title: Novel analysis of cation solvation using a graph theoretic approach.
abstract: A new method for analyzing molecular dynamics simulation data is employed to study the solvent shell structure and exchange processes of mono-, di-, and trivalent metal cations in water. The instantaneous coordination environment is characterized in terms of the coordinating waters' H-bonding network, orientations, mean residence times, and the polyhedral configuration. The graph-theory-based algorithm provides a rapid frame-by-frame identification of polyhedra and reveals fluctuations in the solvation shell shape--previously unexplored dynamic behavior that in many cases can be associated with the exchange reactions of water between the first and second solvation shells. Extended solvation structure is also analyzed graphically, revealing details of the hydrogen bonding network that have practical implications for connecting molecular dynamics data to ab initio cluster calculations. Although the individual analyses of water orientation, residence time, etc., are commonplace in the literature, their combination with graphical algorithms is new and provides added chemical insight.
authors.affiliation: Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 87521, USA.
authors.forename: Barbara Logan
authors.initials: BL
authors.lastname: Mooney
authors.forename: L Rene
authors.initials: LR
authors.lastname: Corrales
authors.forename: Aurora E
authors.initials: AE
authors.lastname: Clark
mesh_terms: D000465:Algorithms; D002412:Cations / Q000737:chemistry*; D006860:Hydrogen Bonding; D008670:Metals / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D002412:Cations; D008670:Metals; D012997:Solvents; D014867:Water