Ion beam synthesis has played a significant role in fabricating metallic or semiconducting nanocrystal arrays in glass for their optical or magnetic properties, but basic questions remain unanswered. What are the microscopic mechanisms that control nanocluster growth, determine their density and size distributions? To what extent can we control these processes in order to tailor the properties? We demonstrate the role of chemistry (redox properties; charge state equilibrium modified by irradiation) in Ag nanocluster nucleation and growth processes in glasses and extend the conclusions to PbS nanocluster synthesis. In the latter case, we show how charge state differences affect diffusion and growth and devise a strategy that produces PbS quantum dots emitting intense photoluminescence at 1.5 μm. In the course of this work, we also showed that the lognormal shape of cluster size distributions signals a loss of information as to the formation process and hence loss of property control.