Bonding Pattern (bonding + pattern)

Distribution by Scientific Domains
Chemistry66%

Kinds of Bonding Pattern

  • hydrogen bonding pattern
    		•

    Selected Abstracts

    Molecular docking studies of selected tricyclic and quinone derivatives on trypanothione reductase of Leishmania infantum

    JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2010
    Santhosh Kannan Venkatesan
    Abstract Visceral leishmaniasis, most lethal form of Leishmaniasis, is caused by Leishmania infantum in the Old world. Current therapeutics for the disease is associated with a risk of high toxicity and development of drug resistant strains. Thiol-redox metabolism involving trypanothione and trypanothione reductase, key for survival of Leishmania, is a validated target for rational drug design. Recently published structure of trypanothione reductase (TryR) from L. infantum, in oxidized and reduced form along with Sb(III), provides vital clues on active site of the enzyme. In continuation with our attempts to identify potent inhibitors of TryR, we have modeled binding modes of selected tricyclic compounds and quinone derivatives, using AutoDock4. Here, we report a unique binding mode for quinone derivatives and 9-aminoacridine derivatives, at the FAD binding domain. A conserved hydrogen bonding pattern was observed in all these compounds with residues Thr335, Lys60, His461. With the fact that these residues aid in the orientation of FAD towards the active site forming the core of the FAD binding domain, designing selective and potent compounds that could replace FAD in vivo during the synthesis of Trypanothione reductase can be deployed as an effective strategy in designing new drugs towards Leishmaniasis. We also report the binding of Phenothiazine and 9-aminoacridine derivatives at the Z site of the protein. The biological significance and possible mode of inhibition by quinone derivatives, which binds to FAD binding domain, along with other compounds are discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source]

    Characterization and crystal structure of D -mannitol hemihydrate

    JOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2004
    Cletus Nunes
    Abstract The objectives of this study were (i) to isolate and characterize mannitol hydrate, and (ii) to solve its crystal structure from high-resolution synchrotron X-ray powder diffraction data. Mannitol hydrate was prepared by freeze-drying aqueous mannitol solutions (5% w/v) under controlled conditions. X-ray powder diffractometry, differential scanning calorimetry, and thermogravimetric analyses indicated that mannitol exists as a hemihydrate (C6H14O6,·,0.5H2O). Synchrotron data were collected on the X3B1 beamline at the National Synchrotron Light Source. The simulated annealing program PSSP was used to solve the structure, which was subsequently refined by Rietveld analysis using the program package GSAS. The compound crystallizes in space group P1, with a,=,9.8963 Å, b,=,10.5424 Å, c,=,4.7860 Å, ,,=,102.589°, ,,=,86.092°, and ,,=,116.079°. The unit cell contains two dissimilar D -mannitol molecules and one water molecule, forming a hydrogen bonding pattern significantly different from that seen in the anhydrous polymorphs. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:2800,2809, 2004 [source]

    X-ray and 13C solid-state NMR studies of N -benzoyl-phenylalanine

    CHEMICAL BIOLOGY & DRUG DESIGN, Issue 4 2000
    M.J. Potrzebowski
    Abstract: A crystalline sample of N -benzoyl- dl -phenylalanine 1 and a polycrystalline sample of N -benzoyl- l -phenylalanine 2 were studied using 13C high-resolution solid-state NMR spectroscopy. The X-ray structure of the dl form was established. Sample 1 crystallizes in a monoclinic form with a P21/c space group, a = 11.338(1) Å, b = 9.185(1) Å, c = 14.096(2) Å, ,,= 107.53(3)°, V = 1400(3) Å3, Z = 4 and R = 0.053. The principal elements of the 13C chemical shift tensors ,ii for 1 and 2, selectively 13C (99%) labeled at the carboxyl groups were calculated. On the basis of 13C ,ii analysis the hydrogen bonding pattern for sample 2 was deduced. Enriched samples were used to establish the intermolecular distance between chemically equivalent nuclei for 1 and spatial proximity in heterogeneous domain for 2, employing the ODESSA pulse sequence. The consistence of the complementary approach covering X-ray data, analysis of the 13C ,ii parameters and ODESSA results is revealed. [source]

    Shape transition of medium-sized neutral silicon clusters

    PHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 3 2003
    A. Sieck
    Abstract Addressing the shape transition of silicon clusters, indicated by mobility experiments on silicon cluster cations with 24 to 30 atoms, we investigate the structure of low energy neutral silicon clusters with 25, 29, and 35 atoms within a density-functional based tight-binding approach. Since there is strong evidence for several nearly degenerate low-energy isomers for clusters of this size, we perform an extensive, but limited global search with Simulated Annealing and statistically analyze for each cluster size the 100 clusters with the lowest energy. We find different dominant shapes in the set of low energy clusters for each size. For neutral silicon clusters with 25 atoms, both prolate and spherical structures with low cohesive energies exist. For clusters containing 29 or 35 atoms, the low-energy isomers exhibit a spherical shape. For each cluster size several stable isomers with similar shapes, and hence similar mobilities, but different bonding patterns exist. The most stable 25 atom cluster resulting from our global search has the lowest energy within DFT-GGA known so far. Finally, we investigate the transition to diamond-like bonding patterns expected for larger silicon clusters. Clusters with up to 239 atoms resemble amorphous silicon rather than the diamond structure and contain several highly coordinated atoms. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

    Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid

    PROTEIN SCIENCE, Issue 2 2008
    Freddie R. Salsbury Jr
    Abstract Cysteine sulfenic acid (Cys-SOH), a reversible modification, is a catalytic intermediate at enzyme active sites, a sensor for oxidative stress, a regulator of some transcription factors, and a redox-signaling intermediate. This post-translational modification is not random: specific features near the cysteine control its reactivity. To identify features responsible for the propensity of cysteines to be modified to sulfenic acid, a list of 47 proteins (containing 49 known Cys-SOH sites) was compiled. Modifiable cysteines are found in proteins from most structural classes and many functional classes, but have no propensity for any one type of protein secondary structure. To identify features affecting cysteine reactivity, these sites were analyzed using both functional site profiling and electrostatic analysis. Overall, the solvent exposure of modifiable cysteines is not different from the average cysteine. The combined sequence, structure, and electrostatic approaches reveal mechanistic determinants not obvious from overall sequence comparison, including: (1) pKas of some modifiable cysteines are affected by backbone features only; (2) charged residues are underrepresented in the structure near modifiable sites; (3) threonine and other polar residues can exert a large influence on the cysteine pKa; and (4) hydrogen bonding patterns are suggested to be important. This compilation of Cys-SOH modification sites and their features provides a quantitative assessment of previous observations and a basis for further analysis and prediction of these sites. Agreement with known experimental data indicates the utility of this combined approach for identifying mechanistic determinants at protein functional sites. [source]

    New pseudopolymorphs of 5-fluorocytosine

    ACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2009
    Maya Tutughamiarso
    In order to better understand the interaction between the pharmaceutically active compound 5-fluorocytosine [4-amino-5-fluoropyrimidin-2(1H)-one] and its receptor, hydrogen-bonded complexes with structurally similar bonding patterns have been investigated. During the cocrystallization screening, three new pseudopolymorphs of 5-fluorocytosine were obtained, namely 5-fluorocytosine dimethyl sulfoxide solvate, C4H4FN3O·C2H6OS, (I), 5-fluorocytosine dimethylacetamide hemisolvate, C4H4FN3O·0.5C4H9NO, (II), and 5-fluorocytosine hemihydrate, C4H4FN3O·0.5H2O, (III). Similar hydrogen-bond patterns are observed in all three crystal structures. The 5-fluorocytosine molecules form ribbons with repeated R22(8) dimer interactions. These dimers are stabilized by N,H...N and N,H...O hydrogen bonds. The solvent molecules adopt similar positions with respect to 5-fluorocytosine. Depending on the hydrogen bonds formed by the solvent, the 5-fluorocytosine ribbons form layers or tubes. A database study was carried out to compare the hydrogen-bond pattern of compounds (I),(III) with those of other (pseudo)polymorphs of 5-fluorocytosine. [source]