Home – Home – Jornals – Journal of Structural Chemistry 2008 number 2

It is shown how the theory developed by the author and regarding the structural transformations of molecules as the result of the resonance mixing between the vibronic wave functions of the corresponding states of subsystems can be extended to the case with an arbitrary number of the resonant and quasiresonant energy levels.

The vast numbers of molecular objects and chemical transformations of a substrate cannot be evaluated even intuitively, which necessitates the development of simple reaction monitoring methods. Here this problem is formulated for the first time, and possible solutions are substantiated.

The electronic structure of a large fragment of the crystal lattice of zircon ZrSiO₄ with a uranium impurity atom replacing the zirconium atom was investigated using the completely relativistic discrete variation (DV) cluster method. The results are compared with the data of a similar calculation of the ideal ZrSiO₄ crystal. An analysis of the overlap populations and effective charges on the atoms of the matrix and impurity showed that chemical binding of uranium with the environment is covalent, and the electron density redistribution caused by this substitution changes not only the impurity and the nearest environment, but also the atoms of the next coordination spheres.

The results of quantum-chemical calculations of the formation energy, equilibrium structure, and potential surface sections along the nonrigid degrees of freedom of the silver trifluoroacetate dimer are presented. Calculations were performed by the B3LYP method with the cc-pVTZ correlation-coherent basis for C, O, and F atoms using the basis and relativistic effective core potentials Stuttgart 1997 RSC for Ag atoms, and, for comparison, by the HF method in the 6-31G(d) basis and MP2 method in the 6-311G(df) basis for C, O, and F atoms using the basis and relativistic effective core potentials SBKJC for Ag atoms. The eight-membered ring is a rigid planar fragment with a bond order of 0.2 between the silver nuclei. The nearly free internal rotation of the CF₃ group affects the geometrical parameters of the ring. It was substantiated that in electron diffraction experiments, the difficulties of interpretation could be explained not only by the presence of decomposition products in the sample, but also by possible oligomerization of silver trifluoroacetate.

In the framework of the MP2/6-311++G**//RHF/6-31G* ab initio approach we investigated the structure and relative stability of the imine (-CHR-CH=N-) and enamine (-CR=CH-NH-) forms of the simplest imines, oximes, and their ethers. Although the enamine form is unstable, double bond migration R₂CH-CH=N- → R₂C=CH-NH- is often regarded as one of the stages of a series of reactions that take place in superbasic media, in particular, synthesis of pyrroles from ketoximes and acetylene. For isomerization of E-ethaneimine CH₃-CH=NH to vinylamine CH₂=CH-NH₂, calculations predict an increase of 4.3 kcal/mol in energy. A close value (4.8 kcal/mol) was obtained for the energy of isomerization of ketimine (CH₃)₂C=NH to 2-aminopropene. The methyl group in CH₃-CH=CH-NH₂ stabilizes the neighboring double bond, and the transformation of E-propane-1-imine into E- and Z-aminoprop-1-ene is accompanied by an increase of 2.8 kcal/mol in energy. After the transition from imines to oximes, the enamine form is drastically destabilized. The highly endothermal character of the CH₃-CH=NOH → CH₂=CH-NHOH rearrangement (16.4 kcal/mol) is retained from acetaldoxime to its methyl ether and decreases by only 1.0 kcal/mol for the isomerization reaction of the vinyl ether of acetaldoxime to N,O-divinylhydroxylamine. These rearrangements are thermodynamically unfavorable probably because of the increased negative charge on the nitrogen atom and, as a consequence, destabilization of the N-O bond.

The applicability of structural analogy to structure elucidation of organic compounds by searching two molecular spectroscopy databases (DBs) is examined. Using structural analogy is based on the representation of DB structures as sets of structural fragments. Of primary concern are the structural fragments that are represented in the search results of both infrared (IR) and mass spectroscopy (MS) DBs. The statistically justified estimates of the efficiency of the combined search depending on the spectral similarity are given.

The wave numbers of trans-2,3-¹³C₂-buta-1,3-diene were calculated using a scaled quantum-chemical force field found at the MP2/6-31G*//MP2/6-31G* level of theory. The obtained results and the theoretical sets of wave numbers for twelve deutero and ¹³C derivatives of the trans form and five deutero and ¹³C derivatives of the gauche form of buta-1,3-diene found previously at the MP2/6-31G*//MP2/6-31G* level are compared with the corresponding experimental vibrational spectra corrected for the Fermi resonance. Combined analysis of the vibrational spectra of the above mentioned isotopomers was performed.

For natural bitumoids, the effects of the structure of vanadyl-porphyrin complexes on the EPR spectra were investigated. The ambiguity of the hyperfine structure (its presence or absence) corresponding to four nitrogen atoms in the spectra of oil vanadyl porphyrins correlates with the changes in the second coordination sphere of the nearest environment of the metal ion, namely, in methine bridges.

The effects of Н₂ and Н₂ + О₂ gas mixtures of varying composition on the state of the surface of the Pt/MoO₃ model catalyst prepared by vacuum deposition of platinum on oxidized molybdenum foil were investigated by X-ray photoelectron spectroscopy (XPS) at room temperature and a pressure of 5-150 Torr. For samples with a large Pt/Mo ratio, the XP spectrum of large platinum particles showed that the effect of hydrogen-containing mixtures on the catalyst was accompanied by the reduction of molybdenum oxide. This effect results from the activation of molecular hydrogen due to the dissociation on platinum particles and subsequent spill-over of hydrogen atoms on the support. The effect was not observed at low platinum contents in the model catalyst (i.e., for small Pt particles). It is assumed for the catalyst that the loss of its hydrogen-activating ability is a consequence of the formation of platinum hydride. Possible participation of platinum hydride as intermediate in hydrogen oxidation to H₂O₂ is discussed.

The approach suggested in this work within the fluctuation theory of the hydrogen bond allows one to correlate the vibrational band shape with the statistical distribution of the geometrical parameters of the О-Н...О hydrogen bridge, generated by the local fluctuations of the molecular surroundings in liquids. The correlation may be established either exclusively from spectral data or by also using the known empirical correlations with structural data. The existing explanations to the anomalous broadening of the spectral bands of associated liquids, namely, the dominant effect of the R_O…O bond length or the j (Н-О...О) bending angle on the OH vibration frequency were tested. Both hypotheses provided an adequate description of the experimental spectra and their temperature dependence. However, the required relationship between the frequency and geometrical parameters conflicts with several empirical facts, indicating that the one-parameter potentials are insufficient for a quantitative description of H-bonds in liquids. A method for the design and verification of more complex potentials containing all geometrical parameters of the hydrogen bridge affecting the H-bond energy is suggested.

The pair distribution functions (DFs) of the oxygen and hydrogen atoms over space around one of the water molecules were calculated during Monte Carlo simulation (Metropolis procedure for the NVT ensemble at normal density and 300 K). An analysis of the isosurfaces of the DF_ОО and DF_OH constructed around the selected water molecule for several fixed values of local density allowed us to obtain detailed information about the most probable localization of water molecules in the second and third coordination spheres.

The thermal effects of dissolution of ammonium bromide in water and its mixtures with formamide (FA) at 277-328 K were studied by the calorimetry method in the region of small additions of the nonaqueous component. The standard values of enthalpy and heat capacity of solution, as well as the temperature changes in the solution entropy and reduced dimensionless Gibbs energy, were calculated. The parameters of electrolyte-amide pair interactions were calculated using the McMillan-Mayer formalism. The contributions of the cation and anion to the pair interaction parameters were determined by the group additivity method. The results are compared with the data obtained previously for solutions of tetrabutyl- and tetraethylammonium bromides in aqueous solutions of FA and hexamethylphoshotriamide (HMPT). At elevated temperatures the system becomes less structured in amide solutions of tetraalkylammonium bromides (except solutions of Et₄NBr in aqueous HMPT) but more structured in solutions of ammonium bromide and in aqueous FA and HMPT.

The structural and thermodynamic characteristics of aqueous solutions of formamide, N-methylformamide, N,N-dimethylformamide, and N,N-diethylformamide were calculated. The specific and nonspecific components of the total energy of intermolecular interactions were determined. The limits of the concentration regions with differently arranged structures of solutions were established, and the preferable solvation parameters of the solution components were evaluated.

The dependence of the binding energies in molecules and crystals on the interatomic distances near the equilibrium position was established in the framework of the Mie equation using the force constants of molecules and the elasticity moduli of solids. To evaluate the repulsion forces, we used the Morse function for molecules and the Born-Landé approach for ionic crystals.

The crystals of a heterobimetallic complex based on lead(II) hexafluoroacetyl acetonate and copper(II) trifluoroacetyl acetonate were investigated by X-ray diffraction. Crystal data for Cu(tfa)₂⋅Pb(hfa)₂: a = 9.3991(4) Å, b = 11.7816(5) Å, c = 13.9736(5) Å, α = 88.311(2)°, β = 89.972(1)°, γ = 76.326(1)°, space group P-1, Z = 2, d_calc = 2.190 g/cm³. The basic structural motif for the complexes is coordination polymer in the form of chains of alternating complex molecules. The Cu(tfa)₂ molecules have a trans configuration. The results of a DTA-TG analysis of the compound are given.

New volatile β-iminoketonate complexes of Ni(L)₂ and Pd(L)₂ were obtained. β-Aminovinylketone C(CH₃)₃C(NH₂)CHC(O)C(CH₃)₃ was used as HL. Synthesis of the compound is described, and element analysis, DTA, and IR spectral data are given. The complexes were investigated by XRPA and XRD. The structures are molecular, consist of the trans complexes, and are isostructural. The central atoms have a square plane environment with a (MO₂N₂) coordination unit. The M-О and M-N distances and the N-M-O valence chelate angles are equal, 1.834 Å, 1.848 Å, and 94.2° for Ni(L)₂ and 1.972 Å, 1.975 Å, and 92.4° for Pd(L)₂.

The crystal structures of the Rh[(EtO)₂PS₂]₃ (I) and Co[(PhO)₂PS₂]₃ (II) chelate compounds were determined from X-ray diffraction (XRD) data (CAD-4 diffractometer, MoK_α radiation, 1193 F_hkl, R = 0.0516 for I and 513 F_hkl, R = 0.0305 for II). Crystals I are monoclinic: a = 14.233(3) Å, b =13.570(3) Å, c = 14.272(3) Å; β = 90.66(3)°, V = 2756.3(10) ų, Z = 4, ρ_calc = 1.587 g/cm³, space group C2/c. Crystals II are trigonal: a = 15.149(2) Å, c = 30.306(6) Å; V = 6023.2(16) ų, Z = 6, ρ_calc = 1.493 g/cm³, space groupR3. Structures I and II consist of discrete mononuclear molecules. The coordination polyhedra of the M atoms (M = Rh, Co) are distorted octahedra formed by six sulfur atoms of three cyclic bidentate ligands.

The molecular and crystal structure of dimethyl-(1,4-dimethyl-7-ethylazulyl)-sulfonium perchlorate and dimethyl-(1,4-dimethyl-7-isopropylazulyl)-sulfonium perchlorate was determined by X-ray diffraction analysis. Their crystal structure is mainly determined by C-H…π intermolecular interactions.

The hydroquinone-dimethyl sulfoxide-toluene system was investigated by thermal and X-ray diffraction analyses. The crystal structure of the 1:1 complex of hydroquinone with dimethyl sulfoxide was determined. Crystal data: C₈H₁₂O₃S, M = 188.24, triclinic system, space group P1, unit cell parameters: a = 7.4202(2) Å, b = 8.4046(3) Å, c = 8.7340(3) Å; α = 100.830(1)°, β = 99.794(1)°, γ = 114.129(1)°; V = 469.35(4) ų, Z = 2, d_calc = 1.332 g/cm³, R1 = 0.028, T = 100 K. The molecules are linked in a supramolecular assembly via D-H…A hydrogen bonds (D = O, C; A = O, π).

Synthesis, X-ray phase analysis (XRPA), and IR spectroscopic study were performed to investigate the structure of [Cu(m-HBH)₂(OH₂)₂]SO₄⋅H₂O, where m-HВН = С₇Н₈О₂N₂ (3-hydroxybenzoylhydrazine); а = 7.154(3) Å, b = 8.012(2) Å, c = 20.061(2) Å, β = 90.56(2)°; P2₁, Z = 2, R(F) = 0.046. The structure of the compound consists of the [Cu(m-HBH)₂(OH₂)₂]²⁺ complex cations, anions, and one water molecule. The copper atom is surrounded by a tetragonal bipyramid; c.n. is 6 = 4 + 2 (the distances are 2.030(5) Å, 2.054(6) Å, 2.061(5) Å, and 2.097(3) Å (equatorial); 2.459(4) Å and 2.53(4) Å (axial)). In complex compounds of 3d metals containing m-HВН, the function of the latter is probably invariable; the distribution of the anions and water molecules in the structure depends on the type of the metal and on the anion shape and geometry for metals with slightly different ionic radii.

A Cu₁O_1.7 oxide film containing a large amout of superstoichiometric oxygen was obtained by low-temperature oxidation of metallic copper in the oxygen plasma. An STM study of the film structure showed that ~10 nm planar copper oxide nanocrystallites with particles packed parallel to the starting metal surface. In an XPS study, the spectral characteristics of the Cu2p and O1s lines indicated that particles with a CuO lattice formed (E_bnd(Cu2p_3/2) = 933.3 eV and a shake-up satellite, E_bnd(O1s) = 529.3 eV). The additional superstoichiometric oxygen is localized at the sites of contact of nanoparticles in the interunit space and is characterized by a state with the binding energy E_bnd(O1s) = 531.2 eV. Due to the formation of a nanostructure in the films during low-temperature plasma oxidation, the resulting copper oxide has a much lower thermal stability than crystalline oxide CuO.

The current state of research on the nature of the chemical bond and the physicochemical properties of binary Th-X (X = H, B, C, N, O, P, S, As, Se, Sb) and ternary (carbonitrides, thorates, and silicates) thorium compounds by modern ab initio methods of the band structure theory is reviewed. The possibilities of the ab initio band structure methods in describing the structural states, phase stability, elasticity characteristics, X-ray emission, absorption, and photoelectron spectra of thorium-containing systems are discussed.

The volatile Fe(dpm)₃ complex was studied by X-ray diffraction at 243 K and 210 K. A phase transition from monoclinic to triclinic structure was found in the temperature range 236-226 K. The packing of complexes in the structures is analyzed by the procedure of translation sublattice isolation. The motif of mutual arrangement of Fe atoms is pseudohexagonal in both modifications. Apart from the differences in the Fe…Fe distances, there are differences in rotation of definite chelate rings.

[RhPy₄Cl₂]₄[Re₆S₈(CN)₆]⋅1.5H₂O (Py is pyridine) was investigated by X-ray analysis. In the cluster anion, the Re-Re distances vary from 2.6063(2) Å to 2.6125(2) Å. For two crystallographically independent complex cations, the distances are 〈Rh-N〉 2.060 Å and 〈Rh-Cl〉 2.336 Å. The motif of the three-layered close packing was found; the [Re₆S₈(CN)₆]^4- anions follow the vertices of a rhombohedron with the parameters a_c ≈ 15.5 Å and α_c ≈ 61°.

The crystal and molecular structure of 1-phenyl-1-fluoro-5-methylquasisilatrane PhFSi(OCH₂CH₂)₂NMe was investigated by X-ray diffraction at 100 K. The coordination polyhedron of the silicon atom in the molecule is a slightly distorted trigonal bipyramid containing fluorine and nitrogen atoms in the axial positions and two endocyclic oxygen atoms and the carbon atom of the phenyl group at three vertices of the equatorial plane.

The products obtained from the Pt_0.25Os_0.75 nonequilibrium solid solution treated by the thermobaric procedure (1.5-2 GPa, 2000°C, 3 min) were investigated by X-ray powder diffraction. The phase compositions were evaluated from quantitative X-ray phase analysis, energy dispersion spectroscopy, and crystal-chemical analysis data for known Pt_хOs_1-х phases.