The unfolding enthalpy of the native state of ubiquitin in solution is 5 to 8 times that of its gaseous ions, as determined by electron capture dissociation (ECD) mass spectrometry. Although two-state folding occurs in solution, the three-state gaseous process proposed for this by Clemmer and co-workers based on ion mobility data is supported in general by ECD mass spectra, including relative product yields, distinct Delta H(unfolding) values between states, site-specific melting temperatures, and folding kinetics indicating a cooperative process. ECD also confirms that the 13+ ions represent separate conformers, possibly with side-chain solvated alpha-helical structures. However, the ECD data on the noncovalent bonding in the 5+ to 13+ ions, determined overall in 69 of the 75 interresidue sites, shows that thermal unfolding proceeds via a diversity of intermediates whose conformational characteristics also depend on charge site locations. As occurs with increased acidity in solution, adding 6 protons to the 5+ ions completely destroys their tertiary noncovalent bonding. However, solvation of the newly protonated sites to the backbone instead increases the stability of the secondary structure (possibly an alpha-helix) of these gaseous ions, while in solution these new sites aid denaturation by solvation in the aqueous medium. Extensive ion equilibration can lead to even more compact and diverse conformers. The three-state unfolding of gaseous ubiquitin appears to involve ensembles of individual chain conformations in a "folding funnel" of parallel reaction paths. This also provides a further caution for characterizing solution conformers from their gas-phase behavior.

The alkali metal ion (M+ = Li+, Na+, K+) affinities of the common DNA and RNA nucleobases are determined in the gas phase by investigating the dissociation of metal ion-bound heterodimers [nucleobase + B]M+, in which B represents a reference base of known affinity (kinetic method). The dimer ion decompositions are assessed at two different internal energies, namely from metastable precursor ions and after collisional activation. This approach makes it possible to deconvolute entropy from enthalpy and, therefore, leads to more accurate affinity (i.e. enthalpy or bond energy) values. For the nucleobases studied, viz. guanine, cytosine, adenine, thymine, and uracil, the corresponding M+−nucleobase bond energies are (kJ mol-1) as follows:  239, 232, 226, 215, and 211 with Li+; 182, 177, 172, 144, and 141 with Na+; and 117, 110, 106, 102, and 101 with K+. The method used also provides quantitative information about the overall entropy change occurring upon the dissociation of the heterodimers; this change is most significant when dissociation alters rotational degrees of freedom. The magnitude of the operating entropy effects gives information on the structures of both the metal ion-bound dimers and the metalated nucleobase monomers. It is found that Li+, Na+, and K+ bind very similarly to the nucleobases. Attachment sites that explain the observed entropic effects and metal ion affinity orders are suggested and discussed. A notable characteristic of several of the resulting structures is their ability to form stabilizing ion pairs (salt bridges).

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Na+ and K+ gas-phase affinities of the three aromatic amino acids Phe, Tyr, and Trp were measured by the kinetic method. Na+ binds these amino acids much more strongly than K+, and for both metal ions the binding strength was found to follow the order Phe < or = Tyr < Trp. Quantum chemical calculations by density functional theory (DFT) gave the same qualitative ordering, but suggested a somewhat larger Phe/Trp increment. These results are in acceptable agreement with predictions based on the binding of Na+ and K+ to the side chain model molecules benzene, phenol, and indole, and are also in reasonable agreement with the predictions from purely electrostatic calculations of the side-chain binding effects. The binding energies were compared with those to the aliphatic amino acids glycine and alanine. Binding to the aromatic amino acids was found to be stronger both experimentally and computationally, but the DFT calculations indicate substantially larger increments relative to alanine than shown by the experiments. Possible reasons for this difference are discussed. The metal ion binding energies show the same trends as the proton affinities.

The Na+ affinities of simple cyclic and linear dipeptides and of selected derivatives are determined in the gas-phase based on the dissociations of Na+-bound heterodimers [peptide + Bi]Na+, in which Bi represents a reference base of known Na+ affinity (kinetic method). The decompositions of [peptide + Bi]Na+ are assessed at three different internal energies; this approach permits the deconvolution of entropic contributions from experimentally measured free energies to thus obtain affinity (i.e. enthalpy or bond energy) values. The Na+ affinities of the peptides studied increase in the order (kJ mol-1) cyclo-glycylglycine (143) < cyclo-alanylglycine (149) < cyclo-alanylalanine (151) < N-acetyl glycine (172) < glycylglycine (177) < alanylglycine (178) < glycylalanine (179) < alanylalanine (180) < glycylglycine ethyl ester (181) < glycylglycine amide (183). The method used provides quantitative information about the difference in bond entropies between the peptide−Na+ and Bi−Na+ bonds, which is most significant when Na+ complexation alters rotational degrees of freedom either in the peptide or in Bi. From the relative bond entropies, it is possible to appraise absolute entropies of Na+ attachment, which are ∼104 and ∼116 J mol-1 K-1 for the cyclic and linear molecules, respectively. The combined affinity and entropy data point out that the cyclic dipeptides bind Na+ in a monodentate fashion through one of their amide carbonyl oxygens, while the linear molecules coordinate Na+ in a multidentate arrangement involving the two carbonyl oxygens and, possibly, the N-terminal amino group. High-level ab initio calculations reveal that the most stable [glycylglycine]Na+ structure arises upon bidentate chelation of Na+ by the two carbonyls and concomitant formation of a hydrogen bond between the amino group and the amide nitrogen. Such a structure agrees very well with the experimental enthalpy and entropy trends observed for the linear molecules. According to theory, zwitterionic forms of [glycylglycine]Na+ are the least stable isomers, as also suggested by the experimental results.