CAT: A Compound Attachment Tool for the Construction of Composite Chemical Compounds

The
continuous improvement of computer architectures allows for
the simulation of molecular systems of growing sizes. However, such
calculations still require the input of initial structures, which
are also becoming increasingly complex. In this work, we present CAT,
a Compound Attachment Tool (source code available at https://github.com/nlesc-nano/CAT) and Python package for the automatic construction of composite
chemical compounds, which supports the functionalization of organic,
inorganic, and hybrid organic–inorganic materials. The CAT
workflow consists in defining the anchoring sites on the reference
material, usually a large molecular system denoted as a scaffold,
and on the molecular species that are attached to it, i.e., the ligands. Usually, ligands are pre-optimized in a conformation
biased toward more linear structures to minimize interligand(s) steric
interactions, a bias that is important when multiple ligands are attached
onto the scaffold. The resulting superstructure(s) are then stored
in various formats that can be used afterward in quantum chemical
calculations or classical force field-based simulations.