Jean-Claude Bradley presents on Open Notebook Science: Transparency in Research on October 23, 2012 at Georgia Tech for Open Access Week. Topics include solubility, melting points, a recrystallization app, the Chemical Information Retrieval class at Drexel University and the Open Chemical Property Matrix (OCPM). YouTube recording here: http://youtu.be/XpRyfdNuMrQ

1. Open Notebook Science:
Transparency in
Research
Georgia Tech Library
Open Access Week
Jean-Claude Bradley
Associate Professor of Chemistry
Drexel University
October 23, 2012

2. Openness in Chemistry
WHY?

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

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

5. What is the current standard for “sufficient
information” in communicating organic
chemistry?
By definition, all peer-reviewed
published documentation has
been approved as sufficient by
authors, editors and reviewers.

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

7. Information from the literature on the target synthesis

8. Information from the literature on the target synthesis

9. Information from the literature on the target synthesis

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

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

12. A failed experiment reveals the importance of aldehyde
solubility

13. Motivation: Faster Science, Better
Science

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

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

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

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

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

19. Discovering outliers for melting points
(stdev/average)

20. Investigating the m.p. inconsistencies of EGCG

21. Investigating the m.p. inconsistencies of
cyclohexanone

22. Most popular data sources

23. Alfa Aesar donates melting points to the public

24. Open Melting Point Explorer
(Andrew Lang)

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

26. Outliers for ethanol: Alfa Aesar and Oxford
MSDS

27. Inconsistencies and SMILES problems within
MDPI dataset

28. MDPI Dataset labeled with High Trust Level

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

30. What is the melting point of 4-benzyltoluene?
American Petroleum Institute5 C
PHYSPROP -30 C
PHYSPROP 125
C
peer reviewed journal (2008) 97.5 C
government database -30 C
government database 4.58 C

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

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

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

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

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

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

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

38. Melting point prediction service

39. Web services for summary data
(Andrew Lang)

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

41. Calling Google App Scripts

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

43. Google Apps Scripts for conveniently
exploring melting point data

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

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

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

47. Google Apps Scripts web services

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

49. Integration of Multiple Web Services to
Recommend Solvents for Reactions
(Andrew Lang)

50. The Recrystallization App
(Andrew Lang)

51. 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

52. 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

53. 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

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

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

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

57. Chemical Information Retrieval 2012
property assignment

58. Melting Point Outlier List

59. Melting Point Outlier example

60. Solubility Outlier List

61. Solubility of benzoic acid in 1-octanol
discrepancies

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

63. Using the InChIKey to find single isomers

64. Chemical Information Validation Sheet 2012

65. Each entry validated with an image

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

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

68. Open Chemical Property Matrix (OCPM)

69. OCPM relationships

70. OCPM melting point sheet

71. 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)