Essential dynamics and sidechain hydrogen bond cluster studies on eosinophil cationic protein

Eosinophil Cationic Protein (ECP) is a member of RNase A superfamily which carries out the obligatory catalytic role of cleaving RNA. It is involved in a variety of biological functions. Molecular dynamics simulations followed by essential dynamics analysis on this protein are carried out with the goal of gaining insights into the dynamical properties at atomic level. The top essential modes contribute to subspaces and to the transition phase. Further, the sidechain-sidechain/sidechain-mainchain hydrogen bond clusters are analyzed in the top modes, and compared with those of crystal structure. The role of residues identified by these methods is discussed in the context of concerted motion, structure and stability of the protein.

Hydrogen-bond dynamics near a micellar surface: Origin of the universal slow relaxation at complex aqueous interfaces

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than 100 ps. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5 kcal/mol.

Influence of the roughness of aggregate surface on the interface bond strength

An experimental investigation on the bond strength of the interface between mortar and aggregate is reported. Composite compact specimens were used for applying Mode I and Mode 11 loading effects. The influence of the type of mortar and type of aggregate and its roughness on the bond strength of the interface has been studied. It has been observed that the bond strength of the interface in tension is significantly low, though the mortars exhibited higher strength. The highest tensile bond strength values have been observed with rough concrete surface with M-13 mortar. The bond strength of the interface in Mode I load depends on the type of aggregate surface and its roughness, and the type of mortar, The bond strength of the interface between mortar M-13 cast against rough concrete in direct tension seems to be about one third of the strength of the mortar. However, it is about 1/20th to 1/10th with the mortar M-12 in sandwiched composite specimens. The bond strength of the interface in shear (Mode IT) significantly increases as the roughness and the phase angle of the aggregate surface increase. The strength of mortar on the interface bond strength has been very significant. The sandwiched composite specimens show relatively low bond strength in Mode I loading. The behavior of the interface in both Mode I and Mode 11 loading effects has been brittle, indicating catastrophic failure. (C) 2002 Elsevier Science Ltd. All rights reserved.

Theory of polymer breaking under tension

We consider the breaking of a polymer molecule which is fixed at one end and is acted upon by a force at the other. The polymer is assumed to be a linear chain joined together by bonds which satisfy the Morse potential. The applied force is found to modify the Morse potential so that the minimum becomes metastable. Breaking is just the decay of this metastable bond, by causing it to go over the barrier. Increasing the force causes the potential to become more and more distorted and eventually leads to the disappearance of the barrier. The limiting force at which the barrier disappears is D(e)a/2,D-e with a the parameters characterizing the Morse potential. The rate of breaking is first calculated using multidimensional quantum transition state theory. We use the harmonic approximation to account for vibrations of all the units. It includes tunneling contributions to the rate, but is valid only above a certain critical temperature. It is possible to get an analytical expression for the rate of breaking. We have calculated the rate of breaking for a model, which mimics polyethylene. First we calculate the rate of breaking of a single bond, without worrying about the other bonds. Inclusion of other bonds under the harmonic approximation is found to lower this rate by at the most one order of magnitude. Quantum effects are found to increase the rate of breaking and are significant only at temperatures less than 150 K. At 300 K, the calculations predict a bond in polyethylene to have a lifetime of only seconds at a force which is only half the limiting force. Calculations were also done using the Lennard-Jones potential. The results for Lennard-Jones and Morse potentials were rather different, due to the different long-range behaviors of the two potentials. A calculation including friction was carried out, at the classical level, by assuming that each atom of the chain is coupled to its own collection of harmonic oscillators. Comparison of the results with the simulations of Oliveira and Taylor [J. Chem. Phys. 101, 10 118 (1994)] showed the rate to be two to three orders of magnitude higher. As a possible explanation of discrepancy, we consider the translational motion of the ends of the broken chains. Using a continuum approximation for the chain, we find that in the absence of friction, the rate of the process can be limited by the rate at which the two broken ends separate from one another and the lowering of the rate is at the most a factor of 2, for the parameters used in the simulation (for polyethylene). In the presence of friction, we find that the rate can be lowered by one to two orders of magnitude, making our results to be in reasonable agreement with the simulations.

Synthesis, crystal structure and catalytic properties of (p-cymene)ruthenium(II) azophenol complexes: azophenyl to azophenol conversion by oxygen insertion to a ruthenium---carbon bond

Azophenol complexes of formulation [(η6-p-cymene)RuCl(Ln)] (1–6, n=1–6) were prepared by two synthetic methods involving either an oxygen insertion to the Ru---C bond in cycloruthenated precursors forming complexes 1 and 2 or from the reaction of [{(η6-p-cymene)RuCl}2(μ-Cl)2] with azophenol ligands (HL3–HL6) in the presence of sodium carbonate in CH2Cl2. The molecular structure of the 1-(phenylazo)-2-naphthol complex has been determined by X-ray crystallography. The complex has a η6-p-cymene group, a chloride and a bidentate N,O-donor azophenol ligand. The complexes have been characterized from NMR spectral data. The catalytic activity of the complexes has been studied for the conversion of acetophenone to the corresponding alcohol in the presence of KOH and isopropanol. Complexes 4 and 6 having a methoxy group attached to the ortho-position of the phenylazo moiety and 2 with a methyl group in the meta-position of the phenolic moiety show high percentage conversion (>84%).

Surfactant-mediated Synthesis of Functional Metal Oxide Nanostructures via Microwave Irradiation-assisted Chemical Synthesis

Nanostructured materials have attracted considerable interest in recent years due to their properties which differ strongly from their bulk phase and potential applications in nanoscale electronic and optoelectronic devices. Metal oxide nanostructures can be synthesized by variety of different synthesis techniques developed in recent years such as thermal decomposition, sol-gel technique, chemical coprecipitation, hydrothermal process, solvothermal process, spray pyrolysis, polyol process etc. All the above processes go through a tedious synthesis procedure followed by prolonged heat treatment at elevated temperature and are time consuming. In the present work we describe a rapid microwave irradiation-assisted chemical synthesis technique for the growth of nanoparticles, nanorods, and nanotubes of a variety of metal oxides in the presence of an appropriate surfactant, without the use of any templates The method is simple, inexpensive, and helps one to prepare nanostructures in a very simple way, and in a very short time, measured in minutes. The synthesis procedure employs high quality metalorganic complexes (typically -diketonates) featuring a direct metal-to-oxygen bond in its molecular structure. The complex is dissolved in a suitable solvent, often with a surfactant added, and the solution then subjected to microwave irradiation in a domestic microwave oven operating at 2.45 GHz frequency with power varying from 160-800 W, from a few seconds to a few minutes, leading to the formation of corresponding metal oxides. This method has been used successfully to synthesize nanostructures of a variety of binary and ternary metal oxides such as ZnO, CdO, Fe2O3, CuO, Ga2O3, Gd2O3, ZnFe2O4, etc. There is an observed variation in the morphology of the nanostructures with the change of different parameters such as microwave power, irradiation time, appropriate solvent, surfactant type and concentration. Cationic, anionic, nonionic and polymeric surfactants have been used to generate a variety of nanostructures. Even so, to remove the surfactant, there is either no need of heat treatment or a very brief exposure to heat suffices, to yield highly pure and crystalline oxide materials as prepared. By adducting the metal complexes, the shape of the nanostructures can be controlled further. In this manner, very well formed, single-crystalline, hexagonal nanorods and nanotubes of ZnO have been formed. Adducting the zinc complex leads to the formation of tapered ZnO nanorods with a very fine tip, suitable for electron emission applications. Particle size and their monodispersity can be controlled by a suitable choice of a precursor complex, the surfactant, and its concentration. The resulting metal oxide nanostructures have been characterized by X-ray diffraction, field emission scanning electron microscopy, transmission electron microscopy, FTIR spectroscopy, photoluminescence, and electron emission measurements.

Influence of growth parameters on the surface morphology and crystallinity of InSb epilayers grown by liquid phase epitaxy

Unintentionally doped homoepitaxial InSb films have been grown by liquid phase epitaxy employing ramp cooling and step cooling growth modes. The effect of growth temperature, degree of supercooling and growth duration on the surface morphology and crystallinity were investigated. The major surface features of the grown film like terracing, inclusions, meniscus lines, etc are presented step-by-step and a variety of methods devised to overcome such undesirable features are described in sufficient detail. The optimization of growth parameters have led to the growth of smooth and continuous films. From the detailed morphological, X-ray diffraction, scanning electron microscopic and Raman studies, a correlation between the surface morphology and crystallinity has been established.

The Drude parameters for metallic PF6 doped polypyrrole

We measured the two components of the complex dielectric function of insulating and metallic PF6 doped polypyrrole up to 4 meV simultaneously. These data are used as an input performed Kramers-Kronig analysis on the higher energy reflection data. This has helped to clarify those results, which were previously deduced from the FIR and UV/VIS data, that could be artifacts.

Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides

Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical `b-ion' series, exhibiting initial backbone cleavage explicitly at the beta-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the `b' or/and the `y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the beta-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the `y-type'. Complementary NMR data showed that, while all metal ions were located around the beta-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent beta-hydroxy acid residue in isariins and the cis peptide bond in isaridins.

An Investigation into the Dependence of the Arc Voltage on the Parameters of the Short-Circuit Current and the Design of the Vacuum Interrupter

The vacuum interrupter is extensively employed in the medium voltage switchgear for the interruption of the short-circuit current. The voltage across the arc during current interruption is termed as the arc voltage. The nature and magnitude of this arc voltage is indicative of the performance of the contacts and the vacuum interrupter as a whole. Also, the arc voltage depends on the parameters like the magnitude of short-circuit current, the arcing time, the point of opening of the contacts, the geometry and area of the contacts and the type of magnetic field. This paper investigates the dependency of the arc voltage on some of these parameters. The paper also discusses the usefulness of the arc voltage in diagnosing the performance of the contacts.

Study of Brittle-to-ductile-transition in Pt-aluminide bond coat using micro-tensile testing method

The Brittle-to-ductile-transition-temperature (BDTT) of free-standing Pt-aluminide (PtAl) coating specimens, i.e. stand-alone coating specimens without any substrate, was determined by micro-tensile testing technique. The effect of Pt content, expressed in terms of the thickness of initial electro-deposited Pt layer, on the BDTT of the coating has been evaluated and an empirical correlation drawn. Increase in the electrodeposited Pt layer thickness from nil to 10 mu m was found to cause an increase in the BDTT of the coating by about 100 degrees C.