Sulfur 1s near-edge x-ray absorption fine structure (NEXAFS) of thiol and thioether compounds

Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems

In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy. In the condensed phase, it is usually very difficult to distinguish direct effects from indirect effects. A straightforward solution for this problem is the use of gas-phase techniques, for instance from the field of mass spectrometry. In this review, we survey mainly experimental but also theoretical work, focusing on radiation-induced intra- and inter-molecular transfer of charge, atoms, and energy within biomolecular systems in the gas phase. Building blocks of DNA, proteins, and saccharides, but also antibiotics are considered. The emergence of general processes as well as their timescales and mechanisms are highlighted.

NEXAFS spectra of model sulfide chains: implications for sulfur networks obtained from inverse vulcanization

Inverse vulcanization is a promising route to stabilize sulfur in lithium-sulfur batteries, but the resulting sulfur strand lengths in the materials are elusive. We address the strand length by characterization via sulfur near edge X-ray absorption fine structure (NEXAFS) spectroscopy. Theoretical predictions of NEXAFS spectra for model molecules containing strands with up to three sulfur atoms are verified by experiment. The near perfect agreement between simulation and experiment on the absolute energy scale allows for the predictions for larger chain lengths also. Inspection and interpretation of NEXAFS spectra from real battery materials on this basis reveals the appearance of single connecting sulfur atoms for very low sulfur content, and of longer strands when the sulfur fraction increases.

High Energy Resolution Fluorescence Detected X-ray Absorption Spectroscopy: An Analytical Method for Selenium Speciation

Selenium is in many ways an enigmatic element. It is essential for health but toxic in excess, with the difference between the two doses being narrower than for any other element. Environmentally, selenium is of concern due to its toxicity. As the rarest of the essential elements, its low levels often provide challenges to the analytical chemist. X-ray absorption spectroscopy (XAS) provides a powerful tool for in situ chemical speciation but is severely limited by poor spectroscopic resolution arising from core-hole lifetime broadening. Here we explore selenium Kα1 high energy resolution fluorescence detected XAS (HERFD-XAS) as a novel approach for chemical speciation of selenium, in comparison with conventional Se K-edge XAS. We present spectra of a range of selenium species relevant to environmental and life science studies, including spectra of seleno-amino acids, which show strong similarities with S K-edge XAS of their sulfur congeners. We discuss strengths and limitations of HERFD-XAS, showing improvements in both speciation performance and low concentration detection. We also develop a simple method to correct fluorescence self-absorption artifacts, which is generally applicable to any HERFD-XAS experiment.

Sulfur Species, Bonding Environment, and Metal Mobilization in Mining-Impacted Lake Sediments: Column Experiments Replicating Seasonal Anoxia and Deposition of Algal Detritus

The oxidation state of sulfur [S] is a primary control on mobility of metals in sediments impacted by legacy mining practices. Coeur d’Alene Lake of northern Idaho, USA, has been impacted by upstream legacy mining practices that deposited an estimated 75 Mt of metal(loid)- and S-rich sediments into the lake. Future lake conditions are expected to include algal blooms, which may alter S and metal remobilization during the seasonal euxinic environment. Cores of the lake sediments were exposed to anoxic and anoxic + algal detritus conditions for eight weeks at 4.5 °C through introduction of a N2 atmosphere and addition of algal detritus. At a location 2.5 cm below the sediment-water interface, anoxic conditions promoted a shift in S species to continually larger concentrations of reduced species and an associated shift in the bonding environment reflective of increased S–metal bonds. Anoxic + algal detritus conditions suppressed the increasing trend of reduced S species and induced greater release of Mn compared to the anoxic-only conditions but did not appear to enhance the release of As, Cd, or Fe. The addition of algal detritus to the sediment-water interface of these Fe- and S-rich sediments enhanced mobilization of Mn likely because of dissimilatory metal reduction where the anaerobic oxidation of the algal detritus stimulated Mn reduction. Results of the study indicate that future metal release from the lake sediments will be altered with the likely deposition of algal detritus, but the effect may not enhance the release of acutely toxic metals, such as As or Cd, or substantially impact Fe cycling in the sediments.

Effect of 1-octanethiol as an electrolyte additive on the performance of the iron-air battery electrodes

It has recently been established that 1-octanethiol in the electrolyte can allow iron electrodes to be discharged at higher rates. However, the effect of thiol additives on the air electrode has not yet been studied. The effect of solvated thiols on the surface positive electrode reaction is of prime importance if these are to be used in an iron-air battery. This work shows that the air-electrode catalyst is poisoned by the presence of octanethiol, with the oxygen reduction overpotential at the air electrode increasing with time of exposure to the solution and increased 1-octanethiol concentration in the range 0–0.1 mol dm−3. Post-mortem XPS analyses were performed over the used air electrodes suggesting the adsorption of sulphur species over the catalyst surface, reducing its performance. Therefore, although sulphur-based additives may be suitable for nickel-iron batteries, they are not recommended for iron-air batteries except in concentrations well below 10 × 10−3 mol dm−3.

Site-Selective Dissociation upon Sulfur L-Edge X-ray Absorption in a Gas-Phase Protonated Peptide

Site-selective dissociation induced by core photoexcitation of biomolecules is of key importance for the understanding of radiation damage processes and dynamics and for its promising use as "chemical scissors" in various applications. However, identifying products of site-selective dissociation in large molecules is challenging at the carbon, nitrogen, and oxygen edges because of the high recurrence of these atoms and related chemical groups. In this paper, we present the observation of site-selective dissociation at the sulfur L-edge in the gas-phase peptide methionine enkephalin, which contains only a single sulfur atom. Near-edge X-ray absorption mass spectrometry has revealed that the resonant S 2p → σ*_C-S excitation of the sulfur contained in the methionine side chain leads to site-selective dissociation, which is not the case after core ionization above the sulfur L-edge. The prospects of such results for the study of charge dynamics in biomolecular systems are discussed.

Elemental characterisation of melanin in feathers via synchrotron X-ray imaging and absorption spectroscopy

Melanin is a critical component of biological systems, but the exact chemistry of melanin is still imprecisely known. This is partly due to melanin’s complex heterogeneous nature and partly because many studies use synthetic analogues and/or pigments extracted from their natural biological setting, which may display important differences from endogenous pigments. Here we demonstrate how synchrotron X-ray analyses can non-destructively characterise the elements associated with melanin pigment in situ within extant feathers. Elemental imaging shows that the distributions of Ca, Cu and Zn are almost exclusively controlled by melanin pigment distribution. X-ray absorption spectroscopy demonstrates that the atomic coordination of zinc and sulfur is different within eumelanised regions compared to pheomelanised regions. This not only impacts our fundamental understanding of pigmentation in extant organisms but also provides a significant contribution to the evidence-based colour palette available for reconstructing the appearance of fossil organisms.

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.

The x-ray absorption spectroscopy model of solvation about sulfur in aqueous L-cysteine

The environment of sulfur in dissolved aqueous L-cysteine has been examined using K-edge x-ray absorption spectroscopy (XAS), extended continuum multiple scattering (ECMS) theory, and density functional theory (DFT). For the first time, bound-state and continuum transitions representing the entire XAS spectrum of L-cysteine sulfur are accurately reproduced by theory. Sulfur K-edge absorption features at 2473.3 eV and 2474.2 eV represent transitions to LUMOs that are mixtures of S-C and S-H σ∗ orbitals significantly delocalized over the entire L-cysteine molecule. Continuum features at 2479, 2489, and 2530 eV were successfully reproduced using extended continuum theory. The full L-cysteine sulfur K-edge XAS spectrum could not be reproduced without addition of a water-sulfur hydrogen bond. Density functional theory analysis shows that although the Cys(H)S⋯H-OH hydrogen bond is weak (∼2 kcal) the atomic charge on sulfur is significantly affected by this water. MXAN analysis of hydrogen-bonding structures for L-cysteine and water yielded a best fit model featuring a tandem of two water molecules, 2.9 Å and 5.8 Å from sulfur. The model included a S(cys)⋯H-O(w1)H hydrogen-bond of 2.19 Å and of 2.16 Å for H(2)O(w1)⋯H-O(w2)H. One hydrogen-bonding water-sulfur interaction alone was insufficient to fully describe the continuum XAS spectrum. However, density functional theoretical results are convincing that the water-sulfur interaction is weak and should be only transient in water solution. The durable water-sulfur hydrogen bond in aqueous L-cysteine reported here therefore represents a break with theoretical studies indicating its absence. Reconciling the apparent disparity between theory and result remains the continuing challenge.