scholarly journals Reactants, Products, and Transition States of Elementary Chemical Reactions Based on Quantum Chemistry

2020 ◽  
Author(s):  
Colin Grambow ◽  
Lagnajit Pattanaik ◽  
William H. Green
Keyword(s):  
Quantum Chemistry ◽  
Energy Surface ◽  
Transition States ◽  
Reaction Times ◽  
Activation Energies ◽  
Reaction Prediction ◽  
Surface Exploration ◽  
Reaction Data ◽  
Automated Methods ◽  
Elementary Chemical

Reaction times, activation energies, branching ratios, yields, and many other quantitative attributes are important for precise organic syntheses and generating detailed reaction mechanisms. Often, it would be useful to be able to classify proposed reactions as fast or slow. However, quantitative chemical reaction data, especially for atom-mapped reactions, are difficult to find in existing databases. Therefore, we used automated potential energy surface exploration to generate 12,000 organic reactions involving H, C, N, and O atoms calculated at the ωB97X-D3/def2-TZVP quantum chemistry level. We report the results of geometry optimizations and frequency calculations for reactants, products, and transition states of all reactions. Additionally, we extracted atom-mapped reaction SMILES, activation energies, and enthalpies of reaction. We believe that this data will accelerate progress in automated methods for organic synthesis and reaction mechanism generation—for example, by enabling the development of novel machine learning models for quantitative reaction prediction.

scholarly journals Reactants, Products, and Transition States of Elementary Chemical Reactions Based on Quantum Chemistry

2019 ◽  
Author(s):  
Colin Grambow ◽  
Lagnajit Pattanaik ◽  
William H. Green
Keyword(s):  
Quantum Chemistry ◽  
Energy Surface ◽  
Transition States ◽  
Reaction Times ◽  
Activation Energies ◽  
Reaction Prediction ◽  
Surface Exploration ◽  
Reaction Data ◽  
Automated Methods ◽  
Elementary Chemical

Reaction times, activation energies, branching ratios, yields, and many other quantitative attributes are important for precise organic syntheses and generating detailed reaction mechanisms. Often, it would be useful to be able to classify proposed reactions as fast or slow. However, quantitative chemical reaction data, especially for atom-mapped reactions, are difficult to find in existing databases. Therefore, we used automated potential energy surface exploration to generate 12,000 organic reactions involving H, C, N, and O atoms calculated at the ωB97X-D3/def2-TZVP quantum chemistry level. We report the results of geometry optimizations and frequency calculations for reactants, products, and transition states of all reactions. Additionally, we extracted atom-mapped reaction SMILES, activation energies, and enthalpies of reaction. We believe that this data will accelerate progress in automated methods for organic synthesis and reaction mechanism generation---for example, by enabling the development of novel machine learning models for quantitative reaction prediction.

scholarly journals Reactants, Products, and Transition States of Elementary Chemical Reactions Based on Quantum Chemistry

2020 ◽  
Author(s):  
Colin Grambow ◽  
Lagnajit Pattanaik ◽  
William H. Green
Keyword(s):  
Quantum Chemistry ◽  
Energy Surface ◽  
Transition States ◽  
Reaction Times ◽  
Activation Energies ◽  
Reaction Prediction ◽  
Surface Exploration ◽  
Reaction Data ◽  
Automated Methods ◽  
Elementary Chemical

Reaction times, activation energies, branching ratios, yields, and many other quantitative attributes are important for precise organic syntheses and generating detailed reaction mechanisms. Often, it would be useful to be able to classify proposed reactions as fast or slow. However, quantitative chemical reaction data, especially for atom-mapped reactions, are difficult to find in existing databases. Therefore, we used automated potential energy surface exploration to generate 12,000 organic reactions involving H, C, N, and O atoms calculated at the ωB97X-D3/def2-TZVP quantum chemistry level. We report the results of geometry optimizations and frequency calculations for reactants, products, and transition states of all reactions. Additionally, we extracted atom-mapped reaction SMILES, activation energies, and enthalpies of reaction. We believe that this data will accelerate progress in automated methods for organic synthesis and reaction mechanism generation—for example, by enabling the development of novel machine learning models for quantitative reaction prediction.

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).

THE H2NO POTENTIAL ENERGY SURFACE EXPLORED WITH HIGH LEVEL AB INITIO AND DENSITY FUNCTIONAL THEORY METHODS

2007 ◽  
Vol 06 (03) ◽  
pp. 549-562
Author(s):  
ABRAHAM F. JALBOUT
Keyword(s):  
Density Functional Theory ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Density Functional ◽  
Energy Surface ◽  
Hybrid Methods ◽  
Transition States ◽  
Basis Set ◽  
Functional Theory ◽  
High Level

The transition states for the H 2 NO decomposition and rearrangements mechanisms have been explored by the CBS-Q method or by density functional theory. Six transition states were located on the potential energy surface, which were explored with the Quadratic Complete Basis Set (CBS-Q) and Becke's one-parameter density functional hybrid methods. Interesting deviations between the CBS-Q results and the B1LYP density functional theory lead us to believe that further study into this system is necessary. In the efforts to further assess the stabilities of the transition states, bond order calculations were performed to measure the strength of the bonds in the transition state.

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