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

  1. Dmitri G. Fedorov1,*,
  2. Kazuo Kitaura1,
  3. Hui Li2,
  4. Jan H. Jensen3,
  5. Mark S. Gordon2

Article first published online: 7 APR 2006

DOI: 10.1002/jcc.20406

Issue

Journal of Computational Chemistry

Journal of Computational Chemistry

Volume 27, Issue 8, pages 976–985, June 2006

Additional Information

How to Cite

Fedorov, D. G., Kitaura, K., Li, H., Jensen, J. H. and Gordon, M. S. (2006), The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO). Journal of Computational Chemistry, 27: 976–985. doi: 10.1002/jcc.20406

Author Information

  1. 1

    National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, 305-8568 Ibaraki, Japan

  2. 2

    Ames Laboratory, US-DOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011

  3. 3

    Department of Chemistry, University of Iowa, Iowa City, Iowa 52242

*National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, 305-8568 Ibaraki, Japan

Publication History

  1. Issue published online: 7 APR 2006
  2. Article first published online: 7 APR 2006
  3. Manuscript Accepted: 5 JAN 2006
  4. Manuscript Received: 17 OCT 2005

Funded by

  • Grant-in-Aid for Scientific Research (Ministry of Education, Culture, Sports, Science and Technology, Japan)
  • NAREGI Nanoscience Project (Ministry of Education, Culture, Sports, Science and Technology, Japan)
  • CREST (JST, Japan)
  • SciDAC grant from the U.S. Department of Energy
  • HEDM grant from the U.S. Air Force Office of Scientific Research
  • NSF. Grant Number: MCB 0209941

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Keywords:

  • fragment molecular orbital;
  • FMO;
  • polarizable continuum model;
  • PCM;
  • GAMESS;
  • parallel;
  • GDDI;
  • protein

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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. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 976–985, 2006

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