Size monodisperse silver nanocrystals have been stabilized by chemisorption of long-chain alkane thiols incorporating a receptor site. When dispersed in a suitable solvent these nanocrystals recognize and selectively bind a long-chain alkane incorporating two complementary substrate sites and are noncovalently linked. The nanocrystal aggregates formed as a result have been studied by NMR, FT-IR, and dynamic light scattering. As a consequence, it has been possible to characterize the interactions between the receptor and substrate sites that lead to nanocrystal aggregation. It has also been possible to gain insights into the factors that affect the size, shape, and internal structure of the nanocrystal aggregates formed. An important insight is that the kinetics of nanocrystal aggregation, and as a consequence the structure of the nanocrystal aggregates formed, depends on the number of receptor sites at the surface of a nanocrystal.