A key to the exploitation of nanoparticle-structured materials for chemical and biological applications is the ability to synthesize and assemble the nanoscale building blocks controllable desired size, shape, composition and spatial properties. We have been investigating molecularly engineered and mediated synthesis and assemblies of nanoparticles as a general bottom-up pathway towards this ability. This presentation focuses on the discussion of recent findings of the synthesis and assembly of gold, alloy and magnetic core@shell nanoparticles. The size, shape, composition, and spatial properties of the nanoparticles and their assemblies are controllable by a combination of molecular/polymeric mediators or templates in solutions. The electronic, optical and magnetic properties of the nanoparticles and assemblies are fine-tunable by manipulating the composition of the nanoparticles, the structure of the mediator, and the interparticle molecular interactions. Recent results from the study of these nanostructured materials for chemical and biological applications will also be discussed.