Analysing π-π-stacking interactions in lignin nanoparticles from molecular simulations - insights and lessons learned.

A special molecular association is π-π-stacking, driven by weak interactions within aromatic compounds. The π-π-stacking interactions can occur in either a sandwich-like or T-shaped manner. In this study, a method to recognise π-π-stacking from classical molecular dynamics trajectories is developed. By applying three criteria, the method is tested for simple lignin dimer, tetramer and octamer systems, with all G units and β-O4' linkages. The criteria are geometric and based on distance between ring centroids, the angle between the planes of the two rings and the lateral displacement of the rings. In addition, a wide-angle X-ray scattering (WAXS) profile was calculated from a tetramer system, in agreement with previous experimental results. However, when the WAXS peak assigned to sandwich-shaped stacking was analysed in-depth, it was found to mainly be caused by other intramolecular structural motifs involving e.g. the α-carbon and ring carbons, rather than π-π-stacking. This finding is important for future analyses of WAXS profiles originating from lignin-based materials and shows the strength of combining X-ray scattering methods with molecular modelling.