Recent advancements in educational technologies have led to an explosion of visualization software for teaching and learning science, particularly chemistry. To varying degrees, visualization tools help teachers and students perceive the imperceptible objects and phenomena of the chemical world. Although some visualization tools have seen great success in the classroom, others have had little impact on student learning and understanding. The present talk explores a novel cognitive model that both motivates the use of computer-based visualization tools for teaching chemistry and explains the variability in learning outcomes that result from their use. First, I argue for a more complete model of teaching and learning in chemistry that empirically defines the role of visualization tools in the classroom. Using data from tandem psychometric and protocol studies, I identify some unique difficulties with learning chemistry that constrain the possible affordances of visualization tools.