Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field

Abstract

The hydration free energy, structure, and dynamics of the zinc divalent cation are studied using a polarizable force field in molecular dynamics simulations. Parameters for the Zn 2+ are derived from gas-phase ab initio calculation of Zn 2+ -water dimer. The Thole-based dipole polarization is adjusted based on the Constrained Space Orbital Variations (CSOV) calculation while the Symmetry Adapted Perturbation Theory (SAPT) approach is also discussed. The vdW parameters of Zn 2+ have been obtained by comparing the AMOEBA Zn 2+ -water dimerization energy with results from several theory levels and basis sets over a range of distances. Molecular dynamics simulations of Zn 2+ solvation in bulk water are subsequently performed with the polarizable force field. The calculated first-shell water coordination number, water residence time and free energy of hydration are consistent with experimental and previous theoretical values. The study is supplemented with extensive Reduced Variational Space (RVS) and Electron Localization Function (ELF) computations in order to unravel the nature of the bonding in Zn 2+ (H 2 O) n (n=1,6) complexes and to analyze the charge transfer contribution to the complexes. Results show that the importance of charge transfer decreases as the size of Zn-water cluster grows due to anticooperativity and to changes in the nature of the metal-ligand bonds. Induction could be dominated by polarization when the system approaches condensed-phase and the covelant effects are eliminated from the Zn(II)-water interaction. To construct an "effective" classical polarizable potential for Zn 2+ in bulk water, one should therefore avoid over-fitting to the ab initio charge transfer energy of Zn 2+ -water dimer. Indeed, in order to avoid overestimation of condensed-phase many-body effects, which is crucial to the transferability of polarizable molecular dynamics, charge transfer should not be included within the classical polarization contribution and should preferably be either incorporated in to the pairwise van der Waals contribution or treated explicitly.

Structure and Thermodynamics of Mg:Phosphate Interactions in Water: A Simulation Study

“…A pre-equilibrated cubic water box with an edge length of 24.857 that contained 511 waters was used to soak the different solutes. [28,30,31] This moderate box size turns out to be sufficient, as shown by the uncertainty analysis below; see Results and Concluding Discussion. Simulations were performed at constant volume and 298 K, by using periodic boundary conditions (PBC), the Berendsen thermostat, [42] and a 1 fs timestep.…”

Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

“…21,22 Piquemal et al developed the SIBFA method which includes non-classical effects such as exchange-polarization. [23][24][25][26][27][28][29][30][31] In the induced dipole model, the induced point dipole at atom site i is proportional to the electric field at the same site (µ i = α i E i , where α i is the atomic polarizability of atom i). The atomic polarizabilities are the key parameters in the induced dipole model.…”

Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies

“…Thanks to high-level electrostatics and full treatment for polarizable effects, MD simulations with AMOEBA [25,26] were able to reproduce structural and dynamical experimental properties of hydrated mono and divalent metal cations [27][28][29][30]. In our previous studies, the AMOEBA polarizable and flexible force field was extended to the lanthanide(III) ions [8][9][10].…”