One of the critical issues in biochemical conversion of lignocellulosic biomass to biofuels is sugar yields. Understanding the kinetics and thermodynamics of the depolymerization process and the sugar loss reactions including degradation and condensation reactions during dilute acid pretreatment is essential to optimize the pretreatment conditions. Car-Parrinello based ab initio molecular dynamics (CPMD) simulations with advanced metadynamics (MTD) technique are used to investigate the reaction mechanisms, the reaction free energies, barriers and rate constants. Protonation is found to be the rate limiting step in both hydrolysis and sugar degradation/condensation reactions. The proton affinity of water structure surrounding the reactants will impact the reaction barriers significantly. In particular, the role of hydrogen bonding interaction on these reactions will be elucidated.