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Mesoporous adsorbents such as MCM-41 are promising materials for use in the separation stage of carbon capture and storage (CCS). Using molecular simulation, we investigated the effectiveness of functionalizing MCM-41 with organic surface groups for CO2/N2 separation from a typical power-plant flue-gas stream. The adsorption isotherms for pure CO2 and ternary flue-gas mixtures were determined in functionalized MCM-41 using grand-canonical Monte Carlo (GCMC) simulations. Both CO2 uptake capacities and CO2/N2 selectivities were studied in order to predict the performance of functionalized materials in the removal of CO2 from flue gases. The effects of pore size, surface group concentration, alkyl chain length, surface group rigidity, and concentration of polar amino moieties on adsorption were studied in detail. Surface functionalization of MCM-41 resulted in materials exhibiting a wide range of CO2/N2 selectivities. Insight from these simulations allowed for the design of a tailor-made surface group encompassing favorable characteristics that was predicted to perform significantly better than the unfunctionalized MCM-41 material in carbon-capture applications.