Open Thread #2

July 25th, 2011

It’s time for a fresh open thread.  Feel free to use the comments to plug things, post random thoughts, ask questions…whatever.

I’ll open with my top 5 favorite Sporcle quizzes on chemistry:

1.  Name the Element Pairs 

2.  Chemistry Laws

3.  Shared Abbreviations   (Elements, States, and Country Domains)

4.  Common Acids

5.  Elements per Letter

Bonus:  6.  One Letter Elements


79 Responses to “Open Thread #2”

  1. andre Says:

    One Letter Elements: Chip vows by funk.

  2. Hoosier Wannabe Says:

    My company’s “improper internet use” banner appears when I try to take one of these!

  3. HowIsThisForRandom Says:

    I’ve got a friend who really wants to take a look at gluten concentrations in soy sauce. Anyone willing to volunteer a few runs on an overnight LCMS, and do a little sample prep (should just involve making a few dilutions in eppendorf tubes, spinning down and making a gluten control); I no longer work in a chemistry lab :(

    We are trying to look at gluten concentrations in soy sauce as some are advertised a gluten free but are interested in gluten concentrations in regular soy sauce….might be interesting and you can take credit for anything interesting that comes out of it.

    you can email me at:

    oldpaper2002@the company that is named after a sound that a cowboy makes.com

    This certainly queues a posting topic…”Weirdest things you’ve been asked to look at as an analytic chemist”.

    I’ve heard ones like: “I think my roommate is poising my orange juice, can you analyze this sample?” are pretty common.

  4. Chemjobber Says:

    Would the Bradford protein assay work? It’d be a lot easier to find a UV/Vis than a LC/MS, and it’d get you the same answer (I think.)

  5. HowIsThisForRandom Says:

    Well it wouldn’t be specific for gluten proteins…there are ELISA kits out there for people who suffer from celiac, but I don’t think they are quantitative.

  6. SN Says:

    What happened to that “Named Reactions Screen Saver” that was going around a few years ago. Lost my copy with an old computer, and now it’s nowhere to be found!

  7. Chemjobber Says:

    Paul, have you seen this Breslow TL comment? Any thoughts? http://dx.doi.org/10.1016/j.tetlet.2011.06.002

  8. Martyn Says:

    @Chemjobber: Best closing sentence ever!

  9. paul - but not paul Says:

    @Chemjobber

    I imagine Breslow sitting at his computer typing his paper thinking “Planet of the apes is lame…. planet of the dinosaurs would be baddass…. “

  10. yonemoto Says:

    +/- Elisa kits can be made quantitative by employing the detection threshold method – keep diluting till you can’t see anything.

  11. Brian Says:

    Just saw a C&EN feature of some enantiomer quantitation from Anslyn’s lab:

    “…synthetic chemists develop methods to selectively synthesize just one enantiomer. Now they can assess the fruits of their labor more easily with a technique that quickly quantifies the relative amount of each mirror image in a racemic mixture…”

    Over and over, the article uses “racemic mixture” to describe a mixture of enantiomers. Usually, I’m not this much of a stickler, but if you’re trying to quantify EE, then you should really know that a racemic mixture, by definition, is 1:1. Another case of sloppy writing/figures in CEN?

  12. wolfie Says:

    Once, I had a colleague, or friend, who is now a full professor pf physics at a minor university in Germany, which I am not. This guy did not even know the chemical difference between sodium and potassium, or that they were different. He was a physicist, and got a habilitation in physical chemistry from the University of Heidelberg.

    At a certain point, he threw me out of his grants, because I was no longer willing or able to secure them.

    Such is the run of the world, sloppily translated.

  13. wolfie Says:

    I thought they had to learn German at Columbia, while studying chemistry, for good reasons. Maybe Sames had not to, but Bengu certainly did.

  14. Lila Guterman, C&EN Says:

    @Brian Thanks for noticing our (yes, sloppy) mistake! We’ve fixed it.

    http://pubs.acs.org/cen/news/89/i31/8931scene4.html

  15. Paul Says:

    Brian is the early favorite to win this thread.

  16. wolfie Says:

    Do you guys know this guy ? It’s Klinsmann.

    http://kress.de/uploads/rte_migration_tt_news/taz-artikel-410.jpg

    He just became the new coach of the US soccer team…

    well, good luck with him, he always tried very hard to be like an American, but …

  17. Chemjobber Says:

    S&P downgrade. Oh, dear.

  18. Paul Says:

  19. Paul Says:

    An excellent teacher:

  20. Paul Says:

  21. Joel Says:

    Is anyone else getting spam from Marinda Li Wu “for ACS President-Elect”? I am tempted to start an anti-Marinda campaign….

  22. Hap Says:

    Yeah, I keep getting it too. It’s annoying.

  23. MJ Says:

    I could do my own lit searching, but I figure someone on here has to have a citation or three handy who actually has some time spent in this field. I don’t want to get overinvested in this one idea that popped into my head, after all.

    Are there are any recent and fairly comprehensive reviews/monographs on origin of life (OoL) research, especially in terms of abiotic chemistry/biochemistry? Even if the actual text glosses over things, as long the bibliography is excellent and provides a solid jumping-off point, that’d be super.

  24. Paul Says:

    @MJ: I think the monograph by Brack is probably the best.

  25. Paul Says:

    There’s a new blog on heterocycles here:

    http://heterocyclist.com/

  26. Paul Says:

  27. Ason Says:

    Sherwood Rowland, RIP. One of those great scientist that not only performed excellent work, but took on an entire community and industry with his findings on CFCs and global warming. Roald Hoffmann calls this The Greatest Nobel, and I tend to agree.

  28. Hap Says:

    1) Did you see this retraction? JOC 2012(77), p. 2578? (PJB addition: link)

    2) Dr. LaClair is part of back-to-back-to-back talks at San Diego: ORGN 749-751. Whee!

  29. Paul Says:

    1) Hadn’t

    2) Looks like La Clair is just giving the first of the three; the second and third might be students or co-workers (?) I won’t be there on Wednesday…and don’t think I could stomach it anyway.

  30. Paul Says:

  31. Hap Says:

    I knew he was only giving the first – he was on the other two.

  32. wolfie Says:

    Real life is unfortunetaly not like chemistry from the ordinary textbook, because it flows above the thermodynamic minima.

  33. Paul Says:

    In retrospect, there surely can be no doubt that *NSYNC was the greatest boy band of the 90s+00s.

  34. Paul Says:

    A most excellent performance featuring chemist (and UNC chancellor) Holden Thorp:

  35. Chemjobber Says:

    So how the heck did you call “Call Me Maybe” in March?

  36. Paul Says:

    Another insignificant accomplishment: the instant I heard “Bad Day” by Daniel Powter I proclaimed to everyone in lab that it would be a smash hit…just watch. It took almost a year (and extensive use on American Idol), but it made it to #1. It also had a great video:

  37. Paul Says:

    This receives my full recommendation:

  38. Paul Says:

    Fantastic. This one has got to get significant radio play…

  39. Hap Says:

    Semi-random question. If you’re doing a total synthesis (mid-range – 10-20 steps), how expensive a starting material would use? Would it matter to you?

    I read this paper. While the paper doesn’t seem bad to me, and the synthesis gives an overall yield of 14% (based on their step yields, the overall yield makes sense), the starting material runs about $78/1g from Sigma-Aldrich (and doesn’t seem like something that you could get on scale cheaper from someone else). I was used to the synthetic problem saw of “$1/g”. Even the racemate is expensive ($14/g, I think), so that you couldn’t cheaply run through iterations of the synthesis. If labor or reagent costs are the major drivers for the decision on what route to use, though, then perhaps an expensive starting material wouldn’t be so bad.

    3-Me-2-cyclopenten-1-one is about $16/g from S-A, and could be converted to SM by Buchwald redn. – I imagine the unsubstituted cyclopentenone would be even cheaper, but I don’t know if I’d like zinc reagents on scale.

  40. Chemjobber Says:

    Great question. Seems to me that to make it through that long of a sequence, you’d need at least ~200 grams. Dunno what kind of deal you could get for that amount…

  41. anonymous for this one Says:

    Hey Paul, can you take a look at this ‘correction’ to an article by Buchwald?

    http://pubs.acs.org/doi/pdf/10.1021/ja3066094

    It seems like it’s a much poorer article and would have trouble getting accepted based on what is described in the correction. I’m guessing some industry types saw a useful reaction and decided to repeat it but couldn’t (a la Sames/Sezen). Of course, you still get product, but the main selling point was selectivity, of which there isn’t much. The first author used this article and the highlight to get a professor job since then, so it feels a bit unfair for those of us looking for professor jobs as well. It’s like you’re not playing on even ground because some big shot from the Buchwald group just makes up yields/selectivity and you never even thought of that. Then if he never gets into funny business ever again in his life, it doesn’t even matter because he already has the professor job. But if this correction is not a big deal, I’ll let my bad feelings go.

    https://medicine.ekmd.huji.ac.il/En/Publications/ResearchersPages/pages/dmitryt.aspx

    I’m writing this in the middle of Yom Kippur because I know there is no way that I can forgive him for this one before the day is over. And he’s never going to forgive me for ruining his professor career by mentioning this on a chemistry blog (as if he’s going to get fired at this point). I’ll probably have to forgive him next year or something. If only I observed Yom Kippur properly and didn’t use electricity and therefore not checked the ASAPs! Then I would have never found out about it until tomorrow.

  42. Paul Says:

    Yeah…can anyone remember someone publishing a correction to note they under-reported a yield or ee? Why is it always the other way around?

    Your story above reminds me that I am working on a post that tracks what has happened to some professors who have had to correct or defend high-profile work from their graduate or postdoc careers.

  43. Hap Says:

    This paper (JOC 77(2012), p. 8174) is another example – the starting cyclohexenone does not seem to be commercially available, and I can’t think of a facile or cheap method to make it. You could perhaps make it racemically by a catalyzed Robinson annulation with acetaldehyde and a pentenone and then resolve it, or by asym. addn. to cyclohexenone and enolate trapping, cleavage of the silyl ether and alpha-formylation, enone formation at the unblocked position, and deformylation, but neither of these seem cheap or easily used on big scale (what you would probably need for a moderate length synthesis). Rich White has related methods for nonracemic 4-substituted cyclohexenones, but I didn’t think they were applicable to 5-substituted ones. What does anyone else think? (I’m not trying to pick on particular authors or classes of authors, but trying to figure out how someone would actually perform the synthesis).

  44. Hap Says:

    The racemate could probably also be made by Birch reduction of m-cresol or its methyl ether, which would be rapid and doable on scale. The resolution, though – ?

  45. Hap Says:

    Coaching and playing, though, are pretty different in scope (although a quarterback or linebacker in football has to know what everyone else is supposed to do on offense or defense in order to function) – a coach has to know everything, first in a specific area of responsibility and then for the team. I don’t think research schools value teaching much at all, where the coaching/prof analogy holds most true, and the organization of a lab (I don’t think, other than maybe Sames?) isn’t usually a professor’s point of failure. The school cares about research good enough to get grants and publicity, and grad students and postdocs are probably selected for their ability to get good research done. In a postdoc in some places (Professor Whitesides’s group, for example, and probably others), the postdoc experience includes organizing a research area and some grant work, so that while success in those fields isn’t known, the candidate has had exposure to them, making them less likely failure points.

  46. Paul Says:

    Hap, I’m going to copy your comment to the other thread.

  47. Hap Says:

    OK.

  48. Hap Says:

    On Harvard’s higher overhead – I’m not sure why they can command it. In theory, the instrumentation that they are using and justifying with the grant money is already paid for under other grants – thus more tools needed implies that more grants were used to get them which doesn’t necessarily justify a higher rate of compensation. In addition, if they get more grants, then the amount of overhead (maintained for presumably a fixed set of professors) would be greater to fund the same amount of facilities and employees.

    My general rule is if there are eight million businesses of a type present (day care, banks), chances are that the business segment is doing well and is not inherently unprofitable (particularly when added competition seems to have no effect on the pricing). Given that it seems like every school on the planet wants to be a research university, it is difficult to believe that schools are merely getting by with current overhead rates (why run to a business that doesn’t generate extra money for the universities?) rather than making lots of money to fund other things.

  49. joel Says:

    Can anyone recommend an RSS feeder to keep up with journal articles and blogs? Google Reader is about to shut down, and the alternatives I have tried so far have been rather unimpressive.

  50. Hap Says:

    Have you seen the In The Pipeline post on this?

    http://pipeline.corante.com/archives/2013/03/14/scientists_and_google_readers_demise.php

    The end of the post has a link to a list of options as well.

  51. joel Says:

    Thanks, Hap. I haven’t been following Derek’s blog as much as I used to.

  52. Hap Says:

    I can’t comment on Chemjobber anywhere but at home – I can’t get my wife’s iPad to enter text into the text boxes there, and I can’t see them at all (or the not-a-robot boxes) at…not home. I haven’t tried this, but I don’t think I’ve had problems with ChemBark.

  53. Paul Says:

    In honor of Memorial Day, what is probably my favorite scene from my favorite TV miniseries:

  54. Paul Says:

    Great new teaching resource page from Minnesota’s Chris Cramer:
    http://pollux.chem.umn.edu/Teaching.html

    There’s orgo, thermo, compo, and how to give a talko.

  55. Hap Says:

    I don’t know where I got this idea, but I was wondering if someone who actually worked with metal catalysts could confirm or invalidate it. I thought (had heard) that if you used precious metal catalysts in lab (not just on industrial scale), they (the waste containing them, presumably) had to be sent back to the manufacturer for recycling. Is this correct, or am I confused?

  56. Paul Says:

    @Hap: I’ve always just tossed precious metals (small quantities), though I’ve seen people collect them if they were running the same experiment a lot. That said, I can’t recall if they ever actually sent the bottle to be recycled.

  57. Hap Says:

    I did that with Pd/C, too.

    I don’t know where I heard the idea about catalyst (precious metal) recycling, and all I can find on the interwebs is information for industrial catalyst users, whereas I was thinking of people like Buchwald, Hartwig, etc. I know someone who had worked for Sanford and she hadn’t heard of it either, so I don’t know if I’m totally confused or just confused industrial catalyst use with lab catalyst use.

  58. SpeedyGonzales Says:

    In some cases, labs get (or got) loans of precious metals from companies such as Johnson Matthey (JM). In those cases the expectation is that they collect the waste containing the metal residue and return it for recycling. You typically see this in older academic papers with Rhodium and Iridium. I doubt they expect a particularly high recovery, so it is a loan with generous terms. I am just speaking from second hand knowledge as I have not been part of a lab receiving such loans at the moment. In my PhD I probably used about 4 grams of iridium COD chloride, and 2 grams of Rhodium salts, which we purchased outright from Strem. There was no expectation of recycling them, but I collected the waste anyway since I just precipitated the catalysts out with diethyl ether at the end of my reaction anyway. As far as I know, the stuff is still sitting in my old hood as I didn’t fancy trying to recycle it myself with aqua regia! I have noticed recently in the literature that some more prominent labs that use platinum metals sometimes thank JM for the gift of metals, which makes me guess JM keeps their philanthropy up, but has given up trying to recoup the small scale residues from labs which are probablly also full of phosphines and other nastiness (just a guess on my part).

  59. Hap Says:

    I thought you worked for Schuster at NYU – he has a Retrospective in JOC (JOC 2013 pp. 6811-6841) that might be interesting to you. It seemed interesting in general.

  60. Paul Says:

    I did work for David, and this retrospective is on my reading list. I find these sorts of pieces fascinating—Dave Evans’ comes to mind, as does Jack Roberts’ autobiography. I am looking forward to reading this one!

  61. Paul Bracher Says:

    This is great:

  62. Hap Says:

    Does anyone know what happened to In The Pipeline? I’ve tried to read it the last two days, and all it gives me is a bunch of Unix for “I’m dead. Come back when I’m not.” I know that Dr. Lowe was planning on moving at some point, but the site had been working okay, and I assume there were issues with moving (content?)

  63. Hap Says:

    Apparently, MS Exploder does not like ITP, though Firefox does – ?!?.

  64. Hap Says:

    Under no circumstances are you allowed to use a laser pointer at someone else’s talk.

    Really? I know people’s minds are heterogeneous, but this seems to require a similar lack of forethought to, say, sealing the rupture disks on your LN2 or LOX cylinders, or giving a talk on erectile dysfunction treatments with an actual live demonstration. It seems like something drunk people would do at a baseball game, or very dumb people.

  65. Retracto Says:

    http://m.sciencemag.org/content/347/6224/834.1

  66. anon Says:

    http://onlinelibrary.wiley.com/doi/10.1002/anie.201410875/abstract

    http://onlinelibrary.wiley.com/doi/10.1002/anie.201500404/abstract

    The second paper was submitted after the first appeared online. My guess is that not many scientists can get away with this. When we mere mortals get scooped our papers don’t go to Angewandte.

  67. eugene Says:

    Where do you see the submitted date?

  68. GiantOctopus Says:

    The “date received” by the journal is at the bottom of the article. The paper from Nova Scotia, Canada was received the 8th November 2014 and published online on the 8th January 2015.

    The paper from Berkeley was received the 15th January 2015 and published online on the 25th February.

    It should be noted that the second paper cites the first as reference 4, therefore there is no doubt that the crucial development in this work was first reported by the Nova Scotia team. It is the decision of the Editor (advised by the reviewers) to have the article accepted into the journal, and if authors feel that they they have a outstanding manuscript that reports a crucial or novel development they should not be criticized for sending the article to publication with the highest impact factor.

    However, it is a pity that the pressure and desire to write articles for very high profile journals means that the excellent Chem. Eur. J., which features a number of important papers by Nobel Prize Winner Prof. J-M Lehn among others, sometimes gets overlooked by experts as a place to publish good manuscripts.

    Perhaps the second paper could ultimately end up highlighting the first?

  69. eugene Says:

    Ah, that’s why I didn’t see it. I’m at home and I was too lazy to log into the library and go through several steps to get the paper. Okay, thanks. Anyways, one week difference is not too bad. It’s not like they did everything in one week, and they were probably preparing to submit for a couple of months beforehand. It’s likely both papers will get cited equally so Andjewandte thought that if it was an important enough topic, they could double their citations. Six months difference, that’s a bit more suspicious. Anyways, congrats to the Andrey team for being first; if I remember correctly, I tried to convince him to go to Nova Scotia over other options, and it worked out. I love the work of the Stradiotto group. It’s not like he’s much of an outsider from Andjewandte and other glamor magz himself.

  70. GiantOctopus Says:

    Jackass?? Anjewandte? What next, Comical Science?

    A good article stands out wherever it is published (excluding predatory journals) and I think sometimes a superb piece of work in a less well known or more specialist journal is a sign of confidence, understanding and knowledge of what is truly cutting edge from the authors. I definitely think a good measure of a scientist is the demonstrated ability to self-discriminate between the good, the excellent, the outstanding and the specialist, rather than just sending a manuscript to the highest IF and hoping for the best.

    Not every single thing that anyone does is utterly novel, outstanding and correct, even though everyone makes the the mistake of thinking that on more than one occasion.

    RE: the one week difference – the crucial thing is that the second paper was submitted after the first paper appeared and cited the first paper, thus acknowledging it’s priority.

  71. eugene Says:

    “Comical Science?” Hah! Good one (and always guaranteed to apply to a paper or two in every journal). Thanks for that one. I’ll be using it pretty often!

    Hey, what do you think of of mine for ‘Chemistry: A Forgotten Journal’? (I mean, European)

  72. GiantOctopus Says:

    I’ve already said that I like Chem. Eur. J. however your proposed alternative title could also apply to Chemistry – An Asian Journal so probably not such a good name.

    Incidentally, I don’t see being Jewish as a negative thing so you if you are going to re-title Angewandte in a mildly humorous fashion in order to show disdain/envy for some of it’s articles you might want to think of a better pun. (How about AngeWTF?)

  73. eugene Says:

    I really don’t see how people can read ‘Jew’ into it. It really never crossed my mind even, since I know German, and the improper way to pronounce the journal if you didn’t know it, would be to say exactly Andjewandte, otherwise, you have to pronounce the ‘g’ differently and not to say it the American ‘dj’ way. So, I really just changed the ‘g’ to a ‘dj’ and the rest of the letters are accidental. Besides, jewels have the word ‘jew’ in it, and most people see them positively. Well… except for me. I think they are a waste of money.

  74. bad wolf Says:

    Whatever you say, Jew-gene. “Just keep fucking that chicken.

  75. Hap Says:

    I think 5% is comparable to the raises we get for going up a level…but there are five levels for us.

    It seems kind of low for what I would have thought tenure and promotion would bring, but I assume the severe oversupply of potential profs has something to do with this.

  76. Paul Bracher Says:

    @Hap: So, here, the bump for tenure+promotion would amount to ~10%…5% for the tenure, and 5% for the promotion in rank from assistant to associate.

    I’m not sure if this is typical of most schools or not.

  77. Hap Says:

    I guess I was taking them separately – but that’s still really only three levels (maybe four?). I would have figured a much larger bump for both of those events, though if annual pay raises are relatively high (please don’t laugh), then that would still end up OK.

  78. anon2 Says:

    “As Professor of Chemistry David MacMillan has said, ‘Graduate students are the fuel for the research engine.'”
    -Princeton Alumni Weekly
    https://paw.princeton.edu/issues/2015/04/01/presidents-page/

    Perhaps a little more honest than intended?

    #burned

  79. kitcatalysis Says:

    @anon (posting February 27th)

    You think that is bad? What about doing a reaction that has already been published more than a year earlier and then publish it in a higher ranking journal.

    Publication 1: http://pubs.acs.org/doi/abs/10.1021/ol300591z?journalCode=orlef7&quickLinkVolume=14&quickLinkPage=1922&selectedTab=citation&volume=14
    (Published online 28th March 2012)

    Publication 2: http://pubs.rsc.org/en/content/articlelanding/2013/sc/c3sc51266e#!divAbstract
    (Submitted 8th May 2013. See ref. 8)


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