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Experiments investigating the role of non-covalent interactions in the structure, properties, and reactivity of gas-phase ion-biomolecule, ion-water, and water-biomolecule complexes in the gas phase are presented and discussed in this dissertation. Ions generated using electrospray ionization and trapped using Fourier transform ion cyclotron resonance mass spectrometers at the University of California, Berkeley, and the FOM Institute for Plasma Physics Rijnhuizen in Nieuwegein, The Netherlands, are probed using infrared photodissociation/infrared multiple photon dissociation (IRPD/IRMPD) spectroscopy and kinetics and electron capture dissociation. IRMPD spectra of alkali metal cationized dipeptides, protonated dipeptides, and trivalent lanthanide cationized polypeptides reported here reveal the role of ion size, formal charge site geometry, peptide sequence, gas-phase basicity, and competition between carbonyl groups and aromatic groups in the structures of these complexes. IRPD spectra of hydrated hydrophobic ions in the gas phase reveal a hydrogen bonding motif that contrasts strongly with those typically seen for more strongly hydrated ions. The role of ion charge state and size in the structures of gas-phase "nanodrops" is discussed based on their IRPD spectra and a computationally inexpensive point-charge model, as well as the dependence of these spectra on the electric field of the ion. These results show that ions can intrinsically affect the hydrogen bond structure of the water network out to three or more solvation shells, in contrast to many recent reports that only the first solvation shell is affected for ions in bulk solution. A new method using IRPD/IRMPD kinetics is demonstrated for directly measuring relative populations of spectroscopically distinguishable ion isomers, and a method for extending IRPD spectroscopic techniques to extensively hydrated ions that dissociate quickly is illustrated. This photodissociation kinetic method is demonstrated for several ion-biomolecule complexes and hydrated biomolecular ions, and relative Gibbs free energies, entropies, and enthalpies for nearly isoenergetic thermal ion populations are obtained with unprecedented precision. Ion nanocalorimetry is used to measure appearance energies for products of the exothermic reaction of a hydrated, doubly protonated dipeptide in the gas phase with a low-energy free electron, and nearly complete quenching of peptide fragmentation is achieved with a very small number of water molecules in the precursor ion complex.