Document Type

Article

Publication Date

2025

Publication Title

ACS Omega

Abstract

Direct dynamics simulations are employed in many areas of chemistry and biochemistry. When paired with an appropriate underlying ab initio, semiempirical, or DFT-based potential energy surface and proper sampling of initial conditions, direct dynamics simulations provide an atomic-level view of the reaction dynamics within the system of interest, yielding considerable fundamental insights. Moreover, when a sufficient number of simulations are conducted, they provide a wealth of information regarding the overall trends in reactivity. However, they also generate large data sets that often require significant manual interpretation through inspection or developing case-specific analysis techniques. Here, we present an analysis method using a multitiered graph theory approach, which automatically highlights the most important mechanistic steps present within an ensemble of direct dynamics simulations. The effectiveness of this approach is demonstrated by examining results from three direct dynamics data sets previously reported for systems relevant to the tandem mass spectrometry community.

Funding Source

GLB and EB acknowledge support from the National Science Foundation Grant No. CHE-2419653. GLB is a member of the MERCURY consortium, which receives support through National Science Foundation Grant No. CHE-2018427. This article was published Open Access thanks to a transformative agreement between Milner Library and ACS.

Creative Commons License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

DOI

10.1021/acsomega.5c04493

Comments

First published in ACS Omega (2025): https://doi.org/10.1021/acsomega.5c04493

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