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Genesys:Automatic reaction networkgeneration using chemo-informaticsNick M. Vandewiele, Kevin M. Van Geem,Marie-Françoise Reyniers, Guy B. MarinLaboratory for Chemical Technology, Universiteit GentEuropean Research Institute of CatalysisLCTLaboratory forChemicalTechnologywww.lct.ugent.be
Computer generated kinetic models Quantitative detailed kinetic models Computer constructed Applications:complex reaction networks:combustion, pyrolysis, industrial chemical processesrmg.mit.eduwww.ensic.inpl-nancy.fr/2
Automated reaction network ineticParametersk2k5k6k7k9k11 k10ReactionrulesKinetic modelenlargementTerminationcriterionk13k12k14k153
Andrew Dalke’s EuroQSAR 2008 Poster FOR REACTION ENGINEERINGMultiple ligands alignment within 3D field potential from Qmol LLC.4
Open source chemo-informaticsOpen Source cheminformatics toolkits:CDKFeatureFile Format SupportAromaticity modelsCanonicalizationStereochemistry3D coordinate generation2D DepictionsCDKOpenBabelOpenBabelRDKitSMARTS SearchingCinfony - Combining disparate cheminformatics resources into a single toolkit, N.M. Boyle et al., ACS Meeting, 2010;Open Source Cheminformatics toolkits: Tools & Data, R. Guha, Bio IT World, 20095
Genesys: ArchitectureGenesysCDK # Library Tools****#species input/outputparsing and generation(InChI, SMILES, etc )substructure searchingspecies internalrepresentationspecies, reactionvisualizationGenesys Code******reaction executionreaction family implementationnetwork generationrule-based terminationthermodynamic properties generationkinetic parameters generationChemistry Development Kit6
Reaction families Add chemistry you know that is relevant; Constrain reaction families as much as possibleE.g. “C-H β scission in presence of doublebond in γ position”RSingle bond between radical C and Hbearing CRRRCCCHCRRRRCCCCRHRCCCCRHRRRRRCCCRRCCR HR HR RCCRRRRCCCCRRRRadical C not part of ringCCRRsp² C’s in double bond, not spRR HRCCHCRRRCCCRR H7
Reaction family definition using a pattern languageSMARTS (Daylight Inc)Submolecular pattern :C C-C(H)-[C;v3]A [C;v3]-C(H)-C CB H-C([C;v3])-C CC C(C C)(H)-[C;v3]Reactive center:Molecule Constraints:Center AMINIMUM Carbon COUNT5MAXIMUM Carbon COUNT10TOTAL NUMBER OF SINGLE ELECTRONS1H3CCCenter “C” IS NOT AROMATICCCHCenter CCenter BCHCHAtom Constraints:CHCHCH3RECIPE:(1) BREAK BOND(2) INCREASE BOND(3) LOSE RADICAL(4) GAIN RADICALB,CA,CA8B
Ideal gas TD Properties: Benson Group AdditivitySabbe et al. J. Phys. Chem. A 2008, 112, 12235–12251Sabbe et al. J. Phys. Chem. A 2005, 109, 7466-74809
Estimation esHave all nonhydrogens beenvisited?Flag matchedatoms as‘visited’ andupdate TDproperties ofspeciesNoPerformSMARTSmatchingTake one GAVfrom libraryOCH3CH3H3CGAV (H)O(H)(C)N(H)2C.ΔH f-42.7S 127.29Cp (300K).NH2.SH10
Filling the Benson Database Group Additive Values GAV Corrections: Ring Strains Non-nearest neighbor interactions Resonance interactions11
Burcat Database: validation of approach ca. 270 from 570 species could be estimatedN.M. Vandewiele et al., Chem. Eng. J. (2012)12
Building kinetic models: Kinetic group additivityHSH2SCH3HS1HC1CH3GAV Library******SMARTS S1log(A)EaSi-(H)Si-(Cd)Si-(CS)Si-(Cd)Si-(Cb). 0.101-0.273-0.788 0.566 0.406-20.2 26.6 22.0 35.1 24.3GAV Library******SMARTS (C).-1.161-0.884-0.342 0.407-0.009-3.6-8.3-14.7-10.6-14.613Sabbe et al. ChemPhysChem 2008, 9, 124 – 140Saeys et al. 2004, AIChE J.
Conclusion Genesys: automatic reaction networkgeneration framework for quantitativemodels– Integrated with open-source chemo-informaticslibrary (CDK)– Generally applicable: Support for many elements Support for many chemistries– Quantitative structure – property relationshipseasily implementable Ideal Gas TD Properties Kinetic expressions for elementary reactions14
Future Directions Applications: kinetic model validations Stereochemistry : accounting for 3Dstructure information Scalability: NP-completeness, multi-CPU,multi-node15
AcknowledgmentsLCT @ UGent: Steven Pyl, Carl Schietekat, Thomas Dijkmans Aäron Vandeputte, Maarten SabbeFunding: Long Term Structural Methusalem Funding by the FlemishGovernment Fund for Scientific Research - Flanders16
THANK YOU!17
Genesys: Automatic reaction network generation using chemo-informatics. . ACS Meeting, 2010; Open Source Cheminformatics toolkits: Tools & Data, . Center B Center C. CH CH CH H H. 3. C CH. 3. Submolecular pattern : Reactive center: Molecule Constraints: MINIMUM Carbon COUNT . 5 .
