RationaleThe mechanism underlying dopant‐assisted atmospheric pressure photoionization's (APPI) formation of ions is unclear and still under debate for many chemical classes. In this study, we reexamined the gas‐phase reaction mechanisms responsible for the generation of [M–H]+ precursor ions, resulting from the loss of a single hydrogen atom, in a series of N‐alkyl‐substituted thieno[3,4‐c]‐pyrrole‐4,6‐dione (TPD) derivatives.MethodsAtmospheric pressure photoionization combined with higher order MS/MSn using high‐resolution mass spectrometry (APPI‐HR‐CID‐MSn) and electronic structure calculations using density functional theory were used to determine the chemical structure of observed [M–H]+ ions.ResultsAs a result, the higher order MSn (n = 3) experiments revealed a reversed Diels–Alder fragmentation mechanism, leading to a common fragment ion at m/z 322 from the studied [M1–5–H]+ ion species. In addition, the calculation for two chemical structure models (N‐alkyl‐TPD1 and N‐alkyl‐TPD5) showed that the fragment structure, resulting from the removal of the hydrogen atom connected to the third carbon atom of the N‐alkyl side chain, has a more stable cyclic form compared with the linear one.ConclusionsThe proposed chemical structure of the N‐alkyl TPD ion species, following the loss of a single hydrogen atom, was revealed during APPI‐HR‐CID‐MSn (n = 3) experiments on the [M–H]+ species. Hydrogen radical (H•) abstraction from the alkyl side chain (e.g., hexyl, heptyl, octyl, 2‐ethylhexyl, and nonyl) triggered a rearrangement in the radical cation structure of the N‐alkyl‐TPD derivatives, initiating cyclization and forming a six‐membered ring that connects the oxygen atom to the third carbon atom in the alkyl chain. In addition, theoretical calculations supported the APPI‐HR‐CID‐MSn (n = 3) experiments by demonstrating that the proposed chemical structure, resulting from the intramolecular cyclization of the N‐alkyl‐TPD ion species, was stable in the presence of chlorobenzene. These findings will aid the structural determination and elucidation of molecules with similar core structures.