Physical nature of interactions within the active site of cytosine-5-methyltransferase

The physical nature of interactions within the active site of cytosine-5-methyltransferase (CMT) was studied using a variation-perturbation energy decomposition scheme defining a sequence of approximate intermolecular interaction energy models. These models have been used to analyze the catalytic activity of residues constituting cytosine-5-methyltransferase active site as well their role in the binding group of de novo designed inhibitors. Our results indicate that Glu119, Arg163, and Arg165 appear to play the dominant role in stabilizing the protonated transition state structure and their influence can be qualitatively approximated by electrostatic interactions alone. The stabilization of neutral structures of the alternative reaction pathway is small, which might suggest the protonated pathway as preferred by the enzyme. Exchange and delocalization terms are negligible in most cases, or they cancel each other to some extent. Interactions of inhibitors with the CMT active site are dominated by electrostatic multipole contributions in analogy with previously studied transition state analogue inhibitors of leucyl aminopeptidase.     

Analysis of charge transport in gels containing polyoxometallates using methods of different sensitivity to migration

Two methods have been used for examination of transport of charge in gels soaked with DMF and containing dissolved polyoxometallates. The first method is based on the analysis of both Cottrellian and steady-state currents and therefore is capable of giving the concentration of the electroactive redox centres and their transport (diffusion-type) coefficient. The second method provides the real diffusion coefficients, i.e. transport coefficients free of migrational influence, for both the substrate and the product of the electrode reaction. Several gels based on poly(methyl methacrylate), with charged (addition of 1-acrylamido-2-methyl-2-propanesulphonic acid to the polymerization mixture) and uncharged chains, have been used in the investigation. The ratio obtained for the diffusion coefficient (second method) and transport coefficient (first method) was smaller for the gels containing charged polymer chains than for the gels with uncharged chains. In part these changes could be explained by the contribution of migration to the transport of polyoxomatallates in the gels. However, the impact of the changes in the polymer-channel capacity at the electrode surface while the electrode process proceeds was also considered. These structural changes should affect differently the methods based on different time domains.     

Molecular-dynamics simulations of the transport properties of a single polymer chain in two dimensions

Molecular-dynamics simulations are conducted to elucidate the critical factors affecting the transport properties of isolated polymer chains in strictly two dimensions. The relevance of surface inhomogeneity is critically examined. We unequivocally find that surface inhomogeneity is critical in obtaining transport behavior consistent with the recent measurements of surface diffusion for polymers adsorbed at the solid-liquid interface. For a systematic investigation of this point, heterogeneity was introduced by decorating the surface with impenetrable elements and we find that chain diffusivity crossed over from Rouse-type behavior to reptationlike with increasing surface coverage of obstacles. This transition in behavior occurred when the mean distance between obstacles is approximately equal to the end-to-end distance, Re, of the two-dimensional chain. Our results underscore the importance of surface disorder (not only literal obstacles but by reasonable extension also to other types of disorder) in determining the transport behavior of chains adsorbed to solids.     

On the influence of microsolvation by argon atoms on the electron affinity properties of water dimer

This work provides a comparison of neutral (H2O)2Ar(n) and negatively charged (H2O)(2-)Ar(n) complexes. The excess electron stabilizes the complexes and leads to the trans to cis rearrangement within the water dimer core. In the case of small complexes (n < or = 4) the microsolvation of the dimer by argon atoms arises on the trans side with respect to the donor water molecule. The stabilization of an excess electron is enhanced by the delocalization of the electronic charge density due to microsolvation. The process of cis to trans rotation is induced by the electric field of the approaching negative charge. The interaction energy decomposition suggests a more ionic character of binding in the negatively charged complexes. The attachment of an electron is controlled by the correlation energy.     

A Geant4 Monte Carlo method for synthesizing radioxenon beta-gamma coincidence spectra

This paper describes a Monte Carlo (MC) simulation method for calculating radioxenon beta-gamma coincidence spectral information. These spectral components include detector response simulations by Geant4 modeling, detector energy and resolution calibrations using the histograms of detector response, beta-gamma coincidence efficiency values and spectral interference ratios. The work presented in this paper demonstrates the feasibility of using the spectral information to create beta-gamma coincidence spectra at various radioxenon activity concentrations. The analysis of these synthetic spectra by XECON software shows an excellent correlation between the analysed radioxenon activity concentration and number of MC samplings.     

Electron localizability indicators ELI–D and ELIA for highly correlated wavefunctions of homonuclear dimers. II. N2, O2, F2, and Ne2

Electron localizability indicators based on the electron pair density ELI–D and ELIA Electron localizability indicators ELI‐D and ELIA based on the electron pair density are studied for the correlated ground‐state wavefunctions of N₂, O₂, F₂, and Ne₂ diatomics. Different basis sets and reference spaces are used for the multireference configuration interaction method following the complete active space calculations to investigate the local effect of electron correlation on the extent of electron localizability in position space determined by the two indicators. The results are complemented by calculations of effective bond order, vibrational frequency, and Laplacian of the electron density at the bond midpoint. It turns out that for O₂ and F₂, the reliable topology of ELI–D is obtained only at the correlated level of theory. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

Geant4 Monte Carlo radioxenon beta-gamma coincidence efficiency simulation for a phoswich detector

In this work, a Monte Carlo (MC) simulation model is established to accurately characterize a phoswich beta-gamma coincidence detector system. This model can be easily used to predict the beta-gamma coincidence efficiencies of xenon radioisotopes at various stable xenon concentrations in the counting cell. The results demonstrate that there is a significant inverse correlation between beta-gamma coincidence efficiency and stable xenon concentration. The influence of stable xenon concentration on beta-gamma coincidence counting efficiency has been investigated for each individual xenon radioisotope. The results indicate that the effect of stable xenon concentration on beta-gamma coincidence efficiency depends on the xenon radioisotope and its decay modes. The coincidence efficiency of ¹³³Xe with 31.0-keV X-ray decay mode is the most affected one; and then followed by ^131mXe, ¹³³Xe with 81.0-keV gamma-ray decay mode, ^133mXe and finally ¹³⁵Xe. The study also indicates that the gamma absorption by xenon gas plays more of a role in the decrease of beta-gamma coincidence efficiency for ¹³³Xe and ¹³⁵Xe, and that the conversion electron spectrum shifting and broadening plays more of a role in the reduction of beta-gamma coincidence efficiency for the metastable radioxenon of ^131mXe and ^133mXe.     

Miniature flowing atmospheric-pressure afterglow ion source for facile interfacing of CE with MS

Here, we present a miniaturized version of the flowing atmospheric-pressure afterglow (miniFAPA) ion source and use it for sheathless coupling of CE with MS. The simple design of the CE-miniFAPA-MS interface makes it easy to separate the electric potentials used for CE and for ionization. A pneumatically assisted nebulization of the CE effluent transfers the analytes from the liquid phase into the gas phase before they are ionized by interacting with reactive species produced by the FAPA. An important advantage of this interface is its high stability during operation: optimization of five different parameters indicated that the interface is not sensitive to minor deviations from the optimum values. Other advantages include ease of construction and maintenance, as well as relatively low cost. Samples with complex matrices, such as yeast extract, soil extract and urine, spiked with the test compounds, were successfully analyzed using the CE-miniFAPA-MS setup.     

Determination of adrenolytic drugs by SPME–LC–MS

Five adrenolytic drugs have been analyzed by liquid chromatography–mass spectrometry (LC–MS). Samples were prepared by solid-phase microextraction (SPME) using polypyrrole fibers coated on stainless steel support as an adsorbent for the drugs. Adsorption efficiencies were 95% and were close for all the drugs investigated. Relative standard deviations (RSD), calculated for samples prepared in standard solutions, were in the range 2.5–13%, however RSD values for the drugs in human plasma were 2.5–4.5%. Using LC–MS the limit of detection (LOD) and the limit of quantification (LOQ) were in the ranges 0.11–0.18 and 0.39–0.54 ng mL⁻¹, respectively, for the five drugs.     

A modular approach to catalytic synthesis using a dual-functional linker for Click and Suzuki coupling reactions

The stable benzylazido-boronate ester 1 is presented as an example of a dual-functional linker that allows the synthetically valuable boronate motif to be clicked onto other molecules under mild conditions. The utility of the azido-boronate motif as a modular building block is demonstrated in the rapid synthesis of drug-like structures employing sequential catalytic azide-alkyne cycloaddition and Suzuki coupling reactions.