Quantitative determination of the local structure of thymine on Cu(1 1 0) using scanned-energy mode photoelectron diffraction

Abstract

The local adsorption structures of the surface species formed by interaction of thymine with a Cu(1 1 0) surface at room temperature, and after heating to ∼530 K, have been investigated. Initial characterisation by soft-X-ray photoelectron spectroscopy and O K-edge near-edge X-ray absorption fine structure (NEXAFS) indicates the effect of sequential dehydrogenation of the NH species and provides information on the molecular orientation. O 1s and N 1s scanned-energy mode photoelectron diffraction shows the species at both temperatures bond to the surface through both carbonyl O atoms and the deprotonated N atom between them, each bonding atom adopting near-atop sites on the outermost Cu surface layer. The associated bondlengths are 1.96 ± 0.03 Å for Cu–N and 1.91 ± 0.03 Å and 2.03 ± 0.03 Å for the two inequivalent Cu--O bonds. The molecular plane lies almost exactly in the close-packed [ 1 1 ¯ 0 ] azimuth, but with a tilt relative to the surface normal of approximately 20°. Heating to ∼530 K, or deposition at this temperature, appears to lead to dehydrogenation of the second N atom in the ring, but no significant change in the adsorption geometry.