Interfacing ab initio quantum mechanical method with classical drude osillator polarizable model for molecular dynamics simulation of chemical reactions

Zhenyu Lu, Yingkai Zhang

Research output: Contribution to journalArticle

Abstract

In order to further Improve the accuracy and applicability of combined quantum mechanical/molecular mechanical (QM/MM) methods, we have interfaced the ab initio QM method with the classical Drude oscillator polarizable MM force field (ai-QM/MM-Drude). Different coupling approaches have been employed and compared: 1. the conventional dual selfconsistent-field (SCF) procedure; 2. the direct SCF scheme, in which QM densities and MM Drude positions are converged simultaneously; 3. the microiterative SCF scheme, in which the Drude positions of the polarizable model are fully converged during each self-consistent field (SCF) step of QM calculations; 4. the one-step-Drude-update scheme, in which the MM Drude positions are updated only once instead of fully converged during each molecular dynamics (MD) step. The last three coupling approaches are found to be efficient and can achieve the desired convergence in a similar number of QM SCF steps comparing with the corresponding QM method coupled to a nonpolarizable force field. The feasibility and applicability of the implemented ai-QM/MM-Drude approach have been demonstrated by carrying out Born-Oppenheimer molecular dynamics simulations with the umbrella sampling method to determine potentials of mean force for both the methyl transfer reaction of the methyl chlorine-chlorine ion system and the glycine intramolecular proton transfer reaction in aqueous solution. Our results indicate that the ai-QM/MM-Drude approach is very promising, which provides a better description of QM/MM interactions while achieving quite similar computational efficiency In comparison with the corresponding conventional ab initio QM/MM method.

Original languageEnglish (US)
Pages (from-to)1237-1248
Number of pages12
JournalJournal of Chemical Theory and Computation
Volume4
Issue number8
DOIs
StatePublished - Aug 2008

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Chlorine
Molecular dynamics
Chemical reactions
chemical reactions
molecular dynamics
Proton transfer
Computer simulation
Computational efficiency
Glycine
field theory (physics)
chlorine
Amino acids
simulation
Ions
Sampling
glycine
self consistent fields
sampling
oscillators
aqueous solutions

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

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title = "Interfacing ab initio quantum mechanical method with classical drude osillator polarizable model for molecular dynamics simulation of chemical reactions",
abstract = "In order to further Improve the accuracy and applicability of combined quantum mechanical/molecular mechanical (QM/MM) methods, we have interfaced the ab initio QM method with the classical Drude oscillator polarizable MM force field (ai-QM/MM-Drude). Different coupling approaches have been employed and compared: 1. the conventional dual selfconsistent-field (SCF) procedure; 2. the direct SCF scheme, in which QM densities and MM Drude positions are converged simultaneously; 3. the microiterative SCF scheme, in which the Drude positions of the polarizable model are fully converged during each self-consistent field (SCF) step of QM calculations; 4. the one-step-Drude-update scheme, in which the MM Drude positions are updated only once instead of fully converged during each molecular dynamics (MD) step. The last three coupling approaches are found to be efficient and can achieve the desired convergence in a similar number of QM SCF steps comparing with the corresponding QM method coupled to a nonpolarizable force field. The feasibility and applicability of the implemented ai-QM/MM-Drude approach have been demonstrated by carrying out Born-Oppenheimer molecular dynamics simulations with the umbrella sampling method to determine potentials of mean force for both the methyl transfer reaction of the methyl chlorine-chlorine ion system and the glycine intramolecular proton transfer reaction in aqueous solution. Our results indicate that the ai-QM/MM-Drude approach is very promising, which provides a better description of QM/MM interactions while achieving quite similar computational efficiency In comparison with the corresponding conventional ab initio QM/MM method.",
author = "Zhenyu Lu and Yingkai Zhang",
year = "2008",
month = "8",
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publisher = "American Chemical Society",
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AU - Lu, Zhenyu

AU - Zhang, Yingkai

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N2 - In order to further Improve the accuracy and applicability of combined quantum mechanical/molecular mechanical (QM/MM) methods, we have interfaced the ab initio QM method with the classical Drude oscillator polarizable MM force field (ai-QM/MM-Drude). Different coupling approaches have been employed and compared: 1. the conventional dual selfconsistent-field (SCF) procedure; 2. the direct SCF scheme, in which QM densities and MM Drude positions are converged simultaneously; 3. the microiterative SCF scheme, in which the Drude positions of the polarizable model are fully converged during each self-consistent field (SCF) step of QM calculations; 4. the one-step-Drude-update scheme, in which the MM Drude positions are updated only once instead of fully converged during each molecular dynamics (MD) step. The last three coupling approaches are found to be efficient and can achieve the desired convergence in a similar number of QM SCF steps comparing with the corresponding QM method coupled to a nonpolarizable force field. The feasibility and applicability of the implemented ai-QM/MM-Drude approach have been demonstrated by carrying out Born-Oppenheimer molecular dynamics simulations with the umbrella sampling method to determine potentials of mean force for both the methyl transfer reaction of the methyl chlorine-chlorine ion system and the glycine intramolecular proton transfer reaction in aqueous solution. Our results indicate that the ai-QM/MM-Drude approach is very promising, which provides a better description of QM/MM interactions while achieving quite similar computational efficiency In comparison with the corresponding conventional ab initio QM/MM method.

AB - In order to further Improve the accuracy and applicability of combined quantum mechanical/molecular mechanical (QM/MM) methods, we have interfaced the ab initio QM method with the classical Drude oscillator polarizable MM force field (ai-QM/MM-Drude). Different coupling approaches have been employed and compared: 1. the conventional dual selfconsistent-field (SCF) procedure; 2. the direct SCF scheme, in which QM densities and MM Drude positions are converged simultaneously; 3. the microiterative SCF scheme, in which the Drude positions of the polarizable model are fully converged during each self-consistent field (SCF) step of QM calculations; 4. the one-step-Drude-update scheme, in which the MM Drude positions are updated only once instead of fully converged during each molecular dynamics (MD) step. The last three coupling approaches are found to be efficient and can achieve the desired convergence in a similar number of QM SCF steps comparing with the corresponding QM method coupled to a nonpolarizable force field. The feasibility and applicability of the implemented ai-QM/MM-Drude approach have been demonstrated by carrying out Born-Oppenheimer molecular dynamics simulations with the umbrella sampling method to determine potentials of mean force for both the methyl transfer reaction of the methyl chlorine-chlorine ion system and the glycine intramolecular proton transfer reaction in aqueous solution. Our results indicate that the ai-QM/MM-Drude approach is very promising, which provides a better description of QM/MM interactions while achieving quite similar computational efficiency In comparison with the corresponding conventional ab initio QM/MM method.

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