Home – Home – Jornals – Journal of Structural Chemistry 2014 number 3

The self-consistency schemes previously developed in J. Struct. Chem ., 30, N 5, p. 3 (1986) are shown to belong to the class of semi-canonical orbital schemes. In the derivation they explicitly involve only a part of canonical Koopmans orbitals in the iteration process. In particular, within the restricted Hartree-Fock method for a non-degenerate case a semi-canonical variational scheme based on the matrix elements of the unrestricted Hartree-Fock method is studied. Errors present in the above mentioned work in the description of the scheme of a varied open shell are corrected. A possible generalization for the case of Roothaan type degeneration is proposed and specific examples of low-spin and high-spin states with a violated Aufbau filling principle are considered.

In order to estimate atomic multipole moments (АММs) and charges in the model of amorphous SiO₂ a hybrid B3LYP functional with 30% of the Hartree-Fock Hamiltonian in the exchange part with the 88-31G*(Si)/8-411G*(O) basis set and the CRYSTAL06 package are used. A 192-atomic unit cell of amorphous SiO₂ is chosen as a model, the calculations with which agree well with the experimental static factor of neutron scattering. The second optimized model of amorphous SiO₂ (a-SiO₂) with a smaller number of defects is prepared with the use of the VASP package and full optimization of the initial a-SiO₂ model. For both models the atomic charges and АММs are calculated (up to the fourth order included) and their approximation is performed. The approximation quality is compared for these models and with a model for crystalline systems whose АММs were previously calculated. The conclusions are drawn about the applicability of charge and АММ estimates within the approaches such as the embedded cluster.

The results of calculations by PM3 and LDA-DFT methods of the structure and properties of six new polymorphic types of diamond, in which all atomic sites are crystallographically equivalent, are presented. The structures of LA5 (Cmca), LA7 (mcm), and LA8 (I4₁/ amd ) phases are obtained as a result of stitching graphene layers and of CA9 (Fd3m), CA10 (R3m), and CA11 (P6₃/mmc) phases by stitching fullerene-like clusters. For these phases the geometrically optimized structures are calculated and the structural parameters, density, sublimation energy, bulk modulus, electron density of states, and X-ray diffraction pattern are measured. It is found that the properties of polymorphic types of diamond depend on the degree of their structure deformation in comparison with the cubic diamond structure.

Quantum chemical calculations of the molecular structure of bis (dipyrrolylmethanates) of cobalt(II), nickel(II), copper(II), zinc(II), cadmium(II), and mercury(II) of the composition [М₂L₂] are performed using the PM6 method within the Gaussian 09W program package. The lengths of M-N coordination bonds, the values of dihedral angles formed by N-M-N bonds, the distances l_M⋯M between the M⋯M atoms are optimized. It is noted that the regularities obtained from the analysis of the results of quantum chemical calculations of the molecular structure of [М₂L₂] helicates reliably reflect the main trends of changes in their physicochemical properties depending on the nature of a complexing agent and the features of the ligand structure.

Based on the characteristic polynomial coefficients (CPCs) of the adjacency matrix A' of heterogeneous molecular graphs of the molecules containing a tetravalent heteroatom >Si< (>Ge<, >Sn<), etc. in the chain, a 13-constant additive scheme for the calculation of their physicochemical properties is obtained. The structural meaning of CPCs of the adjacency matrix A' is established. By the formula obtained the formation enthalpies Δ_fH⁰_{gas, 298 K} of SiC_nH_2n+2 alkylsilanes not studied experimentally are calculated.

IR spectra of 1-germatranol, 1,1-quasi-germatrandiole, 1,1,1-hypogermatrantriole with a general formula (HO)_4-nGe(OCH₂CH₂)_n NR_3-n ( n = 1-3) are obtained. At the B3LYP/ aug-cc-pVDZ density functional level the equilibrium structures and vibrational spectra of these compounds along with their hydrogen-bonded dimers are calculated. Based on the calculations the band assignment is performed in the IR spectra of 1-germatranol, 1,1-quasi-germatrandiole, and 1,1,1-hypogermatrantriole. The existence of dimers is manifested in the IR spectra as the absence of bands in the frequency ranges characteristic of the bending vibrations of Ge-OH groups and the presence of bands in the vibrational range of hydrogen-bonded germatranyl groups.

FT-IR and Raman spectra of methyl(5-[2-thienylcarbonyl]-1H-benzimidazol-2-yl (nocodazole) are experimentally examined in the region of 4000-400 cm ^–1. The optimized geometric parameters, conformational equilibria, normal mode frequencies, and corresponding vibrational assignments of nocodazole (C₁₄H₁₁N₃O₃S) calculated by means of the B3LYP hybrid density functional theory (DFT) method using the 6-31++G(d,p) basis set. Vibrational assignments are made based on the total energy distribution (TED) and the thermodynamic functions, highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO) of nocodazole are calculated. Calculations are employed for four energetically possible conformers of nocodazole (N1, N2, N3 and N4) in the gas phase. A comparison between the experimental and theoretical results indicates that the B3LYP method is able to provide satisfactory results for predicting vibrational wavenumbers if calculated values are scaled properly and the structural parameters.

The structure of 2-(4-hydroxyphenyl)-substituted indan-1,3-dione and phenalene-1,3-dione is investigated using a combination of solid-state NMR, single crystal X-ray analyses and quantum chemical calculations. It is shown that 2-(4-hydroxyphenyl)-1,3-indandione exists as a diketo tautomer while 2-(4-hydroxyphenyl)-1,3-phenalenedione exists in the enol form.

Silicon carbonitride films are synthesized by plasma enhanced chemical vapor deposition from bis(trimethylsilyl)ethylamine and helium or ammonium mixtures. The structure of chemical bonds in the films is studied by X-ray photoelectron and IR spectroscopy. The data on the main types of bonds present in silicon carbonitride films deposited under different synthesis conditions are obtained. It is shown that the use of ammonia at a low deposition temperature provides the synthesis of films with a simultaneous formation of Si-C, Si-N, and C-N bonds. The main bonds in films obtained from a bis(trimethylsilyl)ethylamine and helium mixture are Si-C and Si-N. The chemical structure of films obtained at high synthesis temperatures is close to SiC_x regardless of the type of the additional gas used.

The apparent volumes of the salts in the systems H₂O - NH₄Cl (298 K) and H₂O - NH₄NO₃ (273, 298, and 323 K) are reproduced with an accuracy of 0.03-0.01 cm ³/mol by the equation φ = φ⁰ + Aw₂^0,5 + Вw₂, where w₂ is the salt content (mass fractions). The study shows that there is a correspondence between the critical (for determining the hydration number) structural parameters-the intrinsic volume of the electrolyte and the volume of water in ion hydration shells-and the limiting (at w₂ = 1) partial molar volumes of the components. The hydration numbers at infinite dilution are 6.9 for NH₄Cl at 298 K and 9.1, 6.7, and 6.4 for NH₄NO₃ at 273, 298, and 323 K. The water volume in ion hydration shells decreases in the sequence: NO₃^¯ Cl^-, and NH₄⁺ The hydration numbers decrease with increasing salt concentration. The study shows that within a simpler model φ = φ⁰ + aw₂^0,5, the hydration numbers are temperature independent.

Crystallographic analysis has provided evidence for single cation frameworks formed from preordered cation positions in the individual building blocks (modules) constituting the basis of structures. We propose to call this phenomenon coherence assembly . According to the mechanical wave concept of the crystalline state, coherence assembly dictates the rules of mutual packing of “rigid” structural fragments. This study investigates the typical structures of heteropolyniobates: Na₁₂[Ti₂O₂][SiNb₁₂O₄₀]×4H₂O (I), menezesite Ba₂MgZr₄[BaNb₁₂O₄₂]×12H₂O (II), and the menezesite-isostructural aspedamite □₁₂(Fe³⁺,Fe ²⁺)₃Nb₄×[Th(Nb,Fe³⁺)₁₂O₄₂]×(H₂O,OH)₁₂ (III).

2,6-Di-tert -butyl-p -quinone 1'-phthalazynylhydrazone (HL) is synthesized; the total energies and geometry of the possible hydrazone tautomeric forms are calculated by quantum chemical methods. The hydrazone phthalazone tautomer is shown to be the most stable, which is well consistent with the ¹H NMR spectroscopic data for hydrazone. An X-ray crystallographic analysis is performed of the hydrazone-based Zn(II) trinuclear complex, in which zinc atoms are linked by the diazine bridge of the phthalazine cycle and two pivalate bridges. The geometric properties of the monodeprotonated hydrazone residue in the complex are similar to the calculated data for the phthalazone hydrazone tautomeric form.

Using single crystal X-ray diffraction the structure of polynuclear [Ni₆(OH)₄(Piv)₇(HOC ₄H₈O)(HPiv)₄], {K₄[Ni₁₂(CO₃)₂(Piv)₁₆(OH)₈(HOC₄H₈OH)₂]}HPiv, {[Ni₆(OH)₄(Piv)₆(HOC₄H₈O)(Me₂CO)(HOC₄H₈OH)₂]₄(Piv)₄}, and {K[Ni₂L₂(Piv)₃]} _∞ complexes, where HOC₄H₈OH is 1,4-butanediol, HPiv is pivalic acid, and L is the anion of nitroxyl radical 2,2,5,5-tetramethyl-4-(3',3',3'-trifluoro-2'-oxy-1'-propenyl)-3-imidazolin-1-oxyl is determined.

Two bis-chelates M(tmih)₂ (M = Cu(II), Ni(II), tmih = (CH₃)₃C(NCH₃)CHCOC(CH₃)₃)^- are synthesized and their crystal structures are determined using XRD (Bruker APEX-II diffractometer with a CCD detector, lMo K_a, lCu K_a, graphite monochromator, T = 240(2) K and 296(2) K): Cu(tmih)₂ (I) (space group P2₁/c , a = 12.9670(8) Å, b = 18.4921(9) Å, c = 11.0422(6) Å, β = 93.408(4)°, V = 2643.1(3) ų, Z = 4) and Ni(tmih)₂ (II) (space group P2₁/c , a = 12.810(2) Å, b = 18.529(2) Å, c = 11.243(2) Å, β = 91.959(7)°, V = 2667.1(6) ų, Z = 4). The complexes are isostructural; the coordination polyhedron of metal atoms is a flattened tetrahedron formed from two O atoms (Cu-O of 1.901(2) Å, 1.892(2) Å, Ni-O of 1.845(2) Å, 1.833(2) Å) and two N atoms (Cu-N of 1.976(3) Å, 1.972(3) Å, Ni-N of 1.911(2) Å, 1.920(2) Å) of the ligand; the chelate OMN angles (M = Cu(II), Ni(II)) are in the 87.4-93.1° range; the OMO and NMN angles are 162.2° and 167.2° in I, 171.1° and 173.2° in II. The complexes have the molecular structures formed from isolated molecules bonded by van der Waals interactions. Using a quantum chemical hybrid M06 method, the structures of copper(II) chelates with the H, CH₃, CH₂CH₃, CH(CH₃)₂, and C(CH₃)₃ substituents at the nitrogen atom are calculated. Found that with a bulky substituent at the nitrogen atom, the formation of chelates is hindered due to the intraligand repulsion between the atoms of this substituent and the tert-butyl group.

Three crystal structures of Ni compounds containing bis(pyridine-2-carbaldehyde thiosemicarbazone) ligand (HL), namely (pyridine-2-carbaldehyde thiosemicarbazonato)(pyridine-2-carbaldeyde thiosemicarbazone) nickel(II) nitrate hydrate [Ni(HL)L][NO ₃]×(H ₂O) (1), bis(pyridine-2-carbaldehyde thiosemicarbazone) nickel(II) dinitrate [Ni(HL) ₂][NO ₃] ₂ (2a), and bis(pyridine-2-carbaldehyde thiosemicarbazone) nickel(II) dinitrate dihydrate [Ni(HL) ₂][NO ₃] ₂×2(H ₂O) (2b) are determined by X-ray diffraction methods. Comparative structural studies are carried out.

The structure of double complex salts [Pd(NH₃)₃(NO₂)][Rh(NH₃)₂(NO₂)₄] and [PdEn₂][Rh(NH₃)(NO₂)₅]×0.75H₂O is determined by single crystal X-ray diffraction. In the structures, the main structural moieties are identified.

Compounds [Rh(NH ₃) ₅(NO ₂)](NO ₃) ₂×H ₂O (I) with a = 7.6230(3) Å, b = 7.6230(3) Å, c = 10.3584(4) Å, space group I -42 m , Z = 2, d _calc = 2.026 g/cm ³, V = 601.93(4) Å ³, Rh-NH _{3 eq} = 2.074 Å, Rh-NH _{3 ax} (NO ₂) = 2.048 Å; [Rh(NH ₃) ₅(NO ₂)][Pd(NO ₂) ₄] (II) with a = 8.095(3) Å, b = 22.422(8) Å, c = 7.887(3) Å, b = 98.559(17)°, space group Cc , Z = 4, d _calc = 2.461 g/cm ³, V = 1415.6(9) Å ³, Rh-NH _{3 eq} = 2.069 Å, Rh-NH _{3 ax} = 2.090 Å, Rh-NO ₂ = 2.002 Å; K ₂[Rh(NH ₃)(NO ₂) ₅]×H ₂O (III) with a = 7.5177(5) Å, b = 20.9856(15) Å, c = 7.7017(5) Å, space group Cmc 2 ₁, Z = 4, d _calc = 2.439 g/cm ³, V = 1215.05(14) Å ³, Rh-NH _{3 ax} (NO ₂) = 2.094 Å, Rh-NO _{2 eq} = 2.030 Å are synthesized and studied using single crystal X-ray diffraction.

In treatment of trans-[Ru(NO)(NH₃)₄(OH)]Cl₂ with concentrated sulfuric acid on heating trans -[Ru(NO)(NH₃)₄(SO₄)](HSO ₄)×H₂O (I) is obtained with a yield close to quantitative. In the interaction of the saturated solution of I with a saturated NaNO ₃ solution a trans-[Ru(NO)(NH₃)₄(SO₄)]NO₃×H₂O (II) precipitate forms whose structure is determined by single crystal XRD: space group Р 2 ₁2 ₁2 ₁, a = 6.8406(3) Å, b = 12.6581(5) Å, c = 13.3291(5) Å. A monodentately coordinated sulfate ion is in the trans -position to the nitroso group. Compound II is characterized by IR spectroscopy, powder XRD, and diffuse reflectance spectroscopy. The process of its thermolysis is studied; by differential scanning calorimetry the thermal effect of the dehydration reaction occurring on heating to 120°C (D H = 58.9 ± 1.5 kJ/mol) is estimated. The final product of the thermolysis of II is a mixture of Ru and RuO₂.

Two compounds of 2-ferrocenylmethylidenehydrazono-1,3-dithiane (1) and 2-ferrocenylmethylidenehydrazono-1,3-dithiepane (2) are synthesized and their single crystal structures are determined by the X-ray diffraction method. Compound 1 belongs to the orthorhombic Pca 2 ₁ space group with the cell parameters: a = 13.989(4) Å, b = 5.785(2) Å, c = 18.231(5) Å, V = 1475.4(7) Å ³; while compound 2 crystallizes in a monoclinic symmetry, P 2 ₁/ c space group with a = 15.320(2) Å, b = 5.8028(6) Å, c = 36.584(4) Å, b = 91.932(1)° and V = 3250.4(6) Å ³.

A database study on the N-H⋯S hydrogen bonding ring motif ( R ₂ ²(8)) for 1,2,4-triazole-5-thiones is reported. The R ₂ ²(8) ring is one of the most general ring motifs observed in the crystallographic literature, however, up to now the ring synthon built by the N-H⋯S interaction has not been particularly described. Probably, in multi-heteroatom systems, other structure-determining stronger interactions may take precedence over weaker N-H⋯S interactions. On the other hand, in recent years, considerable importance has been given to structures determined through N-H⋯S interactions. It is also common in the crystals of 1,2,4-triazole-5-thione derivatives.

In the present work alkaline iron oxide nanoparticles are synthesized by a novel solvo thermal approach and characterized exhaustively by various complementary techniques. Field emission scanning electron microscopy (FESEM) studies reveal that the size of nanoparticles is in the range of 31.5 nm to 96.9 nm. Energy-dispersive X-ray spectroscopy spectral analysis reveals the presence of oxygen, carbon, iron, and sodium. The X-ray diffraction studies confirm the formation of tetragonal NaFeO ₂ as the major phase along with orthorhombic NaFeO ₂×H ₂O and rhombohedral FeCO ₃ (siderite) as the minor phases. Fourier transform infrared spectroscopy exhibits peaks due to the stretching and bending vibrations of O-H, C=O, CH ₃-N, CH ₃, C-H, C-N, and Fe-O groups. Differential scanning calorimetry (DSC) results display an endothermic peak at 100.85 °C and a very small endothermic peak at 791.56 °C with 819.73 mJ and 349.28 mJ energies respectively. These DSC peaks can be correlated with thermal gravimetric analysis (TGA) peaks representing 31.04 % weight loss and 7.70 % weight loss respectively in the sample at around 160 °C and 980 °C respectively.

A substantial amount of researches have been carried out on the electron transport properties of gold surfaces. In order to study the role of linkage in the conductive properties of a molecular wire, different linkers such as sulfur, nitrogen, oxygen, CS, SH, NS, and CN are considered in our study. It is found that nitrogen or sulfur linkages can bond Au covalently to cis - and trans -butadiene, whereas on the other hand, oxygen linkage with the same shows a weak interaction and a non-covalent character. Further, this research is also an attempt to study the dependence of the molecular electronic structure of gold-molecule complexes on the external electric field. In addition, electronic conduction has been investigated from the perspective of alteration in shape of molecular orbitals and the development of the HOMO-LUMO gap of molecule-gold complexes under the effect of an electric field.

An X-ray crystallographic study of a new compound is performed and the structure of five sulfin- and sulfonamides of the thiazine series is discussed. The conformation of the thiazine ring in all structures (a distorted boat ) is stabilized by the intramolecular interaction of the C-H…N type. The nitrogen atom of the thiazine ring has a pyramidal configuration. The geometry of isolated molecules is calculated at density functional theory level (PBE1PBE, 6 -31G(d,p)) and compared to that observed in the crystals. In the crystal structures different packing motifs are implemented with the formation of supramolecular associates of different types due to classical hydrogen bonds such as N-H…O.

The review is devoted to the synthesis and properties of branched polymer structures of a controlled molecular architecture. The work considers the main methods to obtain branched macromolecules. The results of both theoretical calculations and experimental studies of the structure and features of the behavior of the mentioned systems in solution are analyzed and generalized. The promising use of branched polymer systems as an alternative to linear systems is noted.

A new volatile complex Ni(mi-aa)₂ [mi-aa = CH₃C(NCH₃)CHC(O)CH₃)] is synthesized and its crystal structure is determined (APEX DUO diffractometer with a 4C CCD detector, lMo K _a, graphite monochromator, T = 100 K). Crystallographic data for Ni(mi-aa) ₂ are as follows: space group Pbca , a = 5.4058(3) Å, b = 11.8684(6) Å, c = 19.8472(10) Å, V = 1273.4(1) ų, Z = 4. The Ni(II) atom is coordinated by the O and N atoms of two ligands. The Ni-O and Ni-N distances are 1.8390(9) Å and 1.926(1) Å; the chelate ONiN angle is 92.52(4)°. The complex has the molecular structure formed from the isolated molecules of Ni(mi-aa)₂ bound by van der Waals interactions. For some complexes, the TG study is performed and the intermolecular interaction energy in the crystals is calculated.

Two new transition metal complexes [Co(tmbpm)Cl₂(H₂O)]×2H₂O (1) and [Zn(tmbpm)Cl₂]×2H₂O (2) (where tmbpm = 4,4',6,6'-tetramethyl-2,2'-bipyrimidine) are synthesized and characterized by IR and single crystal X-ray diffraction. The tmbpm adopts chelating coordination mode in the two mononuclear complexes. Both 1 and 2 form 2D supramolecular structures containing an infinite 1D water chain through hydrogen bonds.

A novel nano-rod mercury(II) coordination compound [Hg (BINH)I ₂] (1), (BINH is the abbreviation of benzylideneisonicotinohydrazide) is synthesized by a hydrothermal method that produces the coordination compound at a nanosize level. The new nanostructure is characterized by scanning electron microscopy, powder X-ray diffraction, elemental analysis, and IR spectroscopy. Compound 1 was structurally characterized by single crystal X-ray diffraction and the single-crystal structure of this complex shows that each mercury(II) center is four-coordinated with two N-donor atoms from tow BINH ligands and tow iodo anions. Self-assembly of this complexes is pereformed by CH⋯I and p-p stacking interactions. The supramolecular features in these complexes are controlled by weak directional intermolecular interactions.

The title compounds bis -tetrazolate ammonium salt (I) and bis -tetrazole monohydrate (II) are synthesized and studied by single crystal and powder X-ray diffraction, IR and elemental analyses. Compound I crystallizes in the monoclinic space group C 2/ m , a = 8.8862(17) Å, b = 11.2334(21) Å, c = 3.7269(7) Å, b = 99.4(6)°, V = 367.03 Å ³ (12), Z = 2. Compound II crystallizes in the monoclinic space group P 2 ₁/ c , a = 5.1701(9) Å, b = 4.7506(8) Å, c = 15.2197(24) Å, b = 107.2(7)°, V = 357.09(10) Å ³, Z = 2. In the structure of I, both ammonium cation and bis -tetrazolate counter-anion are located on twofold crystallographic axes, moreover, the bis -tetrazolate anion has a mirror plane passing through the C1-C1a bond. In the crystal structure of (II), the bis -tetrazole molecule sits on the twofold axis (bisecting the C1-C1a bond), whereas the solvent water molecule occupies a general position. In the crystal structure of (I), the molecules are packed via N-H…N intermolecular interactions. In the crystal structure of (II), the molecules are packed via N-H…O and O-H…O intermolecular interactions. In addition, the crystal packing of both structures is further strengthened by p-p stacking interactions.