The ability of antifreeze glycoproteins to inhibit clathrate-hydrate formation is studied using DFT. A 512 cavity, dodecahedral (H2O)20, and the AATA peptide are used to model the inhibitor–clathrate interaction. The presence of AATA in the vicinity of the water cavities not only leads to the formation of complexes, with different peptide/cavity ratios, but also to the deformation of the cavity and to the elongation of several of the hydrogen bonds responsible for keeping the dodecahedral (H2O)20 together. The complexes are formed through hydrogen bonding between the peptides and the water cavities. The glycoproteins are expected to anchor onto the clathrate surface, blocking the access of new water molecules and preventing the incipient crystals from growing. They are also expected to weaken the clathrate structure. Amide IR bands are associated with the complexes’ formation. They are significantly red-shifted in the hydrogen-bonded systems compared to isolated AATA. The amide A band is the most sensitive to hydrogen bonding. In addition a distinctive band around 3100 cm−1 is proposed for the identification of clathrate–peptide hydrogen-bonded complexes.