期刊
JOURNAL OF CHEMICAL PHYSICS
卷 136, 期 20, 页码 -出版社
AMER INST PHYSICS
DOI: 10.1063/1.4714601
关键词
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资金
- MEXT, Japan
- Computational Materials Science Initiative (CMSI, Japan)
- U.S. National Science Foundation (NSF) [1010674]
A new energy expression is proposed for the fragment molecular orbital method interfaced with the polarizable continuum model (FMO/PCM). The solvation free energy is shown to be more accurate on a set of representative polypeptides with neutral and charged residues, in comparison to the original formulation at the same level of the many-body expansion of the electrostatic potential determining the apparent surface charges. The analytic first derivative of the energy with respect to nuclear coordinates is formulated at the second-order Moller-Plesset (MP2) perturbation theory level combined with PCM, for which we derived coupled perturbed Hartree-Fock equations. The accuracy of the analytic gradient is demonstrated on test calculations in comparison to numeric gradient. Geometry optimization of the small Trp-cage protein (PDB: 1L2Y) is performed with FMO/PCM/6-31(+)G(d) at the MP2 and restricted Hartree-Fock with empirical dispersion (RHF/D). The root mean square deviations between the FMO optimized and NMR experimental structure are found to be 0.414 and 0.426 angstrom for RHF/D and MP2, respectively. The details of the hydrogen bond network in the Trp-cage protein are revealed. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4714601]
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