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Methusalem, Advisory Board Meeting, June 24, 2013Kinetic modeling usingchemo-informatics: GenesysNick Vandewiele, Kevin Van Geem,Marie-Françoise Reyniers, Guy B. MarinLaboratory forChemical Technologyhttp://www.lct.ugent.be1
Methusalem, Advisory Board Meeting, June 24, 2013Kinetic models grow larger and largerT.F. Lu, C.K. Law / Progress in Energy and Combustion Science 35 (2009) 192–2152
Methusalem, Advisory Board Meeting, June 24, 2013Genesys: computer generated kinetic modelsInitialreactantsMechanismAutomatic calculation of : Species thermochemistry Elementary reaction kineticsKinetic modelVandewiele et al. Chem. Eng. J. (2012)http://www.lct.ugent.be/3
Methusalem, Advisory Board Meeting, June 24, 2013Reaction network ineticParametersk2k5k6k7k9k11 k10ReactionrulesKinetic modelenlargementTerminationcriterionk13k12k14k154
Methusalem, Advisory Board Meeting, June 24, 2013Graph representation of molecules Graph theory and algorithms can be applied: mainmethods for chemistry apps: Sub-graph matching functional group query Equivalence test structure database queryInChI ng sub-molecular patterns:SMARTS (SMILES Arbitrary Target Specification)5
Methusalem, Advisory Board Meeting, June 24, 2013Don’t re-invent the wheel: chemo-informaticsAndrew Dalke’s EuroQSAR 2008 Poster(http://www.dalkescientific.com/)Multiple ligands alignment within 3D field potential from Qmol LLC.6
Methusalem, Advisory Board Meeting, June 24, 2013Genesys: integration of CDK7
Methusalem, Advisory Board Meeting, June 24, 2013Reaction families in Genesys 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 H-bearingCRRRCCCHCRRRRCCCCRHsp² C’s in double bond, not spCCCCRRadical C not part of ringHRRRRRCCRRCCR HR HR RCCCRRRRCCCCRRRCCCRRRRR HRCCHCRRRCCCRR 8H
Methusalem, Advisory Board Meeting, June 24, 2013Defining reaction families: pattern, recipe, constraintsSMARTS: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 COUNT 5MAXIMUM Carbon COUNT 10TOTAL NUMBER OF SINGLE ELECTRONS 1CCCCHCenter CH3CCenter BCHCHHCHCH3RECIPE:(1) BREAK BONDB,C(2) INCREASE BOND A,C(3) LOSE RADICALA(4) GAIN RADICALB9
Methusalem, Advisory Board Meeting, June 24, 2013THERMOCHEMISTRYESTIMATION10
Methusalem, Advisory Board Meeting, June 24, 2013Ideal gas TD Properties: Benson Additivity11
Methusalem, Advisory Board Meeting, June 24, 2013Filling the Benson DatabaseNature of GAVs, ca. 1000 unique groupsSabbe et al. J. Phys. Chem. A 2008, 112, 12235–12251Sabbe et al. J. Phys. Chem. A 2005, 109, 7466-748012
Methusalem, Advisory Board Meeting, June 24, 2013NETWORK GENERATION13
Methusalem, Advisory Board Meeting, June 24, 2013Network generation: HMPAGenerated speciesDefine reaction NNPHNCNCH2CNOPPCON14
Methusalem, Advisory Board Meeting, June 24, 2013BUILDING KINETIC MODELS15
Methusalem, Advisory Board Meeting, June 24, 2013Building kinetic models: Kinetic group additivityGAV 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 0.407-0.009-3.6-8.3-14.7-10.6-14.616Sabbe et al. ChemPhysChem 2008, 9, 124 – 140Saeys et al. 2004, AIChE J.
Methusalem, Advisory Board Meeting, June 24, 2013Alkylsulfide thermal decompositionChemistry knowledge:A.G. Vandeputte, The thermochemistry and Decomposition Mechanism ofOrganosulfur and Organophosphorus Compounds, 2012 (Ph.D)Kinetic data:Hydrocarbon reaction families:Additions and β-scissions: Sabbe et al. ChemPhysChem 2008, 9, 124 – 140Hydrogen abstractions: Sabbe et al. PCCP, 2010, 12, 1278–1298Sulfur reaction families:Hydrogen abstractions : Vandeputte et al. PCCP, 2012;14(37):12773-93Homolytic substitutions: Vandeputte et al. 2012 (Ph.D)Generated model:3612 reactions151 species17
Methusalem, Advisory Board Meeting, June 24, 2013Ethyl-methyl-sulfide pyrolysis: validation18
Methusalem, Advisory Board Meeting, June 24, 2013EMS pyrolysis: quantitative analysisEMS conversion: 14%Temperature: 1013KResidence time: 0.2s19
Methusalem, Advisory Board Meeting, June 24, 2013Conclusion Genesys: automatic reaction network generationframework for quantitative models– Integrated with open-source chemo-informaticslibrary (CDK)– Generally applicable: Support for many elements Support for many chemistries– Quantitative structure – property relationships easilyimplementable Ideal Gas TD Properties Kinetic expressions for elementary reactions20
Methusalem, Advisory Board Meeting, June 24, 2013AcknowledgmentsLCT @ UGent: Steven Pyl, Carl Schietekat, Thomas Dijkmans, Ruben De Bruycker Aäron Vandeputte, Maarten Sabbe, Ruben Van de VijverFunding: Long Term Structural Methusalem Funding by the FlemishGovernment Fund for Scientific Research - Flanders21
Methusalem, Advisory Board Meeting, June 24, 2013THANK YOU!22
Methusalem, Advisory Board Meeting, June 24, 2013 Conclusion Genesys: automatic reaction network generation framework for quantitative models - Integrated with open-source chemo-informatics library (CDK) - Generally applicable: Support for many elements Support for many chemistries - Quantitative structure -property .
