{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/troubleshooting-unstable-molecules-in","title":"Troubleshooting Unstable Molecules in Chemical Space","arxiv_id":"2010.02635","date":"2020-10-06","proceeding":null,"authors":["Salini Senthil","Sabyasachi Chakraborty","Raghunathan Ramakrishnan"],"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; of which 3,054 have questionable geometric stability. We successfully troubleshoot 2,988 molecules and ensure a bijective mapping between desired Lewis formulae and final geometries. Our workflow, based on DFT and post-DFT methods, identifies 66 molecules as unstable; 52 contain $-{\\rm NNO}-$, the rest are strained due to pyramidal sp$^2$ C. In the curated dataset, we inspect molecules with long CC bonds and identify ultralong contestants ($r>1.70$~\\AA{}) supported by topological analysis of electron density. We hope the proposed strategy to play a role in big data quantum chemistry initiatives.","url_abs":"http://arxiv.org/abs/2010.02635v2","url_pdf":"http://arxiv.org/pdf/2010.02635v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"troubleshooting-unstable-molecules-in","repo_url":"https://github.com/salinisenthil/ConnGO","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}