Effect of microfibril twisting on theoretical powder diffraction patterns of cellulose Iβ

Abstract

Previous studies of calculated diffraction patterns for cellulose crystallites suggest that distortions that arise once models have been subjected to MD simulation are the result of both microfibril twisting and changes in unit cell dimensions induced by the empirical force field; to date, it has not been possible to separate the individual contributions of these effects. To provide a better understanding of how twisting manifests in diffraction data, the present study demonstrates a method for generating twisted and linear cellulose structures that can be compared without the bias of dimensional changes, allowing assessment of the impact of twisting alone. Analysis of unit cell dimensions, microfibril volume, hydrogen bond patterns, glycosidic torsion angles, and hydroxymethyl group orientations confirmed that the twisted and linear structures collected with this method were internally consistent, and theoretical powder diffraction patterns for the two were shown to be effectively indistinguishable. These results indicate that differences between calculated patterns for the crystal coordinates and twisted structures from MD simulation can result entirely from changes in unit cell dimensions, and not from microfibril twisting alone. Although powder diffraction patterns for models in the 81-chain size regime were shown to be unaffected by twisting, suggesting that a modest degree of twist is not inconsistent with experimental data, it may be that other diffraction techniques are capable of detecting this structural difference. Until such time as definitive experimental evidence comes to light, the results of this study suggest that both twisted and linear microfibrils may represent an appropriate model for cellulose Iβ.

Molecular dynamics simulations of large macromolecular complexes

“…Computer simulations are assisting in the development of cost-effective biofuels from agricultural waste, by studying enzymes and enzymatic complexes employed [18, 74, 75] in cellulose degradation as well as biomass recalcitrance [76, 77]. To avoid the recalcitrance problem, biomass pretreatment methods employ various chemical and thermal conditions to modify the molecular interactions and association of the different biomass components in favor of cellulose accessibility and digestibility [78].…”

A molecular dynamics model for glycosylphosphatidyl-inositol anchors: “flop down” or “lollipop”?

“…[50][51][52] Variation of force field parameters within admissible limits is a one viable strategy to test the sensitivity (and thereby the plausibility) of a certain phenomenology. 53,54 For instance, in discussing how the conformational preferences of the hybrid link Ino-POMe emerge, extensive use has been made of the fact that use of either GLYCAM06-type or AM1-BCC charges led to indistinguishable results, see e.g. Fig.…”

A comparative molecular dynamics study of crystalline, paracrystalline and amorphous states of cellulose

“…Ib crystalline phase is the most common form of cellulose, present in large quantities in plant cells, thus this form has been widely studied both by experiments and molecular dynamics (MD) modeling using the GROMOS force field (Charlier and Mazeau 2012;Chen et al 2012;Bergenstrahle et al 2007Bergenstrahle et al , 2008aMatthews et al 2012;Wohlert et al 2012;Bergenstrahle et al 2010;Hadden et al;Zhang et al 2011;Chen et al 2013). MD simulations provide molecular level insight into the cellulose structure, its organization, surface and interfacial properties that complement experimental studies.…”