Home – Home – Jornals – Journal of Structural Chemistry 2016 number 8

A theoretical description of the relaxation kinetics of photoexcited states in chains of exchange clusters is developed in the mean-field approximation. It is found that in contrast to the analog of this phenomenon in the light-induced electron spin-state trapping (LIESST) effect well known for the conventional spin crossover compounds of Fe(II), the relaxation kinetics in chains of exchange clusters can be self-decelerating due to the different relaxation rates of two types of photoexcited states in the chain. The proposed theoretical approach qualitatively explains the experimentally observed difference in relaxation kinetics at different initial excitation intensities of the system during photoexcitation of breathing crystal compounds.

A model of Li₂MgZn X ₂ half-Heusler compounds with the chalcopyrite structure is considered. The electronic structure is studied from first principles, showing that Li₂MgZn X ₂ are direct-gap crystals, except for pseudo-direct-gap Li₂MgZnP₂, with a band gap of 2.7 eV, 2.2 eV, 3.3 eV, and 2.5 eV for X = N, P, As, and Sb, respectively. The band structure and chemical bonding in the model crystals are found to be similar to those in LiMg X and LiZn X half-Heusler crystals. Total electron density and deformation electron density distributions are obtained. It is found that Mg- X and Zn- X ionic-covalent bonds are stronger than Li- X ionic bonds in Li₂MgZn X ₂ crystals, which allows Li atoms to move in the space between Mg X ₄ and Zn X ₄ cation tetrahedra.

The electronic structure and lattice parameters of several quasi-one-dimensional compounds - known VS₄, NbCl₄, and NbS₃ and hypothetical NbS₄ and VS₃ - are obtained using density functional theory. Comparative analysis of chemical bonding and charge distribution in all these compounds reveals the possible origin of the structural instability of NbS₄ and VS₃.

Density functional theory was used to study pressure-induced phase transitions of zircon to monazite in doped yttrium orthophosphate, Y_{1- х} La _х PO₄, for х = 0, 0.0625, 0.125. The pressures of the phase transition, the elastic moduli and the universal elastic anisotropy index were calculated. It was shown that with increasing lanthanum concentration in Y_{1- x} La _x PO₄, the transition pressure increases. According to the Birch-Murnaghan equation of state, this effect is associated with a decrease in the critical volume. The increased stability of the doped zircon phase compared to YPO₄ is attributed to the more significant increase in the anisotropy and distortions of REO₈ polyhedra and RE-O-P chains found for the optimized structures at critical volumes.

Novel transition metal complexes with the repaglinide ligand [2-ethoxy-4-[N-[1-(2piperidinophenyl)- 3-methyl-1-1butyl] aminocarbonylmethyl]benzoic acid] (HL) are prepared from chloride salts of manganese(II), iron(III), copper(II), and zinc(II) ions in water-alcoholic media. The mononuclear and non-electrolyte [M(L)₂(H₂O)₂]× n H₂O (M = Mn²⁺, n = 2, M = Cu²⁺, n = 5 and M = Zn²⁺, n = 1) and [M(L)₂(H₂O)(OH)]×H₂O (M = Fe³⁺) complexes are obtained with the metal:ligand ratio of 1:2 and the L-deprotonated form of repaglinide. They are characterized using the elemental and molar conductance. The infrared, ¹H and ¹³C NMR spectra show the coordination mode of the metal ions to the repaglinide ligand. Magnetic susceptibility measurements and electronic spectra confirm the octahedral geometry around the metal center. The experimental values of FT-IR, ¹H, NMR, and electronic spectra are compared with theoretical data obtained by the density functional theory (DFT) using the B3LYP method with the LANL2DZ basis set. Analytical and spectral results suggest that the HL ligand is coordinated to the metal ions via two oxygen atoms of the ethoxy and carboxyl groups. The structural parameters of the optimized geometries of the ligand and the studied complexes are evaluated by theoretical calculations. The order of complexation energies for the obtained structures is as follows: Fe(III) complex < Cu(II) complex < Zn(II) complex < Mn(II) complex. The redox behavior of repaglinide and metal complexes are studied by cyclic voltammetry revealing irreversible redox processes. The presence of repaglinide in the complexes shifts the reduction potentials of the metal ions towards more negative values.

A new molecular structural characterization (MSC) method called the molecular vertex eigenvalue correlative index (MVECI) is constructed and used to describe the structures of 122 alkylbenzene compounds. Through multiple linear regression (MLR) and stepwise multiple regression (SMR), a quantitative structure-retention relationship (QSRR) model with correlation coefficient ( R ) of 0.995 is obtained. Through partial least-square regression (PLS), another QSRR model with correlation coefficient ( R ) of 0.991 is obtained. The estimation stability and prediction ability of the two models are strictly analyzed by both internal and external validations. For the internal validation, the cross-validation (CV) correlation coefficients ( R _CV) of the two models are 0.993 and 0.988. For the external validation, the correlation coefficients ( R _test) of the two models are 0.996 and 0.995, respectively. The results show that the stability and predictability of the models are good, and the molecular vertex eigenvalue correlative index can successfully describe the structures of alkylbenzene compounds.

A comparative study of the band structure and magnetic properties of the hexagonal and cubic modifications of aluminum nitride doped with boron, carbon, and oxygen in the nitrogen sublattice has been performed using the ab initio FLAPW-GGA method. Preliminary conclusions on the comparative chemical activity of these phases are drawn from estimates for the energies of substitution of nitrogen atoms by dopants. It has been shown that the doping with boron and nitrogen leads to transition of hexagonal AlN into a magnetic state with high spin polarization of near-Fermi electrons, but for cubic AlN, this effect is absent.

The molecular structures, conformational stabilities, and infrared vibrational wavenumbers of 2-thiophenecarboxaldehyde and 3-thiophenecarboxaldehyde are computed using Becke-3-Lee-Yang-Parr (B3LYP) with the 6-311++G** basis set. From the computations, cis -2-thiophenecarboxaldehyde is found to be more stable than the transfer conformer with an energy difference of 1.22 kcal/mol, while trans -3-thiophenecarboxaldehyde is found to be more stable than the cis conformer by 0.89 kcal/mol. The computed dipole moments, structural parameters, relative stabilities of the conformers and infrared vibrational wavenumbers of the two molecules coherently support the experimental data in the literature. The normal vibrational wavenumbers are characterized in terms of the potential energy distribution using the VEDA4 program. The effect of solvents on the conformational stability of the molecules in nine different solvents is investigated using the polarizable continuum model.

The title compound is synthesized from the precursors 1,2-diaminobenzene and 2,2¢-bipyridine-4,4¢-dicarboxylic acid (dcbpy) and characterized using ESI-Mass, ¹H NMR, FT-IR and single crystal X-ray analysis. We are the first to report the crystal structure of the 4,4¢-bis(benzimidazolyl)-2,2¢-bipyridine (bimbpy) ligand. The photophysical properties of the compound in dimethyl sulfoxide and in the aqueous medium are studied. The interaction studies of bimbpy with bovine serum albumin (BSA) were performed with the fluorescence technique and it strongly binds with BSA.

A Fourier IR spectroscopic study has shown that during injection solubilization of HCl solutions ( V _s/ V _o = 1.0-3.5 vol.%) at a concentration of 1-4 M by Triton N-42 reverse micelles in n -decane, the number of water molecules bound to protons is equal to 2.7±0.1. Protons form (70%) and (30%) cations in equilibrium, which are localized in the aqueous cores of the micelles.

The chlorobenzene (CB)- o -dichlorobenzene ( o -DCB) liquid system has been studied by classical molecular dynamics simulation over the entire range of concentrations. The structure of the solutions is characterized by using radial angular distribution functions for the distances between the planes of benzene rings and the angle between them, using radial distribution functions for the distances between chlorine atoms, and by calculating the self-diffusion coefficients and local dipole moments. Halogen aggregation in the pure components and solutions is analyzed. It is found that in pure CB, chlorine aggregates consisting of four to ten molecules are most likely to form. The sizes of chlorine aggregates increase with increasing o -DCB concentration, and at a o -DCB concentration of 0.50-1.00 ppm, an extended system of chlorine-chlorine contacts is formed. In pure o -DCB, the chlorine aggregation system includes 99% of the molecules of the simulated system. The agglomeration of solute molecules in the range of dilute solutions ( x < 0.1 ppm) is investigated.

Using the aggregation numbers of micelles and the effective sizes of hydrated surfactant ions and counterions of the first coordination sphere, we calculated the average geometric characteristics of the surface layer of ionic spherical micelles in solutions of the sodium n -alkyl sulfate homologues with n _C = 8, 10, 12, and 14 carbon atoms in the molecule; in particular, we established 1) the size of the micelle core; 2) the thickness of the electrical double layer on the surface; 3) the mutual arrangement parameters of hydrophilic and hydrophobic ions; 4) the number of “free” water molecules and showed their dependence on the homologue number and the degree of binding of counterions.

Crystal structures of newly synthesized tetramethylammonium hexafluoridoniobate(V) and hexafluoridotantalate(V) (CH₃)₄N[МF₆] (M=Nb, Ta) have been determined; they crystallize in the tetragonal crystal system, sp. gr. P 4/ nmm . Crystal structures of isostructural compounds (CH₃)₄N[МF₆] (M=Nb, Ta) are formed by virtually regular tetrahedral tetramethylammonium cations (CH₃)₄N⁺ (NMe₄, TMA) and octahedral complex anions [МF₆]^- (M=Nb, Ta), fluorine atoms of the equatorial plane are statistically disordered over two positions. Ionic interactions and weak hydrogen bonds C-H⋯F join the cations and the complex anions in a 3D assembly.

A complex compound [(NH₃)₆Rh₂(m-CO₃)(m-OH)₂](NO₃)₂×H₂O has been obtained and structurally characterized. Crystal data: a = 7.9103(16) Å, b = 9.606(2) Å, c = 11.283(2) Å, a = 103.206(4)°, b = 110.045(4)°, γ = 93.890(5)°, space group P -1, Z = 2, d _x = 2.335 g/cm³. The crystal structure is a packing of dimeric complex rhodium cations [Rh₂(m-OH)₂(m-CO₃)(NH₃)₆]²⁺, nitrate anions, and crystallization water molecules joined by a system of hydrogen bonds. The compound has been investigated with IR spectroscopy and powder X-ray diffraction. The isolated crystalline phase is poorly soluble in water.

A series of six-coordinated Ni(II) complexes, with the general formula Ni(Xan)L₂ (where Xan = isoamyldithiocarbonato and L = 2-bromopyridine, 3-bromopyridine, 4-acetylpyridine, 3-hydroxypyridine and 2-methoxypyridine) are synthesized and characterized by the elemental analysis and various physicochemical techniques such as magnetic susceptibility and conductivity measurements, UV-visible and infrared spectral data. Based on the electronic spectra and magnetic susceptibility measurements, an octahedral geometry is proposed for all the complexes. IR spectral data show that in all these complexes substituted pyridines coordinate to the metal ion through nitrogen atoms occupying the fifth and sixth axial positions, whereas O-alkyldithiocarbonate acts as a monoanion bidentate ligand and occupies the planar positions of octahedral structures. The structure of the adduct with 3-bromopyridine is elucidated by the single crystal X-ray diffraction method. The complex crystallizes in the triclinic space group P -1 with unit cell parameters a = 6.5855(4) Å, b = 9.4984(6) Å, c = 12.4518(8) Å, a = 87.944(5)°, b = 78.843(5)°, g = 77.794(5)°. The crystal structure of the molecule is stabilized by intermolecular C-H…S and C-H…p interactions.

Single crystal X-ray diffraction was applied for re-determination of the crystal structure of a- trans -[Pd(NH₃)₂Cl₂]. It has been demonstrated that, in contrast to the literature data, the structure is disordered. This model does not require excess over-stoichiometric palladium. Two crystals obtained in the same experiment illustrate possible variations in the packing of the molecules of the complex.

Double complex salts (DCS) a-[Pd(NH₃)₄][IrF₆]×H₂O ( P 2₁/ m , a = 6.3181(3) Å, b = 10.8718(5) Å, с = 7.4526(4) Å, b = 103.568(2)°), b-[Pd(NH₃)₄][IrF₆]×H₂O ( P 2₁/ с , a = 8.5773(3) Å, b = 10.8791(4) Å, с = 12.6741(3) Å, b = 122.497(2)°), [Pd(NH₃)₄]₃[IrF₆]₂Cl₂×H₂O ( P- 1, a = 7.6080(2) Å, b = 7.6274(2) Å, с = 11.8070(3) Å, b = 122.497(2)°), and [Pd(NH₃)₄]₂[IrF₆]NO₃ ( Fm -3 m , a = 11.21210(10) Å) have been synthesized and structurally characterized for the first time. The existence of polymorphs for the DCS has been revealed. The influence of the chemical composition of the initial reagents on the reaction course and, respectively, the products, has been demonstrated. A hypothesis on the influence of the second coordination sphere on the formation of one or the other polymorph of the DCS has been suggested. It has been shown that the series a-[Pd(NH₃)₄][МF₆]×H₂O (M = Pt, Pd) exhibits isostructurality.

A novel bimolecular crystal (BMC) of CL-20 and N,N'-dimethyl-N,N'-dinitrooxamide (MNO) has been prepared. Molecular and crystal structures have been determined. Thermal stability has been studied with DSC technique.

Indoline alkaloids kopsinilam and kopsinine extracted from the plant Vinca erecta have been studied by X-ray crystallography; mono and double salts of the latter alkaloid also have been examined. Experimentally determined positions of Н atoms suggest sp ³ hybridization of the indoline nitrogen atom N1 in the bases and the salts. Tetrahedral hybridization of the atom N1 in indoline alkaloids favors the formation of their double salts, what is unlikely for indole and indolinine alkaloids. In the halogen double salts there is an intramolecular Н bond between one of the protons of the NH₂ group and the oxygen of the methoxycarbonyl group, that is absent in the mono salts and pure bases.

A review and comparative analyses of methods for restricting the range of molecular interactions within the concept of atom-atom potentials are presented. Emphasis is placed on the problem of calculating the electrostatic energy in models with periodic boundary conditions. Numerous calculations of the thermodynamic and structural characteristics of water using parallel Monte Carlo computations have shown that the use of functional forms simulating the electric potentials of “screened charges” provides very good results.

Interpretation of X-ray photoelectron spectra (XPS) for p -nitroaniline and the nitroxide radical was carried out by the time-dependent density functional theory (TD-DFT) method using the ( Z +1) ^N-1 approximation. Consideration of satellite transitions in the interpretation of the XPS spectra leads to good agreement with experiment. The shape of the X-ray photoelectron spectra of the radicals mainly depends on the relaxation processes caused by the X-ray hole screening effect and leading to the formation of satellite lines. The structure of the satellites in the XPS spectra depends on the spin state of the system and intermolecular interaction.

Visualization pictures of collective motion of particles are presented, showing the existence of mesoscopic (of the order of tens of angstroms) vortex-like motions at time intervals of at least hundreds of picoseconds in molecular dynamics models of liquid argon.

α-³⁴S has been studied with X-ray crystallography within 100-363 K. Anisotropy of the evolution of the parameters of the orthorhombic unit cell has been examined. The absolute increase in the cell volume is 154 ų, and the relative one is 4.8%. It has been demonstrated that in the studied range the intramolecular S-S bond lengths are shortened at average by 0.006 Å on heating. At the same time, intermolecular contacts S…S shorter than the sum of van der Waals radii demonstrate average elongation of 0.097 Å.

A novel complex [Ag(ptac)]_∞ (1) (ptac = ^t BuC(O)CHC(O)CF₃) has been prepared by interaction of Ag₂O and Hptac, its structure being elucidated by single crystal X-ray diffraction. The complex has a chain polymeric structure originating from tetradentate-m-bridging coordination of the ptac ligands and interactions Ag-Cg between adjacent {Ag(ptac)} fragments. The coordination environment of the silver atom is a distorted square pyramid. The distances Ag-O are 2.362(10)-2.600(10) Å; Ag-Cg - 2.32(2) Å and 2.328(13) Å; Ag···Ag - 3.3497(13) Å and 3.3750(13) Å; the values of chelate angles OAgO fall within 64.6(4)-71.1(3)°. Under thermogravimetric experiment conditions compound 1 decomposes within temperature range 100-385°С with formation of silver metal.

Coordination nickel pyrophosphate [Ni(H₂P₂O₇)(C₁₂H₈N₂)₂]×2.5H₂O (I) is hydrothermally synthesized and characterized by single crystal X-ray diffraction. The title compound crystallizes in the triclinic system, space group P-1, with cell parameters M = 640.07, a = 10.285(2) Å, b = 10.510(3) Å, c = 12.775(3) Å, a = 88.06(2)°, b = 77.87(2)°, g = 89.26(2)°, V = 1349.2(5) ų, Z = 2, R ₁[ I > 2s( I )] = 0.0438, wR ₂[ I > 2s( I )] = 0.1244. This compound displays a new structure of ladder-like 2D layers parallel to (010) consisting of [Ni(H₂P₂O₇)(phen)₂] entities with the distorted octahedral NiN₄O₂ coordination geometry arising from two chelating 1,10-phenanthroline ligands and diphosphate [H₂P₂O₇] ligand bridged through p⋯p stacking interactions between the neighboring 1,10-phen ligands with interplanar distances of 4.425 Å and 4.525 Å. In the compound, the phen ligands bind in a bidentate fashion to the metal atoms and the ladder-like structure of the compound extends into a three-dimensional supramolecular array via hydrogen bonds (O4-H17…O5) between diphosphate groups, which delimits b axis tunnels where water molecules are located.

New complex [Pt(Ph₂bipy)Cl₂] (1) is obtained from the reaction of H₂PtCl₆×6H₂O and 4,4¢-diphenyl-2,2¢-bipyridine (Ph₂bipy) in a mixture of methanol, chloroform, and dimethyl sulfoxide. Suitable crystals of 1 for the diffraction experiment are obtained by slow evaporation of the resulted orange solution at room temperature. This complex is characterized by elemental analysis, IR, ¹H NMR, UV-Vis, and luminescence spectroscopy and its structure is studied by the single crystal X-ray diffraction method. X-ray structure determination shows that in the structure of this compound, the Pt(II) atom is four-coordinated in a distorted square-planar configuration by two nitrogen atoms from a bidentate 4,4¢-diphenyl-2,2¢-bipyridine ligand and two terminal chlorine atoms.

The newly attempted template synthesis involving 1-hydrazinocarbonylmethyl-7-bromo-5-phenyl-1,2-dihydro-3 H -1,4-benzdiazepin-2-one (Hydazepam - HHy) (1), 2-hydroxy-1-naphtaldehyde (HNf) (2) and tin tetrachloride (3) in the solution of iso -propanol has afforded a tin(IV) coordination compound with 1-[(2-hydroxy-1-naphtyl)methylenhydrazino]carbonylmethyl-7-bromo-5-phenyl-1,2-dihydro-3 H -1,4-benzdiazepin-2-one (H₂HyNf) (4) - the product of condensation of 1 with 2. The composition of the complex [Sn(HHyNf)Cl₃] (5) and its structure have been confirmed by a number of physical chemical methods. Its molecular structure has been determined by single crystal XRD. The coordination polyhedron of the tin atom is an octahedron formed by three chlorine atoms, azomethine nitrogen atom and two oxygen atoms of the carbonyl and deprotonated hydroxy group of the ligand.

The structure of a samarium(III) complex with acylhydrazone of N-(2-hydroxyphenyl)iminodiacetic acid and 5-hydroxy-3-methyl-1-phenyl-4-formylpyrazole (Н₅L) of the composition [Sm₂(Н₃L)₃]×С₂Н₅ОН×10Н₂О has been determined by single crystal X-ray diffraction. It has been found that in the dinuclear complex the coordination polyhedra have the geometry of a slightly distorted tri-capped trigonal prism and are linked with three iminodimethylene bridges arranged in a triple helix.

The structures of two novel 8-hydroxyquinoline derivatives with 1,3-tropolonic fragment in the second position of the quinoline ring have been studied as a promising new multidentate system with extended coordination capabilities .

X-ray crystallography has been applied to determine crystal and molecular structures of a co-crystal of malonic acid with acetamide. The crystal symmetry is monoclinic, P 2₁/ c space group, a = 5.042(1) Å, b = 14.022(5) Å, c = 10.593(3) Å, b = 100.61(7)°, V = 736.1(4) ų, Z = 4, d _calc = 1.503 g/cm³, F (000) = 344.