Quantum-dot cellular automata (QCA) is an approach to computing which eliminates the need for transistors by representing binary digits as charge configurations rather than current levels. Coulomb interactions provide device-device coupling without current flow. Molecular QCA uses redox sites of molecules as quantum dots. Clocked control of the device allows power gain, control of power dissipation, and pipelined computation. We present ab initio analyses of both clocked and unclocked molecular QCA cells. We compare the results of calculations using several different levels of theory. We examine the role of the relaxation of the nuclear coordinates. We show how simple molecular QCA devices can be implemented.