L-Alanine in a droplet of water: A density-functional molecular dynamics study
We report the results of a Born-Oppenheimer molecular dynamics study on an L-alanine amino acid in neutral aqueous solution. The whole system, the L-alanine zwitterion and 50 water molecules, was treated quantum mechanically. We found that the hydrophobic side chain (R ) CH3) defines the trajectory...
| Main Authors: | , , , |
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| Format: | Journal Article |
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American Chemical Society
2007
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| Online Access: | http://pubs.acs.org/journals/jpcbfk/index.html http://hdl.handle.net/20.500.11937/18777 |
| _version_ | 1848749842589810688 |
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| author | Degtyarenko, I. Jalkanen, Karl Gurtovenko, A. Nieminen, R. |
| author_facet | Degtyarenko, I. Jalkanen, Karl Gurtovenko, A. Nieminen, R. |
| author_sort | Degtyarenko, I. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | We report the results of a Born-Oppenheimer molecular dynamics study on an L-alanine amino acid in neutral aqueous solution. The whole system, the L-alanine zwitterion and 50 water molecules, was treated quantum mechanically. We found that the hydrophobic side chain (R ) CH3) defines the trajectory path of the molecule. Initially fully hydrated in an isolated droplet of water, the amino acid moves to the droplet's surface, exposing its hydrophobic methyl group and R-hydrogen out of the water. The structure of an L-alanine with the methyl group exposed to the water surface was found to be energetically favorable compared to a fully hydrated molecule. The dynamic behavior of the system suggests that the first hydration shell of the amino acid is localized around carboxylate (CO2-) and ammonium (NH3+) functional groups; it is highly ordered and quite rigid. In contrast, the hydration shell around the side chain is much less structured, suggesting a modest influence of the methyl group on the structure of water. The number of water molecules in the first hydration shell of an alanine molecule is constantly changing; the average number was found to equal 7. The molecular dynamics results show that L-alanine in water does not have a preferred conformation, as all three of the molecule's functional sites (i.e., CH3, NH3 +, CO2-) perform rotational movements around the CR-site bond. |
| first_indexed | 2025-11-14T07:27:22Z |
| format | Journal Article |
| id | curtin-20.500.11937-18777 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T07:27:22Z |
| publishDate | 2007 |
| publisher | American Chemical Society |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-187772018-08-31T07:11:45Z L-Alanine in a droplet of water: A density-functional molecular dynamics study Degtyarenko, I. Jalkanen, Karl Gurtovenko, A. Nieminen, R. We report the results of a Born-Oppenheimer molecular dynamics study on an L-alanine amino acid in neutral aqueous solution. The whole system, the L-alanine zwitterion and 50 water molecules, was treated quantum mechanically. We found that the hydrophobic side chain (R ) CH3) defines the trajectory path of the molecule. Initially fully hydrated in an isolated droplet of water, the amino acid moves to the droplet's surface, exposing its hydrophobic methyl group and R-hydrogen out of the water. The structure of an L-alanine with the methyl group exposed to the water surface was found to be energetically favorable compared to a fully hydrated molecule. The dynamic behavior of the system suggests that the first hydration shell of the amino acid is localized around carboxylate (CO2-) and ammonium (NH3+) functional groups; it is highly ordered and quite rigid. In contrast, the hydration shell around the side chain is much less structured, suggesting a modest influence of the methyl group on the structure of water. The number of water molecules in the first hydration shell of an alanine molecule is constantly changing; the average number was found to equal 7. The molecular dynamics results show that L-alanine in water does not have a preferred conformation, as all three of the molecule's functional sites (i.e., CH3, NH3 +, CO2-) perform rotational movements around the CR-site bond. 2007 Journal Article http://hdl.handle.net/20.500.11937/18777 10.1021/jp0676991 http://pubs.acs.org/journals/jpcbfk/index.html American Chemical Society restricted |
| spellingShingle | Degtyarenko, I. Jalkanen, Karl Gurtovenko, A. Nieminen, R. L-Alanine in a droplet of water: A density-functional molecular dynamics study |
| title | L-Alanine in a droplet of water: A density-functional molecular dynamics study |
| title_full | L-Alanine in a droplet of water: A density-functional molecular dynamics study |
| title_fullStr | L-Alanine in a droplet of water: A density-functional molecular dynamics study |
| title_full_unstemmed | L-Alanine in a droplet of water: A density-functional molecular dynamics study |
| title_short | L-Alanine in a droplet of water: A density-functional molecular dynamics study |
| title_sort | l-alanine in a droplet of water: a density-functional molecular dynamics study |
| url | http://pubs.acs.org/journals/jpcbfk/index.html http://hdl.handle.net/20.500.11937/18777 |