Home – Home – Jornals – Journal of Structural Chemistry 2010 number 4

Some conceptual issues are discussed in the context of the statement of quantum problems in the theory of molecular structure and properties. It is emphasized that the analysis of complex systems requires supplementary information from other fields of science in order to refine the problem definition. It is shown that the statements of quantum problems making them practically applicable for prediction can only result from a combination of the operator (differential equations) and matrix formalism, while these approaches are complementary rather than equivalent. A natural structure of vibronic wave functions is proposed in the form of a linear combination of well-defined basis functions.

DFT/BLYP/DNP method was employed to calculate the total energy of cyclotetramethylene tetranitramine (HMX) derivatives modified with amido groups and the bond dissociation energy of the weakest N-NO₂ bond. The bond dissociation energy decreases with the number of amido groups. Isodesmic reactions were used to calculate standard molar enthalpies of formation of the derivatives; these values increase with the number of amido groups but not according to additivity rules. Entropy and heat capacity were also investigated. NBO analysis was applied to study the bond orders and the second perturbation energy of the N-NO₂ bonds; these parameters decrease regularly with the number of amido groups. Taking a single amido derivative as an example to analyze the vibration frequencies, it is shown that all the strongest vibrations are related with the N-NO₂ bonds.

An ab initio study of the structure of Mn(thd)₂, Fe(thd)₂, and Co(thd)₂ complexes in different electronic states is carried out. Quantum chemical calculations are performed using the PC GAMESS program with relativistic effective core pseudopotentials and Gaussian valence triple-zeta basis sets. Calculation methods: DFT/ROB3LYP and CASSCF followed by the inclusion of dynamic electron correlation through multiconfiguration quasi-degenerate second order perturbation theory (MCQDPT2). All three complexes are shown to have a low-spin electronic ground state with a planar structure of the bicyclic fragment at D_2h molecular symmetry. The M-О bond is mainly ionic, and M(thd)₂ molecules can be considered as an М²⁺ cation coordinated by two negatively charged bidentate ligands.

Calculations of the anthracene crystal structure, 10% isotropic compression of the anthracene crystal and its two dimers linked not through the central atoms of central rings are performed in the density functional theory approximation. Linear lattice parameters a, b, c, interatomic distances, and bond angles coincide with those determined by single crystal X-ray diffraction and previously calculated for an isolated anthracene molecule. The parameter γ is different by 12°, which is due to a weak dependence of the lattice energy on γ (the energy of only a few kcal per mole is required to turn the lattice at this angle). The calculated lattice energy (15 kcal/mol) is close to the enthalpy of sublimation. Dimers of another configuration than those linked through the central atoms of central rings are less energetically favorable. The formation of dimers at high pressure and shear deformation of "sandwiches" composed of anthracene molecules located above each other is shown, and a two-step dimerization scheme is proposed.

One of the current versions of additive schemes to estimate gas chromatographic retention indices of organic compounds not characterized by these constants assumes their structure to be assembled from simpler precursors, and subsequent arithmetical operations are performed with the known indices by the selected schemes. In order to optimize the use of such an algorithm (to confirm the correctness of the selection of structural analogs, to eliminate superposition uncertainty, etc.) it is proposed to use the linear coding system for not complete molecular structures, but only those fragments that mostly affect the chromatographic retention parameters.

The NMR method is used to study the features of the complexation kinetics of paramagnetic lanthanide cations with EDTA in aqueous media at temperature and pD variation. The acidity of solutions is determined by the potentiometric method with a glass electrode. By the dynamic NMR method it is found that the activation enthalpy of the association between EDTA complexones and Ln cations is ΔH^{‡ = 71±5 kJ/mol in a temperature range from 290 K to 368 K (at pD = 1.6). The obtained results indicate that Ho and Pr complexes with EDTA are promising compounds as in vivo NMR thermosensors for biology and medicine.}

X-Ray photoelectron spectroscopy (XPS) is used to study the electronic structure of radiation damaged samples of ZrSiO₄ zircon mineral at early and middle stages of its radiation destruction. The effects of radiation induced atomic disordering are found to be most distinctly manifested in the spectra of O1s states and to a smaller extent in the spectra of Si2p states, and also in the zircon valence band. Based on the quantum chemical calculation results the conclusion is drawn that the observed changes in XPS lines are caused by the formation of oxygen vacancy defects and an increase in the covalency of interatomic bonds near oxygen vacancies. For zircon samples with a low/moderate degree of radiation damage these changes reflect the initial stage of the polymerization of the ZrSiO₄ structure due to the formation of Si-O-Si chain fragments.

Polymorphism is an important characteristic of pharmaceutical products because different polymorphs exhibit different physicochemical stabilities, dissolution rates, etc., which makes them different in therapeutic efficiency. Thus, it is important to control the polymorphic structure of pharmaceutical products. A spectroscopy method based on Fourier transform near infrared (FT-NIR) spectroscopy and chemometric techniques is introduced to classify paracetamol preparations according to polymorphic changes. X-ray diffraction (XRD) and FT-NIR studies were carried out on standard samples, paracetamol preparations (acetaminophen tablet), and also the additives. A direct comparison was performed between the spectroscopic data and those obtained by XRD. The NIR and XRD analyses of paracetamol preparations show some distinct differences, particularly in the Iranian tablet. These differences are found to be related to polymorphism and paracetamol purity. The cluster analysis (CA) and principal component analysis (PCA) were utilized to classify the paracetamol preparations. FT-NIR spectroscopy provides a simple, rapid and accurate qualitative analysis method for the identification of paracetamol polymorphs.

Using the expended chemical bond dielectric theory of complex crystals, we have calculated chemical bond parameters and Mössbauer isomer shift of LnOFeAs as well as AFe₂As₂ which had been chosen due to their layered structures. Results are in good agreement with available experimental data, demonstrating the accuracy of our calculations and theories. The relationship between chemical bond parameters and Mössbauer isomer shift is discussed.

Possible polymorphic transformations of crystals with the non-polar structure of the low-temperature modification are found. The conditions of single domain formation and switching of the bistable structure of these crystals are determined and tabulated. The relations between the characteristics of the low-temperature modifications of secondary and high-order ferroics are established.

The crystal structure of laffittite mineral AgHg(As,Sb)S₃ from the Chauvai deposit (Kyrgyzstan), containing about 10% of Sb atoms in the As³⁺ position, is re-determined (Aa space group, a = 7.7560(3) Å, b = 11.3340(4) Å, c = 6.6650(3) Å, β = 115.233(4)°, V =529.99(4) ų, d = 6.078 g/cm³, Z = 4, R = 0.0229). Crystallographic analysis of the structure reveales the presence of quite regular face-centered cubic cation and anion sublattices, thus confirming the assignment of the structure to the structural type of PbS.
A deviation from the octahedral coordination of cations characteristic of this type is mainly related to a mutual asymmetric displacement of the cation and anion matrices.

The crystal structure of rubidium-ammonium hexachlorotellurate [Rb_0.94(NH₄)_0.06]₂TeCl₆ was determined by X-ray single crystal analysis at room temperature. The space group is Fmm with the lattice parameter a = 10.2503(5) Å and Z = 4. The refinement converged to R(F) = 0.015 and wR(F²) = 0.032. As in the studied [Rb_0.94(NH₄)_0.06]₂TeCl₆ family, this compound has an antifluorite-type arrangement. Tellurium atoms are surrounded by an octahedron of chlorine atoms. The Rb or N atoms are located between TeCl octahedra ensuring the stabilization of the structure by ionic and hydrogen bonding contacts N-H…Cl. The substitution of rubidium by ammonium groups does not affect the structural arrangement, but it leads to a decrease in the a lattice cell dimension. IR and Raman spectroscopic studies at room temperature were performed to confirm the X-ray crystallographic results.

In the MCl-CuCl-HOCH₂C≡CCH₂OH (M = Ca²⁺, C₇H₅N₂H) system, the crystals of two anionic Ca[CuCl₂(HOCH₂C≡CCH₂OH)]₂·4H₂O (1) and (BimH)[CuCl₂(HOCH₂C≡CCH₂OH)] (2) (BimH⁺ is cation of benzimidazole-C₇H₅N₂H) πcomplexes are obtained and studied by single crystal X-ray diffraction. Crystals of 1 are monoclinic: C2/c space group, a = 8.323(3) Å, b = 13.283(4) Å, c = 16.741(5) Å, β = 92.35(3)°, V = 1849.3(10) ų, Z = 4; crystals of 2 are triclinic: space group, a = 6.901(3) Å, b = 9.898(4)Å, c = 9.987(4) Å, α = 94.91(3)°, β = 93.91(3)°, γ = 107.59(4)°, V = 644.7(5) ų, Z = 2. Complex 1 consists of infinite bimetallic chains [{Ca(H₂O)₄}CuCl₂(HOCH₂C≡CCH₂OH)₂]_∞ forming a three-dimensional framework through (Ow)H…Cl and (C)O-H…Cl hydrogen bonds. Compound 2 is built from discrete anions [CuCl₂(HOCH₂C≡CCH₂OH)]^- paired by edge-to-edge packing in the [100] direction and large BimH⁺ cations with face-to-face packing. In both structures, the πcoordinated Cu(I) atom has the trigonal environment involving two Cl^- anions and C≡C 2-butyne-1,4-diol bond (Cu-(C≡C) distance is 1.918(2) Å and 1.910(4) Å for 1 and 2 respectively).

A method is developed to prepare a complex of copper(II) chloride with 3-(hydroxyiminomethyl)-5-(2,5-dimethylphenyl)isoxazole (L) of the composition [Cu₂L₂(μ-Cl)₂Cl₂]. Its molecular and crystal structure is determined by single crystal X-ray diffraction. Examination of the curve μ_ef(Т) within the 2-300 K temperature range reveals the presence of antiferromagnetic interactions between unpaired electrons of copper(II).

This contribution presents the results of a single crystal X-ray diffraction study of three ammine complexes of bivalent platinum and palladium: [Pt(NH₃)₄](NO₃)₂, [Pd(NH₃)₄](NO₃)₂ and [Pd(NH₃)₄]F₂·H₂O. The first two compounds are isostructural; metal atoms are located on inversion centers, all other atoms are in general positions. A three-dimensional framework is built from planar-square complex cations and nitrate ions joined by N-H…O hydrogen bonds. In [Pd(NH₃)₄]F₂·H₂O, palladium atoms, as in the previous cases, are located on inversion centers, while oxygen atoms of water molecules are on the two-fold symmetry axis. A network of strong N-H…F and O-H…F hydrogen bonds linking the cations, anions, and crystallization water molecules is present in the structure.

The structure of the [Au(Dien)Cl]₂[Re₄Te₄(CN)₁₂]·5H₂O compound prepared in an aqueous medium by the reaction of a gold(III) complex [Au(Dien)Cl]Cl₂ with a tetranuclear tetrahedral tellurocyanide cluster complex of rhenium K₄[Re₄Te₄(CN)₁₂]·5H₂O is determined by single crystal X-ray diffraction.

The crystal structures of anhydrous 1-germatranol and its complex with HCCl₃ are centrosymmetrical dimers because of their intermolecular hydrogen bonds. In the germatranol crystal, the axial and equatorial oxygen atoms of its two molecules are hydrogen bonded into an eight-membered coordination cycle. In the complex with HCCl₃, the two molecules of germatranol are likewise linked in dimers, and both axial oxygen atoms are H bonded with HCCl₃. In the investigated structures, the axial Ge-O bond is shorter than the equatorial ones. Depending on the number and strength of the hydrogen bonds, the interatomic Ge-O and Ge ← N distances change markedly. The quantitative estimates of the H bond energy are obtained from quantum chemical calculations of the model systems containing 1-germatranol and HCCl₃ molecules.

The title compound, C₂₉H₂₆O₁₀S, yields two conformational polymorphs concomitantly fr om dichloromethane-methanol mixture; the major polymorph grows as plates (Form I, monoclinic, P2₁/n) and the minor polymorph grows as needles (Form II, triclinic, P-1). The two forms differ mainly in orientation of the tosyl group. In Form I, sulfonyl oxygen of the tosyl group makes intermolecular C-H?KO interactions, wh ereas the same group in Form II is involved in an intramolecular short dipolar S=O?KC=O (sulfonyl-carbonyl) contact. The molecular organization and the influence of various weak non-covalent interactions that stabilize these conformers in the crystal lattices are discussed.

The atomic surface structure of layered dichalcogenide 1T-TiSe₂ is studied by scanning tunneling microscopy (STM) at room temperature. In STM images, the ordered structures in the form of 6×6×6 triangles of Se atoms extending for 0.3±0.20 Å above the crystal surface are observed. The effect of a series of different atomic structural defects on the surface topology of titanium disulphide is modeled on the example of isostructural and isoelectronic 1T-TiS₂ system using the DFTB method. It is determined that a good agreement with the STM experiment is showed by the model of local 1T-TiS₂ packing defects, where the coordination of titanium atoms changes from the octahedral to the prismatic one. For these systems, the calculation results of the electronic structure and defect formation energy are also presented.

With the use of reference polycrystalline α-Al₂O₃ (NIST SRM-1976) and MoO₃ samples we consider the most significant geometric and physical factors affecting the accuracy of X-ray diffraction data obtained on a diffractometer equipped with a flat two-dimensional detector (Debye-Scherrer scheme). A general strategy to measure polycrystalline samples in the amount of 20-30 μg is proposed. By the example of SRM-1976 it is shown that with the proper processing of two-dimensional diffraction patterns and the introduction of certain corrections the angles 2θ can be measured with the accuracy not less than ±0.01°. Even with a strong tendency of particles towards preferred orientation the relative intensities of diffraction reflections are shown to be obtained with the accuracy not less than ±10%.

The structural parameters of tin(II) phthalocyaninate PcSn and tin(IV) bis-phthalocyaninate Pc₂Sn as well as of their cations are determined by B3LYP/SDD and PBE0/SDD quantum chemical methods. The PcSn molecule is characterized by С_4v symmetry, and SnN bond lengths are 2.307/2.299 Å (B3LYP/PBE0). The Sn nucleus is by 1.11 Å (B3LYP, PBE0, single crystal X-ray diffraction analysis) higher than the plane of four neighboring nitrogen nuclei. The "hindered" configuration (D_4d symmetry) with a high (27-30 kcal/mole) internal rotation barrier corresponds to the Pc₂Sn energy minimum. The calculated equilibrium lengths of eight equivalent SnN bonds of 2.366/2.347 Å (B3LYP/PBE0) are similar to the average SnN bond length of 2.347 Å (single crystal X-ray diffraction). Vertical and adiabatic ionization potentials are calculated: I^V 6.40/6.48 eV, I^A 6.38/6.45 eV for PcSn and I^V 5.63/5.66 eV, I^A 5.60/5.63 eV for Pc₂Sn.

In natural apatites, perinaphthenyl radical with spectral parameters g = 2.0018±0.0002, A₁ (¹H) =
0.62±0.01 mT, A₂ (¹H) = 0.2±0.01 mT is identified by EPR. The radical forms during annealing of samples in the air in a range T = 300-500°C and is stable over time for several months after the formation. It is detected in the only genetic type of this polygenic mineral, namely, in supergene insular apatites from guano phosphate ores.

Single crystal X-ray diffraction analysis is used to determine the crystal structure of a newly synthesized molecular complex compound of antimony(III) fluoride with L-leucine of the composition SbF₃(C₆H₁₃NO₂) (orthohombic crystal system: a = 5.7948(8) Å, b = 6.2433(9) Å, c = 28.594(4) Å, Z = 4, P2₁2₁2₁ space group). The structure consists of SbF₃ molecules and L-leucine bound into polymer chains by bidentate bridging carboxyl groups of amino acid molecules. Weak Sb…F(1)^b bonds combine the adjacent chains into polymer ribbons organized by N-H…F and N-H…O hydrogen bonds into a framework.

Single crystal X-ray diffraction analysis is used to determine the structure of iridium(III) trans-trifluoroacetylacetonate at 150 K. The crystallographic data for trans-C₁₅H₁₂F₉O₆Ir are as follows: a = 13.4334(5) Å, b = 14.9136(6) Å, c = 19.4229(8) Å, space group Pcab, V = 3891.2(3) ų, Z = 8, d_x = 2.224 g/cm³, R = 0.0236. The structure is molecular. The metal atom coordinates six oxygen atoms of three β-diketonate ligands of β-diketone. The Ir-O distances are within the range of 2.00 Å to 2.02 Å; the average value is 2.011(6) Å; the average value of the chelate angle ∠О-Ir-O is 95.2(5)°. In the crystal, the molecules are bound only by van der Waals interactions; six shortest Ir…Ir distances in the structure are within the range of 7.469-9.712 Å.

The isostructurality of [Rh(NH₃)₅Cl](WO₄)_x(MoO₄)_1-x (x = 0, 0.5, 1) complex salts is shown, and their thermal properties are compared. In a hydrogen atmosphere, transformations begin at Т ~ 200°C. According to the powder XRD data, the phase composition of the end products is markedly different. For the Rh-Mo system, the dependence (V/Z) of the atomic volume on the composition is presented. The thermal decomposition product [Rh(NH₃)₅Cl](MoO₄) (Т_fin = 800°C) is shown to be the disordered Mo_0.5Rh_0.5 solid solution (а = 2.757(2) Å, с = 4.428(4) Å, P6₃/mmc space group).

The crystal structure of (NH₄)₂Na[Rh(NO₂)₆] previously studied only from the data on polycrystals is refined. The selection of the Fm-3 space group is shown to be unambiguous. Geometrical characteristics of the complex [Rh(NO₂)₆]^3-anion are: Rh-N 2.051 Å, N-O 1.237 Å, ∠O-N-O 119.0°.

Crystals of the rhenium cluster complex (H₃O)₄[(C₂H₅)₄N]₆[Th₂Cl₄(H₂O)₁₂O]₃[Re₄Se₄(CN)₁₂]₄ are obtained in an acidic (HCl) aqueous solution by the reaction of cluster salt K₄[Re₄Se₄(CN)₁₂]·6H₂O with ThCl₄ and (C₂H₅)₄NCl. Single crystal X-ray analysis shows that the title compound is ionic and crystallizes in the cubic crystal system (a = 22.7322(3) Å, V = 11746.93(27) ų, Z = 2, I3m space group, R = 0.0350). It contains [Th₂Cl₄(H₂O)₁₂O]²⁺ cations with two thorium atoms bonded to each other through the bridging oxygen atom forming an angle of 180˚ in the structure.

The crystal structure of 2,2-difluoro-4-(4′-phenylphenyl)-6-methyl-1,3,2-dioxaborin (С₆H₅C₆H₄COCHCOCH₃BF₂) (1) is determined. The effect of the π-stacking interaction on the luminescent properties of compound 1 at 300 K and 77 K is shown.

Zinc di-(4-chlorphenylthioacetate) dihydrate (4-ClC₆H₄SCH₂COO)₂Zn·2H₂O (ZTD) is obtained in the reaction of protatrane 4-chlorphenylthioacetate 4-ClC₆H₄SCH₂COO·N⁺H(CH₂CH₂OH)₃ with zinc dichloride (ZnCl₂) in aqueous alcohol. X-ray diffraction is used to study the crystal structure of ZTD and compare it with related compounds. All intermolecular О…O contacts of the neighboring zinc polyhedra are short in ZTD molecules. Apparently, the short intermolecular О…O contacts cause distortions of the octahedral environment of the zinc atom.

1,3,1′,3′-Tetramethylhydurilic acid (1) and tetramethylalloxantine (5) were prepared by simple novel methods. The crystal structures of the compounds 1 and 5·2(DMSO) are reported.

The crystal structure of the 1:1 ethanol betulin solvate, a widely spread natural compound, is determined. The betulin solvate crystallizes in orthorhombic symmetry in the P2₁2₁2₁ space group, Z = 4. The unit cell parameters are as follows: a = 7.0159(1) Å, b = 12.4425(2) Å, c = 33.7500(5) Å; V = 2946.22(8) ų. Betulin molecules are hydrogen bonded to each other and ethanol molecules, as a result of which the layers are distinguished in the structure, which are perpendicular to the с crystallographic direction. Inside the layer, all molecules are hydrogen bonded, while the layers are linked by van der Waals interactions.

The molecular structure of methyl 1-isopropenyl-5a,5b,8,8,11a-pentamethyl-9-oxo-10-[(E)-1-phenylmethylidene]perhydrocyclopent[a]chrysene-3a-carboxylate II is determined. Compound II С₃₈H₅₂O₃ crystallizes in the non-centrosymmetric P2₁ space group with the cell parameters: а = 11.4450(8) Å, b = 11.1995(8) Å, c = 12.5179(9) Å, β = 93.984(2)°.