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

Van Quan Vuong; Yoshio Nishimoto; Dmitri G. Fedorov; Bobby G. Sumpter; Thomas A. Niehaus; Stephan Irle

doi:10.1021/acs.jctc.9b00108

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

Van Quan Vuong, Yoshio Nishimoto, Dmitri G. Fedorov, Bobby G. Sumpter, Thomas A. Niehaus, Stephan Irle

Research output: Contribution to journal › Article › peer-review

37 Scopus citations

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(N ^1.13-1.28 ), 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.

Original language	English
Pages (from-to)	3008-3020
Number of pages	13
Journal	Journal of Chemical Theory and Computation
Volume	15
Issue number	5
DOIs	https://doi.org/10.1021/acs.jctc.9b00108
State	Published - May 14 2019

Funding

V.Q.V. acknowledges support by an Energy Science and Engineering Fellowship of the Bredesen Center for Interdisciplinary Research and Graduate Education at the University of Tennessee, Knoxville. S.I. acknowledges initial support for the method development by the Laboratory Directed Research and Development (LDRD) Program of Oak Ridge National Laboratory. ORNL is managed by UT-Battelle, LLC, for DOE under Contract No. DE-AC05-00OR22725. SI acknowledges support by the Fluid Interface Reactions, Structures and Transport (FIRST) Center, an Energy Frontier Research Center funded by the U.S. DOE Office of Science for the application of the method to ionic liquids. DGF and YN acknowledge support by JSPS KAKENHI, Grant Number 16K05677 & 19H02682. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility operated under Contract No. DE-AC02-05CH11231.

Funders	Funder number
Bredesen Center for Interdisciplinary Research and Graduate Education at the University of Tennessee
DOE Office of Science
U.S. Department of Energy Office of Science
U.S. Department of Energy
Oak Ridge National Laboratory
Laboratory Directed Research and Development
Japan Society for the Promotion of Science	16K05677, 19H02682

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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(N 1.13-1.28 ), 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.",

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

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