Home – Home – Jornals – Journal of Structural Chemistry 2013 number 1

An exact method (full configuration interaction) and approximate schemes for the calculation of the anisotropy spin coupling matrix and the corresponding zero field splitting D parameter are considered. Calculation algorithms for the exact method and a special case (valence bond (VB) method) are also presented. The results of specific π calculations give evidence that the VB method in fact cannot be recommended for the description of the spin-spin interaction, especially for biradicals with the triplet ground state. At the same time, the Tamm–Dancoff method (taking into account all singly excited configurations) provides on average a good approximation to an accurate description of non-degenerate triplet states. The description of fine spin effects, which is rougher, but better than that in VB, is given by the restricted Hartree–Fock method for open shells.

Quantum chemical calculations of the electronic and geometric structure of the HOO–N=N–OOH intermediate in the activation reaction of molecular nitrogen are performed by the density functional theory method at the B3LYP/6-311++G(3df,3pd) level. For HOO–*N=N*–OOH isotopomers with respect to nitrogen the spectroscopic parameters of the intermediate are characterized, which indicate the possibility of its experimental detection. The reactivity of the high energy state НОО* (²A') in the activation of N₂ is analyzed. The possibility of the generation of singlet oxygen О₂(¹Δ_g ) is considered in the dimerization of radicals with the ground state НОО (²A") followed by the sensitization of excited НОО* (²A'). A substantiated process of bonding of molecular nitrogen is given as an example of the self-organization of a chemical system in the activation of a hard-to-oxidize N₂ substance.

Quantum chemical (DFT) methods are used to study the mechanisms of intramolecular rearrangements (domino-transformations) in O-vinyl-2-tetralone oxime, which potentially can produce both conjugated and non-conjugated dihydrobenzindoles. Transition states of elementary reaction steps are localized. The 1,3-prototropic shift promoted by a mediator molecule (Н₂О) is the limiting step. An activation barrier of the formation of conjugated indole is 4.14 kcal/mol lower than the formation channel on the non-conjugated analog. Activation barriers of syn-(Z)/anti-(E)-isomerization in O-vinyl-2-tetralone oxime are analyzed. It is shown that with regard to barriers of the promoted prototropic shift, Z/E-isomerization is a rapid process.

Based on a cluster approach, the local structure of the rhombic Cu²⁺ center in a ZnF₂ crystal is investigated by using the high-order perturbation formulas of electron paramagnetic resonance (EPR) parameters g-factors g_i (i = x, y, z) and hyperfine structure constants A_i  in rhombically compressed octahedral symmetry. According to the studies, the local axial distortion angle Δα' (≈ 2.9°) in the impurity center is found to be by ~2.5° larger than the host value, which is characterized as a contraction and stretching of the parallel and perpendicular bond lengths by about 0.116 Å and 0.058 Å respectively. This results in a more compressed ligand octahedron because of the Jahn—Teller effect via the interaction of the vibrations of impurity-ligand bonds in the Cu²⁺ center. The reasonableness of the results is also discussed.

To look for the single-source precursors, the structures and properties of (Br₂AlN₃)_n (n = 1—4) clusters, density functional theory (DFT), structural feature, IR spectra, thermodynamic properties clusters are studied at the B3LYP/6-311+G* level. The optimized (Br₂AlN₃)_n (n = 2—4) clusters, density functional theory (DFT), structural feature, IR spectra, thermodynamic properties clusters all possess cyclic structures containing Al—N_α—Al linkages. The relationships between the geometrical parameters and the oligomerization degree n are discussed. The gas-phase structures of the trimers prefer to exist in the boat-twisting conformation. As for the tetramer, the most stable isomers have the S₄ symmetry structure. The IR spectra are obtained and assigned by the vibrational analysis. The thermodynamic properties are linearly related with the oligomerization degree n as well as with the temperature. Meanwhile, the thermodynamic analysis of the gas-phase reaction suggests that the oligomerization be exothermic and favorable under high temperature.

Some structural, electronic, and vibrational properties of the acetylene (C₂H₂) molecule adsorbed at various sites on the Pd(100) surface doped with Sn or Pb are determined theoretically. The calculations were performed using the B3LYP hybrid density functional, and the Sn- or Pb-doped Pd(100) surfaces were represented by a cluster model approach. It is found that the geometry of the C₂H₂ molecule adsorbed in di-σ configurations is highly perturbed with respect to the structure of acetylene in the gas phase. By contrast, the geometry of acetylene adsorbed in π configurations on the doped surfaces shows a much smaller distortion. Apart from calculating the properties of the adsorbed C₂H₂ molecule, the effect of the dopants, i.e. Sn and Pb atoms, on these properties is established by comparing the properties of acetylene adsorbed on the Sn- or Pb-doped Pd(100) surfaces with its properties on the monometallic Pd(100) surface. The results indicate that the geometry of the adsorbed C₂H₂ molecule is similar on the doped and monometallic Pd(100) surfaces.

Combinatorial analysis methods are employed to solve the problem of determining the number and form of X-substituted (X, XY, … are some substituents) of carbometallic derivatives of boranes (C₅H₅)Co(С₂B₉H₁₁) C_1v and (C₅H₅)Co(С₅B₆H₁₁) C_5v (over vertices) based on Polya's theorem. formulas of Z symmetry and generating functions of the number of chiral and achiral substitution stereoisomers are determined. Family distributions of the isomers depending on the form and number of substituents and depending on the number m of possible substitution sites are found. Mono-, di-, and tri-X-substituted (X = CH₃, F, …) isomers of (С₅Н₅)Со(C₅B₆H₁₁) C_5v are identified. Based on the partition of simple (n) and triangular numbers (K₃) of Pascal's triangle, additive schemes are obtained which take into account valence and non-valence pair interactions of atoms in the polyhedron framework and contain 2, 6, and 23 parameters for the calculation of properties of Х-substituted borane (C₅H₅)Co(С₅B₆H₁₁) C_5v.

An EPR study of Li_2–2xZn_2+x(MoO₄)₃ crystals activated by copper ions shows that they occupy the М2 site, one of the three possible sites of both lithium and zinc. In the EPR spectra of Cu²⁺ copper a broadening of HFS lines and a nonequidistant splitting between them, which are unusual for the orientation Н || g_zz, A_zz, are observed. In this work possible reasons for such a broadening of HFS lines from copper ions are analyzed: a distortion of the oxygen octahedron due to the introduction of copper ions, second order perturbation theory corrections, superposition of HFS from ⁶³Cu and ⁶⁵Cu isotopes, and the effect of the charge redistribution in the oxygen octahedron because the cation vacancy providing charge compensation can be located at different distances from the copper ion. It is shown that the first three reasons do not explain the features observed in the EPR spectra. In the case of cation vacancies located in the М3 site and remote at different distances from the copper ion, the charge redistribution in the oxygen octahedron of copper should occur along with the dispersion of HFS parameters and the g-factor. The studies performed in X and Q bands confirm this assumption. The width of HFS lines from copper ions in the EPR spectra measured in the Q band is three times more compared to that measured in the Х band.

An effective strategy of molecular Monte Carlo simulation is proposed. The strategy is based on a combination of two key approaches to parallel computing. The advantage of spatial (domain) decomposition is the high scalability of computing algorithms by splitting "big tasks" into several simultaneously solvable subtasks. However, the domain size in this method can be reduced to a certain limit only. Particle decomposition (division of program loops into portions) is, by contrast, very efficient in the study of small and medium size objects, but is poorly scalable and quickly exhausts the computer system memory with increasing size of the model. The combination of the approaches helps "neutralize" their limitations and create efficient supercomputing programs for the study of molecular models consisting of hundreds of millions of atoms.

The adiabatic compression method is used to determine quantitative solvation parameters such as hydration numbers h, the molar adiabatic compressibility of hydrated complexes β_hV_h, the volume V_1h and compressibility β_1h of water in ion hydration shells, and several other properties in the temperature range 278.15-323.15 K. Hydration numbers are used to determine the verified activity coefficient of the solvent, γ_R. The concentration dependence of the coefficient is shown to be a discontinuous function, with the discontinuity point corresponding to the complete solvation boundary.

The hydration number of α-alanine in aqueous urea solutions is greater than in aqueous NaCl solutions; the ratio of the hydration numbers increases from 0.2 (m = 1) to ≈2 (m = 6). Given the same partial volumes of water, the hydration numbers of α-alanine in the two systems are close to each оthеr.

The features of pseudosymmetry in crystalline compounds with highly symmetric sublattices are discussed. The symmetry of sublattices higher than the crystal symmetry is manifested in elementary excitation spectra in the form of degenerations and quasidegenerations. The topology of spectral branches is not related to the value of the parameter estimating the degree of pseudosymmetry on the basis of the electron density fraction, which is invariant with respect to operations corresponding to additional symmetry.

From the acidified solution of the Na₂WO₄–HNO₃–Sr(NO₃)₂–H₂O system, the white crystals of sodium-strontium paratungstate B Na₆Sr₂[W₁₂O₄₀(OH)₂]∙24H₂O (I) are isolated. By FTIR spectroscopy, the isopoly anion is shown to belong to the structural type of paratungstate B. Using single crystal X‑ray analysis the structure of I is solved: monoclinic, space group P2₁/n, a = 12.5435(3) Å, b = 12.1544(3) Å, c = 18.8080(4) Å, β = 93.440(2)°, V = 2862.28(12) ų at T = 293 K, Z = 2, ρ_calc = 4.207 g/cm³. Found that [W₁₂O₄₀(OH)₂]^10– paratungstate B anions are cross-linked in a layer via the SrO₉ and NaO₆ polyhedra, and cross-linking in a three-dimensional structure occurs via the NaO₆ and NaO₇ polyhedra. By DTA, the thermal properties of the salt are studied. By FTIR spectroscopy, it is found that under annealing of I the [W₁₂O₄₀(OH)₂]^10– paratungstate B anion exists in the structure up to 200 °C.

Previously unknown [ML₂(H₂O)_n] bischelates, where M is Mn(II), Co(II), Ni(II), or Cu(II) and L is deprotonated triformylmethane, are studied by X‑ray diffraction analysis. It is revealed that in the crystals of all compounds there are multiple hydrogen bonds linking bischelate molecules into polymer layers or a single framework. The character of the temperature dependence of the effective magnetic moment [ML₂(H₂O)_n] indicates the existences of weak intracrystalline exchange interactions between the unpaired electrons of the paramagnetic centers.

A new mononuclear Ni(II) N⁶-benzylaminopurine supramolecule [Ni(6-BA-H₂)₂(H₂O)₄]⋅(R)₂⋅4H₂O (1) (6-BA = N⁶-benzylaminopurine (C₅H₂N₃NH)(NH)CH₂(C₆H₅), H₃R = 5-sulfosalicylic acid (C₆H₃)CO₂H(OH)SO₃H) is firstly synthesized by the volatile method. Compound 1 possesses a 3D supramolecular structure built via H-bonds and π—π stacking interactions. In the structure, a mononuclear [Ni(6-BA-H₂)₂(H₂O)₄]⁶⁺ cation, in which the Ni(II) ion is 6-coordinated, bears six positive charges, and a fully deprotonated R³⁻ anion is located in the void surrounding the mononuclear cation to balance the charge.

A new monoclinic Cu(II) salt complex (C₆H₆N)₂⁺ [Cu(2,6-dipico)₂]^2–⋅6H₂O, (2,6-dipico = pyridine-2,6-dicarboxylic acid) is synthesized and characterised by CHN analyses, IR, UV-Vis, magnetic susceptibility measurements, and single crystal X-ray crystallography. The structure contains two pyridine-2,6-dicarboxylate species as tridentate ligands with protonated aniline acting as a counter cation and six uncoordinated water molecules. The complex crystallizes in the monoclinic space group C2/c with unit cell parameters a = 20.9393(4) Å, b = 7.94330(10) Å, c = 19.9093(4) Å, V(ų) = 2932.32(9), Z = 4. Crystal packing is stabilized by N—H…O, O—H…O intermolecular hydrogen bonds and weak π…π interactions. The water molecules are trapped by a cooperative association of coordination interactions forming water clusters as well as by a hydrogen bond to the Cu (II) complex.

The synthesis and X‑ray single crystal study of two mixed-ligand Cu(II) complexes are performed: (CH₃C(NCH₃)CHC(O)CH₃)(CF₃C(O)CHC(O)CF₃)Cu (1) (space group P2₁/c , a = 7.0848(12) Å, b = 17.854(3) Å, c = 11.837(2) Å, β = 100.495(6)°, V = 1472.4(4) ų, Z = 4), (CH₃C(NC₆H₅)CHC(O)CH₃)⋅(CF₃C(O)CHC(O)CF₃)Cu (2) (space group P-1, a = 9.1119(4) Å, b = 9.6954(4) Å, c = 11.1447(6) Å, α = 113.784(2)°, β = 92.383(2)°, γ = 95.402(2)°, V = 893.52(7) ų, Z = 2). The structures are molecular, formed from neutral mixed-ligand copper complexes. The central copper atom has the (3O+N) coordination environment with average Cu–O distances of 1.948 Å and Cu–N of 1.932 Å; the chelate O–Cu–N angle (average) is 94.0°. In the structures, the complexes are linked into dimeric associates with Cu…Cu distances of 3.197 Å (for 1) and 3.246 Å (for 2). The volatility of mixed-ligand complexes 1 and 2 is in between of that of the starting homo-ligand complexes.

Alternating-current electrochemical synthesis is used to obtain for the first time halogenocuprates of an allyl derivative of phosphonium of the composition (CH₂=CHCH₂(C₆H₅)₃P)CuX₂ (X = Br (I), Cl (II)). Compound I crystallizes in the space group P2₁, a = 9.6341(3) Å, b = 12.4167(4) Å, c = 9.9618(4) Å, β = 117.484(5)°, Z = 2. Compound II crystallizes in the space group Р2₁/n , a = 9.9725(5) Å, b = 15.4586(8) Å, c = 13.7557(5) Å, β = 90.429(4)°, Z = 4. In the structures of I and II quasilinear CuX₂^– anions are held by С–H⋯Х hydrogen bonds inside a framework formed by the stacking of phenyl groups from СH₂=СHCH₂(С₆Р₅)₃P⁺ cations. Allyl groups are not involved in coordination with copper (I) atoms.

Data on the synthesis, IR spectroscopy, and single crystal XRD are presented for thiocarbamide compounds of the composition [Ln(H₂O)₉]I₃⋅2CS(NH₂)₂, where Ln = Dy (I) and Yb (II). The structural features of [Ln(H₂O)₉]I₃⋅2CS(NH₂)₂ (Ln = Pr, Nd, Eu, Gd, Dy, Ho, Er, and Yb) are discussed. The compounds of thiocarbamide with Pr, Nd, Eu, Gd, and Dy iodides are found to form the first isostructural series characterized by a continuous network structure, while with Ho, Er, and Yb iodides the second isostructural series with a layered type structure is formed.

A new polymorph of 1-methyl-4-imidazoline-2-thione has been first discovered and studied by X-ray diffraction. The crystal of the new polymorph is monoclinic, the asymmetric part of the cell contains three independent molecules. In the crystal, the key compound is in the form of planar hydrogen-bonded dimers due to the interactions of the N–H…S type. The new modification is of an intensely yellow color in contrast to the previously known colorless forms, is characterized by a lower density but stronger hydrogen bonds; it is formed as a minor impurity to main triclinic polymorph.

A series of three new hydrazone derivatives C₂₂H₁₉N₃O₂ (1), C₁₇H₁₃ClN₄O₃ (2), and C₂₁H₂₄N₄O₂⋅CH₄O (3) obtained by the condensation of 1H-indol-3-acetohydrazide with 2-methoxynaphthaldehyde, 2-chloro-5-nitrobenzaldehyde, and 4-diethylaminosalicylaldehyde, respectively, in methanol, ia prepared. The compounds are characterized by elemental analysis, IR spectra, ¹H NMR spectra, and single crystal X-ray diffraction. Compound 1 crystallizes in the monoclinic space group P2₁/n with unit cell dimensions a = 17.740(2) Å, b = 5.621(1) Å, c = 18.573(3) Å, β = 92.659(2)°, V = 1850.0(6) Å³, Z = 4, R₁ = 0.0610 and wR₂ = 0.1155. Compound 2 crystallizes in the monoclinic space group C2/c with unit cell dimensions a = 29.178(2) Å, b = 8.195(1) Å, c = 14.372(1) Å, Å = 109.446(2)°, V = 3240.5(5) Å³, Z = 8, R₁ = 0.0452 and wR₂ = 0.1028. Compound 3 crystallizes in the monoclinic space group Pc with unit cell dimensions a = 6.579(1) Å, b = 15.112(2) Å, c = 10.676(2) Å, Å = 90.030(2)°, V = 1061.4(3) Å³, Z = 2, R₁ = 0.0535 and wR₂ = 0.1123. The single crystal X-ray structural determination reveals that the molecules of the compounds are much twisted due to the lack of efficient conjugation. Preliminary biological tests indicate that the compounds are effective antibacterial material.

Monoacylated derivatives O-p-anisoyl-D-tartaric acid and its N,N-dimethylammonium salt are synthesized by the partial hydrolysis of O,O'-di-p-anisoyl-D-tartaric acid. Crystal and molecular structures of both compounds have been determined and analyzed. In both of them, some strong and moderate strength [O—H…O] hydrogen bonds exist between the carboxylic units. The intermolecular hydrogen bonds link the adjacent fragments forming infinite one-dimensional chains parallel to the X-axis.

Quantum chemical PBE0 and B3LYP/cc-pVTZ, PBE0, B3LYP, RHF and MP2/6-31G(d,p) methods are employed to calculate the structural parameters of octa(silsesquioxane) H₈Si₈O₁₂ and octa(methylsilsesquioxane) Me₈Si₈O₁₂. These molecules and complexes Н@Me₈Si₈O₁₂, Не@Me₈Si₈O, and Не@Me₈Si₈O₁₂ have highly symmetric (O_h) equilibrium configurations. With the use of the PBE0 method and a cc-pVTZ multicenter basis set common for the complex and its components coincidence is achieved between the calculated polarizability of a free He atom and the experimental value of 0.21 ų and the polarizability depression of 0.17 ų was found for Нe@Me₈Si₈O₁₂. In order to avoid the false conclusion about molecular symmetry the calculations of the structure of silsesquioxanes must be performed with sufficiently high accuracy (Int = ultrafine and Opt = tight in the use of the GAUSSIAN program).

The structure of the [Mn₆(O)₂(Piv)₁₀L₂]_∞ compound, where Piv is the pivalate anion and L is isonicotinamide, is investigated. Its solid phase is found to be formed by polymeric layers within which hexanuclear fragments {Mn₆(O)₂(Piv)₁₀} are bound by bidentate bridging L. The molecules of the solvent (Me₂CO or EtOAc) in which the synthesis was performed are incorporated into the inter-layer space of the crystal.

A new 1D cadmium coordination polymer [Cd(PhCOO)₂(bbbm)]_n (1) (bbbm = 1,1'-(1,4-butanediyl)bis-1H-benzimidazole ) is synthesized under hydrothermal conditions and characterized by elemental analysis, IR, TG, and X-ray single-crystal diffraction. Compound 1 crystallizes in the triclinic system, space group P-1 with a = 10.4289(17) Å, b = 12.5198(9) Å, c = 12.6130(9) Å, α = 118.4260(10)°, β = 95.1990(10)°, γ = 94.3820(10)°, V = 1428.8(3) ų, Z = 2. In the structure of 1, each cadmium center is six-coordinated in a strongly distorted octahedron by two N and four O atoms; an infinite one-dimensional linear chain was built by the flexible bbbm ligand that adopts a bis-monodentate bridging mode linking Cd^II atoms.

A novel viologen(4,4'-bipyridinium)-based compound FeCl₄(4,4'-diethyl-4,4'-bipyH) (1) (bipy = bipyridine), in which 4,4'-diethyl-4,4'-bipyH (MQ⁺) was generated in situ, is synthesized via the hydrothermal reaction and structurally characterized by single crystal X-ray diffraction. The crystal structure analysis reveals that the title compound features an isolated structure based on 4,4'-diethyl-4,4'-bipyH moieties and an iron atom terminally bound by four chlorine atoms. The 4,4'-diethyl-4,4'-bipyH moieties and (FeCl₄)^– anions are interconnected by hydrogen bonds to form a 3D supramolecular framework.

The diacetato-bis(2-methyl-2-propylamine)zinc(II) compound crystallizes in the triclinic system, space group P-1 with unit cell parameters a = 10.0144(10) Å, b = 10.2687(10) Å, c = 10.5149(10) Å, α = 115.184(2)°, β = 97.489(2)°, γ = 114.066(2)°, ν = 830.85(14) ų. The obtained solid state structure of (^tBuNH₂)₂Zn(OOCCH₃)₂ shows both inter- and intramolecular NH---O hydrogen bond interactions which are analyzed.

By X‑ray diffraction the crystal and molecular structure of N-methyl-bis(2-hydroxyethyl)ammonium (4-chlorphenylsulfonyl)acetate 4-ClC₆H₄SO₂CH₂COO^–⋅CH₃N⁺H(CH₂CH₂OH)₂ synthesized by the interaction of (4-chlorphenylsulfonyl)acetic acid with N-methyl-bis(2-hydroxyethyl)amine is studied.

As a result of one-pot three-component condensation of acetone with diethyl oxalate and p -tolyl diazonium chloride of ethyl 3-(4-tolyl)hydrazono-2,4-dioxopentanoates p-tolyl diazonium diethyloxalate and chloride, ethyl ether of 3-(4-tolyl)hydrazono-2,4-dioxopentanoic acid is obtained. The structure of the synthesized compound is studied.

The absolute configuration of 3-acetoxybetulinic acid is determined by single crystal X-ray diffraction.

According to the X‑ray diffraction data, the crystal and molecular structure of tris(2-hydroxyethyl) ammonium fluoride (F^–N⁺H(CH₂CH₂OH)₃, fluoroprotatrane, substantially differs from other halo protatranes X^–N⁺H(CH₂CH₂OH)₃ (X = Cl, Br, and I). At X = F, to the endo-molecular LP of the nitrogen atom the HF molecule having the minimum ionic radius in a series of X^– anions is bonded. The geometry of fluoroprotatrane and the cation packing in the crystal are analyzed.