New Solution to an Old Problem: Exploring Properties of Chemical Reactions in Condensed Phases Using Molecular Simulation

Abstract

The study of chemical reactions is a foundation of chemical engineering, yet there are limited ways to examine how their properties are influenced. Our research has explored the use of molecular simulation to characterize reaction properties in varying environments. First, we use the most common method, Quantum Mechanics (QM) with a Density Functional Theory (DFT) model to study the hydrolysis of a glyosidic bond, which is important for the breakdown of biomass. Previously unknown detailed mechanistic steps were found for the hydrolysis reaction. The reaction was subsequently simulated with a continuum model in several different acid solvents, and the reaction energetics were shown to be directly related to the inverse of the dielectric constant. However, the mechanistic details were unchanged. Based on the trend observed between acid solvents, we set out to learn more about the way the solvents affect reaction properties. In order to accurately determine how solvent molecules affect the reaction, they must be modeled explicitly, as opposed to a continuum model. In order to facilitate fast computation in a reasonable timeframe, we overcame computational limitations stemming from the explicit solvent molecules by pairing a multiscale modeling approach known as metadynamics with the Car Parrinello molecular dynamics method. We observed a stabilizing effect from the solvent. However, after several failed attempts to quantify the barrier heights, we discovered that this approach does not lead to reproducible or accurate estimates for reaction barriers, despite being the consensus approach in literature. Instead of purely using metadynamics, we demonstrated for the first time that a method called “MetaRates” can be used to make estimates of a chemical reaction rate. This was an exciting addition to a method that previously had not been used to study systems with ab initio potentials. In a detailed investigation, we were able to demonstrate that this method is successfully used to predict the energy barrier heights that match with quantum mechanics. Based on our work, we believe that MetaRates can be used to model more complex reactions, such as those taking place in enzymes, on surfaces, and in complex solvents like those we are interested in for continuing biomass reaction research.