Hopkinson, AlanSiu, Michael2018-03-012018-03-012017-03-242018-03-01http://hdl.handle.net/10315/34241In this thesis, we examined the CID spectra of the closed-shell [A4W-Me oxa + H]+ ions, which are completely identical, and indicates sequence scrambling. There are some unique fragmentation patterns from this set of ions that have been analyzed in details. The second part of this thesis is the study of the open-shell [A4W-Me oxa]+ radical cations. In this study, we noticed no sequence scrambling, which is a distinctive characteristic. This is attributed to the formation of a stable structure with a captodative radical at the N-terminus. We also studied the open-shell [A4Yoxa]+ and [A4Moxa]+ ions and summarized some similarities that are shared between the [A4Goxa]+, [A4Yoxa]+, and [A4Moxa]+ ions. All three systems exhibit some isomerization before dissociation; but CID spectra of different sequences are non-identical, with different relative abundances. Loss of CO2 is frequently the most dominant peak in all three systems.enAuthor owns copyright, except where explicitly noted. Please contact the author directly with licensing requests.Physical chemistryElectronic Thesis or Dissertation2018-03-01Collision-induced dissociationSequence scramblingMacrocyclizationEffect of α-methyl on dissociation pathwaysDensity Functional calculationsCIDRadical cationα-methyltryptophan-methyltryptophan