From bioavailability scarcity to energy barriers: limitations of anaerobic microbial reductive defluorination

Abstract

Reductive dehalogenases in organohalide-respiring bacteria underpin anaerobic bioremediation of chlorinated pollutants but rarely effective for reductive defluorination of per- and polyfluoroalkyl substances. However, the physicochemical basis for this selectivity remains unclear. Here, we integrate quantum chemistry and molecular dynamics to evaluate constraints on microbial reductive defluorination. The scarcity of naturally occurring organofluorine has imposed limited evolutionary selective pressure, explaining the absence of robust defluorination pathways. Using quantum mechanical calculation, we show that organoflurines have low bioavailability, due to increasingly unfavorable solvation free energies for fluorinated ethenes in both polar and nonpolar solvents, impeding cellular uptake. Using molecular dynamics simulation, we show that the substrate recognition by reductive dehalogenase is compromised, due to progressively weaker van der Waals energies as chlorines are replaced by fluorines. Tetrafluorinated ligand can form hydrogen bonds with polar residues and preferentially stabilised in a sub-pocket away from the catalytic site. Using quantum mechanics calculation with a cluster model of the active site, we show that the reductive cleavage of C–F bond has prohibitively high energy barriers. Together, these results explain the limited anaerobic microbial reductive defluorination of linear per- and polyfluoroalkyl substances and highlight why engineering applications are unlikely to succeed. The workflow provides a screening framework for assessing biodegradability of new organofluorines prior to industrial deployment.