The electronic properties of an array of monolayer-protected gold nanoclusters (ca. 4.8 +/- 0.5 nm) are investigated with the variation of chain length and molecular structure of the passivating organic molecules. Here, we use a metal-insulator-(monolayers protected nanoclusters)-insulators-metal junction based on self-assembled monolayers at room temperature in air. Nanoparticles are organized on the hydrophobic surface of self-assembled monolayer (SAM)-modified Au(111) substrates through weak van der Waals interaction. The junction consists of a drop of mercury supporting a SAM, in contact with the hydrophobically organized nanoparticles on the SAM-modified Au(111) substrate, i.e., an Au(111)/SAM//AuMPCs//SAM/Hg. This junction is easy to assemble, mechanically quite stable, and reproducible, where the area of the contact can be generated down to 0.01 mm(2) without photolithography. Current-voltage (I-V) results demonstrate a clear Coulomb blockade effect with larger band gaps for clusters passivated with longer chain length, where the fractional residual charge Q. on the center electrode is varied without an external electrode. The aromatic nature of phenyl ring demonstrates nearly linear I-V characteristics. The offset current is found to vary with respect to the chain length, and this effect is accounted for while fitting the I-V data with the standard semiclassical model. Furthermore, the variation of the experimentally obtained conductance gap and transmission probability with the length of capping organic molecules are in good agreement with the theoretically calculated values of capacitance and charging energy using a simple model. These results are significant for designing hybrid nanostructures for molecular electronics as the single-electron tunneling behavior of these Q-dot arrays can be tuned by varying the spacer length and structure of the organic molecules, even for hydrophobically organized clusters.