ChemSpider, how a free community resource of data can support teaching NMR spectroscopy


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ChemSpider is an online database of chemical compounds, reaction syntheses and analytical data. Provided by the Royal Society of Chemistry, our intention is to provide a free internet resource of chemistry related data for the community. ChemSpider is unique in its role of allowing user depositions of chemical structures, synthesis procedures and analytical data and, in so doing, provides an environment for crowdsourced gathering of information. To date over 2000 1D and 2D NMR spectra have been deposited online by the community and are available for reuse. The data have been used as the basis of a spectral game whereby students can learn NMR by interacting with the data. This presentation will provide an overview of the tools and capabilities presently available on ChemSpider to support teaching NMR in the undergraduate curriculum and will outline how the community can participate in enriching this resource for the benefit of all.

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ChemSpider, how a free community resource of data can support teaching NMR spectroscopy

  1. 1. ChemSpider, how a free community resource of data can support teaching NMR spectroscopy
  2. 2. A Pragmatic Vision <ul><ul><li>“ Build a Structure Centric Community to </li></ul></ul><ul><ul><li>Serve Chemists” </li></ul></ul><ul><ul><li>Integrate chemical structure data on the web </li></ul></ul><ul><ul><li>Create a “structure-based hub” to information and data </li></ul></ul><ul><ul><li>Provide access to structure-based “algorithms” </li></ul></ul><ul><ul><li>Let chemists contribute their own data </li></ul></ul><ul><ul><li>Allow the community to curate/correct data </li></ul></ul>
  3. 3. ChemSpider Searches
  4. 4. Search Cholesterol
  5. 5. Search Cholesterol
  6. 6. Linked to Content
  7. 7. Patents Linked
  8. 8. Articles Linked
  9. 9. NMR Spectroscopy on the Internet <ul><li>Access to presentations, tutorials and guidance </li></ul><ul><li>Tables of information – solvent shifts, coupling constants etc </li></ul><ul><li>Spectral data for download – binary files and JCAMP files </li></ul><ul><li>Assigned NMR spectra – tables and interactive displays </li></ul><ul><li>Access to NMR prediction algorithms – free and commercial </li></ul>
  10. 10. ChemSpider : Spectra Linked
  11. 11. Spectra Linked
  12. 12. Spectra Linked
  13. 13. Spectra on ChemSpider
  14. 14. Sources of Spectra <ul><li>Sourced from online sources with permission </li></ul><ul><li>Private collections </li></ul><ul><li>The MAJORITY deposited by ChemSpider users </li></ul>
  15. 15. Spectral Uploading <ul><li>Locate the structure of interest and deposit spectrum </li></ul>
  16. 16. Spectral Uploading <ul><li>Various types of NMR spectra supported </li></ul>
  17. 17. Multiple Spectra for One Structure
  18. 18. ChemSpider ID 24528095 H1 NMR
  19. 19. ChemSpider ID 24528095 C13 NMR
  20. 20. ChemSpider ID 24528095 HHCOSY
  21. 21. ChemSpider ID 24528095 HSQC
  22. 22. ChemSpider ID 24528095 HMBC
  23. 23. Full C13 assignment uploaded
  24. 24. Deposit spectra against new structure <ul><li>If a NEW compound has spectral data then deposit the structure onto ChemSpider first </li></ul>
  25. 25. Available Spectra
  26. 26. Embedding Data
  27. 27. Embedding Structures
  28. 28. Web Services
  29. 29.
  30. 30. Spectral Game
  31. 31. Increasing Complexity
  32. 32. Spectral Game
  33. 33. Data Curation
  34. 34. Reversed Spectrum
  35. 35. Download, reprocess, redeposit
  36. 36. True Curation of Data
  37. 37. 2DNMR Spectral Game
  38. 39. Not Just NMR Data
  39. 40. ChemSpider SyntheticPages
  40. 41. Invitations <ul><li>Spectral data are welcomed from associated syntheses, lab experiments etc </li></ul><ul><li>Upload structures, spectra, analyses etc to ChemSpider to share with the community </li></ul><ul><li>Use and encourage your students </li></ul><ul><li>And presently in beta… </li></ul>
  41. 42. NMRShiftDB
  42. 43. NMRShiftDB:
  43. 45. <ul><li>Flexible search capabilities </li></ul><ul><ul><li>by chemical name </li></ul></ul><ul><ul><li>by structure </li></ul></ul><ul><ul><li>by spectral peaklist </li></ul></ul>
  44. 46. NMR Prediction
  45. 47. Multinuclear NMR Prediction
  46. 48. NMRShiftDB Data Review <ul><li>High quality NMR shift set of ca. 100,000 shifts </li></ul><ul><li>Multiple outliers identified </li></ul><ul><li>Removed followed publication </li></ul>
  47. 49. ChemSpider Integrated NMR Prediction <ul><li>Initial integration in place </li></ul>
  48. 50. Acknowledgments <ul><li>Jean-Claude Bradley, Andrew Lang and Robert Lancashire </li></ul><ul><li>Christoph Steinbeck and Stefan Kuhn </li></ul><ul><li>Wolfgang Robien </li></ul><ul><li>Depositors of data </li></ul>
  49. 51. ChemSpider demos and training <ul><li>ChemSpider demos at booth 301: Royal Society of Chemistry </li></ul><ul><li>Hands-on ChemSpider Training </li></ul><ul><li>Room:  110  </li></ul><ul><li>Location:   Moscone Center </li></ul><ul><li>Date:   Monday 22 nd March   </li></ul><ul><li>Time:   4:00 PM - 6:00 PM </li></ul>
  50. 52. Thank you [email_address] Twitter: ChemSpiderman SLIDES: