Sulfur K-edge X-ray absorption spectroscopy as an experimental probe for S-nitroso proteins

X-ray absorption spectroscopy at the sulfur K-edge (2.4-2.6keV) provides a sensitive and specific technique to identify S-nitroso compounds, which have significance in nitric oxide-based cell signaling. Unique spectral features clearly distinguish the S-nitroso-form of a cysteine residue from the sulfhydryl-form or from a methionine thioether. Comparison of the sulfur K-edge spectra of thiolate, thiol, thioether, and S-nitroso thiolate compounds indicates high sensitivity of energy positions and intensities of XAS pre-edge features as determined by the electronic environment of the sulfur absorber. A new experimental setup is being developed for reaching the in vivo concentration range of S-nitroso thiol levels in biological samples.     

X-ray absorption spectroscopy as a probe of microbial sulfur biochemistry: the nature of bacterial sulfur globules revisited

The chemical nature of the sulfur in bacterial sulfur globules has been the subject of controversy for a number of years. Sulfur K-edge X-ray absorption spectroscopy (XAS) is a powerful technique for probing the chemical forms of sulfur in situ, but two groups have used it with very different conclusions. The root of the controversy lies with the different detection strategies used by the two groups, which result in very different spectra. This paper seeks to resolve the controversy. We experimentally demonstrate that the use of transmittance detection for sulfur K-edge XAS measurements is highly prone to spectroscopic distortions and that much of the published work on sulfur bacteria is very likely based on distorted data. We also demonstrate that all three detection methods used for X-ray absorption experiments yield essentially identical spectra when the measurements are carried out under conditions where no experimental distortions are expected. Finally, we turn to the original question—the chemical nature of bacterial sulfur. We examine isolated sulfur globules of Allochromatium vinosum and intact cells of a strain of magnetotactic coccus and show that XAS indicates the presence of a chemical form of sulfur resembling S₈.     

Experimental and theoretical correlations between vanadium K-edge X-ray absorption and K$$\varvec{\beta} $$ emission spectra

A series of vanadium compounds was studied by K-edge X-ray absorption (XAS) and K\(\beta \) X-ray emission spectroscopies (XES). Qualitative trends within the datasets, as well as comparisons between the XAS and XES data, illustrate the information content of both methods. The complementary nature of the chemical insight highlights the success of this dual-technique approach in characterizing both the structural and electronic properties of vanadium sites. In particular, and in contrast to XAS or extended X-ray absorption fine structure (EXAFS), we demonstrate that valence-to-core XES is capable of differentiating between ligating atoms with the same identity but different bonding character. Finally, density functional theory (DFT) and time-dependent DFT calculations enable a more detailed, quantitative interpretation of the data. We also establish correction factors for the computational protocols through calibration to experiment. These hard X-ray methods can probe vanadium ions in any oxidation or spin state, and can readily be applied to sample environments ranging from solid-phase catalysts to biological samples in frozen solution. Thus, the combined XAS and XES approach, coupled with DFT calculations, provides a robust tool for the study of vanadium atoms in bioinorganic chemistry.     

Metabolization of elemental sulfur in wheat leaves consecutive to its foliar application

The qualitative and quantitative aspects of elemental sulfur metabolization in wheat leaves and its effect upon photosynthetic metabolism were studied through the application of micronized sulfur upon the third leaf. Energy-dispersive x-ray analysis combined with scanning electron microscopy emphasized the existence of a sulfur peak associated with a strong potassium peak in the spectra of different tissue regions for treated leaves only, supplying an original evidence of sulfur uptake. Experiments with³⁵S-labeled micronized sulfur showed that about 2% of the labeled S was absorbed and metabolized into cystine, methionine, glutathione, and sulfate. The close correlation between the excess of oxygen uptake and oxygen needs for sulfur oxidation in conjunction with the absence of hydrogen sulfide released by treated leaves support direct and fast oxidation of sulfur into sulfate according to a pathway still unclear but independent of photosynthetic CO₂ metabolism in treated leaf. The mechanisms involved in the primary metabolism of element sulfur in wheat therefore appear to be different from those in fungi.     

Spectroscopic investigations and hydrogen bond interactions of 8-aza analogues of xanthine, theophylline and caffeine: a theoretical study

The structure, spectral properties and the hydrogen bond interactions of 8-aza analogues of xanthine, theophylline and caffeine have been studied by using quantum chemical methods. The time-dependent density functional theory (TD-DFT) and the singly excited configuration interaction (CIS) methods are employed to optimize the excited state geometries of isolated 8-azaxanthine, 8-azatheophylline tautomers and 8-azacaffeine in both the gas and solvent phases. The solvent phase calculations are performed using the polarizable continuum model (PCM). The absorption and emission spectra are calculated using the time-dependent density functional theory (TD-DFT) method. The results from the TD-DFT calculations reveal that the excitation spectra are red shifted relative to absorption in aqueous medium. These changes in the transition energies are qualitatively comparable to the experimental data. The examination of molecular orbital reveals that the molecules with a small H→L energy gap possess maximum absorption and emission wavelength. The relative stability and hydrogen bonded interactions of mono and heptahydrated 8-azaxanthine, 8-azatheophylline tautomers and 8-azacaffeine have been studied using the density functional theory (DFT) and Møller Plesset perturbation theory (MP2) implementing the 6-311++G(d,p) basis set. The formation of strong N-H…O bond has resulted in the highest interaction energy among the monohydrates. Hydration does not show any significant impact on the stability of heptahydrated complexes. The atoms in molecule (AIM) and natural bonding orbital (NBO) analyses have been performed to elucidate the nature of the hydrogen bond interactions in these complexes.

Studies of Sulfate Utilization by Algae. 7. In vivo Metabolism of Thiosulfate by Chlorella

Chlorella pyrenoidosa Chick (Emerson strain 3) utilizes thiosulfate for growth as effectively as sulfate, and more effectively than a variety of organic sulfur compounds containing sulfur in various oxidation states. Thiosulfates, differentially labeled with ³⁵S in either the SH— or SO₃ — sulfur moieties, were used to follow the incorporation of thiosulfate-sulfur into constituents of the insoluble fraction and of the soluble pools. Labeled sulfate was also used for purposes of comparison. Label from both sulfur atoms of thiosulfate and from sulfate is incorporated into the cysteine, homocysteine, and glutathione of the soluble pools, and into the methionine and cystine of protein in the insoluble fraction. Label from SO₃-sulfur of thiosulfate is incorporated more slowly into protein methionine and cystine than label from the SH-sulfur. Moreover, the SO₃-sulfur of thiosulfate is recovered largely as sulfate in both the soluble pools and the insoluble fraction, while only a trace of SH-sulfur is recovered as sulfate in either case. Consistent with this, the metabolism of the SO₃-sulfur of thiosulfate more closely resembles the metabolism of sulfate. Thus it would appear that exogenous thiosulfate undergoes early dismutation in which the SO₃-sulfur is preferentially oxidized, and the SH-sulfur is preferentially incorporated in a reduced state. These results are discussed in relation to the conversion of sulfate to thiosulfate by cell-free extracts of Chlorella previously described.     

X-ray Absorption Spectroscopy and Magnetism of Synthetic Greigite and Greigite Magnetosomes in Magnetotactic Bacteria

Scanning transmission X-ray microscopy at the Fe 2p (L_2,3), O1s, C1s, and S2p edges was used to study greigite magnetosomes and other cellular content of a magnetotactic bacterium known as a multicellular magnetotactic prokaryote (MMP). X-ray absorption spectrum (XAS) and X-ray magnetic circular dichroism (XMCD) spectra of greigite (Fe₃S₄) nanoparticles, synthesized via a hydrothermal method, were measured. Although XAS of the synthetic greigite nanoparticles and biotic magnetosome crystals in MMPs are slightly different due to partial oxidation of the MMP greigite, the XMCD spectra of the two materials are in good agreement. The Fe 2p XAS and XMCD spectra of Fe₃S₄ are quite different from those of its oxygen analog, magnetite (Fe₃O₄), suggesting Fe₃S₄ has a different electronic and magnetic structure than Fe₃O₄ despite having the same crystal structure. Sulfate and sulfide species were also identified in MMPs, both of which are likely involved in sulfur metabolism.     

Sulfur Species Investigation in Extra- and Intracellular Sulfur Globules of Acidithiobacillus ferrooxidans and Acidithiobacillus caldus

The sulfur chemical speciation in extracellular and intracellular sulfur globules of Acidithiobacillus ferrooxidans and Acidithiobacillus caldus were investigated with an integrated approach including scanning electron microscopy, transmission electron microscopy, energy dispersive spectroscopy and sulfur K-edge X-ray absorption near edge structure spectroscopy (XANES). The results indicated that both strains can accumulate extracellular sulfur globules when grown on thiosulfate, and the major sulfur chemical speciation of which were S₈ for A. ferrooxidans and mixture of ring sulfur and polythionate for A. caldus, respectively. In contrast, A. ferrooxidans can accumulate both linear sulfur and S₈ internally when grown with sulfur powder and thiosulfate, whereas A. caldus did not accumulate intracellular sulfur globules. In addition, the fitted results of sulfur K-edge XANES spectra indicated that the reduced glutathione (containing thiols groups) were involved in sulfur bio-oxidation of both strains and the tetrathionate were the intermediate products during thiosulfate metabolism by two strains.     

X-ray absorption methods for the determination of Ru–Cl bond covalency in olefin metathesis catalysts: On the normalization of chlorine K-edges in ruthenium complexes

A systematic approach to quantitative analysis of Cl K-edge XAS spectra in ruthenium complexes is outlined and applied to ruthenium carbene complexes involved in olefin metathesis catalysis. This method is generally well-suited for probing ligand donor contributions into empty transition metal d orbitals, but overlap of the Ru L_2, 3 edge makes this very difficult in these complexes. A method for removing the Ru L_2, 3 edges from the Cl K-edge spectrum is developed and tested. The normalization procedure makes use of the well-separated Ru L₂ edge and an appropriate L₃/L₂ branching ratio to unambiguously remove contributions from these edges and allow for accurate normalization of the Cl K-edge spectrum. A generalized background subtraction that accounts for variability over the large energy range involved is also described. The methodology should be general for any similarly overlapping edges, as long as one component of the spin–orbit split metal (L- or M-) edge is unperturbed. The results of this study indicate a substantial difference in Ru–Cl bonding depending on the nature of the catalyst.     

Pyrolysis of Sulfur-containing Amino Acids

Sulfur-containing amino acids (l-cysteine, l-cystine and dl-methionine) were pyrolyzed. From pyrolyzed cysteine and cystine were identified 7~8 volatile compounds including 2-methylthiazolidine which is considered to be the product of the reaction of acetaldehyde with mercaptethylamine, and from pyrolyzed methionine were identified 11 volatiles. At the same time, besides these volatile compounds, alanine, cystine and isoleucine, and alanine, isoleucine and methionine were detected in the pyrolyzed products of cysteine and cystine, respectively, but no amino acid was detected from that of methionine. The mixture of seven identified volatiles generated from l-cystine developed a pop-corn like aroma with a roasted sesame like one, and methylmercaptane seemed to be the main contributor to the pickled radish like odor produced from pyrolysis of dl-methionine. Degradation schemes of cystine and methionine were proposed.     

Chloride ligation in inorganic manganese model compounds relevant to Photosystem II studied using X-ray absorption spectroscopy

Chloride ions are essential for proper function of the photosynthetic oxygen-evolving complex (OEC) of Photosystem II (PS II). Although proposed to be directly ligated to the Mn cluster of the OEC, the specific structural and mechanistic roles of chloride remain unresolved. This study utilizes X-ray absorption spectroscopy (XAS) to characterize the Mn–Cl interaction in inorganic compounds that contain structural motifs similar to those proposed for the OEC. Three sets of model compounds are examined; they possess core structures Mn^IV₃O₄X (X=Cl, F, or OH) that contain a di--oxo and two mono--oxo bridges or Mn^IV₂O₂X (X=Cl, F, OH, OAc) that contain a di--oxo bridge. Each set of compounds is examined for changes in the XAS spectra that are attributable to the replacement of a terminal OH or F ligand, or bridging OAc ligand, by a terminal Cl ligand. The X-ray absorption near edge structure (XANES) shows changes in the spectra on replacement of OH, OAc, or F by Cl ligands that are indicative of the overall charge of the metal atom and are consistent with the electronegativity of the ligand atom. Fourier transforms (FTs) of the extended X-ray absorption fine structure (EXAFS) spectra reveal a feature that is present only in compounds where chloride is directly ligated to Mn. These FT features were simulated using various calculated Mn–X interactions (X=O, N, Cl, F), and the best fits were found when a Mn–Cl interaction at a 2.2–2.3 Å bond distance was included. There are very few high-valent Mn halide complexes that have been synthesized, and it is important to make such a comparative study of the XANES and EXAFS spectra because they have the potential for providing information about the possible presence or absence of halide ligation to the Mn cluster in PS II.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-003-0520-1Abbreviations bpea N,N-bis(2-pyridylmethyl)ethylamine - EXAFS extended X-ray absorption fine structure - FT Fourier transform - IPE inflection point energy - OEC oxygen evolving complex - PS II Photosystem II - tacn 1,4,7-triazacyclononane - XANES X-ray absorption near edge structure - XAS X-ray absorption spectroscopy - XRD X-ray diffraction     

Structural Changes of the Oxygen-evolving Complex in Photosystem II during the Catalytic Cycle

The oxygen-evolving complex (OEC) in the membrane-bound protein complex photosystem II (PSII) catalyzes the water oxidation reaction that takes place in oxygenic photosynthetic organisms. We investigated the structural changes of the Mn₄CaO₅ cluster in the OEC during the S state transitions using x-ray absorption spectroscopy (XAS). Overall structural changes of the Mn₄CaO₅ cluster, based on the manganese ligand and Mn-Mn distances obtained from this study, were incorporated into the geometry of the Mn₄CaO₅ cluster in the OEC obtained from a polarized XAS model and the 1.9-Å high resolution crystal structure. Additionally, we compared the S₁ state XAS of the dimeric and monomeric form of PSII from Thermosynechococcus elongatus and spinach PSII. Although the basic structures of the OEC are the same for T. elongatus PSII and spinach PSII, minor electronic structural differences that affect the manganese K-edge XAS between T. elongatus PSII and spinach PSII are found and may originate from differences in the second sphere ligand atom geometry.     

Analysis of the elemental sulfur bio-oxidation by Acidithiobacillus ferrooxidans with sulfur K-edge XANES

Elemental sulfur bio-oxidation by the typical acidophilic sulfur-oxidizing microbe Acidithiobacillus ferrooxidans was investigated by using the technique of sulfur K-edge XANES spectroscopy. Our results showed that the majority of elemental sulfur altered by A. ferrooxidans was dissolved into the organic phase containing carbon disulfide, while a part of it floated. The fitted results of sulfur K-edge XANES spectrum of the floated sulfur showed that the floating part of the elemental sulfur powder was converted to polymeric sulfur and the relative concentration of sulfur in cyclo-octasulfur S₈ and polymeric sulfur was 37.2 and 62.8%, respectively. It seems that the cyclo-octasulfur is converted to the polymeric sulfur and this appears to be necessary for oxidation of elemental sulfur by A. ferrooxidans. The results have important implications for our understanding of the mechanisms for bio-oxidation of elemental sulfur.     

Oxidation of methionine residues in equine growth hormone by chloramine-T

• 1.1. Reactivity of methionine residues towards Chloramine-T was studied in the equine growth hormone.
• 2.2. With a 20.0-fold molar excess of reagent over methionine, full oxidation of the four residues of the protein is achieved.
• 3.3. Methionine 4 is the most reactive group, followed by methionines 72 and 178—methionine 123 being the less reactive residue.
• 4.4. As judged by circular dichroism spectra and binding assays, protein conformation and binding capacity to specific receptors remains unchanged even after full oxidation of all four methionine residues.
• 5.5. Results agree with data previously obtained with bovine growth hormone.

     

Perturbation of hydrogen bonding in hydrated pyrrole-2-carboxaldehyde complexes

The interaction of external water molecules with hydrated pyrrole-2-carboxaldehyde PCL/(H₂O) _n complexes was investigated. The work was supported by both theoretical [DFT/TD-DFT methods using 6-311G++(d,p) basis set in the ground (S₀) and excited (S₁, S₂, S₃)states] and experimental [UV-Vis, FTIR and Raman] verification. The focus of the present work was on the weak intermolecular O–H?O, N–H?O–H hydrogen bonded interaction (I_erHB) between PCL and external water molecules, and the influence of increasing the number of water molecules to form hydrated PCL/(H₂O)_n complexes. Effects were observed on different vibrational normal modes and on electronic transition levels. A hydrogen-bonded network of water induces a shift to higher energy in certain normal modes of PCL to form stable PCL/(H₂O)_n complexes by lowering the barrier energy. Potential energy distribution (PED) analysis indicates a significant charge transfer from PCL to water by creating a water bridge. Hydrogen bonding effects account for the substantial red shift and broadness in ν_NH, ν_CO vibrational modes. Water rearrangement turns out to be the main driving force for hydrated complex formation.

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Graphical abstract Stability of PCL/(H₂O)₄ hydarted complex.

     

Determination of the metabolic origin of the sulfur atom in thiamin of Escherichia coli by mass spectrometry

In this study cells were grown in 34S-sulfate or L-[sulfane-34S]thiocystine, and the effects of unlabeled methionine and cystine on incorporation of sulfur into methionine, cystine and thiamin were determined. Unlabeled methionine effectively suppresses the incorporation of 34S into methionine but not into cysteine or thiamin. In contrast, cystine blocks incorporation of 34S only to approximately the relative ratio of 32S to 34S indicating, that cysteine is closely related to the origin of the sulfur in thiamin, and therefore the sulfane sulfur of thiocystine is also an effective source of the thiamin sulfur.     

Synthesis, structures and spectroscopic properties of platinum(II), copper(I) and zinc(II) complexes bearing 4-(p-dimethylaminophenyl)-6-phenyl-2,2′-bipyridine ligand

The reactions of 4-(p-dimethylaminophenyl)-6-phenyl-2,2′-bipyridine (HL) with three metal salts of platinum(II), copper(I) and zinc(II) provide the new complexes [Pt(L)(PPh₃)]ClO₄ (1), [Cu(HL)₂]BF₄ (2), [Cu(HL)(PPh₃)]BF₄ (3) and [Zn(HL)₂](ClO₄)₂ (4). All the structures of these four complexes have been characterized by single crystal X-ray diffraction, and their spectroscopic properties were investigated. Especially for complex 1, upon protonation, the excited state can be tuned from the intraligand charge transfer (ILCT) to the metal-to-ligand charge transfer (MLCT), and such switching in the excited state is acid/base reversible. The time-dependent density functional theory (TD-DFT) calculation was used to interpret the absorption spectra of complex 1, and the calculated result is consistent with those of experiments results. In contrast with 1, the lowest energy absorption at 410-650 nm of complexes 2 and 3 can be assigned to MLCT excited state. In solid state or solution complex 4 exhibits intense photoluminescence attributed to a ILCT transition in nature.     

Response of rainbow trout to source and level of supplemental dietary methionine

• 1.1. Methionine and total sulfur amino acid (TSAA) requirements of rainbow trout (Salmo gairdneri) were investigated by feeding graded isosulfurous levels of l- and dl-methionine, l-cystine, and the free acid and calcium forms of methionine hydroxy analog (MHA).
• 2.2. Added cystine did not promote growth, survival or prevent cataracts.
• 3.3. l-methionine produced fastest growth, followed by dl-methionine, CaMHA and free acid MHA.
• 4.4. Trout fed CaMHA gained 85.7 and 92.3% as much as those fed l-methionine and dl-methionine.
• 5.5. Within each experiment, the level of L-methionine isomer that prevented cataracts was constant (1.86 g/100g protein in experiment (1), 1.45 in experiment (2) and was lower than for maximum growth (2.89 and 2.15 g) regardless of methionine source.

     

Molecular structure and spectroscopic (FT-IR,FT-Raman, 13C, 1H NMR and UV) studies of 3,4-dihydroxy-l-phenylalanine using density functional theory

Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 3,4-dihydroxy-l-phenylalanine (3,4-DPA) in solid phase were recorded and analysed in this research. Along with this, the IR spectra in CHCl₃ and the use of acetone as solvents of 3,4-DPA were also recorded. The equilibrium geometry, bonding features and harmonic vibrational frequencies were investigated with the help of density functional theory (DFT) method. The ¹H and ¹³C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge including atomic orbital method and compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalisation was analysed using natural bond orbital analysis. The results show that charge in electron density (E _D) in the σ* and π* antibonding orbitals and second-order delocalisation energies E(2) confirms the occurrence of intramolecular charge transfer within the molecule. UV–vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were analysed using the time-dependent (TD)-DFT approach. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound, which showed good agreement with the observed spectra.