The adsorption and stability of sulfur containing amino acids on Cu{531}

The adsorption of L-CySteine and L-methionine amino acids on a chiral Cu{5 3 1} surface was investigated with high resolution X-ray photoelectron spectroscopy (XPS) and carbon K-edge near edge X-ray absorption fine structure (NEXAFS) Spectroscopy using synchrotron radiation. XPS shows that at 300 K L-cysteine adsorbs through two oxygen, a nitrogen and a sulfur atom, in a four point 'quadrangular footprint', whereas L-methionine adsorbs through only two oxygen and a nitrogen atom in a 'triangular footprint'. NEWS was used to clarify the adsorption geometry of both molecules, which suggests a binding orientation to the top layer and second layer atoms in two different orientations associated with adsorption sites on {1 1 0} and {3 1 1} microfacets; of the Cu{5 3 1} surface. (C) 2009 Elsevier B.V. All rights reserved.

Alignment of a model amyloid peptide fragment in bulk and at a solid surface

The alignment of model amyloid peptide YYKLVFFC is investigated in bulk and at a solid surface using a range of spectroscopic methods employing polarized radiation. The peptide is based on a core sequence of the amyloid beta (A beta) peptide, KLVFF. The attached tyrosine and cysteine units are exploited to yield information on alignment and possible formation of disulfide or dityrosine links. Polarized Raman spectroscopy on aligned stalks provides information on tyrosine orientation, which complements data from linear dichroism (LD) on aqueous solutions subjected to shear in a Couette cell. LD provides a detailed picture of alignment of peptide strands and aromatic residues and was also used to probe the kinetics of self-assembly. This suggests initial association of phenylalanine residues, followed by subsequent registry of strands and orientation of tyrosine residues. X-ray diffraction (XRD) data from aligned stalks is used to extract orientational order parameters from the 0.48 nm reflection in the cross-beta pattern, from which an orientational distribution function is obtained. X-ray diffraction on solutions subject to capillary flow confirmed orientation in situ at the level of the cross-beta pattern. The information on fibril and tyrosine orientation from polarized Raman spectroscopy is compared with results from NEXAFS experiments on samples prepared as films on silicon. This indicates fibrils are aligned parallel to the surface, with phenyl ring normals perpendicular to the surface. Possible disulfide bridging leading to peptide dimer formation was excluded by Raman spectroscopy, whereas dityrosine formation was probed by fluorescence experiments and was found not to occur except under alkaline conditions. Congo red binding was found not to influence the cross-beta XRD pattern.

Global and local expression of chirality in serine on the Cu{110} surface

Establishing a molecular-level understanding of enantioselectivity and chiral resolution at the organic−inorganic interfaces is a key challenge in the field of heterogeneous catalysis. As a model system, we investigate the adsorption geometry of serine on Cu{110} using a combination of low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The chirality of enantiopure chemisorbed layers, where serine is in its deprotonated (anionic) state, is expressed at three levels: (i) the molecules form dimers whose orientation with respect to the substrate depends on the molecular chirality, (ii) dimers of l- and d-enantiomers aggregate into superstructures with chiral (−1 2; 4 0) lattices, respectively, which are mirror images of each other, and (iii) small islands have elongated shapes with the dominant direction depending on the chirality of the molecules. Dimer and superlattice formation can be explained in terms of intra- and interdimer bonds involving carboxylate, amino, and β−OH groups. The stability of the layers increases with the size of ordered islands. In racemic mixtures, we observe chiral resolution into small ordered enantiopure islands, which appears to be driven by the formation of homochiral dimer subunits and the directionality of interdimer hydrogen bonds. These islands show the same enantiospecific elongated shapes those as in low-coverage enantiopure layers.

Enantiospecific adsorption of alanine on the chiral Cu{531} surface

We have studied enantiospecific differences in the adsorption of (S)- and (R)-alanine on Cu{531}R using low-energy electron diffraction (LEED), X-ray photoelectron spectroscopy, and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. At saturation coverage, alanine adsorbs as alaninate forming a p(1 4) superstructure. LEED shows a significantly higher degree of long-range order for the S than for the R enantiomer. Also carbon K-edge NEXAFS spectra show differences between (S)- and (R)-alanine in the variations of the ð resonance when the linear polarization vector is rotated within the surface plane. This indicates differences in the local adsorption geometries of the molecules, most likely caused by the interaction between the methyl group and the metal surface and/or intermolecular hydrogen bonds. Comparison with model calculations and additional information from LEED and photoelectron spectroscopy suggest that both enantiomers of alaninate adsorb in two different orientations associated with triangular adsorption sites on {110} and {311} microfacets of the Cu{531} surface. The experimental data are ambiguous as to the exact difference between the local geometries of the two enantiomers. In one of two models that fit the data equally well, significantly more (R)-alaninate molecules are adsorbed on {110} sites than on {311} sites whereas for (S)-alaninate the numbers are equal. The enantiospecific differences found in these experiments are much more pronounced than those reported from other ultrahigh vacuum techniques applied to similar systems.

The adsorption geometry and chemical state of lysine on Cu{110}

Chemisorbed layers of lysine adsorbed on Cu{110} have been studied using X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. XPS indicates that the majority (70%) of the molecules in the saturated layer at room temperature (coverage 0.27 ML) are in their zwitterionic state with no preferential molecular orientation. After annealing to 420 K a less densely packed layer is formed (0.14 ML), which shows a strong angular dependence in the characteristic π-resonance of oxygen K edge NEXAFS and no indication of zwitterions in XPS. These experimental results are best compatible with molecules bound to the substrate through the oxygen atoms of the (deprotonated) carboxylate group and the two amino groups involving Cu atoms in three different close packed rows. This μ4 bonding arrangement with an additional bond through the !-amino group is different from geometries previously suggested for lysine on Cu{110}.

The study of chiral adsorption systems using synchrotron- based structural and spectroscopic techniques: stereospecific adsorption of serine on Au-modified chiral Cu{531} surfaces

We apply modern synchrotron-based structural techniques to the study of serine adsorbed on the pure andAumodified intrinsically chiral Cu{531} surface. XPS and NEXAFS data in combination with DFT show that on the pure surface both enantiomers adsorb in l4 geometries (with de-protonated b-OH groups) at low coverage and in l3 geometries at saturation coverage. Significantly larger enantiomeric differences are seen for the l4 geometries, which involve substrate bonds of three side groups of the chiral center, i.e. a three-point interaction. The l3 adsorption geometry, where only the carboxylate and amino groups form substrate bonds, leads to smaller but still significant enantiomeric differences, both in geometry and the decomposition behavior. When Cu{531} is modified by the deposition of 1 and 2ML Au the orientations of serine at saturation coverage are significantly different from those on the clean surface. In all cases, however, a l3 bond coordination is found at saturation involving different numbers of Au atoms, which leads to relatively small enantiomeric differences.

Surface chemistry of glycine on Pt{111} in different aqueous environments

Adsorption of glycine on Ptf111g under UHV conditions and in different aqueous environments was studied by XPS (UHV and ambient pressure) and NEXAFS. Under UHV conditions, glycine adsorbs in its neutral molecular state up to about 0.15 ML. Further deposition leads to the formation of an additional zwitterionic species, which is in direct contact with the substrate surface, followed by the growth of multilayers, which also consist of zwitterions. The neutral surface species is most stable and decomposes at 360 K through a multi-step process which includes the formation of methylamine and carbon monoxide. When glycine and water are co-adsorbed in UHV at low temperatures (< 170 K) inter-layer diffusion is inhibited and the surface composition depends on the adsorption sequence. Water adsorbed on top of a glycine layer does not lead to significant changes in its chemical state. When glycine is adsorbed on top of a pre-adsorbed chemisorbed water layer or thick ice layer, however, it is found in its zwitterionic state, even at low coverage. No difference is seen in the chemical state of glycine when the layers are exposed to ambient water vapor pressure up to 0.2 Torr at temperatures above 300 K. Also the decomposition temperature stays the same, 360 K, irrespective of the water vapor pressure. Only the reaction path of the decomposition products is affected by ambient water vapor.

Surface chemistry of alanine on Cu{111}: Adsorption geometry and temperature dependence

Adsorption of l-alanine on the Cu{111} single crystal surface was investigated as a model system for interactions between small chiral modifier molecules and close-packed metal surfaces. Synchrotron-based X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy are used to determine the chemical state, bond coordination and out-of-plane orientation of the molecule on the surface. Alanine adsorbs in its anionic form at room temperature, whilst at low temperature the overlayer consists of anionic and zwitterionic molecules. NEXAFS spectra exhibit a strong angular dependence of the π ⁎ resonance associated with the carboxylate group, which allows determining the tilt angle of this group with respect to the surface plane (48° ± 2°) at room temperature. Low-energy electron diffraction (LEED) shows a p(2√13x2√13)R13° superstructure with only one domain, which breaks the mirror symmetry of the substrate and, thus, induces global chirality to the surface. Temperature-programmed XPS (TP-XPS) and temperature-programmed desorption (TPD) experiments indicate that the zwitterionic form converts into the anionic species (alaninate) at 293 K. The latter desorbs/decomposes between 435 K and 445 K.

Observing the in situ chiral modification of Ni nanoparticles using scanning transmission X-ray microspectroscopy

Enantioselective heterogeneous hydrogenation of Cdouble bond; length as m-dashO bonds is of great potential importance in the synthesis of chirally pure products for the pharmaceutical and fine chemical industries. One of the most widely studied examples of such a reaction is the hydrogenation of β-ketoesters and β-diketoesters over Ni-based catalysts in the presence of a chiral modifier. Here we use scanning transmission X-ray microscopy combined with near-edge X-ray absorption fine structure spectroscopy (STXM/NEXAFS) to investigate the adsorption of the chiral modifier, namely (R,R)-tartaric acid, onto individual nickel nanoparticles. The C K-edge spectra strongly suggest that tartaric acid deposited onto the nanoparticle surfaces from aqueous solutions undergoes a keto-enol tautomerisation. Furthermore, we are able to interrogate the Ni L2,3-edge resonances of individual metal nanoparticles which, combined with X-ray diffraction (XRD) patterns showed them to consist of a pure nickel phase rather than the more thermodynamically stable bulk nickel oxide. Importantly, there appears to be no “particle size effect” on the adsorption mode of the tartaric acid in the particle size range ~ 90–~ 300 nm.

Stereochemistry and thermal stability of tartaric acid on the intrinsically chiral Cu{531} surface

Intrinsically chiral metal surfaces provide enantiospecific reaction environments without the need of coadsorbed modifiers. Amongst the intrinsically chiral copper surfaces, Cu{531} has the smallest unit cell and the highest density of chiral sites. XPS, NEXAFS and TPD were employed to investigate the adsorption and decomposition behaviour of the two chiral enantiomers of tartaric acid on this surface. The results obtained from XPS and NEXAFS show that at saturation coverage both enantiomers of tartaric acid adsorb in a μ4 configuration through the two carboxylic groups,which are rotatedwith respect to each other by 90°±≈15°within the surface plane. At intermediate coverage the R,R enantiomer adopts a similar configuration, but the S,S enantiomer is different and shows a high degree of dissociation. Growth of multilayers is observed at high exposures when the sample is kept at below 370 K. TPD experiments show that multilayers desorb between 390 K and 470 K and decomposition of the chemisorbed layer occurs between 470 K and 600 K. The desorption spectra support a two-step decomposition mechanism with a O_C_C_O or HO–HC_CH–OH intermediate that leads to production of CO2 and CO. Enantiomeric differences are observed in the desorption features related to the decomposition of the chemisorbed layer.

Surface chemistry of alanine on Ni{111}

The adsorption of L-alanine on Ni{111} has been studied as a 10 model of enantioselective heterogeneous catalysts. Synchrotron-based X-ray 11 photoelectron spectroscopy and near-edge X-ray absorption fine structure 12 (NEXAFS) spectroscopy were used to determine the chemical state, bond 13 coordination, and out-of-plane orientation of the molecule on the surface. 14 Alanine adsorbs in anionic and zwitterionic forms between 250 and ≈320 K. 15 NEXAFS spectra exhibit a strong angular dependence of the π* resonance 16 associated with the carboxylate group, which is compatible with two distinct 17 orientations with respect to the surface corresponding to the bidentate and 18 tridentate binding modes. Desorption and decomposition begin together at 19 ≈300 K, with decomposition occurring in a multistep process up to ≈450 K. Comparison with previous studies of amino acid 20 adsorption on metal surfaces shows that this is among the lowest decomposition temperatures found so far and lower than typical 21 temperatures used for hydrogenation reactions where modified Ni catalysts are used.

Furan interaction with the Si(001)-(2 x 2) surface: structural, energetics, and vibrational spectra from first-principles

In this work we employ the state of the art pseudopotential method, within a generalized gradient approximation to the density functional theory, to investigate the adsorption process of furan on the silicon (001) surface. A direct comparison of different adsorption structures with x-ray photoelectron spectroscopy (XPS), ultra-violet photoelectron spectroscopy (UPS), high resolution electron energy loss spectroscopy (HREELS), near edge x-ray absorption fine structure (NEXAFS), and high resolution spectroscopy experimental data allows us to identify the [4 + 2] cycloaddition reaction as the most probable adsorbate. In addition, theoretical scanning tunnelling microscopy (STM) images are presented, with a view to contributing to further experimental investigations.

Direct observation of defect levels in hexagonal BN by soft X-ray absorption spectroscopy

Formation of defects in hexagonal boron nitride under low-energy argon bombardment has been studied by near-edge X-ray absorption fine structure (NEXAFS) around B and N K-edges. Breaking of B-N bonds and creation of nitrogen vacancies has been identified from the B K-edge, followed by the formation of molecular nitrogen, N2, at interstitial positions. The presence of N2 produces a sharp resonance in the low-resolution NEXAFS spectra around N K-edge, showing the characteristic vibrational fine structure in high-resolution measurements. Several new peaks in NEXAFS spectra have been assigned to boron or nitrogen interstitials, in good agreement with theoretical predictions. © 2009 Elsevier B.V. All rights reserved.

Formation of defects in boron nitride by low energy ion bombardment

Formation of defects in hexagonal and cubic boron nitride (h -BN and c -BN, respectively) under low-energy argon or nitrogen ion-bombardment has been studied by near-edge x-ray absorption fine structure (NEXAFS) around boron and nitrogen K -edges. Breaking of B-N bonds for both argon and nitrogen bombardment and formation of nitrogen vacancies, VN, has been identified from the B K -edge of both h -BN and c -BN, followed by the formation of molecular nitrogen, N2, at interstitial positions. The presence of N 2 produces an additional peak in photoemission spectra around N 1s core level and a sharp resonance in the low-resolution NEXAFS spectra around N K -edge, showing the characteristic vibrational fine structure in high-resolution measurements. In addition, several new peaks within the energy gap of BN, identified by NEXAFS around B and N K -edges, have been assigned to boron or nitrogen interstitials, in good agreement with theoretical predictions. Ion bombardment destroys the cubic phase of c -BN and produces a phase similar to a damaged hexagonal phase. © 2009 American Institute of Physics.

Decoration of nitrogen vacancies by oxygen atoms in boron nitride nanotubes

Decoration of nitrogen vacancies by oxygen atoms has been studied by near-edge X-ray absorption fine structure (NEXAFS) around B K-edge in several boron nitride (BN) structures, including bamboo-like and multi-walled BN nanotubes. Breaking of B-N bonds and formation of nitrogen vacancies under low-energy ion bombardment reduces oxidation resistance of BN structures and promotes an efficient oxygen-healing mechanism, in full agreement with some recent theoretical predictions. The formation of mixed O-B-N and B-O bonds is clearly identified by well-resolved peaks in NEXAFS spectra of excited boron atoms.