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.

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

Molteni, Elena
Primo
Membro del Collaboration Group
;
Cappellini, Giancarlo
Penultimo
Membro del Collaboration Group
;
2018-01-01

Abstract

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.
2018
Ab initio calculation; DNA; Nucleobase; Optical properties; Reflection anisotropy spectroscopy; silicon; surfaces; electronic, optical and magnetic materials; condensed matter physics
File in questo prodotto:
File Dimensione Formato  
AS5793963733155881515150268348_content_1.pdf

Solo gestori archivio

Descrizione: Articolo principale
Tipologia: versione post-print
Dimensione 1.02 MB
Formato Adobe PDF
1.02 MB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11584/234282
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 3
  • ???jsp.display-item.citation.isi??? 3
social impact