I was mentioning chromatography last week, and I’ve been running several columns this week myself. I’m doing them the new-fangled-with-sufficient-funds way, which has been the standard in the drug industry for many years. You buy the columns of silica gel pre-packed and plug whatever size you need into a machine. Then you load your sample on, tell it what solvents you want to use, put in a rack of test tubes, hit the button and go do something else.
You can set the machine to collect all the solvent that comes off, or (if your compound absorbs ultraviolet light) to only collect when something UV-active starts coming out the other end. Twenty minutes or so later, you come back to a rack of fractions and a printed map showing which UV-active peaks are in which tubes. All this is very nice, and would have caused me to faint with desire if I’d seen it when I was in grad school – not that I could have, since plug-and-play systems like this weren’t on the market back then.
The standard way was (and is, in less well-funded environments) to slurry up your silica gel in solvent, pour that into a glass column, push the solvent through with a stream of air or nitrogen pressure from the top (usually holding it down by hand to keep things from getting out of control), loading your mixture, and eluting fractions into test tubes or Erlenmeyer flasks until you’re sure that your stuff is all out. I wouldn’t want to guess how many columns I’ve run by hand like that over my lab career, but it’s been several years since my last one, and I don’t see another one in my future, with any luck. (For those of you who want to see how it's done, and have twenty minutes to spare, the folks at MIT will tell you all about it).
It’s hard to mess up the automated systems, although you should never underestimate the ingenuity of the user base. But the hand-run columns can easily be loused up in all sorts of ways. Perhaps the most spectacular I’ve seen was when the guy across the hall from me in grad school, who I’ll call “Bob”, since that was his name, decided to run a big column using DMSO as the solvent.
Most of my chemistry readership will have just looked at the screen and said “He did what?” DMSO is a mighty odd choice for a chromatography column. It’s a strong, strong solvent, for one thing, and would mostly just be expected to dissolve everything and sweep it right out the other end. And it’s thick and viscous, too, compared to the solvents that reasonable people use, which means that it would be no fun to get it to come out that other end at a reasonable rate.
But that was Bob’s choice, and he was working on a bunch of nasty, insoluble stuff, so DMSO seemed like a good idea to him at the time. But he didn’t run his column as I’ve described above. He was of another school of setting up columns – apostates, if you ask me – which advocated packing the silica gel into the column dry and running solvent through it before loading the sample. (That always seemed to take longer and use up more solvent, as far as I could tell).
It was a particularly ill-suited method for running a big honking DMSO column. DMSO, as you’ve probably never had the chance to notice, has rather exothermic solvation behavior with silica. In non-PhD language, it gets very hot, very quickly, when it wets the dry powder. So when Bob started, against all odds and a lot of common sense, to force a big bolus of DMSO down his dry column, things shortly got out of hand. Next door, I heard a big “POW!” and ran over to see what it was this time.
There was Bob, staring with dismay at the remains of his column, which had cracked and spewed DMSO-soaked silica all over the bench. In retrospect, he’s lucky that it didn’t shrapnel all over the place. As it was, he had an awful mess to clean up. I never got around to asking him just what he was going to do with all the DMSO fractions he would have taken off the column - evaporating that stuff off is no joke, although it's another problem that yields to sufficient funding. But, then, if sufficient funds had been available back then, Bob never would have been running a column in DMSO in the first place. . .