Andrey Shaporenko

X-ray Absorption Spectroscopy of the Nucleotide Bases at the Carbon, Nitrogen, and Oxygen K-Edges

Near-edge X-ray absorption fine structure spectra of three pyrimidine (viz., cytosine, uracil, and thymine) and two purine (viz., adenine and guanine) nucleobases, which are the key constituents of DNA and RNA, were measured at the C, N, and O K-edges using the self-absorption-free partial electron yield mode. The nucleobase samples were prepared as highly pure native polycrystalline powder films. The spectra are analyzed in terms of the electronic structure of the nucleobases. Subtle chemical effects related to the molecular structures of these heterocyclic compounds with extended pi-electron systems are considered and discussed.

Novel tripod ligands for prickly self-assembled monolayers

The new tridentate thioether ligands PhSi(CH2SMe)3 (1) and Ph-p-C6H4Si(CH2SMe)3 (2) have been synthesised and used for the preparation of the chelates fac-[W(kappa3-1)(CO)3] and fac-[W(kappa3-2)(CO)3], which were characterised by single-crystal X-ray diffraction. 1 and 2 were used as tripodal adsorbate molecules for the fabrication of self-assembled monolayers (SAMs) on gold. Film formation from solution was investigated in situ by second harmonic generation (SHG) and ellipsometry, which revealed a two-stepped process (fast adsorption, followed by slow film ordering). SAMs of 2 on gold were further investigated by ex situ methods, viz. high-resolution X-ray photoelectron spectroscopy (HRXPS), Fourier transform infrared reflection absorption spectroscopy (FTIRRAS), and scanning tunneling microscopy (STM). The latter two methods indicated dense packing of the tripodal anchor groups on the surface, with a substantially lower density of the biphenyl pricks. HRXPS showed three different binding states of sulfur, including a standard thiolate-type and a coordination-type state.

Is X-ray Absorption Spectroscopy Sensitive to the Amino Acid Composition of Functional Proteins?

We report, compare, and analyze near-edge X-ray absorption fine structure (NEXAFS) spectra of powder samples of four different functional proteins, namely, lysozyme, ovalbumin, bovine serum albumin, and type-I collagen, at all relevant absorption edges. The spectra of all of the above proteins were found to be quite similar and to exhibit minor differences only. Nevertheless, despite the general similarity, the spectra of the individual proteins are distinguishable, and some of the respective differences clearly correlate with their amino acid compositions. Further factors affecting the NEXAFS spectra of proteins beyond the building block approach are discussed.

Abrupt change in the structure of self-assembled monolayers upon metal evaporation

We have studied the interaction of vapor-deposited nickel with thiol-terminated self-assembled monolayers (SAMs) of oligophenylthiolates on Au, which can be considered as model systems for molecular electronics. Instead of usually observed disordering of the molecular layer, a drastic decrease in molecular tilt was observed at the initial stage of the deposition. This was attributed to the formation of Ni-thiol complexes at the SAM–ambient interface. The reorientation resulted in the appearance of transient channels for the metal diffusion into the SAM and to the SAM–substrate interface.

Quantitative analysis of temperature effects in radiation damage of thiolate-based self-assembled monolayers

Following our earlier finding of temperature effects in the radiation damage of self-assembled monolayers (SAMs) we investigated in detail the x-ray-induced modification of aliphatic and aromatic thiolate-based SAMs formed from dodecanethiol and biphenylthiol on gold substrates as representative test systems. For six sample temperatures between 50 and 300 K we measured cross sections and saturation behaviour for the most prominent irradiation-induced reactions, including desorption of hydrocarbon fragments, breaking of the headgroup-substrate bond, and formation of cross-linking networks and secondary bonds of the headgroup atoms within the layer. The results are discussed.

A spectroscopic study of self-assembled monolayer of porphyrin-functionalized oligo(phenyleneethynylene)s on gold: the influence of the anchor moiety

Porphyrin-functionalized oligo(phenyleneethynylene)s (OPE) are promising molecules for molecular electronics applications. Three such molecules (1-3) with the common structure P-OPE-AG (P and AG are a porphyrin and anchor group, respectively) and different anchor groups, viz. an acetyl protected thiol, -S-COCH3 (1), an acetyl protected thiol with methylene linker, -CH2-S-COCH3 (2), and a trimethylsilylethynyl group, -C(triple bond)C-Si(CH3)3 (3) have been synthesized and the corresponding self-assembled monolayers (SAMs) on Au(111) substrates have been prepared. The integrity and structural properties of these films were studied by X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy. The results suggest that the films formed from 1 have a high orientational order with an almost upright orientation and dense packing of the molecular constituents, i.e. represent a high quality SAM. In contrast, molecule 2 formed disordered molecular layers on Au, even though the molecule-surface bonding (thiolate) is the same as in the case of molecule 1. This suggests that the methylene linker in molecule 2 has a strong impact on the quality of the resulting film, so that a well-ordered SAM cannot be formed. The silane system, 3, is also able to bind to the gold surface but the resulting SAM has a poor quality, being significantly disordered and/or comprised of strongly inclined molecules. The above results suggest that the nature of the anchor group along with a possible linker is an important parameter which, to a high extent, predetermines the entire quality of OPE-based molecular layers.

Electronically induced modification of thin layers on surfaces

Interactions of thermally and electronically stimulated reactions in thin layers on surfaces are investigated. For self-assembled monolayers, thermal activation promotes many processes primarily induced by electronic excitations. We demonstrate that the film temperature is an important parameter for steering these reactions towards different final products. Using chemisorbed water on Ru(001) as an example, we investigate how the products of an irradiation induced reaction catalyze thermally stimulated dissociation of water molecules.