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!