The document discusses an app that recommends solvents for recrystallizing compounds by using open data sources and algorithms. It summarizes how the app works by looking up solvent properties like boiling point and solubility to predict recrystallization yield. The discussion emphasizes the importance of open data, models and software in chemistry. It provides examples of using open data sources and models to predict properties, validate data, and enable new applications. The conclusions advocate for more openness in chemistry to make science more efficient.

1. The deployment of an app from Open Data feeds
and algorithms: Recommending recrystallization
solvents
ACS-CINF Symposium
Jean-Claude Bradley
Associate Professor of Chemistry
Drexel University
December 13, 2012

2. The importance of recrystallization
• Generally preferred if there is a known
solvent that gives a good yield
• Scales much more easily and cheaply than
chromatography
• However, for new compounds much trial and
error may be needed

3. The Recrystallization App
(Andrew Lang)

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

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

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

7. How does it work?
1. Look up the solvent boiling point
2. Look up the room temperature solubility or predict it via
Abraham descriptors predicted from a model using the
CDK
3. Look up the solute melting point or predict it via a
model using the CDK
4. Use the melting point and the solubility at room
temperature to predict the solubility at boiling
5. Calculate the predicted recrystallization yield

8. Openness in Chemistry
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
WHY?

9. Open Data Collections are essential for this
strategy
Open transparent
Data transformation Open
Data
Open
Data
Transparent chain of provenance

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

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

12. Motivation: Faster Science, Better Science

13. The quest to resolve the melting point
of 4-benzyltoluene: liquid at room temp
and can be frozen <-30C

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

15. Ruling out all melting points above -15C?

16. Oops – 4-benzyltoluene freezes after 16 days at -15C!

17. Measuring the melting point by slowly heating
from -15 C gives 5 C

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

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

20. Melting point prediction service

21. Web services for summary data
(Andrew Lang)

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

23. Calling Google App Scripts

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

25. Never having to leave the Google Spreadsheet
dashboard for access to key info
(Andrew Lang and Rich
Apodaca)

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

27. Google Apps Scripts for conveniently
exploring melting point data

28. Comparison of model with triple validated measurements
Straight chain carboxylic acids from 1 to 10 carbons
Straight chain alcohols from 1 to 10 carbons

29. Cyclic primary amines from 3 to 6 carbons (cyclobutylamine flagged for
validation – only single source available)

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

31. Dibenzalacetone derivatives docking against
tubulin (paclitaxel site)
(Andrew Lang)

32. “Simple” aldol condensation synthesis
Top Hit
(no reports
of synthesis)
In top ten
(a few reports
of synthesis)
(Andrew Lang)

33. Information from the literature on the target synthesis

34. Information from the literature on the target synthesis

35. Searching for aldol condensations of acetone
in the Reaction Attempts database (about
90% of reactions in Open Notebooks are “not
successful”)
(Andrew Lang)

36. An example of a “failed experiment” in an
Open Notebook with useful information

37. A failed experiment reveals the importance of aldehyde
solubility

38. An example of a successful experiment in an Open
Notebook

39. A successful synthesis by avoiding water, dramatically
increasing NaOH and long reaction time

40. Chemical Information Retrieval 2012
property assignment

41. Melting Point Outlier List

42. Melting Point Outlier example

43. Solubility Outlier List

44. Solubility of benzoic acid in 1-octanol
discrepancies

45. Using ChemSpider to ensure all stereocenters
are defined before searching for properties

46. Using the InChIKey to find single isomers

47. Chemical Information Validation Sheet 2012

48. Each entry validated with an image

49. Avoiding redundant property data points with
a single click within the validation sheet

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

51. Open Chemical Property Matrix (OCPM)

52. OCPM relationships

53. OCPM melting point sheet

54. Dibenzalacetone libraries are promising for connecting
the OCPM with useful applications

55. 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)