We start Open Notebook Science at UCC on calculating NMR

Posted on October 10, 2007 by pm286

We are starting an experiment on Open Notebook Science. See (Open Notebook Science Using Blogs and Wikis : Nature Precedings, Drexel CoAS E-Learning: Open Notebook Science, Useful Chemistry: Cameron Neylon on Open Notebook Science, Drexel CoAS talks mp3 podcast: Open Notebook Science ACS March07 (JCB)). ONS seems to be the generally agreed term for scientific endeavour where the experiments are rapidly posted in public view, possibly before being exhaustively checked. It takes bravery as it isn’t fun if you goof publicly. And there are publishers who say that they won’t pblish the science as it is already in the public domain.
We’re going to start doing ONS. One of the current problems of closed data is that the chemical literature is often just plain wrong. Sometimes it’s typos, sometimes it’s misassignments of peaks, bad computational parameters and many other causes. The recent controversy over hexacyclinol – where a published structure seems to be “wrong” – has sparked one good development – the realisation that high-quality QM calculations can predict experimental data well enough to show whether the published structure is “correct”. Joe Townsend has been doing this for crystal structures and shown that the approach can be automated and gives very good results.
We’re now starting to do this for NMR spectra. Henry Rzepa has taken Scott Rychnovksy’s methods for calculating 13C spectra and refined the protocol. Christoph Steinbeck has helped us get 20, 000 spectra from NMRShiftDB and Nick Day (of crystalEye fame) has amended the protocls so we can run hundreds of jobs per day on tne CamGrid Condor cluster.
This results will go directly into public view. (Any delay will be technical not lack of will). For each molecule we shall have the observed peakList and the calculated structure and peakList. (We use CML to hold these which makes it enormously easier to manipulate the system and achieve high-throughput). Each structure will have a web page with the data and a graph comparing observed and calculated shifts.
We’d like user comments. We’re not exactly sure what the best format is – a Wiki with entries for each molecule (can we write to that automatically?); a templated web page with a form for modifying it?  Suggestions welcome.
But we hope to show that the philosophy works, that the method works, and that NMRShiftDB has a measurable high-quality. We expect some variation due to experimental error in the spectra, to misassignment, but also to problems in the calculation – where we can contribute improvements.
Nick and Peter

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7 Responses to We start Open Notebook Science at UCC on calculating NMR

  1. ChemSpiderMan says:
    October 11, 2007 at 3:04 am

    Peter…I support and encourage the ONS. We’re working with Jean-Claude Bradley and helping where we can too.
    In regards to this work you are aware of the study done to apply computer assisted structure elucidation I believe (http://www.chemspider.com/blog/?p=77). A manuscript has just been submitted to J Nat Prod and is in review.
    We have just had a publication accepted to JCIM “Title: “Towards More Reliable 13C and 1H Chemical Shift Prediction: A Systematic Comparison of Neural Network and Least Squares Regression Based Approaches” Author(s): Williams, Antony; Elyashberg, Mikhail; Blinov, Kirill; Smurnyy, Yegor; Churanova, Tatiana”. This related to me finishing up publications from my time at ACD/Labs.
    A lot of work has been done by ACD/Labs to examine the NMRShiftDB database and validate the quality. You’ve seen us (both ACD/labs and ChemSPider) get very vocal about quality in SUPPORT of NMRShiftDB. A manuscript was submitted this week with Christoph Steinbeck (host of NMRShiftDB) as a co-author “”The Performance Validation of Neural Network Based 13C NMR Prediction Using a Publicly Available Data Source.” Authors: Williams, Antony; Blinov, Kirill; Smurnyy, Yegor; Elyashberg, Mikhail; Churanova, Tatiana; Kvasha, Mikhail; Steinbeck, Christoph; Lefebvre, Brent”
    My intuition is that the HOSE-code approach, neural network approach and LSR approach will outperform the GIAO approach. Certainly these approaches would be much faster I believe. It would be good to compare the outcome of your studies with these other prediction algorithms and if the data is open then it will make for a good study.Will it be possible to download the entire dataset with predicted list of shifts in a standard consumable format such as SDF?
    I think ACD/Labs has done a good job validating the quality of the NMRSHIFTDB database and this has been espoused at Ryan’s blog..the last post is http://acdlabs.typepad.com/my_weblog/2007/09/wolfgang-robien.html
    Either wiki or webpage with form for modifying works for me…no preference.
    Is there a timescale for the work? Good luck!

    Reply
  2. ChemSpiderMan says:
    October 11, 2007 at 3:16 am

    Peter…one more comment. Thanks to some very valiant efforts by Bob Lancashire to address Java compatibility issues with JSpecView the applet is now working well (http://www.chemspider.com/news/?p=81). The applet already supports CML from NMRShiftDB so you will likely want to adopt this for spectral viewing? http://sourceforge.net/forum/forum.php?forum_id=707556
    As an NMR jock I’d welcome the opportunity to help in the project. Of course, if Christoph’s engaged you’ll likely have all the bases covered 🙂

    Reply
  3. ChemSpiderMan says:
    October 11, 2007 at 3:42 am

    Just browsing JCIM tonight I noticed the article:
    Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML Vocabulary
    for Spectral Data
    Stefan Kuhn,†,^ Tobias Helmus,† Robert J. Lancashire,‡ Peter Murray-Rust,*,§ Henry S. Rzepa,|
    Christoph Steinbeck,† and Egon L. Willighagen†
    10.1021/ci600531a
    Clearly you know more about the status of JSpecView and CML support than I do 🙂

    Reply

  4. Pingback: First Author » Blog Archive » Open Notebook Science

  5. Jean-Claude Bradley says:
    October 11, 2007 at 1:32 pm

    Peter – it is great to see you contributing to open NMR data processing.
    For a source of raw spectra, we have been and will continue to upload NMRs of our starting materials and isolated products to ChemSpider.
    http://www.chemspider.com/spectra.aspx
    and for example benzaldehyde:
    http://www.chemspider.com/Chemical-Structure.235.html
    I think a lot of the errors in the literature are due to poor quality spectra and improper referencing. It is really useful to verify that the TMS peak is indeed exactly at zero and that phasing was done properly. JSpecView used by us and ChemSpider allows people to expand any part of the spectrum and integrate at will, which is very handy for measuring fine splitting patterns, including J constants in H NMR spectra. The problems with JSpecView and the new Java version have been resolved by Robert Lancashire and fixed on ChemSpider.

    Reply

  6. Pingback: Science in the open » How best to do the open notebook thing…a nice specific example

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