Theoretical and experimental sulfur K-edge X-ray absorption spectroscopic study of cysteine, cystine, homocysteine, penicillamine, methionine and methionine sulfoxide

In Solution Identification of the Lysine-Cysteine Redox Switch with a NOS Bridge in Transaldolase by Sulfur K-Edge X-ray Absorption Spectroscopy

A novel covalent post-translational modification (lysine-NOS-cysteine) was discovered in proteins, initially in the enzyme transaldolase of Neisseria gonorrhoeae (NgTAL) [Nature 2021, 593, 460-464], acting as a redox switch. The identification of this novel linkage in solution was unprecedented until now. We present detection of the NOS redox switch in solution using sulfur K-edge X-ray absorption spectroscopy (XAS). The oxidized NgTAL spectrum shows a distinct shoulder on the low-energy side of the rising edge, corresponding to a dipole-allowed transition from the sulfur 1s core to the unoccupied σ* orbital of the S-O group in the NOS bridge. This feature is absent in the XAS spectrum of reduced NgTAL, where Lys-NOS-Cys is absent. Our experimental and calculated XAS data support the presence of a NOS bridge in solution, thus potentially facilitating future studies on enzyme activity regulation mediated by the NOS redox switches, drug discovery, biocatalytic applications, and protein design.

Non-ergodic fragmentation upon collision-induced activation of cysteine-water cluster cations

Cysteine-water cluster cations Cys(H2O)3,6+ and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collision-induced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies from DFT calculations showing that clusters do not only fragment exclusively by sequential emission of single water molecules but also by the release of small water clusters. Release of clustered water is observed also in the ADMP (atom centered density matrix propagation) molecular dynamics model of small Cys(H2O)3+ and Cys(H2O)3H+ clusters. For large clusters Cys(H2O)6+ and Cys(H2O)6H+ the less computationally demanding statistical Microcanonical Metropolis Monte-Carlo method (M3C) is used to model the experimental fragmentation patterns. We are able to detail the energy redistribution in clusters upon collision activation. In the present case, about two thirds of the collision energy redistribute via an ergodic process, while the remaining one third is transferred into a non-ergodic channel leading to ejection of a single water molecule from the cluster. In contrast to molecular fragmentation, which can be well described by statistical models, modelling of collision-induced activation of weakly bound clusters requires inclusion of non-ergodic processes.

X-ray Induced Fragmentation of Protonated Cystine

We demonstrate site-specific X-ray induced fragmentation across the sulfur L-edge of protonated cystine, the dimer of the amino acid cysteine. Ion yield NEXAFS were performed in the gas phase using electrospray ionization (ESI) in combination with an ion trap. The interpretation of the sulfur L-edge NEXAFS spectrum is supported by Restricted Open-Shell Configuration Interaction (ROCIS) calculations. The fragmentation pathway of triply charged cystine ions was modeled by Molecular Dynamics (MD) simulations. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons. The disulfide bridge breaks for resonant excitation at lower photon energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments initially formed subsequently break into smaller fragments.

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.

Operando Study of Thermal Oxidation of Monolayer MoS2

Monolayer MoS2 is a promising semiconductor to overcome the physical dimension limits of microelectronic devices. Understanding the thermochemical stability of MoS2 is essential since these devices generate heat and are susceptible to oxidative environments. Herein, the promoting effect of molybdenum oxides (MoO x ) particles on the thermal oxidation of MoS2 monolayers is shown by employing operando X-ray absorption spectroscopy, ex situ scanning electron microscopy and X-ray photoelectron spectroscopy. The study demonstrates that chemical vapor deposition-grown MoS2 monolayers contain intrinsic MoO x and are quickly oxidized at 100 °C (3 vol% O2/He), in contrast to previously reported oxidation thresholds (e.g., 250 °C, t ≤ 1 h in the air). Otherwise, removing MoO x increases the thermal oxidation onset temperature of monolayer MoS2 to 300 °C. These results indicate that MoO x promote oxidation. An oxide-free lattice is critical to the long-term stability of monolayer MoS2 in state-of-the-art 2D electronic, optical, and catalytic applications.

Sulfur Molecules in Space by X-rays: A Computational Study

X-ray astronomy lacks high resolution spectra of interstellar dust analogues and molecules, severely hampering interstellar medium studies based on upcoming X-ray missions. Various theoretical approaches may be used to address this problem, but they must first be shown to reproduce reliable spectra compared to the experiment. In this work, we calculate the sulfur K edge X-ray absorption spectra of H₂S, SO₂, and OCS, whose spectra are already known from X-ray experiments and predict the X-ray spectrum of CS, which as far as we are aware has not been measured, thereby hampering its detection by X-ray telescopes. We chose these four molecules as the astrochemistry of sulfur is an unsolved problem and as the four molecules are already known to exist in space. We consider three types of methods for modeling the X-ray spectra: more accurate calculations with the algebraic-diagrammatic construction (ADC) and the CC2, CCSD, and CC3 coupled cluster (CC) approaches as well as more affordable ones with transition potential density functional theory (TP-DFT). A comparison of our computational results to previously reported experimental spectra shows that the core-valence separation (CVS) approaches CVS-ADC(2)-x and CVS-CC3 generally yield a good qualitative level of agreement with the experiment, suggesting that they can be used for interpreting measured spectra, while the TP-DFT method is not reliable for these molecules. However, quantitative agreement with the experiment is still outside the reach of the computational methods studied in this work.

X-ray absorption spectroscopy of organic sulfoxides

Organic sulfoxides, a group of compounds containing the sulfinyl S[double bond, length as m-dash]O group, are widespread in nature, important in health and disease, and used in a variety of applications in the pharmaceutical industry. We have examined the sulfur K-edge X-ray absorption near-edge spectra of a range of different sulfoxides and find that their spectra are remarkably similar. Spectra show an intense absorption peak that is comprised of two transitions; a S 1s → (S-O)σ* and a S 1s → [(S-O)π* + (S-C)σ*] transition. In most cases these are sufficiently close in energy that they are not properly resolved; however for dimethylsulfoxide the separation between these transitions increases in aqueous solution due to hydrogen bonding to the sulfinyl oxygen. We also examined tetrahydrothiophene sulfoxide using both the sulfur and oxygen K-edge. This compound has a mild degree of ring strain at the sulfur atom, which changes the energies of the two transitions so that the S 1s → [(S-O)π* + (S-C)σ*] is below the S 1s → (S-O)σ*. A comparison of the oxygen K-edge X-ray absorption near-edge spectra of tetrahydrothiophene sulfoxide with that of an unhindered sulfoxide shows little change, indicating that the electronic environment of oxygen is very similar.

Mitigation of mercury accumulation in rice using rice hull-derived biochar as soil amendment: A field investigation

Effect of application of 24 t ha^-1 and 72 t ha^-1 rice hull-derived biochar (RHB) on total Hg (THg) and methylHg (MeHg) immobilization and their accumulations by rice plants were studied in a field experiment (Wanshan Hg mine, China). The addition of two doses of RHB significantly increased the biomass of rice plants, and decreased the MeHg concentration in the pore water, as compared to the control. The RHB promoted the partitioning of pore water MeHg to the soil solid phase throughout rice growing season, and pore water THg partitioning only at rice filling stage. Mercury methylation potential was weakly affected by the RHB addition to the soil. Mercury might be immobilized through binding of thiols (e.g., cysteine) presented in the RHB or in the soil induced by RHB addition. Biochar addition decreased MeHg and THg contents in the tissues of rice plants, particularly in the polished rice. We attributed the reduction of THg in the rice to the bio-dilution effect, and of MeHg content in the rice to the decreased MeHg availability in the soil by RHB addition. Results suggest that RHB might be suitable for managing Hg transfer in soil-rice plants at Hg contaminated mining regions in China and beyond.

Phase-driven magneto-electrical characteristics of single-layer MoS2

Magnetism of the MoS2 semiconducting atomic layer was highlighted for its great potential in the applications of spintronics and valleytronics. In this study, we demonstrate an evolution of magneto-electrical properties of single layer MoS2 with the modulation of defect configurations and formation of a partial 1T phase. With Ar treatment, sulfur was depleted within the MoS2 flake leading to a 2H (low-spin) → partial 1T (high-spin) phase transition. The phase transition was accompanied by the development of a ferromagnetic phase. Alternatively, the phase transition could be driven by the desorption of S atoms at the edge of MoS2via O2 treatment while with a different ordering magnitude in magnetism. The edge-sensitive magnetism of the single-layer MoS2 was monitored by magnetic force microscopy and validated by a first-principle calculation with graded-Vs (sulfur vacancy) terminals set at the edge, where band-splitting appeared more prominent with increasing Vs. Treatment with Ar and O2 enabled a dual electrical characteristic of the field effect transistor (FET) that featured linear and saturated responses of different magnitudes in the Ids-Vds curves, whereas the pristine MoS2 FET displayed only a linear electrical dependency. The correlation and tuning of the Vs-1T phase transition would provide a playground for tailoring the phase-driven properties of MoS2 semiconducting atomic layers in spintronic applications.

VUV Photoelectron Spectroscopy of Cysteine Aqueous Aerosols: A Microscopic View of Its Nucleophilicity at Varying pH Conditions

Cysteine (Cys) is unique due to its highly reactive thiol group. It often regulates the biological function of proteins by acting as the redox site. Despite its biological significance, however, the valence electronic structure of Cys under the aqueous environments remains unavailable. Here, we report the VUV photoelectron spectroscopy of Cys aqueous aerosols via a newly built aerosol VUV photoelectron spectroscopy apparatus. The photoelectron spectra of Cys show distinct band shapes at varying pH conditions, reflecting the altered molecular orbital characters when its dominating form changes. The ionization energy of Cys is determined to be 8.98 ± 0.05 eV at low pH. A new feature at a binding energy of 6.97 ± 0.05 eV is observed at high pH, suggesting that the negative charge on the thiolate group becomes the first electron to be removed upon ionization. This work implies that when Cys is involved in redox processes, the charge transfer mechanism may be entirely altered under different pH conditions.

A fluorescence XAFS measurement instrument in the soft X-ray region toward observation under operando conditions

X-ray absorption fine structure (XAFS) measurements are widely used for the analysis of electronic structure. Generally, XAFS in the soft X-ray region is measured under vacuum, but chemical structures under vacuum are typically different from those under operando conditions, where chemical species exhibit their function. Here, we developed an XAFS measurement instrument, as a step toward operando fluorescent, which yields XAFS measurement using synchrotron radiation in the soft X-ray region. We applied this method to analyze the local electronic structure of the sulfur atoms in L-cysteine in different pH solutions. In water at pH 7, the hydrogen atom does not dissociate from the thiol (-SH) group in L-cysteine, which forms a structure surrounded by and interacting with water molecules. The XAFS spectrum of L-cysteine in solution was altered by changing the pH. At pH 9, the hydrogen atom dissociated and a thiolate anion was formed. Although the -SH group was oxidized to SO4 (2-) when L-cysteine was adsorbed on a metal surface and dried, no oxidation was observed in solution. This may be because the water molecules were densely packed and protected the -SH group from oxidation. Our results show that this instrument aimed toward operando fluorescence XAFS measurements in the soft X-ray region is useful for structural analysis of sulfur atoms in organic molecules in air and in solution. The instrument will be applied to the structural analysis of materials containing elements that have absorption edges in soft X-ray region, such as phosphorus and alkali metals (potassium and cesium). It will be also particularly useful for the analysis of samples that are difficult to handle under vacuum and materials that have specific functions in solution.

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.

Microscale characterization of sulfur speciation in lake sediments

Prairie pothole lakes (PPLs) are naturally sulfur-enriched wetlands in the glaciated prairie region of North America. High sulfate levels and dynamic hydrogeochemistry in combination render PPLs a unique environment to explore the speciation of sedimentary sulfur (S). The goals of this research were to define and quantify the solid-phase S pools in PPL sediments and track seasonal dynamics of S speciation. A quantitative X-ray microprobe method was developed based on S 1s X-ray absorption near-edge structure (XANES) spectroscopy and multienergy X-ray fluorescence mapping. Three S pools-pyritic S, reduced organic S (organic mono- and disulfide), and oxidized S (inorganic sulfate, ester sulfate, and sulfonate)-were identified in PPL sediments. No significant seasonal variation was evident for total S, but S speciation showed a seasonal response. During the spring-summer transition, the reduced organic S decreased from 55 to 15 mol %, with a concomitant rise in the oxidized S. During the summer-fall transition, the trend reversed and the reduced organic S grew to 75 mol % at the expense of the oxidized S. The pyritic S, on the other hand, remained relatively constant (∼22 mol %) over time. The seasonal changes in S speciation have strong potential to force the cycling of elements such as mercury in prairie wetlands.

Analytical aspects of waterlogged wood in historical shipwrecks

Conservation methods applied to historical shipwrecks increasingly rely on combining modern analytical techniques to obtain new insights for specially adapted conservation treatments. Crystalline salts formed on waterlogged wood are identified by powder X-ray diffraction while X-ray fluorescence measurements along wood cores show penetration profiles of contaminating elements. Dedicated synchrotron-based X-ray absorption spectroscopy, especially sulfur and iron K-edge XANES, allows speciation of the large amounts of detrimental sulfur and iron compounds that often are found accumulated within the hull timbers, while high resolution X-ray imaging shows the distribution within the wood microstructure. By fitting spectra of model compounds to high quality sulfur K-edge XANES spectra one can obtain the relative amounts of different types of functional sulfur groups. FT-IR, NMR, ESCA, MALDI-TOF mass spectrometry and size exclusion chromatography are other useful techniques to analyze the status of the wood and of the consolidation agent polyethylene glycol. Examples are given from analyses of famous artifacts.

Simulating picosecond iron K-edge X-ray absorption spectra by ab initio methods to study photoinduced changes in the electronic structure of Fe(II) spin crossover complexes

Recent time-resolved X-ray absorption experiments probing the low-spin to high-spin photoconversion in Fe(II) complexes have monitored the complex interplay between electronic and structural degrees of freedom on an ultrafast time scale. In this study, we use transition potential (TP) and time-dependent (TD) DFT to simulate the picosecond time-resolved iron K-edge X-ray absorption spectrum of the spin crossover (SCO) complex, [Fe(tren(py)(3))](2+). This is achieved by simulating the X-ray absorption spectrum of [Fe(tren(py)(3))](2+) in its low-spin (LS), (1)A(1), ground state and its high-spin (HS), (5)T(2), excited state. These results are compared with the X-ray absorption spectrum of the high-spin analogue (HSA), [Fe(tren(6-Me-py)(3))](2+), which has a (5)T(2) ground state. We show that the TP-DFT methodology can simulate a 40 eV range of the iron K-edge XANES spectrum reproducing all of the major features observed in the static and transient spectra of the LS, HS, and HSA complexes. The pre-edge region of the K-edge spectrum, simulated by TD-DFT, is shown to be highly sensitive to metal-ligand bonding. Changes in the intensity of the pre-edge region are shown to be sensitive to both symmetry and π-backbonding by analysis of relative electric dipole and quadrupole contributions to the transition moments. We generate a spectroscopic map of the iron 3d orbitals from our TD-DFT results and determine ligand field splitting energies of 1.55 and 1.35 eV for the HS and HSA complexes, respectively. We investigate the use of different functionals finding that hybrid functionals (such as PBE0) produce the best results. Finally, we provide a detailed comparison of our results with theoretical methods that have been previously used to interpret Fe K-edge spectroscopy of equilibrium and time-resolved SCO complexes.

Glutathione complex formation with mercury(II) in aqueous solution at physiological pH

The mercury(II) complexes formed in neutral aqueous solution with glutathione (GSH, here denoted AH(3) in its triprotonated form) were studied using Hg L(III)-edge extended X-ray absorption fine structure (EXAFS) and (199)Hg NMR spectroscopy, complemented with electrospray ionization mass spectrometric (ESI-MS) analyses. The [Hg(AH)(2)](2-) complex, with the Hg-S bond distances at 2.325 ± 0.01 Å in linear S-Hg-S coordination, and the (199)Hg NMR chemical shift at -984 ppm, dominates except at high excess of glutathione. In a series of solutions with C(Hg(II)) ∼17 mM and GSH/Hg(II) mole ratios rising from 2.4 to 11.8, the gradually increasing mean Hg-S bond distance corresponds to an increasing amount of the [Hg(AH)(3)](4-) complex. ESI-MS peaks appear at -m/z values of 1208 and 1230 corresponding to the [Na(4)Hg(AH)(2)(A)](-) and [Na(5)Hg(AH)(A)(2)](-) species, respectively. In another series of solutions at pH 7.0 with C(Hg(II)) ∼50 mM and GSH/Hg(II) ratios from 2.0 to 10.0, the Hg L(III)-edge EXAFS and (199)Hg NMR spectra show that at high excess of glutathione (∼0.35 M) about ∼70% of the total mercury(II) concentration is present as the [Hg(AH)(3)](4-) complex, with the average Hg-S bond distance 2.42 ± 0.02 Å in trigonal HgS(3) coordination. The proportions of HgS(n) species, n = 2, 3, and 4, quantified by fitting linear combinations of model EXAFS oscillations to the experimental EXAFS data in our present and previous studies were used to obtain stability constants for the [Hg(AH)(3)](4-) complex and also for the [Hg(A)(4)](10-) complex that is present at high pH. For Hg(II) in low concentration at physiological conditions (pH 7.4, C(GSH) = 2.2 mM), the relative amounts of the HgS(2) species [Hg(AH)(2)](2-), [Hg(AH)(A)](3-), and the HgS(3) complex [Hg(AH)(3)](4-) were calculated to be 95:2:3. Our results are not consistent with the formation of dimeric Hg(II)-GSH complexes proposed in a recent EXAFS study.

The iron-site structure of [Fe]-hydrogenase and model systems: an X-ray absorption near edge spectroscopy study

The [Fe]-hydrogenase is an ideal system for studying the electronic properties of the low spin iron site that is common to the catalytic centres of all hydrogenases. Because they have no auxiliary iron-sulfur clusters and possess a cofactor containing a single iron centre, the [Fe]-hydrogenases are well suited for spectroscopic analysis of those factors required for the activation of molecular hydrogen. Specifically, in this study we shed light on the electronic and molecular structure of the iron centre by XAS analysis of [Fe]-hydrogenase from Methanocaldococcus jannashii and five model complexes (Fe(ethanedithiolate)(CO)(2)(PMe(3))(2), [K(18-crown-6)](2)[Fe(CN)(2)(CO)(3)], K[Fe(CN)(CO)(4)], K(3)[Fe(III)(CN)(6)], K(4)[Fe(II)(CN)(6)]). The different electron donors have a strong influence on the iron absorption K-edge energy position, which is frequently used to determine the metal oxidation state. Our results demonstrate that the K-edges of Fe(II) complexes, achieved with low-spin ferrous thiolates, are consistent with a ferrous centre in the [Fe]-hydrogenase from Methanocaldococcus jannashii. The metal geometry also strongly influences the XANES and thus the electronic structure. Using in silico simulation, we were able to reproduce the main features of the XANES spectra and describe the effects of individual donor contributions on the spectra. Thereby, we reveal the essential role of an unusual carbon donor coming from an acyl group of the cofactor in the determination of the electronic structure required for the activity of the enzyme.