Paper Info
Title
The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO).
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 a-helices and P-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 alpha-helices and beta-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. (c) 2006 Wiley Periodicals, Inc.
Year
DOI
Venue
2006
10.1002/jcc.20406
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
Field
DocType
fragment molecular orbital,FMO,polarizable continuum model,PCM,GAMESS,parallel,GDDI,protein
Polarizable continuum model,Electron density,Fragment molecular orbital,Computational chemistry,Chemistry,Solvation,GAMESS,Scaling,Solvent effects
Journal
Volume
Issue
ISSN
27
8
0192-8651
Citations 
PageRank 
References 
11
1.12
5
Authors
5
Name
Order
Citations
PageRank
Dmitri G Fedorov113814.52
Kazuo Kitaura29011.68
Hui Li3111.12
Jan H. Jensen41019.34
Mark S. Gordon528325.73