Exploring the conformers of an organic adsorbate on a metal cluster with Bayesian optimization

[1] Lincan Fang, Xiaomi Guo, Milica Todorovic, Patrick Rinke, Xi Chen. Exploring the conformers of an organic adsorbate on a metal cluster with Bayesian optimization

This dataset shows 1000 sampling points in the configuration space of the cysteine ligand binding with the S site of Au25S18 cluster. For Au25S18 cluster, there are two inequivalent S sites (Au-S-Au-S-Au-S-Au arrow top and side). Here, the binding S site is on "arrow side", we named it "system B". The sampling method is the Bayesian Optimization Structure Search (BOSS), each sampling point consists of structure features and DFT structure energy. The structure features are five dihedral angles of cysteine ligand, d1 (Au-S-C1-C2), d2 (S-C1-C2-N), d3 (C1-C2-N-H), d4 (C1-C2-C3-O1), and d5 (C2-C3-O1-H). The energy was calculated by FHI-aims with PBE functional, tier 2 setting with many-body dispersion corrections. Due to the confined configuration space of this system, we use the energy transformation method (see in manuscript) to tackle one sampling structure that cannot be simulated by DFT or has a huge high DFT energy. For additional details on BOSS search please refer to [1].

The stable local minimum structures from BOSS can be found in NOMAD: https://dx.doi.org/10.17172/NOMAD/2022.08.20-1