Car-Parrinello-based ab initio molecular dynamics simulations (CPMD) combined with metadynamics (MTD) simulations were used to determine the reaction energetics for the beta-D-xylose condensation reaction to form beta-1,4-linked xylobiose in a dilute acid solution. Protonation of the hydroxyl group on the xylose molecule and the subsequent breaking of the C-O bond were found to be the rate-limiting step during the xylose condensation reaction. Water and water structure was found to play a critical role in these reactions due to the proton's high affinity for water molecules. The reaction free energy and reaction barrier were determined using CPMD-MTD. We found that solvent reorganization due to proton partial desolvation must be taken into account in order to obtain the correct reaction activation energy. Our calculated reaction free energy and reaction activation energy compare well with available experimental results.

The acidity constant pKa for polymeric organic acid is expected to be different from its corresponding monomer value due to the change of chemical environment upon polymerization. Thermodynamic cycles were used to determine the free-energy changes for the proton dissociation processes in aqueous solution and the corresponding pKa values for monomer methacrylic acid and several similar carboxylic acids. First-principles calculations and continuum solvation model were used to determine the gas-phase and solvation free energies, respectively. A protocol was developed to use the efficient density functional calculations with B3LYP functional instead of the demanding CBS-QB3 method to determine the gas-phase free energies with relative high accuracy, thus enabling the determination of pKa values for the short oligomers of methacrylic acid. The predicted pKa values for the dimer and trimer of methacrylic acid are higher by about 0.8 pKa units than the predicted monomer value.

Systems of poly(ethylene oxide) with dissolved inorganic salts are used as solid polymer electrolytes in high energy density batteries. Amorphous tetraglyme [CH 3 O(CH 2 CH 2 O) 4 CH 3 ], a model for amorphous PEO, and tetraglyme:LiCF 3 SO 3 (lithium triflate) with an ether oxygen:Li + ratio of 10:1 were studied by molecular dynamics (MD) simulations at 300 and 400 K. Conformational and structural analyses of Li + interactions with tetraglyme and triflate ion oxygens are consistent with decreased Li + coordination by tetraglyme and increased ionic aggregation at the higher temperature. Dihedral angle population density distributions for tetraglyme chains show that the trans conformation is favored for C-O bonds while the more compact gauche conformation is favored for C-C bonds and is enforced by coordination of adjacent oxygens to Li + . Calculated populations of tetraglyme conformational triads indicate that the most stable conformation around Li + -tetraglyme oxygens is tgt. Mean-square radius of gyration and end-to-end distance of pure tetraglyme chains decrease with increasing temperature and upon Li + -tetraglyme oxygen complexation, but increase at 400 vs 300 K for tetraglyme:LiCF 3 SO 3 . The calculated Li + coordination number remains the same with increasing temperature, but triflate ions contribute more oxygens to Li + coordination at 400 K (4.8) than at 300 K (4.6). The MDderived populations of Li + -CF 3 SO 3associated species are compared with vibrational spectral data. The increase in populations of [Li 2 CF 3 SO 3 ] + and [Li 3 CF 3 SO 3 ] 2+ from both MD simulations and IR data implies that Li + -CF 3 SO 3association is increased at higher temperature. Monodentate and bidentate coordination geometries of Li + by CF 3 SO 3were found. The increase in monodentate coordination of Li + by CF 3 SO 3at the higher temperature frees Li + to bridge between different CF 3 SO 3ions.

An oligomeric model for poly(ethylene oxide), tetraglyme, with NaCF 3 SO 3 at an ether oxygen:Na + ratio of 10:1 was used to represent the amorphous phase of PEO:salt systems in molecular dynamics simulations at 300 K and 400 K. Na + -tetraglyme interactions were examined by calculating chain dimensions, dihedral angle population distribution, and conformational triad populations of coordinating tetraglyme chains. All results consistently show that the Na + -ether oxygen coordination induces more compact chains by enforcing a gauche conformation for C-C bonds and introducing a strong preference for tgt conformations in the C-O-C-C-O-C bond sequence. Na + -O(tetraglyme) and Na + -O(triflate) radial distribution functions reveal that triflate ions contribute more oxygens (4.9 at 300 K and 5.3 at 400 K) than tetraglyme (2.2 at 300 K and 2.0 at 400 K) to the first coordination shell of Na + . Populations of aggregates consisting of a triflate ion coordinated to 0-3 Na + were available from vibrational spectra and were also calculated from equilibrated trajectories. Both results agree well, and the computational results indicate that Na + -CF 3 SO 3 -association increases with increasing temperature. The results are compared with results from a previously studied tetraglyme:LiCF 3 SO 3 system. Unlike Li + in the tetraglyme:LiCF 3 SO 3 system, bidentate coordination of Na + by CF 3 SO 3 -becomes more favorable at the higher temperature, at the expense of monodentate and tridentate coordination.