A Polarizable Cationic Dummy Metal Ion Model

Binding of Phosphate Species to Ca2+ and Mg2+ in Aqueous Solution

Phosphate derivatives and their interaction with metal cations are involved in many important biological phenomena, so an accurate characterization of the phosphate-metal interaction is necessary to properly understand the role of phosphate-metal contacts in mediating biological function. Herein, we improved the standard 12-6 Lennard-Jones (LJ) potential via the usage of the 12-6-4 LJ model, which incorporates ion-induced dipole interactions. Via parameter scanning, we fine-tuned the 12-6-4 LJ polarizability values to obtain accurate absolute binding free energies for the phosphate anions H2PO4-, HPO42-, PO43- coordinating with Ca2+ and Mg2+. First, we modified the phosphate 12-6-4 LJ parameters to reproduce the solvation free energies of the series of phosphate anions using the thermodynamic integration (TI) method. Then, using the potential mean force (PMF) method, the polarizability of the metal-phosphate interaction was obtained. We show that the free energy profiles of phosphate ions coordinated to Ca2+ and Mg2+ generally show similar trends at longer metal-phosphate distances, while the absolute binding energy values increased with deprotonation. The resulting parameters demonstrate the flexibility of the 12-6-4 LJ-type nonbonded model and its usefulness in accurately describing cation-anion interactions.

Accurate Metal-Imidazole Interactions

Modeling the interaction between a metal ion and small molecules can provide pivotal information to bridge and close the gap between two types of simulations: metal ions in water and metal ions in metalloproteins. As previously established, the 12-6-4 Lennard-Jones (LJ)-type nonbonded model, because of its ability to account for the induced dipole effect, has been highly successful in simulating metal ion systems. Using the potential of mean force (PMF) method, the polarizability of the metal-chelating nitrogen from two types of imidazole molecules, delta nitrogen protonated (HID) and epsilon nitrogen protonated (HIE), has been parametrized against experiment for 11 metals (Ag(I), Ca(II), Cd(II), Co(II), Cu(I), Cu(II), Fe(II), Mg(II), Mn(II), Ni(II), and Zn(II)) in conjunction with three commonly used water models (TIP3P, SPC/E, and OPC). We show that the standard 12-6 and unmodified 12-6-4 models are not able to accurately model these interactions and, indeed, predict that the complex should be unstable. The resultant parameters further establish the flexibility and the reliability of the 12-6-4 LJ-type nonbonded model, which can correctly describe three-component interactions between a metal, ligand, and solvent by simply tuning the polarizability of the chelating atom. Also, the transferability of this model was tested, showing the capability of describing metal-ligand interactions in various environments.