Home – Home – Jornals – Journal of Structural Chemistry 2015 number 2

Within a slab model the systems of oxygen-containing compounds are investigated. The geometry and the electronic structure are determined for Na₂O₂/NaClO₄(001), K₂O/KClO₃(001) systems using the CRYSTAL09 program package. Parameters of the atomic structure, bond populations, atomic charges, energy distributions, and interaction energies are calculated. It is found that when an oxide and peroxide nanolayer is adsorbed, the bond significantly weakens in chlorate and perchlorate anions.

Using B3LYP/6-311++G(3df,3pd), the electron density distribution (ρ(r)) of trans– and gauche–conformers of normal monohydric alcohols CH₃(CH₂)_nOH (n = 0÷9) is obtained and within the quantum theory of atoms in molecules (QTAIM), the inductive and steric effects are quantitatively studied. Based on the analysis of ρ(r), an additive scheme for calculating the extensive properties is proposed.

The properties of the ground and low-lying excited states of methyl mercaptan (CH₃SH) are studied by using quantum chemistry methods. The geometric parameters and energies of the ground state and the triplet excited state are calculated in this work. It is shown that the calculated geometries of the ground and triplet state are stable and the triplet state potential energy surface has the repulsive feature. The calculated vertical excitation energies and vertical ionization potentials of methyl mercaptan are in best agreement with the experimental values. In addition, the vertical electron affinity and the adiabatic electron affinity of the CH₃SH molecule are also calculated.

The crystalline samples of the orthorhombic phase of H₅O₂⁺ClO₄^– (I) and D₅O₂⁺ClO₄^– (II) are examined by infrared (IR) absorption spectroscopy. Inaccuracies referring to the identification of II found in the literature are corrected. The work shows that a typical evidence of the crystallization of I is the doublet splitting ν(ОН) at 3232 cm^–1 and 3340 cm^–1; and a typical evidence of the crystallization of II is a similar doublet splitting n(ОD) at 2391 cm^–1 and 2484 cm^–1. In order to determine the doublet origin and to make clear how it depends on the concentration of hydrogen isotopes, specially prepared isotopically mixed crystalline samples of the composition (H_1–xD_x)₅O₂⁺ClO₄^– (III, x = 0.17–0.90) are studied. Observations of the concentration dependence of the doublet splitting are used to check the quality of the existing variants of the crystal structure of I. Agreement in the experiments with the samples of III is obtained when the structural model of the cation with the H⁺ and D⁺ positions in the center of a strong Н₂О…Н⁺…ОН₂ and D₂О…D⁺…ОD₂ hydrogen bond (HB) is used. Although we do not exclude the possibility of a symmetrical statistical distribution of H⁺ and D⁺ between two potential energy minima. The results of the spectroscopic analysis agree with the known data of the X-ray crystallographic analysis, showing that the crystals of I have a space symmetry group Pnma . At the same time, they disagree with the recently published data of theoretical calculations of the crystal structure of I (P2₁2₁2₁), these data showing that H⁺ notably shifts from the center of the strong HB towards an oxygen atom of one of the two water molecules.

Raman spectra of tin 2–hydroxy–3,6–di–tert–butyl–para–benzoquianone complexes L₂SnX₂ and LSnX₃ (L is 2–oxy–3,6–di–tert–butyl–para–benzoquianone; X = CH₃, C₂H₅, n–C₄H₉, and C₆H₅) are studied. A comparative analysis of the experimental and calculated spectra is carried out and the vibrational frequencies are conventionally assigned. A new tin(IV) complex based on 2,5–dihydroxy–3,6–di–tert–butyl–para–benzoquianone (L'H₂) containing phenyl substituents at the metal atom is synthesized. Absorption bands of the complexes are interpreted in the low-frequency range of the infrared spectrum that was not considered previously.

In this work, the N,N'-dipyridoxyl(1,2-diaminocyclohexane) [=H₂L] Schiff-base ligand and its square complex [Cu(L)] are newly synthesized and characterized by IR, mass spectroscopy, ¹H NMR, and elemental analysis. The ful optimization of geometries, the ¹H NMR chemical shifts (for the H₂L) and their vibrational frequencies are calculated using the density functional theory (DFT) method. The optimized geometry of the ligand is not planar, but each of two pyridine rings and the cyclohexane moiety are in the separate planes. The tetradentate-dianionic L^2– ligand occupies the four coordination positions of the square comlex in the N, N, O^–, O^– manner.

The effects of tetraphenylammonium (TPhA) on the equilibrium distribution of aluminosilicate oligomers in aqueous and methanolic alkaline aluminosilicate solutions were investigated using ²⁷Al NMR spectroscopy. Alkaline solutions containing both silicate and aluminate ions are of considerable research interest inter alia because of their involvement in the synthesis of zeolites. In the present work, we use ²⁷Al NMR to characterize alkaline aqueous and methanolic tetraphenylammonium (TPhA) aluminosilicate solutions with different Al/Si ratios. Tetraphenylammonium (TPhA) used as a cation template and no alkaline metals are used for preparation of aluminosilicate solutions. The distribution of aluminosilicate species was affected by the presence of the alcohol such as methanol and the method of mixing the silicate and aluminosilicate solutions. To understand the reaction between silicate and aluminate ions in this system, the evolutions of ²⁷Al NMR spectra with time are investigated.

The reaction of 1,4-diaminobutane with 2,2'-diformyl-6,6'-dimethoxy-diphenoxypropane in a mixed solvent of methanol and chloroform results in a new 17-membered macrocyclic Schiff base compound MeO-sal-pn-pn. The title compound is characterized by the elemental analysis (CHN), FT-IR, ¹H NMR spectroscopy, and powder X-ray diffraction. The crystal data are: M_r = 396.5, orthorhombic, P2₁2₁2₁, with unit cell parameters: a = 4.71769(3) Å, b = 19.1524(2) Å, c = 22.9418(2) Å, V = 2072.90(3) ų, and Z = 4.

Water–sodium dodecylsulfate–triethanolamine–1-pentanol–1,1,2,2-tetrafluorodibromoethane microemulsions of five compositions with different water–hydrocarbon ratios at a constant total surfactant+co-surfactant concentration of ~ 22 wt.% are obtained and their specific isobaric heat capacity and specific conductivity are measured. The temperature and concentration dependences of the mentioned properties of microemulsions are analyzed and interpreted from the standpoint of structural changes in the five-component system.

Thermodynamic characteristics are calculated for aqueous solutions of self-associated alkanolamines, which are capable of forming hydrogen bond networks. Correlations are found between the thermodynamic properties and structure of the solutions. The correlation between the entropy and enthalpy characteristics of water-alkanolamine systems with excess packing coefficients suggests that universal interactions determine the structural and energy properties of aqueous solutions of alkanolamines being studied. The structural and thermodynamic characteristics of aqueous solutions of self-associated alkanolamines are found to be similar to the previously obtained parameters of aqueous solutions of diols and oxyethylated glycols.

Crystallographic analysis is used to investigate the mutual packing arrangements of cluster groupings in the structures of KNa₂₃O₄(H₂O)₄₈[{Rh₄O₂(H₂O)₂}(H₂W₉O₃₃)₂] (I), (NH₄)₂[H₃Mo₅₇V₆(NO)₆O₁₈₃(H₂O)₁₈]·53H₂O (II), and Na₆Sr₂[W₁₂O₄₀(OH)₂]·24H₂O (III). It is found that all heavy cations in the clusters are located near the nodes of the single sublattice of the crystal. This arrangement ensures the coherence-assembly of the structural fragments since both the mutual orientation of the fragments and intervals between them are defined by the single cation sublattice.

Thermal transformations of the crystal structure and composition of the h-MoO₃ metastable phase with a transition to the α-МоО₃ stable modification are investigated. The study is performed using submicron phase-pure crystals exhibiting stability during their long storage in the air. By powder XRD, SEM, TGA, CHN, LMS, Raman and IR spectroscopy it is found: the composition of the deposited crystals is expressed by the general formula МоО₃·0.26H₂O; the impurity cationic composition consists of 1.8 wt.% of ammonia groups and a sum of 15 elements detected at a level of 10^–4 wt.%. Thermal treatment of the crystals to T = 350 °C in the air results in the removal of adsorbed and structural water, ОН^–, and NH₄⁺ groups with retaining the h-phase of hygroscopic МоО₃·0.08H₂O. The h-МоО ₃·0.08H₂O crystals obtained show instability during the storage and transform into the α-МоО₃ stable modification. At T = 380 °C the h → a phase transition occurs with the removal of coordinated water and texture transformations resulting in the formation of α-МоО ₃ hygroscopic crystals that at T = 650 °C acquire the platelet shape characteristic of the α-phase.

By cation exchange for clinoptilolite tuff from the Khonguruu deposit (Yakutia) the Mg-, Ca-, Sr-, Ba-modified heulandite-clinoptilolite zeolites are obtained. Based on the data of powder X-ray diffraction and thermal analyses, the properties of these modifications are characterized. Using nitrogen cryosorption, the specific surface areas are determined. Found that the specific surface areas of the cationic modifications obtained increase with the ion charge.

Single crystal X-ray diffraction is used to determine the crystal structure of the coordination metallopolymer {[Co(C₁₁H₂₀N₄O₂)(H₂O)₃], [Co(H₂O)₆](NO₃)₄}_n (I), which is prepared by reacting Co(NO₃)₂×6H₂O with 4,4,10,10-tetramethyl-1,3,7,9-tetraazospiro[5.5]undecane-2,8-dione monohydrate (C₁₁H₂₀N₄O₂×H₂O) in acetone. The crystallographic parameters of I: triclinic structure, sp. gr. P2/c, a = 15.2449(6) Å, b = 9.2600(3) Å, c = 18.4205(6) Å, β = 103.321(4)°, V = 2530.42(15) ų, Z = 2, C₂₂H₆₄N₁₄O₃₄Co₃, d_х = 1.635 g/cm³, T = 298 K, R₁ = 0.051 for 3757 F₀ > 4σ(F), S = 1.03 to 2θ_max = 58.08°. A crystal of I contains octahedral complex cations [Co(H₂O)₆]²⁺, nitrate anions, and metallopolymer chains of the composition [Co(C₁₁H₁₀N₄O₂)(H₂O)₃]_n²ⁿ⁺, in which the molecules of the organic ligand are interconnected by binuclear cobalt complexes.

An analysis is performed of the crystal structures of complex salts [RhL₄Cl₂]X (L=Py, γ- and β-picolines; X are different anions) in light of the effect induced by the nature of the anion X. It is shown that the intermolecular interactions between the anions play a key role in creating the general motif of the structure.

At a temperature of 20 K the crystal structures of two paracetamol polymorphs (monoclinic, form I, SPG P2₁/n and orthorhombic, form II, SPG Pbcа) are solved by single crystal X-ray diffraction and a comparative analysis of the geometric characteristics of intra- and intermolecular interactions is performed. Polymorphous transformations were not observed until cooling to this temperature. It is shown that in form II hydrogen bonds remain longer than those in form I up to a temperature of 20 K, and the density of metastable form II remains higher than that of stable form I. At the same time, in form II, thermal parameters of nitrogen and oxygen atoms remain higher than those in form I. The features observed in the behavior of the heat capacity of both forms at temperatures below 100 K are not directly related to a change in the geometry of hydrogen bonds. The methyl group orientation determined from the electron density maps does not alter as compared to higher temperatures in both modifications. Thus, changes in the Raman spectra observed in the orthorhombic paracetamol form below 100 K are explained by the features of its dynamics rather than a change in the overall average orientation of the methyl group determined by X-ray diffraction.

The results of the study of statistical copolymers of 3,3-bis(azidomethyl)oxetane (BAMO) and 3-azidomethyl-3-methyloxetane (AMMO) with a different molecular weight of monomer units, where А is the non-crystallizable "soft" block of AMMO and B is the “hard” block of BAMO, are reported. By wide angle X-ray diffractometry and IR spectroscopy, the amorphous-crystalline structure of AMMO BAMO copolymers is studied; the degree of crystallinity, crystallite size, and their defects are determined. The domain structure of the statistical copolymers is determined using small angle X-ray diffractometry.

Using methods of molecular mechanics and quantum chemistry in the DFT approximation, a conformational analysis of one of the most biologically active compounds of the class of brassinosteroids, natural brassinolide, and less active natural 24-epibrassinolide and synthetic (22S,23S)-24-epibrassinolide is performed with a subsequent comparison of their side chain structures. Found that the 22R,23R,24S-configuration of two hydroxyl and one methyl groups of brassinolide provides the side chain structures in which its diol system forms an O6…H(O5) intramolecular hydrogen bond. Therewith, the O6H hydroxyl group is free and can participate in the formation of intermolecular hydrogen bonds with a receptor. On the contrary, the 22S,23S,24R-configuration of (22S,23S)-24-epibrassinolide corresponds to the side chain structures in which the O6H hydroxyl group is shielded by the 21-methyl group, which determines a lower biological activity of this hormone.

Flavonoid-metal complexes have anticancer activities. However, the quantitative structure-activity relationship (QSAR) of flavonoid-metal complexes and their anticancer activities has not been known so far. Based on the 14 structures of flavonoid-metal complexes and their anticancer activities for HepG2 from the references, we optimised their structures using the density functional theory (DFT) method, and subsequently calculated 19 quantum chemical descriptors, such as dipole, charge, and energy. Then, we chose several quantum chemical descriptors that are very important for IC₅₀ which represents the anticancer activities of flavornoid-metal complexes for HepG2 through the stepwise linear regression method. Meanwhile, we obtained six new variables through the principal component analysis. Finally, we built QSAR models based on those important quantum chemical descriptors, six new variables as independent variables, and IC₅₀ as a dependent variable using an artificial neural network (ANN). At last, we validated the models using the experimental data from the references. The results show that models presented in this paper are accurate and predictive.

Three (E)-5-bromo-2-methoxy-4-((phenylimino)methyl)phenol derivatives (1-3) are synthesized and characterized by elemental analysis and single-crystal X-ray diffraction. The antibacterial activities of compounds 1-3 against Escherichia coli , Pseudomonas aeruginosa , Bacillus subtilis , and Staphylococcus aureus are evaluated by the MTT method.

The crystal structure of [Pt(En)₂](ReO₄)₂ (En is ethylenediamine) is studied. The crystal chemical analysis is performed and the main factors affecting the packing of moieties in this structure are determined. Shown that thermal decomposition in the He atmosphere at 880 °C results in the formation of the Pt_0.33Re_0.67 solid solution with the hexagonal close packed lattice parameters а = 2.765 Å, c = 4.422 Å and the size of the coherent scattering regions of 42 nm.

Spherical gold nanoparticles with the metal core of 5nm in diameter (according to the data of the transmission electron-microscopy) are prepared by the reduction of chloroauric acid with hydrazine monohydrate in reverse micelles of sodium bis-(2-ethylhexyl sulfosuccinate) (AOT). The photon correlation spectroscopy (PCS) method is used to determine the structure of the gold nanoparticle adsorption layer after their concentration and redispersion in AOT solutions in organic solvents with different polarity (in a series of decane, toluene, and chloroform). It is shown that in case of the abovementioned solvents at low AOT concentrations a gold nanoparticle is surrounded by a monolayer consisting of AOT molecules. When the concentration increases up to 1 M, the absorption layer thickness sharply increases; an increase in the organic solvent polarity enhances this increase. An increase in the temperature (from 20°C to 55 °C) leads to a partial and reversible decrease in the absorption layer thickness.

The X-ray diffraction and conformational study of bis(4-chloroquinoline-N-oxide)hydrogen tribromide is performed. Two conformations corresponding to the minima on the energy curve are found by DFT using the ABINIT software. The model of one of the conformers generally matches with the structure determined experimentally for this compound using X-ray diffraction. In both instances, the structure with the dihedral angle (quinoline - N-O-H) close to 90° is most favorable, which is explained in terms of resonance theory and steric factors. It is concluded that oxygen atoms in the complex are in the sp³ hybridization state and the sp² hybrid state of the oxygen atom is not possible here due to steric factors.

New complex salts (barium and silver tetranitropalladates(II) Ba[Pd(NO₂)₄]×nH₂O (n = 1, 3) and Ag₂[Pd(NO₂)₄]) are synthesized. The compounds are characterized using elemental and X-ray diffraction analyses and IR spectroscopy. The salts crystallize in different space groups. The mutual orientation of nitro groups depending on the outer-sphere counter ion is examined.

The crystal structure of K[Pd(P(CH₂OH)₃)Cl₃] (1) is determined by the single crystal X-ray diffraction analysis. The salt was obtained by the reaction of K₂[PdCl₄] and P(CH₂OH)₃ obtained in situ by the reaction of [P(CH₂OH)₄]Cl with KOH. Crystallographic parameters are: monoclinic, space group P2₁/n, a = 8.4184(2) Å, b = 12.5320(3) Å, c = 11.5579(4) Å, β = 111.292(1)°, V = 1136.12(45) ų, Z = 4, C₃H₉Cl₃KO₃PPd, d_x = 2.198 g/cm³, T = 295 K, R₁ = 0.024 for 2557 F_o > 4δ(F) until 2θ_max = 62°. The crystal structure contains [Pd(P(CH₂OH)₃)Cl₃]^– anions H-bonded with each other and K⁺ cations. Pd atoms are in the square planar environment; Pd-Cl and Pd-P bond lengths are 2.2972(8)¸2.4059(7) Å and 2.2259(7) Å respectively.

The homolytic substitution of chlorine atoms afforded iron(II) clathrochelate bearing two ethanol fragments. The structure of the compound was determined by XRD in the crystalline state and by NMR in solution.

A new end-on azido-bridged polymeric zinc(II) complex [Zn₂ClL(μ_1,1-N₃)]_n , where L is the dianionic form of N,N '-bis(5-fluoro-2-hydroxybenzylidene)-2-hydroxy-1,3-propanediamine, is prepared and structurally characterized by elemental analysis and single crystal X-ray diffraction. The complex crystallizes in the monoclinic space group P2₁/c , with unit cell dimensions a = 9.194(1) Å, b = 22.356(2) Å, c = 9.598(1) Å, β = 95.869(3)°, V = 1962.5(4) ų, Z = 4, R₁ = 0.0691, and wR₂ = 0.1642. The inner Zn atom of the [Zn₂ClL] unit is coordinated by the imino N and phenolate O atoms of L and one azido N atom, forming a square pyramidal geometry. The outer Zn atom of the [Zn₂ClL] unit is coordinated by two phenolate O of L, one Cl ligand, and one N atom of the bridging azide group, forming a tetrahedral geometry. The Zn⋯Zn distance in the [Zn₂ClL] unit is 3.072(2) Å. The [Zn₂ClL] units are linked through end-on azido bridges, forming 1D chains running along the c axis.

A new mixed-ligand copper(II) complex of 1,10-phenanthroline (phen) and benzoate ligands having the general formula [Cu(phen)(C₆H₅CO₂)₂] is prepared and its crystal structure is determined by X-ray crystallography. The complex exists in the monomeric form; the coordination environment around the copper(II) ion is square planar, with the pair of monodentate benzoate ligands being in a cis disposition. In the crystal, the molecules are linked into [001] chains by weak C-H⋯O interactions; no aromatic π-π stacking occurs.

The title compound C₃₂H₂₇NO₅S belongs to the monoclinic system, space group P2₁/c with a = 14.4530(5) Å, b = 13.9185(5) Å, c = 13.5714(4) Å, α = γ = 90°, β = 87.174(3)°, V = 2726.76(16) ų, Z = 4, D_c = 1.310 g/cm³, F(000) = 1128, R = 0.053 and wR = 0.133, S = 1.03, T = 296 K. In the title compound, the naphthalene unit is planar (r.m.s. deviation = 0.0227 Å). The dihedral angle between the naphthalene unit and nitro-benzenesulfonic acid, 2-phenyl-ethyl and 4-phenyl-ethyl are 49.68(05)°, 82.96(06)°, and 81.94(07)° respectively. The structure is stabilized by intra- and intermolecular C-H…O hydrogen bonds.

A novel hydrazide compound (C₁₆H₂₄N₂O₂) is synthesized in a single step by the reaction of pivaloyl chloride with phenylhydrazine in a 2:1 molar ratio in dry DCM. The molecular structure is determined by the single crystal X-ray analysis. The compound crystallized in the monoclinic system, space group P2₁/c with a = 15.4638(17) Å, b = 9.9481(11) Å, c = 10.5276(12) Å, β = 90.194(3)°, Z = 4, V = 1619.5(3) ų.