Wednesday, November 13, 2013

Highly Active, Barely Seen

Bench chemists know it's tough enough to control the multiple variables that go into any one reaction. But what about the ones you never saw coming?

The literature abounds with cautionary tales: Trace nickel (II) in the NHK reaction. Trace phosphate in the GFAJ "arsenic life" saga. "Metal-free" couplings found to rely upon parts-per-billion levels of Pd or Fe contaminants in "pure" sodium carbonate.

In yesterday's post, a volcanic mudpot-dwelling bacterium flourished in lab culture, but only when its growth media was doped with a rare earth element (REE). The authors had quite a bit of trouble eliminating residual metals from the growth media:
"When testing REE dependency (salts > 99% pure), it was observed that standard serum bottles resulted in a highly variable growth. . . Sand is one of the major raw materials of glass and may contain considerable amounts of REE, and Ce may be used as an additive during glass manufacturing. It was concluded that REEs in glass are extractable, at least partly, by the acidic media used."
Whoa! I confess, I've stirred hundreds of acidic solutions in glassware of all shapes and sizes, and never once have I assayed the rare earth content! And the glass wasn't the only cause for concern:
"Contact of the acidic medium with needles used for sampling was minimized as the metal seems to release REE as well. For these experiments, concentrations of trace elements were (in μM): NiCl2, 1; CoCl2, 1; Na2MoO4, 1; ZnSO4, 1; FeSO4, 5; and CuSO4, 10."
For those playing at home, some of these trace metals guest star at the ppm level in this media. Due to the materials used in glass and disposable needle manufacture, I guess there will always be a baseline of (potentially active) metal contaminants in acidic solution.

Want to take bets that one or more play roles in our favorite cross-coupling reactions?


  1. Could they not just use plastic equipment?

    On the subject of cross-couplings: I'm used to dealing with 1-5 mol% loadings at minimum. Is achieving a good coupling with ppb quantities impressive?

    1. Anon: They made the switch to plastic, then were forced to use single-use disposable bottles when they discovered that the REE stuck to the inside of the bottles.

      For commercial-scale preparation, catalyst loadings <1% are favored. Very few metals can achieve ppb-level catalysis, but more are being discovered as we tease apart organometallic mechanisms and incorporate higher-end microscopy.

  2. CoulombicExplosionNovember 13, 2013 9:51 AM

    Plastics have their own issues. Example -

  3. Rare earth elements are actually much more abundant than people often think. Check this link out: (yes I know its wikipedia, there are better scientific articles out there, but I like the graphic).

    "Rare earth elements" are more abundant than silver, iodine and mercury!

  4. One approach to dealing with the potential presence of metals is to just do everything in a huge excess of EDTA or dipicolylethylenediamine