We report mid-infrared spectra and potential energy surfaces of fouranionic, 2′-deoxynucleotide-5′-monophosphates (dNMPs) and the ionic DNA pairs[dGMP-dCMP−H]1−, [dAMP-dTMP−H]1− with a total charge of the complex equal to−1. We recorded IR action spectra by resonant IR multiple-photon dissociation (IRMPD)using the FELIX free electron laser. The potential energy surface study employed an onthe-fly molecular dynamics quenching method (MD/Q), using a semiempirical AM1method, followed by an optimization of the most stable structures using density functionaltheory. By employing infrared multiple-photon dissociation (IRMPD) spectroscopy incombination with high-level computational methods, we aim at a better understanding ofthe hydrogen bonding competition between the phosphate moieties and the nucleobases.We find that, unlike in multimer double stranded DNA structures, the hydrogen bonds inthese isolated nucleotide pairs are predominantly formed between the phosphate groups.This intermolecular interaction appears to exceed the stabilization energy resulting frombase pairing and directs the overall cluster structure and alignment.