Why Organic Chemistry Made Me Feel Dumb

by James

in Teaching

Today I’ll share with you one thing about organic chemistry that made me feel really, really dumb when I took it. And looking back, I didn’t need to. So if it helps at least one person feel less dumb, that’s a win for me.

When I first took ochem, I was well-accustomed to the style of teaching used for math and physics, where instructors often went to the trouble of deriving equations on a board to explain where they came from before pummelling us with them. If it was difficult, it was only difficult because I wasn’t grasping the logic. That’s OK: I at least understood where I was getting things wrong and had faith that things actually made sense.

When I took ochem, the instructor showed us new reactions – addition of OsO4 to alkenes, say – but never told us WHY or HOW it came to be that these reagents “work”. No explanation.  It felt to me like these reagents were being pulled out of a magic hat.

Every time we learned about a new reagent, I’d ask myself, “How did it get decided that OsO4 [for example] is the best reagent for dihydroxylation? Why OsO4 and not, say, RuO4 (which is, after all, one row up the periodic table)? Or, “why palladium (Pd) in the hydrogenation of alkenes and not some other metal?”

It all seemed so arbitrary at the time, and it drove me bonkers. I felt dumb because I thought that I was just “supposed” to know from first principles how and why these reagents did their magic, and my instructor probably thought I was dumb for not knowing this either. I thought I was missing something obvious, and felt ashamed for it.

Many, many years later I realized that my instructor,  even if he was the most brilliant person in the world, could not have predicted from first principles that these reagents do what they did was he in my position. That’s because a great deal any of the things we learn in organic chemistry are the results of discoveries, not deduction. For instance, H.C. Brown, winner of the 1979 Nobel Prize for his application of the hydroboration reaction, discovered it by accident [note 1] not by some sudden flash of insight.  Only once he’d discovered the reaction did he assign an army of graduate students and postdoctoral fellows to explore every facet of the reaction in more detail.

Our knowledge of organic chemistry is hard-won from experiment. The reagents you see thrown up on the chalkboard – AlCl3, BH3, LiAlH4 are the tips of icebergs. You only see the finished result: “BH3 is used for the hydroboration of alkenes”. What you don’t see is the accidents or serendipity that led to its discovery and all the man-years of effort in learning about the reaction in more detail and optimizing the process. You also don’t see all the time spent going down blind alleys exploring reagents that don’t work as well for this process. “It just works”.  That’s why it all seems magical.

The bottom line is this: you’re probably not as dumb as you think.  The course moves really fast, and there isn’t time to go into all the little corners. There are reasons for why these reagents are used, and how they work particularly well, but the tools to fully understand them don’t come until later on in a chemical education (and sometimes the best answer is merely, “we use this reagent because it’s convenient and cheap!”).  And some questions you might scold yourself for thinking as “dumb” – like why OsO4 works so well for dihydroxylation, but RuO4 does not –  lead you down interesting paths. Hold on to these questions for later.  Chemistry is still a living science. We don’t know everything yet, there are many more experiments left to do.

[Note 1] – Actually Brown’s postdoc Dr. B.C. Subba Rao discovered the hydroboration reaction, not Brown himself. From his Nobel Lecture:

In the course of these studies of selective reductions, a minor anomaly resulted in the discovery of hydroboration. My coworker, Dr. B. C. Subba Rao, was examining the reducing characteristics of sodium borohydride in diglyme catalyzed by aluminum chloride[17]. He observed that the reduction of ethyl oleate under our standard conditions, 4 moles of hydride per mole of compound, one hour at 25”, took up 2.37 equivalents of hydride per mole of ester. This contrasted with a value of 2.00 for ethyl stearate. Investigation soon established that the reagent was adding an H-B, bond to the carbon-carbon double bond to form the corresponding organoborane.

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{ 14 comments… read them below or add one }

Jeff M December 5, 2012 at 9:53 am

Great post, James! I’m going to share this with my class because it’s so true for virtually everyone, me included.

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james December 5, 2012 at 5:15 pm

Thanks Jeff!

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mevans December 5, 2012 at 10:20 am

Great post! Makes me think of comparisons of acidity and reactivity. For example, base A has more steric hindrance, but base B has the less electronegative heteroatom…which factor wins? Comparisons like this always drove me nuts, because I felt like there was a secret piece of knowledge I was missing. Truth is, only through experiment (e.g., measuring basicity) and building up one’s mental database of examples can one intuitively recognize the relative importance of some factors.

I bet Ley felt your same frustration :-) (http://www.organic-chemistry.org/abstracts/lit2/906.shtm). I do often ask myself “why THIS metal?!” without getting a satisfactory answer!

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james December 5, 2012 at 5:14 pm

True re: the different factors. Almost like comparing two sports teams with complementary strengths… the way to tell which factor “wins” is just to play the games [except in ochem, the “game” gets played 6.02 x 10^23 times per mol]

I’ve lost the reference, but at some point in grad school I attempted a dihydroxylation with RuO4 under carefully controlled conditions; unsuccessful but apparently it can be done. I also recall [again lost exact reference] a theoretical study which probed the reactivity difference between the two.

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Muhammad December 7, 2012 at 6:38 pm

I recently had the same realization studying before a test. What I still don’t understand is we keep being told to not memorize mechanisms but rather rationalize them. However, in my textbook for example it mentioned that chemists will map out a few possible mechanisms and see which ones are selected for in preference for or to the exclusion of all else, if at the end it just depends on what the experimental results showed, then why would we NOT memorize the mechanism instead of fooling ourselves into thinking like you mentioned that people could not have predicted from first principles what will happen. That being said I know to some extent things can be rationalized to understand the mechanism, but I think professors should just be a bit more candid in some cases and just say “memorize this mechanism!” Especially when the textbook shows you the reaction and then tells you that the mechanism will be learned three chapters laters.

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Susan Farmer December 8, 2012 at 10:00 pm

oh, where were you in 1972 when my Organic Prof was reading Morrison & Boyd (3rd edition to us)!. Not only might I have passed, I think I would have actually *understood* which IMO is much better than merely passing!

One of my co-workers pointed me here because of the cats. Brilliant!

(FWIW, I know where this page was in 1972 — I wound up being a Computer Programmer for close to 20 years, and I know when Tim Berners-Lee sent the first http packet!)

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Diane Castillo December 9, 2012 at 7:29 pm

I realized this about halfway through the semester, and I felt sooooooooooo much better.

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Joel Berglund December 12, 2012 at 5:48 pm

I’m glad you posted this article because I was in a similar situation last fall/winter. It’s kind of like war-time, where you can’t question it, you just need to roll with it. That is why I did better this semester when I had to retake organic chemistry and got A’s and B’s, yet the class just thought I was doing better because I already took it.

But don’t ask me about Physical Chemistry, that stuff is beyond my comprehension. I used to like math, but once I got to calculus, that like started to fade away into the wind and when I went to Physics 221 for the first time, I had no idea what I was doing. It wasn’t as cut and dried as High School physics, but at least I passed it somehow. I hope I can survive another semester of this and not have to retake it.

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Susan V December 12, 2012 at 10:17 pm

Ahhh. Phew. I feel so much better already.

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An Ochem Student March 9, 2013 at 5:17 pm

Thank you for your article. You made this person feel a lot less dumb:)

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Vijay rao December 27, 2013 at 12:33 am

Great article! My grandfather is BC Subbarao! He really enjoyed this.

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James Ashenhurst December 27, 2013 at 12:43 am

If true, then I am greatly honoured.

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Sudha Omprakash January 19, 2014 at 6:54 pm

Yes, I am B. C. Subba Rao’s daughter and Vijay’s aunt. He was touched you mentioned him. We have all shared this page on FB.

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Tom May 4, 2014 at 2:13 pm

Hello James, very cool website. I am just now finishing O chem II at Univ of Akron. The book is phenomenal!! David Klein Organic Chemistry, ever heard of it? Anyways, what do you know about the ACS Organic Chemistry II final exam? I heard horror stories.
Also, I read on the Hydroboration-Oxidation mechanism, our book breaks that down really well too, it has to be the most complex mechanism in all O Chem I, right?

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