RT-TDDFT study of hole oscillations in B-DNA monomers and dimers

Abstract

We employ Real-Time Time-Dependent Density Functional Theory to study hole oscillations within a B-DNA monomer (one base pair) or dimer (two base pairs). Placing the hole initially at any of the bases which make up a base pair, results in THz oscillations, albeit of negligible amplitude. Placing the hole initially at any of the base pairs which make up a dimer is more interesting: For dimers made of identical monomers, we predict oscillations with frequencies in the range $f\approx$ 20–40 THz, with a maximum transfer percentage close to 1. For dimers made of different monomers, $f\approx$ 80–400 THz, but with very small or small maximum transfer percentage. We compare our results with those obtained recently via our Tight-Binding approaches and find that they are in good agreement.

Keywords:

• DNA
• charge transfer in biological systems
• electronic transfer in nanoscale materials and structures

AMS Subject Classifications:

• 87.14.gk 82.39.Jn 73.63.-b

Public Interest Statement

Understanding charge transfer (CT) in DNA is important for many biological and technological applications. CT depends on many extrinsic and intrinsic factors. The purpose of this article is to study the effect of one of the intrinsic factors, i.e. the base sequence. This work is a systematic ab initio study of hole (electron void) oscillations in small DNA segments. It discusses in detail many aspects of the phenomenon and compares its results with those of simpler, semi-empirical methods.

Acknowledgements

This work was supported by computational time granted from the Greek Research & Technology Network (GRNET) in the National HPC facility - ARIS - under [project ID pr002008 - CODNA].

Additional information

Funding

A. Morphis thanks the State Scholarships Foundation-IKY for a PhD research scholarship via ’IKY Fellowships of Excellence’, Hellenic Republic-Siemens Settlement Agreement.

Notes on contributors

M. Tassi

M. Tassi is currently a postdoctoral researcher at the National and Kapodistrian University of Athens (NKUA), Physics Department. Her main research interest is in the area of ab initio calculations studying electronic properties such as charge transfer in molecular systems, e.g. in DNA segments.

A. Morphis

A. Morphis is a PhD student at NKUA, Physics Department. His main research interest is in the study of electronic and optical properties of organic molecules and nanomaterials.

K. Lambropoulos

K. Lambropoulos is a PhD student at NKUA, Physics Department. Currently, he is studying the energy structure and the charge transfer properties of periodic crystalline, quasi-crystalline, fractal, amorphous, random and natural DNA segments.

C. Simserides

C. Simserides is an assistant professor at NKUA, Physics Department. He is mainly interested in charge transfer and transport along DNA, in optical properties of quantum dots and in ferromagnetic properties of diluted magnetic semiconductors.