Proceedings of nanoGe Fall Meeting19 (NFM19)
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: https://github.com/nlesc-nano/CAT
We thank the Netherlands Organization for Scientific Research (NWO) for financial support.
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