We present infrared photodissociation spectra of two protonated peptides that are cooled in a ~10 K quadrupole ion trap and “tagged” with weakly bound H2 molecules. Spectra are recorded over the range 600 – 4300 cm−1 using a table-top laser source, and are shown to result from one-photon absorption events. This arrangement is demonstrated to recover sharp (Δν~6 cm−1) transitions throughout the fingerprint region, despite the very high density of vibrational states in this energy range. The fundamentals associated with all of the signature N-H and C=O stretching bands are completely resolved. To address the site-specificity of the C=O stretches near 1800 cm−1, we incorporated one 13C into the tripeptide. The labeling affects only one line in the complex spectrum, indicating that each C=O oscillator contributes a single distinct band, effectively “reporting” its local chemical environment. For both peptides, analysis of the resulting band patterns indicates that only one isomeric form is generated upon cooling the ions initially at room temperature into the H2 tagging regime.

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Multi-dentate, non-covalent interactions between small molecules and biopolymer fragments are central to processes ranging from drug action to selective catalysis. We present a versatile and sensitive spectroscopic probe of functional groups engaged in hydrogen bonding in such contexts. This involves measurement of the frequency changes in specific covalent bonds upon complex formation, information drawn from otherwise transient complexes that have been extracted from solution and conformationally frozen near 10 Kelvin in gas-phase clusters. Resonances closely associated with individual oscillators are easily identified through site-specific isotopic labeling, as demonstrated by application of the method to an archetypal system involving a synthetic tripeptide known to bind biaryl substrates through tailored H-bonding to catalyze their asymmetric bromination. With such data, calculations readily converge on the plausible operative structures in otherwise computationally prohibitive, high dimensionality landscapes.