Nucleobases (adenine (A), thymine (T), cytosine (C), and guanine (G)) trapped within two metal clusters such as Au-3 undergo expansion. Our investigation reveals that this primarily arises due to the concomitant increase in all the bond lengths in molecules. Such expansion of the molecules can be qualitatively understood on the basis of classical harmonic potentials in the bonds and loss of aromaticity in the rings. Specifically, the highly electronegative O and N elements in the base pairs anchor to Au atoms and form X-Au bonds, which leads to charge redistribution within the molecules. As a very important consequence of this, the nature of the hydrogen bonds (in Au-3-A center dot center dot center dot T-Au-3 and in Au-3-G center dot center dot center dot C-Au-3) change substantially within these electrodes in comparison to gas-phase structures. These hydrogen bonds have a single-well potential energy profile (of the type N center dot center dot center dot H center dot center dot center dot O and N center dot center dot center dot H center dot center dot center dot N) instead of double-well potentials (like N-H center dot center dot center dot O or N- H center dot center dot center dot N/N center dot center dot center dot H-N types). A detailed energy calculation along the proton movement pathway supports our conclusions.