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Theoretical Investigations of Reaction Mechanisms II

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

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 18116

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Dr. Maxim L. Kuznetsov

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

Molecular design, optimization of reaction conditions, and the planning of a chemical synthesis cannot be achieved without knowledge of reaction mechanisms and driving forces of chemical processes. Computational methods of quantum chemistry represent a powerful tool for the understanding of the reaction mechanisms and key factors governing chemical reactions. Such methods are indispensable for the interpretation and analysis of experimental results and provide invaluable information, complementary to the experimental data, about molecular systems and processes. Computational methods are extremely valuable 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. This is a second edition of the Special Issue on this topic. Previously unpublished manuscripts that report mechanistic studies of any organic, inorganic or organometallic reactions with help of computational methods or deal with understanding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

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Keywords

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

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Related Special Issues

Theoretical Investigations of Reaction Mechanisms II in Chemistry (5 articles)
Theoretical Investigations of Reaction Mechanisms in Molecules (17 articles)

Published Papers (9 papers)

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Research

17 pages, 5964 KiB

Open AccessArticle

Performance and Mechanism of Chlorine Dioxide on BTEX Removal in Liquid and Indoor Air

by Anlong Wang, Yina Qiao, Yufan Zhang, Riya Jin, Jiaoqin Liu, Zengdi He, Mengye Jia, Jingshuai Gao and Chengjie Guo

Molecules 2023, 28(11), 4342; https://doi.org/10.3390/molecules28114342 - 25 May 2023

Cited by 1 | Viewed by 1905

Abstract

With the development of the chemical industry, benzene, toluene, ethylbenzene, and xylene (BTEX) have gradually become the major indoor air pollutants. Various gas treatment techniques are widely used to prevent the physical and mental health hazards of BTEX in semi-enclosed spaces. Chlorine dioxide (ClO₂) is an alternative to chlorine as a secondary disinfectant with a strong oxidation ability, a wide range of action, and no carcinogenic effects. In addition, ClO₂ has a unique permeability which allows it to eliminate volatile contaminants from the source. However, little attention has been paid to the removal of BTEX by ClO₂, due to the difficulty of removing BTEX in semi-enclosed areas and the lack of testing methods for the reaction intermediates. Therefore, this study explored the performance of ClO₂ advanced oxidation technology on both liquid and gaseous benzene, toluene, o-xylene, and m-xylene. The results showed that ClO₂ was efficient in the removal of BTEX. The byproducts were detected by gas chromatography-mass spectrometry (GC-MS) and the reaction mechanism was speculated using the ab initio molecular orbital calculations method. The results demonstrated that ClO₂ could remove the BTEX from the water and the air without causing secondary pollution. Full article

(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)

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20 pages, 3450 KiB

Open AccessArticle

Strong External Electric Fields Reduce Explosive Sensitivity: A Theoretical Investigation into the Reaction Selectivity in NH₂NO₂∙∙∙NH₃

by Fu-De Ren, Ying-Zhe Liu, Xiao-Lei Wang, Li-Li Qiu, Zi-Hui Meng, Xiang Cheng and Yong-Xiang Li

Molecules 2023, 28(6), 2586; https://doi.org/10.3390/molecules28062586 - 13 Mar 2023

Cited by 3 | Viewed by 1743

Abstract

Controlling the selectivity of a detonation initiation reaction of explosive is essential to reduce sensitivity, and it seems impossible to reduce it by strengthening the external electric field. To verify this, the effects of external electric fields on the initiation reactions in NH₂NO₂∙∙∙NH₃, a model system of the nitroamine explosive with alkaline additive, were investigated at the MP2/6-311++G(2d,p) and CCSD(T)/6-311++G(2d,p) levels. The concerted effect in the intermolecular hydrogen exchange is characterized by an index of the imaginary vibrations. Due to the weakened concerted effects by the electric field along the −x-direction opposite to the “reaction axis”, the dominant reaction changes from the intermolecular hydrogen exchange to 1,3-intramolecular hydrogen transference with the increase in the field strengths. Furthermore, the stronger the field strengths, the higher the barrier heights become, indicating the lower sensitivities. Therefore, by increasing the field strength and adjusting the orientation between the field and “reaction axis”, not only can the reaction selectivity be controlled, but the sensitivity can also be reduced, in particular under a super-strong field. Thus, a traditional concept, in which the explosive is dangerous under the super-strong external electric field, is theoretically broken. Compared to the neutral medium, a low sensitivity of the explosive with alkaline can be achieved under the stronger field. Employing atoms in molecules, reduced density gradient, and surface electrostatic potentials, the origin of the reaction selectivity and sensitivity change is revealed. This work provides a new idea for the technical improvement regarding adding the external electric field into the explosive system. Full article

(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)

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14 pages, 8100 KiB

Open AccessArticle

Computational Exploration of Dirhodium Complex-Catalyzed Selective Intermolecular Amination of Tertiary vs. Benzylic C−H Bonds

by Xing-Xing Su, Xia-He Chen, De-Bo Ding, Yuan-Bin She and Yun-Fang Yang

Molecules 2023, 28(4), 1928; https://doi.org/10.3390/molecules28041928 - 17 Feb 2023

Cited by 2 | Viewed by 2450

Abstract

The mechanism and origins of site-selectivity of Rh₂(S-tfpttl)₄-catalyzed C(sp³)–H bond aminations were studied using density functional theory (DFT) calculations. The synergistic combination of the dirhodium complex Rh₂(S-tfpttl)₄ with tert-butylphenol sulfamate TBPhsNH₂ composes a pocket that can access both tertiary and benzylic C–H bonds. The nonactivated tertiary C–H bond was selectively aminated in the presence of an electronically activated benzylic C–H bond. Both singlet and triplet energy surfaces were investigated in this study. The computational results suggest that the triplet stepwise pathway is more favorable than the singlet concerted pathway. In the hydrogen atom abstraction by Rh–nitrene species, which is the rate- and site-selectivity-determining step, there is an attractive π–π stacking interaction between the phenyl group of the substrate and the phthalimido group of the ligand in the tertiary C–H activation transition structure. By contrast, such attractive interaction is absent in the benzylic C–H amination transition structure. Therefore, the DFT computational results clearly demonstrate how the synergistic combination of the dirhodium complex with sulfamate overrides the intrinsic preference for benzylic C–H amination to achieve the amination of the nonactivated tertiary C–H bond. Full article

(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)

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21 pages, 7385 KiB

Open AccessArticle

Catalytic Oxidation of Benzoins by Hydrogen Peroxide on Nanosized HKUST-1: Influence of Substituents on the Reaction Rates and DFT Modeling of the Reaction Path

by Darya V. Yurchenko, Anton S. Lytvynenko, Emir N. Abdullayev, Nina V. Peregon, Konstantin S. Gavrilenko, Alina O. Gorlova, Sergey V. Ryabukhin, Dmitriy M. Volochnyuk and Sergey V. Kolotilov

Molecules 2023, 28(2), 747; https://doi.org/10.3390/molecules28020747 - 11 Jan 2023

Cited by 2 | Viewed by 1708

Abstract

In this research, the oxidation of a series of benzoins, R-C(=O)-CH(OH)-R, where R = phenyl, 4-methoxyphenyl, 4-bromophenyl, and 2-naphthyl, by hydrogen peroxide in the presence of nanostructured HKUST-1 (suspension in acetonitrile/water mixture) was studied. The respective benzoic acids were the only products of the reactions. The initial average reaction rates were experimentally determined at different concentrations of benzoin, H₂O₂ and an effective concentration of HKUST-1. The sorption of the isotherms of benzoin, dimethoxybenzoin and benzoic acid on HKUST-1, as well as their sorption kinetic curves, were measured. The increase in H₂O₂ concentration expectedly led to an acceleration of the reaction. The dependencies of the benzoin oxidation rates on the concentrations of both benzoin and HKUST-1 passed through the maxima. This finding could be explained by a counterplay between the increasing reaction rate and increasing benzoin sorption on the catalyst with the increase in the concentration. The electronic effect of the substituent in benzoin had a significant influence on the reaction rate, while no relation between the size of the substrate molecule and the rate of its oxidation was found. It was confirmed by DFT modeling that the reaction could pass through the Baeyer–Villiger mechanism, involving an attack by the HOO⁻ anion on the C atom of the activated C=O group. Full article

(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)

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8 pages, 2332 KiB

Open AccessFeature PaperArticle

A DFT Study of the Reaction of Acrylamide with L-Cysteine and L-Glutathione

by Sandra Ramirez-Montes, Luis A. Zárate-Hernández, Jose A. Rodriguez, Eva M. Santos and Julián Cruz-Borbolla

Molecules 2022, 27(23), 8220; https://doi.org/10.3390/molecules27238220 - 25 Nov 2022

Cited by 2 | Viewed by 2722

Abstract

Thermal processing of certain foods implies the formation of acrylamide, which has been proven to provoke adverse effects on human health. Thus, several strategies to mitigate it have been developed. One of them could be the application of organosulfur compounds obtained from natural sources to react with the acrylamide, forming non-toxic adducts. A DFT study of the acrylamide reaction with the organosulfur model compounds L-cysteine and L-glutathione by Michael addition and a free radical pathway complemented by a kinetic study of these model molecules has been applied. The kinetic evaluation results demonstrate that the L-glutathione reaction exhibited a higher rate constant than the other studied compound. Full article

(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)

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14 pages, 5356 KiB

Open AccessArticle

Nucleophilic Substitution at Tricoordinate Sulfur—Alkaline Hydrolysis of Optically Active Dialkoxysulfonium Salts: Stereochemistry, Mechanism and Reaction Energetics

by Marian Mikołajczyk, Bogdan Bujnicki, Józef Drabowicz and Marek Cypryk

Molecules 2022, 27(23), 8212; https://doi.org/10.3390/molecules27238212 - 25 Nov 2022

Cited by 1 | Viewed by 1553

Abstract

Optically active dialkoxyisopropylsulfonium salts were obtained by methylation (ethylation) of optically active alkyl isopropanesulfinates using methyl (ethyl) trifluoromethanesulfonate. Alkaline hydrolysis of a series of methoxy(alkoxy)sulfonium salts afforded the two sulfinate products methyl isopropanesulfinate and alkyl isopropanesulfinate, both formed with a slightly prevailing inversion of configuration at the sulfur atom. DFT calculations revealed that this substitution reaction proceeded stepwise according to an addition-elimination (A–E) mechanism involving the formation of high tetracoordinate S^IV sulfurane intermediates. In addition, the DFT calculations showed that recombination of the hydroxy anion with the methoxy(alkoxy)sulfonium cation—leading to the parallel formation of the two most stable primary sulfuranes, with the hydroxy and alkoxy groups in apical positions and their direct decomposition—is the most energetically favorable pathway. Full article

(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)

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17 pages, 3281 KiB

Open AccessArticle

A Theoretical Study of the C–X Bond Cleavage Mediated by Cob(II)Aloxime

by Luis E. Seijas, Cesar H. Zambrano, Vladimir Rodríguez, Jorge Alí-Torres, Luis Rincón and F. Javier Torres

Molecules 2022, 27(21), 7283; https://doi.org/10.3390/molecules27217283 - 26 Oct 2022

Viewed by 1671

Abstract

The C–X bond cleavage in different methyl halides (CH₃X; X = Cl, Br, I) mediated by 5,6-dimethylbenzimidazole-bis(dimethylglyoximate)cobalt(II) (Co^IICbx) was theoretically investigated in the present work. An S_N2-like mechanism was considered to simulate the chemical process where the cobalt atom acts as the nucleophile and the halogen as the leaving group. The reaction path was computed by means of the intrinsic reaction coordinate method and analyzed in detail through the reaction force formalism, the quantum theory of atoms in molecules (QTAIM), and the calculation of one-electron density derived quantities, such as the source function (SF) and the spin density. A thorough comparison of the results with those obtained in the same reaction occurring in presence of 5,6-dimethylbenzimidazole-bis(dimethylglyoximate)cobalt(I) (Co^ICbx) was conducted to reveal the main differences between the two cases. The reactions mediated by Co^IICbx were observed to be endothermic and possess higher activation energies in contrast to the reactions where the Co^ICbx complex is present. The latter was supported by the reaction force results, which suggest a relationship between the activation energy and the ionization potentials of the different nucleophiles present in the cleavage reaction. Moreover, the SF results indicates that the lower axial ligand (i.e., 5,6-dimethylbenzimidazole) exclusively participates on the first stage of the reaction mediated by the Co^IICbx complex, while for the Co^ICbx case, it appears to have an important role along the whole process. Finally, the QTAIM charge analysis indicates that oxidation of the cobalt atom occurs in both cases; at the same time, it suggests the formation of an uncommon two-center one-electron bond in the Co^IICbx case. The latter was confirmed by means of electron localization calculations, which resulted in a larger electron count at the Co–C interatomic region for the Co^ICbx case upon comparison with its Co^IICbx counterpart. Full article

(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)

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13 pages, 5258 KiB

Open AccessArticle

Metal-Free Phosphination and Continued Functionalization of Pyridine: A Theoretical Study

by Pan Du, Yuhao Yin, Dai Shi, Kexin Mao, Qianyuan Yu and Jiyang Zhao

Molecules 2022, 27(17), 5694; https://doi.org/10.3390/molecules27175694 - 3 Sep 2022

Cited by 2 | Viewed by 2010

Abstract

This study investigates the mechanism of metal-free pyridine phosphination with P(OEt)₃, PPh₃, and PAr₂CF₃ using density functional theory calculations. The results show that the reaction mechanism and rate-determining step vary depending on the phosphine and additive used. For example, phosphination of pyridine with P(OEt)₃ occurs in five stages, and ethyl abstraction is the rate-determining step. Meanwhile, 2-Ph-pyridine phosphination with PPh₃ is a four-step reaction with proton abstraction as the rate-limiting step. Energy decomposition analysis of the transition states reveals that steric hindrance in the phosphine molecule plays a key role in the site-selective formation of the phosphonium salt. The mechanism of 2-Ph-pyridine phosphination with PAr₂CF₃ is similar to that with PPh₃, and analyses of the effects of substituents show that electron-withdrawing groups decreased the nucleophilicity of the phosphine, whereas aryl electron-donating groups increased it. Finally, TfO⁻ plays an important role in the C–H fluoroalkylation of pyridine, as it brings weak interactions. Full article

(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)

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13 pages, 2261 KiB

Open AccessArticle

Tuning the Intramolecular Chemiexcitation of Neutral Dioxetanones by Interaction with Ionic Species

by Carla M. Magalhães, Joaquim C. G. Esteves da Silva and Luís Pinto da Silva

Molecules 2022, 27(12), 3861; https://doi.org/10.3390/molecules27123861 - 16 Jun 2022

Cited by 4 | Viewed by 1386

Abstract

The intramolecular chemiexcitation of high-energy peroxide intermediates, such as dioxetanones, is an essential step in different chemi- and bioluminescent reactions. Here, we employed the Time-Dependent Density Functional Theory (TD-DFT) methodology to evaluate if and how external stimuli tune the intramolecular chemiexcitation of model dioxetanones. More specifically, we evaluated whether the strategic placement of ionic species near a neutral dioxetanone model could tune its thermolysis and chemiexcitation profile. We found that these ionic species allow for the “dark” catalysis of the thermolysis reaction by reducing the activation barrier to values low enough to be compatible with efficient chemi- and bioluminescent reactions. Furthermore, while the inclusion of these species negatively affected the chemiexcitation profile compared with neutral dioxetanones, these profiles appear to be at least as efficient as anionic dioxetanones. Thus, our results demonstrated that the intramolecular chemiexcitation of neutral dioxetanones can be tuned by external stimuli in such a way that their activation barriers are decreased. Thus, these results could help to reconcile findings that neutral dioxetanones could be responsible for efficient chemi-/bioluminescence, while being typically associated with high activation parameters. Full article

(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms II)

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