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Theoretical Investigations of Reaction Mechanisms
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Theoretical Investigations of Reaction Mechanisms

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

Deadline for manuscript submissions: closed (31 May 2019) | Viewed by 68143

Special Issue Editor

Dr. Maxim L. Kuznetsov

E-Mail Website
Guest Editor
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
Special Issues, Collections and Topics in MDPI journals

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 Previously unpublished manuscripts that report mechanistic studies of any organic, inorganic or organometallic reactions with help of computational methods or deal with understanding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

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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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Published Papers (17 papers)

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Research

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12 pages, 2519 KiB  
Article
A Mechanistic Study on the Tautomerism of H-Phosphonates, H-Phosphinates and Secondary Phosphine Oxides
by Daniella Vincze, Péter Ábrányi-Balogh, Péter Bagi and György Keglevich
Molecules 2019, 24(21), 3859; https://doi.org/10.3390/molecules24213859 - 25 Oct 2019
Cited by 25 | Viewed by 3858
Abstract
H-phosphonates, H-phosphinates and secondary phosphine oxides may be preligands, and are important building blocks in the synthesis of pharmaceuticals, pesticides, and P-ligands. The prototropic tautomerism influenced by substituent effects plays an important role in the reactivity of these species. The [...] Read more.
H-phosphonates, H-phosphinates and secondary phosphine oxides may be preligands, and are important building blocks in the synthesis of pharmaceuticals, pesticides, and P-ligands. The prototropic tautomerism influenced by substituent effects plays an important role in the reactivity of these species. The main goal of our research was to study the tautomerism of the >P(O)H reagents by means of computational investigations applying several DFT methods at different levels. We focused on the effect of implicit solvents, and on explaining the observed trends with physical chemical molecular descriptors. In addition, multiple reaction pathways incorporating three P-molecules were elucidated for the mechanism of the interconversion. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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18 pages, 1123 KiB  
Article
Simplification of Carbon Bond Mechanism IV (CBM-IV) under Different Initial Conditions by Using Concentration Sensitivity Analysis
by Le Cao, Simeng Li, Ziwei Yi and Mengmeng Gao
Molecules 2019, 24(13), 2463; https://doi.org/10.3390/molecules24132463 - 04 Jul 2019
Cited by 5 | Viewed by 2525
Abstract
Carbon Bond Mechanism IV (CBM-IV) is a widely used reaction mechanism in which VOCs are grouped according to the molecular structure. In the present study, we applied a sensitivity analysis on the CBM-IV mechanism to clarify the importance of each reaction under two [...] Read more.
Carbon Bond Mechanism IV (CBM-IV) is a widely used reaction mechanism in which VOCs are grouped according to the molecular structure. In the present study, we applied a sensitivity analysis on the CBM-IV mechanism to clarify the importance of each reaction under two different initial conditions (urban and low-NOx scenarios). The reactions that exert minor influence on the reaction system are then screened out from the mechanism, so that a reduced version of the CBM-IV mechanism under specific initial conditions can be obtained. We found that in a typical urban condition, 11 reactions can be removed from the original CBM-IV mechanism, and the deviation is less than 5% between the results using the original CBM-IV mechanism and the reduced mechanism. Moreover, in a low-NOx initial condition, two more reactions, both of which are nitrogen-associated reactions, can be screened out from the reaction mechanism, while the accuracy of the simulation is still maintained. It is estimated that the reduction of the CBM-IV mechanism can save 11–14% of the computing time in the calculation of the chemistry in a box model simulation. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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12 pages, 1832 KiB  
Article
Formation Mechanism of Benzo(a)pyrene: One of the Most Carcinogenic Polycyclic Aromatic Hydrocarbons (PAH)
by Edina Reizer, Imre G. Csizmadia, Árpád B. Palotás, Béla Viskolcz and Béla Fiser
Molecules 2019, 24(6), 1040; https://doi.org/10.3390/molecules24061040 - 15 Mar 2019
Cited by 26 | Viewed by 9546
Abstract
The formation of polycyclic aromatic hydrocarbons (PAHs) is a strong global concern due to their harmful effects. To help the reduction of their emissions, a crucial understanding of their formation and a deep exploration of their growth mechanism is required. In the present [...] Read more.
The formation of polycyclic aromatic hydrocarbons (PAHs) is a strong global concern due to their harmful effects. To help the reduction of their emissions, a crucial understanding of their formation and a deep exploration of their growth mechanism is required. In the present work, the formation of benzo(a)pyrene was investigated computationally employing chrysene and benz(a)anthracene as starting materials. It was assumed a type of methyl addition/cyclization (MAC) was the valid growth mechanism in this case. Consequently, the reactions implied addition reactions, ring closures, hydrogen abstractions and intramolecular hydrogen shifts. These steps of the mechanism were computed to explore benzo(a)pyene formation. The corresponding energies of the chemical species were determined via hybrid density funcional theory (DFT), B3LYP/6-31+G(d,p) and M06-2X/6-311++G(d,p). Results showed that the two reaction routes had very similar trends energetically, the difference between the energy levels of the corresponding molecules was just 6.13 kJ/mol on average. The most stable structure was obtained in the benzo(a)anthracene pathway. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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10 pages, 1521 KiB  
Article
First-Principles Study of the Reaction between Fluorinated Graphene and Ethylenediamine
by Jin Tian, Yuhong Chen, Jing Wang, Tingting Liu, Meiling Zhang and Cairong Zhang
Molecules 2019, 24(2), 284; https://doi.org/10.3390/molecules24020284 - 14 Jan 2019
Viewed by 3041
Abstract
The reaction process between gauche- and trans-structure ethylenediamine (EDA) and fluorinated graphene (CF) was studied based on density functional theory (DFT). Firstly, the reaction between the most stable gauche-structure EDA and CF was discussed. Some of the reaction results were verified in experiment, [...] Read more.
The reaction process between gauche- and trans-structure ethylenediamine (EDA) and fluorinated graphene (CF) was studied based on density functional theory (DFT). Firstly, the reaction between the most stable gauche-structure EDA and CF was discussed. Some of the reaction results were verified in experiment, but the overall reaction energy barrier was higher. Then, the reaction between the trans-structured EDA and CF was simulated, which concluded that CF is reduced in the main reaction channel and HF is generated at the same time. In this reaction process, the reaction energy barrier is as low as 0.81 eV, which indicates that the reaction may occur spontaneously under natural conditions The Mulliken charge population analysis and the calculation of bond energy prove that the NH bond is more stable than CH and that the H atoms in the CH2 of trans-structure EDA more easily react with CF. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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20 pages, 8928 KiB  
Article
Reaction between Indazole and Pd-Bound Isocyanides—A Theoretical Mechanistic Study
by Girolamo Casella, Maurizio Casarin, Vadim Yu. Kukushkin and Maxim L. Kuznetsov
Molecules 2018, 23(11), 2942; https://doi.org/10.3390/molecules23112942 - 10 Nov 2018
Cited by 3 | Viewed by 3570
Abstract
The mechanism of the addition of indazole (Ind)—a bifunctional aromatic N,NH-nucleophile—to cyclohexyl isocyanide coordinated to the palladium(II) center in the model complex cis-[PdCl2(CNMe)(CNCy)] (1) to give the corresponding aminocarbene ligand was investigated in detail by theoretical (DFT) methods. [...] Read more.
The mechanism of the addition of indazole (Ind)—a bifunctional aromatic N,NH-nucleophile—to cyclohexyl isocyanide coordinated to the palladium(II) center in the model complex cis-[PdCl2(CNMe)(CNCy)] (1) to give the corresponding aminocarbene ligand was investigated in detail by theoretical (DFT) methods. The most plausible mechanism of this reaction is that of the associative type involving nucleophilic attack of Ind by its unprotonated N atom at the isocyanide carbon atom followed by the stepwise proton transfer from the nucleophile molecule to the isocyanide N atom via deprotonation/protonation steps. Two reaction channels based on two tautomeric forms of indazole were found. The channel leading to the experimentally isolated aminocarbene product is based on the less stable tautomeric form. Another channel based on the more stable tautomer of Ind is slightly kinetically more favorable but it is endergonic. Thus, the regioselectivity of this reaction is thermodynamically rather than kinetically driven. The bonding situation in key species was analyzed. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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14 pages, 3123 KiB  
Article
Theoretical Investigations on the Reactivity of Hydrogen Peroxide toward 2,3,7,8-Tetrachlorodibenzo-p-dioxin
by Weihua Wang, Yuhua Wang, Wenling Feng, Wenliang Wang and Ping Li
Molecules 2018, 23(11), 2826; https://doi.org/10.3390/molecules23112826 - 31 Oct 2018
Cited by 4 | Viewed by 3228
Abstract
Acquiring full knowledge of the reactivity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is crucial for the better understanding of the transformation and degradation of TCDD-like dioxins in the environment. To clarify the reactivity of the organic hydroperoxides toward TCDD, in this study, the reactions [...] Read more.
Acquiring full knowledge of the reactivity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is crucial for the better understanding of the transformation and degradation of TCDD-like dioxins in the environment. To clarify the reactivity of the organic hydroperoxides toward TCDD, in this study, the reactions between the neutral/anion of the hydrogen peroxide (H2O2) and TCDD have been systematically investigated theoretically. It was found that the neutral H2O2 is relatively difficult to react with TCDD compared with its anion, exhibiting the pH dependence of the title reaction. As for the anion of H2O2, it reacts with TCDD through two reaction mechanisms, i.e., nucleophilic substitution and nucleophilic addition. For the former, the terminal O atom of HO2− nucleophilically attacks the C atom of the C-Cl bond in TCDD to form an intermediate containing an O-O bond, accompanying the dissociation of the chlorine atom. For the latter, the terminal O atom of HO2− can be easily attached to the C atom of the C-O bond in TCDD, resulting in the decomposition of C-O bond and the formation of an intermediate containing an O-O bond. For these formed intermediates in both reaction mechanisms, their O-O bonds can be homolytically cleaved to produce different radicals. In addition, the selected substitution effects including F-, Br-, and CH3- substituents on the above reactions have also been studied. Hopefully, the present results can provide new insights into the reactivity of the organic hydroperoxides toward TCDD-like environmental pollutants. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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18 pages, 7197 KiB  
Article
Theoretical Investigations on the Reactivity of Methylidyne Radical toward 2,3,7,8-Tetrachlorodibenzo-p-Dioxin: A DFT and Molecular Dynamics Study
by Weihua Wang, Wenling Feng, Wenliang Wang and Ping Li
Molecules 2018, 23(10), 2685; https://doi.org/10.3390/molecules23102685 - 18 Oct 2018
Cited by 1 | Viewed by 3917
Abstract
To explore the potential reactivity of the methylidyne radical (CH) toward 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the reaction mechanism between them has been systematically investigated employing the density functional theory (DFT) and ab initio molecular dynamics simulations. The relevant thermodynamic and kinetic parameters in [...] Read more.
To explore the potential reactivity of the methylidyne radical (CH) toward 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the reaction mechanism between them has been systematically investigated employing the density functional theory (DFT) and ab initio molecular dynamics simulations. The relevant thermodynamic and kinetic parameters in the possible reaction pathways have been discussed as well as the IR spectra and hyperfine coupling constants (hfcc’s) of the major products. Different from the reaction of the CH radical with 2,3,7,8-tetrachlorodibenzofuran, CH radical can attack all the C-C bonds of TCDD to form an initial intermediate barrierlessly via the cycloaddition mechanism. After then, the introduced C-H bond can be further inserted into the C-C bond of TCDD, resulting in the formation of a seven-membered ring structure. The whole reactions are favorable thermodynamically and kinetically. Moreover, the major products have been verified by ab initio molecular dynamics simulations. The distinct IR spectra and hyperfine coupling constants of the major products can provide some help for their experimental detection and identification. In addition, the reactivity of the CH radical toward the F- and Br-substituted TCDDs has also been investigated. Hopefully, the present findings can provide new insights into the reactivity of the CH radical in the transformation of TCDD-like dioxins. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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13 pages, 2781 KiB  
Article
Ab Initio Molecular Dynamics Simulation Study on the Stereo Reactions between Atomic Oxygen Anion and Methane
by Weihua Wang, Wenling Feng, Wenliang Wang and Ping Li
Molecules 2018, 23(10), 2495; https://doi.org/10.3390/molecules23102495 - 29 Sep 2018
Cited by 7 | Viewed by 3201
Abstract
Ion–molecule reaction between atomic oxygen anion (O−) and methane (CH4) has been systematically investigated employing the on-the-fly ab initio molecular dynamics simulations. Besides the major H-abstraction process as the exothermic reaction studied widely, an endothermic pathway to produce OCH [...] Read more.
Ion–molecule reaction between atomic oxygen anion (O−) and methane (CH4) has been systematically investigated employing the on-the-fly ab initio molecular dynamics simulations. Besides the major H-abstraction process as the exothermic reaction studied widely, an endothermic pathway to produce OCH3− and H is also observed in this study. Three typical O− attack modes with reference to the pyramid structure of CH4 fixed in space have been considered. It was found that the internal motions of the radical products are significantly dependent on the O− attack modes. As for the reaction between O− and the thermally vibrating CH4, the major pathway to produce OH− and CH3 is preferred by the direct H-abstraction and the minor pathway to produce H and OCH3− is the roaming reaction via the transient negative ion [HO-CH3]−. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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14 pages, 3335 KiB  
Article
Theoretical Insights into the Electron Capture Behavior of H2SO4···N2O Complex: A DFT and Molecular Dynamics Study
by Wei-Hua Wang, Wen-Ling Feng, Wen-Liang Wang and Ping Li
Molecules 2018, 23(9), 2349; https://doi.org/10.3390/molecules23092349 - 13 Sep 2018
Cited by 2 | Viewed by 3876
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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12 pages, 576 KiB  
Article
One-Electron Reduction Potentials: Calibration of Theoretical Protocols for Morita–Baylis–Hillman Nitroaromatic Compounds in Aprotic Media
by Amauri Francisco da Silva, Antonio João da Silva Filho, Mário L. A. A. Vasconcellos and Otávio Luís de Santana
Molecules 2018, 23(9), 2129; https://doi.org/10.3390/molecules23092129 - 24 Aug 2018
Cited by 3 | Viewed by 3149
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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14 pages, 3305 KiB  
Article
Theoretical Study of the C2H5 + HO2 Reaction: Mechanism and Kinetics
by Nan-Nan Wu, Ming-Zhe Zhang, Shun-Li Ou-Yang and Liang Li
Molecules 2018, 23(8), 1919; https://doi.org/10.3390/molecules23081919 - 01 Aug 2018
Cited by 2 | Viewed by 3350
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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17 pages, 4796 KiB  
Article
A Molecular Electron Density Theory Study of the Competitiveness of Polar Diels–Alder and Polar Alder-ene Reactions
by Luis R. Domingo, Mar Ríos-Gutiérrez and Patricia Pérez
Molecules 2018, 23(8), 1913; https://doi.org/10.3390/molecules23081913 - 31 Jul 2018
Cited by 14 | Viewed by 4378
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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12 pages, 7239 KiB  
Article
Theoretical Studies on Catalysis Mechanisms of Serum Paraoxonase 1 and Phosphotriesterase Diisopropyl Fluorophosphatase Suggest the Alteration of Substrate Preference from Paraoxonase to DFP
by Hao Zhang, Ling Yang, Ying-Ying Ma, Chaoyuan Zhu, Shenghsien Lin and Rong-Zhen Liao
Molecules 2018, 23(7), 1660; https://doi.org/10.3390/molecules23071660 - 07 Jul 2018
Cited by 11 | Viewed by 3409
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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13 pages, 2508 KiB  
Article
A Photophysical Deactivation Channel of Laser-Excited TATB Based on Semiclassical Dynamics Simulation and TD-DFT Calculation
by Wenying Zhang, Jian Sang, Jie Cheng, Siyu Ge, Shuai Yuan, Glenn V. Lo and Yusheng Dou
Molecules 2018, 23(7), 1593; https://doi.org/10.3390/molecules23071593 - 30 Jun 2018
Cited by 3 | Viewed by 3784
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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13 pages, 7290 KiB  
Article
Theoretical Study of the Photolysis Mechanisms of Methylpentaphenyldimetallanes (Ph3MM′Ph2Me; M, M′ = Si and Ge)
by Shih-Hao Su and Ming-Der Su
Molecules 2018, 23(6), 1351; https://doi.org/10.3390/molecules23061351 - 04 Jun 2018
Cited by 2 | Viewed by 3196
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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13 pages, 5160 KiB  
Article
Theoretical Investigations on Mechanisms and Pathways of C2H5O2 with BrO Reaction in the Atmosphere
by Chenggang Lu, Yizhen Tang, Wei Zhang, Xunshuai Qu and Zhihao Fu
Molecules 2018, 23(6), 1268; https://doi.org/10.3390/molecules23061268 - 25 May 2018
Cited by 1 | Viewed by 3139
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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Review

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21 pages, 5671 KiB  
Review
A Trajectory-Based Method to Explore Reaction Mechanisms
by Saulo A. Vázquez, Xose L. Otero and Emilio Martinez-Nunez
Molecules 2018, 23(12), 3156; https://doi.org/10.3390/molecules23123156 - 30 Nov 2018
Cited by 31 | Viewed by 5925
Abstract
The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental [...] Read more.
The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral 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 different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described. Full article
(This article belongs to the Special Issue Theoretical Investigations of Reaction Mechanisms)
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