Machine learning maps reaction space

2021 ◽  
Vol 99 (5) ◽  
pp. 6-6
Author(s):  
Sam Lemonick
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Sina Stocker ◽  
Gábor Csányi ◽  
Karsten Reuter ◽  
Johannes T. Margraf

Abstract Chemical compound space refers to the vast set of all possible chemical compounds, estimated to contain 1060 molecules. While intractable as a whole, modern machine learning (ML) is increasingly capable of accurately predicting molecular properties in important subsets. Here, we therefore engage in the ML-driven study of even larger reaction space. Central to chemistry as a science of transformations, this space contains all possible chemical reactions. As an important basis for ‘reactive’ ML, we establish a first-principles database (Rad-6) containing closed and open-shell organic molecules, along with an associated database of chemical reaction energies (Rad-6-RE). We show that the special topology of reaction spaces, with central hub molecules involved in multiple reactions, requires a modification of existing compound space ML-concepts. Showcased by the application to methane combustion, we demonstrate that the learned reaction energies offer a non-empirical route to rationally extract reduced reaction networks for detailed microkinetic analyses.


2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Zilin Song ◽  
Hongyu Zhou ◽  
Hao Tian ◽  
Xinlei Wang ◽  
Peng Tao

Abstract The bacterial enzyme class of β-lactamases are involved in benzylpenicillin acylation reactions, which are currently being revisited using hybrid quantum mechanical molecular mechanical (QM/MM) chain-of-states pathway optimizations. Minimum energy pathways are sampled by reoptimizing pathway geometry under different representative protein environments obtained through constrained molecular dynamics simulations. Predictive potential energy surface models in the reaction space are trained with machine-learning regression techniques. Herein, using TEM-1/benzylpenicillin acylation reaction as the model system, we introduce two model-independent criteria for delineating the energetic contributions and correlations in the predicted reaction space. Both methods are demonstrated to effectively quantify the energetic contribution of each chemical process and identify the rate limiting step of enzymatic reaction with high degrees of freedom. The consistency of the current workflow is tested under seven levels of quantum chemistry theory and three non-linear machine-learning regression models. The proposed approaches are validated to provide qualitative compliance with experimental mutagenesis studies.


2018 ◽  
Vol 140 (15) ◽  
pp. 5004-5008 ◽  
Author(s):  
Matthew K. Nielsen ◽  
Derek T. Ahneman ◽  
Orestes Riera ◽  
Abigail G. Doyle

2020 ◽  
Vol 43 ◽  
Author(s):  
Myrthe Faber

Abstract Gilead et al. state that abstraction supports mental travel, and that mental travel critically relies on abstraction. I propose an important addition to this theoretical framework, namely that mental travel might also support abstraction. Specifically, I argue that spontaneous mental travel (mind wandering), much like data augmentation in machine learning, provides variability in mental content and context necessary for abstraction.


2020 ◽  
Author(s):  
Mohammed J. Zaki ◽  
Wagner Meira, Jr
Keyword(s):  

2020 ◽  
Author(s):  
Marc Peter Deisenroth ◽  
A. Aldo Faisal ◽  
Cheng Soon Ong
Keyword(s):  

Author(s):  
Lorenza Saitta ◽  
Attilio Giordana ◽  
Antoine Cornuejols

Author(s):  
Shai Shalev-Shwartz ◽  
Shai Ben-David
Keyword(s):  

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