Local electronic structure of the peptide bond probed by resonant inelastic soft X-ray scattering.

The local valence orbital structure of solid glycine, diglycine, and triglycine is studied using soft X-ray emission spectroscopy (XES), resonant inelastic soft X-ray scattering (RIXS) maps, and spectra calculations based on density-functional theory. Using a building block approach, the contributions of the different functional groups of the peptides are separated. Cuts through the RIXS maps furthermore allow monitoring selective excitations of the amino and peptide functional units, leading to a modification of the currently established assignment of spectral contributions. The results thus paint a new-and-improved picture of the peptide bond, enhance the understanding of larger molecules with peptide bonds, and simplify the investigation of such molecules in aqueous environment.

Site-specific electronic structure of imidazole and imidazolium in aqueous solutions.

The occupied and unoccupied electronic structure of imidazole (C3N2H4) and imidazolium (C3N2H5+) in aqueous solutions is studied by X-ray emission spectroscopy (XES) and resonant inelastic soft X-ray scattering (RIXS). Both systems show distinct RIXS fingerprints with strong resonant effects. A comparison with calculated X-ray emission spectra of isolated imidazole and imidazolium suggests only a small influence of hydrogen bonding in the aqueous solution on the electronic structure of imidazole and imidazolium, and allows the attribution of specific spectral features to the non-equivalent nitrogen and carbon atoms in the molecules. In the case of nitrogen, this can also be achieved by site-selective resonant excitation. Furthermore, we find spectator shifts and symmetry selectivity in the RIXS spectra, as well as indications for rapid proton dynamics on the femtosecond timescale of the RIXS process, and derive the HOMO-LUMO gaps for the two molecules in aqueous solution.

X-ray Emission Spectroscopy of Proteinogenic Amino Acids at All Relevant Absorption Edges.

Nonresonant N K, O K, C K, and S L2,3 X-ray emission spectra of the 20 most common proteinogenic amino acids in their solid zwitterionic form are reported. They represent a comprehensive database that can serve as a reliable basis for the X-ray absorption spectroscopy (XES) studies of peptides and proteins. At the most important N and O K edges, clear similarities and differences between the spectra of certain amino acids are observed and associated with the specific chemical structure of these molecules and their functional groups. Analysis of these spectra allows the generation of spectral fingerprints of the protonated amino group, the deprotonated carboxylic group, and, using a building block approach, the specific nitrogen- and oxygen-containing functional groups in the side chains of the amino acids. Some of these fingerprints are compared to the spectra of reference compounds with the respective functional groups; they exhibit reasonable similarity, underlining the validity of the spectral fingerprint approach. The C K and S L2,3 XES spectra are found to be specific for each amino acid, in accordance with the different local environments of the involved C and S atoms, respectively.

Investigation of the Ionic Hydration in Aqueous Salt Solutions by Soft X-ray Emission Spectroscopy.

Understanding the molecular structure of the hydration shells and their impact on the hydrogen bond (HB) network of water in aqueous salt solutions is a fundamentally important and technically relevant question. In the present work, such hydration effects were studied for a series of representative salt solutions (NaCl, KCl, CaCl2, MgCl2, and KBr) by soft X-ray emission spectroscopy (XES) and resonant inelastic soft X-ray scattering (RIXS). The oxygen K-edge XES spectra could be described with three components, attributed to initial state HB configurations in pure water, water molecules that have undergone an ultrafast dissociation initiated by the X-ray excitation, and water molecules in contact with salt ions. The behavior of the individual components, as well as the spectral shape of the latter component, has been analyzed in detail. In view of the role of ions in such effects as protein denaturation (i.e., the Hofmeister series), we discuss the ion-specific nature of the hydration shells and find that the results point to a predominant role of anions as compared to cations. Furthermore, we observe a concentration-dependent suppression of ultrafast dissociation in all salt solutions, associated with a significant distortion of intact HB configurations of water molecules facilitating such a dissociation.

Amino-terminated biphenylthiol self-assembled monolayers as highly reactive molecular templates.

Self-assembled monolayers (SAMs) with amino tail groups are of interest due to their ability of coupling further compounds. Such groups can be, in particular, created by electron irradiation of nitro- or nitrile-substituted aromatic SAMs, which provide a basis for chemical nanolithography and the fabrication of functionalized nanomembranes. An estimate of reactivity of the created amino groups requires a reference system of homogeneous, amino-terminated aromatic SAMs, which can also be used as a highly reactive molecular template. Here, we describe the synthesis of 4'-aminobiphenyl-4-thiol (ABPT) and SAMs prepared from this precursor on Au(111). The monolayers were characterized by X-ray photoelectron spectroscopy and near edge X-ray absorption fine structure spectroscopy, which revealed that they are well defined, chemically uniform, densely packed, and highly ordered. To examine the influence of electron irradiation on the reactivity of the terminal amino groups, ABPT SAMs were exposed to low energy (50 eV) electrons up to a dose of 40 mC/cm(2) and, subsequently, immersed in either trifluoroacetic, pentafluoropropionic, or heptafluorobutyric anhydride. Analysing the amount of the attached anhydride species made it possible to determine the percentage of reactive amino groups as well as the effect of steric hindrance upon the coupling reaction. The above results are compared with those obtained for the well-established nitro-substituted biphenylthiol monolayers.

"Building block picture" of the electronic structure of aqueous cysteine derived from resonant inelastic soft X-ray scattering.

The electronic structure of the amino acid L-cysteine in an aqueous environment was studied using resonant inelastic soft X-ray scattering (RIXS) in a 2D map representation and analyzed in the framework of a "building block" approach. The element selectivity of RIXS allows a local investigation of the electronic structure of the three functional groups of cysteine, namely, the carboxyl, amino, and thiol groups, by measuring at the O K, N K, and S L2,3 edges, respectively. Variation of the pH value allows an investigation of molecules with protonated and deprotonated functional groups, which can then be compared with simple reference molecules that represent the isolated functional groups. We find that such building blocks can provide an excellent description of X-ray emission spectroscopy (XES) and RIXS spectra, but only if all nearest-neighbor atoms are included. This finding is analogous to the building block principle commonly used in X-ray absorption spectroscopy. The building blocks show a distinct spectral character (fingerprint) and allow a comprehensive interpretation of the cysteine spectra. This simple approach opens the path to investigate the electronic structure of more complex biological molecules in aqueous solutions using XES and RIXS.

Orbital-dependent charge transfer dynamics in conjugated self-assembled monolayers.

Femtosecond charge transfer (CT) dynamics in a series of self-assembled monolayers with an oligo(phenylenethynylene) and oligo(phenyl) backbone is addressed by resonant Auger spectroscopy using the core hole clock method. The characteristic CT times are found to depend strongly on the character of the molecular orbital (MO) which mediates the CT process. This demonstrates that the efficiency and rate of CT through molecular frameworks can be controlled by resonant injection of the charge carriers into specific MOs.

Isotope and temperature effects in liquid water probed by x-ray absorption and resonant x-ray emission spectroscopy.

High-resolution x-ray absorption and emission spectra of liquid water exhibit a strong isotope effect. Further, the emission spectra show a splitting of the 1b1 emission line, a weak temperature effect, and a pronounced excitation-energy dependence. They can be described as a superposition of two independent contributions. By comparing with gas phase, ice, and NaOH/NaOD, we propose that the two components are governed by the initial state hydrogen bonding configuration and ultrafast dissociation on the time scale of the O 1s core hole decay.

Exposure of monomolecular lithographic patterns to ambient: an X-ray photoemission spectromicroscopy study.

Patterned self-assembled monolayers (SAMs) of alkanethiolates (AT) on Au and Ag substrates were imaged and characterized by scanning photoelectron microscopy (SPEM). The patterns were prepared in situ by direct writing with the zone-plate-focused X-ray beam provided by the SPEM station. Whereas both AT/Au and AT/Ag behaved alike upon the irradiation, which resulted in similar contrasts in the fabricated patterns and similar microspot spectra from the irradiated areas, the intensity relationship between the patterned and nonpatterned areas changed by different pathways for the Au and Ag substrates after the exposure of the patterns to ambient. The SPEM data imply that weakly bound molecular fragments are desorbed from the irradiated areas upon air exposure in the case of Ag, whereas adsorption of airborne molecules from ambient occurs for the Au substrate. The origin of the observed differences is presumably related to the specific branching patterns of irradiation-induced modification of AT/Au and AT/Ag.

Abnormal temperature dependence of photoemission intensity mediated by thermally driven reorientation of a monomolecular film.

The photoemission intensities of organic molecular layers generally obey the Debye-Waller temperature dependence but not always. With the example of a monomolecular film formed from [1,1';4',1''-terphenyl]-4,4''-dimethanethiol, we show that pronounced deviations from Debye-Waller temperature behavior are possible and are likely caused by temperature-dependent changes in molecular orientation.

Self-assembled monolayers of semifluorinated alkaneselenolates on noble metal substrates.

Self-assembled monolayers (SAMs) formed from semifluorinated dialkyldiselenol (CF(3)(CF(2))(5)(CH(2))(2)Se-)(2) (F6H2SeSeH2F6) on polycrystalline Au(111) and Ag(111) were characterized by high-resolution X-ray photoelectron spectroscopy, infrared reflection absorption spectroscopy, near edge X-ray absorption fine structure spectroscopy, scanning tunneling microscopy, and contact angle measurements. The Se-Se linkage of F6H2SeSeH2F6 was found to be cleaved upon the adsorption, followed by the formation of selenolate-metal bond. The resulting F6H2Se SAMs are well-ordered, densely packed, and contamination-free. The packing density of these films is governed by the bulky fluorocarbon part, which exhibits the expected helical conformation. A noncommensurate hexagonal arrangement of the F6H2Se molecules with an average nearest-neighbor spacing of about 5.8 +/- 0.2 A, close to the van der Waals diameter the fluorocarbon chain, was observed on Au(111). The orientation of the fluorocarbon chains in the F6H2Se SAMs does not depend on the substrate-the average tilt angle of these moieties was estimated to be about 21-22 degrees on both Au and Ag.

Odd-even effects in photoemission from terphenyl-substituted alkanethiolate self-assembled monolayers.

Self-assembled monolayers (SAMs) formed from 4,4'-terphenyl-substituted alkanethiols C6H5(C6H4)2-(CH2)nSH (TPn, n = 1-6) on polycrystalline (111) gold and silver substrates have been characterized by synchrotron-based high-resolution X-ray photoelectron spectroscopy. The intensities, binding energy positions, and width of most photoemission lines exhibited pronounced odd-even effects, i.e., systematic and periodic variation, depending on either odd or even number of the methylene units in the aliphatic linker of the TPn molecules. The detailed analysis of these effects provides important information on the bonding and arrangement of the chemisorbed sulfur headgroups in the TPn films and balance of the structural forces in alkanethiolate SAMs.

Self-assembled monolayers of alkaneselenolates on (111) gold and silver.

Self-assembled monolayers (SAMs) formed from didodecyl diselenide (C12SeSeC12) and didodecyl selenide (C12SeC12) on (111) Au and Ag substrates were extensively characterized by several complementary techniques. C12SeSeC12 was found to form contamination-free, densely packed, and well-ordered C12Se SAMs on both substrates, whereas the adsorption of C12SeC12 occurred only on Au and resulted in the formation of a SAM-like C12SeC12 film with a low packing density and a conformational disorder. The properties of the C12Se SAMs were compared with those of dodecanethiolate (C12S) SAMs. The packing density, orientational order, and molecular inclination in C12Se/Au and C12S/Au were found to be very similar. In contrast, C12Se/Ag exhibited significantly lower packing density, a lower degree of the conformational and orientational order, and a larger molecular inclination than C12S/Ag. The results suggest a sp3 bonding configuration for the selenium atom on Au and Ag and indicate a larger corrugation of the headgroup-substrate binding energy surface in C12Se/Ag than in C12S/Ag.

The effect of halogen substitution in self-assembled monolayers of 4-mercaptobiphenyls on noble metal substrates.

Self-assembled monolayers (SAMs) formed from 4'-substituted 4-mercaptobiphenyls X-(C6H4)2SH (X-BPT, with X = I, Cl, and F) on polycrystalline (111) gold and silver substrates have been characterized by synchrotron-based high-resolution X-ray photoelectron spectroscopy and angle-resolved near-edge X-ray absorption fine structure spectroscopy. The X-BPT molecules were found to form highly oriented and densely packed SAMs on both substrates, with a smaller molecular inclination in the case of Ag. The experimental data show clear evidence for the charge transfer between the 4'-substituent and biphenyl moieties with the direction and extent of the transfer depending on the electronegativity of the halogen substituent. At the same time, no direct evidence of the charge transfer between the 4'-substituent and the thiolate group was observed. However, the substitution of the 4'-hydrogen by a halogen atom seems to affect the detailed packing arrangements of the SAM constituents.

Self-assembled monolayers of aromatic selenolates on noble metal substrates.

Self-assembled monolayers (SAMs) formed from bis(biphenyl-4-yl) diselenide (BBPDSe) on Au(111) and Ag(111) substrates have been characterized by high-resolution X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, infrared reflection absorption spectroscopy, water contact angle measurements, and scanning tunneling microscopy (STM). BBPDSe was found to form contamination-free, densely packed, and well-ordered biphenyl selenolate (BPSe) SAMs on both Au and Ag. Spectroscopic data suggest very similar packing density, orientational order, and molecular inclination in BPSe/Au and BPSe/Ag. STM data give a similar intermolecular spacing of 5.3 +/- 0.4 A on both Au and Ag but exhibit differences in the exact arrangement of the BPSe molecules on these two substrates, with the (2 square root[3] x square root[3])R30 degrees and (square root[3] x square root[3])R30 degrees unit cells on Au and Ag, respectively. There is strong evidence for adsorbate-mediated substrate restructuring in the case of Au, whereas no clear statement on this issue can be made in the case of Ag. The film quality of the BPSe SAMs is superior to their thiol analogues, which is presumably related to a better ability of the selenolates to adjust the surface lattice of the substrate to the most favorable 2D arrangement of the adsorbate molecules. This suggests that aromatic selenolates represent an attractive alternative to the respective thiols.

X-ray absorption spectromicroscopy studies for the development of lithography with a monomolecular resist.

Soft X-ray absorption microscopy was applied to image and characterize molecular patterns produced by electron irradiation of aliphatic and aromatic thiol-derived self-assembled monolayers (SAMs) on Au substrates. The measurements were performed at all relevant absorption edges. The fabricated patterns could be clearly imaged with a lateral resolution better than 150 nm, which, for example, allowed us to distinguish a fine structure of 1 microm features. The X-ray absorption microspot spectra derived from different areas of the SAM patterns provided specific chemical information on pristine and irradiated areas and unexpected features in these patterns. The quality of the microspot spectra is comparable with that of the analogous X-ray absorption spectra acquired with standard equipment from homogeneous SAMs. In particular, a chemical transformation of the functional tail groups within the irradiated areas of the patterned aromatic SAMs could be directly monitored.

Strong temperature dependence of irradiation effects in organic layers.

Radiation damage of self-assembled monolayers, which are prototypes of thin organic layers and highly organized biological systems, shows a strong dependence on temperature. Two limiting cases could be identified. Reactions involving transport of single atoms and small fragments proceed nearly independent of temperature. Reactions requiring transport of heavy fragments are, however, efficiently quenched by cooling. We foresee the combined use of temperature and irradiation by electrons or photons for advanced tailoring of self-assembled monolayers on surfaces. In addition, our results have direct implications for cryogenic approaches in advanced electron and x-ray microscopy and spectroscopy of biological macromolecules and cells.

Depth distribution of irradiation-induced cross-linking in aromatic self-assembled monolayers.

Pristine and strongly irradiated self-assembled monolayers of [1,1':4',1' '-terphenyl]-4,4' '-dimethanethiol (TPDMT) on Au have been characterized by near-edge X-ray absorption fine structure spectroscopy using partial electron yield acquisition mode. The TPDMT films were found to be extremely stable toward electron irradiation, which is explained by cross-linking between the aromatic backbones. In addition, we assume that a large delocalization and a strong relaxation of the initial electronic excitations in the densely packed film contributed to the film stability. The data analysis implies an inhomogeneous distribution of the irradiation-induced dehydrogenation and cross-linking of the terphenyl moieties in the TPDMT film, being most pronounced close to the film-ambient interface. The inhomogeneity was explained by quenching of the electronically excited C-H states via dipole-dipole interaction with the states' image at the metal surface, which has a reduced probability with increasing separation from the metal surface. Generally, the results suggest the importance of relaxation processes for the response of self-assembled monolayers to ionizing radiation.

Irradiation sensitivity of self-assembled monolayers with an introduced "weak link".

The irradiation sensitivity of n-alkanethiolate SAMs can be enhanced by the incorporation of an irradiation-sensitive functionality as a predetermined breaking point into the alkyl chain. Following this general strategy, several different sulfur-derived functional entities with a variable position in the alkyl chain were tested. In some cases, the incorporation of these entities resulted in a noticeable enhancement of the irradiation-induced desorption (by about 30%), even though the chains were not exclusively cut at the position of the incorporated group, but the scission events related to the "weak links" were just added to those in the alkyl matrix. The position of the incorporated group along the alkyl chain was found to be most essential for its performance as a weak link; the enhancement of irradiation-induced desorption was observed only when the groups were placed close to the SAM-ambient interface.