Trying to Make Sense out of Chemical Structures

by Christopher Iceman

So when I was initially informed of my CITE fellowship I had some safe ideas and some wild ones as well. I was happy to find that the folks  at CTL like living a bit on the edge and encouraged me to go for the far fetched (and fun) plan. The motivation for my project is  helping students conceptually and spatially grasp the idea of molecules and their geometries. This is typically a stumbling block for first  semester chemistry students and I’ve always had my eye on virtual reality, 3D and other technologies for chemical viewing.

Newish to the world of 3D stereographic tech is the Oculus Rift, a goggle based 3D platform that stereographically (think 3D at the movies)  presents images so that your brain sees depth in the flat images. This platform has mostly been employed to gaming and one of those  games, Minecraft, is almost ubiquitous amongst youngsters these days. This sandbox world generator allows you to “mine” or create from  mined resources all types of lego like structures and worlds. My own kids love it. So far it has been a challenge for me to really get into it,  until talking with my CITE coordinators when we realized it may be possible to make chemical structures in the game, life sized and  wonderful.

In addition to other molecular viewing software available for the Oculus (Chimera and iView) this suite of visualization tools is being  developed into a laboratory for students to use to understand why water (with three atoms…H2O) is a “bent” molecule but transforms via  the tetrahedral electronic structure group. These principles are conserved up the entire chain of structures all the way to DNA and proteins. Having that baseline understanding allows students to grasp structure function relationships and hopefully a big chunk of chemistry along  the way.

Although we aren’t quite there yet we are getting close.    Current struggles include getting the python programming version of Minecraft  (which uses the python API) to communicate with the Oculus goggles so that students can construct all of these complex molecular shapes  with ease.    I’ve recently invested in another platform, the Raspberry Pi, to assist in these endeavors and that has been a lot of fun too.    I am  a tech geek at heart and so glad to be playing in this world.    I hope that my students are soon doing the same!

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