The thermochemistry of gas-phase ion-molecule interactions and structures of a variety of clusters formed between protonated amino acids and either ammonia or amines have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. The enthalpy changes for the association reactions of protonated Gly, Ala, Val, Leu, Ile, Ser, and Pro with ammonia have been measured as -23.2, -21.9, -21.0, -20.8, -20.6, -22.6, and -20.4 kcal mol(-1), respectively. A very good linear relationship exists between the enthalpy changes and the proton affinities (PAS) of the amino acids, with an exception of Ser, where the hydroxyl substituent forms an extra hydrogen bond with ammonia. For the association reaction of protonated proline and methylamine, the measured enthalpy and entropy changes are -26.6 kcal mol(-1) and -30.1 cal mol(-1) K-1, respectively. The experimental and calculated results indicate that the zwitterionic structure of proline may be well stabilized by CH3NH3+. For the first time, the interaction strengths between these amino acids and NH4+ have been obtained, and comparison with Na+ is discussed. Stabilization of zwitterionic structures of a series of amino acids (Gly, Ala, Val, Ser, and Pro) by various ammonium ions (NH4+, CH3NH3+, (CH3)(2)NH2+, and (CH3)(3)NH+) has been investigated systematically. Energy decomposition analysis has been performed so that the salt bridge interaction strengths between zwitterionic amino acids and ammonium ions have been obtained. Some generalizations with respect to the relative stability of zwitterionic structures may be drawn. First, as the PA of an amino acid increases, within a series of Gly, Ala, Val, the zwitterionic structure becomes more energetically favorable relative to a non-zwitterionic isomer. Second, as the PA of an amine increases, the zwitterionic structure of a given amino acid within the complex becomes gradually less favorable. Third, compared to the other amino acids, Pro, the only secondary amine among the 20 naturally occurring amino acids, has a much more pronounced tendency to form the zwitterionic structure, which has been confirmed by the experimental results. Finally, substitutents on the amino acid backbone that may participate in additional hydrogen bond interactions in non-zwitterionic isomer may render it more stable, as seen in Ser. These organic ammonium ions are found to be able to very effectively stabilize the zwitterionic structure of amino acids, even more effectively than metal ions, which aids significantly in the understanding of why zwitterionic structures exist extensively in biological systems.