Four short ligands; cysteine, cysteamine, dithiothrietol and glycine are examined and compared in their ability to stabilize and assemble silver nanoparticles (AgNPs). Transmission Electron Microscopy (TEM) and UV-visible spectroscopy are used to characterize these nanoparticles in terms of their size (7–16 nm), stability, and capacity for inter-particle assembly and plasmon coupling enforced by hydrogen-bonding. The results show that both sulfhydryl and amine groups can interact with the silver nanoparticle surface. The polydispersity of glycine-stabilized AgNPs can be significantly reduced by centrifugal filtration using an appropriate membrane pore size.