Integrating Chemical Kinetic Data on the webExperiences of the MCM-IUPAC Project

Dr Stephen Pascoe. Centre for Atmospheric Data Archival, STFCStephen.Pascoe@stfc.ac.uk

Dr Hannah Barjat Dr Jenny Young

Photochemical Smog

Global Modelling

Research in Chemical Kinetics

Lab.Experiments

Lab.Experiments

BoxModels

BoxModels

FieldExperiments

FieldExperiments

DynamicModels

DynamicModels

MechanismMechanism

MCMMCMIUPACGas Kinetics

IUPACGas Kinetics

Subcommittee for Gas Kinetic Data Evaluation

Leeds Master Chemical Mechanism

IUPAC Kinetics•900 Gas-phase Datasheets•60 Heterogenious Datasheets

•900 Gas-phase Datasheets•60 Heterogenious Datasheets

http://www.iupac-kinetic.ch.cam.ac.uk/http://www.iupac-kinetic.ch.cam.ac.uk/

MCM

•5660 Chemical Species•13500 Reactions

•5660 Chemical Species•13500 Reactions

Integrating the sites

•Harvest•Update

•Search•Link

Cheminformatics

Open Standards– CML, InChI

OpenSource Tools– OpenBabel, CDK, Jmol, Bioclipse

Open Data-centric websites– PubChem– NIST Webbook– Chemspider

IUPAC Kinetics Databasehttp://www.iupac-kinetic.ch.cam.ac.uk/

IUPAC Datasheets

IUPAC Approach

CML + MathMLCML + MathMLXSLTXSLTLaTeXLaTeX

MCM SearchMCM Search

XHTMLDatasheet

XHTMLDatasheet

XHTMLSummary Table

XHTMLSummary Table

Harvest

CML Usage in IUPAC

CMLReact for reactions Identify species with InChIs Kinetic data as cml:observation/cml:table

Maths expressions in Content MathML

Maths Expressions

Co e f f ic ie n t e xp re s s io n P a ra m e te rs Co m m e n t

*C C, *[M ] Co ns t a nt or e xpr e ss io nde pe n d in g on pr e ss ur ede pe n de ncy

*Ae xp E /T A, E , *[M ] Ar r he nius e xpr e ss io n

*A(T/R e fT) ne E /T A, E , R e fT, n ,*[M ] M odifie d Ar r he niu se xpr e ss io n

*A(T/E )n A, E , n , *[M ] Tr oe e xpr e ss io n

A(1 + [M ]/B ) A, B , [M ] r e le va nt for : H O + CO

Ae xp E/T + B e xp F /T A, B , E , F r e le va nt for H O + a ce tone ;C2 H 5 + O2 ; C 2 H 2 + H O

A[M ]e xp E/T /{ 1 +B [M ]e xp F/T}

A, B , E , F r e le va nt for H O + CH 3SCH 3

MathML Example 1

<apply> <csymbol definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/Arrhenius">Arrhenius</csymbol> <cn definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathML/Pre-exponentialFactor" type="e-notation">5.6<sep/>-34 </cn> <cn definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/Ea_R">300</cn></apply>

<apply><times/> <apply><exp/> <apply><divide/> <csymbol definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathML/temperature">T</csymbol> <cn type="e-notation">5.6<sep/>-34</cn> <cn>300</cn> </apply> </apply></apply>

5.6 . 10-34 e300/TA . eE/T

<math xmlns="http://www.w3.org/1998/Math/MathML"> <apply><eq/> <apply><ci>Fcm3-molecule-s</ci> <csymbol definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/ratecoefficientk"> <ci>k</ci> </csymbol> </apply> <piecewise> <piece>

<apply><csymbol definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/arrhenius">Arrh</csymbol>

<cn definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/Pre-exponentialFactor" type="e-notation"> 7.6<sep />-12 </cn> <apply><csymbol

definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/plusminus">PlusMinus</csymbol> <cn definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/Ea_R">-585</cn> <cn>100</cn> </apply></apply><apply><lt /> <cn>200</cn> <csymbol definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/temperature"> <ci>T</ci> </csymbol> <cn>300</cn></apply>

</piece> </piecewise> </apply></math>

MathML Example 2

Leeds Master Chemical

Mechanismhttp://mcm.leeds.ac.uk/MCM [-devel]

Chemical Identifiers

IUPAC: 2-Methylbutadiene; 2-Methyl-1,3-butadiene; Common: Isoprene; Isopentadiene;

CAS: 78-79-5PubChem: 6557

SMILES: C=CC(C)=C; C(C)=CC=C;C(C=C)C=C; C=C(C=C)C;

CSMILES: C=CC(=C)C

InChI: InChI=1/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3

InChI data model

StereochemistryRadicalsExcited StatesElectronic: O(1D), O(3P)NoInChI=...

Vibrational:

Search: Keep it simple

MCM NameMCM Name

InChIInChI

exact SMILESexact SMILES

SynonymSynonym

SMARTS patternSMARTS pattern

“C5H8”

“isoprene”

“InChI=1/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3”

“InChI=1/C5H8/”

“isopentadiene”

“C=C(C=C)C”

“C=CC=C”

Acknowledgements

University of Cambridge

– Dr Hannah Barjat

– Dr Glenn Carver

University of Leeds

– Dr Jenny Young

– Dr Andrew Rickard

CML

CMLCoreCMLCore

CMLReactCMLReact

CMLSpectCMLSpectCMLCompCMLComp

STMMLSTMML

•Molecules

•Reactions

•Spectra

•Lattices

•Arrays

•Tables

•Matrices

•Metadata

•Equations

168 elements

~200 attributes