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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. Photochemical Smog. Global Modelling. Research in Chemical Kinetics. Box

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integrating chemical kinetic data on the web experiences of the mcm iupac project
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

research in chemical kinetics
Research in Chemical Kinetics

Box

Models

Lab.

Experiments

Field

Experiments

Mechanism

IUPAC

Gas Kinetics

MCM

Subcommittee for

Gas Kinetic Data Evaluation

Leeds Master Chemical Mechanism

Dynamic

Models

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

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

slide6
MCM
  • 5660 Chemical Species
  • 13500 Reactions
integrating the sites
Integrating the sites
  • Harvest
  • Update
  • Search
  • Link
cheminformatics
Cheminformatics
  • Open Standards
    • CML, InChI
  • OpenSource Tools
    • OpenBabel, CDK, Jmol, Bioclipse
  • Open Data-centric websites
    • PubChem
    • NIST Webbook
    • Chemspider
slide9

IUPAC Kinetics Database

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

iupac approach
IUPAC Approach

XHTML

Datasheet

LaTeX

CML + MathML

XSLT

XHTML

Summary Table

Harvest

MCM Search

cml usage in iupac
CML Usage in IUPAC
  • CMLReact for reactions
  • Identify species with InChIs
  • Kinetic data as cml:observation/cml:table
  • Maths expressions in Content MathML
mathml example 1
MathML Example 1

A . eE/T

5.6 . 10-34e300/T

<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>

<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>

mathml example 2
MathML Example 2

<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>

slide16

Leeds Master Chemical Mechanism

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

chemical identifiers
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

inchi data model
InChI data model
  • Stereochemistry
  • Radicals
  • Excited States
    • Electronic: O(1D), O(3P)‏

NoInChI=...

    • Vibrational:
search keep it simple
Search: Keep it simple

MCM Name

“C5H8”

InChI

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

“InChI=1/C5H8/”

Synonym

“isoprene”

“isopentadiene”

exact SMILES

“C=C(C=C)C”

SMARTS pattern

“C=CC=C”

acknowledgements
Acknowledgements
  • University of Cambridge
    • Dr Hannah Barjat
    • Dr Glenn Carver
  • University of Leeds
    • Dr Jenny Young
    • Dr Andrew Rickard
slide26
CML
  • Molecules
  • Reactions
  • Spectra
  • Lattices
  • Arrays
  • Tables
  • Matrices
  • Metadata
  • Equations

CMLCore

CMLReact

STMML

CMLSpect

CMLComp

168 elements

~200 attributes