Simulations of Lignin-Polysaccharide Complexes in the Secondary Cell Wall of Plants for Biofuel Production

We use all-atom molecular dynamics simulations to understand the conformational and dynamical properties of the secondary cell wall components plants. To this end, we specifically model the lignin, hemicelluloses (xylan compounds) and other carbohydrate molecules for Alamo switchgrass plants (Panicium virgatum). First, the influence of hemicellulose in the absence of cellulose on the conformational properties of lignin melt is probed. Subsequently, using hydrated lignin-xylan complex, we analyze the spatial dynamics of water near the lignin-hemicellulose complexes and the structural reorientation of the monolignol and p-hydroxycinnamate subunits of lignin molecules. Finally, an all-atom model, comprising the lignin-carbohydrate complexes with inputs from solid-state NMR experiments, is simulated to understand the organization of the secondary cell wall structure in switchgrass plants. These models will then be used in conjunction with solvents such as tetrahydrofuran (THF) to understand the efficacy of these organic solvents for reducing the recalcitrance of lignin-polysaccharide matrix, thereby leading to effective plant degradation.