the acidity constants (pka) of thirty four (34) ;-substituted carboxylic acids in aqueous solution havebeen calculated using conductor-like polarizable continuum (c-pcm) solvation model. the gasphaseenergies at the density functional theory (dft-mpw1pw91) and solvation energies athartree fock (hf) are combined to estimate the pka values which are very close to the experimentalvalues where, and ...

The properties of lipid bilayer nanometer-scale domains could be crucial for understanding cell membranes. Fluorescent probes are often used to study bilayers, yet their effects on host lipids are not well understood. We used molecular dynamics simulations to investigate perturbations in a fluid DPPC bilayer upon incorporation of three indocarbocyanine probes: DiI-C18:0, DiI-C18:2, or DiI-C12:0...

Macromolecular sedimentation in inhomogeneous media is of great practical importance. Dynamic density gradients have a long tradition in analytical ultracentrifugation, and are frequently used in preparative ultracentrifugation. In this paper, a new theoretical model for sedimentation in inhomogeneous media is presented, based on finite element solutions of the Lamm equation with spatial and te...

By combining the experimental small- and wide-angle x-ray scattering (SWAXS) method with molecular dynamics simulations theoretical ‘complemented-system approach’ it is possible to obtain detailed information about intra- inter-molecular structure of solvation hydration surfactant in organic mixed solvents, e.g., nonionic Brij 35 (C12E23) alcohols aqueous alcohol-rich ternary systems. This firs...

The native state of protein is a resultant of delicate balance of various interactions of protein within itself and with surrounding environment. Disruption of this balance by heat, cold, pressure, pH, denaturant etc., leads to protein denaturation. In the present paper we have investigated the effect of sodium acetate, magnesium acetate calcium acetate, sodium propionate and sodium butyrate on...

The range of interactions between fibre and water and the consequential properties of the bound water are modelled and examined. Dietary fibre may interact with water by means of polar and hydrophobic interactions, hydrogen bonding and enclosure. The results of these interactions vary with the flexibility of the fibre surface. When the fibre is insoluble or junction zones are formed,this may re...

Solvation is essential for protein activities. To study internal solvation of protein, site-directed mutagenesis is applied. Intrinsic fluorescent probe, tryptophan, is inserted into desired position inside protein molecule for ultrafast spectroscopic study. Here we review this unique method for protein dynamics researches. We introduce the frontiers of protein solvation, site-directed mutagene...

We present a statistical mechanical approach for quantifying thermodynamic properties of proteins in mixed solvents. This approach, based on molecular dynamics simulations which incorporate all atom models and the theory of preferential binding, allows us to compute transfer free energies with experimental accuracy and does not incorporate any adjustable parameters. Specifically, we applied our...

Computation of the solvation free energy for chemical and biological processes has long been of significant interest. The key challenges to effective solvation modeling center on the choice of potential function and configurational sampling. Herein, an energy sampling approach termed the “Movable Type” (MT) method, and a statistical energy function for solvation modeling, “Knowledge-based and E...

Differential geometry (DG) based solvation models are a new class of variational implicit solvent approaches that are able to avoid unphysical solvent-solute boundary definitions and associated geometric singularities, and dynamically couple polar and non-polar interactions in a self-consistent framework. Our earlier study indicates that DG based non-polar solvation model outperforms other meth...