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)