The collision-induced dissociations are reported for Cu(II) complexes containing 1,4,7-triazacyclononane (tacn) as the auxiliary ligand and a peptide containing one cystine residue. For six of the complexes examined, cleavage of the S-S bond in the peptide was the dominant fragmentation pathway. The exceptions were for complexes containing the largest peptides, (GlyCys'Gly)(2) and (GlyGlyCys')(2) (Cys' = NHCH(CH(2)S)CO, one half of the cystine residue; terminal H and OH are implicit), for which proton transfer to the auxiliary ligand was the major channel. Cleavage of the C-S bond was observed, but was a minor channel for all complexes. The radical cation (Cys')(2)(*+) was not observed although the complementary ion [Cu(I)(tacn)](+) was present in moderate abundance. Density functional calculations (at B3LYP/6-311++G(d,p)) gave low barriers to fragmentation of (Cys')(2)(*+) by homolytic fission of the C-S bond of the canonical ion (barrier 16.5 kcal mol(-1)) and of the structure at the global minimum, a captodative ion (barrier 17.2 kcal mol(-1)). Peptide radical cations (GlyCys')(2)(*+), (GlyCys'Gly)(2)(*+), (GlyGlyCys')(2)(*+) and (GlyCys'(Cys')Gly)(*+) were observed in low abundances; the first two of these ions dissociated predominantly by fragmentation of the S-S bond, while the other two preferentially cleaved at an amide bond. No cleavage of the C-S bond was observed for the peptide radical cations. Density functional calculations at B3LYP/6-31G(d) established that the cystine in [Cu(II)(tacn)(Cys')(2)](*2+) is bound as a zwitterion through the carboxylate anion with the proton on the distal amino group. The lowest energy complex containing a canonical cystine, coordinated through the carbonyl oxygen and the amino group of the same Cys', is 8.3 kcal mol(-1) higher in enthalpy.