1
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Steffen J. Caracal: A Versatile Ring Polymer Molecular Dynamics Simulation Package. J Chem Theory Comput 2023; 19:5334-5355. [PMID: 37555628 DOI: 10.1021/acs.jctc.3c00568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
A new open-source program package named Caracal covering simulations of molecular systems with ring polymer molecular dynamics (RPMD) is presented. It combines a powerful RPMD implementation including chemical reaction rate calculations and biased periodic and nonperiodic samplings with a collection of easy to set up potential energy surface (PES) methodologies, thus delivering an all-inclusive approach. Most implemented PESs are based on the QMDFF and EVB-QMDFF methods. Where the quantum mechanically derived force field (QMDFF) can be set up for an arbitrary molecular system in a black-box fashion, the empirical valence bond (EVB)-QMDFF connects two QMDFFs and is able to represent the PES of a chemical reaction. With our previously published flavors of this composite method, PESs for almost arbitrary gas phase thermal ground state reactions can be set up. Given an optimized reaction path, the mechanism of the reaction can be classified and RPMD rate constants can be obtained via umbrella sampling and recrossing calculations on an EVB-QMDFF PES. Further, QMDFFs can be polymerized for the description of liquid systems. In this paper, the internal structure as well as the handling philosophy of Caracal are outlined. Further, examples of the different possible kinds of calculations are given.
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Affiliation(s)
- Julien Steffen
- Chair of Theoretical Chemistry, Friedrich-Alexander University Erlangen-Nürnberg, Egerlandstraße 3, 91058 Erlangen, Bavaria, Germany
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2
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Espinosa‐Garcia J. Kinetics study of the OH + SiH
4
hydrogen abstraction reaction: A theoretical analysis. INT J CHEM KINET 2022. [DOI: 10.1002/kin.21593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Joaquín Espinosa‐Garcia
- Departamento de Química Física and Instituto de Computación Científica Avanzada Universidad de Extremadura Badajoz Spain
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3
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Espinosa-Garcia J, Rangel C, Corchado JC. Current Status of the X + C 2H 6 [X ≡ H, F( 2P), Cl( 2P), O( 3P), OH] Hydrogen Abstraction Reactions: A Theoretical Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123773. [PMID: 35744901 PMCID: PMC9228020 DOI: 10.3390/molecules27123773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022]
Abstract
This paper is a detailed review of the chemistry of medium-size reactive systems using the following hydrogen abstraction reactions with ethane, X + C2H6 → HX + C2H5; X ≡ H, F(2P), Cl(2P), O(3P) and OH, and focusing attention mainly on the theoretical developments. These bimolecular reactions range from exothermic to endothermic systems and from barrierless to high classical barriers of activation. Thus, the topography of the reactive systems changes from reaction to reaction with the presence or not of stabilized intermediate complexes in the entrance and exit channels. The review begins with some reflections on the inherent problems in the theory/experiment comparison. When one compares kinetics or dynamics theoretical results with experimental measures, one is testing both the potential energy surface describing the nuclei motion and the kinetics or dynamics method used. Discrepancies in the comparison may be due to inaccuracies of the surface, limitations of the kinetics or dynamics methods, and experimental uncertainties that also cannot be ruled out. The paper continues with a detailed review of some bimolecular reactions with ethane, beginning with the reactions with hydrogen atoms. The reactions with halogens present a challenge owing to the presence of stabilized intermediate complexes in the entrance and exit channels and the influence of the spin-orbit states on reactivity. Reactions with O(3P) atoms lead to three surfaces, which is an additional difficulty in the theoretical study. Finally, the reactions with the hydroxyl radical correspond to a reactive system with ten atoms and twenty-four degrees of freedom. Throughout this review, different strategies in the development of analytical potential energy surfaces describing these bimolecular reactions have been critically analyzed, showing their advantages and limitations. These surfaces are fitted to a large number of ab initio calculations, and we found that a huge number of calculations leads to accurate surfaces, but this information does not guarantee that the kinetics and dynamics results match the experimental measurements.
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4
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Zhou Y, Cao Q, Yang Y, Ma D, Zhu Q, Ma J. Effect of (H 2O) n ( n = 0–3, 13) on the NH 3 + OH reaction in the gas and liquid phases. RSC Adv 2022; 12:28010-28019. [PMID: 36320266 PMCID: PMC9524257 DOI: 10.1039/d2ra04931g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
We studied the effect of water clusters on the NH3 + OH reaction at both the DFT and CCSD(T) levels. The calculated rate constants for the pure reaction are 2.07 × 10−13 and 1.35 × 10−13 cm3 molecule−1 s−1 in the gas and liquid phases, respectively, and the gas-phase rate constants are consistent with the corresponding experimental result (1.70 × 10−13 cm3 molecule−1 s−1), while the liquid-phase rate constants are slightly smaller than the experimental value (5.84 × 10−12 cm3 molecule−1 s−1). In the gas phase, the presence of (H2O)n (n = 1–3) decreases the rate constant compared to the pure NH3 + OH reaction, and these results are in agreement with many reported H2O-catalyzed reactions. For the liquid phase reaction, compared with the case of n = 0–3, when the size of the water molecule cluster surrounding the OH radical is n = 13, the rate constant of the title reaction increases. Our study also shows that proton transfer is also a factor which accelerates the liquid phase NH3 + OH reaction. We used DFT and CCSD(T) methods with PCM solvation model to study the water cluster effect and solvation effect on the NH3 + OH reaction.![]()
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Affiliation(s)
- Yujie Zhou
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, 610065, China
| | - Qi Cao
- Reactor Operation and Application Research Sub-Institute, Nuclear Power Institute of China, Chengdu 610041, China
| | - Yu Yang
- Reactor Operation and Application Research Sub-Institute, Nuclear Power Institute of China, Chengdu 610041, China
| | - Dandan Ma
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, 610065, China
| | - Quan Zhu
- School of Chemical Engineering, Sichuan University, Chengdu, 610065, PR China
- Engineering Research Center of Combustion and Cooling for Aerospace Power, Ministry of Education, Sichuan University, Chengdu, 610065, PR China
| | - Jianyi Ma
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, 610065, China
- Engineering Research Center of Combustion and Cooling for Aerospace Power, Ministry of Education, Sichuan University, Chengdu, 610065, PR China
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5
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Acosta Y, Gerber RB, Varner ME. Oxidation mechanism of ammonia in water clusters. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1983057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Yanitza Acosta
- Chemistry and Biochemistry Department, Iona College, New Rochelle, NY, USA
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, CA, USA
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem, Israel
| | - Mychel E. Varner
- Chemistry and Biochemistry Department, Iona College, New Rochelle, NY, USA
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6
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Saito K, Sugiura Y, Miyazaki T, Takahashi Y, Takayanagi T. Quantum calculations of the photoelectron spectra of the OH -·NH 3 anion: implications for OH + NH 3→ H 2O + NH 2 reaction dynamics. Phys Chem Chem Phys 2021; 23:6950-6958. [PMID: 33729225 DOI: 10.1039/d0cp06514e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present the results of quantum dynamics calculations for analyzing the experimentally measured photoelectron spectra of the OH-·NH3 anion complex. Detachment of an excess electron of OH-·NH3 initially produces a molecular arrangement, which is close to the transition-state structure of the neutral OH + NH3→ H2O + NH2 hydrogen abstraction reaction due to the Franck-Condon principle, and thus finally leads to the OH + NH3 or H2O + NH2 asymptotic channel. We used both the path integral method and the reduced-dimensionality quantum wave packet method to simulate the photoelectron spectra of the OH-·NH3 anion. The calculated spectra were found to be in qualitative agreement with the experimental spectra. It was found that the photodetached complex mainly dissociates into the OH + NH3 channel; however, we found that the hydrogen exchange process also contributes to the photodetachment spectra.
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Affiliation(s)
- Kohei Saito
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan.
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7
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Quasi-Classical Trajectory Study of the CN + NH 3 Reaction Based on a Global Potential Energy Surface. Molecules 2021; 26:molecules26040994. [PMID: 33668582 PMCID: PMC7918900 DOI: 10.3390/molecules26040994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/17/2022] Open
Abstract
Based on a combination of valence-bond and molecular mechanics functions which were fitted to high-level ab initio calculations, we constructed an analytical full-dimensional potential energy surface, named PES-2020, for the hydrogen abstraction title reaction for the first time. This surface is symmetrical with respect to the permutation of the three hydrogens in ammonia, it presents numerical gradients and it improves the description presented by previous theoretical studies. In order to analyze its quality and accuracy, stringent tests were performed, exhaustive kinetics and dynamics studies were carried out using quasi-classical trajectory calculations, and the results were compared with the available experimental evidence. Firstly, the properties (geometry, vibrational frequency and energy) of all stationary points were found to reasonably reproduce the ab initio information used as input; due to the complicated topology with deep wells in the entrance and exit channels and a “submerged” transition state, the description of the intermediate complexes was poorer, although it was adequate to reasonably simulate the kinetics and dynamics of the title reaction. Secondly, in the kinetics study, the rate constants simulated the experimental data in the wide temperature range of 25–700 K, improving the description presented by previous theoretical studies. In addition, while previous studies failed in the description of the kinetic isotope effects, our results reproduced the experimental information. Finally, in the dynamics study, we analyzed the role of the vibrational and rotational excitation of the CN(v,j) reactant and product angular scattering distribution. We found that vibrational excitation by one quantum slightly increased reactivity, thus reproducing the only experimental measurement, while rotational excitation strongly decreased reactivity. The scattering distribution presented a forward-backward shape, associated with the presence of deep wells along the reaction path. These last two findings await experimental confirmation.
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8
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Elishav O, Mosevitzky Lis B, Miller EM, Arent DJ, Valera-Medina A, Grinberg Dana A, Shter GE, Grader GS. Progress and Prospective of Nitrogen-Based Alternative Fuels. Chem Rev 2020; 120:5352-5436. [PMID: 32501681 DOI: 10.1021/acs.chemrev.9b00538] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Alternative fuels are essential to enable the transition to a sustainable and environmentally friendly energy supply. Synthetic fuels derived from renewable energies can act as energy storage media, thus mitigating the effects of fossil fuels on environment and health. Their economic viability, environmental impact, and compatibility with current infrastructure and technologies are fuel and power source specific. Nitrogen-based fuels pose one possible synthetic fuel pathway. In this review, we discuss the progress and current research on utilization of nitrogen-based fuels in power applications, covering the complete fuel cycle. We cover the production, distribution, and storage of nitrogen-based fuels. We assess much of the existing literature on the reactions involved in the ammonia to nitrogen atom pathway in nitrogen-based fuel combustion. Furthermore, we discuss nitrogen-based fuel applications ranging from combustion engines to gas turbines, as well as their exploitation by suggested end-uses. Thereby, we evaluate the potential opportunities and challenges of expanding the role of nitrogen-based molecules in the energy sector, outlining their use as energy carriers in relevant fields.
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Affiliation(s)
- Oren Elishav
- The Nancy and Stephen Grand Technion Energy Program, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Bar Mosevitzky Lis
- The Wolfson Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Elisa M Miller
- Materials and Chemical Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Douglas J Arent
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Agustin Valera-Medina
- College of Physical Sciences and Engineering, Cardiff University, Wales, United Kingdom
| | - Alon Grinberg Dana
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gennady E Shter
- The Wolfson Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Gideon S Grader
- The Nancy and Stephen Grand Technion Energy Program, Technion - Israel Institute of Technology, Haifa 3200003, Israel.,The Wolfson Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
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9
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Espinosa-Garcia J, García-Chamorro M, Corchado JC. Rethinking the description of water product in polyatomic OH/OD + XH (X ≡ D, Br, NH2 and GeH3) reactions: theory/experimental comparison. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-2577-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Liu C, Kelley CT, Jakubikova E. Molecular Dynamics Simulations on Relaxed Reduced-Dimensional Potential Energy Surfaces. J Phys Chem A 2019; 123:4543-4554. [PMID: 31038956 DOI: 10.1021/acs.jpca.9b02298] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulations with full-dimensional potential energy surfaces (PESs) obtained from high-level ab initio calculations are frequently used to model reaction dynamics of small molecules (i.e., molecules with up to 10 atoms). Construction of full-dimensional PESs for larger molecules is, however, not feasible since the number of ab initio calculations required grows rapidly with the increase of dimension. Only a small number of coordinates are often essential for describing the reactivity of even very large systems, and reduced-dimensional PESs with these coordinates can be built for reaction dynamics studies. While analytical methods based on transition-state theory framework are well established for analyzing the reduced-dimensional PESs, MD simulation algorithms capable of generating trajectories on such surfaces are more rare. In this work, we present a new MD implementation that utilizes the relaxed reduced-dimensional PES for standard microcanonical (NVE) and canonical (NVT) MD simulations. The method is applied to the pyramidal inversion of a NH3 molecule. The results from the MD simulations on a reduced, three-dimensional PES are validated against the ab initio MD simulations, as well as MD simulations on full-dimensional PES and experimental data.
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11
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Steffen J. A new class of reaction path based potential energy surfaces enabling accurate black box chemical rate constant calculations. J Chem Phys 2019; 150:154105. [DOI: 10.1063/1.5092589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Julien Steffen
- Institut für Physikalische Chemie, Christian-Albrechts-Universität, Olshausenstraße 40, D–24098 Kiel, Germany
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12
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Nguyen TL, Stanton JF. High-level theoretical study of the reaction between hydroxyl and ammonia: Accurate rate constants from 200 to 2500 K. J Chem Phys 2018; 147:152704. [PMID: 29055339 DOI: 10.1063/1.4986151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hydrogen abstraction from NH3 by OH to produce H2O and NH2-an important reaction in combustion of NH3 fuel-was studied with a theoretical approach that combines high level quantum chemistry and advanced chemical kinetics methods. Thermal rate constants calculated from first principles agree well (within 5%-20%) with available experimental data over a temperature range that extends from 200 to 2500 K. Quantum mechanical tunneling effects were found to be important; they lead to a decided curvature and non-Arrhenius behavior for the rate constant.
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Affiliation(s)
- Thanh Lam Nguyen
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - John F Stanton
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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13
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Espinosa-Garcia J, Corchado JC, Garcia-Chamorro M, Rangel C. F(2P) + C2H6 → HF + C2H5 kinetics study based on a new analytical potential energy surface. Phys Chem Chem Phys 2018; 20:19860-19870. [DOI: 10.1039/c8cp03103g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An exhaustive kinetics study was performed for the title reaction using two theoretical approaches: variational transition-state theory and quasi-classical trajectory calculations, based on an original new analytical full-dimensional potential energy surface, named PES-2018, which has been fitted to high-level ab initio calculations.
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Affiliation(s)
- J. Espinosa-Garcia
- Departamento de Química Física and Instituto de Computacion Cientifica Avanzada
- Universidad de Extremadura
- 06071 Badajoz
- Spain
| | - J. C. Corchado
- Departamento de Química Física and Instituto de Computacion Cientifica Avanzada
- Universidad de Extremadura
- 06071 Badajoz
- Spain
| | - M. Garcia-Chamorro
- Departamento de Química Física and Instituto de Computacion Cientifica Avanzada
- Universidad de Extremadura
- 06071 Badajoz
- Spain
| | - C. Rangel
- Departamento de Química Física and Instituto de Computacion Cientifica Avanzada
- Universidad de Extremadura
- 06071 Badajoz
- Spain
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14
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Affiliation(s)
- Rommel B. Viana
- Departamento de Química e Física Molecular, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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15
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Espinosa-Garcia J, Rangel C, Suleimanov YV. Kinetics study of the CN + CH4 hydrogen abstraction reaction based on a new ab initio analytical full-dimensional potential energy surface. Phys Chem Chem Phys 2017; 19:19341-19351. [DOI: 10.1039/c7cp03499g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed an analytical full-dimensional potential energy surface, named PES-2017, for the gas-phase hydrogen abstraction reaction between the cyano radical and methane.
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Affiliation(s)
- Joaquin Espinosa-Garcia
- Departamento de Química Física and Instituto de Computación Científica Avanzada
- Universidad de Extremadura
- Badajoz
- Spain
| | - Cipriano Rangel
- Departamento de Química Física and Instituto de Computación Científica Avanzada
- Universidad de Extremadura
- Badajoz
- Spain
| | - Yury V. Suleimanov
- Computation-based Science and Technology Research Center
- Cyprus Institute
- Nicosia 2121
- Cyprus
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16
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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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17
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Long B, Tan XF, Wang YB, Li J, Ren DS, Zhang WJ. Theoretical Studies on Reactions of OH with H2SO4…NH3Complex and NH2with H2SO4in the Presence of Water. ChemistrySelect 2016. [DOI: 10.1002/slct.201600194] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Bo Long
- College of Information Engineering; Guizhou Minzu University; Guiyang 550025 China
| | - Xing-Feng Tan
- College of Information Engineering; Guizhou Minzu University; Guiyang 550025 China
| | - Yi-Bo Wang
- Key Laboratory of Guizhou High Performance Computational Chemistry; Department of Chemistry; Guizhou University; Guiyang 550025 China
| | - Jun Li
- Department of Chemistry & Laboratory of Organic; Optoelectronics and Molecular Engineering of the Ministry of Education; Tsinghua University; Beijing 100084 China
| | - Da-Sen Ren
- College of Information Engineering; Guizhou Minzu University; Guiyang 550025 China
| | - Wei-Jun Zhang
- Laboratory of Atmospheric Physico-Chemistry; Anhui Institute of Optics and Fine Mechanics; Chinese Academy of Sciences; Hefei 230031 China
- Key Laboratory of Atmospheric Composition and Optical Radiation; Anhui Institute of Optics and Fine Mechanics; Chinese Academy of Sciences; Hefei 230031 China
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18
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Espinosa-Garcia J, Corchado J, Bonnet L. Quasi-classical trajectory study of the water vibrational distribution for the polyatomic OH/OD+NH3 reactions: Comparison with experiment. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.12.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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19
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Theoretical study on the mechanism and kinetics of atmospheric reactions C n H2n+2 + NH2 (n = 1–3). Struct Chem 2014. [DOI: 10.1007/s11224-014-0500-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Anglada JM, Olivella S, Solé A. Unexpected Reactivity of Amidogen Radical in the Gas Phase Degradation of Nitric Acid. J Am Chem Soc 2014; 136:6834-7. [DOI: 10.1021/ja501967x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Josep M. Anglada
- Departament
de Química Biològica i Modelització Molecular,
(IQAC-CSIC), Jordi Girona,
18-26, E-08034 Barcelona, Catalonia, Spain
| | - Santiago Olivella
- Departament
de Química Biològica i Modelització Molecular,
(IQAC-CSIC), Jordi Girona,
18-26, E-08034 Barcelona, Catalonia, Spain
| | - Albert Solé
- Departament
de Química Física i Institut de Química Teòrica
i Computacional (IQTCUB). Universitat de Barcelona, Martí
i Franqués, 1, E-08028 Barcelona, Catalonia, Spain
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21
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Monge-Palacios M, Corchado JC, Espinosa-Garcia J. Dynamics study of the OH + NH3 hydrogen abstraction reaction using QCT calculations based on an analytical potential energy surface. J Chem Phys 2014; 138:214306. [PMID: 23758370 DOI: 10.1063/1.4808109] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
To understand the reactivity and mechanism of the OH + NH3 → H2O + NH2 gas-phase reaction, which evolves through wells in the entrance and exit channels, a detailed dynamics study was carried out using quasi-classical trajectory calculations. The calculations were performed on an analytical potential energy surface (PES) recently developed by our group, PES-2012 [Monge-Palacios et al. J. Chem. Phys. 138, 084305 (2013)]. Most of the available energy appeared as H2O product vibrational energy (54%), reproducing the only experimental evidence, while only the 21% of this energy appeared as NH2 co-product vibrational energy. Both products appeared with cold and broad rotational distributions. The excitation function (constant collision energy in the range 1.0-14.0 kcal mol(-1)) increases smoothly with energy, contrasting with the only theoretical information (reduced-dimensional quantum scattering calculations based on a simplified PES), which presented a peak at low collision energies, related to quantized states. Analysis of the individual reactive trajectories showed that different mechanisms operate depending on the collision energy. Thus, while at high energies (E(coll) ≥ 6 kcal mol(-1)) all trajectories are direct, at low energies about 20%-30% of trajectories are indirect, i.e., with the mediation of a trapping complex, mainly in the product well. Finally, the effect of the zero-point energy constraint on the dynamics properties was analyzed.
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Affiliation(s)
- M Monge-Palacios
- Departamento de Química Física, Universidad de Extremadura, 06071 Badajoz, Spain
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22
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Anglada JM, Olivella S, Solé A. Atmospheric formation of the NO3 radical from gas-phase reaction of HNO3 acid with the NH2 radical: proton-coupled electron-transfer versus hydrogen atom transfer mechanisms. Phys Chem Chem Phys 2014; 16:19437-45. [DOI: 10.1039/c4cp02792b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The amidogen radical abstracts the hydrogen from nitric acid through a proton coupled electron transfer mechanism rather than by an hydrogen atom transfer process.
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Affiliation(s)
- Josep M. Anglada
- Departament de Química Biològica i Modelització Molecular
- (IQAC – CSIC)
- E-08034 Barcelona, Spain
| | - Santiago Olivella
- Departament de Química Biològica i Modelització Molecular
- (IQAC – CSIC)
- E-08034 Barcelona, Spain
| | - Albert Solé
- Departament de Química Física i Institut de Química Teòrica i Computacional (IQTCUB)
- Universitat de Barcelona
- E-08028 Barcelona, Spain
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23
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Monge-Palacios M, Espinosa-Garcia J. Role of Vibrational and Translational Energy in the OH + NH3 Reaction: A Quasi-Classical Trajectory Study. J Phys Chem A 2013; 117:5042-51. [DOI: 10.1021/jp403571y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Monge-Palacios
- Departamento de Química
Física, Universidad de Extremadura, 06071 Badajoz, Spain
| | - J. Espinosa-Garcia
- Departamento de Química
Física, Universidad de Extremadura, 06071 Badajoz, Spain
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Monge-Palacios M, Espinosa-Garcia J. Bond and mode selectivity in the OH + NH2D reaction: a quasi-classical trajectory calculation. Phys Chem Chem Phys 2013; 15:19180-90. [DOI: 10.1039/c3cp52809j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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