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Vol 60, No 6 (2019)

Article

Homo- and Heteronuclear Architectures of Polynuclear Complexes Containing Anions of Substituted Malonic Acids: Synthetic Approaches and Analysis of Molecular and Crystal Structures

Bazhina E.S., Gogoleva N.V., Zorina-Tikhonova E.N., Kiskin M.A., Sidorov A.A., Eremenko I.L.

Abstract

The review summarizes the data obtained in the studies of transition metal complexes (VIVO, CoII, NiII, CuII, ZnII) with anions of substituted malonic acids, which are not only coordination polymers but also compounds with a discrete molecular structure. The influence of malonic acid substituents and the nature of metal ions (alkali, alkaline earth, and transition metals) on the formation of molecular and polymeric systems is discussed. The crystal structures of recently described heterometallic coordination polymers are analyzed.

Journal of Structural Chemistry. 2019;60(6):855-881
pages 855-881 views

Theoretical Study of the Interaction of Ethanol with the (3,5-Dimethylpyrazole-N2)(N-Salicylidenephenyl-Alaninato-O,N,O′)Copper(II) Complex

Massoud R.A., Makhyoun M.A.

Abstract

The electronic structure of the (3,5-dimethylpyrazole-N2)(N-salicylidenephenyl-alaninato-O,N,O′)copper(II) complex and its ethanol adduct is calculated theoretically using different approaches. A comparison with X-ray data shows that M06/SVP and LC-BLYP/TZVP methods give the best theoretical geometry. The vibrational bands in the range 100–500 cm−1 are assigned by the aid of the Chemcraft software. Unrelaxed potential energy curves of the interaction of ethanol with our compound are obtained and examined.

Journal of Structural Chemistry. 2019;60(6):882-889
pages 882-889 views

Synthesis, Characterization, Crystal Structure, and DFT Study of 4-Bromo-2-(4,6-Dichloro-Phenylimino)-Phenol

Soltani A., Mashkoor R., Khalaji A.D., Raz S.G., Ghoran S.H., Dusek M., Fejfarova K., Kanani Y.

Abstract

The experimental crystal structure of a Schiff base compound 4-bromo-2-(4,6-dichloro-phenylimino)-phenol 1 is determined by single crystal X-ray diffraction and also characterized by FT-IR and 1H NMR spectroscopy. The electronic structure in the gas phase is studied by density functional theory (DFT) calculations.The theoretical results have good agreement with the data obtained from the crystallographic analysis. In addition, theoretical configurations which refer to the title compound are relaxed and studied in terms of the combined analysis of HOMO-LUMO energy gap, total density of states (DOS), partial density of state (PDOS), overlap population density of state (OPDOS), molecular electrostatic potential (MEP), NMR spectra, and harmonic vibrational frequencies.

Journal of Structural Chemistry. 2019;60(6):890-897
pages 890-897 views

Phototautomerism of Isocytosine in a Water Medium: Theoretical and Experimental Study

Dimitrov B.H., Bakalska R.I., Delchev V.B.

Abstract

We have carried out a combined theoretical (at the TDDFT BLYP/6-311++G** level of theory) and experimental study of the mechanism of phototautmerization of the N(3)H oxo tautomer of isocytosine dissolved in a water medium. The study reveals that this photoreaction occurs along the 1πσ* excited-state reaction paths of the oxo and hydroxy tautomers of the compound through conical intersections S0/S1. The last strucutres are located at the CASSCF level for both tautomers.

Journal of Structural Chemistry. 2019;60(6):898-908
pages 898-908 views

An X-ray Spectral Study of the Electronic Structure of Non-Innocent Mono- and Binuclear Platinum Complexes with N-Phenyl-o-Benzosemiquinonediimine

Ivanova T.M., Sidorov A.A., Mazalov L.N., Fedorenko A.D., Kiskin M.A., Savilov S.V., Lunin V.V., Novotortsev V.M., Eremenko I.L., Kalinkin A.V., Fedoseeva Y.V., Okotrub A.V.

Abstract

The electronic structure of mono- and binuclear platinum complexes with N-phenyl-o benzosemiquinondiimine ligands was studied using X-ray photoelectron spectroscopy, X-ray absorption spectroscopy, and the density functional theory. The oxidation state of the central platinum ion corresponds to that of Pt(II). Upon the transition from the trans-complex 1 to the cis-complex 2 and to the binuclear complex 3, the electron density on platinum and nitrogen atoms decreases thus testifying the participation of platinum and nitrogen atoms in the oxidation processes and in the formation of binuclear complex 3.

Journal of Structural Chemistry. 2019;60(6):909-918
pages 909-918 views

The State of Platinum and Structural Features of Pt/Al2O3 Catalysts in the Reaction of NH3 Oxidation

Svintsitskiy D.A., Slavinskaya E.M., Stonkus O.A., Romanenko A.V., Stadnichenko A.I., Kibis L.S., Derevyannikova E.A., Evtushkova A.A., Boronin A.I.

Abstract

The work is related to the fundamental research of the process of ammonia neutralization using catalytic oxidation over Pt/Al2O3 catalysts in an excess of oxygen. The catalysts are synthesized using nitrate precursors on the supports prepared from Pural SCF-55 aluminum hydroxide by the calcination in air at 550°C or 750°C for 4 h. A number of physicochemical methods are used to study morphology, dispersion, structure, and electronic state of the catalyst active component before and after the reduction in hydrogen. It is shown that the synthesized Pt/Al2O3 catalysts are characterized by high dispersion of the active component: the size of deposited platinum particles is in the range from 0.5 nm to 2.0 nm, while the proportion of oxidized and reduced Pt forms varies. Based on the results of kinetic measurements, the catalyst activity and the selectivity to all major products (N2, N2O, NO, NO2) are determined depending on the reaction temperature. The results of the catalytic testing are discussed in relation to the data on dispersion and oxidation state of platinum.

Journal of Structural Chemistry. 2019;60(6):919-931
pages 919-931 views

Structural Manifestations of the Polarizability Effect in 1-Halogensilatranes According to the Dipole-Induced Dipole Mechanism

Tandura S.N., Belyaeva V.V., Baryshok V.P., Gostevsky B.A., Smirnov V.I.

Abstract

A new mechanism of the dipole-induced dipole polarizability effect by the example of

1-halogensilatranes is proposed. The mechanism involves a through-space interaction between the dipole moment μ of the core and the dipole Δμ which is induced on the halogen and, in turn, induces an extra dipole ΔΔμ on the transannular bond Si ← N to make it stronger. This effect explains for the first time the previously discovered contradiction for 1-halogensilatranes where an inverse dependence in the linear correlations between the Si ← N bond length, δ15N, δ1H(CH2N) chemical shifts, and the inductive constant σ are observed. For example, the length of the Si ← N coordination bond is shorter in 1-chlorosilatranе than in 1-fluorosilatrane due to the fact that the polarizability effect is stronger than the inductive effect in the case of the Cl atom.

Journal of Structural Chemistry. 2019;60(6):932-941
pages 932-941 views

Mobility of Water, Urea and Trimethylamine-N-Oxide Molecules in the Vicinity of Globular Protein

Voloshin V.P., Medvedev N.N.

Abstract

Molecular mobility in the hydration shell of the SNase globular protein in an aqueous solution with cosolvents (urea and trimethylamine oxide) is studied using all-atom molecular dynamic simulations. Average displacements of the molecules initially located in the successive layers around the protein are calculated over the same short period of time to characterize the diffusion mobility of the molecules depending on the distance to the protein. It is shown that solvent molecules have lower mobility near the protein, and the mobility of more distant molecules increases irregularly and correlates with the positions of the distribution function maxima of these molecules around the protein. After the second maximum of these functions, the mobility reaches its bulky values both for water and the cosolvent.

Journal of Structural Chemistry. 2019;60(6):942-951
pages 942-951 views

Structure and Properties of the α-Cs2Mo2−xWxO7 Solid Solution

Solodovnikov S.F., Zolotova E.S., Solodovnikova Z.A., Korolkov I.V., Yudin V.N., Uvarov N.F., Plyusnin P.E., Saranchina E.M.

Abstract

The tungsten substitution for molybdenum in cesium dimolybdate Cs2Mo2O7 with the formation of an α-Cs2Mo2−xWxO7 solid solution is studied, and its homogeneity region at 540 °C is found to reach 0 ≤ x ≤ 0.6. It is established that the volume of the monoclinic (pseudo-orthorhombic) unit cell and the solid solution melting point monotonically increase with increasing tungsten content, whereas the phase transition temperature to the orthorhombic phase remains practically constant and is ∼390 °C. The crystals of solid solutions with several compositions are obtained, their structure is determined, and the tungsten atoms are found to be mainly located in octahedral positions of the α-Cs2Mo2O7 structure. As a result of the phase transition at 390 °C the electrical conductivity of Cs2Mo2O7 increases approximately by two orders of magnitude reaching 1.2·10−4S/cm at 460 °C. Due to a large size of Cs+ ions and a high charge of molybdenum cations it is supposed that the charge carriers are oxygen anions. The calculation of bond valence sum (BVS) maps for possible positions of oxygen atoms in the α-Cs2Mo2O7 cell shows the formation of a 3D system of oxygen conductivity channels at boundary BVS isosurface values ≥ 2.13.

Journal of Structural Chemistry. 2019;60(6):952-960
pages 952-960 views

Synthesis and Electrochemical Properties of ((CH3)2NH2)7[P2W17NbO62]

Shmakova A.A., Gushchin A.L., Abramov P.A., Sokolov M.N.

Abstract

The bis(oxalate) complex of niobium (NH4)[NbO(C2O4)2(H2O)2]·3H2O can be used as a source of niobium to incorporate the {NbO}3+ group into a cavity of the monolacunary Dawson-type [α2-P2W17O61]10− anion. The product is isolated from the reaction mixture as dimethylammonium salt (Me2NH2)72-P2W17NbO62]·3H2O (1) and characterized by single crystal XRD, IR and Raman spectroscopy, and elemental analysis. (NBu4)6(Me2NH2)[α2-P2W17NbO62] (2) is obtained by adding Bu4NBr to an aqueous solution of 1. The comparison of the electrochemical properties of complex 2 and (NBu4)6[P2W18O62] shows that the incorporation of niobium atom hinders the anion reduction.

Journal of Structural Chemistry. 2019;60(6):961-966
pages 961-966 views

Synthesis, Structure and Emission Properties of [Cu22-I)2L4] Complex Based on 2-(Methylthio)Pyrazine

Artem’ev A.V., Beresin A.S., Bagryanskaya I.Y.

Abstract

Reaction of 2-(methylthio)pyrazine (L) with CuI (MeCN, r.t.) results in formation of iodide-bridged complex [Cu22-I)2L4], wherein Cu⋯Cu contact of 2.6351(4) Å is observed. The each metal atom of the [Cu22-I)2] core is coordinated by the two ligands via 4-pyrazyl nitrogen atoms. In the solid state at room temperature, the complex obtained emits an orange photoluminescence (λmax = 600 nm) with the average lifetime of 1.66 μs and quantum yield of 17%.

Journal of Structural Chemistry. 2019;60(6):967-971
pages 967-971 views

X-Ray Crystallographic Studies in A Series of Substituted (Fluorinated) 2-(2-Pyridyl)Quinolines

Kopchuk D.S., Slepukhin P.A., Nosova E.V., Khasanov A.F., Zyryanov G.V., Rusinov V.L., Chupakhin O.N.

Abstract

By X-ray crystallography the structures of three compounds of the 2,2′-bipyridine type — 2-(5-phenylpyridin-2-yl)quinolines, including those having a cyclopentylene moiety condensed to the pyridine ring and/or two fluorine atoms at quinoline positions 6 and 7. The effect of fluorine atoms on the geometry of the aromatic system and intermolecular interactions is shown.

Journal of Structural Chemistry. 2019;60(6):972-978
pages 972-978 views

Molecular and Crystal Structures of 4-Cyano-3(2H)-Furanones and Structural Effects in 1H NMR Spectra

Afonin A.V., Vashchenko A.V., Volostnykh O.G., Stepanov A.V., Mal’kina A.G.

Abstract

Features of the molecular structure in crystals of a series of functionalized 4-cyano-3(2H)-furanones with a spiro-cyclohexane substituent or two methyl groups at position 2 of the furanone ring and also an aryl or heteroaryl substituent at position 5 are analyzed in comparison with the literature data. Effects appearing in 1H NMR spectra, which are caused by the features of the molecular structures of these compounds are interpreted. Their crystal structure is considered and intermolecular interactions responsible for the supramolecular architecture of the crystals formed are revealed.

Journal of Structural Chemistry. 2019;60(6):979-989
pages 979-989 views

Experimental and Theoretical Studies on Molecular Structures, Nanostructural Features, and Photophysical Properties of 5-Amino-1-Alkylimidazole-4-Carboxamide Compounds

Das A.

Abstract

A detailed interpretation of experimental spectral data on 1H and 13C NMR chemical shifts of compounds determined from the DFT calculation is reported. The DFT calculated values are in good agreement with the experimental results. The NBO analysis is used to investigate the stability of 1-alkylAICA. The HOMO and LUMO analysis is performed to study the charge transfer property within the molecule as well as various molecular properties viz EHOMO, ELUMO, energy gap, ionization potential, electron affinity, electronegativity, chemical potential, electrophilicity, global hardness as well global softness, and so on. The formation of a 1D nano structure of 1-alkylAICA compounds is detected by SEM studies. The UV and fluorescence study is performed to observe the variation of their photophysical properties on going from the monomer to the nanostructure. TDDFT is applied to analyze experimentally measured absorption and emission spectra. A fluorescence life-time measurement is performed for the series of 1-AlkylAICA.

Journal of Structural Chemistry. 2019;60(6):990-1007
pages 990-1007 views

Geometry, Tautomerism, and Noncovalent Interaction of Bentiromide with a Carbon-Nanotube and γ-Fe2O3 Nanoparticles: A Quantum Mechanical Study

Tanhaei R., Beyramabadi S.A., Behmadi H.

Abstract

A doctor can find out how pancreas is working using bentiromide. This drug can exist as six possible tautomers. Herein, by density functional theory (DFT) and handling the solvent effects with the polarizable continuum model (PCM), the mechanism of its tautomerization, energies, and structural parameters of the tautomers are investigated. Also, the natural bond orbital analysis (NBO) is used for exploring the frontier molecular orbitals. The most stable tautomer of bentiromide has three carbonyl groups in its structure. The amount of other tautomers is negligible in the aqueous solution. The non-covalent interactions of the most stable tautomer of bentiromide with an armchair (5,5) single-wall carbon nanotube and a γ-Fe2O3 nanoparticle are explored. In each case, three possible forms are optimized. Their most stable form is determined. The intermolecular H bonds have a critical role in the energy behavior of the interaction between bentiromide and the γ-Fe2O3 nanoparticle.

Journal of Structural Chemistry. 2019;60(6):1008-1018
pages 1008-1018 views