Home – Home – Jornals – Journal of Structural Chemistry 2016 number 5

Detailed quantum mechanical calculations of the interaction of cyclodextrin (α-, β-, and γ-CD) with 4-nitrophenol (I), 4-nitro-2,6-dimethylphenol (II), 4-nitro-3,5-dimethylphenol (III), and their anions (IV-VI) with the formation of intercalation complexes are carried out for the first time. The calculations of the compounds are performed within the density functional theory by the hybrid Becke-Lee-Yang-Parr (B3LYP) method with LanL2DZ basis sets. For the α-CD+III and α-CD+VI complexes it is shown that a nitrophenol molecule of III and a nitrophenolate anion of VI are not contained in the α-CD torus, which agrees with the experimental equilibrium constants. It is found that the calculated equilibrium constants of the formation of guest-host complexes with phenolate anions are much larger than those of neutral molecules. The most stable CD complexes with nitrophenols and their anions should be expected for γ-CD. The β-CD complexes when the guest enters into the host cavity are formed only with compounds I, V, and VI.

Within the supermolecule theory, the intermolecular interaction of a monomer, a catalyst, and a solvent involved in the polycondensation of pseudochloroanhydrides of aromatic o -ketocarboxylic acids is simulated. A transition state is found in the dimerization reaction of the simplest representative of the class of 3-chloro-3-phenyl phthalylidene monomers under study. It is established that a solvent molecule (nitrobenzene) can coordinate through the functional chlorine atom of 3-chloro-3-phenyl phthalylidene, thus hindering the formation of the active center, and hence, the growth of the polymeric chain. As a rule, in the presence of nitrobenzene the activation energy of the dimerization reaction of 3-chloro-3-phenyl phthalylidene slightly lowers as compared to that in the gas phase.

On the example of a simple mechanical model (a linear chain of three bound atoms) it is shown that the equilibrium conditions of forces and force moments completely determine the linearly elastic properties of the structure and make it possible to find the number of free parameters of the quadratic force field.

A genetic algorithm (GA) coupled with a tight-binding (TB) interatomic potential is used to search for the low-energy structures of medium-sized Ni_n (n = 36-40) clusters. Structural candidates obtained from our GA search are further optimized with first-principles calculations. The medium-sized nickel clusters ranging from 36 to 40 atoms are found to favor the double-icosahedron-based structures with a Ni₇ core (a pentagonal bipyramidal structure) except Ni₃₈ cluster. The lowest-energy structure of Ni₃₈ can be considered to be a magic cluster, which is a typical face-centered cubic structure with large stability and magnetic moment.

In this work, an atrinuclear-oxo-centered complex of the CrFe₂ type with the CF₂ClCOO^- bridging ligand is newly synthesized. The complex is characterized by experimental and theoretical methods. The optimized geometry and theoretical vibrational frequencies are computed using the density functional theory (DFT) method. Also, the AIM analysis was applied to study changes in topological parameters such as the electron density at critical points of all the bonds of the complex. In the optimized geometry of the complex, three metal ions form a trigonal-planar structure with a m₃-O atom in its center. Each of M³⁺ metal ions has an octahedral coordination environment of oxygen atoms. The DFT results are in agreement with the experimental ones, confirming the validity of the optimized geometry for the complex.

The structures and properties of two diamond-like C-LA3 and Si-LA3 phases with crystallographically equivalent atomic sites are calculated by density functional theory with the exchange-correlation potential in the generalized gradient approximation (DFT-GGA). For these phases the structural characteristics, cohesion energies, densities of states, and bulk moduli are determined and powder diffraction patterns are calculated. It is found that the cohesion energies, band gaps, and bulk moduli of C-LA3 and Si-LA3 phases are smaller than the corresponding values of cubic diamond and silicon. Possible methods to obtain experimentally diamond-like C-LA3 and Si-LA3 phases are also analyzed in the paper.

The work demonstrates the results of quantum chemical calculations of ¹⁹F and ¹³С NMR spectra of model fluorocarbon C _n F_{2 n +2} molecules with various configurations and hydrocarbon chain molecules. The possibilities to determine the chain length, formation of branches, identification of fluorine substitution for hydrogen during the fluorination of hydrocarbon paraffins and polymers are discussed.

On the example of bismuth-containing glasses based on InF₃ and ZrF₄ the effect of bismuth on the glass formation, properties, glass structure, and also the appearance of broadband luminescence in the low-wave region of IR spectra of fluorozirconate glasses is considered.

Solid solutions Ba₂In₂O_5-0.5yF_y with the structure of brownmillerite are studied by IR and ¹Н MAS NMR spectroscopy. During the fluorine doping the nearest oxygen environment of indium atoms is distorted and a part of In-O bonds is shortened. It is shown that partial fluoride ion substitution for oxygen atoms results in an increase in the proton mobility in hydrated Ba₂In₂O_5-0.5yF_y x nН₂О phases.

¹⁹F, ¹H NMR and DSC methods are employed to study the ion mobility and phase transitions in hexafluoro complex compounds of tantalum(V), niobium(V), and titanium(IV) with a tetramethyl ammonium cation. It is found that the transformation of NMR spectra observed in the temperature range 77(130)-450 K is due to a change in the form of ion motions in the anionic and cationic sublattices of the compounds under study. The main forms of ion motions in the temperature range 170-450 K are isotropic reorientations of TaF₆, NbF₆, TiF₆ octahedra and tetramethyl ammonium ions. Two endoeffects with the maxima at 232.5 K and 256.5 K for [N(CH₃)₄]TaF₆ and at 235 K and 250 K for [N(CH₃)₄]NbF₆, which are observed in the DSC curve in the range 170-400 K, correspond to phase transitions whose occurrence practically does not affect the parameters of NMR spectra in the temperature range 230-260 K. For the [N(CH₃)₄]₂TiF₆ compound an endoeffect is observed near 422 K, which corresponds to the phase transition from the rhombohedral modification to the cubic one.

Quantum dots (QDs) of zinc sulfide are synthesized by a microwave method in an aqueous medium using sodium dioctyl sulfosuccinate (DS) or 4,4¢-bipyridine (BP). Based on the analysis of X-ray diffraction profiles the conclusion is drawn that QDs obtained have a structure of cubic zinc blende with an average particle size of 5.6 nm for the ZnS_DS sample and 4.8 nm for ZnS_BP. Transmission electron microscopy images show the presence of spherical aggregates of particles only for ZnS_DS. IR data indicate the presence of sulfate ions in both samples; DS remains in the sample, facilitating the QD agglomeration, while BP is effectively washed out. From the optical diffusion scattering spectra the band gap is estimated, which turns out to be larger than the expected one due to the presence of elemental sulfur in the samples and partial oxidation of the QD surface. The QD structure based on ZnS particles is also modeled in the work. The possibility to employ X-ray absorption near-edge spectroscopy for the verification of atomic structural parameters around zinc sites in QDs based on zinc sulfide is demonstrated.

A new numerical method to determine the chirality of water configurations is developed. It consists in the comparison of matrices composed for both initial configuration and its mirror image based on the information of four bound water molecules. The method developed enables the rapid and unambiguous determination of the chirality of an aqueous system.

In a recent work by Zelikman et al.(J. Struct. Chem., 2015, 56(1)), the molecular dynamics simulation of dimers of glycyrrhizic acid (GA), which arise from the spontaneous collision of two GA molecules in water, is performed. Several relatively stable dimer structures are found, and when a cholesterol molecule is inserted, associates are observed that constitute a GA dimer with a cholesterol molecule "stuck" to it. Here, we simulate the associates consisting of three and four GA molecules and a cholesterol molecule. It appears that the cholesterol molecule, as a rule, is also located at the surface of the GA associate. Therewith, trimers do not form any clear characteristic structures, as dimers do, and tetramers can be two stuck dimers.

With an increase in the concentration of additives the hydration numbers of compounds decrease. Thus, in the saturated 54.6 % solution, urea loses approximately 3/4 of the initial amount of water, forming an aquacomplex of the composition (NH₂)₂COxH₂O. In a supersaturated 44% solution, the sodium chloride aquacomplex is dehydrated by 2/3, and in a supersaturated 67% solution, sodium sulfate is dehydrated by 5/6. The density of these solutions is 1.354¸1.360 g/cm³ (44 % NaCl) and 1.800¸1.849 g/cm³ (67 % Na₂SO₄). In the saturated urea solution, NaNO₃, NaCl, and Na₂SO₄ complexes lose 53¸55 % of hydrate water. It is shown here that in the binary water-urea system, interactions somewhat increase the hydration number of the salts (structural hydration). The characteristic important in the structural aspect (density of hydration water) increases in a series of solutions of compounds: urea, NaNO₃, NaCl, and Na₂SO₄. In the same series of additives, an excess volume of binary water-urea and water-salt systems becomes more negative.

Interest in the reduction of NiMoО₄-SiO₂ is related to its promising use as catalysts in hydrodeoxygenation and hydrodesulfurization processes. By means of in situ X-ray diffraction phase transformations occurring during the hydrogen reduction of NiMoO₄-SiO₂ in the temperature range 30-700 °C are studied in this work. It is shown that the reduction of a-NiMoО₄ proceeds in two stages. At the first stage, at 400-500 °C an intermediate state forms, which is a mixed oxide (Ni,Mo,□)O and Ni_{1- x} Mo _x . At the second stage, above 650 °C, two solid solutions form based on Mo and Ni structures. By the Rietveld method the structure of the intermediate state is refined. It is shown that the mixed Ni-Mo oxide forms based on the NiO structure, which contains some amount of cation vacancies.

The reaction of [W₃S₄(H₂O)₉]⁴⁺ with thiourea (tu) in hydrochloric acid produces a new cluster complex [W₃S₄(tu)₈(H₂O)]Cl₄×2H₂O containing coordinated thiourea. The complex is characterized by elemental analysis, thermogravimetry, IR, NMR, UV-Vis spectroscopy, and mass spectrometry. The crystal structure is determined by X-ray analysis. The thermal decomposition of [W₃S₄(tu)₈(H₂O)]Cl₄×2H₂O on heating from 20 °С to 700 °С in He gives WS₂, identified by the X-ray diffraction pattern. DFT calculations for [W₃S₄(tu)₈(H₂O)]⁴⁺ show that HOMO has a comparable contribution from metal- and ligand-centered atomic orbitals.

The new mixed-ligand complex of [Tl(Ph₂phen)Cl₃(DMSO)] (1) is obtained from the reaction of TlCl₃×4H₂O with 4,7-diphenyl-1,10-phenanthroline (Ph₂phen) in a methanol solution. Suitable crystals of 1 are obtained for the X-ray diffraction measurement by methanol diffusion into a DMSO solution. 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.

As a new precursor to prepare nano molybdenum trioxide, methanol {2-[(2-hydroxy-1, 1-dimethyl-ethylimino)-methyl]phenolato}dioxidomolybdenum(VI) complex (1) with the Schiff base ligand (H₂L) is synthesized by two different methods: solvothermal and sonochemical. Nanoparticles of 1 are obtained by one-pot solvothermal treatment of methanolic solutions of the ligand and di-oxomolybdenyl acetylacetonate at 150 °C for 24 h and for improving the quality of nanostructures by sonochemical method with two types of solvents, different concentrations of initial reagents and also different sonication times. The thermal stability of nanosized compound 1 is studied by thermal gravimetric (TG) analysis and differential scanning calorimetry (DSC). Nanoparticles of orthorhombic a-MoO₃ are obtained by calcination of nanostructures of compound 1 at 700 °C. All compounds and the obtained molybdenum trioxide nanostructures are characterized by elemental analysis, FT-IR, UV-Vis spectroscopy, X-ray powder diffraction (XRD), and scanning electron microscopy (SEM).

The titled complex is synthesized from the ethanolic solutions of 1-chloro-2,4-dinitrobenzene, 2-thiobarbituric acid, and 2-methylpyridine and characterized by spectral and elemental analyses. The single crystal X-ray diffraction results for the complex are compatible with the spectral observations. The titled complex exhibits anticonvulsant activity and reduces all phases of convulsion even at a low dosage. Acute toxicity studies of the complex are performed to understand the safer dose concentration for clinical trials.

A new copper(II) complex of 1,10-phenanthroline (C₁₂H₈N₂) and the meta -aminobenzoate ion ( m -amb; ), having the formula Cu(C₁₂H₈N₂)(C₇H₆NO₂)Cl×0.5H₂O, is prepared and characterized by elemental analysis, IR spectroscopy, and single crystal X-ray diffraction. The structure is built up from monomeric units in which the coordination environment around the metal ion is a square plane arising from a bidentate 1,10-phenanthroline molecule, a monodentate m -amb anion, and a chloride ion. A very long (Cu-N = 2.856(5) Å) bond to the nitrogen atom of an adjacent m -amb ion generates [101] polymeric chains in the crystal. The crystal structure is consolidated by N-H⋯O and O-H⋯O hydrogen bonds and C-H⋯O, C-H⋯Cl, and aromatic p-p stacking interactions. Crystal data: C₁₉H₁₅ClCuN₃O_2.5, M _r = 424.33, monoclinic, P 2₁/ n (No. 14), a = 9.8200(5), b = 10.9291(7), c = 16.3803(9) Å, b = 105.293(3)°, V = 1695.74(17) ų, Z = 4, R ( F ) = 0.043, wR ( F ²) = 0.122.

This work is a brief review of the authors’ works on the application of Löwdin-Amos-Hall paired orbitals for the analysis of spin-polarized DFT solutions. The possibilities of this approach are demonstrated on the example (1) of models of Fe(III) hydroxocomplexes with two forms of the terminal oxo center, which are involved in the detachment of methane hydrogen, and (2) models of vanadium oxide during the dissociation of the vanadyl group.

The previous multireference configuration interaction (MRCI) results show that the ground state ⁴S^- of the AlC molecule is basically single configurational in nature. In this paper, the potential energy curve (PEC) of ⁴S^- is calculated with the Brueckner coupled-cluster doubles with perturbative triple and quadruple corrections [BD(TQ)]. Basis set extrapolations with the correlation-consistent basis sets are performed. The efficiency and precision of the methods with different basis sets are compared. The calculated spectroscopic constants are in excellent agreement with the experimental ones. Our results reveal that the correlation from higher order excitations than doubles is very important for this system.

Geometries and properties of the CpW(CO)₂(m-PPh₂)Mo(CO)₅ complex are investigated theoretically through HF and DFT methods. Computational results reveal that the most accurate structural parameters can be predicted at the B2PLYP/SDD level of theory. AIM and NBO analyses are performed to investigate the nature of the Mo-W and the metal-carbonyl interaction in CpW(CO)₂(m-PPh₂)Mo(CO)₅. It is confirmed that there is a Mo-W bond and a semi-bridging carbonyl group in the complex. The formation of the Mo-W bond accompanies the dominant charge transfer interactions: BD(1)Mo1-W2 ® BD*(1)Mo1-W2 and BD(2)Mo1-W2 ® BD*(2)Mo1-W2. The real interaction between W and the CO ligand coordinated to molybdenum explains the observed IR n(CO) band at 1876 cm^-1 at room temperature and d(¹³CO) at 218.69 ppm at 210 K.

The proton acceptor properties of some heterocyclic compounds of a pyrrole series are studied from the data on the self-association of molecules. It is shown that on passing from pyrrole to other compounds of this series a change in the vibrational frequency of the N-H group of associated molecules ν _ас is observed. This change in the frequency is due to the inductive effect of the introduced structural fragments on the equilibrium electronic configuration of the N-H group.

A new manganese(III) complex [Mn(L)(NCS)] (1) is synthesized from the Schiff base ligand N,N¢- O -phenylenebis(4-methoxysalicylideneimine) (H₂L: derived from the condensation of 4-methoxy salicylaldehyde with O -phenylene-diamine) with Mn(NO₃)₂×4H₂O and KSCN in a methanol/water solvent mixture. This complex is characterized by elemental analysis, FT-IR and single crystal X-ray diffraction. It crystallizes in a monoclinic system, with space group P 2₁/ c and four molecules in the unit cell ( Z = 4). The crystal structure shows [Mn(L)(NCS)] units joined together by the Mn⋯S secondary bonding interaction (SBI) to form infinite zigzag chain structures.

A new Cd(II) coordination polymer, namely [Cd(pbmb)(mip)] _n (pbmb = 1,1¢-(1,3-propane)bis-(2-methylbenzimidazole), H₂mip = 5-methylisophthalic acid), is hydrothermally synthesized and characterized by elemental analyses, infrared spectroscopy and single crystal X-ray diffraction analyses. It crystallizes in the triclinic space group P , a = 0.2883(11), b = 11.3409(12), c = 13.2519(14) Å, a = 69.6950(10)°, b = 73.5850(10)°, g = 63.8100(10)°, V = 1285.8(2) ų, Z = 2, C₂₈H₂₈CdN₄O₅, M_r = 612.94, D_c = 1.583 g/cm³, m = 0.896 mm^-1. In the complex, adjacent dinuclear units [Cd₂(pbmb)₂] are bridged by mip^2- ligands in the m₂-h², h¹ coordination modes to construct 1D ladder-like chains which are additionally assembled into a 2D supramolecular network via C-H⋯p interactions. Moreover, the luminescence properties of the complex are described.

A new two-dimensional Cd(II) coordination polymer, [Cd(dtb)(CH₃OH)] _n (H₂DTNB = 5,5'-dithiobis(2-nitrobenzoic acid), has been synthesized by solvothermal method, and characterized by elemental analysis, IR and single-crystal X-ray diffraction analysis. The complex crystallizes in the orthorhombic Pbca space group, with a = 15.1365(19), b = 7.6198(10), c = 31.761(4) Å, b = 90°, V = 3663.2(8) ų, Z = 8, Mr = 538.77, D _c = 1.954 g/cm³ and F (000) = 2128. The final R = 0.040 and wR = 0.0866 for 3603 observed reflections with I > 2s( I ). In the complex, the Cd(II) ion is coordinated with six oxygen atoms from four carboxylate groups of distinct DTNB ligands and one methanol molecule. The adjacent Cd centers are interconnected by the flexible carboxylate ligand to form a two-dimensional (2D) structure.

EPR and luminescence methods are used to study diamonds synthesized in the Mg_0.9-Ge_0.1-C system at high pressures and temperatures (HPHT). In the EPR spectra of the Ge doped samples, along with an impurity nitrogen atom (Р1 center) and a silicon-vacancy defect SiV⁰ (KUL1 center) a new paramagnetic center GeV with the spin S = 1 and D _{3 d} symmetry is detected. The studies performed show that this center has the structure of a double half-vacancy in the center of which there is a germanium atom. The observed GeV center is in the neutral charge state and is responsiblefor the 602 nm systems in the photoluminescence spectra.

The structure of two crystalline modifications of [Pb₃(OH)₄Co(NO₂)₃](NO₂)₂ containing tetrahedral [Pb₃(OH)₄Co(NO₂)₃]²⁺ complex cations is studied. Three lead atoms and one cobalt atom are located in the vertices of a distorted tetrahedron with the edges of 3.39-3.92 Å. The distances from the metal atoms to the oxygen atoms belonging to m₃ bridging hydroxo groups are within 1.910-1.956 Å for Co-O and 2.340-2.439 Å for Pb-O. The packing motifs of the crystal structures are analyzed.

The structure of (CH₃)₃Pt(ptac)Py (ptac = (CH₃)₃C(O)CHC(O)CF₃) is determined by single crystal X-ray diffraction at a temperature of 150 K. The crystallographic data are: space group P 2₁/ c , a = 8.5513(2) Å, b = 16.1089(3) Å, c = 14,0877(3) Å, b = 107.4060(10)°, V = 1851.75(7) ų, Z = 4, R = 0.0365. The structure is of the molecular type; the coordination environment of platinum in the molecule is distorted octahedral. The average Pt-O and Pt-CMe distances are 2.149(1) Å and 2.029(5) Å respectively, Pt-N 2.179(2) Å; the chelate angle O-Pt-O = 89.77(8)°. By thermogravimetry the thermal properties of (CH₃)₃Pt(ptac)Py are studied in the condensed phase.

The first coordination polymer containing a [Re₁₂CS₁₄(SO₂)₃(CN)₆]^6- cluster anion is obtained and structurally characterized. The [{Ni(NH₃)₄}₃´{Re₁₂CS₁₄(m-SO₂)₃(CN)₆}]×14H₂O compound (1) is obtained by the reaction of NiCl₂×6H₂O and K₆[Re₁₂CS₁₄(m-SO₂)₃(CN)₆] in a mixture of NH₃/H₂O and CH₃CN. The compound crystallizes in the triclinic space group P -1 with the unit cell parameters: a = 13.1633(4) Å, b = 14.0464(4) Å, c = 20.7198(7) Å, a = 73.660(1)°, b = 83.101(1)°, g = 65.102(1)°, V = 3334.6(2) ų, Z = 2, d _calc = 3.661 g/cm³. The crystal structure is composed of linear polymeric chains located parallel to the b axis and solvate H₂O molecules bound by hydrogen bonds.