Scientific article
OA Policy
English

Gas-phase reactivity of protonated oxazolone: Chemical dynamics simulations and graph theory-based analysis reveal the importance of ion–molecule complexes

Published inThe Journal of chemical physics, vol. 162, no. 11, 114313
Publication date2025-03-21
First online date2025-03-21
Abstract

This study delves into the fragmentation mechanisms of the oxazolone form (OXA) of protonated cyclo-di-glycine using chemical dynamics simulations at multiple internal energies. While we focus our in-depth analyses on a representative total energy of 178 kcal/mol, we also performed simulations over the 127-187 kcal/mol range. This broader energy sampling reveals how the population of states evolves with increasing internal energy, enabling us to compute rate constants and then effective energy thresholds using a previously introduced three-state model [Perez Mellor et al., J. Chem. Phys. 155, 124103 (2021)]. By transforming molecular geometries into graph representations, we systematically analyze fragmentation processes and identify key intermediates and ion-molecule complexes (IMCs) that play a crucial role in fragmentation dynamics. The study highlights the distinct isomerization landscapes of OXA, driven by IMC formation, which contrasts with the previously reported behavior of cyclic and linear forms [Perez Mellor et al., J. Chem. Phys. 155, 124103 (2021)]. The resulting fragmentation channels are characterized by their unique energetic thresholds and branching ratios and can provide a molecular explanation of what was observed experimentally. Thanks to an accurate analysis of the trajectories using our graph-theory-based tools, it was possible to point out the particular behavior of OXA fragmentation, which is different from other isomers. In particular, the important role of IMCs is shown, which has an impact on populating different isomeric structures.

Research groups
Funding
  • French National Research Agency (ANR) - Development and Application of Direct Dynamics Simulations for Reactivity of Biological Molecules [ANR-14-CE06-0029]
  • Canton de Genève
Citation (ISO format)
PEREZ MELLOR, Ariel Francis, BUERGI, Thomas, SPEZIA, Riccardo. Gas-phase reactivity of protonated oxazolone: Chemical dynamics simulations and graph theory-based analysis reveal the importance of ion–molecule complexes. In: The Journal of chemical physics, 2025, vol. 162, n° 11, p. 114313. doi: 10.1063/5.0245766
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Article (Published version)
Identifiers
Journal ISSN0021-9606
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