Simple position and orientation preconditioning scheme for minimum energy path calculations. Issue 11 (22nd February 2021)

• Record Type: Journal Article
• Authors: Robertson, Christopher; Habershon, Scott
• Is Part Of: Journal of computational chemistry. Volume 42:Issue 11(2021)
• Page Start: 761
• Page End: 770
• Publication Date: 2021-02-22
• Subjects: minimum energy paths -- nudge elastic band -- preconditioning scheme -- reaction discovery -- reaction paths; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.26495
• Languages: English
• ISSNs: 0192-8651

Abstract

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. Abstract : The algorithm starts with reactant and product molecules in any arbitrary orientation and position in space and, through several optimization steps, reorients them into a reasonable initial guess for use in double ended, minimum energy path calculations. The top left‐most cell shows the reactants (top) and product (bottom) molecules arbitrarily oriented. Successively, each stage represented by the dashed cells performs a different operation on the molecules, resulting in the right‐most cell, a reasonable relative initial position and orientation. The resulting reactant and product images can then be used to obtain an approximation to a minimum energy path, as shown in the eight lower cells.