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Abstract The present study is focused on the use of cubic metal-organic frameworks-5 (MOF-5) and its functionalized form in the removal of phenolic pollutants by molecular dynamics (MD) and Well-tempered metadynamics (WTMD) simulation methods. It was found that the adsorption mechanism of MOF-5s/phenolic compounds is mostly due to the van der Waals and π–π interactions. However, electrostatic and hydrogen bond (HB) interactions also play a significant role in removing phenolic pollutants by MOF-5 and its functionalized form. The results show that the fluorine functional group (F-MOF-5) increases the adsorption capacity of phenol compounds on the adsorbent surface. By functionalizing the MOF-5 with a methyl functional group (CH3-MOF-5), the adsorption strength decreases. The WTMD calculation confirmed that at the most stable state, the free energy (FE) value of system II (the most stable system in functionalized systems with –F functional group) is about −289.528 kJ mol−1. This value is ~5.781 and 35.514 kJ mol−1 more negative than the FE of the I and III systems (the most stable systems in the pristine and CH3-MOF-5/pollutant systems, respectively). Altogether, the results indicate that F-MOF-5 can be considered a more suitable adsorbent than MOF-5 and CH3-MOF-5 for phenolic pollutants removal from the environment for more assessment.