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Radical cations of an aliphatic tripeptide prolyl-glycyl-glycine (PGG •+ ) and its sequence ions [a 3 + H] •+ and [b 2 - H] •+ have been generated by collision-induced dissociation of the [Cu(Phen)(PGG)] •2+ complex, where Phen = 1,10-phenanthroline. Infrared multiple photon dissociation spectroscopy, ion-molecule reaction experiments, and theoretical calculations have been used to investigate the structures of these ions. The unpaired electron in these three radical cations is located at different α-carbons. The PGG •+ radical cation has a captodative structure with the radical at the α-carbon of the proline residue and the proton on the oxygen of the first amide group. This structure is at the global minimum on the potential energy surface (PES). By contrast, the [a 3 + H] •+ and [b 2 - H] •+ ions are not the lowest-energy structures on their respective PESs, and their radicals are formally located at the C-terminal and second α-carbons, respectively. Density functional theory calculations on the structures of the ternary copper(II) complex ion suggest that the charge-solvated isomer of the metal complex is the precursor ion that dissociates to give the PGG •+ radical cation. The isomer of the complex in which PGG is bound as a zwitterion dissociates to give the [a 3 + H] •+ and [b 2 - H] •+ ions.

[a 3 + H] 2+ ions generated from Ln 3+ /tripeptide complexes, where Ln = La or Ce, have similar structures to the linear [a n ] + ions but with protonation at both the terminal NH 2 and N═CH 2 groups. Ion stability is favored by having the basic secondary amine of the proline residue at the N-terminus and by an amino acid residue accommodating one of the protons on the side chain. Dissociation of [a 3 + H] 2+ ions derived from peptides containing only aliphatic residues is by cleavage of the second amide bond to give [b 2 ] + or [a 2 ] + ions along with internal [a 1 ] + ions. For [a 3 + H] 2+ ions containing a tryptophan residue in the central location, in addition to cleavage of the amide bond, losses of neutrals NH 3 , HN═CHR, (NH 3 + CO), and HNCO were observed. Dissociations of some unsolvated Ln 3+ /tripeptide complexes gave [b 3 + H] 2+ ions in low abundance; formation of these [b 3 + H] 2+ ions was favored by the presence of a proline residue at the N-terminus and by either a histidine or tryptophan residue in the central position. Dissociation of these [b 3 + H] 2+ ions was by the loss of (H 2 O + CO) and not only CO, indicating that these ions did not have the same type of oxazolone structure as found for [b n ] + ions. Density functional theory calculations suggest that the observed [b 3 + H] 2+ ions of ProGlyGly were formed from [Ce(ProGlyGly)] 3+ complexes in which the peptide was bound to the metal ion as an enolate. Dissociation of the slightly lower-energy complex, where the peptide is bound in the keto form, would produce an oxazolone but the high barrier required to create this isomer of the [b 3 + H] 2+ ion would be sufficient to result in further dissociation. Two isomers of the [b 3 + H] 2+ ion of ProHisGly have been created, one from the [Ce(ProHisGly)] 3+ complex that characteristically dissociates by the combined loss of (H 2 O + CO) and the other by the loss of glycine from [ProHisGlyGly + 2H] 2+ . The [b 3 + H] 2+ ion derived from [ProHisGlyGly + 2H] 2+ dissociated by the loss of only CO.

Collision-induced dissociations of isotopically labeled protonated tetraglycines establish that the [b 4 ] + ion formed by loss of water from the second amide bond (structure II) rearranges to form N 1 -protonated 3,5-dihydro-4H-imidazol-4-one (structure I), the product of water loss from the first amide bond. Structure II is slightly higher in energy than I (ΔH at 0 K is 5.1 kJ mol -1 , as calculated at M06-2X/6-311++G-(d,p)), and the barrier to interconversion is 139.8 kJ mol -1 above I. The dominant dissociation pathway is the loss of methanimine (HN=CH 2 ) from ion I with a barrier of 167.1 kJ mol -1 , giving [GlyGlyGlyGly + H - H 2 O - HN=CH 2 ] + , ion III; a minor channel, loss of NH 3 , has a slightly higher barrier (181.5 kJ mol -1 ). Using labeled glycine ( 13 C α ) it was determined that loss of the imine is from the same residue as that from which water was initially lost. The collision-induced dissociation spectra of ion III derived from both I and II were identical, and their energy-resolved curves were also very similar. Ion III fragments by losses of a glycine molecule (the dominant channel), a water molecule, and a glycine residue (57 Da), giving ions IV, V, and VII, respectively. Isotopic labeling established the origins of each of the neutral molecules that are lost. Using glycine (2,2 D 2 ), rapid deuterium exchange was observed for both ions I and II for the α-hydrogens that are from the same residue as that from which the water had been eliminated.

Peptide radical cations A(n)Y(•+) (where n = 3, 4, or 5) and A5W(•+) have been generated by collision-induced dissociation (CID) of [Cu(II)(tpy)(peptide)](•2+) complexes. Apart from the charge-driven fragmentation at the N-Cα bond of the hetero residue producing either [c + 2H](+) or [z - H](•+) ions and radical-driven fragmentation at the Cα-C bond to give a(+) ions, unusual product ions [x + H](•+) and [z + H](•+) are abundant in the CID spectra of the peptides with the hetero residue in the second or third position of the chain. The formation of these ions requires that both the charge and radical be located on the peptide backbone. Energy-resolved spectra established that the [z + H](•+) ion can be produced either directly from the peptide radical cation or via the fragment ion [x + H](•+). Additionally, backbone dissociation by loss of the C-terminal amino acid giving [b(n-1) - H](•+) increases in abundance with the length of the peptides. Mechanisms by which peptide radical cations dissociate have been modeled using density functional theory (B3LYP/6-31++G** level) on tetrapeptides AYAG(•+), AAYG(•+), and AWAG(•+).

Structural information of gaseous ions can be obtained by comparing their collision cross sections as determined by ion-mobility experiments with those by theoretical modeling. Three theoretical models, the projection approximation (PA), the exact hard-sphere scattering (EHSS), and the trajectory (TJ) models, have been employed to determine the theoretical cross sections of candidate geometries. The accuracy of these models is largely dependent on the empirical parameters used for ion-buffer gas interactions. Optimal empirical parameters for each model have been determined by comparing the experimental cross sections of 20 calibrant ions with their theoretical cross sections obtained by using geometries sampled by density-functional-theory-based molecular dynamics simulations. The maximum absolute deviations of the cross sections of 15.5% (PA), 20.7% (EHSS), and 11.7% (TJ) obtained from the original parameters are reduced to 5.6% (PA), 4.6% (EHSS), and 3.4% (TJ) obtained from the new optimized parameters. The root-mean-square deviations of the predicted cross sections using the new parameters from the experimental values are also drastically reduced to 2.1% (PA), 1.9% (EHSS), and 1.6% (TJ). The new parameters are verified on protonated triglycine, protonated trialanine, and doubly protonated bradykinin.

Histidine, lysine, and arginine radical cations have been generated through collision-induced dissociation (CID) of complexes [CuII(auxiliary ligand)namino acid]*2+, using tri-, bi-, as well as monodentate auxiliary ligands. On the basis of the observed CID products, the existence of two isomeric amino-acid populations is postulated. The Type 1 radical cations of histidine and lysine, stable on the mass spectrometer time scale, were found to lose water, followed by the loss of carbon monoxide under more energetic CID conditions. The arginine Type 1 radical cation behaved differently, losing dehydroalanine. The Type 2 radical cations were metastable and easily fragmented by the loss of carbon dioxide, effectively preventing direct observation. Type 1 radical cations are proposed to result from neutral (canonical) amino-acid coordination, whereas Type 2 radical cations are from zwitterionic amino-acid coordination to copper in the complex. The ratio of Type 1/Type 2 ions was found to be dependent on the auxiliary ligand, providing a method of controlling which radical cation would be formed primarily. Density functional calculations at B3LYP/6-311++G(d,p) have been used to determine the relative energies of five His*+ isomers. Barriers against interconversion between the isomers and against fragmentation have been calculated, giving insight as to why the Type 1 ions are stable, while only fragmentation products of the Type 2 ions are observable under CID conditions.

Comparison of the collision cross-section of the [Fe(III)-protoporphyrin IX]+ ion, hemin+, measured by means of ion-mobility experiments and the cross-sections calculated from theoretical structures based on density functional theory reveals that hemin+, in the gas phase, contains intramolecular hydrogen bonding between its two propionic acid side-chains.

Doubly charged lead monohydrate, [Pb(H2O)]2+, was predicted to be unstable in the gas phase, but it has recently been observed to form in low yield via ligand change between [Pb(CH3CN)]2+ and H2O [Shi, T.; Orlova, G.; Guo, J.; Bohme, D. K.; Hopkinson, A. C.; Siu, K. W. M. J. Am. Chem. Soc. 2004, 126, 7975-7980]. Here we report that abundant [Pb(H2O)]2+ is formed in the gas phase by ligand-exchange reaction between [Pb(N2)n]2+ (n = 1-3) and water after collisional activation. Density functional theory has been used to examine the ligand-exchange reaction profile. A comparison of the potential-energy surfaces between [Pb(N2)]2+ and [Pb(CH3CN)]2+ reacting with H2O provides strong evidence that the ligand-exchange reaction of [Pb(N2)]2+ with H2O to form [Pb(H2O)]2+ is more efficient than that of [Pb(CH3CN)]2+ with H2O.