Local structural investigation of non-crystalline materials at high pressure: the case of GeO2glass.

Local structures play a crucial role in the structural polyamorphism and novel electronic properties of amorphous materials, but their accurate measurement at high pressure remains a formidable challenge. In this article, we use the local structure of network-forming GeO2glass as an example, to present our recent approaches and advances in high-energy x-ray diffraction, high-pressure x-ray absorption fine structure, andab initiofirst-principles density functional theory calculations and simulations. Although GeO2glass is one of the best studied materials in the field of high pressure research due to its importance in glass theory and geophysical significance, there are still some long-standing puzzles, such as the existence of appreciable distinct fivefold[5]Ge coordination at low pressure and the sixfold-plus[6+]Ge coordination at ultrahigh pressure. Our work sheds light on the origin of pressure-induced polyamorphism of GeO2glass, and the[5]Ge polyhedral units may be the dominant species in the densification mechanism of network-forming glasses from tetrahedral to octahedral amorphous structures.

Novel Valence Transition in Elemental Metal Europium around 80 GPa.

Valence transition could induce structural, insulator-metal, nonmagnetic-magnetic and superconducting transitions in rare-earth metals and compounds, while the underlying physics remains unclear due to the complex interaction of localized 4f electrons as well as their coupling with itinerant electrons. The valence transition in the elemental metal europium (Eu) still has remained as a matter of debate. Using resonant x-ray emission scattering and x-ray diffraction, we pressurize the states of 4f electrons in Eu and study its valence and structure transitions up to 160 GPa. We provide compelling evidence for a valence transition around 80 GPa, which coincides with a structural transition from a monoclinic (C2/c) to an orthorhombic phase (Pnma). We show that the valence transition occurs when the pressure-dependent energy gap between 4f and 5d electrons approaches the Coulomb interaction. Our discovery is critical for understanding the electrodynamics of Eu, including magnetism and high-pressure superconductivity.

Metallization of Quantum Material GaTa4Se8 at High Pressure.

Pressure is a unique thermodynamic variable to explore the phase competitions and novel phases inaccessible at ambient conditions. The resistive switching material GaTa4Se8 displays several quantum phases under pressure, such as a Jeff = 3/2 Mott insulator, a correlated quantum magnetic metal, and d-wave topological superconductivity, which has recently drawn considerable interest. Using high-pressure Raman spectroscopy, X-ray diffraction, extended X-ray absorption, transport measurements, and theoretical calculations, we reveal a complex phase diagram for GaTa4Se8 at pressures exceeding 50 GPa. In this previously unattained pressure regime, GaTa4Se8 ranges from a Mott insulator to a metallic phase and exhibits superconducting phases. In contrast to previous studies, we unveil a hidden correlation between the structural distortion and band gap prior to the insulator-to-metal transition, and the metallic phase shows superconductivity with structural and magnetic properties that are distinctive from the lower-pressure phase. These discoveries highlight that GaTa4Se8 is a unique material to probe novel quantum phases from a structural, metallicity, magnetism, and superconductivity perspective.

Pressure induced transformation and subsequent amorphization of monoclinic Nb2O5 and its effect on optical properties.

Pressure-induced phase transitions of monoclinic H-Nb2O5 have been studied by in situ synchrotron x-ray diffraction, pair distribution function (PDF) analysis, and Raman and optical transmission spectroscopy. The initial monoclinic phase is found to transform into an orthorhombic phase at ~9 GPa and then change to an amorphous form above 21.4 GPa. The PDF data reveal that the amorphization is associated with disruptions of the long-range order of the NbO6 octahedra and the NbO7 pentagonal bipyramids, whereas the local edge-shares of octahedra and the local linkages of pentagonal bipyramids are largely preserved in their nearest neighbors. Upon compression, the transmittance of the sample in a region from visible to near infrared (450-1000 nm) starts to increase above 8.0 GPa and displays a dramatic enhancement above 22.2 GPa, indicating that the amorphous form has a high transmittance. The pressure-induced amorphous form is found to be recoverable under pressure release, and maintain high optical transmittance property at ambient conditions. The recoverable pressure induced amorphous material promises for applications in multifunctional materials.

Evolution of a Novel Ribbon Phase in Optimally Doped Bi2Sr2CaCu2O8+δ at High Pressure and Its Implication to High- TC Superconductivity.

One challenge in studying high-temperature superconductivity (HTSC) stems from a lack of direct experimental evidence linking lattice inhomogeneity and superconductivity. Here, we apply synchrotron hard X-ray nanoimaging and small-angle scattering to reveal a novel micron-scaled ribbon phase in optimally doped Bi2Sr2CaCu2O8+δ (Bi-2212, with δ = 0.1). The morphology of the ribbon-like phase evolves simultaneously with the dome-shaped TC behavior under pressure. X-ray absorption studies show that the increasing of TC is associated with oxygen-hole redistribution in the CuO2 plan, while TC starts to decrease with pressure when oxygen holes become immobile. Additional X-ray irradiation experiments reveal that nanoscaled short-range ordering of oxygen vacancies could further lower TC, which indicates that the optimal TC is affected not only by an optimal morphology of the ribbon phase, but also an optimal distribution of oxygen vacancies. Our studies thereby provide for the first time compelling experimental evidence correlating the TC with micron to nanoscale inhomogeneity.

High-energy X-ray focusing and applications to pair distribution function investigation of Pt and Au nanoparticles at high pressures.

We report development of micro-focusing optics for high-energy x-rays by combining a sagittally bent Laue crystal monchromator with Kirkpatrick-Baez (K-B) X-ray focusing mirrors. The optical system is able to provide a clean, high-flux X-ray beam suitable for pair distribution function (PDF) measurements at high pressure using a diamond anvil cell (DAC). A focused beam of moderate size (10-15 µm) has been achieved at energies of 66 and 81 keV. PDF data for nanocrystalline platinum (n-Pt) were collected at 12.5 GPa with a single 5 s X-ray exposure, showing that the in-situ compression, decompression, and relaxation behavior of samples in the DAC can be investigated with this technique. PDFs of n-Pt and nano Au (n-Au) under quasi-hydrostatic loading to as high as 71 GPa indicate the existence of substantial reduction of grain or domain size for Pt and Au nanoparticles at pressures below 10 GPa. The coupling of sagittally bent Laue crystals with K-B mirrors provides a useful means to focus high-energy synchrotron X-rays from a bending magnet or wiggler source.

Local structural distortion and electrical transport properties of Bi(Ni1/2Ti1/2)O3 perovskite under high pressure.

Perovskite-structure materials generally exhibit local structural distortions that are distinct from long-range, average crystal structure. The characterization of such distortion is critical to understanding the structural and physical properties of materials. In this work, we combined Pair Distribution Function (PDF) technique with Raman spectroscopy and electrical resistivity measurement to study Bi(Ni1/2Ti1/2)O3 perovskite under high pressure. PDF analysis reveals strong local structural distortion at ambient conditions. As pressure increases, the local structure distortions are substantially suppressed and eventually vanish around 4 GPa, leading to concurrent changes in the electronic band structure and anomalies in the electrical resistivity. Consistent with PDF analysis, Raman spectroscopy data suggest that the local structure changes to a higher ordered state at pressures above 4 GPa.

Pressure-induced stiffness of Au nanoparticles to 71 GPa under quasi-hydrostatic loading.

The compressibility of nanocrystalline gold (n-Au, 20 nm) has been studied by x-ray total scattering using high-energy monochromatic x-rays in the diamond anvil cell under quasi-hydrostatic conditions up to 71 GPa. The bulk modulus, K0, of the n-Au obtained from fitting to a Vinet equation of state is ~196(3) GPa, which is about 17% higher than for the corresponding bulk materials (K0: 167 GPa). At low pressures (<7 GPa), the compression behavior of n-Au shows little difference from that of bulk Au. With increasing pressure, the compressive behavior of n-Au gradually deviates from the equation of state (EOS) of bulk gold. Analysis of the pair distribution function, peak broadening and Rietveld refinement reveals that the microstructure of n-Au is nearly a single-grain/domain at ambient conditions, but undergoes substantial pressure-induced reduction in grain size until 10 GPa. The results indicate that the nature of the internal microstructure in n-Au is associated with the observed EOS difference from bulk Au at high pressure. Full-pattern analysis confirms that significant changes in grain size, stacking faults, grain orientation and texture occur in n-Au at high pressure. We have observed direct experimental evidence of a transition in compressional mechanism for n-Au at ~20 GPa, i.e. from a deformation dominated by nucleation and motion of lattice dislocations (dislocation-mediated) to a prominent grain boundary mediated response to external pressure. The internal microstructure inside the nanoparticle (nanocrystallinity) plays a critical role for the macro-mechanical properties of nano-Au.

X-ray absorption spectroscopy of GeO2 glass to 64 GPa.

The structural behavior of GeO2 glass has been investigated up to 64 GPa using results from x-ray absorption spectroscopy in a diamond anvil cell combined with previously reported density measurements. The difference between the nearest Ge-O distances of glassy and rutile-type GeO2 disappears at the Ge-O distance maximum at 20 GPa, indicating completion of the tetrahedral-octahedral transition in GeO2 glass. The mean-square displacement σ(2) of the Ge-O distance in the first Ge-O shell increases progressively to a maximum at 10 GPa, followed by a substantial reduction at higher pressures. The octahedral glass is, as expected, less dense and has a higher compressibility than the corresponding crystalline phase, but the differences in Ge-O distance and density between the glass and the crystals are gradually eliminated over the 20-40 GPa pressure range. Above 40 GPa, GeO2 forms a dense octahedral glass with a compressibility similar to that of the corresponding crystalline phase (α-PbO2 type). The EXAFS and XANES spectra show evidence for subtle changes in the dense glass continuing to occur at these high pressures. The Ge-O bond distance shows little change between 45-64 GPa, and this may reflect a balance between bond shortening and a gradual coordination number increase with compression. The density of the glass is similar to that of the α-PbO2-type phase, but the Ge-O distance is longer and is close to that in the higher-coordination pyrite-type phase which is stable above ∼60 GPa. The density data provide evidence for a possible discontinuity and change in compressibility at 40-45 GPa, but there are no major changes in the corresponding EXAFS spectra. A pyrite-type local structural model for the glass can provide a reasonable fitting to the XAFS spectra at 64 GPa.

Absolute x-ray energy calibration over a wide energy range using a diffraction-based iterative method.

In this paper, we report a method of precise and fast absolute x-ray energy calibration over a wide energy range using an iterative x-ray diffraction based method. Although accurate x-ray energy calibration is indispensable for x-ray energy-sensitive scattering and diffraction experiments, there is still a lack of effective methods to precisely calibrate energy over a wide range, especially when normal transmission monitoring is not an option and complicated micro-focusing optics are fixed in place. It is found that by using an iterative algorithm the x-ray energy is only tied to the relative offset of sample-to-detector distance, which can be readily varied with high precision of the order of 10(-5) -10(-6) spatial resolution using gauge blocks. Even starting with arbitrary initial values of 0.1 Å, 0.3 Å, and 0.4 Å, the iteration process converges to a value within 3.5 eV for 31.122 keV x-rays after three iterations. Different common diffraction standards CeO(2), Au, and Si show an energy deviation of 14 eV. As an application, the proposed method has been applied to determine the energy-sensitive first sharp diffraction peak of network forming GeO(2) glass at high pressure, exhibiting a distinct behavior in the pressure range of 2-4 GPa. Another application presented is pair distribution function measurement using calibrated high-energy x-rays at 82.273 keV. Unlike the traditional x-ray absorption-based calibration method, the proposed approach does not rely on any edges of specific elements, and is applicable to the hard x-ray region where no appropriate absorption edge is available.

Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral antibody.

Ibalizumab is a humanized, anti-CD4 monoclonal antibody. It potently blocks HIV-1 infection and targets an epitope in the second domain of CD4 without interfering with immune functions mediated by interaction of CD4 with major histocompatibility complex (MHC) class II molecules. We report here the crystal structure of ibalizumab Fab fragment in complex with the first two domains (D1-D2) of CD4 at 2.2 Å resolution. Ibalizumab grips CD4 primarily by the BC-loop (residues 121-125) of D2, sitting on the opposite side of gp120 and MHC-II binding sites. No major conformational change in CD4 accompanies binding to ibalizumab. Both monovalent and bivalent forms of ibalizumab effectively block viral infection, suggesting that it does not need to crosslink CD4 to exert antiviral activity. While gp120-induced structural rearrangements in CD4 are probably minimal, CD4 structural rigidity is dispensable for ibalizumab inhibition. These results could guide CD4-based immunogen design and lead to a better understanding of HIV-1 entry.

High quality x-ray absorption spectroscopy measurements with long energy range at high pressure using diamond anvil cell.

We describe an approach for acquiring high quality x-ray absorption fine structure (XAFS) spectroscopy spectra with wide energy range at high pressure using diamond anvil cell (DAC). Overcoming the serious interference of diamond Bragg peaks is essential for combining XAFS and DAC techniques in high pressure research, yet an effective method to obtain accurate XAFS spectrum free from DAC induced glitches has been lacking. It was found that these glitches, whose energy positions are very sensitive to the relative orientation between DAC and incident x-ray beam, can be effectively eliminated using an iterative algorithm based on repeated measurements over a small angular range of DAC orientation, e.g., within +/-3 degrees relative to the x-ray beam direction. Demonstration XAFS spectra are reported for rutile-type GeO2 recorded by traditional ambient pressure and high pressure DAC methods, showing similar quality at 440 eV above the absorption edge. Accurate XAFS spectra of GeO2 glass were obtained at high pressure up to 53 GPa, providing important insight into the structural polymorphism of GeO2 glass at high pressure. This method is expected be applicable for in situ XAFS measurements using a diamond anvil cell up to ultrahigh pressures.

Combining solution wide-angle X-ray scattering and crystallography: determination of molecular envelope and heavy-atom sites.

Solving the phase problem remains central to crystallographic structure determination. A six-dimensional search method of molecular replacement (FSEARCH) can be used to locate a low-resolution molecular envelope determined from small-angle X-ray scattering (SAXS) within the crystallographic unit cell. This method has now been applied using the higher-resolution envelope provided by combining SAXS and WAXS (wide-angle X-ray scattering) data. The method was tested on horse hemoglobin, using the most probable model selected from a set of a dozen bead models constructed from SAXS/WAXS data using the program GASBOR at 5 A resolution (q(max) = 1.25 A(-1)) to phase a set of single-crystal diffraction data. It was found that inclusion of WAXS data is essential for correctly locating the molecular envelope in the crystal unit cell, as well as for locating heavy-atom sites. An anomalous difference map was calculated using phases out to 8 A resolution from the correctly positioned envelope; four distinct peaks at the 3.2sigma level were identified, which agree well with the four iron sites of the known structure (Protein Data Bank code 1ns9). In contrast, no peaks could be found close to the iron sites if the molecular envelope was constructed using the data from SAXS alone (q(max) = 0.25 A(-1)). The initial phases can be used as a starting point for a variety of phase-extension techniques, successful application of which will result in complete phasing of a crystallographic data set and determination of the internal structure of a macromolecule to atomic resolution. It is anticipated that the combination of FSEARCH and WAXS techniques will facilitate the initial structure determination of proteins and provide a good foundation for further structure refinement.

Measurements of accurate x-ray scattering data of protein solutions using small stationary sample cells.

In this paper, we report a method of precise in situ x-ray scattering measurements on protein solutions using small stationary sample cells. Although reduction in the radiation damage induced by intense synchrotron radiation sources is indispensable for the correct interpretation of scattering data, there is still a lack of effective methods to overcome radiation-induced aggregation and extract scattering profiles free from chemical or structural damage. It is found that radiation-induced aggregation mainly begins on the surface of the sample cell and grows along the beam path; the diameter of the damaged region is comparable to the x-ray beam size. Radiation-induced aggregation can be effectively avoided by using a two-dimensional scan (2D mode), with an interval as small as 1.5 times the beam size, at low temperature (e.g., 4 degrees C). A radiation sensitive protein, bovine hemoglobin, was used to test the method. A standard deviation of less than 5% in the small angle region was observed from a series of nine spectra recorded in 2D mode, in contrast to the intensity variation seen using the conventional stationary technique, which can exceed 100%. Wide-angle x-ray scattering data were collected at a standard macromolecular diffraction station using the same data collection protocol and showed a good signal/noise ratio (better than the reported data on the same protein using a flow cell). The results indicate that this method is an effective approach for obtaining precise measurements of protein solution scattering.

SNAP-25 is also an iron-sulfur protein.

SNAP-25 has a cysteine cluster located at its linker domain. In vivo, the cysteine residues in this cluster can be palmitoylated, and the hydrophobic palmitate molecules can target SNAP-25 to the presynaptic membrane. Here, we report that the SNAP-25a expressed in Escherichia coli is also an iron-sulfur protein binding an iron-sulfur cluster using the cysteine residues in its cysteine cluster. Therefore, SNAP-25a uses the same cysteine residues to bind two different prosthetic groups (iron-sulfur cluster and palmitate). Because the binding sites of these two prosthetic groups overlap, we suggest that these two modifications occur at different times, and probably at different places in the cell.

Density measurements of noncrystalline materials at high pressure with diamond anvil cell.

We describe an x-ray absorption method for in situ density measurement of non-crystalline materials in the diamond anvil cell using a monochromatic synchrotron x-ray microbeam. Sample thickness, which is indispensable in the absorption method, can be determined precisely by extrapolating the thickness profile of the gasket obtained by x-ray absorption and diffraction measurements. Diamond deformation across the sample chamber becomes noticeable at high pressures above 10 GPa, which can be monitored with a precision better than 1%, as demonstrated by measurements on crystalline Ag. We have applied the developed method to measure densities of the classic network-forming GeO(2) glass in octahedral form at pressures up to 56 GPa. The fit to the pressure-volume data with the Birch-Murnaghan equation from 13 to 56 GPa gives parameters of V(0)=23.2+/-0.4 cm(3)mol and K=35.8+/-3.0 GPa, assuming that K(')=4. This method could be applicable for in situ determination of the density of liquids and other noncrystalline materials using a diamond anvil cell up to ultrahigh pressures.

Distinct thermal behavior of GeO2 glass in tetrahedral, intermediate, and octahedral forms.

One fascinating high-pressure behavior of tetrahedral glasses and melts is the local coordination change with increasing pressure, which provides a structural basis for understanding numerous anomalies in their high-pressure properties. Because the coordination change is often not retained upon decompression, studies must be conducted in situ. Previous in situ studies have revealed that the short-range order of tetrahedrally structured glasses and melts changes above a threshold pressure and gradually transforms to an octahedral form with further pressure increase. Here, we report a thermal effect associated with the coordination change at given pressures and show distinct thermal behaviors of GeO(2) glass in tetrahedral, octahedral, and their intermediate forms. An unusual thermally induced densification, as large as 16%, was observed on a GeO(2) glass at a pressure of 5.5 gigapascal (GPa), based on in situ density and x-ray diffraction measurements at simultaneously high pressures and high temperatures. The large thermal densification at high pressure was found to be associated with the 4- to 6-fold coordination increase. Experiments at other pressures show that the tetrahedral GeO(2) glass displayed small thermal densification at 3.3 GPa arising from the relaxation of intermediate range structure, whereas the octahedral glass at 12.3 GPa did not display any detectable thermal effects.

Annular arrangement and collaborative actions of four domains of protein-disulfide isomerase: a small angle X-ray scattering study in solution.

We presented for the first time a small angle x-ray scattering study of intact protein-disulfide isomerase (PDI) in solution. The restored model revealed that PDI is a short and roughly elliptical cylinder with a molecular mass of 69 kDa and dimensions of 105 x 65 x 40 A, and the four thioredoxin-fold domains in the order a-b-b'-a' are arranged in an annular fashion. Atomic force microscope imaging also supported the finding that PDI appears as an approximately flat elliptical cylinder. A PDI species with apparent molecular mass of 116 kDa measured by using size-exclusion chromatography, previously assumed to be a dimer, was determined to exist mainly as a monomer by using analytical ultracentrifugation. The C-terminal fragment 441-491 contributed to the anomalous molecular mass determination of PDI by size-exclusion chromatography. The annular model of PDI accounted for the cooperative properties of the four domains in both the isomerase and chaperone functions of PDI.

The C-terminal (331-376) sequence of Escherichia coli DnaJ is essential for dimerization and chaperone activity: a small angle X-ray scattering study in solution.

DnaJ, an Escherichia coli Hsp40 protein composed of 376 amino acid residues, is a chaperone with thioldisulfide oxidoreductase activity. We present here for the first time a small angle x-ray scattering study of intact DnaJ and a truncated version, DnaJ (1-330), in solution. The molecular weight of DnaJ and DnaJ (1-330) determined by both small angle x-ray scattering and size-exclusion chromatography provide direct evidence that DnaJ is a homodimer and DnaJ (1-330) is a monomer. The restored models show that DnaJ is a distorted omega-shaped dimeric molecule with the C terminus of each subunit forming the central part of the omega, whereas DnaJ (1-330) exists as a monomer. This indicates that the deletion of the C-terminal 46 residues of DnaJ impairs the association sites, although it does not cause significant conformational changes. Biochemical studies reveal that DnaJ (1-330), while fully retaining its thiol-disulfide oxidoreductase activity, is structurally less stable, and its peptide binding capacity is severely impaired relative to that of the intact molecule. Together, our results reveal that the C-terminal (331-376) residues are directly involved in dimerization, and the dimeric structure of DnaJ is necessary for its chaperone activity but not required for the thiol-disulfide oxidoreductase activity.

Determination of the topological shape of integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria in the detergent solution by small-angle X-ray scattering.

The topological shape of the integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria Rhodobacter spheroides 2.4.1 in detergent solution has been determined from synchrotron small-angle X-ray scattering data using direct curve-fitting by the ellipsoid, ab initio shape determination methods of simulated annealing algorithm and multipole expansion, respectively. The results indicate that the LH2 protein in aqueous solution is encapsulated by a monolayered detergent shell. The detergent-stabilized structure has the shape of an oblate plate, with a thickness of 40 A, a long axis of 110 A, and a short axis of 85 A. After correction for the detergent shell, the shape of the LH2 core is also an oblate plate with a height of 40 A, a long axis of 80 A, and a short axis of 55 A. In contrast to the cylindrical crystal structure with a height of 40 A and a diameter of 68 A, the molecular shape of the LH2 complex in detergent solution clearly deviates from the ringlike crystal structure, with an eccentricity found to be 0.59-consistent with the result of single molecular spectroscopy study of the isolated single LH2 molecules.