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Stirring Bar Contamination

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!

88 comments on “Stirring Bar Contamination”

  1. Anonymous says:

    I remember hearing something similar several years ago with 96-well plates being used for catalyst screening – without any catalyst added the active wells were still active… Not studied to this level of detail of course.

    1. Pharmacologist says:

      Also reminds me of reports of stuff leaching out of microcentrifuge tubes in biology experiments, like plasticizers or dyes used in the colored tubes. I have a batch of purple-capped sterile 50 mL conical centrifuge tubes, they give off quite a strong scent of who-knows-what when you first uncap them and take a whiff. Luckily most experiments don’t seem to be sensitive to that kind of thing, nowadays pretty much everything used in biology is plastic rather than glass.

      1. Isidore says:

        I saw this first-hand. We were preparing samples for MS analysis by MALDI-TOF MS, which for those not familiar involves mixing the protein sample with a UV-absorbing MALDI matrix (e.g. sinapinic acid), depositing on a metal plate and after drying the plate inserting it into the mass spectrometer ion source. However, the samples refused to dry, they would form a kind of viscous gel-like material instead of the protein co-crystalizing with the matrix. The problem was traced to a new lot of 0.5 mL polypropylene tubes used to prepare the samples. As far as the manufacturer would tell us there was no difference between the particular lot and previous lots of the same tubes, which we had been using without ever encountering this problem. We threw away all the tubes from the particular lot.

      2. MrXYZ says:

        We recently saw (smelled) this as well. We were having serious cell viability issues, which was affecting experiments across our company. It took us a while but we finally tracked it down to the 50 ml conicals we used when resuspending cells. Switching to a different vendor solved the issue immediately.

        Several years prior, we had microcentrifuge tubes that inhibited our PCR reactions.

        Caveat emptor!

      3. Free Radical says:

        I’m reminded of a report in J. Nat. Prod. of a supposed fluorinated arene natural product. It was followed by two papers that re-analyzed their results and found that it was a BHT-related compound that was probably leached from plastic. See https://pubs.acs.org/doi/abs/10.1021/np500643g and cited references.

        1. kriggy says:

          Might be stupid question but how could they missed that ? I mean it should be quite obvious from MS that the fluorinated structure does not match? I mean if its possibly the hydroxyderivative or the quinone then the MS should be very different from the fruorinated compound. ALso, all of the compounds are symmetric so the tbutyl groups should have one signal instead of two

  2. A Nonny Mouse says:

    Yes, palladium and glassware was my downfall. Even after going through industrial dishwashers it is still retained. Caused me several weeks of trouble until I gave up before knowing the cause and developed a new simple process to the product (Bis-TMS peroxide).

    As an aside, I once lost a couple of stirrer bars down the sink in the ancient lab that we were in which had open drains (won’t talk about the fire from Italian post-docs/toluene/cigarettes…). Being badly funded I pulled the bench out and, underneath the one inch layer of mercury (!), found about 20 stirrer bars. I repeated this in all the other catch pots and found over 200.

    1. Derek Lowe says:

      All that mercury kept ’em nice and protected down there, I’m sure. What sort of potatohead pours mercury down a sink?

      1. Old Pump Kicker says:

        A chemist friend of mine caught her technician in the process of dumping mercury in the sink. Given that this was at a U.S. Government facility, the sink likely had a label (as I saw at other labs) enumerating specific materials _not_ to be poured down it.
        This stupidity was one of the reasons she transitioned to water treatment QA.

      2. Silver Birch says:

        Last year, we received this email from the University Health and Safety Adviser:

        “At the end of last year an incident occurred on the XXXX campus where someone attempted to incorrectly dispose of a significant mercury by pouring it down a urinal in a men’s toilets. This was only discovered during routine maintenance when the full urinal trap was emptied into a nearby toilet and the mercury was spotted by the plumber. The total amount of mercury disposed of was estimated to be between 100-150ml, far in excess of something like a broken thermometer.”

      3. A Nonny Mouse says:

        Probably about 70 year’s worth of students as the lab hadn’t changed since it was built in the early 1900s!

        These were BIG porcelain pots about 2ft by 1ft and there was about an inch in every one. It did cause quite a stir at the time. I can’t believe that no one had checked in all that time.

    2. KazooChemist says:

      The stir bars sank in the mercury?

    3. Nick K says:

      As a graduate student I managed to save the lab a certain amount of money by discreetly “fishing” for stirrer bars with a magnetic retriever down sinks in other groups’ labs. After soaking them in aqua regia I could reuse them.

      1. A Nonny Mouse says:

        Probably back in the Whiffen Lab where mine were from (as you seemed to spend more time with us than in your building!).

        We did have some good parties, though, didn’t we!

        1. Nick K says:

          The parties with SVL and AGMB are still talked about today!

          1. A Nonny Mouse says:

            Well, at least we are!

            You were very naughty getting involved with “Mick the Nick” and PJ Brockham setting off that bin bag bomb from the GC cylinders (probably the only use it ever had). Only 6 police cars … did dampen the party slightly.

    4. Anonymous says:

      More mercury (and scarier!) stories In The Pipeline, here (link in handle):
      “Chemical Storage, Good and Not So Good”
      10 November, 2016

  3. Hap says:

    Stir-bars are kind of expensive to use once and discard, though, and mechanical stirrers aren’t useful for small reactions. What do you do?

    1. John Wayne says:

      I use the stirbars that you buy for the crimp topped microwave vials (Chemglass CG-4920 and similar). If you negotiate with a larger purchase, you get get them for about a dollar each (a bit more for the larger ones). This is a reasonable price compared with the cost of your time.

      1. t says:

        Yep…everything we use is done in disposable vials with disposable stir bars. Probably cheaper than using a ton of solvents/soap/water/acid/base to clean.

        1. Derek Lowe says:

          I’ve gradually switched over to that over the years as well. Scintillation vials and microwave stir bars, all the way.

          1. An Old Chemist says:

            In my third world country, I used to take little iron bars (occasionally paper clips) to the glassblower and get them sealed in glass. Now, this is as clean a stir bar as you can ever get. I suggest that all the organometallic chemists should give this a try when they are worried about residual metal contaminations affecting their next reactions.

          2. anon electrochemist says:

            Embedded iron in glass is standard practice for hardcore physical-analytical work, like single crystal electrochemistry. You pirahna/aqua-regia clean your glassware after every. single. experiment.

          3. Nick K says:

            How Medchem has changed since the 1980’s! In my time (adopts shaky old man voice) we aimed to make at least a gram (!) of final product, and the smallest vessels we normally used were 50ml RB flasks.

      2. ap says:

        I run the stockroom at a large community college. I can get 1 in stirbars for 75 cents in lots of 100.

    2. Anonymous says:

      Hap, “small reactions”: If you mean really small reactions, then
      1. Into the Vortex (Hammerhead) – brand names: Vortex Genie, Wiggle Bug, Vornado, Vortamixer, others
      2. The Pipettes – give the reaction the old up-down in the pipette (the long skinny tip of a Pasteur pipette). Pull it into a capillary for smaller volumes.
      3. Gemini Syringes (The Flaming Lips) – for even smaller reactions (and I’ve done reactions in melting point capillaries), give the reaction the old in-out in the microliter syringe needle / barrel
      4. What’s the buzz? Tell me what’s a-happenin’ (JC Superstar) – sonicator: you can secure a small vessel (capillary) in a larger vessel (test tube, vial, flask, beaker), add liquid to surround the capillary, and put that outer vessel in the sonicator bath. Some of the buzz still gets through. Adjust for other size vessels.
      5. Le Tourbillon de la Vie (Jeanne Moreau) – if you seal a small vessel (mp capillary; screw cap tube; larger), you can get some mixing by tilting or rotating back and forth. Depends on the viscosity, surface tension, and so. I have mounted reaction vessels (vials, tubes, etc.) on my rotovap axis to let them rotate slowly for hours.
      6. Whip It! (Devo) – seal a capillary and give it a good wrist snap to move liquid from one end to the other. Reverse. Repeat.
      7. Drop It Like It’s Hot (Snoop Dogg) – take a length (~100 cm) of ~4 – 6 mm OD glass tubing; hold it vertically, resting the bottom on a suitable surface (not too hard, not too soft); drop your sealed capillary (liquid at the TOP) down the top of the outer glass tube and watch it bounce few times and propel the liquid to the bottom of the capillary. Invert. Repeat.
      8. Microwaves – Never mind. That’s where this started.

      1. Hap says:

        I haven’t done reactions for a long time (I’m not in lab anymore) but I generally did reactions in 10-25 mL RB flasks, so not so small as you’re talking about (though there are better analytical tools now, so it’d be easier, particularly for optimization, to do runs on that scale). The stir bars were big enough that I wouldn’t want to use and discard them, and too small for mechanical stirring (at least I thought).

        1. Anonymous says:

          Hap: My preferred flasks were 15 mL pears. I bought a bunch and was the only one in that group who used them routinely and I added a nichrome loop to each (for hanging on the balance hook). It was easy to tell when someone had taken my flasks from my bench. Teflon “fleas”, paper-clip stir bars, and others worked fine in the 15 mL pears.

          I also did NMR tube reactions (in deuterated solvents) with a flea or paper clip stir bar. There are NMR-tube sized rubber septa for controlled atmospheres. Use the long neck as an air condenser during reflux. Just use another magnet to slide the stir bar up the inside of the NMR tube and out the top to get a spectrum. Back into the pot if the reaction wasn’t done.

          Rather than add another separate “reply”: Does anyone know the SUBMISSION date of the originally cited paper (paywall), ACS Catal., 2019, 9, pp 3070–3081. DOI: 10.1021/acscatal.9b00294 . Publication Date (Web): March 12, 2019 ? Did they cite the December 10, 2018 “In The Pipeline” at all?

  4. Uncle Al says:

    Cleaning glassware in KOH/EtOH works. Do it in sulfuric acid/dichromate and you have chromated glassware. Clean Plexiglas with sulfonate syndet, see sulfur on medical devices’ surfaces. PPO-PEO syndets probably adsorb…but that is analytically FDA OK.

    Much tax money was NIH-spent trying to create bulk biocompatible engineering materials. Biocompatiblity is but a monolayer deep, as is contamination. One suspects a not insignificant fraction of failed device surfaces (re Kusserow rings) is adsorption or blooming (plastic mold release). Individual cells and all the stuff in blood, plasma, lymph, CSF, you name it, have a different scale of perspective.

    1. UudonRock says:

      I have often seen chrome catylized reactions in glassware cleaned with dichromate. This paper makes me wonder if someone should make a line of pre-catalyzed stirbars for specific reactions. Might be lucrative…

      1. Jeff Evarts says:

        Pd-on-stirbar hydrogenations, anyone?

  5. MTK says:

    I guess if you start seeing some inconsistent results one would have to run control reactions using the exact same glassware, spin bars (and different or new ones) with and without catalyst to make sure you’re not seeing some unknown contaminant from those things.

    ugh.

    1. SP123 says:

      Just write on the stir bars with a Sharpie and you’ll know which one to use when repeating the experiment.

  6. Istvans dog says:

    This is why you should always take an NMR of your stirbars before you use them!

    1. NHR_GUY says:

      Careful what you put out there. I can bet you some first year grad student is about to follow your “advice” and load up their NMR tube with a stir bar even as I write this.

    2. db says:

      That’s just cruel…

    3. Some idiot says:

      What a lovely thought… question is, what would happen? Would it smash before it got in the probe, would it bend and break the tube, or would you have someone going to the person responsible for the machine, and say “I don’t know why, but I can’t get my sample to eject…”

      My hyperactive imagination also hears a somewhat more urgent sound than the usual sound of a sample descending under a controlled decrease in pressure…

      Wonderful mental images… but just not on my 600 please…

      Ooops… last mental image: said instrument responsible removes probehead in order to remove sample (or so they thought…)…

      1. Anonymous says:

        NMR accidents: I was told the story (by a field tech) about a student or tech doing something on the magnet (routine LN2 refill from the top? adjusting screws on the probe from below?) and a small screwdriver got sucked into the bore. (USE BRASS OR NON-MAGNETIC TOOLS NEAR THE NMR!!) The NMR company had to send in their techs to de-energize the magnet, remove the tool, do an inspection, and power it back up. I heard another story (from a field tech) about a screwdriver that got sucked into a magnet, pierced the wall of the bore but did not reach the coils. That one had to be de-energized and rebuilt. …

        Now that I think about, there are some youtube videos of accidents that happened when people were trying to move / relocate energized MRI magnets! One misstep, the magnet quenches, and you get plumes of LN2 , He spewing all over the place. I just googled “MRI Magnet Quench” and there are too many!

        1. Derek Lowe says:

          I can see where it would be tempting to move an energized magnet (time, wear and tear, helium $$), but it sounds like a risky choice with a good chance of costing you all the time and money anyway. . .although nowhere near as bad an idea as bringing anything ferric within close range, that’s for sure.

          1. Nick K says:

            They successfully moved a 300MHz NMR at Pfizer Sandwich in the late 1980’s. The corridor down which the magnet (still cryogenic and superconducting) was taken had metal lockers on either side. Very wisely, these had been securely taped up beforehand.

        2. Annonned says:

          One installation engineer told me of setting-up a new NMR in a new building. The magnet was put together and left alone in the empty room for a couple of weeks with a warning sign waiting to be energized. One morning, few days after they energized it, they found a floor buffer stuck to the bottom of the magnet. The probe was crushed, but I think they said that the magnet was still usable and it did not quench. No one ever came to claim the floor buffer after it was removed.

  7. Magrinho says:

    “higher-order” cyanocuprate reagent to open an epoxide”

    I was once young and idealistic too. It was a coupling vinyl cuprate – alkyl iodide coupling. My batting average was below the Mendoza line.

    1. Derek Lowe says:

      Makes me feel better. My dissertation says “. . .cuprate reagents of all kinds were abandoned after this experience”.

    2. Young Padawan says:

      The Lipshutz cuprate worked nicely for me, although with quite some fluctuations in yield 50-80%. I went for “higher-order” because my iodide was too precious to spent two equivalents per cuprate…

    3. Nick K says:

      Many years ago I had a similar experience with a cyanocuprate. The reaction either worked well (80% yield) or failed completely. We finally traced the problem to the THF ( had to be freshly distilled from Na/benzophenone; Aldrich Dry failed), and to the batch of CuCN.

  8. Rule (of 5) Breaker says:

    Finally! I have wondered about this sort of thing for 20+ years.

  9. NHR_GUY says:

    When I was still in lab I would take my stir bars up in a self made solution of Aqua Regia every six months or so. Not to get rid of trace metals (this solution will tackle even gold) or organics. I did it just to make them more aesthetically pleasing to myself. BTW, haven’t read the paper yet, but I don’t by the “the stir bar ruined my reaction” hypothesis. How much trace material could be on a traditionally “cleaned” stir bar? Probably less than a milligram. Since the MW of the unknown dirt is unknown its hard to calculate how many mmols. If the material was acting stoichiometrically then it would amount to less then 1% of unwanted by product even on a mg scale reaction. Not even noticeable or notable using our typical TLC->LC/MS->NMR analysis of reactions. If it is acting catalytically, then it must be fairly robust with a very quick turn over rate to have a meaningful affect on your reaction outcome. It would be something you’d be interested in and try to isolate if it is so good….haven’t seen anything in the literature to that effect. On the biology side, all bets are off. Who the heck knows what goes on in those systems even when we think we know what we are doing. I’ll go read the paper now and see if I can be convinced of the dirty stir bar phenomena.

    1. Some idiot says:

      Main problem, as I see it, is if a “dirty” stirrer bar was catalysing a reaction. Then others would not give a reaction that worked…

      On the other hand, myself (along time with most process chemists I have known) always kept a special stirrer bar (and spatula) for hydrogenations… mind you, that was just to avoid poisoning…

    2. Anonyanon says:

      Isn’t the whole point of the post the danger of catalytic action? You may as well be adding a pinch of random, finely ground metals to your flask. Presumably the reactions where you want that, you put something in on purpose, and in everything else it just causes problems.

  10. Gilbert Pinfold says:

    My parents were both chemists, and Dad used to keep one or more stirbars in his pocket. It wasn’t until I took high school chemistry did I learn that stirbars did not naturally come smelling of what I now know to be pyridine.

  11. myma says:

    And then there is your magic stuff adsorbing to the pipette tips, leading to less stuff in that little well than you think. I believe there are articles on this too.

    1. zero says:

      I knew someone whose job was to precisely calculate to the ounce how much paint would be required for a production run of packaging bags. They routinely delivered that level of precision or better. That meant knowing exactly how much paint would stick to the walls of the supply vats, the feed lines and the transfer rollers.

      With something as small as a pipette (or small wells), small differences in surface tension and viscosity would have a big difference in how much material gets stuck to the equipment. Sounds like a challenge.

  12. Calvin says:

    Ahh stirrer bar fun. Back in the day we were doing a bunch of Suzukis on a very statically hindered coupling partner. We made this great compound, our breakthrough in terms of potency. But no matter what we did we simply could not remake it. 6 months of effort went with no joy. We were paranoid about whether we’d even made the original compound and so did all analysis we could do to confirm. Eventually, a lab mate suggested we throw in a specific metal salt and hey presto suddenly we could make it again. We were always convinced that the original success was a result of trace silver salts on the stirrer bar (and these were shared across a lab across multiple projects). That was the weirdest coupling I ever saw although we did in the end get away from it with a different partner. But we would never have made that original leap had it not been for the damn contaminated stirrer bar.

    1. Nick K says:

      …and yet people still think Organic Chemistry is an exact science!

  13. Joe Q. says:

    This is the plus and minus of catalysis, in a nutshell. Fantastically huge effects come from small quantities of additives. Figuring out just how those additives work (or even what they are) is another story.

    I remember a case of a “Palladium-free” Heck coupling (or something similar) reported some years back — I think Derek discussed it on the blog — the culprit turned out to be contamination of sodium carbonate used in the reaction by ppm levels of Pd salts.

    1. DRP says:

      Iron-catalysed biaryl Suzuki couplings turned out to be ppm palladium in the base

  14. Marie says:

    Anyone who cooks regularly in nonstick-coated pans (especially at high heat) will not be surprised by this. Doesn’t matter how carefully you wash the stir-fry pan, last night’s garlic and sriracha are still going to be evident if you sniff carefully. And putting the pans in the dishwasher makes the problem worse since it damages the coating and allows more sticking.

  15. anon the II says:

    My sense is that using a dirty stir-bar is more likely to make something happen rather than stopping something from happening. So it’s more likely to help than hurt. So I’ll hang on to that motley collection of stir bars that I’ve accumulated over the years, thank you.
    A new stir bar for every reaction? Seriously? No way!

  16. Anonymous says:

    This topic came up In The Pipeline not too long ago:
    “Ah, Just Pour It Into Salt Water” 10 December, 2018
    (Link in Handle)
    (Note: The Hershberg stirrer, mentioned on 10-Dec, was invented in 1936 by Emanuel B. Hershberg at Harvard:
    Ind. Eng. Chem. Anal. Ed., 1936, 8 (4), pp 313–313
    DOI: 10.1021/ac50102a041 )

    The recent stir bar paper cited by Derek is behind a PAYWALL (aaarrrgggg!). I can’t see the submission date or if they mention being inspired by the 10-Dec discussion In The Pipeline or when they started their analyses.

    Here is some additional info.

    (1) You can make your own micro stir bars from a paper clip and a melting point capillary. Snip off 3-8 mm of paper clip wire; slide down a capillary to the sealed end. Tip off / seal the open end near the metal with a mini-torch. (Note to youngsters: use METAL paper clips, not newfangled plastic paper clips – they will not stir with a magnetic stirrer; hold the capillary in tweezers or a hemostat to avoid burning your fingers; a mini-torch lighter from your local mini-market should work but be careful where you aim it in a chem lab.) You can TEST them by boiling in a suitable solvent (water) and look for air bubbling out from your sealed end. Let cool and look for any solvent that gets sucked back into the capillary upon cooling. When you get good at, you can skip the testing.

    I’ve made a few bigger stir bars from other cheap metal pins or rods and larger diameter glass tubing, but I’m mostly a micro chemist. I usually make “a bunch” of mp capillary stir bars at one time and store them in a vial. Use ’em once; throw ’em away.

    (2) How many of you have used shared high pressure reactors? (I don’t want to bring down homeland security and call it a reaction bee oh em bee.) Even if you use a glass insert, other users might not have and you can still get sloshing around and solvent creep in there. You might think you’ve discovered a new miracle reaction with iron or tin or KHSO4 (avoid using halides in your steel vessels) but you could be experiencing the entire history of that reactor which might include Hg, Pd, Pt, Ir, Rh … and other more potent contaminants embedded in the vessel walls. Another source of irreducibility and disappointment.

    (3) In the early days of microtiter plates, problems were discovered not just with leaching but with non-uniform manufacturing across the plate. People also observed “edge effects” that partially included thermal gradients (wells on the perimeter exposed to ambient temp vs insulated interior wells) and other problems. Billions of plates later, a lot of variability has been reduced and good experiments take known problems into account. But it’s the unknown problems that can still get you!

  17. Peter S. Shenkin says:

    I haven’t run a reaction for over 40 years, but it seems to me that in “the old days” you could purchase magnetic stirring bars sealed into a small glass tube. Not that I ever used one; we used teflon. But is my memory correct? Did they exist? If so, they’d presumably be easier to clean than teflon, and in any case, no worse than the glass vessels one is using anyway.

    1. NHR_GUY says:

      You are not mistaken, glass encapsulated stir bars exist. I’ve seen them, never used them though.

      1. Matthew says:

        I bought and used glass-coated stir bars for running Li-naphthalene reactions, during the 90s if I remember correctly.

    2. John Wayne says:

      You can still get these. They aren’t common because they are pricey, not very small and break easily. They are very useful when using ‘sea of electrons’ chemistry like the Birch, or making things like tin or silyl anions that eat fluoropolymers for lunch.

      1. Derek Lowe says:

        Yep, always had those earmarked for Birch reductions and the like.

        1. milkshake says:

          K-naphthalenide radical anion solution in THF instantly blackens teflon also

  18. physicsguy says:

    A more positive take:
    Can you improve the efficiency of solid catalysts by coating them on a stir bar?

    1. aairfccha says:

      Probably, since you are moving a catalyst-coated surface through the medium.

      1. Scott says:

        That was this business majors first thought on reading Derek’s post!

  19. Benonymous says:

    I heard about a lab running in vivo pain assays for a project. Compounds worked, the project was going well. Then suddenly it didn’t. Someone had used a different pestle and mortar to prepare the sample. Turned out the original one was also used to prepare the standard positive controls for another assay – cox2 ibs. Oops.

  20. Dumbrus says:

    Why not just do the reaction in large scale? It would be nice if 10g scale reaction was contaminate by stir bar. If it did, you would have found a new catalyst.

  21. oldnuke says:

    You learn just how much s/// junk gets adsorbed onto “inert” objects like stir bars when you work with radioisotopes. Just run the GM tube over the “clean” glassware and stir bars, then listen to the speaker go crazy! 🙂

  22. Stephen says:

    I wondered then when the “metal free” coupling reaction papers first came out many years ago how many of were caused by contaminated stirrer bars. I know that Ley suggested it was from contamination from the salts used (e.g. potassium carbonate) but I am not convinced they rigorously ruled out other routes.

    1. A Nonny Mouse says:

      Probably re-use of glassware that had previously seen metals. Impossible to remove even with industrial washers (so I dread to think what a brush in a lab is like).

  23. Barry says:

    We gave up the “chromerge” bath close to 40yrs ago in favor of persulfate (but yes, you eventually have to dispose of the sulfuric acid). And I’ve used aqua regia for cleaning magnetic stir bars for nearly that long. Following either treatment, you want a wash with ammonium hydroxide to be sure you haven’t replaced a spurious metal catalyst with a spurious acidic catalyst on the stir-bar surface.

  24. milkshake says:

    I am doing a small scale peroxyformic acid N-oxidation of a substituted 2,6-lutidine right now. With the formic acid+H2O2 combo being quite touchy, a choice of a stirbar is critical – apart from the danger of the stuff suddenly erupting, a wrong stirbar with the wrong kind of contamination (even a brand new one!) produces plenty of bubbles and none of the desired N-oxide.

    Also, I heard that dioxirane preparation issues are often related to stirbar contamination with metals, and adding some EDTA into the reaction mix improves the reproducibility

  25. Geoffrey Smith says:

    This kind of ‘problem’ has been used to great effect before.

    https://www.sciencedirect.com/science/article/abs/pii/S0926860X12001500?via%3Dihub

  26. Silicon says:

    I worked in an organometallics lab. Always wash stir bars in aqua regia, always retest a working reaction with new stir bars. Problem solved. If it looks like its been through Mount Doom, toss it in the fire Isildur!

    Also, if a reaction isn’t robust enough to handle microscopic amounts of metal or contaminants the reaction probably isn’t going to get used very much anyways so move on to something better and less boutique. I’m sure interesting things could be discovered by examining what on the stir bar caused or stopped a reaction, but who has the time when you gotta publish and graduate.

  27. amidemonkey says:

    Catalyst impregnated 3D printed stirrer bars have been studied by a group at London School of Pharmacy, not sure if they commercially available
    http://generic.wordpress.soton.ac.uk/dial-a-molecule/wp-content/blogs.dir/sites/50/2017/07/Hilton-Dial-a-molecule-2017-pdf-COPY.pdf

  28. Falanx says:

    First thing a materials scientist learns about polyolefins – they are all permeable, to pretty much everything given enough osmotic pressure or hydrostatic pressure. Halogen substituted polyolefins are no different.

  29. xtleyes says:

    Mavens in macromolecular crystallography can relate stories of deep despair from failures to reproduce crystallization procedures affected by trace contaminants in precipitant solutions. This was especially true back in the days of low purity polyethyleneglycols as precipitants. If you’re interested, type “impurities polyethylene glycol protein crystallization” into your favorite internet search engine for fascinating history about this vexation from pioneers Fran Jurnak and Alex McPherson, among others.

  30. Citizen360 says:

    I need expert commentary.
    I have no background in chemistry.

    Straight to the point:
    Is an iron spinbar (magnetic stir bar) embedded inside of PTFE insulated from reacting to the electrolysis process while making colloidal silver?

    Brief Details:
    I make colloidal silver via old-fashioned electrolysis. Power supply provides 30VDC constant voltage. The ‘burn-time’ can be lengthy enough that the two silver bars eventually tend to connect and begin a soft-short, increasing current draw on the power supply and heating the water.

    To avoid this, I manually stir the solution every so often with a glass rod.

    I would like to automate the process by placing the container on a magnetic stirrer and dropping a PTFE spinbar into the container.

    I am concerned that the PTFE will not prevent the embedded iron bar from reacting.

    Is an iron spinbar (magnetic stir bar) embedded inside of PTFE insulated from reacting to the electrolysis process while making colloidal silver?

    I would very much prefer my silver of the uncontaminated variety.

    Thank you in advance for helping!

    1. Anonymous says:

      I’ve done a little bit of electrochemistry and used teflon coated stir bars without any problems. I think you’ll be OK using it in your prep. (I wonder if the silver will precipitate and stick to the teflon.)

      Even though you didn’t ask, “colloidal silver” has also been discussed In The Pipeline a few times. I’ll cut to the chase and link to the Mayo Clinic site (in my handle) which says, “Colloidal silver isn’t considered safe or effective for any of the health claims manufacturers make. Silver has no known purpose in the body. Nor is it an essential mineral, as some sellers of silver products claim. […] Manufacturers of colloidal silver products often claim that they are cure-alls, boosting your immune system, fighting bacteria and viruses, and treating cancer, HIV/AIDS, shingles, herpes, eye ailments and prostatitis. However, no sound scientific studies to evaluate these health claims have been published in reputable medical journals. In fact, the Food and Drug Administration has taken action against some manufacturers of colloidal silver products for making unproven health claims.”

      Colloidal silver is also a topic at Quackwatch:
      http://www.quackwatch.org/ 01QuackeryRelatedTopics/ PhonyAds/silverad.html

      1. Citizen360 says:

        Thank you!

    2. Annonned says:

      I remember seeing and using a few of these Pyrex stir bars, but they were never very wide spread.
      https://www.sigmaaldrich.com/catalog/product/aldrich/z284246?lang=en&region=US

      1. Citizen360 says:

        Thank you for the suggestion. I did look into this for about a minute and discovered that they have generally bad reviews due to the fragility and tendency to easily break (even while tumbling around in a vessel during the stirring process).

        I had high hopes on this for a moment.

  31. Chris Dockendorff says:

    Great thread for practicing chemists…
    Speaking of stir bar contamination, I just stumbled upon this old note from John Eisch in C&EN:
    https://cen.acs.org/articles/85/i4/cautionary-tale-reproducibility.html

  32. BK says:

    In grad school where I was doing A LOT of metal-based catalysis, I ALWAYS used a stirbar only once and then stirred them in concentrated nitric acid over a few days until my cache of stirbars got pretty low. Glassware was always soaked in base bath or no-chromix overnight, depending on what reaction was, and occasionally a nitric rinse was used.

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