Exploring Structure and Energetics of a Helix-Forming Oligomer by Molecular Modeling and Molecular Dynamics Simulation Methods: Dynamics of Water in a Hydrophobic Nanotube
IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata
View Archive Info| Field | Value | |
| Title |
Exploring Structure and Energetics of a Helix-Forming Oligomer by Molecular Modeling
and Molecular Dynamics Simulation Methods: Dynamics of Water in a Hydrophobic
Nanotube
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| Creator |
Sen, Srikanta
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| Subject |
Molecular & Human Genetics
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| Description |
Molecular dynamics simulation studies on the structure, energetics, and dynamics of an all-meta-phenylacetylene
oligomer in helical and coiled conformations in water have been performed in order to understand the physical
basis of helix stabilization in water. It has been demonstrated that the oligomer maintained a dynamically
stable helical structure in aqueous solvent at room temperature, without intrachain H-bonds, in agreement
with experimental observation. The structure obtained from simulation is found significantly different from
the structure presented before based on energy minimization only. The average structure of the helix from
dynamics simulation has been characterized in detail. Comparison of energetics between the helical and coiled
conformations of the oligomer demonstrated that, in addition to the solvophobic effect, the self-energy of the
oligomer also provides a substantial preference toward the helix structure due to favorable van der Waal
interactions. No water bridge stabilizing the helix was found. Interestingly, the helix represents a novel model
double-walled nanotube (DWNT). Although the inside surface of the helix pore is dominantly hydrophobic
in nature, water molecules are allowed to enter into the tube during dynamics but no permeation of water
through the tube was observed over the 0.75 ns trajectory. The water molecules inside the hydrophobic tube
were found to be strongly H-bonded among them with long lifetimes. The overall dynamics of water inside
the tube was quite different from that of water molecules in the bulk.
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| Publisher |
American Chemical Society
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| Date |
2002
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| Type |
Article
PeerReviewed |
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| Format |
application/pdf
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| Identifier |
http://www.eprints.iicb.res.in/770/1/JOURNAL_OF_PHYSICAL_CHEMISTRY_B_106(43)_11343%2D11350_;2002[21].pdf
Sen, Srikanta (2002) Exploring Structure and Energetics of a Helix-Forming Oligomer by Molecular Modeling and Molecular Dynamics Simulation Methods: Dynamics of Water in a Hydrophobic Nanotube. The Journal of Physical Chemistry B, 106 (43). pp. 13453-11350. |
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| Relation |
http://dx.doi.org/10.1021/jp014730k
http://www.eprints.iicb.res.in/770/ |
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