Ionic Liquids (ILs) are salts that are composed of an asymmetric organic cation paired with an organic or inorganic anion. These organic complexes remain in the liquid state at room temperature due to their low charge density and highly structured nature which hinders crystal formation under standard conditions. These ILs are being used as efficient solvents and functional agents in various chemical and industrial applications for having “attractive properties” such as low melting points, non-volatility, nonflammability, high thermal and chemical stability, and tunable properties. Although ILs are often labeled as "green solvents," their environmental persistence may pose a challenge. Studies have demonstrated that many ionic liquids are only partially biodegradable, with a greater potential for biodegradation observed when the alkyl chain has six or more carbon atoms. Various studies have hypothesized that the iron porphyrin in bacterial cytochrome P450’s active site initiates IL biodegradation by oxidatively transforming the alkyl side chain. Cytochrome P450 (CYP450), has been referred to as a “ versatile biocatalyst” for oxidizing a wide range of substrates, producing essential molecules like neurotransmitters and hormones while detoxifying biological systems by using molecular oxygen, two electrons, and two protons. This study employs molecular dynamics (MD) simulations to explore interactions between [Cnmim]Cl (n = 2, 4, 6, 8, 10) and cytochrome P450 BM3 (PDB ID: 1JPZ), focusing on IL binding mechanisms. We investigated the binding dynamics, conformational changes, and stability within the enzyme’s heme active site. Our calculations include residue-level contact analysis, secondary structure alterations using DSSP, protein-ligand dynamics assessed through dynamic cross-correlation matrices (DCCM), and binding free energy calculations via umbrella sampling. Our results reveal specific residues that stabilize IL binding, subtle structural shifts in the enzyme, correlated motions relevant to ligand association, and favorable free energy profiles supporting IL-enzyme interaction. These insights reveal how alkyl chain length influences overall biodegradation efficiency with BM3. By providing an atomic-level understanding of the enzyme-IL complex, this work enhances knowledge of IL fate in microbial systems and informs the design of P450 variants for improved bioremediation, promoting sustainable industrial practices.
