Model calculations of the energy band structures of double stranded DNA in the presence of water and Na ions

Using the ab initio Hartree-Fock crystal orbital method in its linear combination of atomic orbitals form we have calculated the band structures of poly(-) and poly(-). Here, besides the nucleotide bases, the sugar and phosphate parts of the nucleotide were also taken into account together with their first water shell and Na⁺ ions. We use the notation with a tilde above the abbreviation of a base for the whole nucleotide; for instance poly() means a guanine base with the deoxyribose and PO₄⁻ groups to which it is bound. The obtained band structures were compared with previous single chain calculations as well as with the earlier poly(-) and poly(-) calculation without water but in the presence of counterions. One finds that all the bands of poly(-) and poly(-) are shifted considerably upwards as compared to the previous single chain results (poly(), poly(), poly() and poly()). This effect is explained by the ∼0.2e charge transfer from the sugars of both chains to the nucleotide bases. The fundamental gaps between the nucleotide base-type highest filled and lowest unfilled bands are decreased in both cases by 1-3 eV, because the valence bands are purine-type and the conduction bands pyrimidine-type, respectively, while in the case of single homopolynucleotides they belong to the same base. We also pointed out that the LUMO is mainly Na⁺-like in both investigated cases and several unoccupied bands (belonging to the Na⁺ ions, the phosphate group and the water molecules) can be found between this and the first unoccupied pyrimidine-like empty band.