In small nanoclusters/nanocrystals/quantum clusters (my goodness, they have so many names nowadays) in the size range around 13, 55 and 144 metal atoms, the ligands enter a real orbital interaction. They are ligated to the metal core. In spheric clusters, molecular orbital interactions were calculated in which the ligands form orbitals, which are reminiscent to those of atomic orbitals. They are describable in terms of the superatom model and they explain the stability of the compounds. (http://dx.doi.org/10.1002/anie.201310436)

In DNA-ligated gold clusters, the phosphate groups are able to bond to the metal core and substitute the phosphine ligands it had before. (http://dx.doi.org/10.1002/anie.200250235)

In larger nanoparticles, the tendency of the particles to agglomerate is much smaller. Some of them can be measured with TEM (Transmission Electron Microscopy) without full agglomeration. This is not given for the small 13 metal atom clusters. The big particles enter interactions with their surfactants for which the main contribution is given either by van der Waals forces, or by electrostatic interactions.