1
|
Yamashita T, Miyamura N, Kawai S. Classification of the HCN isomerization reaction dynamics in Ar buffer gas via machine learning. J Chem Phys 2023; 159:124116. [PMID: 38127399 DOI: 10.1063/5.0156313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/07/2023] [Indexed: 12/23/2023] Open
Abstract
The effect of the presence of Ar on the isomerization reaction HCN ⇄ CNH is investigated via machine learning. After the potential energy surface function is developed based on the CCSD(T)/aug-cc-pVQZ level ab initio calculations, classical trajectory simulations are performed. Subsequently, with the aim of extracting insights into the reaction dynamics, the obtained reactivity, that is, whether the reaction occurs or not under a given initial condition, is learned as a function of the initial positions and momenta of all the atoms in the system. The prediction accuracy of the trained model is greater than 95%, indicating that machine learning captures the features of the phase space that affect reactivity. Machine learning models are shown to successfully reproduce reactivity boundaries without any prior knowledge of classical reaction dynamics theory. Subsequent analyses reveal that the Ar atom affects the reaction by displacing the effective saddle point. When the Ar atom is positioned close to the N atom (resp. the C atom), the saddle point shifts to the CNH (HCN) region, which disfavors the forward (backward) reaction. The results imply that analyses aided by machine learning are promising tools for enhancing the understanding of reaction dynamics.
Collapse
Affiliation(s)
- Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Naoaki Miyamura
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Shinnosuke Kawai
- Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| |
Collapse
|
2
|
da Silva RS, Ballester MY. A theoretical study of energy transfer in Ar( 1S) + SO 2( X ̃ 1 A ') collisions: Cross sections and rate coefficients for vibrational transitions. J Chem Phys 2018; 149:144309. [PMID: 30316261 DOI: 10.1063/1.5051349] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Vibrational transitions, induced by collisions between rare-gas atoms and molecules, play a key role in many problems of interest in physics and chemistry. A theoretical investigation of the translation-to-vibration (T-V) energy transfer process in argon atom and sulfur dioxide molecule collisions is presented here. For such a purpose, the framework of the quasi-classical trajectory (QCT) methodology was followed over the range of translational energies 2 ≤ Etr/kcal mol-1 ≤ 100. A new realistic potential energy surface (PES) for the ArSO2 system was developed using pairwise addition for the four-body energy term within the double many-body expansion. The topological features of the obtained function are compared with a previous one reported by Hippler et al. [J. Phys. Chem. 90, 6158 (1986)]. To test the accuracy of the PES, additional coupled cluster singles and doubles method with a perturbative contribution of connected triples calculations were carried out for the global minimum configuration. From dynamical calculations, the cross sections for the T-V excitation process indicate a barrier-type mechanism due to strong repulsive interactions between SO2 molecules and the Ar atom. Corrections to zero-point energy leakage in QCT were carried out using vibrational energy quantum mechanical threshold of the complex and variations. Rate coefficients and cross sections are calculated for some vibrational transitions using pseudo-quantization approaches of the vibrational energy of products. Main attributes of the title molecular collision are discussed and compared with available information in the literature.
Collapse
Affiliation(s)
- Ramon S da Silva
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36036-330, Brazil
| | - Maikel Y Ballester
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36036-330, Brazil
| |
Collapse
|
3
|
Liu Y, Huang Y, Ma J, Li J. Classical Trajectory Study of Collision Energy Transfer between Ne and C2H2 on a Full Dimensional Accurate Potential Energy Surface. J Phys Chem A 2018; 122:1521-1530. [DOI: 10.1021/acs.jpca.7b11483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yang Liu
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China
| | - Yin Huang
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China
| | - Jianyi Ma
- Institute
of Atomic and Molecular Physics, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jun Li
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China
| |
Collapse
|
4
|
Li J, Guo H. Permutationally invariant fitting of intermolecular potential energy surfaces: A case study of the Ne-C2H2 system. J Chem Phys 2015; 143:214304. [DOI: 10.1063/1.4936660] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jun Li
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| |
Collapse
|
5
|
Conte R, Qu C, Bowman JM. Permutationally Invariant Fitting of Many-Body, Non-covalent Interactions with Application to Three-Body Methane–Water–Water. J Chem Theory Comput 2015; 11:1631-8. [DOI: 10.1021/acs.jctc.5b00091] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Riccardo Conte
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M. Bowman
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
6
|
Qu C, Conte R, Houston PL, Bowman JM. “Plug and play” full-dimensional ab initio potential energy and dipole moment surfaces and anharmonic vibrational analysis for CH4–H2O. Phys Chem Chem Phys 2015; 17:8172-81. [DOI: 10.1039/c4cp05913a] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The first full-dimensional potential energy surface of CH4–H2O dimer is presented, and vibrational analysis of this dimer is performed.
Collapse
Affiliation(s)
- Chen Qu
- Department of Chemistry and Cherry L. Emerson Centrer for Scientific Computations
- Emory University
- Atlanta
- USA
| | - Riccardo Conte
- Department of Chemistry and Cherry L. Emerson Centrer for Scientific Computations
- Emory University
- Atlanta
- USA
| | - Paul L. Houston
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- Department of Chemistry and Chemical Biology
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Centrer for Scientific Computations
- Emory University
- Atlanta
- USA
| |
Collapse
|
7
|
Conte R, Houston PL, Bowman JM. Trajectory Study of Energy Transfer and Unimolecular Dissociation of Highly Excited Allyl with Argon. J Phys Chem A 2014; 118:7742-57. [DOI: 10.1021/jp5062013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Riccardo Conte
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Paul L. Houston
- School
of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Department
of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, New York 14852, United States
| | - Joel M. Bowman
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
8
|
Conte R, Houston PL, Bowman JM. Classical Trajectory Study of Energy Transfer in Collisions of Highly Excited Allyl Radical with Argon. J Phys Chem A 2013; 117:14028-41. [DOI: 10.1021/jp410315r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Riccardo Conte
- Department of Chemistry and Cherry L. Emerson
Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Paul L. Houston
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson
Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
9
|
Marques JMC, Martínez-Núñez E, Vazquez SA. Trajectory dynamics study of collision-induced dissociation of the Ar + CH4 reaction at hyperthermal conditions: vibrational excitation and isotope substitution. J Phys Chem A 2006; 110:7113-21. [PMID: 16737261 DOI: 10.1021/jp0611929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We investigate the role of vibrational energy excitation of methane and two deuterated species (CD(4) and CH(2)D(2)) in the collision-induced dissociation (CID) process with argon at hyperthermal energies. The quasi-classical trajectory method has been applied, and the reactive Ar + CH(4) system has been modeled by using a modified version of the CH(4) potential energy surface of Duchovic et al. (J. Phys. Chem. 1984, 88, 1339) and the Ar-CH(4) intermolecular potential function obtained by Troya (J. Phys. Chem. A 2005, 109, 5814). This study clearly shows that CID is markedly enhanced with vibrational excitation and, to a lesser degree, with collision energy. In general, CID increases by exciting stretch vibrational modes of the reactant molecule. For the direct dissociation of CH(4), however, the CID cross sections appear to be essentially independent of which vibrational mode is initially excited. In all situations studied, the CID cross sections are always greater for the Ar + CD(4) reaction than for the Ar + CH(4) one, the Ar + CH(2)D(2) being an intermediate situation. A detailed analysis of the energy transfer processes, including their relation with CID, is also presented.
Collapse
Affiliation(s)
- J M C Marques
- Departamento de Química, Universidade de Coimbra, Portugal.
| | | | | |
Collapse
|
10
|
Varandas AJC, Rodrigues SPJ. New Double Many-Body Expansion Potential Energy Surface for Ground-State HCN from a Multiproperty Fit to Accurate ab Initio Energies and Rovibrational Calculations. J Phys Chem A 2005; 110:485-93. [PMID: 16405320 DOI: 10.1021/jp051434p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An accurate single-sheeted double many-body expansion potential energy surface has been obtained for the ground electronic state of the hydrogen cyanide molecule via a multiproperty fit to ab initio energies and rovibrational data. This includes 106 rovibrational levels and 2313 discrete points, which are fit with a rmsd of 4 cm(-1) and 2.42 kcal mol(-1), respectively, and seven zero first-derivatives that are reproduced at three stationary points. Since the potential also describes accurately the appropriate asymptotic limits at the various dissociation channels, it is commended both for the simulation of rovibrational spectra and reaction dynamics.
Collapse
Affiliation(s)
- A J C Varandas
- Departamento de Química, Universidade de Coimbra 3004-535 Coimbra, Portugal
| | | |
Collapse
|
11
|
Marques JMC, Martínez-Núñez E, Fernandez-Ramos A, Vazquez SA. Trajectory Dynamics Study of the Ar + CH4Dissociation Reaction at High Temperatures: the Importance of Zero-Point-Energy Effects. J Phys Chem A 2005; 109:5415-23. [PMID: 16839068 DOI: 10.1021/jp044707+] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Large-scale classical trajectory calculations have been performed to study the reaction Ar + CH4--> CH3 +H + Ar in the temperature range 2500 < or = T/K < or = 4500. The potential energy surface used for ArCH4 is the sum of the nonbonding pairwise potentials of Hase and collaborators (J. Chem. Phys. 2001, 114, 535) that models the intermolecular interaction and the CH4 intramolecular potential of Duchovic et al. (J. Phys. Chem. 1984, 88, 1339), which has been modified to account for the H-H repulsion at small bending angles. The thermal rate coefficient has been calculated, and the zero-point energy (ZPE) of the CH3 product molecule has been taken into account in the analysis of the results; also, two approaches have been applied for discarding predissociative trajectories. In both cases, good agreement is observed between the experimental and trajectory results after imposing the ZPE of CH3. The energy-transfer parameters have also been obtained from trajectory calculations and compared with available values estimated from experiment using the master equation formalism; in general, the agreement is good.
Collapse
Affiliation(s)
- J M C Marques
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal.
| | | | | | | |
Collapse
|
12
|
Martínez-Núñez E, Vázquez SA, Marques JMC. Quasiclassical trajectory study of the collision-induced dissociation of CH[sub 3]SH[sup +]+Ar. J Chem Phys 2004; 121:2571-7. [PMID: 15281855 DOI: 10.1063/1.1769364] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [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 study the dynamics of energy transfer and collision-induced dissociation (CID) of CH(3)SH(+) + Ar at collision energies ranging from 4.34 to 34.7 eV. The relative abundances calculated for the most relevant product ions are found to be in good agreement with experiment, except for the lowest energies investigated. In general, the dissociation to form CH(3)(+) + SH is the dominant channel, even though it is not among the energetically favored reaction pathways. The results corroborate that this selective dissociation observed upon collisional activation arises from a more efficient translational to vibrational energy transfer for the low-frequency C-S stretching mode than for the high-frequency C-H stretching modes, together with weak couplings between the low- and high-frequency modes of vibration. The calculations suggest that CID takes place preferentially by a direct CH(3)(+) + SH detachment, and more efficiently when the Ar atom collides with the methyl group-side of CH(3)SH(+).
Collapse
Affiliation(s)
- Emilio Martínez-Núñez
- Departmento de Química Fisica, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | | | | |
Collapse
|
13
|
Rodrigues SPJ, Varandas AJC. Dynamics Study of the Reaction S + O2 → SO + O and Its Reverse on a Single-Valued Double Many-Body Expansion Potential Energy Surface for Ground-State SO2. J Phys Chem A 2003. [DOI: 10.1021/jp0301305] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- S. P. J. Rodrigues
- Departamento de Química, Universidade de Coimbra, 3004-545 Coimbra, Portugal
| | - A. J. C. Varandas
- Departamento de Química, Universidade de Coimbra, 3004-545 Coimbra, Portugal
| |
Collapse
|
14
|
Riganelli A, Wang W, Varandas AJC. Monte Carlo Simulation Approach to Internal Partition Functions for van der Waals Molecules. J Phys Chem A 1999. [DOI: 10.1021/jp991494t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. Riganelli
- Departamento de Química, Universidade de Coimbra P-3049 Coimbra Codex, Portugal
| | - W. Wang
- Departamento de Química, Universidade de Coimbra P-3049 Coimbra Codex, Portugal
| | - A. J. C. Varandas
- Departamento de Química, Universidade de Coimbra P-3049 Coimbra Codex, Portugal
| |
Collapse
|
15
|
Rodrigues SPJ, Varandas AJC. On the Rate Constant for the Association Reaction H + CN + Ar → HCN + Ar. J Phys Chem A 1999. [DOI: 10.1021/jp9906076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. P. J. Rodrigues
- Departamento de Química, Universidade de Coimbra, P-3049 Coimbra, Portugal
| | - A. J. C. Varandas
- Departamento de Química, Universidade de Coimbra, P-3049 Coimbra, Portugal
| |
Collapse
|
16
|
Varandas A, Rodrigues S, Gomes P. Energy switching potential energy surfaces and spectra of the van der Waals modes for the ArHCN molecule. Chem Phys Lett 1998. [DOI: 10.1016/s0009-2614(98)01159-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|