Home – Home – Jornals – Journal of Structural Chemistry 2012 number 1

A DFT/B3LYP method using the 6-311++G(3df) basis set is employed to calculate the geometric, electronic, and thermodynamic parameters of O=NO-ON=O peroxide as an isomer of N₂O₄ dinitrogen tetraoxide. Calculations of the configuration interaction in a system of three paramagnetic particles with open shells have shown for the first time that the formation of cis-cis peroxide in the oxidation reaction of nitrogen oxide 2NO (²∏) + O₂ (³∑_g) → O=NO-ON=O (¹A) proceeds without an energy barrier in accordance with recently performed studies. The molecular orbital scheme of the barrierless activation of molecular oxygen and the driving force of the NO oxidation reaction are considered. A spontaneous character of the process is based on the idea of spin-catalysis when the reaction proceeds in the two-triplet state with total zero spin. The obtained results are in agreement with the experimental data on a spontaneous and irreversible process characterized by the observed negative activation energy.

DFT, SA-MCSCF, and MRMP/MCQDPT2 methods in the 6-311++G(2d) basis set are employed to consider the features of the formation reaction of key intermediates (SeOO, Se(O₂)) and photochemical dissociation of selenium dioxide with the formation of singlet oxygen. The cross-sections of potential energy surfaces of SeO₂, Se(O₂), and SeOO are constructed and the terms of their ground and excited states are analyzed at the SeOO dissociation limit with regard to spin-orbital interaction. Possible formation channels of ¹О₂ (¹Δ_g, reactive oxygen species during the decay of the excited states of selenium oxocomplexes are revealed. The effect of the spin-orbit interaction on the character of electronic spectrum transitions and zero field splitting in oxygen is estimated.

Equilibrium geometric parameters, normal mode frequencies and intensities in IR spectra, atomization enthalpy, and relative energies of low-lying electronic states of scandium fluoride molecules (ScF, ScF₂, and ScF₃) are calculated by the coupled-cluster method (CCSD(T)) in triple-, quadruple, and quintuple-zeta basis sets with the subsequent extrapolation of the calculation results to the complete basis set limit. The ScF molecule is also studied by the CCSDT technique. The error in the approximate calculation of triple excitations in the CCSD(T) method does not exceed 0.002 Å for the equilibrium internuclear distance R_e, 4 cm^-1 for the vibrational frequency, and 0.2 kcal/mol for the dissociation energy of the molecule. In the ground electronic state ²A₁(C_2v) of ScF₂ molecules, R_e(Sc-F) = 1.827 Å and α_e(F-Sc-F) = 124.2°; the energy barrier to bending (linearization) h = E_min(D_∞h) - E_min(C_2v) = 1652 cm^-1. The relative energies of ²Δ_g and ²Π_g electronic states are 3522 cm^-1 and 14633 cm^-1 respectively. The bond distance in the ScF₃ molecule (, D_3h) is refined: R_e(Sc-F) = 1.842 Å. The atomization enthalpies Δ_at of ScF_k molecules are 139.9 kcal/mol, 289.0 kcal/mol, and 444.8 kcal/mol for k = 1, 2, 3 respectively.

The effect of sublattices on the electronic structure of Zn₂SiO₄ crystals is ab initio studied from the first principles calculations at the density functional theory level. Based on the analysis of band spectra and sublattices the different role of Zn and Si cations in the formation of the valence band structure is determined, which is due to the crystal structure and atomic interactions in SiO₄ and ZnO₄ cationic tetrahedra.

Density functional calculations are performed to study the structures and electronic properties of Al_nCo_m clusters with n = 1-7 and m = 1, 2. Frequency analysis is also performed after structural optimization to make sure that the calculated ground states are real minima. The corresponding total and binding energies, adiabatic electron affinities and ionization potentials are presented and discussed to aid the identification of our calculations. The BSSE correction is also considered in our calculation. Among Al_nCo_m, Al_nCo, and Al_nCo clusters (n = 1-7 and m = 1-2), Al₄Co^-, Al₆Co^-, Al₂Co₂, and Al₆Co₂ are predicted to be more stable. Our results are consistent with the available experimental data.

The structure and thermodynamics of the following phosphorus oxide caged clusters were calculated in the gas phase at STP via both the local density approximation (LDA) and a generalized gradient approximation (BLYP) of density functional theory: the experimentally characterized trioxide (P₄O₆) and pentoxide (P₄O₁₀), and in order of thermodynamic preference, the hypothetical P₂₄O₆₀, P₈O₂₀, P₂₄O₄₈, and P₂₀O₂₀. All of the hypothetical oxides would dissociate to the pentoxide at equilibrium. Secondarily, the LDA calculation of the enthalpy of formation was unexpectedly superior to the BLYP calculation.

A theoretical study of the structure and vibrational spectrum of methyl-β-D-glucopyranoside is performed with allowance for the hydrogen bond effect on them. At the density functional theory level with the use of the B3LYP functional in the 6-31G(d) basis set the structural dynamic models of a free molecule of methyl-β-D-glucopyranoside and its simplest complexes with hydrogen bonding in the form of dimers with different structures are constructed. Energies are minimized; structures, electro optical parameters, force constants, and normal vibrational frequencies in the harmonic approximation and their intensities in IR spectra are calculated; the hydrogen bond energy is estimated. Based on the calculation, the conclusions are drawn about the structure of the methyl-β-D-glucopyranoside sample, the formation and interpretation of its IR spectrum, and the possibilities of the used density functional theory method.

The structure of the synthesized title compound is characterized by IR, UV-Visible spectroscopy, and single-crystal X-ray diffraction (XRD). The new compound (C₁₈H₂₃NS) crystalizes in the monoclinic P2₁/c space group. In addition to the crystal structure from the X-ray experiment, the molecular geometry, vibrational frequencies, atomic charge distribution, and frontier molecular orbital (FMO) analysis of the title compound in the ground state are calculated by density functional teory (B3LYP) with 6-311G(d,p) and 6-31G(d,p) basis sets. The results of the optimized molecular structure are presented and compared with the experimental values. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the observed experimental bands. To determine the conformational flexibility, the molecular energy profile of (1) is obtained by semi-empirical (AM1) and (PM3) calculations with respect to a selected degree of torsional freedom. Moreover, molecular electrostatic potential (MEP) and thermodynamic parameters of the title compound were calculated by the theoretical methods.

The crystal structure, luminescence properties of 2,2-difluoro-4,6-(4-methylphenyl)-1,3,2-dioxaborine (СH₃C₆H₄COCHCOC₆H₄CH₃BF₂) crystals and solutions at different concentrations are examined at T 296 K and 156 K.

By the example of four even members in a homologous series of sodium n-alkyl sulfates (decyl-, dodecyl-, tetradecyl-, and hexadecyl sulfate) and with the use of the Debye-Hueckel theory of strong electrolytes the parameters are calculated that determine electrostatic interactions in micellar solutions of surfactants. Calculation results for the Gibbs electrostatic energy of micellization are compared to those obtained from one of the approximate solutions of the Poisson-Boltzmann equation and also to the results of its numerical integration for spherical micelles. Applicability conditions of the Debye-Hueckel theory are determined with respect to the micelle concentration and size and the number of carbon atoms in a surfactant molecule. It is shown that the Debye-Hueckel theory in the proposed version enables an efficient and quite accurate calculation of all electrostatic properties of micelles and ionic micellar solutions for surfactants with a number of carbon atoms in a molecule starting from 10 and more and at concentrations up to 0.15 mol/dm³.

A molecular dynamics method is used to simulate liquid mixtures of benzene and chlorobenzene at different concentrations. Radial angular distribution functions (RADFs) for distances between the benzene ring planes and the angle between them were calculated to analyze the structure of pure components and mixtures. In chlorobenzene, the highest RADF maximum at a distance between the mass centers of the benzene rings of about 4 Å corresponds to the stacked configurations of molecules, and at 5-7 Å the number of stacked contacts are much less than that at 4 Å and is comparable with the orthogonal ones.
In liquid benzene, the number of stacked and orthogonal configurations is approximately equal in a range from 4 Å to 7 Å. RADF for benzene reveals extended regions of correlation, which gives evidence of the occurrence of agglomerates bound by specific interactions between the benzene rings. These agglomerates are not characteristic of chlorobenzene, but the presence of maxima on the radial distribution function for the distances between chlorine atoms indicates chlorine aggregation. The effect of halogen aggregation on the structure of benzene-chlorobenzene mixtures is considered. The obtained results are compared with the data on molecular light scattering.

An analysis of the formation of solid solutions in MAO₄-(Me_0.5Ln_0.5)AO₄ systems, where Me = Li, Na, K; M = Ca, Sr, Ba, Pb, Cd; Ln = La-Gd, Y, Bi; A = Mo, W, is performed in the approximation of regular solutions. Equations that make it possible to determine the temperature of the transition of limited solid solutions to unlimited ones at heterovalent substitutions M²⁺ ↔are obtained.

Crystal structures are determined by X-ray crystallography for tetrafluoroantimonates(III) of single and double protonated 3-amino-1,2,4-triazolium cations of the composition (C₂H₅N₄)SbF₄ (I) (monoclinic: a = 4.7723(6) Å, b = 19.643(2) Å, c = 7.6974(9) Å, β = 97.239(2)°, Z = 4, Cc space group) and (C₂H₆N₄)(SbF₄)₂ (II) (monoclinic: a = 4.7617(3) Å, b = 15.512(1) Å, c = 7.4365(5) Å, β = 107.706(1)°, Z = 2, P2₁/n space group). The structure of I is built from complex [SbF₄]⁻ anions and single charged (C₂H₅N₄)⁺ cations; the structure of II is built from the same anion and double charged 3-amino-1,2,4-triazolium cation: (C₂H₆N₄)²⁺. In the structure, weak interactions Sb⋯F join the anions in polymeric layers [SbF₄] that are assembled in a 3D framework by N-H⋯F hydrogen bonds. The formation of the double protonated 3-amino-1,2,4-triazolium cation (C₂H₆N₄)²⁺, found in the crystal structure of II, is observed for the first time.

Complex salts of the composition [Co(NH₃)₆](ReO₄)₃·2H₂O (I), [Co(en)₃](ReO₄)₃ (II), [Co(NH₃)₅H₂O](ReO₄)₃·2H₂O (III), and [Co(NH₃)₅Cl](ReO₄)₂·0.5H₂O (IV) are obtained. Their crystal structures are determined by single crystal XRD. Crystallographic characteristics: (I) a = 9.9797(3) Å, b = 12.6994(3) Å, c = 14.7415(4) Å, β = 102.870(1)°, C2/c space group; (II) a = 8.0615(3) Å, b = 8.4483(4) Å, c = 8.8267(4) Å, α = 61.923(2)°, β = 89.552(2)°, γ = 72.295(2)°, P1 space group; (III) a = 8.0086(4) Å, b = 12.9839(6) Å, c = 17.5122(7) Å, β=91.858(1)°, P2₁/n space group; (IV) a = 14.9446(3) Å, b = 14.6562(4) Å, c = 12.2434(4) Å, Cmc2₁ space group.

N,N,N′,N′-tetramethylethylenediamine is obtained by the reaction of ethylenediamine with formaldehyde and formic acid (the Eschweiler-Clarke reaction) and then alkylated with allyl chloride (or bromide) in a ratio of 1:1 or 1:2 to obtain N-allyl-N,N,N′,N′-tetramethylethylenediaminium and N,N′-diallyl-N,N,N′,N′-tetramethylethylenediaminium bromide respectively. [{C₂H₄N₂(H⁺)(CH₃)₄(C₃H₅)}Cu₄Cl₆] (1) and [{C₂H₄N₂(CH₃)₄(C₃H₅)₂}_0.5Cu₂Cl_1.67Br_1.33] (2) π-complexes are obtained from alcohol solutions containing an ethylenediamine derivative and copper(II) chloride by ac-electrochemical synthesis on copper wire electrodes. An XRD study of the complexes is carried out. The crystals are monoclinic; 1: P2₁/n space group, a = 9.0081(6) Å, b = 12.5608(7) Å, c = 16.8610(10) Å, β = 102.061(3)°, V = 1865.7(2) ų, Z = 4; 2: С2/с space group, a = 14.462(2) Å, b = 12.519(1) Å, c = 12.762(2) Å, β = 107.861(5)°, V = 2199.1(4) ų, Z = 8. The structure of 1 consists of infinite copper halide networks with four crystallographically independent copper atoms, one of which coordinates the double bond of the allyl group of the ligand. The [C₂H₄N₂(H)(CH₃)₄(C₃H₅)]²⁺ cations are attached above and below the plane of the network. The individual fragments are bonded via an extensive system of (N)H…Cl and (C)H…Cl hydrogen bonds. The structure of 2 contains a three-dimensional copper halide framework whose cavities contain the [C₂H₄N₂(CH₃)₄(C₃H₅)₂]²⁺ cations that are π-coordinated with copper(I) atoms. In both structures, the Cu(I) atom that coordinates the С=С bond has a trigonal-pyramidal coordination environment consisting of the double С=С bond of the corresponding ligand and three halogen atoms. The other Cu(I) atoms have a tetrahedral environment consisting solely of halogen atoms. The Cu-(C=C) distance is 1.958(1) Å (1) and 1.974(1) Å (2).

The crystal structures of compounds of the composition [Rh(H₂O)₆]₂(SO₄)₃·5H₂O (I) and [Rh(H₂O)₆]PO₄ (II) are determined. Crystallographic data for I: a = 7.272(9) Å, b = 27.047(1) Å, c = 12.464(9) Å, β = 97.038(10)°, P2₁ space group, Z = 4, d_x = 2.184 g/cm³; for II: a = 9.746(6) Å, b = 6.877(7) Å, c = 23.623(6) Å, β = 100.601(10)°, C2/c space group, Z = 8, d_x = 2.611 g/cm³. Compounds are analyzed by IR spectroscopy and powder XRD. Crystalline phase I is well soluble in water, whereas II is almost insoluble.

The structures of three novel octahedral rhenium cluster compounds [Re₆S₈(CN)₂(py)₄]·H₂O (1), [Re₆S₈(CN)₂(4-Mepy)₄] (2), [Re₆S₈(CN)₂(4-Mepy)₄]·4-Mepy (3) (py = pyridine, 4-Mepy = 4-methylpyridine) are determined by X-ray crystallography. Crystal data are: C2/m space group, a = 14.813(1) Å, b = 14.772(1) Å, с = 9.2122(6) Å, β = 119.085(2)°, V = 1761.7(2) ų, d_x = 3.318 g/cm³, R = 0.0585 (1); I4₁/amd space group, a = 16.0018(3) Å, c = 14.7186(5) Å, V = 3768.81(16) ų, d_x = 3.169 g/cm³, R = 0.0489 (2); P2₁/c space group, a = 9.0452(4) Å, b = 15.8065(7) Å, c = 15.2951(6) Å, β = 103.700(2)°, V = 2124.57(16) ų, d_x = 2.957 g/cm³, R = 0.0245 (3). Molecular cluster complexes interact via π-π stacking affording 3D frameworks in 1 and 2 and chains in 3.

The crystal structures of [CuL](NO₃)(ReO₄) and [CuL](ReO₄)₂ (L is 4,6,6-trimethyl-1,9-diamino-3,7-diazanon-3-en) are studied. The square coordination of the copper atom in [CuL](NO₃)(ReO₄) is completed to a distorted octahedron by two oxygen atoms: Cu…O 2.393 Å and Cu…O 2.685 Å, and that in [CuL](ReO₄)₂, by Cu…O 2.468 Å and 2.697 Å. The products of thermolysis of the salts in a hydrogen atmosphere at 800°C are mixtures of nanocrystalline metal powders with coherent scattering regions of ~45 nm.

The reaction products of 8-allylthioquinoline with mercury halides are studied by single crystal X-ray diffraction. It is shown that the products are organomercury derivatives of salts of 2,3-dihydro[1,4]-thiazino[2,3,4-ij]quinoliniuim

Two mercury(II) cyanide complexes of N-ethylthiourea (Ettu) and N-propylthiourea (Prtu) ligands, [Hg(Ettu)₂(CN)₂] (1) and [Hg(Prtu)₂(CN)₂] (2), were prepared and their crystal structures were determined by X-ray crystallography. In both structures, the mercury atom is coordinated to two sulfur atoms of thioureas and two cyanide carbon atoms in a pseudo-tetrahedral mode with the bond angles in the range of 90.52(11)-162.2(3)°. The structures are stabilized by N-H---S, N-H---N, and C-H---N intramolecular and intermolecular hydrogen bonds.

The structural study of two (C₃₀H₄₈O₂) pentacyclic triterpene (PCTT) isomers is presented. These terpenes, known as 30-hydroxy-lup-20(29)-en-3-one (1) and (11α)-11-hydroxy-lup-20(29)-en-3-one (2), were isolated from Maytenus imbricata Mart. Ex Reissek (Celastraceae). The molecular structure of 1 and 2 differs in the position of the hydroxyl group. Both compounds crystallize in non-centrosymmetric space groups with two molecules in the asymmetric unit. The crystal structure of 1 shows a triclinic P1 space group (a = 9.5518(1) Å, b = 9.7083(1) Å, c = 14.4696(2) Å, α = 93.832(1)°, β = 102.833(1)° and γ = 103.307(1)°), while compound 2 crystallizes in a monoclinic P2₁ one (a = 13.4439(16) Å, b = 14.4463(14) Å, c = 13.5224(9) Å and β = 99.703(8)°). The two molecules independent by symmetry of 1 differ slightly due to the presence of static disorder in oxygen atoms. In addition, the intermolecular geometries of 1 and 2 were analysed, and in each isomer the crystal packing is stabilized by O-H⋯O intermolecular hydrogen bonds and van der Waals forces.

Mass spectra of 5-substituted N(3)-acyl-4,6-diaryl-3,4-dihydropyrimidin-2(1H)-ones are studied. The features of the dissociative ionization of their molecular ions, which occurs with ketene elimination from the acyl group, are revealed. The subsequent fragmentation of fragment ions proceeds according to the rules established for pyrimidin-2(1H)-one derivatives.

Literature data on the apparent molar volumes φ of alanine in water and aqueous urea solutions at 298 K are analyzed. It is shown that the slope of the φ dependence on the alanine concentration is not dependent on the urea concentration. The standard partial volume of alanine increases linearly with the increase in the urea concentration (wt.%). The structural characteristics of hydrated complexes of alanine (hydration number, molar volume of water inside and outside the hydration sphere, and proper volume of alanine in solution) are given. The hydration number of alanine decreases by a factor of two in passing from water to a saturated (20m) urea solution. The effects of urea additions on the hydration numbers of alanine and glycine are compared.

A new 2D metal-organic coordination polymer [Cu(trtr)₂]_n (1) (Htrtr = 3-(1,2,4-triazolyl-4-yl)-1H-1,2,4-triazole) is synthesized through the hydrothermal reaction of Cu(ClO₄)₂ with Htrtr. The crystal structure of 1 is determined by a direct method from X-ray diffraction data (Rigaku Mercury CCD, MoK_α radiation). 1 crystallizes in the monoclinic C2/c space group with unit cell parameters: a = 14.158(2) Å, b = 9.8050(14) Å, c = 11.413(3) Å, β = 127.9870(10)°, v = 1248.7(4) ų, z = 4, D_cal = 1.775 g/cm³. 1 features a 2D grid based on the propagation of 28-membered rings, which is further fabricated into a 3D supramolecular framework via the hydrogen bond linkage. The fluorescence of 1 shows a blue emission at 441 nm with a 14 nm red-shift compared to that of free Htrtr, which can be assigned to LMCT.

The crystal structure of [Ni(en)₃](ReO₄)₂ (en is ethylenediamine) is studied: a = 8.3997(2)Å, b = 15.6167(5) Å, c = 14.2406(4) Å, β = 100.378(1)°, V = 1837.46(9) ų, P2₁/c space group, Z = 4, and d_x = 2.673 g/cm³. It is shown that packing of the complex cations can be considered as single-layer pseudohexagonal. Thermal decomposition of the salt in a hydrogen atmosphere at 550°C is used to obtain a mixture of nickel with a nanocrystalline Re_0.87Ni_0.13 solid solution (a = 2.733(2) Å, c = 4.400(3) Å, Р6₃/mmc space group; CSR size is ~14 nm).

It is found that M(AmH)₂(3,5-DNB)₄·8H₂O compounds (where M(II) = Co, Ni; AmH is piperidine PipH = (C₅H₁₀NH₂)⁺ or diethylamine DaH = (C₄H₁₀NH₂)⁺ cations; 3,5-DNB = (C₇H₃N₂O₆)^- is the dinitrobenzoic acid anion) are isotypic. The structure of the Ni(PipH)₂(3,5-DNB)₄·8H₂O single crystal is studied. The crystals have a monoclinic system, P2₁/n space group, Z = 2, a = 6.7694(3) Å, b = 16.0746(6) Å, c = 23.1250(9) Å, β = 97.794(1)°, V = 2493.1(2) ų, T = 153 K. The final value R(F) = 0.0407 was obtained for 8191 independent reflections with I > 2σ(I). The structural units of the compound studied are as follows: [Ni(OH₂)₆]²⁺ complex hexaaquacation, two (PipH)⁺ cations, four (3,5-DNB)^- anions, and two molecules of water of crystallization with the structural formula [Ni(OH₂)₆](PipH)₂(3,5-DNB)₄·2H₂O. Similar compounds of Ni(II) and Co(II) are isostructural.

The crystal and molecular structure of the complex of 2-(1-silatranylmethylthio)-4,5-benzo-1,3-thiazole with СоСl₂ and MeCN (I) is determined by single crystal X-ray diffraction. The geometry of the silatranylmethyl moiety in complex I is compared to the geometry of 1-(2′-benzthiazolylthiomethyl)silatrane. Molecular packing in the crystal is analyzed.

Crystal structures of two solvates (Bu₄N)₂[Mo₆Cl₈(O₃SC₆H₄CH₃)₆]·2CH₃CN (1) and (Bu₄N)₂[Mo₆Cl₈(O₃SC₆H₄CH₃)₆]·2CH₂Cl₂ (2) are determined. Both compounds contain cluster [Mo₆Cl₈(O₃SC₆H₄CH₃)₆]^2- anions. Molybdenum atoms are coordinated with monodentate carboxylate ligands (Mo-O 2.101(3)-2.110(3) Å in 1; 2.088(7)-2.109(2) Å in 2).

Single crystal X-ray diffraction is used to determine the crystal and molecular structure of 4-trifluoro-2-[2-(4-fluorophenyl)hydrazine-1-ylidene]-1-(thiophen-2-yl)butane-1,3-dione. Crystallographic data for C₁₄H₈F₄N₂O₂S are as follows: a = 8.2723(6) Å, b = 9.3009(7) Å, c = 9.9895(7) Å; α = 79.224(2)°, β = 75.851(2)°, γ = 72.337(2)°. Triclinic crystal system, P-1 space group, d_x = 1.622 g/cm³, V = 704.83(9) ų, μ = 0.286 mm^-1, crystal size 0.30×0.20×0.20 mm, R1 = 0.0891, wR2 = 0.1989.