Home – Home – Jornals – Journal of Structural Chemistry 2012 number 2

By means of the ab initio DMol³ method Mo_nSi_m nanoparticles and fragments of Mo₃Si and MoSi₂ crystal lattices are theoretically modeled. For both crystals a few neutral Mo₄Si₆ and Mo₆Si₆ fragments of different shapes and symmetry are considered. In each case, after cluster separation its geometry is optimized, as a result of which the geometric structure noticeably changes and its stability increases. In order to theoretically search for the spatial configurations of Mo₄Si₆ and Mo₆Si₆ nanoparticle, two approaches are used: 1) in the most stable Fe₄C₆ and Fe₆C₆ isomers found previously, iron and carbon atoms are replaced by molybdenum and silicon respectively and then the geometry is optimized to obtain new equilibrium distances and angles; 2) the search for main Mo₄Si₆ and Mo₆Si₆ configurations is performed using the binominal scheme, starting from Mo₂, MoSi, and Si₂ dimers. The nanoparticle structures are found to contain metal atom chains and isolated pairs and triples of silicon atoms. In most cases, the nanoparticle stability proves to be higher than that of the crystal clusters.

Silicon nitride exhibits good mechanical properties and thermal stability at high temperatures. Since experiments have limitations in nanoscale characterization of the chemical structure and related properties, atomistic simulation is a proper way to investigate the mechanism of this unique feature. In this paper, the melt-quench method is used to generate the amorphous structure of silicon nitride; then the structural properties of silicon nitride under tensile deformation were studied by angular pair distribution functions. The corresponding mechanism of tensile stress induced structure rearrangement is explored.

The nature of metal-metal and metal-carbon bonding interactions within the penta- and tetra-ruthenium acetylide complexes [Ru₅(μ₄-C₂)L(CO)₁₃] (1) and [Ru₄(μ₄-C₂)L(CO)₁₀] (2) respectively are investigated using the present topological theories of the chemical bond: AIM and ELF. The electron density analysis within the framework of Atoms in Molecules (AIM) indicates that, in the first complex, only one bond path exists between the Ru4 and Ru5 metal atoms, whereas there is no direct bonding between ruthenium atoms in the second complex. On the other hand, the ELF analysis reveals that in both complexes, all Ru-C bonds belong to closed-shell type interactions and leads to the conclusion that the Ru-Ru bond is predominantly covalent. Moreover, the presence of trisynaptic basins in the first complex points out a three-center bond connecting ruthenium atoms.

Model Pb(II) thiocomplexes with mono- and bidentate ligands of the composition [Pb(L^1,2)_n]^2-n (L¹ is (SC₆H₅)^- (thiophenolate ion), L² is (S₂CN(CH₃)₂)^- (dithiocarbamate ion), n is the number of ligands of 2-6), which simulate fragments of the crystal structures of Pb(II) complex compounds with organic ligands, are studied within density functional theory. Geometric and energy parameters of model complexes with different coordination geometries of the Pb atom are determined and the stereochemical activity of the lone electron pair (LEP, E) of the Pb²⁺ ion is estimated in them. In the studied complexes, the highest Pb-S binding energy is found for the Pb atom surrounded by 2-4 ligands. The geometry of the Pb atom coordinated by S donor atoms can be described in terms of the valence shell electron pair repulsion (VSEPR) model with stereochemically active LEP. The coordination number (cn) of the Pb atom in the most energetically favorable complexes [Pb(SC₆H₅)_n]^2-n is (3+E) - (4+E), and in [Pb(S₂CN(CH₃)₂)_n]^2-n complexes, it is (4+E) and (6+E). Configurations with the mentioned cns are most often observed in the crystal structures of Pb(II) thiocomplex compounds.

According to the data of UB3LYP/6-31G* and UMP2/cc-pVTZ calculations, the adiabatic potential energy surface of the cyclopentane radical cation is very intricate and combines six types of stationary structures of C_s and C₂ symmetry. Ten equivalent C_s structures with the totally symmetric electronic state (C_s (²A′)) correspond to global minima. Conformational transitions between the global minima occur along the inversion and pseudorotation coordinates, for each pair of minima the conformational transition occurring in one stage (through the only transition state). The inversion barrier is ~2 kcal/mol; pseudorotation barriers are ~4-8 kcal/mol. The structure of the potential surface provides the interpretation of the EPR data as a result of dynamic averaging over 20 C_s (²A′) and C₂ (²A) stationary structures.

Ab initio quantum chemical methods are employed to study the spatial and electronic structure of a 1,4-dithiine molecule. Calculations are performed with electron correlation treatment by MP2 and B3LYP methods in 6-311++G(d,p) and 6-311G basis sets. It is found that the macrocyclization of 1,4-dithiine is energetically favorable. The addition of each subsequent dithiine ring decreases the relative energy of the system by ≈0.5÷2.3 kcal/mol. The cycle consisting of 7 dithiine rings is the most comfortable from the standpoint of the internal strain of the macrocycle. With an increase in the number of rings up to 10, the macrocycle starts to break into 4-, 5-, 6-, or 7-membered fragments. The formation of a nanotube based on a 7-membered macrocycle is energetically favorable. The inner diameter of this nanotube is 6.9 Å.

The molecular geometries and vibrational frequencies of the title compounds in the ground state are calculated using the Hartree-Fock (HF) and density functional theory (DFT/B3LYP) methods with the LANL2DZ basis set and compared with the experimental data. The calculated results show that the optimized geometries can well reproduce the crystal structural parameters, and the theoretical vibrational frequencies show good agreement with the experimental values. The energetic behavior of the title compounds in solvent media is examined using the B3LYP method with the LANL2DZ basis set by applying the Onsager and polarizable continuum model (PCM). In addition, molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) analyses of the title compounds are investigated by theoretical calculations.

The local structure and the spin Hamiltonian parameters (the g factors g_i (i = x, y, z) and the hyperfine structure constants A_i) for Cu²⁺-doped Ca(OD)₂ are theoretically investigated from the perturbation formulas of these parameters for a 3d⁹ ion in an orthorhombically elongated octahedron. From the studies, the planar Cu²⁺-OD⁻ bonds are found to experience the relative variation ΔR (≈0.014 Å) along the X and Y axes, while those parallel to the Z axis may undergo the relative elongation ΔZ (≈0.25 Å) due to the Jahn-Teller effect. The theoretical spin Hamiltonian parameters based on the above local lattice distortions agree well with the experimental data. As compared with the previous treatments, the improvements of the theoretical spin Hamiltonian parameters are achieved in this work by adopting the uniform calculation formulas and the tetragonal field parameters based on the superposition model.

An artificial neural network (ANN) is constructed and trained for the prediction of gas to water partition coefficients of various organic compounds. The inputs of this neural network are theoretically derived from molecular descriptors that were chosen by the genetic algorithm-partial least squares (GA-PLS) feature selection technique. These descriptors are: area-weighted surface charge of hydrogen bonding donor atoms (HDCA-2), average bond order of a C atom (P_C), Kier flexibility index (Φ), atomic charge weighted partial positively charged surface area (PPSA-3), and difference between atomic charge weighted partial positive and negative surface areas (DPSA-3). By comparing the results obtained from PLS and ANN models, one can see that statistical parameters (Fisher ratio, correlation coefficient, and standard error) of the ANN model are better than those of the PLS model, which indicates that a nonlinear model can simulate more accurately the relationship between the structural descriptors and the partition coefficients of the investigated molecules.

Absolute intensities are calculated in the harmonic approximation for the IR spectrum of 18 hydrocarbons, oxygen- and nitrogen-containing organic compounds. The quantum chemical calculation is carried out in the 6-311G(3df,3pd) basis set. The calculated data are compared to the experimental values of absolute absorption intensities. It is found that calculations in the HF approximation substantially overestimate (on average by 87%) the integral absolute intensity of fundamental vibrations in the 575-4000 cm^-1 range. Most part of this overestimation falls on the stretching vibrations with large amplitudes (C-H and C=O bonds). When the MP2 method is used without electron correlation treatment, this overestimation decreases to 22% and becomes more uniform in the whole spectral region.

The structure of adducts forming in the solution due to the interaction of bifunctional azo compounds (dimethylpyrazole (DMP) and diphenylformamidine (DPFA)) with hydrogen halides (HF, HCl, and HBr) is found from the data of the IR absorption spectra and quantum chemical calculations. It is shown that in the interaction with HCl or HBr proton donors, proton transfer via the hydrogen bond to the basic N atom of the azo compound occurs with the formation of an NH⁺…Hal^- ionic pair. Strong evidences of proton transfer and the anion-cation pair formation are not found for the DMP-НF structure, and complexes with the molecular N…HF hydrogen bond are the dominant structures. Geometric parameters of the formed structures are calculated. The formation of trimers, containing two molecules of the azo compound and one HHal molecule, with an increase in the nitrogenous base concentration is experimentally proved, and the trimer structure is determined.

NMR and impedance spectroscopy are used to study the ionic mobility and conductivity in crystalline samples in PbSnF₄-MF systems (M = Li, Na, K) in a 150-473 K temperature range. The ¹⁹F NMR spectral parameters, types of ionic motion, and ionic conductivity value in the PbSnF₄ compound doped with alkali metal fluoride is found to be determined by the temperature, nature, and concentration of an alkali cation. The specific conductivity of the crystalline samples in PbSnF₄-MF systems (M = Li, Na, K) is rather high at room temperature and hence, it seems possible to apply them in the development of functional materials with high ionic (superionic) conductivity

The atomic structure of copper(II) complexes based on diacetyl monoxime 1′-phthalazinyl hydrazone is studied by XANES spectral analysis and magnetochemistry. The XANES spectra at the CuK-edge are measured in С₂₄H₂₄N₁₀Cu₂O₂ and С₂₄H₂₄N₁₀Cu₂O₂ complexes. The calculations of the CuK-XANES spectra of the complexes in question are performed for a few structural models based on the full-potential finite difference method. By low-temperature magnetochemistry magnetic exchange parameters are determined, and a quantum chemical simulation of the exchange interaction is carried out within the broken symmetry approximation. Based on a combined analysis of the XANES spectra and magnetic exchange parameters, the most probable structural models of С₂₄H₂₄N₁₀Cu₂O₂ and С₂₄H₂₄N₁₀Cu₂O₂ complexes are found.

By single crystal X-ray analysis, the atomic structure of the crystals of bis-phenanthrolinium hexachlorotellurate(IV) dihydrate (С₁₂Н₉N₂)₂TeBr₆·2H₂O (a = 7.4846(5) Å, b = 13.792(1) Å, c =
14.532(1) Å, β = 99.857(2)°, space group Р2₁/c, Z = 2, d_x = 2.259 g/cm³) is determined. The crystal structure is formed from separate anions [TeBr₆]^2-, cations of phenanthrolinium (С₁₂Н₉N₂)⁺, and water molecules. The electronic and geometrical aspects determining the spectral-luminescent and thermochromic properties of the complex are discussed.

The theory of the dependence of solvation numbers on the temperature is very popular today. However, according to our works, solvation numbers do not depend on temperature until the complete solvation limit is reached. The purpose of this paper is to address this apparent contradiction

The analysis of changes in the partial volume of glycine in solutions of substances that have a different effect on water structure is presented. For glycine in mixtures of water with glycerol and ethylene glycol, we derive a single equation for the dependence on the volume fraction of alcohol. The addition of tert-butyl alcohol, ethylene glycol, glycerol, and urea to water leads to a decrease in the hydration number of the amino acid (glycine dehydrates). In 1m solutions the losses of hydration water are 3.2%, 4.5%, 5.7%, and 7.6% respectively. In a 4m solution of tert-butyl alcohol, glycine loses 44% of hydration water, the same as in a 15m urea solution and a 20m glycerol solution. A contribution of the structural dehydration of glycine is observed in dilute aqueous solutions of t-BuOH. In more concentrated solutions, intermolecular interactions in the binary mixed solvent counteract dehydration. These interactions compensate for 15-22% of water lost by glycine in a 20m solution of urea, glycerol, and ethylene glycol and a 4m solution of t-BuOH. The partial volumes are also discussed within preferential solvation concepts.

A ternary salt system Rb₂MoO₄-Ce₂(MoO₄)₃-Zr(MoO₄)₂ is studied by powder XRD. Single crystals of 5:1:2 ternary rubidium-cerium-zirconium molybdate Rb₅CeZr(MoO₄)₆ are obtained by solution melt crystallization under spontaneous nucleation conditions. The crystal structure is solved by X-ray crystallography (X8 APEX automated diffractometer, МоK_α radiation, 1274 F(hkl), R = 0.0456). The parameters of a trigonal unit cell are: a = b = 10.7248(2) Å, c = 38.796(1) Å, V = 3864.52(14) ų, Z = 6, Rc space group. The three-dimensional complex framework comprises Мо tetrahedra linked to two independent (Ce,Zr)O₆ octahedra. Two types of rubidium atoms occupy large cavities of the framework.

The crystal structure of the coordination compound Na[RuNOCl₃(H₂O)OH]·2H₂O is reported. The complex is studied by IR and NMR spectroscopy, powder and single crystal X-ray diffraction. Crystallographic data determined for H₇Cl₃NNaO₅Ru is: a = 6.648(2) Å, b = 8.216(7) Å, c = 10.063(3) Å, α = 89.75(6)°, β = 70.96(2)°, γ = 78.76(5)°, V = 967.9(2) ų, P1 space group, Z = 4, d_x = 2.165 g/cm³.

New tridentate 2,6-bis(imino)pyridyl ruthenium(II) complexes, [N₃]Ru(H)(Cl)(2,4,6-(CH₃)₃C₆H₂NH₂) (4) and [N₃]Ru(Cl)₂(2,4,6-(CH₃)₃C₆H₂NH₂) (5) ([N₃] = 2,6-(2,4,6-(CH₃)₃C₆H₂N=CCH₃)₂C₅H₃N) have been synthesized and characterized. The crystal of complex 4, which has been grown in benzene/cyclohexane by evaporation at room temperature, was studied by X-ray diffraction. Complex 4 crystallizes in the monoclinic space group C2/c with cell parameters of a = 42.243(4) Å, b = 8.1480(5) Å, c = 23.662(2) Å, β = 117.998(1)°, V = 7191.1(10) ų, and Z = 8. The molecular structure of 4 shows a six coordinate, pseudo-octahedral geometry with a trans arrangement of hydrogen and chloride ligands. The mesityl ligands are oriented approximately perpendicular to the 2,6-bis(imino)pyridyl ligand plane, and form a pocket surrounding the 2,4,6-trimethyl benzenamine ligand. The coordinated 2,4,6-trimethyl benzenamine (2,4,6-(CH₃)₃C₆H₂NH₂) is in the cis to chloride and hydride, trans to pyridine ligand, and lies parallel to one of the mesityl rings.

A new complex of 2-aminopyridine and malonic acid in a 1:1 stoichiometric ratio is obtained. The complex crystallizes in a centrosymmetric P2₁/c space group with a = 3.8522(2) Å, b = 17.5226(8) Å, c = 13.7317(7) Å and β = 94.418(3)°. This complex is held by network of hydrogen bonds between the protonated 2-aminopyridinium cation and the malonate anion. There is no phase transition observed in this complex, which is verified using DSC and single crystal X-ray measurement studies. Unlike 2-aminopyridinium maleate, this complex crystallizes in the centrosymmetric space group and hence, this complex will not exhibit any non-linear optical property.

An X-ray structural examination is carried out for 2,3-dimethyl-5-(2′-methylprop-1′-enyl)-6-(morpholyl-4′-carbonyl)-cyclohex-3-en-1-carboxlic acid that is one of the products of the Diels-Alder reaction of an acyclic monoterpene alloocimene with maleic and citraconic anhydrides followed by the ring opening of adducts with morpholine to corresponding amides. The crystals are triclinic; a = 10.619(1) Å, b = 12.784(2) Å, c = 14.328(2) Å; α = 65.752(1)°, β = 87.932(1)°, γ = 78.120(1)°; V = 1733.0(3) ų, P-1 space group, Z = 4 (two independent molecules). In both molecules, the anti-conformation of the carboxylic group is observed, the conformation being stabilized by an intramolecular hydrogen bond involving the carboxylic hydrogen atom and ketonic oxygen.

The orientation of dihydropyrimidine derivatives containing podand chains is determined in the model receptor using the CiS algorithm. The orientation of compounds with podand chains is compared with the location of compounds without podand chains in the model receptor. The pharmacophore and antipharmacophore parts of the compounds are analyzed. Amino acid residues responsible for the effective interactions of the compounds with podand chains with the binding site of dihydrofolate reductase (DHFR) are identified using the X-ray diffraction data. The mechanism of the action of tuberculostatic compounds with podand chains in their composition is proposed, which assumes the studied molecules to undergo metabolism by cytochrome P450 isoform 3A4 forming metabolites. The most active are the metabolites without the fragments of podand chains, which interact with DHFR. Therefore, the compounds containing podand chains are prodrugs.

A PBE0/6-311G(3d₅f₇,p) quantum chemical method is used to determine the structural parameters of the molecules of sin- and anti-tricyclo[4.2.0.0^2.5]octane, [2.2.2]propellane, tricyclo[3.3.0.0^2.6]octane, prismanes (CH)_2n (n = 1-7), and dicubane С₁₂Н₈. Bond lengths in anti-tricyclo[4.2.0.0^2.5]octane amount to 1.572 Å. The tetratomic ring in tricyclo[3.3.0.0^2.6]octane is a flattened tetrahedron with internuclear distances of 1.551 Å and 2.037 Å. The symmetry of C₈H₈ sin-tricyclo[4.2.0.0^2.5]octa-3,4,7,8-tetrayl moieties in prismanes and metal organic compounds (C₈H₈RhCl₂RhC₈H₈, C₈H₈RhCl₂RhC₇H₈, and C₈H₈PdCl₂) is higher than the symmetry of a free sin-tricyclo[4.2.0.0^2.5]octane molecule.

A series of N-heterocyclic carbene nickel complexes of the type [Ni(N-heterocylic carbene)(NO)(R)] (R = H, Me, HC=CH₂, and C≡CH) are examined to study the influence of a substituent on the molecular structure and bonding of these complexes. Geometrical and AIM analyses of the interaction between Ni and the carbene fragment reveal that for the metal-carbene bond donation is more important than back-donation. The NICS values suggest that aromaticity in the heterocyclic ring is less than in the free heterocycle.

A method to predict the enthalpies of vaporization of ethers with various structures under normal conditions using a modified Randič method is proposed

The temperature dependence of heat capacity of the polycrystalline sample of cobalt(II) clathrochelate in a range of 6-300 K is studied. Based on the smoothed dependence C_p(Т), the entropy and enthalpy values in a temperature range of 8-300 K and their standard values at 298.15 K are calculated. In the C_p(Т) curve in a range of 50-70 K, a process is recorded whose entropy and enthalpy are 1.2 J·(K·mol^-1) and 68 J·mol^-1 respectively. A comparison of the results with the data of a multitemperature X-ray diffraction study makes it possible to attribute this process to the structural phase transition.

From 3-allyl salicylaldehyde and 4-aminoazobenzene (HL), the Schiff-base complex of copper(II) is synthesized and structurally characterized. The crystallographic unit of a CuL₂ (1) single crystal contains two independent molecules of the complex. Coordination polyhedra of copper atoms are slightly distorted squares; azomethine ligands are in the trans-position. The neighboring molecules of the complex are bonded by intermolecular π stacking interactions

Tris(diisopropylammonium)tetrachloridoferrate(III) dichloride crystallizes in the monoclinic space group P2₁/c (a = 7.6685(2), b = 17.6079(3), c = 23.3217(4) Å, β = 91.396(2)°, V = 3148.1(1) ų, Z = 4, T = 113 K) with three diisopropylammonium cations (dip), one tetrachloridoferrate(III) anion, and two chloride anions in the asymmetric unit. The dip cations and the chloride anions form hydrogen bonded one-dimensional polymers along [010]. The tetrachloridoferrate(III) anion, habituated in between these chains, is not involved in any hydrogen bonding. The structural characterization is supported by infrared and Raman spectroscopic data.

In the interaction of Zn(NO₃)₂·6H₂O and adamantane-1,3,5,7-tetracarboxylic acid (H₄atc) in N,N′-dimethyl formamide (DMF) a three-dimensional coordination polymer with the composition [Zn₂(dmf)(H₂O)(atc)]·0.75DMF·0.5H₂O (1) is produced. Its structure is determined by a single crystal X-ray diffraction study