Quantum-dot cellular automata (QCA) is an emerging, promising, future generation computational architecture that encodes binary information into the positions of electrons. The switching and logic function of this transistorless architecture has already been realized in metal QCA and magnetic QCA. 'Bottom-up' molecular implementation may not only circumvent the lithography limits, but also realize room temperature operation, where metal QCAs could not function. A clock scheme is introduced to execute the pipeline calculation and provide the power gain. The clocking electric field can be produced by buried nanowires. Electrostatic force microscopy (EFM) is a direct way to measure the electric field. In our experiments, parallel nanowires were fabricated by electron beam lithography and metal lift off, and applied with different voltages to simulate different clocking phases. The electric forces were measured by the phase signal of EFM. EFM-phase measurement is not well understood here and used mostly for phase-contrast qualitative measurements. We demonstrate quantitative EFM-phase measurements. Also we discuss a source of error in EFM dual-pass measurement, which has been considered in our model for quantitative EFM-phase measurements. Finite element analysis is provided for applications of clocking QCA molecules. The simulations about programmable logic array in QCA and low-power consumption of QCA clocking wires have been demonstrated. Future work about the switching of molecular logic states by electric fields and detection by EFM or Kelvin probe force microscopy will be discussed.