Compound Attachment Tool: Automating the Construction of Chemical Compounds
Bas van Beek a, Felipe Zapata b, Lucas Visscher a, Ivan Infante a c
a Department of Theoretical Chemistry, Vrije Universiteit - NL, Amsterdam, Netherlands
b Netherlands eScience Center, Amsterdam
c Istituto Italiano di Tecnologia (IIT), Genova, Italy, Via Morego, 30, Genova, Italy
nanoGe Fall Meeting
Proceedings of nanoGe Fall Meeting19 (NGFM19)
#NCFun19. Fundamental Processes in Semiconductor Nanocrystals
Berlin, Germany, 2019 November 3rd - 8th
Organizers: Ivan Infante and Jonathan Owen
Poster, Bas van Beek, 392
Publication date: 18th July 2019

The automatic construction of computational nanocrystal models has been a long-standing desire within the group, to which end the Compound Attachment Tool (CAT) has been developed. CAT is a collection of tools for constructing molecules out of constituent components (“ligands” and “cores”),  with a focus on the construction of nanocrystals in particular.
The developed Python package is, among other things, capable of:

* Interfacing with various quantum chemical software using QMFlows [1] and PLAMS; granting the user further flexibility in balancing accuracy versus computational cost.

* Identifying potential anchor sites within ligands using RDKits' [2] functional group recognition.

* Optimizing ligand geometries while minimizing inter-ligand steric repulsion (i.e. finding “non-bulky” conformations).

* Automatically populating the nanocrystal surface with ligands in a chemical intuitive manner.

Large numbers of molecules, ranging from dozens to thousands of atoms, can be constructed within a manner of seconds, making CAT suitable for handling individual molecules or for the screening of entire compound databases. As a secondary focus, two extensions are available for analyzing and storing the resulting structures and/or calculated properties.

Repository link:

We thank the Netherlands Organization for Scientific Research (NWO) for financial support.

© Fundació Scito
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