Articles by: azmanam

#ACSIndy Meetup Monday 6pm Kilroys

Just like the title says. 6-7pm Monday at Kilroys on the corner of Meridian and Georgia st, 2 blocks east of the convention center. See you there!


By September 7, 2013 0 comments fun

#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

#ChemSummer Carnival – Glow Sticks: How Do They Work?

Via Kenneth Freeman

Read other entries in the How Does it Work? series!

This post is part of the #ChemSummer carnival hosted by C&ENews and Rachel Pepling.

Everybody loves summer. And as the sun starts to set, and the fireflies twinkle, and bedtimes are some ancient school-day memory, you crack a glow stick and are amused for hours… and your parents have a way to keep an eye on you.

But how do these wonders of creation work? Why do I have to ‘break’ it before it lights up? How come it doesn’t last forever? Chemistry, my child. Chemistry.

If you were with me when we talked about how Cold-Activated Bottles work (go ask your dad what beer is), we talked about how alkenes absorb light in the ultraviolet region of the electromagnetic spectrum. The alkene will absorb one wavelength better than any others, and we call that λmax. As you chain more and more alkenes together in conjugation, the molecule will absorb longer and longer wavelengths of light, and λmax will increase with the number of pi bonds in conjugation.



Eventually with enough conjugated alkenes, λmax breaks the 400 nm barrier and starts absorbing visible light. Because of subtractive color, white light hits the object, the object absorbs light at λmax, and the rest of the light bounces off into your eye, so we see all the colors that remain after λmax is absorbed. So when lycopene in tomatoes has a λmax of 471 nm, the rest of the light reflected back looks red.

So that’s a bit on how color works, what about how light works?

via Jacobkhed

For something to radiate light, it needs to emit a photon. Incandescent light bulbs work by heating up a filament until it glows and emits photons as a result of the high temperature of the filament (incandescence). Glow-in-the-dark stickers and things that glow under a black light work because a chemical (a fluorophore) absorbs energy from ambient light and excites an electron. When this electron relaxes back down to its ground state, it emits a photon of light. If this relaxation takes a long time to occur, the sticker will continue to emit light even after the lights have been turned off (fluorescence and phosphorescence).

But a glow stick is different. It is similar to fluorescence in that an excited electron is relaxing down to a ground state and emitting a photon, but it is different in how that electron gets excited in the first place. A glow stick doesn’t glow because of incandescence or fluorescence or phosphorescence, it glows because of chemiluminescence. The energy used to excite the electron comes as a byproduct of a chemical reaction. Some chemical reactions release energy as they occur. Most of the time that energy is expressed as thermal energy (heat), but sometimes another molecule absorbs that energy and excites an electron. When the electron relaxes, it emits a photon.

So this sets us up to discuss what we need to make a glow stick. We need a chemical reaction which releases energy. We need a chemical which can absorb that energy and excite an electron. And that same chemical needs to emit a photon of visible light when that electron relaxes to the ground state.

Most modern glow sticks contain all of these components. The reaction which releases energy is the reaction of a diaryl oxalate with hydrogen peroxide. This produces 1,2-dioxetanedione as a highly unstable intermediate. This intermediate decomposes to two molecules of carbon dioxide and releases energy. The glow stick also contains an unreactive molecule which can absorb this energy and excite an electron. When the electron relaxes back to its ground state, it emits a photon. Depending on the structure of this molecule, different colors of glow can be achieved. When the reagents have been completely consumed and the reaction ceases, then no more energy is being released, and no more glowing occurs, and the glow stick goes dark.


But why do I need to break it first? Remember that this is a chemical reaction, and when the reagents have been consumed, the reaction is over. If the manufacturers were to mix all three ingredients together from the start, the reaction would occur during manufacturing and shipment, and by the time you open it the reaction would be complete – there’d be no glow. So we need some way to not have the reaction occur during shipment, and only occur when I’m ready for it to occur. So we need to physically separate the diaryl oxalate and the hydrogen peroxide from each other until we’re ready for glow. To achieve this, your glow stick is actually two concentric cylinders. The outer, flexible, plastic cylinder contains the diaryl oxalate and the dye molecule. Within this cylinder is an inner, glass cylinder containing hydrogen peroxide. Flexing the outer plastic cylinder causes the inner glass cylinder to break, releasing the hydrogen peroxide. When the hydrogen peroxide mixes with the diaryl oxalate, the reaction is able to occur and the glow stick starts glowing.


Will it really last longer if I put it in the freezer? Yes, kind of. The glow is a result of that chemical reaction. Reaction rates can be influenced by temperature. If the temperature is colder, the reaction proceeds slower. If the reaction proceeds slower, the energy is released over a longer period of time, and the glow lasts for a longer time. But if you’re handling the glow stick and waving it around and holding it in your hands, it will warm up pretty quickly and revert to its typical life time.

Glow sticks have a lot of very attractive benefits that have not gone unnoticed. A glow stick is water proof – as long as you don’t puncture the outer plastic tube, a glow stick will work just fine underwater. A glow stick does not need any batteries or external energy source to give off light. The light-emitting phenomenon is completely self-contained. It does not generate an appreciable amount of heat or give off sparks, and it is reasonably inexpensive and disposable. Given these benefits, it is considered the only safe light source to use following some kind of disaster scenario, natural or otherwise. There is no need for external power, and it can withstand most weather conditions. Who knew this little red ring around your neck was so important for first responders, too.

So is this how fireflies work, too? Kinda. Fireflies contain a molecule called luciferin which reacts with atmospheric oxygen to form a similarly strained cyclic 1,2-dioxetane. This decomposes to carbon dioxide and an excited state form of oxyluciferin which relaxes to its ground state and emits that characteristic yellowish glow of a firefly.


Now, child, go run along and play. We can talk about how sparklers work next week (hint: it’s magnesium. And chemistry.)

By July 30, 2013 7 comments fun, Uncategorized