Home – Home – Jornals – Journal of Structural Chemistry 2008 number 5

Changes in the electronic structure and magnetic characteristics of Sr₂FeMO₆ double perovskites were studied by the FLAPW-GGA ab initio band structure method in relation to the type of the cation M = Sc, Ti, …, Ni, Cu.

The modified augmented plane wave method (WIEN2k program) was used to study the electronic energy structure and calculate the SK-absorption spectra of LiBiS₂, NaBiS₂, and KBiS₂. The crystal structures of the compounds were modeled using symmetric structures, in which each sulfur atom was surrounded by three alkali metal atoms and three bismuth atoms in such a way that the alkali metal-sulfur and bismuth-sulfur bond length differed. This difference between bond lengths was calculated from the sum of the ionic radii of the components of compounds and by the geometry optimization of the crystal lattice. The two variants of calculation allowed us to check the applicability of Pauling's idea about preservation of the bond lengths of elements in compounds for modeling the crystal structures of LiBiS₂, NaBiS₂, and KBiS₂. The SK absorption spectra and optically forbidden bands were calculated.

The electronic energy structure of MC, M₆C, and M₁₂C carbide systems and iron martensite in the absence of spin polarization was studied by the local coherent potential method using the cluster version of the МТ approximation in terms of multiple scattering theory. The local partial density of the electronic states of atoms in crystals was calculated and their electronic structures were compared. The peculiarities of chemical bonding in crystals are discussed.

The potential surfaces of the ground and lowest excited states of the [RuCl₅NO]^2- complex ion were studied by density functional theory. The conical intersections between the potential surfaces of the ground and lowest excited states were found and characterized. The possible routes from the conical intersection points to the ground state and metastable bond isomers were traced. A preliminary scheme, describing photoisomerizations in the complex, was suggested.

The results of B3LYP quantum-chemical calculations of the equilibrium structures of [(CX₃COOCu)₂]₃, [(CX₃COOCu)₂]₂, and (CX₃COOCu)₂ oligomers (X = H, F) using the cc-pVTZ correlation-consistent basis for C, O, and F atoms and the Stuttgart 1997 RSC basis and relativistic effective core potential for Cu(I) atoms are presented. The differences in the structures of the free dimer and dimer units in oligomers. The hexamer structure was chosen as the model of a fragment of the crystalline phase. Good agreement was obtained between the experimental and calculated differences between the geometrical parameters of the structures in the "gas phase−crystal" and "acetate−trifluoroacetate" series. Based on the calculated data, the increase in the Cu(I)-Cu(I) bond length in the silver acetate crystal compared with the gas phase can be explained by the effect of the neighboring dimer units of the polymer ribbon and the increase in the Cu(I)-Cu(I) bond length in gaseous trifluoroacetate compared with acetate, by the acceptor effect of fluorine atoms.

Density functional theory (DFT) calculations at B3LYP/6-31G(d,p) level were carried out to investigate the mechanism of the reaction of benzaldehyde (BA) or acetaldehyde (AD) with (1R)-2-endo-bromoacetyl-1,7,7-trimethylbicyclo[2.2.1]heptan-2-ol (endo-2-bromoacetylisoborneol) 1 (Scheme 1). The calculations indicate that the reactions are diastereoselective, in good agreement with the experimental results [1]. Moreover, the calculations show that these reactions proceed via two steps: (1) an aldol-like reaction and (2) the formation of an epoxide. Our calculation study of the transition states demonstrate that the terminal hydroxyl group in compound 1 is vital to the stereoselectivity of the reactions.

The spatial and electronic structures of molecules with three substituents at the germanium atom (tricoordinated germanium) were calculated by the DFT method (Gaussian-98 program package, B3LYP functional, 6-311G(d,p) basis set). The main characteristics of Ge-X bonds in thee molecules were determined by NBO and AIM procedures. It is shown that Ge-X are weak, "intermediate" type bonds. The bond energies were calculated.

The molecular structure of nickel(II) and copper(II) N,N′-ethylene-bis(acetylacetoneiminates), NiO₂N₂C₁₂H₁₈ and CuO₂N₂C₁₂H₁₈, at 442(5) K and 425(5) K, respectively. Both molecules have С₂ symmetry with a nearly planar MN₂O₂ coordination site and internuclear distances r_h1(M-O) = 1.862(10)/1.923(17) Е and r_h1(M-N) = 1.879(10)/1.947(18) Е for Ni(acacen) and Cu(acacen), respectively. The structure of free molecules is close to the structure of molecules in crystal. The DFT/В3LYP quantum-chemical calculations (CEP-31G and 6-31G* basis sets) gave a molecular structure that agreed satisfactorily with the one found in experiment. The low-spin ¹А and high-spin ³А states of the Ni(acacen) molecule were considered. It was found that a change in multiplicity caused significant changes in the geometrical and electronic structure of the MN₂O₂ coordination site. As shown by experiment and calculations for the NiO₂N₂C₁₂H₁₈ molecule, the low-spin ¹А state is the ground state. The internal rotation of CH₃(CN) and CH₃(CO) methyl groups was studied by the В3LYP/CEP-31G method. It was shown that steric hindrances led to a high rotation barrier of the CH₃(CN) group.

The molecular structure of 2-chlorobenzenesulfonyl chloride was studied by electron diffraction and quantum-chemical (МР2/6-31G**, B3LYP/6-311++G**) methods at 337(3) K. Only one (C₁) conformer was found in the gas phase. The following structural parameters were obtained: r_h1(C-H)_av = 1.105(6) Е, r_h1(C-C)_av = 1.398(3) Е, r_h1(C-S) = 1.783(11) Е, r_h1(S=O)_av = 1.427(3) Е, r_h1(S-Cl) = 2.048(4) Е, r_h1(С-Cl) = 1.731(9) Е, ∠(С-S=O1) = 109.9(8)°, ∠(С-S=O2) = 106.9(8)°, ∠(Cl1-S-O1) = 107.3(4)°, ∠(Cl1-S-O2) = 106.4(4)°, ∠C-S-Cl = 102.1(6)°, ∠O=S=O = 122.3(11)°. The C2-C1-S-Cl1 torsion angle that defines the position of the S-Cl bond relative to the plane of the benzene ring was 69.7(8)°. The B3LYP/6-311++G** calculated barriers of internal rotation of the sulfonyl chloride group were V₀₁ = 9.7 kcal/mol and V₀₂ = 3.6 kcal/mol.

The binary molybdate Li₂Zn₂(MoO₄)₃ of a new crystal type was characterized by EPR, optical spectroscopy, and X-ray diffraction methods. The crystals have the Pnma symmetry group and the lattice parameters а = 5.1139(5) Е, b = 10.4926(13) Е, c = 17.6445(22) Е; Z = 4. The crystals possess scintillation properties; emission is caused by the presence of impurity levels in the forbidden band. The EPR studies of the nature of the impurity centers responsible for the scintillation characteristics of the crystal showed that the centers were Cu²⁺ ions substituted for zinc ions in the oxygen octahedra. The directions of the main values of the g and А tensors (g_zz, A_zz) correspond to the direction of O-Cu-O of the oxygen octahedron distorted along the Z axis. The EPR spectra of the copper ions are described by the spin Hamiltonian with the parameters g_|| = 2.38, g_⊥ = 2.06; A_|| = 116 G, А_⊥ = 0 G.

A method is suggested for analyzing the model structures of crystals by calculating the spherical coordinates of the normals to the simplex faces of the simplicial Delaunay partitioning of a set of points (atoms). The normals to the simplex faces of the Delaunay partitioning of the crystal structure characterize the structure at the local level. An algorithm for constructing the invariant of the crystal structure (crystal module) was considered. Crystals modules were constructed for hexagonal and cubic ices.

A simulation of crystallization and a structural study of an overcooled NaCl melt are reported. A criterion is suggested for classifying the structural states of ions in the transition mode of nucleation. It is shown that in the bulk of overcooled liquid, short-lived crystal phase germs appear and vanish. A distribution of the critical clusters according to form and size was found. It was assumed that crystal growth occurred by collective synchronization of particle motions in crystal and liquid near the interface. The NaCl nanocrystals formed during nucleation are cubic crystals with clear-cut faces and edges. Overcooling the liquid to a greater extent led to the formation of defective polycrystalline structures.

The Kirkwood factor g_K of a model polar liquid of dipolar hard spheres (DHSs) was approximated by analytical equations using the approximation of the interaction of the second neighbors within the hindered rotation model. The derived equations describe the temperature and density dependences of the dielectric functions of the DHS liquid.

Isoentropy compressibilities of aqueous magnesium chloride and sulfate were determined based on precision measurements of ultrasound velocity, density, and isobaric heat capacity at low to high concentrations at 278.15-323.15 K. The hydration numbers h and the molar parameters of volume and compressibility were calculated based on thermodynamically correct equations for hydration complexes (V_h, β_hV_h), water in the hydration shell (V_1h, β_1hV_1h), and the void containing a stoichiometric mixture of ions (V_2h, β_2hV_2h). The h and β_hV_h values were found to be independent of the temperature; the molar compressibility of the hydration sphere (β_1hV_1h) and the stoichiometric mixture of ions without a hydration shell (β_2hV_2h) were independent of the concentration under the stated conditions. The effect of the electrostatic field of ions on the temperature dependence of the molar volume of water in the hydration sphere was more significant than the effect of pressure on the temperature dependence of the molar volume of bulk water. This is attributed to changes in the dielectric constant of water in the vicinity of the electrolyte ions.

The results of previous studies of the increments ΔG⁰_CH2, ΔH⁰_CH2, TΔS⁰_CH2 and in hydrocarbon solution processes in water, evaporation, hydration, and transfer from vapor and water to surfactant micelles are summarized. The corresponding thermodynamic cycles were constructed. A micelle was shown to be a bistable structure formed by the contact and water-separated hydrophobic interactions of the alkyl groups of surfactants. The fraction in ΔG⁰_CH2M is -2.3 kJ⋅mol^-1 for the contact associate and -0.7 kJ⋅mol^-1 for the hydrated one. Water is involved in the hydrophobic interaction of each associate. In a dualist micelle, however, ΔG⁰_CH2 = -3.0 kJ⋅mol^-1 equals that of the dispersion interaction after condensation from vapor. The dual nature of the dynamic properties of micelles is discussed.

The crystal structure of the Os₃(μ,η²-O=CC₆H₅)(η³-C₃H₅)(CO)₉ cluster synthesized by the reaction of the (μ-H)Os₃(μ-O=CC₆H₅)(CO)₁₀ complex with allylamine in chloroform was determined by X-ray analysis. Prolonged storage of the reaction mixture led to N-C bond cleavage in allylamine and η³-addition of the allyl fragment at one of the Os atoms (Os-C 2.246 Е, 2.248 Е, and 2.273 Е). The unit cell parameters of the complex are a = 9.494(1) Е, b = 10.479(1) Е, c = 12.474(2) Е, α = 84.55(1)°, β = 70.08(1)°, γ =
70.72(1)°, V = 1255.8(4) Е³, space group Z = 2; C₁₉H₁₀O₁₀Os₃; d_calc = 2.922 g/cm³, 3085 I_hkl > 2σ_I of 3611 collected reflections; R = 0.0252. The structure of Os₃(μ,η²-O=CC₆H₅)(η³-C₃H₅)(CO)₉ is molecular. The plane of the Os₃ triangle and the OsCOOs plane are connected according to the "butterfly" principle with an angle of 103.4° between them. The Os-Os distances in the cluster core vary from 2.836(1) Е to 2.844(1) Е; the Os-C_carb distances are 1.88(1)-1.97(1) Е; the distances to the atoms of the bridging ligands are Os-C 2.11(1), Os-O 2.14(1) Е; the O-C bridging bond is 1.24(1) Е. The conformations of the Os₃(μ,η²-O=CC₆H₅)(η³-C₃H₅)(CO)₉ triosmium cluster were studied theoretically. The potential curve of the internal rotation of the allyl ligand relative to the Os(1)-С(9) bond was determined. The rotation barrier of the allyl ligand in crystal relative to the Os(1)-С(9) bond is 8.38 kJ/mol, and the rotation of the ligand is not hindered. The effects of the intra- and intermolecular interactions on the conformation state of the cluster complex is considered.

An X-ray study of the crystals of bicyclic compounds containing fluorinated aromatic and nonfluorinated heteroaromatic rings, 5,6,7,8-tetrafluoroquinoline, 5,6,8-trifluoroquinoline, 5,7-difluoroquinoline, 5,7,8-trifluoro-2-phenylquinoline, and 5,7,8-trifluoro-6-trifluoromethylquinoline, was carried out. The basic supramolecular motifs and the underlying intermolecular interactions that control the lattice structure of these compounds were investigated. B3LYP DFT quantum-chemical calculations (6-311G(d,p) basis set) and the topological analysis of the electron density distribution in terms of Bader's QTAIM theory were performed for the compounds. It is shown that the intermolecular interactions in question, traditionally regarded as nonvalent interactions, are related, to a definite extent, to the formation of very weak covalent chemical bonds in the intermolecular space due to the overlap of the "tails" of the molecular wave functions.

Three modifier compounds that stabilize the phase state of ammonium nitrate over a wide range of temperatures, 1,3,5-trihydroxyisocyanuric acid dihydrate (1), 4-aminouracil (2), and 4-aminouracil monohydrate (3) were studied by X-ray diffraction. Strong donor-acceptor intermolecular interactions were found for structures 2 and 3. The electronic parameters of the molecules were calculated by quantum-chemical methods, and it was found that additional intermolecular interactions were possible.

An X-ray study of (3Z)-(±)-4-(2′-hydroxypropyl)amino- and (3Z)-4-(2′-hydroxyethyl)aminopent-3-en-2-ones is reported. The bond lengths inside the H ring are equalized due to the classical N-H…O hydrogen bond between the carbonyl oxygen and the amino group. In the 4-(2′-hydroxyethyl)aminopent-3-en-2-one crystal, due to the classical N-H…O bonds, infinite zigzag chains are formed along the 0b axis and arranged into a layered structure due to the weak C-H…O interactions. In (±)-4-(2′-hydroxypropyl)amino-pent-3-en-2-one crystal, however, centrosymmetric dimers are formed, which are then linked by weak
C-H…O intermolecular interactions, which form a layered structure along the a0b plane.

Pseudohalogen-containing compounds have attracted significant interest among nonmetal chemists and theorists, not only owing to their potential use in various fields but also due to difficulties in their experimental preparation and characterization. Since its introduction in 1925, the pseudohalide principle has been used extensively and, therefore, a remarkable progress has been made in the experimental and theoretical research on the compounds of this kind. In this work, we review studies on structural investigations and theoretical characterizations of several pseudohalide-containing compounds in order to contribute to better understanding of the chemistry of many such species.

Non-empirical RHF/6-31G* and MP2/6-31G* quantum chemical methods are used to calculate the molecular structure of trichlorophosphazene compounds: Cl₃P=NC(CF₃)₃ (I) and Cl₃P=NCCl(CCl₃)₂ (II). The corresponding geometric parameters obtained from the calculations are compared with X-ray diffraction analysis data reported in the literature. Conformational differences between the molecules of I and II, previously found by X-ray diffraction in the crystals of these compounds, are confirmed by non-empirical calculations of the molecules in the free state. The features of their geometry caused by intramolecular interactions are discussed.

Based on graph theory fundamentals, a general formula to calculate formal unsaturation of chemical compounds that contain atoms of any valence is deduced and the mathematical meaning of this widely used chemical concept is shown.

Using the results of Monte Carlo simulation, equations of state of hard sphere liquids are calculated for 106 values of the fill factor η = 0.005-0.530 (step of 0.005). In the region of liquid phase stability the absolute accuracy of about 0.00001-0.00008 is reached. Correctness of the accuracy estimate is discussed. The results obtained are compared with reported equations of state of the hard sphere liquid.

Primary data of the X-ray diffraction experiment on DyBr₃ and YbBr₃ aqueous solutions in salt:water molar ratios of 1:20 are presented. The occurrence of a pre-main peak in the curves of normalized scattering intensities determines the average distance between cations in these solutions, and hence, directs to a model description of the structure of solutions. Based on the determination of boundaries of the cation complex and taking into account the deficit of solvent, the model of the cation complex is supposed to consist of two coordination shells involving at least two anions.

The crystal structure and the formation conditions of crystals of the LiFe₅O₈ ordered phase obtained from the solution-melt of the Bi₂O₃-Fe₂O₃-B₂O₃-LiCl quadruple system are refined. The crystals are black, octahedral, of cubic symmetry (space group P4₃32). Unit cell parameters: a = 8.3339(1) Е, V = 578.82(1) Е³, Z = 4, d_calc = 4.753 g/cm³. From 6046 of the collected array I_hkl 358 are independent (R_int = 0.0321). As a result of anisotropic refinement of structural parameters, R₁ factor is found to be 0.0186 (wR₂ = 0.0467). Lithium atoms are in octahedral environment, Li-O is 2.109(1) Е; iron atoms are of two types: in octahedra with Fe-O (by two) distances of 1.9586(9) Е, 2.0152(9) Е, and 2.0652(10) Е and tetrahedra with Fe-O (three) 1.8848(10) Е and 1.914(2) Е. The structure is of inverted spinel type.

Triclinic modification of trans-bis(trifluoroacetylacetonato)copper(II) has been studied by single crystal X-ray diffraction (diffractometer X8 APEX BRUKER, MoK_α radiation, T = 173(2) K). The structure is molecular. Square environment of the Cu atom (Сu-O_av 1.916 Е, ∠O-Сu-O_av 93.4°) is completed to a bi-pyramid by two Сγ atoms of neighboring molecules, Cu…Сγ 3.18 Е and 3.23 Е.

Crystal structure of acrylamide has been re-determined by single crystal X-ray diffraction (133(1) K, BRUKER SMART 1000 CCD, a = 8.228(1) Е, b = 5.759(1) Е, c = 9.760(1) Е, β = 120.04(1)°, V =
400.3(1) Е³, space group P2₁/c, Z = 4, R = 0.0543 for 867 reflections). In the structure strong hydrogen bonds N-H…O join the molecules of C₃H₅NO into bi-molecular layers, which make C…C molecular contacts. It has been demonstrated that the process of sold phase polymerization of acrylamide should proceed through the cleavage of double bonds С(1)=С(2) in the monomers and formation of bonds С(1)-С(1) and С(2)-С(2) between the closest carbon atoms of different layers.

Addition of trichloroacetonitrile to 2,5-dimethyl-1,5-hexadiene in presence of cuprous amine complexes has been studied. Single crystal X-ray diffraction unambiguously proves that the main product is a racemic mixture of the cyclic symmetric nitrile - (1r,3R,6S)- and (1r,3S,6R)-1,3,6-trichloro-3,6-dimethylcycloheptanecarbonitrile. Established relative configuration of the product confirms the ring closure mechanism suggested before. Also, a side product - 2,5-dimethyl-2,5-dichlorohexane has been isolated (the product of hydrochlorination of the starting alkadiene). Low-temperature (190 K) structural examination of this centrosymmetrical molecule indicates that the unit cell comprises one molecule.

The structure of (±)-2-[(1S,3S)-3-acetyl-2,2-dimethylcyclobutyl]-N-(p-tolyl)acetamide has been determined by single crystal X-ray diffraction analysis. The crystal belongs to triclinic system, space group P-1, a = 8.8700(18) Å, b = 10.331(2) Å, c = 10.363(2) Å, α = 71.11(3)°, β = 65.06(3)°, γ = 72.18(3)°, V = 798.6(3) ų, Z = 2, formula unit C₁₇H₂₃NO₂. The title compound has a fragment of 2,2-dimethylcyclobutane and its conformation represents semi-chair. The intermolecular hydrogen bonds N-H...O and C-H...O are revealed.