<p>During the past fifty years, mass spectrometry, often hyphenated with chromatography, has developed into the most widely used technique for the quantitative and qualitative analysis of increasingly complex mixtures of (bio)organic molecules.</p> <p>One important aspect of this development concerns the relationship between the structure (atom connectivity) of a molecule and the mass spectrum obtained by electron ionization (EI). In this context, from 1960 - 1990, a wealth of studies has appeared that uses a variety of novel experimental techniques, often in conjunction with isotope labelling, to probe the structure, stability, reactivity and dissociation characteristics of the radical cations generated by EI of various classes of molecules. One highlight was the discovery of surprisingly stable distonic ions and the role they play in the dissociation chemistry of ionized molecules.</p> <p>However, mechanistic proposals based upon experimental observations can often only be considered as tentative. Synergy between experiment and theory would be ideal to remedy this situation, but it was not until recent spectacular advances in computer technology and software that this approach could be implemented. It has led to the growing realization that many rearrangement reactions of radical cations in the rarefied gas-phase involve catalysis. Proton-transport catalysis (PTC) is a prime example : here, a neutral species induces an ion to isomerize via hydrogen-bridged radical cations (HBRCs) as intermediates. An exemplary case described in this thesis concerns the ion-molecule reaction of the cyanamide ion with a single H₂O molecule : experiment and theory indicate that the H₂O molecule catalyzes the swift transformation of NH₂-CN^·⁺ into the more stable carbodiimide ion HN=C=NH^·⁺.</p> <p>The thesis exploits the synergy of tandem mass spectrometry and computational chemistry to study the role of catalysis in the association and dissociation reactions of several systems of radical cations. During these studies, a new type of a catalyzed reaction was discovered: "ion-catalysis", where an organic cation promotes the otherwise prohibitive rearrangement of a neutral. Ion-catalysis is proposed to explain the unexpected loss of NH₂O^· from low-energy N-hydroxyacetamide ions CH₃C(=O)NHOH^·⁺ : the molecular ion rearranges into the HBRC [O=C-C(H₂)--H--N(H)OH]^·⁺ whose acetyl (cation) component catalyzes the transformation NHOH^· --> NH₂O^·. Another highlight involves a hybrid reaction, in which both the ion and the neutral component of an incipient HBRC catalyze one another to rearrange into more stable isomers.</p> <p>Catalysis may also play an important role in astrochemistry and a question addressed in this context is whether pyrimidine, a key component of DNA, may be generated by ion-molecule reactions. It appears that the acrylonitrile ion (AN) does not react with HCN to produce ionized pyrimidine, instead it isomerizes by PTC. However, the reaction of the ion with its neutral counterpart does not involve catalysis, but rather cyclization into the pyrimidine ion ! A related topic concerns the structures of covalently bound dimers of the ubiquitous interstellar molecules HCN and HNC. Neutralization-Reionization Mass Spectrometry in conjunction with model chemistry calculations leaves little doubt that the elusive dimers HN=C=C=NH and HC=N-C=NH are kinetically stable in the rarefied gas-phase, whereas HC=N-N=CH is not.</p> <p>The structure of ions may also be probed by interactions with selected neutral molecules rather than dissociative collision experiments (MS/MS). An exciting case involves the differentiation of isomeric heterocyclic ions by ion-molecule reactions with dioxygen. Here, too, model chemistry calculations play an essential role in understanding the mechanism and the scope of the reaction.</p> / Doctor of Philosophy (PhD)