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We report the preparation and spectroscopic characterization of a highly elusive copper site bound exclusively to oxygen donor atoms within a protein scaffold. Despite copper generally being considered unsuitable for use in MRI contrast agents, which in the clinic are largely Gd(III) based, the designed copper coiled coil displays relaxivity values equal to, or superior than, those of the Gd(III) analog at clinical field strengths. The creation of this new-to-biology proteinaceous CuOx-binding site demonstrates the power of the de novo peptide design approach to access chemistry for abiological applications, such as for the development of MRI contrast agents.
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Medios de Contraste , Cobre , Cobre/metabolismo , Medios de Contraste/química , Imagen por Resonancia Magnética , Sitios de Unión , PéptidosRESUMEN
Accurate analysis of the rich information contained within X-ray spectra usually calls for detailed electronic structure theory simulations. However, density functional theory (DFT), time-dependent DFT and many-body perturbation theory calculations increasingly require the use of advanced codes running on high-performance computing (HPC) facilities. Consequently, many researchers who would like to augment their experimental work with such simulations are hampered by the compounding of nontrivial knowledge requirements, specialist training and significant time investment. To this end, we present Web-CONEXS, an intuitive graphical web application for democratizing electronic structure theory simulations. Web-CONEXS generates and submits simulation workflows for theoretical X-ray absorption and X-ray emission spectroscopy to a remote computing cluster. In the present form, Web-CONEXS interfaces with three software packages: ORCA, FDMNES and Quantum ESPRESSO, and an extensive materials database courtesy of the Materials Project API. These software packages have been selected to model diverse materials and properties. Web-CONEXS has been conceived with the novice user in mind; job submission is limited to a subset of simulation parameters. This ensures that much of the simulation complexity is lifted and preliminary theoretical results are generated faster. Web-CONEXS can be leveraged to support beam time proposals and serve as a platform for preliminary analysis of experimental data.
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Understanding nature of intermediates/active species in reactions is a major challenge in chemistry. This is because spectator species typically dominate the experimentally derived data and consequently active phase contributions are masked. Transient methods offer a means to bypass this difficulty. In particular, modulation excitation with phase-sensitive detection (ME-PSD) provides a mechanism to distinguish between spectator and reacting species. Herein, modulation excitation (ME) time-resolved (energy dispersive) X-ray absorption spectroscopy, assisted by phase sensitive detection (PSD) analysis, has been applied to the study of a liquid phase process; in this case the classic ferrocyanide/ferricyanide redox couple. Periodic switches of the electrical potential (anodic/cathodic) enabled the use of the ME approach. Structural changes at fractions as low as 2% of the total number of electroactive species were detected within the X-ray beam probe volume containing ~30 pmol of Fe(II)/Fe(III).
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Oxygenase and peroxygenase enzymes generate intermediates at their active sites which bring about the controlled functionalization of inert C-H bonds in substrates, such as in the enzymatic conversion of methane to methanol. To be viable catalysts, however, these enzymes must also prevent oxidative damage to essential active site residues, which can occur during both coupled and uncoupled turnover. Herein, we use a combination of stopped-flow spectroscopy, targeted mutagenesis, TD-DFT calculations, high-energy resolution fluorescence detection X-ray absorption spectroscopy, and electron paramagnetic resonance spectroscopy to study two transient intermediates that together form a protective pathway built into the active sites of copper-dependent lytic polysaccharide monooxygenases (LPMOs). First, a transient high-valent species is generated at the copper histidine brace active site following treatment of the LPMO with either hydrogen peroxide or peroxyacids in the absence of substrate. This intermediate, which we propose to be a CuII-(histidyl radical), then reacts with a nearby tyrosine residue in an intersystem-crossing reaction to give a ferromagnetically coupled (S = 1) CuII-tyrosyl radical pair, thereby restoring the histidine brace active site to its resting state and allowing it to re-enter the catalytic cycle through reduction. This process gives the enzyme the capacity to minimize damage to the active site histidine residues "on the fly" to increase the total turnover number prior to enzyme deactivation, highlighting how oxidative enzymes are evolved to protect themselves from deleterious side reactions during uncoupled turnover.
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Cobre , Histidina , Oxigenasas de Función Mixta , Estrés Oxidativo , CatálisisRESUMEN
The discovery of a new physical process in manganese metal is reported. This process will also be present for all manganese-containing materials in condensed matter. The process was discovered by applying our new technique of XR-HERFD (extended-range high-energy-resolution fluorescence detection), which was developed from the popular high-resolution RIXS (resonant inelastic X-ray scattering) and HERFD approaches. The acquired data are accurate to many hundreds of standard deviations beyond what is regarded as the criterion for `discovery'. Identification and characterization of many-body processes can shed light on the X-ray absorption fine-structure spectra and inform the scientist on how to interpret them, hence leading to the ability to measure the dynamical nanostructures which are observable using the XR-HERFD method. Although the many-body reduction factor has been used universally in X-ray absorption spectroscopy in analysis over the past 30 years (thousands of papers per year), this experimental result proves that many-body effects are not representable by any constant reduction factor parameter. This paradigm change will provide the foundation for many future studies and X-ray spectroscopy.
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The study aims to understand the role of the transient bonding in the interplay between the structural and electronic changes in heteroleptic Cu(I) diimine diphosphine complexes. This is an emerging class of photosensitisers which absorb in the red region of the spectrum, whilst retaining a sufficiently long excited state lifetime. Here, the dynamics of these complexes are explored by transient absorption (TA) and time-resolved infrared (TRIR) spectroscopy, which reveal ultrafast intersystem crossing and structural distortion occurring. Two potential mechanisms affecting excited state decay in these complexes involve a transient formation of a solvent adduct, made possible by the opening up of the Cu coordination centre in the excited state due to structural distortion, and by a transient coordination of the O-atom of the phosphine ligand to the copper center. X-ray absorption studies of the ground electronic state have been conducted as a prerequisite for the upcoming X-ray spectroscopy studies which will directly determine structural dynamics. The potential for these complexes to be used in bimolecular applications is confirmed by a significant yield of singlet oxygen production.
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The design and performance of an electrochemical cell and solution flow system optimized for the collection of X-ray absorption spectra from solutions of species sensitive to photodamage is described. A combination of 3D CAD and 3D printing techniques facilitates highly optimized design with low unit cost and short production time. Precise control of the solution flow is critical to both minimizing the volume of solution needed and minimizing the photodamage that occurs during data acquisition. The details of an integrated four-syringe stepper-motor-driven pump and associated software are described. It is shown that combined electrochemical and flow control can allow repeated measurement of a defined volume of solution, 100â µl, of samples sensitive to photoreduction without significant change to the X-ray absorption near-edge structure and is demonstrated by measurements of copper(II) complexes. The flow in situ electrochemical cell allows the collection of high-quality X-ray spectral measurements both in the near-edge region and over an extended energy region as is needed for structural analysis from solution samples. This approach provides control over photodamage at a level at least comparable with that achieved using cryogenic techniques and at the same time eliminates problems associated with interference due to Bragg peaks.
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Cobre , Oxidación-Reducción , Rayos XRESUMEN
We have investigated the role of oxygen stoichiometry and structural properties in the modulation of Co valence and spin state in single-layer La2-xAxCoO4±Î´ (A = Sr, Ca; 0 ≤ x ≤ 1) perovskites as well as the interplay between their local structural properties and the magnetic and charge-ordering phenomena. We show the results of high angular resolution powder X-ray diffraction and Co K-edge X-ray absorption and emission spectroscopy experiments on polycrystalline and single-crystal samples. The different doping-induced changes in the Co valence and spin state by Ca (or Sr) substitution can be understood in terms of the evolving oxygen stoichiometry. For Ca doping, the interstitial oxygen excess around the La/Ca atoms in underdoped samples is rapidly lost upon increasing the Ca content. The creation of oxygen vacancies leads to the stabilization of a mixed-valence Co2.5+ independently of the Ca content. In contrast, Sr substitution leads to almost stoichiometric samples and a lower oxygen vacancy concentration, which allows higher mixed-valence states for Co up to Co2.9+. The Co mixed-valence state along the two series is fluctuating between two valence states, Co2.4+ as in La2CoO4.2 and Co2.9+ as in LaSrCoO3.91, that become periodically ordered for the charge-ordered phases around the half-doping. The X-ray emission derived spin states agree well with the Co fluctuating mixed-valence state derived from X-ray absorption spectroscopy on consideration of a distribution of high-spin Co2+ and low-spin Co3+. Furthermore, there is no quenching of the orbital contribution for the high-spin Co2+, as concluded from a comparison with macroscopic magnetization measurements. Doping holes are mainly located in the ab plane and have a strong oxygen 2p character. The major lattice distortions, which are different for Sr and Ca doping, occur along the c axis, where changes in the oxygen stoichiometry take place. Moreover, charge-order transitions are clearly shown from the anomalous increase of the c lattice parameter with an increase in the temperature above 500 K but there is no signature for a temperature-dependent spin-state transition.
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Regulation of mitochondrial activity allows cells to adapt to changing conditions and to control oxidative stress, and its dysfunction can lead to hypoxia-dependent pathologies such as ischemia and cancer. Although cytochrome c phosphorylation-in particular, at tyrosine 48-is a key modulator of mitochondrial signaling, its action and molecular basis remain unknown. Here we mimic phosphorylation of cytochrome c by replacing tyrosine 48 with p-carboxy-methyl-l-phenylalanine (pCMF). The NMR structure of the resulting mutant reveals significant conformational shifts and enhanced dynamics around pCMF that could explain changes observed in its functionality: The phosphomimetic mutation impairs cytochrome c diffusion between respiratory complexes, enhances hemeprotein peroxidase and reactive oxygen species scavenging activities, and hinders caspase-dependent apoptosis. Our findings provide a framework to further investigate the modulation of mitochondrial activity by phosphorylated cytochrome c and to develop novel therapeutic approaches based on its prosurvival effects.
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Citocromos c/metabolismo , Mitocondrias/patología , Estrés Oxidativo , Especies Reactivas de Oxígeno/metabolismo , Tirosina/química , Citocromos c/química , Citocromos c/genética , Humanos , Espectroscopía de Resonancia Magnética , Mitocondrias/metabolismo , Mutación , Peroxidasas/metabolismo , Fenilalanina/análogos & derivados , Fenilalanina/química , Fenilalanina/metabolismo , Fosforilación , Conformación Proteica , Transducción de Señal , Tirosina/genética , Tirosina/metabolismoRESUMEN
Complexes with weakly coordinating ligands are often formed in chemical reactions and can play key roles in determining the reactivity, particularly in catalytic reactions. Using time-resolved X-ray absorption fine structure (XAFS) spectroscopy in combination with time-resolved IR (TRIR) spectroscopy and tungsten hexacarbonyl, W(CO)6, we are able to structurally characterize the formation of an organometallic alkane complex, determine the W-C distances, and monitor the reactivity with silane to form an organometallic silane complex. Experiments in perfluorosolvents doped with xenon afford initially the corresponding solvated complex, which is sufficiently reactive in the presence of Xe that we can then observe the coordination of Xe to the metal center, providing a unique insight into the metal-xenon bonding. These results offer a step toward elucidating the structure, bonding, and chemical reactivity of transient species by X-ray absorption spectroscopy, which has sensitivity to small structural changes. The XAFS results indicate that the bond lengths of metal-alkane (W-H-C) bond in W(CO)5(heptane) as 3.07 (±0.06) Å, which is longer than the calculated W-C (2.86 Å) for binding of the primary C-H, but shorter than the calculated W-C (3.12 Å) for the secondary C-H. A statistical average of the calculated W-C alkane bond lengths is 3.02 Å, and comparison of this value indicates that the value derived from the XAFS measurements is averaged over coordination of all C-H bonds consistent with alkane chain walking. Photolysis of W(CO)6 in the presence of HSiBu3 allows the conversion of W(CO)5(heptane) to W(CO)5(HSiBu3) with an estimated W-Si distance of 3.20 (±0.03) Å. Time-resolved TRIR and XAFS experiments following photolysis of W(CO)6 in perfluoromethylcyclohexane (PFMCH) allows the characterization of W(CO)5(PFMCH) with a W-F distance of 2.65 (±0.06) Å, and doping PFMCH with Xe allows the characterization of W(CO)5Xe with a W-Xe bond length of 3.10 (±0.02) Å.
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In order to provide adequate cryogenic cooling of both existing and next-generation crystal monochromators, a new approach to produce an optimum thermal interface between the first crystal and its copper heat exchanger is proposed. This will ensure that the increased heat load deposited by higher X-ray powers can be properly dissipated. Utilizing a cylindrical silicon crystal, a tubular copper heat exchanger and by exploiting the differing thermal and mechanical properties of the two, a very good thermal interface was achieved at liquid-nitrogen temperatures. The surface flatness of the diffracting plane at one end of the cylindrical crystal was measured at room temperature while unconstrained. The crystal was then placed into the copper heat exchanger, a slide fit at room temperature, and then cooled to liquid-nitrogen temperature. At -200°C the slide fit became an interference fit. This room-temperature `loose' fit was modelled using finite-element analysis to obtain the desired fit at cryogenic temperatures by prescribing the fit at room temperature. Under these conditions, the diffraction surface was measured for distortion due to thermal and mechanical clamping forces. The total deformation was measured to be 30â nm, an order of magnitude improvement over deformation caused by cooling alone with the original side-clamped design this concept method is set to replace. This new methodology also has the advantage that it is repeatable and does not require macro-scale tools to acquire a nanometre-accuracy mounting.
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This issue of the Journal of Synchrotron Radiation is a special issue including papers from the Q2XAFS2017 workshop. Here, a brief introduction is given.
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A description of the technical and design details of a scanning four-bounce crystal monochromator that has recently been commissioned for the Versatile X-ray Absorption Spectroscopy (XAS) beamline at Diamond Light Source is presented. This device consists of two independent rotary axes of unique design which are synchronized using a multiple read-head encoder system. This monochromator is shown to be capable of maintaining the flux throughput of the Bragg axes without the need of any external feedback mechanism from 4 to 20â keV. The monochromator is currently equipped with cryogenically cooled crystals with the upstream axis consisting of two independent Si(111) crystals and a pair of channel-cut crystals in the downstream axis. The possibility of installing an additional Si(311) crystal-set to extend the energy range to 34â keV is incorporated into the preliminary design of the device. Experimental data are presented showing the exceptional mechanical stability and repeatability of the monochromator axes.
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This manuscript presents the current status and technical details of the Spectroscopy Village at Diamond Light Source. The Village is formed of four beamlines: I18, B18, I20-Scanning and I20-EDE. The village provides the UK community with local access to a hard X-ray microprobe, a quick-scanning multi-purpose XAS beamline, a high-intensity beamline for X-ray absorption spectroscopy of dilute samples and X-ray emission spectroscopy, and an energy-dispersive extended X-ray absorption fine-structure beamline. The optics of B18, I20-scanning and I20-EDE are detailed; moreover, recent developments on the four beamlines, including new detector hardware and changes in acquisition software, are described.
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ZnO nanoparticles capped with thiol molecules display room temperature ferromagnetism which has been associated with the structural details of the interface formed between the organic molecule and the ZnO core. Although the local order around sulfur atoms at the ZnS/ZnO interface has been related to the occurrence of the ferromagnetic like behavior, no direct structural determination has been obtained yet. We report here a detailed x-ray absorption spectroscopy study performed at the sulfur K-edge to determine the local structure around the sulfur atoms in these systems and how it is modified by varying the length of the organic molecule.
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Here, the novel technique of extended-range high-energy-resolution fluorescence detection (XR-HERFD) has successfully observed the n = 2 satellite in manganese to a high accuracy. The significance of the satellite signature presented is many hundreds of standard errors and well beyond typical discovery levels of three to six standard errors. This satellite is a sensitive indicator for all manganese-containing materials in condensed matter. The uncertainty in the measurements has been defined, which clearly observes multiple peaks and structure indicative of complex physical quantum-mechanical processes. Theoretical calculations of energy eigenvalues, shake-off probability and Auger rates are also presented, which explain the origin of the satellite from physical n = 2 shake-off processes. The evolution in the intensity of this satellite is measured relative to the full Kα spectrum of manganese to investigate satellite structure, and therefore many-body processes, as a function of incident energy. Results demonstrate that the many-body reduction factor S02 should not be modelled with a constant value as is currently done. This work makes a significant contribution to the challenge of understanding many-body processes and interpreting HERFD or resonant inelastic X-ray scattering spectra in a quantitative manner.
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Energy scale calibration and reliable intensity measurement are the main issues related to the collection of good spectroscopy data. The accurate determination of the energy scale is often established by using foils of optimum thickness to calibrate the monochromator. However, mechanical issues with the monochromator, movement of the source, or even the resolution of the spectrometer can have an effect on the measured energy scale. For the issue of accurate intensity measurements, calibrated detectors are necessary to ensure a reliable measurement of the spectroscopic signal, both in transmission and fluorescence detection modes. In this paper a review of the most common techniques used for energy calibration and for collecting X-ray absorption spectroscopy data is given, together with a brief description of the factors that have an impact on the intensity of the measured signal. A brief description of the versatile X-ray absorption spectroscopy beamline, I20, at Diamond Light Source is also presented, giving particular emphasis on how the beamline design has been undertaken to tackle these key issues. In particular, the use of a four-bounce monochromator will be discussed, highlighting the advantages of the device for the measurement of spectroscopy data.
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The coordination structures of U(IV), Np(IV), and Th(IV) in aqueous solution have been determined by studying the X-ray absorption near edge structure (XANES) of the actinide (An) L(3)-edge absorption spectra. The high sensitivity of XANES to the bonding geometry provides an unambiguous determination of the coordination polyhedron. On the basis of the comparison of ab initio computations with the experimental data we conclude that the hydration sphere of the three An(IV) aqua-ions studied is best modeled by 9 water molecules forming a tricapped trigonal prism.
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H/D isotopic substitution neutron scattering and X-ray scattering have been used to investigate the short and intermediate range solution structure in a 1 m aqueous solution of lanthanum chloride. To improve the reliability of the local structural information on the cation environment, information has been incorporated from Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy data into the applied analytical framework. The markedly different structural sensitivities of the experimental probes allow the construction of a detailed three-dimensional atomistic model using the Empirical Potential Structure Refinement (EPSR) technique. The results show that at the investigated concentration La(3+) is hydrated by eight water molecules and one chloride ion, forming an inner-sphere ion complex in which the water molecules maintain angular configurations consistent with a tricapped trigonal prism configuration. This local geometry considerably disrupts the bulk solvent structure.
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A scanning multi-crystal x-ray emission spectrometer to perform photon-in/photon-out spectroscopy at the I20-Scanning beamline at Diamond Light Source is described. The instrument, equipped with three analyzer crystals, is based on a 1 m Rowland circle spectrometer operating in the vertical plane. The energy resolution of the spectrometer is of the order of 1 eV, having sufficient resolving power to overcome the core-hole lifetime broadening of most of the transition metalsK-edges. Examples showing the capability of the beamline for performing high energy resolution fluorescence detection x-ray absorption spectroscopy (HERFD-XAS), non-resonant x-ray emission spectroscopy (XES) and resonant x-ray emission spectroscopy are presented. The comparison of the Zn and MnK-edge HERFD-XANES of ZnO and MnO withab initiocalculations shows that the technique provides enhanced validation of the models by making subtle spectral features more visible.