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

Attila Bende, F. Bogár, János Ladik

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Using the ab initio HartreeFock crystal orbital method in its linear combination of atomic orbitals form we have calculated the band structures of poly(G̃-C̃) and poly(Ã-T̃). 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(G̃) 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(G̃-C̃) and poly(Ã-T̃) calculation without water but in the presence of counterions. One finds that all the bands of poly(G̃-C̃) and poly(Ã-T̃) are shifted considerably upwards as compared to the previous single chain results (poly(G̃), poly(C̃), poly(Ã) and poly(T̃)). 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 1-3eV, 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.

Original languageEnglish
Pages (from-to)301-305
Number of pages5
JournalSolid State Communications
Volume151
Issue number4
DOIs
Publication statusPublished - Feb 2011

Fingerprint

Poly T
Nucleotides
Band structure
energy bands
DNA
nucleotides
deoxyribonucleic acid
Ions
Water
water
ions
Sugars
Phosphates
pyrimidines
Poly G
sugars
Sugar Phosphates
Deoxyribose
phosphates
Guanine

Keywords

  • A. Polymers, elastomers, and plastics
  • C. Crystal structure and symmetry
  • D. Electronic band structure
  • D. Orderdisorder effects

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Chemistry(all)
  • Materials Chemistry

Cite this

Model calculations of the energy band structures of double stranded DNA in the presence of water and Na+ ions. / Bende, Attila; Bogár, F.; Ladik, János.

In: Solid State Communications, Vol. 151, No. 4, 02.2011, p. 301-305.

Research output: Contribution to journalArticle

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N2 - Using the ab initio HartreeFock crystal orbital method in its linear combination of atomic orbitals form we have calculated the band structures of poly(G̃-C̃) and poly(Ã-T̃). 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(G̃) 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(G̃-C̃) and poly(Ã-T̃) calculation without water but in the presence of counterions. One finds that all the bands of poly(G̃-C̃) and poly(Ã-T̃) are shifted considerably upwards as compared to the previous single chain results (poly(G̃), poly(C̃), poly(Ã) and poly(T̃)). 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 1-3eV, 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.

AB - Using the ab initio HartreeFock crystal orbital method in its linear combination of atomic orbitals form we have calculated the band structures of poly(G̃-C̃) and poly(Ã-T̃). 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(G̃) 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(G̃-C̃) and poly(Ã-T̃) calculation without water but in the presence of counterions. One finds that all the bands of poly(G̃-C̃) and poly(Ã-T̃) are shifted considerably upwards as compared to the previous single chain results (poly(G̃), poly(C̃), poly(Ã) and poly(T̃)). 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 1-3eV, 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.

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