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The application of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry to the quantitative study of molecular recognition in the gas phase is reviewed. Because most quantitative measurements are dependent on accurate determination of the pressure of a neutral reagent, methods for accurate pressure measurement in FTICR, including gauge calibration using a reaction with known rate constants (the traditional method), exothermic proton transfer rate measurement (often the best method when accurate neutral pressures in the trapping cell are desired), and linewidth measurement (a little-used, but generally applicable method) are discussed. The use of rate constant measurements in molecular recognition is illustrated with examples employing natural abundance isotopic labeling to study self-exchange and 2 : 1 ligand:metal complex formation kinetics in crown ether-alkali cation systems. Self-exchange rates do not correlate with alkali cation/crown cavity size relationships, whereas 2 : 1 complex formation kinetics correlate strongly with size relationships. The use of exchange equilibrium constant measurements to characterize molecular recognition is illustrated by alkali cation exchanges between 18-crown-6 and the isomers of dicyclohexano-18-crown-6. These experiments show that the alkyl-substituted ligand binds alkali cations better than unsubstituted 18-crown-6 in the gas phase, in accordance with expectations based on the higher polarizability of the alkyl-substituted ligand. Further, the metal binding thermochemistry differs for the two dicyclohexano-18-crown-6 isomers, with the bowl-shaped cis-syn-cis isomer binding all the alkali cations more strongly than the cis-anti-cis isomer. The measurement of entropies and enthalpies associated with one of the most subtle forms of molecular recognition, enantiomeric discrimination, is illustrated by studies of the discrimination between enantiomers of chiral amines by dimethyldiketopyridino-18-crown-6. This chiral ligand binds chiral primary ammonium cations that have the opposite absolute configuration at their stereocenter more strongly than the enantiomer with the same absolute configuration. Gas-phase studies show that this enantiomeric discrimination is enthalpic in origin, likely related to more favorable pi-pi stacking for the preferred enantiomer. Entropy disfavors binding of the preferred enantiomer.

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