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Title: Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube

Abstract

Recently, a collective variable “proton indicator” was purposed for tracking an excess proton solvated in bulk water in molecular dynamics simulations. In this work, we demonstrate the feasibility of utilizing the position of this proton indicator as a reaction coordinate to model an excess proton migrating through a hydrophobic carbon nanotube in combined quantum-mechanics/molecular-mechanics simulations. Our results indicate that applying a harmonic restraint to the proton indicator in the bulk solvent near the nanotube pore entrance leads to the recruitment of water molecules into the pore. This is consistent with an earlier study that employed a multistate empirical valence bond potential and a different representation (center of excess charge) of the proton. We attribute this water recruitment to the delocalized nature of the solvated proton, which prefers to be in high-dielectric bulk solvent. While water recruitment into the pore is considered an artifact in the present simulations (because of the artificially imposed restraint on the proton), if the proton were naturally restrained, it could assist in building water wires prior to proton transfer through the pore. The potential of mean force for a proton translocation through the water-filled pore was computed by umbrella sampling, where the bias potentials were appliedmore » to the proton indicator. The free energy curve and barrier heights agree reasonably with those in the literature. Finally, the results suggest that the proton indicator can be used as a reaction coordinate in simulations of proton transport in confined environments.« less

Authors:
 [1]; ORCiD logo [1]
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  1. Univ. of Colorado, Denver, CO (United States). Chemistry Dept.
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE; National Science Foundation (NSF)
OSTI Identifier:
1480293
Grant/Contract Number:  
CHE-140070; ACI-1053575
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
Additional Journal Information:
Journal Volume: 121; Journal Issue: 36; Journal ID: ISSN 1520-6106
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS

Citation Formats

Duster, Adam W., and Lin, Hai. Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube. United States: N. p., 2017. Web. doi:10.1021/acs.jpcb.7b06657.
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Duster, Adam W., & Lin, Hai. Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube. United States. https://doi.org/10.1021/acs.jpcb.7b06657
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Duster, Adam W., and Lin, Hai. Fri . "Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube". United States. https://doi.org/10.1021/acs.jpcb.7b06657. https://www.osti.gov/servlets/purl/1480293.
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@article{osti_1480293,
title = {Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube},
author = {Duster, Adam W. and Lin, Hai},
abstractNote = {Recently, a collective variable “proton indicator” was purposed for tracking an excess proton solvated in bulk water in molecular dynamics simulations. In this work, we demonstrate the feasibility of utilizing the position of this proton indicator as a reaction coordinate to model an excess proton migrating through a hydrophobic carbon nanotube in combined quantum-mechanics/molecular-mechanics simulations. Our results indicate that applying a harmonic restraint to the proton indicator in the bulk solvent near the nanotube pore entrance leads to the recruitment of water molecules into the pore. This is consistent with an earlier study that employed a multistate empirical valence bond potential and a different representation (center of excess charge) of the proton. We attribute this water recruitment to the delocalized nature of the solvated proton, which prefers to be in high-dielectric bulk solvent. While water recruitment into the pore is considered an artifact in the present simulations (because of the artificially imposed restraint on the proton), if the proton were naturally restrained, it could assist in building water wires prior to proton transfer through the pore. The potential of mean force for a proton translocation through the water-filled pore was computed by umbrella sampling, where the bias potentials were applied to the proton indicator. The free energy curve and barrier heights agree reasonably with those in the literature. Finally, the results suggest that the proton indicator can be used as a reaction coordinate in simulations of proton transport in confined environments.},
doi = {10.1021/acs.jpcb.7b06657},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
number = 36,
volume = 121,
place = {United States},
year = {Fri Aug 18 00:00:00 EDT 2017},
month = {Fri Aug 18 00:00:00 EDT 2017}
}
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https://doi.org/10.1021/acs.jpcb.7b06657
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