Predicting atomic-level reaction mechanisms for SN2 reactions via machine learning

2021 ◽  
Author(s):  
Fanbin Meng ◽  
Yan Li ◽  
Dunyou Wang
Keyword(s):  
Machine Learning ◽  
Reaction Mechanisms ◽  
Atomic Level ◽  
Sn2 Reactions

scholarly journals Reply to the Comment on “On the SN2 Reactions Modified in Vibrational Strong Coupling Experiments: Reaction Mechanisms and Vibrational Mode Assignments”

2021 ◽  
Author(s):  
Clàudia Climent ◽  
Johannes Feist
Keyword(s):  
Strong Coupling ◽  
Reaction Mechanisms ◽  
Vibrational Mode ◽  
Chem Phys ◽  
Sn2 Reactions ◽  
Original Manuscript ◽  
Supplementary Material ◽  
Phys Chem Chem Phys

<div> <div> <div> <p> </p><div> <div> <div> <p>In September 2020, we became aware that a comment (A. Thomas, L. Lethuillier-Karl, J. Moran and T. Ebbesen, 2020, DOI:10.26434/chemrxiv.12982358.v1.) on our recent paper (C. Climent and J. Feist, Phys. Chem. Chem. Phys., 2020, 22, 23545) had been posted to ChemRxiv. Since our attempts in October 2020 to reach out to the authors to discuss the points they raised did not receive a response as of April 2021, and the comment was not submitted as a formal comment to the original journal either, we here provide a brief reply based on the results that were already reported in our original manuscript. Most importantly, we show that we did not “presumably overlook” any data in the supplementary material of their original article, but that our results are actually fully consistent with those data. </p> </div> </div> </div> </div> </div> </div>

Identification of Atomic-Level Mechanisms for Gas-Phase X– + CH3Y SN2 Reactions by Combined Experiments and Simulations

2014 ◽  
Vol 47 (10) ◽  
pp. 2960-2969 ◽  
Author(s):  
Jing Xie ◽  
Rico Otto ◽  
Jochen Mikosch ◽  
Jiaxu Zhang ◽  
Roland Wester ◽  
...  
Keyword(s):  
Gas Phase ◽  
Atomic Level ◽  
Sn2 Reactions

Development of a machine learning-based tool to evaluate correct Lewis acid–base model use in written responses to open-ended formative assessment items

2021 ◽  
Author(s):  
Brandon J. Yik ◽  
Amber J. Dood ◽  
Daniel Cruz-Ramírez de Arellano ◽  
Kimberly B. Fields ◽  
Jeffrey R. Raker
Keyword(s):  
Machine Learning ◽  
Formative Assessment ◽  
Lewis Acid ◽  
Reaction Mechanisms ◽  
Machine Learning Techniques ◽  
Transfer Reactions ◽  
Acid Base ◽  
Written Responses ◽  
Learning Techniques ◽  
Proton Transfer Reactions

Acid–base chemistry is a key reaction motif taught in postsecondary organic chemistry courses. More specifically, concepts from the Lewis acid–base model are broadly applicable to understanding mechanistic ideas such as electron density, nucleophilicity, and electrophilicity; thus, the Lewis model is fundamental to explaining an array of reaction mechanisms taught in organic chemistry. Herein, we report the development of a generalized predictive model using machine learning techniques to assess students’ written responses for the correct use of the Lewis acid–base model for a variety (N = 26) of open-ended formative assessment items. These items follow a general framework of prompts that ask: why a compound can act as (i) an acid, (ii) a base, or (iii) both an acid and a base (i.e., amphoteric)? Or, what is happening and why for aqueous proton-transfer reactions and reactions that can only be explained using the Lewis model. Our predictive scoring model was constructed from a large collection of responses (N = 8520) using a machine learning technique, i.e., support vector machine, and subsequently evaluated using a variety of validation procedures resulting in overall 84.5–88.9% accuracies. The predictive model underwent further scrutiny with a set of responses (N = 2162) from different prompts not used in model construction along with a new prompt type: non-aqueous proton-transfer reactions. Model validation with these data achieved 92.7% accuracy. Our results suggest that machine learning techniques can be used to construct generalized predictive models for the evaluation of acid–base reaction mechanisms and their properties. Links to open-access files are provided that allow instructors to conduct their own analyses on written, open-ended formative assessment items to evaluate correct Lewis model use.

scholarly journals Deep Reinforcement Learning of Transition States

2021 ◽  
Author(s):  
Jun Zhang ◽  
Yao-Kun Lei ◽  
Zhen Zhang ◽  
Xu Han ◽  
Maodong Li ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Reinforcement Learning ◽  
Transition State ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Md Simulations ◽  
Learning Approach ◽  
Machine Learning Approach ◽  
Chemical Reaction Mechanisms

Combining reinforcement learning (RL) and molecular dynamics (MD) simulations, we propose a machine-learning approach, called RL‡, to automatically unravel chemical reaction mechanisms. In RL‡, locating the transition state of a...

scholarly journals Comment on “On the SN2 Reactions Modified in Vibrational Strong Coupling Experiments: Reaction Mechanisms and Vibrational Mode Assignments"

2020 ◽  
Author(s):  
Anoop Thomas ◽  
Lucas Lethuillier-Karl ◽  
Joseph Moran ◽  
Thomas Ebbesen
Keyword(s):  
Reaction Mechanisms ◽  
Recent Article ◽  
Cavity Mode ◽  
Vibrational Mode ◽  
Theoretical Studies ◽  
Vibrational Modes ◽  
Experimental Proof ◽  
Sn2 Reactions ◽  
Vibrational Bands ◽  
Supplementary Material

We welcome the large number of theoretical studies to analyze our experiments on chemistry under VSC. As Climent and Feist state in their recent article, many details are not understood. 1 However, there should be no need to misrepresent our results. In their paper, the authors re-analyze, not the chemistry under VSC, but the reactions that we used that have been studied for over half a century and for which there is no consensus about the details of the mechanism. 2 Secondly, they try to assign the vibrational bands of the reactants. Indeed, as they find, they are often mixed (coupled vibrational modes). For simplicity, it is commonplace in chemistry to describe vibrations according to their main contribution, a convention that we follow in our papers. Since there are differences between our results and their calculations, they assume that our assignments are wrong. Finally, they conclude that we must have coupled the solvent, apparently by a higher cavity mode, despite the experimental proof to the contrary in the original paper.3 The proof that the solvent was not coupled is reproduced below for those who are interested, together with one example of an unequivocal assignment that was in the supplementary material, 4 which Climent and Feist presumably overlooked.

scholarly journals Comment on “On the SN2 Reactions Modified in Vibrational Strong Coupling Experiments: Reaction Mechanisms and Vibrational Mode Assignments"

2020 ◽  
Author(s):  
Anoop Thomas ◽  
Lucas Lethuillier-Karl ◽  
Joseph Moran ◽  
Thomas Ebbesen
Keyword(s):  
Reaction Mechanisms ◽  
Recent Article ◽  
Cavity Mode ◽  
Vibrational Mode ◽  
Theoretical Studies ◽  
Vibrational Modes ◽  
Experimental Proof ◽  
Sn2 Reactions ◽  
Vibrational Bands ◽  
Supplementary Material

We welcome the large number of theoretical studies to analyze our experiments on chemistry under VSC. As Climent and Feist state in their recent article, many details are not understood. 1 However, there should be no need to misrepresent our results. In their paper, the authors re-analyze, not the chemistry under VSC, but the reactions that we used that have been studied for over half a century and for which there is no consensus about the details of the mechanism. 2 Secondly, they try to assign the vibrational bands of the reactants. Indeed, as they find, they are often mixed (coupled vibrational modes). For simplicity, it is commonplace in chemistry to describe vibrations according to their main contribution, a convention that we follow in our papers. Since there are differences between our results and their calculations, they assume that our assignments are wrong. Finally, they conclude that we must have coupled the solvent, apparently by a higher cavity mode, despite the experimental proof to the contrary in the original paper.3 The proof that the solvent was not coupled is reproduced below for those who are interested, together with one example of an unequivocal assignment that was in the supplementary material, 4 which Climent and Feist presumably overlooked.

scholarly journals On the SN2 reactions modified in vibrational strong coupling experiments: reaction mechanisms and vibrational mode assignments

2020 ◽  
Vol 22 (41) ◽  
pp. 23545-23552
Author(s):  
Clàudia Climent ◽  
Johannes Feist
Keyword(s):  
Strong Coupling ◽  
Reaction Mechanisms ◽  
Vibrational Mode ◽  
Vibrational Modes ◽  
Sn2 Reactions

We study the mechanism of SN2 reactions modified in vibrational strong coupling experiments and propose a new assignment of the vibrational modes.

scholarly journals Reply to the Comment on “On the SN2 Reactions Modified in Vibrational Strong Coupling Experiments: Reaction Mechanisms and Vibrational Mode Assignments”

2021 ◽  
Author(s):  
Clàudia Climent ◽  
Johannes Feist
Keyword(s):  
Strong Coupling ◽  
Reaction Mechanisms ◽  
Vibrational Mode ◽  
Chem Phys ◽  
Sn2 Reactions ◽  
Original Manuscript ◽  
Supplementary Material ◽  
Phys Chem Chem Phys

<div> <div> <div> <p> </p><div> <div> <div> <p>In September 2020, we became aware that a comment (A. Thomas, L. Lethuillier-Karl, J. Moran and T. Ebbesen, 2020, DOI:10.26434/chemrxiv.12982358.v1.) on our recent paper (C. Climent and J. Feist, Phys. Chem. Chem. Phys., 2020, 22, 23545) had been posted to ChemRxiv. Since our attempts in October 2020 to reach out to the authors to discuss the points they raised did not receive a response as of April 2021, and the comment was not submitted as a formal comment to the original journal either, we here provide a brief reply based on the results that were already reported in our original manuscript. Most importantly, we show that we did not “presumably overlook” any data in the supplementary material of their original article, but that our results are actually fully consistent with those data. </p> </div> </div> </div> </div> </div> </div>

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