Showing papers in "Journal of Structural Chemistry in 2013"

4-hydroxy-2H-1,2-benzothiazine-3-carbohydrazide 1,1-dioxide-oxalohydrazide (1:1): X-ray structure and DFT calculations

Abstract: The title compound, 4-hydroxy-2H-1,2-benzothiazine-3-carbohydrazide 1,1-dioxide-oxalohydrazide (1:1), is determined using X-ray diffraction techniques and the molecular structure is also optimized at the B3LYP/6-31G(d,p) level using density functional theory (DFT). The asymmetric unit consists of four independent molecules. The oxalohydrazide molecules have the centre of symmetry at the mid-point of the central C-C bond. Each thiazine ring adopts a half-chair conformation. Intermolecular C-H...O, N-H...O and N-H...N hydrogen bonds produce R 2 2 (10), R 2 2 (13), R 3 3 (12) and R 3 3 (15) rings, which lead to one-dimensional polymeric chains. An extensive three-dimensional supramolecular network of N-H...N, N-H...O, C-H...O and O-H...O hydrogen bonds is responsible for crystal structure stabilization.

Solvophobic effects: Qualitative determination and quantitative description

Abstract: Solvophobic effects strongly influence the thermodynamic properties of solutions and are one of the driving forces of self-assembly processes of supramolecular structures. However, the generally accepted definition and a quantitative measure of these effects have so far been absent. Based on the analysis of a large set of experimental data on the thermodynamic functions of solvation in various systems, we propose a qualitative criterion allowing us to judge about whether the solvophobic effects are manifested in the solution or not, and also a method to determine their contributions to the thermodynamic functions of solvation. A feature of the solvophobic effect is a violation of the linear relationship between the Gibbs free energy and the enthalpy of solvation, which is fulfilled for the solutions of different compounds in many non-associated solvents. It is shown that in self-associated solvents the solvophobic effect is observed for any dissolved compounds, including well soluble ones, resulting in an increase in the Gibbs energy of solvation. Previously proposed solvophobicity parameters are considered and compared with our results.

Collective motions in computer models of water. large-scale and long-time correlations

Abstract: Two-particle correlation functions describing the simultaneous motion of a pair of molecules initially separated by a given distance R0 are calculated to study collective effects in the diffusive motion of water molecules in molecular dynamics models. Various types of such functions and their dependences on the interaction potential, temperature, and the number of particles in the model are considered. At short times (of the order of ten picoseconds), these functions exhibit irregular behavior depending on R0. The most nontrivial and unexpected result was the detection of correlations in the displacements of pairs of particles that extend for tens of angstroms and last for hundreds of picoseconds. Such correlations are not observed in the random walk models of noninteracting particles. It is suggested that the observed large-scale correlations reveal the vortex-like motions of the molecules.

Cluster structure of water in accordance with the data on dielectric permittivity and heat capacity

Abstract: In the work the character of water clusterization in the whole existence domain of its liquid state is discussed: from supercooled states to the critical point. Conclusions about the cluster composition of liquid water are drawn based on the analysis: 1) of the features of dielectric relaxation; 2) character of the temperature dependence of its static dielectric permittivity, and 3) the value and temperature dependence of different contributions to the heat capacity of the system. It is shown that near the water crystallization point tetramers prevail in its structure, with an increase in the temperature trimers start to play the main role, and near the critical point of water dimers become the major associates. At temperatures near the water crystallization point the obtained results well agree with the data on emission and absorption X-ray spectroscopy.

A new polymorph of methimazole: Single crystal and powder X-ray diffraction study

Abstract: A new polymorph of 1-methyl-4-imidazoline-2-thione has been first discovered and studied by X-ray diffraction. The crystal of the new polymorph is monoclinic, the asymmetric part of the cell contains three independent molecules. In the crystal, the key compound is in the form of planar hydrogen-bonded dimers due to the interactions of the N-H…S type. The new modification is of an intensely yellow color in contrast to the previously known colorless forms, is characterized by a lower density but stronger hydrogen bonds; it is formed as a minor impurity to main triclinic polymorph.

Crystal structure of potassium 2-thiobarbiturate

Abstract: The crystal and molecular structure of potassium thiobarbiturate C4H3KN2O2S (C4H4N2O2S-2-thiobarbituric acid, H2TBA) is determined. Crystallographic data for KHTBA are as follows: a = 11.2317(17) A, b = 3.8687(6) A, c = 14.557(2) A, β = 97.448(4)°, V = 627.18(17) A3, space group P2/c, Z = 4. Each potassium ion is linked with four oxygen atoms and two S atoms forming a distorted octahedron. N-H…O and C-H…S hydrogen bonds form a branched three-dimensional network. The structure is also stabilized by the π-π interaction of heterocyclic HTBA− ions.

Argon and water

Abstract: Computer simulation of liquid argon and water has shown that the structural inhomogeneity pattern visualized by coloring their instantaneous structures according to the volumes of the Voronoi polyhedra is the same for both liquids. The dynamics of argon atoms in the cavity of a clathrate hydrate and in liquid water is considered. The argon atoms included in the network of hydrogen bonds in liquid water are involved in concerted motion. As a result of this concerted motion, the distance between two argon atoms can fluctuate around some value for a fairly long time. The environment of argon atoms in a liquid aqueous solution differs significantly from their environment in clathrate hydrates.

Culation of partial molar volume and its components for molecular dynamics models of dilute solutions

Abstract: This paper is a review of our recent computational studies of volumetric characteristics using computer models of dilute solutions. Partial molar volume (PMV) and its components are calculated for simple and complex molecules in water (methane, noble gases, surfactants, polypeptides). Advantages and disadvantages of various computational methods are discussed. It is proposed to use the Voronoi-Delaunay technique to determine the reasonable boundary between a solute molecule and solvent molecules and to identify the PMV components related to the molecule, the boundary layer, and the solvent. It is noted that the observed increase in PMV with temperature for large molecules is due to an increase in the volume of voids in the boundary layer, i.e., due to the “thermal volume.” In this case, the solvent gives a negative contribution to the PMV. In contrast, for simple molecules (methane), the contribution from the solvent is positive and is the main factor in the increase in the PMV, which is associated with a specific change in water structure around a spherical hydrophobic particle outside the boundary layer. For surfactant molecules, the contribution from the solvent changes sign (from negative to positive) with increasing temperature.

Formation conditions of a magnetically ordered phase ɛ-Fe2O3. A FMR in situ study

Abstract: The ferromagnetic resonance (FMR) method in situ is used to study the initial stages of the formation of ɛ iron oxide nanoparticles deposited on silica gel at temperatures up to 600°C. It is shown that at high-temperature treatment of starting samples obtained by impregnation with an iron(II) sulfate solution, supermagnetic ɛ-Fe2O3/SiO2 nanoparticles form with a narrow size distribution. An analysis of the FMR data in comparison with the data of other methods enables the formulation of the formation conditions for systems of deposited ɛ-Fe2O3 nanoparticles without other polymorph impurities.

H-H interaction in phenanthrene: Attraction or repulsion?

Abstract: By the example of the structure of phenanthrene the character of the H-H interaction is studied by nonempirical quantum chemical methods. The calculations performed confirm Bader’s conclusions about the attractive character of the H-H interaction, which were made based on the QTAIM analysis, and disprove the repulsive character of the above interaction, which was derived from the EDA procedure.

Lanthanide(III) chelates as MRI contrast agents: A brief description

Abstract: Magnetic resonance imaging (MRI) has become a prominent imaging technique in medicine. Gadoliniumbased contrast agents are extensively used to enhance the contrast between normal and diseased tissues through MRI scans. The article illustrates the paramount significance of such contrast agents in MRI applications. Clinically approved contrast agents as well as those in trial period are discussed. Important parameters, i.e. hydration number, rotational correlation time, and mean residence lifetime, influencing the relaxivity (sensitivity) of such agents are described in detail. Various approaches towards relaxivity enhancement are discussed with appropriate examples from the recent literature. A decrease in the Gdwater proton distance results in significant relaxivity enhancement. A comprehensive classification and explanation of Gd3+-based contrast agents are presented. Each class is explained with suitable examples. The stability of contrast agents is dependent on their chemical structure. Future contrast agents need to be tissue specific of high relaxivity, low toxicity, and lower administered dose for in vivo use.

Crystal structures and antibacterial activity of hydrazone derivatives from 1H-indol-3-acetohydrazide

Abstract: A series of three new hydrazone derivatives C22H19N3O2 (1), C17H13ClN4O3 (2), and C21H24N4O2·CH4O (3) obtained by the condensation of 1H-indol-3-acetohydrazide with 2-methoxynaphthaldehyde, 2-chloro-5-nitrobenzaldehyde, and 4-diethylaminosalicylaldehyde, respectively, in methanol, ia prepared. The compounds are characterized by elemental analysis, IR spectra, 1H NMR spectra, and single crystal X-ray diffraction. Compound 1 crystallizes in the monoclinic space group P21/n with unit cell dimensions a = 17.740(2) A, b = 5.621(1) A, c = 18.573(3) A, β = 92.659(2)°, V = 1850.0(6) A3, Z = 4, R 1 = 0.0610 and wR 2 = 0.1155. Compound 2 crystallizes in the monoclinic space group C2/c with unit cell dimensions a = 29.178(2) A, b = 8.195(1) A, c = 14.372(1) A, β = 109.446(2)°, V = 3240.5(5) A3, Z = 8, R 1 = 0.0452 and wR 2 = 0.1028. Compound 3 crystallizes in the monoclinic space group Pc with unit cell dimensions a = 6.579(1) A, b = 15.112(2) A, c = 10.676(2) A, β = 90.030(2)°, V = 1061.4(3) A3, Z = 2, R 1 = 0.0535 and wR 2 = 0.1123. The single crystal X-ray structural determination reveals that the molecules of the compounds are much twisted due to the lack of efficient conjugation. Preliminary biological tests indicate that the compounds are effective antibacterial material.

Crystal structure of catena -DI(2-thiobarbiturato-O,S)aqualead(II)

Abstract: The crystal structure of catena-di(μ2-2-thiobarbiturato-O,S)aqualead(II) C8H8N4O5S2Pb (C4H4N2O2S is 2-thiobarbituric acid, H2TBA) is determined. Crystallographic data for catena-[Pb(H2O)(μ2-HTBA-O,S)2] are as follows: a = 6.5972(1) A, b = 9.8917(2) A, c = 10.0893(2) A, α = 106.702(1)°, β = 93.395(2)°, γ = 107.48(1)°, V = 593.82(2) A3, space group \(P\bar 1\), Z = 2. The Pb2+ ion is linked with six monodentate HTBA− ligands through two O atoms and four S atoms and also connected with a water molecule. Additionally, there is a shortened Pb-S contact (3.622 A), given which the complex polyhedron represents a distorted square antiprism. Hydrogen bonds N-H…O and O-H…O form a branched three-dimensional network. The structure is also stabilized by the π-π interaction of heterocyclic HTBA− ions.

EFfect of alumina modification on the structure of cobalt-containing Fischer-Tropsch synthesis catalysts according to internal-field 59Co NMR data

Abstract: An internal-field 59Co NMR study of cobalt-containing Fischer-Tropsch synthesis catalysts supported on different alumina modifications was reported. The Co/δ-Al2O3 sample was shown to contain single-domain fcc packing and stacking faults, whereas Co/γ-Al2O3 gave signals from the fcc domain walls, hcp and stacking faults, thus indicating differences in the particle size of the studied samples. T 2 relaxation times were measured; their distribution in a spectrum is non-uniform, which allows signals to be distinguished by their relaxation times. Quantitative measurements of the relative atoms content in different packings revealed that the catalysts have mostly a defect structure. A brief historical background was presented to characterize the internal-field 59Co NMR technique, the related problems, and different approaches to acquired data interpretation.

3,3′-dihydroxy-4,4′-[1,2-cyclohexanediyl-bis(nitrilomethylidyne)]-bis-phenol schiff-base and its Mn(II) complex: Synthesis, experimental, and theoretical characterization

Abstract: In this work, a 3,3′-dihydroxy-4,4′-[1,2-cyclohexanediyl-bis(nitrilomethylidyne)]-bis-phenol [=H2L] Schiff-base ligand and its Mn(II) complex [Mn(L)(H2O)2] are newly synthesized and characterized by elemental analysis, IR and NMR spectroscopies. Also the geometry optimizations, assignment of the IR bands and NMR chemical shifts are computed using the density functional theory (DFT) method. The DFT optimized geometry of the ligand is not planar; each of the cyclohexane and two benzene rings are located in separate planes. The phenolic protons are engaged in the intramolecular-hydrogen-bonding interactions with azomethine nitrogen atoms. In the optimized geometry of the octahedral Mn2+ complex, the dianionic L2− acts as a tetradentate ligand in the N, N, O−, O− manner, where the coordinating atoms occupy the four equatorial positions. The two axial positions are occupied by two H2O ligands. The theoretical and experimental results are in good agreement, confirming the validity of the optimized geometries for the H2L ligand and its Mn complex.

Binuclear cluster complexes of molybdenum containing 2,2′-bipyridine and 1,10-phenanthroline: Synthesis and structure

Abstract: By the interaction between (Et4N)2[Mo2O2S8] and I2 in DMF with a subsequent addition of 2,2′-bipyridine or 1,10-phenanthroline, new binuclear complexes [Mo2O2S2I2(bipy)2] (1) and [Mo2O2S2I2(phen)2] (2) are obtained. The structure of [Mo2O2S2I2(bipy)2] is determined using single crystal X-ray diffraction. The compounds are characterized by elemental analysis and IR spectra. The [MoO(S2)2(bipy)] complex as a product of oxidative destruction of 1 is isolated and characterized.

Experimental and theoretical characterization of N,N′-bis(2,4-dihydroxybenzylidene)-1,2-diaminobenzene schiff base and its Cu(II) complex

Abstract: A new Schiff base ligand N,N′-bis(2,4-dihydroxybenzylidene)-1,2-diaminobenzene [=H2L] and its Cu(II) complex [Cu(L)] are synthesized and characterized by IR, UV-Vis, NMR, mass spectrometry and elemental analysis. Also, the computational prediction of optimized geometries, IR spectra and NMR chemical shifts is performed using the density functional theory (DFT) method. The DFT optimized geometry of the ligand is not planar, so the three benzene rings are located in separate planes. The phenolic protons are engaged in the intramolecular hydrogen-bonding interactions. In the optimized geometry of the square comlex, dianionic L2− acts as a tetradentate ligand, which occupies four coordination positions in the N, N, O−, O− manner. The consistency between the calculated and experimental results confirms the validity of the optimized structures for the H2L ligand and its Cu complex.

Crystal structure of monoclinic modifications of zirconium and hafnium tetrafluoride trihydrates

Abstract: The monoclinic modification of ZrF4·3H2O, isostructural to HfF4·3H2O, is synthesized and structurally studied for the first time. Unlike the triclinic modification of ZrF4·3H2O with a dimeric structure, the synthesized compound has a polymer structure formed from infinite chains composed of ZrF6(H2O)2 groups sharing F…F edges. The crystal structure of HfF4·3H2O, previously determined by the photo method, is refined. The refined data on the geometric characteristics of the coordination polyhedron of the Hf atom and the system of hydrogen bonds in the structure are obtained.

Quantum chemical calculation for the inhibitory effect of compounds

Abstract: The effects of the molecular structure on the corrosion inhibition efficiency are investigated by nine methods of calculations. The selected thio compounds were previously identified as corrosion inhibitors for mild steel in the 1.0 M HCl solution. The electronic properties such as highest occupied molecular orbital (EHOMO) energy, lowest unoccupied molecular orbital (ELUMO) energy, dipole moment (μ), and Fukui indices are calculated and discussed. Results show that the corrosion inhibition efficiency increase with the increase in both EHOMO and μ values, respectively, and decrease in ELUMO. QSAR approach is utilized in this study; a good relationship is found between the experimental corrosion inhibition efficiency (IEexp, %) and the theoretical corrosion inhibition efficiency (IEtheor, %). The calculated inhibition efficiency is found closer to the experimental inhibition efficiency with a coefficient of correlation (R2) of 0.875.

Parallel and distributed computing in problems of supercomputer simulation of molecular liquids by the Monte Carlo method

Abstract: An effective strategy of molecular Monte Carlo simulation is proposed. The strategy is based on a combination of two key approaches to parallel computing. The advantage of spatial (domain) decomposition is the high scalability of computing algorithms by splitting “big tasks” into several simultaneously solvable subtasks. However, the domain size in this method can be reduced to a certain limit only. Particle decomposition (division of program loops into portions) is, by contrast, very efficient in the study of small and medium size objects, but is poorly scalable and quickly exhausts the computer system memory with increasing size of the model. The combination of the approaches helps neutralize their limitations and create efficient supercomputing programs for the study of molecular models consisting of hundreds of millions of atoms.

Structure-determining role of Tl+ in natural and synthetic sulfides

Abstract: A crystallographic analysis is performed for the structures of TlCu2S2, TlCu7S4, TlTaS3, TlIn3S5, TlIn5S8, and TlCr2V3S8. In them the Tl+ cation is included in anion sublattices and stabilizes their regularity. The cation sublattices are substantially distorted and have additional conjugation to the anionic positions of the thallium cations. The monoclinic structures (the last three) have geometrically similar anionic and cationic “forced skeletons,” while in tetragonal (the first two) and orthorhombic symmetries they are modified by symmetry restrictions.

Structural organization of dithiocarbamate heteropolynuclear gold(III)-cadmium complexes from X-ray crystallography and 113Cd MAS NMR spectroscopy data

Abstract: We study the interaction of dialkyl substituted and cyclic cadmium dithiocarbamates with [AuCl4]− anions in 2M HCl medium. The state of the chemisorbents upon contact with AuCl3 solutions is controlled by 113Cd MAS NMR spectroscopy. The result of the heterogeneous reactions involving chemisorption binding of gold(III) from the solutions and partial ion exchange is the formation of heteropolynuclear gold(III)-cadmium complexes. The crystal and molecular structure of the acetone-solvated form of polymeric bis-(N,N-diethyldithiocarbamato-S,S′) gold(III) hexachlorodicadmate is identified by single-crystal XRD. The main structural moieties of the compound are complex [Au{S2CN(C2H5)2}2]+ cations and [Cd2Cl6]2− anions. The structural self-organization of the complex at the supramolecular level is attributed to the secondary Au…S bonds between neighboring isomeric complex gold(III) cations; the bonding results in the formation of linear polymer ([Au{S2CN(C2H5)2}2]+)n chains, with [Cd2Cl6]2− anions alternating to the right and left of the chains.

Unusual crystal and molecular structure of tris (2-hydroxyethyl)ammonium fluoride

Abstract: According to the X-ray diffraction data, the crystal and molecular structure of tris(2-hydroxyethyl) ammonium fluoride (F−N+H(CH2CH2OH)3, fluoroprotatrane, substantially differs from other halo protatranes X−N+H(CH2CH2OH)3 (X = Cl, Br, and I). At X = F, to the endo-molecular LP of the nitrogen atom the HF molecule having the minimum ionic radius in a series of X− anions is bonded. The geometry of fluoroprotatrane and the cation packing in the crystal are analyzed.

Charge distribution and mobility of lithium ions in Li2TiO3 from 6,7Li NMR data

Abstract: A comparative analysis of 6,7Li NMR spectra is performed for the samples of monoclinic lithium titanate obtained at different synthesis temperatures. In the 7Li NMR spectra three lines are found, which differ in quadrupole splitting frequencies vQ and according to ab initio EFG calculations are assigned to three crystallographic sites of lithium: Li1 (vQ ∼ 27 kHz); Li2 (vQ ∼ 59 kHz); Li3 (vQ ∼ 6 kHz). The dynamics of lithium ions is studied in a wide temperature range from 300 K to 900 K. It is found that the narrowing of 7Li NMR spectra as a result of thermally activated diffusion of lithium ions in the low-temperature Li2TiO3 sample is observed at a higher temperature in comparison with a sample of high-temperature lithium titanate. Based on the analysis of 6Li NMR spectra it is assumed that there is mixed occupancy of lithium and titanium sites in the corresponding layers of the crystal structure of low-temperature lithium titanate, which hinders lithium ion transfer over regular crystallographic sites.

Stepwise magnetic behavior of the liquid crystal iron(III) complex

Abstract: EPR and Mossbauer spectroscopy is used to study a new liquid crystal complex of iron(III) with a Schiff base: 4,4′-dodecyloxybenzoyloxybenzoyl-4-oxysalicylidene-2-aminopyridine with a PF 6 − counterion. It is shown that Fe(III) ions exist only in the high-spin (HS, S = 5/2) state. It is found that under the influence of temperature the system demonstrates the stepwise behavior of the product of the integrated intensity of EPR lines (I) and temperature (proportional to χ T, where χ is the magnetic susceptibility) with an inflection point at ∼80 K. Above 80 K a new EPR spectrum is detected due to the excited S = 2 state and the formation of dimeric molecules (through oxygen bridges) with a strong intramolecular antiferromagnetic exchange interaction J 1 = 162.1 cm−1. Below 80 K iron(III) complexes are organized in 1D chains where the exchange value J 2 = 2.1 cm−1. At 80 K there is a structural phase transition in the system: the transition from a 1D chain organization of HS Fe(III) centers to dimeric molecules. Based on quantum chemical calculations a model of the binuclear iron(III) complex is proposed.

Theoretical study of hydrophobicity and hydrophilicity of indole, skatole, and ethanole

Abstract: The structures of indole, skatole, and ethanole complexes with water molecules are calculated by the DFT method. Radial and angular dependences of hydrogen bridge parameters on the number of water molecules are analyzed. Two models are determined which enable the study of the reason for the hydrophobicity of indole and skatole. Frequencies and intensities of absorption bands corresponding to stretching vibrations of the NH bond of indole, skatole, and ethanol in complexes with water are compared. It is shown that the main reason for the domination of the hydrophobic component over the hydrophilic one is the taking into account of the interaction of water molecules with the aromatic system of indole and skatole, finally resulting in a substantial decrease in the HB strength.

Crystal and electronic structure of heteromolecular complexes of 3,6-bis(3,5-dymethylpyrazole-1-yl)-1,2,4,5-tetrazine with azoles

Abstract: X-ray crystallography is used to investigate heteromolecular crystals of 3,6-bis(3,5-dimethylpyrazole-1-yl)-1,2,4,5-tetrazine with NH-donating azole derivatives The effect is studied of the structure of azole on molecular packing in the crystal and the characteristics of covalent bonds in the molecule of 3,6-disubstituted tetrazine The distribution of electron density critical points inside crystal cells is analyzed to identify and quantitatively describe the intermolecular interactions underlying the formation of lateral and stacking motifs

Spectral analysis of acetylcholine halides by density functional theory calculations

Abstract: The optimized molecular structures, vibrational frequencies and 1H and 13C NMR chemical shifts of acetylcholine halides (F, Cl, and Br) have been investigated using density functional theory (B3LYP) method with 6-311G(d) basis set. The comparison of their experimental and calculated IR, R and NMR spectra of the compounds has indicated that the spectra of three optimized minimum energy conformers can simultaneously exist in one experimental spectrum. Thus, it was concluded that the compounds simultaneously exist in three conformations in the ground state. The calculated optimized geometric parameters (bond lengths and bond angles), vibrational frequencies and NMR chemical shifts for the minimum energy conformers were seen to be in a good agreement with the corresponding experimental data. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program.

Crystal structure of [CoEn 3 ] 2 (W 7 O 24 )·6H 2 O

Abstract: Crystal structure of a complex salt [CoEn3]2(W7O24)·6H2O is determined by X-ray crystallography. Powder X-ray diffraction is applied for the phase identification of the products of thermal decomposition of the salt in the helium atmosphere.

A cocrystal of caffeine and dipicolinic acid: synthesis, characterization, X-ray crystallography, and solution studies

Abstract: A reaction between caffeine (caff) and dipicolinic acid = 2,6-pyridine dicarboxylic acid (pydc.H2) in water results in the formation of a cocrystal compound (pydc.H2.H2O)(caff) 1. The characterization of the resulting crystallohydrate is performed using 1H, 13C NMR and IR spectroscopy and X-ray crystallography. X-ray crystal structure analysis reveals the presence of both starting materials and water in the lattice. It also indicates intensive intermolecular H bonding interactions between carboxylic acid, caffeine, and water as well as π-π stacking between the pydc.H2 and caff rings as constituents of the cocrystal. The hydrogen bonding and non-covalent interactions play roles in the formation of the cocrystal. The crystal system is triclinic with the space group P-1 and two formula units per unit cell. The unit cell parameters are a = 6.906(2) A, b = 8.451(3) A, c = 14.68 (4) A with α = 81.51(3)°, β = 78.47(3)°, and γ = 78.14(3)°. The final R value is 0.0660 for 7943 measured reflections.