Spectroscopy and dissociation dynamics of cold, biomolecular ions

The function of a peptide is intimately connected to its structure, which in solution is the result of the balance between non-covalent interactions within the molecule and the molecule-solvent interactions. Theory has the power to predict the properties of a wide variety of molecules, but the accuracy of the theoretical predictions must be verified by experiments. A way to test, and hopefully improve, theory is to study proteins or peptides in the gas-phase. The combination of mass spectrometry and laser spectroscopy is used to investigate properties of biological ions in the gas-phase. Closed-shell biomolecular ions produced by an electrospray source are cooled down in an RF ion trap to less than 10 K and interrogated spectroscopically. Electronic and conformer-specific vibrational spectra have been measured for small protonated peptides applying photofragment-based detection schemes. These measurements allow us to investigate the role of the charge and the influence of the nature and the position of the chromophore in the peptide chain on its conformational preferences. Highly-resolved conformer-specific vibrational spectra of such species, as well as those of a double-chromophore molecule, help elucidate the mechanism of the IR-UV double-resonance methods and provide benchmarks for testing the accuracy of theoretical calculations. This thesis shows also the experimental developments that allow us to use photofragment-based detection scheme to measure highly-resolved electronic spectra of peptides of up to 17 amino acids, containing one or two chromophores, using infrared laser-assisted photofragment spectroscopy (IRLAPS). The fragmentation yield of UV pre-excited molecules increases by as much as two orders of magnitude when they further interact with the CO2 laser. This approach can be also applied in a IR-UV double resonance scheme, allowing measurements of conformer-specific infrared spectra of protonated peptides. The fragmentation channel, which is always greatly enhanced by IRMPE of UV pre-excited molecules, is the loss of the neutral, aromatic side chain via cleavage of the Cα-Cβ bond, independent of the chromophore excited in the peptide. The possible mechanisms, involving the formation of a long-lived intermediate species, that lead to the formation of the observed photofragment are discussed in this thesis work.