Cyclization and Rearrangement Reactions of a n Fragment Ions of Protonated Peptides

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Abstract. It is well-known that oxazolone b 2 ions fragment extensively by elimination of CO to form a 2 ions, which often fragment further to form a 1 ions. Less well-known is that some oxazolone b 2 ions may fragment directly to form a 1 ions. The present study uses energy-resolved collision-induced dissociation experiments to explore the occurrence of the direct b 2 →a 1 fragmentation reaction. The experimental results show that the direct b 2 →a 1 reaction is generally observed when Gly is the C-terminal residue of the oxazolone. When the C-terminal residue is more complex, it is able to provide increased stability of the a 2 product in the b 2 →a 2 fragmentation pathway. Our computational studies of the relative critical reaction energies for the b 2 →a 2 reaction compared with those for the b 2 →a 1 reaction provide support that the critical reaction energies are similar for the two pathways when the C-terminal residue of the oxazolone is Gly. By contrast, when the nitrogen of the oxazolone ring in the b 2 ion does not bear a hydrogen, as in the Ala-Sar and Tyr-Sar (Sar=N-methylglycine) oxazolone b 2 ions, a 1 ions are not formed but rather neutral imine elimination from the N-terminus of the b 2 ion becomes a dominant fragmentation reaction. The M06-2X/6-31+G(d,p) density functional theory calculations are in general agreement with the experimental data for both types of reaction. In contrast, the B3LYP/6-31+G(d,p) model systematically underestimates the barriers of these S N 2-like b 2 →a 1 reaction. The difference between the two methods of barrier calculation are highly significant (PG0.001) for the b 2 →a 1 reaction, but only marginally significant (P=0.05) for the b 2 →a 2 reaction. The computations provide further evidence of the limitations of the B3LYP functional when describing S N 2-like reactions.

Section: Mechanistic Considerationsmentioning

confidence: 99%

Formation of a₁ Ions Directly from Oxazolone b₂ Ions: an Energy-Resolved and Computational Study

Bythell

Harrison

2015

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“…The formation, structure, and reactivity of a n ions have received less attention [28]. a n Ions are formed [5,6,[29][30][31][32] mainly [33] from b n ions by elimination of CO.…”

Section: Introductionmentioning

confidence: 99%

Rearrangement Pathways of the a₄ Ion of Protonated YGGFL Characterized by IR Spectroscopy and Modeling

Paizs

Bythell

Maı̂tre

2012

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The structure of the a 4 ion from protonated YGGFL was studied in a quadrupole ion trap mass spectrometer by 'action' infrared spectroscopy in the 1000-2000 cm -1 ('fingerprint') range using the CLIO Free Electron Laser. The potential energy surface (PES) of this ion was characterized by detailed molecular dynamics scans and density functional theory calculations exploring a large number of isomers and protonation sites. IR and theory indicate the a 4 ion population is primarily populated by the rearranged, linear structure proposed recently (Bythell et al., J. Am. Chem. Soc. 2010, 132, 14766). This structure contains an imine group at the N-terminus and an amide group -CO-NH 2 at the C-terminus. Our data also indicate that the originally proposed N-terminally protonated linear structure and macrocyclic structures (Polfer et al., J. Am. Chem. Soc. 2007, 129, 5887) are also present as minor populations. The clear differences between the present and previous IR spectra are discussed in detail. This mixture of gas-phase structures is also in agreement with the ion mobility spectrum published by Clemmer and co-workers recently (J. Phys. Chem. A 2008Chem. A , 112, 1286. Additionally, the calculated cross-sections for the rearranged structures indicate these correspond to the most abundant (and previously unassigned) feature in Clemmer's work.

“…The amide bond forms the fundamental linkage between monomeric amino acid residues in peptide polymers, and it is important to understand its gas-phase chemistry, which has so far been studied mainly through the decomposition reactions of protonated amides and peptides [27][28][29][30][31]. The mobile proton model [32][33][34][35][36][37] was proposed and applied to the flexible peptides and proteins besides the rigid molecules to describe the mobility of the proton across the protonated species.…”

mentioning

confidence: 99%

Gas Phase Chemistry of Li⁺with Amides: the Observation of LiOH Loss in Mass Spectrometry

Guo

Zhou

Liu

et al. 2012

of N-phenylbenzamide and N-phenylcinnamide. Loss of LiOH was essentially the sole fragmentation reaction observed for the former. For the latter, both losses of LiOH and H 2 O were discovered. The presence of electron-donating substituents of the phenyl ring of these compounds was found to facilitate elimination of LiOH, while that loss was retarded by electron-withdrawing substituents. Proposed fragment ion structures were supported by elemental compositions deduced from ultrahigh resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FTICR-MS/MS) m/z value determinations. Density functional theory-based (DFT) calculations were performed to evaluate potential mechanisms for these reactions.