Molecular dynamics simulation on devitrification: Isothermal devitrification and thermodynamics of PbF2 glasses

The vitrification and devitrification features of lead fluoride are investigated by means of molecular dynamic simulations. The influence of heating rate on the devitrification temperature as well as the dependence of the glass properties on its thermal history, i.e., the cooling rate employed, is identified. As expected, different glasses are obtained when the cooling rates differ. Diffusion coefficient analysis during heating of glass and crystal, indicates that the presence of defects on the glassy matrix favors the transition processes from the ionic to a superionic state, with high mobility of fluorine atoms, responsible for the high anionic conduction of lead fluoride. Nonisothermal and isothermal devitrification processes are simulated in glasses obtained at different cooling rates and structural organizations occurring during the heat treatments are clearly observed. When a fast cooling rate is employed during the glass formation, the devitrification of a single crystal (limited by the cell dimensions) is observed, while the glass obtained with slower cooling rate, allowing relaxations and organization of various regions on the glass bulk during the cooling process, devitrifies in more than one crystalline plane. (C) 2004 American Institute of Physics.

The use of molecular spectra simulation for diagnostics of reactive flows

The C 2 * radical is used as a system probe tool to the reactive flow diagnostic, and it was chosen due to its large occurrence in plasma and combustion in aeronautics and aerospace applications. The rotational temperatures of C 2 * species were determined by the comparison between experimental and theoretical data. The simulation code was developed by the authors, using C++ language and the object oriented paradigm, and it includes a set of new tools that increase the efficacy of the C 2 * probe to determine the rotational temperature of the system. A brute force approach for the determination of spectral parameters was adopted in this version of the computer code. The statistical parameter c 2 was used as an objective criterion to determine the better match of experimental and synthesized spectra. The results showed that the program works even with low-quality experimental data, typically collected from in situ airborne compact apparatus. The technique was applied to flames of a Bunsen burner, and the rotational temperature of ca. 2100 K was calculated.

C-H center dot center dot center dot O and N-H center dot center dot center dot O hydrogen bonds in liquid amides investigated by Monte Carlo simulation

Monte Carlo simulations of liquid formamide, N-methylformamide (MF), and N,N-dimethylformamide (DMF) have been performed in the isothermal and isobaric ensemble at 298 K and 1 atm, aiming to investigate the C-H ... O and N-H ... O hydrogen bonds. The interaction energy was calculated using the classical 6-12 Lennard-Jones pairwise potential plus a Coulomb term on a rigid six-site molecular model with the potential parameters being optimized in this work. Theoretical values obtained for heat of vaporization and liquid densities are in good agreement with the experimental data. The radial distribution function [RDF, g(r)] obtained compare well with R-X diffraction data available. The RDF and molecular mechanics (MM2) minimization show that the C-H ... O interaction has a significant role in the structure of the three liquids. These results are supported by ab initio calculations. This Interaction is particularly important in the structure of MF. The intensity of the N-H ... O hydrogen bond is greater in the MF than formamide. This could explain some anomalous properties verified in MF. (C) 1997 John Wiley & Sons, Inc.

C - H ⋯ 0 and N - H ⋯ 0 hydrogen bonds in liquid amides investigated by monte carlo simulation

Monte Carlo simulations of liquid formamide, N-methylformamide (MF), and N, N-dimethytformamide (DMF) have been performed in the isothermal and isobaric ensemble at 298 K and 1 atm, aiming to investigate the C-H ⋯ O and N-H ⋯ O hydrogen bonds. The interaction energy was calculated using the classical 6-12 Lennard-Jones pairwise potential plus a Coulomb term on a rigid six-site molecular model with the potential parameters being optimized in this work. Theoretical values obtained for heat of vaporization and liquid densities are in good agreement with the experimental data. The radial distribution function [RDF, g(r)] obtained compare well with R-X diffraction data available. The RDF and molecular mechanics (MM2) minimization show that the C-H ⋯ O interaction has a significant role in the structure of the three liquids. These results are supported by ab initio calculations. This interaction is particularly important in the structure of MF. The intensity of the N - H ⋯ O hydrogen bond is greater in the MF than formamide. This could explain some anomalous properties verified in MF. © 1997 John Wiley & Sons, Inc.

Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations

In this work, we report a 20-ns constant pressure molecular dynamics simulation of prilocaine (PLC), in amine-amide local anesthetic, in a hydrated liquid crystal bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at similar to 12 angstrom from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, vertical bar S-CD vertical bar, compared to neat bilayers, is found, in good agreement with experimental H-2-NMR studies. The decrease in vertical bar S-CD vertical bar induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. (C) 2008 Wiley Periodicals, Inc.

Preferential location of prilocaine and etidocaine in phospholipid bilayers: A molecular dynamics study

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

Molecular characterization and phylogenetic analysis of JussuMP-I: A RGD-P-III class hemorrhagic metalloprotease from Bothrops jararacussu snake venom

Snake venom metalloproteases (SVMPs) embody zinc-dependent multidomain enzymes responsible for a relevant pathophysiology in envenomation. including local and systemic hemorrhage. The molecular features responsible for hemorrhagic potency of SVMPs have been associated with their multidomains structures which can target these proteins them to several receptors of different tissues and cellular types. BjussuMP-I. a SVMP isolated from the Bothrops jararacussu venom, has been characterized as a P-III hemorrhagic metalloprotease. The complete cDNA sequence of BjussuMP-I with 1641bp encodes open reading frames of 547 amino acid residues, which conserve the common domains of P-III high molecular weight hemorrhagic metalloproteases: (i) pre-pro-peptide, (ii) metalloprotease, (iii) disintegrin-like and (iv) rich cysteine domain. BjussuMP-I induced lyses in fibrin clots and inhibited collagen- and ADP-induced platelet aggregation. We are reporting, for the first time, the primary structure of an RGD-P-III class snake venom metalloprotease. A phylogenetic analysis of the BjussuMP-1 metalloprotease/catalytic domain was performed to get new insights into the molecular evolution of the metalloproteases. A theoretical molecular model of this domain was built through folding recognition (threading) techniques and refined by molecular dynamics simulation. Then, the final BjussuMP-I catalytic domain model was compared to other SVMPs and Reprolysin family proteins in order to identify eventual structural differences, which could help to understand the biochemical activities of these enzymes. The presence of large hydrophobic areas and some conserved surface charge-positive residues were identified as important features of the SVMPs and other metalloproteases. (C) 2006 Elsevier B.V. All rights reserved.

L-Histidine-europium(III) complex: A spectroscopical study

Chemical characterization as well as spectroscopical study of the L-histidine-europium(III) complex were developed both experimental and theoretically. Molecular mechanics (MM) simulation was performed in order to have indication of the compound structure and the Eu 3+ chemical environment. The Simple Overlap Model (SOM) was applied to predict spectroscopic quantities as 5D 0→ 7F 0/ 5D 0→ 7F 2 intensity ratio, 5D 0→ 7F 1 transition splitting and the intensity Ω λ parameters (λ = 2 and 4). Satisfactory results are obtained with 0.1 and 2/3 as the effective charges of the nitrogen (gN) and oxygen (gO) respectively, and their polarizabilities (α) depend on the distance. © 1999 Elsevier Science B.V. All rights reserved.

Structure and weak hydrogen bonds in liquid acetaldehyde

Monte Carlo simulations have been performed to investigate the structure and hydrogen bonds formation in liquid acetaldehyde. An all atom model for the acetaldehyde have been optimized in the present work. Theoretical values obtained for heat of vaporisation and density of the liquid are in good agreement with experimental data. Graphics of radial distribution function indicate a well structured liquid compared to other similar dipolar organic liquids. Molecular mechanics minimization in gas phase leads to a trimer of very stable structure. The geometry of this complex is in very good agreement with the rdf. The shortest site-site correlation is between oxygen and the carbonyl hydrogen, suggesting that this correlation play a important role in the liquid structure and properties. The O⋯H average distance and the C-H⋯O angle obtained are characteristic of weak hydrogen bonds.

Use of grape polyphenols against carcinogenesis: Putative molecular mechanisms of action using in vitro and in vivo test systems

Polyphenols are present in foods and beverages and are related to sensorial qualities such as color, bitterness, and astringency, which are relevant in wine, tea, grape juice, and other products. These compounds occur naturally in forms varying from simple phenolic acids to complex polymerized tannins. Thus, it is reasonable to expect that grape-derived products elaborated in the presence of skins and seeds, such as wine and grape juice, are natural sources of flavonoids in the diet. Carcinogenesis is a multistep process that is characterized by genetic, epigenetic, and phenotypic changes. With increasing knowledge of these mechanisms, and the conclusion that most cases of cancer are preventable, efforts have focused on identifying the agents with potential anticancer properties. The use of grape polyphenols against the carcinogenesis process seems to be a suitable alternative for either prevention and/or therapeutic purposes. The aim of this article is to show the molecular data generated from the use of grape polyphenols against carcinogenesis using in vivo and in vitro test systems. © Mary Ann Liebert, Inc. and Korean Society of Food Science and Nutrition.

Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations

Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (k cat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes. © 2013 Elsevier B.V. All rights reserved.

Interação do peptídeo MP-I com micela de SDS em solução aquosa: um estudo por dinâmica molecular

Pós-graduação em Biofísica Molecular - IBILCE

Estudos conformacionais por dinâmica molecular de peptídeos antimicrobianos da família dos Mastoparanos em misturas de TFE-água

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Non-inclusion complexes between riboflavin and cyclodextrins

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

Structural and functional properties of Bp-LAAO, a new L-amino acid oxidase isolated from Bothrops pauloensis snake venom

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