Students undertaking courses in the field of chemistry need to integrate their spatial skills and conceptual knowledge. However, model perception along with the understanding of spatial processes and spatial structures of molecules has been a cause of difficulty for students as conventional teaching methods cannot fully aid student comprehension. In this research, we propose a technological solution to aid the spatial learning process by automatically creating a link between two-dimensional (2D) representations of chemical structures and three-dimensional (3D) molecular visualization. The image of a chemical structure is acquired and processed on-the-fly for structure identification and 3D model generation. The 3D molecular model is simplified for real-time interactive rendering. The efficacy of the proposed solution in enhancing spatial ability of individuals is evaluated through an experiment on first year undergraduate students. Our analysis of the results suggests that virtual models and mobile applications are capable of narrowing the performance gap between students with different levels of spatial ability.