Polarizable and Non-Polarizable Force Field Representations of Ferric Cation and Validations

Abstract

The AMOEBA polarizable force field of ferric ion was optimized and applied to study the hydration of ferric ion and its complexation with porphine in the aqueous phase. The nonpolarizable force field was also optimized for comparison. The AMOEBA force field was found to give a more accurate hydration free energy than the nonpolarizable force field with respect to experimental data, and correctly predict the most stable electronic state of hydrated Fe, which is the sextet state, and of the Fe-Por complex, which is the quartet state, consistent with the literature that was carried out using the DFT method. The explicit inclusion of charge transfer between Fe and ligand was found to be important in order to obtain a precise picture of polarization energy and van der Waals energy, which otherwise deviate from the corresponding energy components derived from ab initio calculations. The successful application of the AMOEBA force field in the characterization of aquo Fe-Por complexes suggests that its use may be extended to the study of the dynamics of metalloenzyme containing highly charged metal ions in the condensed phase with reliable treatment of the interactions between metal atom and protein.

Review of Molecular Dynamics Simulations of Phosphonium Ionic Liquid Lubricants

“…The non-reactive force fields for ILs can be classified into two categories: polarizable [32][33][34][35][36][37][38] and non-polarizable [39][40][41][42][43][44]. Non-polarizable force fields handle individual atoms as point masses with fixed atomic charge, and do not explicitly consider the polarization of the atoms as a response to external electric fields, while polarizable force fields include explicit treatment of the polarization effect to improve the calculation of electrostatics [45].…”

Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution

“…31 – 33 Polarizable force fields offer an efficient way to model electrostatic interactions for highly charged species with high fidelity. 34 – 36 Here, we carried out molecular dynamics simulations using the AMOEBA polarizable force field 37 – 38 to investigate the phosphate binding mode of PBPs.…”

“…Molecular dynamics (MD) simulations based on classical force fields have been a valuable tool for the understanding of protein–ligand binding. − The popular fixed-charge force fields have been applied to model neutral ligands and monovalent ions. ,− Highly charged species are more challenging in simulation and often treated by computationally demanding quantum mechanical (QM) methods. − Polarizable force fields offer an efficient way to model electrostatic interactions for highly charged species with high fidelity. − Here, we carried out MD simulations using the AMOEBA polarizable force field , to investigate the phosphate binding mode of PBPs.…”

BuRNN: Buffer Region Neural Network Approach for Polarizable-Embedding Neural Network/Molecular Mechanics Simulations

“…Especially challenging is the coordinative bond between Fe and O as it is somewhat between a covalent bond and an ionic bond and is often addressed with specialized force fields. 32 , 33 …”

“…Especially challenging is the coordinative bond between Fe and O as it is somewhat between a covalent bond and an ionic bond and is often addressed with specialized force fields. 32,33 In our test case, the Fe 3+ ion comprises the inner region, and water molecules up to 0.5 nm are treated as the buffer region, which roughly accounts for the first two solvation shells, where the first solvation shell is expected to be formed by the hexacoordinated waters. During extensive MD simulations (10 ns), the water molecules are freely diffusing between the buffer and outer regions, smoothly switching interactions between the NN (QM) level and the MM level of theory.…”