Two Challenges of Molecular Visualization

1. Designing for learning multiple molecular representations

Molecular representations embed conceptual knowledge that make them useful for problem solving and communication. The use of multiple molecular representations (Figure 1) is common practice in chemistry. For example, planning a chemical synthesis begins by building a 3D model of the target to study its reactivity, and the synthesis is documented with sequential 2D drawings known as Lewis structures. Chemistry learners need to understand the conventions of the different representations to translate between them and integrate the complementary information they provide. In turn, educational designers need to support the learners’ development of representational competence.

Multiple representations of glucose.

Figure 1. Multiple representations of glucose.

Research into how students understand multiple molecular representations is being conducted by Dr. Hsin-Kai Wu at the National Taiwan Normal University. Her work has revealed several ways educational designers can scaffold learning from multiple representations (1).
Integration and dynamic linking
Multiple representations should be shown together and changes in one representation should simultaneously affect the other. For example, when teaching how to balance chemical equations, the number of molecules pictured should update as a student manipulates the chemical formula.
Model progression
Present concrete presentations such as 3D models before more abstract types such as Lewis structures. Learners use the more concrete representation as the basis for understanding the more abstract.
Break down a complex representational task into a series of steps. Show a reaction mechanism as a series of static images and explain the relevant features, then show a dynamic animation of the overall process.
Active engagement
Add interactivity into graphics with multiple representations to promote active learning and retention.

2. The need for specialized software

The Architecture of Molecules by Linus Pauling and Roger Hayward (W.H.Freeman & Co, 1964), features 57 pastel drawings of 3D molecular structures created by Hayward over the course of his two-decade friendship with Pauling. Hayward was an expert draftsman who meticulously measured and rendered the structures based on Pauling’s calculations. A single drawing could take a week to complete.

Today, biomedical illustrators are fortunate enough to have specialized software to create molecular graphics, which makes their more efficient production possible. A subset of chemical drawing applications is provided in Figure 2.

Molecular visualization software

Figure 2. Chemical applications and where they are located within a gradient of functionality from 2D graphics drawing to 3D modelling.

A suite of applications may be required to produce a single image. For example, a workflow might consist of

  1. modelling molecular geometry in Spartan;
  2. importing the geometry into ePMV/Maya or ChemDoodle, customizing the visual appearance, and rendering an initial image;
  3. compositing and further editing in Adobe Photoshop;
  4. final layout and labeling in Adobe Illustrator.

A working knowledge of chemistry or related discipline is a strong asset in this process to help guide decisions about tool choice and molecular representation, and to ensure content accuracy.


  1. Wu, H.-K., & S. Puntambekar. 2012. Pedagogical Affordances of Multiple External Representations in Scientific Processes. Journal of Science Education and Technology 21(6), 754–767.