title: Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules.
abstract: We describe here some tests we made in the SAMPL5 communal event of 'Semi-Explicit Assembly' (SEA), a recent method for computing solvation free energies. We combined the prospective tests of SAMPL5 with followup retrospective calculations, to improve two technical aspects of the field variant of SEA. First, SEA uses an approximate analytical surface around the solute on which a water potential is computed. We have improved and simplified the mathematical model of that surface. Second, some of the solutes in SAMPL5 were large enough to need a way to treat solvating waters interacting with 'buried atoms', i.e. interior atoms of the solute. We improved SEA with a buried-atom correction. We also compare SEA to Thermodynamic Integration molecular dynamics simulations, so that we can sort out force field errors.
authors.affiliation: Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA. emiliano.brini@stonybrook.edu.
authors.forename: Emiliano
authors.identifier: 0000-0002-1314-8405
authors.initials: E
authors.lastname: Brini
authors.affiliation: Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
authors.forename: S Shanaka
authors.initials: SS
authors.lastname: Paranahewage
authors.affiliation: Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Fennell
authors.affiliation: Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA.|Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA.|Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, 11794, USA.
authors.forename: Ken A
authors.initials: KA
authors.lastname: Dill
mesh_terms: D003198:Computer Simulation; D003510:Cyclohexanes / Q000737:chemistry*; D055808:Drug Discovery; D008956:Models, Chemical; D015394:Molecular Structure; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D012995:Solubility; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D003510:Cyclohexanes; D004364:Pharmaceutical Preparations; D012997:Solvents; D014867:Water; C506365:Cyclohexane
keywords: Distribution coefficient; Partitioning; SAMPL; SEA; Solvation free energy