Ion-molecule reactions between molecular oxygen and peptide radicals in the gas phase demonstrate that radical migration occurs easily within large biomolecules without addition of collisional activation energy.

In biochemistry, free radicals are versatile species which can perform diverse functions including: signaling, synthesis, and destructive modification. It is of interest to understand how radicals behave within all biomolecules and specifically within peptides and proteins. The 20 standard amino acids contain a wide range of chemical structures, which give proteins their complexity and ultimately their functionality. Many factors influence how radicals interact with these complex molecules, including the bond dissociation energies (BDEs) for homolytically cleaving any X-H bonds. The BDEs provide a simple measure for comparing the thermodynamic favorability of abstracting hydrogen atoms from various sites within a protein. BDEs for abstractable hydrogen atoms have been calculated for each amino acid, the peptide backbone, and peptide termini in order to compile a roadmap of the relative thermodynamics which influence protein radical chemistry. With this information it is possible to gain insight into what contributions both kinetics and thermodynamics will make to various radical mediated reaction pathways.

Electron capture dissociation (ECD) is an important analytical technique which is used frequently in proteomics experiments to reveal information about both primary sequence and post-translational modifications. Although the utility of ECD is unquestioned, the underlying chemistry which leads to the observed fragmentation is still under debate. Backbone dissociation is frequently the exclusive focus when mechanistic questions about ECD are posed, despite the fact that numerous other abundant dissociation channels exist. Herein, the focus is shifted to side chain loss and other dissociation channels which offer clues about the underlying mechanism(s). It is found that the initially formed hydrogen abundant radicals in ECD can convert quickly to hydrogen deficient radicals via a variety of pathways. Dissociation which occurs subsequent to this conversion is mediated by hydrogen deficient radical chemistry, which has been the subject of extensive study in experiments which are independent from ECD. Statistical analysis of fragments observed in ECD is in excellent agreement with predictions made by an understanding of hydrogen deficient radical chemistry. Furthermore, hydrogen deficient radical mediated dissociation likely contributes to observed ECD fragmentation patterns in unexpected ways, such as the selective dissociation observed at disulfide bonds. Many aspects of dissociation observed in ECD are easily reproduced in well-controlled experiments examining hydrogen deficient radicals generated by non-ECD methods. All of these observations indicate that when considering the means by which electron capture leads to dissociation, hydrogen deficient radical chemistry must be given careful consideration.

Novel p-iodobenzoate-based labelling reagents are shown to be effective photocaged precursors for synthesizing biomolecular radicals site-selectively in the gaseous and condensed phases. In vacuo, a single pulse of UV photons (266 nm) is sufficient to quantitatively photolyse the C-I bond. In aqueous solutions, the photolysis half-life is estimated to be 2.5 minutes when irradiating with a 15 W compact fluorescent lamp (254 nm).

The fragmentation chemistry of anionic deprotonated hydrogen-deficient radical peptides is investigated. Homolytic photodissociation of carbon-iodine bonds with 266 nm light is used to generate the radical species, which are subsequently subjected to collisional activation to induce further dissociation. The charges do not play a central role in the fragmentation chemistry; hence deprotonated peptides that fragment via radical directed dissociation do so via mechanisms which have been reported previously for protonated peptides. However, charge polarity does influence the overall fragmentation of the peptide. For example, the absence of mobile protons favors radical directed dissociation for singly deprotonated peptides. Similarly, a favorable dissociation mechanism initiated at the N-terminus is more notable for anionic peptides where the N-terminus is not protonated (which inhibits the mechanism). In addition, collisional activation of the anionic peptides containing carbon-iodine bonds leads to homolytic cleavage and generation of the radical species, which is not observed for protonated peptides presumably due to competition from lower energy dissociation channels. Finally, for multiply deprotonated radical peptides, electron detachment becomes a competitive channel both during the initial photoactivation and following subsequent collisional activation of the radical. Possible mechanisms that might account for this novel collision-induced electron detachment are discussed.