Post Tagged with: "organic chemistry"

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.

By August 19, 2013 17 comments chem 2.0, chemical education

A year of OChem, as told by a blog stat graph

**Today’s post is a guest post by James Ashenhurst, author of the fantastic blog Master Organic Chemistry**

If Google Analytics is any guide, here’s what a year of teaching organic chemistry looks like.

The typical year’s forecast calls for growing concern from September onwards, peaking in a mid December monsoon. This is followed by a cold January lull, which collides with a hot front of anxiety in February and grows in intensity towards a thundering, extended period of hail from mid-April to mid-May.  Then all becomes calm. Sunshine peeks through the summer clouds, and the months from late May through early August are breezy, steady, and smooth.  Then the cycle begins again.

I’m interpreting seasonal local maxima as popular midterm times; it’s pretty neat that the results show this (and the Thanksgiving lull). Does this jive with your experience, readers?

P.S. A big double fist bump to @azmanam and the other kind folk at the Chemistry Blog for letting me post this and for helping MOC to be such a successful project (600K visitors this year & counting). Thanks!

By September 14, 2012 2 comments chem 2.0, chemical education

Eye-Test Abstracts

Readers: have you noticed the new trend in graphical abstracts? Seems to me that more and more choose the “coloring book” route. (I’ve written about this a few times at Just Like Cooking, but I’ve decided to up the ante and broaden the discussion audience over here)

When designing talks and posters, most chemists will tell you to use color sparingly, say, to accent a particular functional group, or to draw the eye to a key concept. Many shy away from color schemes that won’t translate well at a distance, such as white-on-black, or black-on-orange…

J. Am. Chem. Soc., ASAP, 2012

Marketers have long understood that human beings respond strongly to primary colors; it’s no secret that Coca-Cola and McDonald’s both advertise with bright red signs. But for organic chemistry? If your reaction or concept truly breaks new ground, won’t people recognize it without all the visual hype?

Angew. Chemie, ASAP, 2012

I’m not entirely sure what’s driving this – desire to have your chemistry noticed on a crowded page? Viewers transitioning to mobile phone apps, where your abstract (presumably) fights for space amongst highly-colored games and ads? ‘Artistic’ sensibilities?

Organometallics ASAP, 2012

Readers, what are your thoughts? Do you color in your reaction schemes? Do you find colored abstracts appealing, or annoying?

Update (04/20/12) – Almost forgot Nature Chem’s coverage of the abstract issue. Thanks, Stu!

By April 20, 2012 10 comments Uncategorized

Calvin and Hobbes on Chemistry

Ok, so maybe they were originally talking about his math homework… but the joke’s still funny 🙂

By May 5, 2010 2 comments fun, synthetic chemistry