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A similarity between chemical reactions and self-assembly of nanoparticles offers a strategy that can enrich both the synthetic chemistry and the nanoscience fields. Synthetic methods should enable quantitative control of the structural characteristics of nano-particle ensembles such as their aggregation number or directionality, whereas the capability to visualize and analyze emerging nanostructures using characterization tools can provide insight into intelligent molecular design and mechanisms of chemical reactions. We explored this twofold concept for an exemplary system including the polymerization of bifunctional nanoparticles in the presence of monofunctional colloidal chain stoppers. Using reaction-specific design rules, we synthesized chain stoppers with controlled reactivity and achieved quantitative fine-tuning of the self-assembled structures. Analysis of the nanostructures provided information about polymerization kinetics, side reactions, and the distribution of all of the species in the reaction system. A quantitative model was developed to account for the reactivity, kinetics, and side reactions of nanoparticles, all governed by the design of colloidal chain stoppers. This work provided the ability to test theoretical models developed for molecular polymerization. [ABSTRACT FROM AUTHOR]