NMR Challenge: what can a machine deduce from a thesis?

Posted on November 24, 2007 by pm286

One of the ways of extracting chemical structures from the literature is to use the NMR to constrain the possibilities. So, to give you an amusement for the weekend, here are some problems. I have a thesis (which I’m not identifying, but I know the author and he’s happy for the thesis to yield Open Data). I am not sure whether the compounds are in the public literature yet, but they are in the public domain if you know where to find the paper thesis.
Imagine that some future archaeologist had discovered the thesis and only a few scraps had survived. What could be deduced? I’m starting with smallish (hopefully fairly simple) structures and only feeding you some of the information. Depending on what you answer, I’ll either release more or select more complex compounds. All compounds are distinct.
Compound 172
dH (400 MHz, CDCl3): 1.15 (3H, t, J 7.1, OCH2CH3), 1.24 (3H, d, J 5.2, 6-H x 3), 2.84 (1H, qd, J 5.2, 2.0, 5-H), 3.05 (1H, dd, J 7.0, 2.0, 4-H), 4.07 (2H, q, J 7.1, OCH2CH3), 5.99 (1H, dd, J 15.7, 0.6, 2-H), 6.54 (1H, dd, J 15.7, 7.0, 3-H);
Compound 167
dC (100 MHz, CDCl3): 164.5 (CO), 160.3 (C), 107.5 (C), 95.6 (CH), 40.9 (CH2Cl), 24.7 (CH3 x 2);
compound 156
dC (100 MHz, CDCl3): 83.0 (3-C), 79.6 (2-C), 61.8 (5-C), 51.0 (1-C), 25.8 (SiC(CH3)3 x 1), 23.1 (4-C), 18.3 (SiC(CH3)3), -5.1 (Si(CH3) x 2);
Note that the molecular formula, molecular weight, etc. have all been destroyed by the ravages of time.
You can use any method you like, including searching in commercial databases.
What could a machine do with the information above?

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6 Responses to NMR Challenge: what can a machine deduce from a thesis?

  1. Wolfgang Robien says:
    November 24, 2007 at 10:10 pm

    #156: see JCS-P1,2697(2001) – comp 7
    BTW: IMHO comp 8 in this paper has an assignment error
    #167: CAS-RN 81956-31-2 (hopefully Cambridge University has access to SCIFINDER ;-)) )
    Peter, this was not an amusement for a weekend, this was a 5-minute job. I didnt understand the word ‘CHALLENGE’ in the header with respect to the context … ?
    My personal summary: It was a wise decision of ‘Mother Nature’ that not every ejaculation causes a birth certificate – maybe we could apply this to science too ……

    Reply
  2. pm286 says:
    November 24, 2007 at 10:46 pm

    (1) Thanks – this is great
    Yes – the author of the thesis referred to this paper. I wasn’t sure when the compound’s spectrum had been published. Thanks for alerting us to a misassignment – this is the sort of thing we are looking for.
    It will be perhaps more of a challenge when the compounds are not in the literature or if people are not able to look it up.

    Reply
  3. Wolfgang Robien says:
    November 24, 2007 at 10:47 pm

    Note added in proof:
    —-snip—-
    I am not sure whether the compounds are in the public literature yet
    —-snip/end—–
    The usual way I recommend to my students is simply to use CAS-SciFinder …….

    Reply
  4. Wolfgang Robien says:
    November 24, 2007 at 10:50 pm

    (2)
    Compound 167 is NOT in the collection I have accessed
    Similarity search ( in principle what you call ‘robot’ or ‘machine’) with subsequent ranking gave the -OH derivative (instead -Cl) first, then the unsubstituted skeleton …….

    Reply
  5. Wolfgang Robien says:
    November 24, 2007 at 10:53 pm

    ad (2)
    –snip—
    Thanks for alerting us to a misassignment – this is the sort of thing we are looking for.
    –snip/end—
    I recommend to buy a copy of NMRPredict, you have all the comments directly in the data about (mis)assignments, structure revisions, etc. (GLP)
    Obviously this has a value, therefore it has also a price !

    Reply
  6. pm286 says:
    November 24, 2007 at 11:33 pm

    (4) Thank you for not revealing the answer to others 🙂

    Reply

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