Jean-Claude Bradley presents at the University of Delaware Tuesday Tech Talks on February 12, 2013. The aim is to make a compelling case that openness is valuable to the educational process and augmenting scientific knowledge. Specific examples in chemistry relating to solubility, melting point and recrystallization will be detailed, as well as the technical solutions that have proved most useful.

1. The value of Openness in
Research and Teaching
University of Delaware
Tuesday Tech Talks
Jean-Claude Bradley
Associate Professor of Chemistry
Drexel University
February 12, 2013

2. The story of the enigmatic solvent
Sophomore Organic Chemistry lab at Drexel
University
Lab procedure
required
recrystallization
from ethyl acetate
and synthesis not
reliable

3. Searching for a logical reason
• The synthesis of DBA is widespread in
organic teaching labs
• Methods vary but ethyl acetate is often
used to recrystallize DBA
• Its use traces back to a paper from 1903
• However the solubility of DBA in ethyl
acetate was apparently never reported

4. Developing a rational method to choose a
synthesis and recrystallization solvent – in the
open
Matthew McBride

5. An example of a failed experiment in an Open
Notebook with useful information

6. A failed experiment reveals the importance of aldehyde
solubility

7. An example of a successful experiment in an Open
Notebook
This synthesis will now be used in the revised organic
teaching lab manual at Drexel

8. Incomplete information from the literature
can be very problematic

9. Motivation: Faster Science, Better Science

10. The Recrystallization App
(Andrew Lang)

11. What are good solvents to recrystallize benzoic acid?
(Andrew Lang)

12. Click on the solvent to see temp curve
(Andrew Lang)

13. Deliver melting point data via App
(Andrew Lang)

14. The Recrystallization App produces and uses
Open Data:
• Open Solubility Collection and Models
• Open Melting Point Collection and Models
• Modeling depends mainly on CDK (Open
Source Software with Open Descriptors)
• Open Notebook Science

15. Open Melting Point Datasets
Currently 20,000 compounds with Open MPs

16. Contributing to Science while Teaching it:
Chemical Information Retrieval Class

17. The Chemical Information Validation Sheet
567 curated and referenced measurements from
Fall 2010 Chemical Information Retrieval course

18. Each entry validated with an image

19. Alfa Aesar donates melting points to the public

20. Outliers for ethanol: Alfa Aesar and Oxford MSDS

21. Solubility Outlier List

22. Open Melting Point Explorer
(Andrew Lang)

23. Searching for aldol condensations of acetone
in the Reaction Attempts database
(Andrew Lang)

24. Open Random Forest modeling of Open Melting Point
data using CDK descriptors
(Andrew Lang)
R2 = 0.78, TPSA and nHdon most important

25. Melting point prediction service

26. Web services for summary data
(Andrew Lang)

27. Using a Google Spreadsheet as a “dashboard interface”
for reaction planning and analysis

28. Calling Google App Scripts

29. Calling Google App Scripts
(Andrew Lang and Rich
Apodaca)

30. Google Apps Scripts for conveniently
exploring melting point data

31. A click away from an interactive NMR display (using
JCAMP-DX format and ChemDoodle)
(Andrew Lang)

32. Open Melting Points in Supplementary Data Pages
of Wikipedia (Martin Walker)

33. Google Apps Scripts web services

34. Chemistry Google App Scripts description sheet
(Andrew Lang and Rich
Apodaca)

35. Open Chemical Property Matrix (OCPM)
Boiling point Vapor
pressure
Flash point
Abraham Melting point
descriptors
logP
Aqueous Octanol
solubility solubility

36. Conclusions
More openness in chemistry can make science more efficient
Provide interfaces that make sense to the end users:
Open Data, Open Models and Open Source Software to modelers
Apps (smartphones, Google App Scripts, etc.) for chemists at the bench
Acknowledgements
Andrew Lang (code, modeling)
Bill Acree (modeling, solubility data contribution)
Antony Williams (ChemSpider services, mp data curation)
Matthew McBride and Rida Atif (recrystallization and synthesis)
Kayla Gogarty (OCPM)