Conformational analysis of ester and ether linkages in lignin-arabinoxylan complexes

Molecular dynamics simulations of a guaiacyl beta-O-4 lignin model compound: examination of intramolecular hydrogen bonding and conformational flexibility

The dynamical conformational behavior of a guaiacyl beta-O-4 lignin model compound has been investigated by molecular simulations. The potential energy surface of the molecule in vacuum has been examined by means of an adiabatic map, showing a large accessible conformational space with multiple energy minima separated by low barriers. Molecular dynamics simulations have been performed in vacuum and with explicit solvent molecules for 10 and 2.1 ns, respectively. Molecular dynamics trajectories recorded in vacuum have shown the molecule to be flexible and to visit a large number of conformations. Many intramolecular H-bonds have been observed, existing for more than 90% of the total simulation time. The presence of explicit solvent molecules induces a significant broadening of some regions of the accessible conformational space and also largely reduces the statistical significance of intramolecular H-bonding. Intramolecular H-bonds observed in vacuum do not persist significantly and are preferentially exchanged with intermolecular H-bonds to the surrounding solvent molecules. The theoretical results are in good agreement with experimental NMR data that do not support the existence of strong and persistent intramolecular H-bonds in solution but instead indicate that H-bonds to solvent predominate. Finally, both molecular modeling and NMR approaches predict the guaiacyl beta-O-4 structure to be flexible and indicate that intramolecular H-bonds are not strong and persistent enough to confer rigidity to the molecule in solution.

Molecular modeling of syringyl and p-hydroxyphenyl beta-O-4 dimers. Comparative study of the computed and experimental conformational properties of lignin beta-O-4 model compounds

As a new approach for the study of the ultrastructure of lignin, the conformational preferences of lignin beta-O-4 model compounds have been investigated by molecular modeling. The computed results have been compared with the experimental data (X-ray crystal structures and (3)J(H)(alpha)(H)(beta) NMR coupling constant values) reported in the literature. This comparison has led to an improved understanding of the influence of the structure, stereochemistry, and intramolecular H-bonding upon the conformational properties of the beta-O-4 dimers. A large number of low-energy conformations have been predicted for the structures. It has also appeared that the conformational features are predominantly governed by local steric interactions rather than by differences in the H-bonding interactions. The threo and erythro forms differ significantly in their conformational features, with a preferential extended overall shape for the threo form in which the bulky aromatic groups are distant from each other.