title: Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure.
abstract: Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Thole polarization damping model parametrization was modified based on the ab initio polarization energy computed by a constrained space orbital variation energy decomposition scheme. Excellent agreement has been found with condensed phase experimental results using parameters derived from gas phase ab initio calculations. Additionally, we have observed that the coordination of the calcium cation is influenced by the size of the periodic water box, a recurrent issue in first principles molecular dynamics studies.
authors.affiliation: Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA. jpp@lct.jussieu.fr
authors.forename: Jean-Philip
authors.initials: JP
authors.lastname: Piquemal
authors.forename: Lalith
authors.initials: L
authors.lastname: Perera
authors.forename: G Andrés
authors.initials: GA
authors.lastname: Cisneros
authors.forename: Pengyu
authors.initials: P
authors.lastname: Ren
authors.forename: Lee G
authors.initials: LG
authors.lastname: Pedersen
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Darden
mesh_terms: D000656:Amoeba / Q000378:metabolism*; D000818:Animals; D001703:Biophysics / Q000379:methods*; D002118:Calcium / Q000737:chemistry; D002412:Cations; D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D007477:Ions; D008274:Magnesium / Q000737:chemistry; D008956:Models, Chemical; D015203:Reproducibility of Results; D012984:Software; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D002412:Cations; D007477:Ions; D012997:Solvents; D014867:Water; D008274:Magnesium; D002118:Calcium