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United States Department of Agriculture

Agricultural Research Service

Title: Computational Studies on Carbohydrates in Vacuum: Ii. a Revised Amber Forcefield, Amber99c, for Alpha (1->4) Linkages

Authors
item Momany, Frank
item Willett, Julious

Submitted to: Carbohydrate Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 17, 1999
Publication Date: January 3, 2000

Interpretive Summary: Starch is one of the most important biological molecules known, in addition to being one of the largest renewable crops on the planet. Unfortunately, the 3-dimensional structure of the starch granule has to date defied description at the atomic and molecular level. In this paper, we present results on this subject using powerful computer methods utilized only in our laboratory for carbohydrate studies. With these computational tools, we can relate previous experimental information obtained by other researchers to details on the basic structure. This work has allowed us to better understand the flexibility and electronic organization of several starch components and will lead to the design of new chemical modifications of starch components such as amylose. Such chemical modifications will result in production of biodegradable polymers with new physical properties useful for commercial applications. and will lead to the design of new chemical modifications of starch components such as amylose, as well as important cyclodextrins. Such chemical modifications will result in the production of biodegradable polymers with new physical properties useful for commercial applications.

Technical Abstract: Modifications to the AMBER force field [1] have been made to improve our ability to reproduce observed molecular properties of alpha-linked carbohydrates when calculated using empirical potential energy functions. Molecular structures and energies obtained using gradient optimized density functional methods with ab initio basis sets (B3LYP/6-31G*) on 10 minimum energy conformations of maltose [2] were used to refine the empirical potentials. Theoretical and experimental results on maltose, as well as glucose, alpha-cyclodextrin, beta cyclodextrin, and larger cycloamyloses, were used to refine and test the new potentials by looking at glucose-ring puckering and appearance of disallowed conformational transitions. Solvation studies of medium to large cycloamylose molecules are described in paper III of this series. Results of the tests described here suggest that the revised (AMBER99C) are useful for computational studies of alpha-linked carbohydrates, as found in amylose and amylopectin. In this paper, we describe the development of parameters for AMBER99C using the B3LYP/6-31G* derived structures of maltose.

Last Modified: 9/21/2014
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