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A new approach for the development of nano-sized spectroscopic-based early-warning sensors using molecular electrostatic potentials (MEP) and molecular vibronics (MV) was presented. The use of MEPs allow us to sense and detect specific molecules in elaborated arrays of logical gates which provide the signature of the trapped species and a decision signal of the results of the sensing operation. Molecular vibronics is used to activate/deactivate, control and program the detection process as well as to transmit the information to and from nano-micro interfaces that allow the interaction with microelectronic systems. In order to develop this scenario, it is needed to explain the exact reasons, from an atomistic point of view rather than using phenomenological models the effects of molecules on nanoclusters. We present here a study of silicon-phenyl complexes.