Rational Design of Methodology-Independent Metal Parameters Using a Nonbonded Dummy Model

Abstract

A nonbonded dummy model for metal ions is highly imperative for the computation of complex biological systems with for instance multiple metal centers. Here we present nonbonded dummy parameters of 11 divalent metallic cations, namely, Mg(2+), V(2+), Cr(2+), Mn(2+), Fe(2+), Co(2+), Ni(2+), Zn(2+), Cd(2+), Sn(2+), and Hg(2+), that are optimized to be compatible with three widely used water models (TIP3P, SPC/E, and TIP4P-EW). The three sets of metal parameters reproduce simultaneously the solvation free energies (ΔGsol), the ion-oxygen distance in the first solvation shell (IOD), and coordination numbers (CN) in explicit water with a relative error less than 1%. The main sources of errors to ΔGsol that arise from the boundary conditions and treatment of electrostatic interactions are corrected rationally, which ensures the independence of the proposed parameters on the methodology used in the calculation. This work will be of great value for the computational study of metal-containing biological systems.

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

“…In this respect, it is interesting to note that three recent approaches for improving the description of ion-water interactions at the MM level rely in effect on a weakening of the ion-solvent Coulombic interactions. These are: the induction-type 66,67,104,107,[278][279][280][281]284 force fields, where CT effects are included explicitly, the molecular dynamics in electric continuum (MDEC) approach, [285][286][287] where the ion charge is effectively scaled 75,[77][78][79]288 by a factor of about 0.7-0.9 (in line with QM results 282 ), and the multisite ion description, [289][290][291][292][293][294][295] where the ion charge is redistributed over virtual off-center sites within the ion. The observation made here that the features of the QM/MM RDFs can be reproduced more accurately with a MM model when reducing the nominal charge of the ion to +0.75 e is perfectly in line with these considerations.…”

Development of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data

“…In the case of nickel, the free energy of solvation varies of about 20 kcal mol −1 only considering the well‐known datasets compiled by Noyes, Rosseinsky, and Marcus . Among these, we chose to employ the free energy values reported by Marcus, which are relatively recent and widely used in the literature . The approach devised by Marcus stems from the extrapolation of the proton solvation enthalpy and an estimation of the proton bulk entropy.…”

“…[24] Among these, we chose to employ the free energy values reported by Marcus, [24] which are relatively recent and widely used in the literature. [10,11,18,57] The approach devised by Marcus stems from the extrapolation of the proton solvation enthalpy and an estimation of the proton bulk entropy. Notably, the compiled values do not include the phase potential, that is, they are intrinsic free energy of solvation.…”

“…Moreover, Duarte and coworkers parameterized several octahedrally coordinated metal ions through the use of a spherical droplet system, while Liao and coworkers developed an accurate CC model for Cu(II) able to take into account the Jahn‐Teller effect through an anisotropic charge distribution scheme . More recently, consistent CC models have also been developed for eleven transition metal ions and different water models through an elaborate procedure that in principle allows parameters to be compatible with both periodic and non‐periodic simulative conditions …”

“…[17] More recently, consistent CC models have also been developed for eleven transition metal ions and different water models through an elaborate procedure that in principle allows parameters to be compatible with both periodic and non-periodic simulative conditions. [18] Here, we focus on the parameterization of a multisite model for Ni(II) in solution to be used in classical MD simulations eventually combined with enhanced sampling methods. To ensure an optimal derivation of parameters, we developed the multisite model investigating not only the 12-6 L-J parameters of the core site (equilibrium radius, r8/2, and well-depth, e), but we also compared the performance of CC and NC models (see Fig.…”