A Universal Database of Surface Ligands for Quantum Dots

We introduce a public database of organic molecules, derived by an advanced filtering of the PUBCHEM database, with the aim of building a subset of surface ligands candidates that are potentially suitable to passivate the surface of any colloidal QD. For each ligand in the database, we additionally provide relevant chemical and physical properties, from the boiling and melting points to more specific properties that account for the interactions with the solvent and amongst ligands themselves at the QD surface.

The “smiles to filter” scanning process, excluding (or including) a set of molecules based on structural characteristics like their functional groups was performed using the Python-based library Flamingo. The estimation of COSMO-RS (COnductor-like Screening MOdel for Realistic Solvents) [2] properties was carried out by the Fast Sigma program implemented in AMS (Amsterdam Modelling Suite) [3]. The calculations were automatized and managed via the Compound Attachment Tools (CAT) [4] and sister packages nano-CAT and data-CAT. The calculations of the cone angle are currently performed via the nano-CAT code and preceded by a biased conformational search implemented in CAT and by a geometry optimization at the DFTB level of theory with the GFN1-xTB parameter set [5] using AMS and will be progressively added to the dataset as they become available.

[1] Kim S et al., Nucleic Acids Res., 49(D1):D1388–D1395, 2021.

[2] Klamt A. et al., J. Phys. Chem., 99(7) : 2224–2235, 1995.

[3] te Velde G. et al., J. Comput. Chem., 22(9): 931–967, 2001.

[4] van Beek B. et al., J. Chem. Inf. Model. 2022, 62, 22, 5525–5535.

[5] Grimme S. et al., J. Chem. Theory Comput., 13(5):1989–2009, 2017.