An experimental and theoretical study on fragmentation of protonated N-(2-pyridinylmethyl)indole in electrospray ionization mass spectrometry.

RATIONALE: The dissociation reactions of protonated molecules are the base of structural analysis in electrospray ionization tandem mass spectrometry (ESI-MS(n)). However, general rules for elucidating the numerous fragmentation reactions in ESI-MS(n) are still rather lacking. Therefore, it is very important at all times to carry out mechanistic investigations for fragmentation reactions in the gas phase.
METHODS: The fragmentation reactions of protonated N-(2-pyridinylmethyl)indoles were studied by both of ESI ion trap tandem mass spectrometry and ESI Fourier transform ion cyclotron resonance tandem mass spectrometry in positive-ion mode.
RESULTS: In ESI-MS/MS, the ionizing proton is first bound to the most thermodynamically favored site, the pyridine nitrogen; then it transfers to the dissociative protonation sites and triggers the fragmentation. In the fragmentation of the target compounds, some interesting reactions, such as rearrangement, proton transfer and electron transfer reactions, take place via ion/neutral complexes. The proposed mechanisms are supported by both theoretical calculations and isotopic labeling experiments.
CONCLUSIONS: This study is a case for better understanding the dissociative protonation sites and enriching the knowledge about the role of ion/neutral complexes in ESI-MS. It also provides useful information for the structural analysis of organic compounds, especially drug analysis in pharmaceutical chemistry.