A heuristic model based on dielectric continuum theory for the long-range solvation free energy of a dipolar system possessing periodic boundary conditions (PBCs) is presented. The predictions of the model are compared to simulation results for Stockmayer fluids simulated using three different cell geometries. The boundary effects induced by the PBCs are shown to lead to anisotropies in the app...

NAS21, NAS91 and its derivatives belong to class FabZ inhibitors have been focused to develop better anti-malarial drugs. Library of 17 analogues was designed from NAS21, NAS91 scaffold structure, and NAS75, NAS79 was considered for computational study. Their molecular interactions, binding affinities with FabZ was studied using receptor-centric approaches: glide docking, molecular mechanics us...

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximat...

Using’the concepts of scaled particle theory, an analytical theory is developed to investigate the limiting behavior of solvation free energies at the particle creation limit. The new theory directly incorporates the weakly attractive, dispersion interaction terms into the analytical calculations. For neutral molecular systems, the effects of longer ranged electrostatic interactions are also in...

Piperine is a natural cytotoxic agent aware of various therapeutic acts. The aim this study to look into the effects solvent polarity on solvent-free energy, dipole moment, polarizability, and hyper-polarizability first order, as well molecular properties including chemical hardness softness, potential, electronegativity, electrophilicity index, in order gain better understanding its reactivity...

The treatment of hydration effects in protein dynamics simulations varies in model complexity and spans the range from the computationally intensive microscopic evaluation to simple dielectric screening of charge-charge interactions. This paper compares different solvent models applied to the problem of estimating the free-energy differencebetween two loop conformations in acetylcholinesterase....

The treatment of hydration effects in protein dynamics simulations varies in model complexity and spans the range from the computationally intensive microscopic evaluation to simple dielectric screening of charge-charge interactions. This paper compares different solvent models applied to the problem of estimating the free-energy difference between two loop conformations in acetylcholinesterase...

Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation models. The Lagrangian represe...

Daunorubicin (or daunomycin) and Doxorubicin (or adriamycin or 14-hydroxydaunomycin) are well-known anticancer agents used in cancer chemotherapy. They are anthracycline antibiotics and are commonly used in the treatment of a wide range of cancers. Doxorubicin and Daunorubicin were chemically conjugated to PEO-b-PCL (poly(ethylene oxide)-block-poly( -caprolactone)) nanoparticles. In this resear...

We present a family of alchemical perturbation potentials that enable the calculation hydration free energies small to medium-sized molecules in concerted single coupling step instead commonly used sequence two distinct steps for Lennard-Jones and electrostatic interactions. The are based on softplus function solute-solvent interaction energy designed focus sampling near entropic bottlenecks al...