Soft X-Ray-Induced Decomposition of Amino Acids: An XPS, Mass Spectrometry, and NEXAFS Study

Study on the reversible changes of the surface properties of an L-cysteine self-assembled monolayer on gold as a function of pH

A stimuli-response biological surface of L-cysteine was prepared on a polycrystalline gold surface from aqueous solution. The effect of the pH value of the rinsing solution on the surface composition was studied with X-ray photoelectron spectroscopy (XPS). Qualitative and quantitative analysis of the amino, carboxyl, and thiol functional groups of these self-assembled monolayers indicate that L-cysteine molecules exist in the neutral and zwitterionic forms and that they are sensitive to the pH of the rinsing solution. In addition, the wetting properties of the functionalized surface were studied by contact angle (CA) analysis: they were also dependent on the pH of the rinsing solution. Furthermore, it was shown that this functionalization process was reversible.

Quantum yields of decomposition and homo-dimerization of solid L-alanine induced by 7.2 eV Vacuum ultraviolet light irradiation: an estimate of the half-life of L-alanine on the surface of space objects

One of the leading hypotheses regarding the origin of prebiotic molecules on primitive Earth is that they formed from inorganic molecules in extraterrestrial environments and were delivered by meteorites, space dust and comets. To evaluate the availability of extraterrestrial amino acids, it is necessary to examine their decomposition and oligomerization rates as induced by extraterrestrial energy sources, such as vacuum ultraviolet (VUV) and X-ray photons and high energy particles. This paper reports the quantum yields of decomposition ((8.2 ± 0.7) × 10(-2) photon(-1)) and homo-dimerization ((1.2 ± 0.3) × 10(-3) photon(-1)) and decomposition of the dimer (0.24 ± 0.06 photon(-1)) of solid L-alanine (Ala) induced by VUV light with an energy of 7.2 eV. Using these quantum yields, the half-life of L-Ala on the surface of a space object in the present earth orbit was estimated to be about 52 days, even when only photons with an energy of 7.2 eV emitted from the present Sun were considered. The actual half-life of solid L-Ala on the surface of a space object orbit around the present day Earth would certainly be much shorter than our estimate, because of the added effect of photons and particles of other energies. Thus, we propose that L-Ala needs to be shielded from solar VUV in protected environments, such as the interior of a meteorite, within a time scale of days after synthesis to ensure its arrival on the primitive Earth.

Dopamine adsorption on anatase TiO2(101): a photoemission and NEXAFS spectroscopy study

The adsorption of dopamine onto an anatase TiO(2)(101) single crystal has been studied using photoemission and NEXAFS techniques. Photoemission results suggest that the dopamine molecule adsorbs on the surface in a bidentate geometry, resulting in the removal of band gap states in the TiO(2) valence band. Using the searchlight effect, carbon K-edge NEXAFS spectra indicate that the phenyl rings in the dopamine molecules are orientated normal to the surface. A combination of experimental and computational results indicates the appearance of new unoccupied states arising following adsorption. The possible role of these states in the charge-transfer mechanism of the dopamine-TiO(2) system is discussed.

Characterization of Biomaterials by Soft X-Ray Spectromicroscopy

Synchrotron-based soft X-ray spectromicroscopy techniques are emerging as useful tools to characterize potentially biocompatible materials and to probe protein interactions with model biomaterial surfaces. Simultaneous quantitative chemical analysis of the near surface region of the candidate biomaterial, and adsorbed proteins, peptides or other biological species can be obtained at high spatial resolution via scanning transmission X-ray microscopy (STXM) and X-ray photoemission electron microscopy (X-PEEM). Both techniques use near-edge X-ray absorption fine structure (NEXAFS) spectral contrast for chemical identification and quantitation. The capabilities of STXM and X-PEEM for the analysis of biomaterials are reviewed and illustrated by three recent studies: (1) characterization of hydrophobic surfaces, including adsorption of fibrinogen (Fg) or human serum albumin (HSA) to hydrophobic polymeric thin films, (2) studies of HSA adsorption to biodegradable or potentially biocompatible polymers, and (3) studies of biomaterials under fully hydrated conditions. Other recent applications of STXM and X-PEEM to biomaterials are also reviewed.

Vibrational and electronic characterisation of Staphylococcus aureus wall teichoic acids and relevant components in thin films

This work reports an investigation of S. aureus wall teichoic acid (WTA) and compares this biopolymer with its major occurring components, D: -alanine and glycerol phosphate. Detailed insight into molecular structures and electronic properties is obtained by vibrational and photoemission spectroscopy. Calculations are performed to support the analysis of our experimental vibrational spectra. It is shown that there are contributions of positive and negative charges in WTAs, but the number of negative charges is expected to be higher. The presence of both positive and negative charges on WTA may offer a route for modification of surfaces with the objective of avoiding the formation of biofilms.

New ambient pressure photoemission endstation at Advanced Light Source beamline 9.3.2

During the past decade, the application of ambient pressure photoemission spectroscopy (APPES) has been recognized as an important in situ tool to study environmental and materials science, energy related science, and many other fields. Several APPES endstations are currently under planning or development at the USA and international light sources, which will lead to a rapid expansion of this technique. The present work describes the design and performance of a new APPES instrument at the Advanced Light Source beamline 9.3.2 at Lawrence Berkeley National Laboratory. This new instrument, Scienta R4000 HiPP, is a result of collaboration between Advanced Light Source and its industrial partner VG-Scienta. The R4000 HiPP provides superior electron transmission as well as spectromicroscopy modes with 16 microm spatial resolution in one dimension and angle-resolved modes with simulated 0.5 degrees angular resolution at 24 degrees acceptance. Under maximum transmission mode, the electron detection efficiency is more than an order of magnitude better than the previous endstation at beamline 9.3.2. Herein we describe the design and performance of the system, which has been utilized to record spectra above 2 mbar.

L-tyrosine on Ag(111): universality of the amino acid 2D zwitterionic bonding scheme?

We present a combined study of the adsorption and ordering of the l-tyrosine amino acid on the close-packed Ag(111) noble-metal surface in ultrahigh vacuum by means of low-temperature scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. On this substrate the biomolecules self-assemble at temperatures exceeding 320 K into linear structures primarily following specific crystallographic directions and evolve with larger molecular coverage into two-dimensional nanoribbons which are commensurate with the underlying atomic lattice. Our high resolution topographical STM data reveal noncovalent molecular dimerization within the highly ordered one-dimensional nanostructures, which recalls the geometrical pattern already seen in the l-methionine/Ag(111) system and supports a universal bonding scheme for amino acids on smooth and unreactive metal surfaces. The molecules desorb for temperatures above 350 K, indicating a relatively weak interaction between the molecules and the substrate. XPS measurements reveal a zwitterionic adsorption, whereas NEXAFS experiments show a tilted adsorption configuration of the phenol moiety. This enables the interdigitation between aromatic side chains of adjacent molecules via parallel-displaced pi-pi interactions which, together with the hydrogen-bonding capability of the hydroxyl functionality, presumably mediates the emergence of the self-assembled supramolecular nanoribbons.

Functionalization of Zeolitic Cavities: Grafting NH2 Groups in Framework T Sites of B-SSZ-13 A Way to Obtain Basic Solids Catalysts?

Insertion of B atoms into an Al-free zeolitic framework with CHA topology results in the formation of B-SSZ-13 zeotype with Si/B = 11. B K-edge NEXAFS testifies that B forms [B(OSi)4] units in a Td-like geometry (sp3-hybridized B atoms). According to B K-edge NEXAFS and IR, template burning results in the formation of [B(OSi)3] units in a D3h-like geometry (sp2-hybridized B atoms) with a break of a B-O-Si bond and the formation of a Si-OH group. The activated material contains B(III) Lewis acid centers able to specifically coordinate bases like NH3. Such [B(OSi)3] units are reactive toward ammonia, resulting in the formation of B-NH2 surface functionality inside the pores of B-SSZ-13 already under mild conditions, i.e., 35 mbar of NH3 at 373 K for 30 min and without crystallinity degradation. A minor fraction of Si-NH2 cannot be excluded owing to the presence of two IR doublets at 3500 and 3430 cm-1 and at 1600 and 1550 cm-1. Ab initio B3LYP/6-31+G(d,p) calculations on a cluster model, supported by a single-point MP2 on B3LYP/6-31+G(D,P) optimized structures, found the break by NH3 of a B-O-Si bond of the [B(OSi)3] unit with formation of [SiOH] and [H2N-B(OSi)2] species to be energetically favored. Comparison between experimental and computed frequency shifts shows them to be in semiquantitative agreement. The high stability of the B-NH2 surface functionality is probed by N K-edge NEXAFS spectra collected under UHV conditions. These findings can open a new route in the preparation of shape selective solid basic catalysts.

NEXAFS Spectroscopy of Homopolypeptides at All Relevant Absorption Edges: Polyisoleucine, Polytyrosine, and Polyhistidine

Carefully calibrated high-resolution low-noise near-edge X-ray absorption fine structure spectra of three homopolypetides, viz., polyisoleucine, polytyrosine, and polyhistidine at the C, N, and O K-edges, are compared with the respective spectra of parent amino acids and glycine-derived cyclic dipeptide, 2,5-diketopiperazine. An assignment of the spectral features related to the nitrogen and oxygen atoms constituting the peptide bond is suggested on the basis of a comparative analysis of the experimental spectra as well as theoretical calculations for 2,5-diketopiperazine within the real-space multiple-scattering formalism. A splitting of the pi*-feature in the N K-edge spectra is identified, which is probably sensitive to the dominant conformation type of the peptide molecule (i.e., alpha-helix vs beta-sheet).

Probing enantioselectivity with x-ray photoelectron spectroscopy and density functional theory

The enantioselectivity of gold is investigated by x-ray photoelectron spectroscopy (XPS) and density functional theory (DFT). Cysteine molecules on a chiral Au(17 11 9);{S} surface show enantiospecific core level binding energies in the amino and in the thiol group. The sign and order of magnitude of the XPS core level shifts is reproduced by DFT. Identical preparations of D- and L-cysteine layers lead to D-cysteine molecules in the pure NH2 form, while a small portion of L-cysteine molecules maintains a hydrogen rich amino group (NH3). This implies enantiospecific adsorption reaction pathways and is consistent with DFT that indicates an activated hydrogen abstraction reaction from the amino group, which is downhill for D-cysteine.

Scanning transmission X-ray microscopic analysis of purified melanosomes of the mouse iris

Melanosomes are specialized intracellular membrane bound organelles that produce and store melanin pigment. The composition of melanin and distribution of melanosomes determine the color of many mammalian tissues, including the hair, skin, and iris. However, the presence of melanosomes within a tissue carries potentially detrimental risks related to the cytotoxic indole-quinone intermediates produced during melanin synthesis. In order to study melanosomal molecules, including melanin and melanin-related intermediates, we have refined methods allowing spectromicroscopic analysis of purified melanosomes using scanning transmission X-ray microscopy. Here, we present for the first time absorption data for melanosomes at the carbon absorption edge ranging from 284 to 290 eV. High-resolution images of melanosomes at discrete energies demonstrate that fully melanized mature melanosomes are internally non-homogeneous, suggesting the presence of an organized internal sub-structure. Spectra of purified melanosomes are complex, partially described by a predominating absorption band at 288.4 eV with additional contributions from several minor bands. Differences in these spectra were detectable between samples from two strains of inbred mice known to harbor genetically determined melanosomal differences, DBA/2J and C57BL/6J, and are likely to represent signatures arising from biologically relevant and tractable phenomena.

Nitrogen 1s Near-Edge X-ray Absorption Fine Structure Spectroscopy of Amino Acids: Resolving Zwitterionic Effects

Considerable variation is observed in the near-edge X-ray absorption fine structure (NEXAFS) spectra of amino acids. To unambiguously characterize the chemical origin of this variation, we have acquired the nitrogen 1s NEXAFS spectra of several amino acids and other model compounds and complemented these experimental measurements with ab initio calculations of isolated molecules and molecular clusters. The systematic differences observed between the zwitterionic and un-ionized forms of amino acids arise directly from the structural difference (-NH2 vs -NH3+), which leads to a change in the degree of Rydberg-valence mixing. Further change arises from quenching of this Rydberg character in the spectra of condensed amino acids. Ab initio calculations are used to explore the degree of Rydberg-valence mixing in the solid state.

Characterization of protein immobilization at silver surfaces by near edge X-ray absorption fine structure spectroscopy

Ribonuclease A (RNase A) is immobilized on silver surfaces in oriented and random form via self-assembled monolayers (SAMs) of alkanethiols. The immobilization process is characterized step-by-step using chemically selective near-edge X-ray absorption fine structure spectroscopy (NEXAFS) at the C, N, and S K-edges. Causes of imperfect immobilization are pinpointed, such as oxidation and partial desorption of the alkanethiol SAMs and incomplete coverage. The orientation of the protein layer manifests itself in an 18% polarization dependence of the NEXAFS signal from the N 1s to pi* transition of the peptide bond, which is not seen for a random orientation. The S 1s to C-S sigma* transition exhibits an even larger polarization dependence of 41%, which is reduced to 5% for a random orientation. A quantitative model is developed that explains the sign and magnitude of the polarization dependence at both edges. The results demonstrate that NEXAFS is able to characterize surface reactions during the immobilization of proteins and to provide insight into their orientations on surfaces.

Combined X-ray Absorption Spectroscopy and Density Functional Theory Examination of Ferrocene-Labeled Peptides

A combination of soft X-ray absorption spectroscopy (XAS) measurements and StoBe density functional theory (DFT) calculations has been used to study the electronic structures of the ferrocene-labeled peptides Fc-Pro(n)-OBz (n = 1-4). Excellent agreement between the measured and the simulated data is observed in all cases, and the origin of all major spectral features was assigned. The breaking of the degeneracy of the ferrocene 3e(2u)-like unoccupied molecular orbital under the influence of a substituent attached to a Cp ring was observed experimentally. The influence of the bonding environment on the O 1s and N 1s XAS spectra was examined. A corrected assignment of one of the major features in the Fe 2p XAS spectra of ferrocene is proposed and supported by the DFT simulations, as well as the measured spectra.

Local Hydration Environments of Amino Acids and Dipeptides Studied by X-ray Spectroscopy of Liquid Microjets

The nitrogen K-edge spectra of aqueous proline and diglycine solutions have been measured by total electron yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at neutral and high pH. All observed spectral features have been assigned by comparison to the recently reported spectrum of aqueous glycine and calculated spectra of isolated amino acids and hydrated amino acid clusters. The sharp preedge resonances at 401.3 and 402.6 eV observed in the spectrum of anionic glycine indicate that the nitrogen terminus is in an "acceptor-only" configuration, wherein neither amine proton is involved in hydrogen bonding to the solvent, at high pH. The analogous 1s --> sigma(NH) preedge transitions are absent in the NEXAFS spectrum of anionic proline, implying that the acceptor-only conformation observed in anionic glycine arises from steric shielding induced by free rotation of the amine terminus about the glycine CN bond. Anionic diglycine solutions exhibit a broadened 1s --> pi(CN) resonance at 401.2 eV and a broad shoulder resonance at 403 eV, also suggesting the presence of an acceptor-only species. Although this assignment is not as unambiguous as for glycine, it implies that the nitrogen terminus of most proteins is capable of existing in an acceptor-only conformation at high pH. The NEXAFS spectrum of zwitterionic lysine solution was also measured, exhibiting features similar to those of both anionic and zwitterionic glycine, and leading us to conclude that the alpha amine group is present in an acceptor-only configuration, while the end of the butylammonium side chain is fully solvated.

Carbon speciation in airborne particulate matter with C (1s) NEXAFS spectroscopy

Recent and current research activities on the chemical characterization of carbon in airborne carbonaceous particulate matter with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy are reviewed. NEXAFS spectroscopy uses soft X-rays from synchrotron radiation facilities and allows for the bulk and surface speciation of particulates smaller than 2.5 micrometres (PM 2.5). This relatively novel technique is often superior to TEM-EELS and FTIR spectroscopy. In the extreme case, one single PM particle is sufficient for characterization. Liquids, extracts, solid core and surface functional groups can be quantified. Preliminary data on combustion derived PM such as diesel soot, wood smoke and tobacco smoke are compared with ambient samples.

Innershell Absorption Spectroscopy of Amino Acids at All Relevant Absorption Edges

The C, N, and O K-edge near-edge X-ray absorption fine structure spectra of the 22 most common proteinogenic alpha-amino acids in the zwitterionic form collected from solvent-free polycrystalline powder films in the partial electron yield mode are reported. Spectral features common to all amino acids, as well as distinctive fingerprints of specific subgroups of these compounds, are presented and discussed.

Preferred Conformers and Photochemical (λ > 200 nm) Reactivity of Serine and 3,3-Dideutero-Serine In the Neutral Form

A systematic investigation of the conformational potential energy surface of neutral serine [HOCH2CHNH2COOH] and 3,3-dideutero-serine [HOCD2CHNH2COOH] was undertaken, revealing the existence of 61 different minima. The structures and vibrational spectra of the most stable conformers, which were estimated to have relative energies within 7 kJ mol(-1) and account for ca. 93% of the total conformational population at room temperature, were calculated at both the MP2 and DFT/BLYP levels of theory with the 6-311++G(d,p) basis-set and used to interpret the spectroscopic data obtained for the compounds isolated in low-temperature inert matrixes. The assignment of the main spectral infrared features observed in the range 4000-400 cm(-1) to the most stable conformers of serine was undertaken. In addition, UV irradiation (lambda > 200 nm) of the matrix-isolated compounds was also performed, leading to decarboxylation, which was found to be strongly dependent on the conformation assumed by the reactant molecule.

Surface Chemistry of Ultrathin Films of Histidine on Gold As Probed by High-Resolution Synchrotron Photoemission

Procedures for the vacuum deposition of thin histidine films on polycrystalline Au(111) and their characterization with high-resolution synchrotron-radiation-based photoelectron spectroscopy are reported. The chemical form of histidine (anionic vs zwitterionic) and the nature of its interactions with the substrate (strong ionic-covalent vs weak van der Waals bonding) in mono- and multilayer films are analyzed. It is shown that water adsorption on a pre-prepared histidine film at 100 K results in protonation of histidine molecules and partial formation of hydroxyl anions. These chemical effects are carefully differentiated from spectral changes associated with radiation damage of the histidine films.