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[en] Leaching of toxic metals from fertilizers is a growing concern in an agricultural country like Bangladesh due to the serious consequences in health and food chain. Fertilizers used in farming fields and nurseries (plant sales outlet) in the mid-southern part of Bangladesh were collected for the determination of toxic metals. This study employed the neutron activation method and a relative standardization approach. Three standard/certified reference materials, namely NIST coal fly ash 1633b, IAEA-Soil-7, and IAEA-SL-1 (lake sediment), were considered for elemental quantification. Concentration of As (2.63–16.73 mg/kg), Cr (40.93–261.77 mg/kg), Sb (0.47–63.58 mg/kg), Th (1.44–19.16 mg/kg), and U (1.90–209.41 mg/kg) were determined in fertilizers. High concentrations of Cr, Sb, and U were detected in some compost and phosphate fertilizers (TSP and diammonium phosphate (DAP)) in comparison with the IAEA/European market standard and other studies. Quantum mechanical calculations were performed to understand the molecular level interaction of CrO3, Sb2O3, and AsO3, with DAP by employing density functional theory with the B3LYP/SDD level of theory. Our results indicated that CrO3 and Sb2O3 have strong binding affinity with DAP compared to AsO3, which supports the experimental results. These compounds attached to the phosphate group through covalent-like bonding with oxygen. The frontier molecular orbital calculation indicated that HOMO-LUMO gap of the AsO3-DAP (5.46 eV) and Sb2O3-DAP (6.48 eV) complexes are relatively lower than the CrO3-DAP, which indicates that As and Sb oxides are chemically more prone to attach with the phosphate group of DAP fertilizer.