A significant number of heterogeneously-catalyzed chemical processes occur under liquid conditions, but simulating catalyst function under such conditions is challenging when it is necessary to include the solvent molecules. The bond breaking and forming processes modeled in these systems necessitate the use of quantum chemical methods. Since molecules in the liquid phase are under constant thermal motion, simulations must also include configurational sampling. This means that multiple configurations of liquid molecules must be simulated for each catalytic species of interest. The goal of the protocol presented here is to generate and sample trajectories of configurations of liquid water molecules around catalytic species on flat transition metal surfaces in a way that balances chemical accuracy with computational expense. Specifically, force field molecular dynamics (FFMD) simulations are used to generate configurations of liquid molecules that can subsequently be used in quantum mechanics-based methods such as density functional theory or ab initio molecular dynamics. To illustrate this, in this manuscript, the protocol is used for catalytic intermediates that could be involved in the pathway for the decomposition of glycerol (C 3 H 8 O 3 ). The structures that are generated using FFMD are modeled in DFT in order to estimate the enthalpies of solvation of the catalytic species and to identify how H 2 O molecules participate in catalytic decompositions.
|Original language||English (US)|
|Journal||Journal of Visualized Experiments|
|State||Published - Apr 2019|
Bibliographical noteFunding Information:
This research was funded by the National Science Foundation through award number CBET-1438325. Fellowship support for CJB through NASA Training Grant NX14AN43H is gratefully acknowledged. Simulations were performed on the Palmetto Supercomputer Cluster, which is maintained by the Cyberinfrastructure Technology Group at Clemson University. We thank Dr. Paul J. Meza-Morales for testing the protocol.
© 2019 Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.
- Ab initio molecular dynamics
- Aqueous phase
- Configurational sampling
- Density functional theory
- Force field
- Heterogeneous catalysis
- Issue 146
- Molecular dynamics
- Quantum mechanics/molecular mechanics
- Transition metal surface
- Water/solid interface