Unimolecular Fragmentation Properties of Thermometer Ions from Chemical Dynamics Simulations

Abdul Malik, Riccardo Spezia, William L. Hase

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Thermometer ions are widely used to calibrate the internal energy of the ions produced by electrospray ionization in mass spectrometry. Typically, benzylpyridinium ions with different substituents are used. More recently, benzhydrylpyridinium ions were proposed for their lower bond dissociation energies. Direct dynamics simulations using M06-2X/6-31G(d), DFTB, and PM6-D3 are performed to characterize the activation energies of two representative systems: para-methylbenzylpyridinium ion (p-Me-BnPy+) and methyl,methylbenzhydrylpyridinium ion (Me,Me-BhPy+). Simulation results are used to calculate rate constants for the two systems. These rate constants and their uncertainties are used to find the Arrhenius activation energies and RRK fitted threshold energies which give reasonable agreement with calculated bond dissociation energies at the same level of theory. There is only one fragmentation mechanism observed for both systems, which involves C-N bond dissociation via a loose transition state, to generate either benzylium or benzhydrylium ion and a neutral pyridine molecule. For p-Me-BnPy+ using DFTB and PM6-D3 the formation of tropylium ion, from rearrangement of benzylium ion, was observed but only at higher excitation energies and for longer simulation times. These observations suggest that there is no competition between reaction pathways that could affect the reliability of internal energy calibrations. Finally, we suggest using DFTB with a modified-Arrhenius model in future studies.

Original languageEnglish
Pages (from-to)169-179
Number of pages11
JournalJournal of the American Society for Mass Spectrometry
Issue number1
StatePublished - Jan 6 2021


  • benzhydrylpyridinium ions
  • benzylpyridinium ions
  • chemical dynamics simulations
  • kinetic theories
  • thermometer ions
  • unimolecular dissociation


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