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Periodic density functional theory calculations of bulk and the (010) surface of goethite
BACKGROUND: Goethite is a common and reactive mineral in the environment. The transport of contaminants and anaerobic respiration of microbes are significantly affected by adsorption and reduction reactions involving goethite. An understanding of the mineral-water interface of goethite is critical f...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409307/ https://www.ncbi.nlm.nih.gov/pubmed/18477389 http://dx.doi.org/10.1186/1467-4866-9-4 |
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author | Kubicki, James D Paul, Kristian W Sparks, Donald L |
author_facet | Kubicki, James D Paul, Kristian W Sparks, Donald L |
author_sort | Kubicki, James D |
collection | PubMed |
description | BACKGROUND: Goethite is a common and reactive mineral in the environment. The transport of contaminants and anaerobic respiration of microbes are significantly affected by adsorption and reduction reactions involving goethite. An understanding of the mineral-water interface of goethite is critical for determining the molecular-scale mechanisms of adsorption and reduction reactions. In this study, periodic density functional theory (DFT) calculations were performed on the mineral goethite and its (010) surface, using the Vienna Ab Initio Simulation Package (VASP). RESULTS: Calculations of the bulk mineral structure accurately reproduced the observed crystal structure and vibrational frequencies, suggesting that this computational methodology was suitable for modeling the goethite-water interface. Energy-minimized structures of bare, hydrated (one H(2)O layer) and solvated (three H(2)O layers) (010) surfaces were calculated for 1 × 1 and 3 × 3 unit cell slabs. A good correlation between the calculated and observed vibrational frequencies was found for the 1 × 1 solvated surface. However, differences between the 1 × 1 and 3 × 3 slab calculations indicated that larger models may be necessary to simulate the relaxation of water at the interface. Comparison of two hydrated surfaces with molecularly and dissociatively adsorbed H(2)O showed a significantly lower potential energy for the former. CONCLUSION: Surface Fe-O and (Fe)O-H bond lengths are reported that may be useful in surface complexation models (SCM) of the goethite (010) surface. These bond lengths were found to change significantly as a function of solvation (i.e., addition of two extra H(2)O layers above the surface), indicating that this parameter should be carefully considered in future SCM studies of metal oxide-water interfaces. |
format | Text |
id | pubmed-2409307 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-24093072008-06-04 Periodic density functional theory calculations of bulk and the (010) surface of goethite Kubicki, James D Paul, Kristian W Sparks, Donald L Geochem Trans Research Article BACKGROUND: Goethite is a common and reactive mineral in the environment. The transport of contaminants and anaerobic respiration of microbes are significantly affected by adsorption and reduction reactions involving goethite. An understanding of the mineral-water interface of goethite is critical for determining the molecular-scale mechanisms of adsorption and reduction reactions. In this study, periodic density functional theory (DFT) calculations were performed on the mineral goethite and its (010) surface, using the Vienna Ab Initio Simulation Package (VASP). RESULTS: Calculations of the bulk mineral structure accurately reproduced the observed crystal structure and vibrational frequencies, suggesting that this computational methodology was suitable for modeling the goethite-water interface. Energy-minimized structures of bare, hydrated (one H(2)O layer) and solvated (three H(2)O layers) (010) surfaces were calculated for 1 × 1 and 3 × 3 unit cell slabs. A good correlation between the calculated and observed vibrational frequencies was found for the 1 × 1 solvated surface. However, differences between the 1 × 1 and 3 × 3 slab calculations indicated that larger models may be necessary to simulate the relaxation of water at the interface. Comparison of two hydrated surfaces with molecularly and dissociatively adsorbed H(2)O showed a significantly lower potential energy for the former. CONCLUSION: Surface Fe-O and (Fe)O-H bond lengths are reported that may be useful in surface complexation models (SCM) of the goethite (010) surface. These bond lengths were found to change significantly as a function of solvation (i.e., addition of two extra H(2)O layers above the surface), indicating that this parameter should be carefully considered in future SCM studies of metal oxide-water interfaces. BioMed Central 2008-05-13 /pmc/articles/PMC2409307/ /pubmed/18477389 http://dx.doi.org/10.1186/1467-4866-9-4 Text en Copyright © 2008 Kubicki et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Kubicki, James D Paul, Kristian W Sparks, Donald L Periodic density functional theory calculations of bulk and the (010) surface of goethite |
title | Periodic density functional theory calculations of bulk and the (010) surface of goethite |
title_full | Periodic density functional theory calculations of bulk and the (010) surface of goethite |
title_fullStr | Periodic density functional theory calculations of bulk and the (010) surface of goethite |
title_full_unstemmed | Periodic density functional theory calculations of bulk and the (010) surface of goethite |
title_short | Periodic density functional theory calculations of bulk and the (010) surface of goethite |
title_sort | periodic density functional theory calculations of bulk and the (010) surface of goethite |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409307/ https://www.ncbi.nlm.nih.gov/pubmed/18477389 http://dx.doi.org/10.1186/1467-4866-9-4 |
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