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 NASA-TLX 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 in subjective opinions a out the system's ease of use and ease of learning.