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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: closed (31 October 2024) | Viewed by 5283

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

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Keywords

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

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Published Papers (5 papers)

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Research

17 pages, 4321 KiB  
Article
Theoretical Investigation of Rate Coefficients and Dynamical Mechanisms for N + N + N Three-Body Recombination Based on Full-Dimensional Potential Energy Surfaces
by Chong Xu, Zhenxuan Wei, Huayu Hu, Xixi Hu and Daiqian Xie
Molecules 2024, 29(20), 4933; https://doi.org/10.3390/molecules29204933 - 18 Oct 2024
Viewed by 530
Abstract
Three-body recombination reactions, in which two particles form a bound state while a third one bounces off after the collision, play significant roles in many fields, such as cold and ultracold chemistry, astrochemistry, atmospheric physics, and plasma physics. In this work, the dynamics [...] Read more.
Three-body recombination reactions, in which two particles form a bound state while a third one bounces off after the collision, play significant roles in many fields, such as cold and ultracold chemistry, astrochemistry, atmospheric physics, and plasma physics. In this work, the dynamics of the recombination reaction for the N3 system over a wide temperature range (5000–20,000 K) are investigated in detail using the quasi-classical trajectory (QCT) method based on recently developed full-dimensional potential energy surfaces. The recombination products are N2(X) + N(4S) in the 14A″ state, N2(A) + N(4S) in the 24A″ state, and N2(X) + N(2D) in both the 12A″ and 22A″ states. A three-body collision recombination model involving two sets of relative translational energies and collision parameters and a time-delay parameter is adopted in the QCT calculations. The recombination process occurs after forming an intermediate with a certain lifetime, which has a great influence on the recombination probability. Recombination processes occurring through a one-step three-body collision mechanism and two distinct two-step binary collision mechanisms are found in each state. And the two-step exchange mechanism is more dominant than the two-step transfer mechanism at higher temperatures. N2(X) formed in all three related states is always the major recombination product in the temperature range from 5000 K to 20,000 K, with the relative abundance of N2(A) increasing as temperature decreases. After hyperthermal collisions, the formed N2(X/A) molecules are distributed in highly excited rotational and vibrational states, with internal energies mainly distributed near the dissociation threshold. Additionally, the rate coefficients for this three-body recombination reaction in each state are determined and exhibit a negative correlation with temperature. The dynamic insights presented in this work might be very useful to further simulate non-equilibrium dynamic processes in plasma physics involving N3 systems. Full article
(This article belongs to the Special Issue Molecular Dynamics Study on Chemical Reactions)
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19 pages, 5534 KiB  
Article
A Globally Accurate Neural Network Potential Energy Surface and Quantum Dynamics Studies on Be+(2S) + H2/D2 → BeH+/BeD+ + H/D Reactions
by Zijiang Yang, Furong Cao, Huiying Cheng, Siwen Liu and Jingchang Sun
Molecules 2024, 29(14), 3436; https://doi.org/10.3390/molecules29143436 - 22 Jul 2024
Cited by 1 | Viewed by 813
Abstract
Chemical reactions between Be+ ions and H2 molecules have significance in the fields of ultracold chemistry and astrophysics, but the corresponding dynamics studies on the ground-state reaction have not been reported because of the lack of a global potential energy surface [...] Read more.
Chemical reactions between Be+ ions and H2 molecules have significance in the fields of ultracold chemistry and astrophysics, but the corresponding dynamics studies on the ground-state reaction have not been reported because of the lack of a global potential energy surface (PES). Herein, a globally accurate ground-state BeH2+ PES is constructed using the neural network model based on 18,657 ab initio points calculated by the multi-reference configuration interaction method with the aug-cc-PVQZ basis set. On the newly constructed PES, the state-to-state quantum dynamics calculations of the Be+(2S) + H2(v0 = 0; j0 = 0) and Be+(2S) + D2(v0 = 0; j0 = 0) reactions are performed using the time-dependent wave packet method. The calculated results suggest that the two reactions are dominated by the complex-forming mechanism and the direct abstraction process at relatively low and high collision energies, respectively, and the isotope substitution has little effect on the reaction dynamics characteristics. The new PES can be used to further study the reaction dynamics of the BeH2+ system, such as the effects of rovibrational excitations and alignment of reactant molecules, and the present dynamics data could provide an important reference for further experimental studies at a finer level. Full article
(This article belongs to the Special Issue Molecular Dynamics Study on Chemical Reactions)
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13 pages, 3969 KiB  
Article
The Cholinergic Selectivity of FDA-Approved and Metabolite Compounds Examined with Molecular-Docking-Based Virtual Screening
by Michael D. Gambardella, Yigui Wang and Jiongdong Pang
Molecules 2024, 29(10), 2333; https://doi.org/10.3390/molecules29102333 - 16 May 2024
Cited by 1 | Viewed by 792
Abstract
The search for selective anticholinergic agents stems from varying cholinesterase levels as Alzheimer’s Disease progresses from the mid to late stage. In this computational study, we probed the selectivity of FDA-approved and metabolite compounds against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) with molecular-docking-based virtual [...] Read more.
The search for selective anticholinergic agents stems from varying cholinesterase levels as Alzheimer’s Disease progresses from the mid to late stage. In this computational study, we probed the selectivity of FDA-approved and metabolite compounds against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) with molecular-docking-based virtual screening. The results were evaluated using locally developed codes for the statistical methods. The docking-predicted selectivity for AChE and BChE was predominantly the consequence of differences in the volume of the active site and the narrower entrance to the bottom of the active site gorge of AChE. Full article
(This article belongs to the Special Issue Molecular Dynamics Study on Chemical Reactions)
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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
Cited by 1 | Viewed by 904
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 - 9 Feb 2024
Viewed by 1334
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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