1. Integrating Chemical Kinetic Data on the web Experiences of the MCM-IUPAC Project Dr Stephen Pascoe. Centre for Atmospheric Data Archival, STFC Stephen.Pascoe@stfc.ac.uk Dr Hannah Barjat Dr Jenny Young

2. Photochemical Smog

3. Global Modelling

4. Research in Chemical Kinetics Lab. Experiments Lab. Experiments Box Models Box Models Field Experiments Field Experiments Dynamic Models Dynamic Models Mechanism MCM IUPAC Gas Kinetics IUPAC Gas Kinetics Subcommittee for Gas Kinetic Data Evaluation Leeds Master Chemical Mechanism

5. IUPAC Kinetics 900 Gas-phase Datasheets 60 Heterogenious Datasheets 900 Gas-phase Datasheets 60 Heterogenious Datasheets http://www.iupac-kinetic.ch.cam.ac.uk/

6. MCM 5660 Chemical Species 13500 Reactions 5660 Chemical Species 13500 Reactions

7. Integrating the sites Harvest Update Search Link

8. Cheminformatics  Open Standards –CML, InChI  OpenSource Tools –OpenBabel, CDK, Jmol, Bioclipse  Open Data-centric websites –PubChem –NIST Webbook –Chemspider

9. IUPAC Kinetics Database http://www.iupac-kinetic.ch.cam.ac.uk/

10. IUPAC Datasheets

11. IUPAC Approach CML + MathML XSLT LaTeX MCM Search XHTML Datasheet XHTML Datasheet XHTML Summary Table XHTML Summary Table Harvest

12. CML Usage in IUPAC  CMLReact for reactions  Identify species with InChIs  Kinetic data as cml:observation/cml:table  Maths expressions in Content MathML

13. Maths Expressions

14. MathML Example 1 Arrhenius <cn definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathML/Pre-exponentialFactor" type="e-notation">5.6 -34 300 T 5.6 -34 300 5.6. 10 -34 e 300/T A. e E/T

15. Fcm3-molecule-s k Arrh <cn definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/Pre-exponentialFactor" type="e-notation"> 7.6 -12 PlusMinus -585 100 200 T 300 MathML Example 2

16. Leeds Master Chemical Mechanism http://mcm.leeds.ac.uk/MCMhttp://mcm.leeds.ac.uk/MCM [-devel]

17. Chemical Identifiers IUPAC:2-Methylbutadiene; 2-Methyl-1,3-butadiene; Common:Isoprene; Isopentadiene; CAS: 78-79-5 PubChem: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

18. InChI data model Stereochemistry Radicals  Excited States  Electronic: O( 1 D), O( 3 P)‏ NoInChI=...  Vibrational:

23. Search: Keep it simple MCM Name InChI exact SMILES Synonym SMARTS 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”

25. Acknowledgements  University of Cambridge – Dr Hannah Barjat – Dr Glenn Carver  University of Leeds – Dr Jenny Young – Dr Andrew Rickard

26. CML CMLCore CMLReact CMLSpect CMLComp STMML Molecules Reactions Spectra Lattices Arrays Tables Matrices Metadata Equations 168 elements ~200 attributes