Halogenated biphenyls are worldwide persistent pollutants of great environmental concern. In particular, polychlorinated biphenyls and polybrominated biphenyls have been globally used for industrial purposes until they were found highly toxic, mutagenic and carcinogenic to humans. Therefore, ecological strategies to remove halogenated biphenyls, such as enzyme-catalyzed degradation, are needed. Here, we studied the effect of substitution of F, Cl, Br or I at the 4,4′-positions of 2,3-dihydro-2,3-dihydroxybiphenyl-2,3-dehydrogenase (BphB) on the degradation of halogenated biphenyls by quantum and molecular mechanics. Results show that Boltzmann-weighted average degradation barriers of substituted BphB are all lower than the unsubstituted biphenyl, except for chlorinated biphenyl. The roles of residues nearby the active site, e.g., iso-leucine89, asparagine115, serine142, asparagine143, proline184, methionine187 and threonine189, were also investigated. Keywords Quantum mechanics/molecular mechanics • Polyhalogenated biphenyls • Metabolites • Dehydrogenation • Electrostatic influence Abbreviations BphA Biphenyl dioxygenase BphB 2,3-Dihydro-2,3-dihydroxybiphenyl-2,3-dehydrogenase BphC 2,3-Dihydroxybiphenyl-1,2-dioxygenase BphD 2-Hydroxyl-6-oxo-6-phenylhexa-2,4-dienoic acid hydrolase NAD Nicotinamide adenine dinucleotide (coenzyme) Isoleucine89 Isoleucine and its sequence number in BphB enzyme PFBs Polyfluorobiphenyls PCBs Polychlorinated biphenyls PBBs Polybrominated biphenyls PIBs Polyiodobiphenyls QM/MM Quantum mechanics/molecular mechanics bf-4.0 The degradation pathway of polyfluorobiphenyls degradation bb-4.0 The degradation pathway of polybrominated biphenyls degradation bi-4.0 The degradation pathway of polyiodobiphenyls degradation Electronic supplementary material The online version of this article (