Protein solubility and conformational stability are a result of a balance of interactions both within a protein and between protein and solvent. The electrostatic solvation free energy of oligoglycines, models for the peptide backbone, becomes more favorable with an increasing length, yet longer peptides collapse due to the formation of favorable intrapeptide interactions between CO dipoles, in...

Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with...

A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the electrostatic solvation energy of the system, and equilibrium membrane deformation is obtained by minimizing the electroelastic energy functional with respect to the die...

The binding energy distribution analysis method (BEDAM) for the computation of receptor-ligand standard binding free energies with implicit solvation is presented. The method is based on a well-established statistical mechanics theory of molecular association. It is shown that, in the context of implicit solvation, the theory is homologous to the test particle method of solvation thermodynamics...

A series of gas-phase experiments and extensive theoretical modeling was done on the family of singly protonated peptides AARAA, Ac-AARAA, and AARAA-OMe. (AARAA)H(+) underwent extensive H/D exchange with D(2)O, whereas the other two peptides with blocked termini did not, implying that a salt bridge was involved in the H/D exchange process. Ion mobility measurements and complementary molecular m...

THE RELIABILITY OF FREE ENERGY SIMULATIONS (FES) IS LIMITED BY TWO FACTORS: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too c...

The reaction pathways of PCB-77 in the atmosphere with ·OH, O2, NO x , and 1O2 were inferred based on density functional theory calculations with the 6-31G* basis set. The structures the reactants, transition states, intermediates, and products were optimized. The energy barriers and reaction heats were obtained to determine the energetically favorable reaction pathways. To study the solvation ...

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...

A proton NMR method for the determination of the solvation numbers of alkaline earth cations with dimethylsulfoxide (DMSO) in nitromethane as diluent is described. The method is based on the monitoring of the resonance frequency of DMSO protons as a function of DMSO to metal ion mole ratio while keeping the metal ion concentration constant. The average solvation number of cations at any...

Emission and absorption spectra of many organic dyes in liquid solutions depend on the local electric fields generated by the surrounding polar solvent molecules. This “solvation effect” is a result of intermolecular solutesolvent interaction forces (such as dipole-dipole or dipole-induced dipole) that tend to stretch molecular bonds and shift charge distribution on molecules, altering the ener...