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Jiao P, Zheng W, Cui J, Zhang Q, Jin H. Theoretical Study on the P-C Bond Dissociation Enthalpy in 9,10-Dihydro-9-oxa-10-phosphaphenanthrene-10-oxide Flame Retardants. J Phys Chem A 2024; 128:6167-6182. [PMID: 39038260 DOI: 10.1021/acs.jpca.4c01947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO) flame retardants (DOPO-FRs) have attracted more and more attention in the flame-retardant industry due to their high efficiency, environmental protection, and good molecular design. During the flame-retardant process, the breakage of P-C bonds is very important to the flame-retardant effect. Through the comparison of different density functional theories (DFTs) on P-C BDEs, it was found that MN12-L has the highest calculation accuracy, and the root-mean-square error is the smallest with 1.85 kcal/mol. Therefore, MN12-L was selected to investigate P-C BDEs of different DOPO-FRs including thiophen-amine, benzo[d]thiazol-amine, triazol-amine, and aniline DOPO-FRs. By comparing the theoretical calculation of BDE with the experimental parameters of high limiting oxygen index (LOI) and vertical combustion test (UL-94 test), it was found that the P-C BDEs have a certain correlation with the flame-retardant effect. Finally, based on P-C BDEs, substituent effects, and effective flame-retardant fragments, a series of new DOPO-FRs were designed. The results showed that when only one DOPO fragment was contained, the effective fragments of flame retardants were ranked as furan > thiophene > triazole > imidazole. When bis-DOPO fragment was contained, the flame-retardant effect of diamino-triazole fragments was better than that of benzyldimethylamine fragments. In addition, when the substituents on the effective fragment have two EDGs, the flame-retardant effect is superimposed, which makes the flame-retardant performance more excellent.
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Affiliation(s)
- Peilei Jiao
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Wenrui Zheng
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Jinglei Cui
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Qianxi Zhang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Hao Jin
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
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2
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Nayak SK, Yamijala SSRKC. Computing accurate bond dissociation energies of emerging per- and polyfluoroalkyl substances: Achieving chemical accuracy using connectivity-based hierarchy schemes. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133804. [PMID: 38377911 DOI: 10.1016/j.jhazmat.2024.133804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
Understanding the bond dissociation energies (BDEs) of per- and polyfluoroalkyl substances (PFAS) helps in devising their efficient degradation pathways. However, there is only limited experimental data on the PFAS BDEs, and there are uncertainties associated with the BDEs computed using density functional theory. Although quantum chemical methods like the G4 composite method can provide highly accurate BDEs (< 1 kcal mol-1), they are limited to small system sizes. To address DFT's accuracy limitations and G4's system size constraints, we examined the connectivity-based hierarchy (CBH) scheme and found that it can provide BDEs that are reasonably close to the G4 accuracy while retaining the computational efficiency of DFT. To further improve the accuracy, we modified the CBH scheme and demonstrated that BDEs calculated using it have a mean-absolute deviation of 0.7 kcal mol-1 from G4 BDEs. To validate the reliability of this new scheme, we computed the ground state free energies of seven PFAS compounds and BDEs for 44 C-C and C-F bonds at the G4 level of theory. Our results suggest that the modified CBH scheme can accurately compute the BDEs of both small and large PFAS at near G4 level accuracy, offering promise for more effective PFAS degradation strategies.
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Affiliation(s)
- Samir Kumar Nayak
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036 India; Centre for Atomistic Modelling and Materials Design, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sharma S R K C Yamijala
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036 India; Centre for Atomistic Modelling and Materials Design, Indian Institute of Technology Madras, Chennai 600036, India; Centre for Molecular Materials and Functions, Indian Institute of Technology Madras, Chennai 600036, India; Centre for Quantum Information, Communication, and Computing, Indian Institute of Technology Madras, Chennai 600036, India.
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3
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Poskrebyshev GA. Mechanism of formation of p-benzylenephenol peroxide radical (p-PhC(O 2•)HPhOH). J Mol Model 2024; 30:105. [PMID: 38491309 DOI: 10.1007/s00894-024-05900-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
CONTEXT The reactions of radicals with O2 play the important role in the biological, medicinal, and industrial processes. The mechanism of this reaction is studied previously for the alkane, alkene, alkyne, phenols, and close-related radicals. According to these studies, the formation of intermediates in these reactions is predicted only for the aromatic radicals. Thus, the Van der Waals complexes of O2 with phenyl or benzyl radicals are predicted, as well as the π-π cluster for benzene. However, the possibility of the formation of such intermediate π-π clusters in the case of bisphenol radicals and the thermochemistry of its formation is not studied. Bisphenols are one of the main components of bio-oil, produced during pyrolysis of lignin-contained biomass. Synthetic bisphenols are used in polycarbonate plastics, epoxy resins, and thermal papers. Their mechanism of oxidation is important for the determination of fire safety of these materials, the possibility of using them as additives for fuels for the decreasing and the description of the ignition delays, as well as for the determination of its health risk assessment in medicine. METHODS The five DFT (M06-2X (i = 1), B3LYP (i = 2), wB97XD (i = 3), M08HX (i = 4), MN15 (i = 5)) approaches with 6-311 + + G(d,p) basis set are used for the determination of standard enthalpies of atomization (ΔraHo(Yi)) of considered compounds (molecules, radicals, and transition states). These values of ΔraHo(Yi) are corrected using the empirical linear calibration dependencies, reported previously. The different calibration dependencies are used for the hydrocarbons (including the aromatics and simple oxygenated derivatives) and for the peroxides. The corrected values of ΔraHo(Yi, CORR) are used according to Hess's law for the determination of ΔfHo(Yi, CORR). The most consistent values of ΔfHo(Y, MEAN) are derived from the coordination of the values of ΔfHo(Yi, CORR) using the intersection of their values of standard deviations (3SDi). These values of ΔfHo(Y, MEAN), as well as the B3LYP values of So(Y), which are accounting the frequency correction and internal rotations, as well as their temperature dependencies, are used for the determination of thermochemistry of considered reactions and of the calculation, within transition state theory (TST), of the values of high-pressure limits of the rate constant. The values of Ho(Yi), So(Yi), and Go(Yi) are calculated using the Gaussian 16w program. The temperature dependencies of thermochemical properties and the values of rate constants are determined using the ChemRate program (v.1.5). The optimized structures are visualized using the Chemcraft.
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Affiliation(s)
- Gregory A Poskrebyshev
- V.L. Tal'rose Institute of Energy Problems for Chemical Physics at Federal Research Center for Chemical Physics, Russian Academy of Sciences, Leninsky Prosp., Bldg. 38-2, 119334, Moscow, Russia.
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4
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Poskrebyshev GA. The values of Δ
f
H
o
298.15
and
S
o
298.15
of the radicals formed by the abstraction of
H
atom from the p‐Benzylphenol and Dimethyl Phthalate. INT J CHEM KINET 2022. [DOI: 10.1002/kin.21601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Gregory A. Poskrebyshev
- V.L. Tal'rose Institute of Energy Problems for Chemical Physics at Federal Research Center for Chemical Physics Russian Academy of Sciences Moscow Russia
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5
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Zulueta B, Tulyani SV, Westmoreland PR, Frisch MJ, Petersson EJ, Petersson GA, Keith JA. A Bond-Energy/Bond-Order and Populations Relationship. J Chem Theory Comput 2022; 18:4774-4794. [PMID: 35849729 DOI: 10.1021/acs.jctc.2c00334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report an analytical bond energy from bond orders and populations (BEBOP) model that provides intramolecular bond energy decompositions for chemical insight into the thermochemistry of molecules. The implementation reported here employs a minimum basis set Mulliken population analysis on well-conditioned Hartree-Fock orbitals to decompose total electronic energies into physically interpretable contributions. The model's parametrization scheme is based on atom-specific parameters for hybridization and atom pair-specific parameters for short-range repulsion and extended Hückel-type bond energy term fitted to reproduce CBS-QB3 thermochemistry data. The current implementation is suitable for molecules involving H, Li, Be, B, C, N, O, and F atoms, and it can be used to analyze intramolecular bond energies of molecular structures at optimized stationary points found from other computational methods. This first-generation model brings the computational cost of a Hartree-Fock calculation using a large triple-ζ basis set, and its atomization energies are comparable to those from widely used hybrid Kohn-Sham density functional theory (DFT, as benchmarked to 109 species from the G2/97 test set and an additional 83 reference species). This model should be useful for the community by interpreting overall ab initio molecular energies in terms of physically insightful bond energy contributions, e.g., bond dissociation energies, resonance energies, molecular strain energies, and qualitative energetic contributions to the activation barrier in chemical reaction mechanisms. This work reports a critical benchmarking of this method as well as discussions of its strengths and weaknesses compared to hybrid DFT (i.e., B3LYP, M062X, PBE0, and APF methods), and other cost-effective approximate Hamiltonian semiempirical quantum methods (i.e., AM1, PM6, PM7, and DFTB3).
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Affiliation(s)
- Barbaro Zulueta
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Sonia V Tulyani
- Formerly Chemical Engineering Department, University of Massachusetts Amherst,618 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Phillip R Westmoreland
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | | | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - George A Petersson
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States.,Formerly Hall-Atwater Laboratories of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - John A Keith
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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6
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Poskrebyshev GA. The Corrected Values of Δ
r
H
o
(C
a
H
b
O
d
, a≤16) of Atomization of the Aromatic Compounds and Their Uncertainties Determined Using Several Quantum Mechanical Approaches. ChemistrySelect 2022. [DOI: 10.1002/slct.202104502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gregory A. Poskrebyshev
- V.L. Tal'rose Institute of Energy Problems for Chemical Physics at Federal Research Center for Chemical Physics Russian Academy of Sciences 119334 Moscow Russia Leninsky prosp., bldg. 38–2
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7
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Zhang RM, Chen W, Truhlar DG, Xu X. Master Equation Study of Hydrogen Abstraction from HCHO by OH Via a Chemically Activated Intermediate. Faraday Discuss 2022; 238:431-460. [DOI: 10.1039/d2fd00024e] [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
The abstraction reaction of hydrogen from formaldehyde by OH radical plays an important role in formaldehyde oxidation. The reaction involves a bimolecular association to form a chemically activated hydrogen-bonded reaction...
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8
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Zheng YZ, Deng G, Zhang YC. Multiple free radical scavenging reactions of aurones. PHYTOCHEMISTRY 2021; 190:112853. [PMID: 34214923 DOI: 10.1016/j.phytochem.2021.112853] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/18/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
A series of naturally occurring 3',4'-dihydroxy aurones have been studied with regard to multiple free radical scavenging reactions in the gas and two liquid phases using density functional theory (DFT). All of the aurones prefer to perform (2 + n)-HAT mechanism to trap 2 + n free radicals, where n is the sum of the numbers of catechol and guaiacyl units in the gas and benzene phases. The second HAT reaction favours occurring in the same catechol moiety of the first HAT mechanism occurring OH group due to the formation of a stable quinone and the highly exothermic step of the final stable product formation. The catechol and guaiacyl moieties show increased potency for the second and fourth H+/e‒ reactions. In the water phase, aurones can perform multiple H+/e‒ reactions through n1PL-ET-n2HAT-(n+1-n2)ET mechanism, where n1 is the number of OH groups and n2 is the number of guaiacyl moieties.
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Affiliation(s)
- Yan-Zhen Zheng
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, PR China
| | - Geng Deng
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, PR China
| | - Yu-Cang Zhang
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, PR China.
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9
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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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10
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Pyrolysis and carbonization of polyvinyl chloride under electric field: A computational study. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Poskrebyshev GA. The standard thermochemical properties of the p-Benzylphenol and Dimethyl phthalate, and their temperature dependencies. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Liu X. Hydrogenation of CO 2 Promoted by Silicon-Activated H 2S: Origin and Implications. Molecules 2020; 26:molecules26010050. [PMID: 33374285 PMCID: PMC7796234 DOI: 10.3390/molecules26010050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
Unlike the usual method of COx (x = 1, 2) hydrogenation using H2 directly, H2S and HSiSH (silicon-activated H2S) were selected as alternative hydrogen sources in this study for the COx hydrogenation reactions. Our results suggest that it is kinetically infeasible for hydrogen in the form of H2S to transfer to COx at low temperatures. However, when HSiSH is employed instead, the title reaction can be achieved. For this approach, the activation of CO2 is initiated by its interaction with the HSiSH molecule, a reactive species with both a hydridic Hδ− and protonic Hδ+. These active hydrogens are responsible for the successive C-end and O-end activations of CO2 and hence the final product (HCOOH). This finding represents a good example of an indirect hydrogen source used in CO2 hydrogenation through reactivity tuned by silicon incorporation, and thus the underlying mechanism will be valuable for the design of similar reactions.
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Affiliation(s)
- Xing Liu
- College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
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13
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Wen M, Blau SM, Spotte-Smith EWC, Dwaraknath S, Persson KA. BonDNet: a graph neural network for the prediction of bond dissociation energies for charged molecules. Chem Sci 2020; 12:1858-1868. [PMID: 34163950 PMCID: PMC8179073 DOI: 10.1039/d0sc05251e] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
A broad collection of technologies, including e.g. drug metabolism, biofuel combustion, photochemical decontamination of water, and interfacial passivation in energy production/storage systems rely on chemical processes that involve bond-breaking molecular reactions. In this context, a fundamental thermodynamic property of interest is the bond dissociation energy (BDE) which measures the strength of a chemical bond. Fast and accurate prediction of BDEs for arbitrary molecules would lay the groundwork for data-driven projections of complex reaction cascades and hence a deeper understanding of these critical chemical processes and, ultimately, how to reverse design them. In this paper, we propose a chemically inspired graph neural network machine learning model, BonDNet, for the rapid and accurate prediction of BDEs. BonDNet maps the difference between the molecular representations of the reactants and products to the reaction BDE. Because of the use of this difference representation and the introduction of global features, including molecular charge, it is the first machine learning model capable of predicting both homolytic and heterolytic BDEs for molecules of any charge. To test the model, we have constructed a dataset of both homolytic and heterolytic BDEs for neutral and charged (-1 and +1) molecules. BonDNet achieves a mean absolute error (MAE) of 0.022 eV for unseen test data, significantly below chemical accuracy (0.043 eV). Besides the ability to handle complex bond dissociation reactions that no previous model could consider, BonDNet distinguishes itself even in only predicting homolytic BDEs for neutral molecules; it achieves an MAE of 0.020 eV on the PubChem BDE dataset, a 20% improvement over the previous best performing model. We gain additional insight into the model's predictions by analyzing the patterns in the features representing the molecules and the bond dissociation reactions, which are qualitatively consistent with chemical rules and intuition. BonDNet is just one application of our general approach to representing and learning chemical reactivity, and it could be easily extended to the prediction of other reaction properties in the future.
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Affiliation(s)
- Mingjian Wen
- Department of Materials Science and Engineering, University of California Berkeley CA 94720 USA
- Energy Technologies Area, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Samuel M Blau
- Energy Technologies Area, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Evan Walter Clark Spotte-Smith
- Department of Materials Science and Engineering, University of California Berkeley CA 94720 USA
- Energy Technologies Area, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Shyam Dwaraknath
- Energy Technologies Area, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Kristin A Persson
- Department of Materials Science and Engineering, University of California Berkeley CA 94720 USA
- Molecular Foundry, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
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14
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Zheng YZ, Fu ZM, Deng G, Guo R, Chen DF. Role of C‒H bond in the antioxidant activities of rooperol and its derivatives: A DFT study. PHYTOCHEMISTRY 2020; 178:112454. [PMID: 32692658 DOI: 10.1016/j.phytochem.2020.112454] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Rooperol and its derivatives, derived from the Hypoxis rooperi plant, are polyphenolic and norlignan compounds with excellent antioxidant activities. The reaction enthalpies for the free-radical scavenging by rooperol and its six derivatives were studied using density functional theory. We found that the C-H groups played a significant role in the antioxidant activities in non-polar phases. In the gas and benzene phases, rooperol and its derivatives preferentially underwent the free-radical scavenging process via the 3‒CH group by following the hydrogen atom transfer (HAT) mechanism. In polar phases, the sequential proton loss electron transfer (SPLET) was the most preferred mechanism, and the phenolic O‒H groups played a significant role. Additionally, we found that when the hydrogen atom in the OH group was replaced by a glucose moiety, the antioxidant activity of the adjacent OH group was reduced. ROP, DHROP-I, DHROP-II, ROP-4″-G and ROP-4'G have catechol moiety, they may proceed double step-wise mechanisms to trap free radicals. In the gas and benzene phases, the preferable mechanism is dHAT. In water phase, it is SPLHAT.
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Affiliation(s)
- Yan-Zhen Zheng
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Zhong-Min Fu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Geng Deng
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, PR China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Da-Fu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China.
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15
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Shang Y, Ning H, Shi J, Luo SN. Kinetic modeling of methyl pentanoate pyrolysis based on ab initio calculations. Phys Chem Chem Phys 2020; 22:17978-17986. [PMID: 32749410 DOI: 10.1039/d0cp02821e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Recently, methyl pentanoate (MP) was proposed as a viable biodiesel surrogate to petroleum-based fuels. To better understand the pyrolysis chemistry of MP, the unimolecular decomposition kinetics of MP is theoretically investigated on the basis of ab initio calculations; ten primary channels, including four intramolecular H-shifts and six C-C and C-O bond fissions, are identified. The geometries are optimized at the M06-2X/cc-pVTZ level of theory, and accurate barrier heights are determined using the DLPNO-CCSD(T)/CBS(T-Q) method, which shows a good performance against the CCSD(T)/CBS(T-Q) method with an uncertainty of 0.5 kcal mol-1 for small methyl esters. The atomization enthalpy method is adopted to obtain the thermodynamics of involved species. The Rice-Ramsperger-Kassel-Marcus/master equation theory coupled with one-dimensional hindered rotor approximation is employed to calculate the phenomenological rate constants at 500-2000 K and 0.01-100 atm. The branching ratio analysis indicates that two reactions, MP ↔ CH3OC([double bond, length as m-dash]O)CH3 + CH2CHCH3 and MP ↔ CH3OC([double bond, length as m-dash]O)CH2 + CH2CH2CH3, are the dominant channels at low and high temperatures, respectively. The model from Diévart et al. [Proc. Combust. Inst., 2013, 34(1), 821-829] is updated with our calculations, and the modified model can yield a better prediction in reproducing the ignition delay times of MP at high temperatures. This work provides a comprehensive investigation of MP unimolecular decomposition, and can serve as a prototype for understanding the pyrolysis of larger alkyl esters.
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Affiliation(s)
- Yanlei Shang
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031, P. R. China.
| | - Hongbo Ning
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031, P. R. China.
| | - Jinchun Shi
- The Peac Institute of Multiscale Sciences, Chengdu, Sichuan 610031, P. R. China.
| | - Sheng-Nian Luo
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031, P. R. China.
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16
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Prediction of organic homolytic bond dissociation enthalpies at near chemical accuracy with sub-second computational cost. Nat Commun 2020; 11:2328. [PMID: 32393773 PMCID: PMC7214445 DOI: 10.1038/s41467-020-16201-z] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/15/2020] [Indexed: 12/31/2022] Open
Abstract
Bond dissociation enthalpies (BDEs) of organic molecules play a fundamental role in determining chemical reactivity and selectivity. However, BDE computations at sufficiently high levels of quantum mechanical theory require substantial computing resources. In this paper, we develop a machine learning model capable of accurately predicting BDEs for organic molecules in a fraction of a second. We perform automated density functional theory (DFT) calculations at the M06-2X/def2-TZVP level of theory for 42,577 small organic molecules, resulting in 290,664 BDEs. A graph neural network trained on a subset of these results achieves a mean absolute error of 0.58 kcal mol-1 (vs DFT) for BDEs of unseen molecules. We further demonstrate the model on two applications: first, we rapidly and accurately predict major sites of hydrogen abstraction in the metabolism of drug-like molecules, and second, we determine the dominant molecular fragmentation pathways during soot formation.
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Gao Y, Li X, You X. Reaction kinetics of hydrogen addition reactions to methyl butenoate. Phys Chem Chem Phys 2020; 22:5286-5292. [DOI: 10.1039/c9cp06570a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We study the chemical kinetics of hydrogen addition reactions of unsaturated methyl esters, methyl 2-butenoate and methyl 3-butenoate, and compare the rate constants with those of hydrogen abstraction reactions by H atom.
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Affiliation(s)
- Yage Gao
- Center for Combustion Energy
- Tsinghua University
- Beijing 100084
- China
- Key Laboratory for Thermal Science and Power Engineering of the Ministry of Education
| | - Xiaoyu Li
- Center for Combustion Energy
- Tsinghua University
- Beijing 100084
- China
- Key Laboratory for Thermal Science and Power Engineering of the Ministry of Education
| | - Xiaoqing You
- Center for Combustion Energy
- Tsinghua University
- Beijing 100084
- China
- Key Laboratory for Thermal Science and Power Engineering of the Ministry of Education
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18
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Gao Y, You X. On the Prediction of Standard Enthalpy of Formation of C2-C4 Oxygenated Species. J Phys Chem A 2019; 123:11004-11011. [PMID: 31800247 DOI: 10.1021/acs.jpca.9b08516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, to determine an efficient and accurate method for predicting standard enthalpy of formation (ΔfHo) of oxygenated species, we calculated ΔfHo for several typical C2-C4 oxygenated species using atomization and isodesmic reactions in combination with various quantum chemical methods, including six density functional theory methods, three compound methods, and CCSD(T)/CBS. Compared with experimental values, at the same quantum chemical level, ΔfHo values predicted by using isodesmic reactions are more accurate than those using atomization reactions. Comparing various quantum chemical methods when isodesmic reactions are used, the performance of G4 is the best with a mean unsigned deviation (MUE) of 0.3 kcal/mol and a standard deviation (SD) of 0.3 kcal/mol, while M06-2X can predict ΔfHo efficiently and accurately with an MUE of 0.6 kcal/mol and SD of 0.5 kcal/mol. Using the best methods we have found, we calculated the enthalpies of formation and other thermodynamic properties for dimethyl carbonate (DMC) and its associated species and then applied them in a DMC combustion model for predicting ignition delay times. Better agreement with the experiments is achieved when the newly computed thermodynamic properties are adopted.
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Deraet X, Woller T, Van Lommel R, De Proft F, Verniest G, Alonso M. A Benchmark of Density Functional Approximations For Thermochemistry and Kinetics of Hydride Reductions of Cyclohexanones. ChemistryOpen 2019; 8:788-806. [PMID: 31293871 PMCID: PMC6594353 DOI: 10.1002/open.201900085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/10/2019] [Indexed: 11/21/2022] Open
Abstract
The performance of density functionals and wavefunction methods for describing the thermodynamics and kinetics of hydride reductions of 2-substituted cyclohexanones has been evaluated for the first time. A variety of exchange correlation functionals ranging from generalized gradient approximations to double hybrids have been tested and their performance to describe the facial selectivity of hydride reductions of cyclohexanones has been carefully assessed relative to the CCSD(T) method. Among the tested methods, an approach in which single-point energy calculations using the double hybrid B2PLYP-D3 functional on ωB97X-D optimized geometries provides the most accurate transition state energies for these kinetically-controlled reactions. Moreover, the role of torsional strain, temperature, solvation, noncovalent interactions on the stereoselectivity of these reductions was elucidated. Our results indicate a prominent role of the substituent on the cis/trans ratios driven by the delicate interplay between torsional strain and dispersion interactions.
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Affiliation(s)
- Xavier Deraet
- Department of General Chemistry (ALGC)Vrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
| | - Tatiana Woller
- Department of General Chemistry (ALGC)Vrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
| | - Ruben Van Lommel
- Department of General Chemistry (ALGC)Vrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
- Molecular Design and SynthesisDepartment of Chemistry, KU Leuven, Celestijnenlaan 200F Leuven Chem&Tech, box 24043001LeuvenBelgium
| | - Frank De Proft
- Department of General Chemistry (ALGC)Vrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
| | - Guido Verniest
- Research group of Organic Chemistry (ORGC), Departments of Bio-engineering Sciences and ChemistryVrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
| | - Mercedes Alonso
- Department of General Chemistry (ALGC)Vrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
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Debnath S, Sengupta A, Raghavachari K. Eliminating Systematic Errors in DFT via Connectivity-Based Hierarchy: Accurate Bond Dissociation Energies of Biodiesel Methyl Esters. J Phys Chem A 2019; 123:3543-3550. [DOI: 10.1021/acs.jpca.9b01478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sibali Debnath
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Arkajyoti Sengupta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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Gao Y, He T, Li X, You X. Effect of hindered internal rotation treatments on predicting the thermodynamic properties of alkanes. Phys Chem Chem Phys 2019; 21:1928-1936. [PMID: 30632587 DOI: 10.1039/c8cp07308b] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We compare different vibrational analysis methods and examine the effect of hindered internal rotation treatments on predicting thermodynamic properties.
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Affiliation(s)
- Yage Gao
- Center for Combustion Energy
- Tsinghua University
- Beijing 100084
- China
- Key Laboratory for Thermal Science and Power Engineering of the Ministry of Education
| | - Tanjin He
- Center for Combustion Energy
- Tsinghua University
- Beijing 100084
- China
| | - Xiaoyu Li
- Center for Combustion Energy
- Tsinghua University
- Beijing 100084
- China
- Key Laboratory for Thermal Science and Power Engineering of the Ministry of Education
| | - Xiaoqing You
- Center for Combustion Energy
- Tsinghua University
- Beijing 100084
- China
- Key Laboratory for Thermal Science and Power Engineering of the Ministry of Education
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22
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Morgante P, Peverati R. ACCDB: A collection of chemistry databases for broad computational purposes. J Comput Chem 2018; 40:839-848. [DOI: 10.1002/jcc.25761] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/09/2018] [Accepted: 11/11/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Pierpaolo Morgante
- Chemistry Program; Florida Institute of Technology, 150 W. University Blvd.; Melbourne Florida, 32901
| | - Roberto Peverati
- Chemistry Program; Florida Institute of Technology, 150 W. University Blvd.; Melbourne Florida, 32901
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Wu J, Ning H, Ma L, Ren W. Accurate prediction of bond dissociation energies of large n-alkanes using ONIOM-CCSD(T)/CBS methods. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.03.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Zheng Y, Zheng W, Wang J, Chang H, Zhu D. Computational Study on N-N Homolytic Bond Dissociation Enthalpies of Hydrazine Derivatives. J Phys Chem A 2018; 122:2764-2780. [PMID: 29470086 DOI: 10.1021/acs.jpca.7b12094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydrazine derivatives have been regarded as the important building blocks in organic chemistry for the synthesis of organic N-containing compounds. It is important to understand the structure-activity relationship of the thermodynamics of N-N bonds, in particular, their strength as measured by using the homolytic bond dissociation enthalpies (BDEs). We calculated the N-N BDEs of 13 organonitrogen compounds by eight composite high-level ab initio methods including G3, G3B3, G4, G4MP2, CBS-QB3, ROCBS-QB3, CBS-Q, and CBS-APNO. Then 25 density functional theory (DFT) methods were selected for calculating the N-N BDEs of 58 organonitrogen compounds. The M05-2X method can provide the most accurate results with the smallest root-mean-square error (RMSE) of 8.9 kJ/mol. Subsequently, the N-N BDE predictions of different hydrazine derivatives including cycloalkylhydrazines, N-heterocyclic hydrazines, arylhydrazines, and hydrazides as well as the substituent effects were investigated in detail by using the M05-2X method. In addition, the analysis including the natural bond orbital (NBO) as well as the energies of frontier orbitals were performed in order to further understand the essence of the N-N BDE change patterns.
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Affiliation(s)
- Yuanyuan Zheng
- College of Chemistry and Chemical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Wenrui Zheng
- College of Chemistry and Chemical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Jiaoyang Wang
- College of Chemistry and Chemical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Huifang Chang
- College of Chemistry and Chemical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Danfeng Zhu
- College of Chemistry and Chemical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
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25
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Trends in bond dissociation energies of brominated flame retardants from density functional theory. Struct Chem 2018. [DOI: 10.1007/s11224-018-1078-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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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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27
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Hou D, You X. Reaction kinetics of hydrogen abstraction from polycyclic aromatic hydrocarbons by H atoms. Phys Chem Chem Phys 2017; 19:30772-30780. [PMID: 29134219 DOI: 10.1039/c7cp04964a] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We studied how the PAH structure, site, and size affect the rate constants of hydrogen abstraction reactions of PAH systematically.
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Affiliation(s)
- Dingyu Hou
- 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
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28
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Yu HS, He X, Li SL, Truhlar DG. MN15: A Kohn-Sham global-hybrid exchange-correlation density functional with broad accuracy for multi-reference and single-reference systems and noncovalent interactions. Chem Sci 2016; 7:5032-5051. [PMID: 30155154 PMCID: PMC6018516 DOI: 10.1039/c6sc00705h] [Citation(s) in RCA: 709] [Impact Index Per Article: 88.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/06/2016] [Indexed: 01/12/2023] Open
Abstract
Kohn-Sham density functionals are widely used; however, no currently available exchange-correlation functional can predict all chemical properties with chemical accuracy. Here we report a new functional, called MN15, that has broader accuracy than any previously available one. The properties considered in the parameterization include bond energies, atomization energies, ionization potentials, electron affinities, proton affinities, reaction barrier heights, noncovalent interactions, hydrocarbon thermochemistry, isomerization energies, electronic excitation energies, absolute atomic energies, and molecular structures. When compared with 82 other density functionals that have been defined in the literature, MN15 gives the second smallest mean unsigned error (MUE) for 54 data on inherently multiconfigurational systems, the smallest MUE for 313 single-reference chemical data, and the smallest MUE on 87 noncovalent data, with MUEs for these three categories of 4.75, 1.85, and 0.25 kcal mol-1, respectively, as compared to the average MUEs of the other 82 functionals of 14.0, 4.63, and 1.98 kcal mol-1. The MUE for 17 absolute atomic energies is 7.4 kcal mol-1 as compared to an average MUE of the other 82 functionals of 34.6 kcal mol-1. We further tested MN15 for 10 transition-metal coordination energies, the entire S66x8 database of noncovalent interactions, 21 transition-metal reaction barrier heights, 69 electronic excitation energies of organic molecules, 31 semiconductor band gaps, seven transition-metal dimer bond lengths, and 193 bond lengths of 47 organic molecules. The MN15 functional not only performs very well for our training set, which has 481 pieces of data, but also performs very well for our test set, which has 823 data that are not in our training set. The test set includes both ground-state properties and molecular excitation energies. For the latter MN15 achieves simultaneous accuracy for both valence and Rydberg electronic excitations when used with linear-response time-dependent density functional theory, with an MUE of less than 0.3 eV for both types of excitations.
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Affiliation(s)
- Haoyu S Yu
- Department of Chemistry , Chemical Theory Center , Inorganometallic Catalyst Design Center , Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , USA .
| | - Xiao He
- Department of Chemistry , Chemical Theory Center , Inorganometallic Catalyst Design Center , Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , USA .
- State Key Laboratory of Precision Spectroscopy and Department of Physics , East China Normal University , Shanghai , 200062 , China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China
| | - Shaohong L Li
- Department of Chemistry , Chemical Theory Center , Inorganometallic Catalyst Design Center , Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , USA .
| | - Donald G Truhlar
- Department of Chemistry , Chemical Theory Center , Inorganometallic Catalyst Design Center , Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , USA .
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