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Title: Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms

Abstract

Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM-MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM-MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM-MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.

Authors:
ORCiD logo [1];  [1];  [1]
  1. Univ. of Minnesota, Minneapolis, MN (United States). Dept. of Chemistry
Publication Date:
Research Org.:
Univ. of Minnesota, Minneapolis (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1510997
Grant/Contract Number:  
SC0012702
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Molecules
Additional Journal Information:
Journal Volume: 23; Journal Issue: 6; Journal ID: ISSN 1420-3049
Publisher:
MDPI
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; electrostatics; molecular modeling; multiscale modeling; QM/MM

Citation Formats

Wu, Xin-Ping, Gagliardi, Laura, and Truhlar, Donald. Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms. United States: N. p., 2018. Web. doi:10.3390/molecules23061309.
Wu, Xin-Ping, Gagliardi, Laura, & Truhlar, Donald. Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms. United States. doi:10.3390/molecules23061309.
Wu, Xin-Ping, Gagliardi, Laura, and Truhlar, Donald. Wed . "Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms". United States. doi:10.3390/molecules23061309. https://www.osti.gov/servlets/purl/1510997.
@article{osti_1510997,
title = {Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms},
author = {Wu, Xin-Ping and Gagliardi, Laura and Truhlar, Donald},
abstractNote = {Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM-MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM-MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM-MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.},
doi = {10.3390/molecules23061309},
journal = {Molecules},
issn = {1420-3049},
number = 6,
volume = 23,
place = {United States},
year = {2018},
month = {5}
}

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Works referenced in this record:

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