Modelling water adsorption on Au(210) surfaces: II. Monte Carlo simulations

Canonical Monte Carlo simulations for the Au(210)/H(2)O interface, using a force field recently proposed by us, are reported. The results exhibit the main features normally observed in simulations of water molecules in contact with different noble metal surfaces. The calculations also assess the influence of the surface topography on the structural aspects of the adsorbed water and on the distribution of the water molecules in the direction normal to the metal surface plane. The adsorption process is preferential at sites in the first layer of the metal. The analysis of the density profiles and dipole moment distributions points to two predominant orientations. Most of the molecules are adsorbed with the molecular plane parallel to surface, while others adsorb with one of the O-H bonds parallel to the surface and the other bond pointing towards the bulk liquid phase. There is also evidence of hydrogen bond formation between the first and second solvent layers at the interface. (c) 2007 Elsevier B.V. All rights reserved.

Crystal structure and theoretical calculations of Julocrotine, a natural product with antileishmanial activity

Julocrotine, N-(2,6-dioxo-l-phenethyl-piperidin-3-yl)-2-methyl-butyramide, is a potent antiproliferative agent against the promastigote and amastigote forms of Leishmania amazonensis (L.). In this work, the crystal structure of Julocrotine was solved by X-ray diffraction, and its geometrical parameters were compared with theoretical calculations at the B3LYP and HF level of theory. IR and NMR spectra also have been obtained and compared with theoretical calculations. IR absorptions calculated with the B3LYP level of theory employed together with the 6-311G+(d,p) basis set, are close to those observed experimentally. Theoretical NMR calculations show little deviation from experimental results. The results show that the theory is in accordance with the experimental data. (C) 2007 Wiley Periodicals, Inc.

Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity

In this work, two different docking programs were used, AutoDock and FlexX, which use different types of scoring functions and searching methods. The docking poses of all quinone compounds studied stayed in the same region in the trypanothione reductase. This region is a hydrophobic pocket near to Phe396, Pro398 and Leu399 amino acid residues. The compounds studied displays a higher affinity in trypanothione reductase (TR) than glutathione reductase (GR), since only two out of 28 quinone compounds presented more favorable docking energy in the site of human enzyme. The interaction of quinone compounds with the TR enzyme is in agreement with other studies, which showed different binding sites from the ones formed by cysteines 52 and 58. To verify the results obtained by docking, we carried out a molecular dynamics simulation with the compounds that presented the highest and lowest docking energies. The results showed that the root mean square deviation (RMSD) between the initial and final pose were very small. In addition, the hydrogen bond pattern was conserved along the simulation. In the parasite enzyme, the amino acid residues Leu399, Met400 and Lys402 are replaced in the human enzyme by Met406, Tyr407 and Ala409, respectively. In view of the fact that Leu399 is an amino acid of the Z site, this difference could be explored to design selective inhibitors of TR.

Pressure Perturbation Calorimetry and Guest-Host Chemistry of NDMG and N-MAP with p-Sulfonatocalix[6]arene

The aim of this project is to provide an explanation for recently obtained binding constants for two similar guest molecules, NDMG and N-MAP, with a p-sulfonatocalix[6]arene host in ammonium acetate buffer. This work was done primarily using pressure perturbation calorimetry, which is a technique that determines the coefficient of thermal expansion, α, which is in turn related to the solute molecule's effect on the order of the surrounding water molecules. A series of experiments were designed to test the effects of suspected confounding variables on the validity of PPC data. PPC was then used to study NDMG and N-MAP in ammonium acetate buffer. NDMG exhibited a minimum in α as function of temperature, while N-MAP did not. This difference was theorized to be due to the formation of an intramolecular hydrogen bond in monocationic NDMG that would lower the heat capacity of the molecule and better distribute the molecule's charge. Computational work and nuclear magnetic resonance spectroscopy confirmed that monocationic, ring-closed NDMG has less concentrated charge and more constrained motion than monocationic, ring-open NDMG. This evidence supports the theory that monocationic NDMG forms an intramolecular hydrogen bond and that this may be responsible for the minimum in α. This difference may explain the differences in binding constants between NDMG and N-MAP.

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.

Estudo teórico QTAIM e DFT dos compostos de coordenação: efeito quelato, titanocenos e ligação química

This work is a study of coordination compounds by quantum theory of atoms in molecules (QTAIM), based on the topological analysis of the electron density of molecular systems, both theoretically and experimentally obtained. The coordination chemistry topics which were studied are the chelate effect, bent titanocene and chemical bond in coordination complexes. The chelate effect was investigated according to topological and thermodynamic parameters. The exchange of monodentate ligands on polydentate ligands from same transition metal increases the stability of the complex both from entropy and enthalpy contributions. In some cases, the latter had a higher contribution to the stability of the complex in comparison with entropy. This enthalpic contribution is explained according to topological analysis of the M-ligand bonds where polidentate complex had higher values of electron density of bond critical point, Laplacian of electron density of bond critical point and delocalization index (number of shared electrons between two atoms). In the second chapter, was studied bent titanocenes with bulky cyclopentadienyl derivative π-ligand. The topological study showed the presence of secondary interactions between the atoms of π-ligands or between atoms of π-ligand and -ligand. It was found that, in the case of titanocenes with small difference in point group symmetry and with bulky ligands, there was an nearly linear relationship between stability and delocalization index involving the ring carbon atoms (Cp) and the titanium. However, the titanocene stability is not only related to the interaction between Ti and C atoms of Cp ring, but secondary interactions also play important role on the stability of voluminous titanocenes. The third chapter deals with the chemical bond in coordination compounds by means of QTAIM. The quantum theory of atoms in molecules so far classifies bonds and chemical interactions in two categories: closed shell interaction (ionic bond, hydrogen bond, van der Waals interaction, etc) and shared interaction (covalent bond). Based on topological parameters such as electron density, Laplacian of electron density, delocalization index, among others, was classified the chemical bond in coordination compounds as an intermediate between closed shell and shared interactions

Crystal structure of a myotoxic Asp49-phospholipase A(2) with low catalytic activity: Insights into Ca2+ -independent catalytic mechanism

A myotoxic Asp49-phospholipase A(2) (Asp49-PLA(2)) with low catalytic activity (BthTX-II from Bothrops jararacussu venom) was crystallized and the molecular-replacement solution has been obtained with a dimer in the asymmetric unit. The quaternary structure of BthTX-II resembles the myotoxic Asp49-PLA2 PrTX-III (piratoxin III from B. pirajai venom) and all non-catalytic and myotoxic dimeric Lys49-PLA(2)s. Despite of this, BthTX-II is different from the highly catalytic and non-myotoxic BthA-I (acidic PLA(2) from B. jararacussu) and other Asp49-PLA(2)s. BthTX-II structure showed a severe distortion of calcium-binding loop leading to displacement of the C-terminal region. Tyr28 side chain, present in this region, is in an opposite position in relation to the same residue in the catalytic activity Asp49-PLA(2)s, making a hydrogen bond with the atom 0 delta 2 of the catalytically active Asp49, which should coordinate the calcium. This high distortion may also be confirmed by the inability of BthTX-II to bind Na+ ions at the Ca2+-binding loop, despite of the crystallization to have occurred in the presence of this ion. In contrast, other Asp49-PLA(2)s which are able to bind Ca2+ ions are also able to bind Na+ ions at this loop. The comparison with other catalytic, non-catalytic and inhibited PLA(2)s indicates that the BthTX-II is not able to bind calcium ions; consequently, we suggest that its low catalytic function is based on an alternative way compared with other PLA(2)s. (c) 2008 Elsevier B.V All rights reserved.

Crystal structure of a phospholipase A(2) homolog complexed with p-bromophenacyl bromide reveals important structural changes associated with the inhibition of myotoxic activity

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

Theoretical study of omeprazole behavior: Racemization barrier and decomposition reaction

omeprazole is a substituted benzimidazole which suppresses gastric-acid secretion by means of H+, K+-ATPase inhibition. It is an optically active drug with the sulfur of the sulfoxide being the chiral center. This pro-drug can be easily converted into its respective sulfenamide at low pH. In this work, omeprazole has been studied in relation to racemization barrier and decomposition reaction. Quantum chemistry coupled to PCA chemometric method were used to find all minimum energy structures. Conformational analysis and calculation of racemization barriers were carried out by PM3 semiempirical method (Gaussian 98). The average racemization energy barrier for all minimum energy structures (43.56 kcal mol(-1)) can be related to the velocity constant in Eyring's equation. The enormous half-life time at 100 degrees C (9.04 x 10(4) years) indicates that the process cannot be observed in human time scale. on the other hand, the difference of free energy change (Delta(Delta G) = -266.78 kcal mol(-1)) for the decomposition reaction shows that the process is favorable to the sulfenamide formation. The highly negative Delta(Delta G) obtained for the decomposition reaction shows that this process is extremely exothermic. This result explains why omeprazole decomposes and does not racemize. (C) 2008 Wiley Periodicals, Inc.

Crystal Structure Determination of Mebendazole Form A Using High-Resolution Synchrotron X-Ray Powder Diffraction Data

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

Zirconia needles synthesized inside hexagonal swollen liquid crystals

We report the synthesis of zirconia microneedles by the direct nucleation of particles inside a hexagonal swollen liquid crystal (SLC) (cell parameter a = 27 nm) prepared by mixing with the proper ratio, an aqueous solution of sulfated zirconium colloids, a cationic surfactant (cetylpyridinium chloride), cychlohexane as swelling agent with an oil over water ratio of 2.5 (vol.), and 1-pentanol as cosurfactant. After a slow crystallogenesis that can be enhanced by an initial induction step under moderate temperature, particles in the centimeter range can be obtained, with a very high shape ratio (over 100). These particles are made of crystalline octahydrate zirconium oxychloride containing pores of 20 nm diameter, aligned along the main axis of the liquid crystal, as the fingerprint of the oil cylinders present in the hexagonal phase. The morphology of these particles confirms that the shaping mechanism is based on true liquid crystal templating (TLCT). Further thermal treatment of these particles, after extraction from the SLC, leads to the crystallization of zirconia with the same needlelike morphology as the zirconium oxychloride.

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.

Highly swollen liquid crystals as new reactors for the synthesis of nanomaterials

Synthesis and self-assembly of nanomaterials can be controlled by the properties of soft matter. on one hand, dedicated nanoreactors such as reverse microemulsions or miniemulsions can be designed. on the other hand, direct shape control can be provided by the topology of liquid crystals that confine the reacting medium within a specific geometry. In the first case, the preparation of micro- or miniemulsions generally requires energetic mechanical stirring. The second approach uses thermodynamically stable systems, but it remains usually limited to binary (water + surfactant) systems. We report the preparation of different families of materials in highly ordered quaternary mediums that exhibit a liquid crystal structure with a high cell parameter. They were prepared with the proper ratios of salted water, nonpolar solvent, surfactant. and cosurfactants that form spontaneously swollen hexagonal phases. These swollen liquid crystals can be prepared from all classes of surfactants (cationic, anionic, and nonionic). They contain a regular network of parallel cylinders, whose diameters can be swollen with a nonpolar solvent, that are regularly spaced in a continuous aqueous salt solution. We demonstrate in the present report that both aqueous and organic phases can be used as nanoreactors for the preparation of materials. This property is illustrated by various examples such as the synthesis of platinum nanorods prepared in the aqueous phase or zirconia needles or the photo- or gamma-ray-induced polymerization of polydiacetylene in the organic phase. In all cases, materials can be easily extracted and their final shapes are directed by the structure-directing effect imposed by the liquid crystal.

ONIOM study of dissociated hydrogen and water on ZnO surface

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

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.