Home – Home – Jornals – Journal of Structural Chemistry 2017 number 4

The crystal structures and electronic properties of magnesium and calcium nitrates, magnesium nitrate hexahydrate, and calcium nitrate tetrahydrate are studied at the density functional theory level by a hybrid functional in the basis set of localized atomic orbitals using the CRYSTAL14 program code. Atomic structural parameters, atomic charges, bond populations, energy and electron spatial distributions are calculated. The mainly electrostatic nature of interactions between nitro groups and water molecules is shown. The spectrum of the density of states of crystal hydrates, in comparison with nitrates, contains additional bands due to the presence of water. In the spectra of unoccupied states a gap is observed: the anionic gap is ~6.5 eV and the cationic gap is ~8.8 eV.

By the structural representation of a chemical reaction in the form of a condensed graph a model allowing the prediction of rate constants (logk) of Diels-Alder reactions performed in different solvents and at different temperatures is constructed for the first time. The model demonstrates good agreement between the predicted and experimental logk values: the mean squared error is less than 0.75 log units. Erroneous predictions correspond to reactions in which reagents contain rarely occurring structural fragments. The model is available for users at https://cimm.kpfu.ru/predictor/.

The structural and electronic properties of semiconducting BC₁₉ and AlC₁₉ heterofullerenes as adsorbents for toxic small gas molecules (H₂S and SO₂) are determined by DFT. Structural parameters, energy gaps, natural population analysis, partial density of state, dipole moments, and vibrational frequencies were extracted. The adsorption process and sensitivity to the gases are increased by doping with B or Al. The results show that AlC₁₉ is the most sensitive structure. The good sensing of AlC₁₉ is related to high charge transfer upon gas adsorption. Adsorption of the H₂S on the BC₁₉ has negligible effects on the electronic properties, to be categorized as "harmless adsorption". H₂S is weakly adsorbed on BC₁₉ and AlC₁₉. The H₂S and SO₂ molecules act as electron donating and electron withdrawing molecules, respectively. Notably, the adsorption processes are highly exothermic. In general, BC₁₉ is more reactive than C₂₀ and AlC₁₉ is the most reactive cage. This provides a theoretical basis to fabricate B- and Al-doped C₂₀-based gas sensors.

The spin Hamiltonian parameters (g factors, hyperfine structure constants and superhyperfine parameters) and local structures for Ag²⁺ centers in AgCl and KCl crystals are theoretically studied using the high-order perturbation formulas for a tetragonally elongated 4d⁹ cluster. The impurity centers undergo relative elongations (≈0.05 Å and 0.23 Å for Ag²⁺ in AgCl and KCl, respectively) along the C₄ axis owing to the Jahn-Teller effect. All the calculated spin Hamiltonian parameters show good agreement with the experimental data, and the ligand contributions to the spin Hamiltonian parameters are important and should be taken into account. The unpaired spin densities in the superhyperfine parameters are determined from molecular orbital coefficients based on the cluster approach, instead of being taken as the adjustable parameters in the previous treatments. Increasing tetragonal elongation from AgCl to KCl is attributed to a decrease in chemical bonding (or lower force constant) with increasing Ag²⁺-Cl distance.

Extraction complexes of Eu(III) and Am(III) with two 2,6-dicarboxypyridine diamide-type ligands L-A and L-B (Fig. 1) are studied by density functional theory (DFT). At both B3LYP/6-31G(d)/RECP and MP2/6-31G(d)/RECP levels of theory, the geometrical optimizations of the structures of the complexes can achieve the same accuracy and obtain the same geometrical configuration. At the B3LYP/6-311G(d,p)/RECP level of theory Eu³⁺ and Am³⁺ prefer to form [ML]³⁺ complexes under the solvation conditions, and the Am(III) complexes with L-A are more stable than the corresponding Eu(III) complexes. In the system with the ligand L-B, both [ML]³⁺ and [ML(NO₃)₃] species are very unstable.

Halogen and solvent effects on the conformational, vibrational, and electronic characteristics of thiophene-2-carbaldehyde (T2C, C₅H₄OS) and thiophene-2-carbonyl-halogens [C₅H₃XOS, X = F (T2C-F), Cl (T2C-Cl), and Br (T2C-Br)] are analyzed by the density functional theory (DFT) and time dependent density functional theory (TDDFT), using the B3LYP functional and the 6-31++G(d,p) basis set. Computations consider two conformations of the compounds in both gas phase and solution. The present study aims at the exploration of the halogen and medium effects on the stability, structural parameters, dipole moment, carbonyl stretching vibration, frontier molecular orbitals, ultraviolet (UV) and density-of-states spectra of the conformers. The atypical characteristics of fluorine and chlorine affecting the electrical-optical band gaps, chemical hardness, partial density-of-states plot, absorption band, and the highest occupied molecular orbital are observed correspondingly. The findings of this research will provide insight for future studies considering conformations analogous to the compounds studied.

(NH₄)Sb₄F₁₃ crystals (I) are synthesized and their crystal structure (tetragonal crystal system: a = 9.6431(2) Å, c = 6.5503(2) Å, V = 609.11(3) ų, Z = 2, d_calc = 4.100 g/cm³, F (000) = 664, space group I ) is determined. The main structural units of I are tetranuclear anionic [Sb₄F₁₃]^- complexes and [NH₄]⁺ cations. The anionic complexes are built of four SbF₃ groups linked together by tetrahedral bridging fluorine atom. At room temperature the (NH₄)Sb₄F₁₃ crystals are isostructural to previously studied МSb₄F₁₃ (М = K, Rb, Cs, and Tl). The study of ^121,123Sb NQR spectra of compound I is performed in a range of 77-370 K, which shows that when the temperature decreases (<250 K) the substance exhibits piezoelectric properties, as do other compounds of this group, but with a violation of their isostructurality.

The g factors for Cu²⁺ in meta-zeunerite (Cu(UO₂)₂(AsO₄)₂×3H₂O), kroehnkite (Na₂Cu(SO₄)₂x2H₂O), copper benzoate (Cu(PhCO₂)₂×3H₂O) and diaboleite (Pb₂Cu(OH)₄Cl₂) of the tetragonal phase are uniformly treated by high order perturbation formulas for 3d⁹ ions in tetragonally elongated octahedra. The calculation results are in good agreement with the observed values and systematically analyzed in view of the local structures around Cu²⁺. The g anisotropies Δg (= g_|| - g_|) are largely ascribed to the local tetragonal elongations of the Cu²⁺ sites, characterized by the relative elongation ratios ( R_|| - R_|)/ ≈ 19 %, 21 %, 27 % and 30 % for meta-zeunertie, kroehnkite, copper benzoate and diaboletie, respectively. The anomalous valley (minimum) of relative g anisotropy for copper benzoate is attributed to the modification of the Cu²⁺ electronic states due to the phenyl ring. The ligand orbital contributions are found to be significant due to covalency, and should be taken into account. The present study would be helpful to the unified investigations of structures and properties of the copper oxygen compounds.

The work proposes a method to predict changes in the heat capacity of the liquid-vapor phase transition (298.2) based on modified Randič indices for alkanes and acyclic oxygen-containing compounds: alcohols, aldehydes, ketones, ethers, and esters. Based on the obtained (298.2) values heat capacities in the liquid phase (298.2) are calculated for the compounds under study.

The work analyzes both literature data on the dependence of the internal liquid pressure on thermodynamic parameters of state and theoretical ideas of the nature of the internal pressure. The analysis enables the formulation of a hypothesis: the temperature coefficient of the internal liquid pressure corresponds to the state of its force field and the dynamics of this coefficient follows the course of changes in the macroscopic force field of liquids. The hypothesis underlies the construction of a scale of states of the own force field of liquids. To substantiate this scale, and consequently, the formulated hypothesis, the scale is verified with respect to water. A unified scale of states of force fields of associated liquids is proposed.

By a reaction of [BiX₆]^3- with salts of various N-alkylated pyridine derivatives in 2M HX (X = Cl, Br), (N-BzPy)₄[Bi₂X₁₀] complexes (X = Cl (1), Br (2), (4-MePyH)₄[Bi₂Cl₁₀] (3)) are obtained and structurally characterized.

Crystals of bis(4-aminopyridinium) dichromate (C₅H₇N₂)₂[Cr₂O₇] (1) were isolated via slow solvent evaporation and characterized by energy dispersive spectroscopy (EDS), infrared (IR) and ultratviolet-visible (UV-Vis) spectroscopy, and single crystal X-ray diffraction. The room-temperature (RT; 298 K) phase of 1 crystallizes in the monoclinic space group P2₁/m. Its asymmetric unit consists of two crystallographically independent 4-aminopyridinium cations (A and B) and two halves of symmetry-independent dichromate anions (A and B). Cations and anions are linked with the aid of several moderate N-H⋯O hydrogen bonds and weak C-H⋯O interactions resulting in a three-dimensional supramolecular network. The crystal structure is further stabilized by extensive p-p stacking interactions between adjacent pyridine rings. A comparison of the structure of the RT phase of 1 and that of the low temperature (LT; 150 K) phase is described.

A new organic-inorganic hybrid material (C₁₃H₂₈N₂)₂[Cr₂O₇][Cr₃O₁₀]×H₂O (1) was synthesized by slow solvent evaporation at room temperature, and its crystal structure was determined by single crystal X-ray diffraction. This compound crystallizes in the monoclinic space group P2₁/c. The asymmetric unit contains two crystallographically independent 1,3-bis(4-piperidinium)propane, (H₂bppp)²⁺ cations (A and B), one trichromate anion, one dichromate anion, and one water molecule. All these entities are interconnected into a complicated two-dimensional hydrogen bonded network via N-H⋯O and O-H⋯O hydrogen bonds. Furthermore, this structure is stabilized by a large number of C-H⋯O interactions, thus establishing a three-dimensional network structure. This compound appears to be the first example of chromates containing both Cr₂O₇ and Cr₃O₁₀ groups.

A new complex [Cu(L¹)(NCS)]SCN, where L¹ = 3,14-dimethyl-2,6,13,17-tetraazatricyclo(16.4.0.0^7,12)docosane is prepared and characterized by single crystal X-ray crystallographic analysis. The complex crystallizes in the triclinic space group P with two mononuclear formula units in a cell of dimensions a = 7.9681(2), b = 8.8644(2), c = 18.8165(5) Å, α = 76.758(70), β = 78.490(2) and γ = 77.679(2)°. The Cu(II) ion is five-coordinate in an axially elongated square pyramidal environment, with the four amine N atoms at the equatorial positions and the N atom of one thiocyanate at an apical site. The macrocyclic cyclam moiety adopts a stable trans-III configuration. The Cu-N basal plane bond length has a mean value of 2.037(2) Å. The coordinated Cu-NCS bond length is 2.322(3) Å. The N atom of the thiocyanate anion is connected to the macrocyclic ligand of the cation via an NH…N(CS) hydrogen bond. The UV-visible absorption and IR spectral properties are also discussed.

Two new cadmium(II) coordination polymers, {[Cd(L1)(tbta)]×H₂O}_n (1) and [Cd(L2)(tbta)]_n (2) (L1 = 1,4-bis(5,6-dimethylbenzimidazol-1-ylmethyl)benzene, H₂tbta = tetrabromoterephthalic acid and L2 = 1,4-bis(2-methylbenzimidazol-1-ylmethyl)benzene) are obtained under hydrothermal conditions and structurally characterized by single crystal X-ray diffraction methods, IR spectroscopy, TGA and elemental analysis. The L1 and L2 ligands differ by subtle variation of substituents at semi-rigid bis(benzimidazole) bakcbones. Complex 1 features a 3D threefold interpenetrating dia array with a 4-connected 6⁶ topology. Complex 2 displays a 2D {4⁴.6²} sql/Shubnikov tetragonal plane network. Complexes 1 and 2 possess high thermal stabilities and promising fluorescence behavior in the solid state.

A new Mo₂O₃(dpm)₄ compound (I) is synthesized by the interaction of Mo(CO)₆ with 2,2,6,6-tetramethylheptanedione-3,5 (dpm). The structure of complex I determined by the XRD method is as follows: triclinic crystal system, space group P-1, a = 10.1780(7) Å, b = 10.1817(6) Å, c = 13.3255(9) Å, α = 110.562(2)°, β = 102.233(2)°, γ = 93.9041(19)°, V = 1248.17(14) ų. The compound is characterized by IR spectroscopy, mass-spectrometry and thermogravimetric analysis (TGA).

The crystal structure of 1,1-bis(methoxy-NNO-azoxy)-3,3,3-trinitropropane is studied.

A number of physicochemical characteristics of ten 1,2,3,4-tetrahydroquinoline derivatives synthesized for the first time, along with their third order Wiener and Randič indices are calculated by quantum chemical methods. Correlations between the topological indices, physicochemical parameters, and retention factors of the mentioned compounds are obtained for conditions of reversed-phase high performance liquid chromatography on porous graphitized carbon.

Novel Pd(0) nanocomposites using polycaprolactam as a reducing and stabilizing matrix are synthesized. Data on the nanoparticle formation mechanism in a polycaprolactam matrix under the conditions of changing pH of the medium and reagent concentration ratios are obtained. The nanocomposite structure is studied by electron and infrared spectroscopy, X-ray diffraction analysis, atomic force and transmission electron microscopy. The size of metal-containing particles in the composite composition and their size distribution are determined. The obtained nanocomposites can serve as heterogeneous catalysts.

A quantitative topological analysis of supramolecular structures in ethanol solutions with methanol, propanol, water, benzene, and hexane is performed by the MDGT method previously proposed by the authors. The method is based on a combination of molecular dynamics calculations and the graph theory, which enables the recognition and memorization of supramolecular structures observed in each snapshot of the molecular dynamic trajectory, the averaging of data for any number of these snapshots. Thus, the averaged concentrations of associates (dimers, trimers, etc.) are represented and then the concentrations and characteristics of isomers (e.g., chains, branched chains, rings, etc.), bond lengths, angles, etc. are determined in each group of associates.

The reaction between 1,3,6,8-tetraazatricyclo[4.4.1.1^3,8]dodecane (TATD) and 4-nitrophenol (4-NP) under solvent-free conditions results in the formation of a proton transfer (PT) complex, (TATD)⁺(4-NP)^-x4-NP, (3). This is the first crystal structure of a PT complex of TATD, whose structure is stabilized by N⁺-H⋯O and O^-⋯H-O hydrogen bonds. The characterization was performed using FTIR and ¹H NMR spectroscopy, and X-ray crystallography. From X-ray diffraction data collected at 173(2) K, it is concluded that it crystallizes in the monoclinic system (C2/c space group) containing one 4-nitrophenolate anion and one neutral 4-nitrophenol molecule. The stoichiometry of the proton transfer species in DMSO- d ₆ solution is in agreement with the structural data. A combined theoretical and experimental correlation of the structural parameters of free and protonated TATD are in good agreement. The discrepancies in the C-C bond distances between the experimental and calculated results can be attributed to hyper-conjugative interactions and electron delocalization.

A new caffeic acid derivative ((E)-3-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)acrylic acid, HL¹)) is synthesized from caffeic acid, followed by the preparation of a Cu(II) complex, [Cu₂(L¹)₄DMSO₂]x2DMSO. The structure is determined by single crystal X-ray diffraction, and the urease inhibitory activity of the complex is studied. The results show that IC₅₀ of the complex is 0.56 μmol/L, which is superior to positive control acetohydroxamic acid (AHA, IC₅₀ was 10.95 μmol/l), i.e., the complex has strong inhibitory activity towards urease.

Piperidine is one of the basic skeletons in many of pharmacological active compounds derived from natural or synthetic medicaments. Substitution of various groups in the piperidine ring regulates conformational flexibility due to the nature of the substituent on the nitrogen atom. One of the N-substituted piperidine derivatives, PMDPM, phenyl(3-methyl-2,6-diphenylpiperidin-1-yl)methanone, was crystallized and analysed by X-ray crystallography. The crystallographic data are: C₂₃H₂₅NO, M = 355.46, triclinic, space group Pī, a = 8.2543(7), b = 10.5543(8), c = 12.6184(6) Å, α = 77.901(7), β = 71.270(2)°, γ = 70.390(5)°; V = 974.3(1) ų, Z = 2, d_cal = 1.212 Mg/m³, λ(MoK_α) = 0.71073 Å. The core piperidine ring of PMDPM shows a positional disorder and adopts dual conformations as chair and twisted boat. The phenyl rings are oriented axially to the piperidine ring with the dihedral angle of 22.0(1)° between them. The packing is stabilized by C-H⋯O intra molecular interactions including few C-H⋯π and π⋯π weak interactions.

The crystallographic analysis of the tourmaline structure type with the general formula XY₃Z₆(T₆O₁₈)(BO₃)₃V₃W (R3m, Z = 3, a ≈ 16 Å, c ≈ 7.2 Å) shows that tetrahedrally coordinated T (Si, Al, …) cations, octahedrally coordinated Z (Al, Fe, Mg), and Y (Fe, Mg, Mn, …) form a joint cation framework with a sublattice whose geometry is close to F_cub (a_k ≈ 4.40 Å, a_k ≈ 93°) with 40% vacant positions in it. The anion ordering is less regular.

The crystal structures of isostructural fluoride complexes of indium(III) M[InF₄(H₂O)₂] (M = Rb, Cs) crystallizing in the monoclinic system, space group I2/a, are studied. The structures of M[InF₄(H₂O)₂] (M = Rb, Cs) are formed of isolated centrosymmetric complex [InF₄(H₂O)₂]^- anions with the trans -position of coordinated H₂O molecules and Rb⁺, respectively Cs⁺, cations. The In atom in the complex [InF₄(H₂O)₂]^- anion is surrounded by four F atoms and two oxygen atoms of coordinated H₂O molecules, forming the coordination polyhedron as a slightly distorted octahedron. Via a system of hydrogen O-H⋯F bonds the polyhedra of In atoms are arranged in a three-dimensional framework with the cations located in its channels.

The slow diffusion of ethanol vapor into a Na₈[Ta₆O₁₉]x24.5H₂O solution in 30% hydrogen peroxide leads to the formation of colorless Na₃[TaO₈]x14H₂O crystals (1) whose structure and composition are determined by single crystal XRD.

Сrystals of the previously unknown polymorph of potassium tetrafluoroantimonate(III) (β-KSbF₄) are synthesized and their crystal structure is determined (orthorhombic crystal system: a = 8.1631(5) Å, b = 7.8563(5) Å, c = 6.5396(4) Å, V = 419.40(5) ų, Z = 4, d_calc = 3.751 g/cm³, F(000) = 424, space group Pmn2₁). The main structural units of β-KSbF₄ within the first coordination sphere are dimer complex [Sb₂F₈]^2- anions formed of trigonal SbF₄E and tetragonal SbF₅E bipyramids with a common vertex. The previously described α-KSbF₄ polymorph consists of tetrameric [Sb₄F₁₆]^4- complexes formed of SbF₅E bipyramids.

The crystal structure of a hexanuclear Na(I) complex based on 3,5-dimethyl-1H-pyrazole (C₅H₈N₂) and its anion is determined (space group P2₁/c, a = 12.2194(5) Å, b = 24.1554(9) Å, c = 11.3311(4) Å, β = 109.942(1)°, V = 3143.99(8) ų, Z = 2). The crystal structure is formed by Na₆(C₅H₈N₂)₄(C₅H₇N₂)₆ molecules. Thermogravimetric studies show that the compound exhibits volatility at elevated temperatures. The compound can be used in chemical gas-phase deposition processes.

A new copper(II) complex with acetylacetone and ethylenediamine is obtained using the template synthesis. It is studied by single crystal X-ray diffraction. The crystals are monoclinic: а = 7.7563(4) Å, b = 24.0157(12) Å, c = 24.6353(13) Å, β = 91.9490(10)°, V = 4586.2(4) ų, space group P2(1)/c, Z = 2, d_calc = 1.713 g/cm³, R = 0.0695. The copper atom environment consists of two oxygen and two nitrogen atoms of the ligand, forming a slightly distorted square.

A new zirconium(VI) complex with fluorinated methoxy substituted b-diketonate ZrL₄ is synthesized where L = 1,1,1-trifluoro-5-methoxy-5-methylhexane-2,4-dionate. The complex sublimates without decomposition at a low pressure (10^-2 Torr) at 140 °C. The crystal structure of the complex is molecular and composed of mononuclear ZrL₄ molecules. Crystallographic data for C₃₂H₄₀F₁₂O₁₂Zr are: C2/c, a = 12.193(2) Å, b = 21.922(4) Å, c = 15.585(3) Å, β = 101.51(3)°, V = 4082.1(14) ų, Z = 4, d = 1.523 g/cm³. The coordination environment of the zirconium atom is formed by eight oxygen atoms of four b-diketonate ligands; the coordination polymer is a square antriprism. The Zr-O distances are in the range 2.16-2.19 Å. The thermal properties of the complex are studied by TG-DTA.

The [Zn(H₂O)₄]₃[Re₁₂CS₁₄(μ-SO₂)(μ-S)₂(CN)₆]_0.875[Re₁₂CS₁₄(μ-S)₃(CN)₆]_0.125x6H₂O compound (1) containing a new [Re₁₂CS₁₄(μ-SO₂)(μ-S)₂(CN)₆]^6- cluster anion is synthesized by the reaction of ZnCl₂ and K₆[Re₁₂CS₁₄(μ-S/SO/SO₂)₃(CN)₆] in an aqueous solution and structurally characterized. Compound 1 crystallizes in a rhombic space group Pnma with the following unit cell parameters: a = 22.0834(7) Å, b = 28.2551(9) Å, c = 9.7775(3) Å, V = 6100.9(3) ų, Z = 4, d_calc = 3.806 g/cm³. The crystal structure consists of two cluster anions in the ratio 7:1, occupying the same position, distorted [Zn(H₂O)₄]²⁺ cations, and solvate H₂O molecules linked by hydrogen bonds.

A centrosymmetric binuclear complex of gadolinium(III) nitrate with bicyclic bisurea (2,4,6,8-tetramethyl-2,4,6,8-tetraazabicyclo(3.3.0)octane-3,7-dione, or mebicar, Mk) [Gd(C₈H₁₄N₄O₂)(H₂O)(NO₃)₃]₂×H₂O (I) is synthesized and its atomic structure (CIF file CCDC No. 1450653) is determined. The crystals of I are monoclinic: space group P 2₁/c, a = 10.3861(2) Å, b = 10.80470(10) Å, c = 21.2707(4) Å, β = 128.413(3)°, V = 1870.32 ų, ρ(calc.) = 2.05094 g/cm³, Z = 2. The gadolinium atom occupies a general position and is coordinated by two oxygen atoms of two Mk molecules related by a symmetry-center operation, three bidentate nitrate anions, and a water molecule. The coordination polyhedron of the gadolinium atom is a nine-vertex polyhedron represented by a distorted three-cap trigonal prism; the Gd⋯Gd distance in the complex is 6.8697(4) Å.

A series of Ln(III) dipivaloylmethanates of the composition Ln(dpm)₃ (Ln = La, Tm, Yb) is obtained. It is established that Tm(dpm)₃ and Yb(dpm)₃ complexes are isostructural with Lu(dpm)₃. The crystal structure of [La(dpm)₃]₂ at 150(2) K is determined (space group P2₁/n, a = 12.4412(5) Å, b = 28.0579(12) Å, с = 21.9533(8) Å, β = 105.796(2)°, V = 7373.9(5) ų, Z = 4). The studied compound is isostructural with [Pr(dpm)₃]₂, [Eu(dpm)₃]₂, [Gd(dpm)₃]₂, and [Tb(dpm)₃]₂ complexes. The crystal structure of the complex is formed by dimeric [La(dpm)₃]₂ molecules. Thermogravimetric investigations show that the volatility of Ln(dpm)₃ increases in the series from [La(dpm)₃]₂ to Yb(dpm)₃. Melting points of the complexes are close to the known literature data.

The effect of the formation of Н complexes of some dioxolane derivatives with methyl alcohol on the parameters of stretching bands of the ОН group is studied. The observed changes in the spectral and energy characteristics of the complexes are due to the inductive effect of the introduced structural fragments on the equilibrium electron configuration of the COC group in position 1 of the proton acceptor. Based on the results obtained, the authors make the conclusion that the compounds studied are weak proton acceptors.

The crystal structure of 2-(2-morpholinoacetyl)hydrazinocarbothioamide is determined by single crystal X-ray diffraction.