Home – Home – Jornals – Journal of Structural Chemistry 2015 number 6

Crystal structure parameters, band spectra, distribution maps of the toal and partial electron densities of KN₃ and KSCN are calculated from the first principles using the density functional method and the general properties and distinctions in the band spectra are analyzed. The groups of balance subbands are qualitatively similar; in the upper valence band of KN₃ there is weak hybridization of p states of the complex anion and metal, which is not observed in KSCN. KSCN crystals are direct band gap materials and KN₃ are indirect band gap materials. The existence of weak covalent bonding of complex anions with metal is found from the electron density distribution maps in both crystals and also between metal atoms in KSCN, which is absent in KN₃.

Total, difference, and deformation electron densities are calculated from the first principles using the density functional theory and the sublattice method for LiBX (B = Mg, Ca, Zn; X = N, P, As) crystals with the sphalerite structure. The nature and formation features of the chemical bonding caused by a change in the chemical composition are revealed. A weak bond between Li⁺ ions with X anions enables their displacements in the space between crystal-forming tetrahedral (BX)^- groups. It is found that Ca-X bonds are mainly ionic and in a series of crystals the ionic covalent Li-B bond is traced.

DFT and HF methods implemented in the PC GAMESS-Firefly program package are employed to calculate the spatial and electronic structures of molecules of three-coordinate aluminum compounds with Al-N bonds. NBO and AIM methods are applied to determine the main characteristics of Al-N and N-С bonds in these molecules. It is shown that Al and N atoms interact with each other as closed shell atoms. The N-С bonds are close to covalent ones.

Using first-principles pseudo-potential plane wave method, the formation enthalpy D H , binding energy D E , elastic constants, and electronic structure were calculated and analyzed carefully for NiTiX (X = Cu, Fe) shape memory alloy. The results show that the Cu or Fe element prefers to occupy the Ni site in the NiTi matrix phase respectively. Compared with the NiTi matrix phase, the D H , D E , c ₄₄ and c ¢ of NiTi (Cu) are similar to each other. However, the structural stability of the NiTi phase is improved obviously by the Fe alloying process. Simultaneously, the shear modulus c ₄₄ and c ¢ of NiTi (Fe) are larger than those of the NiTi matrix phase. Furthermore, Milliken population results indicate that Q _Cu-Ti is smaller than Q _Ni-Ti after the Cu alloying process, but Q _Fe-Ti is larger than Q _Ni-Ti. The electron density difference shows that some covalent bonding exists between Fe and Ti elements. Based on the upward analysis, the difference in the phase stability and elastic constants of NiTiX (X = Cu, Fe) is the substantial mechanism for the different M _s of NiTiX (X = Cu, Fe) although Cu or Fe substitutes for the same atom Ni elements in the NiTi matrix phase.

A quantum chemical simulation of the structure of a hydrated phenylalanine zwitterion, dimers and larger phenylalanine associates in an aqueous solution is performed by the hybrid B3LYP density functional method with the 6-31G++( d , p ) basis set. It is shown that the association of the amino acid occurs by the formation of hydrogen bonds between phenylalanine amino carboxyl groups involving water molecules.

³¹P, ¹⁹F, ¹H NMR is used to study fluorophosphatometalates of the composition MHfF₂PO₄×0.5H₂O (M = Rb, Cs) and CsMe₂F₆PO₄×4H₂O (Me = Zr, Hf). The data obtained indicate the isostructurality of compounds in each of these two groups. The lines in the NMR spectra are assigned. Assumptions about the character of the bond of PO₄ groups and F atoms with Me are made and schemes of the crystal structure of fluorophosphatometalates are proposed. The occurrence of several types of crystallization water characterized by different bond strengths and energy barriers of the diffusion motion is found.

By electron paramagnetic resonance spectroscopy the paramagnetic centers are investigated in SiC _x N _y H _z films obtained by plasma-enhanced chemical deposition from hexamethyldisilazane vapor. It is found that the films contain dangling bonds broken at carbon atoms, their concentration considerably increasing with an increase in the deposition temperature. By Raman spectroscopy a deposition temperature range is determined within which the films contain carbon clusters. Similarity in the properties of the films synthesized at high deposition temperatures and the films initially deposited at low temperatures and then annealed is established. The results of the study are interpreted with the use of the known data on the film composition and structure and also the representations described in the literature.

The efficiency of the application of the transmission X-ray diffraction technique implemented with the use of the VEPP-3 synchrotron radiation source to obtain functions of the radial electron density distribution (REDD) is shown. By the example of a poorly crystallized sample of cerium oxalate the possibilities of the obtained REDD functions in the structural diagnostics of X-ray amorphous materials are demonstrated: the oxalate phase is detected, the features of the local structure are revealed, and the size of the atomic ordering region is determined.

The carbon K -edge NEXAFS spectra of initial and fluorinated and hydrogenated single-wall carbon nanotubes (SWCNTs) are analyzed theoretically with regard to the polarization dependence. Differences in the polarized theoretical spectra of SWCNTs with zigzag and chair chiralities are shown. As a result of the comparison of experimental and theoretical carbon K -edge NEXAFS spectra of hydrogenated and fluorinated SWCNTs it is found that it is most probable that hydrogen atoms attach to the outer surface of the tube wall and fluorine atoms to the outer and inner surfaces of the SWCNT wall. Based on the analysis of polarized theoretical spectra of fluorinated and hydrogenated SWCNTs differences in the symmetry of the final states of С-H and С-F bonds are shown.

An express analysis technique for the determination of the structural properties of water clusters with impurities and the number of contained water molecules more than 12 is developed. The technique is based on the derivation of three matrices for a water cluster, which makes it possible to write down the unique code characterizing its structure. The technique significantly decreases the computation time (approximately 10⁴ times) in comparison with the procedure developed previously [1], and consequently, allows the analysis of the structural properties of aqueous systems with a large number of molecules on usual PCs. In order to illustrate the technique the code for the typical configuration of the (H₂O)₁₃ cluster is determined within the water model at a temperature of 268 K and a density of 0.99930 g/cm³.

A study is made of the temperature and concentration dependences for conductance of aqueous sodium decyl sulfate solutions. The nature of hydration of the decyl sulfate anion is discussed within the theories proposed by Samoilov, Gurikov, and Krestov. An analysis is performed of the influence of the hydration type on the critical micelle concentration. The analysis suggests that an increase in temperature stimulates micelle formation given that hydration is negative.

The optimal structures and the vibrational frequencies of H-bonded complexes formed from one-two CBr₃COOH molecules or the CBr₃CO anion with water molecules are calculated by density functional theory (B3LYP/6-31++G( d , p )). The comparison of the obtained results with the known Raman spectra of the CBr₃COOH-H₂O and NaCBr₃CO ×H₂O solutions (with component molar ratios of £1:16) shows that they include stable hydrates: CBr₃COOH×H₂O and CBr₃CO ×(H₂O)₆. The first one has a cyclic form, and the second has a cubic globular form. The vibrational band frequencies of the CBr₃COOH molecule and the CBr₃CO anion in the spectra of both solutions are almost completely determined by the mutual arrangement of units in these hydrates.

The work studies a partial tungsten substitution for cobalt in the structure of nonstoichiometric SrCo_0.8Fe_0.2O_3-d (SCF) perovskite with mixed oxygen electron conductivity. It is shown that samples of the composition SrCo_{0.8- x} Fe_0.2W _x O_3-d (SCFW) at x ³ 0.03 undergo the endotaxial phase separation with the formation of nanosized domains with a structure of ordered Sr₂CoWO₆ double perovskite, which are distributed in the matrix of nonstoichiometric SrCo_{0.8- x} Fe_0.2W _x O_3-d perovskite. For the materials with 0.02 < x < 0.1, a decrease in the oxygen stoichiometry is accompanied by nanostructuring of the matrix: the formation of nanosized domains in which oxygen vacancies are ordered with the formation of the brownmillerite-like structure.

Copper(I) π complexes with 2-allylamino-5-phenyl-1,3,4-thiadiazole (C₁₁H₁₁N₃S) of the composition [CuCl(C₁₁H₁₁N₃S)] (1) and [Cu(C₁₁H₁₁N₃S)(H₂O)(CH₃CN)]₂SiF₆×2CH₃CN (2) are obtained by alternating current electrochemical synthesis and studied by single crystal X-ray diffraction. In both structures, the L molecule coordinates to the Cu(I) atom by the C=C bond of the allyl group and the N3 atom of the 1,3,4-thiadiazole core. In 1, the coordination environment of the metal atom is completed to trigonal by one terminal halogen atom, and in 2, it is completed to the tetrahedral environment by the acetonitrile N atom and the O atom of a water molecule. The bridging function of the organic ligand in 1 leads to the formation of coordination chains {CuCl(C₁₁H₁₁N₃S)}_¥, whereas cationic p complex 2 is formed from monomeric {Cu(C₁₁H₁₁N₃S)(H₂O)(CH₃CN)}⁺ cations and anions. A branched system of O-H⋯F, O-H⋯N, and N-H⋯F hydrogen bonds in compound 2 forms hydrogen-bonded layers.

Two dinuclear complexes [Zn(m-L)(NO₃)(H₂O)]₂ (1) and [Cu₂(m-L)₂(HL)₂](NO₃)₂(C₁₂H₈Br₂)_0.5××H₂O (2), (HL = 3-(2-pyridyl)pyrazole, C₁₂H₈Br₂ = 4,4¢-dibromobiphenyl) are synthesized under hydrothermal conditions and characterized by elemental analysis and X-ray single crystal diffraction. Crystal data for 1: triclinic, P , a = 8.8478(7) Å, b = 15.0550(11) Å, c = 16.4310(12) Å, a = 107.588(4)°, b = 112.498(3)°, g = 115.595(3)°, V = 2099.8(9) ų, Z = 2; for 2: triclinic, P , a = 7.2870(15) Å, b = 8.6840(17) Å, c = 9.3290(19) Å, a = 107.588(4)°, b = 112.498(3)°, g = 115.595(3)°, V = 528.77(18) ų, Z = 1. Complex 1 and 2 are both dinuclear structures which are further packed into a 1D supramolecular chain and a 3D supramolecular framework via weak C-H⋯O hydrogen bond interactions respectively.

The syntheses and crystal structures of the layered coordination polymers M(C₈H₈NO₂)₂ [M = Mn (1), Co (2), Ni (3) and Zn (4)] are described. These isostructural compounds contain centrosymmetric trans -MN₂O₄ octahedra as parts of infinite sheets; the ligand bonds to three adjacent metal ions in m³-N,O,O¢ mode from both its carboxylate O atoms and its amine N atom. In each case, weak intra-sheet N-H⋯O and C-H⋯O hydrogen bonds may help to consolidate the structure. Crystal data: 1, C₁₆H₁₆MnN₂O₄, M _r = 355.25, monoclinic, P 2₁/ c (No. 14), a = 10.6534(2) Å, b = 4.3990(1) Å, c = 15.5733(5) Å, b = 95.1827(10)°, V = 726.85(3) ų, Z = 2, R ( F ) = 0.026, wR ( F ²) = 0.067. 2, C₁₆H₁₆CoN₂O₄, M _r = 359.24, monoclinic, P 2₁/ c (No. 14), a = 10.6131(10) Å, b = 4.3374(4) Å, c = 15.3556(17) Å, b = 95.473(4)°, V = 703.65(12) ų, Z = 2, R ( F ) = 0.041, wR ( F ²) = 0.091. 3, C₁₆H₁₆N₂NiO₄, M _r = 359.02, monoclinic, P 2₁/ c (No. 14), a = 10.6374(4) Å, b = 4.2964(2) Å, c = 15.2827(8) Å, b = 95.9744(14)°, V = 694.66(6) ų, Z = 2, R ( F ) = 0.028, wR ( F ²) = 0.070. 4, C₁₆H₁₆N₂O₄Zn, M _r = 365.68, monoclinic, P 2₁/ c (No. 14), a = 10.6385(5) Å, b = 4.2967(3) Å, c = 15.2844(8) Å, b = 95.941(3)°, V = 694.89(7) ų, Z = 2, R ( F ) = 0.038, wR ( F ²) = 0.107.

A novel coordination polymer [Co₅(OH)₂(dnbpdc)₄(H₂O)₆]×16H₂O (1) (dnbpdc = 6,6¢-dinitro-4,4¢-biphenyl-dicarboxylic acid) is obtained from a hydrothermal reaction. The structure of complex 1 is characterized by elemental analysis, IR spectroscopy, and single crystal X-ray diffraction analysis. The title compound (C₅₆H₇₀Co₅N₈O₅₆, M _r = 2045.85) crystallizes in the triclinic space group P -1 with a = 11.9349(2) Å, b = 12.1895(2) Å, c = 15.420(2) Å, a = 109.390(7)°, b = 94.786(1)°, g = 108.027(9)°, V = 1968.4(4) ų, Z = 1, D _c = 1.726 g/cm³, F (000) = 1045, m(Mo K _a) = 1.154 mm^-1, T = 133(2) K, the final R = 0.0316 and wR = 0.0692 for 7032 observed reflections with I > 2s( I ). The coordination polymer is built of a pentanuclear Co(II) cluster, four dnbpdc ligands, two hydroxyl groups, six coordination water and sixteen crystal water molecules. Ligand oxygen atoms exhibit three types of coordination modes (monodentate, syn-syn bridging bidentate and bridging tridentate). Moreover, the infinite three-dimensional supra-molecular network is generated by coordination and hydrogen bonds. The thermal stability of complex 1 is evaluated by differential scanning calorimetry and thermogravimetric analysis.

Two new Cs₅[{Ln(H₂O)₄(C₂H₆O)}{Re₆Se₈(CN)₆}₂]×2H₂O (Ln = La, Nd) compounds are obtained by the interaction of aqueous Cs₃KRe₆S₈(CN)₆ and LnCl₃ solutions in the presence of ethanol. These compounds are isostructural, and crystallize in the tetragonal crystal system (space group P 4/ ncc ) with the following unit cell parameters: a = 17.9102 Å, c = 19.6694 Å for La, and a = 17.8846 Å, c = 19.6425 Å for Nd. The structure of the compounds consists of corrugated [{Ln(H₂O)₄(C₂H₆O)}{Re₆Se₈(CN)₆}₂]^5-layers. Cesium cations compensating the negative charge are located in both cavities of the corrugated layer and between the layers.

The crystal structure of α-(N-benzoxazoline-2-one) acetic acid is studied in the following forms: hydrate, solvate with formic acid, organic monoethanolammonium salt (NН₂(CH₂)₂OH) in two polymorphs produced by minor changes in the crystallization temperature, and also its ethylenediammonium salt (NН₂(CH₂)₂NH₂) in the 2:1 ratio, where amino groups participate in the deprotonation of two molecules of α-(N-benzoxazoline-2-one) acetic acid. Weak intermolecular hydrogen and dative bonds in the crystals consisting of different molecules are analyzed.

The molecular structures of 5,7-di(tert-butyl)-2-(6,8-dimethyl-4-piperidinoquinoline-2-yl)-3-hydroxytropone and 5,7-di(tert-butyl)-2-(5,8-dimethyl-4-piperidinoquinoline-2-yl)-3-hydroxytropone are determined by the single crystal X-ray diffraction analysis.

The method of single crystal X-ray diffraction (XRD) is used to study the crystal structures of the following trinitromethyl derivatives of 1,3,5-triazine: 2,4-diazido-6-trinitromethyl-1,3,5-triazine (1), 2,4-dimethoxy-6-trinitromethyl-1,3,5-triazine (2), 2,4-bis(N,N-dimethylamino)-6-trinitromethyl-1,3,5-triazine (3). Some features of the structure (geometry) of the trinitromethyl group and its location relative to the 1,3,5-triazine ring is determined.

Two mononuclear manganese(III) complexes, [MnL¹(OH₂)(CH₃OH)]×ClO₄ (1) and [MnL²] (2), where L¹ and L² are the deprotonated forms of N,N¢-bis(5-chloro-2-hydroxybenzylidene)ethane-1,2-diamine and tris{2-[(3,5-dichlorosalicylidene)amino]ethyl}amine, respectively, are obtained by the reaction of Schiff bases with manganese perchlorate in methanol. The complexes were characterized by elemental analysis, IR spectra, and single crystal X-ray determination. In both complexes, Mn atoms are in the octahedral coordination. In the crystal structure of complex 1, the complex molecules are linked by water ligands through intermolecular O-H⋯O hydrogen bonds to form dimers. The perchlorate anions are linked to the complex molecules through intermolecular O-H⋯O hydrogen bonds. In the crystal structure of complex 2, the molecules are stacked along the y axis through p⋯p interactions. The catalytic oxidation on olefins of the complexes is studied.

The method of grazing incidence X-ray diffraction (GIXRD) is used to study the hexagonal boron nitride (h-BN) films produced by plasma-enhanced chemical vapor deposition (PECVD) from borazine and ammonia or helium mixtures. The diffraction patterns of boron nitride layers aligned vertically on the substrate are obtained for the first time. The films deposited consist of the amorphous phase and the nanocrystalline h-BN phase. The nanocrystallite sizes in the films obtained from the mixtures of borazine (B₃N₃H₆) with both ammonia and helium increase with an increase in the synthesis temperature. Nanocrystallites are heteraxial and have a layered structure with the interplanar spacing of ~0.35 nm.

Films of various composition are synthesized by chemical vapor deposition under low pressure using the thermal decomposition of the following initial gas mixtures: ferrocene Fe(C₅H₅)₂ and helium; ferrocene, tris(diethylamino)silane [(C₂H₅)₂N]₃SiH (TDEAS) and helium; ferrocene, 1,1,1,3,3,3-hexamethyldisilazane [(CH₃)₃Si]₂NH (HMDS), and helium. The chemical composition of the films obtained is analyzed by FTIR and Raman spectroscopies. The phase composition of the films is studied by grazing incidence X-ray diffraction (GIXRD). It is determined that the films grown from the gas mixtures of organiosilicon compounds (TDEAS or HMDS), ferrocene, and helium have the same chemical and phase composition (SiC_xN_yFe_z), while the films obtained from the mixture of ferrocene and helium have another composition (SiC_xFe_y).

It is shown that a model system of random walk of particles with superimposed vortex motion simulates the specific behaviors of a two-particle correlation function DP ( t ) = <[r _i ( t ) - r _i (0)]×[r _k ( t ) - r _k (0)]>, which are observed in molecular dynamics models of water and liquid argon. Hence, in liquids there well may be mesoscopic-sized vortices (of the order of ten intermolecular distances).

Crystallographic analysis of the known structure of TlHg₆S₄Br₅ reveals that the Tl⁺ cation occupies the S^2- site, centering the cubic Br subcells in the unit cell. The analysis shows that Tl is located in one sublattice with Br and S anions, and the Hg cationic sublattice, which has a relatively small size and large amount of vacant sites, is coordinated with the anionic one due to the selective site occupation in the former. An algorithm is considered for calculating the compositions with a given proportion of large monovalent cations substituting for S.

Vanadium complexes have been proved to possess an interesting insulin-like activity. The reaction of VO(acac)₂ with N ¢-(3,5-dichloro-2-hydroxybenzylidene)-2-methylbenzohydrazide (H₂L) in methanol affords a new mononuclear vanadium (V) complex [VOL(OMe)(MeOH)]. The structure of the complex is characterized by physicochemical methods and single crystal X-ray diffraction. The complex crystallizes as the monoclinic space group P 2₁/ n , with unit cell parameters a = 7.830(2) Å, b = 23.225(3) Å, c = 10.635(2) Å, b = 101.947(2)°, V == 1892.1(6) ų, Z = 4, R ₁ = 0.0404, wR ₂ = 0.0953, S = 1.037. The X-ray analysis indicates that the V atom in the complex is in the octahedral coordination. The insulin-like activity of the complex is studied.

The title complex is synthesized and analyzed using single crystal X-ray diffraction studies. The asymmetric unit [RuCl₃(CO)(PPh₃)₂] of the title complex contains one half of the molecule. The molecular structure is stabilized by C3-H3…Cl1 and C9-H9…Cl2 intramolecular halogen interactions which result in two S(6) ring motifs. The crystal packing features are the C-H…Cg1 interactions, where Cg1 is the center of gravity of the phenyl ring (C14-C19). No classical hydrogen bond is found in the complex.

The interaction of the quaternary thioselenobromide complex Os₂S₇Se₅Br₈ prepared by the reaction of OsO₄ with a solution of sulfur in Sе₂Br₂ at 100°C with melted 4-CNPy at 165°C leads to the formation of the Os₂S₂Br₄(4-CNPy)₄ complex whose structure is determined by single crystal X-ray diffraction.

A new compound C₆F₅N(H)C(O)CH₃ pentafluoroacetanilide, which is promising for the formation of coordination compounds with metal cations, is synthesized. Its crystal structure is determined (APEX DUO diffractometer, lMo K _a, graphite monochromator, T = 150 K). Crystallographic data for C₈H₄F₅NO are as follows: space group C 2/ c , a = 18.2460(7) Å, b = 10.5840(4) Å, c = 9.4489(4) Å, b = 116.198(1)°, V = 1637.28(11) ų, Z = 8. The compound has a molecular structure formed of isolated pentafluoroacetanilide molecules. The average distances in the phenyl ring are 1.39 Å for C-C and 1.34 Å for C-F. The molecular structure of the studied compound is confirmed by ¹⁹F and ¹H NMR in the solution CCl₄/CDCl₃ = 1:1 (v:v).

The crystal structure and structural features of the 7-phenyl-9,11-dihydrochromeno(4,3-b)pyrazolo(4,3-e)pyridine-6(7 H )-one molecule obtained according to the Biginelli reaction in the interaction of 4-hydroxy-2 H -chromen-2-one, benzaldehyde, and 1 H -pyrazole-5-amine are determined by single crystal X-ray diffraction.

The reaction of diethyl-5-methyl-3-oxo-1,2,3,6-tetrahydro-[1,1¢-diphenyl]-2,6-dicarboxylate with (1-(4-bromophenyl)ethylidene)hydrazine is conducted, and the crystal structure of the product of this reaction (diethyl-5-(2-(1-(4-bromophenyl)ethylidene)hydrazinyl)-3-methyl-1,2-dihydro-[1,1¢-diphenyl]-2,6-dicarboxylate) is determined by single crystal X-ray diffraction. The conformation of the cyclohexadiene ring in the form of a strongly distorted half-chair is determined based on the X-ray diffraction data. The presence of the intramolecular hydrogen bond of the N-Н…О=C type is noted.

The Ir(CO)₂(hfac) complex (hfac = CF₃C(O)CHC(O)CF₃) has been studied by X-ray crystallographic analysis. The crystallographic data are as follows: space group Cmc 2₁, a = 8.680(4) Å, b = 18.951(1) Å, c = 6.491(3) Å, V = 1067.7(8) ų, Z = 4, R = 0.0327. The structure is molecular; the coordination polyhedron of iridium adopts a distorted square geometry. The average Ir-O and Ir-C distances are 2.06(1) Å and 1.82(4) Å respectively. The OIrO and CIrC angles are nearly equal (88.7(5)° and 89(1)° respectively). The thermal properties of the complex have been studied by thermogravimetry.

To the best of our knowledge, it is the first time that the method of chemical vapor deposition (MOCVD) with platinum(II) bis(acetylacetonate) (Pt(acac)₂) is used to obtain platinum coatings on the cathodes and anodes of the electrodes for pacemakers. The deposition processes are carried out under reduced pressure in the presence of oxygen. The phase and elemental composition, structure, and morphology of the coatings are examined by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and energy dispersive spectroscopy (EDS). Platinum coatings with a columnar structure are prepared in the temperature range 280-340°C. An increase in the deposition temperature leads to a change in the structure of the coatings and reduction in their thickness. Cyclic voltammetry (CV) is used to estimate the specific capacities of the platinum coatings on the cathodes and anodes, the maximum values of which are 426 mC/cm² and 1160 mC/cm², respectively.

A tetrahedral cluster complex of rhenium with the composition (PhenH)₄[Re₄Te₄(CN)₁₂]×4H₂O (1) is obtained and structurally characterized. The structure of the salt is determined by single crystal X-ray diffraction. The compound crystallizes in the orthorhombic space group Fdd 2, a = 23.1780(7) Å, b = 50.009(2) Å, c = 11.4274(3) Å, V = 13245.6(7) ų.

It is found that electron delocalization indices can be efficiently used as a sorting tool for the classification of bonds between iodine atoms in a wide range of various covalent and noncovalent I…I/I-I interactions. The characteristics of bonds in a symmetrical triiodide anion can serve as benchmarks allowing to distinguish the I…I halogen bond from the I-I covalent bond.