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United States Department of Agriculture

Agricultural Research Service


Location: Plant Polymer Research

Title: DFTMD study of beta-cellobiose: conformational preference using implicit solvent

item Momany, Frank
item Schnupf, Udo

Submitted to: Carbohydrate Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/6/2011
Publication Date: 3/5/2011
Citation: Momany, F.A., Schnupf, U. 2011. DFTMD study of beta-cellobiose: conformational preference using implicit solvent. Carbohydrate Research. 345(1):619-630.

Interpretive Summary: Cellobiose is a building block of cellulose, important in conversion of cellulosic materials to ethanol. In order to understand the chemical conversion, it is important to understand the solvation process. This research has been carried out to explain some anomalies in structure and energy that we found in previous studies on the optimization of cellobiose conformations, using advanced electronic structure calculations. Advances in computing software and hardware made this work possible. Although the computing time for these highly difficult molecular dynamics studies is counted in months of computer processing usage (CPU) it is a major breakthrough to reduce the integrals to be calculated by a factor of ~10% and thus realize a speedup of the calculations. This work enhances understanding of the solvation process and will be of benefit to other scientists working in this area.

Technical Abstract: Previous DFT in vacuo studies on the conformational preferences for cellobiose showed that upon optimization the Phi-H-anti conformations were of lower energy than the syn forms. Upon optimization using an implicit solvation method, COSMO, the syn or observed form was still not predicted to be of lower energy than the Phi-H-anti form, even though optimization after addition of several explicit water molecules did show a relative energy difference favoring the syn form. In order to examine the predictive ability of COSMO on this carbohydrate, constant energy dynamics, DFTMD,simulations were carried out on low energy syn and Phi-H-anti conformations with and without COSMO included during the dynamics. The resulting analysis confirmed that when COSMO is included in the dynamics, the syn conformations become energetically favored over the Phi-H-anti forms suggesting that both solvent and entropy play roles in dictating the solution conformation of cellobiose. Analysis of the dynamic runs includes distributions of selected dihedral angles with time, conformational transitions,and populations of some quasi-planar, boat, skew forms during the simulations.

Last Modified: 10/20/2017
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