Writing an Online Organic Chemistry Quiz

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.

NOT what my exam questions will look like...

NOT what my exam questions will look like…

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.


  1. We do a blackboard safety quiz and use a ‘pick the hot spot’ style question with photos. The students have to click the area of the photo, a lab scene, where something hazardous is. You could use similar if your software allows to get students to click where the incoming curly arrow lands. The quiz recognises a click n the vicinity of the image coordinates specified as the correct area hot spot.

  2. This is a common-ish issue with many SMILES implementations, as I understand it. There are some “Canonical SMILES” algorithms which should produce consistent representations for the same structure, though ChemDraw apparently doesn’t support them.

    The InChI itself (not the key) should be canonical. This InChI representation is human readable, but there’s a bit of a learning curve. The InChI string is also quite a bit longer than either SMILES or InChI Key.

    If you wanted to do some hacking on Moodle, there might be a way to incorporate ChemDoodle Web Components, which is freely licensed ( http://web.chemdoodle.com/ ). Simple structure sketching and answer checking should be quite doable with this. For mechanism etc., there may be more of a challenge. I think you would be able to extract all molecules and “shapes” (arrows, etc) from the drawing applet and then check the “connectivity” described by the curly arrows. If you wanted a student to draw a molecule *and* give a mechanism on that molecule, things would be complicated by a need to canonicalise the atom IDs before checking curly arrows. It sounds like a bit of a nightmare.

    I wonder if a simpler approach to mechanism would be to present the question with all bonds and atoms numbered/alphabetised, with the student asked to enter, as text, the “from” and “to” identifiers for each curly arrow they propose.

    • Thanks, I’ll look into ChemDoodle. I don’t know that I’ll have the right administrator permissions to do much hacking, but maybe IT will be willing to lend me a hand 🙂

  3. I’m using desire to learn (D2L) as an LMS, and have come to the conclusion that arrow pushing and longer answer questions are things better evaluated manually with pen and paper.

    If time spent grading is the issue you are trying to address, perhaps try some peer evaluation methods or buy some graduate students pizza and *soda* to lend a hand?

    If getting real-time feedback to the students is the issue, perhaps releasing an answer key is the way to go.

    • Good points. I have an overall master plan into which this LMS-graded quiz thing would fit. I’ll talk more about that in a later blog post. Stay tuned 🙂

  4. another option says:

    chemaxon’s marvin for javascript will give consistent SMILES I think.

    Easiest method:
    Draw your structure and click get

    Silghtly harder method.
    Click on the save icon on the top left, then choose smiles as your option.

  5. Rather than reinvent the wheel, you might look at using Sapling Learning. You don’t need whole university or department buy-in, I use it for my biochemistry and organic classes as my own option, and it has full structure drawing and many, many pre-generated questions with hints using those structures. It costs each student $30; I have them buy used textbooks and use the money they save on Sapling– money well worth it. I think SMILES will likely be an impediment to student learning, rather than going to be more fully-fleshed solution.

  6. Nice writeup and a good illustration of an important limitation of SMILES.

    As suggested in the comments, there is something called “Canonical SMILES”. Open Babel (open source software) has one implementation (http://openbabel.org/wiki/Main_Page). Canonical SMILES generated _within_ the same software package for the same molecule will always be identical. However, SMILES generated for the same molecule by two different packages can, and usually do, differ.

    InChI does away with this confusion around canonicalization.

    InChI keys will be canonical (except in very rare cases) and have the advantage of being fixed width. InChI itself is of course canonical, but like SMILES, length can vary.

    I’ve written a high-level overview of InChI and InChI Key.

    It goes without saying that both InChI and SMILES should be hidden from students – they’ll only interfere with learning the rest of the material at the undergrad level.

    By the way, this idea in general sounds interesting. If you’d like to shoot some ideas around, drop me a line.

    • Thanks for the helpful feedback. I’m out of town right now, but I will definitely be getting in touch with you to talk about some of these issues. Thanks for the very helpful links, too 🙂

  7. Hi Az 🙂

    Just to let you know – we are discussing your blog entry at CF:


  8. Organic chemistry is extremely interesting for me because of its comprehensively related theory. Unfortunately drawing molecular structure is kind of pain. Drawing structure by hand is a lot easier and faster than by software.

  9. I’ve developed a suite of question types specifically for organic chemistry instruction. You can check them out in action at http://www.easyochem.com. I use Marvinsketch by Chemaxon for some of them. Marvinsketch can generate extended and unique smiles strings so stereochemistry (R/S and E/Z and o/m/p) is not a problem. You can either use my site ($10/per student) or if you email me I can send you the question types you can install on your own moodle server.

    Here’s an brief overview of the question types;

    Electron Pushing/Curved arrows – Students provide curved arrows in mechanisms and resonance structures. (e.g. Provide curved arrows sowing the flow of electrons in the for the following mechanism?)
    Name-to-Structure – Students must draw a structure based on a question (e.g. Draw (R)-2-butanol in the applet below?)
    Newman Projections – Students construct a Newman projection based on a question. (e.g. Draw (R)-2-butanol looking up the C2-C3 bond?).
    Fischer Projections – Students construct a Fischer projection based on a question. (e.g. Convert the following structure in a Fischer projection using the template below?).
    Reactant/Product/reagent Prediction – Students must complete a reaction scheme drawing either the reactants, products or reagents.
    Selection Quesition – Students must select predefined atoms, groups or molecules. (e.g. Select all chiral centers in the following structure?).
    Lewis Structures – Students must provide lone pairs, radical electrons or charges are various atoms.


  10. We’ve been drawing structures and matching answers in our in house system for almost 20 yrs, currently using Moodle. We started with free applet JME and now JSME. Unique SMILES no matter how it’s drawn.

  11. The quiz recognises a click n the vicinity of the image coordinates specified as the correct area hot spot.

  12. Pingback: Draw Molecules In Blackboard Learn - BlackboardHub.Com

  13. Thanks for the idea, I like it. I’ll ask around in IT if this is doable.. Instagram pva accounts

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