reaction mechanism generator: cheminformatics for kinetic modeling

Massachusetts Institute of Technology

Reaction Mechanism Generator:Cheminformatics for Kinetic Modeling

Richard H. West

William H. Green et al.

ACS Boston, August 2010

email: rwest@mit.edu twitter: richardhwest github: rwest

World temperature is rising

1000 2000-1

1

Year

Tem

per

atur

e an

om

aly

(°C

)

Atmospheric CO2 concentration is rising

1960 2000

315

385

Year

CO

2 co

ncen

trat

ion

(PP

M)

Transport sector contributes 18% globally

Transport

Global CO2 emissions

We need...

ENGINES

FUELS

We need...

ENGINES

FUELS

EFFICIENT-

BIO

Combustion chemistry is complex

1250 715

0.1

10

Initial temperature (K)

Igni

tion

del

ay (m

s)

900

1

Modern kinetic models are large

1 80

1000

C atoms in largest alkane

Sp

ecie

s in

kin

etic

mo

del

Reaction Mechanism Generator

automatically builds detailed kinetic models

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Automatic reaction mechanism generationneeds methods to:

1.Represent molecules (and identify duplicates)

2.Create reactions (and then new species)

3.Estimate thermo and kinetic parameters (quickly!)

CH3+

Molecules are represented as graphs

CH3CH2. C C*

H

H

H H

H

=

Thermochemistry is estimated by Benson group contributions

C-(C)(H)3

C-(C)2(H)2

Cb-(H)

C-(C)(Cb)(O)(H)

Solvation energy predictions enable solution-phase modeling

!

!

A Guide For Proper Use of theAdvanced Chemist ry Development

Logo

Preferred Format

This 2 colour version (Black and PMS 301) ismost preferred. When being reproduced in 4colour process it must always be representedin this format.File name: ACD10logo.eps

To reinforce and strengthen brand recognition, proper logo representation is needed. This sheet contains some guidelinesthat should be followed. If you have any questions or concerns, contact the Marketing and CommunicationsDepartment at marketing@acdlabs.com.

All files were created with Adobe Illustrator and saved in .epsformat, which can be used in both Macintosh and PC formats.

One Colour – PMS 301

Web Banner Do Not Stretch Do Not Alter Background

In the case when only one colour isavailable, choose the PMS 301 version of the logo.

File name: ACD10mono301.eps

One Colour – Black

In the case when only Black isavailable, use this version.

File name: ACD10logoBW.eps

On A Coloured Background

If the background colour is anythingother than white, the logo MUST becontained within a white box.

ALWAYS maintain correct proportionswhen rescaling the logo.

This format is acceptable for webbanner usage when the Prefered format does not suit the specifications of the host page.

File name: ACD10horizlogo.eps

The background colour of thelogo must always be white, donot change the colour or introduce pattern.

Free energies of solvation: prediction vs. experiment

Reaction families propose all possible reactions with given species

•Template for recognizing reactive sites

•Recipe for changing the bonding at the site

•Rules for estimating the ratebond breaking and hydrogen abstraction

intramolecularH-abstraction

Reaction families propose all possible reactions with given species

•Template for recognizing reactive sites

•Recipe for changing the bonding at the site

•Rules for estimating the rate

Octane autoxidation has many pathways

•Some pathways go further than others.

Faster pathways are explored further

AB

CD

E

FG

H

AB

CD

E

F

Octane autoxidation

100 species1000 reactions

15,000 species180,000 reactions

Butanol

Butanol combustion. Michael Harper. Wednesday 11:20am. Caspian/Renaissance. FUEL: Green Fuels.

JP-10 jet fuel

JP-10 combustion. Gregory Magoon. Wednesday 10:15am. 157C. COMP: Success Stories in Computer-Guided Chemistry

Unique Species

Unique Reactions

Literature (2001)

36 174

RMG final model

317 7,715

RMG considered

25,000 1.27m

24/11/2008 12:23AMreaction_paths

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Sta

rtin

g r

eactions

How to cope with combinatorial explosion of model size with large fuel compounds?

Unique Species

Unique Reactions

Start 8 0

1 complete generation

50 1,300

2 complete generations

1,000 40,000

7-component surrogate diesel and O2

How to set up web services for overall vision of chemical kinetics community?

Massachusetts Institute of Technology

Any answers? email: rwest@mit.edu twitter: richardhwest github: rwest

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