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Title: The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding

Abstract

The presently available linear scaling approaches to density-functional tight-binding (DFTB) based on the fragment molecular orbital (FMO) method are severely impacted by the problem of artificial charge transfer due to the self-interaction error (SIE), which hampers the simulation of zwitterionic systems such as biopolymers or ionic liquids. Here we report an extension of FMO-DFTB where we included a long-range corrected (LC) functional designed to mitigate the DFTB SIE, called the FMO-LC-DFTB method, resulting in a robust method which succeeds in simulating zwitterionic systems. Both energy and analytic gradient are developed for the gas phase and the polarizable continuum model of solvation. The scaling of FMO-LC-DFTB with system size N is shown to be almost linear, O(N1.13–1.28), and its numerical accuracy is established for a variety of representative systems including neutral and charged polypeptides. It is shown that pair interaction energies between fragments for two mini-proteins are in excellent agreement with results from long-range corrected density functional theory. The new method was employed in long time scale (1 ns) molecular dynamics simulations of the tryptophan cage protein (PDB: 1L2Y) in the gas phase for four different protonation states and in stochastic global minimum structure searches for 1-ethyl-3-methylimidazolium nitrate ionic liquid clustersmore » containing up to 2300 atoms.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [6]
  1. Univ. of Tennessee, Knoxville, TN (United States)
  2. Kyoto Univ., Kyoto (Japan)
  3. National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  5. Univ. Claude Bernard Lyon 1, Villeurbanne (France)
  6. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Fluid Interface Reactions, Structures and Transport Center (FIRST); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1512513
Alternate Identifier(s):
OSTI ID: 1566991
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 15; Journal Issue: 5; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Vuong, Van Quan, Nishimoto, Yoshio, Fedorov, Dmitri G., Sumpter, Bobby G., Niehaus, Thomas A., and Irle, Stephan. The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding. United States: N. p., 2019. Web. doi:10.1021/acs.jctc.9b00108.
Vuong, Van Quan, Nishimoto, Yoshio, Fedorov, Dmitri G., Sumpter, Bobby G., Niehaus, Thomas A., & Irle, Stephan. The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding. United States. https://doi.org/10.1021/acs.jctc.9b00108
Vuong, Van Quan, Nishimoto, Yoshio, Fedorov, Dmitri G., Sumpter, Bobby G., Niehaus, Thomas A., and Irle, Stephan. 2019. "The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding". United States. https://doi.org/10.1021/acs.jctc.9b00108. https://www.osti.gov/servlets/purl/1512513.
@article{osti_1512513,
title = {The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding},
author = {Vuong, Van Quan and Nishimoto, Yoshio and Fedorov, Dmitri G. and Sumpter, Bobby G. and Niehaus, Thomas A. and Irle, Stephan},
abstractNote = {The presently available linear scaling approaches to density-functional tight-binding (DFTB) based on the fragment molecular orbital (FMO) method are severely impacted by the problem of artificial charge transfer due to the self-interaction error (SIE), which hampers the simulation of zwitterionic systems such as biopolymers or ionic liquids. Here we report an extension of FMO-DFTB where we included a long-range corrected (LC) functional designed to mitigate the DFTB SIE, called the FMO-LC-DFTB method, resulting in a robust method which succeeds in simulating zwitterionic systems. Both energy and analytic gradient are developed for the gas phase and the polarizable continuum model of solvation. The scaling of FMO-LC-DFTB with system size N is shown to be almost linear, O(N1.13–1.28), and its numerical accuracy is established for a variety of representative systems including neutral and charged polypeptides. It is shown that pair interaction energies between fragments for two mini-proteins are in excellent agreement with results from long-range corrected density functional theory. The new method was employed in long time scale (1 ns) molecular dynamics simulations of the tryptophan cage protein (PDB: 1L2Y) in the gas phase for four different protonation states and in stochastic global minimum structure searches for 1-ethyl-3-methylimidazolium nitrate ionic liquid clusters containing up to 2300 atoms.},
doi = {10.1021/acs.jctc.9b00108},
url = {https://www.osti.gov/biblio/1512513}, journal = {Journal of Chemical Theory and Computation},
issn = {1549-9618},
number = 5,
volume = 15,
place = {United States},
year = {2019},
month = {4}
}

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Works referencing / citing this record:

Fantasy versus reality in fragment-based quantum chemistry
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