An app for visualizing chemistry

Wednesday, November 24, 2021

In the field of chemistry, one challenge that students commonly encounter is difficulty visualizing molecules, their arrangements and relationship between atoms in space. While there are some tools already being used to address this difficulty, they each have some disadvantages as well. Molecular model kits are bulky, expensive, require students to spend valuable time building each molecule, and are also limited by the number of pieces in the set. Online visualization tools also exist, however, simply looking at a molecule on a screen removes some of the tangibility and depth perspective that physical models provide.

Looking for an alternative, Thorsten Dieckmann, a biochemistry professor at the University of Waterloo has been developing virtual reality (VR) and augmented reality (AR) molecular visualization approaches. Using VR and AR could be a good compromise between tangible models and computer models – providing the variety of content possibilities of computer models, while introducing the depth and tangibility of model kits into the student experience.

A phone showing an amino acid in artificial reality when pointed at an image of an atom

The AR or VR models developed by Dieckmann will show students interactive 3-dimensional projections of molecules. Professor Dieckmann envisions the AR version used on student’s personal devices in large undergraduate classes, so that students can use their own phones to see the molecules floating in front of them. The VR version would most likely be limited to small upper year undergraduate and graduate level classes, due to the limitations of VR headset numbers and space.

Thorsten Dieckmann holding up images for the AR app to identify

I find that when teaching biochemistry, one of the major roadblocks is to properly visualize spatial relationships. It’s always somewhat abstract,” said Professor Dieckmann. “We want to see if using augmented reality actually makes a difference in terms of teaching and student learning.

The AR app, developed by co-op student Shawna Poechman, has been designed to use a small graphic which indicates to the app which model to display. These pictures could be incorporated into course notes, or displayed on a projector for use in lectures. During class, this would allow professors to supplement their teaching, and work with students using a variety of 3-D models.

The AR and VR tools can be used across many different branches of chemistry, for example: comparing stereocenters and enantiomers in organic chemistry; looking for symmetry elements in inorganic chemistry; or looking at structure function relationships in biochemistry classes.

Professor Dieckmann has also demonstrated that this modeling can be extended past just chemistry, to any model that has a 3-D .obj file describing it. He envisions earth science students being able to see the fluvial pathways in a water basin while virtually standing in the watershed, or seeing the remote site that a sample they are looking at in the lab was obtained from. For biology classes, Professor Dieckmann has already modeled the progression of an egg turning into a tadpole and then a frog in the AR app as an example application.

A student looking at a frog artificial reality image on a computer

Currently the prototype app is functional on both Windows and Android systems. While the app is still evolving to stay up to date with the quickly evolving advances in AR and VR, Professor Dieckmann hopes that the app can be implemented for students to use in their studies soon.

This project was funded in part by the Dean’s Undergraduate Teaching Initiative, an investment of $500,000 towards the improvement of undergraduate teaching and learning activities.