Search

Oxidation of methanethiol (MT) is a significant step in the sulfur cycle. MT is an intermediate of metabolism of globally significant organosulfur compounds including dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS), which have key roles in marine carbon and sulfur cycling. In aerobic bacteria, MT is degraded by a MT oxidase (MTO). The enzymatic and genetic basis of MT oxidation have remained poorly characterized. Here, we identify for the first time the MTO enzyme and its encoding gene (mtoX) in the DMS-degrading bacterium Hyphomicrobium sp. VS. We show that MTO is a homotetrameric metalloenzyme that requires Cu for enzyme activity. MTO is predicted to be a soluble periplasmic enzyme and a member of a distinct clade of the Selenium-binding protein (SBP56) family for which no function has been reported. Genes orthologous to mtoX exist in many bacteria able to degrade DMS, other one-carbon compounds or DMSP, notably in the marine model organism Ruegeria pomeroyi DSS-3, a member of the Rhodobacteraceae family that is abundant in marine environments. Marker exchange mutagenesis of mtoX disrupted the ability of R. pomeroyi to metabolize MT confirming its function in this DMSP-degrading bacterium. In R. pomeroyi, transcription of mtoX was enhanced by DMSP, methylmercaptopropionate and MT. Rates of MT degradation increased after pre-incubation of the wild-type strain with MT. The detection of mtoX orthologs in diverse bacteria, environmental samples and its abundance in a range of metagenomic data sets point to this enzyme being widely distributed in the environment and having a key role in global sulfur cycling.

The speciation of metals in solution controls their reactivity, and this is extremely pertinent in the area of metal salts dissolved in ionic liquids. In the current study, the speciation of 25 metal salts is investigated in four deep eutectic solvents (DESs) and five imidazolium-based ionic liquids using extended X-ray absorption fine structure. It is shown that in diol-based DESs M(I) ions form [MCl2](-) and [MCl3](2-) complexes, while all M(II) ions form [MCl4](2-) complexes, with the exception of Ni(II), which exhibits a very unusual coordination by glycol molecules. This was also found in the X-ray crystal structure of the compound [Ni(phen)2(eg)]Cl2·2eg (eg = ethylene glycol). In a urea-based DES, either pure chloro or chloro-oxo coordination is observed. In [C6mim][Cl] pure chloro complexation is also observed, but coordination numbers are smaller (typically 3), which can be explained by the long alkyl chain of the cation. In [C2mim][SCN] metal ions are entirely coordinated by thiocyanate, either through the N or the S atom, depending on the hardness of the metal ion according to the hard-soft acid-base principle. With weaker coordinating anions, mixed coordination between solvent and solute anions is observed. The effect of hydrate or added water on speciation is insignificant for the diol-based DESs and small in other liquids with intermediate or strong ligands. One of the main findings of this study is that, with respect to metal speciation, there is no fundamental difference between deep eutectic solvents and classic ionic liquids.

The first electrochemical series in a deep eutectic solvent (DES) is described. Speciation resulting from the unusual chemistry of the choline chloride based DES is used to explain both similarities and differences from aqueous media. We give examples of how these differences can be exploited in technologically important systems.

We report the results of X-ray absorption spectroscopy studies on electrochemically deposited iridium oxide films. The emphasis of the study is the correlation of X-ray derived structural data with electrochemically controlled charge state. Data were acquired for films subject to redox cycling in neutral and alkaline aqueous media. In both cases, cyclic voltammetric responses show two redox couples, coulometrically of roughly equal magnitude. Assays of the iridium population (based on the iridium L(3) absorption edge amplitude) and the charge injected (based on integration of the voltammetric response) show that overall an average of ca. one electron per iridium atom is transferred. The absorption edge shifts indicate that the formal charge on the iridium changes, on average, from ca. 3.5+ to ca. 4.5+ across the entire process. EXAFS-derived changes in mean Ir-O distance and their mean square variation have been interpreted in terms of a two-site model, in which the two types of site have distinct redox potentials. Variations of local structure and disorder with potential are discussed and a generic model for structural disorder (parameterized via Debye-Waller factor) with diagnostic capability is developed.

Methane-oxidizing bacteria are ubiquitous in the environment and are globally important in oxidizing the potent greenhouse gas methane. It is also well recognized that they have wide potential for bioremediation of organic and chlorinated organic pollutants, thanks to the wide substrate ranges of the methane monooxygenase enzymes that they produce. Here we have demonstrated that the well characterized model methanotroph Methylococcus capsulatus (Bath) is able to bioremediate chromium(VI) pollution over a wide range of concentrations (1.4-1000 mg L(-1) of Cr(6+)), thus extending the bioremediation potential of this major group of microorganisms to include an important heavy-metal pollutant. The chromium(VI) reduction reaction was dependent on the availability of reducing equivalents from the growth substrate methane and was partially inhibited by the metabolic poison sodium azide. X-ray spectroscopy showed that the cell-associated chromium was predominantly in the +3 oxidation state and associated with cell- or medium-derived moieties that were most likely phosphate groups. The genome sequence of Mc. capsulatus (Bath) suggests at least five candidate genes for the chromium(VI) reductase activity in this organism.

It has been appreciated for some time that the novel properties of particles in the size range 1-10 nm are potentially exploitable in a range of applications. In order to ultimately produce commercial devices containing nanosized particles, it is necessary to develop controllable means of incorporating them into macroscopic samples. One way of doing this is to embed the nanoparticles in a matrix of a different material, by co-deposition for example, to form a nanocomposite film. The atomic structure of the embedded particles can be strongly influenced by the matrix. Since some of the key properties of materials, including magnetism, strongly depend on atomic structure, the ability to determine atomic structure in embedded nanoparticles is very important. This review focuses on nanoparticles, in particular magnetic nanoparticles, embedded in different metal matrices. Extended x-ray absorption fine structure (EXAFS) provides an excellent means of probing atomic structure in nanocomposite materials, and an overview of this technique is given. Its application in probing catalytic metal clusters is described briefly, before giving an account of the use of EXAFS in determining atomic structure in magnetic nanocomposite films. In particular, we focus on cluster-assembled films comprised of Fe and Co nanosized particles embedded in various metal matrices, and show how the crystal structure of the particles can be changed by appropriate choice of the matrix material. The work discussed here demonstrates that combining the results of structural and magnetic measurements, as well as theoretical calculations, can play a significant part in tailoring the properties of new magnetic cluster-assembled materials.

[Ni( salen)] complexes bearing different crown ether receptors were electropolymerized to give films whose voltammetric signatures responded to Ba2+. In line with DFT calculations, X-ray absorption spectroscopy (XAS) near the Ni K-edge showed the nickel local environment in the monomers and their corresponding polymers (in the presence or absence of barium) to be identical. However, the expectation of crown size-dependent barium local environment (based on geometry and donor atom availability) was not found. XAS near the Ba K-edge showed that Ba2+ in the films coordinated to only two oxygen donors, irrespective of crown size. This surprisingly low coordination number (compared to solution species) is accompanied by a higher barium/crown ratio than the anticipated 1:1 stoichiometry. The implications of these effects for design and performance of sensors based on metal ion recognition chemistry are discussed.

We have exploited the intrinsic conformational flexibility of leghemoglobin to reengineer the heme active site architecture of the molecule by replacement of the mobile His61 residue with tyrosine (H61Y variant). The electronic absorption spectrum of the ferric derivative of H61Y is similar to that observed for the phenolate derivative of the recombinant wild-type protein (rLb), consistent with coordination of Tyr61 to (high-spin) iron. EXAFS data clearly indicate a 6-coordinate heme geometry and a Fe-O bond length of 185pm. MCD and EPR spectroscopies are consistent with this assignment and support ligation by an anionic (tyrosinate) group. The alteration in heme ligation leads to a 148mV decrease in the reduction potential for H61Y (-127+/-5mV) compared to rLb and destabilisation of the functional oxy-derivative. The results are discussed in terms of our wider understanding of other heme proteins with His-Tyr ligation.

Gold biosorption by dealginated seaweed waste has been studied to elucidate the mechanisms of metal uptake from solution. Dealginated seaweed was able to retain up to 1 mmol g(-1) of Au from solution at pH 3. FT-IR showed the presence of carboxylate groups on the surface of the biosorbent; however, the changes observed for the Au-bound samples suggested very little sorption to the carboxyl moieties. Colloidal Au formed on the surface of dealginated seaweed by reduction of Au(III) to Au(0) was observed using ESEM and four different types of particles were clearly identified. The Au distribution matched closely that obtained for S atoms indicating a possible link between these elements. EXAFS measurements showed that colloidal Au is present on the surface of the biosorbent. Evidence of gold reduction from Au(III) to Au(I) and Au(0) was also confirmed by the measured bond distances characteristic of the metal. The coordination number obtained by EXAFS indicated that approximately 75% of the Au on the sample was present in the colloidal form and the remaining Au was bound to S as nearest neighbor. The proposed mechanisms for Au removal from solution are reduction of Au species by components on the surface of the biosorbent to form colloidal metal followed by retention of the ionic Au(I) species at the sulfur containing sites. The results show that dealginated seaweed can be used for the cleanup of gold-containing effluents.

The probability of secondary electron shake-off in X-ray absorption is calculated using a model form for the time- and energy-dependent core-hole-photoelectron potential, screened by the single plasmon pole dielectric function of the surrounding material. The resultant excitation probabilities are related to the energy-dependent intrinsic loss function in EXAFS data analysis and compared with experiment. Reasonable agreement is obtained close to the absorption edge although the calculation is less accurate at higher photon energies. The theory described allows the losses to be calculated with little computational effort, making the method suitable for routine EXAFS data analysis.

The probability of multiple-electron excitation in X-ray absorption is calculated using a simple generic model. The model permits calculations to be made for all atoms with little input data or computing effort. The high-energy limit of this probability, which gives the usual EXAFS amplitude reduction factor, is calculated in the 'sudden approximation' using Slater orbitals. Good agreement with experiment is found. The energy dependence of this probability is also calculated using a simple model form of perturbing potential and found to agree well with experiment for rare gas atoms. The effect on the X-ray absorption coefficient of including multiple-electron excitations is also determined and is found to be small, again in agreement with observation.

In real systems, inelastic processes remove photoelectrons from the elastic scattering channel. This reduces the amplitude of the EXAFS. Traditionally the discrepancies between experimental and theoretical amplitudes were treated by including two semi-empirical reduction factors in the data analysis. Some inelastic effects may, however, be modelled more rigorously using a complex exchange and correlation potential, for example the Hedin-Lundqvist (HL) potential used in most EXAFS data-analysis programs. In this paper a systematic study of the effects of the HL potential on the calculated EXAFS amplitudes is presented. Expressions are derived whereby the EXAFS amplitudes may be examined in the presence of an arbitrary complex potential independently to the rest of the EXAFS signal. These results are used to study the effects of the HL potential on EXAFS data analysis in detail.

An outline of the theory of X-ray absorption as applied to X-ray absorption spectroscopy is given, concentrating on EXAFS, showing how structural parameters are contained within the theory. A full description of the scattering problem and of inelastic effects is also included, and a description is given of how structural information may be extracted from experimental data. The emphasis is on curve-fitting methods, including those techniques which allow the inclusion of external constraints.