Adsorption of cytosine and aza derivatives of cytidine on Au single crystal surfaces

Abstract: The adsorption of cytosine on the Au(111) and Au(110) surfaces has been studied using both aqueous deposition and evaporation in vacuum to prepare the samples. Soft X-ray photoelectron spectroscopy (XPS) and near edge X-ray absorption fine structure spectroscopy (NEXAFS) were used to determine the electronic structure and orientation of the adsorbates. In addition, three derivatives of cytosine, 6-azacytosine, 6-azacytidine and 5- azacytidine, were studied. Monolayer films of the latter three samples were adsorbed on Au(111) from aqueous solution, and the nature of bonding was determined. Spectra have been interpreted in the light of published calculations of free cytosine molecules and new ab initio calculations of the other compounds. Surface core level shifts of Au 4f imply that all of these compounds are chemisorbed. Cytosine adsorbs as a single tautomer, but in two chemical states with different surface-molecule bonding. For deposition in vacuum, a flat-lying molecular state bonded through the N(3) atom of the pyrimidine ring dominates, but a second state is also present. For deposition from solution, the second state dominates, with the molecular plane no longer parallel to the surface. This state also bonds through the N(3) atom, but in addition interacts with the surface via the amino group. Two tautomers of 6-azacytosine were observed, and they and 6-azacytidine adsorb with similar geometries, chemically bonding via the azacytosine ring. The ribose ring does not appear to perturb the adsorption of azacytidine compared with azacytosine. The azacytosine ring is nearly but not perfectly parallel to the surface, like 5-azacytidine, which adsorbs as an imino tautomer. ...