JOURNAL OF MASS SPECTROMETRY J. Mass Spectrom. 2006; 41: 141–156 Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/jms.998 SPECIAL FEATURE: PERSPECTIVE Structurally diagnostic ion/molecule reactions: class and functional-group identification by mass spectrometry Marcos N. Eberlin * Institute of Chemistry, State University of Campinas, ThoMSon Laboratory for Mass Spectrometry, 13083-970 Campinas, SP, Brazil Received 28 October 2005; Accepted 7 December 2005 This article discusses the application of gas-phase ion/molecule reactions for fine structural elucidation in mass spectrometry. This approach is illustrated via a representative collection of class- and functional group – selective reactions, a few of historical relevance as well as by more recent and instructive examples, and their applications. The focus is on reactions performed under well-controlled conditions of sequential mass spectrometry, discussing key mechanistic details and potential applications. Recent and innovative strategies that allow these reactions to be performed under ambient conditions, making this fast, selective and sensitive approach for structural investigation much more generally applicable, are also discussed. Copyright  2006 John Wiley & Sons, Ltd. KEYWORDS: ion/molecule reactions; gas-phase reactivity; ion chemistry; mass spectrometry; structure elucidation INTRODUCTION In chemistry there is often a direct, rational and very elegant relationship between structure and reactivity. Many types of structural information can therefore be obtained by screening for the occurrence or lack of a specific reaction. In mass spectrometry, for historical and practical reasons, structure/reactivity relationships have been explored mainly for unimolecular reactions that lead to ion dissociation. 1,2 Many diagnostic fragment ions of fragmentation processes have been found and extensively studied throughout the development of MS for structural investigation. Today, ion dissociation occurring as the result of ionization or induced by extra energy provided by collisions or radiation is by far the most frequent process used in MS to access structural information including atom connectivity and spatial arrangements. Thomson, 3 as early as 1913, noticed that ion/molecule reactions occur efficiently inside mass spectrometers, but these reactions began to be explored in MS only after 1966 when Munson and Field introduced chemical ionization (CI). 4 Many CI gases and reactions have since been developed and used to screen for classes of compounds and to identify specific functional groups. 5,6 These structurally diagnostic L Correspondence to: Marcos N. Eberlin, Institute of Chemistry, State University of Campinas, ThoMSon Laboratory for Mass Spectrometry, 13083-970 Campinas, SP, Brazil. E-mail: eberlin@iqm.unicamp.br Contract/grant sponsor: FAPESP and CNPq. reactions are therefore usually referred to as either class- selective or functional group – selective ion/molecule reactions. In CI, however, ion formation and its further reaction are performed in the same region (ion source) without previous ion isolation; hence the desired reaction may occur con- currently with other reactions involving cogenerated ions. With the development of MS instrumentation, particularly after the introduction of tandem-in-space and tandem-in- time mass spectrometers, reactions of ions with neutral molecules can now be performed with much greater refine- ment than is possible under CI environments. Very efficient multiple-stage mass spectrometers, most particularly the ICR, 7 quadrupole ion traps, 8 flowing afterglows 9 and triple- and penta-quadrupoles, 10 and the many scan modes they offer, make possible the isolation of the desired reacting ion with minimized internal energy, its reaction under low- enough energies to allow for efficient bimolecular reactions accompanied by minimal or no ion dissociation, as well as under controlled and well-defined reaction conditions such as pressure, temperature and time. Using MS n techniques, reactions can be monitored as a function of time with instant structural investigation of product ions employing either CID or a second structurally diagnostic ion/molecule reaction, or a combination of both. The mass spectrometrist, with great refinement and exploiting the outstanding speed, sensitivity and selectiv- ity as well the diverse environments that only MS offers, can therefore use the rational relationship between struc- ture and chemical reactivity to investigate the structure of Copyright  2006 John Wiley & Sons, Ltd.