Jump to main content
Jump to site search

Issue 15, 2021
Previous Article Next Article

Troubleshooting unstable molecules in chemical space

Author affiliations

Abstract

A key challenge in automated chemical compound space explorations is ensuring veracity in minimum energy geometries—to preserve intended bonding connectivities. We discuss an iterative high-throughput workflow for connectivity preserving geometry optimizations exploiting the nearness between quantum mechanical models. The methodology is benchmarked on the QM9 dataset comprising DFT-level properties of 133 885 small molecules, wherein 3054 have questionable geometric stability. Of these, we successfully troubleshoot 2988 molecules while maintaining a bijective mapping with the Lewis formulae. Our workflow, based on DFT and post-DFT methods, identifies 66 molecules as unstable; 52 contain –NNO–, and the rest are strained due to pyramidal sp2 C. In the curated dataset, we inspect molecules with long C–C bonds and identify ultralong candidates (r > 1.70 Å) supported by topological analysis of electron density. The proposed strategy can aid in minimizing unintended structural rearrangements during quantum chemistry big data generation.

Graphical abstract: Troubleshooting unstable molecules in chemical space

Back to tab navigation

Supplementary files

Article information


Submitted
09 Oct 2020
Accepted
27 Feb 2021
First published
02 Mar 2021

This article is Open Access
All publication charges for this article have been paid for by the Royal Society of Chemistry

Chem. Sci., 2021,12, 5566-5573
Article type
Edge Article

Troubleshooting unstable molecules in chemical space

S. Senthil, S. Chakraborty and R. Ramakrishnan, Chem. Sci., 2021, 12, 5566
DOI: 10.1039/D0SC05591C

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. Material from this article can be used in other publications provided that the correct acknowledgement is given with the reproduced material and it is not used for commercial purposes.

Reproduced material should be attributed as follows:

  • For reproduction of material from NJC:
    [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the Centre National de la Recherche Scientifique (CNRS) and the RSC.
  • For reproduction of material from PCCP:
    [Original citation] - Published by the PCCP Owner Societies.
  • For reproduction of material from PPS:
    [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the European Society for Photobiology, the European Photochemistry Association, and RSC.
  • For reproduction of material from all other RSC journals:
    [Original citation] - Published by The Royal Society of Chemistry.

Information about reproducing material from RSC articles with different licences is available on our Permission Requests page.


Social activity

Search articles by author

Spotlight

Advertisements