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Where Chemistry Makes Sense

Why is organic chemistry difficult?

Organic chemistry has a reputation for being a difficult subject. I sometimes think this is self-fulling prophecy, your professor may make it hard because he thinks it should be.

There are many books that have been written to make organic chemistry seem easy. I've looked at many of them. This is what I think they have in common, they are shorter. They are the "Reader's Digest" version of your textbook. They are like a math book that skips topics that are too hard or too lengthy to explain.

Considerable time has passed since I last taught a class. Let me condense my thinking. Our brains are pattern matching machines. Exceptions and ambiguity are the enemies to learning a pattern. In addition, chemistry is complex. The patterns can be difficult to discern and chemical reactions require additional levels of knowledge.

Let’s look at this last issue. If you are a fan of the quiz show Jeopardy, then you would know a question such as, ‘common bonds’ is a more difficult question than “Who is buried in Grant’s tomb?” In common bonds, you must know three facts compared to a single fact.

Chemical reactions are similar to the multipart questions. Chemical reactions contain a string of electron movements. The problems become a string of events that grow beyond what a student can memorize.

There is a solution to this, logic. Our brains can connect information together if it is based upon something we know. For example, a mnemonic is a method to connect two ideas together, i.e., ROY G BIV to the colors of a rainbow.

If you needed to learn the Gettysburg address, you could do it because the words and the ideas are connected by logic. However, if it was in another language, it would either be much harder or impossible depending on the similarity to a language you already knew. The intellectual connection of how the phrases have meaning may be lost. The words create phrases, letters create words, and the shapes create letters. If I asked you to memorize the Gettysburg address in Chinese, it would be impossible if there wasn’t a logic to connect the characters. It would be like trying to draw a Jackson Pollack painting from memory.

The chemical equivalent of logic is a reaction mechanism. Students would ask me how many mechanisms did they need to know. I would answer, “Only those that you wish to answer on a test.”

I have not found this to be a problem as reaction mechanisms have a similarity to each other. It never happens that you would learn one mechanism that did not rely on principles you had learned earlier. The more reactions you know, the easier it becomes to learn additional reactions.

"A Guide to Organic Chemistry Mechanisms" is the opposite to the “Organic Chemistry Demystified” guidebooks. It skips all of the simple parts of organic chemistry. They are already well covered by all of the textbooks and additional guides. Most students do not need my help to learn them. "A Guide to Organic Chemistry Mechanisms" makes learning reaction mechanisms a task that can be reasonably accomplished. I don't think "Organic Chemistry for Dummies" or any other guide books succeed as well.

Herein I discovered another issue, ambiguity. I had given my class five mechanisms and announced they would be on the next test. That was thirty points they can easily earn, or so I thought. I was surprised to discover half of the class could not write a single mechanism. After much thought, I realized the mechanisms lacked a logic to connect the steps together.

If you analyze the Markovnikov addition reaction, the curved arrows are ambiguous. They do not indicate what the product should be. A student has to know what the product is in order to understand the curved arrows. This is a weakness of the curved arrow convention.

This ambiguity is multiplied with each additional step in a reaction. A multistep reaction becomes an abstract jumble of lines and letters lacking the logic to connect them together.

I discovered that dashed lines were sometimes added, especially for a Diels-Alder reaction, to indicate which atoms are to be joined in a bond (Williamson, Chapter 49, Diels-Alder Reaction in Macroscale and Microscale Organic Reactions (Houghton Miflin, 4th edition). I therefore modified the reaction mechanisms by adding a dashed line, a ‘pre-bond’, to indicate which atoms would be joined together. The curved arrows now pointed to the new bond being formed and the curved arrow are now unambiguous. You can predict the products completely from the curved arrows. You don’t have to know anything. The curved arrows give all the information needed to predict the product.

I know this is different than the conventional use of the curved arrows. However, my students preferred this usage and had no trouble adapting to either instance. (Here is a pedagogical challenge. Compare student achievement with the use of ‘pre-bonds’ and conventional curved arrows. It is easy to be critical of the use of ‘pre-bonds’, but that does not prove they are not effective.)

Now that ambiguity has been removed, I can address the second part. If you want to lead a donkey with a carrot, you have to hold the carrot within eyesight. If it is too far away, he won’t know where to go. I broke the reaction mechanisms into steps. At the first level, Part A, a student has to add the curved arrows indicating where the electrons move. This contains the logic of the reaction. In Part B, the same reaction is repeated with the ‘pre-bonds’ and every other intermediate removed. If you understood the logic of the reaction in Part A, you should be able to complete Part B. In order to make navigation easy, the reaction on page 37A is repeated on 37B, 37C, and 37D. If you can succeed in Part B, then you should be able to write the complete mechanism in Part C. Part D contains the completed mechanism.