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It encodes the information in the charge distribution of nanometric molecules and propagates it through local electrostatic intermolecular interaction. This technology promises very high speed at ambient temperatures with minimal power dissipation. The main research focus on molecular FCN is currently either on single-molecule low-level analysis or circuit design based on na\u00efve assumptions. We aim to fill this gap, assessing the potential and feasibility of FCN. We present a bottom-up analysis and design framework that starts from the physical characterization of molecular and technological parameters and enables physical-aware FCN designs. The framework explicitly considers molecular physics, allowing the designer to tame the molecular interaction to ensure the computational capabilities of the final device. The framework permits studying possible physical effects that create cross-implications and correlations among physical and system-level layers considering possible behavior variability. We characterize and verify molecular propagation in increasingly structured layouts to design complex arithmetic circuits. 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