Molecular dynamics simulations of a guaiacyl β‐O‐4 lignin model compound: Examination of intramolecular hydrogen bonding and conformational flexibility

Abstract

The dynamical conformational behavior of a guaiacyl β‐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 β‐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. © 2004 Wiley Periodicals, Inc. Biopolymers 73: 301–315, 2004