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. Air Quality

3. Global Modelling HiHEM: CH3CO2

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

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 XML (CML + MathML)‏ XML (CML + MathML)‏ XSLT LaTeX MCM XHTML Datasheet XHTML Datasheet XHTML Summary Table XHTML Summary Table Harvest Search / Link

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. XML -> XHTML <cml xmlns="http://www.xml-cml.org/schema/cml2/core" xmlns:iKin="http://www.atm.ch.cam.ac.uk/iKin" xmlns:iKinunits="http://www.atm.ch.cam.ac.uk/iKinunits" xmlns:mcm="http://mcm.leeds.ac.uk/ns#" xmlns:inchi="http://www.iupac.org/inchi" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xml-cml.org/schema/cml2/core file:/C:/Documents%20and%20Settings/Hannah/Desktop/cmlreactCopy.xsd"> 2004-03-01 No change since last publication hydroxyl radical InChI=1/HO/h1H isoprene InChI=1/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3 not available <cml xmlns="http://www.xml-cml.org/schema/cml2/core" xmlns:iKin="http://www.atm.ch.cam.ac.uk/iKin" xmlns:iKinunits="http://www.atm.ch.cam.ac.uk/iKinunits" xmlns:mcm="http://mcm.leeds.ac.uk/ns#" xmlns:inchi="http://www.iupac.org/inchi" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xml-cml.org/schema/cml2/core file:/C:/Documents%20and%20Settings/Hannah/Desktop/cmlreactCopy.xsd"> 2004-03-01 No change since last publication hydroxyl radical InChI=1/HO/h1H isoprene InChI=1/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3 not available

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

18. 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

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

20. Search: A “Google” inspired approach 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”

21. 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

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

23. The End http://mcm.leeds.ac.uk/MCMhttp://mcm.leeds.ac.uk/MCM [-devel] http://www.iupac-kinetic.ch.cam.ac.uk/

24. Reserve Slides