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With industry progress, environmental problems have begun to threaten human health. Among them, water pollution is closely related to human life and has attracted researchers’ attention. Hence, coping strategies for these pollutants have become a priority nowadays. Here, we carried out the molecular dynamics (MD) and well-tempered metadynamics simulations to evaluate the interaction of Rhodamine B (Rh B) with a copper (II)-benzene-1,3,5-tricarboxylate metal-organic framework (Cu-BTC/MOF). To design a more efficient dye removal platform, the effect of the -NH2, -OH, and -NO2 functional groups on the efficiency of Cu-BTC/MOF in the adsorption of Rh B is investigated. It is found that the interaction energy of Rh B with -NH2-MOF, -OH-MOF, and -NO2-MOF is about −79.98, −121.87, and −365.55 kJ mol−1, respectively, more than the pristine case. This observation confirms that the functionalization strategy can enhance the Cu-BTC/MOF efficiency. The obtained free energy (FE) values from the metadynamics simulation indicated that for adsorption of Rh B on pristine, -NH2-MOF, -OH-MOF, and -NO2-MOF, the global minimums are located about at −220.47, −234.75, −236.09, and −259.01 kJ mol−1, respectively. The obtained results show that in the two-dimensional FE surfaces, the most stable complex with Rh B belongs to the MOF-NO2 system.

Nowadays, nanomaterials are increasingly being used as drug carriers in the treatment of different types of cancers. As a result, these applications make them attractive to researchers dealing with diagnosis and biomarkers discovery of the disease. In this study, the adsorption behavior of gemcitabine (GMC) on graphene nanosheet (GNS), in the presence and absence of Poly (L-histidine) (PLH) polymer is discussed using molecular dynamics (MD) simulation. The MD results revealed an increase in the efficiency and targeting of the drug when the polymer is covalently attached to the graphene substrate. In addition, the metadynamics simulation to investigate the effects of PLH on the adsorption capacity of the GNS, and explore the adsorption/desorption process of GMC on pristine and PLH- grafted GNS is performed. The metadynamics calculations showed that the amount of free energy of the drug in acidic conditions is higher (− 281.26 kJ/mol) than the free energy in neutral conditions (− 346.24 kJ/mol). Consequently, the PLH polymer may not only help drug adsorption but can also help in drug desorption in lower pH environments. Based on these findings, it can be said that covalent polymer bonding not only can help in the formation of a targeted drug delivery system but also can increase the adsorption capacity of the substrate.

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Glyphosate (GLY) is a nonselective herbicide that has been widely used in agriculture for weed control.