DockOnSurf

DockOnSurf automates the generation and optimization of low-energy adsorption configurations for molecules on extended surfaces and nanoparticles to explore adsorbate–surface interactions.

Key Features:

• Generation and optimization: Systematic generation and optimization of low-energy adsorption configurations for molecules on surfaces and nanoparticles.
• Polyfunctional flexible adsorbates: Explicit handling of polyfunctional flexible adsorbates to account for molecular flexibility and multiple functional groups.
• Configurational space exploration: Division of the exploration into chemically meaningful domains including selection of different conformers, identification of potential surface adsorption sites, determination of adsorbate anchoring points and orientations, and allowance for acidic proton dissociation.
• High-throughput screening: Support for workflows aimed at high-throughput screening of adsorbate–surface configurations.
• Traceability and reproducibility: Customizable, traceable workflows that preserve records of generated structures and computational experiments for reproducibility.

Scientific Applications:

• CO on gold nanoparticles: Application to study CO adsorption on gold nanoparticles.
• Sorbitol on hematite: Application to study sorbitol adsorption on hematite surfaces.
• High-throughput adsorbate screening: Use in high-throughput screening of adsorption configurations and energetics.
• Tribology, catalysis, nanoscience, and surface science: Relevant to studies of molecular adsorption, energetics, and surface interactions in tribology, catalysis, nanoscience, and surface science.

Methodology:

Systematic generation and optimization of adsorption configurations by dividing the configurational exploration into chemically meaningful domains: selecting conformers, identifying potential surface adsorption sites, determining anchoring points and orientations, and allowing dissociation of acidic protons.