scholarly journals Correction to Machine Learning to Predict Diels–Alder Reaction Barriers from the Reactant State Electron Density

Author(s):  
Santiago Vargas ◽  
Matthew R. Hennefarth ◽  
Zhihao Liu ◽  
Anastassia N. Alexandrova
2021 ◽  
Vol 17 (10) ◽  
pp. 6203-6213
Author(s):  
Santiago Vargas ◽  
Matthew R. Hennefarth ◽  
Zhihao Liu ◽  
Anastassia N. Alexandrova

2021 ◽  
Author(s):  
Santiago Vargas ◽  
Matthew Hennefarth ◽  
Zhihao Liu ◽  
Anastassia N. Alexandrova

<div> <div> <div> <p>Reaction barriers are key to our understanding of chemical reactivity and catalysis. Certain reactions are so seminal in chemistry, that countless variants, with or without catalysts, have been studied and their barriers have been computed or measured experimentally. This wealth of data represents a perfect opportunity to leverage machine learning models, which could quickly predict barriers without explicit calculations or measurement. Here, we show that the topological descriptors of the quantum mechanical charge density in the reactant state constitute a set that is both rigorous and continuous, and can be used effectively for prediction of reaction barrier energies to a high degree of accuracy. We demonstrate this on the Diels-Alder reaction, highly important in biology and medicinal chemistry, and as such, studied extensively. This reaction exhibits a range of barriers as large as 270 kJ/mol. While we trained our single-objective supervised (labeled) regression algorithms on simpler Diels-Alder reactions in solution, they predict reaction barriers also in significantly more complicated contexts, such a Diels-Alder reaction catalyzed by an artificial enzyme and its evolved variants, in agreement with experimental changes in <i>k<sub>cat</sub></i>. We expect this tool to apply broadly to a variety of reactions in solution or in the presence of a catalyst, for screening and circumventing heavily involved computations or experiments. </p> </div> </div> </div>


2021 ◽  
Author(s):  
Santiago Vargas ◽  
Matthew Hennefarth ◽  
Zhihao Liu ◽  
Anastassia N. Alexandrova

<div> <div> <div> <p>Reaction barriers are key to our understanding of chemical reactivity and catalysis. Certain reactions are so seminal in chemistry, that countless variants, with or without catalysts, have been studied and their barriers have been computed or measured experimentally. This wealth of data represents a perfect opportunity to leverage machine learning models, which could quickly predict barriers without explicit calculations or measurement. Here, we show that the topological descriptors of the quantum mechanical charge density in the reactant state constitute a set that is both rigorous and continuous, and can be used effectively for prediction of reaction barrier energies to a high degree of accuracy. We demonstrate this on the Diels-Alder reaction, highly important in biology and medicinal chemistry, and as such, studied extensively. This reaction exhibits a range of barriers as large as 270 kJ/mol. While we trained our single-objective supervised (labeled) regression algorithms on simpler Diels-Alder reactions in solution, they predict reaction barriers also in significantly more complicated contexts, such a Diels-Alder reaction catalyzed by an artificial enzyme and its evolved variants, in agreement with experimental changes in <i>k<sub>cat</sub></i>. We expect this tool to apply broadly to a variety of reactions in solution or in the presence of a catalyst, for screening and circumventing heavily involved computations or experiments. </p> </div> </div> </div>


2020 ◽  
Author(s):  
Matthew Hennefarth ◽  
Anastassia N. Alexandrova

<div> <div> <div> <p>External electric fields have proven to be an effective tool in catalysis, on par with pressure and temperature, affecting the thermodynamics and kinetics of a reaction. However, fields in molecules are complicated heterogeneous vector objects, and there is no universal recipe for grasping the exact features of these fields that implicate reactivity. Herein, we demonstrate that topological features of the heterogeneous electric field within the reactant state, as well as of the quantum mechanical electron density – a scalar reporter on the field experienced by the system – can be identified as rigorous descriptors of the reactivity to follow. We scrutinize specifically the Diels-Alder reaction. Its 3-D nature and the lack of a singular directionality of charge movement upon barrier crossing makes the effect of the electric field not obvious. We show that the electric field topology around the dienophile double bond, and the associated changes in the topology of the electron density in this bond are predictors of the reaction barrier. They are also the metrics by which to rationalize and predict how the external field would inhibit or enhance the reaction. The findings pave the way toward designing external fields for catalysis, as well as reading the reactivity without an explicit mechanistic interrogation, for a variety of reactions. </p> </div> </div> </div>


1996 ◽  
Vol 74 (6) ◽  
pp. 839-850 ◽  
Author(s):  
Steven M. Bachrach ◽  
Laureta M. Perriott

All Diels–Alder reactions between 1,3-butadiene and cyclopentadiene or 2H-phosphole have been examined at the MP4SDQ/6-31G*//HF/6-31G* level. There is remarkable similarity between the two systems. The thermodynamic product is the bicyclo[4.2.0]nonadiene while the kinetic product is the norbornene product. There is a slight kinetic preference for the endo addition and for the butadiene to be in the s-trans conformation. Except for the case where butadiene is the diene component and addition is endo, the reactions are concerted and synchronous. In these other two cases, the reaction is stepwise with a diradical intermediate.Key words: phosphole, Diels–Alder reaction, topological electron density analysis.


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