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Unexpected explanation for the enigmatic acid-catalysed reactivity of [Fe4S4X4](2-) clusters.

Density functional calculations show that Fe-S clusters undergo unexpected large structural changes when protonated at S. Protonation of prototypical cubanoid [Fe4S4X4](2-) to [Fe4S3(SH)X4](-) (X = Cl, SR, OR) results in formation of doubly-bridging SH, severance of one Fe-S bond, and creation of a three-coordinate Fe. These findings explain previously enigmatic results concerning the reactivity of these clusters, including the rates of protonation, pKa data, and the kinetics of acid-catalysed ligand substitution.