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Corn stover is an abundant feedstock in the US that can be used for second generation bioethanol production. However, there is little useful data on structure of the lignin of corn stover. The following principal tasks will be addressed to profile the structure of corn stover: (1) separation of corn stover into stem, cob, and leaf; (2) isolation of cellulolytic enzyme lignins (CEL) from extractive-free and the alkali-treated fractions; (3) quantification of p-coumarate and ferulate of fractions by HPLC. The results of alkaline nitrobenzene oxidation and 1H-13C HSQC NMR indicated: (1) the structure of lignin varied in the fractions; (2) a remarkable amount of p-coumarate and ferulate was identified and determined; (3) the remarkable structural changes of lignin induced by alkaline treatment were elucidated.