SummaryOur knowledge on the chemistry across molecular and supramolecular levels is insufficient. Here, we show that inclusion of a guest molecule through quadrupolar interactions leads to a chemical transformation of the molecular system. With covalently bonded dimolybdenum complex units as the electron donor (D) and acceptor (A) and a thienylene group (C4H2S) as the bridge (B), the mixed-valence D-B-A complexes are shaped with clefts in the middle of the molecule. The D-A electron transfer is optically studied under the Marcus-Hush theoretic framework. It is found that in aromatic solvents, the electronic coupling matrix elements (Hab) and electron transfer rate constants (ket) are dramatically reduced. DFT calculations and electrostatic potential map analysis indicate that in the solution, an aromatic molecule is encapsulated in the cleft of the D-B-A array; quadrupole-quadrupole interaction between the guest molecule and the C4H2S group evokes charge redistribution, which increases the HOMO-LUMO energy gap, intervening in the through-bond electron transfer. These results demonstrate that a supramolecular system is unified underlying the characteristics of the assembled molecules through constitutional, electronic and energetic complementarities, thus, sharing the general principles developed in molecular chemistry. This study illustrates the role of site-specific interactions of the aromatic residues in biological systems in governing the charge transfer processes.