Abstract In this chapter, we discuss the importance of noncovalent interactions in functional nanostructures. From layered materials to porous materials to polymers, we detail the underlying noncovalent interactions that define their behavior and dominate their properties and how theory, modeling and simulation is key to accelerate the process of understanding and design. In particular, we highlight how atomic level details of the underlying physicochemical phenomena can be useful for illuminating the connections between experiments and computational approaches.