Enhanced Tetrahedral Ordering of Water Molecules in Minor Grooves of DNA: Relative Role of DNA Rigidity, Nanoconfinement, and Surface Specific Interactions

Confinement and Surface specific interactions call induce Structures otherwise unstable at that temperature and pressure. Here we Study the groove specific water dynamics ill the nucleic acid sequences, poly-AT and poly-GC, in long B-DNA duplex chains by large scale atomistic molecular dynamics simulations, accompanied by thermodynamic analysis. While water dynamics in the major groove remains insensitive to the sequence differences, exactly the opposite is true for the minor groove water. Much slower water dynamics observed in the minor grooves (especially in the AT minor) call be attributed to all enhanced tetrahedral ordering (< t(h)>) of water. The largest value of < t(h)> in the AT minor groove is related to the spine of hydration found in X-ray Structure. The calculated configurational entropy (S-C) of the water molecules is found to be correlated with the self-diffusion coefficient of water in different region via Adam-Gibbs relation D = A exp(-B/TSC), and also with < t(h)>.

Replacement of water on a steel substrate by a surrounding oil reservoir

With an objective to replace a water droplet from a steel surface by oil we study here the impact of injecting a hydrophilic/lipophilic surfactant into the droplet or into the surrounding oil reservoir. Contact angle goniometery, Grazing angle FTIR spectroscopy and Atomic force microscopy are used to record the oil/water interfacial tension, surface energetics of the substrate under the oil and water phases as well as the corresponding physical states of the substrates. Such energetics reflect the rate at which the excess surfactant molecules accumulate at the water/oil interface and desorb into the phases. The molecules diffuse into the substrate from the phases and build up specific molecular configurations which, with the interfacial tension, control the non-equilibrium progress of and the equilibrium status of the contact line. The study shows that the most efficient replacement of water by the surrounding oil happens when a surfactant is sparingly soluble in the supplier oil phase and highly soluble in the recipient water phase.

Local structure of water studied by Compton scattering

This thesis presents a novel application of x-ray Compton scattering to structural studies of molecular liquids. Systematic Compton-scattering experiments on water have been carried out with unprecedented accuracy at third-generation synchrotron-radiation laboratories. The experiments focused on temperature effects in water, the water-to-ice phase transition, quantum isotope effects, and ion hydration. The experimental data is interpreted by comparison with both model computations and ab initio molecular-dynamics simulations. Accordingly, Compton scattering is found to provide unique intra- and intermolecular structural information. This thesis thus demonstrates the complementarity of the technique to traditional real-space probes for studies on the local structure of water and, more generally, molecular liquids.

An acid method for the volumetric estimation of water-soluble dithiocarbamates

Dithiocarbamates have been estimated previously by reaction with a strong acid, the carbon disulfide evolved being converted into a xanthate and the latter estimated iodimetrically. In the present method, a water-soluble dithiocarbamate is reacted with a decinormal mineral acid and the excess acid is determined to compute the amount of dithiocarbamate present. This method is applicable for the determination of a dithiocarbamate in a mixture containing thiuram disulfide.

Jodimetric estimation of water-soluble dithiocarbamates

Iodimetric estimation of dialkyl dithiocarbamate in alcoholic solution is not accurate. The method has not met with success for the water-soluble dithiocarbamates before. A simple and accurate iodimetric method has been developed for the estimation of water-soluble dithiocarbamates. The success of the method is due to the removal of the oxidation product which interferes during the titration with iodine.

Charge transport properties of water dispersible multiwall carbon nanotube-polyaniline composites

The transmission electron microscopy images of in situ prepared multiwall carbon nanotubes (MWNTs)and polyaniline (PANI) composites show that nanotubes are well dispersed in aqueous medium, and the nanofibers of PANI facilitate intertube transport. Although low temperature transport indicates variable range hopping (VRH) mechanism, the dc and ac conductivity become temperature independent as the MWNT content increases. The onset frequency for the increase in conductivity is observed to be strongly dependent on the MWNT weight percent, and the ac conductivity can be scaled onto a master curve. The negative magnetoresistance is attributed to the forward interference scattering mechanism in VRH transport. (C) 2010 American.

Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.

Single-File Diffusion of Water Inside Narrow Carbon Nanorings

We use atomistic molecular dynamics (MD) simulations to study the diffusion of water molecules confined inside narrow (6,6) carbon nanorings. The water molecules form two oppositely polarized chains. It is shown that the effective interaction between these two chains is repulsive in nature. The computed mean-squared displacement (MSD) clearly shows a scaling with time similar to t(1/2), which is consistent with single-file diffusion (SFD). The time up to which the water molecules undergo SFD is shown to be the lifetime of the water molecules inside these chains. Simulations of "uncharged" water molecules inside the nanoring show the formation of several water chains and yield SFD. These observations conclusively prove that the diffusion is Fickian when there is a single chain of water and SFD is observed only when two or more chains are present.

Sacrificial photolysis of water on Ti1−xSnxO2 ultrafine powders

Ultrafine powders of extra pure Ti1−xSnxO2, where o < x < 1, prepared by the hydrothermal method are pale yellow in color. They show photocatalytic activity after platinization, in the visible light (420–550 nm) for H2-production from aqueous solutions containing sacrificial donors such as hypophosphite. The spectral sensitization is shown to be due to peroxotitanium species in the rutile-type structure. Peroxide ion, O22−, arises from the dimerization of O−, the hole centres, produced during the disproportionative decomposition of residual hydroxyls: OH− = O− + H. Higher OH contents in TixSnxO2 is due to the amphoteric chemistry of oxocompounds of tin.

A Note on Diffraction of Water Waves by a Nearly Vertical Barrier

A simplified perturbational analysis is employed, together with the application of Green's theorem, to determine the first-order corrections to the reflection and transmission coefficients in the problem of diffraction of surface water waves by a nearly vertical barrier in two basically important cases: (i) when the barrier is partially immersed and (ii) when the barrier is completely submerged. The present analysis produces the desired results fairly easily and relatively quickly as compared with the known integral equation approach to this class of diffraction problems.

Interaction of water molecules in non-identical protein structures

The interaction of the protein atoms with the surrounding water oxygen atoms has been computed for 392 protein chains from 369 protein structures belonging to 90% non-homologous high resolution (<= 1.5 angstrom) protein Structures with a crystallographic R-factor <= 20%. The percentage composition of the polar atoms is found to be 36.3%. An average of 82.55% of water oxygen atoms are found to be in the primary hydration shell and 15.12% in the secondary hydration shell. The average Percentage of interactions of water oxygen atoms with the polar atoms of the main chain and side chain are 54% and 46%. respectively. The interaction of the acidic residues, aspartate and glutamate, with the water oxygen atoms is more when compared to that of the other residues.