Advances in numerical solutions to integral equations in liquid state theory.

摘要

Solvent effects play a vital role in the accurate description of the free energy profile for solution phase chemical and structural processes. The inclusion of solvent effects in any meaningful theoretical model however, has proven to be a formidable task. Generally, methods involving Poisson-Boltzmann (PB) theory and molecular dynamic (MD) simulations are used, but they either fail to accurately describe the solvent effects or require an exhaustive computation effort to overcome sampling problems. An alternative to these methods are the integral equations (IEs) of liquid state theory which have become more widely applicable due to recent advancements in the theory of interaction site fluids and the numerical methods to solve the equations.It is found that the 3D-IEs provide a qualitative description of the density distributions of the solvent species when compared to MD results, but at a much reduced computational effort in comparison to MD simulations. The thermodynamics of the solvated systems are also qualitatively reproduced by the IE results. The findings of this work show the IEs to be a valuable tool for the study and prediction of solution phase phenomena and that such a theory can be effectively used to study complicated processes such as protein folding or protein-ligand binding strengths which depend on solvation effects.In this work a new numerical method is developed based on a Newton-type scheme coupled with Picard/MDIIS routines. To extend the range of these numerical methods to large-scale data systems, the size of the Jacobian is reduced using basis functions, and the Newton steps are calculated using a GMRes solver. The method is then applied to calculate solutions to the 3D reference interaction site model (RISM) IEs of statistical mechanics, which are derived from first principles, for a solute model of a pair of parallel graphene plates at various separations in pure water. The 3D IEs are then extended to electrostatic models using an exact treatment of the long-range Coulomb interactions for negatively charged walls and DNA duplexes in aqueous electrolyte solutions to calculate the density profiles and solution thermodynamics.