Abstract
Classical molecular models of the goethite mineral are presented for both a periodically replicated bulk slab and for a finite fragment. Potential energy functions for the mineral models were developed within the AMBER force field [Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A. "A second generation force field for the simulation of proteins, nucleic acids and organic molecules," J. Am. Chem. Soc. 117 (1995) 5179-5197], which facilitates biogeochemical applications. Intramolecular potential parameters were chosen to yield a mineral structure with flexible surface hydroxyl groups. The electrostatic potential for a goethite slab was determined from a periodic Unrestricted Hartree-Fock calculation and used to assign point charges to the mineral atoms. The models were solvated in water and their effect on solution structure is shown to be very similar, predicting oscillations in solvent density near the mineral surface and structured orientation of water molecules.
Original language | English |
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Pages (from-to) | 1-11 |
Number of pages | 11 |
Journal | Molecular Simulation |
Volume | 29 |
Issue number | 1 |
DOIs | |
State | Published - Jan 1 2003 |
Externally published | Yes |
Funding
The authors thank Andrew R. Felmy and James R. Rustad for providing goethite mineral coordinate files and for helpful discussion as well as Kevin M. Rosso and Edoardo Apra for assistance with the solid state calculations. The Geosciences Research Program of the U.S. Department of Energy, Office of Basic Energy Sciences supported this work. Computing resources were available through a Computational Grand Challenge Application grant from the Molecular Science Computing Facility in the Environmental Molecular Sciences Laboratory, which is operated with funding from the Office of Biological and Environmental Research. The NWChem 4.0 computational chemistry package for massively parallel computers used in this study was developed by the High Performance Computational Chemistry group, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory. Battelle Memorial Institute operates Pacific North-west National Laboratory for the U.S. Department of Energy.
Keywords
- Goethite-water interface
- Hartree-Fock calculation
- Molecular dynamics simulation
- Water molecules