Home – Home – Jornals – Journal of Structural Chemistry 2016 number 6

Six conformers of O-isopropylmethylfluorophosphonate (IMFP) are revealed. Their geometric parameters, dipole moments, and polarizabilities are calculated. The applicability of methods chosen for the calculation of the structure and mentioned properties of IMFP conformers (phosphoryl compounds not noted for conformational diversity) is evaluated. The features of the IMFP structure and stereochemistry are considered.

In the work the structural and thermodynamic characteristics of zirconium tetrahydroborate Zr(BH₄)₄ are considered. The initial compound organized in a cubic lattice was heated from absolute zero to temperatures exceeding the experimental boiling temperature. Temperature dependences of the parameters of the internal structure, energy, and density of molecules in bulk are obtained. It is found that on heating the compound to 300 K its structure is maintained and on further cooling it returns to the initial state. On heating above 400 K the irreversible destruction of the crystal lattice is observed. On further cooling the compound in the solid phase becomes amorphous. It is shown that in the new state the average binding energy is lower than that in the initial one and the cubic lattice has the highest binding energy among the considered Zr(BH₄)₄ structures.

Within the density functional theory with regard to the dispersion interaction the crystal structure parameters of organic C₁₀H₈N₆O₄ azide are determined.The pressure effect in the range 0-20 GPa on its structural and electronic properties is studied. Parameters of the equation of state in the Vinet and Birch-Murnaghan model are determined. Within the quasi-particle method ( G ₀ W ₀) the energy band structure is calculated. It is shown that the hydrostatic pressure of 20 GPa results in the approach of planes of C₁₀H₈N₆O₄ molecules and their shift relative to each other. This is accompanied by a broadening of the upper valence bands and a decrese in the band gap from 5.07eV to 3.97 eV.

Ab initio calculations are employed to investigate nitrogen inversion as a configuration change that can supply an infinitely useful switchable control mechanism for some complex systems. In this paper, the design of a new pedal-like nano-scale robot is discussed based on nitrogen inversion. This work introduces the design of a nano pedal in which different structures of the arms created two diverse kinds of pedals: a) nano pedal without intersectional motion and b) nano pedal with intersectional motion. In ( a ), due to stereo repellent in the two pedal arms, they were unable to pass each other and could only move back and forth in one direction. However, in ( b ), due to an increase in the axis connecting the two arms, the issue of stereo repellent of nitrogen was looked over and the arms could pass each other and moved in a larger domain.

The current aim of the ab initio crystal structure prediction is to find the possible conformers of the flexible N-(3-chloro-4-fluorophenyl)thiourea (CFT) molecule using gas phase optimisation with an MP2/6-31G( d , p ) basis set, and the lattice energy minimization in the presence of a repulsion-dispersion electrostatic potential. If the molecule deviates from the gas phase conformation, suitable intermolecular interactions are added, and the molecule favours stable packing. The crystal structure is said to be feasible if the intermolecular lattice energy compensates the intermolecular energy penalty associated with the suboptimal gas phase conformers. The idea of the current research is to find the least energy hydrogen bonded crystal structure from a set of rigid conformers in a conformation region, with a significant similarity of packing, which may lead to the prediction of polymorphs associated with the considered CFT molecule.

The prilocaine is a significant amino amide local anaesthetic. This drug can exist as three possible tautomers. Herein, by using density functional theory (DFT), and handling the solvent effects with the PCM model, the structure, energetic behavior, kinetics and mechanism of tautomerization, as well as the natural bond orbital analysis (NBO) of the prilocaine are reported. P1 is the most stable tautomer of the prilocaine, which can be tautomerized to two other tautomers via the intramolecular-proton transfer. Good agreement between the calculated NMR chemical shifts and IR vibrational frequencies with the experimental values approves the suitability of the optimized geometry for the prilocaine. A large HOMO-LUMO energy gap implies a high stability of the prilocaine.

The crystal structure of dichlorobis(dimethylsulfoxide-O)copper(II), [CuCl₂(DMSO)₂] (I), previously determined by Willett and Chang, is reinvestigated. It crystallizes in the orthorhombic system with the space group Pnma (N°62), Z = 4, and unit cell parameters a = 8.053(1) Å, b = 11.642(5) Å, c = 11.347(3) Å. Our structure determination is of a significantly higher precision in terms of bond lengths, angles, and R factors (e.g., Cu1-O1 = 1.9737(24) Å, O1-Cu1-O1ⁱ = 173.08(13)° (symmetry code: ⁱ x , 1/2- y , z ) and R ( F ²) = 0.046 compared to 1.955(4) Å, 173.0(3)° and R ( F ) = 0.075). In contrast to the previous investigation, all H atoms are placed at calculated positions. In the title molecule, the Cu^II atom is five coordinated in a distorted square pyramidal geometry. Thus, as reported previously, it can be shown that the crystal structure consists of [CuCl₂(DMSO)₂] molecules which, by virtue of long Cu-Cl interactions, are tied together to form chains parallel to the [100] direction. The density functional theory (DFT) optimized structure at the B3LYP/6-311++G(2 d ,2 p ) level is compared with the experimentally determined molecular structure. The HOMO-LUMO energy gap and other related molecular properties are also calculated. Comprehensive experimental and theoretical structural studies on the studied complex are carried out by FT-IR and UV-visible spectroscopies.

Captopril disulphide is obtained under hydrothermal conditions. The IR and Raman spectra data are in agreement with the X-ray diffraction results. The disappearance of the band at 2566 cm^-1 (n(SH)) in both spectra of captopril disulphide is consistent with the formation of the S-S bond. The degradation of the captopril drug is investigated by Raman spectroscopy and the results indicate that after 6 weeks of air exposure, a band at 512 cm^-1, assigned as n(SS), is observed, suggesting the formation of captopril disulphide. DFT calculations in the solid state are performed for captopril and captopril disulphide. The results indicate that captopril disulphide is approximately 30 kcal×mol^-1 more stable than captopril. The analysis of the total density of states (DOS) reveals that the captopril valence band contains a significant contribution from the S atom, whereas for captopril disulphide, the O atom is the most important for the valence band.

The electronic structure of free radicals and Cu(II) complexes with the nitronylnitroxyl radical and amino nitron is studied by X-ray photoelectron spectroscopy (XPS). N1 s XPS spectra of nitrogen atoms of Cu(II) complexes with amino nitrons confirm the diamagnetic nature of the ligands. The binding energies of the main peak and the intense satellite structure in the Cu2p_3/2,1/2 spectra of the complexes under study correspond to the Cu(II) state. The structure of the satellite in the Cu2p_3/2,1/2 spectrum depends on the environment of the metal ion.

In the work the double differentiation of functions describing the Pt4 f _7/2 band in the XPS spectra of model supported Pt/SiO₂ catalysts is performed in order to determine the number of different chemical states of platinum particles. The functions for the differentiation are obtained by the deconvolution of the experimental spectral contour into two spin-orbit components. As a result of the performed analysis of the number and position of the minima of the second derivative of the function of Pt4 f _7/2 the conditions of the oxidation of platinum particles in the Pt/SiO₂ sample on treating in a NO + O₂ mixture and the reduction of platinum oxide particles on interacting of the PtO _x /SiO₂ sample with hydrogen are determined.

The existence of hydrate forms of iron(III) oxalate, which noticeably differ from each other in the Mössbauer spectral parameters (isomer shift and quadrupole splitting), is detected. In the assumption of the formation of phases with different structural characteristics the samples of the compound under study are studied by the powder X-ray diffraction analysis (including the application of synchrotron radiation), Mössbauer and IR spectroscopy. It is shown that the phase characterized by new values of the Mössbauer parameters has its own IR spectrum and it is X-ray amorphous and metastable.

By the classical molecular dynamics method liquid chlorobenzene chlorobenzene is modeled in the temperature range 293-363 K. The radial angular distribution functions are calculated for the distances between the benzene ring planes and the angle between them; the radial distribution functions for the distances between the chlorine atoms; self-diffusion coefficients, local dipole moments, and the permittivity. In the whole temperature range the molecules are combined into agglomerates due to contacts between the chlorine atoms (halogen aggregation) and owing to specific interactions of benzene rings which result in their mainly parallel and perpendicular orientations in the first coordination sphere. Molecules in the agglomerates are mostly organized in the 1D motif: chains of chlorine atoms and stacks of benzene rings. With an increase in the temperature the structure of agglomerates is reorganized and changes are most obvious in temperature ranges 293-298 K, 313-323 K, and 343-353 K.

Optimal growth conditions for GdSe_1.85 crystals are found by the thermodynamic simulation of the Gd-Se-I system. The obtained data are used to grow GdSe_1.85 crystals by the transport method using iodine as a transport agent. The grown crystals are identified by microprobe and powder X-ray diffraction analyses. The structure is determined by the single crystal X-ray diffraction analysis and the composition is refined. The crystal structure is in general typical of the structures of REM polychalcogenides, however, the unit cell represents the metric type unknown previously: a = 4.0562(2), b = 8.1065(5), c = 9.2489(5) , a = 115.9990(10), b = 90.000(2), g = 89.9750(10), V = 273.34(3) ³, Z = 4, d _calc = 7.659 g/cm³, space group Pb 11. The experimental material for the X-ray crystallographic analysis is obtained on an automated Bruker X8 APEX diffractometer (Мо K radiation, graphite monochromator, CCD detector resolution 10241024 pixel, distance to the detector L = 50 mm, rotation about the axis 15 min) by the standard procedure, 2274 measured reflections, out of them 1523 independent ( R (int) = 0.0352), R -factor [ I > 2s( I )] = 0.0517, R -factor (all measured) = 0.0694).

Novel supramolecular networks based on an anionic polymolybdophosphate cluster Sr₁₀(H₂O)₁₂[Sr₂P₉HMo₁₂O₇₁] is hydrothermally synthesized and structurally characterized by single crystal X-ray diffraction, thermogravimetric analysis, infrared, ultraviolet spectroscopy, and cyclic voltammetry in an aqueous solution. It crystallizes in the orthorhombic space group Pnmm (No. 59) with a = 12.699(1), b = 14.914(1), c = 23.851(2) Å and Z = 2. The compound is made up of unusual shaped-cage [Sr₂P₉HMo₁₂O₇₁]^20-. The strontium cations are divided in two kinds. The first occupy vacant sites in the [P₉Mo₁₂O₆₈] ^n- polyoxoanions unit and the second [Sr(H₂O)₆]²⁺, [Sr(H₂O)₄]²⁺, and [Sr(H₂O)₂]²⁺ serve to bridge together the adjacent polymolybdophosphate clusters to yield unprecedented three-dimensional pure inorganic assemblies of the shaped-cage polymolybdophosphate clusters.

By single crystal X-ray diffraction and differential thermal analyses tetramethylammonium hexafluoridozirconate (N(CH₃)₄)₂[ZrF₆] is studied. In the temperature range 96-110 C the crystals undergo a reversible phase transition from the low-temperature trigonal modification (space group R ) to the high-temperature cubic one (space group Fmm ). The cubic phase is composed of regular [ZrF₆]^2- octahedra and tetrahedral (CH₃)₄N⁺ cations bound by ionic interactions and С-H⋯F hydrogen bonds.

The syntheses and crystal structures of two one-dimensional coordination polymers, [Mn(C₅HO₂F₆)₂(C₁₆H₂₀N₂)] _n (1) and [Mn(C₅HO₂F₆)₂(C₂₀H₂₀N₂)] _n (2), are described, where is the hexafluoro acetylacetonate anion, C₁₆H₂₀N₂ is 1,6-bis(4-pyridyl)-hexane, and C₂₀H₂₀N₂ is 1,4-bis[2-(3-pyridyl)ethyl]-benzene. In both phases, the metal ion lies on a crystallographic twofold axis and is coordinated by two chelating anions and two bridging bipyridyl ligands to generate a cis -MnN₂O₄ octahedron. The bridging ligands, which are completed by crystallographic inversion symmetry in both compounds, connect the metal nodes into zigzag [20 ] chains in 1 and contorted [001] chains in 2. Intrachain C-H⋯O interactions occur in 1 but not in 2, which may be correlated with the relative orientations of the ligands. Crystal data: 1, C₂₆H₂₂F₁₂MnN₂O₄, M _r = 709.40, monoclinic, C 2/ c (No. 15), a = 9.3475(2) Å, b = 16.6547(3) Å, c = 18.3649(4) Å, b = 91.1135(8)°, V = 2858.50(10) ų, Z = 4, R ( F ) = 0.030, wR ( F ²) = 0.075. 2, C₃₀H₂₂F₁₂MnN₂O₄, M _r = 757.44, monoclinic, C 2/ c (No. 15), a = 19.9198(2) Å, b = 10.6459(2) Å, c = 16.8185(3) Å, b = 119.8344(8)°, V = 3093.91(9) ų, Z = 4, R ( F ) = 0.032, wR ( F ²) = 0.078.

A new mixed-ligand one-dimensional copper(II) coordination polymer [Cu(en)(sal)Cl] _n where en = ethylenediamine(C₂H₈N₂) and Hsal = 2-hydroxybenzoic acid (salicylic acid; C₇H₆O₃) is synthesized and characterized by FTIR spectroscopy and single crystal X-ray diffraction. The structure contains Cu²⁺ ions in two different distorted octahedral coordination environments: an axially extended CuN₄Cl₂ moiety arising from a pair of bidentate en ligands and a CuO₄Cl₂ moiety arising from a pair of asymmetrically coordinated sal^- anions. The chloride ions bridge the copper ions into a zigzag chain propagating in [001]. The structure is consolidated by N-H⋯O and N-H⋯Cl hydrogen bonds which generate a layered network. Crystal data: C₉H₁₃ClCuN₂O₃, M _r = 296.20, monoclinic, P 2₁/ c , a = 13.9179(10) Å, b = 10.4900(8) Å, c = 8.5181(6) Å, b = 105.518(4)°, V = 1198.30(15) ų, Z = 4, R ( F ) = 0.026, wR ( F ²) = 0.068.

After the addition of the saturated NaClO₄ solution to the solution of trans -[Ru(NO)(NH₃)₄SO₄] HSO₄H₂O, trans -[Ru(NO)(NH₃)₄SO₄]ClO₄ perchlorate salt (I) is obtained with an yield of 80 %. The heating of trans -[Ru(NO)(NH₃)₄(H₂O)](HSO₄)SO₄ at a temperature of 220 C results in a complete removal of coordination water and a partial removal of ammonia molecules. At successive treatment of the thermolysis product with sulfuric and hydrochloric acids [Ru(NO)(NH₃)₄SO₄][Ru(NO)(NH₃)₃Cl(SO₄)]HSO₄H₂O crystals (II) are obtained. By X-ray crystallography the structure of the obtained compounds is determined: for I space group P 2₁/ c , a = 6.6949(9), b = 13.7049(19), c = 12.8641(17) , = 101.028(4); for II, space group Р 2₁/ c , a = 14.1304(4), b = 12.4908(3), c = 11.6264(3) , = 94.1980(10).

In the work isomeric complexes of platinum(II) with the (ptac)^-1- Pt((CH₃)₃-CO-CH-CO-CF₃)₂ pivaloyltrifluoroacetonate ion are studied. The synthesis and chromatographic separation of ​ Pt(ptac)₂ isomers is described, TGA data for the separated isomers are given, and the crystal structures of solid phases are studied. The cis -Pt(ptac)₂ complex crystallizes in the space group Р -1, a = 10.7091(4), b = 12.7787(6), c = 16.0154(8) , = 92.389(2), = 90.868(2), = 112.1260(10), V = 2027.39(16) ³, Z = 4, d _calc = 1.918 g/cm³. The trans -Pt(ptac)₂ complex crystallizes in the space group C 2/ m , a = 13.3235(5), b = 8.5515(3), c = 9.6694(3) , = 118.5880(10), V = 967.38(6) ³, Z = 2, d _calc = 2.010 g/cm³. The structures of the complexes are molecular, the Pt atom has a square coordination of four oxygen atoms of two ligands; for cis- Pt(ptac)₂ the Pt-O_av distance is 1.968 , for trans -Pt(ptac)₂ it is 1.980 .

By the single crystal X-ray diffraction analysis in combination with quantum chemical calculations the molecular and crystal structures of energy-intensive 2,4,6-triazipyridine and 2,4,6-triazido-3,5-dibromopyridine are studied; the dependence of structural parameters of their azido groups on the size of substituents in b-positions of the pyridine ring is analyzed. The effect of the intramolecular contact involving the central nitrogen atom of -azido groups in substituted triazides on their structure and properties is revealed.

Silver nanoparticles are synthesized in the medium of an aqueous cysteine-silver solution at different рН values using sodium borohydride as a reductant. By means of dynamic light scattering, electron spectroscopy, and transmission electron microscopy it is found that the size and stability of nanoparticles in this system depend on the рН value that is regulated by alkali and on the concentration of the cysteine-silver solution. Under certain conditions the unimodal distribution of silver nanoparticles with an average size of 40 nm are obtained.

Films of hydrogenated SiC _x N _y O _z :H obtained by plasma-enhanced chemical vapor deposition from a mixture of 1,1,3,3-tetramethyldisilazane with oxygen and nitrogen (TMDS+O₂+ x N₂) in the temperature range 373-973 K are nanocomposites in whose amorphous part nanocrystals belonging to phases of the Si-C-N: -Si_3-x C _x N₄ system and graphite are distributed. A change in the chemical composition of gas mixtures enables the preparation of SiC _x N _y O _z :H films with a broad variation range of the functional properties, such as the 1.45-2.15 variation of the refractive index; the controlled transparency ( T 92-99.7 %) in UV, visible, and IR spectral ranges; tunable characteristics of the band gap (3.5-5.4 eV), and dielectric constants (5.2-5.8).

In order to obtain crystalline photochromic materials combining the advantages of photochroms in liquid and polymeric solutions (high quantum yields) and in the solid state (enhanced resistance to photodegradation) a photochromic adduct consisting of a metal-organic framework [Zn₄(dmf)(ur)₂(ndc)₄] (ndc^2- is 2,6-naphthalenedicarboxylate, ur is urotropine, dmf is N,N-dimethylformamide) and 2,3-bis-(2,5-dimethylthiophen-3-yl-cyclopent-2-en-1-one) is synthesized (compound 1). The photochemistry of the adduct is studied. Solid 2,3-diarylcyclopentenone exhibits photochromism typical of diarylethenes. Quantum yields of the adduct photocoloration and photobleaching turn out to be 1.5 and 3 times higher respectively than those for solid compound 1 and lower than those of solution 1 in acetonitrile by an order of magnitude. The number of photochemical cycles for compound 1 in the solution, the solid state, and the adduct composition is limited by the monomolecular side reaction.

A motif of the supramolecular architecture of соcrystals of 18-crown-6 and polychloropolyfluoro-1,3-phenylenediamines or partially fluorinated 1,3-phenylenediamines (1:1 stoichiometry) is infinite 1D ensembles of alternating components. Mutual coordination of molecules in the ensembles is due to the hydrogen bond between crown ether oxygen atoms and hydrogen atoms of polyfluoroarene amino groups. Parameters of the architecture of соcrystals are determined by the effect of the number and positions of substituents (chlorine and fluorine atoms) in the polyhalogenated aromatic ring.

Carboxylate ligands are very versatile because they can adopt different coordination modes towards metal cations, such as monodentate, bidentate-chelate, bidentate bridging and monoatomic bridging. Because of this versatility, these ligands have been widely used in coordination chemistry. In this study the three dimensional structure of the crystal arrangement of 2,5-thiophenedicarboxylic (H₂TPD), trans-3-(3-pyridyl)acrylic (HPYA), and 4,4¢-sulfonyldibenzoic (H₂SFD) acids are determined in order to investigate their supramolecular properties for coordination polymers and metal-organic framework (MOF) constructions.

Mechanisms of radiation damages in minerals promising for the utilization of highly active radioactive waste (zircon ZrSiO₄, monazite LaPO₄, orthophosphate YbPO₄, lakargiite CaZr_0,8Sn_0,1Ti_0,1O, and Gd₂Zr₂O₇ and Gd₂Ti₂O₇ compounds with the pyrochlore structure) are studied by the computer simulation using the molecular dynamics method. The formation of a damaged region in the structures under study is considered along with the reduction (relaxation) processes in these structures. The number of Frenkel pairs and antistructural defects that form in the structure of these minerals after the pass of the knocked out thorium atom is calculated by the molecular dynamics method. A parameter is proposed that characterizes the mineral tendency to amorphization under the effect of the radiation damage. The obtained results show that one of the main factors determining the radiation stability of minerals is the crystal structure type, compounds with the monazite structure being more radiationally stable than compounds with the zircon structure. It is found that the Gd₂Zr₂O₇ compound and lakargiite have a weaker tendency to amorphization than other minerals such as zircon, monazite, and orthophosphate YbPO₄. A high radiation stability of the studied Gd₂Zr₂O₇ compound as well as a solid solution of the composition CaZr_0.8Sn_0.1Ti_0.1O₃ makes it possible to propose them as a possible matrix for the utilization of highly active radioactive waste.

By the interaction of methyl 1-bromo cyclohexane carboxylate with zinc and N-methyl-2-oxo-2Н-chromene-3-carboxyamide 3-methyl-2,3,4,4a,5,10b-hexahydro-1H-spiro[chromeno[3,4-c]pyridine-1,1-cyclohexane]-2,4,5-trione is obtained and its structure is determined by the single crystal X-ray diffraction analysis.

The structure of ionic cocrystals of piperidinium 2-thiobarbiturate with 2-thiobarbituric acid PipeH⁺(HTBA^-)H₂TBA (I) (Н₂ТВА is 2-thiobarbituric acid, Pipe is piperidine) is determined. The asymmetric unit of I contains a H₂TBA molecule in the form of the thione monocarbonyl tautomer, the HTBA^- ion, and the PipeH⁺ piperidinium ion. The structure is stabilized by the intermolecular O-H⋯O, N-H⋯S, and N-H⋯O hydrogen bonds (HBs) forming a three-dimensional framework. The results of single crystal XRD and IR spectroscopy indicate the formation of a strong O-H⋯O HB. The topological analysis of the HB network in I is performed.

New salt spiropyran is obtained, in which the positive charge is localized on the nitrogen atom of the indoline moiety and the negative charge is localized on the group. The structure of the compound is determined by the single crystal X-ray diffraction analysis.

A new Cu(II) coordination polymer, namely {[Cu₂(btb)₂(sip)(OH)]×(H₂O)_0.25} _n (btb = 4,4¢-bis(1,2,4-triazolyl-1-yl)-biphenyl, H₃sip = 5-sulfoisophthalic acid), is hydrothermally synthesized and characterized by elemental analyses, infrared (IR) spectroscopy, and single crystal X-ray diffraction. It crystallizes in the monoclinic space group P 2₁/ c , a = 14.9676(3) Å, b = 14.3478(3) Å, c = 21.2719(5) Å, b = 125.325(2)°, V = 3727.11(14) ų, Z = 4, C₄₀H_28.50Cu₂N₁₂O_8.25S, M _r = 968.39, D _c = 1.726 g/cm³, m = 1.274 mm^-1. The structural analyses reveal that the compound displays a 2D binodal rarely (4,5)-connected network with 4,5L50 topology. Moreover, the thermal and catalytic properties of the complex for the degradation of the congo red azo dye in a Fenton-like process are investigated.