Conformational analysis of xylobiose by DFT quantum mechanics

Authors: LING, ZHE - Beijing Forestry University; Edwards, Judson - Vince; Nam, Sunghyun; XU, FENG - Beijing Forestry University; French, Alfred - Al

Submitted to: Cellulose
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/16/2019
Publication Date: 1/1/2020
Citation: Ling, Z., Edwards, J.V., Nam, S., Xu, F., French, A.D. 2020. Conformational analysis of xylobiose by DFT quantum mechanics. Cellulose. 27:1207-1224. https://doi.org/10.1007/s10570-019-02874-3.
DOI: https://doi.org/10.1007/s10570-019-02874-3

Interpretive Summary: Xylan molecules are important component of most plant cell walls. They are classified as a hemicellulose by those working with wood and other plants that are harvested for their fiber, and are also dietary components. As with other carbohydrate polymers, their properties depend on their shapes. Among the most interesting interactions involving xylans are with enzymes that break them into smaller molecules. The present work explored the shapes of xylan molecules using quantum mechanics studies of xylobiose, a short fragment of xylan, and compared the results with 283 examples of experimental determinations of xylobiose geometry, mostly when complexed with enzymes or other proteins. The agreement between the predicted shapes and experiment was good but some questions remain. Some experimental results were indicated as probably incorrect. This fundamental study provided results that were compared with similar studies of cellulose that showed why the shapes of the two molecules are different. The importance of several factors in the modeling study was clarified. This work is of interest to scientists working with xylan molecules and those who are simulating other carbohydrate materials.

Technical Abstract: '-1,4-Xylobiose could be regarded as the shortest and simplest xylan, a hemicellulose that closely interacts with cellulose in plants. Those interactions, important in plant growth as well as utilization of wood and cereal grains, depend in part on the conformations of the involved molecules. In this work, the conformations of xylan were modeled with xylobiose using the same density functional theory (DFT) quantum mechanics approach used previously for cellobiose, with both vacuum and solvated models. For any given conformation, xylobiose can make only a single inter-residue hydrogen bond instead of the two simultaneous bonds that are possible for cellobiose or cellulose. The vacuum map shows that compared to cellobiose, there is a reduced preference for the 'Hanti-'Hsyn minimum on the edges of our maps (which allows hydrogen bonding between O3 and O2'. On the other hand, the solvated map prefers, if barely, the central 'Hsyn-'Hsyn minimum where an O3-H···O5 bond could occur. The solution global minimum region accommodates the experimentally observed left-handed, 3-fold helical shape of xylan mono- and dihydrate as well as the substantial majority of di- and oligosaccharide structures from the Crystal Structure Database and the Protein Databank. Because cellobiose has a CH2OH group attached to C5 and xylobiose does not, it was also of special interest to compare the energy surfaces of xylobiose and cellobiose. That comparison, and a similar comparison of non-hydroxyl bearing analogs, showed that the C6 group increased the relative energies of structures having 'C5 values between -100° and +40°. The energy map for the solvated, non-hydroxyl bearing xylobiose analog was surprisingly predictive of the observed experimental crystal structures.