Molecular Computational Studies In Geochemistry and Environmental Chemistry
EMSL Project ID
20900
Abstract
This project is focused on prediction of reaction rates, mechanisms, and associated isotopic fractionation factors of key processes in low-temperature geochemistry. Such processes can play a key role in the environmental fate of contaminants such as those present in the subsurface at DOE nuclear production facilities. This proposal combines several geochemical research threads including electron transfer, proton transfer, and ligand exchange reactions in interfacial geochemistry. In each area, the latest theory and simulation methods are closely coupled to recent experiments capable of assessing mechanistic detail for elementary geochemical reactions in model systems. During the last decade, important methodological advances in computational chemistry at the electronic structure and molecular dynamics levels have allowed progress to be made in understanding rates and mechanisms of chemical reactions in complex media, such as those occurring in aqueous solutions. These computational methods promise the ability to calculate rates for real geochemical reactions using the tools of quantum chemistry, molecular dynamics, and computational kinetics. The rates reflect the accessibility of the reactant site to water molecules and the details of bonding, such as charges and the Brønsted acidities of particular oxygen atoms in the reacting molecule and the energies of electrons in a reaction step. These studies will be combined to assess the extent to which reactivity in geochemical systems can be reduced to knowledge of structure.
Project Details
Project type
Capability Research
Start Date
2006-10-01
End Date
2009-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Bogatko SA, EJ Bylaska, and JH Weare. 2010. "First Principles Simulation of the Bonding, Vibrational, and Electronic Properties of the Hydration Shells of the High-Spin Fe3+ Ion in Aqueous Solutions." Journal of Physical Chemistry A 114(5):2189-2200. doi:10.1021/jp904967n
Bylaska EJ, KL Tsemekhman, SB Baden, JH Weare, and H Jonsson. 2011. "Parallel Implementation of Gamma-Point Pseudopotential Plane-Wave DFT with Exact Exchange." Journal of Computational Chemistry 32(1):54-69.
Bylaska EJ, M Dupuis, and PG Tratnyek. 2008. "One-Electron-Transfer Reactions of Polychlorinated Ethylenes: Concerted and Stepwise Cleavages." Journal of Physical Chemistry A 112(16):3712-3721.
Bylaska EJ, M Valiev, JR Rustad, and JH Weare. 2007. "Structure and Dynamics of the Hydration Shells of the Al3+ Ion ." Journal of Chemical Physics 126(10):Art.no.104505.
Cauet E, SA Bogatko, JH Weare, JL Fulton, GK Schenter, and EJ Bylaska. 2010. "Structure and Dynamics of the Hydration Shells of the Zn2+ Ion from ab initio Molecular Dynamics and Combined ab initio and Classical Molecular Dynamics Simulations." Journal of Chemical Physics 132(19):Article 194502.
Elsasser BM, M Valiev, and JH Weare. 2009. "A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction." Journal of the American Chemical Society 131(11):3869-3871. doi:10.1021/ja807940y
Nichols P, EJ Bylaska, GK Schenter, and WA De Jong. 2008. "Equatorial and Apical Solvent Shells of the UO?²? Ion." Journal of Chemical Physics 128(12):124507. doi:10.1063/1.2884861
Nichols PJ, N Govind, EJ Bylaska, and WA De Jong. 2009. "Gaussian Basis Set and Planewave Relativistic Spin-Orbit Methods in NWChem." Journal of Chemical Theory and Computation 5(3):491-499. doi:10.1021/ct8002892
Rustad JR, and EJ Bylaska. 2007. "Ab Initio Calculation of Isotopic Fractionation in B(OH)?(aq) and BOH??(aq)." Journal of the American Chemical Society 129(8):2222-2223. doi:10.1021/ja0683335
Rustad JR, and P Zarzycki. 2008. "Calculation of Site-specific Carbon-isotope Fractionation in Pedogenic Oxide Minerals." Proceedings of the National Academy of Sciences of the United States of America 105(30):10297–10301. doi:10.1073/pnas.0801571105
Rustad JR, SL Nelmes, VE Jackson, and DA Dixon. 2008. "Quantum-Chemical Calculations of Carbon-Isotope Fractionation in CO2(g), Aqueous Carbonate Species, and Carbonate Minerals." Journal of Physical Chemistry A 112(3):542-555. doi:10.1021/jp076103m
Valiev M, EJ Bylaska, M Dupuis, and PG Tratnyek. 2008. "Combined Quantum Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Solution." Journal of Physical Chemistry A 112(12):2713-2720. doi:10.1021/jp7104709
Wang J, JR Rustad, and WH Casey. 2007. "Calculation of Water-Exchange Rates on Aqueous Polynuclear Clusters and at Oxide-Water Interfaces." Inorganic Chemistry 46(8):2962-2964. doi:10.1021/ic070079