The molecular Field-Coupled Nanocomputing (FCN) is a promising implementation of the Quantum-dot Cellular Automata (QCA) paradigm for future low-power digital electronics. However, most of the literature assumes all the QCA devices as possible molecular FCN devices, ignoring the molecular physics. Indeed, the electrostatic molecular characteristics play a relevant role in the interaction and consequently influence the functioning of the circuits. In this work, by considering three reference molecular species, namely neutral, oxidized, and zwitterionic, we analyze the fundamental devices, aiming to clarify how molecule physics impacts architectural behavior. We thus examine through energy analysis the fundamental cell-to-cell interactions involved in the layouts. Additionally, we simulate a set of circuits using two available simulators: SCERPA and QCADesigner. In fact, ignoring the molecular characteristics and assuming the molecules copying the QCA behavior lead to controversial molecular circuit proposals. This work demonstrates the importance of considering the molecular type during the design process, thus declaring the simulators working scope and facilitating the assessment of molecular FCN as a possible candidate for future digital electronics.