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Special Issue "Theoretical Investigations of Reaction Mechanisms"

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

Deadline for manuscript submissions: 30 November 2018

Special Issue Editor

Guest Editor
Dr. Maxim L. Kuznetsov

Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
Website | E-Mail
Interests: computational chemistry; coordination chemistry; molecular catalysis; oxidation of hydrocarbons; activation of small molecules; reaction mechanism; chemical bond nature; cycloaddition; nitriles

Special Issue Information

Dear Colleagues,

Knowledge of reaction mechanisms and driving forces of chemical processes is crucial for the molecular design, the optimization of reaction conditions, and the planning of a chemical synthesis. Elucidation of reaction mechanisms and key factors controlling chemical reactions may be effectively achieved using computational quantum chemical methods, which represent very powerful tools for the interpretation and understanding of experimental results and provide invaluable information, complementary to the experimental data, about molecular systems and processes. Computational methods are indispensable for mechanistic studies of reactions proceeding via formation of short-lived intermediates that cannot be detected experimentally, being the only possibility to obtain information about intimate details of the chemical processes when experimental methods cannot help in the understanding of the reaction mechanisms. Previously unpublished manuscripts that report mechanistic studies of any organic, inorganic or organometallic reactions with help of computational methods or deal with understanding of the key factors and driving forces governing chemical processes are welcome for this Special Issue.

Dr. Maxim L. Kuznetsov
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 papers will be 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 monthly 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 1800 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

  • reaction mechanism
  • computational chemistry
  • density functional theory
  • ab initio
  • quantum chemical calculations
  • reactivity
  • molecular design
  • activation

Published Papers (8 papers)

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Research

Open AccessArticle Theoretical Insights into the Electron Capture Behavior of H2SO4···N2O Complex: A DFT and Molecular Dynamics Study
Molecules 2018, 23(9), 2349; https://doi.org/10.3390/molecules23092349
Received: 18 August 2018 / Revised: 4 September 2018 / Accepted: 5 September 2018 / Published: 13 September 2018
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Abstract
Both sulfuric acid (H2SO4) and nitrous oxide (N2O) play a central role in the atmospheric chemistry in regulating the global environment and climate changes. In this study, the interaction behavior between H2SO4 and N
[...] Read more.
Both sulfuric acid (H2SO4) and nitrous oxide (N2O) play a central role in the atmospheric chemistry in regulating the global environment and climate changes. In this study, the interaction behavior between H2SO4 and N2O before and after electron capture has been explored using the density functional theory (DFT) method as well as molecular dynamics simulation. The intermolecular interactions have been characterized by atoms in molecules (AIM), natural bond orbital (NBO), and reduced density gradient (RDG) analyses, respectively. It was found that H2SO4 and N2O can form two transient molecular complexes via intermolecular H-bonds within a certain timescale. However, two molecular complexes can be transformed into OH radical, N2, and HSO4 species upon electron capture, providing an alternative formation source of OH radical in the atmosphere. Expectedly, the present findings not only can provide new insights into the transformation behavior of H2SO4 and N2O, but also can enable us to better understand the potential role of the free electron in driving the proceeding of the relevant reactions in the atmosphere. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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Open AccessArticle One-Electron Reduction Potentials: Calibration of Theoretical Protocols for Morita–Baylis–Hillman Nitroaromatic Compounds in Aprotic Media
Molecules 2018, 23(9), 2129; https://doi.org/10.3390/molecules23092129
Received: 30 July 2018 / Revised: 9 August 2018 / Accepted: 11 August 2018 / Published: 24 August 2018
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Abstract
Nitroaromatic compounds—adducts of Morita–Baylis–Hillman (MBHA) reaction—have been applied in the treatment of malaria, leishmaniasis, and Chagas disease. The biological activity of these compounds is directly related to chemical reactivity in the environment, chemical structure of the compound, and reduction of the nitro group.
[...] Read more.
Nitroaromatic compounds—adducts of Morita–Baylis–Hillman (MBHA) reaction—have been applied in the treatment of malaria, leishmaniasis, and Chagas disease. The biological activity of these compounds is directly related to chemical reactivity in the environment, chemical structure of the compound, and reduction of the nitro group. Because of the last aspect, electrochemical methods are used to simulate the pharmacological activity of nitroaromatic compounds. In particular, previous studies have shown a correlation between the one-electron reduction potentials in aprotic medium (estimated by cyclic voltammetry) and antileishmanial activities (measured by the IC50) for a series of twelve MBHA. In the present work, two different computational protocols were calibrated to simulate the reduction potentials for this series of molecules with the aim of supporting the molecular modeling of new pharmacological compounds from the prediction of their reduction potentials. The results showed that it was possible to predict the experimental reduction potential for the calibration set with mean absolute errors of less than 25 mV (about 0.6 kcal·mol−1). Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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Open AccessArticle Theoretical Study of the C2H5 + HO2 Reaction: Mechanism and Kinetics
Molecules 2018, 23(8), 1919; https://doi.org/10.3390/molecules23081919
Received: 24 May 2018 / Revised: 26 July 2018 / Accepted: 27 July 2018 / Published: 1 August 2018
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Abstract
The mechanism and kinetics for the reaction of the HO2 radical with the ethyl (C2H5) radical have been investigated theoretically. The electronic structure information of the potential energy surface (PES) is obtained at the MP2/6-311++G(d,p) level of theory,
[...] Read more.
The mechanism and kinetics for the reaction of the HO2 radical with the ethyl (C2H5) radical have been investigated theoretically. The electronic structure information of the potential energy surface (PES) is obtained at the MP2/6-311++G(d,p) level of theory, and the single-point energies are refined by the CCSD(T)/6-311+G(3df,2p) level of theory. The kinetics of the reaction with multiple channels have been studied by applying variational transition-state theory (VTST) and Rice–Ramsperger–Kassel–Marcus (RRKM) theory over wide temperature and pressure ranges (T = 220–3000 K; P = 1 × 10−4–100 bar). The calculated results show that the HO2 radical can attack C2H5 via a barrierless addition mechanism to form the energy-rich intermediate IM1 C2H5OOH (68.7 kcal/mol) on the singlet PES. The collisional stabilization intermediate IM1 is the predominant product of the reaction at high pressures and low temperatures, while the bimolecular product P1 C2H5O + OH becomes the primary product at lower pressures or higher temperatures. At the experimentally measured temperature 293 K and in the whole pressure range, the reaction yields P1 as major product, which is in good agreement with experiment results, and the branching ratios are predicted to change from 0.96 at 1 × 10−4 bar to 0.66 at 100 bar. Moreover, the direct H-abstraction product P16 C2H6 + 3O2 on the triplet PES is the secondary feasible product with a yield of 0.04 at the collisional limit of 293 K. The present results will be useful to gain deeper insight into the understanding of the kinetics of the C2H5 + HO2 reaction under atmospheric and practical combustion conditions. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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Open AccessArticle A Molecular Electron Density Theory Study of the Competitiveness of Polar Diels–Alder and Polar Alder-ene Reactions
Molecules 2018, 23(8), 1913; https://doi.org/10.3390/molecules23081913
Received: 16 July 2018 / Revised: 27 July 2018 / Accepted: 28 July 2018 / Published: 31 July 2018
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Abstract
The competitiveness of the BF3 Lewis acid (LA) catalyzed polar Diels–Alder (P-DA) and polar Alder-ene (P-AE) reactions of 2-methyl-1,3-butadiene, a diene possessing an allylic hydrogen, with formaldehyde has been studied within the Molecular Electron Density Theory (MEDT) at the MPWB1K/6-311G(d,p) computational level.
[...] Read more.
The competitiveness of the BF3 Lewis acid (LA) catalyzed polar Diels–Alder (P-DA) and polar Alder-ene (P-AE) reactions of 2-methyl-1,3-butadiene, a diene possessing an allylic hydrogen, with formaldehyde has been studied within the Molecular Electron Density Theory (MEDT) at the MPWB1K/6-311G(d,p) computational level. Coordination of BF3 LA to the oxygen of formaldehyde drastically accelerates both reactions given the high electrophilic character of the BF3:formaldehyde complex. As a consequence, these reactions present a very low activation enthalpy—less than 2.2 kcal·mol−1—thus becoming competitive. In dioxane, the P-AE reaction is slightly favored because of the larger polar character of the corresponding transition state structure (TS). In addition, the Prins reaction between hexahydrophenanthrene and the BF3:formaldehyde complex has also been studied as a computational model of an experimental P-AE reaction. For this LA-catalyzed reaction, the P-DA reaction presents very high activation energy because of the aromatic character of the dienic framework. The present MEDT study allows establishing the similarity of the TSs associated with the formation of the C–C single bond in both reactions, as well as the competitiveness between P-AE and P-DA reactions when the diene substrate possesses at least one allylic hydrogen, thus making it necessary to be considered by experimentalists in highly polar processes. In this work, the term “pseudocyclic selectivity” is suggested to connote the selective formation of structural isomers through stereoisomeric pseudocyclic TSs. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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Graphical abstract

Open AccessArticle Theoretical Studies on Catalysis Mechanisms of Serum Paraoxonase 1 and Phosphotriesterase Diisopropyl Fluorophosphatase Suggest the Alteration of Substrate Preference from Paraoxonase to DFP
Molecules 2018, 23(7), 1660; https://doi.org/10.3390/molecules23071660
Received: 2 June 2018 / Revised: 4 July 2018 / Accepted: 5 July 2018 / Published: 7 July 2018
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Abstract
The calcium-dependent β-propeller proteins mammalian serum paraoxonase 1 (PON1) and phosphotriesterase diisopropyl fluorophosphatase (DFPase) catalyze the hydrolysis of organophosphorus compounds and enhance hydrolysis of various nerve agents. In the present work, the phosphotriesterase activity development between PON1 and DFPase was investigated by using
[...] Read more.
The calcium-dependent β-propeller proteins mammalian serum paraoxonase 1 (PON1) and phosphotriesterase diisopropyl fluorophosphatase (DFPase) catalyze the hydrolysis of organophosphorus compounds and enhance hydrolysis of various nerve agents. In the present work, the phosphotriesterase activity development between PON1 and DFPase was investigated by using the hybrid density functional theory method B3LYP. Based on the active-site difference between PON1 and DFPase, both the wild type and the mutant (a water molecule replacing Asn270 in PON1) models were designed. The results indicated that the substitution of a water molecule for Asn270 in PON1 had little effect on the enzyme activity in kinetics, while being more efficient in thermodynamics, which is essential for DFP hydrolysis. Structure comparisons of evolutionarily related enzymes show that the mutation of Asn270 leads to the catalytic Ca2+ ion indirectly connecting the buried structural Ca2+ ion via hydrogen bonds in DFPase. It can reduce the plasticity of enzymatic structure, and possibly change the substrate preference from paraoxon to DFP, which implies an evolutionary transition from mono- to dinuclear catalytic centers. Our studies shed light on the investigation of enzyme catalysis mechanism from an evolutionary perspective. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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Open AccessArticle A Photophysical Deactivation Channel of Laser-Excited TATB Based on Semiclassical Dynamics Simulation and TD-DFT Calculation
Molecules 2018, 23(7), 1593; https://doi.org/10.3390/molecules23071593
Received: 29 May 2018 / Revised: 23 June 2018 / Accepted: 28 June 2018 / Published: 30 June 2018
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Abstract
A deactivation channel for laser-excited 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) was studied by semiclassical dynamics. Results indicate that the excited state resulting from an electronic transition from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular mrbital (LUMO) is deactivated via pyramidalization of the
[...] Read more.
A deactivation channel for laser-excited 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) was studied by semiclassical dynamics. Results indicate that the excited state resulting from an electronic transition from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular mrbital (LUMO) is deactivated via pyramidalization of the activated N atom in a nitro group, with a lifetime of 2.4 ps. An approximately 0.5-electron transfer from the aromatic ring to the activated nitro group led to a significant increase of the C–NO2 bond length, which suggests that C–NO2 bond breaking could be a trigger for an explosive reaction. The time-dependent density functional theory (TD-DFT) method was used to calculate the energies of the ground and S1 excited states for each configuration in the simulated trajectory. The S1←S0 energy gap at the instance of non-adiabatic decay was found to be 0.096 eV, suggesting that the decay geometry is close to the conical intersection. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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Open AccessArticle Theoretical Study of the Photolysis Mechanisms of Methylpentaphenyldimetallanes (Ph3MM′Ph2Me; M, M′ = Si and Ge)
Molecules 2018, 23(6), 1351; https://doi.org/10.3390/molecules23061351
Received: 12 May 2018 / Revised: 28 May 2018 / Accepted: 1 June 2018 / Published: 4 June 2018
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Abstract
The mechanisms of the photolysis reactions are studied theoretically at the M06-2X/6-311G(d) level of theory, using the four types of group 14 molecules that have the general structure, Ph3M–M′Ph2Me (M and M′ = Si and Ge), as model systems.
[...] Read more.
The mechanisms of the photolysis reactions are studied theoretically at the M06-2X/6-311G(d) level of theory, using the four types of group 14 molecules that have the general structure, Ph3M–M′Ph2Me (M and M′ = Si and Ge), as model systems. This study provides the first theoretical evidence for the mechanisms of these photorearrangements of compounds that contain a M–M′ single bond. The model investigations indicate that the preferred reaction route for the photolysis reactions is, as follows: reactant → Franck-Condon (FC) region → minimum (triplet) → transition state (triplet) → triplet/singlet intersystem crossing → photoproducts (both di-radicals and singlets). The theoretical findings demonstrate that the formation of radicals results from reactions of the triplet states of these reactants. This could be because both the atomic radius and the chemical properties of silicon and germanium are quite similar to each other and compared to other group 14 elements, their photolytic mechanisms are nearly the same. The results for the photolytic mechanisms that are studied in this work are consistent with the available experimental observations and allow for a number of predictions for other group 14 dimetallane analogues to be made. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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Open AccessArticle Theoretical Investigations on Mechanisms and Pathways of C2H5O2 with BrO Reaction in the Atmosphere
Molecules 2018, 23(6), 1268; https://doi.org/10.3390/molecules23061268
Received: 20 April 2018 / Revised: 22 May 2018 / Accepted: 23 May 2018 / Published: 25 May 2018
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Abstract
In this work, feasible mechanisms and pathways of the C2H5O2 + BrO reaction in the atmosphere were investigated using quantum chemistry methods, i.e., QCISD(T)/6-311++G(2df,2p)//B3LYP/6-311++G(2df,2p) levels of theory. Our result indicates that the title reaction occurs on both the
[...] Read more.
In this work, feasible mechanisms and pathways of the C2H5O2 + BrO reaction in the atmosphere were investigated using quantum chemistry methods, i.e., QCISD(T)/6-311++G(2df,2p)//B3LYP/6-311++G(2df,2p) levels of theory. Our result indicates that the title reaction occurs on both the singlet and triplet potential energy surfaces (PESs). Kinetically, singlet C2H5O3Br and C2H5O2BrO were dominant products under the atmospheric conditions below 300 K. CH3CHO2 + HOBr, CH3CHO + HOBrO, and CH3CHO + HBrO2 are feasible to a certain extent thermodynamically. Because of high energy barriers, all products formed on the triplet PES are negligible. Moreover, time-dependent density functional theory (TDDFT) calculation implies that C2H5O3Br and C2H5O2BrO will photolyze under the sunlight. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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Graphical abstract

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Tentative Title: A Trajectory-Based Method to Explore Reactions Mechanisms
Authors: Emilio Martínez-Núñez
Affiliation: Departamento de Química Física, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain  
Abstract: The method tsscds, recently developed by the author, discovers chemical reaction mechanisms with minimal human intervention. The method employs accelerated classical trajectories, graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present review, its application to solve mechanistic/kinetics problems in a number of different research areas will be presented: photodissociation dynamics, mass spectrometry, interstellar chemistry, and organometallic catalysis. The source code can be downloaded from: http://forge.cesga.es/wiki/g/tsscds/HomePage
 
Author: György Keglevich 
Affiliation:Dept of Organic Chemistry and Technology, Budapest University of Technology and Economics, HUNGARY
 
Author: Ian Dance
Affiliation: School of Chemistry, UNSW Australia
 
Author: Fillmore Freeman
Affiliation:University of California, Irvine, Department of Chemistry, Irvine, United States 
 
Author: Weichao Zhang
Affiliation: School of Chemistry and Materials Science, Jiangsu Normal University, China
 
Author: Edyta Dyguda-Kazimierowicz
Affiliation: Wrocław University of Science and Technology, Advanced Materials Engineering and Modelling Group, Wroclaw, Poland 
 
Tentative Title: First-principles study of reaction between fluorographeneand ethylenediamine
Authors: Tian Jin; Chen Y.
Affiliation: School of Science, Lanzhou University of Technology, Lanzhou 730050, China
 
Author: Le Cao
Affiliation: Nanjing University of Information Science and Technology, China
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