Chemist at work…please disturb

My mentor is such a joker. As a way to enjoy my lab experience more, one of the grad students offered to play one of the burned CDs accumulated from past and current lab members, of my preference. I saw The Magnetic Fields and thought, that might be good to listen to while working (after a song suggestion, “All My Little Words” from my sister). After he put it into the stereo to play, he left for the day. Of course, my mentor then (jokingly) comments on the music: “Way for Tioga [the grad student] to leave us with shitty music to listen to.” My response: “Hey, I chose this music!” His response? “Oh then, this is pretty good music!” Big grin on his face to hide his previous words. I say: “Oh, you say that now.” And he just laughs. Thanks, Rob -_-


Set up another hydroboration reaction. I’m almost at the point when I can use the glove box with no supervision (but it’s been a few months, so why can’t I get it down already??). How nice of my grad student mentor to come in to help me with the reaction (and mostly to make sure I don’t burn the lab down!), albeit I showed up two hours before he did, believing that he would arrive at the same hour (9:30-10AM) as a normal weekday. This was definitely not the case, so I spent ~2 hours studying in the warm sunny weather (on a nearly deserted campus). After setting up the reaction, I went shopping at Ralphs and bought some lovely champagne. First time I purchased alcohol by myself! Then I made mimosas and drank them by my lonesome self. Surprisingly, I didn’t fall asleep!

and its smell is floating through the apartment. Is it from the salmon I just bought, or could it be the triethylamine? Whatever it is, it stinks! Oh well, back to entertaining myself with these GRE vocab words -_- and this great cross-coupling editorial :]

so what do I currently have playing through my head? Oh, maybe some Beck, Cake, 311, Red Hot Chili Peppers, Interpol, The Eagles, Dirty Heads, Sublime, Slightly Stoopid, and Matisyahu. Not much change from my previous music post, but it’s becoming a great distraction. Oh, and I also spent most of today watching Avatar: The Last Airbender rather than studying….oops.

Another fruitful day (haha not really)! It was spent working up my previous copper-coupling reaction without the ligand, and to be honest, I suspected that it would fail. NMR results of the crude product showed only starting material in the reaction mixture, even after heating it and letting it run for 20 hours. After much deliberation about what could possibly be left in the mixture and some brain-wracking analysis by my mentor and another grad student, we decided to try a different approach: change the starting material so that it is functionalized (before, we used 3-hexyne to make the internal vinyl boronate). Ergo, I set up the reaction of 1-bromo-2-butyne with benzyl alcohol in THF solvent and sodium hydride as the base, in order to first obtain functionalized starting material to do hydroboration and the subsequent coupling reaction on. The setup ran fairly smoothly compared to my first attempt using NaH (traumatizing experience: a clogged needle led to hydrogen gas buildup and the septum popping off). After finishing the setup, I had to run to my GRE Test Prep Course, which lasted until 9:30PM. And now I’m here.

An update on what went down in lab today. I arrived in lab at 9:30AM to see none of the grad students there (so grad students DO leave the lab?? shocking!), but because I wasn’t planning on doing anything major (just a TLC test on my reaction), I decided to suit up in my safety gear. There were no available capillary tubes to take a TLC test with, so I had to pull some pipettes. After setting down the pulled pipette to cool down, I foolishly decided to move one of the ends so it wouldn’t fall on the floor, and burned my finger in the process. A painful blister formed, which left me wincing in pain. I then ran it under cold water for 5 minutes and sealed it up with a band-aid. But enough about that. For today, I worked up the hydroboration of 3-hexyne with pinacolborane. After successfully purifying the product, NMR analysis showed that I obtained a cis/trans mixture of the product. Success! After multiple failed attempts with the reaction, a few changes to the process helped (as discovered by one of the 4th year grad students): a solvent change, and heat!

The vinyl boronate product was then used in a coupling reaction with allyl alcohol, employing copper(II) acetate as catalyst. Whilst obtaining the allyl alcohol, getting rid of the darn bubble in the syringe led to some of the alcohol squirting out. As you may know, allyl alcohol is quite toxic and corrosive, as stated on the MSDS: I thought nothing of this (silly, dumb me), and went ahead with adding everything else to start the reaction. After around 15 minutes or so, a burning sensation started creeping throughout my pointer and middle fingers on my left hand, which was abnormal to me but definitely meant that I had  spilled some allyl alcohol on my hands (weird that it didn’t affect my right hand). I washed my hand with water (the proper response as stated in the MSDS), but this just made it worse (further and more extreme burning!). Allyl alcohol is also a lacrymator:, so of course when my mentor told me this, my suspicions about its leakage onto my gloves were confirmed. I excused myself to the bathroom, where I repeated a washing-and-rinsing ritual to wash the allyl alcohol off. It smelled like a mixture of wasabi and mustard, uggh. The pain is still somewhat there, but hopefully there was only a minimal effect of it on my body (since I was handling only 2-3 mL of the stuff). My mentor then told me a story about a lab worker (not in our lab) a few years ago who spilled one drop of n-di-butyl mercury on herself and died six months later. Now I definitely don’t want something like that to happen to me, so I vowed from then on to always report my clumsy actions to my mentor, cross my heart (but never hoping to die!).


Much of this was talk about my personal dealings in the lab, but now I’ll report on the science-y stuff I am currently doing in lab. Previous members of the lab have been having issues with hydroboration of 3-hexyne, which could effectively produce an internal vinyl boronate, a great starting material that could provide leeway to more internal vinyl boronates to use in the coupling reaction, ones that are functionalized at least at one of the terminal positions (3-hexyne, obviously, has no discerning qualities that could direct the formation of one regio-isomer over another). Re-exploration of the issue has illustrated that the reaction does work with modified conditions from those of last time (not wanting to be at risk for any liability, I’m not going to report what those conditions are; y’all understand what I mean, right?). With my obtained vinyl boronate, the cross-coupling reaction of the product (now as substrate) with allyl alcohol was carried out, using Cu(OAc)2 as catalyst instead of Pd(PPh3)4, which is the usual metal catalyst in the Suzuki reaction. TLC tests after 10, 20, and 30 minutes showed nothing occurring really. Here’s to hoping that running the reaction longer will provide some results!

Saw this on 9gag, laughed when I read it.