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In the past 25 years, a tremendous amount of work has been published on the ion/molecule reactions of organic species. This review provides an overview of the areas where gas phase ion chemistry has made a contribution to our understanding of fundamental organic reaction processes. It is clear that the gas phase work can provide insights into subtle features of reaction mechanisms that could not be addressed by conventional condensed phase methods. The study of ion/molecule reactions has already had a major impact on the way that organic chemists think about reaction mechanisms and interpret substituent effects. Moreover, it has heightened our awareness of the importance of solvation effects and how they can alter not only absolute rates but also relative rates, leading in some cases to complete reversals in reactivity patterns. A large body of work could not be included in this review due to space limitations. For example, the study of thermochemistry in the gas phase (i.e., acidities, basicities, bond strengths, binding energies, etc.) has provided a wealth of data that has been exceptionally useful in interpreting organic reaction mechanisms. This has spilled over into the study of organometallic systems, and several groups are making major headway in using mass spectrometry to probe the stability and reactivity of transition metal species. Finally, work involving chemical ionization has provided abundant information on gas phase reaction mechanisms. The future appears to be very promising for the study of gas phase organic reaction mechanisms. In particular, the emergence of new ionization techniques and more powerful mass analyzers will allow chemists to explore a wider range of species. Although still at an early stage, the gas phase study of biochemical transformations offers great promise and has been facilitated by electrospray and matrix assisted laser desorption ionization methods. In addition, these techniques provide a means for introducing important, metal-centered catalytic species into the gas phase and exploring the details of their reactivity. Finally, mass spectrometry continues to play a major role in the study of atmospheric ion chemistry and is providing important kinetic as well as mechanistic data.

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Over the past several decades, quadrupole ion traps have become important instruments in the study of gas phase ion/molecule reactions. As a part of this work, they have been employed in a number of studies focused on fundamental organic reaction mechanisms. In this review, the general features and limitations of quadrupole ion traps are discussed followed by a description of representative ion trap studies of organic reaction mechanisms such as substitution, elimination, and acyl transfer reactions.