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 »
- Authors:
-
- Univ. of Tennessee, Knoxville, TN (United States)
- Kyoto Univ., Kyoto (Japan)
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Univ. Claude Bernard Lyon 1, Villeurbanne (France)
- 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:
- 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. Thu .
"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},
journal = {Journal of Chemical Theory and Computation},
number = 5,
volume = 15,
place = {United States},
year = {Thu Apr 18 00:00:00 EDT 2019},
month = {Thu Apr 18 00:00:00 EDT 2019}
}
Web of Science
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