Home – Home – Jornals – Journal of Structural Chemistry 2012 number 5

The coupled-cluster singles and doubles with perturbative triples (CCSD(T)) method in triple-, quadruple-, and quintuple-zeta basis sets with extrapolation to the complete basis set limit is used to analyze the properties of MnF₃, FeF₃, and CoF₃ molecules. The relative energies of low-lying electronic states are determined. The Jahn-Teller effect is investigated in the ground electronic state ⁵E′ of the MnF₃ molecule and the first excited electronic state ⁵E″ of the CoF₃ molecule. Geometric parameters, atomization enthalpies, vibrational frequencies, intensities in the infrared and Raman spectra are found with high accuracy. The assignment of the bands observed in the low-frequency region of the IR and Raman spectra of MnF₃ and CoF₃ molecules are revised.

Molecular dynamics (MD) simulation results for the adsorption process of chitosan oligomer on a carbon nanotube (CNT) are presented. An ab initio DFT calculation is performed to obtain the optimal geometric parameters and charge distribution in chitosan. Then by means of classic molecular dynamics the binding energy of a chitosan molecule with CNT calculated. It is found that the character of the interaction between a chitosan molecule and CNT is non-specific.

Vibrational spectra of the isolated complementary guanine-cytosine pair are calculated at the B3LYP/6-311++G(d,p) level. The hydrogen bond effect on the structure, frequency positions, and intensities of normal vibrations of the pair are analyzed in comparison with the spectra of isolated guanine and cytosine molecules. Characteristic spectral features of the formation of the complementary guanine-cytosine base pair are revealed.

Mono- and bis-chelate iron(III)-containing complexes with a tridentate azomethine ligand based on n-dodecyloxybenzoic acid ester derivatives with oxybenzoyl-4-salidene-N′-ethyl-N-ethylenediamine with counterions are obtained. The structure of the compounds is determined by IR spectroscopy, elemental analysis, and mass spectrometry (MALDI-ToF MS). It is found that the complexation of iron salts with tridentate ligands in a mixture of solvents (alcohol:benzene) results in the formation of bis-chelate compounds of the composition 1:2 with octahedral packing of iron in the complex, while in pure alcohol solutions, asymmetric mono-chelate complexes are obtained.

2-Anthrylethylene derivatives 1E-5E and 1Z are synthesized to study the cis-trans photoisomerization. Interestingly, unlike 9-anthrylethylene derivatives, 2-anthrylethylene derivatives 1E to 5E do not exhibit E (trans) to Z (cis) photoisomerization upon direct and triplet sensitization. One-way Z (cis) to E (trans) photoisomerization of 1Z is found to be very efficient under direct and triplet sensitization conditions, demonstrating the involvement of both singlet and triplet states. 1E-5E exhibits excitation wavelength dependent fluorescence indicating the existence of conformers (rotamers) at room temperature, which is confirmed by fluorescence lifetimes measurements of compounds 1E and 2E. Theoretical studies are carried out at DFT and ab initio methodology and the calculated relative energy difference of the conformers is very small; it ranges between 2.9 kJ·mol^-1 to 6.3 kJ·mol^-1 for both ground and excited states.

Heterobimetallic complexes [UO₂Mo^V(CH₂L)(hzd)(H₂O)₂]_n, [ZnMo^V(CH₂L)(hzd)(H₂O)₂]_n and mixed-valence complexes [Mo^VIO₂Mo^V(CH₂L)(hzd)(H₂O)₂]_n (where hzdH₃ = inhH₃, n = 1; slhH₃, n = 2) are synthesized fr om bis(2-hydroxy-1-naphthaldehyde)malonoyldihydrazone (CH₂LH₄) and monometallic precursor complexes [Mo(CH₂LH₂)(hzd)]·nH₂O (n = 0, 1) in ethanol. The composition of the complexes is established based on the data obtained from the elemental analysis. The structure of the complexes is discussed in the light of data obtained from molar conductance, magnetic moment, electronic, EPR, and IR spectroscopic studies. All complexes have μ_B values in the range 1.59-1.64 B.M., slightly lower than that required for one unpaired electron. The heterobimetallic complexes show two bands, while mixed-valence complexes show only one band in the visible region assigned to the d-d transition. The g-values decrease in going from uranyl-to-molybdenyl-to-zinc complexes containing the isonicotinoyldiazenido (inh) group, however, no such regular trend is observed in the case of complexes containing the salicyloyldiazenido (slh) group in the coordination sphere. In all complexes, the principal dihydrazone ligand is present in the enol form as a bridging hexadentate ligand in the anti-cis configuration wh ere hydrazide ligands are coordinated to the metal centre as a trinegative bidentate ligand in the diazenido form.

The electronic structure of a series of phenylsilanes Ph_4-nSiH_n (n = 0-3) is studied by X-ray emission spectroscopy and quantum chemical calculations by the density functional theory method. Based on the calculations theoretical X-ray emission SiKβ₁ spectra of phenylsilanes Ph_4-nSiH_n (n = 0-4) are constructed and their energy structure and shape turn out to be well consistent with experiment. The distribution of the electron density of states with different symmetry of Si, C, H atoms are also constructed. An analysis of the obtained X-ray fluorescent SiKβ₁ spectra and the distribution of the electron density of states in Ph₄Si and Ph₃SiH compounds shows that their energy structure is mainly determined by a system of the energy levels of phenyl ligands weakly perturbed by interactions with valence AOs of silicon. In the energy structure of MOs of the PhSiH₃ compound, energy orbitals related to t₂ and a₁ levels of tetrahedral SiH₄ are mainly presented.

The structural and thermodynamic characteristics of amide solvents are calculated with different types of molecular self-assembly through hydrogen bonding. Under a model-based approach, the specific and nonspecific components of the total energy of intermolecular interactions are identified for primary, secondary, and tertiary amides of carboxylic acids. It is found that similarly to water, primary amides have a network of hydrogen bonds and belong to the class of liquids characterized by an increase in nonspecific interactions with temperature. In secondary amides with the chain self-assembly, the contribution of these interactions is practically independent of temperature, and in tertiary amides it decreases with an increase in temperature. The molar values of the specific and nonspecific components are used to analyze the intermolecular interactions and the structural properties of amides with different degrees of N-substitution.

The published data on the density and velocity of ultrasound are used to determine the ion solvation parameters of sodium, magnesium, and cobalt chlorides. It is shown that the solvation of typical coordination compounds, such as cobalt chloride, is determined by the same underlying systems and interactions as that of electrolytes with ions of alkali and alkaline earth metals.

X-ray crystallography is used to analyze the concomitant polymorphism of KNaNbOF₅ crystals. The second β-modification of the compound, crystallizing in the tetragonal crystal system is found for the first time: space group P4/nmm, a = 5.9352(2) Å, с =8.5487(5) Å, V = 301.14(2) ų, Z = 2, R1 = 0.0095. Parameters of the orthorhombic noncentrosymmetric structure of the α-phase, previously described by Poeppelmeier et al. (J. Am. Chem. Soc., 129, 13963-13969 (2007)), are refined and a comparative analysis of both structures is performed. The structures are characterized by the complete ordering of oxygen and fluorine atoms, the Nb-O distance in the α-phase (1.738(1) Å) being noticeably longer than that in the β-phase (1.709(2) Å). In β-KNaNbOF₅, alternating NbOF₅ and NaOF₅ octahedra share vertices, while in α-KNaNbOF₅, they share both vertices and edges. The existence of the non-polar centrosymmetric β-modification of KNaNbOF₅ cancels the assumption of the substantial contribution of potassium cations to the polar structure of α-KNaNbOF₅.

Single crystal X-ray diffraction is used to study the structure of colorless crystals isolated from the saturated aqueous solution of trivalent iron perchlorate (TIP) in 67.5% perchloric acid. It is found that the compound crystallizes in the trigonal crystal symmetry; parameters of the hexagonal unit cell: a = b = 16.079(2) Å, c = 11.369(2) Å, α = β = 90°, γ = 120°, space group (S₆), Z = 6, ρ_calc = 2.021 g/cm³. The structural form of the crystal hydrate is [Fe(Н₂О)₆]³⁺()₃·3Н₂О. The structure contains two independent complex iron cations. Each of them is in the special position but retains the regular octahedral structure: average bond lengths are r(Fe-O) = 1.997(1) Å, ∠O-Fe-O bond angles differ from 90° by only 0.93°. Independent [Fe(Н₂О)₆]³⁺ cations form short H-bonds (О…О 2.64 Å) with three crystallization water molecules and somewhat longer H-bonds (О…O 2.73 Å) with three anions. The anion is disordered over two positions with occupancies of 0.62(2) and 0.37(2). Both positions correspond to the general position. The outer-sphere crystallization water molecule is characterized by the tetrahedral direction of H-bonds, which it forms with two anions and two independent [Fe(Н₂О)₆]³⁺ cations. All water molecules are in the general position. The Raman spectroscopic study of polycrystalline samples reveals weak bands belonging to the internal vibrations of two types of water molecules. The least broad bands are assigned to the transitions of crystallization water molecules whose symmetry is insignificantly lowered by two anion-molecular H-bonds. Anomalously broad bands are assigned to the transitions of a coordinated water molecule whose symmetry is more lowered by intermolecular and anion-molecular H-bonds.

A new decavanadate compound V₁₀O₂₈[Co(H₂O)₆]₃(C₈H₁₈O₆N₂S₂)₂ (I) is synthesized and characterized by single crystal X-ray diffraction, thermogravimetric analysis, FT-IR spectroscopy, and scanning electron microscopy. The sizes of the monoclinic unit cell are as follows: a = 13.2851(16) Å, b = 22.769(3) Å, c = 13.1883(16) Å, β = 117.555(2)°, V = 3536.7(7) ų, C2/m space group, Z = 2. The studies revealed that different moieties in the compound show a three-dimensional framework structure, in which {CoO₆}, the decavandate cluster anions, and 1,4-piperazinediethanesulfonic acid (PIPES) interact with each other by intermolecular forces and strong hydrogen bonding. Bond valence calculations were used to calculate the valence states of the atoms.

The title compound [Ni(C₂₀H₁₅N₂OS)₂] is prepared by the reaction of metal acetate with the corresponding acylthiourea derivative. The complex is characterized by elemental analysis, IR, ¹H and ¹³C NMR, and its structure is determined by single crystal X-ray diffraction. The Ni(II) ion is coordinated by the S and O atoms of two N-benzoyl-N′,N′-diphenylthiourea ligands in a slightly distorted square-planar coordination geometry. The two O and two S atoms are mutually cis to each other. The substance crystallizes triclinic (P-1 space group) with cell dimensions a = 10.7262(9), b = 12.938(3), c = 14.2085(12) Å, α = 74.650(4), β = 78.398(4), γ = 68.200(5)°, and two formula units in the unit cell. The structure is very close to the related N-(2-furoyl) Ni complex reported previously.

Novel compounds of Gd(III), Tb(III), Er(III), and Tm(III) with 4,4′-bipyridine (4-bpy) and trichloroacetates are prepared. The title compounds are isomorphic and isostructural in the solid state. All atoms in the studied compound lie in general positions of the Cc space group. The coordination polyhedra around central atoms can be described as bicapped trigonal prisms slightly disordered towards a square antiprism. All 4-bpy molecules are located in the outer coordination sphere together with four trichloroacetate anions and four water molecules. One of the nitrogen atoms of one 4-bpy is protonated due to stoichiometry.

The crystal structure of p-[N,N-bis(2-chloroethyl)amino]benzaldehyde-4-phenyl thiosemicarbazone(CEAB-4-PTSC) is described. The compound crystallizes in the monoclinic crystal system, P21/c space group, Z = 4, calculated density = 1.327 Mg/m³, V = 1978.2(6) ų with unit cell parameters a = 16.240(3) Å, b = 12.821(2) Å, c = 9.8543(16) Å, β = 105.382(6)°. The crystal structure reveals that the compound exists in the thione form and S1 and N2 are at trans-conformation to each other with respect to the N3-C12 bond. The packing of molecules in the crystal lattice is stabilized by intramolecular hydrogen bonds.

5-(3,4-Dichlorophenyl)-3-{[4-(2-pyridyl)piperazine-1-yl)]methyl}-1,3,4-oxadiazole-2(3H)-one C₁₈H₁₇Cl₂N₅O₂ (3) is synthesized and characterized by IR, ¹H NMR, ¹³C NMR, elemental analyses, single-crystal X-ray diffraction, and the molecular structure is also optimized at the B3LYP/6-31G(d,p) level using density functional theory (DFT). All data obtained from the spectral studies support the structural properties of 3. The molecules are linked principally by C-H⋯O hydrogen bonds involving carbonyl atoms and carboxylate O atoms, forming (16) and (20) rings that link to give a one-dimensional network of molecules. An extensive two-dimensional network of C-H⋯O hydrogen bonds and π⋯π interactions are responsible for crystal stabilization.

Single crystal X-ray structure characterization of isomeric 2-(2,4,4-trimethyl-3,4-dihydro-2H-benzo[h]chromen-2-yl)-1-naphthyl acetate (1) and 3-(2,4,4-trimethyl-3,4-dihydro-2H-benzo[g]chromen-2-yl)-2-naphthyl acetate (2) is described. Compound 1 crystallizes in the centrosymmetric monoclinic space group P2₁/c with all atoms situated in general positions. Isomeric compound 2 crystallizes in the centrosymmetric triclinic space group P-1 and its structure consists of two crystallographically independent molecules with all atoms located in general positions. In addition to intramolecular C-H⋯O bonding, 2 is involved in two intermolecular C-H⋯O interactions resulting in a one-dimensional H-bonded network.

The single crystal X-ray diffraction study of (pyrazin-1-ium-1-yl)(perfluoropyridin-4-yl) and (4,4′-bipyridin)-1-ium-1-yl(perfluoropyridin-4-yl)amides is performed. In all cases, the N⁺-N^- bond length is less than that of the single N_planar.-N_planar. bond, but considerably more than that of the double N=N bond, which indicates a weak involvement of the N^- lone pair of the C₅NF₄N^- group in conjugation with pyrazine or bipyridine moieties. Quantum chemical calculations by DFT/(PBE/L1), B3LYP/L1, and RI-MP2/L1 methods provide the geometry of amides similar to the experimental one. Crystals of (pyrazin-1-ium-1-yl)(perfluoropyridin-4-yl)amide form stacks mainly through F-π interactions. The stacks are joined in 3D architecture by weak C-H…N and C-H…F hydrogen bonds. In the case of (4,4′-bipyridin)-1-ium-1-yl(perfluoropyridin-4-yl)amide crystals, an essential role is played by the π stacking interactions of heteroaromatic rings.

The molecular structure of 3β,28-diacetoxy-18αH,19βH-ursan-20-en is determined. Compound C₃₄H₅₄O₄ II crystallizes in the P2₁2₁2₁ chiral space group: a = 8.2721(6) Å, b = 11.2728(8) Å, c = 32.559(2) Å.

The trustworthy B3LYP/6-311+G* method is employed to investigate the double hydrogen-bonded system with a special emphasis on the oxidation and hydration effect. Proton transfer occurs spontaneously upon oxidation from the amido group to the adjacent imidazole fragment. The larger the pH value of the environment, the significant the effect on the geometry structure is. The electron population on the HOMO determines the IR vibrational frequency of the H bond, being blue-shift or red-shift. The complex prefers to be oxidized under the basic condition. The weak acidic environment is recommended to prevent the DNA mutation.

Two new compounds based on polyoxotungstate [Co₂(PCA)₄(H₂O)₆][SiW₁₂O₄₀]·8H₂O (1), [Cd₂(PCA)₄(H₂O)₆][SiW₁₂O₄₀]·8H₂O (2) (PCA = pyridine-4-carboxylic acid) are prepared and characterized by single crystal X-ray diffraction, elemental analysis, IR spectroscopy, and thermal analysis. The results of the single crystal X-ray diffraction analysis reveal that 1 and 2 are isomorphic and two water molecules in the compounds act as the bridging groups of two cobalt or cadmium atoms, forming dinuclear coordination cations. The ligand PCA adopts a monodentate coordination mode and its uncoordinated carboxyl oxygen atom and the protonized nitrogen atom form hydrogen bonds with other ligands, by which the cations are linked into a supramolecular 2D network with hexagonal grids. The polyoxotungstate anions are arranged above and below the cationic grids. A strong emission peak at 420 nm of 2 is attributed to a ligand-metal transition.

Thermal deformations and polymorphic transformations of even long chain monoclinic normal paraffins С₃₀Н₆₂ and С₃₂Н₆₆ (homological purity 97-99%) are studied. Thermal deformations and temperature limits of the existence of crystalline (1M_cryst and 2M_cryst), low-temperature rotationally crystalline triclinic (Tc_rot.1), monoclinic (M_rot.1), and orthorhombic (Or_rot.1) and high-temperature rotationally crystalline hexagonal (H_rot.2) phases of these n-paraffins are estimated by the character of changes in their diffraction patterns and unit cell parameters (thermal X-ray diffraction). The molecular structure and conformational composition of these n-paraffins in different phase states are determined (IR spectroscopy). In order to determine the temperatures of phase transitions differential scanning calorimetry is also applied. The data of all three methods are in good agreement with each other. The initial sample of С₃₀Н₆₂ n-paraffin at room temperature is characterized by a two-layer monoclinic 2M crystalline modification. When the melt is rapidly cooled, it crystallizes in monolayer monoclinic 1M and orthorhombic Or modifications (two-phase mixture 1M+Or). The initial sample of С₃₂Н₆₆ n-paraffin at room temperature is characterized by the monolayer monoclinic modification 1M. When the melt is rapidly cooled, as well as С₃₀Н₆₂ n-paraffin, it crystallizes in monolayer monoclinic 1M and orthorhombic Or modifications (two-phase mixture 1M+Or). It is found that both n-paraffin undergo irreversible polymorphic transformations from the crystalline state cryst to the low-temperature rotationally crystalline state rot.1. For С₃₀Н₆₂ n-paraffin the transition is performed by the scheme 2M_cryst → М_rot.1 → Or_rot.1, and for С₃₂Н₆₆ n-paraffin it is performed by the scheme 1M_cryst → Tc_rot.1. Both paraffins do not undergo the transition to the high-temperature rotationally crystalline state rot.2 (hexagonal phase H_rot.2), similarly to monoclinic С₂₈Н₅₈ n-paraffin studied previously. These and previously obtained data allow us to consider that as the molecular chain length increases, differences in the polymorphic modification of initial crystalline phases cease to be significant and the sequence of polymorphic transformations is mainly determined by the length of the molecule.

The experimental and theoretical study of self-assembly and gel formation processes in an aqueous solution of L-cysteine and silver nitrate (CSS) is performed. A method to obtain CSS-based hydrogel is described. Its characteristic feature is the formation of a spatial gel network at a low concentration of the dispersed phase (~0.01%) and the thixotropic behavior. The experimental examination of this system provides the formulation of a phenomenological model of the gel formation. Based on it, an atomistic computer model is made to verify our assumptions. It is shown that due to the formation of donor-acceptor sulfur-silver bonds there form clusters from silver mercaptide (SM) zwitterions, from which in turn filamentous aggregates form. An analysis of the molecular configurations formed shows that the filamentous aggregates are stabilized by the interaction of and -C(O)O^- groups belonging to SM zwitterions in the composition of the neighboring clusters. The obtained conclusions underlie the mesoscopic model based on which we managed to illustrate the processes of generation and growth of filamentous aggregates in large spatial scales.

The X-ray diffraction study of a single crystal with the composition NiTiF₆(Ur)₂·7H₂O is performed, where Ur = C₆H₁₂N₄ is an urotropine (hexamethylenetetramine) molecule. The compound crystallizes in the triclinic P-1 space group: a = 8.7220(5) Å, b = 9.1004(5) Å, c = 17.533(1) Å, α = 75.074(1)°, β = 88.530(1)°, γ = 62.558(1)°, Z = 2, d_x = 1.756 g/cm³, μ = 1.228 mm^-1, R = 0.0351. The crystalline compound is ionic. The structural unit consists of [Ni(OH₂)₆]²⁺ and [TiF₆]^2- ions and Ur and H₂O molecules. The structural formula of the compound is [Ni(OH₂)₆][TiF₆](Ur)₂·H₂O. Hydrogen bonds in the compound are studied and analyzed.

The features of the molecular and crystal structures of 4-bromo-2,2-dimethyl-5-oxy-6,6,7,7,8,8,9,9,9-nonafluorononan-3-one are determined by XRD.

The molecular structure of 1-phenyl-2-nitroguanidine is nonplanar, but contains two almost planar fragments: nitroguanyl and phenyl groups. Unlike previously studied nitroguanidines, in 1-phenyl-2-nitroguanidine, the nitro group is turned to the secondary amino group. However, the structural parameters of the nitroguanyl group are little different from those of nitroguanidine and its alkyl derivatives. In the benzene ring, the symmetry in the geometric parameters is not observed, which is explained by the intermolecular interaction with the neighboring molecule.