Rational Design of Nonbonded Point Charge Models for Divalent Metal Cations with Lennard-Jones 12-6 Potential.

Exploring a metal-involved biochemical process at a molecular level often requires a reliable description of metal properties in aqueous solution by classical nonbonded models. An additional term for considering ion-induced dipole interactions was previously proposed to supplement the widely used Lennard-Jones 12-6 potential (known as the 12-6-4 LJ-type model) with good accuracy. Here, we demonstrate an alternative to modeling divalent metal cations (M) with the traditional 12-6 LJ potential by developing nonbonded point charge models for use with 11 water models: TIP3P, SPC/E, SPC/E, TIP4P-Ew, TIP4P-D, and TIP4P/2005 and the more recent OPC3, TIP3P-FB, OPC, TIP4P-FB, and a99SB-.

Developing and Assessing Nonbonded Dummy Models of Magnesium Ion with Different Hydration Free Energy References.

A large diversity in the targeted hydration free energies (HFEs) during model parameterization of metal ions was reported in the literature with a difference by dozens of kcal/mol. Here, we developed a series of nonbonded dummy models of the Mg ion targeting different HFE references in TIP3P water, followed by assessments of the designed models in the simulations of MgCl solution and biological systems. Together with the comparison of existing models, we conclude that the difference in the targeted HFEs has a limited influence on the model performance, while the usability of these models differs from case to case.