DockOnSurf: A Python Code for the High-Throughput Screening of Flexible Molecules Adsorbed on Surfaces

We
present the open-source python package DockOnSurf which automates
the generation and optimization of low-energy adsorption configurations
of molecules on extended surfaces and nanoparticles. DockOnSurf is
especially geared toward handling polyfunctional flexible adsorbates.
The use of this high-throughput workflow allows us to carry out the
screening of adsorbate-surface configurations in a systematic, customizable,
and traceable way, while keeping the focus on the chemically relevant
structures. The screening strategy consists in splitting the exploration
of the adsorbate-surface configurational space into chemically meaningful
domains, that is, by choosing among different conformers to adsorb,
surface adsorption sites, adsorbate anchoring points, and orientations
and allowing dissociation of (acidic) protons. We demonstrate the
performance of the main features based on varying examples, ranging
from CO adsorption on a gold nanoparticle to sorbitol adsorption on
hematite. Through the use of the presented program, we aim to foster
efficiency, traceability, and ease of use in research within tribology,
catalysis, nanoscience, and surface science in general.