title: An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins.
abstract: An efficient approach that combines the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method with conductor-like polarizable continuum model (CPCM), termed EE-GMFCC-CPCM, is developed for ab initio calculation of the electrostatic solvation energy of proteins. Compared with the previous MFCC-CPCM study [Y. Mei, C. G. Ji, and J. Z. H. Zhang, J. Chem. Phys. 125, 094906 (2006)], quantum mechanical (QM) calculation is applied to deal with short-range non-neighboring interactions replacing the classical treatment. Numerical studies are carried out for proteins up to 3837 atoms at the HF/6-31G* level. As compared to standard full system CPCM calculations, EE-GMFCC-CPCM shows clear improvement over the MFCC-CPCM method for both the total electrostatic solvation energy and its components (the polarized solute-solvent reaction field energy and wavefunction distortion energy of the solute). For large proteins with 1000-4000 atoms, where the standard full system ab initio CPCM calculations are not affordable, the EE-GMFCC-CPCM gives larger relative wavefunction distortion energies and weaker relative electrostatic solvation energies for proteins, as compared to the corresponding energies calculated by the Divide-and-Conquer Poisson-Boltzmann (D&C-PB) method. Notwithstanding, a high correlation between EE-GMFCC-CPCM and D&C-PB is observed. This study demonstrates that the linear-scaling EE-GMFCC-CPCM approach is an accurate and also efficient method for the calculation of electrostatic solvation energy of proteins.
authors: State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.
authors: Xiangyu
authors: X
authors: Jia
authors: Xianwei
authors: X
authors: Wang
authors: Jinfeng
authors: J
authors: Liu
authors: John Z H
authors: JZ
authors: Zhang
authors: Ye
authors: Y
authors: Mei
authors: Xiao
authors: X
authors: He
mesh_terms: D000409:Alanine / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012997:Solvents; D055672:Static Electricity
chemical_list: D009842:Oligopeptides; D011506:Proteins; D012997:Solvents; D000409:Alanine