Analytic Second Derivative of the Energy for Density Functional Theory Based on the Three-Body Fragment Molecular Orbital Method

Date
2015-01-01
Authors
Nakata, Hiroya
Fedorov, Dmitri
Zahariev, Federico
Schmidt, Michael
Kitaura, Kazuo
Gordon, Mark
Nakamura, Shinichiro
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Ames Laboratory
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Chemistry
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Abstract

Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in SN2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.

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The following article appeared in Journal of Chemical Physics 142 (2015): 124101, and may be found at doi:10.1063/1.4915068.

Keywords
Proteins, Polymers, Free energy, Raman spectra, Biochemical reactions
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