Calculation of the total energy per unit cell and of the band structures of the five nucleotide base stacks using the local-density approximation

Abstract

Articles you may be interested inAb initio calculation of the CdSe/CdTe heterojunction band offset using the local-density approximation-1/2 technique with spin-orbit corrections J. Appl. Phys. 111, 073708 (2012) All-electron first-principles total energy electronic structure calculations were carried out for single chains of four nucleotide base stacks ͑composed of adenine, thymine, guanine, and cytosine, respectively͒ in the DNA B conformation ͑3.36 Å stacking distance and 36°screw angle ͒ using the local-density approximation ͑LDA͒ within a helical band structure approach. A uracil stack was also computed in the DNA B conformation and compared with the results obtained for the four DNA base stacks. The total energies per unit cell as a function of the stacking distance ͑at fixed screw angle ϭ36°͒ and of the screw angle ͑at dϭ3.36 Å͒ show in most cases rather good agreement with the experiment. As expected with LDA calculations, the band gaps were underestimated by nearly 50% compared to experimentally suggested values. Finally, some suggestions are given for the improvement of the band structures of the nucleotide base stacks.

Electronic Structure of Genomic DNA: A Photoemission and X-ray Absorption Study

“…It is superimposed by two intense components at about 5 eV (ii) and 9 eV (iii) BE. Note that this general shape had shown up in previous ab initio density of states (DOS) calculations of short poly(dA)−poly(dT) DNA double strands (also shown in Figure ) and that the size of the band gap coincides with that determined in recent scanning tunneling spectroscopy (STS) studies and calculations performed for nucleobases. , …”

Charge transport in DNA in solution: The role of polarons

“…It is seen that the polaron is essentially contained in four sites, although it would be larger in curve a for a smaller value of t 0 , which would agree better with recently calculated values for the transfer integral (21)(22)(23). Most significant are the calculated binding energies.…”

Mechanism of Charge Migration through DNA: Molecular Wire Behavior, Single-Step Tunneling or Hopping?

“…An estimate for the transfer integral b can be obtained by examining the HOMO -HOMO-1 energy difference that can be obtained from ab initio calculation 49 or from the bandwidths obtained from band structure calculations. 50 In this way the electronic coupling between neighboring base pairs can be estimated to range from 0.1 to 0.25 eV depending on the actual bases. The calculations mentioned above refer to perfectly regular B-DNA stacks while in real DNA the coupling will be hindered by static and dynamic fluctuations of the structure and different combinations of bases will give different values for b.…”