L-Alanine in a Droplet of Water: A Density-Functional Molecular Dynamics Study
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- 作者：Ivan M. Degtyarenko ; Karl J. Jalkanen ; Andrey A. Gurtovenko ; Risto M. Nieminen
- 刊名：Journal of Physical Chemistry B
- 出版年：2007
- 出版时间：April 26, 2007
- 年：2007
- 卷：111
- 期：16
- 页码：4227 - 4234
- 全文大小：349K
- 年卷期：v.111,no.16(April 26, 2007)
- ISSN：1520-5207
文摘
We report the results of a Born-Oppenheimer molecular dynamics study on an L-alanine amino acid inneutral aqueous solution. The whole system, the L-alanine zwitterion and 50 water molecules, was treatedquantum mechanically. We found that the hydrophobic side chain (R = CH3) defines the trajectory path ofthe molecule. Initially fully hydrated in an isolated droplet of water, the amino acid moves to the droplet'ssurface, exposing its hydrophobic methyl group and 
-hydrogen out of the water. The structure of an L-alaninewith the methyl group exposed to the water surface was found to be energetically favorable compared to afully hydrated molecule. The dynamic behavior of the system suggests that the first hydration shell of theamino acid is localized around carboxylate (CO2-) and ammonium (NH3+) functional groups; it is highlyordered and quite rigid. In contrast, the hydration shell around the side chain is much less structured, suggestinga modest influence of the methyl group on the structure of water. The number of water molecules in the firsthydration shell of an alanine molecule is constantly changing; the average number was found to equal 7. Themolecular dynamics results show that L-alanine in water does not have a preferred conformation, as all threeof the molecule's functional sites (i.e., CH3, NH3+, CO2-) perform rotational movements around the C-sitebond.
-hydrogen out of the water. The structure of an L-alaninewith the methyl group exposed to the water surface was found to be energetically favorable compared to afully hydrated molecule. The dynamic behavior of the system suggests that the first hydration shell of theamino acid is localized around carboxylate (CO2-) and ammonium (NH3+) functional groups; it is highlyordered and quite rigid. In contrast, the hydration shell around the side chain is much less structured, suggestinga modest influence of the methyl group on the structure of water. The number of water molecules in the firsthydration shell of an alanine molecule is constantly changing; the average number was found to equal 7. Themolecular dynamics results show that L-alanine in water does not have a preferred conformation, as all threeof the molecule's functional sites (i.e., CH3, NH3+, CO2-) perform rotational movements around the C-sitebond.