Collision-induced dissociation pathways of protonated Gly2NH2 and Gly3NH2 in the short time-scale limit by chemical dynamics and ion spectroscopy

Dehydration reactions of protonated dipeptides containing asparagine or glutamine investigated by infrared ion spectroscopy

“…Collision-induced migration of a proton from the most basic site to the amide bond where dissociation occurs, accompanied by a nucleophilic attack by the adjacent backbone carbonyl oxygen or the N-terminal nitrogen are suggested as the reaction pathways to these product ion structures, respectively [10][11][12]. Deviations from this general behavior have also been observed, for instance, b-ions from GlyGlyGly contain both five-and eight-membered ring structures [13]. Furthermore, the side chain can become actively involved in the reaction mechanism for instance in the formation of b2 ions from protonated PheGlnAla (a glutarimide structure) and AlaAsnAla (a succinimide structure) [3].…”

“…However, for protonated GlyGlyGlyGly, water loss occurs from the N-terminal amide group, initiated by a nucleophilic attack of the neighboring amide nitrogen, and hence does not result in an oxazolone structure [40]. While, GlyGly dissociation does not form a b-ion, bions from GlyGlyGly contain both five-and eight-membered ring structures [13]. Tripeptides that contain Asn or Gln have been shown to dissociate along different fragmentation mechanisms [2,3,9].…”

A Trajectory-Based Method to Explore Reaction Mechanisms

“…The prediction of mass spectra remains much of a challenge for the community of computational chemists. The common computational approaches employed for such endeavor include statistical rate theory calculations, MD simulations and electronic structure calculations [102][103][104][105][106][107][108][109][110][111][112][113][114][115][116]. Our automated method is very useful in this regard and can easily be coupled with MD simulations of collisions to generate theoretically-based mass spectra as described below.…”

A Trajectory-Based Method to Explore Reaction Mechanisms

“…The prediction of mass spectra remains much of a challenge for the community of computational chemists. The common computational approaches employed for such endeavor include statistical rate theory calculations, MD simulations and electronic structure calculations [99][100][101][102][103][104][105][106][107][108][109][110][111][112][113]. Our automated method is very useful in this regard and can easily be coupled with MD simulations of collisions to generate theoretically-based mass spectra as described below.…”