This isn’t C&E news concentrates, but I want to cram a few in that I missed over the last few months. I’ve read and loved and you’ll love these advances in the field of chemistry:

First: DOI: 10.1126/science.1152692. Fucking brilliant piece from the Baker lab representing state of the art fuckability of proteins. The title: “De Novo Computational Design of Retro-Aldol Enzymes” gives you a half assed idea of what’s actually going on. Where the typical “state of the art” to select for proteins that do specific chemistry is to essentially make a fuck-ton of proteins and run them on a specially designed column or do some Systematic evolution of ligands by exponential enrichment. The idea is NOT to go and design an active site of a protein and then cut out the active site of another protein and stick your active site in it to do the chemistry you want it to do. My brief description trivializes the difficulty inherent here and may overstate the utility, but it’s a monumental push forward for protein engeneering that relies not upon random insertions or specific point mutations but de novo design of an active site and then finding a protein that is compatible with it.

Second: DOI: 10.1088/1468-6996/9/1/014104. Sir Fraser Stoddart and Bill Goddard collaborated to create one of the most awesome ideas in supramolecular chemistry , which I’ve gushed over here. The paper details the attempt and successful creation of the “quasi-tristable [2]catenane.” Limitations exist in the system and it’s apparent that the design, as it stands, is unlikely to produce the desired results as an unfortunate overlap appears to exist between the absorption and CT bands of the various colored bits, but I’m still undaunted in my interest of a system like this.

Finally: DOI: 10.1002/anie.200800891. The prior post makes this next post a bit more apropos. Design of rotaxanes with strong binding interactions necessarily makes “shuttling” them around rather difficult but the synthesis of interlocked molecules nearly necessitates strong interaction between thread and macrocycle to assemble. A Catch 22, as it were. Leigh and Zerbetto have a rather clever hack which is slightly reminiscent of some of Vogtle’s (and Leigh’s own) work, where the macrocycle is used to direct the chemistry that is going to make the rotaxane in the first place, though they use it in a distinctly clever way by exploiting the copper mediated Cadiot–Chodkiewicz reaction. I have pretty high hopes for this sort of thinking in the design of molecular shuttles.

These are just a few of the articles I read and found very interesting. If I weren’t so goddamn busy I’d give literature more treatment and limit my fluff posts. But, it’s my blog, so blah.

I had to take a break from writing the supporting info for a paper I’m doing. Multi colored NMRs and J values and ChemDraw and various other spectra are driving me batshit crazy. Here is a quick post to answer some common questions about the MPLC:

Q: How many grams can you load?
A: As many as you wish. It becomes cumbersome above 10 grams and hardly worth it below 40 mg. I’ve run as little as 10 mg, however, and gotten pretty good separation.

Q: Can you do gradients?
A: Yes. As stated, the gradients are fully adjustable since it’s very, very ghetto. You have two bottles and one is pulling solvent out of the other. It’s pretty easy math to do on a spreadsheet.

Q: How much does it cost, seriously?
A: If you buy all new parts (and I mean all new parts, including a brand new fraction collector) you can get away with about $5,000 - half that cost being the fraction collector. Generally you can skimp and save a few here and there and pull it off for about $1500. When I wrote that post, I was referencing prices from two years ago when I built it, so things have naturally gone up.

Q: Does it save solvent or silica?
A: Not really a solvent saver. I guess, if you’re into recycling solvent it’s easier to do. I do not recycle my solvent, so it saves me nothing in that regard. It obviously saves a shit load of free silica, since I don’t pack my own columns. If you were to, and you packed them correctly, you could run the same columns over and over again saving yourself a lot of silica gel.

Q: How do you load?
A: Loading is easy. Dissolve your shit up into a syringe and inject it onto the loading column. If your sample is fully dissolved it shouldn’t plug the column up but the beauty of working with this ghetto system, is you can load your sample into the guard column and if you include a bit of dead space above the silica, it doesn’t have to even be soluble in your mobile phase. I.E. dry packing is usually not needed. Not only that, but the guard column keeps nasty shit like dirty used Grubb’s catalyst off your nice column, so it’s a must have.

Q:What about air?
A: In the solvent? That’s no problem. But in the column, you’ll want to avoid it, but it’s not the end of the world. The pressure will usually squish the air into the solvent but you’ll want to pump all the air out before you begin. That’s pretty intuitive, I’d think.

Q: What kind of columns do you recommend?
A: I whole heartedly endorse the use of RT Scientific’s packed glass columns. The inital cost is about $100-$200 for smallish columns but the repacking service is cheap and you can run gallons of chloroform and gallons of methanol through them without doing much damage to them. Eventually, even the best packed column dies (especially if you make a habit of cleaning it with methanol). The problem with RT Scientific is that they’re scatterbrained so, while they offer a superior product, they’re not the best at customer service. Otherwise I use ana logix columns (35 micron pore size silica) since they’re consistently well packed and we get a great deal on them.

Q: Do you really run one column a month?
A: One FLASH COLUMN. I run about two columns a day, sometimes more, depending on what I’m doing. I like to have a full bench. That being said, I take my sweet time running columns. Usually run one during the day and run the other over night. Since it’s automated (with a fraction collector) I’m not really hurried into forcing the shit through the column unless I have to. Most compounds I’ve encountered prefer to take their time on the column and a slow drip produces great separation. That being said, I can crank it up and be done in half an hour - if needed. Obviously, if my ghetto column is running, I can always pack a flash column and run it, so it’s quite possible to separate two things at once.

Q: Does it save you time?
A: Fuck yeah. Why you would run a flash column when you could do it automated is beyond me. And, even though I like to toot my own horn a bit, I’m not as good at flash columns as my MPLC and I’m not very patient with collecting the test tubes. If I had an auto-TLCer that would be great.

Q: What about a UV detector?
A: That might be nice and I’ve got the general electronics figured out if I wanted to make one in the machine shop, but I don’t. The UV detector can’t tell me anything about coeluting shit anyway, which is really more important to me, so I’d have to run a TLC anyway. I guess I could rig up a photo diode array… that would be pretty pimp. But that’s just retarded.

I don’t like to run columns and I generally don’t. My syntheses are so bad assed, I generally work harder at figuring out purification methods that don’t require silica because columns are very, very wasteful and it hurts the earth and Al Gore’s feewings. That being said, most of my shit is purified on a column. But I’m both smart and lazy so I’ve used technology to make my life 900% easier by running flash chromatography once a month. My other column is a ghetto MPLC and I LOVE IT OMG LOL!!!!1!1one!.

An MPLC is the “medium pressure” variant of an HPLC, but they really couldn’t be further from HPLCs. Whereas HPLCs are unmistakably scientific instrumentation, MPLCs never are. They’re simple purification machines and, as such, they shouldn’t cost $6000. (a bargain when you consider the $40,000 an HPLC costs) I provide here the means for you to build your own MPLC for purifying organic goodies for under $1500. If you can’t swing that, you should get another lab. Since I’ve run all kinds of things on this set up, I can promise you that if you can separate it on a flash column, you can separate it better on an MPLC. I list vendors here, but you can buy from anyone. These are just the guys I buy from and I’m not getting any money by mentioning their names (though I should) so I can be candidly honest about all of them.

MPLCs can be divided up into 3 parts: The part that runs the solvent, the place where your shit is separated and the part that collects the solvent as it comes off the column. The first thing you need to consider is a pump and a solvent system. I run a lot of binary gradients, but that doesn’t mean I need to buy two pumps. All it means is I need to buy two bottles, one of which has an awesome screwcap top. The pump I have connected it to is an FMI “Q” Pump. You can find out more about these guys here at their website. The pumps can produce a lot of pulsation, but that’s taken care of down the line. This pump is a cheap one and I’ve let it run dry over a weekend and it still keeps chugging. It’s grade A good shit. The whole thing is about $500. You can control the flow rate by twisting a little knob. It not only gets pretty fast, but you can even make it go backwards, which I have yet to find a use for. That bottle is obviously from an Acros bottle and that PFTE cap was purchased from RT Scientific. Essentially, as a vacuum is created in the brown bottle, it pulls solvent from the clear bottle. This is how I get my gradient. It’s very much a true gradient - as much so as a 50mL prep HPLC binary system can produce. That silver thing the brown bottle is sitting on is an old shitty stir plate, of which most labs have a shitty one lying around.

That’s the first part. The second part involves the actual purification and sample introduction. That’s actually even cheaper. As you need to purchase an $8 disposable column from Ana-logix (you can ask for a free sample pack from a sales rep), a $30 gas tight syringe, a $70 3-way lure lock and a small glass loading column, also available from RT Scientific for something like $100.

The whole assembly is connected with about $20 worth of tubing and I’ve run more than 300 liters of chloroform (seriously) through this set up. Nothing will touch it. The pulse suppressor is probably necessary. You can buy it from FMI (see that link above) for something like $250. That’s a lot of money, but separation is generally unaffected if you keep the pump speed low. If you can afford it, get it. So, that’s pretty much all you need if you want to collect by hand and you’re still under $1000. Collecting by hand is awfully gay and sort of defeats the point of “automation” since I find nothing more enjoyable than setting up my MPLC and going out to lunch or writing a blog post (the MPLC is indeed pumping as I write this). But this isn’t such a big deal. While fraction collectors are notoriously over priced, Ebay always has good deals on them. Indeed, a quick search turned up 66 different items. The best part is, if you pay for it with your own money you can tell people to fuck off if they want to use it and you can take it with you to your next job/postdoc/whatever. I didn’t have to buy my own, but life without it would be the sucks. Indeed, here is an Ebay store selling the older version of what I’m using right now for only $250.

So, there you have it. Automated for under $1200. You can think of it in terms of saving money in solvent and silica (you won’t) or think of it in terms of saving time.

Now… you could be asking yourself “But Kyle, you’re rich and famous. Why are you using such a ghetto-assed-fuggly MPLC set up like that?” To which I would respond: Because. I built it from NOTHING AND MADE IT PERFECT. And no one will use something that looks like a bunch of shit hobbled together so I pretty much get it 100% of the time, even though it kicks so much ass its feet are forever covered in shit.

I don’t want anyone taking the impression that I, Kyle muthafuckin Finchsigmate, am in any way disparaging those who do natural product total synthesis. You may have gotten that since sometimes people read comments and attribute them to the post author and, well, it confuses some people even more. I am not opposed to TS research. But… there are two generalizations about TS that I want to expel. Firstly, structural conformation is necessary by total synthesis and drug targets are often inspired by the complex structures of mother nature. You’ve got to do one to get the other. Secondly, it’s a good place to test new catalysts and methodology. The point of many papers in TS, in fact, appears to be to demonstrate some minutia of chemical intuition is correct under the guise of a giant molecule rather than to set out to make a giant molecule with the ancillary hope that you prove that some minutia of chemical intuition is correct. A bonus third reason is it’s easier to develop synthetic pathways that are flexible so that derivatives could be formed at specific positions - objective more easily done inside a total synthesis lab.

It is frustrating that none of these points were raised in the keyboard gnashing in the last post. A lot was said about the need to “train organic chemists” which isn’t a reason to fund TS but it’s a good reason to do it - a chemist who does nothing but attempts to synthesize the hardest compound they can is likely most qualified to produce compounds for drug testing (though this isn’t necessarily always true.) There was one misguided attempt at claiming certain organometallic reagents originated with TS, but tripping over the first hurdle out of the gate pretty much ends the race. Still I give that person credit for trying. If there is one stereotype about TSers that needs to be addressed it’s that they have no idea why they’re doing what they’re doing. Of all the stereotypes, I encounter that one more often.

On the other hand, there was a lot of name calling and vitriol reserved for TSers, namely for their arrogance. This is a stereotype which lacks true self analysis. I can think of a few of the most arrogant people I know in my department and, to be honest, I can think of only one that I find repulsively arrogant in total synthesis. The rest are in various other groups doing various other things (even BIOCHEMISTRY!). The distribution is pretty broad.

But, as I leave at night, when I look back at the building - most of the labs are dark. The biochemists are clearly gone, the inorganic chemists and computational chemists all have their lights out, indeed, the only lights in the building that remain on are those of the labs that do organic synthesis (including my own). So maybe that sleep depraved determination gives them some legitimacy? I don’t know.

I think my point is, everyone should get out of their labs and walk over to meet other people who do other work or make an effort to read outside your field or go to seminars that aren’t related to what you do. Have the balls to ask a question. I’ll be honest with you I’ve asked some pretty retarded questions in seminar but I don’t give a fuck. They sounded good in my head and I’ve gotten to be WAY too cynical about the notion of “intelligence” to care what other people think of mine. The only way you’ll ever know is if you ask and the only way you’ll ever ask is if you build up the nuts to do so