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At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties

Abstract Motivation BISCAP is a state-of-the-art tool for automatically characterizing biofilm images obtained from Optical Coherence Tomography. Limited availability of other software tools is reported in the field. BISCAP’s first version processes 2D images only. Processing 3D images is a problem of greater scientific relevance since it deals with the entire structure of biofilms instead of their 2D slices. Results Building on the image-processing principles and algorithms proposed earlier for 2D images, these were adapted to the 3D case, and a more general implementation of BISCAP was developed. The primary goal concerns the extension of the initial methodology to incorporate the depth axis in 3D images; multiple improvements were also made to boost computational performance. The calculation of structural properties and visual outputs was extended to offer new insights into the 3D structure of biofilms. BISCAP was tested using 3D images of biofilms with different morphologies, consistently delivering accurate characterizations of 3D structures in a few minutes using standard laptop machines. Low user dependency is required for image analysis. Availability and implementation BISCAP is available from https://github.com/diogonarciso/BISCAP. All images used in the tutorials and the validation examples are available from https://web.fe.up.pt/∼fgm/biscap3d.

Narciso, Diogo A. C. (ORCID:0000000227767477)↗
DOE OSTI2025

Similar but Different: Structural and Spectroscopic Characterization of Series of Neodymium, Europium, Americium, and Curium Coordination Complexes

Series of curium, americium, europium, and neodymium complexes with five different polyoxometalate (POM) ligands were structurally and spectroscopically characterized: Na x Cs y H z [M(XW 11 O 39 ) 2 ]· n H 2 O, where M = Nd 3+ , Eu 3+ , Am 3+ , or Cm 3+ and X = B 3+ , Ga 3+ , Si 4+ , Ge 4+ , or P 5+ . This first “serial approach” on transplutonium chemistry was allowed by minimizing the amount of f-element needed per synthesis down to ∼10 μg. This offers a unique opportunity to contrast structural and spectroscopic properties of trivalent actinide with those of lanthanide compounds under identical conditions. The results showcase that although actinide(III) and lanthanide(III) can make isostructural complexes, their solid-state coordination chemistries deviate significantly. The curium and americium compounds were found to be more uniform than their europium and neodymium counterparts, respectively. The particular symmetry of the Cm-POMs also enables the observation of rarely seen emission bands, which hints at vibronic coupling or new emissive pathways. Additionally, the Cm-POM and Eu-POM complexes were characterized via steady-state and time-resolved excitation and emission spectroscopy in solutions containing five different counterions (Li + , Na + , K + , Rb + , or Cs + ), representing 50 combinations of alkali/[M III (XW 11 ) 2 ] n − complexes. The Cm-POMs respond to the alkali counterions by improving symmetry from Li + to Cs + , while the Eu-POMs do the opposite. The luminescence lifetimes of the Cm-POMs also depart from the ideal Kimura equation. Finally, this study provides a rare, and perhaps the most comprehensive, experimental data set comparing heavy actinides and lanthanides via single crystal XRD plus, solution-state, solid-state, and time-resolved emission spectroscopy and demonstrates that lanthanides are only a coarse approximation for actinide elements.

chemical structure↗
DOE OSTI2022

Characterization of the structure and chemistry of the solid–electrolyte interface by cryo-EM leads to high-performance solid-state Li-metal batteries

Solid-state lithium-metal (Li 0 ) batteries are gaining traction for electric vehicle applications because they replace flammable liquid electrolytes with a safer, solid-form electrolyte that also offers higher energy density and better resistance against Li dendrite formation. Solid polymer electrolytes (SPEs) are highly promising candidates because of their tunable mechanical properties and easy manufacturability; however, their electrochemical instability against lithium metal (Li 0 ), mediocre conductivity, and poorly understood Li 0 /SPE interphases have prevented extensive application in real batteries. In particular, the origin of the low Coulombic efficiency (CE) associated with SPEs remains elusive, as the debate continues as to whether it originates from unfavored interfacial reactions or lithium dendritic growth and dead lithium formation. In this work, we use state-of-the-art cryo-electromicroscopy (cryoEM) imaging and spectroscopic techniques to characterize the structure and chemistry of the interface between Li 0 and a polyacrylate-based SPE. Contradicting the conventional knowledge, we find that no protective interphase forms, owing to the sustained reactions between deposited Li dendrites and polyacrylic backbones and succinonitrile plasticizer. Due to the reaction induced volume change, large amounts of cracks form inside the Li dendrites with a stress corrosion-cracking behavior, indicating that Li0cannot be passivated in this SPE system. Based on this observation, we then introduce additive engineering leveraging on the knowledge of liquid electrolytes, and demonstrate that the Li 0 surface can be effectively protected against corrosion using fluoroethylene carbonate (FEC), leading to densely packed Li 0 domes with conformal and stable solid-electrolyte interphases (SEIs) films. Owing to the high room temperature ionic conductivity of 1.01 mS/cm -1 , the high transference number of 0.57 and the stabilized lithium electrolyte interface, this improved new SPE delivers an excellent lithium plating/stripping CE of 99% and 1800 hours of stable cycling in Li||Li symmetric cells (0.2 mA/cm -2 , 1mAh/cm -2 ). Furthermore, this improved cathodic stability along with the high anodic stability enables record high cycle life of >2000 cycles for Li||LiFePO 4 and >400 cycles for Li||LiCoO 2 full cells.

25 ENERGY STORAGE↗
DOE OSTI2021

A General Framework to Learn Tertiary Structure for Protein Sequence Characterization

During the past five years, deep-learning algorithms have enabled ground-breaking progress towards the prediction of tertiary structure from a protein sequence. Very recently, we developed SAdLSA, a new computational algorithm for protein sequence comparison via deep-learning of protein structural alignments. SAdLSA shows significant improvement over established sequence alignment methods. In this contribution, we show that SAdLSA provides a general machine-learning framework for structurally characterizing protein sequences. By aligning a protein sequence against itself, SAdLSA generates a fold distogram for the input sequence, including challenging cases whose structural folds were not present in the training set. About 70% of the predicted distograms are statistically significant. Although at present the accuracy of the intra-sequence distogram predicted by SAdLSA self-alignment is not as good as deep-learning algorithms specifically trained for distogram prediction, it is remarkable that the prediction of single protein structures is encoded by an algorithm that learns ensembles of pairwise structural comparisons, without being explicitly trained to recognize individual structural folds. As such, SAdLSA can not only predict protein folds for individual sequences, but also detects subtle, yet significant, structural relationships between multiple protein sequences using the same deep-learning neural network. The former reduces to a special case in this general framework for protein sequence annotation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural and magnetic characterization of CeTa 7 ⁢O 19 and YbTa 7 ⁢ O 19 with a two-dimensional pseudospin-$\frac{1}{2}$ triangular lattice

Triangular lattice antiferromagnets are prototypes for frustrated magnetism and may potentially realize novel quantum magnetic states such as a quantum spin-liquid ground state. A recent work suggests NdTa 7 ⁢O 19 with rare-earth triangular lattice is a quantum spin-liquid candidate and highlights the large family of rare-earth heptatantalates as a framework for quantum magnetism investigation. Here, in this paper, we report the structural and magnetic characterization of CeTa 7 ⁢ O 19 and YbTa 7 ⁢ O 19 . Both compounds are isostructural to NdTa 7 ⁢O 19 with no detectable structural disorder. For CeTa 7 ⁢O 19 , the crystal field energy levels and parameters are determined by inelastic neutron scattering measurements. Based on the crystal field result, the magnetic susceptibility data could be well fitted and explained, which reveals that CeTa 7 ⁢O 19 is a highly anisotropic Ising triangular-lattice antiferromagnet (𝑔 𝑧 ⁡/𝑔 𝑥⁢𝑦 ∼ 3) with very weak exchange interaction (J ∼ 0.22 K). For YbTa 7⁢ O 19 , millimeter-sized single crystals could be grown. The anisotropic magnetization and electron spin resonance data show that YbTa 7⁢ O 19 has a contrasting in-plane magnetic anisotropy with 𝑔 𝑧 ⁡/𝑔 𝑥⁢𝑦 ∼ 0.67 similar as that of YbMgGaO 4 . The above results indicate that CeTa7⁢ O 19 and YbTa 7 ⁢O 19 with pseudospin-1/2 ground states might either be quantum spin-liquid candidate materials or find applications in adiabatic demagnetization refrigeration due to the weak exchange interaction.

Pan, Feihao↗
DOE OSTI2023

Multimodal Characterization of Crystal Structure and Formation in Rubrene Thin Films Reveals Erasure of Orientational Discontinuities

Abstract Multimodal multiscale characterization provide opportunities to study organic semiconducting thin films with multiple length scales, across multiple platforms, to elucidate crystallization mechanisms of the various microstructures that impact functionality. With polarized scanning transmission X‐ray and 4D‐scanning transmission electron microscopy, hybrid crystalline structures in rubrene thin films in which large crystalline domains surround a common nucleus and transition to a spherulite morphology at larger radii is observed. These high‐resolution techniques reveal how azimuthal orientational discontinuities at smaller radii are erased as spherulite morphology takes hold. In situ crystallization in the films with optical microscopy is also captured, discovering the importance of considering the initial temperature increase of a film during thermal annealing over the crystallization timescale. This kinetic information of the radial crystallization rate and of corresponding film heating kinetics is used to estimate the temperature at which the larger crystalline regions transition into a spherulite. By combining the results obtained from the different characterization modes, it is learned that thermal conditions can sensitively affect the crystallization of rubrene and other organic thin films. The observations suggest opportunities for more complex temperature‐dependent processing to maximize hybrid structures’ functionality in organic thin films and demonstrate that multimodal studies deepen the understanding of structure‐function dynamics.

Tan, Jenna A.↗
DOE OSTI2023

Structural and spectroscopic characterization of thorium pyrasal complexes

To explore the coordination chemistry of thorium, the most abundant radioactive element on earth, we examine the synthesis and characterization of two Th (IV)-pyrasal complexes, L1 “pyrasal” ((2,2'-((1E,1'E)-(pyrazine-2,3-diylbis(azaneylylidene))bis(methaneylylidene))diphenol), and L2 “naphthylpyrasal” (1,1'-((1E,1'E)-(pyrazine-2,3-diylbis(azaneylylidene))bis(methaneylylidene))bis(naphthalen-2-ol). These complexes demonstrate little or no fluorescence when compared to similar naphthylsalophen thorium complexes previously published. Each complex was synthesized and characterized by IR, NMR (1H), and mass spectrometry. The photometric properties of the complexes were characterized using UV–Vis and fluorescence spectroscopy and their solid-state molecular structures were established by single-crystal X-ray crystallography. The electron-withdrawing effects of the pyrazine ring creates changes in the thorium coordination environment resulting in a secondary solid-state extended structure that minimizes the pi-pi stacking. Further, this subsequently causes an overall decrease in the intensity of fluorescence demonstrated previously in by naphthylsalophen thorium complexes.

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

Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB

Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacterium Bacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 Å, in what appears to be an inactive state. In this conformation, a predicted α-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg 2+ ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ-family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg 2+ -dependent 3'–5' DNA exonuclease. We show that Leu113 aids in coordinating the 3' end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC-induced DNA adducts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural and functional characterization of IgG- and non-IgG-based T-cell-engaging bispecific antibodies

Bispecific T-cell-engaging antibodies are a growing class of therapeutics with numerous molecules being tested in clinical trials and, currently, seven of them have received market approval. They are structurally complex and function as adaptors to redirect the cytotoxicity of T cells to kill tumor cells. T-cell-engaging bispecific antibodies can be generally divided into two categories: IgG/IgG-like and non-IgG-like formats. Different formats may have different intrinsic potencies and physiochemical properties, and comprehensive studies are needed to gain a better understanding of how the differences in formats impact on structural and functional characteristics. In this study, we designed and generated bispecific T-cell-engaging antibodies with IgG-like (DVD-Ig) and non-IgG (BiTE) formats. Both target the same pair of antigens (EGFR and CD3) to minimize the possible influence of targets on functional characterization. We performed a side-by-side comparison to assess differences in the physiochemical and biological properties of these two bispecific T-cell-engaging antibodies using a variety of breast and ovarian cancer cell-based functional assays to delineate the structural–functional relationships and anti-tumor activities/potency. We found that the Fc portion of T-cell-engaging bispecific antibodies can significantly impact antigen binding activity, potency, and stability in addition to eliciting different mechanisms of action that contribute the killing of cancer cells.

cluster of differentiation 3 (CD3)↗
DOE OSTI2025

X-ray Spectroscopy Characterization of Electronic Structure and Metal–Metal Bonding in Dicobalt Complexes

Developing multimetallic complexes with tunable metal–metal interactions has long been a target of synthetic inorganic chemistry efforts due to the unique properties that such compounds can exhibit. However, understanding relationships between metal–metal bonding and chemical properties is challenging due to system-dependent factors that influence metal–metal and metal–ligand interactions, including ligand identity, coordination geometry, and metal–metal distance. In this work, we apply X-ray absorption and emission spectroscopy and quantum chemical calculations to describe electronic structure and bonding in a series of dicobalt complexes. The compounds with silane ligands and pseudo-octahedral coordination geometry exhibit Co–Co σ and multicentered bonding character, which we characterize from both the occupied and vacant perspectives via their contributions to the Co X-ray emission and absorption spectra, respectively. In contrast, the dicobalt complexes with a pseudotetrahedral coordination environment do not exhibit Co–Co bonding due to symmetry constraints on orbital overlap. We extend these insights to the theoretical evaluation of related dicobalt complexes to explain how ligand coordination and symmetry dictate the presence or absence of a Co–Co bond. In conclusion, this work highlights how fundamental insights into electronic structure and bonding through X-ray spectroscopy uncover important factors governing metal–metal interactions and guide the rational design of multimetallic complexes with tunable metal–metal bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Salt-flux synthesis, crystal structure and theoretical characterization of Rb 0.74 Ga 6.62 Ti 0·38 O 11

Here single crystals of Rb 0.74 Ga 6.62 Ti 0·38 O 11 (RGTO) were grown from a mixed RbCl–RbF flux at 850 °C. The compound crystallizes in the RbGa 7 O 11 structure type, which is reminiscent of the hollandite and β-Ga 2 O 3 structure types. RGTO crystallizes in the monoclinic space group P2/m with lattice parameters a = 8.3355 (8) Å, b = 3.0286 (3) Å, c = 9.5028 (9) Å, and β = 114.620 (3)°. The crystal structure of RGTO is comprised of GaO 6 and mixed (Ga/Ti)O 6 octahedra and GaO 4 tetrahedra connected in a complex three-dimensional, anionic framework exhibiting eight-sided channels that are occupied by disordered Rb cations required for charge balance. First-principles calculations in the form of density functional theory were performed, which indicated the complex to be a charge transfer semiconductor.

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

Identifying point defects and ordering in the high-entropy layered oxide Li 1.5 MO 3-δ (M=Mn, Al, Fe, Co, Ni) for energy storage applications

High-entropy layered oxides (HELOs) represent a very promising class of next-generation battery cathodes, combining the well-studied properties of layered cathode materials such as LiCoO 2 with the chemical tunability and stability of high-entropy materials. HELO materials often form particles with complex defects and domain structures, complicating accurate characterization of structure and cation mixing. Understanding disorder and order in HELO materials is necessary for understanding their performance and utility as cathodes. Here we demonstrate the characterization of the HELO Li 1.5 MO 3-δ (M = Mn, Al, Fe, Co, Ni), wherein X-ray powder diffraction, transmission electron microscopy imaging, and electron diffraction patterns are analyzed to reveal the presence of ordering in the HELO, with imaging and diffraction simulation employed to compare experimental results to atomic modeling. Finally, without rigorous characterization at the atomic scale, important features such as defect ordering can be easily overlooked and therefore remain unconsidered when interpreting experimental results.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structural and spectroscopic characterization of an einsteinium complex

The transplutonium elements (atomic numbers 95–103) are a group of metals that lie at the edge of the periodic table. As a result, the patterns and trends used to predict and control the physics and chemistry for transition metals, main-group elements and lanthanides are less applicable to transplutonium elements. Furthermore, understanding the properties of these heavy elements has been restricted by their scarcity and radioactivity. This is especially true for einsteinium (Es), the heaviest element on the periodic table that can currently be generated in quantities sufficient to enable classical macroscale studies. Here we characterize a coordination complex of einsteinium, using less than 200 nanograms of 254 Es (with half-life of 275.7(5) days), with an organic hydroxypyridinone-based chelating ligand. X-ray absorption spectroscopic and structural studies are used to determine the energy of the L 3 -edge and a bond distance of einsteinium. Photophysical measurements show antenna sensitization of EsIII luminescence; they also reveal a hypsochromic shift on metal complexation, which had not previously been observed in lower-atomic-number actinide elements. Here, these findings are indicative of an intermediate spin–orbit coupling scheme in which j–j coupling (whereby single-electron orbital angular momentum and spin are first coupled to form a total angular momentum, j) prevails over Russell–Saunders coupling. Together with previous actinide complexation studies, our results highlight the need to continue studying the unusual behaviour of the actinide elements, especially those that are scarce and short-lived.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The E. coli L‐asparaginase V27T mutant: structural and functional characterization and comparison with theoretical predictions

Bacterial L‐asparaginases have been used for over 40 years as anticancer drugs. Ardalan et al. ( Medical Hypotheses 112, 7–17, 2018) proposed that the V27T mutant of Escherichia coli type II L‐asparaginase, EcAII(V27T), should display altered biophysical and catalytic properties compared to the wild‐type enzyme, EcAII(wt), rendering it more favourable as a pharmaceutical. They postulated that EcAII(V27T) would exhibit reduced glutaminolytic activity and be more stable compared to EcAII(wt). Their postulates, however, were purely theoretical. Here, we characterized experimentally selected properties of EcAII(V27T). We found asparaginolytic activity of this mutant unchanged, whereas its glutaminolytic activity was fourfold lower compared with EcAII(wt). We did not observe significant differences in stabilities of EcAII(wt) and EcAII(V27T). Crystal structures of the complexes with L‐Asp and L‐Glu showed considerable differences in binding modes of both substrates.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro

Abstract In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO 226–234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Structural and biochemical characterization of the exopolysaccharide deacetylase Agd3 required for Aspergillus fumigatus biofilm formation

The exopolysaccharide galactosaminogalactan (GAG) is an important virulence factor of the fungal pathogen Aspergillus fumigatus. Deletion of a gene encoding a putative deacetylase, Agd3, leads to defects in GAG deacetylation, biofilm formation, and virulence. Here, we show that Agd3 deacetylates GAG in a metal-dependent manner, and is the founding member of carbohydrate esterase family CE18. The active site is formed by four catalytic motifs that are essential for activity. The structure of Agd3 includes an elongated substrate-binding cleft formed by a carbohydrate binding module (CBM) that is the founding member of CBM family 87. Agd3 homologues are encoded in previously unidentified putative bacterial exopolysaccharide biosynthetic operons and in other fungal genomes.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Linking structure to performance: Characterization of porous transport layers for high-pressure water electrolysis

Proton exchange membrane (PEM) water electrolysis is a promising technology to produce cost-efficient hydrogen. PEM electrolyzers offer a large current density range and the ability to operate at differential pressure which can be used to minimize both capital and operational expenditures. However, directly producing pressurized hydrogen at the cathode results in pushing the membrane against the anode porous transport layer (PTL). This can lead to detrimental effects, such as membrane deformation or ruptures, which depend on membrane properties as well as PTL material properties such as pore size, structure, and morphology. In this work, a range of sinter and felt-based commercial PTLs are evaluated for their contributions to the cell's electrochemical and H 2 crossover performance at cathode pressures up to 30 bar. X-ray tomography and post-operando optical microscopy are used to assess the morphology of the PTLs, and the PTL induced deformation experienced by the catalyst coated membrane (CCM), respectively. PTL samples with lower porosity were found to reduce both the cell voltage and the amount of H 2 permeating from the cathode to the anode exhaust, which was ascribed to improved catalyst layer contact and reduced membrane deformation, respectively. The best performing PTLs improved electrolyzer efficiency by ~1.5 kWh/kg H2 . Specifically, 1 kWh/kg H2 was gained due to reducing membrane deformation and decreasing H 2 crossover. The remainder 0.5 kWh/kg H2 were achieved by improving the electrical contact at the electrode/PTL interface which decreased cell voltage.

08 HYDROGEN↗