Permeation of small molecule solutes through thin films is typically described by the solution-diffusion model, but this model cannot predict the effects of nanostructure due to self-assembly or additives. Other models focusing on diffusion through isolated nanopores indicate that confining permeation to channels slightly larger than the size of the solute can lead to an increased influence of solute−pore wall interactions on permeation rate. In this study, we analyze how differences in polymer nanostructure affect the relative contributions of solute size and polymer−solute interactions on transport rate. We compared the diffusion rates of several small molecules through two polymer thin films: A cross-linked, homogeneous film of poly(ethylene glycol phenyl ether acrylate) (PEGPEA) and a graft copolymer with a poly(vinylidene fluoride-co-chlorotrifluoroethylene) (P(VDF-co-CTFE)) backbone and PEGPEA side chains that self-assemble into continuous ∼1−3 nm PEGPEA domains through which transport occurs. We correlated these rates with the size of each solute and its chemical affinity to PEGPEA, as measured by the difference between their solubility parameters. Diffusion rate through the homogeneous polymer film was controlled by solute size, whereas diffusion rate through the copolymer was strongly controlled by the difference between the solubility parameters. Furthermore, permeation selectivity between two selected molecules was 2.5× higher for the nanostructured copolymer, likely enhanced by the nanoconfinement effects. These initial results indicate that polymer self-assembly is a promising tool for designing polymeric membranes that can differentiate between solutes of similar size but differing chemical structures. R egulating permeation through materials is crucial for many applications, including selective membranes, controlled drug delivery, and packaging. 1−7 Permeation selectivity is especially critical in membrane separations. Membranes that are capable of separating small molecules of similar size by their chemical structure can potentially have great impact in drug manufacture 8−10 and the petrochemical industry. A better understanding of how to modulate the permeation of small molecules through polymers by manipulating chemical interactions and nanostructure can open up new avenues to such membranes.Most current membrane selective layers are homogeneous polymers 11−13 where permeation is described by the solutiondiffusion model. The solute dissolves in the polymer on the feed side, diffuses, and desorbs into the permeate. The molar flux J A of solute A through the polymer film is given bywhere S A , D A , and P A are the solubility, diffusivity, and permeability of A in the polymer, respectively, z is the polymer film thickness, and ΔC A is the concentration difference between the feed and permeate. The permeability of a solute increases with increasing solubility in the polymer and decreasing solute size. This model works well for most gas separation membranes 11−14 and has been adapted for desalinatio...