Of all sustainable resources, only lignocellulosic biomass can be transformed into organic fuels and chemicals that can integrate well with our current transportation infrastructure due to the inherent convenience, cost, and efficiency advantages of these organic fuels over current fuels. However, the high cost of biofuel conversion technologies poses challenges in large-scale commercialization. Pretreatment is the most expensive operation unit that is responsible for disrupting the naturally recalcitrant lignocellulosic biomass to provide reactive intermediates for production of renewable biofuels and bioproducts through biochemical or thermochemical processes. A better fundamental understanding of biomass pretreatment is essential to bring biofuels to market.

The goal of this dissertation is to study the dissolution chemistry of hemicellulose, cellulose, and lignin for hardwood and softwood during flowthrough and batch pretreatment at temperatures of 140 °C to 270 °C, initial pHs (pH 2-12), and flow rate of 0-25 mL/minute. The complete solubilization of hardwood was achieved to produce insoluble lignin with high purity and mild structural modification (i.e. changes of side chains and Cβ-C5). However, ∼30% softwood lignin was found to be undissolvable and was collected for analysis the first time. Based on wet chemistry and NMR results, unlike hardwood, dilute acid flowthrough pretreatment of softwood led to vigorous C-C5 recondensation resulting in undissolvable lignin structures. On the other hand, High Resolution Sum Frequency Generation Vibrational Spectroscopy (SFG-VS) was developed to selectively and in-situ characterize cellulose for the first time and new structural information was observed. The implementation of the simulation of aqueous pretreatment of cellulose using a heated fluid test bed on cellulose and dynamic SFG-VS analysis indicated a cellulose recrystallization hypothesis, leading to new insights on the effectiveness of biomass pretreatment. In addition, Total Internal Reflection (TIR)-SFG-VS was invented and tested to selectively characterize the cellulose surface of Avicel and the cellulose Iβ crystalline particles. At last, the results of the effects of the biomass comminuting approach on aqueous pretreatment indicated the associations among particle sizes, cutting methods, mass diffusion and sugar yields in pretreatment and enzymatic hydrolysis. The findings of this dissertation provide important fundamental insights to establish the effective biomass pretreatment.