Home – Home – Jornals – Journal of Structural Chemistry 2011 number 3

The electronic structure, geometry, and thermodynamic parameters of the high-energy states of NO₃ and the (NO)₂ dimer are calculated at the DFT B3LYP/6-311++G(3df) level within the symmetrized Kohn-Sham formalism. The results of the DFT calculation of the excited states of NO₃ well agree with the experimental data and precise ab initio calculations. The reactivity of high-energy nitrogen trioxide in the activation of molecular nitrogen and nitrogen protoxide is analyzed. The assumption is substantiated that the Karavaev effect (gain of nitrogen oxides in an air mixture with nitric acid vapors) is due to the photochemical activation of molecular nitrogen in the presence of an NO₃ high-energy state as a decomposition product of nitric acid.

By means of the formula that characterizes the correlation between the parameters of XH…Y linear fragments ( are the bond lengths in free molecules, b^XHX, b^YHY are the dimensional coefficients) r^XX(r^XH) and r^XY(r^YH) dependences are obtained. Given the length of a hydrogen bridge formed by O, N, and F atoms, they enable us to find the proton position in the bridge. The definition "a quasi-symmetric hydrogen bond," based on the invariance of the r^XX distance when the proton shifts by 0.1 Å, is established to be applicable to ОНО, FHF, NHN, and ClHCl fragments. It is shown that the hydrogen bridge length remains almost constant (exceeds the minimum length by no more than 0.1 Å) if its bond orders are above 0.1. Here the displacement of the central proton can reach 0.2-0.3 Å.

This work deals with the interaction between urea and DNA bases (adenine, thymine, guanine, and cytosine). The optimized geometries, binding energies, and harmonic vibrational frequencies are calculated using the DFT/B3LYP functional combined with the 6-31+G(d,p) basis set. Their interactions are studied aiming to understand more about the nature of the intercalation binding forces between urea and DNA. Fourteen stable complexes are found on the potential energy surface. The structures are cyclic; they are stabilized by NH…O/N and CH…O interactions. The binding energies range from -19.9 kJ·mol^-1 to -74.0 kJ·mol^-1. The obtained formation energies indicate that Urea:G and Urea:C are more favorable than Urea:T and Urea:A.
In addition, the Atoms in Molecules theory is performed to study the hydrogen bonds in the complexes.

The structures and conformational stabilities of phenylphosphonic and phenylthiophosphonic acids are investigated using calculations mostly at the DFT/6-311G** level and ab initio ones at the MP2/6-311G** level (no frequency calculations in the latter case), because we know from our previous results that the addition of diffuse functions to a valence triple zeta basis with polarization functions might lead to an unbalanced basis set. Further, the experience tells that for large energy differences between conformers, DFT works very well. From the calculations the molecules are predicted to exist in a conformational equilibrium consisting of two non (near)-planar conformers that are identical by symmetry. Interestingly, in the internal rotation potential functions the planar conformer appears to be a stable minimum (also optimization converges to planar), however the vibrational frequencies were computed and the planar conformer exhibited an imaginary one, indicating that it is a maximum with respect to one of the internal coordinates. Only optimization without any restrictions and starting from a non (near)-planar structure converged to a real minimum with a non (near)-planar geometry. In the minimum structure, vibrational infrared and Raman spectra are calculated and those for phenylphosphonic acid are compared to experimental ones, showing satisfactory agreement. The rather low intensity of the OH bands in the experimental infrared spectrum (as compared to normal organic acids) indicates rather weak hydrogen bonding with at most dimers present. Normal coordinate calculations are carried out and potential energy distributions are calculated for the molecules in the non (near)-planar conformations providing a complete assignment of the vibrational modes to atomic motions in the molecules. From the rather low rotational barriers we conclude, in agreement with the results from the literature (for other P=O compounds) based on localized orbitals, that conjugation effects are absent - or at least negligible - as compared to electrostatic and steric ones.

By X-ray photoelectron spectroscopy (XPS), using the technique of layer-by-layer analysis, the films of (HfO₂)_x(Al₂O₃)_1-x solid solutions synthesized by chemical vapor deposition are studied. The possibility to determine the structure of solid binary solutions based on the analysis of the XPS spectra is demonstrated.

A strict approach to determine the adiabatic compressibility of a solvent at constant entropy of the solution is developed. It is shown that the apparent adiabatic compressibility of a solute is not strictly equal to the pressure derivative of the apparent molar volume of a solute at constant entropy of a solution in the general case. With this approach, the equation for hydration numbers and adiabatic compressibility of hydrate complexes is obtained thermodynamically correctly. Parameters of the hydration of potassium chloride, bromide, and iodide are found.

Cyclohexane and 2,3-dimethylbutane molecules are the most compact among saturated С6-hydrocarbons. They have a similar size and are arranged in the liquid phase like atoms in simple liquids. However, the cyclohexane density is higher approximately by 20% than that of 2,3-dimethylbutane. The reasons of this distinction are discussed. It can be explained within the concepts of the physics of simple liquids. According to them, a small variation of the radius of a particle hard core or the pair interaction energy can lead to appreciable changes in the structure and density of a liquid. The obtained results give grounds to discard the explanations based exclusively on the features of the shape of the given molecules.

The formation of solid solutions in the Re-Rh system upon thermobaric treatment (P = 4 GPa, T = 1600°C) of nanocrystalline composite mixtures containing rhodium and rhenium is studied. The boundaries of the decomposition region of solid solutions in the Re-Rh system under high pressure are found. It is shown that they coincide with the boundaries found at normal pressure.

In the Bi₂O₃-SiO₂-O₅ system, single crystal solid solutions of the sillenite family of the general composition Bi₂₄(Bi,Si,V)₂O₄₀ are obtained by a hydrothermal method and for the first time characterized by neutron and X-ray diffraction analysis. The tetrahedral position is found to contain vanadium ions with different formal charges (V⁴⁺ and V⁵⁺) responsible for green and orange colors, respectively, of the samples. For the first time, for some sillenites of this system dissymmetrization of the structure (a transition from the I23 space group into P23) is revealed, which is caused by the presence of several atoms in one crystallographic position and also by crystal growth conditions.

Crystallographic analysis is used to study the structure of (Cd,Pb)Bi₂S₄ (kudriavite), Bi₃In₅S₁₂, Pb₄In₃Bi₇S₁₈, Pb_1.6In₈Bi₄S₁₉, Pb₄In₂Bi₄S₁₃, Bi₂In₄S₉ lozenge-like sulfides (with the m plane perpendicular to the translation ~4 Å). It is shown that the structure bases contain regular cation and anion sublattices whose conjugation within the common translation cell is determined by the cation/anion ratio. The independent collective ordering of cations results in complex variants of their occupation of separate crystallographic sites. Sometimes independent anionic ordering leads to unusual coordination environments.

For the first time, new hybrid organic-inorganic layered zirconium pentafluorides of methylammonium, glycinium, and β-alanine with the composition (CH₃NH₃)ZrF₅·0.5H₂O, (H₃NCH₂COOH)ZrF₅·2H₂O, and (H₃N(CH₂)₂COOH)ZrF₅ are synthesized and their structures are analyzed. In the studied compounds, CN of the Zr atom is 8, and its coordination polyhedron represents a dodecahedron sharing its 6 vertex with three neighboring Zr polyhedra. The Zr dodecahedra are joined with each other in planar netlike anion layers of the composition . The anion layers are hydrogen bonded into a three-dimensional structure by H₂O cations and molecules.

Using the single crystal X-ray diffraction data (150 K, Bruker X8 Apex CCD autodiffractometer, МоK_α radiation), the crystal structure of the [Cd₂L₂Cl₄]·CH₂Cl₂ (L = pyrazolylquinoline, the derivative of monoterpenoid (+)-3-carene) compound is determined. Crystals are monoclinic, unit cell parameters are: a = 10.7005(4) Å, b = 16.8491(4) Å, c = 11.9658(4) Å, β = 93.308(1)°, Р2₁ space group. The structure is formed from discrete acentric molecules of a binuclear [Cd₂L₂Cl₄] complex and uncoordinated CH₂Cl₂ molecules. The Cd²⁺ ions coordinate N atoms of bidentate chelating ligands L, which leads to the closure of two five-membered chelate CdN₃C rings. The coordination sphere of Cd atoms also includes three Cl atoms (two bridging and one terminal), consequently, two CdCl₃N₂ coordination sites and a Cd₂Cl₂ metal ring are formed. The Cl₃N₂ polyhedra have the form of distorted tetragonal pyramids. The CH₂Cl₂ molecules located in the channels formed by the complexes are linked with them by weak H-bonds. The excitation spectra of L and the CdLCl₂ compound contain bands with λ_max of 352 nm and 360 nm respectively. At 300 K and λ_excit 350 nm, in the photoluminescence spectrum of L a rather intense broad split band with λ_max 372 nm and 386 nm is observed. The photoluminescence spectrum of the CdLCl₂ compound contains a broad band with λ_max 418 nm. The photoluminescence intensity of this compound is significantly lower than that of L.

For 12 acetylacetonates of the composition M(acac)_n (n = 2, 3, or 4) and M(acac)(С₂Н₄)₂ (М is a metal) the total area (⁰S) of the faces of Voronoi-Dirichlet polyhedra (VDP) corresponding to all intermolecular contacts of one molecule in the crystal structure and the total volume of pyramids (⁰V), whose bases are formed of such faces and the vertices are occupied by the nuclei of atoms participating in intermolecular contacts, are determined. The key features of non-bonded interactions are considered. The existence of a linear dependence of the sublimation enthalpy of acetylacetonates on the ⁰S or ⁰V parameters of their molecular VDP is revealed. It is shown that the sublimation enthalpy of Ga(acac)₃ requires the refinement and theoretically should be 124 kJ/mol.

Crystal structures of two modifications of a binuclear Pd₂(μ-ac)₂(acac)₂ complex are studied at 150 K and 297 K (ac = acetate; acac = acetylacetonate). It is demonstrated that in both cases, the packing of the complexes can be considered as pseudohexagonal, the molecules forming infinite chains by interactions between chelate rings with the shortest contacts Pd…C_γ ~ 3.3 Å

The structures of volatile pyridine adducts of trimethylplatinum(IV) β-diketonates derived from acetylacetone (Hacac) and dipivaloylmethane (Hdpm) are studied for the first time. Their preparation is reported and the data of thermal studies obtained by the DTA technique are presented. The structures of the compounds in question comprise monomeric complexes. The platinum atom is coordinated to three carbon atoms of methyl groups, two oxygen atoms of β-diketone, and the nitrogen atom of the pyridine molecule. The (PtC₃O₂N) coordination core has the shape of a slightly distorted octahedron. The geometrical characteristics of the coordination cores are the following: in all complexes, the values of Pt-O, Pt-C_Me,
Pt-N bond lengths and O-Pt-O chelate angles fall within 2.122-2.146 Å, 1.986-2.079 Å, 2.131-2.186 Å and 89.3-90.6° respectively.

Novel complex salts [Au(en)₂]Cl(ReO₄)₂ (I) and [Au(en)₂](ReO₄)₃ (II), en = ethylenediamine, are obtained. Their crystal structures are determined by single crystal X-ray diffraction. Complex I crystallizes in the triclinic crystal system: a = 6.2172(7) Å, b = 7.1644(8) Å, c = 8.8829(8) Å, α = 96.605(4)°, β = 110.000(4)°, γ = 97.802(4)°, Р-1 space group, Z = 1, d_x = 3.905 g/cm³; complex II crystallizes in the monoclinic crystal system: a = 15.244(2) Å, b = 7.6809(8) Å, c = 9.3476(12) Å, β = 127.004(3)°, С2 space group, Z = 4, d_x =
4.057 g/cm³.

The complex of terbium(III) with dipivaloylmethane (2,2,6,6-tetramethylheptane-3,5-dione = Htmhd) [Tb(tmhd)₃]₂ (1) and two its adducts with bipyridyl (Bipy) and phenanthroline (Tb(tmhd)₃·Bipy (2) and Tb(tmhd)₃·Phen (3)) are synthesized and analyzed by single crystal X-ray diffraction. The crystals of [Tb(tmhd)₃]₂ (1) belong to the monoclinic crystal system: P2₁/n space group, a = 12.2238(2) Å, b = 27.6369(5) Å, с = 21.8740(4) Å, β = 105.146(1)°, V = 7133.0(2) ų, Z = 4; the crystals of Tb(tmhd)₃·Bipy (2) and Tb(tmhd)₃·Phen (3) belong to the triclinic crystal system with unit cell parameters: (2) space group, a = 11.0554(6) Å, b = 12.2761(7) Å, с = 17.7096(8) Å, α = 77.457(2)°, β = 85.557(2)°, γ = 69.659(2)°, V = 2199.8(2) ų, Z = 2; (3) space group, a = 10.8814(3) Å, b = 12.2852(4) Å, с = 18.3590(6) Å, α = 80.463(1)°, β = 87.587(1)°, γ = 68.640(1)°, V = 2253.6(1) ų, Z = 2. The structures of the complexes are molecular and involve isolated [Tb₂(tmhd)₆] (1), Tb(tmhd)₃·Bipy (2), and Tb(tmhd)₃·Phen (3) molecules. The thermal properties of the obtained terbium complexes are studied by TG-DTA.

The NH₄[Eu^III(Cydta)(H₂O)₂]·4.5H₂O (I) (H₄Cydta = trans-1,2-cyclohexanediamine-N,N,N′,N′-tetraacetic acid) and K₂(pdta)₂(H₂O)₂]·6H₂O (II) (H₄pdta = propylenediamine-N,N,N′,N′-tetraacetic acid) complexes are prepared by heat-refluxing and acidity-adjusting methods respectively, and their composition and structures are determined by elemental analyses and single crystal X-ray diffraction techniques. The complex I has a mononuclear structure, crystallizes in the triclinic crystal system with the space group; the central Eu^III ion is eight-coordinated by a hexadentate Cydta ligand and two water molecules. The crystal data are as follows: a = 8.653(4), b = 10.041(4), c = 14.405(6) Å, α = 88.469(6), β = 74.892(6), γ = 88.256(7)°, V = 1207.5(9) ų, Z = 1, D_c = 1.731 g/cm³, μ = 2.669 mm^-1, F(000) = 638, R = 0.0257, and wR = 0.0667 for 3807 observed reflections with I ≥ 2σ(I). The EuN₂O₆ part in the [Eu^III(Cydta)(H₂O)₂]^- complex anion forms a pseudo-square antiprismatic polyhedron. The complex II is eight-coordinate as well; it is a binuclear structure that crystallizes in the monoclinic crystal system with the C₂/c space group; half of the central Eu^III ion is coordinated by two nitrogen atoms from one hexadentate pdta ligand and six oxygen atoms from the same pdta ligand, one water molecule and carboxylic group from the neighboring pdta ligand respectively. The crystal data are as follows: a = 19.866(3), b = 9.1017(12), c = 21.010(3) Å, β = 104.972(2)°, V = 3670.1(9) ų, Z = 8, D_c = 2.046 g/cm³, μ = 3.710 mm^-1, F(000) = 2240, R = 0.0213 and wR = 0.0460 for 4183 observed reflections with I ≥ 2σ(I). Otherwise, the two EuN₂O₆ parts in the (pdta)₂(H₂O)₂]^2- complex anion form a pseudo-square antiprismatic polyhedron.

The (NH₄)₃[Yb^III(ttha)]·5H₂O (I) (H₆ttha = triethylenetetramine-N,N,N′,N″,N′′′,N′′′-hexaacetic acid) and (NH₄)[Yb^III(pdta)(H₂O)₂]·5H₂O (II) (H₄pdta = propylenediamine-N,N,N′,N′-tetraacetic acid) complexes are synthesized by heat-refluxing and acidity-adjusting methods, and their structures are determined by single crystal X-ray diffraction techniques. These two complexes are all mononuclear structures. The complex I crystallizes in the monoclinic crystal system with the P2₁/c space group. The central Yb^III ion is nine-coordinated only by one ttha ligand, and one non-coordinate carboxyl group is left. The crystal data are as follows: a = 10.321(4), b = 12.744(5), c = 23.203(9) Å, β = 91.082(6)°, V = 3051(2) ų, Z = 4, D_c =
= 1.754 g/cm³, μ = 3.150 mm^-1, F(000) = 1636, R = 0.0357, and wR = 0.0672 for 6203 observed reflections with I ≥ 2σ(I). The YbN₄O₅ part in the [Yb^III(ttha)]³⁻ complex anion forms
a pseudo-monocapped square antiprismatic polyhedron. The complex II is coordinated with one pdta ligand and two water molecules, which form an eight-coordinate structure, and crystallizes in the triclinic crystal system with the space group. The YbN₂O₆ part in the [Yb^III(pdta)(H₂O)₂]⁻ complex anion makes a pseudo-square antiprismatic polyhedron. The crystal data are as follows: a = 9.8923(9), b = 10.9627(10), c = 12.2618(11) Å, α = 67.284(5)°, β = 70.956(6)°, γ = 68.741(5)°, V = 1115.97(18) ų, Z = 2, D_c = 1.843 g/cm³, μ = 4.264 mm^-1, F(000) = 618, R = 0.0177, and wR = 0.0409 for 4036 observed reflections with I ≥ 2σ(I).

3,5-Dimethyl-1Н-pyrazolide of 3-O-acetyl ursolic acid (II) is obtained in the course of the interaction of 3-O-acetyl ursolic acid acyl chloride (I) and 3,5-dimethyl-1Н-pyrazole. The crystal structure of compound II is determined from the single crystal XRD data (150 K, Вruker X8 Apex CCD autodiffractometer, МоK_α radiation). The crystals are rhombic, the unit cell parameters are as follows: a = 10.6034(2) Å, b = 12.4096(2) Å, c = 24.5972(5) Å, Р2₁2₁2₁ space group. The structure consists of discrete acentric molecules. When pyrazolide II is boiled in the alcohol alkali solution, secondary hydroxyl is deacetylated and 3,5-dimethyl-1H-pyrazolide of ursolic acid IV is formed. Compounds II and IV are studied by NMR spectroscopy.

The title compound is analyzed by X-ray diffraction. ONIOM(B3LYP/6-31G(d,p):PM3) is used to investigate the optimized calculation and the frequency analysis of the molecule, in which the PM3 method was used for carbon and hydrogen atoms of the benzene ring and the B3LYP/6-31G(d,p) method was used for the other parts. Energy changes in the molecule are numerically investigated by the flexible scan at PM3 level. The nature of intramolecular interactions that stabilize the structure in vacuo and solid is studied. The results reveal that the molecule is flexible and molecular conformations can easily be mutually transformed through very small potential barriers.

The title compound 2-{[3-Methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]-hydrazonomethyl}-phenol (C₂₁H₂₁N₃S₁O₁) crystallizes in the P-1 triclinic space group with a = 5.8880(4), b = 9.5618(5), c = 17.0484(10) Å, α = 80.214(5)°, β = 80.532(5)°, γ = 80.116(5)°. In addition to molecular geometry and packing from X-ray experiment, we have also calculated the molecular geometry and vibrational frequencies of the title compound in the ground state using density functional theory DFT (B3LYP) with the 6-31G(d,p) basis set. Apart from this, the structure of the title compound is characterized by ¹H NMR, ¹³C NMR, IR and UV-vis. Spectra, and the experimental emission energies are compared with the HOMO-LUMO energy gaps calculated by the DFT method.

Crystal structure parameters (coordination numbers, interatomic distances, unit cell volumes), characteristics of phase transformations, and physical properties of macrosamples can depend on the size of crystal grains. The size effect is especially significant in the electrophysical properties of crystals, including the effect of dispersed powders on the properties of polar liquids contacting with them.

The crystal structure of a newly synthesized molecular adduct of antimony(III) fluoride with L-phenylalanine of the composition SbF₃(C₉H₁₁NO₂) is determined for the first time (monoclinic crystal system: a = 5.8742(1) Å, b = 6.2079(1) Å, c = 15.5401(3) Å, β = 90.741(1)°, Z = 2, P2₁ space group). The structure consists of SbF₃ molecules and L-phenylalanine bound into polymer chains by bidentate bridging carboxyl groups of amino acid molecules. Weak Sb…F(3)^b bonds organize the adjacent chains into polymer ribbons that are bound into layers by N-H…F and N-H…O hydrogen bonds

A cadmium(II) complex, tetrakis(N,N′-diethylthiourea)sulfatocadmium(II), [Cd(Detu)₄SO₄] (1) was prepared and its crystal structure was determined by x-ray crystallography. The crystal structure of the complex consists of an independent molecule with the central cadmium atom coordinated to four thione sulfur atoms of Detu and two oxygen atoms of the sulfate ligand. The Cd atom has a pseudo-octahedral coordination environment with the cis angles varying from 57.68 to 126.57°, while the trans angles fall in the range of 142 to 169°. The new complex was also characterized by IR and NMR spectroscopy and the spectroscopic data are discussed in terms of the nature of bonding.

A novel bimetallic 4f-3d metal-isonicotinic acid inorganic-organic hybrid complex [Tb_0.5(C₆NO₂H₅)₃(H₂O)₂]_2n·(H₃O)_4n(ZnCl₅)_n(ZnCl₄)_2n (1) is synthesized. It has a one-dimensional polycationic chain-like structure. Photoluminescent investigation reveals that it displays interesting emissions in the violet, blue, green, and yellow regions.

The title compound (C₂₀H₁₈FN₃O₂, Mr = 351.37) is prepared and its crystal structure is determined by single crystal X-ray diffraction. The crystal is tetragonal, the P-42(1)c space group with a = 11.0922(6), b = 11.0922(6), c = 28.6271(15) Å, V = 3522.2(3) ų, Z = 8, d_x =
= 1.325 g/cm³, F(000) = 1472, μ = 0.095 mm^-1, MoK_α radiation (λ = 0.71073), R = 0.0505, wR = 0.1090 for 2433 observed reflections with I > 2σ(I). The X-ray diffraction analysis reveals that all ring atoms in the benzo[4,5]furo[3,2-d]pyrimidinone moieties are almost coplanar.

3-chloro-N-(8′-quinolyl)benzo[b]thiophene-2-carboxamide was synthesized from 3-chlorobenzo[b] thiophene -2-carboxyl chloride and 8-aminoquinoline in the presence of triethylamine. The single crystal X-ray structure determination confirmed the earlier proposed structure and also characterized by ¹HNMR, and Mass spectroscopy. Crystallographic study reveals that the structure crystallizes in monoclinic system, a = 14.878(4), b = 8.4292(15), c = 25.461(7) Å, β = 112.022(18)°, Z = 8, V = 2960.20(12) ų with space group C2/c (No. 15). In the structure packing, three kinds of interactions are responsible for the stability of the structure. Infinite two-dimensional stair-like layered chains are formed by relatively strong intermolecular hydrogen bonds [C14-H14…O1]. These parallel chains are connected by several
π-π and CH-π interactions, alternatively. There are two such parallel chains with 70.53°, which are in contact by van der Waals interactions.