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Science Updates

Webinar by Chaya Stern: Fragmenting molecules for QC torsion drives (Jun 4, 2019)

Posted on 24 May 2019 by Karmen Condic-Jurkic and Chaya Stern

You can watch this webinar on YouTube and access slides on Zenodo.

Chaya Stern (Chodera lab) will give a webinar on Jun 4 at 11 am (EDT) under title “Fragmenting molecules for QC torsion drives”, based on her talk presented at the ACS Orlando conference (Mar 31 - Apr 4, 2019). Join the webinar in real time via Zoom link ( or for those who can’t make it, Chaya’s talk will be recorded and shared on the website.

Abstract: The torsion energy term describes the energy of a molecule as it rotates around its bonds and is commonly given as a sum of cosine terms with periodicities that are chosen using chemical expertise. To decrease the computational cost of fitting torsions in large molecules, it is common practice to fragment them into smaller entities that should reproduce the chemistry about each torsion of interest. However, most existing cheminformatics fragmentation schemes fragment molecules for synthetic accessibility and do not consider electronic properties.

In order to automate and generalize the process, several problems need to be addressed. These are:

  • intelligent fragmentation of compounds for quantum chemistry (QC) calculations to reduce misrepresentation of the chemical environment of the torsion;
  • automation of many QC torsion scans;
  • automated parameter fitting and model selection,
  • finding the correct granularity of chemical environments for transferable torsion types.

This talk focuses on the open-source and modular software developed to solve these problems within Open Force Field Initiative framework. The QC calculations are captured, indexed with several canonical chemical identifiers, and deposited to the open QCArchive database for future use.