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Results of an investigation of hydrogen-bonding mediated interparticle assembling and spatial properties from extremely dilute concentrations of the mediation agent are reported. Nanoparticles consisting of highly monodispersed decanethiolate-capped gold nanocrystal cores and alpha,omega-mercapto-alkanoic acids are highlighted as a model system. The formation of a stable ordered array is demonstrated via manipulating the constituents in solution. Infrared reflection spectroscopy, spectrophotometry, transmission electron microscopy, and atomic force microscopy have been utilized to probe the interparticle structural and spatial properties. A "squeezed" interparticle spatial model involving both hydrogen-bonding at the carboxylic acid groups and cohesive van der Waals interaction through interdigitation of the capping decanethiolate molecules is concluded to be responsible for the interparticle assembling forces. This interparticle spatial property depends on the relative amount of the hydrogen-bonding mediation agent, nanocrystal core size, and size monodispersity. Implications of these findings to the creation of well-defined nanostructures from nanoscale building blocks toward functional nanomaterials are also discussed.