Apparatus and process for preparing reactive lignin with high yield from plant biomass for production of fuels and chemicals

Provided are methods for aqueous isolation of depolymerized lignin in high yield from a lignin-containing biomass composition, comprising positioning a lignin-containing biomass composition into a flowthrough thermal reactor chamber to provide for passage of an aqueous fluid therethrough, contacting the lignin biomass composition with the aqueous fluid under elevated temperature conditions sufficient to provide for lignin release and depolymerization, flowing the aqueous fluid through the reactor chamber under the elevated temperature conditions, to provide an output aqueous fluid comprising released depolymerized lignin, and collecting the depolymerized lignin. Particular aspects further comprise hydrogenation and/or hydrodeoxygenation (HDO) of the released depolymerized lignin with a catalyst or catalyst system for deconstruction of the released depolymerized lignin into lower molecular weight reactive lignin moieties and oligomers amenable for subsequent removal of oxygen to produce hydrocarbon fuels and/or chemicals and/or compounds. Systems for practicing the methods are also provided, along with highly purified depolymerized lignin.