scholarly journals New Insight into the Chloroacetanilide Herbicide Degradation Mechanism through a Nucleophilic Attack of Hydrogen Sulfide

2018 ◽  
Vol 19 (10) ◽  
pp. 2864 ◽  
Author(s):  
José Mora ◽  
Cristian Cervantes ◽  
Edgar Marquez
Keyword(s):  
Hydrogen Sulfide ◽  
Reaction Mechanism ◽  
Activation Barrier ◽  
Degradation Mechanism ◽  
Reaction Force ◽  
Transition States ◽  
Reaction Coordinate ◽  
Basis Sets ◽  
Nucleophilic Attack ◽  
Intrinsic Reaction Coordinate

The nucleophilic attack of hydrogen sulfide (HS−) on six different chloroacetanilide herbicides was evaluated theoretically using the dispersion-corrected hybrid functional wB97XD and the 6-311++G(2d,2p) Pople basis sets. The six evaluated substrates were propachlor (A), alachlor (B), metolachlor (C), tioacetanilide (D), β-anilide (E), and methylene (F). Three possible mechanisms were considered: (a) bimolecular nucleophilic substitution (SN2) reaction mechanism, (b) oxygen assistance, and (c) nitrogen assistance. Mechanisms based on O- and N-assistance were discarded due to a very high activation barrier in comparison with the corresponding SN2 mechanism, with the exception of compound F. The N-assistance mechanism for compound F had a free activation energy of 23.52 kcal/mol, which was close to the value for the corresponding SN2 mechanism (23.94 kcal/mol), as these two mechanisms could occur in parallel reactions with almost 50% of each one. In compounds A to D, an important electron-withdrawing effect of the C=O and C=S groups was seen, and consequently, the activation free energies in these SN2 reactions were smaller, with a value of approximately 18 kcal/mol. Instead, compounds E and F, which have a CH2 group in the β-position, presented a higher activation free energy (≈22 kcal/mol). Good agreement was found between experimental and theoretical values for all cases, and a reaction force analysis was performed on the intrinsic reaction coordinate profile in order to gain more details about the reaction mechanism. Finally, from the natural bond orbital (NBO) analysis, it was possible to evaluate the electronic reorganization through the reaction pathway where all the transition states were early in nature in the reaction coordinate (δBav < 50%); the transition states corresponding to compounds A to D turned out to be more synchronous than those for compounds E and F.

scholarly journals On the 3D → 2D Isomerization of Hexaborane(12)

Chemistry ◽  
2021 ◽  
Vol 3 (1) ◽  
pp. 28-38
Author(s):  
Josep M. Oliva-Enrich ◽  
Ibon Alkorta ◽  
José Elguero ◽  
Maxime Ferrer ◽  
José I. Burgos
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Transition States ◽  
Three Dimensional ◽  
Reaction Coordinate ◽  
Intrinsic Reaction Coordinate ◽  
Limiting Factor ◽  
Two Dimensional ◽  
Axis Of Rotation

By following the intrinsic reaction coordinate connecting transition states with energy minima on the potential energy surface, we have determined the reaction steps connecting three-dimensional hexaborane(12) with unknown planar two-dimensional hexaborane(12). In an effort to predict the potential synthesis of finite planar borane molecules, we found that the reaction limiting factor stems from the breaking of the central boron-boron bond perpendicular to the C2 axis of rotation in three-dimensional hexaborane(12).

Reaction mechanism of 1,2-hydrogen migration of hydrogen peroxide

1990 ◽  
Vol 68 (5) ◽  
pp. 666-673 ◽  
Author(s):  
Enric Bosch ◽  
José M. Lluch ◽  
Juan Bertrán
Keyword(s):  
Hydrogen Peroxide ◽  
Reaction Mechanism ◽  
Water Molecule ◽  
Energy Barrier ◽  
Electron Distribution ◽  
Reaction Path ◽  
Bifunctional Catalyst ◽  
Reaction Coordinate ◽  
Intrinsic Reaction Coordinate ◽  
Hydrogen Migration

The 1,2-hydrogen migration of hydrogen peroxide has been investigated by abinitio methods and the Intrinsic Reaction Coordinate (IRC) has been constructed. An analysis of the evolution of the electron distribution along the reaction path has shown that the shifting hydrogen behaves as a proton. This transferring proton polarizes the O—O bond of the hydrogen peroxide that becomes broken at the transition state. If a water molecule is allowed to participate in the reaction, the energy barrier is noticeably lowered, this water molecule acting as a bifunctional catalyst. Keywords: 1,2-hydrogen migration, hydrogen peroxide, proton transfer, bifunctional catalyst, Intrinsic Reaction Coordinate.

scholarly journals The reaction force: Three key points along an intrinsic reaction coordinate

2005 ◽  
Vol 117 (5) ◽  
pp. 467-472 ◽  
Author(s):  
Peter Politzer ◽  
Alejandro Toro-Labbé ◽  
Soledad Gutiérrez-Oliva ◽  
Bárbara Herrera ◽  
Pablo Jaque ◽  
...  
Keyword(s):  
Reaction Force ◽  
Reaction Coordinate ◽  
Intrinsic Reaction Coordinate ◽  
Key Points

scholarly journals Automating the IRC Analysis within Eyringpy

2021 ◽  
Author(s):  
Alan Quintal ◽  
Eugenia Dzib ◽  
Filiberto Ortíz ◽  
Pablo Jaque ◽  
Albeiro Restrepo Cossio ◽  
...  
Keyword(s):  
Chemical Property ◽  
Human Error ◽  
Dipole Moments ◽  
Reaction Force ◽  
Chemical Properties ◽  
Reaction Coordinate ◽  
Intrinsic Reaction Coordinate ◽  
Data Set ◽  
Wiberg Bond Indices ◽  
Input Format

To analyze the evolution of a chemical property along the reaction path, we have to extract all the necessary information from a set of electronic structure computations. However, this process is time-consuming and prone to human error. Here we introduce IRC-Analysis, a new extension in Eyringpy, to monitor the evolution of chemical properties along the intrinsic reaction coordinate, including complete reaction force analysis. IRC-Analysis collects the entire data set for each point on the reaction coordinate, eliminating human error in data capture and allowing the study of several chemical reactions in seconds, regardless of the complexity of the systems. Eyringpy has a simple input format, and no programming skills are required. A tracer has been included to visualize the evolution of a given chemical property along the reaction coordinate. Several properties can be analyzed at the same time. This version can analysis the evolution of bond distances and angles, Wiberg bond indices, natural charges, dipole moments, and orbital energies (and related properties).

Theoretical Study of the Mechanism of the 1CBr2 + 3O2 Reaction

2011 ◽  
Vol 356-360 ◽  
pp. 31-34
Author(s):  
Cong Yun Shi ◽  
Jiao Zhang ◽  
Xing Zhong Liu
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Reaction Mechanisms ◽  
Energy Surface ◽  
Theoretical Study ◽  
Transition States ◽  
Reaction Coordinate ◽  
Intrinsic Reaction Coordinate ◽  
Singlet Potential Energy Surface

A detailed theoretical study was done in order to clarify the reaction mechanisms of the singlet dibromocarbene (1CBr2) with3O2on the singlet potential energy surface (PES). All the geometries of reactants, intermediates, transition states and products were obtained at the B3LYP/6-311++G(d,p) level. Intrinsic reaction coordinate (IRC) calculations at the same level were carried out to confirm the connections between transition states and intermediates. It is found that the initial adduct Br2COO (Cs) is formed via a barrierless association in the1CBr2+3O2reaction, and then some isomerizations and breakages of bonds take place, generating P1(BrCO + BrO), P2(CO + Br2O), P3(CO2+ Br2) and P4(CO2+ 2Br). P3(CO2+ Br2) is the most competitive channel kinetically and thermodynamically. P4(CO2+ 2Br) is the least favorable one kinetically.

scholarly journals Homogeneous Gold Catalysis: Mechanistic Investigation of Hydroalkoxylation of Various Alkynes

2021 ◽  
Author(s):  
◽  
Zhi Xiang Wong
Keyword(s):  
Density Functional ◽  
Activation Barrier ◽  
Gold Atom ◽  
Gold Catalysis ◽  
Basis Sets ◽  
Nucleophilic Attack ◽  
Enol Ether ◽  
Hydrogen Migration ◽  
Mechanistic Investigation ◽  
Internal Alkyne

<p>The reaction mechanism of the gold(III)-catalysed hydroalkoxylation of alkynes is studied to provide a deeper understanding of homogeneous gold catalysis. The study is conducted computationally using Density Functional Theory (DFT), with the PBE0 and BP86 functionals and basis sets of triple-ζ quality (aug-cc-pVTZ and aug-cc-pVTZ-PP for the gold atom). It emphasises the mechanisms undergone by various alkynes when they are activated by gold(III) catalysts towards nucleophilic attack to first form an enol ether and followed by a second nucleophilic attack to form a ketal as the final product. Hydrogen bonding networks formed by the solvent methanols are found to play a crucial role in the mechanism especially in the hydrogen migration steps that follow after the nucleophilic attacks. The first nucleophilic attacks are predicted to have rather low activation energies and hence they are expected to proceed fast while the second additions vary in activation barriers, depending on the steric effects in the substrates. The activation barrier for the last hydrogen migration is highest for all of the three reactions investigated and is expected to be the rate determining step. Investigations of internal alkyne reactions reveal that each elementary step requires a higher activation energy compared to terminal alkynes, which explains the low experimental rate of such reactions. Due to the regioselectivity problem in internal alkyne reactions, this results in a mixture of products which is difficult to isolate due to the similarities in their reaction energies. The study also highlights the calculated thermodynamics and kinetics of the reactions, which can be useful in predicting experimental outcomes. Arrhenius plots of concentration of each intermediate species against time were produced to further help the understanding of these mechanisms, whether or not the reactions go to full completion or stop at the formation of enol ether.</p>

scholarly journals Prediction of Mechanism and Thermochemical Properties of O3+ H2S Atmospheric Reaction

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Morteza Vahedpour ◽  
Reza Baghary ◽  
Freshte Khalili
Keyword(s):  
Hydrogen Sulfide ◽  
Reaction Mechanism ◽  
Oxygen Atom ◽  
Atmospheric Pressure ◽  
Vibrational Frequency ◽  
Main Reaction ◽  
Intrinsic Reaction Coordinate ◽  
Thermochemical Properties ◽  
Frequency Calculation ◽  
Atmospheric Reaction

Ozone and hydrogen sulfide reaction mechanism including a complex was studied at the B3LYP/6-311++G(3df,3pd) and CCSD/6-311++G(3df,3pd)//B3LYP/6-311++G(3df,3pd) levels of computation. The interaction between sulfur atom of hydrogen sulfide and terminal oxygen atom of ozone produces a stable H2S-O3complex with no barrier. With the decomposition of this complex, four possible product channels have been found. Intrinsic reaction coordinate, topological analyses of atom in molecule, and vibrational frequency calculation have been used to confirm the suggested mechanism. Thermodynamic data atT= 298.15 K and the atmospheric pressure have been calculated. The results show that the production of H2O + SO2is the main reaction channel with ΔG° = −645.84 kJ/mol. Rate constants of H2S + O3reaction show two product channels, SO2 + H2O and HSO + HOO, which compete with each other based on the temperature.

scholarly journals Homogeneous Gold Catalysis: Mechanistic Investigation of Hydroalkoxylation of Various Alkynes

2021 ◽  
Author(s):  
◽  
Zhi Xiang Wong
Keyword(s):  
Density Functional ◽  
Activation Barrier ◽  
Gold Atom ◽  
Gold Catalysis ◽  
Basis Sets ◽  
Nucleophilic Attack ◽  
Enol Ether ◽  
Hydrogen Migration ◽  
Mechanistic Investigation ◽  
Internal Alkyne

<p>The reaction mechanism of the gold(III)-catalysed hydroalkoxylation of alkynes is studied to provide a deeper understanding of homogeneous gold catalysis. The study is conducted computationally using Density Functional Theory (DFT), with the PBE0 and BP86 functionals and basis sets of triple-ζ quality (aug-cc-pVTZ and aug-cc-pVTZ-PP for the gold atom). It emphasises the mechanisms undergone by various alkynes when they are activated by gold(III) catalysts towards nucleophilic attack to first form an enol ether and followed by a second nucleophilic attack to form a ketal as the final product. Hydrogen bonding networks formed by the solvent methanols are found to play a crucial role in the mechanism especially in the hydrogen migration steps that follow after the nucleophilic attacks. The first nucleophilic attacks are predicted to have rather low activation energies and hence they are expected to proceed fast while the second additions vary in activation barriers, depending on the steric effects in the substrates. The activation barrier for the last hydrogen migration is highest for all of the three reactions investigated and is expected to be the rate determining step. Investigations of internal alkyne reactions reveal that each elementary step requires a higher activation energy compared to terminal alkynes, which explains the low experimental rate of such reactions. Due to the regioselectivity problem in internal alkyne reactions, this results in a mixture of products which is difficult to isolate due to the similarities in their reaction energies. The study also highlights the calculated thermodynamics and kinetics of the reactions, which can be useful in predicting experimental outcomes. Arrhenius plots of concentration of each intermediate species against time were produced to further help the understanding of these mechanisms, whether or not the reactions go to full completion or stop at the formation of enol ether.</p>

DFT studies on the diastereoselectivity of four-component Ugi reaction

2018 ◽  
Vol 17 (06) ◽  
pp. 1850039 ◽  
Author(s):  
Elaheh Sadat Sharifzadeh ◽  
Nader Zabarjad Shiraz
Keyword(s):  
Reaction Mechanism ◽  
Ring Opening ◽  
Transition States ◽  
Ugi Reaction ◽  
Ring Closure ◽  
Nucleophilic Attack ◽  
Dft Studies ◽  
Acid Base ◽  
Bond Rotation ◽  
Iminium Ion

In this study, mechanism and stereochemistry of four-component Ugi reaction was investigated theoretically. Structures of reagents, products, intermediates, and transition states were optimized at B3LYP/6-31[Formula: see text]G(d,p) level of theory. Mechanism and stereoselectivity of the reaction depended on several processes, including bond rotation, ring closure ring opening, acid-base, nucleophile-electrophile competitions, and rearrangements. These diverse phenomena were studied to provide a clearer picture of the mechanism of this valuable reaction, especially in terms of stereochemistry considerations. According to the results, (E)-oxazolidinols were considered as proper intermediates in Ugi reaction mechanism. In addition, the key point of diastereoselectivity of the reaction was under kinetic and thermodynamic controls of nucleophilic attack of isocyanide to less hindered re-face (E[Formula: see text] compared to 10.19[Formula: see text]kcal/mol for si-face) of chiral (E)-iminium ion.

scholarly journals Quantum chemical study of reaction mechanism between plutonium and Nitrogen

2021 ◽  
Author(s):  
Zhao-Yang Zhao ◽  
Guo-Liang Wang ◽  
Xu-Dan Chen ◽  
Chun-Bao Qi ◽  
Xin-Li Sun
Keyword(s):  
Reaction Mechanism ◽  
Potential Energy ◽  
Transition State ◽  
Density Functional ◽  
Transition States ◽  
Reaction Pathways ◽  
Stationary Points ◽  
Main Reaction ◽  
Intrinsic Reaction Coordinate ◽  
Phase Reaction

Abstract The study of the reaction between plutonium and nitrogen is helpful to further understand the interaction between plutonium and air gas molecules. For the nitridation reaction of plutonium, there is no report on the microscopic reaction mechanism of this system at present. Therefore, the microcospic mechanism of gas phase reaction of Pu with N 2 is studied in this paper based on the density functional theory (DFT) using different functions. In this paper, the geometry of stationary points on the potential energy surface is optimized. In addition, the transition states are verified by the frequency analysis method and the intrinsic reaction coordinate (IRC) method. Finally, we obtain the reaction potential energy curve and the micro reaction pathways. The analysis of reaction mechanism shows that the reaction of Pu with N 2 has two pathways. The pathway-1 (Pu+N 2 →R1→TS1→PuN 2 ) has a T-shaped transition state and the pathway-2 (Pu+N 2 →R 2 →TS 2 →PuN+N) has a L-shaped transition state. Moreover, both transition states have only one virtual frequency. The energy analysis shows that pathway-1 is the main reaction pathway. The nature of the Pu-N bonding evolution along the pathways is studied by atoms in molecules (AIM) and electron localization function (ELF) topological approaches. In order to analyse the role of 5f orbital of plutonium atom in the reaction, the variation of density of state along the pathways is performed. The results show that the 5f orbital makes major contributions to the formation of Pu-N bonds. Meanwhile, the influence of different temperatures on the reaction rate is revealed by calculating the rate constants of the two reaction pathways.

Sign in / Sign up

Export Citation Format

Share Document