Automated transition state theory calculations of abstraction reactions by hydroperoxyl, compared to literature model values
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This study used automated transition state theory (AutoTST) calculations to determine rate constants for hydrogen abstraction reactions by hydroperoxyl radicals (HOO), and compared the results to 72 published kinetic models. The researchers identified 331 relevant H abstraction reactions from the models, generated transition state geometries for 316 of them using distance geometry, and successfully calculated rate constants for 228 reactions using AutoTST. Analysis found the AutoTST approach matched existing models for 68.9% of reactions, with ongoing work seeking to improve accuracy and apply the method to new fuels.
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Automated transition state theory calculations of abstraction reactions by hydroperoxyl, compared to literature model values
- 1. Automated transition state theory calculations of abstraction reactions by hydroperoxyl, compared to literature model values Nathan Harms, Belinda Slakman, Jason Cain, Richard West Department of Chemical Engineering Northeastern University, Boston, MA 10th U.S. National Combustion Meeting April 24, 2017 1 .edu/comocheng
- 2. Combustion involves many steps… R’ + Alkene High Temp, Heat R’ + R” Heat Fuel Radical (R) X = Abstractor •OH, •H, , O•, •CH3, O2 Low Temp O2 RO2 … •H, •CH3 + Unsaturated Hydrocarbons Alkene + HO2• QOOH O2QOOH O2 O2 HO2• + HO2• H2O2 + O2 Intermed. Temp OQ’OOH + •OH Hydrocarbon Growth 2 OQ’O + •OH Heat C6H6 + PAHs Fuel + XH HO2•
- 3. … but we’re focusing on this reaction (for now). H Abstraction by Hydroxyl Radical 3 Fuel Radical (R) Fuel + + H2O2 HO2•
- 4. All Combustion Reactions Putting this in context 4
- 5. All Combustion Reactions Putting this in context 4 Hydrogen Abstraction Reactions
- 6. All Combustion Reactions Putting this in context 4 Hydrogen Abstraction Reactions H Abstraction by OOH
- 7. All Combustion Reactions Putting this in context 4 Hydrogen Abstraction Reactions H Abstraction by OOH Published Kinetics
- 8. All Combustion Reactions Putting this in context 4 Hydrogen Abstraction Reactions H Abstraction by OOH Published Kinetics
- 9. All Combustion Reactions Putting this in context 4 Hydrogen Abstraction Reactions H Abstraction by OOH Published Kinetics
- 10. Some methods rely on rate rules to determine reaction kinetics… 5 Advantages • Fast • Many rules exist Disadvantages • Chemistry doesn’t always follow the rule • Rules are misapplied CH + RH → Products D. L. Baulch et al, Evaluated Kinetics Data for Combustion Modeling, J. Phys. Chem. 2005 CH4 C2H6C4H10 C3H8
- 11. … others rely on transition state theory calculations to determine kinetics. V X‡ Reaction coordinate Energy Reactants Products 6 Advantages • More accurate than rate rules Disadvantages • High computational time • Requires initial guess of transition state geometry
- 12. We would like to estimate fewer of our important reaction rates 7 Measured Calculated Estimated Confidence level
- 13. We would like to estimate fewer of our important reaction rates 7 Measured Calculated Estimated Confidence level
- 14. Our group has automated the entire TST process 8 ⇌RMG Estimate Distances Create TS Geometry TS Search and Validation Determine Kinetics Y X H CanTherm P. Bhoorasingh et al, FigShare (2016).
- 15. dXH: 1.332 dHY: 0.831 dXY: 2.160 Use group additivity and a hierarchical tree database to predict distances 9 R O H C O H O R C HO R X H dXH: 1.242 dHY: 0.874 dXY: 2.111 dXH: 1.336 dHY: 0.998 dXY: 2.334 dXH: 1.301 dHY: 0.906 dXY: 2.205 C HC R Functional Group X-H H-Y X-Y 1.235 0.875 2.104 1.242 0.873 2.109 1.241 0.873 2.109 1.243 0.873 2.112 1.248 0.874 2.119 1.329 0.999 2.328 1.334 0.998 2.332 1.337 0.997 2.334 1.338 0.998 2.336 1.341 0.999 2.340 1.338 0.829 2.163 1.332 0.830 2.159 1.332 0.831 2.161 1.325 0.835 2.158 R O H C HO R C O H O R Training Set Group Tree Bhoorasingh & West Phys. Chem. Chem. Phys. 17, 32173–32182 (2015).
- 16. Generate the 3D transition state estimate using distance geometry 10 ⇌RMG Molecule Connectivity 3D Structure RDKit: Open-source cheminformatics. http://www.rdkit.org/
- 17. Generate the 3D transition state estimate using distance geometry 10 ⇌RMG Molecule Connectivity Atoms List AtomsList Upper limits Lower limits Generate distance matrix Embed in 3D RDKit: Open-source cheminformatics. http://www.rdkit.org/
- 18. Generate the 3D transition state estimate using distance geometry 10 ⇌RMG Molecule Connectivity Atoms List AtomsList Upper limits Lower limits Generate distance matrix Atoms List AtomsList Embed in 3D Edit distance matrix RDKit: Open-source cheminformatics. http://www.rdkit.org/
- 19. New workflow is slightly more robust, using a series of partial optimizations. 11
- 20. Comparing literature kinetics against automatic TST calculations for H abstraction by OOH radical Calculate the reaction rate using AutoTST Filter for reaction of interest Gather models published Identify species involved Compare the results 12
- 21. We have collected 72 different models so far… PCI2013/353-Malewicki PCI2017/037-Sakai PCI2017/032-Cheng PCI2017/082-Hemken PCI2017/111-Jin PCI2017/052-Stagni PCI2017/022-Thion PCI2017/052-Li PCI2017/058-Sun PCI2017/024-Bohon PCI2017/145-Sun PCI2017/051-Pelucchi PCI2017/012-Felsmann PCI2017/047-Rodriguez PCI2017/038-Labbe-Zhao(30Torr-10Atm) PCI2017/087-Tran PCI2017/036-Rashidi PCI2017/025-Sudholt EL24115 CombFlame2013/2712-Sarathy CombFlame2013/1958-Zhao CombFlame2013/487-Schenk CombFlame2013/1541-Zhang CombFlame2013/17-Malewicki CombFlame2013/1315-Chang CombFlame2013/1939-Cai CombFlame2013/2291-Somers CombFlame2013/1609-Veloo CombFlame2013/2680-Vranck MB-Dooley Narayanaswamy H2-3 Shamel-Propane Reduced-DRG-GRI-mech PCI2015/0409-Zhang PCI2015/0325-Nawdiyal PCI2015/0153-Marshall AramcoMech_1.3 USC_Mech_ii n-Heptane CombFlame2015/3755-Konnov Chernov MB-Farooq GRI-mech-3.0 CombFlame2014/405-Cai CombFlame2014/65-Darcy CombFlame2014/885-Xiong CombFlame2014/1135-Dames CombFlame2014/84-Wang CombFlame2014/657-Jin CombFlame2014/798-Cai CombFlame2014/818-Zhang AramcoMech_2.0 Biomass H2 MB-Fisher MatheuCH4 Gasoline_2 GRI-17-species-mech Gasoline_Surrogate IJCK2013/638-Metcalfe PCI2013/269-Matsugi PCI2013/401-Liu PCI2013/335-Wang PCI2013/325-Husson PCI2013/297-Herbinet PCI2013/361-Malewicki PCI2013/599-Veloo PCI2013/259-Labbe PCI2013/225-Somers PCI2013/527-Sheen PCI2013/411-Darcy PCI2013/289-Dagaut 13 Gather models published Identify species involved Filter for reaction of interest Calculate the reaction rate using AutoTST Compare the results
- 22. … and each one has slightly different naming conventions for each molecule 14 MVOX IIC4H7Q2-T C3H5-A C3H5-SC6H101OOH5-4 TC4H8O2H-I C4H8O1-3 C3KET21 CH3COCH2O2H Gather models published Identify species involved Filter for reaction of interest Calculate the reaction rate using AutoTST Compare the results
- 23. CH4 + HO2• → CH3• + H2O2 CH2O + HO2• → HCO + H2O2 C2H6 + CH3• → C2H5• + CH4 PCI2013/353-Malewicki C2H6 + HO2• → C2H5• + H2O2 ••• PCI2013/353-Malewicki C2H6 + HO2• → C2H5• + H2O2 PCI2013/353-Malewicki CH4 + HO2• → CH3• + H2O2 Using python scripts, the existing models are filtered for OOH Abstraction reactions 15 Gather models published Identify species involved Filter for reaction of interest Calculate the reaction rate using AutoTST Compare the results
- 24. CH4 + HO2• → CH3• + H2O2 CH2O + HO2• → HCO + H2O2 C2H6 + CH3• → C2H5• + CH4 PCI2013/353-Malewicki C2H6 + HO2• → C2H5• + H2O2 ••• PCI2013/353-Malewicki C2H6 + HO2• → C2H5• + H2O2 PCI2013/353-Malewicki CH4 + HO2• → CH3• + H2O2 Using python scripts, the existing models are filtered for OOH Abstraction reactions 15 Gather models published Identify species involved Filter for reaction of interest Calculate the reaction rate using AutoTST Compare the results
- 25. The filtered reactions were given to AutoTST to calculate reaction rates 16 PCI2013/353-Malewicki CH4 + HO2• → CH3• + H2O2 Gather models published Identify species involved Filter for reaction of interest Calculate the reaction rate using AutoTST Compare the results
- 26. The filtered reactions were given to AutoTST to calculate reaction rates 16 PCI2013/353-Malewicki CH4 + HO2• → CH3• + H2O2 Gather models published Identify species involved Filter for reaction of interest Calculate the reaction rate using AutoTST Compare the results
- 27. Rates from existing models then compared to AutoTST rates and other models 17 Gather models published Identify species involved Filter for reaction of interest Calculate the reaction rate using AutoTST Compare the results 🆚
- 28. Rates from existing models then compared to AutoTST rates and other models 17 Gather models published Identify species involved Filter for reaction of interest Calculate the reaction rate using AutoTST Compare the results PCI2013/353-Malewicki CombFlame2014/405-Cai CH4 + HO2• → CH3• + H2O2 🆚 PCI2017/082-Hemken CH4 + HO2• → CH3• + H2O2 CombFlame2014/405-Cai CH4 + HO2• → CH3• + H2O2
- 29. Looking at AutoTST vs previously published models 18
- 30. Looking at AutoTST vs previously published models 18
- 31. Looking at specific reactions 19 C4H8 + HO2• → C4H7• + H2O2
- 32. All Combustion Reactions Hydrogen Abstraction Reactions H Abstraction by OOH Published Kinetics Scope of this project 20
- 33. Finding our bugs and measuring our progress 21 Step in the Methods Number of Reactions Percent of Reactions Plausible Reactions Identified from Models 407 N/A Reaction Attempted 407 N/A Matched an H-Abstraction Reaction in RMG 331 100% Started Making TS Geometry 316 95.5% Started Canonical TST Calculations 246 74.3% Overall Successes 228 68.9%
- 34. Finding our bugs and measuring our progress 21 Step in the Methods Number of Reactions Percent of Reactions Plausible Reactions Identified from Models 407 N/A Reaction Attempted 407 N/A Matched an H-Abstraction Reaction in RMG 331 100% Started Making TS Geometry 316 95.5% Started Canonical TST Calculations 246 74.3% Overall Successes 228 68.9%
- 35. Finding our bugs and measuring our progress 21 Step in the Methods Number of Reactions Percent of Reactions Plausible Reactions Identified from Models 407 N/A Reaction Attempted 407 N/A Matched an H-Abstraction Reaction in RMG 331 100% Started Making TS Geometry 316 95.5% Started Canonical TST Calculations 246 74.3% Overall Successes 228 68.9%
- 36. Finding our bugs and measuring our progress 21 Step in the Methods Number of Reactions Percent of Reactions Plausible Reactions Identified from Models 407 N/A Reaction Attempted 407 N/A Matched an H-Abstraction Reaction in RMG 331 100% Started Making TS Geometry 316 95.5% Started Canonical TST Calculations 246 74.3% Overall Successes 228 68.9%
- 37. Ongoing and future efforts 22 • Complete Imported OOH Kinetics • Improve the robustness and accuracy of AutoTST • Look at OOH Abstraction of new fuels All Combustion Reactions Hydrogen Abstraction Reactions H Abstraction by OOH Published Kinetics
- 38. Acknowledgements • Nathan Harms, Belinda Slakman, Jason Cain, Dr. Pierre Bhoorashingh • ACS Petroleum Research Fund • National Science Foundation Grant No.1605568 • Northeastern University, Department of Chemical Engineering 23
- 39. Contributions • Identified 331 “RH + ·OOH ⇌ ·R + H2O2” reactions from published kinetic models. • Found and validated (with IRC) transition states for 228 of them and calculated k(T) • Developed tools to do the above automatically. 24 r.west@neu.edu richardhwest rwest Richard H. West 24 April 2017