Abundant Dipositively Charged Protonated a2 and a3 Ions from Diproline and Triproline

Calculation of Mass Spectra with the QCxMS Method for Negatively and Multiply Charged Molecules

Analysis and validation of a mass spectrometry (MS) experiment are usually performed by comparison to reference spectra. However, if references are missing, measured spectra cannot be properly matched. To close this gap, the Quantum Chemical Mass Spectrometry (QCxMS) program has been developed. It enables fully automatic calculations of electron ionization (EI) and positive ion collision-induced dissociation (CID) mass spectra of singly charged molecular ions. In this work, the extension to negative and multiple ion charge for the CID run mode is presented. QCxMS is now capable of calculating structures carrying any charge, without the need for pretabulated fragmentation pathways or machine learning of database spectra. Mass spectra of four single negatively charged and two multiple positively charged organic ions with molecular sizes from 12 to 92 atoms were computed and compared to reference spectra. The underlying Born-Oppenheimer molecular dynamics (MD) calculations were conducted using the semiempirical quantum mechanical GFN2-xTB method, while for some small molecules, ab initio DFT-based MD simulations were performed. Detailed insights into the fragmentation pathways were gained, and the effects of the computed charge assignments on the resulting spectrum are discussed. Especially for the negative ion mode, the influence of the deprotonation site to create the anion was found to be substantial. Doubly charged fragments could successfully be calculated fully automatically for the first time, while higher charged structures introduced severe assignment problems. Overall, this extension of the QCxMS program further enhances its applicability and underlines its value as a sophisticated toolkit for CID-based tandem MS structure elucidation.

Doubly Charged Small Organic Fragments Derived from [Ce(tripeptide)(CH3CN)m]3+ Complexes: Observation of the Elusive [bn + H]2+ Ions

[a₃ + H]²⁺ ions generated from Ln³⁺/tripeptide complexes, where Ln = La or Ce, have similar structures to the linear [a_n]⁺ ions but with protonation at both the terminal NH₂ and N═CH₂ 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 [a₃ + H]²⁺ ions derived from peptides containing only aliphatic residues is by cleavage of the second amide bond to give [b₂]⁺ or [a₂]⁺ ions along with internal [a₁]⁺ ions. For [a₃ + H]²⁺ ions containing a tryptophan residue in the central location, in addition to cleavage of the amide bond, losses of neutrals NH₃, HN═CHR, (NH₃ + CO), and HNCO were observed. Dissociations of some unsolvated Ln³⁺/tripeptide complexes gave [b₃ + H]²⁺ ions in low abundance; formation of these [b₃ + 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 [b₃ + H]²⁺ ions was by the loss of (H₂O + 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 [b₃ + 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 [b₃ + H]²⁺ ion would be sufficient to result in further dissociation. Two isomers of the [b₃ + H]²⁺ ion of ProHisGly have been created, one from the [Ce(ProHisGly)]³⁺ complex that characteristically dissociates by the combined loss of (H₂O + CO) and the other by the loss of glycine from [ProHisGlyGly + 2H]²⁺. The [b₃ + H]²⁺ ion derived from [ProHisGlyGly + 2H]²⁺ dissociated by the loss of only CO.

Infrared multiple-photon dissociation spectroscopy of tripositive ions: lanthanum-tryptophan complexes

Collision-induced charge disproportionation limits the stability of triply charged metal ion complexes and has thus far prevented successful acquisition of their gas-phase IR spectra. This has curtailed our understanding of the structures of triply charged metal complexes in the gas phase and in biological environments. Herein we report the first gas-phase IR spectra of triply charged La(III) complexes with a derivative of tryptophan (N-acetyl tryptophan methyl ester), and an unusual dissociation product, a lanthanum amidate. These spectra are compared with those predicted using density functional theory. The best structures are those of the lowest energies that differ by details in the π-interaction between La(3+) and the indole rings. Other binding sites on the tryptophan derivative are the carbonyl oxygens. In the lanthanum amidate, La(3+) replaces an H(+) in the amide bond of the tryptophan derivative.

Doubly charged protonated a ions derived from small peptides

Protonated a(2) and a(3) (therefore doubly charged) ions in which both charges lie on the peptide backbone are formed in collision-induced dissociations of [La(III)(peptide)(CH(3)CN)(m)](3+) complexes. Abundant (a(3)+H)(2+) ions are formed from triproline (PPP) and peptides with a proline residue at the N-terminus; these peptides are the most effective in producing ions of the type (a(2)+H)(2+) and (a(3)+H)(2+). A systematic study of the effect of the location of the proline residue and other residues of aliphatic amino acids on the generation of protonated a ions is reported. Density functional theory calculations at B3LYP/6-311++G(d,p) gave the proton affinity of the a(3) ion derived from PPP to be 167.6 kcal mol(-1), 2.6 kcal mol(-1) higher than that of water. The protonated a(2) ions of diglycine and diproline and a(3) ions of triglycine have lower proton affinities and are only observed in lower abundances, possibly due to proton transfer to water in ion-molecule reactions.