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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Quantification of Dynamic Scattering Effects in Molecular Crystals using Large Angle Rocking Beam Electron Diffraction

Electron crystallography provides a pathway to solve structure of small crystals (< 1um) in size, and thus overcomes difficult synthesis constraints involved in growing large crystals. Generally, electron diffraction data is collected in the form of integrated intensity using continuous rotation or by precession. The measured intensities in 3D are utilized for structure solution. Using this approach, structure solution of difficult crystals, such as small crystals of zeolites, metal-organic frameworks, molecular crystals, and proteins , can be solved by electron diffraction. However, electron structure solutions are regularly reported with higher Rvalues than x-ray or neutron diffraction. While similar structures are found despite the high R-values, the differences in the measure intensity and theory calculated intensity limit information that can be extracted by electron diffraction. Previous work demonstrated that including multiple-scattering effects significantly reduce the R-values . Thus, it is critical to be able to quantify the dynamical diffraction effects in molecular crystals.

Crystallography↗
DOE OSTI2021

Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide

Oxidized dGTP (8-oxo-7,8-dihydro-2´-deoxyguanosine triphosphate, 8-oxodGTP) insertion by DNA polymerases strongly promotes cancer and human disease. How DNA polymerases discriminate against oxidized and undamaged nucleotides, especially in error-prone double strand break (DSB) repair, is poorly understood. High-resolution time-lapse X-ray crystallography snapshots of DSB repair polymerase μ undergoing DNA synthesis reveal that a third active site metal promotes insertion of oxidized and undamaged dGTP in the canonical anti-conformation opposite template cytosine. The product metal bridged O8 with product oxygens, and was not observed in the syn-conformation opposite template adenine (A t ). Rotation of A t into the syn-conformation enabled undamaged dGTP misinsertion. Exploiting metal and substrate dynamics in a rigid active site allows 8-oxodGTP to circumvent polymerase fidelity safeguards to promote pro-mutagenic double strand break repair.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Effect of Laser Beam Profile on Rotating Lattice Single Crystal Growth in Sb2S3 Model Glass

Laser heating of chalcogenide glasses has successfully produced rotating lattice single crystals through a solid-solid transformation. To better understand the nature of complex, orientation-dependent lattice rotation, we designed heat profiles of the continuous wave laser by beam shaping, fabricated larger Sb2S3 crystal dots in Sb2S3 glass, and investigated the lattice rotation where the crystal could grow in all radial directions under a circular thermal gradient. The results show that the rate of lattice rotation is highly anisotropic and depends on crystallographic direction. The nature of this rotation is the same in crystals of different orientation relative to the surface. The growth directions that align with the slip planes show the highest rate of rotation and the rotation rate gradually decreases away from this direction. Additionally, the presence of multiple growth directions results in a complicated rotation system. We suggest that the growth front influences the density of dislocations introduced during growth under confinement and thus affects the lattice rotation rate in these crystals.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography

XynII is a family 11 glycoside hydrolase that uses the retaining mechanism for catalysis. In the active site, E177 works as the acid/base and E86 works as the nucleophile. Mutating an uncharged residue (N44) to an acidic residue (D) near E177 decreases the enzyme’s optimal pH by ~ 1.0 unit. D44 was previously suggested to be a second proton carrier for catalysis. To test this hypothesis, we abolished the activity of E177 by mutating it to be Q, and mutated N44 to be D or E. These double mutants have dramatically decreased activities. Our high-resolution crystallographic structures and the microscopic pK a calculations show that D44 has similar position and pK a value during catalysis, indicating that D44 changes electrostatics around E177, which makes it prone to rotate as the acid/base in acidic conditions, thus decreases the pH optimum. Our results could be helpful to design enzymes with different pH optimum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural Characterization of Alzheimer DNA Promoter Sequences from the Amyloid Precursor Gene in the Presence of Thioflavin T and Analogs

Understanding DNA-ligand binding interactions requires ligand screening, crystallization, and structure determination. In order to obtain insights into the amyloid peptide precursor (APP) gene-Thioflavin T (ThT) interaction, single crystals of two DNA sequences 5'-GCCCACCACGGC-3' (PDB 8ASK) and d(CCGGGGTACCCCGG) 2 (PDB 8ASH) were grown in the presence of ThT or its analogue 2-((4-(dimethylamino)benzylidene)amino)-3,6-dimethylbenzo[d]thiazol-3-ium iodide (XRB). Both structures were solved by molecular replacement. In the case of 8ASK, the space group was H3 with unit cell dimensions of a = b = 64.49 Å, c = 46.19 Å. Phases were obtained using a model generated by X3DNA. The novel 12-base-pair B-DNA structure did not have extra density for the ThT ligand. The 14-base-pair A-DNA structure with bound ThT analog XRB was isomorphous with previously the obtained apo-DNA structure 5WV7 (space group was P 4 1 2 1 2 with unit cell dimensions a = b = 41.76 Å, c = 88.96 Å). Binding of XRB to DNA slightly changes the DNA's buckle parameters at the CpG regions. Comparison of the two conformations of the XRB molecule: alone and bound to DNA indicates that the binding results from the freedom of rotation of the two aromatic rings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Application of Dislocation Theory to Minimize Defects in Artificial Solids Built with Nanocrystal Building Blocks

Conspectus. Oriented atomic attachment of colloidal inorganic nanocrystals represents a powerful synthetic method for preparing complex inorganic superstructures. Examples include fusion of nanocrystals into dimer and superlattice structures. If the attachment were perfect throughout, then the resulting materials would have single crystal-like alignment of the individual nanocrystals' atomic lattices. While individual colloidal nanocrystals typically are free of many defects, there are a multitude of pathways that can generate defects upon nanocrystal attachment. These attachment generated defects are typically undesirable, and thus developing strategies to favor defect-free attachment or heal defective interfaces are essential. There may also be some cases where attachment-derived defects are desirable. In this Account, we summarize our current understanding of how these defects arise, in order to offer guidance to those who are designing nanocrystal derived solids. The small size of inorganic nanocrystals means short diffusion lengths to the surface, which favor the formation of nanocrystal building blocks with pristine atomic structures. Upon attachment, however, there are numerous pathways that can lead to atomic scale defects, and bulk crystal dislocation theory provides an invaluable guide to understanding these phenomena. As an example, an atomic step edge can be incorporated into the interface leading to an extra half-plane of atoms, known as an edge dislocation. These dislocations can be well described by the Burgers vector description of dislocations, which geometrically identifies planes in which a dislocation can move. Our in situ measurements have verified that bulk dislocation theory predictions for 1D defects hold true at few-nanometer length scales in PbTe and CdSe nanocrystal interfaces. Ultimately, the applicability of dislocation theory to nanocrystal attachment enables the predictive design of attachment to prevent or facilitate healing of defects upon nanocrystal attachment. We applied similar logic to understand formation of planar (2D) defects such as stacking faults upon nanocrystal attachment. Again concepts from bulk crystal defect crystallography can identify attachment pathways that can prevent or deterministically form planar defects upon nanocrystal attachment. The concepts we discuss work well for identifying favorable attachment geometries for nanocrystal pairs ; however it is currently unclear how to translate these ideas to near-simultaneous multiparticle attachment. Geometric frustration, which prevents nanocrystal rotation, and yet-to-be considered defect generation pathways unique to multiparticle attachment complicate defect-free superlattice attachment. New imaging methods now allow for the direct observation of local attachment trajectories and may enable improved understanding of such multiparticle phenomena. With further refinement, a unified framework for understanding and ultimately eliminating structural defects in fused nanocrystal superstructures may well be achievable in coming years.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Structural characterization of influenza group 1 chimeric hemagglutinins as broad vaccine immunogens

Chimeric hemagglutinins (cHA) appear to be promising for the design and development of universal influenza vaccines. Influenza A group 1 cHAs, cH5/1, cH8/1, and cH11/1, comprising an H1 stem attached to either an H5, H8, or H11 globular head, have been used sequentially as vaccine immunogens in human clinical trials and induced high levels of broadly protective antibodies. Using X-ray crystallography and negative-stain electron microscopy, we determined structures of cH5/1, cH8/1, and cH11/1 HAs in their apo (unliganded) and antibody Fab-bound states. Stem-reactive antibodies 3E1 and 31.b.09 recognize their cognate epitopes in cH5/1, cH8/1, and cH11/1 HAs. However, with cH5/1, the head domains are rotated by 35 to 45° around the threefold axis of the HA trimer compared to native HA with a more splayed-open conformation at the stem base. cH11/1 with 3E1 is structurally more native-like but resembles cH5/1 with 31.b.09, whereas cH8/1 with 31.b.09 exhibited a range of closed-to-open stem configurations with some separation of head and stem domains. Furthermore, all of these group 1 cHAs effectively bound a broad head trimer interface antibody and other broad stem antibodies. Thus, the cHAs exhibit structural plasticity without compromising the stem and head trimer interface epitopes for elicitation of influenza A group 1 cross-reactive antibodies.

Science & Technology - Other Topics↗
DOE OSTI2025

Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization

Introduction: Numerous X-ray crystal structures of the c-Src SH3 domain have provideda large sampling of atomic-level information for this important signaling domain. Multiple crystalforms have been reported, with variable crystal lattice contacts and chemical crystallizationconditions. Materials and Methods: We crystallized the c-Src SH3 domain in a crystallization buffercontaining NiCl2. Results: A unique crystal structure of the Src SH3 domain in the trigonal space group H32 isdetermined to 1.45 Å resolution. Crystal packing and anomalous scattering reveal that this crystalform is mediated by two ordered nickel ions provided by the crystallization buffer. Nickelcoordination occurs in a 2:2 stoichiometry, which dimerizes two SH3 domain monomers across apseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, asurface-exposed histidine residue, and ordered water molecules. Discussion: This study provides an example of metal-mediated crystallization and metal binding byN-terminal protein residues, contrasting with the Amino-Terminal Copper and Nickel Binding(ATCUN) motif. Conclusion: Alternative avenues help widen the potential for future crystallography-based studiesof the c-Src SH3 domain.

Biochemistry & Molecular Biology↗
DOE OSTI2025

A Trichomonas vaginalis C2-XYPPX-repeat protein with a structured C2 domain displaying dampened flexibility upon binding calcium

C2 domains are ubiquitous membrane-binding modules of ∼130 residues in eukaryotes that are often associated with proteins involved in membrane trafficking and lipid modification. The genome of Trichomonas vaginalis, the most common, non-viral, sexually transmitted human pathogen, encodes eight genes that contain a N-terminal C2 module linked to a XYPPX-repeat domain of more than four XYPPX repeats (C2-XYPPX). While the function of the XYPPX-repeat domain remains unknown, its multiple association with C2 domains in T. vaginalis suggests it is important. Here, the C2 domain from one of these C2-XYPPX-repeat proteins, Tv-C2-1, was structurally and physically characterized using X-ray crystallography and NMR spectroscopy. The crystal structure for Tv-C2-1 shows that this domain shares a fold common to all C2 domains, a compact Greek-key motif composed of eight anti-parallel β-strands in the type-2 topology. An NMR chemical shift perturbation study with Ca 2+ showed that Tv-C2-1 bound two Ca 2+ atoms primarily via two loops (loop-1 and loop-3) on the predicted calcium binding face of the protein with K d s of 58.0 ± 0.1 μM and 232 ± 6 μM. Estimations of the overall rotational correlation time, τ c , in the apo (11.1 ns) and Ca 2+ -bound (9.2 ns) state suggests the protein becomes more compact upon Ca 2+ binding, consistent with a decrease in dynamics in loop-3 and marginally in loop-1 suggested by amide 15 N heteronuclear steady-state { 1 H}- 15 N NOEs. Showing Tv-C2-1 binds calcium and adopts a compact Greek-key motif structure, two primary features of C2 domains, suggests understanding the function of the XYPPX-repeat domain may be warranted.

NMR spectroscopy↗
DOE OSTI2022

Nontrivial nanostructure, stress relaxation mechanisms, and crystallography for pressure-induced Si-I → Si-II phase transformation

Crystallographic theory based on energy minimization suggests austenite-twinned martensite interfaces with specific orientation, which are confirmed experimentally for various materials. Pressure-induced phase transformation (PT) from semiconducting Si-I to metallic Si-II, due to very large and anisotropic transformation strain, may challenge this theory. Here, unexpected nanostructure evolution during Si-I → Si-II PT is revealed by combining molecular dynamics (MD), crystallographic theory, generalized for strained crystals, and in situ real-time Laue X-ray diffraction (XRD). Twinned Si-II, consisting of two martensitic variants, and unexpected nanobands, consisting of alternating strongly deformed and rotated residual Si-I and third variant of Si-II, form {111} interface with Si-I and produce almost self-accommodated nanostructure despite the large transformation volumetric strain of -0.237. The interfacial bands arrest the {111} interfaces, leading to repeating nucleation-growth-arrest process and to growth by propagating {110} interface, which (as well as {111} interface) do not appear in traditional crystallographic theory.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Oblique diffraction geometry for the observation of several non-coplanar Bragg reflections under identical illumination

A method to determine the strain tensor and local lattice rotation with dark-field X-ray microscopy is presented. Using a set of at least three non-coplanar symmetry-equivalent Bragg reflections, the illuminated volume of the sample can be kept constant for all reflections, facilitating easy registration of the measured lattice variations. This requires an oblique diffraction geometry,i.e.the diffraction plane is neither horizontal nor vertical. We derive a closed analytical expression that allows determination of the strain and lattice rotation from the deviation of experimental observables (e.g.goniometer angles) from their nominal values for an unstrained lattice.

Chemistry↗
DOE OSTI2024

Birefringent Color Filter by Layered Metal‐Organic Chalcogenides: In‐Plane Anisotropy and Odd/Even Effect

Anisotropic 2D materials are gaining interest recently as building blocks for angular‐dependent optical/electrical devices. However, the fundamental understanding of their structure‐property‐relationship is limited, which hinders further modulation of their unique characteristics via structure tailoring. Here the in‐plane structural anisotropy and the tunable optical/electrical properties of a series of radiation‐sensitive (X‐ray, e‐beam) metal‐organic chalcogenide (MOC) single crystals are comprehensively revealed with ligands of variable length/parity. Their monoclinic crystallography is determined at atomic resolution by a simple method that couples X‐ray/electron diffraction with first‐principles calculations. The in‐plane inorganic backbone of the MOCs exhibits a strong lattice anisotropy with odd/even alternations, which originates from that of the out‐of‐plane organic motifs via organic/inorganic accommodation. Such structural anisotropy is implied mechanically by the preferred orientation of crystal cleavage. It triggers a maximum ≈8 × distinction of in‐plane electrical conductivity of the semiconducting MOCs, plus a distinct birefringence (maximum Δn ≈ 0.03) with a dispersive orientation of dielectric axes, which rotate up to 25.7° from UV to visible‐light regime, inspiring an emerging pathway for color filtering via single crystal rotation. Such in‐plane optical characteristics also exhibit odd/even alternation and can be flexibly tuned by the designable out‐of‐plane ligands.

birefringence↗
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 OSTI2021

Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I.

Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines. In the RT structure of PS I, we also observe conformational differences between the two branches in the reaction center around the secondary electron acceptors A 1A and A 1B . The π-stacked Phe residues are rotated with a more parallel orientation in the A-branch and an almost perpendicular confirmation in the B-branch, and the symmetry breaking PsaB-Trp673 is tilted and further away from A 1A . These changes increase the asymmetry between the branches and may provide insights into the preferential directionality of electron transfer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Deep Bayesian local crystallography

Abstract The advent of high-resolution electron and scanning probe microscopy imaging has opened the floodgates for acquiring atomically resolved images of bulk materials, 2D materials, and surfaces. This plethora of data contains an immense volume of information on materials structures, structural distortions, and physical functionalities. Harnessing this knowledge regarding local physical phenomena necessitates the development of the mathematical frameworks for extraction of relevant information. However, the analysis of atomically resolved images is often based on the adaptation of concepts from macroscopic physics, notably translational and point group symmetries and symmetry lowering phenomena. Here, we explore the bottom-up definition of structural units and symmetry in atomically resolved data using a Bayesian framework. We demonstrate the need for a Bayesian definition of symmetry using a simple toy model and demonstrate how this definition can be extended to the experimental data using deep learning networks in a Bayesian setting, namely rotationally invariant variational autoencoders.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Detector alignment for X-ray crystallography using Millepede-II

I describe a method for accurately refining the geometrical parameters of segmented X-ray area detectors on the basis of serial crystallography data, using 'Millepede' – an algorithm created for a very similar problem in high-energy physics. The Millepede method for serial crystallography builds on the approach of Brewster et al. [Acta Cryst. (2018), D74, 877–894], in which the detector parameters are refined simultaneously with the parameters for each individual crystal. This accounts for the mutual dependency between the parameters and thereby avoids the bias and slow convergence problems that have afflicted older approaches in which the deviations between observed and calculated Bragg peak positions were taken directly as the updates for the detector panel positions. The Millepede method uses the special structure of the least-squares normal equations to reduce them to a much smaller form that can be solved very quickly, even compared with the sparse matrix methods used previously. This makes it practical to refine the detector geometry frequently and thereby maintain accurate calibration without specialized alignment campaigns. Tilts of detector panels out of the plane can be reliably refined, as can the overall distance of the detector in the beam direction. With a simulated test case, the new method produced panel shifts within 7% of the correct values with only one iteration, and produced almost exactly correct shifts after a second iteration. A simulated out-of-plane panel rotation was correctly determined to within 0.001°. Applied to experimental data from an X-ray free-electron laser, the method increased the indexable fraction of frames from 30% to 91% in a single iteration, and to 96% after two further iterations. Computing the geometry updates on the basis of 2060 crystals took only 0.819 s on desktop computing hardware, including the time taken to read the required data from disk. The scaling was found to be very close to linear for up to 100 980 sets of crystal parameters, which took only 78.2 s to process under the same conditions. The method has been applied as part of a real-time feedback system at a synchrotron radiation beamline, in which an out-of-plane detector tilt of 0.04° was detected and corrected. Possible further applications are also described here.

Millepede-II↗
DOE OSTI2025

Reuniting crystallography with real space: Ab initio structure elucidation with 4D-STEM

Structure elucidation via single-crystal methods has historically lacked experimental access to real-space information, instead relying exclusively on diffraction-space measurements of Bragg reflections. Here we exploit the dual-space imaging power of 4D scanning transmission electron microscopy to meaningfully integrate real-space information into the crystallographic workflow. We show that virtual apertures assembled by segmentation of high-angle annular dark-field images enable i) pixel-by-pixel separation of coherent Bragg signal from clusters of closely spaced nanocrystals and ii) selective extraction of integrated intensities from thinner subregions of individual specimens, facilitating retroactive tuning of multiple scattering artifacts. This strategy empowers us to simply pick and choose whichever nanoscale regions of interest generate the highest-quality diffraction patterns, allowing us to solve several independent structures of the metal-organic framework UiO-66 from specimens whose agglomerated morphology proved intractable for conventional microcrystal electron diffraction. Our method is compatible with both rotational and serial approaches to data processing, ultimately divulging the first scanning nanobeam electron diffraction structures determined by direct methods at subangstrom resolution.

Saha, Ambarneil↗