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The properties of materials can be created and improved either by confining their dimensions in the nanoscale or by controlling their nanostructure. We have combined these two concepts, and here we describe a new class of nanostructured nanosized materials that show ordered phase-separated domains at an unprecedented molecular length scale. Scanning tunnelling and transmission electron microscope images of monolayer-protected metal nanoparticles, with ligand shells composed of a mixture of molecules, show that the ligands phase-separate into ordered domains as small as 5 Angstrom. Importantly, the domain shape and dimensions can be controlled by varying the ligand composition or the metallic core size. We demonstrate that the formation of ordered domains depends on the curvature of the underlying substrate, and that novel properties result from this nanostructuring. For example, because the size of the domains is much smaller than the typical dimensions of a protein, these materials are extremely effective in avoiding non-specific adsorption of a variety of proteins.