reaction mechanism generator: cheminformatics for kinetic modeling
DESCRIPTION
This is my 6-minute CINFlash Talk in the Cheminformatics session at the ACS Meeting in Boston, August 2010. For more about RMG visit http://facebook.com/rmg.mit or http://rmg.sourceforge.net/TRANSCRIPT
Massachusetts Institute of Technology
Reaction Mechanism Generator:Cheminformatics for Kinetic Modeling
Richard H. West
William H. Green et al.
ACS Boston, August 2010
email: [email protected] 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
facebook.com/rmg.mitr m g . s o u rc e f o r g e . n e t
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 [email protected].
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
Page 1 of 1file:///Users/rwest/XCodeProjects/RMG/software/python/rxnpath2.dot.svg
Scale = 1.9e-10
-
0.0556 1
24/11/2008 12:23AMreaction_paths
Page 1 of 1file:///Users/rwest/XCodeProjects/RMG/software/python/rxnpath2.dot.svg
Scale = 1.9e-10
-
0.0556 1
24/11/2008 12:23AMreaction_paths
Page 1 of 1file:///Users/rwest/XCodeProjects/RMG/software/python/rxnpath2.dot.svg
Scale = 1.9e-10
-
0.0556 1
24/11/2008 12:23AMreaction_paths
Page 1 of 1file:///Users/rwest/XCodeProjects/RMG/software/python/rxnpath2.dot.svg
Scale = 1.9e-10
-
0.0556 1
24/11/2008 12:23AMreaction_paths
Page 1 of 1file:///Users/rwest/XCodeProjects/RMG/software/python/rxnpath2.dot.svg
Scale = 1.9e-10
-
0.0556 1
24/11/2008 12:23AMreaction_paths
Page 1 of 1file:///Users/rwest/XCodeProjects/RMG/software/python/rxnpath2.dot.svg
Scale = 1.9e-10
-
0.0556 1
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: [email protected] twitter: richardhwest github: rwest
facebook.com/rmg.mitr m g . s o u rc e f o r g e . n e t