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

Abstract

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.

Conformation-Specific Spectroscopy of Peptide Fragment Ions in a Low-Temperature Ion Trap

“…In addition to oxazolone structures, cyclic isomers were reported for the b 3 and the b 4 ions in these experiments [29,32,34,35], while b 2 ions seem to exhibit exclusively an oxazolone structure [32,55]. A linear but rearranged structure was identified as a major isomer for the a 4 ion [6,56], but cyclic intermediates have been proposed to contribute as well [35].…”

“…The spectra nevertheless provide strong support for the proposed rearrangement reaction [5,56]. In Figure 8, we compare them to theoretical predictions for rearranged isomers to obtain further information about the conformational structures.…”

“…A major rearrangement that leads to a transfer of the phenylalanine side chain of the C-terminal residue to the N-terminal side of the molecule (see Scheme 2) has only recently been confirmed from theoretical calculations and IRMPD spectroscopy [5,56]. A corresponding cyclization/rearrangement pathway resulting in an amide structure has recently also been confirmed for a 5 ions [25], and cyclization reactions were proposed [71] and confirmed [40] for smaller a-type fragments before as well.…”

“…Structures of the YG b 2 ion were taken from Reference [55]. Structures for the b 4 and a 4 ions were taken from previous PES scans [34,35,56], which were refined in the present work by including additional species at the higher theoretical levels. Theoretical vibrational spectra were calculated in the harmonic approximation on B3LYP/6-31+G(d,p) level using Gaussian 03 [62] or Gaussian 09 [63].…”

“…In Figure 8, we compare them to theoretical predictions for rearranged isomers to obtain further information about the conformational structures. The shown structures represent the global minimum isomer from another study [56] (structure a) and two further rearranged conformations, which differ mainly in their orientation of the tyrosine OH group (structures b and c).…”