In the condensed phase, the peptide gramicidin S is often considered as a model system for a β-sheet structure. Here, we investigate gramicidin S free of any influences of the environment by measuring the mid-IR spectra of doubly protonated (deuterated) gramicidin S in the gas phase. In the amide I (i.e., C═O stretch) region, the spectra show a broad split peak between 1580 and 1720 cm−1. To deduce structural information, the conformational space has been searched using molecular dynamics methods and several structural candidates have been further investigated at the density functional level. The calculations show the importance of the interactions of the charged side-chains with the backbone, which is responsible for the lower frequency part of the amide I peak. When this interaction is inhibited via complexation with two 18-crown-6 molecules, the amide I peak narrows and shows two maxima at 1653 and 1680 cm−1. A comparison to calculations shows that for this complexed ion, four C═O groups are in an antiparallel β-sheet arrangement. Surprisingly, an analysis of the calculated spectra shows that these β-sheet C═O groups give rise to the vibrations near 1680 cm−1. This is in sharp contrast to expectations based on values for the condensed phase, where resonances of β-sheet sections are thought to occur near 1630 cm−1. The difference between those values might be caused by interactions with the environment, as the condensed phase value is mostly deduced for β-sheet sections that are embedded in larger proteins, that interact strongly with solvent or that are part of partially aggregated species.