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Parker K, Bollis NE, Ryzhov V. Ion-molecule reactions of mass-selected ions. MASS SPECTROMETRY REVIEWS 2024; 43:47-89. [PMID: 36447431 DOI: 10.1002/mas.21819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Gas-phase reactions of mass-selected ions with neutrals covers a very broad area of fundamental and applied mass spectrometry (MS). Oftentimes, ion-molecule reactions (IMR) can serve as a viable alternative to collision-induced dissociation and other ion dissociation techniques when using tandem MS. This review focuses on the literature pertaining applications of IMR since 2013. During the past decade considerable efforts have been made in analytical applications of IMR, including advances in one of the major techniques for characterization of unsaturated fatty acids and lipids, ozone-induced dissociation, and the development of a new technique for sequencing of large ions, hydrogen atom attachment/abstraction dissociation. Many advances have also been made in identifying gas-phase chemistry specific to a functional group in organic and biological compounds, which are useful in structure elucidation of analytes and differentiation of isomers/isobars. With "soft" ionization techniques like electrospray ionization having become mainstream for quite some time now, the efforts in the area of metal ion catalysis have firmly moved into exploring chemistry of ligated metal complexes in their "natural" oxidation states allowing to model individual steps of mechanisms in homogeneous catalysis, especially in combination with high-level DFT calculations. Finally, IMR continue to contribute to the body of knowledge in the area of chemistry of interstellar processes.
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Affiliation(s)
- Kevin Parker
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois, USA
| | - Nicholas E Bollis
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois, USA
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois, USA
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2
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Bigagli N, Savin DW, Will S. Laser Scheme for Doppler Cooling of the Hydroxyl Cation (OH +). J Phys Chem A 2023; 127:8194-8199. [PMID: 37738380 DOI: 10.1021/acs.jpca.3c03248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
We report on a cycling scheme for Doppler cooling of trapped OH+ ions using transitions between the electronic ground state X3Σ- and the first excited triplet state A3Π. We have identified relevant transitions for photon cycling and repumping, have found that coupling into other electronic states is strongly suppressed, and have calculated the number of photon scatterings required to cool OH+ to a temperature where Raman sideband cooling can take over. In contrast to the standard approach, where molecular ions are sympathetically cooled, our scheme does not require co-trapping of another species and opens the door to the creation of pure samples of cold molecular ions with potential applications in quantum information, quantum chemistry, and astrochemistry. The laser cooling scheme identified for OH+ is efficient despite the absence of near-diagonal Franck-Condon factors, suggesting that broader classes of molecules and molecular ions are amenable to laser cooling than commonly assumed.
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Affiliation(s)
- Niccolò Bigagli
- Department of Physics, Columbia University, New York, New York 10027, United States
| | - Daniel W Savin
- Columbia Astrophysics Laboratory, Columbia University, New York, New York 10027, United States
| | - Sebastian Will
- Department of Physics, Columbia University, New York, New York 10027, United States
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3
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Salvi M, Uma NN, Dinesan H, Roy A, Kumar SS. A versatile 16-pole ion trap setup for investigating photophysics of biomolecular ions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:093203. [PMID: 37721505 DOI: 10.1063/5.0160407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/26/2023] [Indexed: 09/19/2023]
Abstract
A linear 16-pole ion trap-based experimental setup has been designed, implemented, and characterized to investigate the photophysics of biomolecules in the gas phase. Electrospray ionization is employed to generate the ions in the gas phase at atmospheric pressure. The voltage configuration on the ion funnel, the ion optic device in the first vacuum interface, is used to control the energy of the ions. A home-built quadrupole mass-filter is utilized for the mass-selection of the ions of interest. A 16-pole ion trap designed and built in-house is implemented for ion trapping. The instrument's versatility and capability are showcased by demonstrating the fragmentation patterns of protonated and deprotonated tryptophan, as well as describing the photodetachment decay of deprotonated indole.
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Affiliation(s)
- M Salvi
- Department of Physics and the Center for Atomic, Molecular, and Optical Sciences & Technologies (CAMOST), Indian Institute of Science Education and Research Tirupati, AP, Tirupati 517507, India
| | - N N Uma
- Department of Physics and the Center for Atomic, Molecular, and Optical Sciences & Technologies (CAMOST), Indian Institute of Science Education and Research Tirupati, AP, Tirupati 517507, India
| | - Hemanth Dinesan
- CNRS Laboratoire de Physique des Lasers (LPL), Université Sorbonne Paris Nord Villetaneuse, Villetaneuse 93430, France
| | - Abheek Roy
- Department of Physics and the Center for Atomic, Molecular, and Optical Sciences & Technologies (CAMOST), Indian Institute of Science Education and Research Tirupati, AP, Tirupati 517507, India
| | - S Sunil Kumar
- Department of Physics and the Center for Atomic, Molecular, and Optical Sciences & Technologies (CAMOST), Indian Institute of Science Education and Research Tirupati, AP, Tirupati 517507, India
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4
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Venkataramanababu S, Li A, Antonov IO, Dragan JB, Stollenwerk PR, Guo H, Odom BC. Enhancing reactivity of SiO + ions by controlled excitation to extreme rotational states. Nat Commun 2023; 14:4446. [PMID: 37488115 PMCID: PMC10366143 DOI: 10.1038/s41467-023-40135-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 07/11/2023] [Indexed: 07/26/2023] Open
Abstract
Optical pumping of molecules provides unique opportunities for control of chemical reactions at a wide range of rotational energies. This work reports a chemical reaction with extreme rotational excitation of a reactant and its kinetic characterization. We investigate the chemical reactivity for the hydrogen abstraction reaction SiO+ + H2 → SiOH+ + H in an ion trap. The SiO+ cations are prepared in a narrow rotational state distribution, including super-rotor states with rotational quantum number (j) as high as 170, using a broad-band optical pumping method. We show that the super-rotor states of SiO+ substantially enhance the reaction rate, a trend reproduced by complementary theoretical studies. We reveal the mechanism for the rotational enhancement of the reactivity to be a strong coupling of the SiO+ rotational mode with the reaction coordinate at the transition state on the dominant dynamical pathway.
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Affiliation(s)
- Sruthi Venkataramanababu
- Applied Physics Program, Northwestern University, Evanston, 60208, IL, USA
- Department of Physics, Northwestern University, Evanston, 60208, IL, USA
| | - Anyang Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China.
| | - Ivan O Antonov
- Lebedev Physical Institute, Samara, 443011, Russian Federation
| | - James B Dragan
- Department of Physics, Northwestern University, Evanston, 60208, IL, USA
| | | | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, 87131, NM, USA
| | - Brian C Odom
- Department of Physics, Northwestern University, Evanston, 60208, IL, USA.
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5
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Okada K, Sakimoto K, Schuessler HA. Rotational Cooling Effect on the Rate Constant in the CH 3F + Ca + Reaction at Low Collision Energies. J Phys Chem A 2022; 126:4881-4890. [PMID: 35857026 DOI: 10.1021/acs.jpca.2c01063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rotational cooling effect on the reaction rate constant of the gas-phase ion-polar-molecule reaction CH3F + Ca+ → CH3 + CaF+ was experimentally studied at low collision energies. Fluoromethane molecules showed higher reactivity as the rotational temperature decreased. The experimental rate constants were compared with the capture rate constants which were obtained by the Perturbed Rotational State (PRS) theory assuming the rotational level distribution corresponding to the experimental conditions. The PRS result shows a strong dependence of the capture rate constants on the rotational level distribution in accordance with the experimental findings. However, the PRS capture rate constants deviate from the measurement values as the average collision energy increases especially when the fluoromethane molecules are rotationally cooled far below room temperature. The present paper suggests that the rotational state distribution significantly affects the rate constants of ion-polar-molecule reactions and is one of the important issues to be considered in the study of molecular synthesis in the interstellar medium, where the thermal equilibrium is not necessarily established.
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Affiliation(s)
- Kunihiro Okada
- Department of Materials and Life Sciences, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan
| | - Kazuhiro Sakimoto
- Department of Materials and Life Sciences, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan
| | - Hans A Schuessler
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843-4242, United States
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6
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Zhu Y, Li R, Song H. Kinetic and dynamic studies of the NH 2+ + H 2 reaction on a high-level ab initio potential energy surface. Phys Chem Chem Phys 2022; 24:25663-25672. [DOI: 10.1039/d2cp03859e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The dynamics and kinetics of the NH2+ + H2 reaction are investigated on a newly developed ab initio potential energy surface using the quasi-classical trajectory method.
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Affiliation(s)
- Yongfa Zhu
- School of Chemistry and Chemical Engineering, Hubei Polytechnic University, Huangshi 435003, China
| | - Rui Li
- School of Chemistry and Chemical Engineering, Hubei Polytechnic University, Huangshi 435003, China
| | - Hongwei Song
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
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7
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Temperature dependence of the rate coefficient of formation of CN radical from C + NH. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Kovalenko A, Roučka Š, Tran TD, Rednyk S, Plašil R, Dohnal P, Glosík J. The reaction of O +( 4S) ions with H 2, HD, and D 2 at low temperatures: Experimental study of the isotope effect. J Chem Phys 2021; 154:094301. [PMID: 33685178 DOI: 10.1063/5.0036049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The reactions of the O+ ions in the 4S electronic ground state with D2 and HD were studied in a cryogenic 22-pole radio-frequency ion trap in the temperature range of 15 K-300 K. The obtained reaction rate coefficients for both reactions are, considering the experimental errors, nearly independent of temperature and close to the values of the corresponding Langevin collisional reaction rate coefficients. The obtained branching ratios for the production of OH+ and OD+ in the reaction of O+(4S) with HD do not change significantly with temperature and are consistent with the results obtained at higher collisional energies by other groups. Particular attention was given to ensure that the O+ ions in the trap are in the ground electronic state.
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Affiliation(s)
- A Kovalenko
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - Š Roučka
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - T D Tran
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - S Rednyk
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - R Plašil
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - P Dohnal
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - J Glosík
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 180 00 Prague, Czech Republic
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9
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Novikov IS, Shapeev AV, Suleimanov YV. Ring polymer molecular dynamics and active learning of moment tensor potential for gas-phase barrierless reactions: Application to S + H2. J Chem Phys 2019; 151:224105. [DOI: 10.1063/1.5127561] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ivan S. Novikov
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Nobel St. 3, Moscow 143026, Russia
| | - Alexander V. Shapeev
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Nobel St. 3, Moscow 143026, Russia
| | - Yury V. Suleimanov
- Computation-Based Science and Technology Research Center, Cyprus Institute, 20 Kavafi Street, Nicosia 2121, Cyprus
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10
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Menéndez M, Jambrina PG, Zanchet A, Verdasco E, Suleimanov YV, Aoiz FJ. New Stress Test for Ring Polymer Molecular Dynamics: Rate Coefficients of the O( 3P) + HCl Reaction and Comparison with Quantum Mechanical and Quasiclassical Trajectory Results. J Phys Chem A 2019; 123:7920-7931. [PMID: 31461272 DOI: 10.1021/acs.jpca.9b06695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the past decade, ring polymer molecular dynamics (RPMD) has emerged as a very efficient method to determine thermal rate coefficients for a great variety of chemical reactions. This work presents the application of this methodology to study the O(3P) + HCl reaction, which constitutes a stringent test for any dynamical calculation due to rich resonant structure and other dynamical features. The rate coefficients, calculated on the 3A' and 3A″ potential energy surfaces (PESs) by Ramachandran and Peterson [ J. Chem. Phys. 2003 , 119 , 9590 ], using RPMD and quasiclassical trajectories (QCT) are compared with the existing experimental and the quantum mechanical (QM) results by Xie et al. [ J. Chem. Phys. 2005 122 , 014301 ]. The agreement is very good at T > 600 K, although RPMD underestimates rate coefficients by a factor between 4 and 2 in the 200-500 K interval. The origin of these discrepancies lies in the large contribution from tunneling on the 3A″ PES, which is enhanced by resonances due to quasibound states in the van der Waals wells. Although tunneling is fairly well accounted for by RPMD even below the crossover temperature, the effect of resonances, a long-time effect, is not included in the methodology. At the highest temperatures studied in this work, 2000-3300 K, the RPMD rate coefficients are somewhat larger than the QM ones, but this is shown to be due to limitations in the QM calculations and the RPMD are believed to be more reliable.
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Affiliation(s)
- M Menéndez
- Departamento de Química Física I, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , 28040 Madrid , Spain
| | - P G Jambrina
- Departamento de Química Física, Facultad de Ciencias Químicas , Universidad de Salamanca , 37008 Salamanca , Spain
| | - A Zanchet
- Departamento de Química Física I, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , 28040 Madrid , Spain
| | - E Verdasco
- Departamento de Química Física I, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , 28040 Madrid , Spain
| | - Y V Suleimanov
- Computation-based Science and Technology Research Center , Cyprus Institute , 20 Kavafi Strasse , Nicosia 2121 , Cyprus.,Department of Chemical Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - F J Aoiz
- Departamento de Química Física I, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , 28040 Madrid , Spain
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11
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Zhu Y, Lu Y, Song H. Thermal rate coefficients and kinetic isotope effects of the reaction HO + H2O → H2O + OH. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2495-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Garcia E, Jambrina PG, Laganà A. Kinetics Of The H + CH 2 → CH + H 2 Reaction At Low Temperature. J Phys Chem A 2019; 123:7408-7419. [PMID: 31373813 DOI: 10.1021/acs.jpca.9b06212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A quasiclassical trajectory study of the kinetics of the title astrochemical reaction in a range of temperatures varying from 5 to 1000 K (corresponding to both the outer and the inner regions of the protostar and the circumstellar envelopes) was carried out and a clear dependence of the rate coefficient on the temperature is given, in contrast with the constant value adopted in kinetics astrochemical databases. Levering the massive nature of the performed calculations and of the detailed dynamical investigation of the reactive process, a rationalization of the temperature dependence of the released translational energy and of the rovibrational population of the CH and H2 diatomic products is also provided. Furthermore, the effect of the initial rovibrational energy of CH2 on the state-specific rate coefficients and cross sections is analyzed in order to single out the role played by the different regions of the potential energy surface on the dynamical outcomes and on the modeling the temperature dependence of the reactive efficiency of the investigated process. This led to a parametrization of the computed rate in terms of the following double Arrhenius expression (in cm3 s-1), k(T) = 2.50 × 10-10 exp(- 1.67/T) + 5.98 × 10-11 exp(- 280.5/T), alternative to the piecewise formulation into the three subintervals of temperature in which the overall 5-1000 K interval can be divided.
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Affiliation(s)
- Ernesto Garcia
- Departamento de Química Física , Universidad del País Vasco (UPV/EHU) , Paseo de la Universidad 7 , 01006 Vitoria , Spain
| | - Pablo G Jambrina
- Departamento de Química Física , Universidad de Salamanca , Plaza de los Caı́dos , 37008 Salamanca , Spain
| | - Antonio Laganà
- UOS Perugia , CNR ISTM , via Elce di sotto 8 , I-06123 Perugia , Italy.,Master UP srl , Strada Sperandio 15 , I-06125 Perugia , Italy
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13
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Bhowmick S, Bossion D, Scribano Y, Suleimanov YV. The low temperature D + + H 2→ HD + H + reaction rate coefficient: a ring polymer molecular dynamics and quasi-classical trajectory study. Phys Chem Chem Phys 2018; 20:26752-26763. [PMID: 30324962 DOI: 10.1039/c8cp05398g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction between D+ and H2 plays an important role in astrochemistry at low temperatures and also serves as a prototype for a simple ion-molecule reaction. Its ground X[combining tilde]1A' state has a very small thermodynamic barrier (up to 1.8 × 10-2 eV) and the reaction proceeds through the formation of an intermediate complex lying within the potential well with a depth of at least 0.2 eV, thus representing a challenge for dynamical studies. In the present work, we analyze the title reaction within the temperature range of 20-100 K by means of ring polymer molecular dynamics (RPMD) and quasi-classical trajectory (QCT) methods over the full-dimensional global potential energy surface developed by Aguado et al. [A. Aguado, O. Roncero, C. Tablero, C. Sanz and M. Paniagua, J. Chem. Phys., 2000, 112, 1240]. The computed thermal RPMD and QCT rate coefficients are found to be almost independent of temperature and fall within the range of 1.34-2.01 × 10-9 cm3 s-1. They are also in very good agreement with previous time-independent quantum mechanical and statistical quantum method calculations. Furthermore, we observe that the choice of asymptotic separation distance between the reactants can markedly alter the rate coefficient in the low temperature regime (20-50 K). Therefore it is of utmost importance to correctly assign the value of this parameter for dynamical studies, particularly at very low temperatures of astrochemical importance. We finally conclude that the experimental rate measurements for the title reaction are highly desirable in future.
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Affiliation(s)
- Somnath Bhowmick
- Computation-based Science and Technology Research Center, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
| | - Duncan Bossion
- Laboratoire Univers et Particules de Montpellier, UMR-CNRS 5299, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Yohann Scribano
- Laboratoire Univers et Particules de Montpellier, UMR-CNRS 5299, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Yury V Suleimanov
- Computation-based Science and Technology Research Center, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
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