Home – Home – Jornals – Journal of Structural Chemistry 2013 number 2

The previously developed scheme of the full configuration interaction for magnetic perturbations of π systems is transformed into a scheme for calculations in the finite field. It helps create “magnetic portraits” of molecules, reflecting the essentially non-linear behavior of conjugated systems in a strong field. In particular, possible latent paramagnetism of aromatic systems and correspondingly latent diamagnetism of antiaromatic ones is easily detected. The degree of the π electron shell openness as well as the singlet-triplet splitting in the field are evaluated. From the data obtained it follows that in the strong magnetic field an aromatic molecule becomes as a rule biradicaloid and non-aromatic. Accordingly, an antiaromatic system dramatically reduces its initial biradicaloid character and thus loses its antiaromaticity.

In the present research, we have mainly concentrated on the survey of interactions in Ln³⁺ (Ln = La, Ce, Nd and Sm) ternary complexes of 5,7-dichloroquinoline-8-ol (DCQ) and 4-vinyl pyridine (VP), [Ln(VP)₂(DCQ)₃]³⁺ by means of density functional theory, Hartree-Fock and Sparkle/PM3 semi-empirical computational methods. For VP and DCQ ligands, the cation binding energy sequence follows the order La³⁺ > Ce³⁺ > Nd³⁺ > Sm³⁺ as expected based on increasing in the hardness and decreasing in the ionic radius of this lanthanide cation series. A similar trend was observed in the calculated binding energy of the aforesaid ligands with the hydrated lanthanide cation series [Ln(H₂O)₉]³⁺, while the computed values of deformation energy of ligands upon complexation demonstrated an opposite order in the lanthanide cation series. Moreover, the solvent effects are considered via a polarized continuum model and provided a significant increase in the binding strength while the relative magnitude of binding energies is the same as that in the gas phase. Combining quantum and statistical mechanical calculations, we have also determined quantitatively a reliable estimate of the conformational distribution of the [Sm(VP)₂(DCQ)₃]³⁺ complex at various temperatures in the gas phase by computing the molecular partition functions and consequently the analysis of the conformational equilibrium constants.

Calculations using conventional ab initio theory are performed to investigate the reaction mechanism associated with the gas-phase ion/molecule reaction of isobutenyl anion with N₂O. As a result, our theoretical findings strongly suggest that the main pathway is the reaction pattern of end-N attack and that the corresponding reaction mechanism basically relates to hydrogen migration, which may yield products cis-CH₂(CH₃)CCN^–₂, trans-CH₂(CH₃)CCN^–₂, and H₂O. Those are in good agreement with the experimental observations. Moreover, based on the NBO, Activation Strain model and methyl group effect analysis, we also explored the characters of rate-determining step of the main pathway.

The effects of the molecular structure on the corrosion inhibition efficiency are investigated by nine methods of calculations. The selected thio compounds were previously identified as corrosion inhibitors for mild steel in the 1.0 M HCl solution. The electronic properties such as highest occupied molecular orbital (EHOMO) energy, lowest unoccupied molecular orbital (ELUMO) energy, dipole moment (μ), and Fukui indices are calculated and discussed. Results show that the corrosion inhibition efficiency increase with the increase in both EHOMO and m values, respectively, and decrease in ELUMO. QSAR approach is utilized in this study; a good relationship is found between the experimental corrosion inhibition efficiency (IE_Exp%) and the theoretical corrosion inhibition efficiency (IE_Theo%). The calculated inhibition efficiency is found closer to the experimental inhibition efficiency with a coefficient of correlation (R²) of 0.875.

The numerical solution algorithm of the Schrödinger equation proposed in [1-5] is described, in which the electron-nucleus interaction operator has an integral representation over the nuclear distribution, and the equation itself is written in separable variables of electrons and nuclei.

A heterometallic complex of Pd(II)–Cu(II) with 1-aminoethylidene-1,1-diphosphonic (AEDP) acid (C₄H₂₂CuN₂O₁₆P₄Pd)_n (І) is synthesized. Single crystals of compound І are obtained; its crystal structure is determined by X-ray crystallography. The crystals are orthorhombic, space group Pbcn , a = 18.366(3) Å, b = 9.7661(17) Å, c = 20.198(4) Å, V = 3622.8(11) ų, Z = 8, d_x = 2.376 g/cm³. The compound crystallizes as a coordination polymer; the square environment of Pd(II) is formed by nitrogen atoms of amino groups and oxygen atoms of phosphonic groups, while at two non-equivalent copper atoms the octahedral environment is formed by oxygen atoms of phosphonic groups and water molecules. The crystal structure of compound I is characterized by the formation of a branched network of hydrogen bonds. Based on the analysis of the temperature dependence of the magnetic susceptibility it is found that for the heterometallic complex of Pd(II)–Cu(II) with AEDP antiferromagnetic interactions between the paramagnetic centers are dominant.

The optimized molecular structures, vibrational frequencies and ¹H and ¹³C NMR chemical shifts of acetylcholine halides (F, Cl and Br) have been investigated using density functional theory (B3LYP) method with 6-311G( d) basis set. The comparison of their experimental and calculated IR, R and NMR spectra of the compounds has indicated that the spectra of three optimized minimum energy conformers can simultaneously exist in one experimental spectrum. Thus, it was concluded that the compounds simultaneously exist in three conformations in the ground state. The calculated optimized geometric parameters (bond lengths and bond angles), vibrational frequencies and NMR chemical shifts for the minimum energy conformers were seen to be in a good agreement with the corresponding experimental data. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program.

The reasons are investigated for the prepeak and the asymmetry of the second peak in the structure factor curve that are observed in a variety of metallic melts. The prepeak is observed as an additional maximum in the left wing of the main peak of the structure factor for multicomponent melts and is attributed to their chemical short-range order (CSRO). The asymmetry of the second peak in the structure factor, which is usually explained by the “icosahedral” (polytetrahedral) order in the melt, is observed both for multicomponent systems and for pure metals. However, some aluminum alloys with transition metals exhibit the two features simultaneously, which requires an explanation. An X-ray diffraction study of the liquid ternary Al_66.6Mn_16.7Co_16.7 alloy is performed at 1393 K and that of liquid copper at 1353 K, 1403 K, and 1553 K. The reverse Monte Carlo (RMC) method is used to derive structural models of these and other melts. Structural analysis of these melts is conducted using Delaunay simplices. A theoretical simulation of CSRO is performed in the model of liquid aluminum, the structure factor of which does not have these features. It is discussed that CSRO can exist in a melt regardless of the presence of the polytetrahedral order.

We use our own and literature data on density, ultrasound propagation velocity, and isobaric heat capacity to study the concentration, temperature, and pressure dependences of solvation numbers in aqueous NaCl solutions. We show that, in the parameter range: m = 0-6.0 mol×kg ^–1, p = 1-1000 bar, and T = 283.15-323.15 K, the solvation numbers decrease with increasing concentration, pressure, and temperature.

A technique is proposed for directed synthesis of 6,11-dichloro-9-dimethylthio-7,8-dicarba- nido-undecaborane [6,11-Cl₂-9-SMe₂-7,8-С₂В₉Н₉]. Single-crystal X-ray diffraction is used to identify the molecular and crystal structure of the compound.

New layered metal-organic coordination polymers [Zn₃(bpdc)₃(DMA)₂]·3DMA (1) (H₂bpdc = 4,4′-bi-phenyldicaboxylic acid, DMA = N,N' -dimethylacetamide) and [Zn₃(bdc) ₃(im)₂]·1.5H₂O (2) (H₂bdc = tere-phtalic acid, im = imidazole) are synthesized and characterized by X-ray crystallography.

By X‑ray diffraction the crystal and molecular structure of quasigermatranediol (HO)₂Ge(OCH₂CH₂)₂NH at 155 K is determined. By quantum chemical method using second-order Møller–Plesset perturbation theory (MP2) and a split-valence 6-311++G(d,p) basis set with polarization and diffuse functions for all types of atoms, the structural parameters of this molecule are calculated. In the crystal, the quasigermatranediol molecules are arranged in columns due to O–H…O and N–H…O hydrogen bonds of medium strength. The columns are linked together via weak O–H…O and N–H…O hydrogen bonds. By calorimetry, the phase transition in a crystal of quasigermatranediol at 150-145 K is revealed.

Dihydrocaffeic acid С₉H₁₀O₄ is a natural antioxidant. The crystal structure of dihydrocaffeic acid is determined; the crystallographic data at 100 K are: a = 11.3189(4) Å, b = 5.5824(1) Å, c = 13.8431(4) Å, b = 109.248(4)°, and V = 825.80(4) ų; the space group is P2₁/c, Z = 4. In addition to the formation of hydrogen bonds that are typical of acids, the compound has features that are important from the viewpoint of reactivity of dihydrocaffeic acid molecules. The position of one of the hydroxyl hydrogen atoms in the catechol group is disordered even at 100 K. The crystal structure of caffeic acid does not show such a disordering.

A coordination polymer {[Mn(H₂O)₂(C₁₁H₂₀N₄O₂)₂]²⁺⋅2(NO₃^–)}_n is synthesized and its structure is determined. The crystals are monoclinic: space group P2₁/c, a = 12.3771(3) Å, b = 14.8775(3) Å, c = 18.1388(4) Å, β = 106.611(2)°, V = 3200.70(12) ų, d_x = 1.44 g/cm ³, Z = 4. Manganese ions are coordinated with four oxygen atoms of four organic ligands (two unique) and two water molecules. The coordination polyhedron is a distorted octahedron; the О–Mn–O angles between the adjacent oxygen atoms fall within 83.96(5)-98.11(5)°. The nitrate anions are in the outer coordination sphere. The Mn…Mn distances in the polymer are 8.56 Å. In the crystal, polymeric coordination chains are joined in layers perpendicular to the b axis by hydrogen bonds involving the organic ligands, water molecules, and nitrate anions.

A new compound EnrH₃[SnBr_3.46Cl_2.54]⋅H₂O, where EnrH₃²⁺ is the enrofloxacinium cation (C₁₉H₂₄FN₃O₃²⁺), is synthesized and its crystal and molecular structure is determined. Crystallographic data for enrofloxacinium tetrabromidodichloridostannate(IV) monohydrate are as follows: a = 17.1262(19) Å, b = 10.3435(11) Å, c = 17.2582(19) Å, β = 119.203(1)°, V = 2640.5(4) ų, space group P2₁/c, Z = 4. Hydrogen bonds form a branched three-dimensional network linking EnrH₃²⁺, [SnBr_3.46Cl_2.54]^2–, and water molecules. The structure is also stabilized by the π–π interaction of EnrH₃²⁺ aromatic rings.

The structure of methyl 4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-1-methyl-1H-pyrazol-5-carboxylate is determined by X-ray crystallography and further used to elucidate the structure of methyl 4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-1-methyl-1H-pyrazol-3-carboxylate, using the data of homo- and heteronuclear 2D NMR correlation spectroscopy.

By the example of multilayer MoS₂ nanotubes the capabilities of the X-ray diffraction method in determining possible polytypic forms of layered metal dichalcogenides, which may appear due to the nanostructuring of these compounds, are discussed. The conclusion about a low information value of the X-ray diffraction method is drawn, therefore the experimental analysis of the polytypic composition of nanostructures of metal dichalcogenides needs to attract electron microscopy and electronой tomography methods.

Two zinc(II) complexes [Zn(6,6'-dimethyl-2,2'-bipy)Cl₂]_n (1) and [Zn(6,6'-dimethyl-2,2'-bipy)I₂]_n (2) are synthesized from the reaction of the 6,6'-dimethyl-2,2'-bipy ligand with ZnCl₂ and ZnI₂. Zinc(II) oxide nanoparticles are synthesized by the thermolysis of [Zn(6,6'-dimethyl-2,2'-bipy)Cl₂]_n (1) and [Zn(6,6'-dimethyl-2,2'-bipy)I₂]_n (2) at two different temperatures. The ZnO nanoparticles are characterized by X-ray diffraction and scanning electron microscopy (SEM). SEM images show the average size of the ZnO nanoparticles produced of 50 nm and 60 nm in compounds 1 and 2 respectively.

From solutions in 2-picoline (2-methylpyridine), depending on the temperature of crystallization, the universal clathratogen — 1,1'-binaphthyl-2,2'-bicarboxylic acid (BBA) — precipitates as crystals of three types with different composition and structure. Under normal conditions (room temperature), the precipitate is crystals of BBA disolvate with 2-picoline; a temperature reduction of 20°C results in the crystallization of monosolvate dihydrate; and a temperature increase of the same level results in the precipitation of monosolvate. That is, as the temperature of crystallization rises, the number of included guest molecules gradually decreases and the space where they are located becomes more closed. In 1:1:2 BBA/2-picoline/H₂O solvate (space group P2₁/n, a = 11.991(2) Å, b = 9.317(2) Å, c = 22.283(5) Å, β = 99.77(3)°, V = 2453.3(9) ų, Z = 4), the carboxyl groups of the BBA molecule at the С21 atom are deprotonated and the released proton goes to the nitrogen atom of 2-picoline. BBA molecules interact with those of 2-picoline and water via H bonds to form infinite chains in direction [111], which, in their turn, join together into infinite two-dimensional sheets parallel to plane (–101). 2-Picoline molecules are located in the channels. In BBA/2-picoline disolvate (space group С₂/с, a = 11.7523(11) Å, b = 13.8563(13) Å, c = 17.9615(13) Å, β = 108.044(9)°, V = 2781.1(4) ų, Z = 4), one BBA molecule and two H bond 2-picoline molecules form a 0-dimensional associate of the type G–H–G. The solvent molecules are also located in the channels. In BBA/2-picoline monosolvate (space group P2₁/с, a = 9.299(5) Å, b = 12.727(5) Å, c = 19.011(5) Å, β = 95.248(5)°, V = 2240.5(16) ų, Z = 4), each BBA molecule is H-bonded with a 2-picoline molecule to form a 0-dimensional associate of the type H–G. Guest molecules are located in closed cavities.

A brief review of works on the crystal chemical features of the structure and methods of describing crystal structure types is presented. A variant of the universal system of a symbolic description of crystal structure types and modular structures with the use of structure codes is proposed. The structure code is based on a description of the geometry and topology of the basic structure module. Structure codes are intended for the identification and systematization of the structure types of compounds, the formalization of topological structural transformations, the determination of structural modules, and the derivation of genetic relationships between the structures.

The results are reported of a study of hydrogen bonding between various N-substituted caproamides and tetrahydrofuran as an O-electron donor by means of FTIR spectroscopy. The spectroscopic characteristics for N—H…O hydrogen bonded complexes are given. The B3LYP functional with 6-31G** basis set has been used to calculate the structural parameters of the studied hydrogen bonded complexes. It can be assumed that both inductive and steric effects play an important role in the stability of these hydrogen bonded complexes.

The title compound, 4-hydroxy-2H-1,2-benzothiazine-3-carbohydrazide 1,1-dioxide-oxalohydrazide (1:1), is determined using X-ray diffraction techniques and the molecular structure is also optimized at the B3LYP/6-31G( d, p) level using density functional theory (DFT). The asymmetric unit consists of four independent molecules. The oxalohydrazide molecules have the centre of symmetry at the mid-point of the central C—C bond. Each thiazine ring adopts a half-chair conformation. Intermolecular C—H…O, N—H…O and N—H…N hydrogen bonds produce R₂²(10), R₂²(13), R₃³(12) and R₃³(15) rings, which lead to one-dimensional polymeric chains. An extensive three-dimensional supramolecular network of N—H…N, N—H…O, C—H…O and O—H…O hydrogen bonds is responsible for crystal structure stabilization.

A cluster complex Cs₃Nb₂I₉ is obtained by a high-temperature reaction of niobium, iodine, and cesium iodide. Its crystal structure is determined: trigonal space group P6₃/mmc, a = 8.2463(3) Å, c = 19.5419(14) Å, V = 1150.84(10) ų, R( F) = 0.0614. The compound obtained is characterized by temperature independent paramagnetism in the temperature range 70-290 K.

The hydration number of the glycine amino acid in aqueous sodium chloride solution is less than in aqueous urea solution; the difference increases significantly with increasing concentration of the nonaqueous component. Given the same partial volume of water, the hydration numbers of glycine in the two systems are close together (δ ≈ 5%).

The crystal structures of triclinic and monoclinic modifications of Nb thiobromide NbS₂Br₂ are determined by X-ray analysis. Both modifications possess layered structures in which {Nb₂(µ-S₂)₂}⁴⁺ cluster units are connected by bridging bromides into 2D layers _∞²[Nb₂(S₂)₂Br_8/2]. The two polymorphs differ only in the way in which the layers are stacked. Interatomic distances and bond angles are identical for both polymorphs.

The crystal structure of the [Ta₆Br₁₂(H₂O)₆](BPh₄)₂⋅4H₂O salt (1), obtained from Ta₆Br₁₄⋅7H₂O and NaBPh₄, is determined by X-ray crystallographic analysis. The structure contains a network of hydrogen bonds, which organizes the cluster cations into layers.

A rhenium cluster complex [Ni(NH₃)₆]_2.5⋅NH₄[Re₁₂CS₁₇(CN)₆]⋅8.5H₂O is obtained and structurally described. The compound crystallizes in the triclinic space group P-1 with the unit cell parameters: a = 11.0856(13) Å, b = 15.242(2) Å, c = 21.232(3) Å, α = 90.158(4)°, β = 97.439(4)°, γ = 90.051(4)°, V = 3557.3(8) ų, Z = 2, d_calc = 3.287 g/cm³. The crystal structure represents a packing of [Ni(NH₃)₆]²⁺ and NH₄⁺ cations, [Re₁₂CS₁₇(CN)₆]^6– cluster anions, and crystallization water molecules bound by a system of hydrogen bonds.

The crystal structure of a new energetic compound of 4,4"-dinitro-[3,3':4,3"]-tris-[1,2,5]-oxadiazole is studied.

By a single crystal X‑ray diffraction study the molecular structure of 3,7-dimethyl-9-thia-3,7-diazabicyclo[3.3.1]nonane-9,9-dioxide having a chair-chair conformation with a diequatorial arrangement of methyl groups at nitrogen atoms is determined. Compound 1 C₈H₁₆N₂O₂S crystallizes in the space group Pnma with the following cell parameters: a = 11.0262(3) Å, b = 14.4490(3) Å, c = 6.1780(3) Å.

The molecular structure of 5-[(triphenylphosphoranylidene)hydrazono]-exo-3-azatricyclo[5.2.1.0^2.6]decane-4-one is determined. The C₂₇H₂₆N₃OP compound crystallizes in the space group P-1: a = 9.2163(9) Å, b = 11.1102(11) Å, c = 11.9397(12) Å, α = 74.284(2)°, β = 78.532(2)°, γ = 72.004(2)°.

The salt (η⁵-pentamethylcyclopentadienyl){bis(pentafluorophenyl)thiomethylphenylphosphine-κ₂S,P)chloroiridium(III) tetrafluoroborate, [(η⁵-C₅Me₅)IrCl{κ₂S,P-(C₆F₅)₂PC₆H₄SMe-2}]BF₄, crystallizes as a conglomerate in the orthorhombic crystal system in space group P2₁2₁2₁ with unit cell parameters a = 9.9621(9) Å, b = 16.7793(15) Å, c = 18.5040(16) Å, V = 3093.1(5) ų, Z = 4, d_calc = 2.014 g⋅cm^–3. The structure of the S_Ir, S_S stereoisomer reveals three-legged piano stool geometry about Ir, with Cp*—Ir, Ir—P, Ir—S and Ir—Cl distances of 1.847(5), 2.2791(14), 2.3451(13) and 2.3840(12) Å respectively.

Reaction of cobalt hydroxide with the α,ω-dicarboxylic acid and 1,12-dodecanedioic acid under ambient conditions results in the formation of a trihydrate Co(C₁₂H₂₀O₄)(H₂O)₃ (1). Single crystal X-ray diffraction studies show 1 to crystallise in the orthorhombic space group Pccn with cell parameters a = 40.2343(7) Å, b = 8.1519(1) Å, c = 9.1011(2) Å. The structure has a very pronounced two dimensional character, with a separation of hydrophobic n-alkyl chains from the carboxylate groups, the Co²⁺ cations and the water of crystallisation. The structure is discussed in respect of the structures of other known compositionally related compounds, including the dihydrate Co(C₁₂H₂₀O₄)(H₂O)₂.