The effect of the replacement of the H-bonds (HBs) that hold nucleic acid base pairs together by halogen bonds (XBs) is examined by DFT calculations. When in its Hoogsteen configuration, XBs involving Cl reduce the interaction energy within the adenine-thymine (AT) pair by the most, followed by Br. I substitutions have little effect on the total binding. Similar reductions arise in the guanine-cytosine (GC) pair, although XBs involving I can enhance the interaction energy. With regard to Watson-Crick pairings, the replacement of two of the H atoms by I yields a stronger GC binding energy, while Cl and Br XBs weaken the interaction. Atoms in Molecules (AIM) analysis allows conclusions to be drawn concerning the contributions of each individual interaction, whether HB or XB, to the full energy.

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