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

Abstract

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( G ̃ – C ̃ ) and poly( A ̃ – T ̃ ). 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( G ̃ ) means a guanine base with the deoxyribose and PO 4 − groups to which it is bound. The obtained band structures were compared with previous single chain calculations as well as with the earlier poly( G ̃ – C ̃ ) and poly( A ̃ – T ̃ ) calculation without water but in the presence of counterions. One finds that all the bands of poly( G ̃ – C ̃ ) and poly( A ̃ – T ̃ ) are shifted considerably upwards as compared to the previous single chain results (poly( G ̃ ), poly( C ̃ ), poly( A ̃ ) and poly( T ̃ )). This effect is explained by the ∼0.2 e 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.