Location: Plant Polymer Research
Title: Molecular Dynamics Simulations of a Cyclic DP-240 Amylose Fragment in a Periodic Cell: Glass Transition Temperature and Water Diffusion Authors
Submitted to: Carbohydrate Polymers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 17, 2009
Publication Date: September 27, 2009
Citation: Momany, F.A., Willett, J.L., Schnupf, U. 2009. Molecular Dynamics Simulations of a Cyclic DP-240 Amylose Fragment in a Periodic Cell: Glass Transition Temperature and Water Diffusion. Carbohydrate Polymers. 78(1):978-986. Interpretive Summary: Computational studies of large molecular fragments of amorphous amylose (starch) give us knowledge of the movement of the carbohydrate and the water molecules imbedded in the material. Molecular dynamic simulations are carried out on a periodic cell containing one molecule made up of 240 glucose residues linked to form a large cyclic structure. Water molecules are dispersed throughout the cell to give specific hydration concentrations. At a particular temperature, each simulation is repeated many times, while the cell volume, material density and potential energy are monitored. Glass transition temperatures (Tg) are found by noting the discontinuity in slope of the three parameters listed when plotted against temperature. The calculated Tg values are in good agreement with experimental values. To investigate the effect of structural modifications to the amylose fragment, randomly selected residues were modified to mannose residues and new Tg values determined. No significant change in Tg was found as a result of the modifications. Diffusion coefficients were also determined and found to fit known experimental values. This work has application to vitreous behavior of food ingredients such as oligosaccharides, important information for food and polymer scientists. This work will help scientists understand the transitions between brittle and rubbery forms in the creation and stabilization of food materials.
Technical Abstract: Molecular dynamics simulations using AMB06C, an in-house carbohydrate force field, (NPT ensembles, 1atm) were carried out on a periodic cell that contained a cyclic-DP-240 amylose fragment and TIP3P water molecules. Molecular conformation and movement of the amylose fragment and water molecules at different temperatures were examined. The periodic cell volume, density, and potential energy were determined at temperatures above and below the glass transition temperature (Tg) in 25 K degree increments. The amorphous cell was constructed as described previously, through successive dynamic equilibration steps at temperatures above the assumed Tg value and the temperature successively lowered until several temperature points were obtained below Tg. Each temperature run was repeated three times. Each molecular dynamics simulation was continued for at least 500 picoseconds or until the volume drift stopped and remained constant for several hundred picoseconds. The Tg values were found by noting the discontinuity in slope of the volume (V), potential energy (PE), or density (delta) versus 1/T. The changes in flexibility and motion of the amylose chain as well as differences in self diffusion coefficients of water molecules are described. The final average Tg value found (316 K) is in agreement with experimental values, i.e. approximately 320 K. Eleven randomly selected residues were structurally modified to alpha-mannose (2-position axial) residues in order to investigate the effect of doping on the amylose sequence. The cell volume at any given temperature increased when the glucose residues were modified, but the Tg value of the doped c-DP-240 fragment was approximately 313 K, nearly the same as the original c-DP-240 within the error limits.