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An S, Patel P, Liu C, Skodje RT. Computational Aspects of Single-Molecule Kinetics for Coupled Catalytic Cycles: A Spectral Analysis. J Phys Chem A 2022; 126:3783-3796. [PMID: 35658508 DOI: 10.1021/acs.jpca.2c02153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalysis from single active sites is analyzed using methods developed from single-molecule kinetics. Using a stochastic Markov-state description, the observable properties of general catalytic networks of reactions are expressed using an eigenvalue decomposition of the transition matrix for the Markov process. By the use of a sensitivity analysis, the necessary eigenvalues and eigenvectors are related to the energies of controlling barriers and wells located along the reaction routes. A generalization of the energetic span theory allows the eigenvalues to be computed from several activation energies corresponding to distinct barrier-well pairings. The formalism is demonstrated for model problems and for a physically realistic mechanism for an alkene hydrogenation reaction on a single-atom catalyst. The spectral analysis permits a hierarchy of timescales to be identified from the single-molecule signal, which correspond to specific relaxation modes in the network.
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Affiliation(s)
- Suming An
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Prajay Patel
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60639, United States
| | - Cong Liu
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60639, United States
| | - Rex T Skodje
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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2
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An S, Ranjan S, Yuan K, Yang X, Skodje RT. The role of the three body photodissociation channel of water in the evolution of dioxygen in astrophysical applications. Phys Chem Chem Phys 2021; 23:9235-9248. [PMID: 33885109 DOI: 10.1039/d1cp00565k] [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
A recent experiment at the Dalian Coherent Light Source (DCLS) has provided measurements of the partial cross sections for the photodissociation of water vapor over an unprecedented range of wavelengths in the vacuum ultraviolet (VUV) region. It was found that the three body dissociation channel, H + H + O(3P/1D), becomes prominent at wavelengths shorter than the Lyman α-line at 121.6 nm. The present work explores the kinetic consequences of this discovery for several astrophysically motivated examples. The irradiation of a dilute low-temperature gas by unscreened solar radiation, similar to early stage photochemical processing in a comet coma, shows significant increase in the production of O2-molecules at shorter times, <1 day, that might physically correspond to the photochemical reaction zone of the coma. Several examples of planetary atmospheres show increased O-atom production at high altitudes but relatively little modification of the equilibrium O2 concentrations predicted by conventional models.
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Affiliation(s)
- Suming An
- Department of Chemistry, University of Colorado, Boulder, CO 80309-215, USA.
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3
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Zaleski DP, Sivaramakrishnan R, Weller HR, Seifert NA, Bross DH, Ruscic B, Moore KB, Elliott SN, Copan AV, Harding LB, Klippenstein SJ, Field RW, Prozument K. Substitution Reactions in the Pyrolysis of Acetone Revealed through a Modeling, Experiment, Theory Paradigm. J Am Chem Soc 2021; 143:3124-3142. [PMID: 33615780 DOI: 10.1021/jacs.0c11677] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The development of high-fidelity mechanisms for chemically reactive systems is a challenging process that requires the compilation of rate descriptions for a large and somewhat ill-defined set of reactions. The present unified combination of modeling, experiment, and theory provides a paradigm for improving such mechanism development efforts. Here we combine broadband rotational spectroscopy with detailed chemical modeling based on rate constants obtained from automated ab initio transition state theory-based master equation calculations and high-level thermochemical parametrizations. Broadband rotational spectroscopy offers quantitative and isomer-specific detection by which branching ratios of polar reaction products may be obtained. Using this technique, we observe and characterize products arising from H atom substitution reactions in the flash pyrolysis of acetone (CH3C(O)CH3) at a nominal temperature of 1800 K. The major product observed is ketene (CH2CO). Minor products identified include acetaldehyde (CH3CHO), propyne (CH3CCH), propene (CH2CHCH3), and water (HDO). Literature mechanisms for the pyrolysis of acetone do not adequately describe the minor products. The inclusion of a variety of substitution reactions, with rate constants and thermochemistry obtained from automated ab initio kinetics predictions and Active Thermochemical Tables analyses, demonstrates an important role for such processes. The pathway to acetaldehyde is shown to be a direct result of substitution of acetone's methyl group by a free H atom, while propene formation arises from OH substitution in the enol form of acetone by a free H atom.
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Affiliation(s)
- Daniel P Zaleski
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States.,Department of Chemistry, Colgate University, Hamilton, New York 13346, United States
| | - Raghu Sivaramakrishnan
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Hailey R Weller
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States.,Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nathan A Seifert
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - David H Bross
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Branko Ruscic
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, 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
| | - Andreas V Copan
- Emmanuel College, Natural Sciences Department, Franklin Springs, Georgia 30639, United States
| | - Lawrence B Harding
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Stephen J Klippenstein
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Robert W Field
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kirill Prozument
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
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4
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Sivaramakrishnan K, Puliyanda A, Tefera DT, Ganesh A, Thirumalaivasan S, Prasad V. A Perspective on the Impact of Process Systems Engineering on Reaction Engineering. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b00280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Kaushik Sivaramakrishnan
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Anjana Puliyanda
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Dereje Tamiru Tefera
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Ajay Ganesh
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Sushmitha Thirumalaivasan
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Vinay Prasad
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
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5
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Magnotti GM, Wang Z, Liu W, Sivaramakrishnan R, Som S, Davis MJ. Sparsity Facilitates Chemical-Reaction Selection for Engine Simulations. J Phys Chem A 2018; 122:7227-7237. [PMID: 30102539 DOI: 10.1021/acs.jpca.8b05436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analysis of large-scale, realistic models incorporating detailed chemistry can be challenging because each simulation is computationally expensive, and a complete analysis may require many simulations. This paper addresses one such problem of this type, chemical-reaction selection in engine simulations. In this computationally challenging case, it is demonstrated how the important concept of sparsity can facilitate chemical-reaction selection, which is the process of finding the most important chemical reactions for modeling a chemical process. It is difficult to perform accurate reaction selection for engine simulations using realistic models of the chemistry, as each simulation takes processor weeks to complete. We developed a procedure to efficiently accomplish this selection process with a relatively small number of simulations using a form of global sensitivity analysis based on sparse regression. The chemical-reaction selection leads to an analysis of the ignition chemistry as it evolves within the compression-ignition engine simulations and allows for the spatial development of the selected chemical reactions to be studied in detail.
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6
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Global Sensitivity Analysis of Large Reaction Mechanisms Using Fourier Amplitude Sensitivity Test. J CHEM-NY 2018. [DOI: 10.1155/2018/5127393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Global sensitivity analysis (GSA) of large chemical reaction mechanisms remains a challenge since the model with uncertainties in the large number of input parameters provides large dimension of input parameter space and tends to be difficult to evaluate the effect of input parameters on model outputs. In this paper, a criterion for frequency selection to input parameter is proposed so that Fourier amplitude sensitivity test (FAST) method can evaluate the complex model with a low sample size. This developed FAST method can establish the relationship between the number of input parameters and sample size needed to measure sensitivity indices with high accuracy. The performance of this FAST method which can allow both the qualitative and quantitative analysis of complex systems is validated by a H2/air combustion model and a CH4/air combustion model. This FAST method is also compared with other GSA methods to illustrate the features of this FAST method. The results show that FAST method can evaluate the reaction systems with low sample size, and the sensitivity indices obtained from the FAST method can provide more important information which the variance-based GSA methods cannot obtain. FAST method can be a remarkably effective tool for the modelling and diagnosis of large chemical reaction.
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7
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Davis MJ, Liu W, Sivaramakrishnan R. Global Sensitivity Analysis with Small Sample Sizes: Ordinary Least Squares Approach. J Phys Chem A 2017; 121:553-570. [PMID: 28001400 DOI: 10.1021/acs.jpca.6b09310] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new version of global sensitivity analysis is developed in this paper. This new version coupled with tools from statistics, machine learning, and optimization can devise small sample sizes that allow for the accurate ordering of sensitivity coefficients for the first 10-30 most sensitive chemical reactions in complex chemical-kinetic mechanisms, and is particularly useful for studying the chemistry in realistic devices. A key part of the paper is calibration of these small samples. Because these small sample sizes are developed for use in realistic combustion devices, the calibration is done over the ranges of conditions in such devices, with a test case being the operating conditions of a compression ignition engine studied earlier. Compression-ignition engines operate under low-temperature combustion conditions with quite complicated chemistry making this calibration difficult, leading to the possibility of false positives and false negatives in the ordering of the reactions. So an important aspect of the paper is showing how to handle the trade-off between false positives and false negatives using ideas from the multiobjective optimization literature. The combination of the new global sensitivity method and the calibration are sample sizes a factor of approximately 10 times smaller than were available with our previous algorithm.
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Affiliation(s)
- Michael J Davis
- Chemical Sciences and Engineering Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Wei Liu
- Chemical Sciences and Engineering Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Raghu Sivaramakrishnan
- Chemical Sciences and Engineering Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
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8
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Bai S, Skodje RT. The sum over histories representation for chemical kinetics: a quantitative theory based on chemical pathways. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1220774] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Burke MP. Harnessing the Combined Power of Theoretical and Experimental Data through Multiscale Informatics. INT J CHEM KINET 2016. [DOI: 10.1002/kin.20984] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Michael P. Burke
- Department of Mechanical Engineering; Department of Chemical Engineering, and Data Science Institute; Columbia University; New York NY 10027
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne IL 60439
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10
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Bai S, Davis MJ, Skodje RT. Sum over Histories Representation for Kinetic Sensitivity Analysis: How Chemical Pathways Change When Reaction Rate Coefficients Are Varied. J Phys Chem A 2015; 119:11039-52. [DOI: 10.1021/acs.jpca.5b07655] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shirong Bai
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Michael J. Davis
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Rex T. Skodje
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
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11
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Burke MP, Goldsmith CF, Klippenstein SJ, Welz O, Huang H, Antonov IO, Savee JD, Osborn DL, Zádor J, Taatjes CA, Sheps L. Multiscale Informatics for Low-Temperature Propane Oxidation: Further Complexities in Studies of Complex Reactions. J Phys Chem A 2015; 119:7095-115. [DOI: 10.1021/acs.jpca.5b01003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael P. Burke
- Department of Mechanical Engineering, Department
of Chemical Engineering, and Data Sciences Institute, Columbia University, New York, New York, United States
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois, United States
| | - C. Franklin Goldsmith
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois, United States
- School of Engineering, Brown University, Providence, Rhode Island, United States
| | - Stephen J. Klippenstein
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois, United States
| | - Oliver Welz
- Combustion Research Facility, Sandia National Laboratories, Livermore, California, United States
| | - Haifeng Huang
- Combustion Research Facility, Sandia National Laboratories, Livermore, California, United States
| | - Ivan O. Antonov
- Combustion Research Facility, Sandia National Laboratories, Livermore, California, United States
| | - John D. Savee
- Combustion Research Facility, Sandia National Laboratories, Livermore, California, United States
| | - David L. Osborn
- Combustion Research Facility, Sandia National Laboratories, Livermore, California, United States
| | - Judit Zádor
- Combustion Research Facility, Sandia National Laboratories, Livermore, California, United States
| | - Craig A. Taatjes
- Combustion Research Facility, Sandia National Laboratories, Livermore, California, United States
| | - Leonid Sheps
- Combustion Research Facility, Sandia National Laboratories, Livermore, California, United States
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12
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Karwat DMA, Wooldridge MS, Klippenstein SJ, Davis MJ. Effects of new Ab initio rate coefficients on predictions of species formed during n-butanol ignition and pyrolysis. J Phys Chem A 2015; 119:543-51. [PMID: 25560388 DOI: 10.1021/jp509279d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Experimental, time-resolved species profiles provide critical tests in developing accurate combustion models for biofuels such as n-butanol. A number of such species profiles measured by Karwat et al. [ Karwat, D. M. A.; et al. J. Phys. Chem. A 2011 , 115 , 4909 ] were discordant with predictions from a well-tested chemical kinetic mechanism developed by Black et al. [ Black, G.; et al. Combust. Flame 2010 , 157 , 363 ]. Since then, significant theoretical and experimental efforts have focused on determining the rate coefficients of primary n-butanol consumption pathways in combustion environments, including H atom abstraction reactions from n-butanol by key radicals such as HO2 and OH, as well as the decomposition of the radicals formed by these H atom abstractions. These reactions not only determine the overall reactivity of n-butanol, but also significantly affect the concentrations of intermediate species formed during n-butanol ignition. In this paper we explore the effect of incorporating new ab initio predictions into the Black et al. mechanism on predictions of ignition delay time and species time histories for the experimental conditions studied by Karwat et al. The revised predictions for the intermediate species time histories are in much improved agreement with the measurements, but some discrepancies persist. A rate of production analysis comparing the effects of various modifications to the Black et al. mechanism shows significant changes in the predicted consumption pathways of n-butanol, and of the hydroxybutyl and butoxy radicals formed by H atom abstraction from n-butanol. The predictions from the newly revised mechanism are in very good agreement with the low-pressure n-butanol pyrolysis product species measurements of Stranic et al. [ Stranic, I.; et al. Combust. Flame 2012 , 159 , 3242 ] for all but one species. Importantly, the changes to the Black et al. mechanism show that concentrations of small products from n-butanol pyrolysis are sensitive to different reactions than those presented by Stranic et al.
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Affiliation(s)
- Darshan M A Karwat
- Department of Mechanical Engineering and ‡Department of Aerospace Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
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13
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Hakalla R, Zachwieja M, Szajna W. First analysis of the 1-v″ progression of the Ångström (B1Σ+-A1Π) band system in the rare 13C17O isotopologue. J Phys Chem A 2013; 117:12299-312. [PMID: 24138166 DOI: 10.1021/jp4077239] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The 1-v″ progression of the Ångström band system, so far unobserved in the rare (13)C(17)O isotopologue, was obtained under high resolution as an emission spectrum using a high accuracy dispersive optical spectroscopy. In the studied region 22,700-24,500 cm(-1), 146 spectral lines were observed, among which 118 were interpreted as belonging to the 1-0 and 1-1 bands of B-A system, and the next 28 were interpreted as extra lines belonging to the 1-1 band of B(1)Σ(+)-e(3)Σ(-) intercombination system, also unobserved in the (13)C(17)O molecule so far. All those lines were precisely measured with an estimated accuracy better than 0.0025 cm(-1), and rotationally analyzed. As a result the following in the (13)C(17)O molecule were calculated for the first time: the merged rotational constants B1 = 1.790227(23) cm(-1), D1 = 6.233(47) × 10(-6) cm(-1), and ΔG1/2 = 2010.9622 (69) cm(-1) and the equilibrium constants, ωe = 2076.04(57) cm(-1), ωexe = 32.54(28) cm(-1), Be = 1.824678(15) cm(-1), αe = 2.2967(24) × 10(-2) cm(-1), De = 5.226(25) × 10(-6) cm(-1), and βe = 6.71(48) × 10(-7) cm(-1) for the B(1)Σ(+) Rydberg state, as well as the individual rotational constant B0 = 1.50485(78) cm(-1), and the equilibrium constants ωe = 1463.340(21) cm(-1), Be = 1.49902(12) cm(-1), αe = 1.7782(49) × 10(-2) cm(-1), De = 7.36(56) × 10(-6) cm(-1) for the A(1)Π state, and σe = 21,854.015(51) cm(-1), RKR turning points, Franck-Condon factors (FCF), relative intensities, and r centroids for the Ångström band system. With the help of the strong and vast A(1)Π (v = 0) ∼ e(3)Σ(-) (v = 1) interaction, the experimental parameters of the e(3)Σ(-) (v = 1) perturbing state were established in the (13)C(17)O molecule for the first time.
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Affiliation(s)
- Rafał Hakalla
- Materials Spectroscopy Laboratory, Center for Innovation and Transfer of Engineering and Natural Science Knowledge, University of Rzeszów , 35-959 Rzeszów, Poland
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14
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Som S, Liu W, Zhou DDY, Magnotti GM, Sivaramakrishnan R, Longman DE, Skodje RT, Davis MJ. Quantum Tunneling Affects Engine Performance. J Phys Chem Lett 2013; 4:2021-2025. [PMID: 26283246 DOI: 10.1021/jz400874s] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We study the role of individual reaction rates on engine performance, with an emphasis on the contribution of quantum tunneling. It is demonstrated that the effect of quantum tunneling corrections for the reaction HO2 + HO2 = H2O2 + O2 can have a noticeable impact on the performance of a high-fidelity model of a compression-ignition (e.g., diesel) engine, and that an accurate prediction of ignition delay time for the engine model requires an accurate estimation of the tunneling correction for this reaction. The three-dimensional model includes detailed descriptions of the chemistry of a surrogate for a biodiesel fuel, as well as all the features of the engine, such as the liquid fuel spray and turbulence. This study is part of a larger investigation of how the features of the dynamics and potential energy surfaces of key reactions, as well as their reaction rate uncertainties, affect engine performance, and results in these directions are also presented here.
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Affiliation(s)
| | | | - Dingyu D Y Zhou
- §Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Gina M Magnotti
- ∥Department of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | | | | | - Rex T Skodje
- §Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
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