A computational study of model NCX (X = F, Cl, Br) species found that protonation at the N end leads to significant changes in their halogen bonding characteristics. The positive potential on the surface of X is substantially increased by the attached proton, which leads to more stable complexes in some instances. On the other hand, the halogen bond was completely destabilized in some complexes, particularly those containing the NCF subunit. (C) 2014 Elsevier B.V. All rights reserved.