Results of density functional theory (DFT) calculations on the protonation of the [FeFe]-hydrogenase model complex, Fe2(μ-pdt)(CO)4(PMe3)2 (pdt = propane-1,3-dithiolate), show that diiron bridging-hydride species are more stable than iron terminal-hydride, sulfur-hydride, or formyl isomers. Consistent with experimental observation, the transoid basal/basal forms are more stable than other μ-H isomers. With an ether as the proton carrier, [Et2OH]+, the favoured reaction pathways appear to involve weak coordination to CO followed by transfer of the proton from ether to an iron terminal site rather than directly to the bridging site. These kinetically favoured terminal-hydride species isomerize through a low-energy Ray-Dutt twist to produce the apical/basal bridging-hydride isomer. This isomer rearranges over somewhat higher barrier Bailar twists to the cisoid and transoid basal/basal isomers, the former finally rearranging to the latter isomer.