In Silico understanding of the cyclodextrin–phenanthrene hybrid assemblies in both aqueous medium and bacterial membranes

[Display omitted] •Two hetero-assemblies, βCD1–Phe1, and βCD2–Phe1 were observed in water solution.•Distinct membrane-binding patterns for βCD, Phe, and their complexes were found.•Minor Phe trans-membrane energy barrier confirmed its membrane penetration ability.•Huge energy barriers for βCD-involved assemblies denied their membrane penetration.•Phe separation from βCD1–Phe1 was easier than that from βCD2–Phe1. The explicit-solvent molecular dynamic (MD) simulation and adaptive biased forces (ABF) methods were employed to systemically study the structural and thermodynamic nature of the β-cyclodextrin (βCD) monomer, phenanthrene (Phe) monomer, and their inclusion complexes in both the aqueous and membrane environments, aiming at clarifying the atomic-level mechanisms underlying in the CD-enhanced degradation of polycyclic aromatic hydrocarbons (PAHs) by bacteria. Simulations showed that βCD and Phe monomers could associate together to construct two distinctive assemblies, i.e, βCD1–Phe1 and βCD2–Phe1, respectively. The membrane-involved equilibrium simulations and the data of potential of mean forces (PMFs) further confirmed that Phe monomer was capable of penetrating through the membranes without confronting any large energy barrier, whereas, the single βCD and βCD-involved assemblies were unable to pass across the membranes. These observations clearly suggested that βCD only served as the carrier to enhance the bioavailability of Phe rather than the co-substrate in the Phe biodegradation process. The Phe-separation PMF profiles indicated that the maximum of the Phe uptake by bacteria would be achieved by the “optimal” βCD:Phe molar ratio, which facilitated the maximal formation of βCD1–Phe1 inclusion and the minimal construction of βCD2–Phe1 complex.