Based on the known experimental Ah receptor binding affinities of 18 kinds of polybrominated diphenyl ethers (PBDEs), the quantitative structure-activity relationships (QSAR) model for PBDEs’ Ah receptor binding affinities was established via 13 substituent parameters (total number of substituent, substituent number in different position, substituent positional relationship parameters, substituent difference between two rings) to complement unknown binding affinities of other 191 PBDEs. Then, the full factorial experiment with 10 factors which correlated with each substituent position and 2 level (0,1) was applied to analyze the main effect and second-order interaction effect of each substituent position on PBDEs’ Ah receptor binding affinities. Meanwhile, different analysis methods were used for the views of the total number of substituent, the similarity of different phenyl ring in single congener and the distribution of substituents on single phenyl ring to expound the correlation between substituent characteristics and Ah receptor binding affinities of PBDEs comprehensively. The obtained results have shown that: PBDEs’ Ah receptor binding affinities are significantly affected by the main effect and second-order interaction effect of substitution positions, especially, the ortho-substituents can weaken the PBDEs’ Ah receptor binding affinities and para-substituents have the opposite effect. The order of the importance for different position is presented as: para>ortho>meta. The main effect of meta-substituent is small which often affects the Ah receptor binding affinities of PBDEs by representing the second-order interaction effects combined with ortho/para-substituent. For other substituent characteristics, the total number of substituent and the similarity of different phenyl ring in single congener cannot control the Ah receptor binding affinities of PBDEs effectively, but the more decentralized for substituents on single phenyl ring, the smaller Ah receptor binding affinities for PBDEs.
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