Automatic discovery of chemical reactions using imposed activation

Lavigne, Cyrille; Gomes, Gabriel; Pollice, Robert; Aspuru‐Guzik, Alán

doi:10.26434/chemrxiv.13008500.v2

Cited by 4 publications

(4 citation statements)

References 66 publications

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“…Reactions 29–38 represent a slightly modified form of the test set for pericyclic reactions by Houk and co-workers . Moreover, we added the small molecule test set of Lavigne et al (reactions 25.4 and 39–44). With reactions 45–50 we include transition-metal-chemistry test cases from ref .…”

Section: Resultsmentioning

confidence: 99%

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Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks

Unsleber

Grimmel

Reiher

2022

J. Chem. Theory Comput.

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Fueled by advances in hardware and algorithm design, large-scale automated explorations of chemical reaction space have become possible. Here, we present our approach to an open-source, extensible framework for explorations of chemical reaction mechanisms based on the first-principles of quantum mechanics. It is intended to facilitate reaction network explorations for diverse chemical problems with a wide range of goals such as mechanism elucidation, reaction path optimization, retrosynthetic path validation, reagent design, and microkinetic modeling. The stringent first-principles basis of all algorithms in our framework is key for the general applicability that avoids any restrictions to specific chemical systems. Such an agile framework requires multiple specialized software components of which we present three modules in this work. The key module, Chemoton, drives the exploration of reaction networks. For the exploration itself, we introduce two new algorithms for elementary-step searches that are based on Newton trajectories. The performance of these algorithms is assessed for a variety of reactions characterized by a broad chemical diversity in terms of bonding patterns and chemical elements. Chemoton successfully recovers the vast majority of these. We provide the resulting data, including large numbers of reactions that were not included in our reference set, to be used as a starting point for further explorations and for future reference.

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Section: Resultsmentioning

confidence: 99%

“…Consider as an example reaction 41, where a long alkyl chain undergoes ring closure as depicted in Figure . This example was taken from the work by Lavigne et al that exploits the conformational exploration of activated structures.…”

Section: Resultsmentioning

confidence: 99%

Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks

Unsleber

Grimmel

Reiher

2022

J. Chem. Theory Comput.

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show abstract

“…Consider as an example reaction 42, where a long alkyl chain undergoes ring closure as depicted in Figure 11. This example was taken from the work by Lavigne et al [105 ] that exploits the conformational exploration of activated structures. As can be understood from Figure 10, bimolecular reference reactions were less likely to be found than unimolecular ones with detection rates of 75 % and 82 %, respectively.…”

Section: Resultsmentioning

confidence: 99%

Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks

Unsleber,

Grimmel,

Reiher

2022

Preprint

View full text Add to dashboard Cite

Fueled by advances in hardware and algorithm design, large-scale automated explorations of chemical reaction space have become possible. Here, we present our approach to an open-source, extensible framework for explorations of chemical reaction mechanisms based on the first principles of quantum mechanics. It is intended to facilitate reaction network explorations for diverse chemical problems with a wide range of goals such as mechanism elucidation, reaction path optimization, retrosynthetic path validation, reagent design, and microkinetic modeling. The stringent first-principles basis of all algorithms in our framework is key for the general applicability that avoids any restrictions to specific chemical systems. Such an agile framework requires multiple specialized software components of which we present three modules in this work. The key module, Chemoton,drives the exploration of reaction networks. For the exploration itself, we introduce two new algorithms for elementary-step searches that are based on Newton trajectories. The performance of these algorithms is assessed for a variety of reactions characterized by a broad chemical diversity in terms of bonding patterns and chemical elements. We reproduce and significantly extend what is known about these reactions and provide the resulting data to be used as a starting point for further explorations and for future reference.

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“…For our own group's research program, we wanted to have available a lightweight workflow management system that could be readily deployed to new and varied computational facilities and local workstations with minimal effort. This system had to support our existing shellbased and Python-based scripts, and be flexible enough for rapid prototyping all the way to large-scale computational campaigns, and provide an embeddable solution that can be bundled within other software (Lavigne et al, 2020). Finally, we were looking for a tool that could integrate data generation and storage, to avoid the common practice of transforming the filesystem into what is effectively a schema-less database.…”

Section: Statement Of Needmentioning

confidence: 99%