Abstract Recent advances in machine learning technologies and their applications have led to the development of diverse structure–property relationship models for crucial chemical properties. The solvation free energy is one them. Here, we introduce a novel ML-based model, which calculates from pairwise atomistic interactions. novelty proposed model consists simple architecture: two encoding fu...

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time-consuming setup of such calculations. We introduce...

Thermodynamic measurements of the solvation of salts and electrolytes are relatively straightforward, but it is not possible to separate total solvation free energies into distinct cation and anion contributions without reference to an additional extrathermodynamic assumption. The present work attempts to resolve this difficulty using molecular dynamics simulations with the AMOEBA polarizable f...

A global optimization method is described for identifying the global minimum energy conformation, as well as lower and upper bounds on the global minimum conformer of solvated peptides. Potential energy contributions are calculated using the ECEPP/3 force eld model. In considering the eeects of hydration, two implicit free energy models are compared. One method is based on the calculation of so...

The fluctuating charge (FQ) force field, a polarizable potential model in which point charges on atomic sites fluctuate in response to the environment, is applied to the aqueous solvation of acetamide and transand cisN-methylacetamide (NMA). Two parameters are assigned to each kind of atom, corresponding to an electronegativity and a hardness. The FQ model accurately reproduces both the gas-pha...

Using molecular mechanics force field partial atomic charges, we show the nonuniqueness of the parametrization of continuum electrostatics models with respect to solute atomic radii and interior dielectric constant based on hydration (vacuum-to-water transfer) free energy data available for small molecules. Moreover, parameter sets that are optimal and equivalent for hydration free energy calcu...