The structure and binding of thiol molecular linker to gold surfaces and nanoparticles is central to the understanding of the electronics properties of SAM´s and to nanoscale assemblages consisting of molecular wires and metal nanoparticles. The thiol group attaches strongly to gold clusters and can thus be used as an interconnect in molecular wires based on conjugated organic molecules.Therefore, the prediction and understanding of the electronic transport properties requires a detailed knowledge of the thiolate-gold cluster interaction.

In this work we performed a quantum mechanical investigation of the binding of different thiol- and dithiol-terminated molecular linkers such as methanethiol, benzenethiol and benzenedithiol with different gold magic number nanoparticles (13, 19, 20, 38 atoms) to compare the effect of the nanoparticle electronic structure on the thiolate bonding.

We studied stability of the different adsorption sites and found that the most stable site is dependent on the size of the nanoparticle. For the smallest nanoparticles, the hollow site is the most stable while for the medium-size clusters (20 atoms) the monocoordinated sites are preferred. The binding energy of methanethiolate on the different nanoparticles is around 60 kcal/mol, indicating that they are more reactive than flat surfaces. We also compared the energetics and electronic structure changes as a function of the nanoparticle surface coverage.

Quantum mechanical calculations were performed at the density functional level of theory using the Amsterdam Density Functional program. The Becke-Perdew exchange-correlation functional was used. Relativistic effects were considered using the ZORA approximation.