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Infrared multiple photon dissociation spectra of the proton-bound heterodimers of phenylalanine/glycine (Phe·H + ·Gly) and pentafluorophenylalanine/glycine (F 5 -Phe·H + ·Gly) have been acquired in the 975–1975 cm −1 region. Exhaustive basin hopping molecular dynamics searches and subsequent DFT calculations predict four low energy intermolecular binding motifs. The spectrum of F 5 -Phe·H + ·Gly is assigned predominantly to isomers exhibiting a N H + ⋯O intermolecular interaction between nitrogen-protonated Gly and the carbonyl oxygen atom of F 5 -Phe. In contrast, the spectrum Phe·H + ·Gly is found to consist of a mixture of isomers exhibiting the N H + ⋯O between nitrogen-protonated Gly and the carbonyl oxygen of neutral Phe, and isomers exhibiting a N H + ⋯N interaction between nitrogen-protonated Phe and the neutral Gly moiety. Cation-π effects also seem to influence the cluster geometries, especially in the case of the Phe·H + ·Gly global minimum structure where the phenyl ring orients with the site of protonation so as to maximize charge-quadrupole interactions.

Gas-phase clusters of protonated methylamine and phenylalanine (Phe) derivatives have been studied using infrared multiple photon dissociation (IRMPD) spectroscopy in combination with electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. Experiments were performed on several Phe derivatives including 4-chloro-l-phenylalanine (4Chloro-Phe), 4-nitro-l-phenylalanine (4Nitro-Phe), 3-cyano-l-phenylalanine (3Cyano-Phe), and 3-trifluoromethyl-l-phenylalanine (3CF3-Phe). Through comparisons between experimental IRMPD spectra and stimulated spectra obtained by electronic structure calculations, charge-solvated structures were found to be prevalent in both 4Chloro-Phe and 4Nitro-Phe, whereas 3Cyano-Phe favored zwitterionic structures and 3-CF3-Phe likely have both zwitterionic and charge-solvated structures present.

The binding motifs in the halide adducts with tyrosine ([Tyr + X]−, X = Cl, Br, I) have been investigated and compared with the analogues with 3-nitrotyrosine (nitroTyr), a biomarker of protein nitration, in a solvent-free environment by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy over two IR frequency ranges, namely 950–1950 and 2800–3700 cm−1. Extensive quantum chemical calculations at B3LYP, B3LYP-D3 and MP2 levels of theory have been performed using the 6-311++G(d,p) basis set to determine the geometry, relative energy and vibrational properties of likely isomers and interpret the measured spectra. A diagnostic carbonyl stretching band at ∼1720 cm−1 from the intact carboxylic group characterizes the IRMPD spectra of both [Tyr + X]− and [nitroTyr + X]−, revealing that the canonical isomers (maintaining intact amino and carboxylic functions) are the prevalent structures. The spectroscopic evidence reveals the presence of multiple non-covalent forms. The halide complexes of tyrosine conform to a mixture of plane and phenol isomers. The contribution of phenol-bound isomers is sensitive to anion size, increasing from chloride to iodide, consistent with the decreasing basicity of the halide, with relative amounts depending on the relative energies of the respective structures. The stability of the most favorable phenol isomer with respect to the reference plane geometry is in fact 1.3, −2.1, −6.8 kJ mol−1, for X = Cl, Br, I, respectively. The change in π-acidity by ring nitration also stabilizes anion–π interactions yielding ring isomers for [nitroTyr + X]−, where the anion is placed above the face of the aromatic ring.

A combination of infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory calculations have been employed to study the structures and mode-specific dissociation pathways of the proton-bound dimer of 3-trifluoromethylphenylalanine (3-CF3-Phe) and trimethylamine (TMA). Three structural motifs are identified: canonical (charge-solvated), zwitterionic (charge-separated), and TMA-bridged. In the 1000-1350 cm(-1) region, similar spectra are observed in the TMA·H(+) and 3-CF3-Phe·H(+) product channels. At wavenumbers above 1350 cm(-1), infrared excitation of charge-solvated structures leads exclusively to production of protonated TMA, while excitation of zwitterionic or TMA-bridged structures results exclusively in production of protonated 3-CF3-Phe. The cluster potential energy landscape is topologically mapped and mechanisms for isomerization and mode-selective dissociation are proposed. In particular, cluster transparency as a result of IR-induced isomerization is implicated in deactivation of some IRMPD channels.

The rate constants for H-D exchange reactions of sodiated polyglycines (GnNa(+), n = 2-8) and polyalanines (AnNa(+), n = 2, 3 and 5) with ND3 have been measured in the cell of an FT-ICR mass spectrometer. All peptides except G2Na(+) are found to undergo three exchange reactions, all of which are consecutive with no sign of multiple exchanges within a single collision event. This information has been used to construct full mechanistic scenarios with the help of detailed quantum chemical calculations of the possible reaction paths for H-D exchange. The first exchange is always located at the C terminus however with different mechanisms depending upon whether the peptide termini can (larger peptides) or cannot (smaller peptides) interact directly without strong energy penalty. The most favourable mechanisms for the second and third exchanges of the N terminus protons, are found to be different from those for the first for all peptide sizes. The peptide distortions that are necessary in order for some of these reactions to occur are made possible by the energy reservoir provided by the favorable interaction of the peptide ion with ND3. Their occurrence and variety preclude any general relationship between H-D exchange kinetics and the most stable ion structures. There is however a break at G7Na(+) in the kinetics trend, with a first exchange rate which is much smaller than for all other peptide sizes. This break can be directly related to a different structural type in which the C terminus is neither free nor close to the N terminus.