MiniSymp2011 Bradley
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Transcript of MiniSymp2011 Bradley
The Impact of Openness on the Quality of Chemistry Data and Implications for Organic
Synthesis
Jean-Claude Bradley
September 29, 2011
Drexel Chemistry Mini Symposium
Associate Professor of ChemistryDrexel University
The Trusted Source ModelBefore online databases (early 90s) searching for properties like melting
points using ONE “trusted source” was practical and acceptable as part of the
chemistry culture.• CRC Handbook•Merck Index• Chemical Vendor Catalogs (e.g. Sigma-Aldrich)• Peer-Reviewed Journals
Single values don’t tend to be contradicted
Question Assumptions
Using technology, we can begin to replace the “trusted source”
model with one based on transparency and provenance
The Chemical Information Validation Sheet
567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course
Discovering outliers for melting points (stdev/average)
Investigating the m.p. inconsistencies of EGCG
Investigating the m.p. inconsistencies of cyclohexanone
Most popular data sources
Alfa Aesar donates melting points to the public
Open Melting Point Explorer
(Andrew Lang)
OutliersMDPI
datasetEPI (donated all data to public
also)
Outliers for ethanol: Alfa Aesar and Oxford MSDS
Inconsistencies and SMILES problems within MDPI dataset
MDPI Dataset labeled with High Trust Level
Open Melting Point DatasetsCurrently 27,000 mps for 20,000 compounds
American Petroleum Institute 5 CPHYSPROP -30 CPHYSPROP 125 Cpeer reviewed journal (2008) 97.5 Cgovernment database -30 Cgovernment database 4.58 C
What is the melting point of 4-benzyltoluene?
The quest to resolve the melting point of 4-benzyltoluene: liquid at room temp and can be frozen <-30C (Evan Curtin)
Open Lab Notebook page measuring the melting point of 4-benzyltoluene
Motivation: Faster Science, Better Science
Ruling out all melting points above -15C?
Oops – 4-benzyltoluene freezes after 16 days at -15C!
Measuring the melting point by slowly heating from -15 C gives 5 C
There are NO FACTS, only measurements embedded
within assumptions
Open Notebook Science maintains the integrity of data
provenance by making assumptions explicit
Open Random Forest modeling of Open Melting Point data using CDK descriptors
(Andrew Lang)
R2 = 0.78, TPSA and nHdon most important
Melting point prediction service
Melting point predictions and measurements on iPhone/iPad (Andrew Lang and Alex Clark)
Using melting point for temperature dependent solubility prediction
Web services for summary data
(Andrew Lang)
Publication of double+ validated melting point dataset to Nature
Precedings and LuLu
Reaction Attempts Book
Reaction Attempts Book: Reactants listed Alphabetically
Google Apps Scripts web services
Google Apps Scripts for conveniently exploring melting
point data
Straight chain carboxylic acids from 1 to 10 carbons
Straight chain alcohols from 1 to 10 carbons
Comparison of model with triple validated measurements
Cyclic primary amines from 3 to 6 carbons (cyclobutylamine flagged for validation – only single source available)
Google Apps Scripts for planning reactions and creating schemes
Open Melting Points in Supplementary Data Pages of Wikipedia (Martin Walker)
All ONS web services
Predicting Best Solvent for Imine Formation
(Evan Curtin)
Predicting Yield of Imine Formation in Ethanol
(Evan Curtin)