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 journalArticlepeer-review

156 Scopus citations


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
Issue number8
StatePublished - Jun 2006
Externally publishedYes


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

ASJC Scopus subject areas

  • General Chemistry
  • Computational Mathematics


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