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

24 February 2021, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

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.

Keywords

adsorption energies
Interface
high-throughput computation
Computational screening
Python package
adsorption mode

Supplementary materials

Title
Description
Actions
Title
SI DockOnSurf
Description
Actions
Title
input files
Description
Actions

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.