Home – Home – Jornals – Journal of Structural Chemistry 2008 number 4

The electronic structure of anthracene, its dimer, and intermediate structures composed of two anthracene molecules were calculated in the density functional theory. The calculated potential barrier to anthracene dimerization is ~55 kcal/mol; the dissociation barrier is ~45 kcal/mol. The pressure required for the reaction to reach the transition state and acting on the anthracene crystal is ~60 kbar. Lower pressures, ~10 kbar, are required for molecules to approach each other to distances of ~3 Å, at which tunnel dimerization is possible for photoexcited molecules.

The electron density distribution in [Re₄Q₄X₁₂]^4- cubane-like clusters (Q = S, Se, Te; X = F, CN) was investigated by the AIM and ELF topological quantum-chemical methods. The Re-Re, Re-Q, and Re-X interatomic interactions are characterized by bcp type critical binding points and are strained.

The profile of the reaction СН₃ОН + МОН → СН₃ОМ + Н₂О in the presence of an alkali (МОН, М = Li, Na, K) was investigated by the ab initio quantum-chemical method for the gas phase (with allowance for the solvent) within the continuum model. The proton transfer and the formation of the alkaline methoxide molecule in МОН/DMSO/СН₃ОН systems (М = Li, Na, K) in the alkali-methanol pre-reaction complexes can take place without their preliminary dissociation and are barrier-free reactions.

The parameters of the geometrical configuration of octachlorotrisilane Si₃Cl₈ were determined by quantum-chemical and gas-phase electron diffraction methods at 303±2 K. The calculated barrier to the internal rotation of SiCl₃ groups relative to the Si-Si bond was calculated.

The geometrical structure, force fields, and vibrational spectra of CeX₄ (X = F, Cl, Br, I) were investigated by second, third, and fourth order Möller-Plesset perturbation theory, CISD+Q configuration interaction method, and the CCSD(T) coupled cluster method. Calculations on CeF₄ were also performed by multiconfiguration second order perturbation theory MCQDPT2/CASSCF. The wave function of the ground state of CeX₄ molecules was found to be appreciably non-one-configurational; this property increases from cerium fluorides to iodides and leads to the divergence of the series of Möller-Plesset perturbation theory. The calculated data point to a tetrahedral equilibrium nuclear configuration in CeX₄ molecules. The energy barriers to the inversion of the tetrahedral CeX₄ molecules via the square configurations are high enough, 74-89 kJ/mol. The calculated vibration frequencies, effective internuclear distances, and mean amplitudes of nuclear vibrations in CeF₄ agree with IR and Raman spectroscopic and high-temperature gas-phase electron diffraction data.

A theoretical study of the interaction between N–nitrosodiethanolamine (NDELA) molecule and one to five molecules of water has been performed at the B3LYP level using a large polarized basis set. The calculated complexation energies (corrected for BSSE and ZPVE)
of NDELA with one, two, three, four and five molecules of water are –4.62, –9.83, –15.29, –21.60, and –25.10 kcal/mol respectively at the B3LYP/6–311++G** level. In all complexes studied there are red shifts in the vibrational frequencies of the O–Hs of NDELA and water molecules along with increases in the corresponding IR intensities.

The IR spectra of L- and DL-serines HN-CH(CH₂OH)-COO^- (without diluents) were investigated in the temperature range 93-413 K; the changes in the IR spectra due to temperature variations were correlated with previously obtained diffraction data on anisotropic compression of structure and changes in the geometrical parameters of the hydrogen bonds.

The microwave spectrum of 5-methyl-1,3-dioxane was studied in the frequency range 12-35 GHz. The а and с type rotation transitions with J ≤ 30 were identified. The rotational constants А =
4658.5244(33) MHz, В = 2383.3930(12) MHz, and С = 1724.28907(88) MHz and the quartic constants of the centrifugal distortion of the molecule in the ground vibrational state were determined. The components of the dipole moment were found, μ_а = 1.76 ± 0.01 D and μ_с = 1.10 ± 0.01 D; the net dipole moment of the molecule is μ = 2.08 ± 0.01 D. 5-Methyl-1,3-dioxane was calculated by the B3PW91/aug-cc-pVDZ density functional theory method. The calculated data are compared with the experimental data. The most stable conformation is the chair conformation with an equatorial orientation of the methyl group.

The spatial isomers of the new synthetic analogs of ethyl permithrinic ether and permethrin were investigated by NMR (¹Н, ¹³С, DEPT (distortionless enhancement by polarization transfer), COSY (correlation spectroscopy), CHCORR (heteronuclear (C, H) shift correlation spectroscopy), ROESY (rotating-frame Overhauser effect spectroscopy)). Several tendencies were revealed in the ¹Н and ¹³С chemical shifts of the α atoms of the substituents in the 2nd and 3rd positions of the cyclopropane ring. For substituents cis-orientated relative to the ester group, the spectra show a paramagnetic shift of the ¹Н signals and the diamagnetic shift of the ¹³С signals relative to the trans-orientated substituents. The ¹Н and ¹³С chemical shifts of the α atoms of the substituents in the 2nd and 3rd positions of the cyclopropane ring permit an unambiguous determination of the stereochemistry of ethyl permethrinic ether and permethrin analogs.

The antisymmetry of proton configurations was studied for the hexagonal water rings with different conformations. The change in the direction of all hydrogen bonds was used as an additional symmetry operation. The ring configuration energies were calculated using the intermolecular interaction potentials. For different ring conformations, the relationships between antisymmetry and energy were analyzed and compared.

The antisymmetry of small water clusters of various configurations with three to five molecules, which are stable according to the ab initio calculated data, was analyzed. The antisymmetry operation was alteration of the direction of all hydrogen bonds including the direction of the external unrealized Н-bonds. It was found that most configurations of small clusters were antisymmetric. Other configurations form pairs of antipode configurations with very close energies.

The apparent molar volume of urea φ in aqueous solution in the range Т = 273-323 K and m = 1-10 (molality) depends linearly on m^1/2. An equation for φ(m, T) was derived. The partial molar characteristics of urea and water (volume, dilatability, and temperature coefficients of volumes) were calculated. The dependences have characteristic points (extrema, inflection points), shifted to the region of lower temperatures for dilute solutions. The dependences for 2m and 4m of the urea solution retain the characteristics of the Y₁(T) of pure water. In these solutions, the proper structure of water is preserved.

In equations for the partial volume, dilatability, heat capacity, and adiabatic compressibility of aqueous urea, the properties are "fitted" to the singular temperature T_s of overcooled water T_s = 227.15 K
(R. J. Speedy, J. Phys. Chem., 91, 3354 (1987)). The equations for the characteristics of D₂O-(ND₂)₂CO and Т₂O-(NТ₂)₂CO systems were obtained by scaling the temperature to 6 and 9.4 K, respectively. The properties of infinitely dilute solutions did not reveal the sign reversal of the isotope effect. The isoconcentrates of the partial volumes and dilatability form wagging lines in the region of low temperatures. The temperature dependences of the properties have extrema and inflection points, while the isotope effects in solutions of finite concentrations experience sign reversal. The maximum density temperature (MDT) of the solution decreases as the urea concentration increases, and also on passing from D₂O-(ND₂)₂CO to H₂O-(NH₂)₂CO. Thus, for the 8m solution, the MDT is 259.6 K (protium system) and 266.7 K (deuterium system). The difference is almost equal to the shift of the MDT after the H₂O → D₂O transition (7.2 K).

The concentration dependence of normalized absorbance (to the total number of moles of components in one liter) of HF solutions in acetonitrile (1:12-10:1) is analyzed. It is found that in the binary liquid system (BLS) under study molecular complexes with stoichiometric 1:1 and ~10:1 ratios of molecules occur along with the heteroassociates (HAs) found previously with the ratio HF:CH₃CN of 4:1. For each of the HAs the concentration range at which it is formed in BLS is evaluated, and the positions of HF stretching vibrational bands are found. Optimum configurations and vibrational frequencies of molecular complexes (HF)_m⋅(CH₃CN)_n (m = 1-6, n = 1-2) of various topology are calculated using the density functional method (B3LYP/6-31 ++ G (d, p)). Their relative stability and the structure peculiarities are studied; complexation tendencies in the HF-CH₃CN system are revealed. The structure of HAs with 1:1 and 4:1 stoichiometric ratios of molecules is determined by comparing the results of calculations and experiment.

Interaction and reorganization contributions to solvation enthalpies of nonelectrolytes in aqueous solutions of amides of carboxylic acids with different degree of N-substitution and N-methylpyrrolidone are calculated. The data are discussed using structurally thermodynamic characteristics of water-amide systems obtained by us previously. It is found that the type of concentration dependence of the solvation enthalpy of nonelectrolytes in all solutions investigated is determined by the type of reorganization component. It is shown that the highest solvation exothermicity of nonelectrolytes in water is due to the lowest value of the reorganization contribution in spite of that nonelectrolytes interact weaker with water than with non aqueous components.

Rubidium and cesium chlorites are prepared and studied by single crystal and powder X-ray diffraction. The compounds are isostructural; crystallize in the orthorhombic system; space group Cmcm, Z = 4. Unit cell parameters: a = 6.3464(8) Å, b = 6.4223(8) Å, c = 7.7493(9) Å for RbClO₂ and a = 6.5998(9) Å, b = 6.6116(9) Å, c = 8.3161(11) Å for CsClO₂. The structures can be represented as 3D frameworks formed by metal cations and chlorite anions acting as tetradentate bridging and bidentate chelating oxygen ligands.

The structure of Nb₂Mo₃O₁₄ double oxide is refined from powder data using synchrotron radiation and the anomalous scattering effect; space group P2₁m is found for the material. It is demonstrated that in the tetragonal unit cell with parameters а = 23.173 Å, с = 4.0027 Å Nb⁵⁺ and Мо⁶⁺ ions are stochastically distributed in МО₆ octahedra and МО₇ pentagonal bipyramids of the polygonal network structure of the Мо₅О₁₄ type.

Four structural models of volborthite Cu₃(OH)₂(V₂O₇)⋅2H₂O (a = 10.646(2) Å, b = 5.867(1) Å, c =
14.432(2) Å, β = 95.19(1)°, V = 897.7(5) ų, Z = 4, R/R_w = 0.038/0.046) calculated in the space groups determined from the systematic absences are compared. Based on the structure balance and the similarity of constituting polyhedra, values of the R factor, and isotropic thermal parameters, the space group Ia is found to be preferable, which is the only possible asymmetric and uniform variant. Hydrogen atoms of ОН-groups, oxygen atoms and, partially, hydrogen atoms of water are localized.

A polyhydrate of the tetraisoamylammonium salt of linear (uncrosslinked) polyacrylate (~25 monomeric units in the polyacrylate chain) is described and compared to polyhydrates of cross-linked tetraisoamylammonium polyacrylates (0.5-3% of cross-linking with divinylbenzene or divinylsulfide). Powder X-ray diffraction reveals that the polyhydrate containing a linear polyacrylate molecule has the same structure (hexagonal, a = 12.26 Å, c = 12.71 Å at 3°C) as polyhydrates of the cross-linked polyacrylate molecules. A single crystal of the polyhydrate obtained from an aqueous solution of linear tetraisoamylammonium polyacrylate is studied by X-ray diffraction at -173°C. The structure is hexagonal; space group P-6m2; the polyhydrate framework is a slightly distorted variant of the hexagonal structure-I of clathrate hydrates.

The complex Ru₄(μ₄-S)(μ,η³-C₃H₅)₂(CO)₁₂ is prepared and examined by IR and NMR spectroscopy; its crystal structure is determined (an automatic Bruker-Nonius X8 Apex four-circle diffractometer equipped with a 2-D CCD-detector, 100 K, graphite-monochromated molybdenum source, λ = 0.71073 Å). The crystal belongs to the orthorhombic crystal system with unit cell parameters a = 19.3781(9) Å, b = 12.2898(7) Å, c = 10.1726(4) Å, V = 2422.6(2) ų, space group Pnma, Z = 4, composition C₁₈H₁₀O₁₂Ru₄S, d_x = 2.343 g/cm³. The molecule of point symmetry C₁ is situated on the mirror plane of the space group Pnma, two carbonyl groups at Ru2 and Ru3 atoms overlapping with the allylic ligand with a weight of 50% so that carbon atoms coincide. Thus, we have a racemic structure with two overlapping enantiomers of the molecule of Ru₄(μ₄-S)(μ,η³-C₃H₅)₂(CO)₁₂.

The title compounds, (NH₄)₂[Mn^II(edta)(H₂O)]⋅3H₂O (H₄edta = ethylenediamine-N,N,N′,N′-tetraacetic acid), (NH₄)₂[Mn^II(cydta)(H₂O)]⋅4H₂O (H₄cydta = trans-1,2-cyclohexanediamine-N,N,N′,N′-tetraacetic acid) and K₂[Mn^II(Hdtpa)]⋅3.5H₂O (H₅dtpa = diethylenetriamine-N,N,N′,N″,N″-pentaacetic acid), were prepared; their compositions and structures were determined by elemental analysis and single-crystal X-ray diffraction technique. In these three complexes, the Mn²⁺ ions are all seven-coordinated and have a pseudo-monocapped trigonal prismatic configuration. All the three complexes crystallize in triclinic system in P-1 space group. Crystal data: (NH₄)₂[Mn^II(edta)(H₂O)]⋅3H₂O complex, a = 8.774(3) Å, b = 9.007(3) Å, c = 13.483(4) Å, α = 80.095(4)°, β = 80.708(4)°, γ = 68.770(4)°, V = 972.6(5) ų, Z = 2, D_c
= 1.541 g/cm³, μ = 0.745 mm^-1, R = 0.033 and wR = 0.099 for 3406 observed reflections with I ≥ 2σ(I); (NH₄)₂[Mn^II(cydta)(H₂O)]⋅4H₂O complex, a = 8.9720(18) Å, b = 9.4380(19) Å, c = 14.931(3) Å, α = 76.99(3)°, β = 83.27(3)°, γ = 75.62(3)°, V = 1190.8(4) ų, Z = 2, D_c = 1.426 g/cm³, μ = 0.625 mm^-1, R = 0.061 and wR = 0.197 for 3240 observed reflections with I ≥ 2σ(I); K₂[Mn^II(Hdtpa)]⋅3.5H₂O complex, a = 8.672(3) Å, b = 9.059(3) Å, c = 15.074(6) Å, α = 95.813(6)°, β = 96.665(6)°, γ = 99.212(6)°, V = 1152.4(7) ų, Z = 2, D_c = 1.687 g/cm³, μ = 1.006 mm^-1, R = 0.037 and wR = 0.090 for 4654 observed reflections with I ≥ 2σ(I).

The molecular structure of 1-methyl-1-fluoroquasisilatrane (2-methyl-2-fluoro-1,3-dioxa-6-aza-2-silacyclooctane) MeFSi(OCH₂CH₂)₂NH (I) is determined by single crystal X-ray diffraction at 100 K. The coordination polyhedron of the silicon atom in this molecule is a slightly distorted trigonal bipyramid with an NH group and a strongly electron-withdrawing fluorine atom in the axial positions, and two endocyclic oxygen atoms and a СН₃ group in three vertices of the equatorial plane. The axial angle N→SiF is 171°. The length of the transannular donor-acceptor bond N→Si (2.058 Å) is as small as in 1-fluorosilatrane. The axial bond F-Si (1.660 Å) is longer than that in 1-fluorosilatrane and tetrahedral silicon compounds.

In large-scale molecular objects (nanostructures) such as dendromers, supramolecules, polymers, nanotubes, etc. external perturbations may have local character. When the perturbation is removed, atomic wave motions of a rather complex type may arise in the nanostructure. They can not only transfer signals inside the nanoobject, but also generate standing waves and antinodes and accumulate energy in other domains of the nanostructure, i.e., give rise to energy traps. These problems have not been addressed before. In this paper we propose a method to calculate the time-dependent evolution of these phenomena for large-scale molecular structures of arbitrary structure and size.

X-ray diffraction analysis of four perfluorinated homophthalic (2-carboxymethylbenzoic) acids is carried out. In the crystals of 2-carboxymethyl-3,4,5,6-tetrafluorobenzoic acid (1) the chains (1D architecture) form with the usual dimeric carboxylic C(O)OH:::O(HO)C synthon. The aromatic carboxylic group is disordered in the ratio 0.58:0.42 over two positions. In the crystals of 2-(carboxydifluoromethyl)-3,4,5,6-tetrafluorobenzoic (2) and 2-(1-carboxy-2,2,2-trifluoroethyl)-3,4,5,6-tetrafluorobenzoic acids (3) the layers (2D architecture) with dimeric and chain-like synthons C(O)OH…O(HO)C are found. In the crystals of 2-[methoxycarbonyl(difluoromethyl)]-3,4,5,6-tetrafluorobenzoic acid (4) only dimers (0D architecture) form with the chain synthon that incorporates both an ester and a carboxylic group. In the crystals of 1 and 2 intermolecular Н-O…π interactions, in the crystals of 4 C-F…π interactions, and in 3 both types of interactions are observed.

By the reaction of [Mo₃S₄(C₂O₄)₃(H₂O)₃]^2- with PdCl₂ and NH₄H₂PO₂ as a reducing agent, followed by the addition of PPh₃, a new oxalate cuboidal cluster complex [Mo₃(PdPPh₃)S₄(C₂O₄)₃(H₂O)₃]^2- is obtained. It was isolated and structurally characterized as K₂[Mo₃(PdPPh₃)S₄(C₂O₄)₃(H₂O)₃]⋅0.5H₂O.

By the high-temperature reaction of Nb₂S₄Br₄ and TlBr a thallium salt of the anionic cluster complex [Nb₂S₄Br₈]^4- is obtained. Its crystal structure is determined by X-ray structural analysis. The complex is also characterized by Raman spectroscopy and electrospray-mass-spectrometry.

By means of X-ray diffraction the chain structure of [Cu(l-Arg)₂]Hg₂Cl₆ (monoclinic, a = 10.2348(9) Å, b = 9.1386(7) Å, c = 14.8521(14) Å, β = 97.455(11)°, space group P2₁) is established. The chains are formed by square-planar [Cu(l-Arg)₂]²⁺ cations of the type trans-[Cu(N)₂(О)₂] (l-Аrg is the zwitter-ion of arginine; Cu-N 1.992 Å and 1.938(6) Å, Cu-O 1.953 Å and 1.967(4) Å) that are bonded to two adjacent binuclear [Cl₂Hg(μ-Cl)₂HgCl₂]^2- ions through its clorine atoms Cl (Hg-Cl bonds are within 2.34-2.78 Å). With these two additional Cu…Cl contacts Cu adopts the geometry of an elongated octahedron with two apical Cl (Cu-Cl 2.961 Å and 3.064(3) Å).

The X-ray analysis of a single crystal of Mg(C₁₂H₁₃N₄O₄S)₂⋅11H₂O, where (C₁₂H₁₃N₄O₄S)^- is the anion of 4-p-aminobenzenesulfamido-2,6-dimethoxypyrimidine (sulfadimethoxine) is carried out. Unit cell parameters are: а = 19.753(4) Å, b = 34.031(7) Å, c = 13.859(3) Å; β = 125.37(3)°, C2/c, Z = 8, R(F) = 0.042. The structure is built of [Mg(OH₂)₆]²⁺, (C₁₂H₁₃N₄O₄S)^-, and water molecules and corresponds to the formula [Mg(OH₂)₆](C₁₂H₁₃N₄O₄S)₂⋅5H₂O. The IR bands of ν_asymSO₂ and ν_symSO₂ are bathochromically shifted as a result of their participation in hydrogen bonding, and not because of any direct coordination of sulfadimethoxinate anion to the complexing atom through oxygen.

The structure of the syn-isomer of 2-N,N′-dimethylamino-5-methylbenzophenone oxime is studied by X-ray diffraction and mass-spectrometry. This molecular compound crystallizes in the triclinic system. Unit cell parameters are: a = 19.5318(10) Å, с = 19.5439(17) Å, V = 6456.9(7) ų, Z = 18, space group The molecules are linked into centrosymmetric pseudo dimers by hydrogen bonds О-H…N formed by the oxime groups. The pathway of the electron-impact induced decomposition of the compound is discussed.

An X-ray diffraction analysis and quantum chemical calculations of hydrated 2-thenoyltrifluoroacetone show that the planar diketone, form of ТТА found in its metal complexes, does not occur in the free ligand. Hydrated ТТА with two geminal hydroxo groups has a non-planar structure stabilized by an intramolecular hydrogen bond.

X-ray structure of 6,11-dihydro-6,11-methano-5H-benzo[5,6]cyclohepta[1,2-b]pyridinol-11 is determined.

Two benzodiazepine derivatives, C₂₃H₂₂N₂O (I), 2-methyl-8-methoxy-2,4-diphenyl-2,3-dihydro-1H-1,5-benzodiazepine, and C₂₂H₁₇N₃O₂Br₂ (II), 2-methyl-7-nitro-2,4-bis(4′-bromophenyl)-2,3-dihydro-1H-1,5-benzodiazepine, were studied by single crystal X-ray diffraction method. Compound (I) crystallizes in the monoclinic system, space group P2₁/c, a = 13.1703(17), b = 11.1990(14), c = 12.9093(16) Å, β = 107.831(2)°, V = 1812.6(3) ų, Z = 4. Compound (II) crystallizes in the monoclinic system, space group P2₁/n, a = 11.7345(12), b = 12.7477(13), c = 13.5965(14) Å, β = 95.221(2)°, V = 2025.4(4) ų, Z = 4. The molecules of (I) and (II) have T-shape form with the diazepine ring at the junction point. The seven membered central benzodiazepine ring in both structures adopt a twist-boat conformation. The crystal packing is stabilized by C-H…π (in I) and C-H…O (in II) interactions.