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United States Department of Agriculture

Agricultural Research Service


Location: Plant Polymer Research

Title: DFT molecular simulations of solvated glucose dimers: explicit vs. implicit water

item Momany, Frank
item Schnupf, Udo

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 5/17/2012
Publication Date: 8/23/2012
Citation: Momany, F.A., Schnupf, U. 2012. DFT molecular simulations of solvated glucose dimers: explicit vs. implicit water. Meeting Abstract. #.

Interpretive Summary:

Technical Abstract: The behavior of Glucose dimers in solution is investigated at the DFT level of theory via optimization and constant energy DFT molecular dynamics. The effect of the solvent on the dimer is treated two different ways: using the implicit solvation method COSMO alone to treat the bulk water behavior and further, in addition to COSMO a super-molecule with ten explicit water molecules surrounding the dimer is used. Different configurations of the glucose dimer and of water molecules around the dimers are examined. To obtain a subset of low energy configurations the explicit waters are arranged to optimize the hydrogen bonding interactions with the glucose dimer. The subset of configurations are pre-optimized using an in house developed empirical AMBER potentials for carbohydrates and then optimized at the DFT level of theory using a reduced basis set method. As the molecular dynamics simulations proceeds, the DFT optimized glucose dimers (either with and without explicit waters) dissociate, as one would expect. What is not expected that the time scale for the dimer dissociation is very different for the implicit solvated states vs. the explicit solvated states. Analysis of the simulations suggests that explicit waters use bridging configurations to hold the glucose molecules together for longer periods of time, compared to the COSMO implicit solvent method.

Last Modified: 10/16/2017
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