Uracil-like nucleobases on Si(001): effect of molecule adsorption, geometry and chemical substitutions on the electronic and optical properties of the silicon surface

Molteni1,2, G. Onida1,2, G. Fratesi1,2 and G. Cappellini3

1.Department of Physics, Universita’ degli Studi di Milano, via Celoria 16, 20133 Milano, Italy

2.European Theoretical Spectroscopy Facility (ETSF)

3.Department of Physics and CNR-IOM SLACS Cagliari, Universita’ degli Studi di Cagliari,

Cittadella Universitaria di Monserrato, S.P. Monserrato – Sestu, Km. 0.700, 09042 Monserrato (CA),


The adsorption of nucleobases on silicon surfaces is relevant both for the possibility of incorporating molecular functionalities within the semiconductor technology[1], and for the role of prebiotic molecules in models of the origin of life[2].

In this work we study the electronic properties of uracil-like nucleobases, thymine (THY), uracil (URA) and 5-fluorouracil (5-FU), adsorbed on the Si(001) surface[3], with first principles methods, based on density functional theory (DFT) with pseudopotentials and plane wave basis set. We investigate both the effects of chemical substitutions and of molecule orientation, finding important changes in band dispersion and energy gaps as a function of molecular tilting with respect to the surface normal.

We then extend our analysis to the study of optical properties[4] of the functionalized silicon surface, focusing on optical absorption and reflectance anisotropy spectra (RAS) and on their dependence on molecule adsorption, chemical substitutions and geometric details of the adsorbate. RAS is in fact a surface sensitive technique[5], which could be successfully used for in-situ, non-destructive surface monitoring. We obtain that the optical response of the Si(001) surface is strongly modified by the presence of the adsorbed molecules. We analyze molecule and substrate contributions to absorption and RAS spectra of the Si(001):X systems (X=THY,URA,5-FU), by considering additional model systems to disentangle the geometric and electronic effects of molecule adsorption. Our results may be of interest for applications in hybrid silicon/biomolecule-based nanodevices.

[1] W. G. Schmidt et al., Appl. Phys. A 85 (2006) 387.

[2] G. Malloci et al., Astronomy & Astrophysics 432 (2005) 585.

[3] E. Molteni, G. Onida, G. Cappellini, Eur. Phys. J. B 89 (2016) 98.

[4] E. Molteni, G. Onida, G. Fratesi, G. Cappellini, in preparation.

[5] K. Seino, W. G. Schmidt, Surf. Sci. 548 (2004) 183.