A surface constrained all-atom solvent model for effective simulations of polar solutions

Abstract

A consistent simulation of ionic or strongly polar solutes in polar solvents presents a major challenge from both fundamental and practical aspects. The frequently used method of periodic boundary conditions (PBC) does not correctly take into account the symmetry of the solute field. Instead of using PBC, it is natural to model this type of system as a sphere (with the solute at the origin), but the boundary conditions to be used in such a model are not obvious. Early calculations performed with our surface constrained soft sphere dipoles (SCSSD) model indicated that the dipoles near the surface of the sphere will show unusual orientational preferences (they will overpolarize) unless a corrective force is included in the model, and thus we implemented polarization constraints in this spherical model of polar solutions. More recent approaches that treated the surface with stochastic dynamics, but did not take into account the surface polarization effects, were also found to exhibit these nonphysical orientational preferences. The present work develops a surface constrained all-atom solvent (SCAAS) model in order to consistently treat the surface polarization effects in all-atom molecular dynamics simulations. The SCAAS model, which was presented in a preliminary way in previous works, introduces surface constraints as boundary conditions in order to make the necessarily finite system behave as if it was part of an infinite system. The performance of the model with regard to various properties of bulk water is examined by comparing its results to those obtained by PBC simulations. The results obtained from SCAAS models of different sizes are found to be similar to each other and to the corresponding PBC results. The performance of the model in simulations of solvated ions is emphasized and a comparison of the results obtained with spheres of different sizes demonstrates that the model does not possess significant size dependence. This indicates that the model can be used with a relatively small number of solvent molecules for convergent simulation of structure, energetics, and dynamics of polar solutions. The much simpler fixed center Langevin dipoles (FCLD) model is also examined and found to provide a powerful tool for estimating solvation free energies. Finally, a preliminary study of the dielectric properties of the SCAAS model is reported and the potential of this model for exploring the correct implementation of the solvent reaction field is discussed.