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Molecular Dynamics Study on Chemical Reactions
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Molecular Dynamics Study on Chemical Reactions

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: 31 May 2024 | Viewed by 1754

Special Issue Editor

Dr. Yongle Li

E-Mail Website
Guest Editor
Department of Physics, Shanghai University, Shanghai, China
Interests: semiclassical dynamics; molecular dynamics; phase transitions

Special Issue Information

Dear Colleagues,

Molecular dynamics is a powerful tool under the union of theoretical chemistry and computational science. It reveals the real-time trajectory of a system in real space. Additionally, it provides both thermodynamic and kinetic information. In the area of research of chemical reactions, it has invaluable power in answering the cardinal question of chemistry: how the reaction occurs. Energized by the cutting-edge advances of both theories and computational techniques, today’s molecular dynamics can simulate both the electronic and nuclear quantum effects, be applied in a wide range of gas phases, surfaces, and condensed phases, and includes a huge amount of degree of freedom. All of these advances have contributed to revealing the details of chemical reactions. The main focus of this Special Issue is thus on articles describing novel theories, technologies, algorithms, software and novel applications, including classical molecular dynamics, semiclassical dynamics, and quantum dynamics, combined with force field, QM/MM, ab initio calculations and machine learning, in studying a varity of chemical reactions. By collecting contributions from scientists specializing in the field, this Special Issue will provide an overview of the latest advances and newest developments in various fields, revealing time-dependent information of reaction systems. We invite investigators to contribute research articles and reviews describing recent findings involving applying or developing novel methods of molecular dynamics to investigate chemical reactions.

Dr. Yongle Li
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular dynamics
  • chemical reactions
  • mechanism
  • kinetics
  • quantum dynamics
  • semiclassical dynamics

Published Papers (2 papers)

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Research

13 pages, 7186 KiB  
Article
State-to-State Quantum Dynamics Study of Intramolecular Isotope Effects on Be(1S) + HD (v0 = 2, j0 = 0) → BeH/BeD + H/D Reaction
by Hongtai Xu and Zijiang Yang
Molecules 2024, 29(6), 1263; https://doi.org/10.3390/molecules29061263 - 13 Mar 2024
Viewed by 471
Abstract
The dynamic mechanisms and intramolecular isotope effects of the Be(1S) + HD (v0 = 2, j0 = 0) → BeH/BeD + H/D reaction are studied at the state-to-state level using the time-dependent wave packet method on a high-quality [...] Read more.
The dynamic mechanisms and intramolecular isotope effects of the Be(1S) + HD (v0 = 2, j0 = 0) → BeH/BeD + H/D reaction are studied at the state-to-state level using the time-dependent wave packet method on a high-quality potential energy surface. This reaction can proceed along the indirect pathway that features a barrier and a deep well or the smooth direct pathway. The reaction probabilities, total and state-resolved integral cross sections, and differential cross sections are analyzed in detail. The calculated dynamics results show that both of the products are mainly formed by the dissociation of a collinear HBeD intermediate when the collision energy is slightly larger than the threshold. As the collision energy increases, the BeH + D channel is dominated by the direct abstraction process, whereas the BeD + H channel mainly follows the complex-forming mechanism. Full article
(This article belongs to the Special Issue Molecular Dynamics Study on Chemical Reactions)
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24 pages, 28213 KiB  
Article
Reactivity of the Ethenium Cation (C2H5+) with Ethyne (C2H2): A Combined Experimental and Theoretical Study
by Vincent Richardson, Miroslav Polášek, Claire Romanzin, Paolo Tosi, Roland Thissen, Christian Alcaraz, Ján Žabka and Daniela Ascenzi
Molecules 2024, 29(4), 810; https://doi.org/10.3390/molecules29040810 - 09 Feb 2024
Viewed by 706
Abstract
The gas-phase reaction between the ethyl cation (C2H5+) and ethyne (C2H2) is re-investigated by measuring absolute reactive cross sections (CSs) and branching ratios (BRs) as a function of collision energy, in the thermal and [...] Read more.
The gas-phase reaction between the ethyl cation (C2H5+) and ethyne (C2H2) is re-investigated by measuring absolute reactive cross sections (CSs) and branching ratios (BRs) as a function of collision energy, in the thermal and hyperthermal energy range, via tandem-guided ion beam mass spectrometry under single collision conditions. Dissociative photoionization of C2H5Br using tuneable VUV radiation in the range 10.5–14.0 eV is employed to generate C2H5+, which has also allowed us to explore the impact of increasing (vibrational) excitation on the reactivity. Reactivity experiments are complemented by theoretical calculations, at the G4 level of theory, of the relative energies and structures of the most relevant stationary points on the reactive potential energy hypersurface (PES) and by mass-analyzed ion kinetic energy (MIKE) spectrometry experiments to probe the metastable decomposition from the [C4H7]+ PES and elucidate the underlying reaction mechanisms. Two main product channels have been identified at a centre-of-mass collision energy of ∼0.1 eV: (a) C3H3++CH4, with BR = 0.76±0.05 and (b) C4H5++H2, with BR = 0.22±0.02. A third channel giving C2H3+ in association with C2H4 is shown to emerge at both high internal excitation of C2H5+ and high collision energies. From CS measurements, energy-dependent total rate constants in the range 4.3×10−11−5.2×10−10 cm3·molecule−1·s−1 have been obtained. Theoretical calculations indicate that both channels stem from a common covalently bound intermediate, CH3CH2CHCH+, from which barrierless and exothermic pathways exist for the production of both cyclic c−C3H3+ and linear H2CCCH+ isomers of the main product channel. For the minor C4H5+ product, two isomers are energetically accessible: the three-member cyclic isomer c−C3H2(CH3)+ and the higher energy linear structure CH2CHCCH2+, but their formation requires multiple isomerization steps and passages via transition states lying only 0.11 eV below the reagents’ energy, thus explaining the smaller BR. Results have implications for the modeling of hydrocarbon chemistry in the interstellar medium and the atmospheres of planets and satellites as well as in laboratory plasmas (e.g., plasma-enhanced chemical vapor deposition of carbon nanotubes and diamond-like carbon films). Full article
(This article belongs to the Special Issue Molecular Dynamics Study on Chemical Reactions)
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