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United States Department of Agriculture

Agricultural Research Service


item French, Alfred - Al
item Kelterer, Anne-marie
item Johnson, Glenn
item Dowd, Michael - Mike
item Cramer, Christopher

Submitted to: Journal of Computational Chemistry
Publication Type: Peer reviewed journal
Publication Acceptance Date: 6/20/2000
Publication Date: N/A

Interpretive Summary: Molecular modeling is widely used in many industries to help understand the properties of molecules both as an aide to experiment and for prediction of new uses. However, these methods are not as well developed for carbohydrates, molecules that are extremely important in agriculture. The prediction of the shapes of molecules is an important step in understanding many of their properties. Although these predictions have been getting better, there is a large controversy regarding whether the shapes depend on the inherent nature of the molecule or if they are mostly governed by the environment. This work used a fundamental, quantum mechanics calculation of the energy of all possible shapes of 12 different molecules that resemble various carbohydrates. The quantum mechanics calculations predicted the shapes of the molecules well. In these analyses, cellulose, the important constituent of cotton fiber, appears to be slightly distorted by other cellulose molecules during crystallization just after biosynthesis. Other molecules included table sugar, starch, callose and trehalose. These other molecules validated the approach. The role of the atoms that were not included in the analysis was most obvious for the analog of maltose, the basic unit of starch. Other work had shown that including the missing oxygen atoms resulted in better predictions of shape. This work is of primary interest to chemists and molecular biologists.

Technical Abstract: Quantum mechanical HF/6-31G* theory was used to calculate Ramachandran energy surfaces for analogs of 12 disaccharides. The analogs were made by replacing glucose with tetrahydropyran and fructose with 2-methyltetrahydrofuran. The set of analogs included molecules with zero, one and two anomeric carbon atoms, and di-axial, axial-equatorial and diequatorial linkages. Despite the inability of analogs to make hydrogen bonds, their energy surfaces account fairly well for the conformations that are observed in crystals of the disaccharides. Thus, torsional energy and the simple bulk of ring structures are major factors in determining the disaccharide conformations. The shapes around the global minima depended on the number of anomeric carbons involved in the linkage, and the propensity for possibly important secondary minima with relative energies of 2 to 4 kcal/mol depended on whether the bond was axial or equatorial. Partition function values show that the di-axial trehalose analog with no anomeric centers is most flexible. Reproduction of these surfaces is recommended as a simple, "necessary but not sufficient" test of force fields for modeling carbohydrates. Also, these surfaces can be used in a simple hybrid method for calculating disaccharide energy surfaces.

Last Modified: 8/24/2016
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