Augmented Chemistry (AC) is an application that utilizes a tangible user interface (TUI) for organic chemistry education. The empirical evaluation described in this paper compares learning effectiveness and user acceptance of AC versus the more traditional ball-and-stick model (BSM). Learning effectiveness results were almost the same for both learning environments. User preference and rankings, using NASATLX and SUMI, showed more differences and it was therefore decided to focus mainly on improving these aspects in a re-design of the AC system. For enhanced interaction, keyboard-free system configuration, and internal/external database (DB) access, a graphical user interface (GUI) has been incorporated into the TUI. Three-dimensional (3D) rendering has also been improved using shadows and related effects, thereby enhancing depth perception. The re-designed AC system was then compared to the old system by means of a small qualitative user study. This user study showed an improvement i...