My Organic Chemistry Story – What’s Yours?

Late one Friday night in building 18 at MIT a few years ago I synthesized a molecule called dideoxyverticillin. It looks like this.


It’s part of a family of molecules that had evaded synthesis for over 40 years and required solving some particularly tough synthetic problems.  Our work was published in Science, arguably the world’s most prestigious scientific journal, and the synthesis was covered in chemical news sites like C&E NewsTotally Synthetic, and even given its own chapter in the book, “Classics In Total Synthesis III “.

You might think that in order to be part of an achievement like this, I must have been an organic chemistry prodigy, born with the ability to memorize reactions with ease,  do synthesis in my sleep, and draw perfect hexagons from the age of 4.

That’s far from accurate. Actually, my grade in sophomore organic chemistry was 68 – a C+ in the Canadian system.

In other words, mediocre. Class-average.

And it’s not like I slacked off. From the moment I knew I would have to take organic chemistry,  I was excited to learn about it and determined to do well in my class. I was aware of its reputation for being difficult so I decided I would work as hard as I could to succeed.

Here’s some of the work I put into the class:

  • worked through five chapters worth of problems the summer before taking organic chemistry
  • Went to class regularly, sitting at the front (which I never did)
  • went through the professors’ recommended list of practice problems
  • had a solid 7 days to study for the final and spent it studying and doing problems, as well as making comprehensive flashcards.

I never had as much concentrated time to prepare for an exam. And I don’t recall a single class from my undergraduate career where I had wanted to do well as badly as in introductory organic chemistry.

And despite all of this – I still got a C! 

I desperately needed a result in the 80’s to bring my mark up to the low B-range, but instead I got something like a 64. I went to the instructors office after we got our exams back, on the verge of tears, wondering where I went wrong. In the pressure of the exam, I missed things like seeing that CH2O can be used as a “reagent” to form acetals, for example.

Here’s the unfortunate lesson I took away from my experience in organic:

No matter how hard I try in organic, I’m bound to fail. I’m not smart enough to do organic chemistry. Other people smarter than me were lucky enough to be born with the ability to do organic, but not me. 

And for years, I believed that. It’s a long story, but eventually, I realized that organic chemistry was the intellectual love of my life, and came back to it.

Unfortunately, many take the same lesson from organic chemistry as I initially did, and it scars them in some way. To this day sometimes when I tell people I’m an organic chemist they say, “ugh, I [frickin’] hated that class!”.

Here’s some lessons I wish I had taken away from my organic chemistry experience instead.


  • Focus less on memorizing long sequences of arrows, and chunk mechanisms into steps – like this. Look deeply for recurring patterns: “nucleophile attacks electrophile” is the key pattern of almost every reaction in organic chemistry. Understand which parts of molecules are electron rich, and which are electron poor.
  • I probably worked alone too much. Don’t be too proud to strike up conversations with strangers in your class to find people – at your level, hopefully – to study with.
  • After doing a practice problem, I should have asked myself what I learned from it, instead of just mentally ticking it off and moving on to the next one.
  • I should have kept a journal of mistakes that I made and reviewed it regularly.


  • College is a kind of  tournament. My class was a tournament. Of course my instructors job was to teach, but he also expected to produce a roughly bell-shaped distribution of grades at the end of the semester. Sadly, it was not always in his interest to point out common points where students trip up, because these could be prime trick-question material.
  • This means: my grade is not my intelligence, my grade reflects my exam performance in the tournament.  I was far too hard on myself thinking I was “dumb” for not doing better in organic.
  • Some instructors design the “tournament” in different ways. Some courses test at a highly conceptual level, requiring you to apply key concepts.  Others have long lists of reactions with blank “product” boxes. This is why you have one group of people telling you “don’t memorize, learn the concepts”, and another saying, “it’s all memorization”.
  • Organic chemistry isn’t like math, where a genius like Ramanujan can logically deduce a great deal from a given set of principles. Which is not to say it’s illogical –  it’s just that there are many variables in play, sometimes acting in opposite directions, and it’s hard to predict which of these variables will dominate in different situations. Organic chemistry is an empirical discipline, where knowledge is hard-won by experiment. Markovnikov may have made the observation about addition of HX to alkenes, but he didn’t predict it in advance nor did he understand exactly why alkene addition reactions happen that way. It only looks obvious in retrospect.
  •  If you find yourself mystified by certain reactions and reagents,  that is a perfectly reasonable response. Instructors (and textbooks) have a bad habit of presenting certain new reagents and reactions like they are obvious logical extensions of concepts explored previously and don’t convey the depth of experimentation and failure that went into their development. It’s possible to cover the Sharpless epoxidation in 15 minutes of lecture, but that doesn’t convey the dozens of man-years  of experimentation that went into its development. Introductory courses don’t give you the full story.
  • Organic chemistry is so incredibly deep that a two semester course doesn’t do it justice. Instructors are under pressure to cover a lot of material in 12 weeks of lecture (24 for Org 1 + 2), and a lot of the important conceptual underpinnings that would help students to understand the material more deeply are poorly developed.

I could go on about how I am still bitter that my instructor didn’t do a better job of explaining some of these latter concepts but I don’t want to belabour the point. I will say that part of the reason I started MOC was in the hope that I could reach people who are struggling with organic chemistry and help coach them through the course in a way I never was, and maybe help them avoid the wasted years of feeling “dumb” that I experienced.

What’s your organic chemistry story?

What have you learned from taking organic chemistry?

Reply in the comments.



Comment section

13 thoughts on “My Organic Chemistry Story – What’s Yours?

  1. Hi James. I really appreciated reading your story. I am currently studying a MSc in Chemistry after a two-year break working in combustion. I have had to take courses in organic chemistry this year, something I was trying to avoid for the rest of my life! In my exam here at DTU I got the equivalent of a D grade despite studying so hard :-( I am struggling with the “I am not smart enough” mantra. I will persevere and use your website as an aid and hopefully, I will improve with time!

  2. Hi James! I really enjoyed reading your story. It must have been great to see in retrospect all your development from the C grade up to your science paper. I am a master student of materials science in Brazil and I am really passionate about organic chemistry although I don’t use it in my research work. Sometimes I like to think about the molecules dynamics, the chemical bonds, the electron densities around each part of the molecule but I has been a long time since I don’t touch my Paula Bruice’s book. I found your testimonial after searching for a book about organic chemistry that wouldn’t be too technical and offered some sort of narrative, like “the selfish gene” is a book about biology and genetics but anyone who completed high school can understand it. Do you know such a book? Thank you again, best regards

  3. Thanks for that! I really felt like I was the only one without any expertise in organic! No matter how hard I try, this thing always seems to elude me!

  4. I hated my first quarter of organic chemistry (although I ended up somehow with an A- through a lot of blood, sweat, and tears).

    You see my instructor didn’t understand or at least didn’t present one of the KEY lessons you described. In fact he presented organic chemistry as if it was EXACTLY LIKE MATH. As if, I could predict all the reactions in the world through knowledge and logical deduction.

    The funny thing is, I already knew that wasn’t the case, I had already taken physical chemistry, so I knew the impracticality of telling someone to predict all sorts of reactions using some arbitrary set of qualitative rules. So I challenged him on it, I went to about 3 office hours and basically argued with him about how he was presenting the reactions was not scientifically correct, and how A) I can’t be expected figure out exactly what happens when there are competing affects, and, B) many reactions go completely against the rules he’s taught us.

    Needless to say it got me nowhere, he wouldn’t listen and I’d just get angry. Come midterm time he’d still put a question asking us the rank the acidity of several compounds that would be extremely varied like methanethiol and toluene, all the while telling us in class that memorization of pKa’s is totally not necessary.

    Despite the fact that I wasn’t doing poorly in the class, I considered dropping it many times and just changing my major because of how infuriated I was. I looked to find some solace online, where I found sites like yours and learned organic chemistry is not as bad as it was being presented to me. I’m much happier now in my second quarter of o. chem with a different instructor. I truly think ones appreciation o. chem, perhaps even more so than other subjects, is greatly dependent on the quality of the instructor and the method in which the material is presented.

      1. Nothing’s worst than a professor that gets mad when you question him about something you don’t understand and he says memorize it. Memorize it? Huh? But I still don’t understand! I quit!

  5. James,

    Wow! Love the honesty. Coming from an expert like you, and hearing about your first experience with the subject you eventually went on to master is super inspiring.

    This is a testament to 2 things: (1) Complex subjects like Orgo truly are friggin hard, and there’s usually no quick answer – not everything is black and white; (2) Your first experience with a subject is just that, a first experience – and it doesn’t determine your eventual success or failure; (3) Thankfully there’s a method to the madness – and despite how painful your initial experience was, you went back to it and eventually figured it out (AND are now sharing it with us). Well, guess that was 3 things.

    Nonetheless, I’m really glad you shared this – and most of all for the students out there who are stuck, and need a roadmap (which you deliver!).

  6. That was a great post!
    I am studying for iit jee. I agree with your point that we must ask ourselves what we learnt from a particular question rather than just putting a tick mark and moving ahead.

  7. I love your spirit and humility. I am finished with org but I keep reading your posts because I can tell that you care and you are real. I found org to be crazy frustrating and totally beautiful at the same time. I am no hippie although I sound like one but org really made me pay attention to the natural world.

  8. Here is my short story with Organic Chemistry.. I just got M.Sc in Organic Chemistry after struggling with studying, working and my social life as a wife and a mother..

    It was really difficult for me, as a part time student in Organic Chemistry but I made it.

    You know what when I talk to people about Chemistry, they say u love it… and I ask myself do I really love Chemistry, I enjoy studying it … I have no idea if I really love Chemistry :)


  9. Hi James,

    Thanks for your efforts on creating this site! I’ve got A- on intro organic chemistry. I have learned so much from you! Thanks again!

    Wai Ling

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