Jean-Claude Bradley provides examples of how detailed monitoring of chemical mixing can be advantageous for new discoveries and Green Chemistry. The role of openness to successfully accomplish this goal is also discussed.

1. The Chemical Rediscovery
Survey and the role of
Openness in Chemistry
Research Mini-Symposia
Drexel University Department of Chemistry
Jean-Claude Bradley
Associate Professor of Chemistry
Drexel University
March 6, 2014

2. Forms of Openness in Science
1. Open Access Peer-Reviewed
Publication
2. Informal Discussions
3. Open Source Software
4. Open Datasets and Models
5. Open Notebook Science
6. Open Research Proposals

3. Top 5 questions in chemistry
according to Scientific American
(Nov 5, 2013)
1. Can we unravel the puzzle of life’s
origins?
2. Can we ever beat photosynthesis?
3. How do we make chemistry
environmentally friendly?
4. Can we design the perfect drug?
5. How do we sell chemistry to the
public?

4. The current paradigm of doing and
sharing science in chemistry
1. Design experiments based on
established or potentially new theories.
2. Execute and record experimental
outcomes in private notebooks.
3. When a sufficient narrative emerges
selective experimental data are
combined to publish, with a limited
amount of “supplementary supporting
data”

5. What kind of (chemical) worldview
has this approach created?
1. Selective bias towards which
experiment are even attempted.
2. Overconfidence in our understanding
since deviant or ambiguous results are
rarely reported.

6. Filling in the blind spots with the
Chemical Rediscovery Survey
(chemrs.wikispaces.com)
1.
2.
3.
4.
Randomize the mixture of chemicals with
certain criteria*
Identify “what happens” after convenient*
periods of time.
Follow up on unexpected behavior with the
traditional scientific method.
Openly share the entire process, including all
raw data and preliminary hypotheses and
discoveries as it happens.

7. The current CRS criteria
1. Only small common cheap organic
compounds
2. Only select relatively “Green”
compounds
3. Avoid excessively unpleasant
compounds (stench!)

8. Co-axial NMR tubes are used to isolate
the reaction from the deuterated solvent

9. An example of a Chemical
Rediscovery Survey experiment

10. The overall reaction is easily
identified by NMR

11. Raw NMR data is provided for open
analysis

12. The experiment is represented in a
machine readable matrix: mole fractions

13. All assignable NMR peaks are also
archived for machine readability

14. Report discoveries as they happen

15. Example of a more human readable format

16. In the case of ethanol, hemiacetal OH
appears as doublet (7.3 Hz)

17. This level of detail for monitoring
chemical interactions is not typically
available from the chemical literature
(Open or Not)
Using NMR spectroscopy in this way to
create an Open Survey of chemical
behavior is analogous in astronomy to
creating a new Survey of Space by
introducing a new telescope

18. NMR requires a homogeneous solution
for proper measurement
However once an interesting reaction has
been observed to occur slowly at 25C and
low concentration, preparative scale-up
conditions can be estimated (i.e. reaction
rate doubles about every 10C)

19. The Recrystallization App (Open)
(Andrew Lang)

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

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

22. The role of Openness in rethinking how to
tackle the “big chemistry questions”
Q3. How do we make chemistry
environmentally friendly?
By limiting ourselves to relatively Green
compounds and by sharing all data in real time
we are much more likely to find Green reactions
from the CRS project and encourage others to
benefit.
This would reduce student exposure in teaching
labs and lower costs for waste disposal

23. Q4. Can we design the perfect drug?
We can try to do Open Drug Discovery – we have
found active lead compounds against malaria for
example and working on Taxol analogs
(Andrew Lang)

24. Q5. How do we sell chemistry to the public?
We are approaching 1000 queries a day for
specific solubility and melting point data.
Some originate from academia and industry
but many from high schools and the
general public.
By concentrating on “Green” non toxic and
readily available compounds and by
providing Open resources to encourage
their curiosity the public will become more
engaged and understand the importance of
chemistry.

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

26. Chemical Information Validation Sheet 2012

27. Each entry validated with an image

28. Alfa Aesar donates melting points to the public

29. Outliers for ethanol: Alfa Aesar and Oxford MSDS

30. Outliers
MDPI
dataset
EPI (donated all
data to public also)

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

32. What is the melting point of 4-benzyltoluene?
American Petroleum Institute
PHYSPROP
PHYSPROP
peer reviewed journal (2008)
government database
government database
5C
-30 C
125 C
97.5 C
-30 C
4.58 C

33. Open Lab Notebook page measuring the
melting point of 4-benzyltoluene

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

35. A failed experiment reveals the importance of aldehyde
solubility

36. Information from the literature on the target synthesis

37. Motivation: Faster Science, Better Science

38. There are NO FACTS,
only measurements embedded
within assumptions
Open Notebook Science maintains
the integrity of data provenance by
making assumptions explicit

39. An example of a successful experiment in an Open
Notebook that was used to improve the teaching lab
manual

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

41. Melting point prediction service

42. Web services for summary data
(Andrew Lang)

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

44. Calling Google App Scripts

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

46. Google Apps Scripts web services

47. Conclusions
More openness in chemistry can make science more efficient and
address many of the key current questions challenging chemistry
community
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, Cuepil Choi, Matthew McBride, Alex Turfa (CRS)