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The unique strength observed in molecular thin films consisting of assemblies of nanoparticles encoded with short organic chains opens an intriguing new realm of controllable materials. Here the fundamental mechanisms underlying this unique mechanical strength are probed by molecular dynamics simulations. Using nanoparticles encoded with short hydrocarbon chains, we show that the mechanical response and failure of single nanoparticle thick membranes depend on subtle changes of the coating. Extremely high moduli were observed in agreement with experiment. We calculate Young's modulus for the membrane system based on properties of the individual components and find that ligand end-group interactions explain the observed changes in mechanical properties. Specifically, for dodecanethiol chains on 6 nm diameter gold cores, Young's modulus is 2.5 GPa for CH_{3} terminated chains and increases by 50% when end groups are replaced by COOH.