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Day Off

Rather than speculate about the UK this morning, which does seem to be the thing to do, I’m going to plead illness instead. I’m fighting off a sinus infection, which I could certainly have done without, and I’m functioning at less than peak levels. The frontiers of sciences are going to have to do without me until Monday, and the politicians, well, they pretty much seem to do without me all the time. Which I suppose is one reason why some people voted “Leave”, now that I think about it, although I’ll bet that some of them are now thinking that they didn’t expect quite so many people to vote it alongside them. . .

Update: after a few days, I am much improved. I have to say, I’m glad that there are still infections out there that are susceptible to good old amoxicillin (and I’m also glad that that’s the kind I encountered!)

40 comments on “Day Off”

  1. TroyBoy says:

    Get better soon, Derek!!

  2. Mark Thorson says:

    Since we’re not getting anything new today, I thought I’d ask the audience what is the weirdest unexplained phenomenon you’ve run across. Like maybe a highly colored compound that should be completely colorless. Or a reaction that runs faster at low temperature.

    1. Ben T. says:

      This doesn’t count as unexplained, but during my few years doing synthesis I once made a compound with two completely chemically distinct neighboring protons that had, coincidentally, near enough to identical 1H chemical shifts that they didn’t split each other. They showed up as a perfectly shaped singlet (in a 500 MHz spectrum no less). Caused me a lot of confusion until I took a spectrum in methanol instead of CDCl3 and the protons showed up as doublets like half a ppm apart. Added a drop of methanol to the CDCl3 tube and the “singlet” split apart.

      I guess theory says that’s going to happen, statistically, every once in awhile, but it was freaky to see it in real life!

      1. Richard Blaine says:

        Had the same thing happen back in grad school, although back then only had a 200 MHz magnet. Still, a sharp singlet in some solvents, and an AB quartet in others. Also could be driven one direction or another to some extent with temperature. This was my introduction to NMR weirdness.

    2. A Nonny Mouse says:

      0% conversion with potassium carbonate; 95% with sodium carbonate.

      And, yes, I am one of the ones who are now wondering if I did the right thing but it’s too late to change now……………

      1. Vasili says:

        Most probably the carbonate that worked was the finely grounded one and the other was granular.

    3. Curious Wavefunction says:

      “Or a reaction that runs faster at low temperature.”

      Cold denaturation of proteins comes to mind. It’s probably because the energy barriers are lowered at cold temperatures.

      1. Peter S. Shenkin says:

        Protein denaturation (including cold denaturation) is in general a thermodynamic phenomenon, not a kinetic phenomenon, and as such has nothing to do with barriers. It is the consequence of the fact that denaturation exhibits a negative Delta-H at low temperatures and a positive Delta-Cp of reaction. It was recognized early on that such parameters are also exhibited for the dissolution of hydrophobic compounds in water, and this analogy led to the hypothesis that protein folding is driven by agglomeration of hydrophobic groups in the interior, away from water. Of course, it’s more complicated than this, but this simple picture explains cold denaturation on purely thermodynamic grounds.

    4. old man says:

      prepared a solution of lysine in a mixture of water and THF that was homogeneous when cold but biphasic when warmed up. Could cycle the phase split with a hot air gun. Probably a hydrogen bonding phenomenon.

      1. Richard Blaine says:

        Possibly related effect to what you observed, there is a well-known, although rare, phenomenon in polymer science known as the Lower Critical Solution Temperature. It stems from changes in the relative strengths of polymer-polymer, solvent-solvent, and polymer-solvent interactions with temperature. This behavior can lead to the seemingly impossible observation of a solid crashing out of from a perfectly homogeneous solution upon heating, then re-dissolving on cooling.

        I discovered one example of this back in grad school by sheer dumb luck. My advisor was totally fascinated. He spent hours that afternoon happily playing with a test tube of polymer + THF and a hot gun, repeatedly driving the stuff in and out of solution. Simple things for simple minds, we thought…

        1. PS says:

          Also referred to as ‘Cloud Point’

        2. Mark Thorson says:

          Hmmm . . . maybe could make a toy out of this. Or a lava lamp that doesn’t have all that stuff congealed at the bottom when it’s cold. It’s totally clear cold, and then the circulating stuff appears when it comes up to temperature.

      2. Triton says:

        This phenomenon can be used to isolate membrane proteins from soluble with Triton X114!
        See paper [Phase separation of integral membrane proteins in Triton X-114 solution.]

    5. Slurpy says:

      I recently had a 10 L waste container that’s used for 1 M nitric acid, potassium iodide, and the metal we colorimetrically quantify go quickly from its normal orange-yellow color to dark purple and start venting a lovely brown gas, which I assumed was NOx as I rushed it to the fume hood.

      After it happened a second time, I started badgering everyone until I determined that one of our other groups had “borrowed” it from our shelf after filling all of their containers, and it had probably had 75 or a hundred mLs of IPA waste still sloshing around at the bottom after our waste service did their half-a$$ed dumping.

      Not exactly an unexplained phenomenon, unless you talk to the lab tech that did it. She still doesn’t understand why that was bad.

      1. newnickname says:

        Bretherick (Handbook of Reactive Chemical Hazards) describes alcohol – nitric acid as “unstable … rocket fuel.” http://www.ab.ust.hk /hseo /tips /ls /ls005.htm

        I’ve seen the aftermath of a few such explosions. No matter how many times it’s mentioned at safety seminars, it doesn’t seem to sink in until someone is rushed to the hospital or the hazmat team shows up.

    6. GladToMoveToProcess says:

      Had a Lewis acid catalyzed Diels-Alder that showed poorer selectivity at lower temperatures. Guessed that at lower T, two LAs were binding to the dienophile, leading to reversed regioselectivity; never figured out how to test this, though.

  3. ksr15 says:

    Oh man, sinus infections are the worst! Get better soon!

  4. Hap says:

    I don’t know. I was trying to react a guanidine with an a-keto aldehyde and got lots of colored foams (rainbow-colored, not just black or red tar) which fell apart when I tried to chromatograph them.

  5. Nick K says:

    The Unicorn reaction – only worked once, and could never be repeated, despite many attempts.

    1. Dalibor Sames says:

      Was Bengu Sezen by chance in your lab at the time

      1. Nick K says:

        No, I did the reaction myself, and it actually did work, albeit only once, unlike Bengu Sezen’s chemistry, which never worked.

    2. HFM says:

      That’s not unexplained, really; it’s a general law of the lab.

      Experiments do not work on the first run-through. Ever.

      If you believe your experiment worked the first time, woe unto you, for it will never work again. If you’ve excitedly showed the results to your boss, even worse; you’ll be spending the next months of your life in a futile effort to reproduce them.

      Whatever went wrong the first time – and something did – produced a result that you interpreted as “correct”. But you don’t know what went wrong, so you can’t do it again.

  6. bacillus says:

    In keeping with Derek’s opening statement, I’m now a guy who went to bed a European and woke up an Englishman. Although exit is going to be a long drawn out affair, I wonder how it might ultimately affect the location of various Big Pharma sites. This might get especially interesting if the Donald is triumphant. BTW this is just a musing, not an excuse to turn this into a Brexit discussion, there’s already hundreds of them today.

    Therefore, in keeping with the spirit of the thread, and speaking as a biologist not a chemist, the most interesting phenomenon I’ve experienced first and second hand is the finding that vaccination sometimes enhances the susceptibility of experimental animals to the target pathogen compared to unvaccinated controls. I’d put it down as God messing with my mind, but I’m an atheist.

    1. Hap says:

      “The universe is a recalcitrant b@$%ard.” Robert Parker

    2. Mark Thorson says:

      This reminds me of tuberculin. Today, we use tuberculin in the tine test and Mantoux test for tuberculosis. But in the early 20th century it was also used as therapy. Tuberculous patients would be injected with tuberculin, they have a bad reaction, and then they’d get some more up to the limit of what they could stand. And this would be repeated until they got well. It was thought that this would provoke the body to attack the bacteria. But it became increasingly obvious that this was not a very effective therapy, and it fell out of favor. During the period when it was controversial, advocates were saying the critics were getting bad results because they weren’t using the right dose. They didn’t really do proper RCT’s back in those days, so who knows? Maybe somebody should do a proper RCT of tuberculin therapy just to nail down whether or not it works. You can still buy vials of injectable tuberculin (for the Mantoux test), so no problem obtaining it.

    3. user says:

      Antibody-mediated enhancement for viruses/intracellular pathogens (e.g. dengue virus), biasing immunodominant epitopes to ineffective ones (influenza), pushing the immune response to the wrong type (e.g. Th2 response when a Th1 would be best for leprosy), or non-optimal innate immune stimulation that leads to tolerogenic response.

    4. NJ BugHunter says:

      Weakly binding antibodies fail to neutralize viruses and can trigger infection of macrophages through the Fc receptor. This phenomenon is responsible for severe hemorrhagic disease in Dengue patients who have had prior infections with a different serotype of the virus. I’d imagine something similar is at play in your vaccinated animals.

  7. MoMo says:

    First failed Cat Allergy vaccines now Brexit. You are doomed, UK, DOOMED!

    Time to hold a parade for the Queen.

  8. Me says:

    Most inexplicable reaction: dithionite reduction of nitro.

    Almost as inexplicable as my compatriots voting Brexit…..

    1. milkshake says:

      dithionite works as a source of HSO2(-) which is the reducing agent, but is pretty unstable in solution. Rongalite HOCH2SO2Na is another variant of the same

  9. Petros says:

    Another key impact of Brexit on the pharma industry will be the removal of the European Medicines Agency from London to somewhere in the EU. Significant changes will have to be made, when the British politicians can be bothered, to permit UK approval of certain classes of drugs such as biologicals.

  10. jomki says:

    The next thing is to build Walls.. what a shame.

    1. Mark Thorson says:

      And make the Scots pay for it!

  11. Insilicoconsulting says:

    What works best against sinus infections? I know there’s healthy skepticism here, but try Quercetin with bromelein . As someone who has repeatedly suffered in the last 3 years, it’s the only orally ingestible thingie that seems to work. (Not counting nasal drips , steam etc)

    1. Crocodile Chuck says:

      Thanks, insilico-I’ve got a horrible one. Will try today.
      Oh, & hope you’re on the mend, Derek

  12. Pennpenn says:

    Ugh, gotta hate a sinus infection. Made me wish I could just remove the front half of my skull and flush it out with a hose. Of just replace it with a clean copy.

    And yeah, Brexit was a dumb idea to begin with, ruin the country all to appease some xenophobic idiots who are congenitally unpleasable. And it may well end up costing them Scotland since the Scots voted in favour of staying (and “You get to stay in the EU” was one of the major draws in staying with the UK during the last independence referendum).

  13. gippgig says:

    Might be of interest:
    NCIS June 28 on CBS at 8PM EDT – “Abby is trapped in a pharmaceutical lab when armed men enter the building and take hostages.”

  14. Dave says:

    Hope you feel better, Derek.

    I would have gladly traded your sinus infection for my intestinal virus last week. Fortunately, the thrust was pretty evenly balanced, so I didn’t go rocketing off into the sky. 🙁

  15. ppjm says:

    Here is just a tiny consequence of the Brexshit clusterfuck:

    http://www.huffingtonpost.co.uk/wayne-beynon/brexit-what-now-for-intel_b_11196522.html?utm_hp_ref=uk-news

    A lot of pharma is going to head to the European mainland…

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