The Web is now a standard tool for information access and dissemination in higher education. The prospect of Web-based, simulated learning platforms and technologies, however, remains underexplored. We have developed a Web-based tutorial program (ChemVoyage) for a third-year organic chemistry class on the topic of pericyclic reactions to illustrate this approach with scaffolding and visual auxiliaries. The questions in the tutorial are tiered to simulate the pyramidal structure of knowledge and interlinked to form concept maps required to aid student learning. Visual cues and remedial exercises are linked to advanced questions to facilitate integration of knowledge. Students advance through lower levels to reach higher levels at their own pace. This Web-based learning program provides flexible delivery for the learner and records the learning history of an individual user for the instructor. The diagnostic information helps with reflective teaching and facilitates independence of the learner. Student feedback shows that this is an effective approach in improving their learning outcomes.