Green Shit

This post is for my organic buddies and their recent adventure with colorful things.

Behold, the formation of green shit upon the introduction of UV light[1]:



Photochromism for the win!

[1] I am not clever enough to have come up with the name of this compound. Instead, I derived it from the YouTube page.

[Hat tip: The Sceptical Chymist]

Roto-Vap Woes and Amazing Colors

The roto-vaps in the undergraduate lab suck. No, wait. They don't suck. That is, their vacuum simply is non existent. That means if you have a lot of solvent to get rid of, expect to take several hours. unless you're ingenious like me and ice the mofo down.

The multi-colored bowls on the side are acting as awesome molding for the ice.

But when push came to shove, I just went to another lab that had a REAL vacuum pump for their roto-vaps and stayed there. I even had a little friend while I did several filtrations to remove the DCU from the oil. [1] S/he ran several laps around the lip of the water bath before disappearing.
So with as much of the DCU filltered out as I am willing to fight for, onward to step two.
Thus, for the past two hours I have been adding the obtained oil from the first reaction into a D-Lysine and sodium bicarbonate solution in a THF:water mixture. Now, we have some pretty colors. Before adding dropwise:

Notice the cloudiness. Now, add some oil in a THF solution (~140 ppm oil):

The cloudiness is gone. Sort of. It's definitely a lot less cloudy. Once all the oil has been added, you get this: [2]

Let this stir for about two hours and then bring the pH down to 2 by adding 0.5 M HCl dropwise to the reaction vessel. That's my next step before synthesis class begins at 7:30am. Woohoo!

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[1] The best technique to remove the greatest quantity was to wait a couple of hours to allow the DCU to crystallize and crash to the bottom of the flask. Apparently DCU makes pretty spindly white crystals when allowed to.
[2] Sorry for the blurry images. My brother was the photography major, so all the steady handedness I could have inherited went to him.

Previous Outburst

The previous outburst was generated by a frustrating aspect of my senior synthesis project. The full schematic is shown below:
The product (1) seems simple enough of a reaction to me. But, the cursed side product (dicyclohexylurea, DCU, a white solid) is driven strongly by Le Chatelier's principle. So, to slow it down, it's a good idea to stick it in a refrigerator once dicyclohexylcarbodiimide (DCC) had been added (if the reaction vessel wasn't iced, expect everything to crash out VERY quickly) [1].

So I thought I did everything well according to procedure. Prepare a round bottom flask with ~250mL THF, and dissolve the ether-acetic acid and hydroxysuccinimide in the vessel. Dissolve the DCC in ~50mL THF [2]. Ice both for ~30 minutes. Pour. Cap. Stick in refridgerator. Have beer.

So you would expect some DCU. But I didn't expect 13.8g, especially when I used ~14g of the DCC. Granted, I haven't done the calculations to determine how much of my DCC was lost to DCU, but ~13.8g seems like a bit much.

And I haven't even gotten all of it out of my reaction vessel. DCU is stubborn and wants to stay in my reaction vessel and not come out of solution. Plus, I think the pumps to the roto-vap lack sucking power and create a poor vacuum to remove the THF from the r.b.f.

At the end of the day I need a 140ppm solution of the pyrole-ether-acetate product. Hope for the best? If not, expect more inane bitching about synthesis. [3]

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[1] DCC is disgusting to use. It's a very chunky solid that requires chiseling to obtain. Secondly, it's very, very soluble in organic solvents and oils, particularly those found on your skin. So, it's readily absorbed through your skin. And, it's a sensitizer, so I feel bad for anyone who continuously uses DCC, like protein chemists. (Oh, and I know there's worse chemicals, but I'm not working with those at the moment)
[2] Oh, did I mention DCC has a high vapor pressure as a solid? Scared now? Muhahaha!
[3] Why oh why did i not change my concentration to chemical physics? The silly notion of being a well-rounded chemist has given me headaches, lol!

I'm About to Make Something Cool

Spring break is approaching, and that means projects are around the corner. First up for discussion on this blog is the project for my synthesis class. I will be synthesizing N_ε-2-(2-(2-methoxyethoxy)ethoxy)acetyl- L-Lysine-N-carboxyanhydride (see figure). [1]
I like long names for chemical species whose synthesis is actually relatively easy.[2] The only precautions are anhydrous conditions for the recrystallization of your final product and a step that needs to be done under inert atmosphere. And all the other QC controls, like not sneezing into the solution container.

The choice isn't random. The professor of the synthesis lab wants to use the N-carboxyanhydride as a monomer for poly(N_ε-2(2-(2-methoxyethoxy)ethoxy)acetyl-lysine). This homopolypeptide is α-helical in water at ambient temperature. If I remember correctly, he wants to use it as a chiral medium for other compounds in his work. Though that isn't the only application of such a polymer, as reading [1] shows.

All the products are white solids or clear oils, so the synthesis will be boring to view. But it will empower me with the ability to say: "Yes, I did a synthesis. Yes, I hated it. That's why I'm a physical chemist".


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[1] Bellomo, E.; Davidson, P.; Imperor-Clerc, M.; Deming, T. J. Am. Chem. Soc. 2004, 126, 9101-9105. DOI: 10.1021/ja047932d
[2] See the supplemental materials to Bellemo et al. above.