Realization of three-dimensional solvation-structures from the site-site radial distribution functions in liquids

We propose a new procedure to realize a three-dimensional (3D) solvation structure around a solute molecule from a set of radial distribution functions (RDF), or distance information. The method consists of the minimization of a penalty function defined as the mean-square difference of the solute-solvent interatomic distances obtained from trial 3D configurations and from target RDFs. The hydration structures around several different solute molecules are visualized to demonstrate the method. The solvation structures realized with the present method correspond to the most plausible solvation structure (MPSS), which looks like a snap shot of the molecular dynamics trajectory. However, the MPSS is essentially different from the snap shot, since it represents an average configuration, and is therefore an observable quantity. The present procedure was originally developed for analyses of the RDF results obtained from the reference interaction site model (RISM), but can be applied straightforwardly to RDFs from other sources, such as molecular simulations and scattering experiments.