Stir bars – it was the stirring bars all along. That’s the take-home from this paper, which shows definitively that (A) you cannot truly clean one of the things and that (B) the stuff that’s stuck to them can be influencing the next reaction they’re used in. At one level, I think that few organic chemists will be surprised that the Teflon-coating little thingies can be contaminated. We’ve all seen them in various stages of discoloration, and not just the jet-black surface that they emerge with if you use one to stir a Birch reduction. No, they pick up grey, brown, yellow, and orange tints with time. Some of that is ferroelectric dust particles from who knows where (a bit like the dust experiments on the Mars rovers), and some of it, as this new paper shows, is material from past reactions that gets imbedded in surface defects on the coating itself.

The chapter-and-verse on those defects is one of the striking things about this. The paper cites a number of examples that have already shown up in the literature on stirring bar contamination, but this is the first detailed look at this level. Micrographs show the sorts of damage that accumulate on the surface of the Teflon, and you can see the metal particles lodged in there. What’s more, it appears that these actually have a thermodynamic affinity for the fluorinated surface once it’s been microscopically damaged. The binding is both mechanical and chemical. Shown is one of the scanning electron microscope images, along with EDX (energy-dispersive X-ray) analysis of the same region. Anyone with experience in metal-catalyzed chemistry will appreciate the problem, and there are a lot more images like that (and worse) in the paper and its supporting information.

To be sure, the advice is always to use fresh stir bars in any sort of crucial reaction, but there are still a lot of grungy-looking (and not-so-grungy-looking to the naked eye) specimens that are getting used all the time, and surely affecting reactions in unrealized ways. Platinum, cobalt, iron, gold, palladium, nickel, chromium – all these and more show up, and as very small high-surface-area particles. Interestingly, some of the discolored-looking stir bars the authors examined didn’t seem to have all that much metal contamination, while others that looked more appealing definitely did. Cleaning under the usual conditions did not remove all of the metals, and cleaning under more vigorous conditions will damage the surface further, leading to still more contamination at the first opportunity.

As the authors show, you can get effects from leaching out of these contaminants into the solution, from combination of different metals with a catalytic system already in use in the reaction, or even promotion of side reactions in situations where you weren’t even thinking about metal catalysis at all. This could explain a synthetic mystery of my own, perhaps – while doing my graduate work, I had a reaction using a “higher-order” cyanocuprate reagent to open an epoxide. It worked twice, with high yields, on a scale of hundreds of milligrams, and then it never, ever worked again. Just stopped dead. Nothing I tried ever produced a trace of product – same old reagents, fresh new reagents, artificially aged reagents, same bottle of THF, new bottle of THF, rigorous drying or exclusion of oxygen, rigorous intentional exposure to varying amounts of water or oxygen. Nothing, nothing. If I hadn’t had the product from those first two runs sitting on my bench with its TLC and NMR right in front of me, I’d have thought the whole thing was a hallucination. Now I wonder if it was the stir bars!