Molecular and product design are intertwined with process intensification. To this end, we will develop a framework that integrates superstructure optimization and computer-aided molecular design. Particularly, the superstructure will be constructed in a stage-by-stage manner, and the pairwise phenomena interactions of each stage will be enumerated. For the reaction phenomena at each stage, we will consider the molecular design subproblems for designing reaction products, whereby discrete decisions are made regarding the selection of functional groups (or union of functional groups) and their connections. Finally, through molecular dynamics simulations, we will validate these optimally designed products to elucidate the molecular interactions that govern the products' properties. To account for chemical systems that existing force-field parameterization does not predict well (e.g., charged systems involving polarization and reactive systems), we intend to explore other forms of potential function and develop a new parameterization by integrating Bayesian optimization, experimental data, and molecular dynamics simulations.