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Chen W, Zhang P, Truhlar DG, Zheng J, Xu X. Identification of Torsional Modes in Complex Molecules Using Redundant Internal Coordinates: The Multistructural Method with Torsional Anharmonicity with a Coupled Torsional Potential and Delocalized Torsions. J Chem Theory Comput 2022; 18:7671-7682. [PMID: 36441527 DOI: 10.1021/acs.jctc.2c00952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identification of internal-rotation modes in the normal-mode analysis of complex molecules is important for accurately describing the thermodynamic properties and kinetics of complex molecules when it is necessary to treat the anharmonicity of torsions and the multiconformer anharmonicity caused by the internal rotations. However, identifying and distinguishing torsional modes are very challenging because they are coupled to one another. In this work, we present a new strategy to automatically identify torsional vibrations and separate them from the other vibrational modes. By combining a redundant-internal-coordinate auto-generation procedure with torsional projection techniques, we automate the procedure of identifying and separating the coupled torsions, and we show that we can obtain robust and consistent results with various reasonable definitions of redundant-internal-coordinate sets. This model has been implemented in a new development version of the MSTor program to reduce the user input needed for multistructural and torsional anharmonicity (MS-T) calculations. The new method is called multistructural and torsional anharmonicity with a coupled torsional potential and delocalized torsions ([MS-T(CD)]. As example applications, we consider MS-T(CD) calculations on three molecules (2-hexyl radical, n-propylbenzene, and 5-hydroperoxy-6-oxohexanoylperoxy radical) that have multiple rotors and that provide challenges to choosing good sets of nonredundant-internal coordinates, and we compare the performance of the new strategy to five other torsion identification methods. The new strategy is demonstrated to be efficient in separating the torsional and nontorsional elements in the Hessian matrix, as well as in providing reasonable projected nontorsional frequencies to be used for calculations of partition function and thermochemistry.
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Affiliation(s)
- Wenqi Chen
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing100084, China
| | - Pengchao Zhang
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing100084, China
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MinnesotaMN55455-0431, United States
| | - Jingjing Zheng
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut06492, United States
| | - Xuefei Xu
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing100084, China
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2
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Passos MO, Lins IA, Venâncio MF, Alves TV. Differences in the torsional anharmonicity between reactant and transition state: the case of 3-butenal + H abstraction reactions. Phys Chem Chem Phys 2021; 23:25414-25423. [PMID: 34751697 DOI: 10.1039/d1cp03981d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermal rate coefficients for the hydrogen-abstraction reactions of 3-butenal by a hydrogen atom were obtained applying multipath canonical variational theory with small-curvature tunneling (MP-CVT/SCT). Torsional anharmonicity due to the hindered rotors was taken into account by calculating the rovibrational partition function using the extended two-dimensional torsional (E2DT) method. For comparison, rovibrational partition functions were also estimated using the multistructural method with torsional anharmonicity based on a coupled torsional potential (MS-T(C)). By contrast, with (E)-2-butenal reactions, the abstraction reactions of 3-butenal proceed via five reaction channels (R1)-(R5). In a conformational search, 45 distinguishable structures of transition states were found, including enantiomers, which were separated into six conformational reaction channels (CRCs). The individual reactive paths were constructed, the recrossing and semiclassical transmission coefficients estimated, and the multipath rate constants were obtained. High torsional barriers between the wells of CRC2/CRC6 indicate a harmonic behavior. Consequently, a difference between the torsional anharmonicity of 3-butenal and the transition states is responsible for the increase in the thermal rate constants for channel (R2). Analysis of the contributions of each conformer of the transition state shows an important contribution of the high-energy rotamers in the total flux of (R1)-(R5). After fitting the rate constants in a four-parameter equation, the activation energy estimation showed a strong temperature dependence.
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Affiliation(s)
- Maiara Oliveira Passos
- Departamento de Físico-Química, Instituto de Química - Universidade Federal da Bahia, Rua Barão de Jeremoabo, 147, Salvador, Bahia, 40170-115, Brazil.
| | - Igor Araujo Lins
- Departamento de Físico-Química, Instituto de Química - Universidade Federal da Bahia, Rua Barão de Jeremoabo, 147, Salvador, Bahia, 40170-115, Brazil.
| | - Mateus Fernandes Venâncio
- Departamento de Físico-Química, Instituto de Química - Universidade Federal da Bahia, Rua Barão de Jeremoabo, 147, Salvador, Bahia, 40170-115, Brazil.
| | - Tiago Vinicius Alves
- Departamento de Físico-Química, Instituto de Química - Universidade Federal da Bahia, Rua Barão de Jeremoabo, 147, Salvador, Bahia, 40170-115, Brazil.
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3
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Li W, Li J, Ning H, Shang Y, Luo SN. Multistructural Variational Reaction Kinetics of the Simplest Unsaturated Methyl Ester: H-Abstraction from Methyl Acrylate by H, OH, CH 3, and HO 2 Radicals. J Phys Chem A 2021; 125:5103-5116. [PMID: 34082530 DOI: 10.1021/acs.jpca.1c01788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The H-abstraction reaction kinetics of methyl acrylate (MA) + H/OH/CH3/HO2 radicals have been investigated theoretically in the present work. For these reactions, the reaction energies and barrier heights are first computed using several density functionals and compared to the coupled cluster CCSD(T)-F12/jun-cc-pVTZ benchmark calculations. The M062X/maug-cc-pVTZ method shows the best performance with the smallest mean unsigned deviation (MUD) of 0.42 kcal mol-1. Combined with the electronic structure calculations using the M062X/maug-cc-pVTZ method, the multistructural canonical variational transition-state theory (MS-CVT) with small-curvature tunneling (SCT) is employed to calculate the reaction rate constants at 500-2000 K. The variational effect is between 0.56 and 1.0, the multistructural torsional anharmonicity factor ranges from 0.004 to 4.57, and the tunneling coefficient is in the range of 0.5-4.70. Notably, given the existence of reactant complexes (RCs) between reactants and transition states for the reaction systems MA + OH/HO2, we further compare the rate constants under the low-pressure limit (LPL) kinetic model, which treats the reaction as a single-step process and neglects RCs, and the pre-equilibrium model, which takes RCs into account in the reaction and treats the reaction as a two-step process. The rate constants calculated by these two models are similar within the combustion temperature range, and apparent differences occur at lower temperatures. In addition, we determine the branching ratios as a function of temperature and find that the methyl site (S3) abstractions by OH and H radicals are dominant in the low- and high-temperature ranges, respectively. Moreover, we update the kinetic model with the calculated H-abstraction rate constants to simulate the ignition delay times of MA. The simulations of the updated model are in good agreement with experimental results. The accurate reaction kinetics determined in this work are useful for the understanding and prediction of consumption branching fractions and ignition properties of the unsaturated methyl esters.
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Affiliation(s)
- Wenrui Li
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, China.,Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Jun Li
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, China
| | - Hongbo Ning
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Yanlei Shang
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Sheng-Nian Luo
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
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4
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Viegas LP. Simplified Protocol for the Calculation of Multiconformer Transition State Theory Rate Constants Applied to Tropospheric OH-Initiated Oxidation Reactions. J Phys Chem A 2021; 125:4499-4512. [PMID: 33902279 DOI: 10.1021/acs.jpca.1c00683] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical kinetics plays a fundamental role in the understanding and modeling of tropospheric chemical processes, one of the most important being the atmospheric degradation of volatile organic compounds. These potentially harmful molecules are emitted into the troposphere by natural and anthropogenic sources and are chemically removed by undergoing oxidation processes, most frequently initiated by reaction with OH radicals, the atmosphere's "detergent". Obtaining the respective rate constants is therefore of critical importance, with calculations based on transition state theory (TST) often being the preferred choice. However, for molecules with rich conformational variety, a single-conformer method such as lowest-conformer TST is unsuitable while state-of-the-art TST-based methodologies easily become unmanageable. In this Feature Article, the author reviews his own cost-effective protocol for the calculation of bimolecular rate constants of OH-initiated reactions in the high-pressure limit based on multiconformer transition state theory. The protocol, which is easily extendable to other oxidation reactions involving saturated organic molecules, is based on a variety of freeware and open-source software and tested against a series of oxidation reactions of hydrofluoropolyethers, computationally very challenging molecules with potential environmental relevance. The main features, advantages and disadvantages of the protocol are presented, along with an assessment of its predictive utility based on a comparison with experimental rate constants.
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Affiliation(s)
- Luís P Viegas
- Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, Buildings 1630-1632, Aarhus 8000, Denmark
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5
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Passos MO, Lins IA, Alves TV. Rate coefficients and product branching ratios for (E)-2-butenal + H reactions. Phys Chem Chem Phys 2020; 22:14246-14254. [PMID: 32555895 DOI: 10.1039/d0cp02142c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermal rate constants for the hydrogen abstraction reactions of (E)-2-butenal by hydrogen atoms were calculated, for the first time, using the multipath canonical variational theory with small-curvature tunneling (MP-CVT/SCT). After a torsional potential energy surface exploration, ten conformations of the transition states (including the mirror images) were found and separated into four conformational reaction channels (CRCs). Individual energy paths of each CRC were built, recrossing and quantum tunneling effects estimated, and the thermal rate constants obtained. Due to the hindered rotors, the torsional anharmonicity was incorporated in the rate coefficient through the calculations of the rovibrational partition functions using the extended two-dimensional torsional method (E2DT). For comparison, the one-well (1W-CVT/SCT) and harmonic multipath (MP-CVT/SCT) thermal rate constants were also estimated. In addition, kinetic Monte Carlo (KMC) simulations were performed to predict the product branching ratios. For all kinetic approaches, the formation of products of (R1) is predominant. Compared to the harmonic multipath estimation, the percentage of reaction (R4) increases by approximately 9% when the torsional anharmonicity is taken into account. For the reactions (R2) and (R3), the product branching ratio is slightly decreased when compared with the harmonic simulation.
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Affiliation(s)
- Maiara Oliveira Passos
- Departamento de Físico-Química, Instituto de Química - Universidade Federal da Bahia, Rua Barão de Jeremoabo, 147, Salvador, Bahia, 40170-115, Brazil.
| | - Igor Araujo Lins
- Departamento de Físico-Química, Instituto de Química - Universidade Federal da Bahia, Rua Barão de Jeremoabo, 147, Salvador, Bahia, 40170-115, Brazil.
| | - Tiago Vinicius Alves
- Departamento de Físico-Química, Instituto de Química - Universidade Federal da Bahia, Rua Barão de Jeremoabo, 147, Salvador, Bahia, 40170-115, Brazil.
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6
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Xing L, Wang Z, Truhlar DG. Multistructural Anharmonicity Controls the Radical Generation Process in Biofuel Combustion. J Am Chem Soc 2019; 141:18531-18543. [PMID: 31637914 DOI: 10.1021/jacs.9b09194] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The OH radical plays an important role in combustion, and isopentanol (3-methylbutan-1-ol) is a promising sustainable fuel additive and second-generation biofuel. The abstractions of H atoms from fuel molecules are key initiation steps for chain branching in combustion chemistry. In comparison with the more frequently studied ethanol, isopentanol has a longer carbon chain that allows a greater number of products, and experimental work is unavailable for the branching fractions to the various products. However, the site-dependent kinetics of isopentanol with OH radicals are usually experimentally unavailable. Alcohol oxidation by OH is also important in the atmosphere, and in the present study we calculate the rate constants and branching fractions of the hydrogen abstraction reaction of isopentanol by OH radical in a broad temperature range of 298-2400 K, covering temperatures important for atmospheric chemistry and those important for combustion. The calculations are done by multipath variational transition state theory (MP-VTST). With a combination of electronic structure calculations, we determine previously missing thermochemical data. With MP-VTST, a multidimensional tunneling approximation, multiple-structure anharmonicity, and torsional potential anharmonicity, we carried out more realistic rate constant calculations than can be computed by conventional single-structure harmonic transition state theory or by the empirical relations that are currently used in atmospheric and combustion modeling. The roles of various factors in determining the rates are elucidated, and we show that recrossing, tunneling, and multiple structures are all essential for accurate work. We conclude that the multiple structure anharmonicity is the most important correction to conventional transition state theory for this reaction, although recrossing effects and tunneling are by no means insignificant and the tunneling depends significantly on the path. The thermodynamic and kinetics data determined in this work are indispensable for the gas-phase degradation of alcohols in the atmosphere and for the detailed understanding and prediction of ignition mechanisms of biofuels in combustion.
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Affiliation(s)
- Lili Xing
- Energy and Power Engineering Institute , Henan University of Science and Technology , Luoyang , Henan 471003 , China.,Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minnesota 55455-0431 , United States
| | - Zhandong Wang
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei , Anhui 230029 , PR China
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minnesota 55455-0431 , United States
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7
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Chi Y, You X. Kinetics of Hydrogen Abstraction Reactions of Methyl Palmitate and Octadecane by Hydrogen Atoms. J Phys Chem A 2019; 123:3058-3067. [PMID: 30893997 DOI: 10.1021/acs.jpca.8b08802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen abstractions play a crucial role in the consumption of fuel molecules during fuel pyrolysis and combustion processes. In this study, a generalized energy-based fragmentation approach was used to obtain CCSD(T)-F12a/cc-pVTZ energy barriers of hydrogen abstraction reactions by hydrogen atoms from methyl palmitate (C15H31COOCH3), a key component of biodiesel. The accuracy of M06-2X/6-311++G(d,p) for obtaining the energy barriers was evaluated against the CCSD(T) results. Based on the quantum chemical results, the high-pressure-limit rate constants for C15H31COOCH3 + H were calculated and compared with those of octadecane ( n-C18H38) reacting with H. The treatment of hindered internal rotations for such long-chain molecules was discussed and the rate rules for different abstraction sites were summarized. The results show that in the C15H31COOCH3 + H system, the α hydrogen abstraction no longer plays a dominant role as in small methyl esters, and the hydrogen atoms of CH2 groups far away from the ester group are more easily abstracted than those near the ester group.
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Affiliation(s)
- Yawei Chi
- Center for Combustion Energy , Tsinghua University , Beijing 100084 , China.,Key Laboratory for Thermal Science and Power Engineering of Ministry of Education , Tsinghua University , Beijing 100084 , China
| | - Xiaoqing You
- Center for Combustion Energy , Tsinghua University , Beijing 100084 , China.,Key Laboratory for Thermal Science and Power Engineering of Ministry of Education , Tsinghua University , Beijing 100084 , China
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8
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Yin C, Takahashi K. Effect of unsaturated substituents in the reaction of Criegee intermediates with water vapor. Phys Chem Chem Phys 2018; 20:20217-20227. [PMID: 30027942 DOI: 10.1039/c8cp02064g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Criegee intermediates (CIs), formed in the reactions of unsaturated hydrocarbons with ozone, are very reactive carbonyl oxides and have recently been suggested as important oxidants in the atmosphere. In this work, we studied the substituent effect on the water monomer and dimer reaction with CIs which include up to three carbon atoms at the QCISD(T)/CBS//B3LYP/6-311+G(2d,2p) level. Our calculation showed that for saturated CIs with a hydrogen atom on the same side as the terminal oxygen atom, the reaction with water vapor would likely dominate the removal processes of these CIs in the atmosphere. On the other hand, for unsaturated CIs, the reactivity toward water vapor decreases compared to the saturated species allowing them to survive in humid atmospheric environments. We also evaluated the kinetic isotope effect in the reaction between CI and water vapor by performing calculations with deuterated water. We found that tunneling is not important and the kinetic isotope effect mainly comes from the difference in the zero point energy between water and deuterated water.
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Affiliation(s)
- Cangtao Yin
- Institute of Atomic and Molecular Sciences, Academia Sinica, PO-Box 23-166, Taipei, 10617, Taiwan.
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9
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Ferro-Costas D, Martínez-Núñez E, Rodríguez-Otero J, Cabaleiro-Lago E, Estévez CM, Fernández B, Fernández-Ramos A, Vázquez SA. Influence of Multiple Conformations and Paths on Rate Constants and Product Branching Ratios. Thermal Decomposition of 1-Propanol Radicals. J Phys Chem A 2018; 122:4790-4800. [DOI: 10.1021/acs.jpca.8b02949] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Bao JL, Xing L, Truhlar DG. Dual-Level Method for Estimating Multistructural Partition Functions with Torsional Anharmonicity. J Chem Theory Comput 2017; 13:2511-2522. [DOI: 10.1021/acs.jctc.7b00232] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry, Chemical Theory
Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Lili Xing
- Department of Chemistry, Chemical Theory
Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory
Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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11
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Li X, You X, Law CK, Truhlar DG. Kinetics and branching fractions of the hydrogen abstraction reaction from methyl butenoates by H atoms. Phys Chem Chem Phys 2017; 19:16563-16575. [DOI: 10.1039/c7cp01686g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We studied hydrogen abstraction reactions at various sites of unsaturated methyl esters by H atoms, including variational effects, tunneling and multi-structural torsional anharmonicity.
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Affiliation(s)
- Xiaoyu Li
- Center for Combustion Energy
- Tsinghua University
- Beijing
- China
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education
| | - Xiaoqing You
- Center for Combustion Energy
- Tsinghua University
- Beijing
- China
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education
| | - Chung K. Law
- Center for Combustion Energy
- Tsinghua University
- Beijing
- China
- Department of Mechanical and Aerospace Engineering
| | - Donald G. Truhlar
- Department of Chemistry
- Chemical Theory Center, and Minnesota Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
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12
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Bao JL, Truhlar DG. Variational transition state theory: theoretical framework and recent developments. Chem Soc Rev 2017; 46:7548-7596. [DOI: 10.1039/c7cs00602k] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications.
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Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry
- Chemical Theory Center, and Minnesota Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
| | - Donald G. Truhlar
- Department of Chemistry
- Chemical Theory Center, and Minnesota Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
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13
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Bao JL, Zheng J, Truhlar DG. Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory. J Am Chem Soc 2016; 138:2690-704. [PMID: 26841076 DOI: 10.1021/jacs.5b11938] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry. We employ a new calibration procedure for quantum Rice-Ramsperger-Kassel (QRRK) unimolecular rate theory within a chemical activation mechanism to calculate the pressure-falloff effect of a radical association with an aromatic ring. The new theoretical framework is applied to the reaction of H with toluene, which is a prototypical reaction in the combustion chemistry of aromatic hydrocarbons present in most fuels. Both the hydrogen abstraction reactions and the hydrogen addition reactions are calculated. Our system-specific (SS) QRRK approach is adjusted with SS parameters to agree with multistructural canonical variational transition state theory with multidimensional tunneling (MS-CVT/SCT) at the high-pressure limit. The new method avoids the need for the usual empirical estimations of the QRRK parameters, and it eliminates the need for variational transition state theory calculations as a function of energy, although in this first application we do validate the falloff curves by comparing SS-QRRK results without tunneling to multistructural microcanonical variational transition state theory (MS-μVT) rate constants without tunneling. At low temperatures, the two approaches agree well with each other, but at high temperatures, SS-QRRK tends to overestimate falloff slightly. We also show that the variational effect is important in computing the energy-resolved rate constants. Multiple-structure anharmonicity, torsional-potential anharmonicity, and high-frequency-mode vibrational anharmonicity are all included in the rate computations, and torsional anharmonicity effects on the density of states are investigated. Branching fractions, which are both temperature- and pressure-dependent (and for which only limited data is available from experiment), are predicted as a function of pressure.
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Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States
| | - Jingjing Zheng
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States
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14
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Bao JL, Sripa P, Truhlar DG. Path-dependent variational effects and multidimensional tunneling in multi-path variational transition state theory: rate constants calculated for the reactions of HO2 with tert-butanol by including all 46 paths for abstraction at C and all six paths for abstraction at O. Phys Chem Chem Phys 2016; 18:1032-41. [DOI: 10.1039/c5cp05780a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Multi-path variational transition state theory (MP-VTST) provides a conformationally complete framework for calculating gas-phase rate constants.
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Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry
- Chemical Theory Center
- and Supercomputing Institute
- University of Minnesota
- Minneapolis
| | - Pattrawan Sripa
- Department of Chemistry
- Chemical Theory Center
- and Supercomputing Institute
- University of Minnesota
- Minneapolis
| | - Donald G. Truhlar
- Department of Chemistry
- Chemical Theory Center
- and Supercomputing Institute
- University of Minnesota
- Minneapolis
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15
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Bao JL, Meana-Pañeda R, Truhlar DG. Multi-path variational transition state theory for chiral molecules: the site-dependent kinetics for abstraction of hydrogen from 2-butanol by hydroperoxyl radical, analysis of hydrogen bonding in the transition state, and dramatic temperature dependence of the activation energy. Chem Sci 2015; 6:5866-5881. [PMID: 29861912 PMCID: PMC5950756 DOI: 10.1039/c5sc01848j] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 06/15/2015] [Indexed: 01/20/2023] Open
Abstract
The goal of the present work is modeling the kinetics of a key reaction involved in the combustion of the biofuel 2-butanol. To accomplish this we extended multi-path variational transition state theory (MP-VTST) with the small curvature tunneling (SCT) approximation to include multistructural anharmonicity factors for molecules with chiral carbons. We use the resulting theory to predict the site-dependent rate constants of the hydrogen abstraction from 2-butanol by hydroperoxyl radical. The generalized transmission coefficients were averaged over the four lowest-energy reaction paths. The computed forward reaction rate constants indicate that hydrogen abstraction from the C-2 site has the largest contribution to the overall reaction from 200 K to 2400 K, with a contribution ranging from 99.9988% at 200 K to 88.9% at 800 K to 21.2% at 3000 K, while hydrogen abstraction from the oxygen site makes the lowest contribution at all temperatures, ranging from 2.5 × 10-9% at 200 K to 0.65% at 800 K to 18% at 3000 K. This work highlights the importance of including the multiple-structure and torsional potential anharmonicity in the computation of the thermal rate constants. We also analyzed the role played by the hydrogen bond at the transition state, and we illustrated the risks of (a) considering only the lowest-energy conformations in the calculations of the rate constants or (b) ignoring the nonlinear temperature dependence of the activation energies. A hydrogen bond at the transition state can lower the enthalpy of activation, but raise the free energy of activation. We find an energy of activation that increases from 11 kcal mol-1 at 200 K to more than 36 kcal mol-1 at high temperature for this radical reaction with a biofuel molecule.
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Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry , Chemical Theory Center and Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-043 , USA .
| | - Rubén Meana-Pañeda
- Department of Chemistry , Chemical Theory Center and Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-043 , USA .
| | - Donald G Truhlar
- Department of Chemistry , Chemical Theory Center and Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-043 , USA .
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Franzen S, Skalski B, Bartolotti L, Delley B. The coupling of tautomerization to hydration in the transition state on the pyrimidine photohydration reaction path. Phys Chem Chem Phys 2014; 16:20164-74. [DOI: 10.1039/c4cp02160f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Yue L, Xie HJ, Qin XM, Lu XX, Fang WJ. A DFT study on the thermal cracking of JP-10. J Mol Model 2013; 19:5355-65. [DOI: 10.1007/s00894-013-2029-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
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Seal P, Oyedepo G, Truhlar DG. Kinetics of the hydrogen atom abstraction reactions from 1-butanol by hydroxyl radical: theory matches experiment and more. J Phys Chem A 2013; 117:275-82. [PMID: 23244297 DOI: 10.1021/jp310910f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the present work, we study the H atom abstraction reactions by hydroxyl radical at all five sites of 1-butanol. Multistructural variational transition state theory (MS-VTST) was employed to estimate the five thermal rate constants. MS-VTST utilizes a multifaceted dividing surface that accounts for the multiple conformational structures of the transition state, and we also include all the structures of the reactant molecule. The vibrational frequencies and minimum energy paths (MEPs) were computed using the M08-HX/MG3S electronic structure method. The required potential energy surfaces were obtained implicitly by direct dynamics employing interpolated variational transition state theory with mapping (IVTST-M) using a variational reaction path algorithm. The M08-HX/MG3S electronic model chemistry was then used to calculate multistructural torsional anharmonicity factors to complete the MS-VTST rate constant calculations. The results indicate that torsional anharmonicity is very important at higher temperatures, and neglecting it would lead to errors of 26 and 32 at 1000 and 1500 K, respectively. Our results for the sums of the site-specific rate constants agree very well with the experimental values of Hanson and co-workers at 896-1269 K and with the experimental results of Campbell et al. at 292 K, but slightly less well with the experiments of Wallington et al., Nelson et al., and Yujing and Mellouki at 253-372 K; nevertheless, the calculated rates are within a factor of 1.61 of all experimental values at all temperatures. This gives us confidence in the site-specific values, which are currently inaccessible to experiment.
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Affiliation(s)
- Prasenjit Seal
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USA
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