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United States Department of Agriculture

Agricultural Research Service

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Location: Cotton Structure and Quality Research

2011 Annual Report

1a. Objectives (from AD-416)
Overall project objectives include: Collecting the best available information on the structures within the cotton fiber; Constructing fundamental models of these structures at different size scales; Providing additional fundamental models that have partial surfaces of hydrophobic molecules; and Monitoring moisture movement through the model structure during molecular dynamics simulations. Specific aspects of this work to be carried out by the CCRC include development of improvements of atomistic models of cotton cellulose and their interaction with water.

1b. Approach (from AD-416)
The main feature of this effort will be to examine the abilities of an improved version of the water model (TIP5P) and a parameter set that utilizes explicit lone pairs of electrons. The models will be examined for reproduction of known properties such as unit cell dimensions and retention of the geometric features of the cellulose structure. Distinctions in results between molecular dynamics and energy minimization will be explored. Necessary adjustments will be made to the modeling parameters to develop a final set. A model involving several smaller crystals will be devised to mimic a portion of a cotton fiber, and the behavior of interacting water will be observed. An ultimate goal, possibly not practical within the scope of this project, will be to gain insight on the division between “bound water” and “bulk water” and the sensitivity of the results to the exact details of the simulation. Deviations from the above plan are not necessarily expected but can be accommodated. For example, water models other than TIP5P might be more helpful, or other force field modifications other than the addition of explicit lone pairs may be more useful.

3. Progress Report
Previous molecular dynamics studies of cellulose microfibrils using force field models found that the microfibrils adopted a right-handed twist upon simulation. This twist appeared to be inconsistent with experimental cellulose structural data. The computer program Groningen Machine for Chemical Simulations (GROMACS) allows simulations of periodic cellulose microfibrils down the length of what is essentially an “infinite” microfibril. This type of simulation is being used to examine the effect of model size on simulation outcome. Models currently under investigation are 1x1, 3x3, 5x5, 7x7, and 9x9 bundles, all simulated to be “infinitely” long. As seen in previous “finite” simulations, bundles larger than 1x1 twist as a bulk. In order to build “infinite” models of bundles larger than 1x1 that are not artificially constrained to linearity due to the nature of the simulation, the models must be built in a way that the periodic unit of the bundle will be repeated to infinity and contain the appropriate number of beta-glucose units to form a complete twist. This will allow the twist to be accommodated should the model attempt to twist over the course of the simulation. In order to satisfy this prerequisite, we are running a series of “finite” model simulations to determine the angle of twist for each bundle. From this, the number of beta-glucose units necessary to create appropriate periodic units can be determined. This permits simulation of “infinite” cellulose microfibrils that are not artificially constrained to linearity, and allows the effect of model length to be thoroughly investigated. A new series of calculations has been initiated to look at other potential problems in using the Glycam potential energy force field for cotton cellulose and other carbohydrates, so as to learn whether the results from a Glycam calculation are the same as those from a quantum mechanics calculation. The molecules being studied are simpler than the cellobiose molecule in that they have no hydroxyl groups. Still, the quantum mechanics energy maps for the simple analog models are predictive for the solid state experimental structures. Another factor that became apparent is that the unit cell dimensions for the tunicate cellulose are noticeably different from those of cotton. This is attributed to the smaller crystallite size of cotton, which lacks the long range vander Waals forces that could compress a larger crystal and give shorter unit cell dimensions perpendicular to the chain axis. The methods used to monitor activities for this agreement were e-mails and interactions, presentations at scientific meetings, and publications.

4. Accomplishments

Last Modified: 2/23/2016
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