Xinguo Hong

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.

Polyhedral units and network connectivity in GeO2 glass at high pressure: An X-ray total scattering investigation

We report a pressure-induced dense tetrahedral intermediate state via Ge–O–Ge rotation formed at 3–5 GPa and the polyhedral relations in GeO2 glass up to 17.5 GPa using in situ X-ray total scattering and X-ray absorption (XAFS) techniques. It was found that the nearest-neighbor Ge-Ge correlations show a decrease reaching a minimum between 4 and 6 GPa, and exhibit negative compression behavior at 7–17.5 GPa. The Ge–Ge distance determined by XAFS shows a substantial reduction, i.e., normal compression behavior, at 7–17.5 GPa. The comparison with the theoretical g(r) function for rutile-type GeO2 (16.1 GPa) indicates that the negative compression of intermediate range order reflects the direct formation of GeO6 octahedral units. Results of coordination number analysis show that GeO2 glass undergoes a transition from tetrahedral GeO4, to GeO5 units (possibly triangular bipyramidal), and finally to octahedral GeO6 units. The present investigation provides the structural details of the polyhedral units and thei...

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.

High resolution pair-distance distribution function P(r) of protein solutions

A high resolution pair-distance distribution function P(r) of protein molecules has been obtained from the complete solution scattering curve made by combining accurate small-angle and wide-angle x-ray scattering data out to 2.15 A resolution. Both indirect and direct Fourier transforms exhibit two distinct peaks at 1.4 and 5.1 A in P(r). X-ray crystallographic data demonstrate that these peaks correspond to two intramolecular distances: the average bond length between C, N, and O atoms and the pitch of an α-helix, respectively. Hence some high resolution aspects of the structure and function of a protein may be investigated in a solution.

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.

Structural phase transitions in SrTiO3 nanoparticles

Understanding the structural phase diagram of nano scale SrTiO3 has important implications on the basic physics and applications of the general class of transition metal oxide perovskites. Pressure dependent structural measurements on monodispersed nanoscale SrTiO3 samples with average diameters of 10 to ~80 nm were conducted. A robust pressure independent polar structure was detected in the 10 nm sample for pressures of up to 13 GPa while a size dependent cubic to tetragonal transition occurs (at P = Pc) for larger particle sizes. The results suggest that the growth of ~10 nm STO particles on substrates with large lattice mismatch will not alter the polar state of the system for a large range of strain values, possibly enabling device use.

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.

Absolute x-ray energy calibration and monitoring using a diffraction-based method

In this paper, we report some recent developments of the diffraction-based absolute X-ray energy calibration method. In this calibration method, high spatial resolution of the measured detector offset is essential. To this end, a remotely controlled long-translation motorized stage was employed instead of the less convenient gauge blocks. It is found that the precision of absolute X-ray energy calibration (ΔE/E) is readily achieved down to the level of 10−4 for high-energy monochromatic X-rays (e.g. 80 keV). Examples of applications to pair distribution function (PDF) measurements and energy monitoring for high-energy X-rays are presented.

High-pressure pair distribution function (PDF) measurement using high-energy focused x-ray beam

In this paper, we report recent development of the high-pressure pair distribution function (HP-PDF) measurement technique using a focused high-energy X-ray beam coupled with a diamond anvil cell (DAC). The focusing optics consist of a sagittally bent Laue monochromator and Kirkpatrick-Baez (K–B) mirrors. This combination provides a clean high-energy X-ray beam suitable for HP-PDF research. Demonstration of the HP-PDF technique for nanocrystalline platinum under quasi-hydrostatic condition above 30 GPa is presented.

High-energy X-ray focusing and high-pressure pair distribution function measurement

In this paper, we report recent progress in high-energy X-ray focusing by using Kirkpatrick-Baez (K–B) mirrors in combination with a sagittally bent Laue monochromator. This combination of optics provides a high flux X-ray beam, which can significantly reduce the data acquisition time for high-pressure pair distribution function (HP-PDF) measurements using the diamond anvil cell (DAC). Demonstration of the HP-PDF technique for the compression/relaxation of nanocrystalline platinum at high pressures is presented.