A nanogap formed by a metal nanoparticle and a flat metal substrate is one kind of “hot site” for surface-enhanced Raman scattering (SERS). In this sense, the characteristics of 1,4-phenylenediisocyanide (1,4-PDI) trapped in a nanogap formed by a flat Au or Ag substrate and 60nm-sized Au or Ag nanoparticles have been examined by means of Raman scattering spectroscopy. It is noteworthy that the NC stretching band of 1,4-PDI is very susceptible to the measurement condition. The NC stretching band is observed at 2177, 2173, and 2174cm−1 when 1,4-PDI is trapped in the Au–Au, Ag–Au, and Au–Ag nanogaps, respectively, but the corresponding peak shifts linearly with a slope of as much as 22.4, 28.5, and 31.2cm−1V−1, respectively, in the electrochemical environment. On the other hand, the NC stretching peak is found to blue-shift by up to 8, 3, and 5cm−1, respectively, when the Au–Au, Ag–Au, and Au–Ag nanogaps are exposed to acetic acid. In contrast, in the presence of ammonia, the NC stretching peak is red-shifted by up to 9, 4, and 5cm−1, respectively. This can be understood by presuming that acetic acid acts as an electron acceptor, while ammonia acts as an electron donor when these volatile organics interact with Au or Ag, thereby resulting in either the increase or the decrease in the surface potential of the nanogap electrodes.