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 st ructure around a solute molecule from a set of radial distribution function s (RDF), or distance information. The method consists of the minimization o f a penalty function defined as the mean-square difference of the solute-so lvent interatomic distances obtained from trial 3D configurations and from target RDFs. The hydration structures around several different solute molec ules 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 diff erent from the "snap shot," since it represents an average configuration, a nd is therefore an observable quantity. The present procedure was originall y developed for analyses of the RDF results obtained from the reference int eraction site model (RISM), but can be applied straightforwardly to RDFs fr om other sources, such as molecular simulations and scattering experiments.