Adsorption of Thymine on Gold Single-Crystal Electrodes

Abstract

We have examined the adsorption of thymine on (111), (100), and (210) gold single-crystal surfaces. The adsorption behavior on these three surfaces has been investigated by classical electrochemical methods like cyclic voltammetry and capacitance−potential measurements. Additionally in situ scanning tunneling microscopy (STM) and ex situ photoelectron spectroscopy (XPS) measurements have been performed for the adsorption of thymine on the (111) surface. The capacitance measurements as well as cyclic voltammetry investigations show the three adsorption states of thymine on all Au electrodes. The first adsorption state refers to a random adsorption of thymine molecules at negative surface charges. The second state can be characterized as a condensed but weakly adsorbed adlayer on the (100) and (111) crystals, whereas a noncondensed state has been found on the (210) surface. The condensed thymine film is stabilized mainly by hydrogen bonding. High-resolution STM images for this film on the (111) electrode point to an ordered adlayer with a unit cell which is incommensurate with the underlying Au surface. The images indicate flat adsorbing thymine molecules in this state. The third adsorption state is characterized by charge transfer from deprotonated thymine molecules to the gold surface. XPS data show one chemically modifed nitrogen atom for the chemisorbed thymine film. This adsorption state shows a commensurate 2√3 × 2√3 overstructure in the STM image. The STM images are interpreted by stacks of adsorbed thymine molecules with the molecular plane perpendicular to the surface. The stacks are connected by coadsorbed water molecules. The molecules are bound by a deprotonated nitrogen to the surface.

Interaction of Self-Assembled Monolayers of DNA with Electrons: HREELS and XPS Studies

“…This discrepancy between the conclusions based on the two techniques might arise from the fact that each of the techniques is sensitive to a different region of the monolayer. Whereas HREELS probes mainly the end of the molecules facing the vacuum, as most processes are region position ss-poly(C) ss-poly(A) ss-poly(T) literature [29][30][31][32][33][34][35] due to impact mechanisms, XPS probes the coverage on the gold itself. It is quite possible that, although the layer is not dense and fully ordered near the substrate, the long molecules arrange themselves in such a way that their tails, facing the vacuum, are well-ordered.…”

Spectroscopic quantification of covalently immobilized oligonucleotides

“…It could also be the result of DNA base interactions with the Al substrate. The growth (or appearance in the case of thymine) of the lower energy peak upon the interaction of various purines and pyrimidines with metals has been reported for thymine on gold, 45 aminopyrimidine on copper 46 and mercaptopurine on gold. 47 Each of the studied sequences has a unique C 1s spectrum, as shown in Fig.…”

Surface‐Structure‐Sensitive Adsorption of Adenine on Gold Electrodes

“…[2][3][4] The structure and properties of adsorbed nucleobase films deduced from electrochemical studies have been confirmed by several in situ spectroscopy techniques, such as subtractively normalized interfacial Fourier-transform infrared spectroscopy (SNIFTIRS), [5] surface-enhanced infrared reflection-absorption spectroscopy with the attenuated total reflection technique (ATR-SEIRAS), [4,6] surface-enhanced Raman spectroscopy (SERS), [7] surface X-ray scattering (SXS), [8] X-ray photoelectron spectroscopy (XPS), [9] and scanning tunnelling microscopy (STM). [9][10][11][12] These techniques, however, were mostly used to obtain information on monolayer films adsorbed on smooth basal planes or single-crystal surfaces with a low density of monotamic steps and hence reduced surface atomic corrugation. Although the macroscopic information that can be obtained by electrochemical techniques may not reflect the entire complexity of interfacial phenomena, it has long been used to assess the average systematic effect of surface atomic structure details such as regular monoatomic steps and kinks on, for example, the ionic and organic adsorption, electrocatalysis, under-potential deposition and two-dimensional film condensation.…”