A theoretical study of linear and cyclic clusters of (HCN)(n) and (HNC)(n) (up to n = 10) has been carried out by means of DFT and MP2 ab initio methods. The transition states linking the cyclic clusters show high energetic barriers that prevent the spontaneous transformation of the high-energy clusters, (HNC)(n), into the low-energy ones, (HCN)(n). The effect of the protonation/deprotonation of the linear clusters has also been explored. The results show that (HNC)(n) clusters with n values larger than six are thermodynamically more stable as charged systems than as neutral ones. The geometrical results have been analyzed using a Steiner-Limbach plot. The electron density and its Laplacian at the bond critical points correlate with the corresponding bond distances by means of two exponential functions, one for the open shell and another for the closed shell cases.