Integrating Chemical Kinetic Data on the webExperiences of the MCM-IUPAC Project
Dr Stephen Pascoe. Centre for Atmospheric Data Archival, [email protected]
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