In the present study atomistic models of three-terminal Y junctions with D-3h symmetry were built by the covalent assembly of single-walled armchair carbon nanotubes and the energetic properties were evaluated using quantum chemical methods at the PM6 level of theory. The theoretical study follows the influence of the relative position of the heptagonal ring defects on the structure and stability of the junction. The deformation of the attached nanotube branches is discussed in terms of the evaluated geometric parameters. Results indicate that the size of the junction and the diameter of the nanotube will determine the proper position of the defects corresponding to the energetically favourable cluster.