In this work, we employ density functional theory to assign vibrational signatures of [FeFe]-hydrogenase intermediates to molecular structures. For this purpose, we perform an exhaustive analysis of structures and harmonic vibrations of a series of CN and CO containing model clusters of the [FeFe]-hydrogenase enzyme active site considering also different charges, counterions, and solvents. The pure density functional BP86 in combination with a triple-xi polarized basis set produce reliable molecular structures as well as harmonic vibrations. Calculated CN and CO stretching vibrations are analyzed separately. Scaled vibrational frequencies are then applied to assign intermediates,in [FeFe]-hydrogenase's reaction cycle. The. " results nicely complement the previous studies of Darensbourg and The infrared spectrum of the H-ox form is in very good agreement with the calculated Spectrum of the (FeFeII)-Fe-I-model complex featuring a free coordination site at the distal Fe atom, as well as, With the calculated spectra of the complexes in which H-2 or H2O are coordinated at this site The spectrum of H-red measured from Desulfovibrio desulfuricans is compatible with a mixture of a (FeFeI)-Fe-I species with all terminal COs, and a (FeFeI)-Fe-I species with protonated dtma ligand, while the spectrum of H-red recently measured from Chlamydomonas reinhardtii is compatible with a mixture of a (FeFeI)-Fe-I species with a bridged CO, and a (FeFeII)-Fe-II species with a terminal hydride bound to the Fe atom.