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United States Department of Agriculture

Agricultural Research Service


Location: Plant Polymer Research

Title: DFTr optimization and DFTr-MD studies of glucose, ten explicit water molecules enclosed by an implicit solvent, COSMO)

item Momany, Frank
item Schnupf, Udo

Submitted to: Computational and Theoretical Chemistry
Publication Type: Peer reviewed journal
Publication Acceptance Date: 12/12/2013
Publication Date: 12/22/2013
Publication URL:
Citation: Momany, F.A., Schnupf, U. 2013. DFTr optimization and DFTr-MD studies of glucose, ten explicit water molecules enclosed by an implicit solvent, COSMO. Computational and Theoretical Chemistry. 1029(1):57-67.

Interpretive Summary: Computer modeling of glucose, the simplest sugar, was carried out where ten molecules of water were placed around it. The computer model was used to determine if water was attracted to a specific site on glucose or if the water restricted the movements of the atoms present in glucose. The results we obtained show that although water is attracted to many sites on the glucose, there are no preferential sites. This result will be of use to organic chemists, biochemists, and pharmacologists as glucose comes into contact with water in all living things.

Technical Abstract: DFTr optimization studies are carried out on alpha/beta-glucose surrounded by ten explicit water molecules and the glucose/water super-molecule completely enclosed by an implicit solvation model, COSMO. Twenty one starting configurations of the explicit waters were first optimized empirically with the AMB06C/TIP3P force field, and further optimized 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. Glucose hydroxymethyl conformations included gg, gt, and tg forms, with the hydroxyl group’s conformations reverse clockwise, ‘r’, and clockwise, ‘c’, forms. The empirical force field optimized configurations were in general agreement with the DFTr results in hydrogen bonding distances from glucose to water molecules, but not in such good agreement in water molecule orientation, a result of lack of lone-pair orientation within the TIP3P force field. The individual energies of all components of the super-molecule complex (i.e. water-water, water-glucose), with and without COSMO) allows analysis of the hydration and interaction energies. Examination of the hydroxyl and hydroxymethyl low energy conformations suggests that the hydrated configurations with gg-r and gg-c conformers are preferred in water.

Last Modified: 8/24/2016
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