Home – Home – Jornals – Journal of Structural Chemistry 2016 number 3

By means of B3LYP/6-311++G(3df,3pd) the electron density distribution in the propargyl radical CH₂CCH is obtained. Within the Quantum Theory of Atoms in Molecules the phenomenon of conjugation and the spin density distribution of the unpaired electron in CH₂CCH are studied at the qualitative level. Characteristics of the electronic structure of CH₂CCH and its parent molecules CH₃-C≡CH and CH₂=C=CH₂ are compared. With the use of the rigid rotator-anharmonic oscillator model the thermodynamic properties of the propargyl radical and enthalpies of bond cleavage in propyne and allene are calculated in the temperature range 298-1500 K. The relationship between the electronic and thermodynamic properties of CH₂CCH is considered and its conjugation energy is calculated.

Within density functional theory the experimentally observed stereoeffects of the ligand environment in low-spin bis-chelates of Ni(II), Pd(II), and Pt(II) with aromatic azomethines is modeled. It is shown that complexes with the MN₂O₂ coordination core are characterized by the trans -configuration and in complexes with MN₂S₂ or MN₂Se₂ cores the stabilization of the cis -configuration occurs. The relationship is found between the composition of metal cycles and their conformation (an inflection along the donor atom line), the degree of steric hindrances in the cis -configuration due to the interligand interaction of R substituents at azomethine nitrogen atoms and the relative stability of cis - and trans -isomers of the complex.

In the work a prediction method based on modified Randic indices to estimate the enthalpies of vaporization under standard conditions D_vap H ⁰(298.2) is proposed for esters with different structures and numbers of ester groups. It is shown that the proposed method enables the prediction of enthalpies of vaporization of esters with an accuracy as good as experimental.

Based on density functional theory with regard to the dispersion interaction the crystal structure and electronic properties of C₄H₈N₁₂O₆ and C₄H₈N₁₀Cl₂O₈ are studied. Atomic structural parameters, bond populations, atomic charges, energy and spatial electron distributions are calculated. Differences in the studied characteristics caused by the non-equivalence of atoms are shown. A partially covalent nature of anion-cation bonds is revealed. The cationic nature of the lower unoccupied states is established, which results in a small band gap of ~1.7 eV as compared to other nitrates and perchlorates.

Ab initio calculations are employed to investigate nitrogen inversion as a configuration change that can supply an extremely useful switchable control mechanism for some complex systems. In this paper, the design of a new artificial rotary molecular machine based on nitrogen inversion is discussed. The introduced design of a molecular rotator is based on the reciprocating motion of a substituent due to the inversion phenomenon, leading to the rotary motion in the molecule. Since simple secondary amines easily face the inversion process at room temperature, aziridine is selected as the initial driver for the molecular motion. The most obvious finding from this study is that, following the displacement of the substituent attached to the aziridine nitrogen atom, two rotary motions occurr in the molecule, one clockwise and another counterclockwise with a 39.52 to 150.09° angle domain.

By the low-gradient Čzochralski method, both undoped and copper ion activated Li_{2-2 x}Mg_{2+ x}(MoO₄)₃ crystals are grown. The charge state and structural position of impurity copper ions are determined using EPR. Investigations of the luminescence properties reveal that luminescence with a maximum at λ = 520 nm is observed for Li_{2-2 x}Mg_{2+ x}(MoO₄)₃ crystals. A decrease in the temperature increases the intensity of this luminescence. It is found that the doping of Li_{2-2 x}Mg_{2+ x}(MoO₄)₃ crystals with copper ions also increases the luminescence intensity with a maximum at λ = 520 nm. It is supposed that cation vacancies, which provide the charge compensation when copper ions substitute for lithium ions, are responsible for the luminescence.

4-Amino-1,2,4-triazolium hexafluoridoniobate(V) and hexafluoridotantalate(V) (C₂H₅N₄)MF₆ (M = Nb, Ta) crystallizing in the monoclinic system (space group P 2₁/ n ) are synthesized for the first time and their crystal structures and spectroscopic features are studied by single crystal X-ray diffraction and ¹H and ¹⁹F NMR spectroscopy. The crystal structures of isostructural (C₂H₅N₄)MF₆ compounds are formed of octahedral complex [MF₆]^- anions (M = Nb, Ta) and monoprotonated heterocyclic 4-amino-1,2,4-triazolium cations (C₂H₅N₄)⁺ organized in a three-dimensional structure via N-H⋯F and N-H⋯N hydrogen bonds. The character and types of ion motions in the fluoride sublattice of (C₂H₅N₄)MF₆ are determined in a wide temperature range.

An iron(II) complex with tris(pyrazol-1-yl)methane (HC(Pz)₃) of the composition [Fe(HC(Pz)₃))₂]xEu(dipic)₂(Hdipic)]x2H₂O, containing an outer-sphere complex anion, is synthesized. The compound is examined by single crystal and powder X-ray diffraction, UV-Vis and IR spectroscopies, and static magnetic susceptibility. The investigation of the temperature dependence χ(T) in the temperature range 80-470 K reveals that the polycrystalline phase of the compound undergoes spin-crossover ¹А₁ <=> ⁵Т₂. The transition is accompanied by thermochromism (color change pink <=> white).

New biligand complexes of iron(III) are synthesized based on 3,4,5-tri(tetradecyloxy)benzoyloxy-4-salicylidene-N'-ethyl-N-ethylenediamine azomethine with the outer sphere NO3, PF6, Cl^-, BF4, Cl4, and CNS^- anions. All the target compounds are characterized by gel exclusion chromatography, elemental analysis, and electron, IR, and NMR spectroscopy. The presence of complex-forming ions is confirmed by FT-IR spectra in the far region. The formation of biligand polychelate complexes with an octahedral packing of the iron ion is observed. Phase transitions in the resulting coordination compounds are studied by differential scanning calorimetry and optical polarizing thermomicroscopy. The presence of several polymorphic crystalline modifications, as well as mesophases, is established. Mesomorphic properties are found for complexes with chloride and tetrafluoroborate anions.

An in silico study of semiconductor quantum dots of the CdTe family doped with atoms of rare earth elements is performed based of density functional theory. An ab initio computer design of quantum dots based on CdTe nanoparticles doped with Eu и Gd atoms is carried out. Partial densities of states of CdTe:Eu and CdTe:Gd quantum dots are calculated and analyzed. X-ray absorption near edge (XANES) spectra near the Eu K-, L₁-, and L₃- and Gd K-, L₁-, and L₃-edges of CdTe:Eu and CdTe:Gd quantum dots are calculated. The sensitivity of XANES spectroscopy for the verification of parameters of a nanosized atomic structure of quantum dots based on CdTe particles doped with atoms of rare earth elements and the determination of the local atomic structure around the atoms of rare earth elements in quantum dots is demonstrated.

The total lifetime distributions for hydrogen bonds in snapshots of molecular dynamics simulations of water serve as a basis to identify a class of proper hydrogen bonds. Proper bonds emerge and break up when restructuring the surrounding area of the hydrogen bond networkwhich weakly depend on the properties of this individual bond, i.e., almost randomly. Therefore, the distribution of the bond lifetimes is described by an exponential function similar to the distribution of the mean free path time in gas. It is shown that proper hydrogen bonds are strong, long-lived, and tetrahedrally oriented bonds. They account for about 80% of the bonds in each snapshot. Thus, these bonds form the basis or framework of the hydrogen bond network of water. The other, improper bonds have a substantially shorter lifetime; these are weak, bifurcated, and quickly switching bonds.

X-ray diffractometry and positron annihilation life-time spectroscopy are applied to study the structural features of polymetallophenylsiloxane (PMOS) samples with the Si/M ratio corresponding to the metal valence state, namely, interplanar spacings ( d₀₀₁), coherentscattering region (CSR) sizes, cross-section areas of polymer chains ( s ) calculated by the Miller-Boyer method, and the degree of amorphousness (β). It is demonstrated that the direct proportional dependence between the logarithm of the interplanar spacing d₀₀₁ and the logarithm of the cross-section area s is observed for PMOSs. This is an inverse dependence relative to changes in the crystal chemical ion radius. The extraction of the iron ion from polyferrophenylsiloxane leads to a sharp decrease in the interplanar spacing, which turns out to be less than d ₀₀₁ in polyphenylsiloxanes, and also CSR increases due to a decrease in the diameter of the polymer chain. The positron annihilation life-time spectroscopy data show the observed direct dependence of the annihilation intensity ( I₃), the annihilation rate ( K₃), the degree of amorphousness on the PMOS cross-section area.

The results of a crystallographic analysis of the structures of CsFe₂S₃, Tl₂PbZrS₄, and Tl₂PbGeS₄ with a 1:1 cation-anion ratio are used to identify a joint F sublattice for Cs and S in the first compound and two separate F sublattices for cations and anions in the second compound (the PbS structural type). The substitution of the small Ge⁴⁺ (with its tetrahedral coordination by sulfur) for Zr⁴⁺ in the composition results in an increase in the unit cell volume, i.e., a decrease in the packing density for both cations and anions in the structure of the third compound. In the absence of regular F sublattices, there are “two-dimensional” orderings, typical of the PbS type, for the atomic positions in the projections of this structure.

A crystallographic analysis is conducted of the structures of orthorhombic mineral sicherite TlAg₂(As,Sb)₃S₆, monoclinic synthetic sulfide Tl₃Ag₃Sb₂S₆ , and triclinic mineral raberite Tl₅Ag₄As₆SbS₁₅. In the first two structures, the large and heavy Tl⁺ cation forms, together with the other cations, ordered “skeletal” frameworks with F and I cation sublattices that are close to cubic ones. In the structure of raberite, the Tl and Ag cations undergo, together with the sulfur anions, two-dimensional ordering by a zone of closely packed crystallographic planes, which generate a pseudohexagonal symmetry. The deviations from the 1 cation/anion stoichiometry are compensated: in the second structure, by a local consolidation of cations (to a distance Tl-Ag = 2.96 Å) and, in the third structure, through the formation of a dumbbell pair As-Ag (2.68 Å), which occupies one position in the sublattice.

A novel trinuclear nickel(II) ONO pincer complex [Ni(pydc)₂]₂[Ni(H₂O)₅]×2H₂O×2(C₆H₁₅N) (1) (H₂pydc = 2,6-pyridinedicarboxylic acid) is synthesized by the reaction between Ni(OAc)₂ and H₂pydc in acetonitrile in the presence of triethylamine. A detailed study through single crystal XRD reveals that the compound crystallizes in the triclinic space group P -1 with cell parameters a = 11.6646(3) Å, b = 14.0999(4) Å, c = 16.4633(5) Å, a = 80.189(2)°, b = 75.539(2)°, g = 67.017(2)°. Both terminal Ni(II) centers are coordinated to two ONO pincer ligands (pydc) bridged by the nickel penta aqua unit. Further, triethyl ammonium neutralizes the trinuclear complex.

The [Pd(dpa)(tsser)] complex (1) is prepared from the reaction of PdCl₂ and 2,2'-dipyridylamine (dpa) with 4-toluenesulfonyl-L-serine (tsserH₂). This complex is characterized by spectral methods (IR, UV-Vis, ¹H NMR, and luminescence), elemental analysis, thermal analysis (TG, DTA), and single crystal X-ray diffraction. X-ray structure determinations show that in this complex, Pd^II atoms are four-coordinated in a distorted square-planar configuration by two N atoms from a bidentate 2,2'-dipyridylamine ligand and one N atom and one O atom from a bidentate tsser^2- ligand.

For the first time, a mononuclear biligand complex of lanthanum nitrate with bicyclic bisurea (4,4,10,10-tetramethyl-1,3,7,9-tetraazospiro[5.5]undecane-2,8-dione, or spirocarbon, Sk) [La(C₁₁H₂₀N₄O₂)₂(H₂O)₂× ×(NO₃)₃] (I) is synthesized and its structure is determined by direct single crystal XRD. The crystals of I are monoclinic: space group P 2₁/ c , a = 11.1989(15) Å, b = 13.015(2) Å, c = 24.153(2) Å, b = 101.129(12)°, V = 3454.3(8) ų, d _calc = 1.618 g/cm³, Z = 4, CCDC 985760. The structure is molecular. The lanthanum cation is coordinated by two oxygen atoms of two organic ligand molecules, two water molecules, and three bidentate nitrate anions. The coordination number of lanthanum is ten; the coordination polyhedron is an irregular 10-vertex polyhedron. The crystal of I represents a non-merohedral twin with the components turned by 180° along the a axis; the relative weights of the components are 0.76:0.24. To confirm the purity of the sample of I, the powder XRD pattern was refined using the Rietveld method; the unit cell parameters at room temperature are as follows: a = 11.2777(4) Å, b = 13.0774(5) Å, c = 24.3453(9) Å, b = 101.129(3)°, V = 3523.0(2) ų.

The structure of xymedone iodo methylate is determined by X-ray crystallography. The molecular and crystal structure of the compound is analyzed in comparison with xymedone whose X-ray crystallographic data have been obtained previously. The molecular and electronic structures of both compounds and noncovalent interactions in the ionic pair of xymedone iodo methylate are analyzed using the data of the quantum topological calculations. It is shown that the presence of the iodine anion results in an increase in the delocalization of the p electron density inside the heterocyclic moiety, the charge redistribution inside the molecule, and consequently, in significant distinctions in crystal packings.

By small-angle X-ray scattering a gadolinium triacetate-undecane-water system is studied at hydrotrope concentrations of 0.05-0.5 М on the line of saturation with undecane at 298 K. In the ternary system mixed hydrotrope/undecane lamellar micelles form with lateral dimensions of hydrophilic and hydrophobic plates of 0.4 nm. It is shown that the Gibbs energy of the hydrophobic interaction and the micelle shape are determined by a joint (cooperative) effect of the hydrotrope and hydrocarbon on water.

The review includes comprehensive NMR data on platinum metals (^99,101Ru, ¹⁰³Rh, ¹⁰⁵Pd, ¹⁸⁷Os, ¹⁹⁵Pt) and ligand donor atoms (¹H, ¹³C, ^14,15N, ¹⁷O, ¹⁹F, ³¹P) of metal complexes in aqueous solutions. A systematic analysis of NMR spectroscopy techniques is presented with focus on the measurements of NMR parameters in these systems. A novel concept referred to as coordinate shift is introduced, allowing interpretation of NMR spectra of platinum metal complexes. The review contains an encyclopedic NMR database covering a period of over 50 years from the first measured NMR spectra of platinum metals to 2014.

The radial distribution of hydrogen on C_20(cage) and C₁₉Si_(cage), and C₁₉B_(cage) fullerene structures is investigated at different temperatures (273, 293, 320, and 400 K) for the pressure range between 1 MPa and 30 MPa using the (N,V,T) Monte Carlo simulation. The gravimetric storage capacity and radial distribution function parameters show that, under the identical temperature and pressure conditions, the magnitude of the hydrogen radial distribution on the C₁₉B surface is larger than that on C₁₉Si and C₂₀. The calculated maximum of the gravimetric storage capacity for C₁₉B at 273 K and 30 MPa is 7.6 %.

A procedure of the X-ray diffraction study of thin layers using a single crystal X-ray diffractometer equipped with a microfocus tube is described. It is demonstrated that a-cobalt phthalocyanine layers deposited by thermal vacuum evaporation onto polished surfaces of substrates (glass, quartz) have a perfectly oriented polycrystalline structure. The (00 l ) planes of all crystallites are oriented along the surface of the substrate. The structural organization of layers is analyzed.

The structure of 5,7-di( tert -butyl)-2-(6,8-dimethyl-4-chloroquinoline-2-yl)-3-hydroxytropone with a hydrogen atom, possibly equally distributed over two N and O centers and involved in the intramolecular hydrogen bond, is determined by the single crystal X-ray diffraction analysis.

The structure of [Pb₃(OH)₄Co(NO₂)₃](NO₃)(NO₂)×2H₂O is determined by single crystal X-ray diffraction. The crystallographic characteristics are as follows: a = 8.9414(4) Å, b = 14.5330(5) Å, c = 24.9383(9) Å, V = 3240.6(2) ų, space group Pbca , Z = 8. The Co(III) atoms have a slightly distorted octahedral coordination formed by three nitrogen atoms belonging to nitro groups (Co-N_av is 1.91 Å) and three oxygen atoms belonging to hydroxyl groups (Co-O_av is 1.93 Å). The hydroxyl groups act as m₃-bridges between the metal atoms. The geometric characteristics are analyzed and the packing motif is determined.

A novel form of anhydrous dicalcium phosphate CaHPO₄ (monetite) is synthesized hydrothermally and characterized by single crystal X-ray diffraction. It crystallizes in the orthorhombic space group Ccm 2₁ with a = 6.242(1) Å, b = 6.994(2) Å, c = 7.003(3) Å, V = 305.73(16) ų and it has four independent unit formulas in the unit cell ( Z = 4). A three-dimensional crystal structure can be described by {HPO₄} _n infinite zigzag chains linked by Ca-O bonds. The comparison to the crystal structures of other polymorphs is given.

Single crystals of 1-cyclohexylpiperazine-1,4-diium dichromate(VI), (C₁₀H₂₂N₂)[Cr₂O₇], were obtained by slow evaporation at room temperature from an aqueous solution of potassium dichromate, hydrochloric acid and 1-cyclohexylpiperazine. (C₁₀H₂₂N₂)[Cr₂O₇] is triclinic ( P ) with a = 10.351(2) Å, b = 12.766(3) Å, c = 6.111(1) Å, a = 91.50(2)°, b = 104.26(3)°, g = 94.91(2)°, V = 778.8(3) ų, and Z = 2. The structure determination performed from single crystal X-ray diffraction data leads to R ₁/ wR ₂ reliability factors of 0.032/0.078. The asymmetric unit of the title salt consists of one 1-cyclohexylpiperazine-1,4-diium dication and one dichromate dianion. These entities are linked together by N-H⋯O hydrogen bonds to form {(C₁₀H₂₂N₂)[Cr₂O₇]} _n infinite chains lying parallel to the (100) plane and running along the c axis. The intermolecular N-H⋯O hydrogen bonds link these chains into a two-dimensional network structure consolidated through C-H⋯O weak interactions.