Octanol-to-water solvation free energies of acetyl amino amides (Ac-X-amides) [Fauchère, J.L., & Pliska, V. (1983) Eur. J. Med. Chem. --Chim. Ther. 18,369] form the basis for computational comparisons of protein stabilities by means of the atomic solvation parameter formalism of Eisenberg and McLachlan [(1986) Nature 319, 199]. In order to explore this approach for more complex systems, we have...

A Gaussian solvent-exclusion model for the solvation free energy is developed. It is based on theoretical considerations and parametrized with experimental data. When combined with the CHARMM 19 polar hydrogen energy function, it provides an effective energy function (EEF1) for proteins in solution. The solvation model assumes that the solvation free energy of a protein molecule is a sum of gro...

stabilities and quantum molecular descriptors of cyclophoshphamide (an anticancer drug)-functionalized (8,0) zigzag and (4,4) armchair carbon nanotubes (cnts) complexes in water were studied using density functional theory (dft) calculations. two attachments namely the sidewall- and tip-attachments are considered for the model constructions. calculations of the total electronic energy (et) and ...

We develop force field parameters for the divalent cations Mg(2+), Ca(2+), Sr(2+), and Ba(2+) for molecular dynamics simulations with the simple point charge-extended (SPC/E) water model. We follow an approach introduced recently for the optimization of monovalent ions, based on the simultaneous optimization of single-ion and ion-pair properties. We consider the solvation free energy of the div...

A new method is proposed for calculating aqueous solvation free energy based on atom-weighted solvent accessible surface areas. The method, SAWSA v2.0, gives the aqueous solvation free energy by summing the contributions of component atoms and a correction factor. We applied two different sets of atom typing rules and fitting processes for small organic molecules and proteins, respectively. For...

Molecular dynamics simulations of electron and ion transfer reactions near a smooth surface are presented, analyzing the effect of the geometrical constraint of the surface and the interfacial electric field on the relevant solvation properties of both a monovalent negative ion and a neutral atom. The simulations show that, from the solvation point of view, ion adsorption is an uphill process d...

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...