Accuracy of reaction coordinate based rate theories for modelling chemical reactions: insights from the thermal isomerization in retinal
Fuente:
arXiv
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Preprint |
| Published: |
2023
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866913421519224832 |
|---|---|
| author | Ghysbrecht, Simon Donati, Luca Keller, Bettina G. |
| author_facet | Ghysbrecht, Simon Donati, Luca Keller, Bettina G. |
| contents | 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 disparities of up to four orders of magnitude. 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2312_12948 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Accuracy of reaction coordinate based rate theories for modelling chemical reactions: insights from the thermal isomerization in retinal Ghysbrecht, Simon Donati, Luca Keller, Bettina G. Chemical Physics 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 disparities of up to four orders of magnitude. 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. |
| title | Accuracy of reaction coordinate based rate theories for modelling chemical reactions: insights from the thermal isomerization in retinal |
| topic | Chemical Physics |
| url | https://arxiv.org/abs/2312.12948 |