Evaluation of coarse-grained mapping schemes for polysaccharide chains in cellulose

TitleEvaluation of coarse-grained mapping schemes for polysaccharide chains in cellulose
Publication TypeJournal Article
Year of Publication2013
AuthorsMarkutsya S, Devarajan A, Baluyut JY, Windus TL, Gordon MS, Lamm MH
Journal TitleJournal of Chemical Physics
Volume138
Pages214108
Date Published06
Type of ArticleArticle
ISBN Number0021-9606
Accession NumberWOS:000320138900010
Keywordsalgorithms, biomolecular systems, crystal-structure, highly efficient, hydrogen-bonding system, model, molecular-dynamics simulations, neutron fiber diffraction, pretreatment, synchrotron x-ray
Abstract

A fundamental understanding of the intermolecular forces that bind polysaccharide chains together in cellulose is crucial for designing efficient methods to overcome the recalcitrance of lignocellulosic biomass to hydrolysis. Because the characteristic time and length scales for the degradation of cellulose by enzymatic hydrolysis or chemical pretreatment span orders of magnitude, it is important to closely integrate the molecular models used at each scale so that, ultimately, one may switch seamlessly between quantum, atomistic, and coarse-grained descriptions of the system. As a step towards that goal, four multiscale coarse-grained models for polysaccharide chains in a cellulose-I alpha microfiber are considered. Using the force matching method, effective coarse-grained forces are derived from all-atom trajectories. Performance of the coarse-grained models is evaluated by comparing the intrachain radial distribution functions with those obtained using the all-atom reference data. The all-atom simulation reveals a double peak in the radial distribution function for sites within each glucose residue that arises from the distinct conformations sampled by the primary alcohol group in the glucose residues. The three-site and four-site coarse-grained models have sufficient degrees of freedom to predict this double peak while the one-site and two-site models do not. This is the first time that coarse-grained models have been shown to reproduce such subtle, yet important, molecular features in a polysaccharide chain. The relative orientations between glucose residues along the polysaccharide chain are evaluated and it is found that the four-site coarse-grained model is best at reproducing the glucose-glucose conformations observed in the all-atom simulation. The success of the four-site coarse-grained model underscores the importance of decoupling the pyranose ring from the oxygen atom in the glycosidic bond when developing all-atom to coarse-grained mapping schemes for polysaccharides. (C) 2013 AIP Publishing LLC.

URL<Go to ISI>://WOS:000320138900010
DOI10.1063/1.4808025