MiniSymp2011 Bradley

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Jean-Claude Bradley presents a 15 minute summary of current research in his lab on September 29, 2011 at the Drexel University Department of Chemistry Faculty Mini-Symposium. The main project discussed is the Open Melting Point Collection done in collaboration with Andrew Lang and Antony Williams. Work by Evan Curtin is also shown, demonstrating the application of melting point and solubility in reaction design

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MiniSymp2011 Bradley

  1. 1. The Impact of Openness on the Quality of Chemistry Data and Implications for Organic Synthesis<br />Drexel Chemistry Mini Symposium<br />Jean-Claude Bradley<br />Associate Professor of Chemistry<br />Drexel University<br />September 29, 2011<br />
  2. 2. The Trusted Source Model<br />Before online databases (early 90s) searching for properties like melting points using ONE “trusted source” was practical and acceptable as part of the chemistry culture.<br /><ul><li>CRC Handbook
  3. 3. Merck Index
  4. 4. Chemical Vendor Catalogs (e.g. Sigma-Aldrich)
  5. 5. Peer-Reviewed Journals</li></ul>Single values don’t tend to be contradicted<br />
  6. 6. Question Assumptions<br />Using technology, we can begin to replace the “trusted source” model with one based on transparency and provenance<br />
  7. 7. The Chemical Information Validation Sheet <br />567 curated and referenced measurements from <br />Fall 2010 Chemical Information Retrieval course<br />
  8. 8. Discovering outliers for melting points (stdev/average)<br />
  9. 9. Investigating the m.p. inconsistencies of EGCG<br />
  10. 10. Investigating the m.p. inconsistencies of cyclohexanone<br />
  11. 11. Most popular data sources<br />
  12. 12. Alfa Aesar donates melting points to the public<br />
  13. 13. Open Melting Point Explorer<br />(Andrew Lang)<br />
  14. 14. Outliers<br />MDPI <br />dataset<br />EPI (donated all data to public also)<br />
  15. 15. Outliers for ethanol: Alfa Aesar and Oxford MSDS<br />
  16. 16. Inconsistencies and SMILES problems within MDPI dataset<br />
  17. 17. MDPI Dataset labeled with High Trust Level<br />
  18. 18. Open Melting Point Datasets<br />Currently 27,000 mps for 20,000 compounds<br />
  19. 19. What is the melting point of 4-benzyltoluene?<br />American Petroleum Institute5 C<br />PHYSPROP-30 C<br />PHYSPROP 125 C<br />peer reviewed journal (2008)97.5 C<br />government database-30 C<br />government database4.58 C<br />
  20. 20. The quest to resolve the melting point <br />of 4-benzyltoluene: liquid at room temp <br />and can be frozen <-30C (Evan Curtin)<br />
  21. 21. Open Lab Notebook page measuring the melting point of 4-benzyltoluene<br />
  22. 22. Motivation: Faster Science,Better Science<br />
  23. 23. Ruling out all melting points above -15C?<br />
  24. 24. Oops – 4-benzyltoluene freezes after 16 days at -15C!<br />
  25. 25. Measuring the melting point by slowly heating from -15 C gives 5 C<br />
  26. 26. There are NO FACTS, <br />only measurements embedded within assumptions<br />Open Notebook Science maintains the integrity of data provenance by making assumptions explicit<br />
  27. 27. Open Random Forest modeling of Open Melting Point data using CDK descriptors<br />(Andrew Lang)<br />R2 = 0.78, TPSA and nHdon most important<br />
  28. 28. Melting point prediction service<br />
  29. 29. Melting point predictions and measurements on iPhone/iPad (Andrew Lang and Alex Clark)<br />
  30. 30. Using melting point for temperature dependent solubility prediction<br />
  31. 31. Web services for summary data<br />(Andrew Lang)<br />
  32. 32. Publication of double+ validated melting point dataset to Nature Precedings and LuLu<br />
  33. 33.
  34. 34.
  35. 35. Reaction Attempts Book<br />
  36. 36. Reaction Attempts Book: Reactants listed Alphabetically<br />
  37. 37.
  38. 38. Google Apps Scripts web services<br />
  39. 39. Google Apps Scripts for conveniently exploring melting point data<br />
  40. 40. Comparison of model with triple validated measurements<br />Straight chain carboxylic acids from 1 to 10 carbons<br />Straight chain alcohols from 1 to 10 carbons<br />
  41. 41. Cyclic primary amines from 3 to 6 carbons (cyclobutylamine flagged for validation – only single source available) <br />
  42. 42. Google Apps Scripts for planning reactions and creating schemes<br />
  43. 43. Open Melting Points in Supplementary Data Pages of Wikipedia (Martin Walker)<br />
  44. 44. All ONS web services<br />
  45. 45. Predicting Best Solvent for Imine Formation <br />(Evan Curtin)<br />
  46. 46. Predicting Yield of Imine Formation in Ethanol <br />(Evan Curtin)<br />

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