Accuracy of Reaction Coordinate Based Rate Theories for Modelling Chemical Reactions : Insights From the Thermal Isomerization in Retinal

Bibliographische Detailangaben
Veröffentlicht in:	Journal of computational chemistry. - 1984. - 46(2024), 1 vom: 05. Jan., Seite e27529
1. Verfasser:	Ghysbrecht, Simon (VerfasserIn)
Weitere Verfasser:	Donati, Luca, Keller, Bettina G
Format:	Online-Aufsatz
Sprache:	English
Veröffentlicht:	2025
Zugriff auf das übergeordnete Werk:	Journal of computational chemistry
Schlagworte:	Journal Article diffusion kramers metadynamics path collective variable rate theory retinal square root approximation umbrella sampling

Beschreibung
Zusammenfassung:	© 2024 The Author(s). Journal of Computational Chemistry published by Wiley Periodicals LLC. Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability to studying chemical reactions remains uncertain due to the high and sharp energy barriers and complex reaction coordinates involved. This study focuses on the thermal cis-trans isomerization in retinal, employing molecular simulations and comparing rate constant estimates based on one-dimensional rate theories with those based on sampling transitions and grid-based models for low-dimensional collective variable spaces. Even though each individual method to estimate the rate passes its quality tests, the rate constant estimates exhibit considerable disparities. Rate constant estimates based on one-dimensional reaction coordinates prove challenging to converge, even if the reaction coordinate is optimized. However, consistent estimates of the rate constant are achieved by sampling transitions and by multi-dimensional grid-based models
Beschreibung:	Date Revised 13.12.2024 published: Print Citation Status PubMed-not-MEDLINE
ISSN:	1096-987X
DOI:	10.1002/jcc.27529