Diffraction Intensity Data Research Articles

EDIC intensity correction of electron diffraction

Transmission electron microscopy (TEM) has recently become indispensable in determining crystal structures. The location of atoms in crystals can be determined using electron diffraction (ED) intensity data series if the diffracted intensities are directly proportional to the square of the structure factor (|Fhkl|2). However, due to the crystal thickness, the used electron wavelength and the potential misalignment of the measured crystal the detected intensities differ from the ideal values. A method, Electron Diffraction Intensity Correction (EDIC), and a computer program have been developed to recover the ideal |Fhkl|2 proportional intensities from experimental data for kinematic scattering, for further structure studies.

High-resolution and high-sensitivity X-ray ptychographic coherent diffraction imaging using the CITIUS detector.

Ptychographic coherent diffraction imaging (PCDI) is a synchrotron X-ray microscopy technique that provides high spatial resolution and a wide field of view. To improve the performance of PCDI, the performance of the synchrotron radiation source and imaging detector should be improved. In this study, ptychographic diffraction pattern measurements using the CITIUS high-speed X-ray image detector and the corresponding image reconstruction are reported. X-rays with an energy of 6.5 keV were focused by total reflection focusing mirrors, and a flux of ∼2.6 × 1010 photons s-1 was obtained at the sample plane. Diffraction intensity data were collected at up to ∼250 Mcounts s-1 pixel-1 without saturation of the detector. Measurements of tantalum test charts and silica particles and the reconstruction of phase images were performed. A resolution of ∼10 nm and a phase sensitivity of ∼0.01 rad were obtained. The CITIUS detector can be applied to the PCDI observation of various samples using low-emittance synchrotron radiation sources and to the stability evaluation of light sources.

Linking B-factor and temperature-induced conformational transition

The crystallographic B-factor, also called temperature factor or Debye-Waller factor, has long been used as a surrogate for local protein flexibility. However, the use of the absolute B-factor as a probe for protein motion requires reproducible validation against conformational changes against chemical and physical variables. Here we report the investigation of the thermal dependence of the crystallographic B-factor and its correlation with conformational changes of the protein. We obtained the crystal protein structure coordinates and B-factors at high resolution (1.5 Å) over a broad temperature range (100 K to 325 K). The exponential thermal dependence of B-factor as a function of temperature was equal for both the diffraction intensity data (Wilson B-factor) and for all modeled atoms of the system (protein and non-protein atoms), with a thermal diffusion constant of about 0.0045 K−1, similar for all atoms. The extrapolated B-factor at zero Kelvin (or zero-point fluctuation) varies among the atoms, although with no apparent correlation with temperature-dependent protein conformational changes. These data suggest that the thermal vibration of the atom does not necessarily correlate with the conformational dynamics of the protein.

Data-analysis software framework 2DMAT and its application to experimental measurements for two-dimensional material structures

An open-source data-analysis framework 2DMAT has been developed for experimental measurements of two-dimensional material structures. 2DMAT offers five analysis methods: (i) Nelder-Mead optimization, (ii) grid search, (iii) Bayesian optimization, (iv) replica exchange Monte Carlo method, and (v) population-annealing Monte Carlo method. Methods (ii) through (v) are implemented by parallel computation, which is efficient not only for personal computers but also for supercomputers. The current version of 2DMAT is applicable to total-reflection high-energy positron diffraction (TRHEPD), surface X-ray diffraction (SXRD), and low-energy electron diffraction (LEED) experiments by installing corresponding forward problem solvers that generate diffraction intensity data from a given dataset of the atomic positions. The analysis methods are general and can be applied also to other experiments and problems. Program summaryProgram Title: 2DMATCPC Library link to program files:https://doi.org/10.17632/c2t3vzbx9f.1Developer's repository link:https://www.pasums.issp.u-tokyo.ac.jp/2dmat/Code Ocean capsule:https://codeocean.com/capsule/7260490Licensing provisions: GNU General Public License v3.0Programming language: Python 3External routines/libraries: Numpy, Scipy, Tomli, mpy4pyNature of problem: Analysis of experimental measurement data.Solution method: Optimization, grid-based global search, Monte Carlo method.

What Kind of Measurements Can Be Made with an X-ray Free Electron Laser at SACLA?

Three-dimensional structural information is indispensable to understand the function of proteins in living organisms and X-ray crystallography plays a major role in determining the three-dimensional structure. X-ray free-electron laser (XFEL), which is intense and femtosecond X-ray pulses, enables us to obtain X-ray diffraction intensity data before the destruction of protein molecules, and is expected to be a technology to obtain dynamic structural information. This year marks the 10th anniversary of SPring-8 Angstrom Compact Free Electron Laser (SACLA), Japan's X-ray free electron laser facility. In this review, I describe the damage-free crystal structure analysis, de novo crystal structure determination using single wavelength anomalous dispersion by serial femtosecond crystallography (SFX), and time-resolved X-ray crystallography that have been performed at SACLA.

Convolution and deconvolutional treatment on sample transparency aberration in Bragg–Brentano geometry

Exact and approximate mathematical models for the effects of sample transparency on the powder diffraction intensity data are examined. Application of the formula based on the first-order approximation about the deviation angle is justified for realistic measurement and computing systems. The effects of sample transparency are expressed by double convolution formulas applying two different scale transforms, including three parameters, goniometer radius R, penetration depth μ−1, and thickness of the sample t. The deconvolutional treatment automatically recovers the lost intensity and corrects the peak shift and asymmetric deformation of peak profile caused by the sample transparency.

Sodium rare earth metal amides Na3 RE(NH2)6 (RE = La–Nd, Er, Yb) from ammonothermal synthesis

Abstract The amides Na3 RE(NH2)6 have been obtained from the metals in supercritical ammonia under ammonobasic conditions at 573 K and 70 MPa for RE = La–Nd, and at 473 K and 40 MPa for RE = Er, Yb. All compounds are formed in the hot zone within a temperature gradient, indicating a retrograde solubility under the applied process conditions. These amides represent soluble intermediates in ammonothermal binary rare earth metal nitride synthesis. All compounds were obtained as microcrystalline powders, while single crystals of those amides containing the heavier rare earth metals could be isolated. The crystal structures were solved and refined from single-crystal and powder X-ray diffraction intensity data. The results of vibrational spectroscopy are reported. Thermal analysis measurements under inert gas atmosphere demonstrated a decomposition to the respective black binary rare earth metal nitrides REN1−δ .

An Aggregation-Induced Emission Optical Highlighter for the Studies of Endoplasmic Reticulum-Lipid Droplet Content Dynamics

An Aggregation-Induced Emission Optical Highlighter for the Studies of Endoplasmic Reticulum-Lipid Droplet Content Dynamics

Likelihood-based estimation of substructure content from single-wavelength anomalous diffraction (SAD) intensity data.

SAD phasing can be challenging when the signal-to-noise ratio is low. In such cases, having an accurate estimate of the substructure content can determine whether or not the substructure of anomalous scatterer positions can successfully be determined. Here, a likelihood-based target function is proposed to accurately estimate the strength of the anomalous scattering contribution directly from the measured intensities, determining a complex correlation parameter relating the Bijvoet mates as a function of resolution. This gives a novel measure of the intrinsic anomalous signal. The SAD likelihood target function also accounts for correlated errors in the measurement of intensities from Bijvoet mates, which can arise from the effects of radiation damage. When the anomalous signal is assumed to come primarily from a substructure comprising one anomalous scatterer with a known value of f'' and when the protein composition of the crystal is estimated correctly, the refined complex correlation parameters can be interpreted in terms of the atomic content of the primary anomalous scatterer before the substructure is known. The maximum-likelihood estimation of substructure content was tested on a curated database of 357 SAD cases with useful anomalous signal. The prior estimates of substructure content are highly correlated to the content determined by phasing calculations, with a correlation coefficient (on a log-log basis) of 0.72.

Indium Ammoniates from Ammonothermal Synthesis: InAlF6(NH3)2, [In(NH3)6][AlF6], and [In2F(NH3)10]2[SiF6]5 ∙ 2 NH3

The ammonothermal synthesis of three ammoniates of indium, namely InAlF6(NH3)2, [In(NH3)6][AlF6], and [In2F(NH3)10]2[SiF6]5 ∙ 2 NH3 was successful from near-ammononeutral conditions in the presence of fluoride ions. Initially, all these compounds were obtained upon corrosion of the applied liner and crucible material Si3N4, which also contains small amounts of aluminum. The syntheses were performed in supercritical ammonia (T = 753 K, p up to 307 MPa). The crystal structures were solved and refined from single crystal X-ray diffraction intensity data. InAlF6(NH3)2 crystallizes as a typical layer-type structure with corner-sharing [InF4(NH3)2]– and [AlF6]3− octahedra. [In(NH3)6][AlF6] features isolated [In(NH3)6]3+ and [AlF6]3− octahedra. The crystal structure of [In2F(NH3)10]2[SiF6]5 ∙ 2 NH3 contains [(NH3)5In–F–In(NH3)5]5+ octahedra doubles next to [SiF6]2− octahedra and ammonia molecules. All intermediates have strong hydrogen bonding systems. The results from vibrational spectroscopy are reported.

Ammonothermal Synthesis and Characterization of First Amidozincate Hydroxides

AbstractThe first alkali metal amidozincate hydroxides Na3[Zn(NH2)4](OH) and Na3[Zn(NH2)3](OH)2were obtained from supercritical ammonia under ammonobasic conditions at 823 K and 250 MPa, and 623 K and 159 MPa, respectively. Crystal structures have been refined against single crystal X‐ray diffraction intensity data. Coordination environments of the cations as well as the rather open crystal structure and low density of Na3[Zn(NH2)4](OH) suggest the initial formation of a monoammoniate, prior loss of ammonia during depressurizing and recovery of the product. While Na3[Zn(NH2)4](OH) contains mutually isolated amidozincate ions next to hydroxide ions, Na3[Zn(NH2)3](OH)2is the first amidozincate realizing a condensation of the complex anionic substructure so far. Both compounds are regarded possible intermediates in an ammonothermal zinc nitride synthesis and give insights into the action of impurities during ammonothermal processes. Raman spectroscopic measurements support the assignment of amide and hydroxide groups.

Twisted Intramolecular Charge Transfer—Aggregation-Induced Emission Fluorogen with Polymer Encapsulation-Enhanced Near-Infrared Emission for Bioimaging

Fluorescence probes with strong near-infrared (NIR) emission and water solubility are considered useful visualization tools for localization marking as well as investigating cell migration and tran...

Trial Direct Phasing Calculation of A Thyroid Hormone Receptor Alpha Structure (4LNW)

A thyroid receptor alpha structure (PDB ID: 4LNW) was studied for ab initio phasing. With the diffraction intensity data, protein sequence, and ligand structure as the only input, a high-resolution structure was successfully reconstructed by using an iterative projective method based on the hybrid input–output (HIO) algorithm.

Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27

The IBARAKI biological crystal diffractometer (iBIX) was used in single-crystal time-of-flight neutron diffraction experiments on manganese catalase from Thermus thermophilus. The unit-cell dimensions were 133 × 133 × 133 Å, which is close to the designed maximum limitation of iBIX (135 × 135 × 135 Å). The optimum integration box sizes were set and the degree of integration box overlap was calculated for each Laue spot. Using the overlap ratio as the criterion, the selection of the diffraction intensity data was performed to give a minimum R p.i.m.. Subsequently, diffraction intensity data from Laue spots with overlap ratios ≤0.1 were selected and a complete reflection data set with d min = 2.35 Å was obtained. Joint X-ray and neutron structure refinements were also successfully performed. It was difficult to determine the structures and protonation states of all the oxygen atoms in the manganese cluster owing to the disordered structure. No hydrogen atom was observed on the ordered μ-bridging oxygen atom O1003. Instead, this oxygen atom probably forms a hydrogen bond with Thr39. In addition, the refinements clearly showed the protonation states of the amino acid residues and hydrogen bonds, as observed in Tyr192, Glu167 and Glu280. This first neutron crystal structure of manganese catalase shows that iBIX can provide acceptable diffraction data for neutron single-crystal analyses of at least 2.4 Å resolution within the original targeted unit-cell dimensions of 135 × 135 × 135 Å.

Strontium-modification in the stepwise solidification of A319 Al alloy: An in-situ neutron diffraction study

The modification of cast Al-Si alloys with trace Sr is common practice for the improvement of material properties. In addition to the typical morphological transformation of the eutectic Si particles, research has shown that Sr can significantly influence the evolution of multiple other phases that are observed in complex industrial Al alloys. In this study, the solidification sequence and characteristics of unmodified and Sr-modified A319 Al alloy was investigated using in-situ neutron diffraction to obtain a novel perspective of the mechanism of its phase transformations. Neutron diffraction intensity data was collected during stepwise alloy solidification from 630 to 200 °C. This enabled the production of fraction solid curves, isolated for the individual Al, Si, Al15(Fe,Mn)3Si2, Al5Mg8Cu2Si6, and Al2Cu phases in the alloy, which corresponded well with the curves simulated using FactSage™ software. The solidification analysis was complimented with optical and scanning electron microscopy, which revealed the production of a unique and fascinating microstructure in the Sr-modified alloy. As a result of the combined action of Sr-induced undercooling and long holding times during stepwise cooling, the Al15(Fe,Mn)3Si2 phase was completely and significantly transformed into numerous, fine, uniformly-dispersed polyhedrons. The unmodified, acicular growth of the Si particles was then enabled, by using the polyhedral phase as substrates for nucleation. Hence, no undercooling of the Al-Si eutectic reaction was observed for the Sr-modified alloy.

Topology of electron density and electrostatic potential of HIV reverse transcriptase inhibitor zidovudine from high resolution X-ray diffraction and charge density analysis

Azidothymidine (AZT) is a first anti-HIV drug namely Zidovudine used for HIV treatment, which binds to the viral DNA primer and inhibits the HIV reverse transcription. The side effects of this powerful drug are severe and the detailed understanding of its electronic structure helps to design new drugs from the AZT molecule. Present study aims to determine the structure of AZT at electronic level from the experimental charge density analysis as well as the solid state DFT calculations. AZT was crystallized and low temperature high resolution X-ray diffraction intensity data has been measured up to sin (θ/λ)max = 1.1 Å−1 at 100.0 (2) K. The crystal structure of AZT was determined, which reveals the information that the AZT compound crystallizes with two molecules in the asymmetric unit which are conformationally different and linked through strong hydrogen bonding interactions (dimer). The Hirshfeld surface of both molecules shows the locations of weak and strong interactions. Further, a multipole model refinement was carried out using Hansen-Coppens multipole formalism. The experimental topological properties of electron density of AZT molecules were determined and compared with the results of theoretical DFT calculations based on solid state and gas phase studies. The charge density distribution of the two molecules in the asymmetric unit is unequal and shows some difference. The topological properties of O–H⋅⋅⋅O, O–H⋅⋅⋅N, C–H⋅⋅⋅N, H⋅⋅⋅H and azide⋅⋅⋅azide group interactions are also determined. The electrostatic potential (ESP) surface of both AZT molecules in the crystal exhibits high electronegative regions around the O, N atoms and also around the azide group, however, ESP regions of molecules (I) and (II) are not similar.

Crystalline-Phase Solidification Analysis Using In Situ Neutron Diffraction

In situ neutron diffraction was utilized to examine the solidification behavior of aluminum and magnesium alloys for further understanding of solidification, hot tearing, and grain refinement. The experiments consisted of melting samples and allowing them to cool while being irradiated by neutrons. During solidification, solid phases enabled diffraction of neutrons. The diffraction profiles were collected at each temperature step and were used to interpret the growth of individual planes and phases. In situ neutron diffraction enabled determination of fraction solid curves for individual planes and phases, which was not possible with traditional thermal analysis and computational techniques. This paper outlines the method of generation of fraction solid curves from neutron diffraction intensity data, including a technique to account for the effects of the Debye–Waller factor. This method was successful in revealing detailed insights into crystalline solidification. It showed promise in quantifying many other phenomena beyond those discussed.

PDFgetN3: atomic pair distribution functions from neutron powder diffraction data using ad hoc corrections

PDFgetN3, a new software tool for the extraction of pair distribution functions (PDFs) from neutron powder diffraction intensity data, is described. Its use is demonstrated with constant-wavelength neutron data measured at the new powder diffractometer PEARL at the Delft University of Technology. PDFgetN3 uses an ad hoc data collection protocol similar to PDFgetX3. The quality of the resulting PDFs is assessed by structure refinement and by comparison with established results from synchrotron X-ray scattering.

Deconvolution–convolution treatment on powder diffraction data collected with CuKα X-ray and NiKβ filter

A method to remove small CuKβ peaks and step structures caused by NiK-edge absorption as well as CuKα2 sub-peaks from powder diffraction intensity data measured with Cu-target X-ray source and Ni-foil filter is proposed. The method is based on deconvolution–convolution treatment applying scale transform of abscissa, Fourier transform, and a realistic spectroscopic model for the source X-ray. The validity of the method has been tested by analysis of the powder diffraction data of a standard LaB6 powder (NIST SRM660a) sample, collected with the combination of CuKα X-ray source, Ni-foil Kβ filter, flat powder specimen and one-dimensional Si strip detector. The diffraction intensity data treated with the method have certainly shown background intensity profile without CuKβ peaks and NiK-edge step structures.

Analysis of eutectic silicon modification during solidification of Al-6Si using in-situ neutron diffraction

Aluminum-silicon alloys contain coarse, acicular Si plates that are detrimental to material properties. However, trace additions of Sr have been found to modify the eutectic Si to have a fine, fibrous structure, which improves elongation, strength, and thermal conductivity. In this study, in-situ neutron diffraction was conducted during the solidification of unmodified and Sr-modified binary Al-6 wt.% Si to obtain a novel view of the modification mechanism. Neutron diffraction intensity data was collected at temperatures ranging from 660 °C to 200 °C and was integrated to create fraction solid curves for the individual Al and Si phases in each alloy. Scanning electron microscopy revealed that the Sr-modified alloy microstructure contained many micro-sized Al-Si-Sr intermetallics scattered about the eutectic regions at the Al-Si interfaces, and a few Si flakes close to some β-(Al,Si,Fe) intermetallics, suggesting important interactions between both the Fe-bearing phases and Sr in the solidification of eutectic Si. Comparing the isolated phase evolution temperatures for each alloy revealed in-situ for the first time that Sr suppresses the nucleation temperatures of both the eutectic Al and eutectic Si phases by several degrees. Accordingly, the eutectic reaction was observed to evolve at a higher primary Al solid fraction with Sr modification.