Home – Home – Jornals – Journal of Structural Chemistry 2013 number 5

The action of a strong electric field on conjugated π-systems is studied within the method of full configuration interaction. The behavior of systems in the field is analyzed by means of the electron unpairing measure: the number N_eff of effectively unpaired electrons. For N_eff formal asymptotic rules are derived, which correspond to extreme values of the external field. Field induced biradicaloid π-states are studied in detail.

The phonon spectra of a series of А²В⁴С⁵₂ and А¹В³С⁶₂ crystals with the chalcopyrite structure are calculated in the Keating model in the basis set of polarization vectors of their sublattices. The dependences of frequency values and partial contributions of sublattices to the polarization vectors on the chemical composition are studied. The effect of the mass ratio and the strengths of covalent bonds between the compound components on the phonon spectrum formation is found.

The adsorption of CO and C₂H₂ molecules on the perfect basal surface of graphite is investigated by adopting cluster models in conjunction with quantum chemical calculations. The noncovalent interaction potential energy curves for three different orientations of CO and C₂H₂ molecules with respect to the inert basal plane of graphite are calculated via semi-empirical and Möller-Plesset ab initio methods. Then, we have considered the effects of interaction energies on the C≡O and C≡C bond lengths by performing the partial geometry optimization procedure on the CO-graphite and C₂H₂-graphite systems in various intermolecular distances. The computational analysis of all physical noncovalent potential energy curves reveals that the relative configurations in which CO and C₂H₂ molecules approach the graphite sheet from out of the plane have stronger interaction energy and so is more favorable from the energetic viewpoint. This means that the graphite layer prefers to increase its thickness via the chemical vapor deposition of CO and C₂H₂ on the graphite.

Within DFT (B3LYP) methods the potential surface of the interaction between 1-iodopropan-2-one and 1,2,3-benzotriazole resulting in the formation of 1,3-bis(2-oxopropyl)-3Н-1,2,3-benzotriazolium triiodide is studied. A mechanism consisting of four steps (N-1-alkylation of 1,2,3-benzotriazole, elimination of molecular iodine during partial reduction of 1-iodopropan-2-one with hydrogen iodide, formation of the triiodide structure, and formation of 1,3-bis(2-oxopropyl)-3Н-1,2,3-benzotriazolium) is proposed. Thermodynamic and kinetic parameters of these steps are obtained.

The molecular structure of chromium and cobalt tris-acetylacetonates is studied by the synchronous electron diffraction and mass spectrometric experiment and quantum chemically. It is found that molecules have the D₃ symmetry with internuclear distances r_h1(Cr–O) = 1.960(4) Å and r_h1(Co–O) = 1.893(4) Å. Quantum chemical calculations by the DFT methods with different basis sets yield a structure well consistent with that found in the experiment. Changes in the structural parameters of chromium and cobalt b-diketonate complexes whose ligands differ in –CH₃, –C(CH₃)₃, –CF₃ substituents are considered.

The ferromagnetic resonance (FMR) method in situ is used to study the initial stages of the formation of ε iron oxide nanoparticles deposited on silica gel at temperatures up to 600°C. It is shown that at high-temperature treatment of starting samples obtained by impregnation with an iron(II) sulfate solution, supermagnetic ε-Fe₂O₃/SiO₂ nanoparticles form with a narrow size distribution. An analysis of the FMR data in comparison with the data of other methods enables the formulation of the formation conditions for systems of deposited ε-Fe₂O₃ nanoparticles without other polymorph impurities.

Single crystal XRD is used to determine the structures of the complexes (H₂TMEDA)[Mg(ptac)₃]₂ (1, TMEDA = Me₂N(CH₂)₂NMe₂, ptac = ^tBuCOCHCOCF₃) and (H₂TMEDA)[Mg(hfac)₃](hfac) (2, hfac = CF₃COCHCOCF₃) at a temperature of 150 K. The crystallographic data for complex 1: a = 10.2919(3) Å, b = 10.9492(4) Å, c = 15.4159(6) Å, α = 87.117(1)°, β = 89.686(1)°, γ = 79,864(1)°, space group Z = 1, R = 0.0573; for complex 2: a = 12.9446(2) Å, b = 23.0035(4) Å, c = 13.1473(3) Å, α = 90°, β = 98.779(1)°, γ = 90°, space group P2₁/n, Z = 4, R = 0.0605. The structures are ionic; the metal atom coordinates six oxygen atoms of three β-diketonate ligands. The distances Mg–O in complex 1 are in the range 2.036(2)-2.0920(19) Å; the same distances in complex 2 are in the range 2.051(2)-2.076(2) Å. The spatial packing is determined by the system of hydrogen bonds between the (H₂TMEDA)²⁺ cations and [Mg(ptac)₃]^– (1) or hfac^– (2) anions. A thermogravimetric study of complex 1 is carried out.

The structure of supports (ceria and zirconia) for supported copper catalysts for the processes of hydrogen obtaining and purification is studied. The formation features of the structure of zirconia annealed at 300-1000°C are identified at different levels: the atomic one and the level of the structural arrangement of secondary particles when the formation of agglomerated block structures with large number of grain interfaces occurs. The formation process of copper oxides on different supports is studied.

N1s and O1s X-ray photoelectron spectra of stable nitroxyl radicals (substituted piperidine-1-oxyl, 2-imidazoline-1-oxyl, and 2-imidazoline-3-oxide-1-oxyl) and also diamagnetic derivatives with a {ONCNO} fragment are measured. It is shown that the structure of N1s and O1s X-ray photoelectron spectra of nitroxyls is determined by charge transfer processes between different parts of the molecule to screen the X-ray hole and the spin-spin interaction of unpaired electrons on the HOMO and 1s level.

An X-ray photoelectron and X-ray emission study of the charge state of thiacalix[4]arenes is performed with a comparison with the data of quantum chemical calculations. Relaxation corrections between the Kohn–Sham orbital energies calculated by the DFT method and experimental parameters of the X-ray emission and photoelectron spectra of the studied compounds are estimated. It is shown that the formation of a cyclic aromatic system in thiacalixarenes results in a decrease in the energy of orbitals involving р–π interactions of the bridging sulfur atoms and aromatic moieties, which determines the features of the X-ray emission spectra of the studied compounds.

In the samples of the Na₂MoO₄–MgMoO₄ system quenched in the air at above 600°C, by powder X‑ray diffraction two double molybdates of variable composition are detected: monoclinic alluaudite-like Na_4–2xMg_1+x(MoO₄)₃ (0.05 ≤ x ≤ 0.35) and triclinic Na_{2–2 y}Mg_2+y(MoO₄)₃ (0.10 ≤ y ≤ 0.40) isostructural to previously studied Na₂Mg₅(MoO₄)₆. Sodium-magnesium molybdate of the Li₃Fe(MoO₄)₃ structure type is not revealed in this system. By spontaneous flux crystallization, the crystals are obtained and the structures of two triclinic double molybdates of the Na₂Mg₅(MoO₄)₆ structure type (space group P1, Z = 1) containing magnesium and manganese are determined. The results of the refinement of site occupancies made it possible to determine the composition of the studied crystals: for the compound with magnesium (Na)_0.5(Na_0.25⟩_0.75)(Na_0.75Mg _0.25)Mg₂(MoO₄)₃ or Na_1.50Mg_2.25(MoO₄)₃ (a = 6.9577(1) Å, b = 8.6330(2) Å, c = 10.2571(2) Å, α = 106.933(1)°, β = 104.864(1)°, γ = 103.453(1)°, R = 0.0188); for the compound with manganese (Na)_0.5(Na_0.32⟩_0.68)(Na_0.82Mn_0.18)Mn₂(MoO₄)₃ or Na _1.64Mn_2.18(MoO₄)₃ (a = 7.0778(2) Å, b = 8.8115(2) Å, c = 10.4256(2) Å, α = 106.521(1)°, β = 105.639(3)°, γ = 103.233(1)°, R = 0.0175). The Na₂Mg₅(MoO₄)₆ structure is redetermined and it is shown that actually it corresponds to the composition Na_1.40Mg_2.30(MoO₄)₃.

A new azido-coordinated nickel(II) complex [NiL¹(N₃)] (1) and a new thiocyanato-coordinated nickel(II) complex [NiL²(NCS)] (2), where L¹ and L² are the monoanionic forms of Schiff bases 2-[(2-isopropylaminoethylimino)methyl]-6-methylphenol and 2-[(2-dimethlaminoethylimino)methyl]-6-methylphenol respectively, are prepared and structurally characterized by elemental analysis, IR spectra, and single crystal X-ray crystallography. Complex 1 crystallizes in the triclinic space group P-1 with unit cell dimensions a = 8.812(2) Å, b = 9.433(3) Å, c = 9.488(2) Å, α = 81.933(2)°, β = 69.925(2)°, γ = 84.591(2)°, V = 732.5(3) ų, Z = 2, R₁ = 0.0291, and wR₂ = 0.0734. Complex 2 crystallizes in the monoclinic space group P2₁/n with unit cell dimensions a = 7.4497(4) Å, b = 6.1933(3) Å, c = 31.5126(18) Å, β = 92.484(2)°, V = 1452.57(13) ų, Z = 4, R₁ = 0.0307, and wR₂ = 0.0668. The Ni atom in each of the complexes is coordinated by three donor atoms of the Schiff base ligand and by one N atom of the azide or thiocyanate ligand, forming a square planar geometry. The azide and thiocyanate anions readily coordinate to the complexes as secondary ligands.

X-ray crystallographic analysis is used to determine the crystal structures of [Ru(NH₃)₆](MoO₄)Cl×3H₂O and [М(NH₃)₆](ReO₄)₃×2H₂O (M = Ru, Ir) complex salts. The features of the fragment packing are studied.

Complex rhodium(III) salts with the composition trans-М[Rh(NH₃)₂(NO₂)₄], where М = K⁺, Cs⁺, Ag⁺, and N(CH₃)₄⁺, are prepared and characterized. The molecular and crystal structures are determined by X-ray crystallography.

A coordination polymer {[Cu(C₁₁H₂₀N₄O₂)₂(H₂O)]²⁺×2(NO₃^–)}_n (I) is synthesized and analyzed using single-crystal XRD. The crystals are monoclinic: space group P2/c, a = 12.5237(6) Å, b = 7.3310(3) Å, c = 16.8926(8) Å, β = 92.569(4)°, V = 1549.38(13) ų, r_calc = 1.47 g/cm³, and Z = 2. The copper atom is in a special position in the second-order axis. The coordination polyhedron of the metal is a trigonal bipyramid. In the axial direction, it is coordinated by two oxygen atoms O(1) of the organic ligand molecules connected by the symmetry operation [–x, y, 0.5–z]; the angle O(1)Cu(1)O(1)ⁱ is 175.16(15)°. In the equatorial direction, the copper atom is coordinated by oxygen atoms O(2) of two ligand molecules connected with the reference molecule by the symmetry operations [–x, y, 0.5–z] and [x, 1–y, –0.5+z] and the water molecule О(6) in a special position on the twofold axis. The OCuO angles between the equatorial oxygen atoms are 96.80(16)-131.60(8)°, and those between the axial and equatorial atoms are 87.58(8)-91.60(10)°. It is noteworthy that the length of the Cu–O(1) bond (1.955(2) Å) with the axial carbonyl oxygen atom is somewhat shorter than the bond (2.060(3) Å) with the equatorial atom. Nitrate anions are outside the coordination sphere of the metal. The Cu…Cu distance in the polymer is 8.33 Å. To confirm the purity of the sample of I, the powder X-ray pattern is refined by the Rietveld method; the lattice parameters at room temperature are: a = 12.535(4) Å, b = 7.3161(13) Å, c = 16.841(5) Å, β = 92.11(2)°, and V = 1543.4(7) ų.

1'-Phthalazinylhydrazones of salicylaldehyde, its substituted derivatives, and 2-diphenylphosphinebenzaldehyde are synthesized and studied. A description is given of the structures salicylaldehyde 1'-phthalazinylhydrazone (1а) and 2-diphenylphosphinebenzaldehyde 1'-phthalazinylhydrazone (2), which exist in the crystal in the hydrazonophthalazone tautomeric form. Molecules of hydrazone 1а form in the crystal infinite stacks of hydrogen bonded dimers with intermolecular π-stacking interactions. A quantum chemical calculation is made of the geometry and total energy of the possible tautomers in vacuum and in aqueous and chloroform solutions. The hydrazonophthalazone tautomers are shown to be the most stable in all cases. The X-ray crystallography results are compared with the calculated data.

By quantum chemical DFT M06-2X/6-31G(d,p) method, the equilibrium parameters of rigid and stable hydrocarbon clusters of icosahedral symmetry with a dodecahedron structure whose sites are occupied by 20 adamant-1,3,5-triyl moieties linked with each other either directly or through bridges containing two or four carbon atoms are determined. The radius of the smallest studied quasispherical molecules is 1.05 nm and that of the largest one is 1.76 nm. The radius of the inner cavity in them varies from 0.37 nm (C₂₀₀H₂₆₀) to 1.06 nm (C₃₂₀H₂₆₀). Perfluorination increases the outer and decreases the inner radius of super dodecahedrane.

In the structure of Tl₂S, the pseudo translational sublattice of Tl and S atoms with a rhombohedral primitive subcell a_P = 3.09 Å, α_P = 81.87° is determined. As opposed to the common PbS structure type, in which single (close-packed) layers of cations and anions alternate, in the structure of Tl₂S, there is an alternation of double cationic layers with single anionic layer, while the general geometry of atomic positions (skeleton) of the PbS structure type is retained. Therewith, the atoms of a part of cationic layers occupy the atomic sites of the anionic layers and vice versa.

The crystal structure of catena-di(μ₂-2-thiobarbiturato-O,S)aqualead(II) C₈H₈N₄O₅S₂Pb (C₄H₄N₂O₂S is 2-thiobarbituric acid, H₂TBA) is determined. Crystallographic data for catena-[Pb(H₂O)(μ₂-HTBA-O,S)₂] are as follows: a = 6.5972(1) Å, b = 9.8917(2) Å, c = 10.0893(2) Å, α = 106.702(1)°, β = 93.395(2)°, γ = 107.48(1)°, V = 593.82(2) ų, space group P1, Z = 2. The Pb²⁺ ion is linked with six monodentate HTBA ⁻ ligands through two O atoms and four S atoms and also connected with a water molecule. Additionally, there is a shortened Pb–S contact (3.622 Å), given which the complex polyhedron represents a distorted square antiprism. Hydrogen bonds N–H⋯O and O–H⋯O form a branched three-dimensional network. The structure is also stabilized by the π–π-interaction of heterocyclic HTBA⁻ ions.

A novel Zn(II) coordination polymer [Zn₂(phen)₂]L₄×3H₂O(1) is synthesized by the reaction of Zn(NO₃)₂, Phen(1,10-phenanthroline), and L(2-mercaptonicotinic acid) at room temperature and structurally characterized by X-ray single crystal diffraction along with IR spectra and elemental analysis. Title complex 1 belongs to the triclinic system with the space group ( P-1), a = 10.9373(11) Å, b = 11.6201(12) Å, c = 13.1371(14) Å; α = 116.100(1)°, β = 97.717(2)°, γ = 108.652(2)°, V = 1344.4(2) ų; Z = 2, ρ_calcd = 1.596 g×cm^–3, F(000) = 664, R₁ = 0.0708 and wR₂ = 0.1823 independent reflections for 18523 observed ones (I > 2σ(I)), and the zinc atom is rendered five-coordinated in a distorted tetragonal pyramid coordination geometry by two nitrogen atoms from the phen molecule, two oxygen atoms from two L molecules, and an oxygen atom from the H₂O molecule. Complex 1 forms a 1D chain by O—H⋯O hydrogen bonds from free-water, while the 2D layer structure is formed by C—H⋯O hydrogen bonds through the L ligand of adjacent chains. These compounds further result in a 3D network structure by the intermolecular π⋯π stacking interaction of the neighbouring layers.

A novel coordination polymer constructed with [Co(3,3'-bpbc)(H₂O)₃]×H₂O(I) (3,3'-bpbc = 2,2'-bipyridine-3,3'-dicarboxylic acid) is successfully synthesized at room temperature and characterized by elemental analysis and IR spectra. The crystal structure of the complex is determined by single crystal X-ray diffraction. The unit cell parameters for complex I are: a = 9.9606(11) Å, b = 9.2552(10) Å, c = 16.0258(17) Å, β = 96.731(0)°, V = 1467.2(3) ų, Z = 4, space group P2(1)/n. In the crystal, the cobalt(II) ion adopts a hexa-coordinate environment, and the structure units aggregate together to give birth to infinite 1D chains. The 2D and 3D framework is constructed via intermolecular hydrogen bonds.

A new compound of 6-ferrocenyl-3-phenyl-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole is synthesized and its single crystal structure is determined by X-ray diffraction method. The compound belongs to the monoclinic P2₁/c space group with cell parameters: a = 10.5523(12) Å, b = 13.8414(16) Å, c = 11.4303(13) Å, V = 1603.5(3) ų.

The crystal structure of tetra(m-acetato)-bis{[1-ethyl-3-(pyridine-2-yl)carbamide]copper} Cu₂(L)₂(CH₃COO)₄ (I), where L is 1-ethyl-3-(pyridine-2-yl)carbamide, is determined. The asymmetric unit cell of the crystal structure of I contains a copper complex with two acetate ions and a monodentate molecule of 1-ethyl-3-(pyridine-2-yl)carbamide, which is coordinated via the pyridine nitrogen atom. Due to the symmetry center, binuclear complexes form in the crystal, in which the acetate ions act as bridges between the metal atoms. In them, the coordination polyhedron of the central copper atoms represents an almost ideal tetragonal pyramid. Its base is formed from the oxygen atoms of acetate ions. In the crystal of the binuclear complex, hydrogen bonds form between the acetate ions and the L ligand along with an intramolecular hydrogen bond, which stabilize the conformation of the organic L molecule. Between the neighboring complexes in the crystal, the van der Waals interaction occurs.

A reaction between caffeine (caff) and dipicolinic acid = 2,6-pyridine dicarboxylic acid (pydc.H ₂) in water results in the formation of a cocrystal compound (pydc.H₂.H₂O)(caff) 1. The characterization of the resulting crystallohydrate is performed using ¹H, ¹³C NMR and IR spectroscopy and X-ray crystallography. X-ray crystal structure analysis reveals the presence of both starting materials and water in the lattice. It also indicates intensive intermolecular H-bonding interactions between carboxylic acid, caffeine, and water as well as π—π stacking between the pydc.H₂ and caff rings as constituents of the cocrystal. The hydrogen bonding and non-covalent interactions play roles in the formation of the cocrystal. The crystal system is triclinic with the space group P- 1 and two formula units per unit cell. The unit cell parameters are a = 6.906(2) Å, b = 8.451(3) Å, c = 14.68 (4) Å with α = 81.51(3°), β = 78.47(3°), and γ = 78.14(3°). The final R value is 0.0660 for 7943 measured reflections.