Archive for July, 2008

Look at me. I’m cleaning two NMR tubes AT THE SAME TIME for pennies. I learn so much with my blog.

SO, from the comments below. This is about 1000x easier to assemble. Indeed, you’d have to be pretty much a retard to need a diagram. It even allows for multi-tube cleaning just by sticking more needles through the septum! I dunno if that septum is resistant to chloroform and DMSO but the tubes look pretty clean. I grabbed that from a bag of septa we have for 29/40 flasks. It fits perfectly and gives a nice tight vacuum.

We have something in the lab that I like to call the Soviet Eyewash station. It consists of a long needle sticking straight out of a sliced squeeze bottle attached to an aspirator. One of our visiting students made it for us and it was to replace the NMR tube cleaner Aldrich charges a brazillion dollars for (though that 5 NMR tube washing thing is pretty sweet.) Nevertheless, funding was tight and when some clever scholar broke our expensive aldrich NMR tube cleaner so we needed a cheap alternative:

The concept is simple and I think it’s actually on the internet already, but for those of you who aren’t familiar, here is a simple scheme that I made whilst practicing my Adobe Illustrator skills. (Am I the only one that feels like a retard with that Pen tool?) You stick the NMR tube on the long needle and squirt solvent into that ghetto fucking cup there and the suction takes it through the tube and on out. You can pretty much use whatever solvent you want. I like to soak mine in Nitric acid and slurp it out and wash with DI water for that extra sparkle clean. Chloroform followed by acetone also seems to be a good system for most things. I’ve never had the urge to squirt DMSO into there, but I assume it would work.

And there you have it. For some reason the pngs look like shit. But I’m hoping it’s visible. Hope this helps anyone who hasn’t seen it before. *HINT* the best NMR washing solution is nitric acid followed by acetone. (JUST kidding. Please don’t try that. You may blow your face off.)

Through his distinguished career, Julius Rebek has done some profoundly interesting chemistry and I’ll admit that I’m a blushing fan of his work. I like his style and I like it a lot, so take this criticism of his recent Angew paper (“Gas Behavior in Self-Assembled Capsules” DOI: 10.1002/anie.200802023 ) as little more than a cynical interpretation. Sometimes intellectual masturbation’s grand finish results in a one-odd shot straight in the eye and, from what I hear, that stings quite a bit.

Forgive me for not updating the uninitiated – one can simply explore Rebek’s rather snazzy website (which has audio commentary for the really lazy) to get a better understanding of his self assembling sporting goods.  This paper describes the encapsulation of butane and cyclopropane inside of a capsule, which is formed from a 1:1 association of resorcinarene derived molecules (see left) and it looks like your standard drug capsule. Because cyclopropane is a gas and because all gases should immediately be subjected to the ideal gas law it was determined that the insides of these capsules are filled with somewhere between 270 to 1000 atm of pressure (depending on who you ask)! Holy flying shit balls. (Using PV=nRT I got 282.8 atm at 293 K…) But this is WRONG. Making pressure the variable is nonsense since the experiment clearly involved bubbling the gas into solution, which means the solution could never have gotten above 1 atmosphere. The real question is… how hot are they? Well… In reality, using the same numbers (n=5e-24 moles, R=.0820, V=4.25e-25 L and, just for fun, P=1 atm) they’re actually 1 K. Seriously. One Kelvin.  The notion of a Nanogun was recently brought up at a conference I was attending when Rebek announced these findings. I think not. Nanorefrigerators. Global warming is officially fixed.

But let’s step out of Stupidland for a second and really consider something that’s actually true:

1. The ideal gas law was made up by Godless communists. Trust it at your own peril.

2. The three molecules of cyclopropane inside of that capsule are not “gas”. It’s tempting to think of things we see in big people land as being the exact same in Nanoland, where bulk materials retain their properties even when they’re reduced down single molecules, but (alas) this isn’t the case.  It isn’t the case here and it won’t be the case anywhere else.  At some point someone will have to draw the line between supramolecular chemistry and materials chemistry and demand people stop stealing shit from either side to dramatize their results.

The paper goes to some lengths to state that such an analysis is indeed nonsense. Clearly, you cannot have capsules that are 1 K in solution or the whole solution would freeze and everyone would die all Cat’s Cradle style. This is not so, obviously. Thus we are left with the more logical choice: the capsules are pressurized to over 280 times that of their surroundings and kept from going nucular only with hydrogen bonds.  *shrug*

Now, as stated previously, I saw Rebek give this talk and someone asked him if it were possible to create a “nanogun,” betraying two very interesting points, the most intriguing of which was that Rebek didn’t do a very good job in his talk emphasizing that using the ideal gas law was an academic exercise and not an actual, meaningful measurement. (He tried.  I was there.  He made an honest effort to politically place the result in an academic context.) The other, far more pitiful point, is that there are people out there that just don’t get it and they’re chemistry profs at major universities and they review papers.

Photoreactions are a pain in the nuts quite often because you have to stick them next to light sources that often heat the sample up to a billion degrees. This, of course, isn’t always wanted, which means you’re either going to have to cool your sample or fit a reflux condenser on it. Even more of a pain in the ass comes if you want to bubble oxygen or something into the system. Suddenly your cute little photochemical reaction is a goddamn nightmare.

(Some people will wonder why I bitch about this. After all, isn’t the point of photochemistry to get out a bunch of awesome glassware? No. That’s a huge pain in the balls. As is trying to synthesize a product that decomposes in refluxing solvent. So I would have to use a jacketed flask… PAIN IN THE BALLS. Work smart, not hard folks.)

Thus, in my case (and presumably many others) why go to the trouble of generating heat at all when you can have ultra blinding light that doesn’t get your sample any warmer than 30 degrees? I dunno. Let me introduce you to something I invented last night at about 1:30am in a WalMart.1

As you can see to your left, with a few bucks I went out and purchased a lamp socket holder thing for lizard cages or some shit and found the biggest fucking compact fluorescent bulb I could find2. MISSION ACCOMPLISHED. According to the box, a 45W compact fluorescent bulb is about equivalent to a 200W incandescent bulb. Since the only wavelengths I loose in CF bulbs are those at the pesky (and useless in my case) near IR and above, I figured it was one helluva deal, as the bulb I had been running was a 200 watt tungsten heat lamp that was generating more heat than Dave Evan’s thighs in a full sprint. I tossed that bitch out and plugged this one in and never. looked. back.

Wrapped it up in foil and BLAM! My little heat sensitive photoreaction went in less than 20 minutes with almost no solvent evaporation (it was open to the air so I could bubble oxygen into the flask) and the bulb remained cool enough to touch the whole time.

So, it may not be the PERFECT solution to EVERY photochemical reaction, but for the ones I want to do on the bench at low temp, it’s fucking fantastic. Not only that, but it makes Al Gore’s weewee spring into a giant boner, since I’m saving about 3 pounds of CO2 when I run it instead of my big honking sun lamp.

[1] I may not have invented this. If someone else did, I’m taking credit for it. So suck it Tesla, the radio is MINE!
[2] The bulb is about 10″ long with a diameter of about 3″. No shit. It also pumps out about 3,000 lumens (new). If I want to go bigger, I can get a 200 Watt compact fluorescent bulb that spits out 23,520 lumens.


Rajeev S. Muthyala may or may not be trying to fuck with us in this Org Lett ASAP (DOI: 10.1021/ol801204s), but I certainly felt fucked with.  See, part of what I like to do here is not only point out the well written, well thought out science but also the bull shit and this article entitled “Carbonyl Groups as Molecular Valves to Regulate Chloride Binding to Squaramides” is a giant floating turd.  The stage is set in the intro paragraph:

“Smart” artificial chloride ion receptors whose binding cavities can be opened and closed in response to changes in the environment can be useful in regulating ion transport1 as well as in other areas including environmental remediation5 and sensor design.6

hmmm..  Sounds like a good idea.  Something smart, which can open and close in response to a changing environment.  Here is how they hope to accomplish this:

Some people may find utility in this whole thing.  I, for my part, do not.  The ability of solvents to disrupt hydrogen bonding isn’t amazingly interesting, nor is the binding of chloride to squaramides.  What the world really needs is a novel chloride binding motif which possesses a fluorescence signature.  In this, they almost have – but not really enough for an Org Lett, IMHO.  This notion of “gating” is grossly misrepresentative of what they’ve actually produced which is nothing more than a molecule which displays solvent dependent intramolecular hydrogen bonding.  The fact that they get chloride bonding in acetonitrile (Ka of ~80-500) in the presence of a competing conformer is… well… uninspiring and certainly not a “gate.”  Boo hiss boo on the reviewers for letting this through and especially the editor.  Honestly, who the fuck falls for this shit?