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...

• The widely used GAFF parameters are evaluated and refitted in a system- component-specific manner. Large-scale calculations of solvation transfer free energies ionic liquids performed. Finite-size artifacts energy more pronounced than the mass density. Thermodynamic perspectives charge scaling presented compared with bulk-property-derived one. General guidelines for molecular modelling fixed-...

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...

This work introduces a model, solvation model 6 with temperature dependence (SM6T), to predict the temperature dependence of aqueous free energies of solvation for compounds containing H, C, and O in the range 273-373 K. In particular, we extend solvation model 6 (SM6), which was previously developed (Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1, 1133) for predict...

We undertake steps to overcome four challenges that have hindered the understanding of ZnO/biomolecule interfaces at atomic scale: parametrization a classical force field, ZnO surface termination and amino acid protonation state in methanol, convergence enhanced sampling molecular dynamics simulations. predict adsorption free energies for histidine, serine, cysteine, tryptophan remarkable agree...

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 ...

Implicit solvation models are popular alternatives to explicit solvent methods due to their ability to "pre-average" solvent behavior and thus reduce the need for computationally-expensive sampling. Previously, we have demonstrated that Poisson-Boltzmann models for polar solvation and integral-based models for nonpolar solvation can reproduce explicit solvation forces in a low-charge density pr...