Meditations on Bicyclic Aminobenzene Synthesis

Well today was the last official day of organic lab. Woo hoo. Truth be told, I’m going to miss it…in fact, I already miss the nice Suzuki couplings and “easy” stuff we did earlier in the year. Call me lucky, but something just clicked for me in that class for labs 2 and 3 (Suzuki coupling and halogen-metal exchange + nucleophilic attack on a carbonyl).

Then came lab 4, the independent project.

The concept seemed simple enough: mix some diaminopyridine and glyoxal together in refluxing ethanol, and out comes a bicyclic, fully conjugated diamino compound. Hydrogenate this using sodium borohydride and TFA, and voila, a bicyclic diaminopyridine. I just had to make one slight change, and use diaminobenzene instead of diaminopyridine…BAM! Everything goes to hell.

The fully conjugated compound in my reference was a white powder. My fully conjugated compound (confirmed by NMR, so yes I did get it [albeit with a few impurities, although GC called it pure]) was a brown oil. After running a column on my product from the first step, it came out more impure than it was when I put it in the column. Christ.

Preliminary results are showing that the hydrogenation step went so-so. I expected a color change because of the loss of conjugation, but that didn’t happen. Running a column on the crude product (per the reference procedure) proved to be a pain in the ass, but then, what column isn’t? I only had time to isolate and submit the first thing out of the column, unfortunately.

I suppose it didn’t go that badly…I just didn’t get as lucky this time as I’ve gotten before. Also it’s been neat trying to figure out the mechanism for the first step…i’m thinking something along the lines of nuclophilic attack by the nitrogens on the carbonyl carbons of glyoxal, followed by double protonation of the glyoxal O’s (by ethanol) and elimination of water.



  1. I miss that class. My independent project didn’t work well either since it was one of his crazy ideas rather than a lit reference. This only meant that I was used to his crazy ideas not working when I started in the lab…predictably enough, this has not changed.


  2. Thanks! The great irony there is that the day after the poster competition we heard back from the engineers that the compound we thought was super-awesome actually does NOTHING in solar cells. Sigh.


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