Solid State Communications 151 (2011) 301–305 Contents lists available at ScienceDirect Solid State Communications journal homepage: www.elsevier.com/locate/ssc Model calculations of the energy band structures of double stranded DNA in the presence of water and Na + ions Attila Bende a,c , Ferenc Bogár b,c , János Ladik c,* a Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Str. Donath 65-103, C.P. 700, Cluj-Napoca RO-400293, Romania b Supramolecular and Nanostructured Materials Research Group of the Hungarian Academy of Sciences, University of Szeged, Dóm tér 8., 6720 Szeged, Hungary c Chair for Theoretical Chemistry and Laboratory of the National Foundation for Cancer Research, Friedrich-Alexander-University-Erlangen-Nürnberg, Egerlandstr. 3, 91058 Erlangen, Germany article info Article history: Received 31 July 2010 Received in revised form 12 November 2010 Accepted 1 December 2010 by V. Pellegrini Available online 8 December 2010 Keywords: A. Polymers, elastomers, and plastics C. Crystal structure and symmetry D. Electronic band structure D. Order–disorder effects 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 ∼0.2e 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. © 2010 Elsevier Ltd. All rights reserved. 1. Introduction Early quantum chemical models of DNA supposed the strict helical symmetry of the system and used a band-like description (Hartree–Fock Crystal Orbital (HFCO) theory). With these approx- imations they successfully described several important features of the electronic structure of DNA (see Ref. [1] and the references therein). In two recent papers [2,3] we applied the HFCO method for the calculation of the energy band structures of the four, single stranded, homopolynucleotides (poly(guanylic acid), polycytidine, poly(adenylic acid), and polythymidine) in the presence of water and Na + ions. (We shall subsequently denote the four nucleotides as ˜ G, ˜ C, ˜ A and ˜ T.) In our solid state physical model the chemical non-periodicity, the flexibility of DNA (the deviation from the perfect helical sym- metry) and also the fluctuating interactions with the environment * Corresponding author. Tel.: +49 9131 996600; fax: +49 9131 85 27736. E-mail addresses: bende@itim-cj.ro (A. Bende), bogar@sol.cc.u-szeged.hu (F. Bogár), Janos.Ladik@chemie.uni-erlangen.de (J. Ladik). are neglected. Growing experimental evidence indicates that this model cannot be applied directly for the description of charge transport in DNA in a biological environment (for a recent review see Ref. [4]). Several theoretical works investigated the effect of relaxing some constraints invoked in the solid state physical model. Arta- cho et al. [5,6] used a periodic model for poly( ˜ G– ˜ C) in its A-DNA form but with a unit cell containing 11 nucleotide pairs (with and without helical constraint). The calculated bandwidths using the strict helical symmetry were compared to the energy fluctuations caused by the vibrations or aperiodicity of base-sequence (one ˜ G– ˜ C pair was swapped in the unit cell). They found that the fluctua- tions are considerably larger than the bandwidths, which make the coherent transport of electrons in DNA impossible. The influence of water and ions surrounding DNA in a biologi- cal environment was studied by Gervasio et al. using density func- tional Car–Parrinello method [7]. Their model system was based on the experimental crystal structure of ˜ G– ˜ C dodecamer in its Z-DNA conformation. The periodic model had twelve ˜ G– ˜ C pairs in 0038-1098/$ – see front matter © 2010 Elsevier Ltd. All rights reserved. doi:10.1016/j.ssc.2010.12.001