skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: An analysis of hydrated proton diffusion in ab initio molecular dynamics

Abstract

A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ~2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP–D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300–330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and aftermore » successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions. Furthermore, the correlations of the neighboring water atoms are identified as the fourth water approaches the hydronium. Finally, the temperature effects on structural and dynamical properties are studied« less

Authors:
 [1];  [2];  [1]
  1. Univ. of Chicago, IL (United States). James Franck Inst., and Computation Inst., Dept. of Chemistry
  2. Argonne National Lab. (ANL), Argonne, IL (United States). Leadership Computing Facility
Publication Date:
Research Org.:
Univ. of Chicago, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); U.S. Department of Defense (DOD); National Science Foundation (NSF); Croucher Foundation; Engineer Research and Development Center (ERDC)
OSTI Identifier:
1512306
Alternate Identifier(s):
OSTI ID: 1228466; OSTI ID: 1582235
Grant/Contract Number:  
SC0005418; AC02-06CH11357; CHE-1214087
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 142; Journal Issue: 1; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
74 ATOMIC AND MOLECULAR PHYSICS

Citation Formats

Tse, Ying-Lung Steve, Knight, Chris, and Voth, Gregory A. An analysis of hydrated proton diffusion in ab initio molecular dynamics. United States: N. p., 2015. Web. doi:10.1063/1.4905077.
Tse, Ying-Lung Steve, Knight, Chris, & Voth, Gregory A. An analysis of hydrated proton diffusion in ab initio molecular dynamics. United States. https://doi.org/10.1063/1.4905077
Tse, Ying-Lung Steve, Knight, Chris, and Voth, Gregory A. 2015. "An analysis of hydrated proton diffusion in ab initio molecular dynamics". United States. https://doi.org/10.1063/1.4905077. https://www.osti.gov/servlets/purl/1512306.
@article{osti_1512306,
title = {An analysis of hydrated proton diffusion in ab initio molecular dynamics},
author = {Tse, Ying-Lung Steve and Knight, Chris and Voth, Gregory A.},
abstractNote = {A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ~2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP–D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300–330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions. Furthermore, the correlations of the neighboring water atoms are identified as the fourth water approaches the hydronium. Finally, the temperature effects on structural and dynamical properties are studied},
doi = {10.1063/1.4905077},
url = {https://www.osti.gov/biblio/1512306}, journal = {Journal of Chemical Physics},
issn = {0021-9606},
number = 1,
volume = 142,
place = {United States},
year = {Wed Jan 07 00:00:00 EST 2015},
month = {Wed Jan 07 00:00:00 EST 2015}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 50 works
Citation information provided by
Web of Science

Figures / Tables:

TABLE I TABLE I: The density functional, basis set, plane wave cutoff, simulation length, and linear fit to constant $NVE$ instantaneous temperature as a function of time (picoseconds) for all AIMD trajectories examined in this study. Here, the instantaneous temperature is defined to be the average of kinetic energy divided by 1.5more » $$k$$B for each data frame. For each density functional approximation, the first and last two rows correspond to pairs of simulations equilibrated at the target temperatures 300 and 330 K, respectively, in the constant $NVT$ ensemble. The B3LYP simulations were equilibrated only at one target temperature of 300 K.« less

Save / Share:

Works referenced in this record:

Structure and Dynamics of Concentrated Hydrochloric Acid Solutions
journal, July 2010


Potential models for simulations of the solvated proton in water
journal, October 1998


Molecular Dynamics Simulation of Liquid Water:  Hybrid Density Functionals
journal, March 2006


Structure and dynamics of orientational defects in ice I
journal, March 2004


Ab Initio Molecular Dynamics Simulation of the Solvation and Transport of H3O+ and OH- Ions in Water
journal, April 1995


Quantum effects and the excess proton in water
journal, November 1997


An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport
journal, January 2008


The nature of the hydrated excess proton in water
journal, February 1999


The Self-Consistent Charge Density Functional Tight Binding Method Applied to Liquid Water and the Hydrated Excess Proton: Benchmark Simulations
journal, May 2010


Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel
journal, November 2013


New generalized gradient approximation functionals
journal, January 2000


Ions in water: The microscopic structure of a concentrated HCl solution
journal, January 2004


Effect of Environment on Hydrogen Bond Dynamics in Liquid Water
journal, February 1996


Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited
journal, July 2005


Accurate description of van der Waals complexes by density functional theory including empirical corrections
journal, January 2004


Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach
journal, April 2005


Communication: Electronic structure of the solvated chloride anion from first principles molecular dynamics
journal, May 2013


Empirical potential Monte Carlo simulation of fluid structure
journal, January 1996


On the recombination of hydronium and hydroxide ions in water
journal, December 2011


Hydrogen-bond patterns in liquid water
journal, November 1973


A bond-order analysis of the mechanism for hydrated proton mobility in liquid water
journal, January 2005


The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations
journal, December 1999

  • Lippert, Gerald; Hutter, Jürg; Parrinello, Michele
  • Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 103, Issue 2
  • https://doi.org/10.1007/s002140050523

Multiconfiguration molecular mechanics algorithm for potential energy surfaces of chemical reactions
journal, February 2000


Behavior of the Eigen Form of Hydronium at the Air/Water Interface
journal, June 2011


Special Pair Dance and Partner Selection: Elementary Steps in Proton Transport in Liquid Water
journal, August 2008


The nature and transport mechanism of hydrated hydroxide ions in aqueous solution
journal, June 2002


A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
journal, April 2010


The Curious Case of the Hydrated Proton
journal, August 2011


A conjecture concerning collective excitations in liquid water
journal, December 1981


Defining Condensed Phase Reactive Force Fields from ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton
journal, September 2010


Density‐functional thermochemistry. III. The role of exact exchange
journal, April 1993


Concerted Hydrogen-Bond Dynamics in the Transport Mechanism of the Hydrated Proton: A First-Principles Molecular Dynamics Study
journal, November 2009


Hydrated Excess Protons Can Create Their Own Water Wires
journal, September 2014


Characterization of the Solvation and Transport of the Hydrated Proton in the Perfluorosulfonic Acid Membrane Nafion
journal, September 2006


Proton transfer through the water gossamer
journal, July 2013


Dispersion corrected RPBE studies of liquid water
journal, August 2014


Communication: The effect of dispersion corrections on the melting temperature of liquid water
journal, March 2011


Canonical sampling through velocity rescaling
journal, January 2007


Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
journal, January 1988


Proton Solvation and Transport in Aqueous and Biomolecular Systems:  Insights from Computer Simulations
journal, May 2007


Multistate Empirical Valence Bond Model for Proton Transport in Water
journal, July 1998


Proton Transport Mechanism of Perfluorosulfonic Acid Membranes
journal, July 2014


A second generation multistate empirical valence bond model for proton transport in aqueous systems
journal, September 2002


Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water
journal, July 1995


The quantum dynamics of an excess proton in water
journal, February 1996


A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions
journal, November 2006


The role of the umbrella inversion mode in proton diffusion
journal, April 2014


ReaxFF:  A Reactive Force Field for Hydrocarbons
journal, October 2001


Separable dual-space Gaussian pseudopotentials
journal, July 1996


Pressure and temperature dependence of self-diffusion in water
journal, January 1978


Auxiliary Density Matrix Methods for Hartree−Fock Exchange Calculations
journal, July 2010


The statistics of electric field fluctuations in liquid water
journal, February 2009


The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water
journal, January 2005


The Grotthuss mechanism
journal, October 1995


First Principles Simulations of the Infrared Spectrum of Liquid Water Using Hybrid Density Functionals
journal, March 2011


Hydroxylation Structure and Proton Transfer Reactivity at the Zinc Oxide−Water Interface
journal, April 2011


Bulk Liquid Water at Ambient Temperature and Pressure from MP2 Theory
journal, October 2013


Ab initio molecular dynamics using hybrid density functionals
journal, June 2008


Kinetics and Mechanism of Water Cluster Equilibria
journal, January 2014


Toward a Unified Picture of the Water Self-Ions at the Air–Water Interface: A Density Functional Theory Perspective
journal, May 2014


The distribution of rings of hydrogen‐bonded molecules in a model of liquid water
journal, May 1987


The computer simulation of proton transport in water
journal, November 1999


Re-examining the properties of the aqueous vapor–liquid interface using dispersion corrected density functional theory
journal, September 2011


Proton and deuteron mobility in normal and heavy water solutions of electrolytes
journal, January 1974

  • Roberts, Noel K.; Northey, Helen L.
  • Journal of the Chemical Society, Faraday Transactions 1: Physical Chemistry in Condensed Phases, Vol. 70, Issue 0
  • https://doi.org/10.1039/f19747000253

Exploring the behaviour of the hydrated excess proton at hydrophobic interfaces
journal, January 2013


Molecular Dynamics Simulations of Proton Transport in 3M and Nafion Perfluorosulfonic Acid Membranes
journal, April 2013


Benchmark oxygen-oxygen pair-distribution function of ambient water from x-ray diffraction measurements with a wide Q -range
journal, February 2013


Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
journal, November 1994


Indication of a Very Large Proton Diffusion in Ice I h
journal, July 2008


Autoionization in Liquid Water
journal, March 2001


Application of the SCC-DFTB Method to Neutral and Protonated Water Clusters and Bulk Water
journal, May 2011


Multiscale reactive molecular dynamics
journal, December 2012


Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD)
journal, November 2001


Works referencing / citing this record:

Reactive molecular dynamics simulations of an excess proton in polyethylene glycol-water solutions
journal, December 2018


Correlated Dynamics in Aqueous Proton Diffusion
text, January 2018


A simple and effective solution to the constrained QM/MM simulations
journal, April 2018


Hydrated excess protons and their local hydrogen bond transport network as measured by translational, librational, and vibrational frequencies
journal, June 2019


Aqueous proton-selective conduction across two-dimensional graphyne
journal, March 2019


Correlated dynamics in aqueous proton diffusion
journal, January 2018


Calculation of solvation free energy utilizing a constrained QM/MM approach combined with a theory of solutions
journal, March 2019


Entropic barriers in the kinetics of aqueous proton transfer
journal, July 2019


Recent advances in quantum‐mechanical molecular dynamics simulations of proton transfer mechanism in various water‐based environments
journal, May 2019


Hydrated proton and hydroxide charge transfer at the liquid/vapor interface of water
journal, July 2015


Aqueous proton-selective conduction across two-dimensional graphyne
journal, March 2019


Predicting the Ionic Product of Water
journal, August 2017


Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.