Home – Home – Jornals – Journal of Structural Chemistry 2010 number 1

Using a fully relativistic DV cluster method, we study the electronic structure of a large fragment of the crystal lattice of zircon ZrSiO₄ with a plutonium dopant atom replacing a Zr⁴⁺ zirconium atom. Three possible states of the impurity center are considered: Pu⁴⁺ (isovalent substitution), Pu³⁺ (non-isovalent substitution), and Pu³⁺ with an oxygen vacancy in the nearest environment that provides charge compensation. Relaxation of the ZrSiO₄ crystal lattice near a defect is simulated using a semi-empirical method of atomic pair potentials (GULP program). An analysis of overlap populations and effective charges on atoms shows that the chemical bonding of plutonium with a matrix is covalent, while isovalent substitution yields a more stable system than a Pu³⁺ impurity. In the presence of vacancies the structure of chemical bonding is intermediate with respect to substitutions Pu⁴⁺ → Zr⁴⁺ and Pu³⁺ → Zr⁴⁺.

Using the density functional theory method at the B3LYP/6-31G(d,p) theory level, the formation of hydrogen bonded complexes of L-cysteine with selenious and selenic acids is studied. In both cases, complexes formed through the carboxyl group of cysteine mostly arise, their enthalpy of formation being of -19 kcal/mol to -21 kcal/mol and the free energy of -6 kcal/mol to -9 kcal/mol. The primary act of interaction in the system of hydroxyl-containing selenium compound - α-aminoacid, including the mutual orientation of reactant molecules and the formation of intermolecular hydrogen bonds is likely to a serve as prerequisite for the thiol group to be able to participate in the next stages (including deeper chemical transformations) of biologically significant reactions.

Correlations of topological indices with physicochemical parameters of N-alkylcarboxylimides of cyclic dicarboxylic acids are investigated and a comparative analysis of the obtained results with the correlations binding these parameters is carried out.

Gas electron diffraction is used to study the structure of a zinc(II) N,N′-ethylene-bis(acetylacetoniminate) molecule, ZnO₂N₂C₁₂H₁₈, at a temperature T = 503(5) K. It is found that the molecule has the symmetry of the С₂ equilibrium configuration with a nonplanar structure of the ZnN₂O₂ coordination fragment and internuclear distances r_h1(Zn-O) of 1.958(13) Å and r_h1(Zn-N) of 2.012(16) Å. Quantum chemical calculations by the DFT/В3LYP/СЕР,TZV method gives the molecular structure consistent with that found in the experiment.

The structure and vibrational spectra of twelve tautomers are calculated in the B3LYP/6-311+G(d,p) approximation and analyzed. Spectral manifestations of isomeric uracil transformations into one out of the twelve tautomeric forms and cis-trans-isomeric transformations of the tautomers themselves are considered. All tautomeric transformations are shown to be characterized by the presence of at least one vibration, whose frequency is different by ~100-200 cm^-1 from a similar vibrational frequency of the precursor and also by a pronounced change in the intensity of bending vibrations of ОН hydroxyl groups and stretching vibrations of СО bonds.

Solid solutions of double orthophosphates of zirconium and rare earth lanthanum and ytterbium (La_0.33Zr₂(PO₄)₃-Yb_0.33Zr₂(PO₄)₃) that belong to the NASICON (NZP) structural type are synthesized and studied by IR spectroscopy. The factor-group analysis of P-O vibrations in phosphates with (La_0.33Zr₂(PO₄)₃) and (Yb_0.33Zr₂(PO₄)₃) space groups allows us to assign the intermediate representatives of this series to two different space groups by their IR spectra, which is difficult to perform based on powder X-ray diffraction results. A morphotropic transition → с is found to occur near the La_1/18Yb_5/18Zr₂(PO₄)₃ composition.

Synthesis procedures for mix-ligand complexes with a composition of Fe(Htrz)_3(1-x)(NH₂trz)_3xSiF₆·mH₂O, 0 ≤ x ≤ 1, m = 1, 2 are developed. Solid phases are isolated from water-ethanol solutions and studied by X-ray phase analysis, the method of static magnetic susceptibility (temperature range of 100 K to 400 K), IR and Mössbauer spectroscopy (at 200 K and 298 K). The temperatures of direct and inverse transitions are shown to depend on the complex composition.

Co-crystals formed between benzoic acid and 4,6-dimethyl-2-aminopyrimidine in 1:1 molar ratio (C₆H₉N₃·C₇H₆O₂) have been prepared and studied. According to single crystal XRD analysis, the structure is monoclinic, P2₁/c, a = 6.7019(9), b = 7.647(1), c = 25.285(3) Å, β = 91.36(2)°, V = 1295.4(3) ų, Z = 4. The asymmetric unit contains 2-amino-4,6-dimethylpyrimidine and benzoic acid molecules linked to each other by two hydrogen bonds
[O1-H1…N1, H…N = 1.819; N3-H3A…O2, H…O = 2.157 Å]. Calculations of band structure, density of states, absorption and reflectivity spectra have been performed in the frame of density functional theory using the CASTEP code, and the corresponding experimental optical properties have been investigated. The theoretical results indicate that C₆H₉N₃·C₇H₆O₂ single crystal is a wide band-gap semiconductor with the theoretical direct band gap 3.0271 eV. The title co-crystal may become promising host for fluorescence-emitting; it can absorb ultraviolet radiation.

Fluctuations of the number of nearest neighbors M_λ inside the coordination sphere of a given radius λ in a hard sphere liquid (M_λ is the total number of neighbors for all N particles of the system) are analyzed. For the probability density distribution of this random value, an exact asymptotic decomposition over the number of particles N in the system has been derived, and the decomposition coefficients were recorded in terms of the semi-invariants of the random value of M_λ. The result coincides completely with the asymptotic decomposition in the central limiting theorem of the probability theory. Due to this, the number of nearest neighbors in a liquid of N hard spheres can be represented as the sum of N independent random values with equal distributions. The hard sphere liquid of N particles was simulated by the Monte Carlo method in the canonical Gibbs ensemble over a wide range of densities (N = 864, periodic boundary conditions, occupancy η from 0.005 to 0.500). The theoretical equations are in good agreement with the results of simulation.

The aim of this work was to determine the structure of stable heteroassociates (HAs) with the stoichiometric ratios 1:2, 2:1, and 4:1 of molecules formed in the HF-(C₂H₅)₂O binary liquid system. The stretching frequencies of HF molecules found for each HA using a special procedure for processing IR spectra were compared with the calculated frequencies ν_HF of the stable molecular complexes (HF)_m·((C₂H₅)₂O)_n (m = 1, 2, 4, 8; n = 1, 2) with different topologies by the density functional method (B3LYP/6-31++G(d,p)). As a result, it was shown that the most stable (among H-bonded complexes with the same stoichiometric ratio of molecules) HAs HF·((C₂H₅)₂O)₂, (HF)₄·((C₂H₅)₂O)₂, and (HF)₈·((C₂H₅)₂O)₂ formed in HF solutions in diethyl ether. All of them had a cyclic structure and a common peculiarity of structure: only one lone electron pair of the oxygen atom of the (C₂H₅)₂O molecules is involved in hydrogen bonding.

The thermal expansion α, isothermal compressibility β_T, and internal pressure coefficients of Н₂О-(NH₂)₂CO and D₂O-(ND₂)₂CO π systems at 278 K, 298 K, and 318 K and aquamolality m ≤ 1.5 were calculated. The changes in the isotope differences Δα, Δβ_T, and Δπ at different solute concentrations and temperature are discussed. In contrast to Δα and Δπ, Δβ_T is almost independent of the urea concentration already at 298 K and independent of m at 318 K. The derivative ∂π/∂Т increased in dilute solution, at lower temperatures, and on passing from protium to deuterium system, which corresponded to increased structuring. The isotope difference for the Grüneisen constant at given temperatures and concentrations is shown to be independent of the urea content.

By chemical vapor deposition Ir and Ir-Al₂O₃ coatings are obtained with a thickness of up to 40 μm on steel substrates precoated with a layer of Al₂O₃. Tris-acetylacetonates of iridium(III) and aluminium(III) are used as precursors. The deposition processes are carried out at atmospheric pressure in the presence of oxygen. The obtained coatings are studied by X-ray diffraction, X-ray photoelectron spectroscopy, and scanning electron microscopy. The dependences of coating structures and compositions on the preparation conditions are found. An increase in the deposition temperature results in the formation of Ir coatings with loose discontinuous structure, an increase in the size of metal crystallites, and the growth of the oxygen concentration in their composition. An increase in the concentration of precursor vapors in the deposition zone at a constant deposition temperature results in the formation of Ir coatings that consist of differently structured layers (compact, columnar, and granular). Mixed Ir-Al₂O₃ coatings which composed of metal Ir and amorphous Al₂O₃ crystallites, which exhibit a pronounced iridium texture in the [111] direction, have the most perfect compact structure. The introduction of the oxide phase in the coating composition halves the Ir crystallite size.

Copper(II) chloride complexes with bis(3,5-dimethyl-4-iodopyrazol-1-yl)methane (L) with a composition of CuLCl₂ (1), [Cu₂(μ₂-Cl)₂L₂(H₂O)₂]Cl₂·2(CH₃)₂CO (2), and [Cu₃(μ₂-Cl)₆L₂]·(CH₃)₂CO (3) are synthesized. Single crystal X-ray diffraction is used to determine the molecular and crystal structures of these compounds. In the structures of compounds 2 and 3, shortened non-valent I…Cl contacts with a length of 3.222(1)-3.439(2) Å are found. They involve uncoordinated and coordinated chloride ions and iodine atoms of organic ligands.

The structure of the interaction products of (NH₄)₂[Ru(NO)Cl₅] solution with ammonium acetate on heating is studied. The crystal structure of the [Ru(NO)(NH₃)₃(H₂O)Cl][Ru(NO)(NH₃)₃(OH)Cl]×
[Ru(NO)(NH₃)Cl₄]₂Cl·2H₂O compound (compound I) containing a previously unknown anion of the nitrosomonoammine series is determined: Cc space group; a = 33.530(7) Å, b = 8.202(2) Å, c = 11.844(2) Å; β = 101.54(3)°.

Structures of four tetraphenylporphyrinatotin(IV) bis(carboxylato) complexes [Sn(tpp)(OCOR)₂] have been determined by single crystal X-ray diffraction. All complexes have typical octahedral geometry. The average Sn-N bond lengths for R = CH₃, CHCl₂, CF₃ and H are 2.091, 2.084, 2.082 and 2.086 Å, respectively. The Sn-O bond lengths are 2.096, 2.091, 2.109 and 2.090 Å respectively. These bond lengths and those of all other reported Sn(tpp) complexes of O-bound anionic ligands are compared. There is an inverse correlation between the Sn-N and Sn-O bond lengths, indicating that stronger electron donation by the axial anionic ligand results in an expansion of the porphyrin core. Correlation of the Sn-O bond lengths with the pK_a of the conjugate acids of the axial ligands shows that the stronger the acid, the longer the Sn-O bonds, indicating that the bonding is dominated by electrostatic effects.

Using physicochemical methods, the crystal and molecular structure of 1,1′-bis-(acetoacetyl)ferrocene is studied. The compound crystallizes in the form of two crystallographically independent molecules with slightly different conformations and mutually perpendicular orientation. Crystals are monoclinic, C₁₈H₁₈FeO₄, a = 35.68(1) Å, b = 5.733(2) Å, c = 30.30(1) Å; β = 96.831(5)°; V = 6154(3) ų, Z = 16, d_x = 1.529 g/cm³, С2/с space group. The molecule consists of the ferrocene fragment and two acetylacetonyl substituents.

Previously unknown bis{[2-(4-tert-butyl)phen]ethyl}phosphine sulfide is obtained with a high yield from 4-tert-butyl styrene, red phosphorus, and elemental sulfur. Using single crystal XRD, multinuclear NMR, IR, and UV spectroscopy, it is found that the phosphorus atom is four-coordinated in the bis{[2-(4-tert-butyl)phen]ethyl}phosphine sulfide molecule (regardless of the phase state of the compound: crystal, solution). By the example of phosphorylation of bis{[2-(4-tert-butyl)phen]ethyl}phosphine sulfide acetylene in the KОН-DMSO system it is shown that the reaction proceeds by double addition with the participation of phosphorus-centered nucleophiles.

A method to calculate electronic and vibrational energy levels in nanoobjects with a periodic internal structure is proposed. The approach allows us to reduce the general problem to a set of order problems corresponding to the repeating atomic arrangement. Further refinement is performed using perturbation theory.

Rietveld structure refinement and simulation of the diffraction patterns of partially disordered materials are used to study the real structure of nanoscale pseudoboehmite samples obtained by different technologies. The effect of various violations in the structure of these nanomaterials on diffraction patterns is analyzed. The introduction of corrections for the Lorentz and polarization factors in the determination of the cell parameter b by the position of the 020 diffraction peak in the pattern is shown to be important. A model for the atomic structure of pseudoboehmite is proposed. The model involves additional water molecules as compared to the structure of boehmite. The water molecules in the interlayer space of the layered boehmite structure are found to violate its regularity, which results in a decrease in the size of crystallites.

Calculated by DFT (PBE/3z) based on the experimental crystal atom coordinates, the molecular pair (MP) interaction energies are used to analyze the crystal packing for compounds 1-6. Supplementing the visual geometric approach used in the PLATON and MERCURY programs, the MP interaction energies make it possible to describe the crystal architecture more completely and structurally, to identify supramolecular motifs more reliably, and to determine their hierarchy.

Molecular pair (MP) interaction energies, DFT calculated (PBE/3z) based on the experimental crystal atomic coordinates, are used to analyze the crystal packing of enaminoimine and related enaminoketones complexes with dioxane and pyridine. The sign of the interaction energy of enaminoimine molecules in the chain (complex 4) and in the supermolecule (complex 5) indicates that they are held in the observed position by the intermolecular interaction with solvent. The enaminoketone molecules in complexes 6 and 7 are, on the contrary, linked by N-H…O hydrogen bonds into dimers, which interacting with solvent molecules form chains (complex 6) and supermolecules (complex 7). In addition to the visual geometrical approach of PLATON and MERCURY programs, the MP interaction energies allow a more complete and structural description of the crystal architecture, a more reliable determination of supramolecular motifs and their hierarchy.

The work describes the procedure for performing a quantitative powder X-ray diffraction analysis in the Debye-Scherrer scheme on a single crystal diffractometer equipped with a flat two-dimensional detector. Specially prepared mixtures of polycrystalline phases (α-Al₂O₃, Si, α-SiO₂, and W) with substantially different linear absorption coefficients are analyzed. It is shown that even when crystallites are most prone to preferred orientation, it is possible to perform measurements with an accuracy no worse than traditional 5 wt.%.

A quantum chemical study of the hydrogen bond in the complex is carried out using topological methods: quantum theory of atoms in molecules (QTAIM) and of electron localization f unction (ELF) theory. In the complex, three lone electron pairs on the oxygen atom in Ph₃PO are found to be combined in one ELF basin, and they all participate in the hydrogen bond formation. The observed topological features of the complex are compared to the topological features of related complexes and the literature data.

Within the first principle FLAPW-GGA band method we predict the structural, electronic, and magnetic properties of CaCNi₃, SrCNi₃, and BaCNi₃ hypothetical antiperovskites. The results are discussed in comparison to the MgCNi₃ isostructural superconductor.

Using X-ray phase analysis, the Rb₂MoO₄-Nd₂(MoO₄)₃-Zr(MoO₄)₂ ternary salt system is studied. The crystals of rubidium-neodymium-zirconium triple molybdate are grown by solution-melt crystallization under spontaneous nucleation. According to the X-ray diffraction data (automatic X8 APEX diffractometer, МоK_α radiation, 1345 F(hkl), R = 0.0356), the crystal structure and its composition is determined: Rb_4.7Nd_0.7Zr_1.3(MoO₄)₆. The sizes of the trigonal unit cell are as follows: a = b = 10.7561(2) Å, c = 38.7790(12) Å, V = 3885.41(16) ų, Z = 6, space group. The three-dimensional mixed framework structure consists of Мо tetrahedra and two types of octahedra: (Nd,Zr)O₆. The distribution of Nd³⁺ and Zr⁴⁺ cations over two crystallographic sites is also refined. Two types of rubidium atoms are located in large cavities of the framework.

A new compound [pefloxacindium tetrachlorocuprate(II)], C₁₇H₂₀FN₃O₃ - 1-ethyl-6-fluoro-1,4-dihydro-4-oxo-7-(4-methyl-1-piperazinyl)-3-quinoline carboxylic acid (pefloxacin, PefH) is synthesized and characterized by single crystal X-ray diffraction technique. The crystal structure of the compound contains one cation and one anion. The supramolecular architecture of the crystal is determined.

An X-ray phase and X-ray structural analysis of M(Aet)₂·8H₂O compounds, where M(II) = Sr and Ba; (Aet)^- = (C₁₀H₁₁N₄O₂S₂) is the sulfaethiodole (2-(para-aminobenzene-sulfamido)-5-ethyl-1,3,4-thiadiazole) anion is carried out. Symmetry and unit cell parameters of Sr(Aet)₂·8H₂O and Ba(Aet)₂·8H₂O are found: P2₁/c, Z = 4, а = 10.390(2) Å, b = 14.609(3) Å, c = 21.931(5) Å, β = 92.42(2)°, R = 0.041; and P2₁/c, Z = 4, а = 9.793(2) Å, b = 15.408(4) Å, c = 22.553(6) Å, β = 94.98(2)° respectively. The considered compounds are isostructural. The structure of Sr(Aet)₂·8H₂O is fully studied; the crystals of the compound are composed of the complex centrosymmetric dimeric [(H₂O)₅Sr(Aet)₂Sr(OH₂)₅]²⁺ cations, (Aet)^- anions, and water molecules; the independent part of the structural formula of the compound is [Sr(Aet)(OH₂)₅](Aet)·3H₂O. The sulfaethiodole anion is coordinated to the complexing metal atom by oxygen and nitrogen atoms with the formation of a four-membered ring.

A double complex salt [Co(N₂C₂H₈)₃][AuBr₄]₂Br is obtained and characterized using single crystal X-ray diffraction analysis. The crystallographic data of C₆H₂₄Au₂Br₉CoN₆ are as follows: a = 21.6479(17) Å, b = 14.9085(12) Å, c = 8.2676(7) Å, β = 110.820(2)°, V = 1538.92(12) ų, C2/c space group, Z = 4, d_x = 3.602 g/cm³. Square planar coordination of the gold atom in the complex anion is completed to a tetragonal pyramid by an additional bromine atom of the adjacent complex anion at the Au…Br distance of 3.677 Å.

The compound fac-[Co(NH₂CH₂CH₂O)₃]·3H₂O (I) was synthesized and its crystal structure determined. Crystal data for C₆H₂₄CoN₃O₆: a = 14.5236(3) Å, c = 4.9346(2) Å, V = 901.43(5) ų, T = 90 K, space group R3, Z = 3, ρ_calc = 1.620 g/cm³. In the complex, the octahedral environment of the Со(III) atom is formed by three monoethanolamine ligands using N and O atoms. The structure is disordered in such a way that the two oppositely orientated CoN₃O₃ octahedra are superimposed on each other at an angle.

Using the X-ray structural analysis the atomic structure of luminescent terbium methacrylate is determined (orthorhombic crystal system, a = 14.791(1) Å, b = 12.9306(8) Å, c = 7.6869(5) Å, Cmc2₁ space group, Z = 4, ρ_x = 1.867 g/cm³). The crystal structure is represented by continuous chains of C₁₂H₁₅TbO₆ molecules along the crystallographic c axis, which are linked by the van der Waals interaction.