In order to contribute to the access of blind and visually impaired (BVI) people to the study of chemistry, we are developing Navmol, an application that helps BVI chemistry students to interpret molecular structures. This application uses sound to transmit the information about the structure of the molecules. Navmol uses voice synthesis and describes the molecules using the clock polar type coordinates. In order to help the users to mentally conceptualize the molecular structure representations more easily, we propose to use 2D spatial audio. This way, the audio signal generated by the application gives the user the perception of sound originating from the directions of the bonds between the atoms in the molecules. The sound spatialization is obtained with head related transfer functions. The results of a usability study show that the combination of spatial audio with the description of the molecules using the clock reference system helps BVI users to understand the molecules’ structure.