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One reason that metal nanoparticles encapsulated in metal-organic frameworks are of interest is that confinement effects on the particle size and shape may lead to superior catalytic activity. The interior of a metal-organic framework has the potential to influence nucleation and aggregation of metal nanoparticles and to strongly affect their in situ shape and electronic properties. We apply density functional theory and ab initio molecular dynamics (AIMD) to model the nucleation and diffusion of Cun (n = 1-19) clusters on the tetratopic 1,3,6,8-(p-benzoate)pyrene (TBAPy4-) linkers of NU-1000 frameworks. We find that Cu atoms and Cu clusters are stabilized by the TBAPy linker, especially by the edge site of aromatic rings. The stabilization increases when the Cu cluster interacts with two linkers. We identified the most favorable site for Cu cluster adsorption as the window site that connects the c pore and the triangular pore. A Pt atom is found to bind much more strongly than a Cu atom on the TBAPy linker, and AIMD simulations show that this promotes Pt atom diffusion from the center of a Cu15 cluster to the interface between the linker and the cluster. The strong interaction between a Pt atom and a linker is attributed to the greater metal-to-linker charge transfer.