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Simple position and orientation preconditioning scheme for minimum energy path calculations
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Robertson, Christopher and Habershon, Scott (2021) Simple position and orientation preconditioning scheme for minimum energy path calculations. Journal of Computational Chemistry, 42 (11). pp. 761-770. doi:10.1002/jcc.26495 ISSN 0192-8651.
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WRAP-Simple-position-orientation-preconditioning-scheme-minimum-energy-path-calculations-2021.pdf - Accepted Version - Requires a PDF viewer. Download (1878Kb) | Preview |
Official URL: https://doi.org/10.1002/jcc.26495
Abstract
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.
Item Type: | Journal Article | ||||||||
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Subjects: | Q Science > QD Chemistry | ||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Chemistry Faculty of Science, Engineering and Medicine > Science > Chemistry > Computational and Theoretical Chemistry Centre |
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Library of Congress Subject Headings (LCSH): | Molecular orbitals , Reaction mechanisms (Chemistry) , Chemical kinetics -- Mathematical models | ||||||||
Journal or Publication Title: | Journal of Computational Chemistry | ||||||||
Publisher: | Wiley-Blackwell Publishing Ltd. | ||||||||
ISSN: | 0192-8651 | ||||||||
Official Date: | 30 April 2021 | ||||||||
Dates: |
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Volume: | 42 | ||||||||
Number: | 11 | ||||||||
Page Range: | pp. 761-770 | ||||||||
DOI: | 10.1002/jcc.26495 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Reuse Statement (publisher, data, author rights): | "This is the peer reviewed version of the following article: Robertson, C, Habershon, S. Simple position and orientation preconditioning scheme for minimum energy path calculations. J Comput Chem. 2021; 42: 761– 770, which has been published in final form at https://doi.org/10.1002/jcc.26495. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions." | ||||||||
Access rights to Published version: | Restricted or Subscription Access | ||||||||
Date of first compliant deposit: | 25 March 2021 | ||||||||
Date of first compliant Open Access: | 22 February 2022 | ||||||||
RIOXX Funder/Project Grant: |
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