They’re teaching you Organic Chemistry wrong, and here’s why

(Special thanks to Dr. Lawrence Williams and Dr. Jeehiun Lee for their edits and suggestions)

In my previous article, I talked about my frustration about “magic-box” functions. Now although that was in the context of Software Development, the idea is so applicable to every single discipline.

The idea of a “magic-box” is this: You give an input and put it into the magic box. Then, the magic box does xyz, in other words, God knows what, and out comes your brand-new output. The more obstructed your view of the box’s functions, the more magical the box is.

This is inherently a bad paradigm for many, many reasons. For me personally, it fundamentally goes against the way I think. Material effects should be explained by material causes. The less cohesive and cogent the explanation is, the more you have to rely on memorization or taking the information “as-is”. Learning new sciences and disciplines start from the ground-up, where each new concept is explained by the previous concept.

I took a special course on Organic Chemistry with Professor Lawrence Williams a year ago, and had the opportunity to learn Orgo or Ochem in a different way than the curriculum that is generally taught to pre-med students who are dreading the course before it even starts.

I want to compare a few key differences between the way that I learned Orgo, which I believe is the right way, and the “wrong way” of learning organic chemistry.

My takeaway of organic chemistry is essentially this: it is the flow of electrons between different substances, almost like a game of pinball. Electrons bounce around different molecules and have a finite set of actions they can take. Basically, they can stay in the same place or they can move to a new location. That’s pretty much it. The game (i.e, the reaction) ends when the pinball gets stuck (when they find their most stable configuration and have nowhere else to move).

Now, if I were to ask you, how would you teach pinball to a baby?

It would be silly to ask a baby to learn how the ball interacts with each of these parts of the table before explaining how the ball works.

Now, I don’t mean that students shouldn’t be taught nomenclature or how to draw diagrams. All of that is critical and it should definitely be taught early on.

Rather, what I mean is that more time needs to be spent explaining the fundamental rules that govern electrons and electron pairs. For most organic chemistry courses, explaining orbitals and hybridization is merely an afterthought. It is simply consumed and learned by students as a review of Chemistry I concepts, rather than understanding that this is the fundamental chapter that will dictate the rest of Organic Chemistry.

Mainly, I want to focus on orbitals, especially in regards to MO/PMO theory, and identifying the HOMO (Highest Occupied Molecular Orbital) and LUMO (Lowest Unoccupied Molecular Orbital). Consider the following Molecular Orbital Diagram.

Clayden, Greeves, & Warren. (2001). Organic Chemistry. Oxford University Press. (A diagram from the Organic Chemistry textbook I used in Prof. Williams’s class.)

If you hadn’t learned Organic Chemistry without learning molecular orbital theory, or understanding anti-bonding orbitals first, this diagram might be meaningless to you. However, if the first concept you learned was how to use your previous knowledge from Chem I and II to construct and interpret these diagrams, you’d be learning so much without memorizing anything.

I’ll break down the information that I can extract from this diagram, even though I haven’t studied Organic Chemistry in almost a year. Firstly the π and the π* orbitals. Those indicate a possible interaction between two atoms. They’re mixing their regular (p/sp/sp2/sp3) orbitals to produce a new way to bond. If they bond, it’ll form an oval shaped orbital between This took me a little time to learn, but the π* orbital has a shape too! It exists behind the two tips of that oval shape, meaning it has one location behind the C and one behind the O. This is the only new information you need to construct and interpret this diagram. Everything else can be done with simple Chem I and II logic. Let’s break it down into steps.

1. We want to explore the possible interactions in the C-O bond. We are mixing orbitals, so first we want to figure out the placement of the C. I’ll put the C on one side and put that p orbital in an arbitrary orientation. All that matters is it being relatively correct compared to other atoms.
2. We need to place the O atom somewhere. We have three options: higher, lower, or at the same energy level (height) that we put the carbon atom at. We can use basic Chem I to figure this out. Oxygen is more electronegative, so it holds onto electrons more tightly. If that’s the case, the electrons are less likely to go running away, so we can say that the O-electrons are more stable, or have less energy. That means, we can put Oxygen’s orbitals lower than the carbon.
3. Mix! Orbitals are orbitals. So p orbitals can be in-phase relative to each other (i.e. bonding) or out-of-phase (i.e. antibonding), even if they’re new π or π* orbitals and they follow the same rules. Their orbitals would be lower than a C-C bond because the oxygen adds stability to the orbitals. That would pull them all down.
4. Add in your electrons. We have one electron from each atom, so our new bonding orbital will have two electrons in it.
5. Pinball!

From here, we can start asking some very important, interesting questions that define the rest of organic chemistry. For example, what is an anti-bonding, or π* orbital? Simply put, it’s the orbital where if you put electrons into it, it’ll destabilize the bond and cause the bond to break.

What if we have another π orbital that we can put electrons into? It should mean added stability, aka another bond!

How can we “shoot” our pinballs, or our electrons? Well, we can just compare the different orbitals. If we have two molecules, we can see if there are any high-energy orbitals that have electrons in them (the HOMO). If there is a bonding orbital (e.g. an antibonding orbital) available that is at a lower energy level (the LUMO), then we can have a new bond formed. The molecule with the high-energy orbitals would be considered the Nucleophile, and now we can start talking about Nucleophilic attack.

Learning Orgo by first gaining an understanding of the fundamental concept that governs the majority of basic chemical reactions is a much better way to approach a difficult, puzzle-based discipline like Organic Chemistry. We can use these theories to provide best-fit arguments to explain the experimentally observed phenomena, rather than using a “magic-box” theory.

Wouldn’t it be better to understand Sn1 and Sn2 reactions in terms of material, even visual interactions using basic geometry and chemistry, rather than approaching Organic Chemistry head-on? Typically, when you get to Sn1 and Sn2 reactions, you have no framework to understand why is A a nucleophile and why is B an electrophile? You almost have to take a leap of faith to understand why an Sn1 reaction might maintain its stereochemistry, while an Sn2 reaction must reverse it.

I think that Organic Chemistry is a unique discipline because it is one of the few opportunities to learn in its purest form. Most disciplines such as biology rely largely on a posteriori knowledge, rather than a priori. Organic Chemistry, although largely experimentally based, allows students to use established models to make deductive conclusions. Teaching Organic Chemistry in a brute force way largely reduces those opportunities, and turns the discipline into more of an arms-race to memorize and do the most practice problems humanly possible.

Uthman Qureshi is an undergraduate researcher studying at Rutgers University in Professor Jeehiun Lee’s lab.