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United States Department of Agriculture

Agricultural Research Service


Location: Plant Polymer Research

Title: DFT studies of carbohydrate solvation: II. MD-DFTr of a super-molecule complex of glucose, explicit waters, and an implicit solvent (COSMO)

item Momany, Frank
item Schnupf, Udo

Submitted to: Computational and Theoretical Chemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/13/2012
Publication Date: 10/13/2012
Citation: Momany, F.A., Schnupf, U. 2012. DFT studies of carbohydrate solvation: II. MD-DFTr of a super-molecule complex of glucose, explicit waters, and an implicit solvent (COSMO). Computational and Theoretical Chemistry . xx.

Interpretive Summary: Computer modeling of glucose, a simple sugar, was carried out with ten water molecules, as reported in the first paper of this series. Allowing the molecular system to reach room temperature we could follow the way the molecules move and observe how the application of solvent changed the movements relative to the vacuum state. Water molecules did not stick to the glucose molecule for very long times during this simulation. This result is important for scientists to understand the role of solvent in molecular reactions.

Technical Abstract: MD-DFTr studies are carried out on the super-molecule solvated complexes of glucose described in paper I. Included were ten explicit water molecules and an implicit solvation model, COSMO, superimposed upon the complex. Starting configurations were taken from DFTr optimized complexes resulting from using a reduced basis set (B3LYP/4-31G) on the sugar carbon atoms and the full (B3LYP/6-31+G*) level on all other atoms. Molecular dynamics (MD-DFTr) calculations of 5, 10, or 30 ps were examined in order to study the residence time and mobility of the explicit water molecules energy optimized around the glucose molecule, and to observe the removal and time of migration of explicit water molecules into the COSMO solvent layer. MD-DFTr studies provide an estimate of the residence times of the water molecules at particular sites around the glucose molecule. After 5-10 ps of MD-DFTr the results suggest that more than one-half of the previously optimized explicit water molecules have moved from around the glucose molecule, either into the implicit solvent system, or hydrogen bounded to other water molecules in the COSMO layer, but not interacting closely with glucose. Approximately ~2-5 waters remain attached to the glucose after these short MD-DFTr times, thus producing an indirect measure of the binding of explicit water molecules. Upon dynamics fluctuating orientations of the hydroxyl hydrogen atoms occur, but the hydroxymethyl groups remain near their starting conformations, with the exception of the tg forms which in all but one case studied moved to the gt conformation during the simulation. Figures at different picosecond times allow one to observe the movement of the water molecules with time and shows that water molecules above or below the ring move away from glucose faster in the beta-forms than in the alfa-forms. H---O interaction lengths are presented for the optimized configurations, during dynamics, and at the end of each dynamics run. Glucose polarization differences from either explicit water molecules or COSMO were negligible, any differences being overshadowed by differences that are a result of dynamic motion.

Last Modified: 07/25/2017
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