At the molecular level, chemical processes involve the rearrangement of atoms in space and time. Students often struggle with visualizing the 3D spatial characteristics of molecules and transition states, as well as recognizing the dynamic nature of chemistry. Both visual spatial skills and representational competence should be explicitly trained to avoid misconceptions regarding how molecules approach each other in space, and how chemical reactions occur in time. Visual spatial skills and representational competence are critical in the path to master organic chemistry. This is especially true for visually demanding reactions involving several stereocenters such as the Diels-Alder reaction. This project was focused on the development of a Virtual Reality Learning Environment (VRLE) where students could practice their spatial skills while acquiring representational competence, to support their ability to extract, represent, and predict stereochemical outcomes for the Diels-Alder reaction. This dissertation begins with the compilation and operationalization of a network of pedagogical frameworks that support and reinforce each other synergistically to ground the design and development of a VRLE. From the frameworks compiled, a model was created to recognize 3D characteristics from 2D representations of transition states, centered on the use of a hexagonal prism as an external reference frame. Following the description of the applications and limitations of the Hexagonal Prism Reference Model (HPRM), this project describes the technical and mathematical considerations that were necessary to build the VRLE, as well as a novel tool to convert computational chemistry calculations into formats compatible with 3D modeling software. Finally, a qualitative study was conducted to compare visual spatial skills, challenges and strategies between graduate and undergraduate students as they extract, represent, and predict stereochemical outcomes for the Diels-Alder reaction. Therein, a profile of the most prominent visual spatial skills for both groups was described. Afterwards, this study described how multiple and simultaneous visual spatial skills compose different spatial strategies and how these strategies were applied to visualize Diels-Alder reaction outcomes. A set of spatial difficulties and an optical illusion were characterized. The results revealed the importance of Visual Orientation and Visual Discrimination to recognize spatial characteristics, identify accurate representations, and predict stereochemical outcomes. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com.bibliotheek.ehb.be/en-US/products/dissertations/individuals.shtml.]