The hydrophobic cavity of the active site of [FeFe]-Hydrogenase is mimicked by two cyclodextrin molecules which surround a 2Fe2S synthetic analogue of the active site, outfitted with an aryl sulfonate to promote inclusion into beta-cyclodextrin. The X-ray crystal structure of the clathrate shows an increased torsion angle between the apical CO ligands indicating that the supramolecular cage destabilizes the eclipsed geometry typical of diiron model complexes. Inclusion in the model second coordination sphere also has important effects on the electrochemical properties of the model complex including an similar to 80 mV shift of the Fe(1)fe(1)/Fe(1)fe(0) reduction and a change in the potential at which electrocatalytic reduction of protons by the diiron complex occurs.