DONKEY: A Flexible and Accurate Algorithm for Clustering DOI Creative Commons

Janaka Kara,

Kyle Acheson,

Adam Kirrander

et al.

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: May 2, 2025

We propose an accurate clustering algorithm suitable for the varied and multidimensional data sets that correspond to temporal snapshots from on-the-fly nonadiabatic trajectory-based simulations of photoexcited dynamics. The approximates underlying probability density function using variable kernel estimation, with local maxima corresponding cluster centers. Each point is then assigned one by employing a maximization procedure. Finally, clusters artificially separated minor fluctuations in are merged. does not require parameter tuning, which ensures flexibility reduces risk bias. It tested on several synthetic sets, where it consistently outperforms conventional algorithms. As final example, applied excited dynamics norbornadiene ⇌ quadricyclane (C7H8) molecular photoswitch, demonstrating how distinct reaction pathways can be identified.

Language: Английский

Simulating the Energy Capture Process in Push–Pull Norbornadiene-Quadricyclane Photoswitches DOI Creative Commons
Michał Andrzej Kochman, Bo Durbeej

The Journal of Physical Chemistry Letters, Journal Year: 2025, Volume and Issue: unknown, P. 4315 - 4325

Published: April 23, 2025

Molecular switches based on the norbornadiene-quadricyclane (NBD-QC) isomer pair are among most promising candidates for applications in molecular solar thermal energy storage (MOST). In these compounds, is captured through a photoinduced [2 + 2] cycloaddition reaction whose mechanism only partially understood. This holds true especially NBD derivatives containing type of push-pull substitution pattern that was previously proven necessary to attain reasonable photoisomerization quantum yields. present contribution, we report computational investigation photochemistry NBD-QC with precisely such pattern. Static calculations provide information structures excited electronic states involved reaction, and topographies relevant ground- excited-state potential surfaces. Furthermore, nonadiabatic dynamics (NAMD) simulations allow an estimation time scale yield. The simulation results paint detailed picture capture process: begins spectroscopically bright state switch. model compound which performed NAMD simulations, ring closing takes place roughly 150 fs, makes it one fastest known reactions.

Language: Английский

Citations

0
DONKEY: A Flexible and Accurate Algorithm for Clustering DOI Creative Commons

Janaka Kara,

Kyle Acheson,

Adam Kirrander

et al.

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: May 2, 2025

We propose an accurate clustering algorithm suitable for the varied and multidimensional data sets that correspond to temporal snapshots from on-the-fly nonadiabatic trajectory-based simulations of photoexcited dynamics. The approximates underlying probability density function using variable kernel estimation, with local maxima corresponding cluster centers. Each point is then assigned one by employing a maximization procedure. Finally, clusters artificially separated minor fluctuations in are merged. does not require parameter tuning, which ensures flexibility reduces risk bias. It tested on several synthetic sets, where it consistently outperforms conventional algorithms. As final example, applied excited dynamics norbornadiene ⇌ quadricyclane (C7H8) molecular photoswitch, demonstrating how distinct reaction pathways can be identified.

Language: Английский

Citations

0