Friday, September 18, 2009

fun weekend

Esther came to town for a visit this last weekend, and we got to do some fun stuff. In addition to the fun stuff we ran into some interesting and odd things too, two of which I thought I would share.

On Saturday we thought we would go to Old Town Alexandria and check out the Torpedo Factory. We'd never been and heard it was neat, if the chance arises to go there, I recommend it. that place was pretty damn cool.

On the way out of town to go there we knew it was going to be a long day, so we stopped off at the CVS to get some water bottles to take. And the expected customers for a Saturday morning were milling around the store. Only one thing stood out, and I wouldn't have noticed it at all if I hadn't happened to look over at just the right time. There was a little old lady browsing in an aisle who looked for all the world like any middle America grandmother except for one thing. She had no nose. Where her nose had once, presumably, been was a flat spot covered by a triangular band-aid. For just a moment I involuntarily thought of Vincent D'Onofrio's character Pooh-Bear from the Salton Sea, and subsequently of his pet/torture device badger Captain Stubing. Rather an odd juxtaposition for a nameless granny.

I couldn't find a pic of him without the bad prosthesis, sorry

The other encounter happened when we went to a movie one night. We saw District 9, and pretty early on I had to go to the bathroom, and I felt it would be best to get it out of the way before all the crazy action really started in earnest. It just so happened that there was a unisex singlr bathroom right outside our theater that was open. As I approached it, I could see through the slightly open door that someone had already vomited in there. I peeked my head in to see how bad it was, to determine if I could still use it, or would need to look for another. I was shocked to see that not only had someone basically turned their entire alimentary canal inside out, but they had placed the bulk of the detritus as far from the toilet and trash can as possible while still residing in the same room.

In addition to the grotesque landscape was a not unpleasant odor of blueberries or raspberries. So I was able to use the bathroom in relative comfort, even in that state. I went back after the movie to snap these pics and the odor had persisted.

Wednesday, September 16, 2009

sweet, sweet buzzwords

I saw this beauty this morning while having my morning tea, and it just cements in my mind how badly people want to latch onto popular, and often useless, nomenclature. Perhaps the best example of worthless jargon that is used frequently is "chemoselective" which appears to have no proper definition, and adds nothing to the chemist's lexicon that wasn't already available, but a close second these days seems to be "organocatalytic".

David MacMillan appears to be a great chemist, and an ok guy, but the real fame in his chosen area seems to be based largely on sales tactics. His classic contributions to the area are merely improvements on existing methods. Is that bad? Of course not, but now everyone else wants in on the game.

I think it's a bit odd to call most of these things "organo" catalized reactions anyway, because the active centers typically are nitrogen. Anchimeric assistance is often provided by oxygen or other nitrogens, and the hydrocarbon organic portion is typically scaffolding, as in many inorganocatalized reactions.

In today's example the authors most likely wanted to add some pizazz to their paper with needless, and inappropriate, jargon. It's too bad, really, because the method is actually quite nice, and doesn't need the added tripe. While the title proudly claims the method is organocatalytic, the graphical abstract has a nice large fluorine cation, and no carbon to be seen.

The fact that it says salts in the title should be a giveaway, but it never hurts to look on a bit further. The first depiction of the catalyst is given in scheme 2, where we see it's N-fluoropyridinium
triflate. That's like calling a reduction with tetrabutylammonium borohydride organostoichiometric.

Some very quick math shows that the hydrocarbon portion of the salt is only 31.2% of the mass of the compound, and that the inorganic active fluorine is just below that at 30.8%. To really beat this dead horse lets look at a heavily skewed example of a common inorganic catalyst, tetrakis(triphenylphosphine)palladium. This common catalyst and catalyst precursor has more than 10 times the hydrocarbon mass per mole and the portion of the catalyst that is hydrocarbon is over 80%, that's even better than the carbon rich MacMillan catalyst (5S)-(−)-2,2,3-trimethyl-5-benzyl-4-imidazolidinone monohydrochloride at 69% hydrocarbon.

Suffice to say I wish people's chemistry would stand on its own two feet but it seems everyone knows that massaging the system works better, and if someone else has laid the groundwork why not capitalize on it.

Sunday, September 6, 2009

lab accidents

I'm pretty lucky in that I have very few of them, and they tend to be minor. Oddly, however, the worst lab accidents have always been doing mundane things. The things that can really go awry are usually surrounded by a lot of care and multiple layers of safety and protection, so if things go wrong it's not too bad. Messy, but not damaging.

The few accidents I have had that involved personal injury typically come from things I really didn't expect, and therefore I wasn't watching like the paranoid neurotic I typically am. Quite a while ago I was doing a liquid liquid extraction and, since I wear glasses anyway, I wasn't wearing safety glasses. A lone drop flew off the drip tip of the funnel and arced perfectly over my glasses into my eye. I don't remember what was exactly in the funnel at the time, but it was probably the usual mix of aqueous mineral acid and product mixture in organic solvent. I do remember that it was so stunningly painful that it took specific effort on my part to maintain my grip on the funnel, and keep my hands and arms from involuntarily relaxing and dropping it.

My eye picked up a slight yellow tint for the rest of the day, and shortly thereafter I grew some small bumps on my lower eyelid in a cluster. I don't know if they came from that incident or not, but they were an almost daily reminder of it for about 10 years until they grew out and fell off earlier this year.

In grad school, on two separate occasions, I was putting the cap on an NMR tube, and the tube broke directly between the two sets of fingers holding the tube and cap respectively. Both times I accidentally pushed the shards into either hand. The first time it was about 2 am, and I wanted to get one last NMR in before I left. I was bleeding so bad from one of the cuts I couldn't really do anything but hold a paper towel on it, and there was no one left in the lab, or on my floor that I could find. I had to sit there like an idiot until it stopped bleeding sufficiently that I could tape it shut with label tape. We were, of course, out of band aids. When I got home much later, after cleaning up the mess I had made, I changed the tape out for a bandage. It was interesting/gross to see that I had cut a question mark shaped hole as the tube attempted to get a core sample, and it was a challenge to remove the tape off without the flap peeling up and separating from the fat and collagen layers. I now throw out severely chipped and cracked NMR tubes, and put the caps on very very carefully.

Earlier this week I was getting ready to go home for the night, and was shutting everything down at my hood and bench. I kneeled, turned off my pump, and raised the trap out of the dry ice/acetone filled dewar. The dewar tipped over and poured its contents down the front of my shin and into my shoe. I was happy to see it hadn't broken and sent glass flying while deafening me, while at the same time I was stomping and shaking my shoe to remove the acetone from around my ankle. Oddly, and thankfully, there was little damage. My sock did soak up quite a bit in the front and freeze, unfortunately. An immediate survey showed the damage was minor, I finished shutting down and split. When I got home, I figured I would photograph it for fun. I have a great series of a fluid filled, swollen, and highly colored ankle healing from hitting my shin a few years ago, you just never know when this stuff will come in handy.

I apologize for the shitty pictures. Apparently my recently replaced phone had a protective film covering the INSIDE of the lens cover that I was unaware of until today.

The night of the "incident"
the hair was already gone,
too many cheap ski boots took care of that in my youth

As you can't really see, the affected area is reddened and swollen pretty evenly. There is already a bit of ridging where the elastic of the sock was. It felt a lot like a reasonably bad sunburn.

Several days later:

Most of the swelling and redness are gone except in the most burned part. Doesn't hurt anymore except for when direct pressure is applied. Usually on accident, and is quite a surprise.


Look at how clear that is when you remove that little piece of fucking plastic! The color is somewhat unpleasant looking, but it feels fine, and is healing well.

Interestingly, a few days ago the same thing happened, and without any surprise or real thought my knee shot forward to catch the dewar and balance it until I had a hand free to right it. I think perhaps it's time to reevaluate my pump trap system.