The focus of this study is students' learning with a Connected Chemistry unit, CC1 (denotes Connected Chemistry, chapter 1), a computer-based environment for learning the topics of gas laws and kinetic molecular theory in chemistry (Levy and Wilensky 2009). An investigation was conducted into high-school students' learning with Connected Chemistry, based on a conceptual framework that highlights several forms of access to understanding the system (submicro, macro, mathematical, experiential) and bidirectional transitions among these forms, anchored at the common and experienced level, the macro-level. Results show a strong effect size for embedded assessment and a medium effect size regarding pre-post-test questionnaires. Stronger effects are seen for understanding the submicroscopic level and bridging between it and the macroscopic level. More than half the students succeeded in constructing the equations describing the gas laws. Significant shifts were found in students' epistemologies of models: understanding models as representations rather than replicas of reality and as providing multiple perspectives. Students' learning is discussed with respect to the conceptual framework and the benefits of assessment of learning using a fine-tuned profile and further directions for research are proposed.