Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from Bacteroides fragilis complexed with imipenem

Herein, we present results from MD simulations of the Michaelis complex formed between the dizinc beta-lactamase from B. fragilis and imipenem. We considered two catalytically important configurations, which differ in the presence or absence of a hydroxide bridge connecting the two zinc ions in the active site. The structural and dynamical effects induced by substrate binding, the specific roles of the conserved residues and the zinc-bound water molecules, the near attack conformers of the Michaelis complex, and so forth, are discussed in detail. The relative stability of the two configurations was estimated from QM linear scaling calculations on the enzyme-substrate complex combined with Poisson-Boltzmann electrostatic calculations and normal mode calculations. Importantly, we find that the two configurations have similar energies, indicating that these two structures could readily be interchanged, thereby facilitating catalysis. The configuration with the hydroxide bound to the two zinc ions is predicted to be the resting form of the enzyme, while the configuration without the bridge is the reactive form that was found to place the hydroxide in position to attack the carbonyl of the beta-lactam ring. Thus, we propose that the enzyme initiates catalysis by converting from the hydroxide bridge form into the configuration that lacks the hydroxide bridge. This interconversion increases the nucleophilicity of the hydroxide ion and exposes it to the beta-lactam carbonyl, which ultimately facilitates nucleophilic attack. The implications of the observed modes of binding, the possible influence of mutating the Lys184 and Asn193 residues on substrate binding, and the reaction mechanism are also discussed in detail.     

Sensitive determination of diquat by a kinetic method using the stopped-flow mixing technique

A simple, sensitive, selective, fast and inexpensive assay for the determination of diquat is proposed. The method is based on the reduction of the herbicide to a strongly fluorescent monocation radical with sodium dithionite. The initial rate of this reaction is directly proportional to the diquat concentration. The stopped-flow mixing technique was used because the kinetic data can be obtained in only 7 s, meaning that the method can be automated. The calibration graph is linear over the range 5-500 ng ml-1 and the precision (RSD) is close to 1.2%. The applicability of the method was demonstrated by determining the herbicide in different kinds of samples.     

Thermal oxidation of cellulose investigated by chemiluminescence. The effect of magnesium and calcium carbonates and of different pHs

Whatman cellulose impregnated with calcium and magnesium carbonates was oxidized and chemiluminescence accompanying this oxidation has been measured. It was shown that magnesium ions in deacidified cellulose pulp promote the light emission significantly. On the other hand, acid papers give the more pronounced light signals at temperatures close to ambient. The relation between chemiluminescence runs and paper degradation has been implicated, with an attempt to extrapolate half-lives of paper samples to conditions close to ambient. To cite this article: J. Rychlý et al., C. R. Chimie 9 (2006).     

A Study of the Hydration of Lime-Pozzolan Binders

DTA/TG and TG/DTG thermal studies and XRD investigations were carried out on pastes of lime-pozzolan binders to examine the relative hydration process. The binders were prepared with two natural pozzolans and hydrated lime, mixed together in different proportions. The main hydrated phases formed in the pastes are calcium silicate hydrate (CSH) and mono-carboaluminate. The growth of CSH was greater for the paste of the pozzolan richer in reactive constituents. For pastes with a higher lime/pozzolan ratio, a slowing of the formation of CSH was observed, while the formation of monocarboaluminate was more intense. The calcium hydroxide contents of the pastes obtained by thermogravimetric analysis made it possible to determine the pozzolanic activities of the two pozzolans under examination. The mortars for the various lime-pozzolan binders displayed characteristic hardening. This revised version was published online in July 2006 with corrections to the Cover Date.     

Neutron activation analysis for chromium(III) and (VI) in lixiviated liquid through a calcined chromium(VI) adsorbed hydrotalcite

Summary Electrophoresis followed by neutron activation analysis was utilized to determine chromium(III) and (VI) in mixed solutions. These solutions proceeded from Cr(VI) adsorbed hydrotalcites heated at 800 °C to partially immobilize Cr in the Mg-Al oxide solid solution. Immobilization was studied by Cr lixiviation with NaCl solutions through the heated hydrotalcites. The results have shown that Cr lixiviated was in the form of CrO₄^2- ions, mainly because some Cr(VI) was not completely reduced to Cr(III) during heating. Chromium lixiviated from HT-Cr sample, heated at 800 °C and γ-irradiated at 1000 kGys, was found, as well, in the form of CrO₄^2- ions. Although γ-irradiation increases Cr immobilization in the solid, it does not reduce completely all CrO₄^2- ions present in the solid and, therefore, some Cr is lixiviated through the solid in the form of CrO₄^2- ion.     

Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations

To investigate the molecular details of the phosphoryl-transfer mechanism catalyzed by cAMP-dependent protein kinase, we performed quantum mechanical (QM) calculations on a cluster model of the active site and molecular dynamics (MD) simulations of a ternary complex of the protein with Mg(2)ATP and a 20-residue peptide substrate. Overall, our theoretical results confirm the participation of the conserved aspartic acid, Asp(166), as an acid/base catalyst in the reaction mechanism catalyzed by protein kinases. The MD simulation shows that the contact between the nucleophilic serine side chain and the carboxylate group of Asp(166) is short and dynamically stable, whereas the QM study indicates that an Asp(166)-assisted pathway is structurally and energetically feasible and is in agreement with previous experimental results.     

Adsorption and microcalorimetric investigations ofn-butylamine intercalation in α- and γ-zirconium phosphates

The intercalation process ofn-butylamine was investigated. The adsorption ofn-butylamine in interlamellar space had stepwise character in case of both crystalline forms of zirconium phosphate. The intercalatedn-butylamine existed at low concentration as bilayered complex. The reaction heat was determined by a microcalorimetric method. It was found that about 90% of it refers to the neutralization ofn-butylamine and only about 10% is related with surface adsorption (ion exchange). The steps of adsorption are 6.0 J/g and 1.0 J/g reaction heat values, respectively. The enthalpy balance of total process in dilute solution system (c ₀=3.0 vol%) is 14.67 kJ/mol. The calculated value for ion adsorption (exchange) was 1.37 kJ/mol.     

On-line preconcentration of inorganic mercury and methylmercury in sea-water by sorbent-extraction and total mercury determination by cold vapour atomic absorption spectrometry

A comparative study of three mercury chelate forming reagents [diethyldithiocarbamate, pyrrolidin-1-yldithioformate and diphenylthiocarbazone (dithizone)] has been carried out for the preconcentration of ultratrace amounts of inorganic mercury and methylmercury in silica C(18) minicolumns as the solid sorbent. Sample flow injection in-line sorbent extraction was coupled with continuous cold vapour atomic absorption spectrometry (CVAAS) for detection. Results showed the superiority of the carbamate type reagents over the dithizone for the on-line formation and preconcentration of the corresponding mercury chelates. Using diethyldithiocarbamate (DDC) as reagent, aqueous sample volumes of 100 ml can be preconcentrated with 100% efficiency for both inorganic mercury and methylmercury. Quantitative release of the retained DDC chelates was obtained for volumes of eluent (ethanol) of 50 microl. Following the proposed procedure, detection limits of 16 ng/l. of mercury were achieved for sample volumes of 25 ml. The relative standard deviation was +/- 3.4% at 0.5 microg/l. Hg(II) levels. The method has been successfully applied to the determination of low levels of mercury in sea-water.     

Synthese von 4H-Pyrano[2,3-d]pyrimidinen

Summary Good yields of substituted 5-(5R-2-furyl)-4H-pyrano[2,3-d]pyrimidines4 were obtained in the reaction of 2-ethoxymethyleneamino-3-cyano-4H-pyranes2 with ammonia. Compounds2 were prepared by the condensation of the starting 2-amino-5-acetyl-3-cyano-6-methyl-4H-pyranes1 with ethyl orthoformate. Spectral properties of the bicyclic system4 in relation to compounds3 are discussed.

     

Comprehensive kinetic studies on isothermal and non-isothermal reactions of some aluminium compounds

Residual differences after model fitting were investigated in both isothermal and non-isothermal kinetics in order to make numerical comparisons between several models and various parameter-estimating methods. Data from two independent experimental series were evaluated. A large data set, collected earlier under isothermal conditions from decompositions and hydrothermal reactions of aluminium hydroxides and oxides, was processed first. It showed that mechanical activation of the starting gibbsite affected reactivity of samples in several subsequent reactions for all model equations tried. The relative residual deviation concept is introduced, and statistics were applied to find a model that fits a certain reaction in most of the cases. In the second study, the sulphate decomposition step of aluminium sulphate octadecahydrate was investigated. TG curves were measured using a constant heating rate. Dynamic models were fitted by three mathematical methods, including a new general purpose one. Fitting ability of the methods with various complexity were compared on the basis of residual deviations obtained after integration of the model equations. As well as evaluating the best fit, this new parameter-estimating method provides a statistical analysis of the reliability of the whole model fitting process.