Geochemical reaction mechanism discovery from molecular simulation
Andrew G. Stack A C and Paul R. C. Kent B
+ Author Affiliations
- Author Affiliations
A Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
B Center for Nanophase Materials Sciences and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
C Corresponding author. Email: stackag@ornl.gov
Andrew G. Stack is a Senior R&D Staff Member in the Geochemistry and Interfacial Sciences Group, Chemical Sciences Division at Oak Ridge National Laboratory. He is a geochemist who specialises in understanding the kinetics and mechanisms of mineral reactions, and how these inherently molecular-level processes manifest themselves at larger scales. Reactions he has examined include mineral growth and dissolution, incorporation of impurities, electron transfer and ligand exchange. He studies these using a variety of computational, experimental and theoretical approaches. He is currently the Division Chair for the American Chemical Society, Geochemistry Division. |
Paul R. C. Kent is a Senior R&D Staff Member at the Center for Nanophase Materials Sciences and the Computer Science and Mathematics Division at Oak Ridge National Laboratory. He is a physicist specialising in the atomistic simulation of materials, primarily using quantum mechanics-based methods. A particular focus is the development, implementation and optimisation of these methods on high performance computers. He is currently member at large of the Division of Computational Physics of the American Physical Society. |
Environmental Chemistry 12(1) 20-32 https://doi.org/10.1071/EN14045
Submitted: 1 March 2014 Accepted: 2 August 2014 Published: 10 November 2014
Environmental context. Computational simulations are providing an increasingly useful way to isolate specific geochemical and environmental reactions and to test how important they are to the overall rate. In this review, we summarise a few ways that one can simulate a reaction and discuss each technique’s overall strengths and weaknesses. Selected case studies illustrate how these techniques have helped to improve our understanding for geochemical and environmental problems.
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. Some common methods are summarised that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and their strengths and weaknesses are also discussed. 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 effect that molecular simulation has had on our understanding of geochemical reactivity is 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.
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