Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality
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59 BASIC BIOLOGICAL SCIENCES↗
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Instrument-model refinement in normalized reciprocal-vector space for X-ray Laue diffraction
Abstract not provided
Kami↗
The AUREX cell: a versatile operando electrochemical cell for studying catalytic materials using X-ray diffraction, total scattering and X-ray absorption spectroscopy under working conditions
Understanding the structure–property relationship in electrocatalysts under working conditions is crucial for the rational design of novel and improved catalytic materials. This paper presents the Aarhus University reactor for electrochemical studies using X-rays (AUREX) operando electrocatalytic flow cell, designed as an easy-to-use versatile setup with a minimal background contribution and a uniform flow field to limit concentration polarization and handle gas formation. The cell has been employed to measure operando total scattering, diffraction and absorption spectroscopy as well as simultaneous combinations thereof on a commercial silver electrocatalyst for proof of concept. This combination of operando techniques allows for monitoring of the short-, medium- and long-range structure under working conditions, including an applied potential, liquid electrolyte and local reaction environment. The structural transformations of the Ag electrocatalyst are monitored with non-negative matrix factorization, linear combination analysis, the Pearson correlation coefficient matrix, and refinements in both real and reciprocal space. Upon application of an oxidative potential in an Ar-saturated aqueous 0.1 M KHCO 3 /K 2 CO 3 electrolyte, the face-centered cubic (f.c.c.) Ag gradually transforms first to a trigonal Ag 2 CO 3 phase, followed by the formation of a monoclinic Ag 2 CO 3 phase. A reducing potential immediately reverts the structure to the Ag (f.c.c.) phase. Following the electrochemical-reaction-induced phase transitions is of fundamental interest and necessary for understanding and improving the stability of electrocatalysts, and the operando cell proves a versatile setup for probing this. In addition, it is demonstrated that, when studying electrochemical reactions, a high energy or short exposure time is needed to circumvent beam-induced effects.
Frank, Sara (ORCID:0000000163218363)↗
Illustrated formalisms for total scattering data: a guide for new practitioners
The total scattering method is the simultaneous study of both the real- and reciprocal-space representations of diffraction data. While conventional Bragg-scattering analysis (employing methods such as Rietveld refinement) provides insight into the average structure of the material, pair distribution function (PDF) analysis allows for a more focused study of the local atomic arrangement of a material. Generically speaking, a PDF is generated by Fourier transforming the total measured reciprocal-space diffraction data (Bragg and diffuse) into a real-space representation. However, the details of the transformation employed and, by consequence, the resultant appearance and weighting of the real-space representation of the system can vary between different research communities. As the worldwide total scattering community continues to grow, these subtle differences in nomenclature and data representation have led to conflicting and confusing descriptions of how the PDF is defined and calculated. This paper provides a consistent derivation of many of these different forms of the PDF and the transformations required to bridge between them. Some general considerations and advice for total scattering practitioners in selecting and defining the appropriate choice of PDF in their own research are presented. This contribution aims to benefit people starting in the field or trying to compare their results with those of other researchers.
36 MATERIALS SCIENCE↗
rmc-discord : reverse Monte Carlo refinement of diffuse scattering and correlated disorder from single crystals
A user-friendly program has been developed to analyze diffuse scattering from single crystals with the reverse Monte Carlo method. The approach allows for refinement of correlated disorder from atomistic supercells with magnetic or structural (occupational and/or displacive) disorder. The program is written in Python and optimized for performance and efficiency. Refinements of two user cases obtained with legacy neutron-scattering data demonstrate the effectiveness of the approach and the developed program. It is shown with bixbyite, a naturally occurring magnetic mineral, that the calculated three-dimensional spin-pair correlations are resolved with finer real-space resolution compared with the pair distribution function calculated directly from the reciprocal-space pattern. With the triangular lattice Ba 3 Co 2 O 6 (CO 3 ) 0.7 , refinements of occupational and displacive disorder are combined to extract the one-dimensional intra-chain correlations of carbonate molecules that move toward neighboring vacant sites to accommodate strain induced by electrostatic interactions. The program is packaged with a graphical user interface and extensible to serve the needs of single-crystal diffractometer instruments that collect diffuse-scattering data.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Nanoscale structural correlations in a model cuprate superconductor
Understanding the extent and role of inhomogeneity is a pivotal challenge in the physics of cuprate superconductors. While it is known that structural and electronic inhomogeneity is prevalent in the cuprates, it has proven difficult to disentangle compound-specific features from universally relevant effects. Here, in this study, we combine advanced neutron and x-ray diffuse scattering with numerical modeling to obtain insight into bulk structural correlations in HgBa 2 CuO 4+δ . This cuprate exhibits a high optimal transition temperature of nearly 100 K, pristine charge-transport behavior, and a simple average crystal structure without long-range structural instabilities, and is therefore uniquely suited for investigations of intrinsic inhomogeneity. We uncover diffuse reciprocal-space patterns that correspond to prominent nanoscale correlations of atomic displacements perpendicular to the CuO 2 planes. The real-space nature of the correlations is revealed through three-dimensional pair distribution function analysis and complementary numerical refinement. We find that relative displacements of ionic and CuO 2 layers play a crucial role, and that the structural inhomogeneity is not directly caused by the presence of conventional point defects. The observed correlations are therefore intrinsic to HgBa 2 CuO 4+δ , and thus likely important for the physics of cuprates more broadly. It is possible that the structural correlations are closely related to the unusual superconducting fluctuations and Mott-localization in these complex oxides. As advances in scattering techniques yield increasingly comprehensive data, the experimental and analysis tools developed here for large volumes of diffuse scattering data can be expected to aid future investigations of a wide range of materials.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Data-driven discovery of dynamics from time-resolved coherent scattering
Coherent X-ray scattering (CXS) techniques are capable of interrogating dynamics of nano- to mesoscale materials systems at time scales spanning several orders of magnitude. However, obtaining accurate theoretical descriptions of complex dynamics is often limited by one or more factors—the ability to visualize dynamics in real space, computational cost of high-fidelity simulations, and effectiveness of approximate or phenomenological models. In this work, we develop a data-driven framework to uncover mechanistic models of dynamics directly from time-resolved CXS measurements without solving the phase reconstruction problem for the entire time series of diffraction patterns. Our approach uses neural differential equations to parameterize unknown real-space dynamics and implements a computational scattering forward model to relate real-space predictions to reciprocal-space observations. This method is shown to recover the dynamics of several computational model systems under various simulated conditions of measurement resolution and noise. Moreover, the trained model enables estimation of long-term dynamics well beyond the maximum observation time, which can be used to inform and refine experimental parameters in practice. Finally, we demonstrate an experimental proof-of-concept by applying our framework to recover the probe trajectory from a ptychographic scan. Our proposed framework bridges the wide existing gap between approximate models and complex data.
36 MATERIALS SCIENCE↗
In situ high-temperature X-ray diffraction study of Sc-doped titanium oxide nanocrystallites
Titanium dioxide is an inexpensive wide-gap highly ionic semiconductor with striking photocatalytic capabilities in several heterogeneous photoredox reactions. A small crystal size is desirable to maximize the surface area, since photocatalytic reactions occur at the surface of a photocatalyst. Presented in this work are the synthesis and microstructural characterization of 4 at.% Sc-doped TiO 2 (4SDT) prepared by water-based co-precipitation. The crystal structure of 4SDT was examined via in situ high-temperature powder X-ray diffraction experiments from 25 to 1200°C. Rietveld analysis revealed single-phase anatase up to 875°C, while at 900°C the anatase-to-rutile phase transformation occurred and at higher temperatures additional reflections of Sc-rich phases (Sc 2 TiO 5 from 975°C and Ti 3 Sc 4 O 12 or Sc 2 O 3 at 1200°C) were observed. Debye function analysis (DFA) was applied to model the total scattering pattern directly in reciprocal space, allowing the reconstruction of Ti vacancies. Both Rietveld and DFA methods were applied to estimate the nanocrystallite size and shape with consistent growth in crystallite size with temperature: an ellipsoid shape with equatorial ~4.7 nm / axial (001) ~6.9 nm at 25°C to equatorial ~27.9 nm / axial (001) ~39.6 nm at 900°C refined by Rietveld analysis, versus a cylinder shape with D a , b = 4.3 nm and size dispersion σ ab = 1.5 nm, L c = 4.9 nm and σ c = 2.3 nm at 25°C to D a , b = 21.4 nm, σ ab = 8.3 nm, L c = 23.9 and σ c = 10.9 nm at 900°C estimated by DFA. The microstructural changes obtained by Rietveld and DFA methods were supported by high-resolution transmission electron microscopy image analysis, as well as by the less direct nitrogen sorption techniques that provide information on the size of non-agglomerated and dense particles. The Ti site-occupancy factor showed a linear increase from 0.6–0.8 at 25°C to unity at 900°C for anatase, and from ~0.7 at 900°C to unity at 1200°C for rutile, via Rietveld analysis and DFA.
36 MATERIALS SCIENCE↗
Atomic structures determined from digitally defined nanocrystalline regions
Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based ab initio solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography.
36 MATERIALS SCIENCE↗
AUTOIGNITION DELAY TIMES FOR REFORMATE GAS MIXTURES FROM METHANE GAS ENGINES
Methane slip is a prominent issue in natural gas reciprocating engines that are used in transportation and marine applications. The incomplete combustion that results in methane slip can be resolved with the introduction of hydrogen within the combustion mixture to improve methane oxidation and further enable combustion within the engine crevices where methane has previously remained unreacted. Steam methane reforming (SMR) is a common method used to produce hydrogen and can be used to design an onboard device to reduce methane slip from reciprocating engines. The development of this reformer device requires the validation of high-fidelity chemical kinetic models at the low temperatures of the crevice volumes of these engines. In this work, auto-ignition data is obtained using a shock tube at lean (φ—0.714 or λ—1.4) and stoichiometric (φ, λ = 1) equivalence ratios spanning a temperature range of 1042–1234 K at the 80-bar operating pressure of the test engine. Blends of methane, hydrogen, and reformate products from the SMR reaction are shock-heated in synthetic air, with the ignition delay time measured using an OH* chemiluminescence detector at 310 nm and a CH* detector at 430 nm. The experimental results are compared to several state-of-the-art chemical kinetic mechanisms from the literature. In general, most of the mechanisms show very good agreement with experiments at higher temperatures, with simulation results showing little deviation from experiments at lower temperatures. A sensitivity analysis was conducted, and the results reveal that the reaction H2 + CH3O2 = H + CH3O2H has a very significant role in determining low-temperature ignition delay times (IDTs) of SMR mixtures. These findings provide valuable insights into the chemical kinetics governing methane reformate combustion and contribute to the optimization of onboard reformer designs aimed at mitigating methane slip in natural gas-fueled engines.
Fraze, Matthew↗