Doubly charged protonated a ions derived from small peptides

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.

A RRKM study and a DFT assessment on gas-phase fragmentation of formamide-M(2+) (M = Ca, Sr)

A kinetic study of the unimolecular reactivity of formamide-M(2+) (M = Ca, Sr) systems was carried out by means of RRKM statistical theory using high-level DFT. The results predict M(2+), [M(NH2)](+) and [HCO](+) as the main products, together with an intermediate that could eventually evolve to produce [M(NH3)](2+) and CO, for high values of internal energy. In this framework, we also evaluated the influence of the external rotational energy on the reaction rate constants. In order to find a method to perform reliable electronic structure calculations for formamide-M(2+) (M = Ca, Sr) at a relatively low computational cost, an assessment of different methods was performed. In the first assessment twenty-one functionals, belonging to different DFT categories, and an MP2 wave function method using a small basis set were evaluated. CCSD(T)/cc-pWCVTZ single point calculations were used as reference. A second assessment has been performed on geometries and energies. We found BLYP/6-31G(d) and G96LYP/6-31+G(d,p) as the best performing methods, for formamide-Ca(2+) and formamide-Sr(2+), respectively. Furthermore, a detailed assessment was done on RRKM reactivity and G96LYP/6-31G(d) provided results in agreement with higher level calculations. The combination of geometrical, energetics and kinetics (RRKM) criteria to evaluate DFT functionals is rather unusual and provides an original assessment procedure. Overall, we suggest using G96LYP as the best performing functional with a small basis set for both systems.

Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide

BACKGROUND

Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations.

METHODS

MSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds.

RESULTS

We were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation.

CONCLUSIONS

These results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification.

Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]2+ gas phase unimolecular reactivity via chemical dynamics simulations

In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)](2+), in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar + [Ca(urea)](2+) collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex.