Lately, I’ve been very interested in using my university’s Learning Management System (we use Moodle, others use Blackboard or something else) to administer quizzes to my students, but as an organic chemist, I’ve been hesitant to do so. Primarily because I don’t want to ask a bunch of multiple choice questions. That’s not what my exam will be. Most of my exam answers will be structure based, so any LMS-administered quiz would need to accept structure-based answers.
I know some publishers have platforms for just this, but our university doesn’t subscribe to the service. So in some respects, I’m admittedly reinventing the wheel here.
At first I thought the LMS would be able to grade my students’ work if they type in the IUPAC name for each structure. But many of the structures have IUPAC names which can be rather large and/or outside of the scope of IUPAC nomenclature my students learn. And our ChemDraw license does not include the structure-to-name feature. So I needed something else.
I thought SMILES would be a good choice. SMILES is a condensed version of the structure, almost human readable, and ChemDraw can copy a structure directly in SMILES format. Perfect! I like the human readable aspect, as students can glance through their SMILES to check for some potential errors.
So I wrote up a pilot quiz with tutorial videos. I coded the correct SMILES into the grader – as well as some of the common errors for feedback purposes – and released it to my students. For testing purposes, I also had them upload a .jpg version of the structure so I could check it visually myself if there were any discrepancies. I’m glad I did.
The first thing I noticed when looking at the responses is that most of the students got most of the tutorial questions incorrect! I didn’t understand why. All they had to do was follow along bond for bond with my tutorial video and get the correct answer. When I checked their .jpg structures, all of the structures appeared to be correct! What is going on?
After some testing of my own, I came to a disappointing conclusion: ChemDraw gives different SMILES for the same structure depending on the order in which you draw the bonds. If you start from the left side, you get one SMILES, from the right you get a different SMILES. Start in the middle, and you get a third SMILES still. Don’t believe me? Watch this, and try it yourself:
I’ve let the ChemDraw people know, and they said they’d pass my comments along to developers. I understand that all of these are valid SMILES, but I feel that one structure should give the same SMILES from ChemDraw, regardless of how the molecule happened to be drawn. So now, I’m going to use InChI Key for my grading system. It’s not human readable, but at least the same structure seems to give the same InChI Key regardless of how the structure is drawn.
I still haven’t figured out a convenient way to code arrow-pushing mechanisms or multi-step synthesis answers using this method. If anyone has any suggestions, let me know! It needs to be something unambiguous that the students can use and the non-chemistry quiz grading software can interpret the answer.