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ManyHF-based full-dimensional potential energy surface development and quasi-classical dynamics for the Cl + CH3NH2 reaction. J Chem Phys 2023; 159:134306. [PMID: 37791624 DOI: 10.1063/5.0166680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/06/2023] [Indexed: 10/05/2023] Open
Abstract
A full-dimensional spin-orbit (SO)-corrected potential energy surface (PES) is developed for the Cl + CH3NH2 multi-channel system. Using the new PES, a comprehensive reaction dynamics investigation is performed for the most reactive hydrogen-abstraction reactions forming HCl + CH2NH2/CH3NH. Hartree-Fock (HF) convergence problems in the reactant region are handled by the ManyHF method, which finds the lowest-energy HF solution considering several different initial guess orbitals. The PES development is carried out with the Robosurfer program package, which iteratively improves the surface. Energy points are computed at the ManyHF-UCCSD(T)-F12a/cc-pVDZ-F12 level of theory combined with basis set (ManyHF-RMP2-F12/cc-pVTZ-F12 - ManyHF-RMP2-F12/cc-pVDZ-F12) and SO (MRCI+Q/aug-cc-pwCVDZ) corrections. Quasi-classical trajectory simulations show that the CH3-side hydrogen abstraction occurs more frequently in contrast to the NH2-side reaction. In both cases, the integral cross sections decrease with increasing collision energy (Ecoll). A reaction mechanism shifting from indirect to direct stripping can be observed from the opacity functions, scattering angle, and translation energy distributions as Ecoll increases. Initial attack angle distributions reveal that chlorine prefers to abstract hydrogen from the approached functional group. The collision-energy dependence of the product energy distributions shows that the initial translational energy mainly transfers to product recoil. The HCl vibrational and rotational energy values are comparable and nearly independent of collision energy, while the CH2NH2 and CH3NH co-products' vibrational energy values are higher than the rotational energy values with more significant Ecoll dependence. The HCl(v = 0) rotational distributions are compared with experiment, setting the direction for future investigations.
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Probing the location of the unpaired electron in spin-orbit changing collisions of NO with Ar. Phys Chem Chem Phys 2020; 22:22289-22301. [PMID: 33005915 DOI: 10.1039/d0cp04228e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the molecular forces that drive a reaction or scattering process lies at the heart of molecular dynamics. Here, we present a combined experimental and theoretical study of the spin-orbit changing scattering dynamics of oriented NO molecules with Ar atoms. Using our crossed molecular beam apparatus, we have recorded velocity-map ion images and extracted differential and integral cross sections of the scattering process in the side-on geometry. We observe an overall preference for collisions close to the N atom in the spin-orbit changing manifold, which is a direct consequence of the location of the unpaired electron on the potential energy surface. In addition, a prominent forward scattered feature is observed for intermediate, even rotational transitions when the atom approaches the molecule from the O-end. The appearance of this peak originates from an attractive well on the A' potential energy surface, which efficiently directs high impact parameter trajectories towards the region of high unpaired electron density near the N-end of the molecule. The ability to orient molecules prior to collision, both experimentally and theoretically, allows us to sample different regions of the potential energy surface(s) and unveil the associated collision pathways.
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Active stereo-control of the Cl + CH 4(ν 3 = 1) reaction: a three-dimensional perspective. Phys Chem Chem Phys 2020; 22:10949-10956. [PMID: 32377655 DOI: 10.1039/d0cp01502d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The transition state in Cl + CH4 is of Cl-H-C collinear geometry. As the reactant CH4 is vibrationally excited by a linearly polarized infrared (IR) light to the antisymmetric-stretching state of ν3 = 1, all four C-H bonds are collectively excited and any one of the H-atoms can be reactive. Yet, a strong alignment of the excited CH4(ν3 = 1), as evidenced from the striking stereo-specificity in the Cl + CH4 reaction, was clearly revealed in a previous, exploratory study. Reported here is the full account of that investigation at two collisional energies of Ec = 4.8 and 2.7 kcal mol-1, using a crossed molecular-beam, product-imaging approach. By active control of the polarization direction of an IR laser under judiciously chosen beam-geometries, a complete set of polarization-dependent differential cross sections is disentangled from the CH3(00) product images. To our surprise, the quantitative results appear nearly identical to those obtained for the isotope-substituted reaction of Cl + CHD3(ν1 = 1) → HCl(ν) + CD3(00). A detailed discussion is presented to elucidate the underlying physics for such an intriguing similarity in stereo-reactivity between a spherical-top and a symmetric-top reactant.
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Benchmark ab initio and dynamical characterization of the stationary points of reactive atom + alkane and SN2 potential energy surfaces. Phys Chem Chem Phys 2020; 22:4298-4312. [DOI: 10.1039/c9cp04944d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review composite ab initio and dynamical methods and their applications to characterize stationary points of atom/ion + molecule reactions.
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Morphophysiological and molecular evidence supporting the augmentative role of Piriformospora indica in mitigation of salinity in Cucumis melo L. Acta Biochim Biophys Sin (Shanghai) 2019; 51:301-312. [PMID: 30883647 DOI: 10.1093/abbs/gmz007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 01/27/2023] Open
Abstract
Salinity is one of the major limiting factors in plant growth and productivity. Cucumis melo L. is a widely cultivated plant, but its productivity is significantly influenced by the level of salinity in soil. Symbiotic colonization of plants with Piriformospora indica has shown a promotion in plants growth and tolerance against biotic stress. In this study, physiological markers such as ion analysis, antioxidant determination, proline content, electrolyte leakage and chlorophyll measurement were assessed in melon cultivar under two concentrations (100 and 200 mM) of NaCl with and without P. indica inoculation. Results showed that the endophytic inoculation consistently upregulated the level of antioxidants, enhanced plants to antagonize salinity stress. The expression level of an RNA editing factor (SLO2) which is known to participate in mitochondria electron transport chain was analyzed, and its full mRNA sequence was obtained by rapid amplification of cDNA ends (RACE). Under salinity stress, the expression level of SLO2 was increased, enhancing the plant's capability to adapt to the stress. However, P. indica inoculation further elevated the expression level of SLO2. These findings suggested that the symbiotic association of fungi could help the plants to tolerate the salinity stress.
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Rotational-mode specific effects on the stereo-requirement in the reaction of prealigned-CHD3(v1 = 1; |JK = |10 or |1 ± 1) with the chlorine atom. J Chem Phys 2018; 148:244307. [DOI: 10.1063/1.5037892] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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7
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Spiers Memorial Lecture : Introductory lecture: quantum dynamics of chemical reactions. Faraday Discuss 2018; 212:9-32. [DOI: 10.1039/c8fd00131f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This Spiers Memorial Lecture discusses quantum effects that can be calculated and observed in the chemical reactions of small molecules.
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A Combined Theoretical and Experimental Study of Sarin (GB) Decomposition at High Temperatures. J Phys Chem A 2017; 121:6200-6210. [PMID: 28704051 DOI: 10.1021/acs.jpca.7b04282] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Theoretical and experimental results are presented for the pyrolytic decomposition of the nerve agent sarin (GB) in the gas phase. High-level quantum chemistry calculations are performed together with a semiclassical transition-state theory for describing quantum mechanical tunneling. The experimental and theoretical results for the temperature dependence of the survival times show very good agreement, as does the calculated and measured activation energy for thermal decomposition. The combined results suggest that the thermal decomposition of GB, for temperature ranging from 350 to 500 °C, goes through a pericyclic reaction mechanism with a transition state consisting of a six-membered ring structure.
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11
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Recent advances in quantum scattering calculations on polyatomic bimolecular reactions. Chem Soc Rev 2017; 46:7625-7649. [DOI: 10.1039/c7cs00526a] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review surveys quantum scattering calculations on chemical reactions of polyatomic molecules in the gas phase published in the last ten years.
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12
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Differential steric effects in Cl reactions with aligned CHD3(v1 = 1) by the R(0) and Q(1) transitions. II. Abstracting the unexcited D-atoms. J Chem Phys 2016; 145:144306. [DOI: 10.1063/1.4964653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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13
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Differential steric effects in Cl reactions with aligned CHD3(v1 = 1) by the R(0) and Q(1) transitions. I. Attacking the excited C–H bond. J Chem Phys 2016; 145:144305. [DOI: 10.1063/1.4964652] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Vibrational Control of Bimolecular Reactions with Methane by Mode, Bond, and Stereo Selectivity. Annu Rev Phys Chem 2016; 67:91-111. [DOI: 10.1146/annurev-physchem-040215-112522] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Angular Scattering Dynamics of the CH4 + Cl → CH3 + HCl Reaction Using Nearside-Farside, Local Angular Momentum, and Resummation Theories. J Phys Chem B 2016; 120:2020-32. [PMID: 26625096 DOI: 10.1021/acs.jpcb.5b10189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The differential cross section (DCS) for the CH4 + Cl → CH3 + HCl reaction is studied at six total energies where all of the species are in their ground states. The scattering (S) matrix elements have been calculated by the rotating line umbrella method for a dual-level ab initio analytic potential energy surface. We make the first application to this reaction of nearside-farside (NF) and local angular momentum (LAM) techniques, including resummation orders (r) of 0, 1, 2, and 3 for the partial-wave series representation of the full scattering amplitude. We find that resummation usually cleans the NF r = 0 DCSs of unphysical oscillations, especially at small angles. This cleaning effect is typically most pronounced when changing from no resummation (r = 0) to r = 1; further resummations from r = 1 to r = 2 and from r = 2 to r = 3 have smaller effects. The NF DCS analyses show that the reaction is N-dominated at sideward and large angles, whereas at small angles there are oscillations caused by NF interference. The NF LAM analysis provides consistent and complementary information, in particular for the total angular momenta that contribute to the reaction at different scattering angles. The NF analyses also provide justification for simpler N-dominant dynamical theories such as the semiclassical optical model, which provides an explanation for the distorted mirror image effect for the moduli of the S matrix elements and the DCSs, as well as the use of a hard-sphere DCS over limited angular ranges.
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Rotational Mode Specificity in Cl + CH4(v3=1,|jNl⟩): Role of Reactant’s Vibrational Angular Momentum. J Phys Chem A 2016; 120:4799-804. [DOI: 10.1021/acs.jpca.5b12156] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Reduced-Dimensionality Semiclassical Transition State Theory: Application to Hydrogen Atom Abstraction and Exchange Reactions of Hydrocarbons. J Phys Chem A 2015; 119:12015-27. [DOI: 10.1021/acs.jpca.5b04379] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Nonadiabatic Transition State Theory and Trajectory Surface Hopping Dynamics: Intersystem Crossing Between 3B1 and 1A1 States of SiH2. J Phys Chem A 2015; 119:1332-8. [DOI: 10.1021/jp509515e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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22
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Quantum reaction dynamics study of vibrational excitation effects on the Cl+CHD3/CD4→HCl/DCl+CD3 reactions. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.04.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Reaction Dynamics of Methane with F, O, Cl, and Br on ab Initio Potential Energy Surfaces. J Phys Chem A 2014; 118:2839-64. [DOI: 10.1021/jp500085h] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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How to measure a complete set of polarization-dependent differential cross sections in a scattering experiment with aligned reagents? J Chem Phys 2014; 140:084202. [DOI: 10.1063/1.4865673] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Crossed-beam and reduced dimensionality studies of the state-to-state integral cross sections of the Cl+HCD3(v)→HCl(v′)+CD3 reaction. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.09.038] [Citation(s) in RCA: 7] [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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27
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Quantum effects in the abstraction reaction by H atoms of primary and secondary hydrogens in n-C4H10: a test of a new potential energy surface construction method. Phys Chem Chem Phys 2013; 15:1222-31. [PMID: 23223355 DOI: 10.1039/c2cp42911j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recently, von Horsten et al. suggested an efficient method to construct two dimensional potential energy surfaces (PESs) for use in quantum scattering simulations, in which they utilised the minimum energy path (MEP) and assumed harmonic behaviour of the PES near the MEP. In the same paper, the authors applied this method to various H-abstraction reactions from C1-C3 alkane molecules. In this work we demonstrate an alternative PES construction method, and apply it to the more challenging H-abstraction from n-C(4)H(10) reactions. The geometry optimizations and frequency calculations are done at the MP2/cc-pVTZ level of theory, while the energies are calculated with the CCSD(T) method with the same basis set. The calculations give adiabatic energy barrier heights of 45.9 kJ mol(-1) and 34.4 kJ mol(-1) for the primary and secondary hydrogens in n-C(4)H(10). When compared to purely classical transition state theory, quantum scattering calculations show that quantum tunnelling and zero-point effects have large contributions at low temperatures, typically below 500 K. The branching ratio study suggests that the abstraction of secondary hydrogen in n-C(4)H(10) dominates the overall reaction rate at low temperatures. The rate constants for the two abstraction channels become more comparable as the temperature increases.
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A reduced dimensionality quantum mechanical study of the H + HCF3 ↔ H2 + CF3 reaction. Phys Chem Chem Phys 2013; 15:18530-8. [DOI: 10.1039/c3cp52170b] [Citation(s) in RCA: 6] [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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29
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Translational energy dependence of the Cl + CH4(vb = 0, 1) reactions: a joint crossed-beam and quasiclassical trajectory study. Mol Phys 2012. [DOI: 10.1080/00268976.2012.662600] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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30
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Revealing the stereospecific chemistry of the reaction of Cl with aligned CHD3(ν1 = 1). Nat Chem 2012; 4:636-41. [DOI: 10.1038/nchem.1383] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 05/17/2012] [Indexed: 11/09/2022]
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31
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Accurate ab initio potential energy surface, thermochemistry, and dynamics of the Cl(2P, 2P3/2) + CH4 → HCl + CH3 and H + CH3Cl reactions. J Chem Phys 2012; 136:044307. [DOI: 10.1063/1.3679014] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Quantum dynamics study of the Cl + CH4 → HCl + CH3 reaction: reactive resonance, vibrational excitation reactivity, and rate constants. Phys Chem Chem Phys 2012; 14:13656-62. [DOI: 10.1039/c2cp41917c] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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An efficient route to thermal rate constants in reduced dimensional quantum scattering simulations: Applications to the abstraction of hydrogen from alkanes. J Chem Phys 2011; 135:094311. [DOI: 10.1063/1.3625960] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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