Computational insights of noncovalent interactions in xylan hydrate crystal

This study investigates the H atomic coordinates of hydroxyl and water in xylan hydrate crystals through an integrated computational approach combining density functional theory (DFT) and molecular dynamics (MD) simulations, with the objective of establishing the complete crystal structure of this important hemicellulose component of plant secondary cell walls. We implemented a three-step refinement protocol consisting of: (1) conformational coarse searching, (2) DFT optimization, and (3) MD simulation. Initial structural configurations were determined through semi-empirical force field energy minimization to identify the most probable hydroxyl group orientations at C2 and C3 positions, followed by DFT refinement of water hydrogen coordinates. Our results demonstrate that both C2 and C3 hydroxyl dihedral angles (∠H-C-O-H) converge to approximately ±60°, corresponding to a cis-cis configuration. MD simulations further elucidate the critical role of water molecules in crystallizing and stabilizing the xylan/water complex through formation of 2.49 hydrogen bonds per residue. Energy decomposition analysis using a low-dimensional fragment approach revealed distinct interaction mechanisms: electrostatic forces dominate xylan-water cohesion, while dispersion interactions (rather than hydrogen bonding) primarily stabilize xylan-xylan chain packing. These findings provide fundamental insights into the molecular interactions governing plant cell wall assembly and offer valuable guidance to develop advanced applications for lignocellulosic materials.