Integrating Chemical Kinetic Data on the web

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• Integrating Chemical Kinetic Data on the web
• Experiences of the MCM-IUPAC Project

Dr Stephen Pascoe. Centre for Atmospheric Data
Archival, STFC Stephen.Pascoe_at_stfc.ac.uk
Dr Hannah Barjat Dr Jenny Young
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Air Quality
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Global Modelling
HiHEM CH3CO2
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Research in Chemical Kinetics
Box Models
Lab. Experiments
Field Experiments
Mechanism
IUPAC Gas Kinetics
MCM
Subcommittee for Gas Kinetic Data Evaluation
Leeds Master Chemical Mechanism
Dynamic Models
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IUPAC Kinetics

• 900 Gas-phase Datasheets
• 60 Heterogenious Datasheets

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MCM

• 5660 Chemical Species
• 13500 Reactions

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Integrating the sites

• Harvest
• Update

• Search
• Link

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Cheminformatics

• Open Standards
• CML, InChI
• OpenSource Tools
• OpenBabel, CDK, Jmol, Bioclipse
• Open Data-centric websites
• PubChem
• NIST Webbook
• Chemspider

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IUPAC Kinetics Database
http//www.iupac-kinetic.ch.cam.ac.uk/
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IUPAC Datasheets
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IUPAC Approach
XHTML Summary Table
XML (CML MathML)?
LaTeX
XSLT
XHTML Datasheet
Harvest
MCM
Search / Link
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CML Usage in IUPAC

• CMLReact for reactions
• Identify species with InChIs
• Kinetic data as cmlobservation/cmltable
• Maths expressions in Content MathML

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Maths Expressions

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MathML Example 1
A . eE/T
5.6 . 10-34 e300/T
ltapplygtlttimes/gt ltapplygtltexp/gt
ltapplygtltdivide/gt ltcsymbol
definitionURL"http//www.iupac-kinetic.ch.cam.ac.
uk/mathML/temperature"gtTlt/csymbolgt ltcn
type"e-notation"gt5.6ltsep/gt-34lt/cngt
ltcngt300lt/cngt lt/applygt lt/applygt lt/applygt
ltapplygt ltcsymbol definitionURL"http//www.iupac
-kinetic.ch.cam.ac.uk/mathml/Arrhenius"gtArrheniuslt
/csymbolgt ltcn definitionURL"http//www.iupac-ki
netic.ch.cam.ac.uk/mathML/Pre-exponentialFactor"
type"e-notation"gt5.6ltsep/gt-34 lt/cngt ltcn
definitionURL"http//www.iupac-kinetic.ch.cam.ac.
uk/mathml/Ea_R"gt300lt/cngt lt/applygt
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MathML Example 2
ltmath xmlns"http//www.w3.org/1998/Math/MathML"gt
ltapplygtlteq/gt ltapplygtltcigtFcm3-molecule-slt/cigt
ltcsymbol definitionURL"http//www.iupac-ki
netic.ch.cam.ac.uk/mathml/ratecoefficientk"gt
ltcigtklt/cigt lt/csymbolgt
lt/applygt ltpiecewisegt ltpiecegt ltapplygtltcs
ymbol definitionURL"http//www.iupac-kinetic.ch.c
am.ac.uk/mathml/arrhenius"gtArrhlt/csymbolgt ltcn
definitionURL"http//www.iupac-kinetic.ch.cam.ac.
uk/mathml/Pre-exponentialFactor"
type"e-notation"gt 7.6ltsep /gt-12 lt/cngt
ltapplygtltcsymbol definitionURL"http//www.iupac-ki
netic.ch.cam.ac.uk/mathml/plusminus"gtPlusMinuslt/cs
ymbolgt ltcn definitionURL"http//www.iupac-ki
netic.ch.cam.ac.uk/mathml/Ea_R"gt-585lt/cngt
ltcngt100lt/cngt lt/applygt lt/applygt ltapplygtltlt
/gt ltcngt200lt/cngt ltcsymbol definitionURL"http
//www.iupac-kinetic.ch.cam.ac.uk/mathml/temperatu
re"gt ltcigtTlt/cigt lt/csymbolgt
ltcngt300lt/cngt lt/applygt lt/piecegt
lt/piecewisegt lt/applygt lt/mathgt
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XML -gt XHTML
lt?xml version"1.0" encoding"UTF-8"?gt ltcml
xmlns"http//www.xml-cml.org/schema/cml2/core"
xmlnsiKin"http//www.atm.ch.cam.ac.uk/iKin"
xmlnsiKinunits"http//www.atm.ch.cam.ac.uk/iKinu
nits" xmlnsmcm"http//mcm.leeds.ac.uk/ns"
xmlnsinchi"http//www.iupac.org/inchi"
xmlnsmml"http//www.w3.org/1998/Math/MathML"
xmlnsxsi"http//www.w3.org/2001/XMLSchema-instan
ce" xsischemaLocation"http//www.xml-cml.org/s
chema/cml2/core file/C/Documents20and20Setting
s/Hannah/Desktop/cmlreactCopy.xsd"gt
ltdescription title"Dates and Versions"gt
ltlistgt lt!-- Dates given in American format
(yyyy-mm-dd standard for xsddate) --gt
ltscalar dictRef"iKinPubDate"gt2004-03-01lt/scalargt
ltscalar dictRef"iKinRecValueDate"gt2004-03
-01lt/scalargt ltscalar dictRef"iKinTextChang
eDate"gt2004-03-01lt/scalargt ltscalar
dictRef"iKinLatestChange"gtNo change since last
publicationlt/scalargt lt/listgt
lt/descriptiongt ltreactionList id"II_A2_10"gt
ltreaction id"II_A2_10_(1)"gt
ltreactantListgt ltreactant count"1"
title"HO"gt ltmolecule title"HO"gt
ltname convention"iKinpreferredname"gthydrox
yl radicallt/namegt ltformula concise"H
1 O 1"/gt ltidentifiergt
ltinchibasicgtInChI1/HO/h1Hlt/inchibasicgt
lt/identifiergt lt/moleculegt
lt/reactantgt ltreactant count"1"
title"CH_2C(CH_3)CHCH_2"gt ltmolecule
title"CH_2C(CH_3)CHCH_2"gt ltname
convention"iKinpreferredname"gtisoprenelt/namegt
ltformula concise"C 1 H 2"/gt
ltidentifiergt ltinchibasicgt
InChI1/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3lt/inchibasic
gt lt/identifiergt
lt/moleculegt lt/reactantgt
lt/reactantListgt ltproductListgt
ltproduct title"generic products"/gt
lt/productListgt ltpropertyListgt
ltproperty title"Heat of reaction"
dictRef"iKinhreact"gt ltscalar
units"iKinUnitskJ-mol"gtnot availablelt/scalargt
lt/propertygt
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Leeds Master Chemical Mechanism
http//mcm.leeds.ac.uk/MCM -devel
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Chemical Identifiers
IUPAC 2-Methylbutadiene 2-Methyl-1,3-butadie
ne Common Isoprene Isopentadiene
CAS 78-79-5 PubChem 6557
SMILES CCC(C)C C(C)CCC C(CC)CC
CC(CC)C CSMILES CCC(C)C
InChI InChI1/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3
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InChI data model

• Stereochemistry
• Radicals
• Excited States
• Electronic O(1D), O(3P)?
• NoInChI...
• Vibrational

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Search A Google inspired approach
MCM Name
C5H8
InChI
InChI1/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3
InChI1/C5H8/
Synonym
isoprene
isopentadiene
exact SMILES
CC(CC)C
SMARTS pattern
CCCC
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Summary

• So far
• IUPAC Datsheets machine readable
• Species links between MCM and IUPAC
• Intuitive species search in MCM
• Todo
• Update MCM from IUPAC
• Dedicated Search Site
• Standardised CML output of MCM

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Acknowledgements

• University of Cambridge
• Dr Hannah Barjat
• Dr Glenn Carver
• University of Leeds
• Dr Jenny Young
• Dr Andrew Rickard

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The End
http//www.iupac-kinetic.ch.cam.ac.uk/
http//mcm.leeds.ac.uk/MCM -devel
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Reserve Slides
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