The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)

Dmitri G. Fedorov, Kazuo Kitaura, Hui Li, Jan H. Jensen, Mark S. Gordon

Research output: Contribution to journalArticle

105 Citations (Scopus)

Abstract

The polarizable continuum model (PCM) for the description of solvent effects is combined with the fragment molecular orbital (FMO) method at several levels of theory, using a many-body expansion of the electron density and the corresponding electrostatic potential, thereby determining solute (FMO)-solvent (PCM) interactions. The resulting method, denoted FMO/PCM, is applied to a set of model systems, including α-helices and β-strands of alanine consisting of 10, 20, and 40 residues and their mutants to charged arginine and glutamate residues. The FMO/PCM error in reproducing the PCM solvation energy for a full system is found to be below 1 kcal/mol in all cases if a two-body expansion of the electron density is used in the PCM potential calculation and two residues are assigned to each fragment. The scaling of the FMO/PCM method is demonstrated to be nearly linear at all levels for polyalanine systems. A study of the relative stabilities of α-helices and β-strands is performed, and the magnitude of the contributing factors is determined. The method is applied to three proteins consisting of 20, 129, and 245 residues, and the solvation energy and computational efficiency are discussed.

Original languageEnglish (US)
Pages (from-to)976-985
Number of pages10
JournalJournal of Computational Chemistry
Volume27
Issue number8
DOIs
StatePublished - Jun 1 2006

Fingerprint

Continuum Model
Molecular orbitals
Fragment
Solvation
Helix
arginine glutamate
Carrier concentration
Solvent Effect
Electron
Relative Stability
Arginine
Model Error
Computational efficiency
Energy Efficiency
Mutant
Alanine
Electrostatics
Computational Efficiency
Energy efficiency
Scaling

Keywords

  • FMO
  • Fragment molecular orbital
  • GAMESS
  • GDDI
  • PCM
  • Parallel
  • Polarizable continuum model
  • Protein

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO). / Fedorov, Dmitri G.; Kitaura, Kazuo; Li, Hui; Jensen, Jan H.; Gordon, Mark S.

In: Journal of Computational Chemistry, Vol. 27, No. 8, 01.06.2006, p. 976-985.

Research output: Contribution to journalArticle

Fedorov, Dmitri G. ; Kitaura, Kazuo ; Li, Hui ; Jensen, Jan H. ; Gordon, Mark S. / The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO). In: Journal of Computational Chemistry. 2006 ; Vol. 27, No. 8. pp. 976-985.
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