The continuous minituarization of integrated circuits may reach atomic scales in a couple of decades. Some researchers have already built simple computation engines by manipulating individual atoms on metal surfaces. This paper presents a systematic approach to automate the design of logic gates using molecule cascades. Temporal logic is used to characterize molecular interactions and specify the behavior of logic gates. Model-checking techniques are used for the exploration of structures behaviorally equivalent to the logic gates. As an example, a complete library of combinational logic gates has been designed using a particular molecular system. This new approach provides a methodology to bridge the gap between physical chemists and computer scientists in seeking computational structures at atomic scales.