title: Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water.
abstract: Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion-oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters.
authors.affiliation: Department of Chemistry, Department of Biochemistry and Molecular Biology, Michigan State University , 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Li
authors.forename: Lin Frank
authors.initials: LF
authors.lastname: Song
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Merz
mesh_terms: D004583:Electrons; D008670:Metals / Q000737:chemistry*; D008958:Models, Molecular; D046588:Nanoarchaeota / Q000201:enzymology; D010088:Oxidoreductases / Q000737:chemistry; D011487:Protein Conformation; D014867:Water / Q000737:chemistry*
chemical_list: D008670:Metals; D014867:Water; D010088:Oxidoreductases; C121849:superoxide reductase