Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching

Abstract

The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at ‘hotspots’ that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems.This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

Failure and Redemption of Statistical and Nonstatistical Rate Theories in the Hydroboration of Alkenes

“…There has been some contention over the best way to model the energy loss, but on the whole such models have been highly successful for gas-phase calculations, and have started to see use in condensed phases. 6,7,8,9 Importantly, the selectivity expected for propene in the absence of collisional cooling would be lower than experiment while the selectivity expected if INT (R = Me) cooled fully is higher than experiment. As a result, any model for the energy loss would necessarily be able to reproduce experiment with a fitted cooling parameter.…”

Methyl group transfer upon gas phase decomposition of protonated methyl benzoate and similar compounds

“…Full geometry optimizations and energy calculations were performed, within DFT framework at B3LYP/6‐311++G(d,p) level of theory because B3LYP (Becke, 3‐parameter, Lee‐Yang‐Parr) is one of the most popular functional and can be applied for many different systems . 6‐311++G(d,p) basis set (augmented with diffuse and polarization functions) is recommended for calculations for simple molecules that include electronegative elements and for comparisons with experiment .…”

Reactive molecular dynamics: From small molecules to proteins

“…41 More recently, this has been extended to other types of reactions, including bimolecular reactions 42,43 or the association and dissociation of CH 3 from diamond surfaces. 44 Furthermore, several generalizations have been suggested to the original EVB method allowing its application to a wider class of problems. 35,45,46 2.3 | Reactive MD: Mixing potential energy surfaces in time and energy Time-resolved experiments have contributed heavily to our understanding of chemical reactivity over the past 20 years.…”