TY - JOUR
T1 - An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins
AU - Jia, Xiangyu
AU - Wang, Xianwei
AU - Liu, Jinfeng
AU - Zhang, John Z.H.
AU - Mei, Ye
AU - He, Xiao
PY - 2013/12/7
Y1 - 2013/12/7
N2 - 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 (DC-PB) method. Notwithstanding, a high correlation between EE-GMFCC-CPCM and DC-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.
AB - 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 (DC-PB) method. Notwithstanding, a high correlation between EE-GMFCC-CPCM and DC-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.
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U2 - 10.1063/1.4833678
DO - 10.1063/1.4833678
M3 - Article
C2 - 24320361
AN - SCOPUS:84903362087
SN - 0021-9606
VL - 139
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
IS - 21
M1 - 214104
ER -