Organic Chemistry Curriculum: A Step in the Right Direction

Alison Flynn’s latest in the Journal of Chemical Education is an instant classic. She describes a redesign of the organic chemistry curriculum at the University of Ottawa that tackles head on the issue of “curved arrows as decorations” that has been well documented by Cooper, Bhattacharyya, and others.

Her approach begins with four units on the basics of organic structure and physical properties, which is standard stuff. An entire unit on reaction mechanisms that precedes the first reaction covered comes next, and this is really the pièce de résistance of the design. Acid-base reactions come next (pretty standard), followed by nucleophilic additions to π electrophiles and electrophilic addition to π electrophiles, including reactions of alkenes and arenes. That’s organic 1. Note the complete absence of substitution and elimination—a huge plus in my opinion!

Organic 2 begins with eliminations and oxidations—love how these two are grouped together, as many oxidations are glorified eliminations. Next come activated π nucleophiles (enols and enolates), π electrophiles with a leaving group (e.g., acid chlorides), and π electrophiles with a “hidden” leaving group (e.g., imine formation). Seems a little odd to loop back to carbonyl chemistry at the end of organic 2 after hitting nucleophilic addition to carbonyls near the beginning of organic 1, but let’s not allow “we’ve always done it this way” to rationalize away the change. Continue reading →


Chain Mechanisms and Catalysis: What’s the Difference?

In a recent authoring project on organic chemistry, I came across the following statement:

A chain mechanism involves two or more repeating steps.

Is this a true statement? Well, yes and no. Yes, a chain mechanism involves the same process happening again and again. But so does a catalytic mechanism—are both mechanisms the same? If they were, we’d just call all chain mechanisms catalytic (it sounds much better, right?). In fact, the two are not the same, and there’s far more to the definition of a chain mechanism than two repeating steps.

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Naively, chain initiators (let’s use radical initiators for the present discussion) look a lot like catalysts. They’re around in substoichiometric amounts and they promote the combination of reactants that would otherwise sit dormant. Clearly then, they decrease the activation energy of the reaction relative to a situation without initiator. However, radical initiators are missing a key feature of catalysts: they are consumed by the reaction. They’re about as close as one can get to a catalyst without being a catalyst!  Continue reading →

Chemical Education Roundup, 7-22-12

Has it really been almost a year since I last published a roundup? Wow. I confess that I’ve been putting much more effort recently into another project, The Organometallic Reader. With BCCE 2012 coming on soon, it seems an appropriate time to start the roundup train going again. I can’t make it to BCCE this year, unfortunately, but the e-program looks fascinating. Follow my man Jeff Raker on Twitter for nods to talks he finds interesting.

So what’s new in the world of chemical education research? What are the cool jams? What is everybody up to? Here are some of my favorite papers over the past year, in no particular order.

On the theoretical side, all organic chemists should check out the hybrid orbital controversy that erupted in the pages of J. Chem. Educ. earlier this year. At issue is whether hybrid orbitals are “real” and whether they should be taught to general and organic chemistry undergraduates. Rebuttals to the original paper brilliantly come to the defense of hybrid orbitals. As an educator, I feel more confident teaching and discussing hybrid orbitals with students after reading this series.

I’ve been waiting on this one for a while: in April, Grove & Cooper’s article on representational competence while drawing organic reaction mechanisms was finally published. Although the papers’ results left me wanting more, the authors’ conclusions will resonate with any organic chemistry teacher. They found that many students avoid using mechanistic approaches to solving organic chemistry problems when mechanisms are not the direct goal, as in “predict-the-product” questions. However, among students who did draw mechanisms, a disturbing trend emerged: the proportion of students who drew nonsensical mechanisms containing cyclic electron flow actually increased with time! On the positive side, the most notable trend over time is a decrease in “nucleophile-attacks-nucleophile” and “electrophile-attacks-electrophile” mechanisms. Still, the (understandable) disrespect that students develop for physically correct mechanisms over time is staggering. Organic chemical educators must be relentless! Continue reading →

Speaking the Same (Chemical) Language

The organic chemistry course I teach makes use of a problem-solving website built on MarvinSketch to collect and evaluate student responses. This feature of the course has the awesome effect of forcing students and instructors to “speak the same language” when it comes to chemical structures and reaction mechanisms. The letters of our alphabet, so to speak, are the atoms, bonds, and curved arrows provided by the software. Since we all use the same software, and it doesn’t allow certain nonsensical drawings (such as a curved arrow pointing to nothing) a lack of clarity in student responses has become almost a non-issue.

For organic chemistry courses relying on paper and pencil, it’s very important for instructors to be clear about the drawing conventions and standards to which they expect students to adhere. As a former grader of mountains of orgo exams, I can profess that nonsensical errors and ambiguity are the most common sources of confusion for graders (and lost points for students). But it doesn’t have to be this way! With just a few words and illustrative examples, instructors can make their standards clear and help students avoid “nonsense errors.” If we tell our students the syntax and grammar of our chemical language and communicate our expectations, we can expect students to speak that language.

I’ve prepared an example of a list of these kinds of standards for my own use. Feel free to adapt it for use in your own courses (but a nod to the blog would be nice :-D).

Standards for Drawing Organic Reaction Mechanisms

Reaction Mechanisms as Narratives

The other day, a colleague and I were discussing the value of narratives in education—how teachers can use stories to make ideas stick, fit new content into existing mental models, and bring enthusiasm and relevance to a topic. Chemistry is full of narratives, in both a practical and metaphorical sense. On the one hand, the entirety of chemistry can be viewed as one big metaphor, because as one chemical educator put it, “you can’t see the damn stuff.” On the other hand, there are all kinds of stories of achievement and discovery in chemistry that bring fame and fortune to the scientific methods and ideas involved. For instance, I’m something of a named reactions nut. Despite seeing the transformation countless times, I used to be unable to remember what the Vilsmeier-Haack reaction was—it’s a reaction just obscure enough to warrant forgetting, but common enough to make you go “damn, I should know that” on a regular basis.

Then I found PIHKAL, the story of Alex Shulgin’s life as a scientist studying psychoactive organic compounds. The second half of the book contains procedures for synthesizing a variety of phenethylamines. Notwithstanding your ethical take of Shulgin’s work, his procedures will make the Vilsmeier-Haack reaction stick to your memory forevermore. The reaction is central to Shulgin’s synthetic strategy—formylate an aromatic ring, then nitroaldol condensation followed by reduction provides the desired phenethylamine. The V-H reaction below is used in the synthesis of MDMA.

The Vilsmeier-Haack reaction...for those stubbornly inaccessible benzaldehydes!

Most organic chemists have good stories associated with their favorite reactions. But what about “metaphorical” stories? Reaction mechanisms are the most common “metaphorical stories” of organic chemistry that come to my mind. Reaction mechanisms tell the tales of electrons, and figuring out how electrons are likely to behave in a never-before-seen reaction is a lot like figuring out how a fictional character would behave under new conditions. Take Captain Hook out of Neverland and plunk him down in a modern elementary school…I think we can all imagine what would happen! He certainly wouldn’t be friendly to the students.

Extending the “electrons as characters” idea, we can also imagine that the number of “plot elements” in reaction mechanisms is limited. There are a limited number of things electrons can do, when we take a sufficiently general view. However, there are countless variations on these themes, and a massive number of ways to chain steps together. Many students get the idea that these variations are what make organic chemistry hard. Yet…in both chemistry and the study of literature, seeing the forest through the trees—that is, recognizing when a new situation (story, reaction, mechanism, etc.) fits an existing general paradigm—is a critically important skill. The most interesting fictional characters live by general maxims, and we like to believe nature does too!

An Unsung Classic

I recently discovered Miguel Alonso’s The Art of Problem Solving in Organic Chemistry among my research group’s collection. This book makes a great companion to Grossman’s The Art of Writing Reasonable Organic Reaction Mechanisms, which is more exhaustive but, in my opinion, less compelling in the problems it presents. Alonso’s book is chock full of compelling mechanism problems, which will require even the most astute organic chemist to bust out paper and pencil and start drawing molecules. Perhaps the only downside of the book is its misleading title, which suggests generalized organic chemistry problem solving—the book is limited to mechanism problems, so don’t look to it for other subjects. It’s also a shame that this book hasn’t seen an update since the late 80’s…organometallic and radical chemistry are hard to find in its pages.

School has been crazy recently. I promised a post on chemoinformatics in education, and I will deliver soon…just not today 🙂 I’ll leave you with an interesting problem from Alonso’s book, inspired by a recent post on Can you provide mechanisms that explain the formation of all observed products in the reaction below?

Grignard reagents and propargyl chlorides