺) and anionic (Н₂О-Cl^- and Н₂О-NO₃^-) systems is calculated.

The X-ray in-situ study of [Cu(NH₃)₄](ReO₄)₂ complex salt is carried out on heating up to 500 K. The product obtained at this temperature is a new crystalline phase [Cu(NH₃)₂(m-ReO₄)₂] _n with the following unit cell parameters: a = 14.7523(3) Å, b = 5.8559(1) Å, c = 5.6290(1) Å, b = 111.387(1)°, V = 452.799(2) ų, space group C 2/ m , Z = 2, d_x = 4.386 g/cm³. The coordination polyhedron of the Cu atom is a distorted octahedron formed by two nitrogen atoms (Cu-N 2.195 Å), and four oxygen atoms (Cu-О 2.306 Å). The structure consists of infinite [Cu(NH₃)₂(m-ReO₄)₂] _n chains, the shortest N(H)…O distances between the chains being 2.82 Å.

Structural organization and thermal behavior of a new polymeric heteronuclear of gold(III)-zinc-dibutylammonium complex ([NH₂(C₄H₉)₂][Au{S₂CN(C₄H₉)₂}₂][ZnCl₄]) _n (I), obtained by a heterogeneous reaction between freshly precipitated binuclear zinc dibutyldithiocarbamate [Zn₂{S₂CN(C₄H₉)₂}₄] and a H[AuCl₄] solution in 2M HCl, is studied. According to single crystal XRD data the crystal structure of the obtained compound is determined and its main structural units are complex [NH₂(C₄H₉)₂]⁺ and [Au{S₂CN(C₄H₉)₂}₂]⁺ cations and complexе [ZnCl₄]^2- anions. Dibutylammonium cations are hydrogen bonded to tetrachlorozincate ions, forming zigzag polymer chains. On the side of the chains there are discrete complex [Au{S₂CN(C₄H₉)₂}₂]⁺ cations characterized by a planar tetragonal structure and a uniform spatial orientation. The thermal behavior of I is investigated by synchronous thermal analysis. The multistage process of thermal destruction involves the thermolysis of the cation and anion parts (with the release of metallic gold, zinc chloride and a partial formation of zinc sulfide).

Three new complexes [Cd(Hflu)₂(NO₃)](NO₃) 1, [Cd(H₂O)(Hflu)₂(Hmalo)](NO₃)×2(H₂O) 2, and [Cd(H₂O)(Hflu)₂(Hfum)](NO₃)×2(H₂O) 3 (Hflu = [2-(2,4-difluorophenyl)-1,3-bis(1,2,4-triazol-1-yl)-propan-2-ol], H₂fum = fumaric acid, H₂malo = malonate acid) are synthesized by a solution diffusion method and characterized by single crystal X-ray diffraction methods, elemental analyses, IR spectroscopy as well as thermal analyses. In compound 1, Cd(II) cations are bridged by fluconazole ligands to form 2D Cd-Hflu layers, and these layers are further connected by C-H⋯F hydrogen bonds to form a complicated 3D structure with the topology of (4×6×8)(4×6⁴×8⁴×10)(6×3). Compounds 2 and 3 are isostructural, and in them the Cd(II) cations are bridged by fluconazole ligands to form a 2D network, which is connected by C-H⋯O hydrogen bonds to form a complicated 3D (3,4)-connected framework with the topology of (4×8²)(4×8⁵).

The [Eu(HDTBA)₃] _n complex (I), HDTBA is 1,3-diethyl-2-thiobarbituric acid (C₈H₁₂N₂O₂S) is synthesized and its structure is determined by X-ray crystallography. The crystals of I are triclinic: a = 11.0205(2) Å, b = 11.8811(3) Å, c = 12.7312(2) Å, a = 100.933(1)°, b = 109.704(1)°, g = 101.161(1)°, V = 1479.88(5) ų, space group P -1, Z = 2. Each of three independent DETBA^- ions is a bridging m₂-O,O¢-coordinated ligand. The coordination polyhedron of Eu(III) is a distorted octahedron. Bridging DETBA^- organize the octahedra into an infinite two-dimensional layer. The structure contains intramolecular hydrogen bonds but intermolecular hydrogen bonds and the p-p interaction are absent. The results of IR spectroscopy and photoluminescence agree with the single crystal X-ray diffraction data. The main product of the thermal decomposition of I at 900°С is oxysulfate Eu₂O₂SO₄.

A structural interpretation of the catalytic action of carbon nanotubes on the curing of epoxy polymers is proposed. It is based on the fractal analysis ideas. It is shown that essentially the only factor determining the kinetics of the curing process is the microgel structure characterized by its fractal dimension. The most important conclusion from the obtained results is the fact that the reaction rate dependences on the structural parameters are described by the same correlation for the epoxy polymer curing reaction both in the presence and absence of carbon nanotubes. This means that the catalytic effect of carbon nanotubes consists in a change in the structure of microgels.

BaTi_{1- x} Nb _x O₃ compounds (with x = 0.00, 0.01, 0.03, 0.06, and 0.09) are synthesized by the microwave-hydrothermal (MH) method. The donor concentration effect on the structural properties is investigated. The new MH method is used instead of the previous solid state reaction for the BaTiO₃+Nb₂O₃ system. In the MH process, as the niobium incorporation rate increases, the particle growth substantially slows down. The synthesis of Nb-doped BaTiO₃ is investigated under the MH conditions subjected to 150 °C for only 2 h using C₁₆H₃₆O₄Ti (tetra-n-butyl orthotitanate), Ba(OH)₂×8H₂O, and NbCl₅ as Ba, Ti, and Nb sources respectively. For the phase evolution studies, X-ray diffraction patterns are analyzed and Raman spectroscopy is performed. The transmission electron microscope and the field emission scanning electron microscope images are taken for the detailed analysis of the grain size, surface, and morphology of the compound.

The [Co₂(tbb)Cl₄]×4DMF complex, where tbb is meso -1,2,3,4-tetra(1H-benzo[ d ]imidazol-2-yl)butane, is synthesized and characterized by single crystal X-ray diffraction. For the complex: C₄₄H₅₄Co₂C_l4N₁₂O₄, M_r = 1074.65, monoclinic crystal system, space group P 21/ n , a = 9.2350(13) Å, b = 11.3566(15) Å, c = 23.879(3) Å, b = 90.547(2)°, V = 2504.3(6) ų, Z = 2, D_c = 1.425 g/cm³, l = 0.71073 Å, m(Mo K _a) = 0.929 mm^-1, F (000) = 1112, S = 1.047, R = 0.0765, and wR = 0.2110 for 13668 observed reflections with I > 2 s( I ) . It is a neutral dinuclear complex. One meso -1,2,3,4-tetra(1H-benzo[ d ]imidazol-2-yl)butane coordinates two cobalt(II) ions. Each cobalt(II) ion is formed by two tbb nitrogen atoms and two chloride ions. The antiproliferative activities of the complex are screened by MTT assay against Eca109 cancer cells. The complex exhibits inhibition on the growth of Eca109 cancer cells with IC₅₀ of 22.1±6.7 mM after 48 h treatment. The cobalt complex has potential application in treatment of Eca109 cancer. CCDC 1015791.

We report the optical and structural properties of ZnO and MgO nanoparticles. The samples are obtained by a simple method using a new template of hexamethylene tetramine. The optical properties of the samples are studied by UV-visible spectroscopy. Their crystal structure and morphology are studied by XRD and scanning electron microscopy. The absorption spectra of MgO and ZnO show that the optical band gaps are 4.27 eV and 3.02 eV, respectively. In this investigation the photocatalytic degradation of indigo carmine (IC) in water is studied. The effects of some parameters such as pH, amount of catalyst, initial concentration of dye, are examined.

Tungsten tetraiodide WI₄ (1) is produced by a high-temperature reaction of WTe₂ and I₂ in a vacuum sealed ampoule. The crystals of 1 belong to the triclinic crystal symmetry, space group P -1, Z = 4, a = = 7.9291(3) Å, b = 10.7695(4) Å, c = 10.8117(4) Å, a = 85.668(1)°, b = 71.772(1)°, g = 71.559(1)°, V = = 831.60(5) ų, d _calc = 5.523 g/cm³. The structure of 1 consists of tetrameric W₄I₁₆ molecules in which W atoms are in a distorted octahedral environment formed by I atoms.

The crystal structure of nitrate tris(4-allylthiosemicarbazide)chromium(III) hydrate [CrL₃](NO₃)₃(H₂O)_1.05 (I) , where L is 4-allylthiosemicarbazide, is determined. The asymmetric unit of the cell of the crystal structure of I contains a complex of a chromium ion with three bidentate coordinated molecules L. The outer coordination sphere of the central atom contains a disordered water molecule and three nitrate ions. The coordination polyhedron of the chromium atom in complex I is an octahedron. In the crystal, the complexes of the compound under study are joined with each other by the outer-sphere nitrato groups into a three-dimensional branched net of hydrogen bonds.

For the first time the crystal structure and absolute configuration of 28- O -acetylbetulin are determined by the X-ray crystallographic analysis.

The crystal and molecular structures of 1-(iodmethyl)silatrane and 1-(iodpropyl)silatrane are determined by X-ray diffraction. The effect of the iodine heteroatom upon silatrane moieties of the molecules through one- and three-carbon chains is studied based on the geometric characteristics of the molecules and the analysis of their packings.