ChemBark

Yes, you read that title correctly: Jean-Luc Picard, the greatest starship captain of all-time, failed organic chemistry at Starfleet Academy. In his defense, it was probably less to do with intelligence and more to do with being distracted:

I pulled that video clip so I can show it to my students during our opening lecture. It should go well with the “How to Win Orgo” handout.

Update (5/1): Thanks to a tip in the comments from “bad wolf”, I went and pulled a clip from Star Trek: Generations where it is revealed that one of Picard’s ancestors won the Nobel Prize in Chemistry. It makes his failure in orgo all the more astonishing.

Perfectionists take note: even titans of catalysis make embarrassing mistakes with their chemistry. Just look at this little oopsie that was caught by an astute reader in the Midwest.

It seems like there might be a bit of confusion hanging over the chemists developing methods for anti-Markovnikov hydroamination of alkenes at the Center for Enabling New Technologies Through Catalysis (CENTC):

Ummm….yeah….that’s not the difference between Markovnikov and anti-Markovnikov addition.

Those of you who’ve taken sophomore organic chemistry will remember that Markovnikov’s rule states that protic functional groups (e.g., H-NR’R') will typically add to double bonds such that the hydrogen adds to the less substituted carbon (and the other group, e.g., -NR’R', adds to the more substituted carbon.) What Hartwig and coworkers have drawn as the Markovnikov product is still anti-Markovnikov. The products they’ve drawn might charitably be called conformational isomers, but they’ve failed to note any 3-D structure.

Of course, the true Markovnikov product would place the amine on the same carbon as the R group.

There is nothing like a trip to my mailbox to bring a nice little blogging hiatus to a crashing halt. While attacking my pile of C&ENs, I caught this ad for TOSOH Organic Chemical Company on page 43 of the 11 June 2012 edition:

I guess the hair net and painter’s mask ensure that—unlike my Orange Chicken at Panda Express—these products arrive free of human hair. Matters of lab attire aside, what actually piqued my interest in the ad were the compounds for sale:

Sigh. That is not how I was taught to name organic compounds. My orgo professor—on the recommendation of IUPAC—told us to start by numbering the longest chain of carbons. Thus, 1-bromo-2-ethylbutane is properly named 3-(bromomethyl)pentane, and 1-bromo-2-ethylhexane should be 3-(bromomethyl)heptane.

Avid readers of ChemBark know that I love trick questions, and structures like the ones above make for great nomenclature practice. Many students will instinctively assume the carbon chain extending from left to right is the longest. When I taught orgo, I had to purchase red pens by the dozen.

Today’s edition of What’s Wrong with this Picture? was sent in by an astute reader from Atlanta:

I’ve been a reader for a while, and when I saw these doors and signs on all of the chemistry labs at the new Undergraduate Learning Commons at Georgia Tech today, I immediately thought of your blog.

Incidentally, the missing “T” in the first picture is not the answer (the theft of “T”s from campus signs is a tradition at Georgia Tech). The problem, of course, is the myriad of Texas carbons in these Lewis structures. While I love the H₂C= groups bonded directly to the benzene rings, what really gets me going are the triple bonds at the bridgeheads of the fused ring systems. Brilliant.

I think I’ll have to retire the WWWTP genre, because I can’t think of a worse place to post fakakta Lewis structures than the entrance of an orgo lab designed to teach undergrads to learn chemistry. This is the Sgt. Pepper’s of chemistry mistakes. Game over.

Pre-meds often wonder whether they really need a year of organic chemistry, but what about prospective Starfleet officers? Will organic chemistry still be important for explorers in the 24th century?

Apparently not. (Skip to 7:45)

I have made it a rule not to participate in blog carnivals. There is something disturbing about them. Perhaps it’s the association of carnivals with fun, which I try to limit in my life. Instead of organizing and participating in “carnivals”, I do exactly the same thing and call them “roundtables”. It’s so much more professional and so much less fun.

But ever since neutrinos decided to disobey the speed limit, I’ve been reconsidering my adherence to all of the rules in my life—including my self-imposed prohibition of carnivals. The good people at C&EN are hosting a blog carnival this month in honor of the International Year of Chemistry, and I feel strangely compelled to participate. The subject: “Your favorite chemical reaction”.

Fortunately, I didn’t need to conduct my usual 200 hours of background research to write this post, because I actually wrote it in January 2007. My favorite reaction is the same now as it was then:

I came across the above reaction while thumbing through a random issue of Chemical Reviews whilst consuming a carton of curry chicken from Yenching Restaurant. It looks like the reaction can be traced to this paper by Mukaiyama from 1970. Much like Charlie Brown’s obsession with a bit of cartoon strumpet known to him only as the little red-haired girl, I find myself in the predictament of having fallen in love with a reaction that has no name. But a reaction so lovely should not have to go nameless for a minute longer. Henceforth, the reaction shall be known as the Mukaiyama Thioester Synthesis in all lands and kingdoms for perpetuity. Go forth and spread the gospel. Yields are risen.

Here is what I believe to be the (shorthand) mechanism for this dandy:

What do I find so compelling about this beauty of a reaction? Perhaps it’s the involvement of my favorite compounds, thioesters? Perhaps it is the generation of a notoriously strong phosphorus-oxygen bond to serve as the driving force for the reaction? Perhaps it is the neat nucleophilic attack of the phosphine on the disulfide in a process that must be similar to thiol-disulfide interchange? Perhaps it is the fact that this single reaction has all of these things wrapped into one? I don’t know.

And that’s all I have to say about that.  Having looked over the other entries in the carnival, I find it unfortunate how far off-base the other contributors have been.  There is nothing about any other reaction that could justify its being someone’s favorite above Mukaiyama Thioester Synthesis. The reaction is clearly the greatest in history.