Fast screening of homogeneous catalysis mechanisms using graph-driven searches and approximate quantum chemistry

Robertson, Christopher; Habershon, Scott

doi:10.1039/c9cy01997a

Cited by 21 publications

(44 citation statements)

References 48 publications

(64 reference statements)

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“…31 We have also shown that when combined with semiempirical or ab initio electronic structure calculations, our GDS scheme can correctly identify the accepted "correct" mechanism of catalysis by an organometallic complex. 38 These same successful calculations have also highlighted two important algorithmic issues in our GDS approach. First, our approach currently does not account for permutational invariance among reactive atoms and molecules when searching for reaction mechanisms.…”

Section: Introductionmentioning

confidence: 72%

Identifying Barrierless Mechanisms for Benzene Formation in the Interstellar Medium Using Permutationally Invariant Reaction Discovery

Robertson

Hyland

Lacey

et al. 2021

J. Chem. Theory Comput.

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Complex chemical reaction environments, such as those found in combustion engines, the upper atmosphere, or the interstellar medium, can contain large numbers of different reactive species participating in similarly large numbers of different chemical reactions. In such settings, identifying the most-likely multistep reaction mechanisms which lead to the production of a particular defined product species is an extremely challenging problem, requiring search and evaluation over a large number of different possible candidate mechanisms while also addressing the permutational challenges posed when considering a large number of reaction routes available to sets of identical molecular species. In this article, the problem of generating candidate reaction mechanisms which form a defined product from a diverse set of reactive molecules is cast as a discrete optimization of a permutationally invariant cost function describing similarity between the target product and the product generated by a trial reaction mechanism. This approach is demonstrated by generating 2230 candidate reaction mechanisms which form benzene from diverse sets of reactive molecules which have been experimentally identified in the interstellar medium. By screening this set of autogenerated mechanisms, using dispersion-corrected DFT to evaluate reaction energies and activation barriers, we identify several candidate barrierless reaction mechanisms (both previously proposed and new) for benzene formation which may operate in the low temperatures found in the interstellar medium and could be investigated further to supplement existing microkinetic models.

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Section: Introductionmentioning

confidence: 72%

Identifying Barrierless Mechanisms for Benzene Formation in the Interstellar Medium Using Permutationally Invariant Reaction Discovery

Robertson

Hyland

Lacey

et al. 2021

J. Chem. Theory Comput.

Self Cite

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“…The method also benefits from working in graph space, where reactions are simply graph transformations. This has been shown to be a practical way to explore reactive events by Habershon and co‐workers 26,27,97–100 …”

Section: Methodsmentioning

confidence: 99%

“…This has been shown to be a practical way to explore reactive events by Habershon and co-workers. 26,27,[97][98][99][100] The workflow of ChemKnow is detailed as follows:…”

Section: Chemical Knowledge (Chemknow)mentioning

confidence: 99%

AutoMeKin2021: An open‐source program for automated reaction discovery

et al. 2021

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AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare‐event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond‐order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin

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“…Most relevant to our work, we anticipate that this algorithm may be of particular utility in the context of automated, high‐throughput schemes to attempt de novo design of potential molecular catalysts 17,19,20,24,26,30–35 . As well as preconditioning the position and orientation of molecules, deciding whether the product and reactant molecules require conformational intermediates and providing reasonable guesses (prior to PES evaluations) of these would be a natural next step to implement, and for which work is currently underway.…”

Section: Discussionmentioning

confidence: 99%

Simple position and orientation preconditioning scheme for minimum energy path calculations

Robertson

Habershon

2021

J Comput Chem

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Minimum‐energy path (MEP) calculations, such as those typified by the nudged elastic band method, require input of reactant and product molecular configurations at initialization. In the case of reactions involving more than one molecule, generating initial reactant and product configurations requires careful consideration of the relative position and orientations of the reactive molecules in order to ensure that the resulting MEP calculation proceeds without converging on an alternative reaction‐path, and without requiring excessive numbers of optimization iterations; as such, this initial system set‐up is most commonly performed “by hand,” with an expert user arranging reactive molecules in space to ensure that the following MEP calculation runs smoothly. In this Article, we introduce a simple preconditioning scheme which replaces this labor‐intensive, human‐knowledge‐based step with an automated deterministic computational scheme. In our approach, initial reactant and product configurations are generated such that steric hindrance between reactive molecules is minimized in the reactant and product configurations, while also simultaneously requiring minimal structural differences between the reactants and products. The method is demonstrated using a benchmark test‐set of >3400 organic molecular reactions, where comparison of the reactant/product configurations generated using our approach compare very well to initial configurations which were generated on an ad hoc basis.

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Fast screening of homogeneous catalysis mechanisms using graph-driven searches and approximate quantum chemistry

Abstract: Automatic analysis of competing mechanisms.

Cited by 21 publications

References 48 publications

Identifying Barrierless Mechanisms for Benzene Formation in the Interstellar Medium Using Permutationally Invariant Reaction Discovery

Identifying Barrierless Mechanisms for Benzene Formation in the Interstellar Medium Using Permutationally Invariant Reaction Discovery

AutoMeKin2021: An open‐source program for automated reaction discovery

Simple position and orientation preconditioning scheme for minimum energy path calculations

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