Connected Chemistry (named CC1 to denote Connected Chemistry Chapter 1) is a computer-based environment for learning the topics of gas laws and kinetic molecular theory in chemistry. It views chemistry from an "emergent" perspective, how macroscopic phenomena result from the interaction of many submicroscopic particles. Connected Chemistry employs agent-based models built in NetLogo (Wilensky, NetLogo, Northwestern University, Evanston, 1999a), embedded in scripts that structure and log the students' activities. A conceptual framework was developed to structure students' experiences and learning through exploring the models. The framework describes three spheres of knowledge (conceptual, symbolic and physical) and four forms of access to understanding the system (submicro, macro, mathematical and experiential). Activities were designed to help students build an integrated view of the chemical system, by focusing on understanding within each form of access, and promoting transitions between the spheres of knowledge. The macro-level descriptions were used to bridge between the three spheres and support these shifts. The conceptual framework for the Connected Chemistry curriculum is discussed and demonstrated. Further development directions are suggested.