Home – Home – Jornals – Journal of Structural Chemistry 2011 number 5

Based on the previously proposed solution for the Schrödinger equation, which corresponds to the representation of a molecule as a dynamically stable geometric figure [1-3] and explicitly reflects the continuous correlation between electronic and nuclear motions with retaining the separation of variables, expressions for the matrix elements of the dipole transition are obtained. It is shown that the equation common for all states has the matrix form. The appearance of parameters having simple meanings and simultaneously affecting both vibrational and electronic components of the general wave function and electron vibrational energy levels is noted. This enables the statement and solution of the corresponding inverse spectral problems.

The results of the DFT studies of the band structure, Fermi surface, and chemical bond in ultrathin graphene/MnO(001) and MnO(001) films are presented, and the features of the interatomic interactions at the initial stage of the growth of graphene islands on the manganese oxide surface are considered. The features of spin state in the valence band and at the Fermi level in these systems are discussed. The magnetic moment on the Mn atom is estimated, and the effect of spin polarization on oxygen and carbon atoms is found. Their nature is discussed. Based on the structural energy calculations of 2D graphene/MnO(001) and 2D MnO(001), the stability of the systems is established, and the chemical bond energy is determined.

Lithium absorption in silicon is studied at the DFT level. By means of the developed method of modeling the structure of amorphous silicon, including with impurities, it is shown that with an increase in the lithium concentration intermediate amorphous Li_xSi_y phases, up to the crystalline Li₁₅Si₄ phase, form in crystalline silicon. An increase in the silicon cell volume, as it is filled with lithium, is calculated. A nonlinear dependence of silicon voltage on lithium intercalation is found. The lithium diffusion coefficient in crystalline silicon at a low lithium concentration is calculated and it is demonstrated for amorphous silicon that lithium diffusion is substantially accelerated by the lattice deformation inherent in amorphous silicon. The calculated values can be used in the production of high-capacity lithium ion batteries with a silicon anode.

The Са²⁺-regulated photoprotein obelin determines the luminescence of the marine hydroid Obelia longissima. Bioluminescence is initiated by calcium and appears as a result of the oxidative decarboxylation related to the coelenterazine substrate. The luciferase of the luminescent marine coral Renilla muelleri (RM) also uses coelenterazine as a substrate. However, three proteins are involved in the in vivo bioluminescence of these animals: luciferase, green fluorescent protein, and Са²⁺-regulated coelenterazine-binding protein (СВР). In fact, CBP that contains one strongly bound coelenterazine molecule is the RM luciferase substrate in the in vivo bioluminescent reaction. Coelenterazine becomes available for oxygen and the reaction with luciferase only after binding CBP with calcium ions. Unlike Са²⁺-regulated photoproteins, the coelenterazine molecule is not activated by oxygen in the CBP molecule. In this work, by means of quantum chemical methods the behavior of substrates in these proteins is analyzed. It is shown that coelenterazine can form different tautomers: CLZ(2H) and CLZ(7H). The formation of 2-hydroperoxy-coelenterazine is studied. According to the obtained data, these proteins use different forms of the substrates for the reaction. In obelin, the substrate is in the CLZ(2H) form that affords hydrogen peroxide. In RM, coelenterazine is in the CLZ(7H) form, and therefore, CBP is not activated by oxygen.

In a number of theoretical works, the cis-trans isomerization of bis(glycinato)copper(II) and its interaction with water molecules is investigated. The interactions with the water medium modeled either by adding water molecules explicitly or through the Polarized Continuum Model (PCM) are investigated by the density functional (B3LYP) method in order to question the reliability of theoretical results. The crucial dependence of theoretical energies on the accuracy of PCM corrections is established. It is shown that for bis(glycinato)copper(II) the differences of isomer energies are of the order of the upper limit of the reliability of PCM corrections. Based on the calculation results, two possible mechanisms for the cis-trans isomerization are proposed. It is shown that only the inclusion of two explicit water molecules enables the modeling of the isomerization mechanism involving the interchange of glycine and water oxygen atoms in copper coordination.

Based on the ³¹P NMR data, equilibriums in the [RuNO(NO₂)₄OHZn(TPPO)₃]-Py system are quantitatively described, and equilibrium constants of dissociation of the initial complex and organic ligand substitution are determined. The stability of heterometallic complexes is found to increase in passing from TPPO to pyridine. The mixed ligand [RuNO(NO₂)₄OHZn(TPPO)₂Py] complex is structurally characterized, and it is shown that the TPPO molecule in the trans-position to the μ₂-bridging hydroxo group is substituted first.

The forms and structure of comenic acid and its salts with Na⁺ and Li⁺ in solution and solid state are studied by multinuclear NMR spectroscopy. The formation of dimeric structures of comenic acid in the solid state is shown. It is found that disubstituted sodium and lithium salts have different structures.

A new ellipsometric method is proposed to measure adsorption in thin layers directly in a stream of vapors of volatile liquid and inert gas at atmospheric pressure. The method enables the determination of the main structural parameters of nano- and microporous materials: the average pore size, pore surface, size pore distribution, and the total porosity of sorbents. A procedure to find the Young modulus in nanoscale porous layers with the use of a spectroellipsometer is described.

A method to obtain previously unknown layered structure composed of stacks of perforated graphene sheets is developed. The method consists in the thermal decomposition of graphite oxide in the concentrated H₂SO₄ and H₃PO₄ medium. In order to confirm the presence of holes in graphene layers, a large set of chemical and physicochemical analysis methods are applied. Based on a new matrix, treated thermally and chemically, layered compounds are obtained: oxide, fluoride, and fluoroxide of two types. The obtained compounds are analyzed by transmission electron microscopy, infrared absorption spectroscopy, Raman spectroscopy, X-ray photoelectron spectroscopy, thermogravimetric analysis, and powder X-ray diffraction.

The diffusion of ammonia vapors to the magnesium/manganese/nickel nitrate solution results in the formation of their respective metal hydroxides, while the diffusion of ammonia vapors to copper and zinc nitrate solutions results in the crystallization of layered hydroxysalts. The PXRD patterns show that highly crystalline phases of samples are obtained. Infrared spectra were used to get information on the local coordination of ions. The thermogravimetric analysis justifies the phases concluded from powder X-ray diffraction and infrared spectroscopy. This clearly demonstrates that the crystal structure is mainly dictated by the nature of the metal ion, its site selectivity and specificity under identical synthesis conditions.

Crystal structures of [Со(NH₃)₅Cl]MoO₄ and [Со(NH₃)₅Cl]WO₄ complex salts are determined by single crystal X-ray diffraction. It is demonstrated for both salts that within the temperature range T = -123-20°C there is a negative thermal expansion (about 0.26%) towards the с axis of the orthorhombic unit cell (Pnma space group). Thermal properties of the salts are investigated. The phase composition of the products obtained on heating the salts in different gas atmospheres is studied.

The crystal structure of a double complex salt of the composition [Au(en)₂]₂[Cu(C₂O₄)₂]₃·8H₂O (en = ethylenediamine) at 150 K is determined by single crystal X-ray diffraction. The crystal data for C₂₀H₄₈Au₂Cu₃N₈O₃₂ are: a = 9.1761(3) Å, b = 16.9749(6) Å, c = 13.4475(5) Å, β = 104.333(1)°, V = 2029.43(12) ų, P2₁/c space group, Z = 2, d_x = 2.450 g/cm³. It is demonstrated that the thermal decomposition of the double complex salt in a helium or hydrogen atmosphere affords the solid solution Au_0.4Cu_0.6.

A new compound C₁₈H₂₂FN₃O·[CdBr₄]^2-·2H₂O, C₁₈H₂₀FN₃O₄-levofloxacin (LevoH) is synthesized and its crystal and molecular structure is determined. Crystallographic data for levofloxacindi-um cadmium tetrabromide dihydrate C₁₈H₂₆CdBr₄FN₃O₆ are as follows: a = 8.3815(8) Å, b = 27.318(3) Å, с = 12.066(1) Å, β = 107.105(1)°, V = 2640.5(4) ų, P2₁ space group, Z = 4. Hydrogen bonds form a branched three-dimensional network linking LevoH CdBr and water molecules. The structure is also stabilized by the π-π interaction of LevoHaromatic rings.

Two complexes [Zn(SALIMP)(CH₃CO₂)]₂ (1) and [Cu(SALIMP)Cl] (2) are obtained by the reactions of zinc(II) and copper(II) salts with a tridentate Schiff base ligand 2-[[(2-pyridinylmethyl)imino]methyl]phenol (HSALIMP). Their structure is determined by single crystal
X-ray diffraction. Data for complex 1: C₃₀H₂₈N₄O₆Zn₂, CCDC number: 668213, M_r = 671.3, monoclinic, C2/c, with a = 34.670(5) Å, b = 15.266(2) Å, c = 23.464(4) Å, β = 114.045(2)°, V = 11341(3) ų, Z = 16, F(000) = 5504, GOOF(F²) = 0.894, the final R = 0.0520 and wR =
= 0.1272 for 10515 observed reflections with I > 2σ(I); complex 2: C₁₃H₁₂N₂OClCu, CCDC number: 668211, M_r = 311.24, triclinic, P-1, with a = 7.4050(8) Å, b = 10.2369(11) Å, c = 16.2873(17) Å, α = 87.728(2)°, β = 87.818(2)°, γ = 78.279(2)°, V = 1207.4(2) ų, Z = 4, F(000) = 632, GOOF(F²) = 1.077, the final R = 0.0326 and wR = 0.0381 for 4209 observed reflections with I > 2σ(I).

The crystal and molecular structure of 2-ferrocenyl-2-propanol is studied by means of physicochemical methods. The compound crystallizes in the form of three crystallographically independent molecules with slightly different conformations. Crystals are monoclinic, C₁₃H₁₆FeO: a = 6.2687(7) Å, b = 36.614(4) Å, c = 15.291(2) Å; β = 97.86(2)°; V = 3477.2(7) ų, Z = 12, d_x = 1.396 g/cm³, P2₁/n space group. The molecule consists of the ferrocene fragment and the isopropyl carbinol substituent.

We present a thermogravimetric study of the thermolysis of trans-[Ru(NO)(NH₃)₄(H₂O)](HSO₄)SO₄ in a helium atmosphere. The intermediate product of thermolysis (at 186°C) is treated with a 2 M H₂SO₄ solution to obtain the first example of a sulfate ammine complex of nitrosoruthenium [Ru(NO)(NH₃)₄(SO₄)](HSO₄)·H₂O (I) with a ~70% yield. The product of higher temperature thermolysis (220°C) is treated with acids (H₂SO₄ and HCl) to obtain a triammine complex [Ru(NO)(NH₃)₃Cl(SO₄)]·2H₂O (II). The structure of the compounds is found by single crystal XRD: Pna2₁ space group, a = 10.8005(2) Å, b = 14.9032(3) Å, c = 7.7603(1) Å) (I) and P2₁/n space group, a = 8.9397(1) Å, b = 8.3276(1) Å, c = 13.8993(2) Å; β = 97.358(1)° (II).

A new 3-D europium sulfate Eu₂(H₂O)₄(SO₄)₃ 1 is synthesized solvothermally and characterized by single crystal X-ray diffraction, IR spectrum, TG, powder XRD, and ultraviolet excitation and emission spectrum. This compound crystallizes in the triclinic system with the space group P-1, a = 6.7520(9) Å, b = 9.1077(12) Å, c = 10.5910(14) Å, α = 94.432(2)°, β =
= 107.1170(10)°, γ = 99.160(2)°, V = 609.17(14) ų, Z = 2. The open framework of the title compound is an eight-membered ring channel along the crystallographic a-axis, which is built up by EuO₈ polyhedra and SO₄ tetrahedra.

The title compound 1′-Benzyl-8-(4-fluorobenzyl)-8-azaspiro[bicyclo[3.2.1] octane-3,4′-imidazolidine]-2′,5′-dione, C₂₃H₂₃FN₃O₂ is synthesized and the structure is investigated by X-ray diffraction studies. The compound crystallizes in the triclinic crystal class in the P1 space group. The hydantoin ring adopts a planar conformation and is affected by the π conjugation. The pyrrolidine and piperidine rings in the bicyclo octane moiety adopt envelope and chair conformations respectively. The structure exhibits both inter- and intramolecular hydrogen bonds of the type N-H…O, C-H…O, and C-H…N. The oxygen atom in the hydantoin ring simultaneously accepts two hydrogen bonds to form a three-centered hydrogen bonding pattern.

The phase diagram of the phloroglucinol (1,3,5-trioxybenzol)-dimethyl sulfoxide system is studied. The system is found to form a 1:1 molecular complex of phloroglucinol with dimethyl sulfoxide. The crystal structure of the complex is determined. The crystallographic data for C₈H₁₂O₄S, M = 204.24, monoclinic system, P2₁/n space group, unit cell parameters: a = 9.0345(2) Å, b = 9.6895(3) Å, c = 10.9960(3) Å, β = 98.865(1)°, V = 951.09(4) ų, Z = 4, d_x = 1.426 g/cm³, R1 = 0.0283, T = 150 K. The molecules are joined in a supramolecular ensemble via O-H⋯O hydrogen bonds.

FT-IR and photon correlation spectroscopy methods are used to study the distribution of free (bulk) and bound (hydration) water in Triton N-42 reverse micelles under the conditions of injection solubilization of hydrochloric acid solutions. The amount of each type of water is calculated depending on the solubilization capacity* (V_s /V_o) and HCl concentration in the aqueous pseudophase. According to the IR spectroscopy data, the distribution of water is largely determined by the solubilization capacity of the micellar solution, while the fraction of bulk water exceeds significantly the value calculated by the geometric approach based on the photon correlation spectroscopy data. The difference shows that there is bulk water in the surface layer formed by oxyethyl groups of Triton N-42 molecules in spherocylindrical micelles.

FT-IR spectroscopy is used to study the distribution of bulk (free) and hydration (bound) water during the extraction of Pt(IV) and Au(III) from acid sulfate-chloride media by Triton N-42 reverse micelles. The bulk water fraction in Triton N-42 micelles reduces from 44% to 23% with an increase in the sodium sulfate concentration up to 3.5 mol/l in the feed. A decrease in the total concentration of micellar water and bulk water fraction complies well with an increase in the Pt(IV) and Au(III) distribution coefficients and concentration during the extraction by Triton N-42 reverse micelles.

By X-ray diffraction the crystal and molecular structure of N-(1-silatranylmethyl)phthalimide (SMP) is determined. The coordination polyhedron of the silicon atom in SMP, as in all silatranes, is a trigonal bipyramide; the phthalimide cycle is planar. The data presented indicate that the silatranylmethyl group almost does not affect the geometry of the phthalimide moiety.

2-(4-chlorophenyl)-5,7-dimethoxyquinolin-4-yl phenyl bis(2-chloroethyl)phosphoramidate is synthesized and characterized by NMR, IR and single crystal X-ray crystallography. The crystal is triclinic, P1 space group, with a = 9.5188(19), b = 12.856(3), c = 13.250(3) Å, V =
= 1412.0(5) Å)³, and Z = 2 (at 291(2) K). The crystal packing arrangement indicates that the molecule is stacked through π…π aromatic stacking interactions.

A general approach to the solution of the electronic vibrational problem with imposed conditions on possible vibrational nuclear motions in a double-minimum potential well is proposed.

The quantum chemical (U)B3LYP/6-31G(d₅,p) method is used to determine the structural parameters and ionization potentials of aluminum(III) (μ-oxo)bis[phthalocyaninate] and monophthalocyaninate PcAlCl. Two (PcAl)₂O structures with similar energies are obtained: an eclipsed high-symmetry (D_4h) structure with a rectangular AlOAl group and a retarded low-symmetry (C_s) structure with the AlOAl bond angle of 167.5°. The AlO bonds include a substantial π component. The energy needed for the detachment of two electrons from a free (PcAl)₂O molecule is 13.46 eV.

Data of ¹³С NMR and quantum chemical methods is used to show that a change in the oxidation degree of 12-nuclear rhenium cluster complexes [Re₁₂CS₁₇(CN)₆]^n- from n = 6 to n = 8 leads to electron vacancy localization on the rhenium atoms surrounding the central carbon atom.

Two isostructural compounds (C₁₇H₂₂FN₃O₃)[MCl₄]·H₂O (M = Cd, Hg), C₁₇H₂₀FN₃O₃ is 1-ethyl-N-methyl-6-fluoride-1,4-dihydro-4-oxo-7-(4-methyl-1-piperazinyl)-3-quinoline carboxylic acid (PefH, pefloxacin), are synthesized and their crystal structure is determined. The crystals contain PefH₃²⁺ and MCL₄^2- ions. The neighboring [MCl₄]^2- ions are bonded together by two bridging water molecules through four Cl⋯(H-O-H)₂⋯Cl hydrogen bonds with the formation of the supramolecular motif R₂⁴(8) The supramolecular architecture of crystals is analyzed.

The cocrystallization method is used to obtain a new volatile heterometallic complex of the composition [Cu(ki)₂·Pb(hfa)₂]₂, where ki = 2-iminopentan-4-onate and hfa = hexafluoroacetylacetonate. The crystallographic data for C₂₀H₁₈CuF₁₂N₂O₆Pb: a = 10.6729(5) Å, b = 10.7712(5) Å, c = 13.4779(5) Å; α = 79.1020(10)°, β = 84.5140(10)°, γ = 66.2470(10)°, Р-1 space group, Z = 2, d_x = 2.102 g/cm³. The compound has a molecular structure built of individual Cu…Pb…Pb…Cu-type tetramers. The Cu…Pb and Pb…Pb distances in the tetramer are 3.454 Å and 4.122 Å respectively; the Cu-Pb-Pb angle is 160.7°.

The interaction of Ta₂O₅ with sodium hydroxide at 400°C yields Na₈[Ta₆O₁₉], which can be recrystallized from an aqueous solution in the form of Na₈[Ta₆O₁₉]·24.5H₂O. The complex is characterized by IR spectroscopy, thermogravimetry, powder XRD, and single crystal XRD: hexagonal system, P6₃ space group, a = 12.3622(2) Å, c = 31.4305(7) Å, V = 4159.81(13) ų, d_x = 3.217 g/cm³, R = 0.0195.

Two new linear Cu^II complexes [Cu(L¹)₂] (I) (HL¹ = (E)-3,5-dichloro-2-hydroxy benzaldehyde O-methyl oxime) and [Cu(L²)₂] (II) (HL² = (E)-3,5-dichloro-2-hydroxy benzaldehyde
O-ethyl oxime) are synthesized and characterized by elemental analysis, IR, UV-Vis, and
X-ray diffraction methods. X-ray crystallographic analyses indicate that complexes I and II have a similar structure consisting of one Cu^II ion and two L^- units. In the complexes, the Cu^II ion lying on an inversion centre is four-coordinated in a trans-CuN₂O₂ square planar geometry by two phenolate O and two oxime N atoms from two symmetry-related N,O-bidentate oxime-type ligands. However, the crystal structure of the two complexes is different: complex I forms an infinite three-dimensional supramolecular network structure through intermolecular hydrogen bonding and π⋯π interaction, while complex II forms an infinite one-dimensional supramolecular structure through intermolecular hydrogen bonds.

A mixed-ligand silver(I) complex of triphenylphosphine and N,N′-dibutylthiourea (Dbtu), [Ag(Ph₃P)₂(Dbtu)₂]NO₃, is prepared and its structure in the solid state is determined by X-ray crystallography. X-ray structure of this complex shows that it is mononuclear with the silver atom coordinated by two PPh₃ and two dibutylthiourea ligands adopting a distorted tetrahedral geometry. The crystal structure shows the formation of 1-D chains through intermolecular hydrogen bonding interactions between N-H of Dbtu and nitrate ions. The new complex is also characterized by IR and NMR (¹H and ³¹P) spectroscopy. The spectroscopic data are discussed in terms of the nature of bonding. A similar mixed-ligand complex is also prepared for tetramethylthiourea (Tmtu), but the structure of the resulting compound shows that it is a bis(phosphine) complex, [Ag(PPh₃)₂NO₃] rather than a mixed-ligand complex.

The molecular and crystal structure of methyl 1-isopropenyl-5a,5b,8,8,14a-pentamethyl-1,2,3,3a,4,5,5a,5b, 6,7,7a,8,9,14,14a,14b,15,16,16a,16b-icosahydrocyclopenta-[7,8]phenenthro[2,1-b]carbazole-3a-carboxylate is determined. Compound C₃₇H₅₁NO₂ II crystallizes in the C2 chiral space group: a = 27.0380(5) Å, b = 7.9817(15) Å, c = 18.1980(3) Å, β = 123.580(3)°.

The complex of 2-ethylthio-4,5-benzo-1,3-thiazole with CoCl₂ of the 2:1 composition is synthesized. By X-ray diffraction, its crystal and molecular structure is determined. The coordination polyhedron of the cobalt atom is a tetrahedron formed from two chlorine and two nitrogen atoms. The nitrogen atoms belong to two ligand conformations of the studied complex

The composition of the coordination polyhedron of the complex of copper(II) acetate with 2-[2-hydroxyphenyl]-4,4-diphenyl-1,2-dihydro-4H-3,1-benzoxazine in the solid state and solutions of ethanol and chloroform is studied. Using the angular overlap model, the interaction energy of the copper(II) ion with donor atoms of the ligand is calculated. The temperature dependence of the molar magnetic susceptibility (χ_М) of the complex in the solid state is studied; the occurrence of the exchange interaction of the antiferromagnetic type between two copper ions is found (2J = -57.8 cm^-1).

The adduct of 2-aminobenzothiazole (1) and 2-hydroxy-3-naphthoic acid (2) is synthesized by the normal temperature volatilization method. The crystal belongs to the monoclinic system, P2₁/c space group. It crystallizes with two independent molecules in the unit, the two independent molecules forming helices through hydrogen bonds. The luminescence property of 1, 2, and the adduct (1·2) were studied at room temperature.