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

Air Quality

Global Modelling HiHEM: CH3CO2

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

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

MCM 5660 Chemical Species Reactions 5660 Chemical Species 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 Database

IUPAC Datasheets

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

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

MathML Example 1 Arrhenius <cn definitionURL=" type="e-notation"> T e 300/T A. e E/T

Fcm3-molecule-s k Arrh <cn definitionURL=" type="e-notation"> PlusMinus T 300 MathML Example 2

XML -> XHTML <cml xmlns=" xmlns:iKin=" xmlns:iKinunits=" xmlns:mcm=" xmlns:inchi=" xmlns:mml=" xmlns:xsi=" xsi:schemaLocation=" file:/C:/Documents%20and%20Settings/Hannah/Desktop/cmlreactCopy.xsd"> 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=" xmlns:iKin=" xmlns:iKinunits=" xmlns:mcm=" xmlns:inchi=" xmlns:mml=" xmlns:xsi=" xsi:schemaLocation=" file:/C:/Documents%20and%20Settings/Hannah/Desktop/cmlreactCopy.xsd"> 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

Leeds Master Chemical Mechanism [-devel]

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

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

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”

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

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

The End [-devel]

Reserve Slides