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 towards handling polyfunctional flexible adsorbates. The use of this high-throughput workflow allows 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 on splitting the exploration of the adsorbate-surface configurational space into chemically meaningful domains, i.e., by choosing among different conformers to adsorb, surface adsorption sites, adsorbate anchoring points, 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.