Research shows that computer-based simulations and animations are especially helpful in fields such as chemistry where concepts are abstract and cannot be directly observed. Bio-Organic Reaction Animations (BioORA) is a freely available 3D visualization software program developed to help students understand the chemistry of biomolecular events. This paper introduces BioORA, presents a qualitative research study exploring the different features of the program that faculty and students perceive as educationally beneficial, and addresses the value of using 3D simulations in education. Findings reveal faculty and student experiences with the software as well as aspects of their experiences within the field, and also suggest how other software programs can be developed and used for education.