Herein, our primary motivation was to elucidate the electronic and physicochemical properties of a novel molecular dyad consisting of ferrocene (Fc; electron donor), urea (u; linker), and amphoteric benzimidazole (BI; electron acceptor) entities. The sensor responses were investigated for various divalent transition metal cations (Mn, Fe, Co, Ni, Cu, and Zn) and the selectivity of this cationophore molecule (Fc-u-BI) to copper ion (Cu) was demonstrated by using B3LYP/LANL2DZ method. According to the thermochemical calculations, we justified that Fc-u-BI⋯Cu reached to the lowest binding energy (∆E), enthalpy (∆H), and Gibbs free energy (∆G) changes. In the light of the calculated global descriptors, Fc-u-BI⋯Cu was found to be the softer and thus the most reactive complex. The complex stabilities and their corresponding non-covalent interactions were also investigated by NBO and NCI analyses, respectively. The mechanistic insight into metal cation sensing by the modeled cationophore dyad.