An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins

Xiangyu Jia, Xianwei Wang, Jinfeng Liu, John Z.H. Zhang, Ye Mei, Xiao He

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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 (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.

Original languageEnglish (US)
Article number214104
JournalJournal of Chemical Physics
Volume139
Issue number21
DOIs
StatePublished - Dec 7 2013

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ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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