crystals and dissapointment

Well, a picture of the crystals just to show you how big they were. Unfortunately the camera I was using does not take very good close-up shots. There are two whole crystals shown in the J. Young tube, with a penny for size comparison. These were blocky, and I could actually tell you the space group just by looking at the facets on the crystals if I were to take the time to look them up. Unfortunately careful 11B and 13C NMR analysis indicates almost certainly that these are not what I thought they were, and to boot, they are pretty common and easy to obtain, which explains why I got such huge crystals.

some crystals

Finally a break. The liquid pearl mentioned in the previous blog was painstakingly filtered (4 hours on a Buechner) and a quick 13C NMR said the prize was in the filtrate. Weird because the pearly part stayed on the filter, but I think there was just a wee bit of pearl in a bulk of dull white crap. Cooling the filtrate overnight in the fridge gave some nice flakey crystals, clear but with a significant iridescence, kind of like mica. While this is well and good, they aren't really X-ray quality crystals because they are just thin plates, nor are they worth getting a structure of anyway.

And in better news, a vial that's been in the box freezer for almost a month now (haven't looked at it in a few weeks) has yielded big fat blocks of clear crystals. Theres one thats nearly 3 mm square, almost neutron diffractable. Almost. More to the point, these are definitely X-ray quality, and they're of an unreported complex, so they might be worth collecting data on. I doubt it though, but we'll see what Prof. Heller thinks.

X-ray quality crystals were grown from a solution of THF over several weeks in a -40 C freezer.

Liquid pearl

For reasons I may explain later (or not, it doesn't matter) I was converting some phloroglucinol to 3,5-dihydroxybenzenesulfonate. The prep calls for diluting the aqueous solution with ethanol in order for the product to crystallize overnight. Whatever, this didn't happen. After a few other attempts I evaporated all of the solvent and then tried to dissolve it into a minimum of water, which didn't work at all for some unknown reason (it was soluble in water to start out with - maybe a pH issue). It did give a suspension which looked remarkably like liquid pearl. Pretty as it is, this stuff turns out to be nearly impossible to filter because the particles are so fine. These particles are however, soluble in neat ethanol, and hopefully some crystals can be coaxed out of solution this way.

Long time, no work

Sorry to disappoint the many many fans who I know attentively watch this blog on a daily basis. The promising reaction I spoke of nearly a month ago now? No crystals, just some gummy crap at the bottom of the vial. Where has our fearless author been this past month? Well, for the first part of it I was feverishly working on a research proposal project as a requirement for staying in the graduate program. The proposal outlines the synthetic plan necessary to synthesize Moebius molecules. I rendered a computer simulation of the molecule for the conclusion, and I've included it here. Obviously its not going to really look red and blue, thats just the coloring used to define the rails and rungs of the Moebius strip. I haven't gotten much feedback on the proposal yet from my committee, but I figure that no news is good news in this particular case. Professor Heller did at least acknowledge it and said he liked the proposal. Good enough for me.

So that covers the first two weeks of my absence, the last two weeks have been spent feverishly preparing for group meeting which I gave yesterday. Mostly this was spent trying to scrape together some results in the wee bit of time I had left in between finishing the proposal and giving the group meeting presentation. All in all I thought it went rather well, and now its time to settle back into some solid, non-feverishly done research.

THF solvent bomb

After improperly refilling the tetrahydrofuran solvent bomb, the color of the sodium benzophenone ketal was no longer dark purple, not even bright blue or even green, it was yellow, indicating a total loss of the flask's integrity. I emptied the bomb and quenched the remaining sodium. In the process of vacuum transferring new THF into the freshly made bomb flask, the convection in the condensed THF was so strong that it created a little fountain in the center of the bomb, with a well about 1 cm deep and spray that came up and spattered the sides of the flask. I called over Jake and Derrik to look at it but they were not as impressed with it as I was. Regardless, its a very pretty blue color.

a promising reaction

Finally, a promising reaction. The salt metathesis reaction I ran last week appears to have worked, although the NMR spectra indicate ~ 85% purity, and a pretty unassignable mess of chemical shifts. Nonetheless, I think crystallization might succeed, and if I can get some good single crystals then it will be up to Warren, the staff crystallographer, to do the rest. The first attempt will be slow evaporation of the reaction mixture.

stir plate repair

We don't have enough working stir plates. I attempted to repair one by stripping it down and washing the moving parts with hexane. No dice. I regreased it with some Loctite N-5000 (the packaging proudly proclaims "Nickel-based anti-seize lubricant for the Nuclear Power Industry") but still, no dice. I began removing parts I thought looked extraneous. This worked somewhat, and as it turns out the piece that was obstructing the bar magnet was the cooling fan. When I say it worked "somewhat" I mean that it worked until the motor overheated and seized, in spite of the newly applied Ni-based nuclear power grease. At the very least this is now a valid state of disrepair to warrant tossing the old plate and ordering a new one. A view of the carnage...


The pieces in the foreground are some of the amputated bits. The washer and lock washer appeared to have no purpose whatsoever. The shiny bits are what remains of the cooling fan after being torn out of the middle of the stir plate.

Student Grades

Well, grades are in for the class I'm a TA for. As you can see from the neatly constructed histogram, there are some winners and there are some losers in this bunch.
I don't know if it's luck of the draw, or actual TA influence, but the three high grades are from my section, and the three low grades are not. I'd like to think I personally had something to do with it, but I fear that the sample size isn't large enough to get too snobby. I'll wait to see what the TA evaluations look like before making any more presumptuous claims.

March Madness

It's tough to convince a bunch of chemistry grad students that a NCAA bracket is a good idea, even for a small amount of money. Are grad students a bunch of squares? Well, there is one bracket racket going on in the department, but the buy in is a six pack of beer, and really, who wants to win 40 six-packs of low quality beer? Someone who wants to throw a low quality party, that's who. And although I'm not so out of touch with normal society as to not want to participate, there is also enough square in me to not want to play for what is essentially the right to host a drunken frat party with all of my not so square friends.

Exam proctoring

The class for which I TA had their exam today. I helped Prof. Heller out by going over the exam questions ahead of time, just to make sure that the poor little babies weren't overly challenged. (We wouldn't want to hurt their confidence going into exam week, now would we?)

For one of the questions, Heller wanted to use some data that was actually obtained by one of the students in the class. I dug it up for him but it wasn't exactly to his liking. "Do you think you could find a spectrum which has minor impurity peaks in it?" I told him I couldn't, but I said I would have no problem inventing the data in excel and producing a fake spectrum which was indistinguishable from the real thing. This is apparently not something your PhD adviser likes to hear, although he wasn't so appalled as to not use the spectrum. It was a little frightening how easy it was to make a plausible looking spectrum from completely falsified data. A test for the reader....three of the following spectra are real, the fourth is invented. Can you tell the difference? (click on the image to enlarge it)

Drinking

Yesterday, Labmate Jake, with nothing but grading to do for the rest of the day, decides to have an afternoon beer at his desk. Soon after, three beers have been consumed and the severity of his red pen has become decidedly more docile. This will come into play later in the evening.

Our dear friend in another lab has completed his post-doc position and will be returning to his home in Europe on Thursday. In his honor, our lab as well as Prof. Heller (our fearless adviser) go out for a few beers after work at the University Inn Pub. Several snippets:

Krista: (pulls out pouch of tobacco and rolling papers, begins to roll a cigarette)
Prof. Heller: Wow, I haven't seen anyone roll their own cigarettes since I lived with my parents.
Derrik: Your father rolled his own, did he?
Prof. Heller: No, my mother was a truck driver in the army. She could roll 'em with one hand while the other was still on the wheel.
(Slight pause as the group forms their own mental pictures of Heller's mother in a truck rolling a cigarette one-handed, meanwhile Heller finishes half his beer in one pull.)

later on...

Jake: (finishes beer, sets empty glass on table)
Prof. Heller: Looks like you're empty (grabs pitcher, begins to pour Jake another beer)
Jake: (a little slurred) Oh, that's OK, I've probably had enough.
Prof. Heller: What? (continues to pour beer)
Jake: Um, maybe just half.
Prof. Heller: Nonsense (finishes pouring Jake's beer)
Jake: Hmmm (picks up beer, almost misses his mouth with it.)
Prof. Heller: (signals to waitress, holds up empty pitcher) Miss, we seem to've gone dry, could we get another?

Sublimation mixed results

After taking care of the details such as fixing thermometers and getting dry NMR solvent, the results of the purification are in. A partial success! The final material is more pure in that there are fewer products present (3 as opposed to 7) however only about 50% product, down from about 75%. Looks like I'll have to make a new batch from scratch.