Organic chemistry. If you are pre-med, pre-dentistry, pre-pharmacy, a biology major, going into the health care or pharmaceutical industry, or any kind of science kid, you will, at some point, have to tackle this beast. You hear all the rumors, know all the people who’ve had to retake it for one reason or another. You sign up for the class (almost invariably scheduled for 8 or 9am, and you buy the model set. But you still aren’t really prepared.
Before taking O chem, I had a year of general bio, a year of anatomy & phys, several other bio classes (immunology, cell bio, molecular bio), and a year of gen chem. You would think that would be good preparation, and it was definitely better than not having that background, but O chem is a beast of a different nature. It is nothing like gen chem, which is full of chemical reactions and equations, measurements, masses, temperatures and (somewhat) straightforward physical laws. The first few days of O chem review some things from gen chem (oribital hybridization, VSEPR and molecular shapes), but from then on it is all new material, like nothing you have ever seen before. My prof always said that’s part of the point, to see how you handle something completely new.
It was the hardest class I’ve ever taken. You have to practice, practice, practice and then practice some more. Some people think of organic chemistry as a lot of memorization, and there certainly are a lot of things to remember, but it’s more about learning systems. First there is the nomenclature system. As Walter White says, “The nomenclature alone is enough to make your head spin.” It’s a system called IUPAC and there are lots of rules for naming compounds. I don’t think we had any exam all year that didn’t start with naming. But then these compounds they react, and that’s where it gets really dicey.
I always think it is so hard to explain organic chemistry to someone who hasn’t taken it because it’s just so unlike anything else. You can’t just memorize or balance or measure reactions. You have to know where the electrons go at every little intermediate step and write out these things called mechanisms, showing the electrons making and breaking bonds. Sometimes you protonate and deprotonate (adding and subtracting Hydrogen ions) over and over in a single reaction. And if the electrons move in a way that leaves one atom in the molecule with a positive or negative charge and you forget to write it in? Bad kitty.
Here is a fun video, a play on the trailer for Inception (watch this real one first), all about the dreaded mechanism.
So there are mechanisms. And you probably have to learn about two hundred of these reactions and the mechanisms that go with them. But it’s not like you can just memorize the reaction, you have to know the steps, the concepts and then apply it to any molecule treated with the same reagents under the same conditions. And then you also have to consider the stereochemistry, or the chirality, the 3D spatial orientation of molecules, because switching a stereocenter can make a molecule react completely differently. Some reactions keep the stereocenters the same (ex. opening an epoxide under basic conditions), some flip them (Sn2 reactions), some reactions will flip some stereocenters but not others (for example, an Sn2 on a molecule where only one stereocenter is affected, leading to diastereomers). And some remove the stereocenters, meaning it can go either way (Sn1, leading to racemic mixtures of enantiomers). There is a similar thing about double bonds. Some reactions lead to double bonds where the heavier parts will end up on the same side as each other, Z alkenes (ex. Lindlar’s cat on an alkyne) or the heavier parts can end up on opposite sides, E alkenes (ex. dissolving metal reduction of an alkyne).
You also have to do something called synthesis. You have to start with a simple molecule, usually something like benzene or propane, and get to some end product using any series of reactions you have learned that year. But then there are other rules, like you can only add three carbons at a time, or everything must start from propane, or all your carbons must come from an alcohol. It is hard! Sometimes synthesis problems can involve up to 20 reactions to get to your end product. And there are so many conditions to remember, like if you have an alcohol on your molecule, you can’t use a Gignard reagent, or you can’t do a Friedel-Crafts alkylation or acylation on a deactivated benzine ring.
There is something called HNMR, a form of spectroscopy that is used to analyze molecules. This part was actually a little bit fun. I don’t even know how to describe it. It’s kind of like a little puzzle. You have to figure out the structure of the molecule based on the data. Usually you are given the molecular formula, like C11H19NO2 and you have to determine what it looks like based on the data.
This probably all sounds like gibberish and sometimes it feels that way. It is a world onto itself. And every class period you are learning new concepts, new reactions, new mechanisms, new naming procedures, new stereochemistry, and you have to start applying it, incorporating this new thing into everything you’ve already been doing.
Around the end of the first term of this three-term sequence, is when I started hearing all the war analogies. It does sort of feel that way, like you’re in this epic and really long and relentless battle. You get your study buddies (one of mine loved to open the door to marathon study sessions saying, “Welcome to Hell!”) and you hunker down, practicing until you’re on the verge of tears and beyond. And then even when you get together for complete mind numbing relaxation (like say, watching The Bachelor or going out for drinks and scoping out guys or ordering way too much pizza hut because you’re too exhausted to cook even though you know you’re getting fatter and fatter from all your stress eating), just to unwind, the conversation can’t help but return, over and over, to o chem. It’s this super intense thing that you share with each other that you can’t quite share with the civilian world. Your own language that no one else can understand. I think that’s one of the reasons I got so into Breaking Bad, because Walt and the show speak that language and connect to this unique experience that can’t easily be shared.
And the bond that you share feels stronger and stronger as the year goes on. You work together all the time, support each other, wonder aloud to each other if anyone has ever brought firearms to an organic chem class or admit that the other day while drinking wine in the bathtub, you wondered if your professor would feel guilty if you drowned yourself with your o chem book open beside you or you start crying in a coffeeshop when you can’t understand oxymercuration. You remind each other that one of the student workshop leaders who took the class last year swore to you that the day you wake up at the end of the year when O chem is all over is literally better than sex. You feel like giving up about a thousand times a week. You start planning to burn your books and your two hundred plus reaction mechanism notecards in a huge bonfire once the class is over, and you start this plan in the first term.
IN April, you go through this really long and horrific chapter on enols and enolates and it is the lowest of the low. You have been at this for seven or eight months and it is just pushing you beyond your limit. You’re already feeling burned out and this just threatens to knock you dead.
And then, after you finish the enolate chapter and start to be able to breathe again, you actually sorta reluctantly kinda…start to like organic chemistry. You start to see the patterns in the mechanisms more clearly, stereochemistry becomes more second nature, and synthesis becomes (grudgingly, of course) fun. You know so many reactions, you’ve had it drilled into you to not use Grignards on an alcohol or FC alkylate a deactivated benzene. Synthesis becomes like a really challenging but fun 10,000 piece puzzle and it just becomes enjoyable to start putting it together, rearranging when necessary, and thinking through the synthesis. Maybe it’s a bit of Stockholm Syndrome, but whatever the reason, you’re kinda diggin’ it. You find yourself at an end-of-year party actually laughing at an O chem joke.
And then it’s over. And you’re so relieved. And the relief that it’s over is almost better than sex. Almost. But then you develop this weird feeling. Will you ever be challenged like this again? What if nothing is ever this intense again? What if no other class makes you work this hard? It sounds good on the surface but it also leads to a little bit of angst, some ennui. What do you do with yourself now that this is over? You relax, you enjoy the break, but in the back of your mind there is this little voice wondering if you will miss the intensity, the challenge.
P.S. This post was originally written pretty soon after I finished my year of organic chemistry. It is now almost three years later, and I have to say that in those three years, that feeling of missing the o chem challenge quickly developed into a huge love for o chem. It is, by far and away, my favorite subject to tutor. I would do o chem problems for fun anyday. Awhile ago, a friend said to me that I walk around with a big, pink Valentine’s heart that says “o chem” and there’s some truth to that. I went on and took classes in advanced o chem and spectroscopy when I didn’t have to for any requirements, purely for fun. Sometimes I even think of going to grad school for organic chem. I LOVE it, especially NMR and synthesis!
The question about bringing firearms to class reminded me of an actual story in the news years ago, about a doctoral student in mathematics who pulled out a hammer and pounded an abusive faculty member to death. Not saying it was right, but as a former grad assistant I can sympathize.
Hahaha, it was a friend of mine who made that comment. We were just sitting there in o chem lecture, learning reactions and she leaned over and whispered the question.
The prof was actually amazing, I never lost sight of that even in the depths of despair during that class. I was really lucky, because it was sort of a scheduling accident.
But yeah, I have heard about a lot of abuse of grad students. One of the reasons I’m not thinking the grad route as much (plus not a lot of jobs for organic chemists).