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Vol 60, No 12 (2019)

Article

Structural and Electronic Properties and Chemical Bonding in Layered 1111-Oxyarsenides LaRhAsO and LaIrAsO: AB Initio Simulation

Bannikov V.V., Shein I.R.

Abstract

Structural and electronic properties, Fermi surface topology, and chemical bonding features in layered 1111-oxyarsenides LaRhAsO and LaIrAsO are studied and compared using ab initio simulations. The nonmagnetic metal LaIrAsO is found to be weakly sensitive to both electronic and hole doping. However, the Rh-containing phase is predicted to exhibit weak band magnetism and can turn into a nonmagnetic state by hole doping. Therefore, the LaRhAsO oxyarsenide can be considered as a possible “electronic” analogue of the LaFeAsO compound, the basic phase of layered FeAs superconductors.

Journal of Structural Chemistry. 2019;60(12):1859-1867
pages 1859-1867 views

Crystal and Electronic Structures of Alluaudite-Type Double Molybdates of Scandium and Indium

Suetin D.V., Baklanova Y.V., Medvedeva N.I., Savina A.A., Khaykina E.G., Pletneva E.D., Denisova T.A.

Abstract

Double molybdates of indium and scandium with alluaudite structure are prepared by the solid-phase synthesis method. The crystal structure of the indium containing compound is refined and optical characteristics of Na5R(Mo04)4(R = Sc, In) are determined. Electronic structures of Na5R(Mo04)4(R = Sc, In) molybdates are studied within the ab initio method taking account of Na/Sc(In) positional disordering. Calculations of the imaginary part of dielectric function predict the optical gap of ~3.8 eV, in accordance with absorption spectroscopy data. It is established that formation energy of sodium vacancies strongly depends on sodium position and Sc(In) concentration. As a result, various diffusion mechanisms may be activated in alluaudite-type compounds with high and low contents of metal R.

Journal of Structural Chemistry. 2019;60(12):1868-1876
pages 1868-1876 views

Structural Features of the Inclusion Compound Based on the trans-[Co(en)2Cl2]+ Complex and Cucurbit[8]Uril: A DFT Study

Grishaeva T.N., Masliy A.N., Kuznetsov A.M.

Abstract

Structural features of the inclusion compound based on the cobalt(III) trans-[Co(en)2Cl2]+ complex and the cucurbit[8]uril macrocycle are studied within the density functional theory. It is shown that water molecules fix the complex inside the macrocycle cavities to form various structures. The main structural characteristics of trans-[Co(en)2Cl2]+·nH2O@CB[8] supramolecules obtained from quantum chemical calculations are compared with available XRD data. Thermodynamic parameters concerning the formation of this inclusion compound are estimated.

Journal of Structural Chemistry. 2019;60(12):1877-1884
pages 1877-1884 views

Coordination Numbers and Critical Topology of Centrosymmetric Hydrocarbons

Banaru A.M., Gridin D.M.

Abstract

Various types of coordination numbers in molecular crystals are discussed. The relationship between parameter R of the Delone system, coordination number (CN), topological type, and the intermolecular interaction energy is studied on the example of crystal structures of centrosymmetric hydrocarbons. The first coordination sphere of a molecule takes 86.2±1.6% of the lattice energy; the interactions providing molecular arrangement take at least 50% of the lattice energy for CN ≥ 6. The nets characterizing the framework of intermolecular interactions in this series of structures tend to the lowest cyclomatic number of the quotient graph.

Journal of Structural Chemistry. 2019;60(12):1885-1895
pages 1885-1895 views

Synthesis of Ethyl-2-Dicyanomethylene-4-Methyl-6-Phenyl-3-Cyclohexene-1-Carboxylate and Molecular Agglomerates in Its Crystal Structure

Ismiev A.I., Potekhin K.A., Maleev A.V., Maharramov A.M.

Abstract

Three-component condensation of benzylideneacetone, ethyl acetoacetate, and malononitrile in the 1:1:1 molar ratio, respectively, in the presence of equimolar quantities of piperidine and glacial acetic acid is studied. The crystal structure of the reaction product (ethyl-2-dicyanomethylene-4-methyl-6-phenyl-3-cyclohexene-1-carboxylate) determined from XRD data by the method of atom-atom potentials contains energy traps in the form of double planar and double two-sided catchers. The energy traps lead to molecular agglomerates occurring in the crystal in the form of slightly deformed translationally identical hexagonal networks.

Journal of Structural Chemistry. 2019;60(12):1896-1905
pages 1896-1905 views

DFT Investigation of a Charge-Transfer Complex Formation Between p-Phenylenediamine and 3,5-Dinitrosalicylic Acid

Madi F., Laafifi I., Cheriet M., Issaoui N., Nouar L., Merdes R., Athmani A.S.

Abstract

This study presents a computational investigation of p-phenylenediamine (PPD) interaction with 3,5-dinitrosalicylic acid (DNS) within PPD/DNS charge transfer (CT) complex. All calculations were performed by M06-2X/6-311+G(d,p) levels of theory in vacuum, water and methanol. EDA analysis was used to control the complexation process and suggested that electrostatic and dispersion energies contributes greatly in stabilizing PPD/DNS CT complex. The results of energy optimization showed that PPD/DNS CT complex is stable with negative complexation energy; the obtained geometries showed that ammonium group of PPD is closed to carboxylate one of DNS enabling the establishment of large number of interactions. Additionally, different analyses were performed on obtained optimized structures: TD-DFT, NBO, QTAIM and NCI. Consequently, NBO, QTAIM and NCI analysis give that PPD/DNS CT complex is stabilized by hydrogen bonding and van der Waals interactions.

Journal of Structural Chemistry. 2019;60(12):1906-1916
pages 1906-1916 views

Synthesis, Crystal Structure, and DFT Study of a New Compound 6-(2-Fluorophenyl)-N-(p-Tolyl)Imidazo[1,2-A]Pyridine-2-Carboxamide

Qin Y., Long D., Zhu X., Zhou Z., Chai H., Zhao C.

Abstract

6-(2-Fluorophenyl)-N-(p-tolyl)imidazo[1,2-a]pyridine-2-carboxamide is an organic intermediate having both functions of azabicyclo and amide groups. In this paper, the title compound is obtained by the ring closure reaction, the Suzuki reaction, the hydrolysis and amidation reactions. The structure of the compound is confirmed by FT-IR, lH NMR, 13C NMR spectroscopy, and MS. At the same time, a single crystal of the title compound is measured by X-ray diffraction and subjected to crystallographic and conformational analyses. The molecular structure is further calculated using density functional theory (DFT) and compared with the X-ray diffraction value. The results of the conformation analysis indicate that the molecular structure optimized by DFT is consistent with the crystal structure determined by single crystal X-ray diffraction. In addition, the molecular electrostatic potential and frontier molecular orbitals of the title compound are further investigated using DFT, revealing some physicochemical properties of the compound.

Journal of Structural Chemistry. 2019;60(12):1917-1924
pages 1917-1924 views

Electronic Structure of Eu(III) Adducts with OP(C6H5)3 and OP[NMe2]3

Shurygin A.V., Vovna V.I., Korochentsev V.V., Mirochnik A.G., Sergienko V.I.

Abstract

Ultraviolet photoelectron spectroscopy in the gas phase (UPS, HeI), X-ray photoelectron spectroscopy in the condensed phase (XPS, MgKα), and quantum chemical methods (DFT) are used to study the adducts of Eu(III) tris-hexafluoroacetylacetonate with two molecules of four-coordinated phosphorus, namely HMPA (OP[N(CH3)2]3) and TPPO (OP(C6H5)3). Spectral bands of valence and core levels are interpreted using energy calculations and localization of Kohn-Sham orbitals. It is shown that TPPO and HMPA molecules influence the electronic structure of the complexes; positions and localizations of molecular orbitals are determined, the nature of bonding between Eu(III) and three chelate ligands and two neutral molecules is established. The differences in positions and compositions of occupied and vacant orbitals participating in energy transfer under excitation are shown. It is estimated that the bonding energy between Eu(hfac)3 and the two molecules is 10.91 eV for OP(C6H5)3, 12.62 eV for OP[NMe2]3, and 24.9 eV for SP[NMe2]3. It is shown how the differences between the energies and localizations of HOMOs of neutral molecules affect the structure, localization of adducts by the frontier molecular orbital (MO) and HOMO-LUMO gaps and how these differences determine the parameters of “antenna” ligand effects and the relative quantum yield of the luminescence of the adduct.

Journal of Structural Chemistry. 2019;60(12):1925-1939
pages 1925-1939 views

A Mass Spectrometric Study of Copper Bis(Acetylacetonate) with Allowance for the Isotopic Composition of the Metals

Kostyuk N.N., Dik T.A., Kazak M.S., Metelsky Y.M.

Abstract

Copper bis(acetylacetonate) is studied using mass spectrometry taking account of the natural isotopic composition of the metal. Valid data are obtained for the intensity of copper cations in the mass spectrum, which are confirmed by expected intensity ratios of copper-containing signals in the form of doublets. A new scheme for the main directions of Cu(acac)2 destruction is proposed. The assignment of cation signals in the mass spectrum is performed with a special software by representing Cu(acac)2 as a special discrete structure, a labeled simple graph G.

Journal of Structural Chemistry. 2019;60(12):1940-1945
pages 1940-1945 views

Crystallographic Analysis of SiO2 Polymorphs

Borisov S.V., Pervukhina N.V., Magarill S.

Abstract

The crystallographic analysis of six SiO2 phases (α-quartz, β-tridymite, α- and β-cristobalite, coesite, and stishovite) is performed. The effect of the local symmetry of SiO4 tetrahedra on the symmetry of phases tending either to highly symmetrical cubic P-cristobalite or hexagonal P-tridymite is shown. The parameters of cation, anion, and joint pseudotranslational sublattices characterizing the atomic configurations of the structures and their individual features are calculated. The relative stability of the phases is considered.

Journal of Structural Chemistry. 2019;60(12):1946-1958
pages 1946-1958 views

Crystal Structure of Three Ionic Compounds of Levofloxacin

Vasiliev A.D., Golovnev N.N.

Abstract

The structures of three ionic compounds of levofloxacin (LevoH or Ci18H20FN3O4) − LevoH3[CoCl4]-H2O (I), LevoH3[ZnBr4]·H2O (II), LevoH3[CuBr4]-H2(III) are determined. The crystals of I-III are monoclinic; in compound III, the particles are packed so that the direction of the screw axis does not coincide with the largest unit cell parameter. The asymmetric unit of the unit cell contains two LevoH32+ and CoCl42− ions and two crystallization water molecules in I; two LevoH32+ and MBr42− (M = Cu, Zn) ions and two crystallization water molecules in II and III. The absolute structure of the crystals and the configuration of the chiral center of the levofloxacinium cation S are determined. The structures are stabilized by multiple hydrogen bonds, X−Y π and π-π interactions.

Journal of Structural Chemistry. 2019;60(12):1959-1964
pages 1959-1964 views

Metal-Organic Coordination Polymers Based on the Anions of Perfluorinated Dicarboxylic Acids

Cheplakova A.M., Samsonenko D.G., Fedin V.P.

Abstract

Two new coordination polymers are obtained: layered [Hdabco][Sc2(H20)2(OH)(tFBDC)3]-3/2C4HgO2 (1) (dabco=1,4-diazabicyclo[2.2.2]octane) and chain-like [Zn(CH3OH)4(oFBPDC)]-2CH3OH (2). They are formed by anions of perfluorinated terephthalic (tFBDC2) and biphenyl-4,4'-dicarboxylic (oFBPDC2) acids. The composition and structure of the obtained compounds are determined by the single crystal X-ray diffraction analysis.

Journal of Structural Chemistry. 2019;60(12):1965-1970
pages 1965-1970 views

A Dinuclear Paddle-Wheel Cu(II) Complex [Cu2(L)4(H2O)2]·2H2O [HL=2-(Methoxycarbonyl)Benzoic Acid)]: Crystallographic, Magnetic, and Theoretical Analyses

Vakil F., Mantasha I., Shahid M., Ahmad M.

Abstract

A dinuclear paddle-wheel Cu(II) complex [Cu2(L)4(H2O)2]·2H2O (1) [HL=2-(methoxycarbonyl)benzoic acid)] is crystallized and characterized by spectral and magnetic analyses and single crystal X-ray crystallography. Single crystal XRD reveals that the complex crystallizes in the triclinic P-1 space group and has a square pyramidal environment around each copper(II) atom with a Cu ··· Cu intramolecular distance of 2.631 Å. Noncovalent C-Hπp interactions generate a 1D chain, thus consolidating the crystal lattice. Such non-covalent interactions are verified theoretically by the Hirshfeld surface analysis, while a theoretical approach of molecular docking discloses the binding affinity of the complex with DNA which occurs interestingly in the major groove region through the free ester group present in the complex. Moreover, the temperature-variable magnetic data measured under an applied dc field of 0.1T in the temperature range 2-300 K show the presence of strong antiferromagnetic interactions between the two Cu(II) centres of the complex.

Journal of Structural Chemistry. 2019;60(12):1971-1982
pages 1971-1982 views

1D Copper(I) Coordination Polymer [Cu2(µ-(2,4-Cl-ba)2bn)(µ-I2)]n with a Flexible Schiff Base Ligand: Synthesis, Crystal Structure, and Thermal Stability

Khalaji A.D., Peyghoun S.J., Dusek M., Eigner V.

Abstract

In this paper, bis-monodentate Schiff base ligand (2,4-Cl-ba)2bn and its 1D copper(I) coordination polymer [Cu2(μ-(2,4-Cl-ba)2bn)(μ-I2)]n are synthesized and characterized by the elemental analysis (CHN), FT-IR and 1H NMR spectroscopy. Their crystal structure is determined from the single crystal X-ray diffraction analysis. The thermal behavior of the complex is studied using thermogravimetry in order to evaluate its thermal stability and thermal decomposition pathway. The X-ray results show that the free Schiff base ligand (2,4-Cl-ba)2bn is centrosymmetric and coordinated to copper(I) ions via two iminic nitrogen atoms as a bis-monodentate bridging ligand. The coordination geometry around the copper ions is a distorted triangle formed by one nitrogen and two iodine atoms. The distance between the two symmetry-related copper atoms is very short: 2.4756(8) Å.

Journal of Structural Chemistry. 2019;60(12):1983-1988
pages 1983-1988 views

Binuclear Niobium Complex with Coordinated N-Heterocyclic Carbene

Petrov P.A., Golubitskaya E.A., Kompankov N.B., Eltsov I.V., Sukhikh T.S., Sokolov M.N.

Abstract

By the interaction of Nb(NMe2)5 and 1,3-(2,6-diisopropylphenyl)imidazolium (IPr·HBF4) tetrafluoroborate a binuclear complex with coordinated N-heterocyclic carbene [(IPr)Nb(=NMe)(NMe2)(μ-F)2(μ-NMe2) NbF2(NMe2)] (1) is obtained. The reaction of Nb(NMe2)5 and 1,3-(2,4,6-trimethylphenyl)imidazolium (IMes·HBF4) tetrafluoroborate yields [(IMes)2H][NbF6] salt (2). The structure of the complexes is determined by single crystal X-ray diffraction.

Journal of Structural Chemistry. 2019;60(12):1989-1994
pages 1989-1994 views

Crystal Structure and Luminescent Property of a new Three-Dimensional Polymer Based on 3,5-Di(1H-Benzimidazol-1-yl)Pyridine

Zhang C., Tao J., Wang J.

Abstract

A three-dimensional Cd(II) complex [Cd(L)(BPDC)]-3H2O (1) (L = 3,5-di(1H-benzimidazol-1-yl)pyridine, H2BPDC = biphenyl-4,4-dicarboxylic acid) is synthesized and characterized using single crystal X-ray diffraction, IR spectroscopy, and elemental analysis. The single crystal X-ray diffraction analysis reveals that complex 1 is a novel twofold interpenetrating 4-connected net with a (65·8) topology. Moreover, complex 1 exhibits an emission band at 400 nm with an inconspicuous shoulder at 525 nm (λex = 329 nm).

Journal of Structural Chemistry. 2019;60(12):1995-2000
pages 1995-2000 views

Determination of the Diameter Distribution Function of Single-Wall Carbon Nanotubes by the X-Ray Diffraction Data

Salamatov I.N., Yatsenko D.A., Khasin A.A.

Abstract

A method to construct an atomic model of bundles consisting of single-wall carbon nanotubes with different diameters is proposed. It takes into account the appearing distortions of the close packing and helps calculate X-ray diffraction patterns by the Debye scattering equation. This method is demonstrated on a Tuball™(OCSiAl) sample. Its application provides information on the diameter distribution function of nanotubes.

Journal of Structural Chemistry. 2019;60(12):2001-2008
pages 2001-2008 views

Synthesis, Crystal Structure, and Anti-Gastric Cancer Activity of Ethyl 3-(3-Amino-4-(Methylamino)-N-(Pyridin-2-Yl) Benzamido)Propanoate

Liu L., Peng K., Yue F., Li X., Zhang L.

Abstract

A new heterocyclic compound ethyl 3-(3-amino-4-(methylamino)-N-(pyridin-2-yl)benzamido)propanoate (1), designed using 4-(methylamino)-3-nitrobenzoic acid (2) as a starting material is successfully obtained via a multiple synthesis route and finally characterized by IR, 1H NMR, and single crystal X-ray crystallography. In addition, the in vitro anti-cancer activity of newly synthesized complex 1 is emulated against three human gastric cancer cell lines SGC-790, MKN-4, and MKN45.

Journal of Structural Chemistry. 2019;60(12):2009-2014
pages 2009-2014 views

Features of the Real Structure of Metallic Silver Nanoparticles Located in Channels of Mesoporous Silicate SBA-15

Zyuzin D.A., Cherepanova S.V., Moroz E.M., Moroz B.L., Gerasimov E.Y., Bukhtiyarov V.I.

Abstract

The features of diffraction on silver nanoparticles located in channels of mesoporous silicate SBA-15 are analyzed. A computer simulation of diffraction patterns is performed for crystallites with different sizes, the cubic structure, and stacking faults. The experimental diffraction patterns are compared with simulated ones. Together with the stacking fault concentration, the average crystallite sizes are determined in the direction normal to the close packed layers and along the layers in the crystal structure.

Journal of Structural Chemistry. 2019;60(12):2015-2024
pages 2015-2024 views

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