Home – Home – Jornals – Journal of Structural Chemistry 2012 number 3

A first - principles method of density functional theory with a gradient approximation of the exchange-correlation potential in the form of PBE implemented in the PWscf program of the Quantum ESPRESSO software using the Grimme′06 scheme is used to calculate the crystal structure of naphthaline and anthracene at a hydrostatic pressure ranging from 0 GPa to 2 GPa and from 0 GPa to 20 GPa respectively; their equations of states are analyzed. It is shown that under pressure the volume decreases due to voids, and the molecules themselves are practically not deformed. The Grüneisen parameter is calculated in the Slater-Dugdale-MacDonald-Zubarev-Vashchenko model. This parameter decreases from the equilibrium values of 2.356 (anthracene) and 3.226 (naphthaline) with an increase in the pressure. With the use of the Mie-Grüneisen equation under the additional Hugoniot-Renkin condition the impact pressure is calculated, which increases compared to the cold one at a relative compression V/V₀, below 0.7.

A method to solve the problem of the electron-nuclear states of molecules with internal rotation and the smeared positions of nuclei due to this rotation is proposed. It is shown how to state the Hamiltonian for the description of the electron motion with regard to this smearing and the total electron-nuclear Hamiltonian.

At the DFT level with the B3LYP hybride functional the structure and relative stability of geometric isomers of bi- and trithiazolidine-4-ones are calculated. Based on Bader's analysis of the electron density distribution the presence of intramolecular hydrogen bonds and van der Waals interactions is found in the studied isomers. Energies of these interactions are calculated. It is shown that the presence of a substituent in the thiazolidine ring affects the stabiliyty of the studied geometric isomers.

The energies of the Pt-NH₃ and Pt-Cl bonds of cisplatin are calculated by means of a density functional theory method with the B3LYP functional and various basis sets. The calculated bond energies of 37.38 kcal·mol^-1 and 64.35 kcal·mol^-1 for Pt-NH₃ and Pt-Cl, respectively, agree well with the experimental values (37.28 kcal·mol^-1 and 69.31 kcal·mol^-1 respectively) derived from enthalpy changes. The proton and lithium ion affinities of cisplatin are also obtained with the B3LYP functional. Structural characterizations for the protonated and lithiated cisplatin complexes are given. Protonation and lithiation alter the geometric parameters, and the gas-phase proton affinity (198.71 kcal·mol^-1) is much higher than the lithium ion affinity (70.32 kcal·mol^-1).

To construct artificial neural network (ANN) models for the prediction of reactivity parameters (u, v), density functional theory (DFT) calculations are carried out for 55 vinyl monomers, at the B3LYP level of theory with a 6-31G(d) basis set. After the generation of quantum chemical descriptors, the stepwise multiple linear regression (MLR) analysis and the ANN method are used to develop quantitative structure-property relationship (QSPR) models of parameters u and v. The ANN models produced test set root-mean-square (rms) errors of 0.35 for the parameter u and 0.34 for the parameter v. Research results indicate that the QSPR models based on DFT calculations and ANN techniques are accurate and possess the ability to generalize.

Methods to measure the bond rupture force are considered. It is proposed to use a quartz resonator as an active element rather than simply a sensor. When the surface oscillation amplitude of an AT quartz resonator increases smoothly (rupture event scanning), a particle attached to the quartz surface is removed by inertial forces, and from their values it is easy to obtain the bond dissociation value. This procedure provides reliable measurements of the rupture force of about 10 pN. As the atomic force microscopy method, the rupture event scanning does not apply electromagnetic radiation, but has simpler instrumental set-up. The scanning requires minimum sample preparation, can be performed in various media (vacuum, air, liquid), and takes only a few minutes.

A new tetradentate N,N′-dipyridoxyl(1,2-ethylenediamine) [=H₂ES] Schiff-base ligand and its Cu(II) salen complex [Cu(ES)(H₂O)] are synthesized and characterized by IR, UV-Vis, ¹H NMR, mass spectrometry, and elemental analysis. Their optimized geometries and theoretical vibrational frequencies are computed by using the density functional theory method where the B3LYP functional was used. Also, the ¹H NMR chemical shifts of the H₂ES ligand are calculated at the same computational level. In the optimized structure of the free ligand, two pyridine rings are not in the same plane. In the structure of the complex, the Schiff-base ligand acts as a dianionic tetradentate ligand in the N,N,O^-,O^- manner, so that the coordinating atoms occupy equatorial positions. The H₂O ligand occupies the axial position of the square-pyramidal complex. The calculated results are consistent with the experimental ones, confirming the suitability of the optimized structures for the H₂ES ligand and its Cu(II) complex.

We investigate the applicability of a variational method with a new reference system (square-well model) to the description of the structure and thermodynamics of liquid metals. An expression for the system entropy for a one-component fluid is derived. The three parameters of the model (the hard-sphere diameter and the width and depth of the square well) are determined by the variational method using the local pseudopotential approximation. The approach is used for liquid Na and K, and the calculated results are compared with experiment. It is shown that the approach can provide a realistic description of the properties of liquid metals.

The Monte Carlo method is used to simulate similar sized hard sphere systems in a wide range of densities (from η 0.005 to 0.530 with a step of η = 0.005). The models are used to calculate the coefficients of the thermodynamic perturbation theory series for SW fluids up to the fourth order. The width of the attraction zone of the SW potential λ is varied from 1 to 2.5 sphere diameters. The analytical expressions approximating the obtained coefficients by polynomials with respect to the variables η and λ are determined. The absolute accuracy of the approximation is estimated to be better than ±0.001. All the necessary data for the calculation of the Helmholtz free energy of SW fluids up to the fourth-order perturbation theory are given.

The data on the solubility of helium in water and aqueous solutions of sodium chloride at a temperature of T = 293-353 K and a He partial pressure of p₂ = 0.1-20 MPa are used to calculate the standard parameters of the Sechenov salt effect and estimate, within the formalism of the McMillan-Mayer theory, the parameters of the pairwise solute-solute interaction.

The vibrational spectra of a series of HF solutions in acetone (1:20-8.9:1) are analyzed with the help of special techniques. It is shown that three types of strong heteroassociates (HAs) with 1:1, 4:1, and ≥10:1 stoichiometric ratios of the molecules are formed in the HF-(CH₃)₂CO binary liquid system. The concentration ranges of the existence of HAs in the solution and the stretching vibrational frequency of their constituent HF molecules are estimated. The density functional method (B3LYP/6-31++G(d,p)) is used to calculate the optimal configurations and IR spectra of the (HF)_m·((CH₃)₂CO)_n molecular complexes (m = 1, 2, 4, 8, n = 1, 2) of different structure. The relative stability of the latter is studied. By comparing the calculated and experimental data, the composition (2:2 and 4:1) and structure of two types of HAs are determined.

The structures of two salts [Co(NH₃)₆][Rh(NO₂)₆] (I) and [Co(NH₃)₆][(NO₂)₃Rh(μ-NO₂)_1+x(μ-OH)_2-x Rh(NO₂)₃]·(2-x)(H₂O), x = 0.17 (II) are solved. Single crystals of the salts are obtained by the counter diffusion method through the gel of aqueous solutions of [Co(NH₃)₆]Cl₃ and Na₃[Rh(NO₂)₆]. The structure of [Co(NH₃)₆][Rh(NO₂)₆] is consistent with the diffraction data for a polycrystalline sample of poorly soluble fine salt formed in the exchange reaction between aqueous solutions of [Co(NH₃)₆]Cl₃ and Na₃[Rh(NO₂)₆]. The structure of [Co(NH₃)₆][(NO₂)₃Rh(μ-NO₂)_1+x(μ-OH)_2-xRh(NO₂)₃]·(2-x)(H₂O), x = 0.17 exhibits the stabilizing effect of a large cation in the formation of novel, unknown previously coordination ions: [(NO₂)₃Rh(μ-NO₂)(μ-OH)₂Rh(NO₂)₃]^3- and [(NO₂)₃Rh(μ-NO₂)₂(μ-OH)Rh(NO₂)₃]^3-.

A novel copper(II) complex {[Cu(BIX)₂(H₂O)₂](PhCOO)₂}_n (1) (BIX = 1,4-bis(imidazole-1-methyl))benzene) is synthesized and characterized by elemental analysis, IR, TG, and single crystal X-ray diffraction. Complex 1 crystallizes in the triclinic crystal system with the P-1 space group, Z = 1, a = 9.465(2) Å, b = 9.703(2) Å, c = 12.060(2) Å, α = 77.26(3), β = 70.37(3), γ = 67.14(3)°, and V = 956.1(3) ų. The crystal structural analysis of complex 1 shows that the copper center is six-coordinated in an elongated octahedral geometry by four N atoms from four different BIX and two O atoms from two water molecules; two neighboring Cu(II) cations are bridged by two BIX extending into an infinite 1D double chain structure.

At T = 150 K, the crystal structures of [Pd(En)₂](ReO₄)₂, [Pd(En)₂](NO₃)₂, and [PdL₂](ReO₄)₂ (L is N,N′-diisopropylideneethane-1,2-diamine) are studied. Crystal chemical analysis is performed, and the main factors affecting the packing of fragments in these structures are determined.

Four complex salts with the polyatomic [Rh(NH₃)₆]³⁺ cation are synthesized and studied by X-ray diffraction. The crystallographic characteristics of [Rh(NH₃)₆](WO₄)Cl are determined and the structures of [Rh(NH₃)₆]Cl₃, [Rh(NH₃)₆](ReO₄)₃·2H₂O, and [Rh(NH₃)₆](MoO₄)Cl·3H₂O are solved. The features of mutual packing of the fragments are studied.

Two new double complex salts [Pd(NH₃)₄]₃[Rh(NO₂)₆]₂ (I) and [Pd(NH₃)₄]₃[Rh(NO₂)₆]₂·H₂O (II) are synthesized and characterized. The techniques to produce one-phase residues of the salts are developed. The crystallographic data for I: a = 18.915(2) Å, V = 6767.4 ų, F-43c space group, Z = 8, d_x = 2.548 g/cm³; II: a = 21.160(6) Å, b = 8.085(7) Å, c = 21.363(4) Å, β = 91.71(4)°, V = 3661.1(6) ų, P2₁/c space group, d_x = 2.357 g/cm³. Thermal properties of the obtained compounds in the hydrogen and helium atmosphere are studied. It is shown that the final product of their decomposition both in the inert and reducing atmosphere is a powder consisting of bimetallic nanosized particles (nanoalloy) of Pd_0.59Rh_0.41 (Fm-3m space group, a = 3.856(2) Å, crystallite size of 8-11 nm).

Bis-(3,3-dinitroazetidinyl)-oxamide ((DNAZ-CO)₂) is an acyl derivative of 3,3-dinitroazetidine (DNAZ). It is prepared and its crystal structure is determined. The crystal is orthorhombic, Fdd2 space group, a = 13.136(14) Å, b = 19.48(3) Å, c = 10.326(14) Å, V = 2642 (6) ų, Z = 8. A density functional theory (DFT) method of the Amsterdam Density Functional (ADF) package is used to calculate the geometry, frequencies, and properties. The optimized geometry, frontier orbital energy, and main atomic orbital percentage are obtained. The thermal behavior is studied under a non-isothermal condition by DSC and TG/DTG methods. The apparent activation energy (E_a) and pre-exponential factor (A) of the exothermic decomposition reaction of (DNAZ-CO)₂ are 164.10 kJ·mol^-1 and 10^13.38 s^-1 respectively. The critical temperature of thermal explosion is 272.20 °C. The values of ΔS^≠, ΔH^≠, and ΔG^≠of this reaction are 6.44 J·mol^-1··K^-1, 163.76 kJ·mol^-1 and 160.34 kJ·mol^-1 respectively.

Single crystal XRD is used to study the crystals of salts of indole alkaloid norfluorocurarine: hydrochloride recrystallized from absolute alcohol, dihydrate hydrochloride recrystallized from water, methochloride monohydrate recrystallized from water, solvate form of methochloride obtained from ethanol, and methobromide monohydrate. Intra- and intermolecular hydrogen bonds are analyzed in these crystals. The crystal structures of norfluorocurarine methochloride and methobromide monohydrates are isomorphic. In norfluorocurarine salts, the orientation of the carbonyl group is determined by the intramolecular С19=О…H-N1 hydrogen bond that is absent in the solvate form with ethanol.

X-ray diffraction studies of the ultradisperse products of the solid-phase oxidative thermolysis of iron oxalate dehydrate are performed. Models are considered and diffraction patterns are calculated for the nanopowders of different crystalline modifications of iron oxide. Calculations are performed for the particles of various shapes and sizes, starting from one unit cell. Despite that the final product is the hematite phase, the reaction is shown to pass through the formation of particles with the ferrihydrite structure.

Alloys of the composition Re_0.65Pt_0.35 are prepared by thermal reduction of a bimetallic complex salt (NH₄)₂[ReCl₆]_0.65[PtCl₆]_0.35 in the hydrogen atmosphere and also by thermal-baric treatment of a mixture of nanosized powders of rhenium and platinum. The products are examined by powder X-ray diffraction and HRTEM. The compositions of the obtained phases are estimated using EDS and crystal chemical analysis of phases known for the Re-Pt system.

Ab initio RHF/3-21G** and ММ+ molecular mechanics method are employed to calculate the structural chemical parameters of molecular nanoparticles of petroleum asphaltenes. It is found that naphtheno-aromatic rings have a non-planar cup-like character. The values of dihedral angles α₁ between the planes of aromatic and naphthene rings, which are calculated by the RHF/3-21G** method, are within 156-163°. The values of dihedral angles α₂, which were calculated by the molecular mechanics method, are within 156-164°.

The crystal structure is solved for a 1:1 molecular complex of pyrogallol and dimethylsulfoxide. Crystal dat a: C₈H₁₂O₄S, M = 204.24, orthorhombic, Pna2₁ space group; unit cell parameters: a = 10.9620(4) Е, b = 10.9542(4) Е, c = 8.0561(3) Е, V = 967.38(6) Е³, Z = 4, d_x = 1.402 g/cm³, R1 = 0.0216, T = 150 K. The molecules are joined in a supramolecular ensemble by O-HпO and C-HпА hydrogen bonds.

A systematic computational study was carried out to determine the structural stability of salicylic acid derivatives as well as the acidic properties of the protonation-deprotonation site and excitation parameters of the considered drugs at different temperatures using quantum chemical calculations. For further structural information, the dipole moment and differences in the energy of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) as Δ(HOMO-LUMO) were compared. A high stability of the salicylic acid derivatives was referred to the large HOMO-LUMO band gap. The result of the current study may give useful information about the drug biochemical functionality based on the physical and chemical nature at different temperatures, and in this way the study on the structural features of analogous molecules of salicylic acid derivatives with higher drug functionality would be possible.

Enthalpies of formation ((g)) are calculated for syn and anti conformers of FC(O)SCF₃ and ClC(O)SCF₃ using the atomization methods with the Gaussian-n composite methods for which experimental values do not exist. DFT approaches and MP2 methods are employed to optimize the molecular geometries of XC(O)SCF₃ (X = F and Cl). Excellent results are obtained with the reported experimental data.

Heyrovskyite mineral Pb₆Bi₂S₉ from fumarole exhalations of the Kudryavyi volcano (Iturup island, Kurils, Russia) is studied by X-ray crystallography (Bruker Nonius X8 Apex with a 4K CCD detector, R = 0.0405). Unit cell parameters are: a = 4.1457(1) Å, b = 13.7421(5) Å, c = 31.5005(12) Å, V = 1794.6(1) ų, Z = 4, d_x = 7.216 g/cm³, Cmcm space group, R=0.0405. The resulted structure is similar to the known structures of heyrovskyites from other deposits with some variation in the cation composition.

Exposure of dichloromethane solution of [OEPFe^IIICl], where OEP is the dianion of octaethylporphyrin, to dioxygen results in its transformation into the ј-oxo bridged compound [(OEPFe)₂O)]. The structure of [(OEPFe)₂O)] is determined by X-ray diffraction analysis. It contains binuclear centrosymmetric [(OEPFe)₂O]. The Fe atom is five-coordinated to four N atoms of the porphyrin ring and to one bridging O atom. The compound is characterized by an average Fe-N bond length of 2.096 Е. The Fe-O bond distance is 1.7739(12) Е, the Fe-O-Fe bond angle is 180.0° and the two porphyrin rings are parallel. Crystal dat a: triclinic crystal system, a = 10.915(4), b = 12.951(4), c = 13.403(4) Е, ± = 118.06(1)°, І = 100.33(1)°, і = 102.43°, P space group, V = 1144.5(1) Е³, Z = 1.

A new mononuclear complex Mn(bbbi)₂(H₂O)₄(ClO₄)₂·(bbbi)₂·(H₂O)₂ 1 (bbbi = 1,4-bis(benzimidazol-1-yl)-2-butene) is synthesized under hydrothermal conditions and characterized by IR spectroscopy, elemental analysis, and single crystal X-ray structural analysis. Crystal data for 1: triclinic, P, a = 8.8478(7) Å, b = 15.0550(11) Å, c = 16.4310(12) Å, α = 108.657(7)°, β = 104.044(7)°, γ = 99.317(7)°, V = 1942.2(3) ų, Z = 1, final R = 0.0621. Each manganese atom is octahedrally coordinated by four aqua ligands and two nitrogen atoms of two distinct bbbi ligands. The molecule is stabilized by hydrogen bonding and π⋯π interactions.

A new complex CuL₂ 1 [HL = 2-((E)-(p-tolylimino) methyl)-6-bromo-4-chlorophenol] is obtained and characterized using the single crystal X-ray diffraction analysis. The crystal belongs to the monoclinic system, P2₁/c space group, with a = 13.3203(13), b = 12.3052(11), c = 17.8664(17) Å, β = 105.3420(10)°, V = 2824.1(5) ų, Z = 4, D_c = 1.672 g/cm³, R₁ = 0.0686. The geometry around copper(II) is intermediate between square planar and tetrahedral. The units of the complex are linked via weak inter-molecular Br…Br contracts, leading to the formation of one-dimension (1D) chains along the b axis; the multipoint Cu…Cl intermolecular interactions extend the 1D chain into a 2D layer.

N,N-phthaloyl-glycine is synthesized under microwave activation without solvent. Its nanoporous solvate is obtained by recrystallization. The solvate is studied by single crystal and powder XRD, thermogravimetry, and mass spectrometry. The crystals are composed of dimers that form a framework structure with infinite channels of about 4 Å in diameter, containing a non-stoichiometric amount of chloroform (the mole fraction is close to 0.35). The nature of the incorporated solvate molecules is determined by high-resolution mass spectrometry, and their quantity is found by thermogravimetry.

The structure of the complex of nickel(II) bis-(1,1,1-trifluoro-5,5-dimethyl-2,4-hexanedionate) with 1,3-diaminopropane is determined by single crystal X-ray diffraction at a temperature of 150 K. Crystallographic data for C₂₀H₃₄F₆N₂NiO₅: a = 17.5446(8) Å, b = 18.1171(10) Å, c = 18.6654(7) Å, β =
115.4150(10)°, space group C2/c, V = 5358.8(4) ų, Z = 8, d_calc = 1.376 g/cm³, R = 0.0435. The structure is molecular; the metal atom coordinates four oxygen atoms of two β-diketonate ligands and two nitrogen atoms of propylenediamine. In the crystal, the molecules are bonded only by van der Vaals interactions.

X-ray diffraction is used to determine the crystal and molecular structure of the complex of N-(1-silatranylmethyl)-3,5-dimethylpyrazole with cobalt dichloride (I). This is yet another example of the participation of the endocyclic oxygen atom of the silatrane fragment in complexation with a metal atom. Metal dichloride interconnects two heterocyclic systems of dimethylpyrazole (DMP) and silatrane (Sa). The coordination polyhedron of the cobalt atom is a tetrahedron.