Hydride transfer changes the charge structure of the reactant and thus, may induce reorientation/reorganization of solvent molecules. This solvent reorganization may in turn alter the energetics of the reaction. In the present work, we investigate the intramolecular hydride transfer by taking Lewis acid catalyzed glucose to fructose isomerization as an example. The C2-C1 hydride transfer is the...

A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model [Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. 104, 527 (2006); J. Chem. Phys. 124, 084905 (2006)]. In the level-set method, a possible solute-solvent interface is represented by the zero level set (i.e., the zero lev...

Both KNI-10033 and KNI-10075 are high affinity preclinical HIV-1 protease (PR) inhibitors with affinities in the picomolar range. In this work, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method has been used to investigate the potency of these two HIV-1 PR inhibitors against the wild-type and mutated proteases assuming that potency correlates with the affinity of the drugs...

The aim of this communication was to expand the results of numerical analyses performed by Sun et al. on their experimental solubility of fenofibrate in aqueous mixtures of ethanol and acetone at 298.15 K, in terms of the evaluation of the preferential solvation of this compound by the organic solvents and water in the saturated mixtures based on the inverse Kirkwood-Buff integrals (IKBI). ...

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...

Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review "alchemical" approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies ...

Most proteins perform their function in aqueous solution. The interactions with water determine the stability of proteins and the desolvation costs of ligand binding or membrane insertion. However, because of experimental restrictions, absolute solvation free energies of proteins or amino acids are not available. Instead, solvation free energies are estimated based on side chain analog data. Th...

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...

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We study the bulk thermodynamics and interfacial properties of electrolyte solution mixtures by accounting for electrostatic interaction, ion solvation, and inhomogeneity in the dielectric medium in the mean-field framework. Difference in the solvation energy between the cations and anions is shown to give rise to local charge separation near the interface, and a finite Galvani potential betwee...