Home – Home – Jornals – Journal of Structural Chemistry 2009 number 3

Structurization of water in the cavity of cucurbit[6]uryl was studied using the highly effective PRIRODA quantum-chemical program package, the PBE functional, and the TZ atomic basis. The structural and energy characteristics of the formation of small water clusters in the cavitand void were calculated. The maximum possible number of molecules in the void was found to be six.

It was shown that the resonance mixing of states on large molecules can increase the probability of reaction. This effect is similar to a decrease in the activation threshold or the action of an external catalyst.

Gas diffusion in porous layers of varying structure was simulated numerically. Mesoporous mesophase material (MMM) and silica gel layers were studied. The former were a set of ordered cylinders; the latter were disordered packings of spheres. The average residence time of a molecule in a layer (return time) and dispersion of this time in relation to the layer depth were calculated. For the same porosity and specific surface of layers, the average return time is independent of the pore structure and increases with the layer depth as a linear function. This is the consequence of the general theoretical result, according to which the duration of molecule wandering in a pore depends only on the ratio of the pore volume to the section area of its windows. Dispersion of the wandering time is sensitive to the pore structure; it is slightly smaller for regular pores than for a complex pore system. The functional dependence of return time dispersion on the layer depth is the same for different layers (the cubic root of dispersion changes with the layer depth as a linear function). This work helps us to understand recent experimental data, which showed that using MMM for gas chromatographic columns increased the efficiency of the latter compared with other columns based on silicon oxide.

Localization and molecular mobility of the ligands ([C₈H₄O₄]²⁺ and [C₆H₁₂N₂]⁰) of the host lattice and (CH₃)₂NCHO dimethyl formamide guest molecules in the inclusion compound [Zn₂(C₈H₄O₄)₂(C₆H₁₂N₂)]·
n(H₃C)₂NCHO were studied on the basis of ¹H NMR data. At room temperature, the longest axes of the dimethyl formamide guest molecules are ordered in parallel to the С₄ symmetry axes, and the symmetry planes of these molecules are disordered, while preserving the tetragonal crystal system of the inclusion compound. At lower temperatures, a phase transition takes place in view of the ordering in the guest sublattice.

This paper reports on our study of the formation of an interface of layered structures in the Fe-Si system by reflected electron energy loss spectroscopy (REELS). Quantitative element analysis was performed using the product of the mean length of the inelastic free path by the inelastic scattering cross-section of electrons. It is shown that the Fe-Si interface is quite uniform.

The X-ray photoelectron spectra (XPS) of the core electrons of the carbon, oxygen, nitrogen, and fluorine atoms of antibiotics from the class of quinolones (nalidixic acid, norfloxacin, and enoxacin), having different antibacterial activities, were measured and interpreted. The integrated intensities of the π-π* and n-π* transition bands in the absorption spectra of the compounds were analyzed. The maxima of the luminescence spectral bands are given along with the lifetimes of the excited states and quantum yields of the protolytic forms of the compounds in aqueous media. The XPS data were compared with the Mulliken charges on heteroatoms obtained by quantum-chemical calculations.

The charged state of the 3d metal ions in layered cation-substituted disulfides CuCr_1-xV_xS₂ was studied by X-ray photoelectron spectroscopy. An analysis of the energy positions and structure of the Cu2p_3/2 and Cr2p_3/2 X-ray photoelectron lines showed that the corresponding polycrystalline samples of CuCr_1-xV_xS₂ contained mixed-valence chromium and copper ions. It was shown that the charged states of chromium and copper ions depended on the concentration of vanadium cations (x). The presence of mixed-valence Cu¹⁺ and Cu²⁺ ions in CuCr_1-xV_xS₂ may be correlated with the crystal structure of the corresponding layered disulfides.

It was proven that after averaging over the canonical Gibbs ensemble, the mean perturbation energy was singled out of the classical partition function before the expansion in a series of perturbation theory. Therefore, the term that formally coincides with first order perturbation theory in a decomposition of the Helmholtz free energy bears no relationship to perturbation theory. Then the proper series of the thermodynamic perturbation theory always starts with a second order infinitesimal. Therefore, the well-known condition of applicability of the thermodynamic perturbation theory, "…the requirement that the perturbation energy per particle be small compared with Т…" (L. D. Landau and E. M. Livshits, Statistical Physics, Vol. V, Pt. I), can be substantially weakened. The most important factor for applicability of thermodynamic perturbation theory is the value of many-particle correlations in an unperturbed system, but not the smallness of the perturbation potential.

The results of measurements of the temperature dependence of the relaxation rate (1/Т₁) of protons in seawater with 35‰ salinity and salt solutions with different concentrations at temperatures from -22°C to +120°C are presented. The possibility of approximating the temperature dependence of the magnetic relaxation rate by different functions in pure water, seawater, and solutions of the salts of the latter was studied. The parameters of this dependence and their variation under the influence of salt components are given. The least mean square deviation was obtained, and the best convergence was determined according to the statistical criteria for aqueous electrolytes of moderate concentrations for the function in the form of the sum of exponentials, in which the number of terms depended on the solution concentration. It is shown that the parameters of the thermal dependence of the relaxation rate represented by different functions can be used in combination for studying the dynamic properties of the solutions of low and moderate concentrations.

Reconstructive phase transitions and their conditions in perovskite, ilmenite, pyrochlore, and other structures were considered on the basis of the experimental structural data on oxide compounds. It is shown that such transitions depend on the pressure, temperature, chemical composition, and defective structure.

The behavior of the manganese−alumina system with Mn:Al = 1:1 on heating in air and vacuum was studied. The starting samples were mixtures of β-Mn₃O₄, α-Mn₂O₃, and γ-Al₂O₃. On heating to 950°C in air, the samples were partially oxidized into α-Mn₂O₃, and corundum α-Al₂O₃ formed along with mixed manganese−alumina cubic spinel, whose composition was close to Mn₂AlO₄. In vacuum at 1200°C, the starting sample with a ratio of Mn:Al = 1:1 transformed into the manganese−alumina spinel Mn_1.5Al_1.5O₄, which retained its cubic structure after slow cooling in vacuum. When cooled in air, this solid solution delaminated, and a nanocrystalline Mn_2.8Al_0.2O₄ phase formed, whose structure was β-Mn₃O₄ type tetragonal spinel.

The crystal structures of compounds from the series [M(NH₃)₅Cl](NO₃)₂, (M = Ir, Rh, Ru) were described. The compounds crystallized in the tetragonal crystal system, space group I4, Z = 2. Crystal data for [Ir(NH₃)₅Cl](NO₃)₂ (I): a = 7.6061(1) Å, b = 7.6061(1) Å, c = 10.4039(2) Å, V = 601.894(16) ų, ρ_calc =
2.410 g/cm³, R = 0.0087; [Rh(NH₃)₅Cl](NO₃)₂ (II): a = 7.5858(5) Å, b = 7.5858(5) Å, c = 10.41357(7) Å, V =
599.24(7) ų, ρ_calc = 1.926 g/cm³, R = 0.0255; [Ru(NH₃)₅Cl](NO₃)₂ (III): a = 7.5811(6) Å, b = 7.5811(6) Å, c = 10.5352(14) Å, V = 605.49(11) ų, ρ_calc = 1.896 g/cm³, R = 0.0266. The compounds were defined by IR spectroscopy and XRPA and thermal analyses.

The atomic structure of europium acrylate crystals [Eu₂(Acr)₅OH·3H₂O]·2(0.5H₂O) was studied by X-ray analysis (a = 24.360(3) Å, b = 18.466(2) Å, c = 8.5818(9) Å, β = 96.087(2)°, space group C2/c, Z = 6, ρ_calc = 2.036 g/cm³). The crystal structure involves chains of binuclear [Eu₂(C₃H₃O₂)₅OH·3H₂O] molecules, running infinitely in the [101] direction and having pairs of C₉H₉EuO₇H₂O molecules alternating with C₆H₆EuO₄OH·2H₂O molecules that link the pairs. The infinite chains are linked by hydrogen bonds and van der Waals interactions. The thermal behavior of luminescence of the europium(III) complex is discussed.

The new salts of pyridine-4-aldehyde thiosemicarbazone: perchlorate (I) and trifluoromethane sulfonate (II) HN⁺C₅H₄-CH=N-NH-C(S)-NH₂·X^- (X = ClO₄, CF₃SO₃) were synthesized and studied by IR and NMR spectroscopy and X-ray diffraction analysis. The compounds were synthesized by a reaction of pyridine-4-aldehyde thiosemicarbazone with chloric or trifluoromethane sulfonic acid, respectively. Compound I crystallized in the triclinic crystal system, space group P-1, a = 6.8691(2) Å, b = 9.5406(4) Å, c =
9.6348(4) Å, α = 78.838(1)°, β = 77.618(1)°, γ = 69.661(1)°, Z = 2. Compound II crystallized in the monoclinic crystal system, space group P2₁/c, a = 7.3149(8) Å, b = 11.9830(16) Å, c = 15.143(2) Å, β = 96.949(4)°, Z = 4. The structures are formed by hydrogen-bonded ions. Moreover, the cations are linked in "dimmers" due to the weak N-H…S hydrogen bonds.

The crystal structures of ethyl-4-(5-bromo-2-hydroxyphenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine- 5-carboxylate and ethyl-1-methyl-15-oxo-2-oxa-14,16-diazatetracyclo[11.3.1.0^3.12.0^6.11]heptadeca-3,5,7, 9,11-pentaene-17-carboxylate were determined by XRD, and the conformations of their structures were determined.

The molecular and crystal structure of quinoline-2-aldehyde thiosemicarbazone is determined. The thiosemicarbazide fragment has cis-arrangement of terminal nitrogen atoms relative to the central N-C bond. The structure is based on a centrosymmetric dimer formed by hydrogen bonds between NH groups and sulfur atoms of thiosemicarbazide fragments of the neighboring molecules. In the crystal, the dimers are joined with each other through a system of hydrogen bonds and intermolecular π-π interactions.

X-ray photoelectron spectroscopy and diffraction (XPS and XPD) are applied to analyze oxygen-induced surface structures on the Nb(110) face formed due to oxygen segregation from the crystal bulk on thermal annealing to 2000 K in vacuum and/or oxygen adsorption in situ at temperatures above 1100 K. The Nb3d, O1s electronic states and valence band spectra of the NbO_x/Nb(110) surface are studied by XPS, and the results are compared with data for NbO, NbO₂, and Nb₂O₅ oxides. It is shown that niobium atoms entering the composition of surface oxide structures on Nb(110), from the standpoint of the nearest environment and chemical bond, are similar to metal states in NbO. The NbO_x layer thickness is estimated to be 0.5 nm. Two chemically inequivalent oxygen states are distinguished on Nb(110), which are, presumably, atomic chemisorbed oxygen on the parts of the clean surface of the Nb monolayer with hexagonal packing and oxygen in the composition of NbO_x-like linear clusters on Nb(110). A model of the NbO_x/Nb(110) surface takes into account a distortion of the structure of NbO_x clusters: a periodic vertical shift of metal atoms in Nb-chains and changes in Nb-O bond angles.

The discovery in 2008 of superconducting transition (T_c ~ 38 K) for BaFe₂As₂ arsenide doped with potassium has stimulated works on synthesis, studies of structural and electromagnetic properties, and simulation of this and similar materials. A brief review of the current state of studies on novel superconducting arsenides in the mentioned aspects is presented.

Based on FLAPW-GGA calculations, a comparative study of the features of interatomic interactions in LaFeAsO, SrFe₂As₂, and LiFeAs layered crystals (basic phases of new 18-56 K superconductors) is carried out.

The vaporization enthalpy of monohydric alcohols with different structures under normal conditions is calculated using a modified Randič method with an error comparable to the experimental one. The energy of hydrogen bonds in alcohols is determined and shown to be constant and independent on the alcohol structure.

Instability in the formation of KNbO₃ with perovskite structure is complicated by its structural instability. The structural instability accounts for the existence of phases different in their symmetry and cell parameters (rhombic, tetragonal, and cubic) at room temperature.

Crystals of binary praseodymium and hafnium molybdate of Pr₂Hf₃(MoO₄)₉ composition are grown by solution-melt crystallization under spontaneous nucleation conditions. By the X-ray diffraction data (X8 Apex automated diffractometer, МоK_α radiation, 2262 F(hkl), R = 0.0170) its composition and crystal structure are determined. Parameters of the trigonal unit cell are: a = b = 9.8001(1) Å, c = 58.7095(8) Å, V = 4883.15(10) ų, Z = 6, space group R3c. The crystal structure is composed of three types of polyhedra: МоО₄ tetrahedra, HfO₆ octahedra, and nine-vertex PrO₉. All three types of polyhedra are bonded among themselves by common oxygen vertices of bridging МоО₄ tetrahedra forming an openwork three-dimensional structure.

XRD is used to determine the structure of Cp′Ir(cod) at a temperature of 150(2) K. Crystallographic data for C₁₄H₁₉Ir are: a = 10.8272(5) Å, b = 9.7746(4) Å, c = 10.9180(5) Å, β = 97.3310(10)°, monoclinic symmetry, space group P2₁/n, V = 1146.02(9) ų, Z = 4, d_calc= 2.199 g/cm³, R = 0.0246. The structure is molecular, built of neutral molecules. The metal atom coordinates carbon atoms of two cyclic ligands:
5-methylcyclopentadienyl-ion (Cp′) and 1,5-cyclooctadiene (cod). Five Ir-C_Cp′ distances lie in the range of 2.21-2.28 Å; four Ir-C_cod distances differ insignificantly, and their average value is 2.114(13) Å. The С₁₁С₁₂С₁₃С₁₄С₁₅ and C₁C₂C₅C₆ planes of ligand fragments are almost parallel, and the angle between normals is 1.9°. In the crystal, molecules are bonded only by van der Waals interactions; in the structure, the eight shortest Ir…Ir distances are in the range of 5.608-7.257 Å.

The structure of Ir(CO)₂(acac) is determined by XRD at room temperature. Crystallographic data for C₇H₇IrO₄ are: a = 6.4798(5) Å, b = 7.7288(5) Å, c = 9.1629(10) Å, α = 105.738(2)°, β = 90.467(3)°, γ = 100.658(2)°, space group P1 V= 433.24(6) ų, Z = 2, d_calc = 2.662 g/cm³, R = 0.0167. The structure is built of isolated mononuclear molecules. The central iridium atom has a square coordination environment formed by two oxygen atoms that belong to the acetylacetonate ligand and two carbon atoms of carbonyl groups. The average Ir-O and Ir-C bond lengths are 2.045(3) Å and 1.832(6) Å respectively. Molecules are stacked in such a way that the planes of coordination squares turn out to be parallel to the Ir…Ir distances between the nearest neighbors in the stack of 3.242 Å and 3.260 Å.

The structure of the product formed on boiling [RuNO(NH₃)₃(NO₂)(ОH)]Cl·0.5H₂O in 3 M HNO₃ is determined by XRD. The crystals belong to monoclinic symmetry. Crystallographic data for H₁₁ClN₆O₈Ru are: a = 13.7924(4) Å, b = 6.9114(2) Å, c = 12.3577(4) Å, β = 111.863(1)°, V = 1093.27(6) ų, Z = 4, d_calc = 2.185 g/cm³, space group Cc. The structure is built of complex [RuNO(NH₃)₃(H₂O)Cl]²⁺ cations and anions NO^-₃. The compound is studied by IR spectroscopy and X-ray phase analysis.

In the crystals of [Ca(H₂O)₅][Cr(Ida)₂]₂·4H₂O (triclinic symmetry, a = 10.1056(10) Å, b = 13.0077(11) Å, c = 13.1185(13) Å, α = 70.186(11)°, β = 81.248(11)°, γ = 78.996(11)°, Z = 2, space group P1) cyclic centrosymmetric tetramers are present. In them calcium ions are bonded to oxygen atoms of the carboxyl groups of two octahedral complex cis(N)-[Cr(Ida)₂]^- ions (Ida is the iminodiacetic acid anion). The О atoms of five water molecules complete the Са atom environment to a distorted pentagonal bipyramid. Isolated [Cr(Ida)₂]^- ions of a similar structure neutralize the positive charge of tetramers.

The carbonylation reaction of 2,3-dichlorobiphenyl proceeds with a substitution of the chlorine atom in position 3 and results in the formation of 2-chloro-3-phenylbenzoic acid. The structure of this acid is revealed by single crystal XRD. It is determined by steric interactions of substituents in positions 2,4,2′, and 6′, a stable carboxyl supramolecular synthon, and weak interactions with the participation of the carbonyl oxygen atom and the chlorine atom.

Single crystal XRD is used to study the crystal structure of 1-(4-bromobutyl)-3,6-dimethyluracil and 1,3-dimethyl-5-(5-bromopentyl)-isocyanurate in comparison with structurally similar compounds studied previously. It is shown that unlike macrocyclic compound, for which the crystal structure is determined by the presence of the stacking effect, in the crystals of their artificial precursors stacking interactions are not observed. For 1-(4-bromobutyl)-3,6-dimethyluracil, C-H…O interactions and С=O…Br interactions for 1,3-dimethyl-5-(5-bromopentyl)-isocyanurate are found.