New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations.

Herein, we demonstrate a convenient approach to systematically investigate chemical reaction dynamics using the metadynamics (MetaD) family of enhanced sampling methods. Using a symmetric SN2 reaction as a model system, we applied infrequent metadynamics, a theoretical framework based on acceleration factors, to quantitatively estimate the rate of reaction from biased and unbiased simulations. A systematic study of the algorithm and its application to chemical reactions was performed by sampling over 5000 independent reaction events. Additionally, we quantitatively reweighed exhaustive free-energy calculations to obtain the reaction potential-energy surface and showed that infrequent metadynamics works to effectively determine Arrhenius-like activation energies. Exact agreement with unbiased high-temperature kinetics is also shown. The feasibility of using the approach on actual ab initio molecular dynamics calculations is then presented by using Car-Parrinello MD+MetaD to sample the same reaction using only 10-20 calculations of the rare event. Owing to the ease of use and comparatively low-cost of computation, the approach has extensive potential applications for catalysis, combustion, pyrolysis, and enzymology.

Characterizing the catalyzed hydrolysis of ß-1,4 glycosidic bonds using density functional theory.

Unraveling the mechanistic details of biomass deconstruction at ambient conditions has remained a challenge for many years. In this study we examine a crucial step in the pretreatment of biomass: the hydrolytic cleavage of the glycosidic bond present in many forms of biomass and other oligomeric saccharides. We present the detailed mechanistic steps found using density functional theory and transition state calculations on the acid catalyzed hydrolysis of a pyranose dimer linked by a ß-1,4 glycosidic bond in a vacuum and various continuum solvation models. The order that the bonds in the double displacement reaction form and break was revealed along with the transition state energies and an overall intrinsic reaction pathway for the two-step mechanism. The uncatalyzed hydrolysis reaction, mediated by a single water splitting event, was also determined with DFT calculations and a detailed comparison to the two-step catalyzed reaction was performed. The effects of the surrounding solvent on the reaction energetics were studied by systematically changing the dielectric strength and polarity of the solvent model. For acidic solvents, a trend was observed that related the transition state energy barrier to the inverse of the dielectric constant whereas solvents that varied slightly in dielectric strength but strongly in polarity (e.g., alcohols) did not significantly change the reaction energetics. The effects of the substituents on the model sugar were also studied by changing from a model pyranose dimer to xylobiose and cellobiose. Irrespective of the solvent choice or model sugar characteristics we observed identical ordering of all bond breaking/forming in both transition states in the double displacement mechanism.