Structure analysis of thiouracil on Ag(111) and graphite (0001) by x-ray diffraction and scanning tunneling microscopy

The geometric structures of ordered monolayers of large organic molecules (thiouracil) adsorbed to the surface of Ag(111) and graphite (0001) were analyzed using surface x-ray diffraction and scanning tunneling microscopy (STM), respectively. Although the substrates are different, in both cases the molecules are found to be arranged in parallel zig-zag rows. On graphite (0001) the molecules form a unit cell similar to the (111)plane of the bulk crystal whereas on Ag(111) the detailed x-ray analysis gives evidence that, in contrast to the bulk structure, all but one of the intermolecular hydrogen bonds present in the bulk are broken. The intact pyrimidine rings are tilted by about 30° with respect to the Ag surface in comparison to flat lying molecules on graphite. An elongation of the C=S bond distance by 0.16(7) A and an increase of the intra-pyrimidine-ring distances by about 0.11(10) A relative to the bulk is observed which can be attributed to the covalent interaction of the molecule with the substrate. We conclude that for an inert surface like graphite, where the molecules merely interact by van der Waals forces, the molecules build a unit cell mainly determined by intermolecular hydrogen bridge bonds and therefore almost unchanged with respect to the bulk, whereas even in the case of a weakly interacting surface like Ag( 111) the crystal structure can considerably be altered with respect to the bulk.