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

Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy

Near-edge X-ray absorption mass spectrometry (NEXAMS) around the nitrogen and oxygen K-edges was employed on gas-phase peptides to probe the electronic transitions related to their protonation sites, namely at basic side chains, the N-terminus and the amide oxygen. The experimental results are supported by replica exchange molecular dynamics and density-functional theory and restricted open-shell configuration with single calculations to attribute the transitions responsible for the experimentally observed resonances. We studied five tailor-made glycine-based pentapeptides, where we identified the signature of the protonation site of N-terminal proline, histidine, lysine and arginine, at 406 eV, corresponding to N 1s → σ*(NHx+) (x = 2 or 3) transitions, depending on the peptides. We compared the spectra of pentaglycine and triglycine to evaluate the sensitivity of NEXAMS to protomers. Separate resonances have been identified to distinguish two protomers in triglycine, the protonation site at the N-terminus at 406 eV and the protonation site at the amide oxygen characterized by a transition at 403.1 eV.

Role of the redox state of cerium oxide on glycine adsorption: an experimental and theoretical study

The role of the oxidation state of cerium cations in a thin oxide film in the adsorption, geometry, and thermal stability of glycine molecules was studied. The experimental study was performed for a submonolayer molecular coverage deposited in vacuum on CeO₂(111)/Cu(111) and Ce₂O₃(111)/Cu(111) films by photoelectron and soft X-ray absorption spectroscopies and supported by ab initio calculations for prediction of the adsorbate geometries, C 1s and N 1s core binding energies of glycine, and some possible products of the thermal decomposition. The molecules adsorbed on the oxide surfaces at 25 °C in the anionic form via the carboxylate oxygen atoms bound to cerium cations. A third bonding point through the amino group was observed for the glycine adlayers on CeO₂. In the course of stepwise annealing of the molecular adlayers on CeO₂ and Ce₂O₃, the surface chemistry and decomposition products were analyzed and found to relate to different reactivities of glycinate on Ce⁴⁺ and Ce³⁺ cations, observed as two dissociation channels via C-N and C-C bond scission, respectively. The oxidation state of cerium cations in the oxide was shown to be an important factor, which defines the properties, electronic structure, and thermal stability of the molecular adlayer.

Mineralogical control on methylotrophic methanogenesis and implications for cryptic methane cycling in marine surface sediment

Minerals are widely proposed to protect organic carbon from degradation and thus promote the persistence of organic carbon in soils and sediments, yet a direct link between mineral adsorption and retardation of microbial remineralisation is often presumed and a mechanistic understanding of the protective preservation hypothesis is lacking. We find that methylamines, the major substrates for cryptic methane production in marine surface sediment, are strongly adsorbed by marine sediment clays, and that this adsorption significantly reduces their concentrations in the dissolved pool (up to 40.2 ± 0.2%). Moreover, the presence of clay minerals slows methane production and reduces final methane produced (up to 24.9 ± 0.3%) by a typical methylotrophic methanogen—Methanococcoides methylutens TMA-10. Near edge X-ray absorption fine structure spectroscopy shows that reversible adsorption and occlusive protection of methylamines in clay interlayers are responsible for the slow-down and reduction in methane production. Here we show that mineral-OC interactions strongly control methylotrophic methanogenesis and potentially cryptic methane cycling in marine surface sediments.

Adsorption of methylamines onto clay minerals provides a hitherto unrecognised control on methane production in marine surface sediment.

Soft X-ray Absorption Spectroscopy of Aqueous Solutions Using a Table-Top Femtosecond Soft X-ray Source

We demonstrate the feasibility of soft X-ray absorption spectroscopy in the water window using a table-top laser-based approach with organic molecules and inorganic salts in aqueous solution. A high-order harmonic source delivers femtosecond pulses of short wavelength radiation in the photon energy range from 220 to 450 eV. We report static soft X-ray absorption measurements in transmission on the solvated compounds O=C(NH₂)₂, CaCl₂, and NaNO₃ using flatjet technology. We monitor the absorption of the molecular samples between the carbon (∼280 eV) and nitrogen (∼400 eV) K-edges and compare our results with previous measurements performed at the BESSYII facility. We discuss the roles of pulse stability and photon flux in the outcome of our experiments. Our work paves the way toward table-top femtosecond, solution-phase soft X-ray absorption spectroscopy in the water window.

Soft X-ray Spectroscopy of the Amine Group: Hydrogen Bond Motifs in Alkylamine/Alkylammonium Acid-Base Pairs

We use N K-edge absorption spectroscopy to explore the electronic structure of the amine group, one of the most prototypical chemical functionalities playing a key role in acid-base chemistry, electron donor-acceptor interactions, and nucleophilic substitution reactions. In this study, we focus on aliphatic amines and make use of the nitrogen 1s core electron excitations to elucidate the roles of N-H σ* and N-C σ* contributions in the unoccupied orbitals. We have measured N K-edge absorption spectra of the ethylamine bases Et _xNH_{3- x} ( x = 0...3; Et- = C₂H₅-) and the conjugate positively charged ethylammonium cation acids Et _yNH_{4- y}⁺ ( y = 0...4; Et- = C₂H₅-) dissolved in the protic solvents ethanol and water. Upon consecutive exchange of N-H for ethyl-groups, we observe a spectral shift, a systematic decrease of the N K-edge pre-edge peak, and a major contribution in the post-edge region for the ethylamine series. Instead, for the ethylammonium ions, the consecutive exchange of N-H for ethyl groups leads to an apparent reduction of pre-edge and post-edge intensities relative to the main-edge band, without significant frequency shifts. Building on findings from our previously reported study on aqueous ammonia and ammonium ions, we can rationalize these observations by comparing calculated N K-edge absorption spectra of free and hydrogen-bonded clusters. Hydrogen bonding interactions lead only to minor spectral effects in the ethylamine series, but have a large impact in the ethylammonium ion series. Visualization of the unoccupied molecular orbitals shows the consecutive change in molecular orbital character from N-H σ* to N-C σ* in these alkylamine/alkylammonium ion series. This can act as a benchmark for future studies on chemically more involved amine compounds.

Influence of Local Environment on Inner Shell Excitation Spectra, Studied by Electron and X-ray Spectroscopy and Spectromicroscopy

Inner shell excitation spectroscopy is a local probe of the unoccupied electronic structure in the immediate vicinity of the core excited atom. As such, one might expect the inner shell spectrum of a given unit (a molecular fragment or a repeat unit of a solid) to be largely independent of where that unit is located. This is often an implicit assumption in spectral analysis and analytical applications. However, there are situations where inner shell excitation spectra exhibit significant sensitivity to their local environment. Here I categorize the ways in which inner shell spectra are affected by their local environment, and give examples from a career dedicated to developing a better understanding of inner shell excitation spectroscopy, its experimental techniques, and applications.

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p-Aminobenzoic Acid

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO–LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs and σ* shape resonances in the NEXAFS spectra. This provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute–solvent interactions.

Sulfur 1s near edge x-ray absorption fine structure spectroscopy of thiophenic and aromatic thioether compounds

Thiophenic compounds are major constituents of fossil fuels and pose problems for fuel refinement. The quantification and speciation of these compounds is of great interest in different areas such as biology, fossil fuels studies, geology, and archaeology. Sulfur 1s Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy has emerged as a qualitative and quantitative method for sulfur speciation. A firm understanding of the sulfur 1s NEXAFS spectra of organosulfur species is required for these analytical studies. To support this development, the sulfur 1s NEXAFS spectra of simple thiols and thioethers were previously examined, and are now extended to studies of thiophenic and aromatic thioether compounds, in the gas and condensed phases. High-resolution spectra have been further analyzed with the aid of Improved Virtual Orbital (IVO) and Δ(self-consistent field) ab initio calculations. Experimental sulfur 1s NEXAFS spectra show fine features predicted by calculation, and the combination of experiment and calculation has been used to improve the assignment of spectroscopic features important for the speciation and quantification of sulfur compounds. Systematic differences between gas and condensed phases are also explored; these differences suggest a significant role for conformational effects in the NEXAFS spectra of condensed species.

Binding geometry of hydrogen-bonded chain motif in self-assembled gratings and layers on Ag(111)

Upon adsorption on the (111) facet of Ag, 4-[trans-2-(pyrid-4-yl-vinyl)] benzoic acid (PVBA) self-assembles into a highly ordered, chiral twin chain structure at submonolayer coverages with domains that can extend for micrometers in one dimension. Using polarization-dependent measurements of C and N K-shell excitations in near-edge X-ray absorption fine structure (NEXAFS) spectra, we determine the binding geometry of single PVBA molecules within this unique ensemble for both low and high coverage regimes. At submonolayer coverage, the molecule is twisted to facilitate the formation of hydrogen bonds. The gas-phase planarity is gradually recovered as the coverage is increased, with complete planarity coinciding with loss of order in the overlayer. Thermal treatment of the PVBA film results in deprotonation of the carboxyl tail of the molecule, but despite the suppression of the stabilizing hydrogen-bonds, the overlayer remains ordered.

Excitons at the B K edge of boron nitride nanotubes probed by x-ray absorption spectroscopy

We have performed a near-edge x-ray absorption fine-structure (NEXAFS) investigation of multi-walled boron nitride nanotubes (BNNTs). We show that the one-dimensionality of BNNTs is clearly evident in the B K edge spectrum, while the N K edge spectrum is similar to that of layered hexagonal BN (h-BN). We observe a sharp feature at the σ* onset of the B K edge, which we ascribe to a core exciton state. We also report a comparison with spectra taken after an ammonia plasma treatment, showing that the B K edge becomes indistinguishable from that of h-BN, due to the breaking of the tubular order and the formation of small h-BN clusters.

Monopeptide versus monopeptoid: insights on structure and hydration of aqueous alanine and sarcosine via X-ray absorption spectroscopy

Despite the obvious significance, the aqueous interactions of peptides remain incompletely understood. Their synthetic analogues called peptoids (poly-N-substituted glycines) have recently emerged as a promising biomimetic material, particularly due to their robust secondary structure and resistance to denaturation. We describe comparative near-edge X-ray absorption fine structure spectroscopy studies of aqueous sarcosine, the simplest peptoid, and alanine, its peptide isomer, interpreted by density functional theory calculations. The sarcosine nitrogen K-edge spectrum is blue shifted with respect to that of alanine, in agreement with our calculations; we conclude that this shift results primarily from the methyl group substitution on the nitrogen of sarcosine. Our calculations indicate that the nitrogen K-edge spectrum of alanine differs significantly between dehydrated and hydrated scenarios, while that of the sarcosine zwitterion is less affected by hydration. In contrast, the computed sarcosine spectrum is greatly impacted by conformational variations, while the alanine spectrum is not. This relates to a predicted solvent dependence for alanine, as compared to sarcosine. Additionally, we show the theoretical nitrogen K-edge spectra to be sensitive to the degree of hydration, indicating that experimental X-ray spectroscopy may be able to distinguish between bulk and partial hydration, such as found in confined environments near proteins and in reverse micelles.

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.