chem 2.0

#WheresCarmen at ACSIndy?

C&E News reporter Carmen Drahl is covering the ACS Conference in Indianapolis in September, and she needs your help. She’s crowd sourcing which events to cover. You can vote on the C&E News Facebook page. Help shape the journalistic coverage of ACSIndy!

By August 29, 2013 1 comment chem 2.0, fun, science events

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 18 comments chem 2.0, chemical education


Chemis-Trees have been all the raged on the chemistry Reddit this season. A select few are shown below. If you have one feel free to leave it in the comments and we’ll add it to the list.

from The University of Malta (@detox29)


from (@Fluorophore1)


from (@KeithLav)


from (@heckler_heckler)


from (@wych_)


from (@Tepaps)

By December 21, 2012 2 comments Chemistry Reddit - Chemit

Reality Show of Chemistry Undergrads

Reality TV for Chemists

MIT has fully embraced the power of the internet to educate outside the walls of its lecture halls. It offers anyone with an internet connection the ability to watch lectures from a large variety of classes through its OpenCourseWare (OCW) initiative. However, they have taken it a step further this year, and present the travails of a small cohort of chemistry freshman as they learn basic fundamental lab techniques in a crammed 4-week laboratory course. The top students in the class will be offered an opportunity to do research with a faculty member.

In many ways this is a smart program. It’s a nice way to make sure that undergrad researchers have basic skills before they ever step into a research lab. Below I’ve included their trailer and episodes 1 and 2 for your viewing pleasure. New episodes can be found at ChemLab Boot Camp as they get placed on the web.

More info:


Episode 1: Great Expectations

Episode 2: Overwhelmed

It should be fun seeing how this pans out.


By September 25, 2012 0 comments chem 2.0