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At least 757 records · Page 42

Dicarbonyl[10,10-dimethyl-5,15-bis(pentafluorophenyl)biladiene]ruthenium(II): discovery of the first ruthenium tetrapyrrole cis -dicarbonyl complex by X-ray and electron diffraction

Dicarbon­yl[10,10-dimethyl-5,15-bis­(penta­fluoro­phen­yl)biladiene]ruthenium(II), [Ru(C 33 H 16 F 10 N 4 )(CO) 2 ] or Ru(CO) 2 [DMBil1], is the first reported ruthenium(II) cis-dicarbonyl tetra­pyrrole complex. The neutral complex sports two carbonyls and an oligo­tetra­pyrrolic biladiene ligand. Notably, the biladiene adopts a coordination geometry that is well distorted from square planar and much more closely approximates a seesaw arrangement. Accordingly, Ru(CO) 2 [DMBil1] is not only the first ruthenium cis-dicarbonyl with a tetra­pyrrole ligand, but also the first metal biladiene complex in which the tetra­pyrrole does not adopt a (pseudo-)square-planar coordination geometry. Ru(CO) 2 [DMBil1] is weakly luminescent, displaying λ em = 552 nm upon excitation at λ ex = 500 nm, supports two reversible 1 e – reductions at –1.45 and –1.73 V (versus Fc + /Fc), and has significant absorption features at 481 and 531 nm, suggesting suitability for photo­catalytic and photosensitization applications. While the structure of Ru(CO) 2 [DMBil1] was initially determined by X-ray diffraction, a traditionally acceptable quality structure could not be obtained (despite multiple attempts) because of consistently poor crystal quality. Furthermore, an independent structure obtained from electron diffraction experiments corroborates the structure of this unusual biladiene complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa

The role of seemingly non-enzymatic proteins in complexes interconverting UDP-arabinopyranose and UDP-arabinofuranose (UDP-arabinosemutases; UAMs) in the plant cytosol remains unknown. To shed light on their function, crystallographic and functional studies of the seemingly non-enzymatic UAM2 protein from Oryza sativa (OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low-dose vector data acquisition. Using size-exclusion chromatography, it is shown that the protein is monomeric in solution. Finally, limited proteolysis was employed to demonstrate DTT-enhanced proteolytic digestion, indicating the existence of at least one intramolecular disulfide bridge or, alternatively, a requirement for a structural metal ion.

59 BASIC BIOLOGICAL SCIENCES↗

Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions

Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper–oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallo­graphy provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. Here, to characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.

Neurospora crassa↗

The crystal structures of Fe-bearing MgCO 3 sp 2 - and sp 3 -carbonates at 98 GPa from single-crystal X-ray diffraction using synchrotron radiation

The crystal structure of MgCO 3 -II has long been discussed in the literature where DFT-based model calculations predict a pressure-induced transition of the carbon atom from the sp 2 to the sp 3 type of bonding. We have now determined the crystal structure of iron-bearing MgCO 3 -II based on single-crystal X-ray diffraction measurements using synchrotron radiation. We laser-heated a synthetic (Mg 0.85 Fe 0.15 )CO 3 single crystal at 2500 K and 98 GPa and observed the formation of a monoclinic phase with composition (Mg 2.53 Fe 0.47 )C 3 O 9 in the space group C 2/ m that contains tetrahedrally coordinated carbon, where CO 4 4- tetrahedra are linked by corner-sharing oxygen atoms to form three-membered C 3 O 9 6- ring anions. The crystal structure of (Mg 0.85 Fe 0.15 )CO 3 (magnesium iron carbonate) at 98 GPa and 300 K is reported here as well. In comparison with previous structure-prediction calculations and powder X-ray diffraction data, our structural data provide reliable information from experiments regarding atomic positions, bond lengths, and bond angles.

Chariton, Stella (ORCID:0000000155220498)↗

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2–3 × 10 −4 (Δ E / E ). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (Δ E / E = 3 × 10 −3 ) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.

59 BASIC BIOLOGICAL SCIENCES↗

A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs

One often observes small but measurable differences in the diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and may reveal the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step that could extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can be obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). To the extent that different states adopt different molecular structures, one expects to observe differences in the crystals; each of the polystates will create a polymorph of the crystals. After mixed-state diffraction data have been measured, deliberately or inadvertently, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here, this problem is addressed using a simple multi-factor clustering approach that classifies each data set using independent observables, thereby assigning each data set to the correct location in conformational space. This procedure is illustrated using two independent observables, unit-cell parameters and intensities, to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. It is observed that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin.

36 MATERIALS SCIENCE↗

In situ characterization of residual stress evolution during heat treatment of SiC/SiC ceramic matrix composites using high-energy X-ray diffraction

Volumetric strains were measured in silicon carbide/silicon carbide melt-infiltrated ceramic matrix composites (CMCs) at ambient and high temperatures using high-energy synchrotron X-ray diffraction (XRD). Both silicon and silicon carbide constituents were interrogated utilizing a broad spectrum of diffracting planes that would be largely inaccessible to common laboratory XRD equipment. Residual room-temperature principal strains in the melt-infiltrated silicon phase were found to be approximately 1100 mu epsilon in compression, corresponding to stresses of approximately 300 MPa using simplifying constitutive assumptions. Residual room-temperature principal strains in silicon carbide particles found throughout the matrix were approximately 500 mu epsilon in tension, corresponding to approximately 300 MPa. Residual strains were found to decrease considerably as temperatures increased from ambient temperature to 1250 degrees C. Additionally, residual strains returned to approximately preheat treatment values after cool-down to ambient temperature. Strain measurements in the silicon phase were found to be significantly affected by dissolved boron dopant levels causing contraction of the silicon lattice. This contraction must be accounted for in high-temperature experiments for accurate calculation of stresses in the silicon phase.

36 MATERIALS SCIENCE↗

Evidence for phonon hardening in laser-excited gold using x-ray diffraction at a hard x-ray free electron laser

Studies of laser-heated materials on femtosecond timescales have shown that the interatomic potential can be perturbed at sufficiently high laser intensities. For gold, it has been postulated to undergo a strong stiffening leading to an increase of the phonon energies, known as phonon hardening. Despite efforts to investigate this behavior, only measurements at low absorbed energy density have been performed, for which the interpretation of the experimental data remains ambiguous. By using in situ single-shot x-ray diffraction at a hard x-ray free-electron laser, the evolution of diffraction line intensities of laser-excited Au to a higher energy density provides evidence for phonon hardening.

36 MATERIALS SCIENCE↗

Multiple origins of extra electron diffractions in fcc metals

Diffuse intensities in the electron diffraction patterns of concentrated face-centered cubic solid solutions have been widely attributed to chemical short-range order, although this connection has been recently questioned. This article explores the many nonordering origins of commonly reported features using a combination of experimental electron microscopy and multislice diffraction simulations, which suggest that diffuse intensities largely represent thermal and static displacement scattering. A number of observations may reflect additional contributions from planar defects, surface terminations incommensurate with bulk periodicity, or weaker dynamical effects.

36 MATERIALS SCIENCE↗

Visualizing the strong field–induced molecular breakup of C 60 via x-ray diffraction

Laser-driven dynamics in polyatomic molecules poses a complex many-body problem. Understanding intense light-matter interaction is crucial for steering intramolecular quantum dynamical processes. Here, we record time-resolved x-ray diffraction images of C 60 molecules during and after their interaction with intense near-infrared fields, giving direct access to structural changes of the molecules and their fragmentation in real time. Tuning the intensity of the excitation pulses, we uncover a transition from a weak-field regime of excited but stable molecules to a high-field regime dominated by Coulomb explosion. In the transition region, the molecules expand by up to 50% of their initial size within just 140 fs, with major fragmentation only setting in afterward. This work demonstrates that x-ray diffractive imaging is capable of retrieving time-resolved structural information of large molecules reshaped by intense laser fields. Laser-driven fragmentation is a first step toward observing molecular processes modified by laser fields of increasing intensity.

Schnorr, Kirsten [Paul Scherrer Inst. (PSI), Villi↗

Exploring the Limits of Bottom-Up Gold Filling to Fabricate Diffraction Gratings

Gold deposition on rotating disk electrodes, Bi 3+ adsorption on planar Au films and superconformal Au filling of trenches up to 45 μm deep are examined in Bi 3+ -containing Na 3 Au(SO 3 ) 2 electrolytes with pH between 9.5 and 11.5. Higher pH is found to increase the potential-dependent rate of Bi 3+ adsorption on planar Au surfaces, shortening the incubation period that precedes active Au deposition on planar surfaces and bottom-up filling in patterned features. Decreased contact angles between the Au seeded sidewalls and bottom-up growth front also suggest improved wetting. The bottom-up filling dynamic in trenches is, however, lost at pH 11.5. The impact of Au concentration, 80 mmol/L versus 160 mmol/L Na 3 Au(SO 3 ) 2 , on bottom-up filling is examined in trenches up to ≈ 210 μm deep with aspect ratio of depth/width ≈ 30. The microstructures of void-free, bottom-up filled trench arrays used as X-ray diffraction gratings are characterized by scanning electron microscopy (SEM) and Electron Backscatter Diffraction (EBSD), revealing marked spatial variation of the grain size and orientation within the filled features.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single-frame far-field diffractive imaging with randomized illumination

Contains a transmission ptychography dataset collected from a chrome on glass Siemens star under optical illumination. The probe is generated by a randomized zone plate under illumination from a spatially filtered green laser. A single diffraction pattern was removed from the dataset and reported in a separate cxi file. In addition, a single exposure collected after manually defocusing the probe is reported. The ptychography dataset is used for calibration of the probe function, and the remaining diffraction patterns can be reconstructed via randomized probe imaging.

Ptychography, Randomized Probe Imaging↗

Single-frame far-field diffractive imaging with randomized illumination

Contains two transmission ptychography datasets, one collected from a Siemens star, and the second from an Fe/Gd multilayer. Both samples are under illumination from the same randomized zone plate. Each dataset has a single diffraction pattern removed, and these patterns are reported in a separate cxi file. Either ptychography dataset can be used for calibration of the probe function, and the remaining diffraction patterns can be reconstructed via randomized probe imaging.

BESSY II↗

NEURAL NETWORK FOR COHERENT DIFFRACTION IMAGE INVERSION

A deep neural network model plus automatic differentiation is developed for retrieving phase information from 3D coherent diffraction images. The model is implemented using Tensorflow and the training dataset is generated using physics-based atomistic simulations. Custom codes are written to handle the resampling of diffraction images to oversampling ratios appropriate for the neural network model.

CHAN, HENRY↗

Thermal x-ray diffraction and near-field phase contrast imaging

Using higher-order coherence of thermal light sources, the resolution power of standard x-ray imaging techniques can be enhanced. Here in this work, we applied the higher-order measurement to far-field x-ray diffraction and near-field phase contrast imaging (PCI), in order to achieve superresolution in x-ray diffraction and obtain enhanced intensity contrast in PCI. The cost of implementing such schemes is minimal compared to the methods that achieve similar effects by using entangled x-ray photon pairs.

47 OTHER INSTRUMENTATION↗

High x-ray resolving power utilizing asymmetric diffraction from a quartz transmission crystal measured in the 6 keV to 22 keV energy range

We report a Cauchois-type spectrometer utilizing the (203) lattice planes at an oblique angle of 11.53° to the normal to the surface of a quartz transmission crystal recorded the Kα and Kβ spectral lines of six elements from Fe to Ag in the 6–22 keV energy range from a laboratory x-ray source. After deconvolving the natural lifetime widths and the image plate detector broadening from the observed spectral linewidths, the intrinsic crystal resolving power was determined to be 4000 at the lower energies and decreasing to 1000 at the higher energies. Previously, a Si wafer crystal exhibited twice this resolving power when the (331) planes had been used in asymmetric geometry. The investigation of diffraction with this quartz crystal, with a very similar lattice spacing and therefore spectral coverage, was motivated by the larger integrated reflectivity of quartz due to its well-known quasimosaicity upon elastic bending. The measured spectral linewidths were in good agreement with the widths calculated by accounting for various broadening mechanisms, including source size, crystal thickness, crystal height, crystal rocking curve width, geometrical aberrations, and possible spectrometer configuration errors. This is the first, to the best of our knowledge, demonstration of high resolving power achieved by asymmetric diffraction over a wide energy range (6–22 keV) and with detailed comparisons with theoretical broadenings. Finally, based on these results, Cauchois spectrometers employing asymmetric planes of perfect quartz and silicon crystals can be reliably designed and optimized for high-resolution spectroscopy in the >6 keV energy range.

36 MATERIALS SCIENCE↗

Single-frame far-field diffractive imaging with randomized illumination

We introduce a single-frame diffractive imaging method called randomized probe imaging (RPI). In RPI, a sample is illuminated by a structured probe field containing speckles smaller than the sample’s typical feature size. Quantitative amplitude and phase images are then reconstructed from the resulting far-field diffraction pattern. The experimental geometry of RPI is straightforward to implement, requires no near-field optics, and is applicable to extended samples. When the resulting data are analyzed with a complimentary algorithm, reliable reconstructions which are robust to missing data are achieved. To realize these benefits, a resolution limit associated with the numerical aperture of the probe-forming optics is imposed. RPI therefore offers an attractive modality for quantitative X-ray phase imaging when temporal resolution and reliability are critical but spatial resolution in the tens of nanometers is sufficient. We discuss the method, introduce a reconstruction algorithm, and present two proof-of-concept experiments: one using visible light, and one using soft X-rays.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

High accuracy single-layer free-space diffractive neuromorphic classifiers for spatially incoherent light

Free-space all-optical diffractive systems have shown promise for neuromorphic classification of objects without converting light to the electronic domain. While the factors that govern these systems have been studied for coherent light, the fundamental properties for incoherent light have not been addressed, despite the importance for many applications. Here we use a co-design approach to show that optimized systems for spatially incoherent light can achieve performance on par with the best linear electronic classifiers even with a single layer containing few diffractive features. This performance is limited by the inherent linear nature of incoherent optical detection. We circumvent this limit by using a differential detection scheme that achieves greater than 94% classification accuracy on the MNIST dataset and greater than 85% classification accuracy for Fashion-MNIST, using a single layer metamaterial.

Léonard, François (ORCID:0000000249736743)↗