Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential

Abstract

Presented are parameters for mono-, di-, and trivalent cations compatible with the CHARMM additive force field and the TIP3P water model. Thermodynamic perturbation molecular dynamics simulations were performed for the cations located at the center of a TIP3P water sphere under a solvent boundary potential. A series of perturbations generated free energies of hydration indexed by the two Lennard-Jones parameters, ε and R(min). Interpolating the experimental free energies of hydration showed that multiple combinations of ε and R(min) values reproduced the free energies of hydration for each ion. To overcome this nonunique parameter problem, the hydration shell model in combination with an empirical scaling parameter was applied to assign values for each ion. R(min) values were then identified via interpolation of the calculated free energies of hydration. The presented parameters are anticipated to be of utility for simulations of ions, including ions complexed to proteins.

Structure and Dynamics of FosA-Mediated Fosfomycin Resistance in Klebsiella pneumoniae and Escherichia coli

“…Parameters for the protein and K ϩ ion were taken from the CHARMM36 force field (30,31). The water model was the CHARMM-modified TIP3P (32)(33)(34), and Mn 2ϩ parameters were taken from work by Won (35). Parameters for fosfomycin were generated using CGenFF (36).…”

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, because of the restraint provided by the preservation of net charge, the parameterization is achieved through a modulation of the 12‐6 Lennard‐Jones (L‐J) potential only, leaving little room to simultaneously match and reproduce all the experimental observables. Spherical models have been widely employed in MD simulations, and attempts to treat transition metals within this theoretical framework have also been reported . Among these, we mention the modified 12‐6‐4 L‐J potential model proposed by Li and Merz …”

“…Spherical models have been widely employed in MD simulations, and attempts to treat transition metals within this theoretical framework have also been reported. [10] Among these, we mention the modified 12-6-4 L-J potential model proposed by Li and Merz. [9,11] In parallel to the development of spherical models, a distinct strategy to treat ions in classical MD simulations has been reported.…”