Graphene and its derivatives are useful building blocks for the bottom-up assembly of advanced functional materials. Noncovalently functionalized graphene networks offer a wide range of applications. We investigated the formation of sandwich-like three-layered nanostructures with graphene. Novel architectures have been generated by stacking selected suitable organic molecules based on their characterized donor and acceptor strengths vertically on the graphene surface. This paper describes the adsorption of electron-acceptor and electron-donor molecules on the graphene layer through noncovalent interactions. Cluster and crystal models of the graphene surface have been selected to design sandwich-like two-layered and three-layered structures, and their stabilities have been verified using density functional theory calculations. Further, stability of the complexes has been confirmed on the basis of factors such as interaction energy and charge transfer. The stability of the macrostructures has been tested by metadynamics simulations. We have found that the most stable complex C4···HAT-CN···TAB prefers the double-sandwich state over the dissociated state.