ConspectusCarbon-based two-dimensional (2D) functional materials exhibit potential across a wide spectrum of applications from chemical separations to catalysis and energy storage and conversion. In this Account, we focus on recent advances in the manipulation of 2D carbonaceous materials and their composites through computational design and simulations to address how the precise control over material structure at the atomic level correlates with enhanced functional properties such as gas permeation, selectivity, membrane transport, and charge storage. We highlight several key concepts in the computational design and tuning of 2D structures, such as controlled stacking, ion gating, interlayer pillaring, and heterostructure charge transfer.The process of creating and adjusting pores within graphene sheets is vital for effective molecular separation. Simulations show the power of controlling the offset distance between layers of porous graphene in precisely regulating the pore size to enhance gas separation and entropic selectivity. This strategy of controlled stacking extends beyond graphene to include covalent organic frameworks (COFs) such as covalent triazine frameworks (CTFs). Experimental assembly of the layers has been achieved through electrostatic interactions, thermal transformation, and control of side chain interactions.Graphene can interface with ionic liquids in various forms to enhance its functionality. A computational proof-of-concept showcases an ion-gating concept in which the interaction of anions with the pores in graphene allows the anions to dynamically gate the pores for selective gas transport. Realization of the concept has been achieved in both porous graphene and carbon molecular sieve membranes. Ionic liquids can also intercalate between graphene layers to form interlayer pillaring structures, opening the slit space. Grand canonical Monte Carlo simulations show that these structures can be used for efficient gas capture and separation. Experiments have demonstrated that the interlayer space can be tuned by the density of the pillars and that, when fully filled with ionic liquids and forming a confined interface structure, the graphene oxide membrane achieves much higher selectivity for gas separations. Moreover, graphene can interface with other 2D materials to form heterostructures where interfacial charge transfers take place and impact the function. Both ion transport and charge storage are influenced by both the local electric field and chemical interactions.Fullerene can be used as a building block and covalently linked together to construct a new type of 2D carbon material beyond a one-atom-thin layer that also has long-range-ordered subnanometer pores. The interstitial sites among fullerenes form funnel-shaped pores of 2.0-3.3 Å depending on the crystalline phase. The quasi-tetragonal phases are shown by molecular dynamics simulations to be efficient for H2 separation. In addition, defects such as fullerene vacancies can be introduced to create larger pores for the separation of organic solvents.In conclusion, the key to imputing functions to 2D carbonaceous materials is to create new interactions and interfaces and to go beyond a single-atom layer. First-principles and molecular simulations can further guide the discovery of new 2D carbonaceous materials and interfaces and provide atomistic insights into their functions.