Defying Entropy: Forming Large Head‐to‐Tail Macrocycles in the Gas Phase

Abstract

Spektrale Fingerabdrücke: Kollisionsinduzierte Dissoziation (CID) von protonierten Peptiden in der Gasphase führt zu linearen Ionenfragmenten mit fünfgliedrigem Oxazolon‐Ring am terminalen Kohlenstoff‐Atom. Mit Infrarotspektroskopie wird gezeigt, dass kleinere Fragmente eine Oxazolonstruktur bilden. Für mittlere und große Fragmente wird Kopf‐Schwanz‐Isomerisierung zu Makrocyclen beobachtet (siehe Bild).

Insights into the fragmentation pathways of gas-phase protonated sulfoserine

“…IRMPD spectroscopy thus serves as a direct structural probe of gas-phase ions and can be used for structural elucidation of said ions, especially when combined with theoretical infrared (IR) frequency calculations and/or comparison to experimental spectra of synthetic standards. This technique has proven successful in many areas, including the study of PTMs [18][19][20][21] and of the fragmentation chemistry of peptides [22][23][24][25] and remains promising for many additional future applications.…”

Linkage and Anomeric Differentiation in Trisaccharides by Sequential Fragmentation and Variable-Wavelength Infrared Photodissociation

“…While nominally, a C 2 fragment from a larger oligosaccharide corresponds to the same building block as a reference disaccharide, the present experiments in fact give strong evidence that these structures are chemically equivalent. The dissociation of larger entities into fragments may, in principle, proceed via a number of chemical pathways involving rearrangement reactions and, thus, giving rise to complex product ion structures; complex rearrangement chemistry has been attested in numerous studies on peptide fragmentation pathways [54,55], which can complicate structural analysis. It appears that such concerns are not merited in the case of oligosaccharide dissociation, where the glycosidic bond and other chemical moieties are conserved upon ion activation [21].…”

DNA Oligonucleotide Fragment Ion Rearrangements Upon Collision-Induced Dissociation

“…Sequencescrambling in peptides and proteins are believed to occur through macrocyclization and subsequent reopening at internal amide bonds to generate product ions with rearranged amino acid sequences [21]. Though the impact of rearrangements on sequence coverage of peptides in amino acid sequencing is uncertain [22,23], positive identification of permuted fragment ions and mechanistic understandings of their generation could help improve sequencing algorithms.…”

“…We hypothesized that similar to CID of peptide fragment ions [18][19][20][21], CID of DNA fragment ions could also result in generation of secondary fragment ions with rearranged atomic structures (relative to precursor ion structures). For this study, we chose to focus on CID of w type fragment ions for two reasons: (1) w type ions (along with a-B type ions) are the most commonly observed fragment ions in CID of DNA ions [3] and are, thus, often used for sequencing [7][8][9][10][11]; (2) w type ions retain all of the bases in the precursor ion series (unlike a-B type ions, which lack nucleobases at various positions [3]).…”