Fragment calculation of electronic structures of polyatomic molecules in the ground state. I. A method of intermediate fragment

A method is proposed for fragment calculation of electronic structures of polyatomic molecules in the ground state. The wave function of a molecule in the ground state in single-determinantal representation of a closed shell is employed. The concise formulation allows efficient calculation of the electronic structures of polyatomic molecules taking into account possible charge transfer between interacting molecular fragments. V.I. Vernadskii Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences. Translated fromZhurnal Struktumoi Khimii, Vol. 36, No. 3, pp. 387–394, May–June, 1995. Translated by I. Izvekova     

Parametric method for computing the structure of the excited states and the vibronic spectra of complex molecules. Absorption and fluorescence spectra of perylene

The structures of the perylene molecule in the first excited 1¹ 0B_2u state and the band shape (vibrational structure) of its fluorescence and absorption spectra are computed by the parametric method. A fragmentary approach and the molecular fragments H/1C= with the parameters obtained for acenes and polyenes are used to form molecular models in the excited state. It is shown that a model that corresponds to the choice of fragments with the parameters of acenes is the most optimal. The theoretical spectra satisfactorily reproduce both qualitatively and quantitatively, the basic specific features of the vibrational structure of the experimental spectra. Calculation results show high degree of transfer of the parameters of the method in a series of related molecules not only for acenes with “linear” arrangement of the rings (benzene, naphthalene, anthracene, etc.) but also for more complex structures (perylene). It is shown that the parametric method developed is efficient for predicting the vibronic spectra and the structure of the excited states of complex molecules. Translated fromZhurnal Struktumoi Khimii, Vol.40, No. 2, pp. 242–250, March–April, 1999.     

Fast atom bombardment mass spectrometric (FAB MS) study of the molecular structure of DI-Μ-guanino-Μ-guanine BIS(CIS-Chlorodiammineplatinum(II))

A new compound of cis-chlorodiammineplatinum(II) with normal and deprotonated guanine has been synthesized and studied by FAB MS. The compound has a molecular structure of a binuclear complex. The mass spectrometric behavior of the complex is dictated by the variable valence of platinum and chemical ionization of fragments by protons, as well as by the fact that the guanine molecule bridges the two cis-PtCl(NH₃)₂ groups by its N7 and OC6 atoms and the two gpanine anions bridge the groups by their N1 and OC6 atoms. The differences in the mutual arrangement of the anions and the guanine molecule are responsible for the formation of the head-to-head and head-to-tail structural isomers. Translated fromZhurnal Strukturnoi Khimii, Vol. 38, No. 3, pp. 503–510, May–June, 1997.     

A Central Partition of Molecular Conformational Space. III. Combinatorial Determination of the Volume Spanned by a Molecular System

In the first work of this series (Gabarro-Arpa, Comp. Biol. Chem. 27 (2003) 153–159) it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the space into a hierarchical set of cells that can be encoded by the face lattice poset of the arrangement. The model however, lacked explicit rotational symmetry, which made impossible to distinguish rotated structures in conformational space. This problem was solved in a second work (Gabarro-Arpa, Proc. 26th Ann. Int. Conf. of the IEEE EMBS (San Franciso, 2004) 3007–3010) by sorting the elementary 3-dimensional components of the molecular system into a set of morphological classes that can be properly oriented in a standard 3-D reference frame. This also made possible to find a solution to the problem that is being addressed in the present work: for a molecular system immersed in a heat bath we want to enumerate the subset of cells in conformational space that are visited by the molecule in its thermal wandering. If each visited cell is a vertex on a graph with edges to the adjacent cells, here it is explained how such graph can be built.     

Parametric method in the theory of vibronic spectra of complex molecules. Excited state structure and fluorescence spectrum of stilbene

The parameters of the adiabatic model of the stilbene molecule in the excited state and the vibrational structure of the fluorescence spectrum are calculated by the parametric method of the theory of vibronic spectra of complex molecules. The first and second orders of theory are used. The molecular models are constructed by the fragment method. Satisfactory agreement with experiment is obtained. The parameters of molecular fragments are shown to be highly transferable. The model and the spectrum max be refined in the second order of theory using only one additional parameter for CCC angles (optimal values were obtained). The parametric method under discussion makes it possible to predict variations of structural parameters due to excitation and to calculate the vibrational structure of the electronic spectra of complex molecules, including characteristic variations of the spectra in series of related molecules (stilbene-di-phenylpolyenes). This method surpasses all previous procedures (in particular, the correlation method) in completeness and accuracy of results. Translated fromZhurnal Strukturnoi Khinii, Vol. 41, No. 2, pp. 369–378, March–April, 2000.     

Fragment calculation of electronic structures of polyatomic molecules in the ground state. II. A method of delocalized states of fragments

A fragment method is proposed to calculate the electronic structures of polyatomic molecules in the ground state. Localization and delocalization of the electronic states of molecular fragments are calculated simultaneously. The compact formulation of the method allows algorithmically efficient calculations of the electronic structures of interacting molecular fragments as well as of the whole molecules. V. I. Vernadskii Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences. Translated fromZhurnal Struktumoi Khimii, Vol. 36, No. 3, pp. 395–400, May–June, 1995. Translated by I. Izvekova     

Syntheses,crystal structures,and properties of two molecular double-supporting polyoxotungstates

Two molecular double-supporting polyoxotungstates [SiW₁₂O₄₀{M(phen)₂H₂O}₂] · nH₂O (phen = 1,10′-phenanthroline, M = Mn 1, n = 2; M = Co 2, n = 3) were synthesized hydrothermally and characterized by elemental analyses, IR, TG, and X-ray single-crystal diffraction. The variable-temperature magnetic susceptibilities were measured at 2–300 K. The double-supporting polyoxotungstate molecule consists of a Keggin-type dodecatungstosilicate anion and a pair of transition metal complex fragments which are covalently linked to opposite sides of the Keggin anion. The transition metal ion locates in the center of a distorted octahedron. Multiple H-bonding interactions are observed between the coordinated waters of the transition metal complex fragments and terminal oxygen atoms of Keggin units and also between the bridging oxygen atoms of Keggin units and the lattice waters, which creates one-dimensional chains or two-dimensional layers. Between the layers or chains there are weak CH···O hydrogen bonding interactions and van der Waals forces. The molecular double-supporting polyoxotungstosilicate begins to decompose at ca. 500 °C. The variable-temperature magnetic behavior of 1 shows weak antiferromagnetic characteristics with a small value of θ = −0.289 K.     

Structure-guided fragment-based<Emphasis Type="Italic"> in silico</Emphasis> drug design of dengue protease inhibitors

An in silico fragment-based drug design approach was devised and applied towards the identification of small molecule inhibitors of the dengue virus (DENV) NS2B-NS3 protease. Currently, no DENV protease co-crystal structure with bound inhibitor and fully formed substrate binding site is available. Therefore a homology model of DENV NS2B-NS3 protease was generated employing a multiple template spatial restraints method and used for structure-based design. A library of molecular fragments was derived from the ZINC screening database with help of the retrosynthetic combinatorial analysis procedure (RECAP). 150,000 molecular fragments were docked to the DENV protease homology model and the docking poses were rescored using a target-specific scoring function. High scoring fragments were assembled to small molecule candidates by an implicit linking cascade. The cascade included substructure searching and structural filters focusing on interactions with the S1 and S2 pockets of the protease. The chemical space adjacent to the promising candidates was further explored by neighborhood searching. A total of 23 compounds were tested experimentally and two compounds were discovered to inhibit dengue protease (IC₅₀ = 7.7 μM and 37.9 μM, respectively) and the related West Nile virus protease (IC₅₀ = 6.3 μM and 39.0 μM, respectively). This study demonstrates the successful application of a structure-guided fragment-based in silico drug design approach for dengue protease inhibitors providing straightforward hit generation using a combination of homology modeling, fragment docking, chemical similarity and structural filters.     

Crystal and molecular structure of (1S,2S,4aS, 8aS)-N-(N-allyldiaminomethanethione)-1-(2-hydroxy-2,5,5,8a-tetramethyldecahydronaphthalenyl) acetamide

Crystal and molecular structure of a new homodrimanic compound (1S,2S,4aS, 8aS)-N-(N-allyldiaminomethanethione)-1-(2-hydroxy-2,5,5,8a-tetramethyldecahydronaphthalenyl) acetamide has been determined by X-ray diffraction analysis. The crystal is monoclinic, unit cell parameters are: a = 9.577(2) Å, b = 7.414(1) Å, c = 16.856(3) Å; β = 94.83(3)°, space group P2₁, Z = 2, of composition C₂₀H₃₅N₃O₂S. Two cyclohexan fragments have ordinary structure and chair-configuration typical of this compound class in homodrimanic skeleton. Ethanol molecule is located in the outer sphere. The withdrawal of carbon atoms from planar fragments of cyclohexan rings varies within the limits from 0.722(5) Å to − 0.634(5) Å. A dihedral angle between the mean-square planes of the latter equals 16.0(2)°, torsion angle (5)-(5)-(10)-(16) 171.0(1)° indicates their trans-joint. In the side non linear chain allyl group is connected to terminal nitrogen atom of thiosemicarbazide molecule. Intermolecular hydrogen bonds between carbonyl atom of acetamide fragment, ethanol molecule, and donor-acceptor groups of thiosemicarbazide moiety play the main part in crystal structure organization. Original Russian Text Copyright ? 2005 by E. P. Styngach, S. T. Malinovskii, L. P. Bets, L. A. Vlad, M. Gdanets, and F. Z. Makaev __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 46, No. 4, pp.785–789, July–August, 2005.     

Computational modeling of amorphous silica. 3. Modeling the initial structures. Silica gel

A qualitative algorithm for construction of large clusters of silica gel model structures is used. According to this algorithm and in line with our classification of dispersive silicas, silica gel is regarded as cyclosilica, which is characterized by loose packing of the cycles of silicon-oxygen tetrahedra. A model of silica gel structure is proposed, where the primary structural fragments are hollow frameworks with a network surface. The units of the surface network are formed by nonplanar [SiO₄] chain cycles of various sizes. This structural model makes it possible to explain the peculiarities of the vibration spectra of the framework, hydroxyl, and aqueous components of silica gels. Institute of Surface Chemistry, Ukrainian Academy of Sciences. Russian University of Peoples' Friendship. Translated fromZhurnal Strukturnoi Khimii, Vol. 35, No. 3, pp. 27–34, May–June, 1994. Translated by O. Kharlamova     

Structural data representation and search for structural analogs in molecular spectroscopy databases

A method for encoding structural formulas of organic compounds using two varieties of the tree code is suggested. The tree code is a sequence of symbols, each corresponding to an edge of a molecular graph traced around in width or in depth. The deep tree code provides compact storage of structural formulas and rapid substructure search. The wide tree code is a basis for a structure collection classifier providing quick access to structurally related compounds. Three techniques for selecting structural analogs of the compound using the classifier are proposed. Databases on mass and¹³C NMR spectra serve as illustrations. Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 6, pp. 1129–1139, November–December, 1996. Translated by L. Smolina     

EPMA and X-Ray Diffraction of the Degraded Fuel Bundle from the Phebus FPT1 Test

 The degraded fuel rod bundle from the second Phebus test (FPT1) was examined at ITU, Karlsruhe. Metallographic and microprobe analysis of the degraded fuel pieces were carried out. The fuel samples from the upper bundle and cavity edge were porous and had remnants of thick oxidised cladding adhering to them. Electron microprobe analysis line scans across the cladding-fuel interface showed interdiffusion of U and Zr, with U diffusing down the grain boundaries of the oxidised cladding, while point analyses revealed noticeable amounts of Zr (1.5–4.2 wt%) in the UO₂ fuel. EPMA oxygen measurements revealed in the upper part of the bundle a superstoichiometry of x = 0.3–0.4 in UO _2 + x , indicating that fuel fragments in this position had undergone considerable oxidation. X-ray diffraction of the corium pool disclosed a deformed cubic fluorite lattice of UO₂. The lattice parameter of a = 5.2984 ? was considerably reduced compared with pure, stoichiometric UO₂ and was consistent with a lattice containing approximately 45 mol% ZrO₂ that had undergone little oxidation. The corium’s nominal composition of (U_0.5Zr_0.5) O₂ also corresponded to its observed single phase microstructure.     

Synthesis and properties of a novel photochromic luminophore

A photochemically bifunctional compound was obtained. Its molecule includes the spironaphthoxazine and dansylamino fragments. This compound exhibits both photochromic and luminescent properties. Its spectroscopic characteristics were studied in different solvents. The electronic systems of two constituent fragments do not interact with each other. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2802–2805, December, 2005.     

Geometrical design of ligands for spherical ions

New types of ligands for spherical ions have been designed as part of the molecular design strategy for supramolecular compounds. In particular, symmetric conformers of macrocycles, built of −(CH₂)_n−O−(n=3,4,5) fragments, which envelope the spherical ion in a complementary way, have been constructed. Alos, new types of “bracelentands” with different, “hardening” fragments are suggested. Using the molecular mechanics methods, the selectivity of complex formation of the ligands with respect to alkaline metal ions has been investigated. A. V. Bogatskii Physicochemical Institute, Ukrainian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 5, pp. 879–883, September–October, 1995. Translated by L. Smolina     

Propane transformations on aluminum chloride—cobalt chloride clusters: a quantum chemical study

Density functional PBE/TZ2p quantum chemical calculations of activated complexes and pathways of model catalytic transformations of propane under the action of aluminum chloride-cobalt chloride ionic bimetallic complexes were carried out. The formation of an intermediate with a broken C-C bond can occur on the cationic cluster CoAlCl₄ ⁺ characterized by the strongest coordination of propane molecule. The activation barrier to the reaction is ΔG = 25.0 kcal mol⁻¹. Activation of alkane C-H bonds follows the alkyl pathway involving the formation of bimetallic alkyl complexes. The interaction of activated hydrocarbon fragments bound to transition metal atoms in cobalt-chloroaluminate clusters can result in alkane metathesis products (in this case, ethane and a polymetallic cluster containing an extendedchain alkyl radical).     

Embedded cluster calculation of the Ce3+ impurity in Lu2SiO5 crystals including crystal lattice relaxation and polarization

Results of electronic structure studies of the Ce³⁺ impurity in Lu₂SiO₅ crystals allowing for lattice polarization and relaxation are given. The calculations were performed by the embedded cluster method combining the scattered wave and molecular static methods. The effect of lattice deformation induced by the defect on the results of calculations is discussed. Translated fromZhurnal Strukturnoi Khimii, Vol. 38, No. 6, pp. 1046–1052, November–December, 1997.     

Influence of structure of the crystal lattice of nickel(II) complex with amide-containing ligand on its stability and adsorption properties

The characteristic of the crystal lattice of the hydrate of a nickel complex with a tetradentate amide-containing ligand is the presence of hexamers of the metal complex molecule, united by intermolecular hydrogen bonds which are retained during adsorption and desorption of polar molecules. The lattice of this material is characterized by a definite lability which arises during interaction with methanol. __________ Translated from Teoreticheskaya i éksperimental’naya Khimiya, Vol. 43, No. 1, pp. 47–51, January–February, 2007.     

Calculations of concentration dependences of chemical shifts for acrylamide in water—DMSO mixed solvent

The lattice model of associated solutions was used to calculate the concentration dependences of the chemical shifts of¹³C magnetic nuclei in the acrylamide molecule in water—DMSO solvent. Each pair of bonds between the acrylamide group containing a magnetic nucleus and the neighboring solvent molecule was assumed to additively contribute to the change in the chemical shift of the nucleus in question. The new approach affords the same accuracy in describing the experimental data at any ratios of the solution components. It was shown that the chemical shifts and the excess heat of mixing of the water—DMSO binary solution can be simultaneously described using the same set of energy parameters of the model. The model makes it possible to employ experimental data on chemical shifts for studying intermolecular interactions in solutions. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1983–1987, October, 1998.