Abstract The nucleophilic halogenases 5′-fluoro-5′-deoxyadenosine synthase (FDAS) and salinosporamide synthase (SalL) share 35% sequence identity, and both have been shown to catalyze chlorination, though only SalL does so under native conditions. High-resolution crystal structures of both enzymes support SN2 as the substitution mechanism, and thus desolvation of the halide through the exchange of protein residues for water must be a key component for both catalytic processes. QM/MM calculations and Molecular Dynamics (MD) simulations indicate that microsolvation of the nucleophile within the active site can serve to dramatically weaken the interaction between the chloride and a critical backbone amide. The resulting exposure of an otherwise shielded backbone amide is shown to induce structural disorder in the protein, thereby reducing the enzyme’s catalytic efficiency. This model highlights the importance of excluding water from the vicinity of a backbone amide through inclusion of a tightly bound halide ion, and raises the possibility that desolvation is driven, in part, by a need serve to preserve the integrity of the protein structure of the nucleophilic halogenases.