Most of the leading chemical pretreatment technologies that have been described herein are effective on one or more factors that contribute to lignocellulosics recalci­trance. Despite much research that has been dedicated to understanding the chemistry and the plant cell wall structure changes during various pretreatment technologies, the insufficient knowledge of cell wall structure, ultra structure, and pretreatment effects still limits the economics and effectiveness of pretreatment. For instance, the biological and chemical properties of plants are very complex in terms of composi­tion, structure, and ultra-structure [162]. Although researchers have put significant

effort into optimizing the pretreatment effectiveness, the fundamental science behind these optimizations is still not fully understood. Furthermore, there has been a lack of mechanistic understanding of the ultrastructural and physicochemical changes oc­curring within the cell wall at the molecular level and the cellular/tissue scale during various pretreatment technologies. It is thus essential to understand the effects of pretreatment on plant cell walls at a more fundamental level, in order to develop a cost-effective pretreatment technology with maximum fermentable sugar recovery, minimum inhibitor production and energy input, low demand of post-pretreatment processes, and low capital costs for reactors, water, and chemicals. In addition, ad­vances in the analytical chemistry would provide useful tools to investigate the cell wall deconstruction and understand the recalcitrance during the pretreatment process [163, 164].

Acknowledgments The authors are grateful for the financial support from the US Department of Energy (DOE biorefinery project: DE-EE0003144) for these studies.