Calculating solvation energies by means of a fluctuating charge model combined with continuum solvent model

Abstract

Continuum solvent models have shown to be very efficient for calculating solvation energy of biomolecules in solution. However, in order to produce accurate results, besides atomic radii or volumes, an appropriate set of partial charges of the molecule is needed. Here, a set of partial charges produced by a fluctuating charge model-the atom-bond electronegativity equalization method model (ABEEMσπ) fused into molecular mechanics is used to fit for the analytical continuum electrostatics model of generalized-Born calculations. Because the partial atomic charges provided by the ABEEMσπ model can well reflect the polarization effect of the solute induced by the continuum solvent in solution, accurate and rapid calculations of the solvation energies have been performed for series of compounds involving 105 small neutral molecules, twenty kinds of dipeptides and several protein fragments. The solvation energies of small neutral molecules computed with the combination of the GB model with the fluctuating charge protocol (ABEEMσπ∕GB) show remarkable agreement with the experimental results, with a correlation coefficient of 0.97, a slope of 0.95, and a bias of 0.34 kcal∕mol. Furthermore, for twenty kinds of dipeptides and several protein fragments, the results obtained from the analytical ABEEMσπ∕GB model calculations correlate well with those from ab initio and Poisson-Boltzmann calculations. The remarkable agreement between the solvation energies computed with the ABEEMσπ∕GB model and PB model provides strong motivation for the use of ABEEMσπ∕GB solvent model in the simulation of biochemical systems.

Reaction mechanism of NO with hydrolysates of NAMI‐A: an MD simulation by combining the QM/MM(ABEEM) with the MD‐FEP method

“…Wilson and Ichikawa and Torrent‐Sucarrat and coworkers pointed out that the charge transfer between atoms in a molecule is overestimated by using the polarization basis sets. Huzinaka et al, Jakalian et al, Watanabe et al, and our group have shown that the use of higher levels of basis sets overestimates the overlap between their respective basis functions belonging to two atoms in a molecule. Bayly and his coworkers pointed out that when the 6‐31G* basis set is used, the polarity of a molecule calculated by the partial charges is overestimated by 10%–15% .…”

A model of atoms in molecules based on potential acting on one electron in a molecule: I. Partition and atomic charges obtained from ab initio calculations

“…Atomic charges of this type are based on the concept of electronegativity. Some methods based on the electronegativity equalization principle in DFT have been developed, such as Mortier's electronegativity equalization method (EEM); the split charge equilibration (SQE) model; Rappé and Goddard's QEq; York and Yang's chemical potential equilibration (CPE); the partial equalization of orbital electronegativity proposed by Gasteiger et al and Scheraga and coworker; the methods proposed by Mullay and Abraham and coworkers; and Yang's atom‐bond electronegativity equalization method (ABEEM), among others …”

The electronegativity equalization method fused with molecular mechanics: a fluctuating charge and flexible body potential function for [Emim][Gly] ionic liquids

“…Based on the electronegativity equalization method (EEM) 31,32 originally developed in the context of density functional theory (DFT), 33,34 the fluctuating charge model has been applied to many systems, such as water, microporous inorganic solids, organic molecules, dense and biomolecular systems, and so on. [35][36][37][38][39][40][41][42][43] Currently, a small number of fluctuating charge models for IL compounds are available. In 2008, Siehl et al 44 applied the consistent charge equilibration (CQEq) method to guanidinium chloride IL systems.…”