the value of openness in research and teaching

The value of Openness in Research and

Teaching

Jean-Claude Bradley

February 12, 2013

University of Delaware

Associate Professor of ChemistryDrexel University

Tuesday Tech Talks

The story of the enigmatic solvent

Sophomore Organic Chemistry lab at Drexel University

Lab procedure required

recrystallization from ethyl

acetate and synthesis not

reliable

Searching for a logical reason

• The synthesis of DBA is widespread in organic teaching labs

• Methods vary but ethyl acetate is often used to recrystallize DBA

• Its use traces back to a paper from 1903

• However the solubility of DBA in ethyl acetate was apparently never reported

Developing a rational method to choose a synthesis and recrystallization solvent – in

the open

Matthew McBride

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

A failed experiment reveals the importance of aldehyde solubility

An example of a successful experiment in an Open Notebook

This synthesis will now be used in the revised organic teaching lab manual at Drexel

Incomplete information from the literature can be very problematic

Motivation: Faster Science, Better Science

The Recrystallization App

(Andrew Lang)

What are good solvents to recrystallize benzoic acid?

(Andrew Lang)

Click on the solvent to see temp curve

(Andrew Lang)

Deliver melting point data via App

(Andrew Lang)

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

Open Melting Point DatasetsCurrently 20,000 compounds with Open MPs

Contributing to Science while Teaching it:

Chemical Information Retrieval Class

The Chemical Information Validation Sheet

567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course

Each entry validated with an image

Alfa Aesar donates melting points to the public

Outliers for ethanol: Alfa Aesar and Oxford MSDS

Solubility Outlier List

Open Melting Point Explorer

(Andrew Lang)

Searching for aldol condensations of acetone in the Reaction Attempts

database

(Andrew Lang)

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

Web services for summary data

(Andrew Lang)

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

Calling Google App Scripts

Calling Google App Scripts

(Andrew Lang and Rich Apodaca)

Google Apps Scripts for conveniently exploring melting

point data

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

(Andrew Lang)

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

Google Apps Scripts web services

Chemistry Google App Scripts description sheet

(Andrew Lang and Rich Apodaca)

Open Chemical Property Matrix (OCPM)

logP

Abraham descriptors

Melting point

Aqueous solubility

Octanol solubility

Vapor pressure

Flash point

Boiling point

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 modelersApps (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)