Reaction of Aplysia limacina metmyoglobin with hydrogen peroxide

Myoglobin (Mb) from gastropod mollusc Aplysia limacina shows only 20% sequence homology to the 'prototype' sperm whale Mb but exhibits a typical Mb fold and can reversibly bind oxygen. An intriguing feature of aplysia Mb is that it lacks the distal histidine and displays a ligand stabilisation based on an arginine. Here we report the reaction of aplysia metMb with hydrogen peroxide studied by optical and electron paramagnetic resonance (EPR) spectroscopies. Two electron oxidation of the protein by H2O2 results in formation of two intermediates typical for this class of reactions, the oxoferryl haem state and a globin-bound free radical. An unusual characteristic of the aplysia Mb reaction is formation, prior to haem oxidation, of an optically distinct compound with an EPR spectrum typical of the low spin Fe3+ haem state. This compound is interpreted as the complex between H2O2 and the ferric haem state (Compound), formed prior to cleavage of the dioxygen bond. We conclude that H2O2 is singly deprotonated in Compound which can thus be notated as [Fe3+--OOH]. A new low spin ferric haem state has been observed over the period of Compound decay, and hypotheses have been formulated as to its identity and role. The location of the protein bound radical observed in aplysia Mb is discussed in light of the fact that the protein does not have any tyrosine residues, the most common site of free radical formation in the haem protein/peroxide systems. All intermediates of the reaction are kinetically characterised.     

Formation of supported size-controlled nanoparticles of sulfated zirconia

Methods of the preparation of catalysts for alkane skeletal isomerization based on uniform nanoparticles of sulfated zirconia anchored to different supports were investigated. These catalysts were characterized by using the ICP, HRTEM and BET techniques. The activities of the catalysts in the reaction of n-butane isomerization were measured and compared with those of bulk catalysts.     

Thermal and mechanical properties of PE/organoclay nanocomposites

Polyethylene/montmorillonite clay nanocomposites were obtained via direct melt intercalation. The clay was organically modified with four different types of quaternary ammonium salts. The objective of this work is to study the use of montmorillonite clay in the production of nanocomposites by means on rheological, mechanical and crystallization properties of nanocomposites and to compare to the properties of the matrix and PE/unmodified clay nanocomposites. In general, the tensile test showed that the yield strength and modulus of the nanocomposites are close to the pure PE. Apparently, the mixture with Dodigen salt seems to be more stable than the pure PE and PE/unmodified clay.     

Sequential Injection Lab‐on‐Valve Procedure for the Determination of Amantadine Using Potentiometric Methods

Amantadine potentiometric detectors were developed, evaluated and incorporated in a SIA‐LOV manifold in order to accomplish the control of pharmaceutical formulations and urine. The electrodes incorporate α‐cyclodextrin as ionophore, dibutyl phthalate or 2‐fluorophenyl 2‐nitrophenyl ether as plasticizers and potassium tetrakis[3,5‐bis‐(trifluoromethyl)phenyl]borate (KTFPB) as cationic additive. The slope increased from 61.2 to 63.8 mV decade^?1 and the practical limit of detection from 2.6×10^?6 mol L^?1 to 2.5×10^?5 mol L^?1 when the plasticizer was changed from 2‐fluorophenyl 2‐nitrophenyl ether to dibutyl phthalate. When incorporated in the flow‐manifold the membranes composed by dibutyl phthalate or with 2‐fluorophenyl 2‐nitrophenyl ether presented slopes and a practical limit of detection of 69.8 mV decade^?1 and 1.5×10^?4 mol L^?1 or 73.7 mV decade^?1 and 5.4×10^?5 mol L^?1, respectively. The electrode presented stable responses for over a year, and were highly selective concerning the representative species of the two sample matrices assayed as interferents. Comparison of obtained results with those provided by reference methods and recovery assays, revealed adequate accuracy for control assays.     

The isobutylene-isobutane alkylation process in liquid HF revisited

Details on the mechanism of HF catalyzed isobutylene-isobutane alkylation were investigated. On the basis of available experimental data and high-level quantum chemical calculations, a detailed reaction mechanism is proposed taking into account solvation effects of the medium. On the basis of our computational results, we explain why the density of the liquid media and stirring rates are the most important parameters to achieve maximum yield of alkylate, in agreement with experimental findings. The ab initio Car-Parrinello molecular dynamics calculations show that isobutylene is irreversibly protonated in the liquid HF medium at higher densities, leading to the ion pair formation, which is shown to be a minimum on the potential energy surface after optimization using periodic boundary conditions. The HF medium solvates preferentially the fluoride anion, which is found as solvated [FHF](-) or solvated F(-.)(HF)(3). On the other hand, the tert-butyl cation is weakly solvated, where the closest HF molecules appear at a distance of about 2.9 Angstrom with the fluorine termination of an HF chain.     

Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition

Sequence dependence of DNA conformation plays a crucial role in its recognition by proteins and ligands. To clarify the relationship between sequence and conformation, it is necessary to quantify the conformational energy and specificity of DNA. Here, we make a systematic analysis of dodecamer DNA structures including all the 136 unique tetranucleotide sequences at the center by molecular dynamics simulations. Using a simplified conformational model with six parameters to describe the geometry of adjacent base pairs and harmonic potentials along these coordinates, we estimated the equilibrium conformational parameters and the harmonic potentials of mean force for the central base-pair steps from many trajectories of the simulations. This enabled us to estimate the conformational energy and the specificity for any given DNA sequence and structure. We tested our method by using sequence-structure threading to estimate the conformational energy and the Z-score as a measure of specificity for many B-DNA and A-DNA crystal structures. The average Z-scores were negative for both kinds of structures, indicating that the potential of mean force from the simulation is capable of predicting sequence specificity for the crystal structures and that it may be used to study the sequence specificity of both types of DNA. We also estimated the positional distribution of conformational energy and Z-score within DNA and showed that they are strongly position dependent. This analysis enabled us to identify particular conformations responsible for the specificity. The presented results will provide an insight into the mechanisms of DNA sequence recognition by proteins and ligands.     

Anisotropic local motions and location of amide protons in proteins

A new method has been developed to obtain dynamic and structural information about peptide planes in proteins by a combination of measurements of weak short-range cross-correlation rates R(H(N)N/NC') that are due to concerted fluctuations of the H(N)-N and N-C' dipole-dipole interactions and stronger long-range cross-correlation rates R(C'H(N)/H(N)N) and R(NH(N)/H(N)C(alpha)). The rates were interpreted using the axially symmetric Gaussian axial fluctuation model (GAF). The oscillation amplitudes as well as the positions of H(N) atoms with respect to peptide planes in ubiquitin were determined. Most N-H(N) bonds were found not to lie exactly along the bisector of the N-C' and N-C(alpha) bonds but to be slightly tilted toward the carbon-terminal side of the peptide.     

Interplay between Auger and ionization processes in nanocrystal quantum dots

We study the interplay between Auger effects and ionization processes in the limit of strong electronic confinement in core/shell CdSe/ZnS semiconductor nanocrystal quantum dots. Spectrally resolved fluorescence decay measurements reveal a monotonic increase of the photoluminescence decay rate on excitation density. Our results suggest that Auger recombination accelerates ionization processes that lead to the occupation of dark, nonemissive nanocrystal states. A model is proposed in the quantized Auger regime describing these experimental observations and providing an estimate of the Auger assisted ionization rates.     

High-resolution electron spin resonance spectroscopy of XeF* in solid argon. The hyperfine structure constants as a probe of relativistic effects in the chemical bonding properties of a heavy noble gas atom

Xenon fluoride radicals were generated by solid-state chemical reactions of mobile fluorine atoms with xenon atoms trapped in Ar matrix. Highly resolved electron spin resonance spectra of XeF* were obtained in the temperature range of 5-25 K and the anisotropic hyperfine parameters were determined for magnetic nuclei 19F, 129Xe, and 131Xe using naturally occurring and isotopically enriched xenon. Signs of parallel and perpendicular hyperfine components were established from analysis of temperature changes in the spectra and from numerical solutions of the spin Hamiltonian for two nonequivalent magnetic nuclei. Thus, the complete set of components of hyperfine- and g-factor tensors of XeF* were obtained: 19F (Aiso=435, Adip=1249 MHz) and 129Xe (Aiso=-1340, Adip=-485 MHz); g(parallel)=1.9822 and g(perpendicular)=2.0570. Comparison of the measured hyperfine parameters with those predicted by density-functional theory (DFT) calculations indicates, that relativistic DFT gives true electron spin distribution in the 2Sigma+ ground-state, whereas nonrelativistic theory underestimates dramatically the electron-nuclear contact Fermi interaction (Aiso) on the Xe atom. Analysis of the obtained magnetic-dipole interaction constants (Adip) shows that fluorine 2p and xenon 5p atomic orbitals make a major contribution to the spin density distribution in XeF*. Both relativistic and nonrelativistic calculations give close magnetic-dipole interaction constants, which are in agreement with the measured values. The other relativistic feature is considerable anisotropy of g-tensor, which results from spin-orbit interaction. The orbital contribution appears due to mixing of the ionic 2Pi states with the 2Sigma+ ground state, and the spin-orbit interaction plays a significant role in the chemical bonding of XeF*.