Nonadiabatic coupling of the dynamical structure to the superconductivity in YSr2Cu2.75Mo0.25O7.54 and Sr2CuO3.3.

A crucial issue in cuprates is the extent and mechanism of the coupling of the lattice to the electrons and the superconductivity. Here we report Cu K edge extended X-ray absorption fine structure measurements elucidating the internal quantum tunneling polaron (iqtp) component of the dynamical structure in two heavily overdoped superconducting cuprate compounds, tetragonal YSr2Cu2.75Mo0.25O7.54 with superconducting critical temperature, Tc = 84 K and hole density p = 0.3 to 0.5 per planar Cu, and the tetragonal phase of Sr2CuO3.3 with Tc = 95 K and p = 0.6. In YSr2Cu2.75Mo0.25O7.54 changes in the Cu-apical O two-site distribution reflect a sequential renormalization of the double-well potential of this site beginning at Tc, with the energy difference between the two minima increasing by ∼6 meV between Tc and 52 K. Sr2CuO3.3 undergoes a radically larger transformation at Tc, >1-Šdisplacements of the apical O atoms. The principal feature of the dynamical structure underlying these transformations is the strongly anharmonic oscillation of the apical O atoms in a double-well potential that results in the observation of two distinct O sites whose Cu-O distances indicate different bonding modes and valence-charge distributions. The coupling of the superconductivity to the iqtp that originates in this nonadiabatic coupling between the electrons and lattice demonstrates an important role for the dynamical structure whereby pairing occurs even in a system where displacements of the atoms that are part of the transition are sufficiently large to alter the Fermi surface. The synchronization and dynamic coherence of the iqtps resulting from the strong interactions within a crystal would be expected to influence this process.

Resonant inelastic X-ray scattering using a miniature dispersive Rowland refocusing spectrometer.

X-ray absorption spectroscopy (XAS) beamlines worldwide are steadily increasing their emphasis on full photon-in/photon-out spectroscopies, such as resonant inelastic X-ray scattering (RIXS), resonant X-ray emission spectroscopy (RXES) and high energy resolution fluorescence detection XAS (HERFD-XAS). In such cases, each beamline must match the choice of emission spectrometer to the scientific mission of its users. Previous work has recently reported a miniature tender X-ray spectrometer using a dispersive Rowland refocusing (DRR) geometry that functions with high energy resolution even with a large X-ray spot size on the sample [Holden et al. (2017). Rev. Sci. Instrum. 88, 073904]. This instrument has been used in the laboratory in multiple studies of non-resonant X-ray emission spectroscopy using a conventional X-ray tube, though only for preliminary measurements at a low-intensity microfocus synchrotron beamline. This paper reports an extensive study of the performance of a miniature DRR spectrometer at an unfocused wiggler beamline, where the incident monochromatic flux allows for resonant studies which are impossible in the laboratory. The results support the broader use of the present design and also suggest that the DRR method with an unfocused beam could have important applications for materials with low radiation damage thresholds and that would not survive analysis on focused beamlines.

Local lattice distortions and dynamics in extremely overdoped superconducting YSr2Cu2.75Mo0.25O7.54.

A common characteristic of many "overdoped" cuprates prepared with high-pressure oxygen is Tc values ≥ 50 K that often exceed that of optimally doped parent compounds, despite O stoichiometries that place the materials at the edge or outside of the conventional boundary between superconducting and normal Fermi liquid states. X-ray absorption fine-structure (XAFS) measurements at 52 K on samples of high-pressure oxygen (HPO) YSr2Cu2.75Mo0.25O7.54, Tc = 84 K show that the Mo is in the (VI) valence in an unusually undistorted octahedral geometry with predominantly Mo neighbors that is consistent with its assigned substitution for Cu in the chain sites of the structure. Perturbations of the Cu environments are minimal, although the Cu X-ray absorption near-edge structure (XANES) differs from that in other cuprates. The primary deviation from the crystal structure is therefore nanophase separation into Mo- and Cu-enriched domains. There are, however, indications that the dynamical attributes of the structure are altered relative to YBa2Cu3O7, including a shift of the Cu-apical O two-site distribution from the chain to the plane Cu sites. Another effect that would influence Tc is the possibility of multiple bands at the Fermi surface caused by the presence of the second phase and the lowering of the Fermi level.

Local structure of Sr2CuO3.3, a 95 K cuprate superconductor without CuO2 planes.

The local structure of the highly "overdoped" 95 K superconductor Sr2CuO3.3 determined by Cu K X-ray absorption fine structure (XAFS) at 62 K in magnetically oriented samples shows that 1) the magnetization is perpendicular to the c axis; 2) at these levels of precision the Cu sublattice is tetragonal in agreement with the crystal structure; the O sublattice has 3) continuous -Cu-O- chains that orient perpendicular to an applied magnetic field; 4) approximately half-filled -Cu-O- chains that orient parallel to this field; 5) a substantial number of apical O vacancies; 6) O ions at some apical positions with expanded Cu-O distances; and 7) interstitial positions that imply highly displaced Sr ions. These results contradict the universally accepted features of cuprates that require intact CuO2 planes, magnetization along the c axis, and a termination of the superconductivity when the excess charge on the CuO2 Cu ions exceeds 0.27. These radical differences in charge and structure demonstrate that this compound constitutes a separate class of Cu-O-based superconductors in which the superconductivity originates in a different, more complicated structural unit than CuO2 planes while retaining exceptionally high transition temperatures.

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature.

Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.

Efficient xylem transport and phloem remobilization of Zn in the hyperaccumulator plant species Sedum alfredii.

Sedum alfredii is one of a few species known to hyperaccumulate zinc (Zn) and cadmium (Cd). Xylem transport and phloem remobilization of Zn in hyperaccumulating (HP) and nonhyperaccumulating (NHP) populations of S. alfredii were compared. Micro-X-ray fluorescence (µ-XRF) images of Zn in the roots of the two S. alfredii populations suggested an efficient xylem loading of Zn in HP S. alfredii, confirmed by the seven-fold higher Zn concentrations detected in the xylem sap collected from HP, when compared with NHP, populations. Zn was predominantly transported as aqueous Zn (> 55.9%), with the remaining proportion (36.7-42.3%) associated with the predominant organic acid, citric acid, in the xylem sap of HP S. alfredii. The stable isotope (68)Zn was used to trace Zn remobilization from mature leaves to new growing leaves for both populations. Remobilization of (68)Zn was seven-fold higher in HP than in NHP S. alfredii. Subsequent analysis by µ-XRF, combined with LA-ICPMS (laser ablation-inductively coupled plasma mass spectrometry), confirmed the enhanced ability of HP S. alfredii to remobilize Zn and to preferentially distribute the metal to mesophyll cells surrounding phloem in the new leaves. The results suggest that Zn hyperaccumulation by HP S. alfredii is largely associated with enhanced xylem transport and phloem remobilization of the metal. To our knowledge, this report is the first to reveal enhanced remobilization of metal by phloem transport in hyperaccumulators.

Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode.

The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this "probe-before-destroy" approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as well as the ligand environment, critical for understanding the functional role of redox-active metal sites. Kß(1,3) XES spectra of Mn(II) and Mn(2)(III,IV) complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to >100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. The technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II.

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals.

Most of the dioxygen on earth is generated by the oxidation of water by photosystem II (PS II) using light from the sun. This light-driven, four-photon reaction is catalyzed by the Mn(4)CaO(5) cluster located at the lumenal side of PS II. Various X-ray studies have been carried out at cryogenic temperatures to understand the intermediate steps involved in the water oxidation mechanism. However, the necessity for collecting data at room temperature, especially for studying the transient steps during the O-O bond formation, requires the development of new methodologies. In this paper we report room temperature X-ray diffraction data of PS II microcrystals obtained using ultrashort (< 50 fs) 9 keV X-ray pulses from a hard X-ray free electron laser, namely the Linac Coherent Light Source. The results presented here demonstrate that the "probe before destroy" approach using an X-ray free electron laser works even for the highly-sensitive Mn(4)CaO(5) cluster in PS II at room temperature. We show that these data are comparable to those obtained in synchrotron radiation studies as seen by the similarities in the overall structure of the helices, the protein subunits and the location of the various cofactors. This work is, therefore, an important step toward future studies for resolving the structure of the Mn(4)CaO(5) cluster without any damage at room temperature, and of the reaction intermediates of PS II during O-O bond formation.

Br-rich tips of calcified crab claws are less hard but more fracture resistant: a comparison of mineralized and heavy-element biological materials.

We find that the spoon-like tips of the chelipeds (large claws) of the crab Pachygrapsus crassipes differ from the rest of the claw in that they are not calcified, but instead contain about 1% bromine--thus they represent a new example of a class of structural biological materials that contain heavy elements such as Zn, Mn, Fe, Cu, and Br bound in an organic matrix. X-ray absorption spectroscopy data suggest that the bromine is bound to phenyl rings, possibly in tyrosine. We measure a broad array of mechanical properties of a heavy-element biological material for the first time (abrasion resistance, coefficient of kinetic friction, energy of fracture, hardness, modulus of elasticity and dynamic mechanical properties), and we make a direct comparison with a mineralized tissue. Our results suggest that the greatest advantage of bromine-rich cuticle over calcified cuticle is resistance to fracture (the energy of fracture is about an order of magnitude greater than for calcified cuticle). The greatest advantage relative to unenriched cuticle, represented by ant mandible cuticle, is a factor of about 1.5 greater hardness and modulus of elasticity.The spoon-like tips gain additional fracture resistance from the orientation of the constituent laminae and from the viscoelasticity of the material. We suggest that fracture resistance is of greater importance in smaller organisms, and we speculate that one function of heavy elements in structural biological materials is to reduce molecular resonant frequencies and thereby increase absorption of energy from impacts.

Photoreduction of the active site of the metalloprotein putidaredoxin by synchrotron radiation.

X-ray damage to protein crystals is often assessed on the basis of the degradation of diffraction intensity, yet this measure is not sensitive to the rapid changes that occur at photosensitive groups such as the active sites of metalloproteins. Here, X-ray absorption spectroscopy is used to study the X-ray dose-dependent photoreduction of crystals of the [Fe(2)S(2)]-containing metalloprotein putidaredoxin. A dramatic decrease in the rate of photoreduction is observed in crystals cryocooled with liquid helium at 40 K compared with those cooled with liquid nitrogen at 110 K. Whereas structural changes consistent with cluster reduction occur in the active site of the crystal measured at 110 K, no such changes occur in the crystal measured at 40 K, even after an eightfold increase in dose. When the structural results from extended X-ray absorption fine-structure measurements are compared with those obtained by crystallography on this and similar proteins, it is apparent that X-ray-induced photoreduction has had an impact on the crystallographic data and subsequent structure solutions. These results strongly indicate the importance of using liquid-helium-based cooling for metalloprotein crystallography in order to avoid the subtle yet important changes that can take place at the metalloprotein active sites when liquid-nitrogen-based cooling is used. The study also illustrates the need for direct measurement of the redox states of the metals, through X-ray absorption spectroscopy, simultaneously with the crystallographic measurements.

Where water is oxidized to dioxygen: structure of the photosynthetic Mn4Ca cluster.

The oxidation of water to dioxygen is catalyzed within photosystem II (PSII) by a Mn(4)Ca cluster, the structure of which remains elusive. Polarized extended x-ray absorption fine structure (EXAFS) measurements on PSII single crystals constrain the Mn(4)Ca cluster geometry to a set of three similar high-resolution structures. Combining polarized EXAFS and x-ray diffraction data, the cluster was placed within PSII, taking into account the overall trend of the electron density of the metal site and the putative ligands. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 angstrom-resolution x-ray structures or other previously proposed models.

X-ray damage to the Mn4Ca complex in single crystals of photosystem II: a case study for metalloprotein crystallography.

X-ray absorption spectroscopy was used to measure the damage caused by exposure to x-rays to the Mn(4)Ca active site in single crystals of photosystem II as a function of dose and energy of x-rays, temperature, and time. These studies reveal that the conditions used for structure determination by x-ray crystallography cause serious damage specifically to the metal-site structure. The x-ray absorption spectra show that the structure changes from one that is characteristic of a high-valent Mn(4)(III(2),IV(2)) oxo-bridged Mn(4)Ca cluster to that of Mn(II) in aqueous solution. This damage to the metal site occurs at a dose that is more than one order of magnitude lower than the dose that results in loss of diffractivity and is commonly considered safe for protein crystallography. These results establish quantitative x-ray dose parameters that are applicable to redox-active metalloproteins. This case study shows that a careful evaluation of the structural intactness of the active site(s) by spectroscopic techniques can validate structures derived from crystallography and that it can be a valuable complementary method before structure-function correlations of metalloproteins can be made on the basis of high-resolution x-ray crystal structures.

Patenting inventions arising from biological research.

Patents are the most important way in which researchers can protect the income that might come from ideas or technologies they have developed. This article describes the steps involved and the considerations needed for successful granting of a patent. For instance, inventions must be novel and not obvious, adequately described, and useful, and they should not be disclosed publicly before a patent is applied for.

Integrated instrumentation for combined polarized single-crystal XAS and diffraction data acquisition for biological applications.

Single-crystal X-ray absorption spectroscopy (XAS) instrumentation, allowing sequential integrated XAS and crystallographic data acquisition during the same experiment and on the same beamline, has been developed for SSRL beamline 9-3, a wiggler side station dedicated to general user biological XAS. The implementation includes a Huber kappa goniometer, Canberra 30-element Ge detector for XAS data collection, open-flow LHe and LN2 crystal coolers, a microscope for crystal alignment in the beam, and a MarCCD crystallography detector. The kappa goniometer allows a large accessible angular range with an open geometry, affording access to detectors and open stream coolers, as well as future instrumentation. Applicable standard hardware on SSRL crystallography beamlines has been incorporated, with crystallographic data collection controlled via the Blu-Ice software developed by the SSRL SMB macromolecular crystallography group. XAS data collection is handled through the SSRL standard XAS-Collect software. Initial diffraction and XAS data from single crystals using an open-flow cryostat are presented. The instrument will be available to general users after the SPEAR3 upgrade in 2004, and future expansion for use in high-throughput structural genomics XAS is proposed.

Mo K- and L-edge X-ray absorption spectroscopic study of the ADP.AlF4--stabilized nitrogenase complex: comparison with MoFe protein in solution and single crystal.

The utility of using X-ray absorption spectroscopy (XAS) to study metalloproteins and, specifically, the enzyme complex nitrogenase, is highlighted by this study comparing both the structural and Mo-localized electronic features of the iron-molybdenum cofactor (FeMoco) in isolated MoFe protein and in the ADP.AlF4--stabilized complex of the MoFe protein with the Fe protein. No major differences are found at Mo between the two protein forms. The excellent quality of the data at both the Mo K and L edges will provide a baseline for analysis of other intermediates in the nitrogenase cycle. A new capability to delineate various contributions in the resting state of FeMoco is being pursued through polarized single-crystal XAS. The initial results point to the feasibility of using this technique for the analysis of scattering from the as yet unidentified atom at the center of FeMoco.

Liquid helium cryostat with internal fluorescence detection for x-ray absorption studies in the 2-6 keV energy region.

X-ray absorption spectroscop (XAS) in the intermediate x-ray region (2-6 keV) for dilute biological samples has been limited because of detector/flux limitations and inadequate cryogenic instrumentation. We have designed and constructed a new tailpiece/sample chamber for a commercially available liquid helium cooled cryostat which overcomes difficulties related to low fluorescence signals by using thin window materials and incorporating an internal photodiode detector. With the apparatus, XAS data at the Cl, S, and Ca K edges have been collected on frozen solutions and biological samples at temperatures down to 60 K. A separate chamber has been incorporated for collecting room-temperature spectra of standard compounds (for energy calibration purposes) which prevents contamination of the cryostat chamber and allows the sample to remain undisturbed, both important concerns for studying dilute and radiation-sensitive samples.

Structural Change of the Mn Cluster during the S2→S3 State Transition of the Oxygen-Evolving Complex of Photosystem II. Does It Reflect the Onset of Water/Substrate Oxidation? Determination by Mn X-ray Absorption Spectroscopy.

The oxygen-evolving complex of Photosystem II in plants and cyanobacteria catalyzes the oxidation of two water molecules to one molecule of dioxygen. A tetranuclear Mn complex is believed to cycle through five intermediate states (S0-S4) to couple the four-electron oxidation of water with the one-electron photochemistry occurring at the Photosystem II reaction center. We have used X-ray absorption spectroscopy to study the local structure of the Mn complex and have proposed a model for it, based on studies of the Mn K-edges and the extended X-ray absorption fine structure of the S1 and S2 states. The proposed model consists of two di-µ-oxo-bridged binuclear Mn units with Mn-Mn distances of ~2.7 Å that are linked to each other by a mono-µ-oxo bridge with a Mn-Mn separation of ~3.3 Å. The Mn-Mn distances are invariant in the native S1 and S2 states. This report describes the application of X-ray absorption spectroscopy to S3 samples created under physiological conditions with saturating flash illumination. Significant changes are observed in the Mn-Mn distances in the S3 state compared to the S1 and the S2 states. The two 2.7 Å Mn-Mn distances that characterize the di-µ-oxo centers in the S1 and S2 states are lengthened to ~2.8 and 3.0 Å in the S3 state, respectively. The 3.3 Å Mn-Mn and Mn-Ca distances also increase by 0.04-0.2 Å. These changes in Mn-Mn distances are interpreted as consequences of the onset of substrate/water oxidation in the S3 state. Mn-centered oxidation is evident during the S0→S1 and S1→S2 transitions. We propose that the changes in Mn-Mn distances during the S2→S3 transition are the result of ligand or water oxidation, leading to the formation of an oxyl radical intermediate formed at a bridging or terminal position. The reaction of the oxyl radical with OH-, H2O, or an oxo group during the subsequent S state conversion is proposed to lead to the formation of the O-O bond. Models that can account for changes in the Mn-Mn distances in the S3 state and the implications for the mechanism of water oxidation are discussed.

Structural Effects of Calcium Depletion on the Manganese Cluster of Photosystem II: Determination by X-ray Absorption Spectroscopy.

The structural consequences of calcium depletion of Photosystem II (PS II) by treatment at pH 3.0 in the presence of citrate has been determined by Mn K-edge X-ray absorption spectroscopy. X-ray absorption edge spectroscopy of Ca-depleted samples in the S1', S2', and S3' oxidation states reveals that there is Mn oxidation on the S1'-S2' transition, although no evidence of Mn oxidation was found for the S2'-S3' transition. This result is in keeping with the results from EPR studies where it has been found that the species oxidized to give the S3' broad radical signal found in Ca-depleted PS II is tyrosine Yz. The S2' state can be prepared by two methods: illumination followed by dark adaptation and illumination in the presence of DCMU to limit to one turnover. Illumination followed by dark adaptation was found to yield a lower Mn K-edge inflection-point energy than illumination with DCMU, indicating vulnerability to reduction of the Mn complex, even over the relatively short times used for dark adaptation (~15 min). EXAFS measurements of Ca-depleted samples in the three modified S states (referred to here as S' states) reveals that the Fourier peak due to scatterers at ~3.3 Å from Mn is strongly diminished, consistent with our previous assignment of a Ca-scattering contribution at this distance. Even after Ca depletion, there is still significant amplitude in the third peak, further supporting our conclusions from earlier studies that the third peak in native samples is comprised of both Mn and Ca scattering. The Mn-Mn contributions making up the second Fourier peak at ~2.7 Å are largely undisturbed by Ca-depletion, but there is some evidence that S1'-state samples contain significant amounts of reduced Mn(II), which is then photooxidized in the preparation of higher S' states.