Various heteroatoms (N, P and S) were substituted at different positions of the cluster to study the influence of heteroatoms toward the activation of hydrogen. In the presence of heteroatoms, the dissociation energy of hydrogen molecule was considerably decreased compared to that of pure carbon nanotubes. To understand the role of hetero atoms in hydrogen activation in carbon nanotubes, the calculations were performed to estimate the value of activation energy value of each of the steps of hydrogen activation and migration within the framework of Transition state theory.