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 ◽  
...  
Author(s):  
Alan Quintal ◽  
Eugenia Dzib ◽  
Filiberto Ortíz ◽  
Pablo Jaque ◽  
Albeiro Restrepo Cossio ◽  
...  

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).


2018 ◽  
Vol 19 (10) ◽  
pp. 2864 ◽  
Author(s):  
José Mora ◽  
Cristian Cervantes ◽  
Edgar Marquez

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.


Chemistry ◽  
2021 ◽  
Vol 3 (1) ◽  
pp. 28-38
Author(s):  
Josep M. Oliva-Enrich ◽  
Ibon Alkorta ◽  
José Elguero ◽  
Maxime Ferrer ◽  
José I. Burgos

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).


1990 ◽  
Vol 68 (5) ◽  
pp. 666-673 ◽  
Author(s):  
Enric Bosch ◽  
José M. Lluch ◽  
Juan Bertrán

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.


ChemInform ◽  
2016 ◽  
Vol 47 (4) ◽  
pp. no-no
Author(s):  
Satoshi Maeda ◽  
Yu Harabuchi ◽  
Yuriko Ono ◽  
Tetsuya Taketsugu ◽  
Keiji Morokuma

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