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Copan AV, Moore KB, Elliott SN, Mulvihill CR, Pratali Maffei L, Klippenstein SJ. Radical Stereochemistry: Accounting for Diastereomers in Kinetic Mechanism Development. J Phys Chem A 2024. [PMID: 38683599 DOI: 10.1021/acs.jpca.4c01060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Recent work in combustion and atmospheric chemistry has revealed cases in which diastereomers must be distinguished to accurately model a reacting flow. This paper presents an open-source framework for introducing such stereoisomer resolution into a kinetic mechanism. We detail our definitions and algorithms for labeling and enumerating the stereoisomers of a molecule and then generalize our system to describe the transition state (TS) of a reaction. This allows for the stereospecific enumeration of reactants and products while accounting for "fleeting" stereochemistry that is unique to the TS. We also present the AutoMech Chemical Identifier (AMChI), an InChI-like string identifier that accounts for stereocenters omitted by InChI. This identifier is extended to describe the TSs of reactions, providing a universal lookup key for specific reaction channels. The final piece of our methodology is an analytic formula to remove redundancy from a stereoresolved mechanism when its enantiomers exist as a racemic mixture, making it as compact as possible while fully accounting for the differences between diastereomers. In applying our methodology to two subsets of the NUIGMech1.1 mechanism, we find that our approach reduces the extra species added for large-fuel oxidation from 2231 (133%, full expansion) to 694 (41%, nonredundant expansion). We also find that for pyrolysis more than a quarter of the species in the expanded mechanism cannot be properly described by an InChI string, requiring an AMChI string to communicate their identity. Finally, we find that roughly one-quarter of the large-fuel oxidation reactions and one-third of the pyrolysis reactions include fleeting TS stereochemistry, which may have relevant effects on their kinetics.
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Affiliation(s)
- Andreas V Copan
- College of Engineering, University of Georgia, Athens, Georgia 30602, United States
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Kevin B Moore
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Sarah N Elliott
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Clayton R Mulvihill
- Department of Mechanical Engineering, Baylor University, Waco, Texas 76798, United States
| | - Luna Pratali Maffei
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Milano 20133, Italy
| | - Stephen J Klippenstein
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
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Demireva M, Au K, Hansen N, Sheps L. Time-resolved quantification of key species and mechanistic insights in low-temperature tetrahydrofuran oxidation. Phys Chem Chem Phys 2024; 26:10357-10368. [PMID: 38502092 DOI: 10.1039/d3cp06227a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
We investigate the kinetics and report the time-resolved concentrations of key chemical species in the oxidation of tetrahydrofuran (THF) at 7500 torr and 450-675 K. Experiments are carried out using high-pressure multiplexed photoionization mass spectrometry (MPIMS) combined with tunable vacuum ultraviolet radiation from the Berkely Lab Advanced Light Source. Intermediates and products are quantified using reference photoionization (PI) cross sections, when available, and constrained by a global carbon balance tracking approach at all experimental temperatures simultaneously for the species without reference cross sections. From carbon balancing, we determine time-resolved concentrations for the ROO˙ and ˙OOQOOH radical intermediates, butanedial, and the combined concentration of ketohydroperoxide (KHP) and unsaturated hydroperoxide (UHP) products stemming from the ˙QOOH + O2 reaction. Furthermore, we quantify a product that we tentatively assign as fumaraldehyde, which arises from UHP decomposition via H2O or ˙OH + H loss. The experimentally derived species concentrations are compared with model predictions using the most recent literature THF oxidation mechanism of Fenard et al., (Combust. Flame, 2018, 191, 252-269). Our results indicate that the literature mechanism significantly overestimates THF consumption and the UHP + KHP concentration at our conditions. The model predictions are sensitive to the rate coefficient for the ROO˙ isomerization to ˙QOOH, which is the gateway for radical chain propagating and branching pathways. Comparisons with our recent results for cyclopentane (Demireva et al., Combust. Flame, 2023, 257, 112506) provide insights into the effect of the ether group on reactivity and highlight the need to determine accurate rate coefficients of ROO˙ isomerization and subsequent reactions.
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Affiliation(s)
- Maria Demireva
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551, USA.
| | - Kendrew Au
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551, USA.
| | - Nils Hansen
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551, USA.
| | - Leonid Sheps
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551, USA.
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Li T, Li J, Chen S, Zhu Q, Li Z. Investigating the kinetics of the intramolecular H-migration reaction class of methyl-ester peroxy radicals in low-temperature oxidation mechanisms of biodiesel. Phys Chem Chem Phys 2023; 25:32078-32092. [PMID: 37982313 DOI: 10.1039/d3cp03376g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Biodiesel is a promising, sustainable, and carbon-neutral fuel. However, studying its combustion mechanisms comprehensively, both theoretically and experimentally, presents challenges due to the complexity and size of its molecules. One significant obstacle in determining low-temperature oxidation mechanisms for biodiesel is the lack of kinetic parameters for the reaction class of intramolecular H-migration reactions of alkyl-ester peroxy radicals, labeled as R(CO)OR'-OO˙ (where the 'dot' represents the radical). Current biodiesel combustion mechanisms often estimate these parameters from the analogous reaction class of intramolecular H-migration reactions of alkyl peroxy radicals in alkane combustion mechanisms. However, such estimations are imprecise and neglect the unique characteristics of the ester group. This research aims to explore the kinetics of the reaction class of H-migration reactions of methyl-ester peroxy radicals. The reaction class is divided into 20 subclasses based on the newly formed cycle size of the transition state, the positions of the peroxy radical and the transferred H atom, and the types of carbons from which the H atom is transferred. Energy barriers for each subclass are calculated by using the CBS-QB3//M06-2X/6-311++G(d,p) method. High-pressure-limit and pressure-dependent rate constants ranging from 0.01 to 100 atm are determined using the transition state theory and Rice-Ramsberger-Kassel-Marcus/master-equation method, respectively. It is noted that the pressure-dependent rate constants calculated for each individual isomerization channel could bring some uncertainties while neglecting the interconnected pathways. A comprehensive comparison is made between our values of selected reactions and high-level calculated values of the corresponding reactions reported in the literature. The small deviation observed between these values indicates the accuracy and reliability of the energy barriers and rate constants calculated in this study. Additionally, our calculated high-pressure-limit rate constants are compared with the corresponding values in combustion mechanisms of esters, which were estimated based on analogous reactions of alkyl peroxy radicals. These comparative analyses shed light on the significant impact of the ester group on the kinetics, particularly when the ester group is involved in the reaction center. Finally, the high-pressure-limit rate rule and pressure-dependent rate rule for each subclass are derived by averaging the rate constants of reactions in each subclass. The accurate and reasonable rate rules for methyl-ester peroxy radicals developed in this study play a crucial role in enhancing our understanding of the low-temperature oxidation mechanisms of biodiesel.
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Affiliation(s)
- Tao Li
- School of Chemical Engineering, Sichuan University, Chengdu 610065, P. R. China.
| | - Juanqin Li
- School of Chemical Engineering, Sichuan University, Chengdu 610065, P. R. China.
| | - Siyu Chen
- School of Chemical Engineering, Sichuan University, Chengdu 610065, P. R. China.
| | - Quan Zhu
- School of Chemical Engineering, Sichuan University, Chengdu 610065, P. R. China.
- Engineering Research Center of Combustion and Cooling for Aerospace Power, Ministry of Education, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Zerong Li
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
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Kandpal SC, Otukile KP, Jindal S, Senthil S, Matthews C, Chakraborty S, Moskaleva LV, Ramakrishnan R. Stereo-electronic factors influencing the stability of hydroperoxyalkyl radicals: transferability of chemical trends across hydrocarbons and ab initio methods. Phys Chem Chem Phys 2023; 25:27302-27320. [PMID: 37791466 DOI: 10.1039/d3cp03598k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The hydroperoxyalkyl radicals (˙QOOH) are known to play a significant role in combustion and tropospheric processes, yet their direct spectroscopic detection remains challenging. In this study, we investigate molecular stereo-electronic effects influencing the kinetic and thermodynamic stability of a ˙QOOH along its formation path from the precursor, alkylperoxyl radical (ROO˙), and the depletion path resulting in the formation of cyclic ether + ˙OH. We focus on reactive intermediates encountered in the oxidation of acyclic hydrocarbon radicals: ethyl, isopropyl, isobutyl, tert-butyl, neopentyl, and their alicyclic counterparts: cyclohexyl, cyclohexenyl, and cyclohexadienyl. We report reaction energies and barriers calculated with the highly accurate method Weizmann-1 (W1) for the channels: ROO˙ ⇌ ˙QOOH, ROO˙ ⇌ alkene + ˙OOH, ˙QOOH ⇌ alkene + ˙OOH, and ˙QOOH ⇌ cyclic ether + ˙OH. Using W1 results as a reference, we have systematically benchmarked the accuracy of popular density functional theory (DFT), composite thermochemistry methods, and an explicitly correlated coupled-cluster method. We ascertain inductive, resonance, and steric effects on the overall stability of ˙QOOH and computationally investigate the possibility of forming more stable species. With new reactions as test cases, we probe the capacity of various ab initio methods to yield quantitative insights on the elementary steps of combustion.
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Affiliation(s)
| | - Kgalaletso P Otukile
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa.
| | - Shweta Jindal
- Tata Institute of Fundamental Research, Hyderabad 500046, India.
| | - Salini Senthil
- Tata Institute of Fundamental Research, Hyderabad 500046, India.
| | - Cameron Matthews
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa.
| | | | - Lyudmila V Moskaleva
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa.
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Damerau A, Ahonen E, Kortesniemi M, Gudmundsson HG, Yang B, Haraldsson GG, Linderborg KM. Docosahexaenoic acid in regio- and enantiopure triacylglycerols: Oxidative stability and influence of chiral antioxidant. Food Chem 2023; 402:134271. [DOI: 10.1016/j.foodchem.2022.134271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/01/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022]
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Zádor J, Martí C, Van de Vijver R, Johansen SL, Yang Y, Michelsen HA, Najm HN. Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces. J Phys Chem A 2023; 127:565-588. [PMID: 36607817 DOI: 10.1021/acs.jpca.2c06558] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Automation of rate-coefficient calculations for gas-phase organic species became possible in recent years and has transformed how we explore these complicated systems computationally. Kinetics workflow tools bring rigor and speed and eliminate a large fraction of manual labor and related error sources. In this paper we give an overview of this quickly evolving field and illustrate, through five detailed examples, the capabilities of our own automated tool, KinBot. We bring examples from combustion and atmospheric chemistry of C-, H-, O-, and N-atom-containing species that are relevant to molecular weight growth and autoxidation processes. The examples shed light on the capabilities of automation and also highlight particular challenges associated with the various chemical systems that need to be addressed in future work.
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Affiliation(s)
- Judit Zádor
- Combustion Research Facility, Sandia National Laboratories, Livermore94550, California, United States
| | - Carles Martí
- Combustion Research Facility, Sandia National Laboratories, Livermore94550, California, United States
| | | | - Sommer L Johansen
- Combustion Research Facility, Sandia National Laboratories, Livermore94550, California, United States
| | - Yoona Yang
- Combustion Research Facility, Sandia National Laboratories, Livermore94550, California, United States
| | - Hope A Michelsen
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder80309, Colorado, United States
| | - Habib N Najm
- Combustion Research Facility, Sandia National Laboratories, Livermore94550, California, United States
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Doner A, Zádor J, Rotavera B. Stereoisomer-dependent unimolecular kinetics of 2,4-dimethyloxetane peroxy radicals. Faraday Discuss 2022; 238:295-319. [DOI: 10.1039/d2fd00029f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2,4,dimethyloxetane is an important cyclic ether intermediate that is produced from hydroperoxyalkyl (QOOH) radicals in low-temperature combustion of n-pentane. However, reaction mechanisms and rates of consumption pathways remain unclear. In...
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Klippenstein SJ. Spiers Memorial Lecture: theory of unimolecular reactions. Faraday Discuss 2022; 238:11-67. [DOI: 10.1039/d2fd00125j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One hundred years ago, at an earlier Faraday Discussion meeting, Lindemann presented a mechanism that provides the foundation for contemplating the pressure dependence of unimolecular reactions. Since that time, our...
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