These calculations are computer simulations of the time evolution of atoms based upon their velocities and potential energies due to interactions with the other atoms in the system. In Car-Parrinello molecular dynamics (CPMD) (23,24) approach the potential energy due to the interactions of the atoms in the system is determined by conducting quantum mechanical
calculations of the valence and semi-core electrons in each atom. The CPMD code is based on density functional theory and is capable of simulating chemical reaction pathways for systems of up to several thousand atoms. The valence electrons were treated using the density functional developed by Becke (25) and Lee et al. (26), BLYP, and were assumed to exist in a psuedopotential exerted by the nuclei and the core electrons. The BLYP functional was shown to be appropriate to describe the liquid water (27, 28). The valence and semi-core electrons were treated with the Troullier-Martin norm-conserving pseudopotential (20). Plane waves were used as the basis functions in these calculations and the simulations were conducted using a time step of 0.125 fs in our calculations. The plane-wave basis set cut-off used was 70 Ry, which was shown to be sufficient for biomolecular simulations in aqueous solution (28). Three-dimensional periodic boundary conditions were applied. During simulations of sugar decomposition reactions in vacuum, the calculations were carried out with a (12 x 12 x 12 A3) unit cell containing one protonated sugar molecule surrounded by sufficient vacuum space to separate the interactions between the neighboring sugar molecules. Protonation was assumed to initiate the sugar degradation reactions. All probable protonation sites of the sugar molecule were investigated including the hydroxyl groups on the sugar ring and the ring oxygen. The simulations were carried out at 500 K. A total of 2 ps simulation time was carried out on a high-speed Linux PC machine. Each step took about 60 seconds of CPU time. The initial atomic coordinates of the xylose molecule were taken from the optimized structure of the CPMD calculations without the proton. The events simulated are qualitative, not quantitative in nature.

Simulations of xylose in water were carried out with each sugar molecule surrounded by 32 water molecules in a unit cell of with a lattice parameter of 11.5 A. Each sugar molecule had approximately two hydration shells. In addition, one proton was added to the system to mimic the acidic medium. Ab initio MD was carried out at constant temperature of500 K, which is at the higher end of the pretreatment temperature. Because these calculations sampled a large portion of the conformational space, they were ideally suited for finding low energy structures in sugars and in identifying likely reaction pathways.