Optical Properties of Free and Si(001)-Adsorbed Pyrimidinic Nucleobases

In this work, we predict and analyze the optical spectra of pyrimidinic uracil-like nucleobases thymine (THY), uracil (URA), and 5-fluorouracil (5-FU) and their reflection anisotropy spectra (RAS) upon adsorption on the silicon (001) surface. First-principles results based on plane-wave density functional theory show chemically sensitive features in gas phase optical absorption spectra that redshift/blueshift according to the orbitals involved in the corresponding transition. In the RAS, a characteristic lineshape is found, typical of the energetically favored "dimer bridge" configuration, and remarkably similar for all the investigated Si(001):X systems (X=THY, URA, 5-FU). We show that molecular tilting and breaking of the glide plane symmetry have a negligible effect on the optical spectra, despite their influence on the surface bandstructure. Contrarily to gas phase spectra, chemically sensitive RAS features only appear above 4.5eV, and can be recognized as molecular contributions consistent with gas phase optical absorption results whereas substrate effects dominate at lower energies.