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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Synthesis, characterization, and structure determination of bis-oxazolidine complexes of rhenium

A tetradentate fused bis-oxazolidine ligand (FOX) is used to coordinate to rhenium carbonyl. The ligand binds in a κ 3 -NNN fashion to a Re(CO) 3 + fragment, giving an octahedral complex. The hydroxymethyl group can be deprotonated with CsOH, leading to a κ 3 -ONN variation in the binding of the ligand. Furthermore, loss of CO from this compound proved difficult, impeding further reactivity.

09 BIOMASS FUELS↗
DOE OSTI2021

IMS Rapid Response FY21 Summary Report for: Integrating Patterned Probes with Four-Dimensional Scanning Transmission Electron Microscopy for Unrivaled Crystallographic Structure Determination in Nanomaterials

The initial goal of our 4-dimensional scanning transmission electron microscopy (4D-STEM)-based project was to develop strain resolution two orders of magnitude better than what is now currently possible with electron-based scattering techniques, all while collecting scattering information from 7 different tilt axes at one time [multi-beam electron diffraction (MBED)1 ] through the development of a new electron probe-forming aperture with non-circular features (patterned probes 2 ). We set out to accomplish this through a collaboration with Drs. Colin Ophus and Ben Savitsky at Lawrence Berkeley Laboratory (they are the world-leading experts in developing the complex computational codes required to perform orientation analysis and quantitative strain mapping on our 4D-STEM data sets. We are motivated to invest in this area as it will be the only technique sensitive enough to perform three- dimensional automated crystallographic orientation mapping (ACOM) and strain mapping for materials exposed to external stimulus (a focus of our larger efforts).

36 MATERIALS SCIENCE↗
DOE OSTI2024

On the performance of composite schemes in determining equilibrium molecular structures

Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, in this study, the performance of two different ab initio composite approaches for obtaining equilibrium structures, “energy scheme” and “geometry scheme,” is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules. The ab initio calculations were performed using three tiers of composite chemical recipes. The current results show that as the overall rigor of calculation is increased, the semi-experimental and the ab initio numbers agree to within 0.0003 Å for all molecules in the test set. The composite approach based on correcting the potential energy surface (energy scheme) and the one based on correcting the geometry directly (geometry scheme) show excellent agreement with each other. This work represents a step toward development of efficient and highly accurate procedures for computing ab initio equilibrium structures.

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

FMX – the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425 , 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493 , 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015 , 1741 , 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5–30 keV photon energy range and delivers a flux of 4.0 × 10 12 photons s −1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 10 12 photons s −1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods – serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25 , 1362–1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ , 5 , 238–246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5 , 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE

AlphaFold has recently become an important tool in providing models for experimental structure determination by X-ray crystallography and cryo-EM. Large parts of the predicted models typically approach the accuracy of experimentally determined structures, although there are frequently local errors and errors in the relative orientations of domains. Importantly, residues in the model of a protein predicted by AlphaFold are tagged with a predicted local distance difference test score, informing users about which regions of the structure are predicted with less confidence. AlphaFold also produces a predicted aligned error matrix indicating its confidence in the relative positions of each pair of residues in the predicted model. The phenix.process_predicted_model tool downweights or removes low-confidence residues and can break a model into confidently predicted domains in preparation for molecular replacement or cryo-EM docking. These confidence metrics are further used in ISOLDE to weight torsion and atom–atom distance restraints, allowing the complete AlphaFold model to be interactively rearranged to match the docked fragments and reducing the need for the rebuilding of connecting regions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Integrating crystallographic and computational approaches to carbon-capture materials for the mitigation of climate change

Here, this article presents an overview of the current state of the art in the structure determination of microporous carbon-capture materials, as discussed at the recent NIST workshop “Integrating Crystallographic and Computational Approaches to Carbon-Capture Materials for the Mitigation of Climate Change”. The continual rise in anthropogenic CO 2 concentration and its effect on climate change call for the implementation of carbon capture technologies to reduce the CO 2 concentration in the atmosphere. Porous solids, including metal–organic frameworks (MOFs), are feasible candidates for gas capture and storage applications. However, determining the structure of these materials represents a significant obstacle in their development into advanced sorbents. The existing difficulties can be overcome by integrating crystallographic methods and theoretical modeling. The workshop gathered experimentalists and theorists from academia, government, and industry to review this field and identify approaches, including collaborative opportunities, required to develop tools for rapid determination of the structures of porous solid sorbents and the effect of structure on the carbon capture performance. We highlight the findings of that workshop, especially in the need for reference materials, standardized procedures and reporting of sorbent activation and adsorption measurements, standardized reporting of theoretical calculations, and round-robin structure determination.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization

For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein–solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54 , e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO , a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE . The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

Abstract Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan , respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.

59 BASIC BIOLOGICAL SCIENCES↗