Application of a new reverse Monte Carlo algorithm to polyatomic molecular systems. I. Liquid water

Using a new reverse Monte Carlo algorithm, we present simulations that reproduce very well several structural and thermodynamic properties of liquid water. Both Monte Carlo, molecular dynamics simulations and experimental radial distribution functions used as input are accurately reproduced using a small number of molecules and no external constraints. Ad hoc energy and hydrogen bond analysis show the physical consistency and limitations of the generated RMC configurations. (C) 2001 American Institute of Physics.

The valuable role of renucleation rate in ultrananocrystalline diamond growth

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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.

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.

Peirce's mathematical-logical approach to discrete collections and the premonition of continuity

According to Peirce one of the most important philosophical problems is continuity. Consequently, he set forth an innovative and peculiar approach in order to elucidate at once its mathematical and metaphysical challenges through proper non-classical logical reasoning. I will restrain my argument to the definition of the different types of discrete collections according to Peirce, with a special regard to the phenomenon called premonition of continuity (Peirce, 1976, Vol. 3, p. 87, c. 1897). © 2012 Copyright Taylor and Francis Group, LLC.

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.

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

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Síntese de perovskitas nanométricas com estrutura 'PB IND.1-x''M IND.X''TI''O IND.3'(M='BA', 'CA' e 'SR')

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

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Ativação da ligação c-h no metano por espécies MOm n+ (M = Nb, Fe; m = 0, 1; n = 0, 1, 2): estrutura eletrônica, mecanismo de reação e reatividade

The need for renewal and a more efficient use of energy resources has provided an increased interest in studies of methane activation processes in the gas phase by transition metal oxides. In this respect, the present work is an effort to assess , by means of a computational standpoint, the reactivity of NbOm n+ and FeOm n+ (m = 1, 2, n = 0, 1, 2) oxides in the activation process of the methane C-H bond, which corresponds to the first rate limiting step in the process of converting methane to methanol. These oxides are chosen, primarily, because the iron oxides are the most experimentally studied, and iron ions are more abundant in biological mediums. The main motive for choosing niobium oxides is the abundance of natural reserves of this mineral in Brazil (98%), especially in Minas Gerais. Initially, a thorough investigation was conducted, using different theoretical methods, to analyze the structural and electronic properties of the investigated oxides. Based on these results, the most reliable methodology was selected to investigate the activation process of the methane C-H bond by the series of iron and niobium oxides, considering all possible reaction mechanisms known to activate the C-H bond of alkanes. It is worth noting that, up to this moment and to our knowledge, there are no papers, in literature , investigating and comparing all the mechanisms considered in this work. I n general, the main results obtained show different catalytic tendencies and behaviors throughout the series of monoxides and dioxides of iron and niobium. An important and common result found in the two studies is that the increase in the load on the metal center and the addition of oxygen atoms to the metal, clearly favor the initial thermodynamics of the reaction, i.e., favor the approach of the metal center to methane, distorting its electron cloud and, thereby, decreasing its inertia. Comparing the two sets of oxides, we conclude that the iron oxides are the most efficient in activating the methane C-H bond. Among the iron oxides investigated, FeO + showed better kinetic and thermodynamic performance in the reaction with methane, while from the niobium oxides and ions NbO 2+ and NbO2 2+, showed better catalytic efficiency in the activation of the methane C-H bond.

Análise das interações moleculares em blendas sintéticas tipo biodiesel/diesel por espectroscopia dielétrica e vibracional de absorção na região do infravermelho

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As vogais médias pretônicas na variedade do interior paulista

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

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)