Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0.

Metabolic problems lead to numerous failures during clinical trials, and much effort is now devoted to developing in silico models predicting metabolic stability and metabolites. Such models are well known for cytochromes P450 and some transferases, whereas less has been done to predict the activity of human hydrolases. The present study was undertaken to develop a computational approach able to predict the hydrolysis of novel esters by human carboxylesterase hCES2. The study involved first a homology modeling of the hCES2 protein based on the model of hCES1 since the two proteins share a high degree of homology (congruent with 73%). A set of 40 known substrates of hCES2 was taken from the literature; the ligands were docked in both their neutral and ionized forms using GriDock, a parallel tool based on the AutoDock4.0 engine which can perform efficient and easy virtual screening analyses of large molecular databases exploiting multi-core architectures. Useful statistical models (e.g., r (2) = 0.91 for substrates in their unprotonated state) were calculated by correlating experimental pK(m) values with distance between the carbon atom of the substrate's ester group and the hydroxy function of Ser228. Additional parameters in the equations accounted for hydrophobic and electrostatic interactions between substrates and contributing residues. The negatively charged residues in the hCES2 cavity explained the preference of the enzyme for neutral substrates and, more generally, suggested that ligands which interact too strongly by ionic bonds (e.g., ACE inhibitors) cannot be good CES2 substrates because they are trapped in the cavity in unproductive modes and behave as inhibitors. The effects of protonation on substrate recognition and the contrasting behavior of substrates and products were finally investigated by MD simulations of some CES2 complexes.

Calmodulin/KCa3.1 channel interactions as determinant to the KCa3.1 Ca2+ dependent gating : theoretical and experimental analyses

Differentes études ont montré que la sensibilité au Ca2+ du canal KCa3.1, un canal potassique indépendant du voltage, était conférée par la protéine calmoduline (CaM) liée de façon constitutive au canal. Cette liaison impliquerait la région C-lobe de la CaM et un domaine de $\ikca$ directement relié au segment transmembranaire S6 du canal. La CaM pourrait égalment se lier au canal de façon Ca2+ dépendante via une interaction entre un domaine de KCa3.1 du C-terminal (CaMBD2) et la région N-lobe de la CaM. Une étude fut entreprise afin de déterminer la nature des résidus responsables de la liaison entre le domaine CaMBD2 de KCa3.1 et la région N-lobe de la CaM et leur rôle dans le processus d'ouverture du canal par le Ca2+. Une structure 3D du complexe KCa3.1/CaM a d'abord été générée par modélisation par homologie avec le logiciel MODELLER en utilisant comme référence la structure cristalline du complexe SK2.2/CaM (PDB: 1G4Y). Le modèle ainsi obtenu de KCa3.1 plus CaM prévoit que le segment L361-S372 dans KCa3.1 devrait être responsable de la liaison dépendante du Ca2+ du canal avec la région N-lobe de la CaM via les résidus L361 et Q364 de KCa3.1 et E45, E47 et D50 de la CaM. Pour tester ce modèle, les résidus dans le segment L361-S372 ont été mutés en Cys et l'action du MTSET+ (chargé positivement) et MTSACE (neutre) a été mesurée sur l'activité du canal. Des enregistrements en patch clamp en configuration ``inside-out`` ont montré que la liaison du réactif chargé MTSET+ au le mutant Q364C entraîne une forte augmentation du courant, un effet non observé avec le MTSACE. De plus les mutations E45A et E47A dans la CaM, ont empêché l'augmentation du courant initié par MTSET+ sur le mutant Q364C. Une analyse en canal unitaire a confirmé que la liaison MTSET+ à Q364C cause une augmentation de la probabilité d'ouverture de KCa3.1 par une déstabilisation de l'état fermé du canal. Nous concluons que nos résultats sont compatibles avec la formation de liaisons ioniques entre les complexes chargés positivement Cys-MTSET+ à la position 364 de KCa3.1 et les résidus chargés négativement E45 et E47 dans la CaM. Ces données confirment qu'une stabilisation électrostatique des interactions CaM/KCa3.1 peut conduire à une augmentation de la probabilité d'ouverture du canal en conditions de concentrations saturantes de Ca2+.

Acid dye biodegradation using saccharomyces cerevisiae immobilized with polyethyleneimine-treated sugarcane bagasse

Chemical reagents used by the textile industry are very diverse in their composition, ranging from inorganic compounds to polymeric compounds. Strong color is the most notable characteristic of textile effluents, and a large number of processes have been employed for color removal. In recent years, attention has been directed toward various natural solid materials that are able to remove pollutants from contaminated water at low cost, such as sugarcane bagasse. Cell immobilization has emerged as an alternative that offers many advantages in the biodegradation process, including the reuse of immobilized cells and high mechanical strength, which enables metabolic processes to occur under adverse conditions of pH, sterility, and agitation. Support treatment also increases the number of charges on the surface, thereby facilitating cell immobilization processes through adsorption and ionic bonds. Polyethyleneimine (PEI) is a polycationic compound known to have a positive effect on enzyme activity and stability. The aim of the present study was to investigate a low-cost alternative for the biodegradation and bioremediation of textile dyes, analyzing Saccharomyces cerevisiae immobilization in activated bagasse for the promotion of Acid Black 48 dye biodegradation in an aqueous solution. A 1 % concentration of a S. cerevisiae suspension was evaluated to determine cell immobilization rates. Once immobilization was established, biodegradation assays with free and immobilized yeast in PEI-treated sugarcane bagasse were evaluated for 240 h using UV-vis spectrophotometry. The analysis revealed significant relative absorbance values, indicating the occurrence of biodegradation in both treatments. Therefore, S. cerevisiae immobilized in sugarcane bagasse is very attractive for use in biodegradation processes for the treatment of textile effluents. © 2012 Springer Science+Business Media Dordrecht.

Usos de membranas de quitosana na remoção de cobre em águas residuais

In this work a chitosan (CS) ionically crosslinked were manufactured by treatment with sulfuric acid solution for application in the treatment of wastewater from oil industry. Two crosslinking process were developed: homogeneous and heterogeneous. In the homogeneous process the ratio molar of SO42-/ NH3+ (1:6 and 1:4) were the variable analyzed, denominated CS16 and CS14 respectively. In the heterogeneous process the soaking time of the membranes in sulfuric acid solution were the variable studied, being used times of 5 (CS5) and 30 (CS30) minutes. FTIR-ATR results indicated no changes in the characteristics of chitosan after homogeneous crosslinking process, while heterogeneous crosslinking showed formation of ionic bonds between protonated groups from chitosan and the crosslinking agent sulfate ions. TG/DTG and XRD analysis confirmed the formation of these interactions, as also shown the new structure on the surface region of CS5 and CS30 membranes compared to CS, CS16 e CS14. Swelling test in aqueous medium have shown that crosslinking process reduced the membrane sorption capacity. Swelling test in acid medium demonstrated that CS16 and CS14 membranes increasing the adsorption capacity up to a maximum percentage of 140% approximately, whereas the CS5 e CS30 reached a maximum of 60%. The mechanical properties indicated the stiff and ductile behavior of crosslinked membrane. Adsorption experiments of CuCl2 results that CS16 membranes reached the efficiency maximum with 73% of copper removal at pH 5.0 and 87% at pH 4.0. The experiments with CuSO4 also obtained efficiency maximum to the CS16 membrane and 80% to the removal of Cu2+ ions. Also was verified that the increase of concentration and temperature cause a decrease in the adsorption capacity for all membranes. Kinetics study indicated that pseudo-second-order obtained characterized better the membranes. Equilibrium studies demonstrated that the CS, CS16 and CS14 follow the Langmuir model, whereas CS5 and CS30 follows Freundlich model. Filtration experiments results with rejection maximum to the CS16 and CS5 membranes, reaching 92 and 98% respectively.

Usos de membranas de quitosana na remoção de cobre em águas residuais

In this work a chitosan (CS) ionically crosslinked were manufactured by treatment with sulfuric acid solution for application in the treatment of wastewater from oil industry. Two crosslinking process were developed: homogeneous and heterogeneous. In the homogeneous process the ratio molar of SO42-/ NH3+ (1:6 and 1:4) were the variable analyzed, denominated CS16 and CS14 respectively. In the heterogeneous process the soaking time of the membranes in sulfuric acid solution were the variable studied, being used times of 5 (CS5) and 30 (CS30) minutes. FTIR-ATR results indicated no changes in the characteristics of chitosan after homogeneous crosslinking process, while heterogeneous crosslinking showed formation of ionic bonds between protonated groups from chitosan and the crosslinking agent sulfate ions. TG/DTG and XRD analysis confirmed the formation of these interactions, as also shown the new structure on the surface region of CS5 and CS30 membranes compared to CS, CS16 e CS14. Swelling test in aqueous medium have shown that crosslinking process reduced the membrane sorption capacity. Swelling test in acid medium demonstrated that CS16 and CS14 membranes increasing the adsorption capacity up to a maximum percentage of 140% approximately, whereas the CS5 e CS30 reached a maximum of 60%. The mechanical properties indicated the stiff and ductile behavior of crosslinked membrane. Adsorption experiments of CuCl2 results that CS16 membranes reached the efficiency maximum with 73% of copper removal at pH 5.0 and 87% at pH 4.0. The experiments with CuSO4 also obtained efficiency maximum to the CS16 membrane and 80% to the removal of Cu2+ ions. Also was verified that the increase of concentration and temperature cause a decrease in the adsorption capacity for all membranes. Kinetics study indicated that pseudo-second-order obtained characterized better the membranes. Equilibrium studies demonstrated that the CS, CS16 and CS14 follow the Langmuir model, whereas CS5 and CS30 follows Freundlich model. Filtration experiments results with rejection maximum to the CS16 and CS5 membranes, reaching 92 and 98% respectively.

A microscopic view of substitution reactions solvated by ionic liquids

The solvation effect of the ionic liquid 1-N-butyl-3-methylimidazolium hexafluorophosphate on nucleophilic substitution reactions of halides toward the aliphatic carbon of methyl p-nitrobenzenesulfonate (pNBS) was investigated by computer simulations. The calculations were performed by using a hybrid quantum-mechanical/molecular-mechanical (QM/MM) methodology. A semiempirical Hamiltonian was first parametrized on the basis of comparison with ab initio calculations for Cl(-) and Br(-) reaction with pNBS at gas phase. In condensed phase, free energy profiles were obtained for both reactions. The calculated reaction barriers are in agreement with experiment. The structure of species solvated by the ionic liquid was followed along the reaction progress from the reagents, through the transition state, to the final products. The simulations indicate that this substitution reaction in the ionic liquid is slower than in nonpolar molecular solvents proper to significant stabilization of the halide anion by the ionic liquid in comparison with the transition state with delocalized charge. Solute-solvent interactions in the first solvation shell contain several hydrogen bonds that are formed or broken in response to charge density variation along the reaction coordinate. The detailed structural analysis can be used to rationalize the design of new ionic liquids with tailored solvation properties. (c) 2008 American Institute of Physics.

Design and characterization of novel biopolymeric structure using biocompatible ionic liquids

The main objective of this thesis was the development of polymeric structures from the dissolution of FucoPol, a bacterial exopolysaccharide (EPS), in a biocompatible ionic liquid, choline acetate. The FucoPol was produced by the bacteria Enterobacter A47 using glycerol as carbon source at controlled temperature and pH (30ºC and 7, respectively). At the end of 3 days it was produced 7 g/L of FucoPol. The net yield of Fucopol in glycerol (YP/S) was 0.22 g/g and the maximum productivity 2.37 g/L.d This polymer was characterized about its composition in sugars and acyl groups (by High-Performance Liquid Chromatography - HPLC), containing fucose (35 % mol), galactose (21 % mol), glucose (29 % mol), rhamnose (3% mol) and glucuronic acid (12% mol) as well as acetate (14.28 % mol), pyruvate (2.15 % mol) and succinate (1.80 % mol). Its content of water and ash was 15% p/p and 2% p/p, respectively, and the chemical bonds (determined by Infrared Spectroscopy - FT-IR) are consistent to the literature reports. However, due to limitations in Differential Scanning Calorimetry (DSC) equipment it was not possible to determine the glass transition temperature. In turn, the ionic liquid showed the typical behavior of a Newtonian fluid, glass transition temperature (determined by DSC) -98.03ºC and density 1.1031 g/cm3. The study of chemical bonds by FT-IR showed that amount of water (8.80%) influenced the visualization of the bands predicted to in view of their chemical structure. After the dissolution of the FucoPol in the ionic liquid at different temperatures (50, 60, 80 and 100 ° C) it was promoted the removal of this by the phase inversion method using deionized water as a solvent, followed by drying in an oven at 70 ° C. The mixtures before and after the phase inversion method were characterized through the studies mentioned above. In order to explore possible application field’s biocompatibility assays and collage on balsa wood tests were performed. It was found that the process of washing with water by the phase inversion method was not totally effective in removing the biocompatible ionic liquid, since all FucoPol – IL mixtures still contained ionic liquid in their composition as can be seen by the DSC results and FT-IR. In addition, washing the mixtures with water significantly altered the composition of FucoPol. However, these mixtures, that developed a viscous behavior typical of a non-Newtonian fluid (shear-thinning), have the potential to be applied in the biomedical field as well as biological glues.

Ionic-covalent transition in titanium oxides

The nature of the chemical bond in three titanium oxides of different crystal structure and different formal oxidation state has been studied by means of the ab initio cluster-model approach. The covalent and ionic contributions to the bond have been measured from different theoretical techniques. All the analysis is consistent with an increasing of covalence in the TiO, Ti2O3, and TiO2 series as expected from chemical intuition. Moreover, the use of the ab initio cluster-model approach combined with different theoretical techniques has permitted us to quantify the degree of ionic character, showing that while TiO can approximately be described as an ionic compound, TiO2 is better viewed as a rather covalent oxide.

Stabilization of the ionic form of weak acid cation exchange resins

Weak acid cation exchange (WAC) resins are used in the chromatographic separation of betaine from vinasse, a by-product of sugar industry. The ionic form of the resin determines the elution time of betaine. When a WAC-resin is in hydrogen form, the retention time of betaine is the longest and betaine elutes as the last component of vi-nasse from the chromatographic column. If the feed solution contains salts and its pH is not acidic enough to keep the resin undissociated, the ionic form of the hydrogen form resin starts to alter. Vinasse contains salts and its pH is around 5, it also contains weak acids. To keep the metal ion content (Na/H ratio) of the resin low enough to ensure successful separation of betaine, acid has to be added to either eluent (water) or vinasse. The aim of the present work was to examine by laboratory experiments which option requires less acid. Also the retention mechanism of betaine was investigated by measuring retention volumes of acetic acid and choline in different Na/H ratios of the resin. It was found that the resulting ionic form of the resin is the same regardless of whether the regeneration acid is added to the eluent or the feed solution (vinasse). Be-sides the salt concentration and the pH of vinasse, also the concentration of weak acids in the feed affects the resulting ionic form of the resin. The more buffering capacity vinasse has, the more acid is required to keep the ionic form of the resin desired. Vinasse was found to be quite strong buffer solution, which means relatively high amounts of acid are required to prevent the Na/H ratio from increasing too much. It is known that the retention volume of betaine decreases significantly, when the Na/H ratio increases. This is assumed to occur, because the amount of hydrogen bonds between the carboxylic groups of betaine and the resin decreases. Same behavior was not found with acetic acid. Choline has the same molecular structure as betaine, but instead of carboxylic group it has hydroxide group. The retention volume of choline increased as the Na/H ratio of the resin increased, because of the ion exchange reaction between choline cation and dissociated carboxylic group of the resin. Since the retention behavior of choline on the resin is opposite to the behavior of be-taine, the strong affinity of betaine towards hydrogen form WAC-resin has to be based on its carboxylic group. It is probable that the quaternary ammonium groups also affect the behavior of the carboxylic groups of betaine, causing them to form hydrogen bonds with the carboxylic groups of the resin.

Azolium-based systems: application of an anion exchange resin (A- form) method and 1H NMR analysis of the charged-assisted (CH)+·anion hydrogen bonds

The counteranion exchange of quaternary 1,2,3-triazolium salts was examined using a simple method that permitted halide ions to be swap for a variety of anions using an anion exchange resin (A¯ form). The method was applied to 1,2,3-triazolium-based ionic liquids and the iodideto- anion exchange proceeded in excellent to quantitative yields, concomitantly removing halide impurities. Additionally, an anion exchange resin (N3¯ form) was used to obtain the benzyl azide from benzyl halide under mild reaction. Likewise, following a similar protocol, bis(azidomethyl)arenes were also synthesized in excellent yields. The results of a proton NMR spectroscopic study of simple azolium-based ion pairs are discussed, with attention focused on the significance of the charged-assisted (CH)+···anion hydrogen bonds of simple azolium systems such as 1-butyl-3-methylimidazolium and 1-benzyl-3-methyl-1,2,3-triazolium salts.

Azolium-based systems: application of an anion exchange resin (A- form) method and 1H NMR analysis of the charged-assisted (CH)+·anion hydrogen bonds

The counteranion exchange of quaternary 1,2,3-triazolium salts was examined using a simple method that permitted halide ions to be swap for a variety of anions using an anion exchange resin (A¯ form). The method was applied to 1,2,3-triazolium-based ionic liquids and the iodideto- anion exchange proceeded in excellent to quantitative yields, concomitantly removing halide impurities. Additionally, an anion exchange resin (N3¯ form) was used to obtain the benzyl azide from benzyl halide under mild reaction. Likewise, following a similar protocol, bis(azidomethyl)arenes were also synthesized in excellent yields. The results of a proton NMR spectroscopic study of simple azolium-based ion pairs are discussed, with attention focused on the significance of the charged-assisted (CH)+···anion hydrogen bonds of simple azolium systems such as 1-butyl-3-methylimidazolium and 1-benzyl-3-methyl-1,2,3-triazolium salts.

Azolium-based systems: application of an anion exchange resin (A- form) method and 1H NMR analysis of the charged-assisted (CH)+·anion hydrogen bonds

The counteranion exchange of quaternary 1,2,3-triazolium salts was examined using a simple method that permitted halide ions to be swap for a variety of anions using an anion exchange resin (A¯ form). The method was applied to 1,2,3-triazolium-based ionic liquids and the iodideto- anion exchange proceeded in excellent to quantitative yields, concomitantly removing halide impurities. Additionally, an anion exchange resin (N3¯ form) was used to obtain the benzyl azide from benzyl halide under mild reaction. Likewise, following a similar protocol, bis(azidomethyl)arenes were also synthesized in excellent yields. The results of a proton NMR spectroscopic study of simple azolium-based ion pairs are discussed, with attention focused on the significance of the charged-assisted (CH)+···anion hydrogen bonds of simple azolium systems such as 1-butyl-3-methylimidazolium and 1-benzyl-3-methyl-1,2,3-triazolium salts.

Platinum Electrodeposition in an Ionic Liquid Analogue. Solvent Stability Monitoring

The use of ionic liquid analogues as solvents has increased in order to substitute the aqueous solvents in some applications in which the side reactions are undesirable. However these solvents prepared from the mixture in the eutectic proportion of species establishing hydrogen bonds are susceptible of electrochemical reactions. The study of platinum deposition on vitreous carbon in an ionic liquid analogue (2 urea: choli ne chloride) is presented; the electrochemical study has permitted to interpret the sequence of the metal deposition process and simultaneously to analyze the behavior of the ionic liquid analogue along the process. Reduction reactions of the solvent relat ed both to the electronation of choline and hydrogen formation have been detected. Different substrata have been used in order to test the possibility and the extent of these reactions depending on the nature of material. The results indicate that the feas ible electrochemical window of the substrate/solvent is highly dependent of the kind of substrate; the negative limit is tied by the massive hydrogen reaction, reaction enhanced by the electrocatalytic character of the substrate.

Ionic-covalent transition in titanium oxides

The nature of the chemical bond in three titanium oxides of different crystal structure and different formal oxidation state has been studied by means of the ab initio cluster-model approach. The covalent and ionic contributions to the bond have been measured from different theoretical techniques. All the analysis is consistent with an increasing of covalence in the TiO, Ti2O3, and TiO2 series as expected from chemical intuition. Moreover, the use of the ab initio cluster-model approach combined with different theoretical techniques has permitted us to quantify the degree of ionic character, showing that while TiO can approximately be described as an ionic compound, TiO2 is better viewed as a rather covalent oxide.

Ultrasonic chemical oxidative degradations of 1,3-dialkylimidazolium ionic liquids and their mechanistic elucidations

A highly efficient process for oxidative degradation of 1,3-dialkylimidazolium ionic liquids in hydrogen peroxide/acetic acid aqueous medium assisted by ultrasonic chemical irradiation is, for the first time, described. It is shown that more than 93% of the 1,3-dialkylimidazolium cation with the corresponding Cl-, Br-, BF4- and PF6- counter-anions at a concentration of 2.5 mM can be degraded at 50 degrees C within 12 h while at 72 h the conversions approach 99%. A tentative mechanism for the degradation of these ILs is for the first time proposed through a detailed kinetic analysis of several characteristic transients and/or immediate products, which are identified during the ILs degradation using GC-MS. The results clearly indicate that three hydrogen atoms in the imidazolium ring are the first sites preferably oxidized, followed by cleavage of the alkyl groups attached to the N atoms from the ring. The nature of the alkyl chain length on the imidazolium ring and the type of counter anion do not seem to affect the degradation process. Further, selective fragmentations of C-N bonds of the imidazolium or derived ring lead to ring opening, forming degraded intermediates. It is also shown that acetoxyacetic acid and biurea are the final kinetically stable degraded products from the ILs under the degradation conditions.