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Results for “rotation crystallography”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Ligand‐Mediated Quantum Yield Enhancement in 1‐D Silver Organothiolate Metal–Organic Chalcogenolates

X-ray free electron laser (XFEL) microcrystallography and synchrotron single-crystal crystallography are used to evaluate the role of organic substituent position on the optoelectronic properties of metal–organic chalcogenolates (MOChas). MOChas are crystalline 1D and 2D semiconducting hybrid materials that have varying optoelectronic properties depending on composition, topology, and structure. While MOChas have attracted much interest, small crystal sizes impede routine crystal structure determination. A series of constitutional isomers where the aryl thiol is functionalized by either methoxy or methyl ester are solved by small molecule serial femtosecond X-ray crystallography (smSFX) and single crystal rotational crystallography. While all the methoxy examples have a low quantum yield (0-1%), the methyl ester in the ortho position yields a high quantum yield of 22%. Here, the proximity of the oxygen atoms to the silver inorganic core correlates to a considerable enhancement of quantum yield. Four crystal structures are solved at a resolution range of 0.8–1.0 Å revealing a collapse of the 2D topology for functional groups in the 2- and 3- positions, resulting in needle-like crystals. Further analysis using density functional theory (DFT) and many-body perturbation theory (MBPT) enables the exploration of complex excitonic phenomena within easily prepared material systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Deep residual networks for crystallography trained on synthetic data

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive

Serial crystallography at conventional synchrotron light sources (SSX) offers the possibility to routinely collect data at room temperature using micrometre-sized crystals of biological macromolecules. However, SSX data collection is not yet as routine and currently takes significantly longer than the standard rotation series cryo-crystallography. Thus, its use for high-throughput approaches, such as fragment-based drug screening, where the possibility to measure at physiological temperatures would be a great benefit, is impaired. On the way to highthroughput SSX using a conveyor belt based sample delivery system – the CFEL TapeDrive – with three different proteins of biological relevance (Klebsiella pneumoniae CTX-M-14 β-lactamase, Nectria haematococca xylanase GH11 and Aspergillus flavus urate oxidase), it is shown here that complete datasets can be collected in less than a minute and only minimal amounts of sample are required.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Resolving the Chemical Formula of Nesquehonite via NMR Crystallography, DFT Computation, and Complementary Neutron Diffraction

Nesquehonite is a magnesium carbonate mineral relevant to carbon sequestration envisioned for carbon capture and storage of CO 2 . Its chemical formula remains controversial today, assigned as either a hydrated magnesium carbonate [MgCO 3 · 3H 2 O], or a hydroxy- hydrated- magnesium bicarbonate [Mg(HCO 3 )OH · 2H 2 O]. Here, the resolution of this controversy is central to understanding this material‘s thermodynamic, phase, and chemical behavior. In an NMR crystallography study, using rotational-echo double-resonance 13 C{ 1 H} (REDOR), 13 C- 1 H distances are determined with precision, and the combination of 13 C static NMR lineshapes and density functional theory (DFT) calculations are used to model different H atomic coordinates. [MgCO 3 · 3H 2 O] is found to be accurate, and evidence from neutron powder diffraction bolsters these assignments. Refined H positions can help understand how H-bonding stabilizes this structure against dehydration to MgCO 3 . More broadly, these results illustrate the power of NMR crystallography as a technique for resolving questions where X-ray diffraction is inconclusive.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Likelihood-based docking of models into cryo-EM maps

Optimized docking of models into cryo-EM maps requires exploiting an understanding of the signal expected in the data to minimize the calculation time while maintaining sufficient signal. The likelihood-based rotation function used in crystallography can be employed to establish plausible orientations in a docking search. A phased likelihood translation function yields scores for the placement and rigid-body refinement of oriented models. Optimized strategies for choices of the resolution of data from the cryo-EM maps to use in the calculations and the size of search volumes are based on expected log-likelihood-gain scores computed in advance of the search calculation. Tests demonstrate that the new procedure is fast, robust and effective at placing models into even challenging cryo-EM maps.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2005

Microfocus/Polycapillary-Optic Crystallographic X-Ray System

A system that generates an intense, nearly collimated, nearly monochromatic, small-diameter x-ray beam has been developed for use in macromolecular crystallography. A conventional x-ray system for macromolecular crystallography includes a rotating-anode x-ray source, which is massive (.500 kg), large (approximately 2 by 2 by 1 m), and power-hungry (between 2 and 18 kW). In contrast, the present system generates a beam of the required brightness from a microfocus source, which is small and light enough to be mounted on a laboratory bench, and operates at a power level of only tens of watts. The figure schematically depicts the system as configured for observing x-ray diffraction from a macromolecular crystal. In addition to the microfocus x-ray source, the system includes a polycapillary optic . a monolithic block (typically a bundle of fused glass tubes) that contains thousands of straight or gently curved capillary channels, along which x-rays propagate with multiple reflections. This particular polycapillary optic is configured to act as a collimator; the x-ray beam that emerges from its output face consists of quasi-parallel subbeams with a small angular divergence and a diameter comparable to the size of a crystal to be studied. The gap between the microfocus x-ray source and the input face of the polycapillary optic is chosen consistently with the focal length of the polycapillary optic and the need to maximize the solid angle subtended by the optic in order to maximize the collimated x-ray flux. The spectrum from the source contains a significant component of Cu K (photon energy is 8.08 keV) radiation. The beam is monochromatized (for Cu K ) by a nickel filter 10 m thick. In a test, this system was operated at a power of 40 W (current of 897 A at an accelerating potential of 45 kV), with an anode x-ray spot size of 41+/-2 microns. Also tested, in order to provide a standard for comparison, was a commercial rotating-anode x-ray crystallographic system with a pyrolytic graphite monochromator and a 250-micron pinhole collimator, operating at a power of 3.15 kW (current of 70 mA at an accelerating potential of 45 kV). The flux of collimated Cu K radiation in this system was found to be approximately 16 times that in the rotatinganode system. Data on x-ray diffraction from crystals of tetragonal form of lysozyme (protein) in this system were found to be of high quality and to be reducible by use of standard crystallographic software.

Joy, Marshall↗
NASA NTRS1999

First Results from a Microfocus X-Ray System for Macromolecular Crystallography

The design and performance of a 40 Watt laboratory crystallography system optimized for the structure determination of small protein crystals are described. This system combines a microfocus x-ray generator (40 microns FWHM spot size at a power level of 40 Watts) and a short focal length (F = 2.6 mm) polycapillary collimating optic, and produces a small diameter quasi-parallel x-ray beam. Measurements of x-ray flux, divergence and spectral purity of the resulting x-ray beam are presented. The x-ray flux in a 250 microns diameter aperture produced by the microfocus system is 14.7 times higher .than that from a 3.15 kW rotating anode generator equipped with graphite monochromator. Crystallography data taken with the microfocus system are presented, and indicate that the divergence and spectral purity of the x-ray are sufficient to refine the diffraction data using a standard crystallographic software. Significant additional improvements in flux and beam divergence are possible, and plans for achieving these coals are discussed.

Gubarev, Mikhail↗
DOE OSTI2025

Dislocation‐Driven Formation of Oriented Macroperiodic Metastructures of Curved Single Crystal Lattices in Glass

Abstract Single crystals fabricated in glass by localized heating can develop uniquely deformed lattices stabilized by the surrounding amorphous medium. The development of lattice curvature appears to be intrinsic to the crystal growth process in some systems, while the result of the locally changing crystallography in others. In this work, a model laser‐fabricated rotating lattice Sb 2 S 3 crystal grown in stoichiometric glass is used to demonstrate fabrication of novel macroperiodic metastructures that utilize intrinsic lattice curvature superimposed with subtle crystallographic influences. The limited availability of slip systems drives the lattice curvature magnitude to vary with crystal growth direction, maximizing for lattices aligned with the predominant Burgers vector along with corresponding increases in dislocation density. Misaligned lattice orientations form smaller secondary lattice curvatures arising from misaligned Burgers vectors with further elastic contributions. Over extended crystal growth, these secondary components align the lattice to rotate about either the <001> or <010> crystal axes forming repeating metastructures of lattice orientation with periodicity 20–160 microns in length. The mechanistic approach used in this work may be expanded to other systems with known slip systems to better understand and design macroperiodic metastructures.

36 MATERIALS SCIENCE↗
NASA NTRS2000

Characterization of X-Ray Diffraction System with a Microfocus X-Ray Source and a Polycapillary Optic

We present here an optimized microfocus x-ray source and polycapillary optic system designed for diffraction of small protein crystals. The x-ray beam is formed by a 5.5mm focal length capillary collimator coupled with a 40 micron x-ray source operating at 46Watts. Measurements of the x-ray flux, the divergence and the spectral characteristics of the beam are presented, This optimized system provides a seven fold greater flux than our recently reported configuration [M. Gubarev, et al., J. of Applied Crystallography (2000) 33, in press]. We now make a comparison with a 5kWatts rotating anode generator (Rigaku) coupled with confocal multilayer focusing mirrors (Osmic, CMF12- 38Cu6). The microfocus x-ray source and polycapillary collimator system delivers 60% of the x-ray flux from the rotating anode system. Additional ways to improve our microfocus x-ray system, and thus increase the x-ray flux will be discussed.

Gubarev, Mikhail↗
DOE OSTI2022

Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations

The mechanism of rotatory catalysis in ATPhydrolyzing molecular motors remains an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multistep rotation process. Here, using vacuolar or V 1 -type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using Xray crystallography, a new intermediate or “dwell” is identified, which enables the release of an inorganic phosphate (or P i ) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transformations and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the side-chain-level interactions transcend into larger-scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. An inspection of all known rates encompassing the 4-step rotation mechanism implicates the overcoming of the ADP interactions with V 1 -ATPase to be the rate-limiting step of motor action.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Plug-and-play polymer microfluidic chips for hydrated, room temperature, fixed-target serial crystallography

The practice of serial X-ray crystallography (SX) depends on efficient, continuous delivery of hydrated protein crystals while minimizing background scattering. Of the two major types of sample delivery devices, fixed-target devices offer several advantages over widely adopted jet injectors, including: lower sample consumption, clog-free delivery, and the ability to control on-chip crystal density to improve hit rates. In this study we present our development of versatile, inexpensive, and robust polymer microfluidic chips for routine and reliable room temperature serial measurements at both synchrotrons and X-ray free electron lasers (XFELs). Our design includes highly X-ray-transparent enclosing thin film layers tuned to minimize scatter background, adaptable sample flow layers tuned to match crystal size, and a large sample area compatible with both raster scanning and rotation based serial data collection. The optically transparent chips can be used both for in situ protein crystallization (to eliminate crystal handling) or crystal slurry loading, with prepared samples stable for weeks in a humidified environment and for several hours in ambient conditions. Serial oscillation crystallography, using a multi-crystal rotational data collection approach, at a microfocus synchrotron beamline (SSRL, beamline 12-1) was used to benchmark the performance of the chips. Furthermore, high-resolution structures (1.3–2.7 Å) were collected from five different proteins – hen egg white lysozyme, thaumatin, bovine liver catalase, concanavalin-A (type VI), and SARS-CoV-2 nonstructural protein NSP5. Overall, our modular fabrication approach enables precise control over the cross-section of materials in the X-ray beam path and facilitates chip adaption to different sample and beamline requirements for user-friendly, straightforward diffraction measurements at room temperature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Elucidating metal–organic framework structures using synchrotron serial crystallography

Metal organic frameworks (MOFs) are porous crystalline materials that display a wide variety of physical and chemical properties. Their single crystal structure determination is often challenging because in most cases micro- or nano-sized crystals spontaneously form upon MOF synthesis, which cannot be recrystallized. The production of larger single crystals for structure determination involves optimizing, and thus modifying, the conditions of synthesis, in which success cannot be guaranteed. Failure to produce crystals suitable for single-crystal X-ray diffraction leaves the 3D structure of the MOF compound unknown, and scientists must resort to more challenging structure solution methods based on X-ray powder or electron diffraction data. These laborious tasks can be avoided by using serial crystallography techniques which merge data collected on many micro-crystals. Here, we report the application of three synchrotron serial crystallography methods. We call these “mesh”, “grid” and “mesh&collect” scans. “Still” images (no rotation) are collected in the mesh scan approach, whereas small rotational wedges are collected in the grid scan method. The third protocol, mesh&collect, combines the acquisition of still images and rotational wedges. Using these means, we determine the ab initio structure of benchmark MOFs, MIL-100(Fe) and ZIF-8, that differ largely in unit cell size. These methods are expected to be widely applicable and facilitate structure determination of many MOF microcrystalline systems.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Approach and rotation of reconnecting topological defect lines in liquid crystal

Topological defects are a universal concept across many disciplines, such as crystallography, liquid-crystalline physics, low-temperature physics, cosmology, and even biology. In nematic liquid crystals, topological defects called disclinations have been widely studied. For their three-dimensional (3D) dynamics, however, only recently have theoretical approaches dealing with fully 3D configurations been reported. Further, recent experiments have observed 3D disclination line reconnections, a phenomenon characteristic of defect line dynamics, but detailed discussions were limited to the case of approximately parallel defects. In this paper, we focus on the case of two disclination lines that approach at finite angles and lie in separate planes, a more fundamentally 3D reconnection configuration. Observing and analyzing such reconnection events, we find the square-root law of the distance between disclinations and the decrease of the interdisclination angle over time. We compare the experimental results with theory and find qualitative agreement on the scaling of distance and angle with time, but quantitative disagreement on distance and angle relative mobilities. To probe this disagreement, we derive the equations of motion for systems with reduced twist constant and also carry out simulations for this case. These, together with the experimental results, suggest that deformations of disclinations may be responsible for the disagreement. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗
DOE OSTI2024

Approach and rotation of reconnecting topological defect lines in liquid crystal

Topological defects are a universal concept across many disciplines, such as crystallography, liquid-crystalline physics, low-temperature physics, cosmology, and even biology. In nematic liquid crystals, topological defects called disclinations have been widely studied. For their three-dimensional (3D) dynamics, however, only recently have theoretical approaches dealing with fully 3D configurations been reported. Further, recent experiments have observed 3D disclination line reconnections, a phenomenon characteristic of defect line dynamics, but detailed discussions were limited to the case of approximately parallel defects. In this paper, we focus on the case of two disclination lines that approach at finite angles and lie in separate planes, a more fundamentally 3D reconnection configuration. Observing and analyzing such reconnection events, we find the square-root law of the distance between disclinations and the decrease of the interdisclination angle over time. We compare the experimental results with theory and find qualitative agreement on the scaling of distance and angle with time, but quantitative disagreement on distance and angle relative mobilities. To probe this disagreement, we derive the equations of motion for systems with reduced twist constant and also carry out simulations for this case. These, together with the experimental results, suggest that deformations of disclinations may be responsible for the disagreement.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Crystal structures and rotational dynamics of a two-dimensional metal halide perovskite (OA) 2 PbI 4

The extended charge carrier lifetime in metal halide perovskites is responsible for their excellent optoelectronic properties. Recent studies indicate that the superb device performance in these materials is intimately related to the organic cation dynamics. Here, we focus on the investigation of the two-dimensional hybrid perovskite, (C 8 H 17 NH 3 ) 2 PbI 4 (henceforth, OA + = C 8 H 17 NH 3 + ). Using elastic and quasielastic neutron scattering techniques and group theoretical analysis, we studied the structural phase transitions and rotational modes of the C 8 H 17 NH 3 + cation in (OA) 2 PbI 4 . Here, our results show that, in the high-temperature orthorhombic ( T > 310 K) phase, the OA + cation exhibits a combination of a twofold rotation of the NH 3 –CH 2 head group about the crystal c -axis with a characteristic relaxation time of ~6.2 ps, threefold rotations (C 3 ) of NH 3 and CH 3 terminal groups, and slow librations of the other atoms. Contrastingly, only the C 3 rotation is present in the intermediate-temperature orthorhombic (238 K < T < 310 K) and low-temperature monoclinic ( T < 238 K) phases.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Refining perovskite structures to pair distribution function data using collective Glazer modes as a basis

Structural modelling of octahedral tilts in perovskites is typically carried out using the symmetry constraints of the resulting space group. In most cases, this introduces more degrees of freedom than those strictly necessary to describe only the octahedral tilts. It can therefore be a challenge to disentangle the octahedral tilts from other structural distortions such as cation displacements and octahedral distortions. This paper reports the development of constraints for modelling pure octahedral tilts and implementation of the constraints in diffpy-CMI, a powerful package to analyse pair distribution function (PDF) data. The model in the program allows features in the PDF that come from rigid tilts to be separated from non-rigid relaxations, providing an intuitive picture of the tilting. The model has many fewer refinable variables than the unconstrained space group fits and provides robust and stable refinements of the tilt components. It further demonstrates the use of the model on the canonical tilted perovskite CaTiO 3 which has the known Glazer tilt system α + β – β – . The Glazer model fits comparably to the corresponding space-group model Pnma below r = 14 Å and becomes progressively worse than the space-group model at higher r due to non-rigid distortions in the real material.

36 MATERIALS SCIENCE↗
NASA NTRS1965

Rotating filters permit wide range of optical pyrometry

Gear-driven dual filter disks of graduated density vary linearly with respect to rotation, allowing a wide range of photographic pyrometry. this technique is applicable in metallurgy, glass, plastics and refractory research, and crystallography.

Exton, R. J.↗