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Abstract
We predict UV reflectance anisotropy spectra (RAS) of the organically functionalized silicon (001) surface covered by pyrimidinic uracil-like nucleobases. First-principles results based on density functional theory show characteristic spectral features appearing in the UV range between 3 and 7 eV, besides the expected quench in the well-known two-minima RAS signal of clean Si(001). Nucleobase adsorption in the energetically favored ``dimer bridge'' configuration gives rise to a characteristic RAS line shape, common to thymine, uracil, and 5-fluorouracil. We trace back the origin of such spectral features by singling out RAS structures induced by relaxation and passivation effects on the Si surface, and those directly associated with molecular excitations. The former turn out to be the same for the three nucleobases, and are totally unaffected by molecular tilting. The sign and position of the latter RAS peaks at higher energy exhibit a moderate nucleobase dependence, and can be fully rationalized in terms of the molecular orbitals involved. The present theoretical results call for a RAS experimental study in the UV region extending up to $\ensuremath{\simeq}6--7$ eV.
Highlights
Functionalized solid surfaces have acquired a fundamental role in many fields of research, ranging from DNA sequencing [1,2] to semiconductor devices with novel functionalities [3,4,5], taking advantage of the great flexibility of organic chemistry in tuning the molecular electronic and optical properties [6,7,8]
In agreement with the experimental results of Lopez et al [17], density functional theory (DFT) results have shown that uracil molecules absorb vertically, with Si-O and Si-H bonds, indicating that hydrogen atoms are cleaved from the molecule, and move to saturate dangling bonds of Si surface atoms
We calculated the optical properties, including reflectance anisotropy spectra (RAS), for the Si(001) surface covered with thymine, uracil, and 5-fluorouracil molecules in the “dimer bridge” configuration, taking into account a possible tilting of the adsorbed molecules with respect to the surface normal
Summary
Functionalized solid surfaces have acquired a fundamental role in many fields of research, ranging from DNA sequencing [1,2] to semiconductor devices with novel functionalities [3,4,5], taking advantage of the great flexibility of organic chemistry in tuning the molecular electronic and optical properties [6,7,8]. A broad variety of molecular assemblies can form upon adsorption of organic molecules on metal, semiconductor, and insulating surfaces: a controlled growth process may lead to self-organized overstructures, with different geometries depending on the experimental conditions during growth. In this landscape, nucleobases have attracted much attention in view of their fundamental role in molecular biology and their simplicity with respect to larger biomolecules (peptides or even some amino acids) [9]. In agreement with the experimental results of Lopez et al [17], DFT results have shown that uracil molecules absorb vertically, with Si-O and Si-H bonds, indicating that hydrogen atoms are cleaved from the molecule, and move to saturate dangling bonds of Si surface atoms
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