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Title: Geochemical Reaction Mechanism Discovery from Molecular Simulation

Abstract

Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineral surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.

Authors:
 [1];  [2]
+ Show Author Affiliations
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1163589
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Environmental Chemistry
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1448-2517
Publisher:
CSIRO Publishing
Country of Publication:
United States
Language:
English
Subject:
58 GEOSCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Stack, Andrew G., and Kent, Paul R. C. Geochemical Reaction Mechanism Discovery from Molecular Simulation. United States: N. p., 2014. Web. doi:10.1071/EN14045.
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Stack, Andrew G., & Kent, Paul R. C. Geochemical Reaction Mechanism Discovery from Molecular Simulation. United States. https://doi.org/10.1071/EN14045
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Stack, Andrew G., and Kent, Paul R. C. Mon . "Geochemical Reaction Mechanism Discovery from Molecular Simulation". United States. https://doi.org/10.1071/EN14045. https://www.osti.gov/servlets/purl/1163589.
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@article{osti_1163589,
title = {Geochemical Reaction Mechanism Discovery from Molecular Simulation},
author = {Stack, Andrew G. and Kent, Paul R. C.},
abstractNote = {Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineral surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.},
doi = {10.1071/EN14045},
journal = {Environmental Chemistry},
number = 1,
volume = 12,
place = {United States},
year = {Mon Nov 10 00:00:00 EST 2014},
month = {Mon Nov 10 00:00:00 EST 2014}
}
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