Structures of gaseous ions by infrared multiple photon dissociation (IRMPD) spectroscopy

The technique of infrared multiple photon dissociation (IRMPD) spectroscopy has shown its ability to determine the 3D (dimensional) structure of gaseous ions. Using this technique, the structures of small biologically relevant ions such as amino acids and nucleic acid bases bound with a proton or metal cations in the gas-phase were determined. The necessity of employing computational methods to analyze and interpret the experimental data has been demonstrated. However, the computational results must be analyzed with extreme caution to prevent any incorrect conclusions. Among the parameters one has to consider when dealing with the computational results is the experimental method used to obtain the data. For example, the simulated IR spectra for only two of the four lowest-energy protonated adenine dimer isomers were similar to the experimental IRMPD while, based on gas-phase calculations, the four lowest-energy structures were almost isoenergetic. Since the ions were produced by electrospray ionization (ESI) from the solution phase, the effect of water as a solvent was considered by applying two independent computational approaches to take solvation effects into account. Polarizable continuum model (PCM) calculations as well as microsolvation with five explicit water molecules calculations showed that water only preferentially stabilizes these two observed isomers, consistent with the interpretation of the IRMPD spectra. The results suggest great caution is required when using gas-phase calculations to predict the structures of gaseous ions borne in solution by ESI.;Due to the importance of m-DNA (metalated-DNA), an attempt to investigate the structure of singly hydrated thymine zinc ion-bound dimer was initiated. It was found that thymine loses one proton in the presence of zinc. Therefore, the [(Thy2-H)-Zn-(H2O)]+ cluster was singly charged. Solely comparing the IRMPD spectrum in the 3100-3850 cm -1 and simulated IR spectra was not sufficient to assign only one structure to the observed spectrum. Based on thermodynamical values, the two lowest energy structures were assigned as possible structures under the experimental conditions. In the most stable structure, the water is directly attached to the zinc in the zinc ion-bound dimer in which the An2+ is shared between the two atheneums at N3O4 sites. Furthermore, computational data suggested that recording an IRMPD spectrum in the 1800-2800 cm-1 region might be useful to distinguish between the two lowest energy structures. Therefore, recording the spectrum for the [(Thy2-H)Zn-(H 2O)]+ cluster in this lower energy region is part of the future work.;To investigate the influence of solvent on the structure of ions, an experimental method was developed to produce solvated ions in the gas-phase. These solvated ions then were investigated by IRMPD spectroscopy and blackbody infrared radiative dissociation (BIRD) to obtain kinetic and thermodynamic data. The solvation of electrosprayed ions occurs in the accumulation/collision hexapole of a hybrid quadrupole-Fourier transform mass spectrometer (Q-FTMS) by introducing the solvent into the collision cell. The most sensitive parameters based on our experience were the collision energy in the hexapole, the pressure of both collision gas and solvent in the hexapole, ion accumulation time, and the chemical nature of the species. This method was successfully applied to adenine and thymine cluster ions to produce multiply hydrated ions. The structures of singly hydrated ions were determined by IRMPD spectroscopy.