Alright, so you spent most of the day nailing down a certain reaction, and just in time you found a promising lead in the literature. The only thing left now to be able to run your desired reaction is going through the details. It is then you don’t want any of these.

1. Questionable purity and identification

“Pale yellow” may be somewhat of a bad sign, but in most cases not a deal-breaker. However, purity according to TLC is quite disturbing, especially in the year of 2013.

Purity by TLC
Org. Commun. 2013, 6, 95-101. (No DOI – thank Heaven – but full version here)

2. Yield by GC

Has anybody ever seen a better yield after work-up compared to a GC estimated yield on the crude material? Rhetorical question, guys. Yield by GC sucks, and nothing in the world can change that.

Yield by GC
Angew. Chem. Int. Ed. 2012, 51, 11487-11490. (DOI: 10.1002/anie.201207148)

3. No experimental details, and a reference to nowhere

Tetrahedron Letters doesn’t have the best of reputations when it comes to experimental details, but contrary to mainstream opinion, I don’t think the journal is entirely shit. Maybe because I happen to have a couple of papers in it :) This example, however, is shit.

Lack of experimental details
Tetrahedron Lett. 2005, 46, 8391-8394. (DOI: 10.1016/j.tetlet.2005.09.156)

4. Journals no-one has access to

Can you access this figure? Congratulations! You belong to the <.1 % of scholars who can. I had to go to great lengths to lay my hands on this.

Unavailable articles
Heterocycles 2009, 77, 1185-1208. (DOI: 10.3987/COM-08-S(F)97)

5. Outdated or unintelligible methods

Here is a favorite. Patents, especially older ones, are littered with techniques, which I assume few living chemists are able to reproduce today. How about this one, for example?

Molecular weight determination
US Pat. 3,784,571, 1974 (full version here)

I’m sure you can name a number of additional annoyances. Hit me hard!

 

38 Responses to Five things synthetic chemists hate

  1. Andrew says:

    A key paper for my thesis has a comment along these lines: “synthesis and characterisation of the compounds this paper is entirely about will be reported later”. Five/six years later and we’re still waiting.

    • drfreddy says:

      +1 for _synthesis_ being performed later.

    • fluorogrol says:

      Not directly related to actually making stuff, but the phrase ‘mechanistic studies are under way and will be reported in due course’ at the end of a paper makes my eyes swivel right back into my head. No they’re not and no they bloody well won’t be!

  2. Jess says:

    Sigma aldrich quote purity by TLC on occasion *head desk*

  3. Srdjan says:

    My boss have given me a reference which I had to try to reproduce in which yield was determined using spectroscopy. Bad thing is that getting solid material substance in pure state is little harder then playing with numbers in some spectral tables. That have been waste of my time…

  4. fluorogrol says:

    ‘Characterisation data were in accordance with those previously reported in the literature[23]’

    Look up the compound in ref 23…

    ‘Characterisation data were in accordance with those previously reported in the literature[12]’

    Look up the compound in ref 12…

    ‘Characterisation data were in accordance with those previously reported in the literature[16]’

    Look up the compound in ref 16 (we’re now back in pre-war JACS)…

    ‘bp 268 F (23.8 Torr), distinctive taste of rancid pork’

  5. Tom says:

    @Jess:
    If done correctly, TLC purity can be quantified using a standardized method with dedicated TLC plate scanner and integrator, which is exactly how they do it in industry. Just because synthetic chemists normally use TLC for day-to-day quick-and-dirty purity estimation (as probably happened in the above reference), doesn’t mean it cannot be used as a highly sensitive and reproducible method in the hands of an analytical chemist.

  6. Stephen says:

    My pet hate is the experimental that manages to leave one or more critical quantities out, while describing everything else very carefully.

  7. wildfyr says:

    Tha angawante one is the scariest. That is supposed to be a top flight journal. All the others are mediocre to bush league

  8. See Arr Oh says:

    “The compound was prepared by the usual methods”

    WHAT USUAL METHODS? The ones you had to attend your exact college in 1958 to learn?

  9. sarah says:

    Super-sekrit abbreviations are always fun… I remember trying to follow an experimental from Trost during my PhD that used the reagent BSA, with no further clues to its identity. In our lab, BSA meant benzeneseleninic anhydride, which was unlikely in the extreme in this case. Figured it meant ‘Barry’s Secret Additive’. This being circa 1990, we called him – turned out it was something involving silicon.

  10. mamid says:

    For #3, a quick search on Google scholar, Scopus, Web of Knowledge etc. will give you the reference. In this case, 10.1016/j.molcata.2005.09.034. Not the greatest of efforts, for sure. It happens now and then, when 2 or more related papers are submitted roughly at the same time, to different publications.

  11. Andy Lund says:

    BSA: N,O-bis(trimethylsilyl)acetamide.

    Agree with Tom, just because you’ve never quoted a yield by TLC doesn’t mean it can’t be done. It is, frequently, and is a very valuable method for awkward compounds.

  12. bad wolf says:

    @Tom and Andy Lund

    Please see above comment re: the year we’re living in.

  13. JB says:

    Apparently I am one of the few… the proud… the ones who have access to Heterocycles. But what’s with dedicating papers for elderly birthdays? I hope someone gets me something better than a research paper when I’m that old.

    “This paper is dedicated to Professor Emeritus Keiichiro Fukumoto on the occasion of his 75th birthday.”

  14. sylvain B. says:

    “Work in progress” is quite like the web pages giving a “page under construction”.
    Why to mention that work is in progress if you’re supposed to be at work???
    why?

  15. Dr Octopus says:

    Dedicating journal issues to academics’ birthdays is a scam to coerce their former students into submitting papers.

  16. K Yosce says:

    BSA = bovine serum albumin :)
    Very commonly used protein every biologist/biochemist knows. Remembered this from doing conjugation chemistry to develop antibody assays back in the day. I really hate unelucidated abbreviations . . .

  17. Dr Matt says:

    #5 Melting point depression was part of the AP Chem curriculum when I was in high school, which was only 13 years ago. We used S8 in naphthalene heated with an open flame on the benchtop. I think the teacher cleaned the glassware with benzene afterwards.

    • drfreddy says:

      For determination of molecular weight?

      • Dr Matt says:

        Not of an unknown, we knew it was S8. Like most experiments at that level the goal was just to roughly match the theoretical value without setting the apparatus on fire. Still, it is not complicated.

        • drfreddy says:

          Everybody knows how useful mp is for purity and identification. High school chem. No-one knows — anylonger — how to use it to determine the MW of an unknown compound. That is something else.

  18. Knight Rider says:

    I don’t see anything wrong with a TLC purity estimate. HPLC is no better, and possibly worse. You cannot measure purity by HPLC unless you know the impurities. At least TLC (>1 eluent system) can, with staining, show non-UV absorbing impurities, such as salts.

    • drfreddy says:

      Well, since none of the details were disclosed a mere “Purity >90 & by TLC” has absolutely no bearing. One can do pretty amazing shit with TLC. For example, I like 2D TLC. And for isotope labeled compounds, TLC is the shit (but it requires fancy machines). Bottom-line: DETAILS

  19. Myron Wilde says:

    I’ve actually done molecular weight by freezing point depression in industry. It is an empirically solid technique if you have the instrumentation and training. It is actually quite useful if you should ever need the average molecular weight for a distribution of substances. Its also highly sensitive to impurities since they throw the final value off. As opposed to whatever is hiding among the fragmentation peaks in MS.

  20. HeddyMurphy says:

    I make silica particles, and that field is the absolute worst for deciphering experimentals! They list things like, “to prepare particles, the molar ratio of water:tetraethoxysilane:ammonia:ethanol used was 2:1:0.5:8″, or a convoluted description like “the silane was dissolved in ethanol and added to the water in ammonia such that the final silane content was 5%”. Um, just list the damn volume! And I can’t tell you how many times they forget to include concentrations. ugh.

  21. Young Padawan says:

    Hey Dr. Freddy, can you somehow turn off these annoying adds that pop up and try to make me use Twitter?

    • drfreddy says:

      Hi, I think you mean Facebook. The pop-over is set to be shown a maximum of two times per user – ever. If for some reason that setting isn’t working, please tell me, and I will look into it.

  22. Young Padawan says:

    I stop by on a regular basis from only 2 different computers and I’ve had the message appear far more than 4 times.

    • drfreddy says:

      Hm… have you tried clicking “never show this message again”?

      Does anybody else have the same negative experience?

Leave a Reply

Your email address will not be published. Required fields are marked *

You may use these HTML tags and attributes: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>

Current ye@r *