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Title: Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method

Abstract

The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

Authors:
 [1];  [2];  [3];  [4];  [5];  [2]
  1. Tokyo Institute of Technology
  2. Ames Laboratory
  3. National Institute of Advanced Industrial Science and Technology (AIST)
  4. Kobe University
  5. Nakamura Lab
Publication Date:
Research Org.:
Ames Laboratory (AMES), Ames, IA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1166910
Report Number(s):
IS-J 8503
Journal ID: ISSN 1089-5639
DOE Contract Number:
DE-AC02-07CH11358
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Physical Chemistry. A, Molecules, Spectroscopy, Kinetics, Environment, and General Theory; Journal Volume: 118; Journal Issue: 41
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE

Citation Formats

Nakata, Hiroya, Schmidt, Michael W, Fedorov, Dmitri G, Kitaura, Kazuo, Nakamura, Shinichiro, and Gordon, Mark S. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method. United States: N. p., 2014. Web. doi:10.1021/jp507726m.
Nakata, Hiroya, Schmidt, Michael W, Fedorov, Dmitri G, Kitaura, Kazuo, Nakamura, Shinichiro, & Gordon, Mark S. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method. United States. doi:10.1021/jp507726m.
Nakata, Hiroya, Schmidt, Michael W, Fedorov, Dmitri G, Kitaura, Kazuo, Nakamura, Shinichiro, and Gordon, Mark S. Thu . "Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method". United States. doi:10.1021/jp507726m.
@article{osti_1166910,
title = {Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method},
author = {Nakata, Hiroya and Schmidt, Michael W and Fedorov, Dmitri G and Kitaura, Kazuo and Nakamura, Shinichiro and Gordon, Mark S},
abstractNote = {The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.},
doi = {10.1021/jp507726m},
journal = {Journal of Physical Chemistry. A, Molecules, Spectroscopy, Kinetics, Environment, and General Theory},
number = 41,
volume = 118,
place = {United States},
year = {Thu Oct 16 00:00:00 EDT 2014},
month = {Thu Oct 16 00:00:00 EDT 2014}
}
  • The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted Hartree-Fock, second-order Møller-Plesset perturbation, and density functional theories. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262,144 CPU cores, are also discussed.
  • We extended the fragment molecular orbital (FMO) method interfaced with density functional theory (DFT) into spin unrestricted formalism (UDFT) and developed energy gradients for the ground state and single point excited state energies based on time-dependent DFT. The accuracy of FMO is evaluated in comparison to the full calculations without fragmentation. Electronic excitations in solvated organic radicals and in the blue copper protein, plastocyanin (PDB code: 1BXV), are reported. The contributions of solvent molecules to the electronic excitations are analyzed in terms of the fragment polarization and quantum effects such as interfragment charge transfer.
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  • 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 evaluatedmore » 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 S{sub N}2 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.« less
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