Currently, first-year chemistry students learn about three-dimensional molecular structures using a combination of lectures, tutorials, and practical hands-on experience with molecular chemistry kits. We have developed a basic 3D molecule construction simulation, called <i>MolyPoly</i>. The system was designed to augment the teaching of organic chemistry by helping students grasp the concepts of chemistry through visualisation in an immersive environment, 3D natural interaction, and audio lesson feedback. This paper presents the results of a pilot study conducted with a first-year chemistry class at the University of Tasmania. Participating students were split into two groups: <i>MolyPoly</i> group (no lecturer in the sessions) and traditional classroom group during the four in-semester classroom sessions over a period of two weeks. We present our comparative analyses over the knowledge-based pretest and posttest of the two groups, by discussing the overall improvement as well as investigating the improvement over the test questions with different knowledge difficulty levels and different required spatial knowledge.