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When fractionating corn cobs using the acetosolv process, the type of acid catalyst and their concentrations significantly affect the structure of the resulting lignin fraction as well as its catalytic deconstruction to aromatic monomers. Gel permeation chromatography (GPC) results show that the average molecular weight (~55,750 g/mol) of the sulfuric acid-pretreated corn cob lignin (H2SO4-CCL) is much greater than that (~39,400 g/mol) of hydrochloric acid-pretreated corn cob lignin (HCl-CCL) at similar acid concentrations, suggesting increased condensation reactions when using sulfuric acid. Further, a significant amount of bound sulfur content (~2900 ppm) was measured in H2SO4-CCL. This sulfur presence poisons the Pd/C catalyst used in the downstream catalytic conversion of the lignin in methanol to form monolignols and derivatives thereof. X-ray photoelectron spectroscopy (XPS) results reveal that both sulfide and sulfate groups are formed with the surface Pd sites, rendering them inactive and amenable to possible leaching. Elemental mapping of spent catalysts using scanning transmission electron microscopy-high angle annular dark field (STEM-HAADF)/energy dispersive x-ray (EDX) technique corroborate overlapping presence of Pd, S and O in the micrographs. 2D 1H/13C HSQC nuclear magnetic resonance (NMR) spectroscopy reveals that the use of H2SO4 preserves aryl ether linkages only at low concentrations. In contrast, the use of HCl in the acetosolv process preserves such linkages even at high concentrations while also mitigating sulfur poisoning of the Pd/C catalyst. Consequently, the yield of aromatic monomers during catalytic fractionation of HCl-CCL was doubled compared to H2SO4-CCL at identical operating conditions.