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United States Department of Agriculture

Agricultural Research Service

Title: Molecular Dynamics Calculations on Amylose Fragments. I. Glass Transition Temperatures of Maltodecaose at 1%, 5%, 10% and 15.8% Hydration


Submitted to: Biopolymers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 27, 2001
Publication Date: N/A

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. The main components of starch are large carbohydrate polymers namely amylose and amylopectin, that are made up of long chains of glucose sugar units. Despite numerous efforts to understand the shapes of these molecules, a detailed understanding of how amylose and amylopectin pack to form starch granules is still lacking. In this paper we present results on the prediction of glass transition temperatures of amorphous amylose fragments using new computer simulation methods developed in our laboratory. With these computational tools, we can relate previous experimental information obtained by researchers to details concerning the basic structure of the components of starch. This work has allowed us to better understand the size and organization of said components, as well as to more accurately define the role of water in the starch granule. It is hoped that this work will lead to the design of new chemical modifications of starch that will result in properties useful for commercial applications.

Technical Abstract: Molecular dynamics simulations (NPT ensembles, 1atm.) using the all atom force field AMB99C(1)(2), are applied to a periodic cell containing ten maltodecaose fragments and TIP3P water molecules. Simulations were carried out at 25 K intervals over a range of temperatures above and below the expected glass transition temperature, T, for different water concentr- ations. The amorphous cell was constructed through successive dynamic equilibration steps at temperatures above glass transition and the temperature lowered until several points of reduced slope (1/Tv.s. volume) were obtained. This procedure was carried out at each hydration level. Each dynamics simulation was continued until the volume remained constant without up or down drift for at least the last 100 ps. For a given temperature, most simulations required 400-600 ps to reach an equilibrium state, but longer times were necessary as the amount of water in the cell was reduced. A total of more than 30 ns of simulations were required for the complete study. The glass transition for each hydrated cell was taken as that point at which a discontinuity in slope of the volume (V), potential energy (PE), or density (r) versus 1/T was observed. The average calculated glass transition values were 311 K, 337 K, 386 K, and 477 K for hydration levels of 15.8%, 10%, 5%, and 1% respectively, in generally good agreement with experimental values. The glass transition for anhydrous amylose is above the decomposition temperature for carbo- hydrates and so cannot be easily measured. However, it has also been difficult to obtain a value of glass transition for anhydrous amylose using simulation methods. Other molecular parameters such as end-to-end dis- tances, mean square distributions, and pair distributions are discussed.

Last Modified: 9/10/2014
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