A new vision of the DNA triple-helix: structural, spectroscopic and electronic parameters for hydrogen bonding for Watson-Crick and Hoogsteen pairing

Through the B3LYP/6-31+G(d,p) calculations, the intermolecular structures of double and triple DNA helix formed by Thymine (T) Adenine (A) were fully optimized. Based on analysis of structural parameters, vibrational modes and infrared absorption intensities, specific hydrogen bonds on the scaffolds of the purine and pyrimidine were identified. On behalf of charge transfer criterion between the HOMO and LUMO frontier orbitals of the proton receptor and donor respectively, the application of the NBO and ChElPG protocols have provided unsatisfactory results. Meanwhile, all hydrogen bonds were characterized through the QTAIM descriptors, by which new intermolecular profiles have been pointed out to both of double (TA) and (TAT) triple-DNA helix.