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, September 26, 2006

Chemistry in zeroGee

I think space travel is cool. Not that anyone is actually doing any, they're basically flying in circles for no reason. And NASA are a bunch of wimps, always waffling, all reluctant to go up and service the Hubble although that's the one thing they have up there that makes pretty pictures - which are probably a good thing as far as taxpayer relations - hey, I'll go fix the Hubble. I mean, 98% chance of survival in a Shuttle flight, that isn't too bad, I'll be a hero otherwise I'll be dead but it'll hopefully not be slow and painful at least. 98%, I'd do it. I'll do it myself, it doesn't take a huge crew, c'mon, that thing needs the pilot to push like one button the whole time! I love the Shuttle though, like when they say that it always leaves a trail of broken foam and other junk behind it. I had a car like that once.

Anyway, I think zero G would be cool. And if I was to go up to fix the Hubble, I'd want to bring my cat. Because if I didn't come back, nobody else would want him. Mainly I'd love to see him in zero G. Imagine 25 pounds of angry teeth, claws, and flab, floating helplessly in the middle of the air while desperately seeking to claw or bite something. That'd be awesome.

But I've been wondering - what would chemistry be like in zero G? Sure, you could run reactions in sealed flasks. But good luck heating them in an oil or water bath, there goes the hotplate - maybe microwave reactions would be better? Those are cool, sealed-tube and nice even heat, I have a lot of fun with those. Sep funnels would just not be a very good idea. Flash chromatography would probably work. Filtration would be an interesting operation, too, wouldn't it? Probably people would use some sort of frit-bottomed vial with a cap at both ends.

And distillation - I've never seen a distillation setup that doesn't rely on gravity. Gravity keeps the liquids down and the vapors up, condensing and dripping back down a fractional column, all that fun stuff. Could it be done in zero gravity? I suppose the distillation apparatus would probably basically be a centrifuge of some sort, wouldn't it have to be?

And I bet magnetic stirplates would need modification - they really mostly don't attract the stirbar that much that it would work without gravity, right? But pulling harder on it might make it stick. That'd be a total challenge.

Or come to think of it, how come magnetic stirplates suck so much now? You always end up watching your stirbar feebly twitch. So you turn it up a bit, and it threatens to spin, goes for a bit, then flings itself to the side of the flask, oops, too fast! Frustrated, you try it just on the bare plate and it works, so is it the viscosity of your mixture or that extra 1/8" of glass that so frustrates the magnetic field that it just cannot do the job? Been using these things for years and I guess I've amassed a collection of "lucky" stirbars at this point. I honestly don't know why they even made some of them.

So this makes me appreciate biological systems, which do all sorts of fascinating chemistry and work nearly fine in zero G. Sure, that last astronaut who fainted was kind of wobbly when she got back, but she was fine until she got back into gravity, and this is probably some systemic effect, individual cells are plugging away just fine. Yet I can't imagine how one could do, for example, a fractional distillation under vacuum in zero gravity. It's something neat to think about.

And maybe if NASA lets me ride a shuttle I'll bring some glassware to mess around with. That and a cat. Honestly, all an astronaut has to do is push one button anyway, I could sure do that, I could fly the Shuttle. And only 1 chance in 50 of fiery death, what a deal!

Thursday, September 14, 2006

Fun with CaCl2

In my earlier post on "Harry Potter Chemistry", I ranted on the popular portrayal of chemistry as leaving out workup/purification of the reaction mixture in order to obtain a pure product. In this installment, I'm gonna just rant about wash liquids.

So you've got your reaction mixture, in some sort of organic solvent, and you want to clean it up. There's all sorts of aqueous - water based - solutions you can wash your mixture with to clean it up. Suppose there's base in your reaction mixture, you can remove it by shaking it up with aqueous acid. Or you can remove acidic impurities by washing with aqueous base. Easy and fun. Maybe you want to remove something more exotic. Like iodine, for example? Wash with aqueous sodium sulfite, it'll reduce it to iodide which is soluble in water and you can just get rid of it that way.

Here's a crazy wash liquid I've been using - 10% aqueous CaCl2. I've been using it to remove fluoride from various reactions that I have been doing. Sometimes it's important to get rid of every last trace of fluoride from a reaction. Suppose fluoride removes a protecting group, and then you take that deprotected compound on to a coupling with another compound containing the same protecting group - a little bit of leftover fluoride can really make a huge mess, especially if you're working microscale and have nothing to waste. And it's not readily visible on 1H NMR, or TLC, you could totally be fooled if you don't bother to take a careful 19F NMR and even that isn't necessarily a guarantee of freedom from fluoride. So if I want to get rid of F-, I always do, as my final wash, a calcium chloride wash these days just to be extra, extra paranoid. Sure, water will extract the vast majority of it, but I'm disinclined to take chances with fluoride these days.

Aqueous CaCl2 is rather a weird wash liquid, because unlike most wash liquids it doesn't solubilize F-. In fact, fluoride is completely insoluble in CaCl2 solution! It falls right out as CaF2.

That's fine with me, though, it's totally fine. CaF2 is plenty inert, so long as there's no acid around, so it won't screw up the next step so bad even if a little stays in. And I can just filter it out later on, when I'm filtering off my drying agent anyway. One thing I worry about though... if I get CaF2 in my glassware it's not going to be removed by water, or soap, or any solvents..... hopefully I can remove most by scrubbing .... but the rest will just lurk and lurk until one day I add some acid and poof! It's nasty, reactive, glass-etching, poisonous as heck hydrofluoric acid! Well, that's why this is pretty much a microscale technique for me.

Sure I could just put the reaction through a calcium-salt packed column, but like I said, valuable milligrams. This is a goofy workup, but it works for me, and in the end what matters is what makes me happy, right? And what makes you happy. So think of calcium chloride next time you have to clean up fluoride from your reaction.

Thursday, September 07, 2006

Today's post brought to you by.....

Ah... the joy of getting paid to do your hobby. You see, the driver leasing service that I am currently employed with has me on a minimum 8 hours per day 5 day per week contract. And today the unnamed engine plant that has become my home away from home is not shipping any engines today, so I'm home early and getting paid the princely sum of 14$ per hour to write this. The down side is that unless aliens show up and destroy Toyota and Honda, or something equally unlikely (like American car manufacturers regaining their traditional marketshare) I'm not going to see a dime of overtime 'til I get off my ass and get a real job. I could do that at any time, but as you know from reading my first post, I'm too lazy. Sure I'd like better clothes, better food, vacations where I actually vacate the area, but that would require me to quit this job where 9 days out of 10 I put in about 5 hours on duty, and spend at least half of it sitting on my ass talking to friends on the phone. That ain't gonna happen.

The best thing about having a CDL (commercial drivers license in case you forgot) is that you NEVER have to TRY to look for a job again. EVER! As long as you have at least 2 years verifiable experience, and have a clean enough record, it's a slam dunk shooting fish in a barrel no brainer. Let me ask you often do people cold call you and offer a 30-60 K/year position? I'm sure the answer for most of you is no. And the few of you who could retort with something like "60 K a year? ROFL thats a joke" or "in my field I'm in such demand...bla bla bla" let me ask you a follow up question; "Have you had at least 10 different employers in the last 3 years, and have you quit last minute and pulled no call/no shows on at least half of them?" My last interview went something like this:

Me: "Yeah I haven't worked for the past few months, cause....well... I just kinda got sick of trying, and I'm tired of it all, but I ran out of money from my tax return and they're about to cut off my internet access .... I figure it's you guys or JB Hunt."

My current Employer: "Let me show you our best account, when can you start?"

CAN YOU BELIEVE THAT SHIT? I remember job hunting in my Pre CDL days. It was like weeks of nothing, nothing and more nothing, then when a guy would tell me that he had a few people he was considering and he'd get back to me I felt like I was back in school and trying to find a girl to go to a dance. Lying awake wondering if I was good enough, showering and putting on my best clothes beforehand, trying to look as happy and pleasant while holding back how nervous I was while presenting myself. Then afterwords staring at the phone, wondering if i should call and ask if a decision was made , or just wait it out and not seem so pushy. And of course the ego crushing devastation at the inevitable rejection. Did I mention that at the aforementioned truckdriver interview I wasn't even showered?

Ok, so finding work isn't the hard part. Finding a GOOD job is just as hard as it is for anyone though. Drivers get paid in many different ways, hourly, by the mile, percentage (pretty much all Owner operators go this way or by the mile) or some convoluted formula based on weight, miles number of packages, phase of the moon, or some junk. And how you get paid has a lot to how you drive. Also there's the issue of quality of life. I could make a lot more if i was willing to spend a LOT more time in the truck. And you have to consider where you go, how long you spend away from home, and the pressure you will be under to get the load there.

I was going to talk about many of these issues this post but this looks like it's about as long as the human attention span, and if i get into the details it will run way too long, so ill go into that later, now its time for me to call Dweezil and tell him to format and spellcheck this ( yes I'm THAT lazy). Til next time, keep on trucking.

Wednesday, September 06, 2006

Alchemy and chemotherapy

The popular conception of alchemy is that it was the art of making gold from other metals. But really, there's no sharp dividing line between alchemy and chemistry. Not all "alchemists" actually really believed in the transmutation of metals - more on that in another entry. I'd bet that talking about gold was all about getting funded. A very important thing for any academic to worry about! I'd guess that every research proposal back then would have, in the "future goals" section, "making gold".

Anyway, alchemy is really based on a beautiful theoretical view of the universe. To us moderns, the world is basically built out of tiny particles which make up atoms which make up molecules which make up things. But to an alchemist, the world was much more of an organic whole, where even the mineral kingdom was alive. If we see a field of daisies, we imagine that they all somehow grew from a single daisy which spread its offspring over the years - and we're probably right! An alchemist who saw a rich vein of ore would similarly imagine that it grew from a Seed of Metals. He was probably wrong. In fact, he definitely was wrong. But it was a nice theory. And working from that sort of a theoretical framework, making gold shouldn't be harder than growing daisies. Too bad that the alchemists were wrong.

But they did some cool stuff. Like brew up poisonous medicines. One day we were having a seminar in grad school and we had each looked up the toxicity of a different heavy metal - this was just an informal grad-student thing - anyway I'd been assigned antimony, "Sb". Turns out that although there isn't a whole lot of antimony poisoning going on these days, a certain 15th Century alchemist, Basil Valentine, liked to poison people with antimony-based medicines. He could treat depression and also cancer (I'm assuming something like that was meant) this way, with certain side effects:

"The Dose of it before Coagulation is eight Grains taken in Wine. It makes a man very young again, delivers him from all Melancholy, and whatsoever in the Body of man grows and increaseth, as the Hairs and Nails fall off..."

oh yeah, and just about everything else was treatable this way too:

"If anyone hath laboured long with grievous Diseases, and will for some time dayly use this Oil, his Hairs and Nayls will fall off"

Well you know when it's working, don't you? I wonder just how long people lived after this sort of treatment? Wonder how their bone marrow and other vital organs held up?

Too bad that I didn't get a cooler metal like lead or mercury. Poor antimony. Yet it's really cool because someone had to work long and hard to poison people with it, they couldn't just spew it out of tailpipes or make paint out of it, it took real effort.

Tuesday, September 05, 2006

A day at the office

Hi, my name is Smokey Clutch, and I am a lousy truck driver. Holy shit, the lights not on! What are you fucking doing? That fucking light isn't on? What are you doing in my fucking trailer? Sorry about that.

I'm a lousy truck driver, not because I run over people or break things, but because I'm basically lazy. How lazy am I? Well, for starters, I'm not even typing this. Dweezil's taking dictation over my cell phone.

I'm currently at an engine plant, operated by one of the Big 3 automakers in southeast Michigan, and I'm sitting around getting paid for doing nothing. Well, at least most of the time. This job is great for a truck driver like me. I don't work for the Big 3, I don't work for the motor carrier that's hauling these engines for the Big 3, I work for a driver leasing company - think temp agency. You see, the forklift drivers here are so lazy that the owner-operators (real truckers) can't make any money doing this. So the invisible hand of capitalism has placed me, to sit here, while the lazy union dockworker makes up his mind whether to load the next rack of engines or continue having the lunch that he spent his entire lunch hour purchasing and now must eat, at some point.

The truck I drive is your low-end International day cab, which does not belong to any of the aforementioned companies but, is leased from yet another company. If you're not familiar with the trucks, think the Ford Escort of commercial vehicles. These things are basically the worn out whores of the truck world, and I've driven several of them of various vintages at the many shit jobs I've had. Anyway, it's the new style interior and at least this time around, they've at least moved the cupholder away from the gearshift so it doesn't dump your coffee in your lap when you hit third. The biological unit of this whole operation (me) is the same sort of just-in-time thrown-together "it'll do" ...

See, I never really learned how to drive a truck. My last job, before I entered the exciting world of commercial hauling, was as an under-the-table food delivery guy living in my parents house using the car my parents bought. Unfortunately impending fatherhood necessitated a change of lifestyle and a serious career. So I did what every white, Oakland County, multiple college dropout does in times like these. I begged Daddy for $6000 to go to truck driving school. Let me tell you, these guys are awesome. I chose the school on the criteria that it was the first truck driving school on the employment page and I didn't feel like making 2 phone calls. Plus the salesman sounded convincing. The good side is that $6000 buys you a CDL in Michigan. I could get your dog a commercial drivers license. The bad news is that I never really learned how to drive a truck. Most of the tuition that didn't go into the owner's pockets and the extensive recruiting and advertising budget, didn't go towards equpiment or training materials or anything like that. It went to the State-certified driving test administrator, a former employee of the school.

The last 5 years have, to say the least, been interesting and eye-opening. In that time, I've bounced between many jobs, driven dozens of trucks, through about 25 States, I've been to hundreds of docks, and spent countless hours just realizing how amazingly intricate and stupid the world around me really was. During this time I've collected the fuel for hours of mindless ranting. And these rants are too good to remain solely in the world of truck drivers.

As soon as I get around to pounding out another entry, I'll let you all in on just what the men and women go through who bring you everything, and I mean everything, you will ever buy.

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.

Welcome to the Oil Bath

The Oil Bath keeps your gears lubricated, your toolbits cool, and your chemical reactions hot.