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I'm working on replicating methods from Klarich et al. [1] and the authors do not provide the reaction SMARTS used for synthesizing secondary amine + carboxylic acid building blocks.

Does anyone have a good set of reaction smarts for forming a bond between a secondary amine and a carboxylic acid? The basic format is:

[*:1]N[*:2].[*:3]C(=O)O>>[*:1]N([*:2])C(=O)[*:3]

But I'm looking for a more robust version with full SMARTS syntax.

Reference

  1. Klarich, K.; Goldman, B.; Kramer, T.; Riley, P.; Walters, W. P. Thompson Sampling─An Efficient Method for Searching Ultralarge Synthesis on Demand Databases. J. Chem. Inf. Model. 2024, 64 (4), 1158–1171. DOI: 10.1021/acs.jcim.3c01790.
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    $\begingroup$ This could be better suited at matter modeling. I personally think it's a fine question, but since I've never worked with SMARTS I can't help. $\endgroup$ Commented Apr 16 at 0:04
  • $\begingroup$ @Karl You describe a reaction with mapped atoms to prevent a manual-only search in a db (like open reaction db, or chemical reaction base e.g. for reactions with furfural (visual preview)). And now, you want to probe in advance what structures the SMARTS string of a reagent/product might cover, if an * any atom better is a CX4? $\endgroup$
    – Buttonwood
    Commented Apr 16 at 11:05

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