Chemical Information Retrieval 2012

Jean-Claude Bradley

September 28, 2012

First Class

Associate Professor of ChemistryDrexel University

CHEM367/767 Drexel University

Finding reliable chemical information

can be really hard

After this class,you should feel that

you can never blindly trust

chemical data sources again

But…You will learn how to do the best you can

with imperfect information

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 20,000 compounds with Open MPs

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

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

“Simple” aldol condensation synthesis

Top Hit(no reports of synthesis)

In top ten(a few reports of synthesis)(Andrew Lang)

Information from the literature on the target synthesis

Information from the literature on the target synthesis

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

information

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

time

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

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)

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

Google Apps Scripts web services

Integration of Multiple Web Services to Recommend Solvents

for Reactions

(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)

Web services from data collected in this class will be added here

In this class you will learn

How to search Science1.0 resources

•Peer-Reviewed journals•Commercial databases•Patents•Conference Proceedings

In this class you will learn

How to participate in Science2.0

•wikis (Wikipedia, class wiki)•blogs•interactive databases (ChemSpider)•social software (Twitter, FriendFeed)

In this class you will learnHow to leverage Science3.0

(via collaboration with Andrew Lang)

•machine readable web-services

Now lets take a look at the class wiki