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Data for Simple position and orientation preconditioning scheme for minimum energy path calculations
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Robertson, Christopher and Habershon, Scott (2021) Data for Simple position and orientation preconditioning scheme for minimum energy path calculations. [Dataset]
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FIGURE3.dat - Published Version Available under License Creative Commons Attribution 4.0. Download (22Kb) |
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Plain Text (Raw data)
FIGURE4.dat - Published Version Available under License Creative Commons Attribution 4.0. Download (95Kb) |
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 labour-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 >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: | Dataset | ||||||
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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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Type of Data: | Experimental data | ||||||
Library of Congress Subject Headings (LCSH): | Molecular orbitals, Reaction mechanisms (Chemistry), Chemical kinetics -- Mathematical models | ||||||
Publisher: | University of Warwick, Department of Chemistry | ||||||
Official Date: | 22 January 2021 | ||||||
Dates: |
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Status: | Not Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Media of Output (format): | .dat | ||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||
Copyright Holders: | University of Warwick | ||||||
Description: | Data record consists of two ASCII data files in plain text format, corresponding to figure 3 and figure 4 in the related publication. |
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Date of first compliant deposit: | 29 January 2021 | ||||||
Date of first compliant Open Access: | 12 April 2021 | ||||||
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