In-situ infrared spectroscopic and scanning tunneling microscopy investigations of the chemisorption phases of uracil, thymine, and 3-methyl uracil on Au(111) electrodes

The complementary techniques of in-situ infrared spectroscopy and scanning tunneling microscopy (STM) have been used in this study to build detailed structural models for the chemisorbed forms of uracil, thymine, and 3-methyl uracil on Au(lll) electrodes. The infrared spectra, in water and D2O electrolytes, show that both uracil and thymine adopt similar coordination forms with the surface with both exocyclic oxygen atoms and a deprotonated N3 facing in toward the surface in a vertically oriented chemisorbate. 3-Methyl uracil cannot exhibit such a surface coordination and its IR signature in the carbonyl stretching region is quite different. This is interpreted as the chemisorbate interacting through its deprotonated N1 and C2=O. STM has been used to characterize and compare the molecular ordering of the three respective adsorbates. Uracil exhibits the highest coverage structure c(3 x root 3), while thymine exhibits smaller ordered domains which are expanded in one direction to allow for the spatial requirements of the methyl group on thymine. The domain size for the thymine chemisorbate could be improved by temperature annealing the electrode in-situ and a "pseudo c(root 3 x 4)" structure was observed. Both the uracil and thymine chemisorbate structures feature chains of molecules, stacked like "rolls of coins", close enough for rr-stacking to occur. The structure of thymine overlayers differs from uracil, since there are a number of different possible orientations of adjacent molecular rows, which results in a high frequency of stacking faults. These differences are discussed. 3-Methyl uracil is quite different, exhibiting a rather low coverage, albeit a highly ordered structure (5 x 2 root 3) which cannot allow rr-stacking. On the basis of these observations, the factors governing the formation of the respective chemisorbed phases are discussed.