University of LeedsDepartment of Chemistry

The MCM Website

Andrew Rickard, Stephen Pascoe, Louise Whitehouse, Claire Bloss, Mike Jenkin, Sam Saunders and Mike Pilling

Navigational Features: Homepage

• Updated to McMv3.1 (including Box and PTM models)

• Improve User Experience:

• Better navigation• Search/Extract tools

• Simplify update and maintenance:

• More integrated data representation

• Facilitate inclusion of contextual information:

• Protocol methodology• Reaction source• Rate uncertainty

• Provide base for future development

www.mcm.leeds.ac.uk/MCM

Navigational Features: Homepage

● Menu Bar

● Mark species for later processing

● Three main functions– Browse– Search– Extract

Navigational Features: Search

● Enter SMILES string

– e.g. isoprene: C=C(C)C=C

● Enter a MCM species name

– e.g. n-butane: NC4H10

Navigational Features: Search Results

● Structure image linked to reaction listing.

Navigational Features: Reaction Listing

● Reaction source information

● Add species to Mark List

Navigational Features: Source information

● Information based on Protocol papers

● Hyperlinked citations

Reaction Categorisation

KEY

Initial reactionsIntermediate reactionsRO

2reactions

Product reactions

VOC

h OH NO3 O3

R

RO

RO2

[Criegee]*Criegee

Cl Removal

Carbonyls RONO2 ROONO2

Rxns of unsaturated degradation products

ROOH RC(O)OOH

RC(O)OONO2

RC(O)OH

ROH Multi-functional h

RO2 + NORO2 + NO2 (acyl and CH3O2)RO2 + NO3

RO2 + HO2

RO2 + RO2 (permutation)

further degradation

paper-sectionS - Saunders 2003J - Jenkin 1997

S-4.1.1S-4.4.1

S-4.5.1

S-4.2.1S-4.3.1

S-4.8.1

S-4.6.2

S-4.7.1

S-4.6.1

S-4.7.2

S-4.6.3

S-4.6.4

S-4.6.5

J-3.10.2 J-3.10.3

J-3.9.1

J-3.10.1 J-3.10.4 J-3.10.5 J-3.10.6

J-3.10.7 J-3.10.8 J-3.10.9S-4.9.1

paper-sectionS - Saunders 2003J - Jenkin 1997

S-4.1.1S-4.4.1

S-4.5.1

S-4.2.1S-4.3.1

S-4.8.1

S-4.6.2

S-4.7.1

S-4.6.1

S-4.7.2

S-4.6.3

S-4.6.4

S-4.6.5

J-3.10.2 J-3.10.3

J-3.9.1

J-3.10.1 J-3.10.4 J-3.10.5 J-3.10.6

J-3.10.7 J-3.10.8 J-3.10.9S-4.9.1

Navigational Features: Extract

Use Mark List as primaryspecies

Choose output format- HTML- FACSIMILE- FORTRAN- XML- KPP

Navigational Features: Extract Listing

Feedback: Mailing List

• Keep up-to-date with

updates and improvements

to the MCM and website

• Provides a forum for

suggestions and error

reporting

Under the Hood Improvements: Database

• The central MCM database has been converted to a MySQL integrated and interactive database on the web server.

• The updating and maintenance of the MySQL database is facilitated via OBDC (open database connectivity) through the usual Access/Accord front end.

Accord data

Name

Species

Accord data

Name

Species

Reaction category

Rate expression

Reaction expression

Reactions

Reaction category

Rate expression

Reaction expression

Reactions

Structural information

Canonical number

SMILES

Name

Species

Structural information

Canonical number

SMILES

Name

SpeciesLocal Tables

Reaction category

Rate expression

Reaction expression

Reactions

Reaction category

Rate expression

Reaction expression

Reactions

MySQL Tables

AccessAccord ODBCParametersParameters

Under the Hood Improvements: Design

MySQL

Reactions Species Parameters

MySQL

Reactions Species Parameters

apache

TemplateSystem

MCMModules

mod_python

ImagingModule

MechgenModules

apache

TemplateSystem

MCMModules

apache

TemplateSystem

MCMModules

mod_python

ImagingModule

MechgenModules

file system

StaticContent

TemplatesCachedContent

file system

StaticContent

TemplatesCachedContent

file system

StaticContent

TemplatesCachedContent

Access /Accord DB

ODBCAccess /

Accord DB

ODBC

File systemsFTP

File systemsFTP

Web BrowserWeb Browser

Maintainer's PC Web Server User's PC

MCMThe Future: Areas Requiring Revision

– Development so far focused on mechanism development.

– Updates tended to target portions of the mechanism only.

– Some areas still based on 1990’s chemistry (Protocol 1).

– Aimed mainly at boundary layer chemistry.– Difficult to update. Rate constants from SARs are hard-

wired.– Not subject to peer review (except protocol papers).

– Over the next few years the MCM will be rigorously reviewed and updated. – A series of “modular” protocols are being developed to address a number

of key areas:•Initiation reactions (excluding ozonolysis and photolysis)

• - hydrocarbons and halocarbons (OH, NO3, Cl)

• - oxygenated species (OH, NO3, Cl, Br and isomerisation)

•Initiation by ozonolysis• - including Criegee reactions•Initiation by photolysis

•Reactions of RO2 intermediates

• - including isomerisation of RO2

•Reactions of RO intermediates

• - including reactions with NO and NO2

MCMPlanned Developments

T & p dependent

MCMPlanned Developments

–The development of each of these protocols will be overseen by an international panel of experts established by ACCENT:

MJ Pilling (Leeds), AR Rickard (Leeds), ME Jenkin (Imperial), RA Cox (Cambridge), J Hjorth (JRC, Ispra), W Mellouki (Orleans), L Vereecken (Leuven), R Atkinson (UCRiverside) and TJ Wallington (Ford Dearborn)

–Database of updated rate constants is to be used by Luc Vereecken in order to develop SARs based on quantum chemical calculation.

–MCM database will be extended to free tropospheric conditions (e.g. p dependence for photolysis, T for oxy reactions).

–Automatic determination of T dependent rate parameters from SARs is being investigated through the development of structural recognition software (Leeds).

MCMLinks to IUPAC (1)

– IUPAC database provides kinetic and photochemical data evaluated by the IUPAC Subcommittee for Gas Kinetic Data Evaluation:

www.iupac-kinetic.ch.cam.ac.uk– Many explicit rate constants in MCM come from

IUPAC evaluated database. – European and US panel evaluation.

MCMLinks to IUPAC (2)

– Knowledge Transfer funding received for the integration and co-development of the MCM and IUPAC databases (Leeds, Cambridge, BADC):

o Development and synchronisation of the IUPAC and MCM databases in line with developments being made by the chemo-informatics communities using standardised formats and nomenclature so that data can be shared across each database and other community databases.

o Ease of MCM maintenance enhanced by linking of IUPAC datasheets to the appropriate reactions in the database.

o Common web-based tools will be developed for clear simultaneous searching of both databases and easy extraction of data.

These updates will make the MCM more robust and sustainable and help it retain its reputation as a state of the art, highly detailed

“benchmark” organic chemistry mechanism.