Computational Studies to Understand Nitrile Imine Reactivity in Photocrosslinking to Peptides in Gas-Phase Ions

Abstract

Computational methods were applied to explore the behavior of nitrile imines as photocrosslinkers in gas-phase peptide ions. Irradiating peptide-2,5-diaryltetrazole conjugates (peptide-tet)at 250 and 213 nm yielded nitrile imines, which crosslinked with amide carbonyl and side-chain groups in the peptides. Structural and compositional analysis of crosslinked products was conducted using collision-induced dissociation (CID), ultraviolet photodissociation (UVPD) tandem mass spectrometry, and cyclic ion mobility mass spectrometry (c-IMS). Photodissociation tandem mass spectrometry was studied at two wavelengths to probe the energetics of nitrile-imine intermediate formation and its effect on crosslinking. Theoretical calculations were performed using Born-Oppenheimer molecular dynamics for conformational analysis and density-functional theory (DFT) to evaluate isomer energies. Ion trajectory methods were used to calculate collision cross sections (CCS) of precursors and potential intermediates. Integrating computational data with experimental mass spectra and c-IMS measurements provided a comprehensive understanding of nitrile imine's role as a peptide photocrosslinker in gas-phase ions.