The Oil Bath

A blog mainly about chemistry and driving trucks, describing how the world looks from the bench of a lab and how the world looks from the seat of a cab.

Tuesday, August 29, 2006

No, it DOESN'T crystallize. It doesn't even precipitate!


So these past few days I've been doing some synthesis. Not that I'm at liberty to mention what the compounds are, or even what kind of compounds they are, but I have definitely been making something. Or trying to. And it's making me mad enough to eat a glass stirrer rod, or at least chew it to pieces.

One of the chemicals I need has been previously reported in the literature. Good old-fashioned chemistry from the days when FDR was president. The kind where you use large quantities of material, don't use any fancy reagants, play with really noxious stuff, and crystallize things a lot. It's cool if you're working with compounds that are kind enough to be treated this way. And there's something magical about seeing 20 grams of product crystallize in the largest flask you've got. Old school.

But when it doesn't work it just sucks.

In this one problematic reaction I'm trying to remove a trityl protecting group from an alcohol. Easy stuff, right? Dissolve up the compound in neat acetic acid, doing about 5 - 10 grams because I'm kicking it old school. Ancient reference recommends heating to get it all in. I just use the sonicator instead. It's cool, everything goes on in. Cool solution in a bath of cold, but not icy, water. Do that, easy, it all stays in solution. Fancy digital thermometer reads exactly what I want. Add in appropriate quantity of hydrogen bromide dissolved in acetic acid, okay, precipitate of trityl bromide forms and is filtered off, super easy. Pour filtrate into cold water, extract with chloroform, dry it and evaporate it and pump under vacuum to get a syrup.

Reference cheerfully informs me that upon adding anhydrous ether, the syrup will crystallize. And then I can recrystallize again from chloroform and ether, and it'll be done!

But it doesn't crystallize. It actually does the exact opposite of crystallize. The syrup and the ether actually immediately mix. As far as I can tell the syrup and the ether actually mix in all conceivable proportions.

So I evaporate it and I try it again. Evaporate, try it again. No hope at all! Okay, add hexane to the syrup and beat the hell out of it with a glass rod. The syrup becomes snot. Anybody have a better word for it? It sure looks like snot. Pour off the hexane, do it again, snot hardens up a bit. Pump on the vacuum overnight, the snot becomes foam. Hard foam. The kind you can break up into a white powder. It's a solid! It's a solid!

It's the kind of solid that is 100%, as much as I can tell, to the infinite degree, perfectly and completely SOLUBLE in ether! It will never crystallize. It will never even precipitate. Try chloroform/ether/hexane, get oil, well my fault for doing the mixed-solvent thing too muchl. Chloroform/hexane, get oil. Ether/hexane, get oil. Do I have any other crystallization solvents? Maybe I should just try every solvent I have.

Alright, screw this dinosaur chemistry. Bring on the NMR. Almost certainly the product is in there. But it's damned dirty. Do some TLC, which sucks a lot because this compound has no real chromophores and is only slightly visualized by permanganate stain. There are 2 spots, but they're really close to each other. Running a column is going to suck. We have a fancy flash chromatography machine with programmable gradients and triggerable steps and all that good stuff, that machine gets a lot of love around here, but it's really not a lot of fun without using UV detection which won't work for this damned compound.

Maybe there's still a lot of acetic acid in there that is making it soluble, but c'mon - white powder? How much acetic acid can that stuff possibly be soaking up? And I've pumped, and pumped, and pumped.

Do the prep again. More intractable syrup that can be converted to intractable white powder. Give up, scoop the white powder together, dissolve it in ether (an incredibly tiny amount of ether, I might add), shove it in the freezer. Wow it's forming two layers! Maybe tomorrow I'll play with them.

This reaction sux. This description is a pack of lies.

Just another day, being humiliated by the chemists of the old days, men who were giants back when giants walked the Earth.

Monday, August 28, 2006

Harry Potter Chemistry


One of my pet peeves is how most people think chemists spend their day. The general conception most people have, fed by popular culture, is that we mix chemicals together in a flask of some sort. Then we hold it up in the air, letting the light catch it in a dramatic manner, and shout "Eureka" when we've gotten what we want.

The best example that I can think of in popular culture isn't explicitly about chemists at all, but it's really the same thing. I refer to the Harry Potter books, Potions class. The eager students, under Snape's baleful gaze, will put one thing after another into their cauldrons. They'll heat them, cool them, stir them clockwise or counterclockwise, and at the end they'll have a cauldron full of the desired Potion. All ready to use.

But really, it doesn't usually take a lot of time to put the chemicals together. This is often pretty easy. Then you have to wait and wait and wait. But I've got other stuff to do that takes up a lot of my time anyway, so I don't really mind.

What I spend most of my time doing is purification. After a reaction finished, almost always you don't just get something useful appearing in the flask. Usually you've got a mixture of product and a whole lot of other things that you don't want. Then you can waste hours and days purifying the one thing that you want out of this mixture of things that you don't want. There are many ways to purify the product - but a lot of the time the chemist spends the whole day packing a glass tube full of silica gel or something like that, pouring his mixture into the top of the thing, and just pouring solvents into the top and waiting for different things to come out of the bottom. One of which is, hopefully, the product that the chemist wants.

You always see chemists mixing chemicals on TV. You never see them hopping up on a stepladder to pour stuff into the top of a giant tube, and then filling up lots of test tubes from the bottom of it. But that's really the usual timesink.

Figuring out that you've actually gotten what you want is even more work. There's lots of machines involved. Just holding it up in the air does not usually help.

It would be nice to just mix chemicals until we get what we want. Too bad that real life isn't more like Harry Potter.

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