Onsager-Machlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways

For sampling multiple pathways in a rugged energy landscape, we propose a novel action-based path sampling method using the Onsager-Machlup action functional. Inspired by the Fourier-path integral simulation of a quantum mechanical system, a path in Cartesian space is transformed into that in Fourier space, and an overdamped Langevin equation is derived for the Fourier components to achieve a canonical ensemble of the path at a finite temperature. To avoid "path trapping" around an initially guessed path, the path sampling method is further combined with a powerful sampling technique, the replica exchange method. The principle and algorithm of our method is numerically demonstrated for a model two-dimensional system with a bifurcated potential landscape. The results are compared with those of conventional transition path sampling and the equilibrium theory, and the error due to path discretization is also discussed.Comment: 20 pages, 5 figures, submitted to J. Chem. Phy

The reaction mechanism of polyalcohol dehydration in hot pressurized water

The use of high-temperature liquid water (HTW) as a reaction medium is a very promising tech- nology in the field of green chemistry. In order to fully exploit this technology, it is crucial to unravel the reaction mechanisms of the processes carried out in HTW. In this work, the reaction mecha- nism of 2,5-hexanediol dehydration in HTW has been studied by means of three different ab initio simulations: string method, metadynamics and molecular dynamics in real time. It is found that the whole reaction involving the protonation, bond exchange and the deprotonation occurs in a single step without a stable intermediate. The hydrogen bonded network of surrounding water has a vital role in assisting an efficient proton relay at the beginning and at the end of the reaction. It is confirmed that the reaction is energetically most favorable in the SN2 pathway with an estimated barrier of 36 kcal/mol, which explains the high stereoselectivity and the reaction rate observed in experiment. The mechanistic insights provided by our study are relevant for a prominent class of reactions in the context of sustainable biomass processing, namely dehydration reactions of polyalcohol molecules

Refined metadynamics through canonical sampling using time-invariant bias potential: A study of polyalcohol dehydration in hot acidic solutions

We propose a canonical sampling method to refine metadynamics simulations a posteriori, where the hills obtained from metadynamics are used as a time‐invariant bias potential. In this way, the statistical error in the computed reaction barriers is reduced by an efficient sampling of the collective variable space at the free energy level of interest. This simple approach could be useful particularly when two or more free energy barriers are to be compared among chemical reactions in different or competing conditions. The method was then applied to study the acid dependence of polyalcohol dehydration reactions in high‐temperature aqueous solutions. It was found that the reaction proceeds consistently via an SN2 mechanism, whereby the free energy of protonation of the hydroxyl group created as an intermediate is affected significantly by the acidic species. Although demonstration is shown for a specific problem, the computational method suggested herein could be generally used for simulations of complex reactions in the condensed phase

Understanding competition of polyalcohol dehydration reactions in hot water

Dehydration of biomass-derived polyalcohols has recently drawn attention in green chemistry as a prototype of selective reactions controllable in hot water or hot carbon- ated water, without any use of organic solvents or metal catalysts. Here we report a free energy analysis based on first-principles metadynamics and blue-moon ensemble simulations to understand the mechanism of competing intramolecular dehydration re- actions of 1,2,5-pentanetriol (PTO) in hot acidic water. The simulations consistently predict that the most dominant mechanism is the proton-assisted SN2 process where the protonation of the hydroxyl group by water and the C-O bond breaking and formation occurs in a single step. However the free energy barriers are different between the reac- tion paths: those leading to five membered ether products, tetrahydrofurfuryl alcohol (THFA), are few kcal/mol lower than those leading to six membered ether products, 3-hydroxytetrahydropyran (3-HTHP). A slight difference is seen in the timing of the protonation of the hydroxyl group of THFA and 3-HTHP on their reaction pathways. The detailed mechanism found from the simulations shows how the reaction paths are selective in hot water and why the reaction rates are accelerated in acidic environments, thus giving a clear explanation of experimental findings for a broad class of competing dehydration processes of polyalcohols