Eur. Phys. J. Special Topics 227, 1681-1692 (2019)
https://doi.org/10.1140/epjst/e2019-800157-0

Regular Article

Diamondoid-functionalized nanogaps: from small molecules to electronic biosensing

¹ Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
² Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, IL 60439, USA

^a e-mail: mfyta@icp.uni-stuttgart.de

Received: 1 October 2018
Received in final form: 25 October 2018
Published online: 8 March 2019

Abstract

The potential of reading-out DNA molecules using functionalized electrodes embedded in nanopores is discussed here. Focus is given on functionalization using tiny diamond-like hydrogenated cages, the diamondoids. A derivative known as memantine of the smallest diamondoid is taken. This offers hydrogen bonding possibilities. Based on quantum-mechanical calculations, we first assess the interaction details of memantine with DNA units, the nucleotides. At a next step, nucleotides are placed within the nanogap formed by the diamondoid-functionalized electrodes. Quantum transport calculations are performed and show the high sensitivity of the electrodes in distinguishing among the different nucleotide types. We proceed by qualitatively revealing the influence of the DNA molecules by simply rotating the nucleotide within the nanogap. The effect of an aqueous environment is also included and the dynamic behavior of the conductance across the functionalized electrodes is addressed. In the end, we discuss the relevance of our results in detecting DNA sequences.