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Updated: Feb 7, 2026

In Vitro Analysis of E3 Ubiquitin Ligase Function
Published on: May 14, 2021
CHD3 dissociation on Pt(111): A comparison of the reaction dynamics based on the PBE functional and on a specific
H Chadwick1, D Migliorini1, G J Kroes1
1Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
Abstract:
We present a comparison of ab initio molecular dynamics calculations for CHD3 dissociation on Pt(111) using the Perdew, Burke and Ernzerhof (PBE) functional and a specific reaction parameter (SRP) functional. Despite the two functionals predicting approximately the same activation barrier for the reaction, the calculations using the PBE functional consistently overestimate the experimentally determined dissociation probability, whereas the SRP functional reproduces the experimental values within a chemical accuracy (4.2 kJ/mol). We present evidence that suggests that this difference in reactivity can at least in part be attributed to the presence of a van der Waals well in the potential of the SRP functional which is absent from the PBE description. This leads to the CHD3 molecules being accelerated and spending less time near the surface for the trajectories run with the SRP functional, as well as more energy being transferred to the surface atoms. We suggest that both these factors reduce the reactivity observed in the SRP calculations compared to the PBE calculations.
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