Chessistry
Your back’s against the wall. Your time is limited, but you’ve got to make a move. You’ve got to do something…but what? This move could make or break you…bring home the win, or send you back to square one. How do you respond?!
To some, the previous paragraph may sound like a scene from an action movie or the climax of a classic sporting event. Students of organic chemistry may find it eerily similar to the feelings they experience during examinations…and chess fanatics out there might hear echoes of their emotions at a critical moment during a chess game. The core idea that unites all of these scenarios is the pressure of prediction—the emotional roller coaster associated with predicting the future. Using our observations of the past to predict the future and choose a “move” is a key skill involved in science, sport, chess and staying alive in an action movie.
Prediction cannot happen without rhyme or reason! Unlike the base instinct for self-preservation modeled by most action heroes, chess and organic chemistry have rules. The rules delineate what we can and cannot do, and thus help limit and direct the thought process. In chess, the rules are very clear: no two opposing pieces can occupy the same square, the game is over when one side’s king is captured, etc. To a master of organic chemistry, the rules of organic chemistry are just as clear: orbitals must overlap for reactions to occur, carbocations cannot serve as electron sources, etc. To a novice of organic chemistry, these rules are understandably much less apparent…worst of all, most instructors of organic chemistry make little to no effort to remedy this problem in the classroom.
Organic chemistry is rarely taught in a way that promotes understanding and creative application of the rules of organic chemical structure and reactivity.
The Walking Dead? Organic Chemistry Lectures Online
AMC’s The Walking Dead is one of my favorite shows on television these days. On top of excellent acting and a compelling storyline, the show is legendary for its special effects, which hold nothing back in terms of violence and gore. Zombies have taken over the world, and the show follows a small group of human survivors as they cling to life in and around Atlanta. How exactly did a bunch of mindless, flesh-eating, slow-walking undead best the United States military, Interpol, nuclear bombs, etc.? Good question…
Here’s a (somewhat) related question, about a situation just as ugly: how could a subject as compelling as organic chemistry be given as dull a treatment as those currently available on iTunes U? The linked lectures are by J. Michael McBride at Yale, and are (long story short) the “best” organic chemistry lectures available on that platform. The problem? They’re a poster child of God-awful teaching. Where do I even begin…?
More compelling: zombies from The Walking Dead or organic chemistry lectures online?
Let me start by calmly stating that I have no problem with the content that McBride covers, per se. His content is fine, and cuts a nice swath across a variety of topics. If the student buys in, she’ll leave McBride’s course with a solid awareness of important results and thought processes in many areas of organic chemistry. What he teaches is largely irrelevant, but I take enormous issue with how he teaches.
I probably don’t have to tell this audience that good teaching should reflect how people learn, not how a discipline is structured—or even how knowledge is structured in a professor’s mind. Good teaching must include live practice and feedback, right at the moment of learning, in the classroom. Good teaching must feature concrete, attainable learning goals. Good teaching should be a conversation, not an oration. If it must be an oration, the structure of good teaching should invite the student to consider a problem or challenge her current worldview. McBride’s lectures—and most other organic chemistry lectures I’ve seen online—do none of this. He assumes, erroneously, that his responsibility is simply to say words in class. Even so, his words don’t challenge, confront, or question…his videos are as good as Reusch’s Virtual Textbook of Organic Chemistry (which, by the way, is a phenomenal resource). One might argue that the videos are even worse than text, insofar as they aren’t searchable and may be a waste of the student’s time. In spite of its flaws, Khan’s organic chemistry series does a better job of presenting compelling problems and asking the student to consider them than McBride’s series. That the community of organic chemical educators would relegate good teaching to the likes of Salman Khan is downright embarrassing. That McBride actually taught in a live classroom at Yale is also disheartening!
MOOCs have captured the world’s attention in recent months, which means that online educational content is seeing more scrutiny lately than it usually gets. Some educators have been optimistic about the situation, others cynical. Me? I’m still on the fence, but I welcome the opportunity to have my teaching put under the microscope. In spite of what Bill Gates says, chemistry content online is not what it should be, and pales in comparison to comparable content in…political philosophy, let’s say. Reusch’s VTOC has entered its teen years with no comparable interactive replacement. Opportunities to practice organic chemistry and learn interactively are very few and far between right now. Our situation is frustrating, but inspiring to the extent that we have a lot of room to grow.
Perhaps I’m over-reacting…I have a tendency to do that. Still, I would rather be chemical education’s harshest critic than hear the same legitimate criticisms from outside the field. Would love to hear your thoughts about chemical education’s relation to the MOOC craze, and how you think we’re doing. Thanks for reading!
#ChemCoach: My Story
Hey all! This is my contribution to See Arr Oh‘s ChemCoach project. Interested in what a chemical educator does all day? How I got here? Stalking me? Whatever it is, you’ve gotten this far; keep reading…
What would you say…ya do here?
I’m currently a graduate student studying organic chemistry and chemical education at the University of Illinois, Urbana-Champaign. I also work part time as a Graduate Affiliate at UIUC’s Center for Teaching Excellence, teach CHEM 332 (Elementary Organic Chemistry II) at UIUC, and run the website + create content for Organic Reactions. Most of my time is spent teaching and preparing materials for teaching…but then again, I have a very flexible definition of what counts as “teaching materials,” and my teaching and research practices often overlap (more on that later). I strongly believe that chemical education researchers should also be good teachers, and if they aren’t good teachers, they’re “doing it wrong.” You’d be surprised how many brilliant chemical education researchers fit this description…but that’s a tale for another time. My research involves the development and evaluation of educational technologies for organic chemistry.
Take us through a typical day…for you.
A “typical” day can vary for me, but here’s a broad overview. I teach at 8 am on Monday, Wednesday, and Friday, which forces me to get to work by 7:30 on these mornings. After I teach, I generally deal with teaching responsibilities and preparing materials for teaching in the morning—it’s just a weird habit I’ve gotten into. In the early afternoon I’ll do CTE stuff: meet with TA’s, do class observations, prepare presentations, eat the world’s most delicious mints (seriously, they’re like crack for me), etc. The later afternoon and evening are usually reserved for research. My research responsibilities vary somewhat across projects, but I’ll go through alternating periods of creating content, writing code, collecting data, and carrying out data analysis. As I’m not a computer programmer by trade (although I always loved it), writing code probably takes me the most time…it’s a toss-up between that and drawing flippin’ structures in ChemDraw. Many of the products of my research are turned back over to students—to help them overcome difficulties, work more intimately with molecules, etc. There is one constant in my day: coffee.
What kind of schooling, training, or experience helped you get where you are?
I graduated from the University of Kentucky with a B.S. in Chemistry, and I can’t say enough about how my experiences there (good and bad) inform my teaching and research. During my time there, I fell in love with teaching, and jumped on an opportunity to serve as an undergraduate workshop leader for organic chemistry at UK. Advice for those who want to become chemical educators: start early. There’s a tired old fogey out there waiting for your youth and enthusiasm. Start reading the literature and critiquing the literature early, before you “get” everything—do not fear the chemical literature. It’s just vicious rumor, after all! Once at UIUC, I took a course on college teaching that opened the door to opportunities at the Center for Teaching Excellence, and I’ve been networking with other faculty and academic professionals on campus interested in teaching ever since. Again, you’d be surprised—there are more of us around than you think.
This seems like a good place to warn you that being a great chemical educator is not for the faint of heart. My committee is 75% “wet organic chemists,” and dealing with them is not an easy experience. You will be misunderstood, ridiculed, kicked when you’re down, and marginalized throughout your career—however, this is not an excuse to shy away from these experiences! On the contrary, value your interactions with practicing chemists. This is perhaps the most important thing graduate school has taught me. If you just want to crawl into a hole and teach, you’re part of the problem, not the solution!
How does chemistry inform your work?
Naturally, organic chemistry is central to what I teach. My exam problems come from the chemical literature, and I read journals daily. Chemistry is also central to the way I develop software: I think about how to “systematize” chemical principles so they can be encoded in computer programs. I consider how software can help students create and work with chemical structures more efficiently. I think about how machine-readable chemical data can expose common misconceptions and help students spot their weak areas. The list goes on, but thinking about the relationship between chemistry and technology fascinates me. The future is bright!
A unique, interesting, or funny anecdote about your career
So many stories…goodness. I think I hold the UIUC record for most hours spent on video on campus—I’ll even take the journalism department to task on that. I’ve recorded online videos for both non-major organic chemistry courses (approaching one thousand students per semester), so I get a lot of weird looks walking across campus, which I do almost every day. Once, a student ran up behind me on the quad and poked me on the shoulder…she had recognized me by solely by my voice! In the live classroom, I tend to be rather brash and vulgar. For example, what some would call “figuring out the bonds made and broken in a reaction,” I affectionately refer to as “cutting out the bullshit.” I also enjoy anthropomorphizing: past activities include “your hands are enantiotopic,” “surf’s up with pericyclic reactions,” and “the human orbital diagram.”
I blog here (naturally), and I keep my organometallic skills sharp over at The Organometallic Reader.
Demo This!: Smash Glow Crystals
It’s time for a nod to one of my favorite chemistry-themed YouTube channels, NurdRage. NurdRage’s channel is basically a laundry list of awesome, little-known chemistry experiments…with a creepy yet soothing voice-changer voice to boot. One of his recent videos is especially cool: he synthesizes blue triboluminescent crystals from copper thiocyanate, pyridine, and PPh3, then grinds them up. The experiment is based on a recent JCE article from Marchetti et al. The reaction itself is straightfoward to perform: mix everything up, heat to dissolve, wait for cystallization, and wash! The copper salt, pyridine, and triphenylphosphine react to form the coordination complex (SCN)Cu(py)2(PPh3). Grinding of the crystals produces a stunning blue light.
NurdRage’s explanation of triboluminescence (the direct transduction of mechanical energy to light) is clear and concise—check it out below! Long story short, charge separation occurs in the crystal upon mechanical agitation, and recombination of the charges produces a blue light.
Chemoinformatics Curiosities: A Chemical Educator’s Perspective on InChI
Organizations supporting machine-readable molecular formats.
When it comes to machine-readable representations of molecules, I grew up with SMILES. A SMILES string reflects the connectivity and stereochemistry of a molecular structure, and may be generated from any number of other machine-readable formats, such as MOL and CML. SMILES strings are becoming ubiquitous on the web, thanks to giants like Wikipedia. They’re nice because they’re fairly short and readable—the SMILES string for ethane is simply “CC,” for example.
That said, the limitations of SMILES are difficult to ignore. The same readability that makes SMILES appealing to human eyes limits its scope significantly. The innards of the SMILES algorithm(s) are fairly simple from a chemist’s perspective, and do not take into account spontaneous structural changes like tautomerization (or even the structural equivalence of resonance forms). There are multiple algorithms, meaning there is not, strictly speaking, a one-to-one relationship between structure and SMILES string. Finally, SMILES is a proprietary format whose algorithms are kept under lock and key—with the notable exception of the OpenSMILES project.
IUPAC, chemistry’s own group of nerds with a nomenclature fetish, has been working to remedy this situation for over a decade. Their machine-readable format, the International Chemical Identifier or “InChI” (en-chee), reflects a completely different philosophy from the SMILES approach. The goal of InChI is not to fully represent molecular structure, but to generate a unique identifier for a particular compound, given a structural representation. The InChI folks recognized that molecules can be represented with varying levels of detail, and that we may not necessarily need all the details to uniquely identify a particular compound. Many species, for example, can be singled out by their molecular formulas and connectivity alone. H2 is a nice example—to uniquely identify H2, all we really need is its molecular formula and knowledge that the H’s are bound together. More complex compounds, such as those that may possess stereoisomers, need more details in their identifier. Read the rest of this entry »
Demo This!: Trautz-Schorigin Reaction of Polyphenols in Green Tea
Periodically, I plan to cover a new demonstration from the recent chemical education literature in a feature I’m calling Demo This! Today’s featured demonstration comes from a recent J. Chem. Educ. article, which highlights the use of polyphenols in green tea for the luminescent Trautz-Schorigin reaction.
Background
Pyrogallol, or what we might call 1,2,3-trihydroxybenzene, undergoes an interesting set of transformations under oxidative conditions. In the presence of water, formaldehyde, base, and hydrogen peroxide, pyrogallol is oxidized and excited singlet oxygen is produced. Relaxation of singlet oxygen to its ground state produces red luminescence.
The Trautz-Schorigin Reaction: see if you can draw a mechanism for this beast!
A quick literature search has revealed that this reaction has been understudied (or at least underpublished) over the years. See if you can draw a mechanism accounting for all the products! All manner of oxygen-containing species may be present under these harsh conditions, including superoxide anion and hydroperoxide anion.
This reaction can be slowed or prevented by treatment with boric acid (forming cyclic borate esters, which are resistant to oxidation) or by treatment with ascorbic acid, which can reduce the 1,2-keto intermediate back to pyrogallol and (in a separate reaction) react with singlet oxygen. Considering these quenching reagents, this demonstration has all the trappings of a “green,” easy-to-prepare experiment.
Experiment
This demo can be carried out either with the parent pyrogallol or with polyphenols found in green tea. Either way, set up is straightforward, and the article claims that the entire kit and kaboodle takes less than one hour. Assuming that a tea bag holds about 2 grams of tea leaves, infusing for ~3 minutes in 200 mL of hot water is long enough to push a sufficient quantity of polyphenols into the water. Paraformaldehyde and sodium carbonate are then added to the hot tea with stirring, and the solution is allowed to cool to room temperature in a water bath. The pH of the solution is checked using pH paper or indicator before adding hydrogen peroxide (it should be ~11). 50 mL of the pH 11 solution are transferred to an empty beaker, and the lights are killed. Finally, 50 mL of dilute (3%) hydrogen peroxide are added. Luminescence should be instantaneous, and lasts for 5-10 seconds.
Ascorbic acid completely shuts down the reaction, while boric acid only slows it down. These quenching reagents should be added just before the lights are killed, right before the addition of hydrogen peroxide.
Source
Panzarasa, G.; Sparnassi, K. J. Chem. Educ. 2012, ASAP. doi: 10.1021/ed200810c
