Multi-scale structural description of siloxane-PPO hybrid ionic conductors doped by sodium salts

Alkaline metal doped organic - inorganic hybrids have potential applications in the field of portable energy sources. Attractive sol - gel derived urea cross-linked polyether, siloxane - PPO ( poly( propylene oxide)) hybrids doped with sodium salts ( NaClO4 and NaBF4) were examined by multi-spectroscopic approach that includes complex impedance, X-ray powder diffraction (XRPD), small angle X-ray scattering (SAXS), Si-29 and Na-23 magic-angle spinning nuclear magnetic resonance (NMR/MAS), Na K-edge X-ray absorption near edge structure (XANES) and Raman spectroscopies. The goals of this work were to determine which cation coordinating site of the host matrix ( ether oxygen atoms or carbonyl oxygen atoms) is active in each of the materials analyzed, its influence on the nanostructure of the samples and its relation with the thermal and electrical properties. The main conclusion derived from this study is that the NaBF4 salt has a much lower solubility in the hybrid matrix than the NaClO4 salt. Furthermore, the addition of a large amount of salt plays a major role in the hybrid nanostructure and electrical properties, modifying the PPO chain conformation, weakening or breaking the hydrogen bond of the polyether - urea associations and changing the polycondensation and aggregation processes involving the siloxane species.

Structure characterization of molecular complexes for non-linear optical materials. II. 1 : 1 complexes of 4-methyl-morpholine-N-oxide (1) and 3-picoline-N-oxide (2) with 2,4,6-trinitrophenol, studied by X-ray, AM1 and DFT calculations

(1) C6H2N3O7- center dot C5H12NO2+, Mr = 346.26, P2(1)/c, a = 7.2356(6), b = 10.5765(9), c = 19.593(2) angstrom, 3 beta=95.101(6)degrees, V = 1493.5(2) angstrom(3), Z = 4, R-1 = 0.0414; (2) C6H2N3O7- center dot C6H8NO+, Mr = 38.24, P2(1)/n, a = 7.8713(5), b = 6.1979(7), c = 28.697(3) angstrom, beta = 90.028(7)degrees, V = 1400.0(2) angstrom(3), Z = 4, R-1 = 0.0416. The packing units in both compounds consist of hydrogen bonded cation-anion pairs. The (hyper)polarizabilities have been calculated for the crystallographic and optimized molecules, by AM1 and at the DFT/B3LYP(6-31G**) level.

Synthesis, structure, and electronic and EPR spectra of copper(II) complexes containing the [CuBr4]2- anion and triphenylarsine oxide

The preparation and characterization of (Ph3AsOH)2[CuBr4] and [Cu(Ph3AsO)4][CuBr4] are reported (Ph3AsO = triphenylarsine oxide). Crystallographic analysis of the monoclinic crystals of (Ph3AsOH)2[CuBr4] (space group C2/c, a = 17.569 (3) Å, b = 13.090 (2) Å, c = 16.933 (2) Å, and β = 105.64 (2)°, R = 0.055 and Rw = 0.057) revealed the presence of compressed [CuBr4]2- tetrahedra of C2 symmetry with Cu-Br distances of 2.340 (1) and 2.437 (1) Å and trans-Br-Cu-Br angles of 139.2 (1) and 122.4 (1)°. The oxonium cations hydrogen bond to the bromine atoms involved in the longer Cu-Br bonds and the smaller trans-Br-Cu-Br angle. Single-crystal electronic and EPR spectra are interpreted in terms of the observed [CuBr4]2- geometry. Analysis of the electronic and EPR spectra of [Cu(Ph3AsO)4][CuBr4] led to the postulation of the presence of planar [Cu(Ph3AsO)4]2+ cations and distorted tetrahedral [CuBr4]2- anions. © 1992 American Chemical Society.

Structure of tick anticoagulant peptide at 1.6 Å resolution complexed with bovine pancreatic trypsin inhibitor

The structure of tick anticoagulant peptide (TAP) has been determined by X-ray crystallography at t.6 Å resolution complexed with bovine pancreatic trypsin inhibitor (BPTI). The TAP-BPTI crystals are tetragonal, a = b = 46.87, c = 50.35 Å, space group P41, four complexes per unit cell. The TAP molecules are highly dipolar and form an intermolecular helical array along the c-axis with a diameter of about 45 Å. Individual TAP units interact in a head-to-tail fashion, the positive end of one molecule associating with the distal negative end of another, and vice versa. The BPTI molecules have a uniformly distributed positively charged surface that interacts extensively through 14 hydrogen bonds and two hydrogen bonded salt bridges with the helical groove around the helical TAP chains. Comparing the structure of TAP in TAP-BPTI with TAP bound to factor Xa(Xa) suggests a massive reorganization in the N-terminal tetrapeptide and the first disulfide loop of TAP (CyS5(T)- Cys 15(T)) upon binding to Xa. The Tyr1(T)OH atom of TAP moves 14.2 Å to interact with Asp189 of the S1 specificity site, Arg3(T)CZ moves 5.0 Å with the guanidinium group forming a cation-π-electron complex in the S4 subsite of Xa, while Lys7(T)NZ differs in position by 10.6 Å in TAP-BPTI and TAP-Xa, all of which indicates a different pre-Xa-bound conformation for the N- terminal of TAP in its native state. In contrast to TAP, the BPTI structure of TAP-BPTI is practically the same as all those of previously determined structures of BPTI, only arginine and lysine side-chain conformations showing significant differences.

Structure of thrombin complexed with selective non-electrophilic inhibitors having cyclohexyl moieties at P1

The crystal structures of five new non-electrophilic β-strand-templated thrombin active-site inhibitors have been determined bound to the enzyme. Four co-crystallize with hirugen and inhibitor isomorphously to produce thrombin-hirugen crystals (monoclinic, space group C2), while one co-crystallizes in the hexagonal system, space group P65. A 1,4-substituted cyclohexyl moiety is conserved at the P1 position of all the inhibitors, along with a fused hetero-bicyclic five- and six-membered ring that occupies the P2 site. Amino, amidino and aminoimidazole groups are attached to the cyclohexyl ring for recognition at the S1 specificity site, while benzylsulfonyl and diphenyl groups enhance the binding at the S3 subsite. The cyclohexyl groups at the P1 positions of three of the inhibitors appear to be in the energetically favored chair conformation, while the imidazole-substituted cyclohexyl rings are in a boat conformation. Somewhat unexpectedly, the two cyclohexyl-aminoimidazole groups bind differently in the specificity site; the unique binding of one is heretofore unreported. The other inhibitors generally mimic arginyl binding at S1. This group of inhibitors combines the nonelectrophilicity and selectivity of DAPA-like compounds and the more optimal binding features of the S1-S3 sites of thrombin for peptidic molecules, which results in highly potent (binding constants 12 nM-16 pM, one being 1.1 μM) and selective (ranging from 140 to 20 000 times more selective compared with trypsin) inhibitors of thrombin. The binding modes of these novel inhibitors are correlated with their binding constants, as is their selectivity, in order to provide further insight for the design of therapeutic antithrombotic agents that inhibit thrombin directly at the active site.

Molecular model of shikimate kinase from Mycobacterium tuberculosis

Tuberculosis (TB) resurged in the late 1980s and now kills approximately 3 million people a year. The reemergence of tuberculosis as a public health threat has created a need to develop new anti-mycobacterial agents. The shikimate pathway is an attractive target for herbicides and anti-microbial agents development because it is essential in algae, higher plants, bacteria, and fungi, but absent from mammals. Homologs to enzymes in the shikimate pathway have been identified in the genome sequence of Mycobacterium tuberculosis. Among them, the shikimate kinase I encoding gene (aroK) was proposed to be present by sequence homology. Accordingly, to pave the way for structural and functional efforts towards anti-mycobacterial agents development, here we describe the molecular modeling of M. tuberculosis shikimate kinase that should provide a structural framework on which the design of specific inhibitors may be based. © 2002 Elsevier Science (USA). All rights reserved.

The structural origin and biological function of pH-sensitivity in firefly luciferases

Firefly luciferases are called pH-sensitive because their bioluminescence spectra display a typical red-shift at acidic pH, higher temperatures, and in the presence of heavy metal cations, whereas other beetle luciferases (click beetles and railroadworms) do not, and for this reason they are called pH-insensitive. Despite many studies on firefly luciferases, the origin of pH-sensitivity is far from being understood. This subject is revised in view of recent results. Some substitutions of amino-acid residues influencing pH-sensitivity in firefly luciferases have been identified. Sequence comparison, site-directed mutagenesis and modeling studies have shown a set of residues differing between pH-sensitive and pH-insensitive luciferases which affect bioluminescence colors. Some substitutions dramatically affecting bioluminescence colors in both groups of luciferases are clustered in the loop between residues 223-235 (Photinus pyralis sequence). A network of hydrogen bonds and salt bridges involving the residues N229-S284-E311-R337 was found to be important for affecting bioluminescence colors. It is suggested that these structural elements may affect the benzothiazolyl side of the luciferin-binding site affecting bioluminescence colors. Experimental evidence suggest that the residual red light emission in pH-sensitive luciferases could be a vestige that may have biological importance in some firefly species. Furthermore, the potential utility of pH-sensitivity for intracellular biosensing applications is considered. © The Royal Society of Chemistry and Owner Societies.

Structural insights into selectivity and cofactor binding in snake venom l-amino acid oxidases

l-Amino acid oxidases (LAAOs) are flavoenzymes that catalytically deaminate l-amino acids to corresponding α-keto acids with the concomitant production of ammonia (NH 3) and hydrogen peroxide (H 2O 2). Particularly, snake venom LAAOs have been attracted much attention due to their diverse clinical and biological effects, interfering on human coagulation factors and being cytotoxic against some pathogenic bacteria and Leishmania ssp. In this work, a new LAAO from Bothrops jararacussu venom (BjsuLAAO) was purified, functionally characterized and its structure determined by X-ray crystallography at 3.1å resolution. BjsuLAAO showed high catalytic specificity for aromatic and aliphatic large side-chain amino acids. Comparative structural analysis with prokaryotic LAAOs, which exhibit low specificity, indicates the importance of the active-site volume in modulating enzyme selectivity. Surprisingly, the flavin adenine dinucleotide (FAD) cofactor was found in a different orientation canonically described for both prokaryotic and eukaryotic LAAOs. In this new conformational state, the adenosyl group is flipped towards the 62-71 loop, being stabilized by several hydrogen-bond interactions, which is equally stable to the classical binding mode. © 2012 Elsevier Inc.

Kinetic parameters for thermal decomposition of supramolecular polymers derived from diclofenac-meglumine supramolecular adducts

Meglumine is an aminocarbohydrate able to form supramolecular adducts with organic acids. The recognition is based on hydrogen bonds and the structures resulting from the complexation have high solubility in water. This property has been exploited by the pharmaceutical industry in the improvement of existing drugs, and the successful example of this approach involves the poorly soluble non-steroidal anti-inflammatory drugs (NSAIDs). Investigation of the thermal behavior of adduct obtained from meglumine and the NSAID diclofenac revealed that a polymer-like material is formed from the self-assembly of diclofenac-meglumine adducts in the melt. This polymer showed a high molecular weight around 2.0×105kDa. The kinetic parameters for the thermal decomposition step of the polymer were determined by the Capela-Ribeiro non-linear isoconversional method. From data for the TG curves in nitrogen atmosphere and heating rates of 5, 10, 15 and 20°Cmin-1, the Eα and Bα terms could be determined, and consequently the pre-exponential factor, Aα, as well as the kinetic model, g(α). © 2012 Elsevier B.V.

Estudos de confinamento quântico em ligações de hidrogênio

Pós-graduação em Biofísica Molecular - IBILCE

Estudo de N-metilformamida em meio não aquoso. O caso NMF-acetona

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudos estruturais e filogenéticos com fosfolipases e serino proteases de venenos de serpentes botrópicas nativas e quimicamente modificadas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A hybrid neutron diffraction and computer simulation study on the solvation of N-methylformamide in dimethylsulfoxide

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Protonation Pattern, Tautomerism, Conformerism, and Physicochemical Analysis in New Crystal Forms of the Antibiotic Doxycycline

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)