Quantum-dot cellular automata (QCA) may provide a novel way to bypass the transistor paradigm to form ultrasmall computing elements. In the QCA paradigm information is represented in the charge configuration of a QCA cell, which maps naturally to a binary model. Molecular QCA implementations are being explored where the quantum dots in the cell take the form of redox centers in a molecule. Clocking has proved important in QCA cells synthesized so far. Here we examine a method to clock molecular QCA cells which are assembled at an interface. The clocking signals in this scheme originate from wires buried below the QCA surface. We present a simplified model of this clocking method and examine its behavior as a molecular shift register.