Analytic gradient for second order Moller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method

Takeshi Nagata, Dmitri G. Fedorov, Hui Li, Kazuo Kitaura

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

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 Å for RHF/D and MP2, respectively. The details of the hydrogen bond network in the Trp-cage protein are revealed.

Original languageEnglish (US)
Article number204112
JournalJournal of Chemical Physics
Volume136
Issue number20
DOIs
StatePublished - May 28 2012

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Pulse code modulation
Molecular orbitals
molecular orbitals
perturbation theory
fragments
continuums
proteins
gradients
polypeptides
Static Electricity
solvation
Hydrogen
Proteins
free energy
Solvation
Surface charge
electrostatics
hydrogen bonds
deviation
formulations

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Analytic gradient for second order Moller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method. / Nagata, Takeshi; Fedorov, Dmitri G.; Li, Hui; Kitaura, Kazuo.

In: Journal of Chemical Physics, Vol. 136, No. 20, 204112, 28.05.2012.

Research output: Contribution to journalArticle

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