First-principles density functional theory calculations of synthetic models of [FeFe]-hydrogenase are used to show that the theoretical methods reproduce observed structures and infrared spectra to high accuracy. The accuracy is demonstrated for synthetic Fe(I)Fe(I) models ([(mu-PDT)Fe-2(CO)(6)] and [(CN)(CO)(2)(mu-PDT)Fe-2-(CO)(2)(CN)](2-)), for which we show that their infrared spectra are sensitive to the geometric arrangement of their CO/CN ligands and can be used in conjunction with quantum-mechanical total energies to predict the correct ligand geometry. We then analyze and predict the structure of mixed-valence Fe(II)Fe(I) models ([(mu-MeSCH2C(Me)(CH2S)(2))Fe-2(CO)(4)(CN)(2)](x-)). These capabilities promise to distinguish among the various structural isomers of the enzyme's active site which are consistent with the limited accuracy of the X-ray observations.