Home – Home – Jornals – Journal of Structural Chemistry 2011 number 2

Quantum chemical calculations are applied to study the structure and energy of the complexes of a series of Schiff bases (SBs) with acetic acid. The results of the calculations give evidence that a weak hydrogen bond occurs between the oxygen atoms of the acid and SB aromatic protons in these complexes along with the CH₃СOOH…N=CH Н-bond. The structure of the complexes is confirmed experimentally by measuring the nuclear Overhauser effect. The effect of the properties of SB terminal substituents on the stability of SB-acid complexes is analyzed.

A quantum chemical study of the internal rotation of CX₃ (X = H, F, CH₃) radical substituents in scandium and calcium β-diketonate complexes is performed. Calculations are carried out using the GAUSSIAN-03 program at the HF and DFT/B3LYP levels with relativistic effective core pseudo-potentials and valence double zeta basis sets. Analytical expressions V(ϕ) are obtained that describe the potential energy variation during the rotation of СХ₃ groups. The rotation of CH₃ and CF₃ groups is shown to be described by a simple potential of the form V = V₀/2 + V₃cos(3ϕ), while for the description of the rotation of tert-butyl groups it is required to use a more complex function V = V₀/2 + V₃cos(3ϕ) + V₆cos(6ϕ). Based on the obtained expressions for V(ϕ), the effective torsion angles ϕ_ef of the rotation of СХ₃ groups are calculated for different temperatures. It is shown that ϕ_ef obtained based on the quantum chemical calculations are close to the values obtained in electron diffraction experiments.

A systematic study on the structural characteristics of the 2-pyranone ring containing molecules with bromine, nitrile, and amide substituents at the C-3 position in the ring is conducted in the electronic ground (S₀) state by DFT calculations using the B3LYP/6-311++G** method. The geometrical structure of the bromine substituted compound, which shows potent hepatoprotective activity, is studied both in the ground (S₀) and first excited singlet (S₁) states using RHF/6-311++G** and CIS/6-311++G** methods respectively. The molecules are found to exist in two isomeric forms gauche and trans that have the enthalpy difference of less than 3.32 kcal/mol; the latter is the preferred orientation in the gaseous phase. The S₁ state is a ¹(π,π*) state that arises π-electron transfer from the region of a double bond in the pyranone ring to the region of the internuclear bond connecting the 2-pyranone and benzene rings. A complete vibrational analysis is conducted for the 3-bromo-6-(4-Chlorophenyl)-4-thiomethyl-2H-pyran-2-one molecule based on the experimental infrared spectra in the 50-4000 cm^-1 region and DFT/6-311++G** computations of vibrational frequencies for the gauche and trans isomeric forms. Spectral assignments based on the potential energy distribution along the internal coordinates confirm the non-planar structure of the molecule.

2-Chloro-1,3,2-dioxaphosphorinane-2-oxide, -sulfide, and -selenide are studied at the DFT/B3LYP level and several ab initio methods using a 6-311G** basis set. Our energy optimizations by all these methods show that for oxide DFT and ab initio methods are not much different, while for the sulfide and the selenide the DFT relative energies are higher by about a kcal/mol as compared to those of MP2, MP3, MP4(SDTQ)//MP2, and CCSD(T)//MP2 (//MP2 indicates that a single-point calculation based on the MP2 optimized geometry is performed). However, regardless of rather large relative energies, that does not change the fact that in all three cases the conformational equilibrium mixture contains more than 95 % of the lowest, chair-equatorial conformer (this indicates that the P=X bond is in equatorial position). This one and the next higher conformer (chair-axial) are confirmed to be real conformers (energy minima) in all cases. The energetically much higher twist and boat forms are probably just stationary states and local maxima because in many cases, geometry optimizations do not converge to them. Only for MP2 and the selenide do all optimizations converge to the desired stationary state. The relative energies could all be explained in terms of anomeric effects and ring strains. The decreasing covalent character of the P=X bond, with X changing from O to S and to Se, shows itself in the increasing bond lengths and the decreasing strength of anomeric effects.

2-Chloro-1,3,2-dioxaphosphorinane-2-oxide, -sulfide, and -selenide are studied with the help of DFT/B3LYP and several ab initio methods using a 6-311G** basis set. However, due to rather large relative energies of higher conformers in all three cases, the conformational equili-brium mixture contains more than 95 % (see the preceding paper in this Journal) of the lowest chair-equatorial conformer (this indicates that the P=X bond is in the equatorial position), so we do not find any conformer bands in the experimental spectra and calculate our theoretical ones for the assignment only fr om the chair-equatorial conformer. The vibrational infrared and Raman spectra were calculated and are in fair agreement with their experimental counterparts. Potential energy distribution calculations are performed, and the theoretical modes wh ere an experimental counterpart could be found to symmetry coordinates are assigned.

The splitting of the ν(С=О) absorption band (AB) of about 12 cm^-1 is found in the IR spectra of diphenylphthalide (DPP) in the crystalline phase and CCl₄ solution. In the crystalline phase, this splitting is likely to be caused by the inequivalence of DPP molecules in the crystallographic cell, while in the solution, by the dimerization of DPP molecules via dipole-dipole and/or hydrogen bonds. A theoretical low-frequency shift of the ν(С=О) AB for a complex of two DPP molecules (in comparison with a single molecule) is 14 cm^-1 in the PBE/3ξ approximation, which is close to the experimentally observed splitting. In two quantum chemical approximations (B3LYP/6-311G(d,p) (I) and PBE/3ξ (II)) the optimal structure and vibrational spectrum of DPP are calculated. Approximation I better reproduces the intensities, whereas approximation II better reproduces the IR frequencies of the DPP spectrum. Almost all 48 ABs of the IR spectrum of DPP are assigned to theoretical normal vibrations (modes). Based on the potential energy distribution over natural coordinates and the visualization of vibrations, experimental ABs (and the corresponding modes) are assigned to the stretching and bending vibrations of certain bonds in the DPP molecule. In particular, ABs at 1107 cm^-1 and 970 cm^-1 are assigned to the ν(-OC-O-) and ν(-C-O-) stretching vibrations, respectively, of the DPP lactonic ring, which differs from the previously accepted assignment. The results of the interpretation of the DPP spectrum are used to assign a number of ABs in the IR spectrum of polydiphenylenephthalide (PDP), for which DPP is a model compound. According to the calculations in approximation II of the vibrational spectrum of a model valence-bonded dimeric molecule, the intense complex AB at 800-870 cm^-1 in the IR spectrum of PDP is mainly due to the out-of-plane bending vibrations of C-Н bonds in the 1,4-substituted benzene rings of polymer biphenyl moieties and the bending vibrations of the lactonic ring.

Phosphoryl chloride is used as a starting material to synthesize new diazaphosphole, (1) and diazaphosphorinane, (2). The products are characterized by ¹H, ¹³C, ³¹P NMR and IR spectroscopy. A high value ²J(PNH) = 17.0, 17.2 Hz is measured for two non-equivalent NH protons of endocyclic nitrogen atoms in compound 1, while it greatly decreases to 4.5 Hz in 2. Also, great amounts are obtained for two ²J(P,C) as well as two ³J(P,C) in the ¹³C NMR spectrum of 1, but they are zero in 2. Here, the effect of ring strain and ring size on the structural and spectroscopic parameters is observed. The ³¹P NMR spectra reveal that δ(³¹P) of compound 1 is far much more downfield (12.63 ppm) relative to that of compound 2 (-10.39 ppm). Furthermore, ab initio quantum chemical calculations are performed to optimize the structures of these molecules by density functional theory (B3LYP) and Hartree-Fock (HF) methods, using the standard 6-31+G** basis set. The stabilization energies are calculated by the equation ΔE_{stabilization} = E_molecule - ∑E_i, where i = atom. To obtain the atomic hybridizations, NBO computations are made at the B3LYP/6-31+G** level. Also, by NMR calculations the ¹H, ¹³C, ³¹P chemical shifts are obtained and compared with the experimental ones.

The structure of the resonant electron emission (REE) spectra of UO₂ (REE appears under the excitation with synchrotron radiation near the O_4,5(U) absorption edge at ~100 eV and ~110 eV) is studied with regard to the X-ray O_4,5(U) absorption spectrum of UO₂ and a quantitative scheme of molecular orbitals based on the X-ray electron spectroscopy data and the results of a relativistic calculation of the electronic structure of UO₂. The structure of the REE spectra of U₃O₈ and UO_2+x is studied for comparison, and the effect of the uranium chemical environment in oxides on it is found. The appearance of such a structure reflects the processes of excitation and decay involving the U5d and electrons of the outer valence MOs (OVMOs, from 0 to ~13 eV) and inner valence MOs (IVMOs, from ~13 eV to ~35 eV) of the studied oxides. It is noted that REE spectra show the partial density of states of U6p and U5f electrons. Based on the structure of REE spectra, it is revealed that U5f electrons directly participate (without losing the f nature) in the chemical bonding of uranium oxides and are delocalized within CMOs (in the middle of the band), which results in the enhancement of the intensity of the REE spectra of CMO electrons during resonances. The U6d electrons are found to be localized near the bottom of the outer valence band and are observed in the REE spectra of the studied oxides as a characteristic maximum at 10.8 eV. It is confirmed that U6p electrons are effectively involved in the formation of IVMOs, which leads to the appearance of the structure in the region of IVMO electron energies during resonances. This structure depends on the chemical environment of uranium in the considered oxides.

A method based on the statements of molecular association theory and a simple lattice model (ASL = Associated Solution + Lattice) is used to calculate the solubility of a series of porphyrin macrocycles (blood porphyrins) in binary solvents (tetrachloromethane-ethyl acetate, tetrachloromethane-methanol). Separate contributions to solubility are identified and the relative role of different factors determining the solubility dependence on the mixed solvent composition is analyzed. The calculated solubility values are in good agreement with the experimental data obtained for the studied systems by the isothermal saturation method with a spectrophotometric control of concentrations.

An X-ray diffraction study and simulation of the structure of ternary Al_81.6Ni_14.9Fe_3.5, Al_71.6Ni₂₃Fe_5.4, and Al_61.1Ni_31.1Fe_7.3 melts by the reverse Monte Carlo method are conducted. An analysis of the structural models of melts is performed by the Voronoi-Delaunay partition. It is shown that the prepeak on the structure factor curves in the diffraction vector range of 13 nm^-1 to 22 nm^-1 is due to two factors: chemical ordering of atoms and non-crystalline close packing. The origin of the icosahedral short-range order in the melts as one of the variants of ordering of atoms in non-crystalline close packed clusters is discussed.

The Tikhonov regularization of the reference intensity ratio (RIR) method integrated within the information retrieval system of X-ray phase analysis together with the method of cluster phase identification is reported. The possibilities of the methods are discussed by the example of the X-ray phase analysis of test mixtures from Round Robin on QPA held by the International Union of Crystallography Commission for Powder Diffraction (CPD).

The local structure of aluminas obtained from hydroxides (pseudo-boehmites) synthesized by different methods is studied using the radial density distribution function,. The occupancy of the cation sites of different types (tetrahedral and octahedral, spinel and non-spinel) in the structure of the studied oxides is analyzed.

Pure titania, zirconia, and mixed oxides (3-37 mol.% of ZrO₂) are prepared using the sol-gel method and calcined at different temperatures. The calcined samples are characterized by Raman spectroscopy, X-ray powder diffraction, scanning electron microscopy, transmission electron microscopy, and nitrogen adsorption porosimetry. Measurements reveal a thermal stability of the titania anatase phase that slightly increases in the presence of 3-13 mol.% of zirconia. Practically, the titania anatase-rutile phase transformation is hindered during the temperature increase above 700 °C. The mixed oxide with 37 mol.% of ZrO₂ treated at 550 °C shows a new single amorphous phase with a surface area of the nanoparticles double with respect to the other crystalline samples and the formed srilankite structure (at 700 °C). The anatase phase is not observed in the sample containing 37 mol.% of ZrO₂. The treatment at 700 °C causes the formation of the srilankite (Ti_0.63Zr_0.37O_x) phase.

A composite constituted by zirconia supported on magnesia is thermally treated. Depending on temperature, several crystal sizes and crystalline zirconia structures are obtained. At low temperatures, cubic zirconia crystals are found to be deposited on the crystalline magnesia matrix. As temperature increases, the cubic zirconia phase transforms to the tetragonal and the monoclinic phases. They form clusters supported on the MgO matrix. All these results are supported by different analytical techniques and a catalytic test.

By the hydration of MVO(SeO₄)₂ with saturated water vapors at room temperature a series of isostructural complex compounds of vanadium(V) of the composition M[VO₂(SeO₄)(H₂O)₂]·H₂O (K, Rb, NH₄) are synthesized and their physicochemical properties are studied. Based on the X-ray and neutron diffraction data, it is found that their crystal structure is composed of VO₆ octahedra linked in infinite chains by bridging SeO₄ tetrahedra. Each of the VO₆ octahedra has two short terminal V-O bonds forming a bent dioxovanadium group Two water molecules are coordinated by vanadium and one molecule is out of the first coordination sphere in the interchain space. The vibrational spectra of the studied compounds are completely consistent with their structural features.

Double complex salts (DCSs) [Co(NH₃)₆][Fe(CN)₆] (I) and [Co(NH₃)₆]₂[Cu(C₂O₄)₂]₃ (II) and complex [Co(NH₃)₆]₂(C₂O₄)₃·4H₂O (III) are synthesized and investigated by single crystal XRD, crystal optics, and elemental analysis. The crystalline phases of I, II, and III (R-3, P2₁/c, and Pnnm space groups respectively) have the following crystallographic characteristics: a = 10.9804(2) Å, b = 10.9804(2) Å, c = 10.8224(3) Å, V = 1130.03(4) ų, Z = 3, d_x = 1.65 g/cm³ (I); a = 9.6370(2) Å, b = 10.2452(2) Å, c = 13.2108(3) Å, V = 1932.90(9) ų, Z = 2, d_x= 1.97 g/cm³ (II), and a = 11.7658(3) Å, b = 11.7254(3) Å, c = 14.1913(4) Å, V = 1304.34(5) ų, Z = 2, d_x = 1.68 g/cm³ (III). This paper investigates the products of DCS thermolysis in a hydrogen atmosphere: the intermetallic compound CoFe with the bcc parameter а = 2.852 Å for I and a heterogeneous mixture of Co and Cu in the decomposition of II. The coordinated CN^- and groups then turn into NH₃, hydrocarbons, and CO₂. The dominant hydrocarbon is methane.

Two metal-organic coordination polymers [Cu(bpy)₂(H₂O)₂](NO₃)₂·4.5C₂H₅OH (1) and [Cu₂(bpy)(H₂O)(L-pha)₂](NO₃)₂·H₂O (2) (L-Hpha = L-phenylalanine, bpy = 4,4′-bipyridyl) are prepared by slow evaporation of an aqueous alcoholic solution of copper nitrate, L-phenylalanine, and 4,4′- bipyridyl. The structure and composition of the obtained compounds are determined by single crystal XRD. The framework of compound 1 is positively charged and forms two types of intersecting channels. Compound 2 is a homochiral metal-organic coordination polymer whose structure contains L-phenylalanine anions.

Single crystal X-ray diffraction is used to investigate two synthesized β-diketonate complexes of copper(II) with aminopyridine: Cu(4-NH₂Py)(aa)₂ (I) and Cu(4-NH₂Py)(hfa)₂ (II). The crystals of I and II have a monoclinic system; the unit cell parameters of I are: P2₁/n space group, a = 8.2921(3) Å, b = 14.7243(5) Å, с = 13.4970(4) Å, β = 102.426(1)°, V = 1609.32(9) ų, Z = 4; for II: С2/c space group, a = 23.5704(5) Å, b = 11.4977(2) Å, с = 16.0285(3) Å, β = 109.265(1)°, V = 4100.6(1) ų, Z = 8. The structures of I and II are molecular; they are composed of isolated molecules. The coordination polyhedron of the copper atom is formed by the О atoms of two acetylacetonate ligands (Cu-O 1.940(2)-2.171(2) Å) in I and the O atoms of two hexafluoroacetylacetonate ligands (Cu-O 1.940(2)-2.215(3) Å) in II. The molecules of 4-NH₂Py are bonded to the copper atom via the nitrogen atom of the aromatic ring (Cu-N 2.008(2) Å in I and Cu-N 1.978(3) Å in II). Noncoordinated amino groups join the molecules of the complexes together by means of N-H…O hydrogen bonds.

Polymeric complexes of [Cu₂Cl₂L₂]_∞ copper(I) chloride (1) (L = N¹,N²-bis(5-methylpyridin-2-yl)-oxalamide)) and {[Cu₂(C₂O₄)Cl₂L](L)·2H₂O}_∞ copper(II) chloride (2) are obtained. The complexes are studied by powder and single crystal XRD. It is found that during the reaction of L with copper(II) chloride in the formation of complex 1 copper(II) is reduced to copper(I), while the formation of complex 2 is accompanied by the hydrolysis of the ligand.

The crystal structures of double complex salts [M(NH₃)₅Br][AuBr₄]₂·H₂O (M = Ir, Rh) are determined by single crystal XRD. The compounds crystallize in the triclinic system, P-1 space group, Z = 4. Crystallographic characteristics: [Ir(NH₃)₅Br][AuBr₄]₂·H₂O: a = 8.2982(3) Å, b = 15.3045(4) Å, c = 17.4378(6) Å, α = 73.064(1)°, β = 88.938(1)°, γ = 86.221(1)°, V = 2113.95(12) ų, d_x = 4.419 g/cm³, R = 0.0469; [Rh(NH₃)₅Br][AuBr₄]₂·H₂O: a = 8.2855(2) Å, b = 15.2881(3) Å, c = 17.4053(4) Å, α = 73.015(1)°, β = 88.913(1)°, γ = 86.267(1)°, V = 2104.08(8) ų, d_x = 4.165 g/sm³, R = 0.0480. The crystal structure of [Ir(NH₃)₅Br]Br₂ is determined. The compound crystallizes in the orthorhombic system, Pnma space group, Z = 4. Crystallographic characteristics: a = 13.8521(3) Å, b = 10.8570(2) Å, c = 6.9908(1) Å, V = 1049.31(3) ų, d_x = 3.273 g/cm³, R = 0.0127.

A crystal structure of a new layered [Nb₄OI₈][Mo₆I₁₄]_2∞ polymer containing a previously unknown niobium cluster {Nb₄(μ₄-O)I₈}²⁺ with a μ₄ oxygen atom is determined. The compound crystallizes in the triclinic space group with unit cell parameters a = 10.1842(6) Å, b = 10.1880(6) Å, c = 11.5700(6) Å, α = 78.058(2)°, β = 77.944(2)°, γ = 80.738(2)°, V = 1139.85(11) ų, Z = 1, R_f = 0.0414. The electronic structure of the [{Nb₄(μ₄-O)I₈}I₄]^2- cluster complex is calculated.

A cluster complex of the composition [Zn₂(NH₃)₆(μ-OH)][Zn(NH₃)₄]_0.5[Re₄Te₄(CN)₁₂]·5H₂O is obtained by the interaction of an aqueous solution of K₄[Re₄Te₄(CN)₁₂]·5H₂O with an aqueous ammonia solution of ZnCl₂. The compound crystallizes in the C2/m (12) monoclinic space group with unit cell parameters a = 23.233(2) Å, b = 14.5906(16) Å, c = 14.3825(15) Å, β = 125.169(1)°, V = 3985.5(7) ų, Z = 4, d_x = 3.290 g/cm³. The structure is built from cluster [Re₄Te₄(CN)₁₂]⁴⁻ anions and complex [Zn₂(NH₃)₆(μ-OH)]³⁺ and [Zn(NH₃)₄]²⁺ cations; the latter is disordered over two positions.

The compounds of Eu(III) with nicotinic acid and enrofloxacin are synthesized. Their composition and structure are proved by the data of elemental analysis, IR and luminescence spectroscopy, powder and single crystal X-ray diffraction. By single crystal X-ray diffraction, the structure of the compound of Eu with nicotinic acid is identified as a centrosymmetric dimer with 4 carboxylate bridges of the composition Eu₂(C₆H₄NO₂)₆·4H₂O. The Stark structure of the ⁵D₀-⁷F_j transitions in the mixed-ligand compounds of Eu(III) with nicotinic acid and enrofloxacin is determined. The bands of IR spectra are assigned; the conclusion about the bidentate coordination of ligands is made

A novel oxazole-5-one derivative 2-o-tolyl-4-(3-N,N-dimethylaminophenylmethylene)-oxazol-5-one (TDPO) C₁₉H₁₈N₂O₂ is synthesized and characterized and the crystal structure is determined by X-ray crystallography. TDPO is monoclinic in the P2₁/c space group. The molecule adopts the Z configuration. To enlighten the flexibility of TDPO, the sel ected torsion angle is varied fr om -180° to 180° in each 10° separately, and the molecular energy profile is calculated and analyzed by density functional calculations. In addition, Bader′s QTAIM analysis is performed to investigate the intramolecular weak interactions.

The current state of studies on binary complex compounds [M¹L_a]_x·[M²A_b]_y (М¹ and М² are the central ions, L and А are ligands) is considered, notably: synthesis, composition, structures, magnetic properties, and thermal decomposition.

B3LYP/6-311+G(d,p) and MP2/6-31G(d,p) methods are used to study the electronic structure of a 1,2,4-triazine molecule. Quantitative characteristics of the reactivity are obtained in the form of atomic charges and Fukui coefficients. Thermodynamic characteristics are determined for the protonation reaction and addition of the hydride anion to a 1,2,4-triazine molecule.

In the microwave spectrum of 4,4-dimethyl-1,3-dioxane, the rotational transitions of a, b, and c types with J ≤ 54 are identified in the ground vibrational state of the molecule in the frequency range of 12 GHz to 37 GHz. Rotational constants, quartic centrifugal distortion constants, and the dipole moment of the molecule are determined. The revealed transitions are found to belong to the chair conformer. The B3PW91/aug-cc-pVDZ method is used to calculate the geometric parameters of 1,3-dioxane, 4-methyl-1,3-dioxane, and 4,4-dimethyl-1,3-dioxane. Alkyl substitution is shown to cause changes in the geometry of the 1,3-dioxane core.

Changes in the structure of synthetic Mg_xAl_y(OH)_z layered double hydroxides are studied during the sorption of organic compounds.

The crystal structure of Na₂[ReCl₆]·6H₂O is determined. The crystallographic characteristics are as follows: a = 6.6955(2) Å, b = 7.0926(2) Å, c = 8.3667(3) Å; α = 102.567(1)°, β = 98.853(2)°, γ = 107.236(1)°; V = 360.08(2) ų, P-1 space group, Z = 1, d_x = 2.550 g/cm³. The thermal properties of Na₂[ReCl₆]·6H₂O are studied in the hydrogen atmosphere. During the thermolysis of Na₂[ReCl₆]_0.50[PtCl₆]_0.50·6H₂O double complex salt in the hydrogen atmosphere, Re_xPt_1-x nanocrystalline solid solutions were obtained.