Metal ions play significant roles in biochemical systems. Almost one-third of the proteins in Protein Data Bank database contain metal ions. Molecular mechanics (MM) involves a potential function representation that can give insights into macromolecular systems at the atomic level. There are several ways to simulate metal ions using MM including the bonded model, the nonbonded model and the cationic dummy atom model. The 12-6 Lennard-Jones (LJ) nonbonded model is widely used due to its simple form and excellent transferability. But there are no systematic and consistent parameter sets available that span from monovalent to high-valent ions. We have built 12-6 LJ nonbonded parameter sets for cations with charges from +1 to +4 and halide anions (in total 63 different ions) for three widely used water models (TIP3P, SPC/E and TIP4P<sub>EW</sub>), respectively, using the particle mesh Ewald (PME) method to treat long-range electrostatic interactions. Concomitantly we created 12-6-4 LJ-type nonbonded models and parameterized it for 55 different ions for the three water models using the PME method as well. In this presentation we will cover the details of the benefits of the 12-6-4 model over the 12-6 model in the accurate representation of metal ions in aqueous solution.

Systematic parameterization of an accurate nonbonded model for ions

251st National Meeting (2016)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.