Charge and temperature effects on biomolecule hydration: an experimental and computational investigation

Abstract

The focus of this dissertation is on the role of charge and temperature on the structure of hydrated cluster ions. This is investigated using a combination of infrared photodissociation (IRPD) spectra and geometry and frequency calculations. The particular cluster ions examined here include hydrated rubidium cluster ions and hydrated sodium- and potassium-containing tryptamine, 2-amino-1-phenylethanol and ephedrine. In every case, there are significant differences between spectra obtained at different temperatures as well as those containing different metal ions. The argon tagging method, which was used to facilitate the temperature comparisons, had an unintended consequence: the cluster formation process trapped high-energy isomers in the experiments performed at lower temperatures. In addition, thermodynamic calculations showed the important role of entropy in determining the structures formed at warm temperatures. Both of these observations make it clear that the identification of one or two minimum-energy isomers based on zero-point energy calculations is not sufficient to mimic the isomer populations which are present during the experiments. A summary of the methods used to explore the potential energy surfaces of the various cluster ions is also given. An in-house Monte Carlo simulation program was originally written to aid the discovery of M+(H2O)n structures and was later expanded to include additional ligands in the clusters. More recent efforts have focused on using molecular dynamics to explore the conformations of the more complex M+(Biomolecue)(H2O)n cluster ions