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García-Andrade X, García Tahoces P, Pérez-Ríos J, Martínez Núñez E. Barrier Height Prediction by Machine Learning Correction of Semiempirical Calculations. J Phys Chem A 2023; 127:2274-2283. [PMID: 36877614 PMCID: PMC10845151 DOI: 10.1021/acs.jpca.2c08340] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/19/2023] [Indexed: 03/07/2023]
Abstract
Different machine learning (ML) models are proposed in the present work to predict density functional theory-quality barrier heights (BHs) from semiempirical quantum mechanical (SQM) calculations. The ML models include a multitask deep neural network, gradient-boosted trees by means of the XGBoost interface, and Gaussian process regression. The obtained mean absolute errors are similar to those of previous models considering the same number of data points. The ML corrections proposed in this paper could be useful for rapid screening of the large reaction networks that appear in combustion chemistry or in astrochemistry. Finally, our results show that 70% of the features with the highest impact on model output are bespoke predictors. This custom-made set of predictors could be employed by future Δ-ML models to improve the quantitative prediction of other reaction properties.
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Affiliation(s)
| | - Pablo García Tahoces
- Department
of Electronics and Computer Science, University
of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Jesús Pérez-Ríos
- Department
of Physics, Stony Brook University, Stony Brook, New York 11794, United States
- Institute
for Advanced Computational Science, Stony
Brook University, Stony
Brook, New York 11794-3800, United States
| | - Emilio Martínez Núñez
- Department
of Physical Chemistry, University of Santiago
de Compostela, Santiago
de Compostela 15782, Spain
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2
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A Trajectory-Based Method to Explore Reaction Mechanisms. Molecules 2018; 23:molecules23123156. [PMID: 30513663 PMCID: PMC6321347 DOI: 10.3390/molecules23123156] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/23/2018] [Accepted: 11/29/2018] [Indexed: 12/02/2022] Open
Abstract
The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present review, its application to solve mechanistic/kinetics problems in different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described.
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Pérez-Soto R, Vázquez SA, Martínez-Núñez E. Photodissociation of acryloyl chloride at 193 nm: interpretation of the product energy distributions, and new elimination pathways. Phys Chem Chem Phys 2016; 18:5019-26. [DOI: 10.1039/c5cp07759a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of an automated TS search method leads to the finding of novel HCl elimination pathways.
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Affiliation(s)
- Raúl Pérez-Soto
- Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Campus Vida
- Universidade de Santiago de Compostela
- Santiago de Compostela
- Spain
| | - Saulo A. Vázquez
- Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Campus Vida
- Universidade de Santiago de Compostela
- Santiago de Compostela
- Spain
| | - Emilio Martínez-Núñez
- Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Campus Vida
- Universidade de Santiago de Compostela
- Santiago de Compostela
- Spain
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Vázquez SA, Martínez-Núñez E. HCN elimination from vinyl cyanide: product energy partitioning, the role of hydrogen–deuterium exchange reactions and a new pathway. Phys Chem Chem Phys 2015; 17:6948-55. [DOI: 10.1039/c4cp05626d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A schematic diagram of HCN elimination channels from vinyl cyanide including a new CCdiss pathway.
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Affiliation(s)
- Saulo A. Vázquez
- Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares
- Campus Vida
- Universidade de Santiago de Compostela
- Santiago de Compostela
- Spain
| | - Emilio Martínez-Núñez
- Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares
- Campus Vida
- Universidade de Santiago de Compostela
- Santiago de Compostela
- Spain
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Homayoon Z, Vázquez SA, Rodríguez-Fernández R, Martínez-Núñez E. Ab Initio and RRKM Study of the HCN/HNC Elimination Channels from Vinyl Cyanide. J Phys Chem A 2011; 115:979-85. [DOI: 10.1021/jp109843a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zahra Homayoon
- Departamento de Química Física y Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71454, Iran
| | - Saulo A. Vázquez
- Departamento de Química Física y Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Roberto Rodríguez-Fernández
- Departamento de Química Física y Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Emilio Martínez-Núñez
- Departamento de Química Física y Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Vázquez SA, Martínez-Núñez E. Translational energy distributions in the photodissociation of fluorobenzene. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Xu H, Kiefer JH, Sivaramakrishnan R, Giri BR, Tranter RS. Shock tube study of dissociation and relaxation in 1,1-difluoroethane and vinyl fluoride. Phys Chem Chem Phys 2007; 9:4164-76. [PMID: 17687466 DOI: 10.1039/b703124f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper reports measurements of the thermal dissociation of 1,1-difluoroethane in the shock tube. The experiments employ laser-schlieren measurements of rate for the dominant HF elimination using 10% 1,1-difluoroethane in Kr over 1500-2000 K and 43 < P < 424 torr. The vinyl fluoride product of this process then dissociates affecting the late observations. We thus include a laser schlieren study (1717-2332 K, 75 < P < 482 torr in 10 and 4% vinyl fluoride in Kr) of this dissociation. This latter work also includes a set of experiments using shock-tube time-of-flight mass spectrometry (4% vinyl fluoride in neon, 1500-1980 K, 500 < P < 1300 torr). These time-of-flight experiments confirm the theoretical expectation that the only reaction in vinyl fluoride is HF elimination. The dissociation experiments are augmented by laser schlieren measurements of vibrational relaxation (1-20% C(2)H(3)F in Kr, 415-1975 K, 5 < P < 50 torr, and 2 and 5% C(2)H(4)F(2) in Kr, 700-1350 K, 6 < P < 22 torr). These experiments exhibit very rapid relaxation, and incubation delays should be negligible in dissociation. An RRKM model of dissociation in 1,1-difluoroethane based on a G3B3 calculation of barrier and other properties fits the experiments but requires a very large DeltaE(down) of 1600 cm(-1), similar to that found in a previous examination of 1,1,1-trifluoroethane. Dissociation of vinyl fluoride is complicated by the presence of two parallel HF eliminations, both three-center and four-center. Structure calculations find nearly equal barriers for these, and TST calculations show almost identical k(infinity). An RRKM fit to the observed falloff again requires an unusually large DeltaE(down) and the experiments actually support a slightly reduced barrier. These large energy-transfer parameters now seem routine in these large fluorinated species. It is perhaps a surprising result for which there is as yet no explanation.
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Affiliation(s)
- Hui Xu
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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Martínez-Núñez E, Vázquez S. Rovibrational distributions of HF in the photodissociation of vinyl fluoride at 193 nm: a direct MP2 quasiclassical trajectory study. J Chem Phys 2006; 121:5179-82. [PMID: 15352810 DOI: 10.1063/1.1782531] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Quasiclassical trajectory calculations were performed to calculate rovibrational distributions of the nascent HF fragment in the photodissociation of vinyl fluoride at 193 nm. The trajectories were initiated at the transition states of the four-center (4C) and three-center (3C) HF elimination channels, using a microcanonical, quasiclassical normal-mode sampling. In general, the calculated distributions are in reasonably good agreement with experiment. In particular, the trajectory distributions show bimodal character, although not as pronounced as that observed experimentally. The calculations predict that the 3C and 4C distributions are rather similar to each other, which suggests that the low-J and high-J components of the rotational distributions cannot be specifically assigned to each of these channels.
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Affiliation(s)
- Emilio Martínez-Núñez
- Departamento de Quimica Fisica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Lee SH, Chen WK, Chaudhuri C, Huang WJ, Lee YT. Photodissociation dynamics of vinyl fluoride (CH2CHF) at 157 and 193nm: Distributions of kinetic energy and branching ratios. J Chem Phys 2006; 125:144315. [PMID: 17042598 DOI: 10.1063/1.2357946] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using photofragment translational spectroscopy and tunable vacuum-ultraviolet ionization, we measured the time-of-flight spectra of fragments upon photodissociation of vinyl fluoride (CH2CHF) at 157 and 193 nm. Four primary dissociation pathways--elimination of atomic F, atomic H, molecular HF, and molecular H2--are identified at 157 nm. Dissociation to C2H3 + F is first observed in the present work. Decomposition of internally hot C2H3 and C2H2F occurs spontaneously. The barrier heights of CH2CH --> CHCH + H and cis-CHCHF --> CHCH + F are evaluated to be 40+/-2 and 44+/-2 kcal mol(-1), respectively. The photoionization yield spectra indicate that the C2H3 and C2H2F radicals have ionization energies of 8.4+/-0.1 and 8.8+/-0.1 eV, respectively. Universal detection of photoproducts allowed us to determine the total branching ratios, distributions of kinetic energy, average kinetic energies, and fractions of translational energy release for all dissociation pathways of vinyl fluoride. In contrast, on optical excitation at 193 nm the C2H2 + HF channel dominates whereas the C2H3 + F channel is inactive. This reaction C2H3F --> C2H2 + HF occurs on the ground surface of potential energy after excitation at both wavelengths of 193 and 157 nm, indicating that internal conversion from the photoexcited state to the electronic ground state of vinyl fluoride is efficient. We computed the electronic energies of products and the ionization energies of fluorovinyl radicals.
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Affiliation(s)
- Shih-Huang Lee
- National Synchrotron Radiation Research Center (NSRRC), 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 30076, Taiwan.
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Martínez-Núñez E, Vázquez S. Rotational distributions of HBr in the photodissociation of vinyl bromide at 193nm: An investigation by direct quasiclassical trajectory calculations. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Martínez-Núñez E, Vázquez S. Quasiclassical trajectory calculations on the photodissociation of CF2CHCl at 193 nm: product energy distributions for the HF and HCl eliminations. J Chem Phys 2006; 122:104316. [PMID: 15836324 DOI: 10.1063/1.1859276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Quasiclassical trajectory calculations were carried out to determine product energy distributions for the HCl and HF eliminations that take place in the photodissociation of 2-chloro-1,1-difluoroethylene at 193 nm. The trajectories were initiated at the transition states of the HCl and HF elimination channels under microcanonical, quasiclassical conditions, and were propagated with the energies and gradients taken directly from density functional theory calculations. Good agreement with experiment is found, except for the translational energy distribution of the HF elimination channel and the average vibrational energy of the HCl fragment. Possible sources of disagreement are discussed.
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Affiliation(s)
- Emilio Martínez-Núñez
- Departamento de Química Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Kunsági-Máté S, Végh E, Nagy G, Kollár L. Quantum chemical investigations on the dynamics of hydrogen halide elimination from vinyl-halides: influence of the molecular environment. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.02.075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Vázquez SA, Aoiz FJ, Bañares L, Santamarı́a J, Martı́nez-Núñez E, Fernández-Ramos A. Quasi-classical trajectory study of H2 elimination in the photodissociation of difluoroethylenes at 193 nm. J Chem Phys 2003. [DOI: 10.1063/1.1559678] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Affiliation(s)
- John E Baldwin
- Department of Chemistry, Syracuse University, Syracuse, New York 13203, USA
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González-Vázquez J, Fernández-Ramos A, Martínez-Núñez E, Vázquez SA. Dissociation of Difluoroethylenes. I. Global Potential Energy Surface, RRKM, and VTST Calculations. J Phys Chem A 2003. [DOI: 10.1021/jp021901s] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jesús González-Vázquez
- Departamento de Química Física, Universidad de Santiago de Compostela, Santiago de Compostela, E-15706, Spain
| | - Antonio Fernández-Ramos
- Departamento de Química Física, Universidad de Santiago de Compostela, Santiago de Compostela, E-15706, Spain
| | - Emilio Martínez-Núñez
- Departamento de Química Física, Universidad de Santiago de Compostela, Santiago de Compostela, E-15706, Spain
| | - Saulo A. Vázquez
- Departamento de Química Física, Universidad de Santiago de Compostela, Santiago de Compostela, E-15706, Spain
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Kunsági-Máté S, Végh E, Nagy G, Kollár L. Influence of the Molecular Environment on the Three-Center versus Four-Center Elimination of HBr from Vinyl Bromide: A Theoretical Approach. J Phys Chem A 2002. [DOI: 10.1021/jp014512r] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sándor Kunsági-Máté
- Department of General and Physical Chemistry, University of Pécs, H-7624 Pécs, Hungary, Department of Inorganic Chemistry, University of Pécs, H-7624 Pécs, Hungary, and Research Group for Chemical Sensors of the Hungarian Academy of Sciences, H-7624 Pécs, Hungary
| | - Eszter Végh
- Department of General and Physical Chemistry, University of Pécs, H-7624 Pécs, Hungary, Department of Inorganic Chemistry, University of Pécs, H-7624 Pécs, Hungary, and Research Group for Chemical Sensors of the Hungarian Academy of Sciences, H-7624 Pécs, Hungary
| | - Géza Nagy
- Department of General and Physical Chemistry, University of Pécs, H-7624 Pécs, Hungary, Department of Inorganic Chemistry, University of Pécs, H-7624 Pécs, Hungary, and Research Group for Chemical Sensors of the Hungarian Academy of Sciences, H-7624 Pécs, Hungary
| | - László Kollár
- Department of General and Physical Chemistry, University of Pécs, H-7624 Pécs, Hungary, Department of Inorganic Chemistry, University of Pécs, H-7624 Pécs, Hungary, and Research Group for Chemical Sensors of the Hungarian Academy of Sciences, H-7624 Pécs, Hungary
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Martínez-Núñez E, Marques JMC, Vázquez SA. A direct dynamics study of the H2 elimination from 2,5-dihydrofuran. J Chem Phys 2001. [DOI: 10.1063/1.1409359] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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18
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McKee ML. Proposed fluorination mechanism of CB(5)H(6)(-) and CB(9)H(10)(-) with HF. Evidence of kinetic control in the formation of 2-CB(5)H(5)F(-) and 6-CB(9)H(9)F(-). Inorg Chem 2001; 40:5612-9. [PMID: 11599961 DOI: 10.1021/ic010176h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Two pathways have been considered in the fluorination of CB(5)H(6)(-) and CB(9)H(10)(-) by HF. In the ionic HF fluorination pathway, the monocarborane anion cage is first protonated in a BBB face followed by H(2) elimination and fluoride anion addition. In the covalent HF fluorination pathway, HF is first coordinated through hydrogen to the BBB face. Next, the fluorine can add to either an axial or equatorial boron atom which opens the cage to a nido structure with an endo fluoride substituent. Endo to exo rearrangement occurs with a small activation barrier followed by H(2) elimination. In both pathways, fluorination at the equatorial boron position is predicted to have smaller activation barriers even though substitution at the axial position leads to the more stable products.
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Affiliation(s)
- M L McKee
- Department of Chemistry, Auburn University, Auburn, Alabama 36849, USA
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Martínez-Núñez E, Vázquez SA. Anharmonic Quasiclassical Barrier Samplings in Trajectory Calculations and Their Influence on the Computed Product Energy Distributions. J Phys Chem A 2001. [DOI: 10.1021/jp004267w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Emilio Martínez-Núñez
- Departamento de Química Física, Universidad de Santiago de Compostela, Santiago de Compostela E-15706, Spain
| | - Saulo A. Vázquez
- Departamento de Química Física, Universidad de Santiago de Compostela, Santiago de Compostela E-15706, Spain
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