Home – Home – Jornals – Journal of Structural Chemistry 2010 number 5

A new form of the Hamiltonian is proposed, for which additional conditions are imposed from the very beginning specifying the localization of the nuclear motions in the region corresponding to the structural isomer. In the Hamiltonian for the electronic state problem, a potential is introduced to describe the action of the diffuse positive charge.

The formula has previously been proposed and successfully tested in the description of the experimental data for OHN fragments. It characterizes the correlation between bond lengths in hydrogen bridges formed by different atoms (XHY). Here b^XHX, b^YHY are the dimension coefficients unambiguously determined based on the average XH, YH bond lengths in free molecules ( and ) and bond lengths in symmetric X…H…X, Y…H…Y hydrogen bridges. The present work analyzes the applicability of this formula to describe dependences between parameters of OHN и OHCl fragments calculated by density functional theory (B3LYP/6-31++G(d,p)) in neutral, positively and negatively charged molecular complexes. It is shown to well reproduce the correlation between bond lengths in hydrogen bridges close to linear ones, and hence, it may be used to solve a wide range of problems, in particular, when single crystal X-ray diffraction is unable to localize the position of the central proton.

The quantum chemical DFT method with the B3LYP hybrid functional in 6-31++G(d,p) and 6-311+G(d,p) basis sets is used to calculate the equilibrium geometric parameters of different conformations of 5-(4-oxo-1,3-thiazolidine-2-ylidene)-rhodanine and its substituted form ethyl-5-(4-oxo-1,3-thiazolidine-2-ylidene)-rhodanine-3′-acetic acid applied in the synthesis of indoline and some other sensitizing dyes for solar cells. The thermodynamic parameters of four conformers and their synthesis reactions are calculated. The effect of substituents on the thermodynamic stability of the studied isomers is shown.

A molecular mechanics method in the ММ⁺ semi-empirical field potentials and a quantum chemical method in the РМ3 approximation are used to calculate the geometric and energy parameters of a biocarnosine molecule in two tautomeric forms of the imidazole ring. The electronic structures of monomeric and dimeric complexes of both carnosine forms with zinc are investigated.

A Quantitative Structure - Property Relationship (QSPR) model based on Genetic Algorithm (GA), Multiple Linear Regression (MLR) and Artificial Neural Network (ANN) techniques was developed for the prediction of water-to-polydimethylsiloxane partition coefficients (log K_PDMS-water) of 139 organic compounds. A suitable set of molecular descriptors was calculated and important descriptors were selected by genetic algorithm and stepwise multiple regression. These descriptors were: Minimum Atomic Orbital Electronic Population (P_μμ), Kier Shape Index (order 3) (³κ), Polarity Parameter / Square Distance (PP), and Complementary Information Content (order 2) (²CIC). In order to find a better way to depict the nonlinear nature of the relationships, these descriptors were used as inputs for a generated ANN. The root mean square errors for the neural network calculated log K_PDMS-water of training, test, and validation sets were 0.116, 0.179, and 0.183, respectively, which are smaller than those obtained by MLR model (0.422, 0.425, and 0.480, respectively). The results obtained showed the ability of developed artificial neural network to predict water-to-polydimethylsiloxane partition coefficients of various organic compounds. Also, the results revealed the superiority of the artificial neural network over the multiple linear regression model.

Correlations of the theoretical informational indices with the acid ionization constants and melting points of N-alkylcarboxyimides of hexachlorobicycloheptene-, hexachlorotricycloundecene-, and hexachlorotetracyclododecene-1,2-dicaboxylic acids are analyzed, and the prognostic capabilities of these indices are revealed.

The vibrational spectra of an isolated complementary adenine-thymine pair are calculated in the B3LYP/6-311++G(d,p) approximation and analyzed. The effect of hydrogen bonds on the structure is shown along with the position of frequencies and intensities of normal vibrations of the pair in comparison with the spectra of isolated thymine and adenine molecules. A comparative analysis of the hydrogen bonding effect on the IR and Raman spectra of thymine and adenine is performed.

The NMR (¹⁹F and MAS NMR ¹⁹F), IR, and Raman spectroscopic methods are used to study the ionic mobility and structure of a series of new glasses in ZrF₄-BiF₃-MF₂ (M = Sr, Ba, Pb) systems in a temperature range of 180 K to 500 K. The temperature range, in which diffusion of fluorine ions becomes the dominant form of ionic motion, is determined by the nature of the M²⁺ cation. The factors determining the basic model of the structure of glasses in ZrF₄-BiF₃-MF₂ (M = Sr, Ba, Pb) systems and conditions under which bismuth polyhedra can participate in the construction of the glass network are considered. According to the data of impedance spectroscopy, the studied glasses have relatively high ionic conductivity (σ ≥ 10^-4 S/cm above 480 K).

A silver atom in synthetic beryl is investigated by the EPR and electron spin echo (ESE) spectroscopy. It is established that silver ions were first introduced into the structural channels of beryl by thermodiffusion at 800°C. The Ag⁺ ions are then converted to the Ag⁰ state by the X-ray irradiation of samples at room temperature. Charge changes in manganese and chromium impurities located at the aluminum positions are observed at the same conditions. Four different Ag⁰ centers with isotropic hyperfine interactions (HFI) with ¹⁰⁷Ag and ¹⁰⁹Ag nuclei and hyperfine constants less than those for the free Ag atom are revealed by the EPR method. ESE investigations enable us to confirm the positions of silver atoms that are stable up to 230°C.

The electronic structure of polyvinylsiloxane polymeric chains (Si₂O₃(CHCH₂)₂)_n is studied by X-ray photoelectron spectroscopy and quantum chemistry in the DFT approximation. The binding energy of С and О 1s electrons occupying inequivalent positions in the polymer coincides within the experimental accuracy. The binding energies for С and О (284.9 eV and 532.4 eV) and for Si2p-electrons (102.7 eV) well agree with the values for related compounds. The experimental data for the binding energy are reproduced in HF and DFT calculations only with the extended 6-311**(d) basis set. The highest occupied levels of the polymer are π orbitals of vinyl groups.

By the example of aqueous solutions of sodium chloride an approach is developed to obtain the hydration number, molar volume and compressibility of hydrate complexes using the data on adiabatic and isothermal compressibility. It is shown that the results of calculations based on isothermal and adiabatic compressibility are consistent with each other.

A synthesis method with the use of polymer-salt compositions (calcination temperature 800°C) provides the preparation of various solid solutions of a La_1-xCa_xFeO_3-δ series in the 0 ≤ x ≤ 0.7 range, which belong to the perovskite structure type. A morphotropic phase transition occurs from the orthorhombic perovskite modification (0 ≤ x ≤ 0.4) to the cubic one (0.5 ≤ x ≤ 0.7). A growing number of microdistortions in the perovskite structure and the formation of a microblock structure in the morphotropic phase transition region are observed with increasing degree of calcium substitution for lanthanum. Calcination of solid solutions with х = 0.6 and 0.7 at temperatures above 1000°C in the air or under conditions of reduced oxygen partial pressure (laboratory vacuum of 10^-3 Torr) results in the formation of a nanostructured state with coherently grown blocks of perovskite and Grenier phase, which is due to irreversible oxygen loss.

The crystal structure of As-schwatzite Cu₆(Cu_5.26Hg_0.75)(As_2.83Sb_1.17)S₁₃ (Aktash deposit, Altai mountains) is refined. Tetrahedrally shaped dark-gray single crystals of the mineral belong to the cubic crystal system: I3m space group, a = 10.2890(1) Å, V = 1089.2(1) ų, d = 4.99 g/cm³, Z = 2 for the composition Cu_11.26Hg_0.75As_2.83Sb_1.17S₁₃, R = 0.0177. The structure is based on the sphalerite-like framework comprising identically oriented (Cu,Hg)S₄ tetrahedra ((Cu,Hg)-S 2.3452(8) Å) and (As,Sb)S₃ pyramids ((As,Sb)-S 2.311(1) Å) sharing their vertices. The centers of [Cu₆] octahedra in the (000) and (1/2 1/2 1/2) positions coinciding with the centers of the cluster anionic vacancies [□]₄ are occupied by the so-called thirteenth sulfur atom. Quantum chemical calculations of the electron density are carried out for the [As₄S₁₃Cu₆]^6- fragment. The calculation results confirm the presence of strain in the [As₄S₁₃Cu₆]^6- moiety, which exists due to the support of the surrounding symmetric framework including the external sulfur atoms of the fragment. The possibility of inclusion of mercury into the framework, which is much richer in arsenic than in antimony, is demonstrated. High stability of the framework determines significant compression of the S-centered [SCu₆] octahedron in its interstices, bringing together copper atoms to 3.145(1) Å and shortening the Cu-S distances to 2.224(1) Å.

The crystal structure of L-leucinium tetrafluoroantimonate(III) of the composition (C₆H₁₄NO₂)SbF₄ (orthorhombic symmetry: a = 6.1459(6) Å, b = 14.994(1) Å, c = 24.789(2) Å, Z = 8, P2₁2₁2₁ space group) synthesized for the first time is determined. The (C₆H₁₄NO₂)SbF₄ structure represents a new structure type of tetrafluoroantimonate(III). It is formed by (C₆H₁₄NO₂)⁺ cations and chain complex [Sb₂F₈] anions composed of Sb₂F₈ dimers linked into chains by bridging F atoms. The Sb₂F₈ dimers consist of SbF₃ and SbF₅ groups bound by bridging fluoride atoms of the SbF₅ group. Chains in the structure are linked by N-H…F, N-H…O, and O-H…F hydrogen bonds into a three-dimensional framework.

Crystals of MСl₂·2CONH₃ (M = Cu²⁺, Mn²⁺) are synthesized from low-temperature water-formamide solutions and studied by crystal optical, single crystal X-ray diffraction, and infrared spectroscopy methods. The crystal structures of CuСl₂·2CONH₃ and MnСl₂·2CONH₃ are solved by direct methods and refined in the Ptriclinic space group, R1 = 0.043 and 0.038 for 501 and 686 reflections with F₀ > 4σ(F₀) respectively. Unit cell parameters for Cu and Mn salts are: a = 3.705(1) Å and 3.685(1) Å, b = 7.049(2) Å and 7.136(2) Å, c = 7.375(2) Å and 7.779(2) Å, α = 113.57(3)° and 117.17(2)°, β = 96.17(3)° and 95.35(2)°, γ = 94.85(3)° and 92.23(2)° respectively, Z = 1. In the studied crystal structures, MCl₄O₂ octahedra share Cl-Cl edges and form chains along the [100] direction. This direction corresponds to a morphological elongation of the obtained crystals and orientation of the maximum refractive index. The FT infrared spectra obtained in a range from 4000 cm^-1 to 300 cm^-1 are very close to the spectrum of liquid formamide, but exhibit better resolution of absorption bands.

Chelate complexes of copper(II) and nickel(II) with anions of nitroxide radical ethyl-2-(1-oxyl-2,2,5,5-tetramethylimidazolidin-4-yliden)-3-oxopropanoate (HL) are synthesized. The compounds have molecular structure and zero magnetic dimensionality. CuL₂ crystallizes as two polymorphs having mononuclear structure. Ni₂L₄ forms dimeric molecules by virtue of the bridging function of the aldehyde oxygen atoms. Magnetic properties of Ni₂L₄ are determined by antiferromagnetic exchange interactions between the Ni(II) ions (-48(1) K) propagated through the oxygen bridges.

The synthesis and determination of the crystal and molecular structure of the binuclear complex μ-4,4′-bipyridyl-bis-[trans-С,О-nitrate-2-(2′-thienyl-3-ido)pyridine-palladium] is described (C₂₈H₂₀N₆O₆Pd₂S₂: a = 12.3914(11) Å, b = 9.8929(7) Å, с = 12.4058(12) Å, α = 90(0)°, β = 105.440(40)°, γ = 90(0)°, V = 1465.9(0) ų, monoclinic symmetry, P2₁/n (14), Z = 4, d_x = 1.843 g/cm³). The pyridine rings of 4,4′-bipyridyl are shown to be in the orthogonal position with respect to the coordination planes of palladium centers both in the solid state and solution.

Based on the X-ray diffraction data for polycrystals, the crystal structures of double complex salts [Rh(NH₃)₅Cl][ReBr₆] and [Ir(NH₃)₅Cl][ReBr₆] are refined. The structure of [Rh(NH₃)₅Cl][IrBr₆] is determined. Initial models are constructed using the Monte Carlo method in the straight space. Further refinement is made by the Rietveld method. It is shown that such an approach is suitable for the refinement of crystal structures composed of isolated rigid polyhedra and can be used to determine the structure of salts without structural analogues.

It is revealed that at 300 K Sm(Phen)(i-Bu₂PS₂)₃ (I) and Sm(2,2′-Bipy)(i-Bu₂PS₂)₃ (II) complexes have photoluminescence properties typical of the Sm³⁺ ion. In the spectra, three bands are observed with λ_max = 564 nm, 600 nm, and 645 nm. Single crystals of Sm(Phen)(i-Bu₂PS₂)₃·MeCN (III) are grown, and the structure of the compound is determined based on the X-ray diffraction data (X8 Apex diffractometer, MoK_α radiation, 7685 F_hkl, R = 0.0258). Crystals of III are triclinic, unit cell parameters are a = 11.0554(3) Å, b = 15.0446(3) Å, c = 15.4849(4) Å; α = 89.218(1)°, β = 75.555(1)°, γ = 73.484(1)°, V = 2386.6(1) ų, Z = 2, ρ_calc = 1.391 g/cm³, P space group. The structure of III is formed from the molecules of mononuclear complex I and MeCN molecules. A coordination polyhedron of the Sm atom is an N₂S₆ tetragonal antiprism. It is shown that the structure of III includes dimeric assemblies of the molecules of complex I.

In the ¹H and ¹³C NMR spectra of methyl 6,7-endo,sin-dibromo-7-anti-(phenylsulfonyl)bicycle-
[3.1.1]heptane-6-exo-carboxylate, H(1) and H(5) protons as well as C(1) and C(5) carbon atoms show their chemical inequivalence determined by the hindered rotation of sulfonyl and ester groups about simple C-S and C-C bonds due to the existence of donor-acceptor interaction between the carbonyl C atom and the oxygen atom of the SO₂Ph group. This interaction is indicated by the single crystal X-ray diffraction study detecting the shortened intramolecular contacts (2.49 Å with the sum of the C…O van der Waals radii of 3.00 Å). Other features of the norpinane skeleton conformation and the spatial orientation of substituents in the single crystal are discussed. By ¹H NMR methods, the parameters of the dependence of molecular conformations on the temperature of DMSO-d₆ solution and the activation free energy = 80.1 kJ/mol of conformational transitions are determined. By a quantum chemical DFT calculation of the potential energy surface it is revealed that the hindered rotation of the ester group makes the main contribution to the barrier of conformational transitions.

The FLAPW-GGA band method is used to analyze the structural, electronic, and magnetic properties of rhodium hydrides RhH_x depending on the hydrogen content (x = 0.25, 1.00, and 1.33). The RhH monohydride is a magnetic metal. A decrease in the hydrogen content in the system or formation of vacancies in the Rh sublattice results in a transition of RhH_x to the non-magnetic state.

The ab initio pseudopotential method (VASP package) within the gradient approximation (GGA) for the exchange-correlation potential is used to study the effect of Li and Na substitution for Be atoms on the electronic and magnetic properties of wurtzite-like beryllium monoxide BeO with an impurity concentration of 0.028. When Li impurity is introduced into ВеО, the system is found to remain non-magnetic. At the same time, the BeO:Na system adopts magnetic moments (~0.8 μ_В per cell) through the spin polarization of the 2р-state of oxygen atoms surrounding the impurity center. After lithium incorporation into ВеО, the spectrum of ВеО:Li becomes metal-like, while the introduction of sodium results in the magnetic semimetal type of the ВеО:Na spectrum.

The results of a comparative study on the modification of the properties of glassy and crystalline silicon dioxide under the radiation induced structural rearrangement are presented. The patterns of a non-linear change in the spectral parameters of bending vibrations of the Si-O-Si bonds in the function of fast neutron flux are revealed. The radiation kinetics of the peak value of the reflection coefficient and the respective frequency modes in the silicon dioxide modifications are compared. The graphs are found to demonstrate a dose dependence of the spectral parameters of special points. They are considered to be related to a radiation-induced rearrangement of the original structure accompanied by a deformation of the bridging bond angles.

Three-component condensation of N1-phenylthiocarbamide with salicylaldehyde and with the ether of acetoacetic acid in the presence of trifluoroacetic acid provides a productive synthesis of ethyl 9-methyl-10-phenyl-11-thioxo-8-oxa-10,12-diazatricyclo[7.3.1.0^2.7]trideca-2(7),3,5-trien-13-carboxylate I. Single crystal XRD is used to determine the crystal structure of I and to identify the conformation properties of the structures.

A new compound (pefloxacindium tetrachlorozincate(II)), C₁₇H₂₀FN₃O₃ 1-ethyl-N-methyl-6-fluoro-1,4-dihydro-4-oxo-7-(4-methyl-1-piperazinyl)-3-quinoline carbonic acid (PefH, pefloxacin) is synthesized, and its crystal structure is determined. The crystal contains and ions. The supramolecular architecture of the crystal is analyzed

By heating in the air [НBW₁₁O₃₉]^8- with [Rh₂(CH₃COO)₄(H₂O)₂] in the excess of tungstate followed by crystallization in the presence of CsCl, a double salt of Cs₈[α-BW₁₂O₄₀][RhCl₆]·5.5H₂O is obtained and structurally characterized. Its crystal structure is determined by single crystal X-ray diffraction. The structure is ionic with Cs⁺ cations, [BW₁₂O₄₀]^5- anions with the Keggin structure, and [RhCl₆]^3- octahedral anions.

The products of the extraction treatment of Rh(III) and Pd(II) nitrate-nitrite solutions are studied. The [Rh(Thio)₆](NO₃)₃·3H₂O and [Pd(Thio)₄](NO₃)₂ complex salts are extracted and an X-ray diffraction analysis of single crystals is performed (BRUKER X8 APEX automated diffractometer, MoK_α radiation, graphite monochromator, two-dimensional CCD-detector). [Rh(Thio)₆](NO₃)₃·3H₂O crystallographic characteristics are as follows: a = 15.1857(3) Å, b = 10.7292(2) Å, c = 18.8524(4) Å, β = 105.165(1)°, P2₁/c space group, Z = 4; [Pd(Thio)₄](NO₃)₂: a = 5.8013(4) Å, b = 7.0981(5) Å, c = 11.4991(8) Å, α = 99.963(2)°, β = 101.410(2)°, γ = 102.229(2)°, P -1 space group, Z = 1.

A single crystal X-ray diffraction study of the crystals of methyl 4-methyl-3,5-dioxo-1-phenyl-2-oxaspiro[5.5]undecane-4-carboxylate shows that phenyl and methoxycarbonyl substituents are in the equatorial position on the one side of the dioxopyran ring with twist boat conformation.

Single crystal X-ray diffraction is used to determine the crystal structure of 1-(4-bromo-9-methyl-11-thioxo-8-oxa-10,12-diazatricyclo[7.3.1.0^2.7]trideca-2,4,6-trien-13-yl)ethanone and identify its conformation characteristics.

Single crystal X-ray diffraction is used to determine the crystal structure of 4,5-bis-phenyl-8а-phenyl-3,4,4а,5,6,8а-hexahydro-1Н,8Н-pyrimido[4.5-d]pyrimidine-2,7-dione and identify its conformation characteristics.