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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Melting temperature of bismuth to 55 GPa using synchrotron X-ray phase contrast imaging

The melting temperature of elemental bismuth under high pressure has been measured to 55 GPa using synchrotron X-ray phase-contrast imaging in the laser-heated diamond anvil cell. Imaging of solid-liquid interface formation, combined with radiometric temperature and X-ray diffraction measurements, reveals a pronounced reduction in melting boundary slope in Bi-V with pressure. The unusually steep initial slope is attributed to low configurational entropy of melting, arising from structural ordering and coordination matching in the cool liquid, while slope reduction is driven by entropy increase correlated with significant liquid structure changes with rising pressure and temperature. Finally, the data rule out kinetic effects on melting in shock compression experiments and demonstrate the need for improved theoretical phase diagrams.

Materials science↗
DOE OSTI2021

Synthesis, Electronic Structure, and Reactivity of a Planar Four‐Coordinate, Cobalt–Imido Complex

Abstract A four‐coordinate cobalt–imido complex, ( t Bu mPNP)Co=NMes ( t Bu mPNP=modified PNP pincer ligand) has been synthesized from addition of 2,4,6‐trimethylphenylazide (Mes–N 3 ) to the corresponding dinitrogen complex. The solid‐state structure determined by X‐ray diffraction established a rare, idealized planar geometry with a Co=N bond distance of 1.716(2) Å. Magnetic measurements revealed an S =1 ground state with CAS‐SCF calculations supporting radical character on the imide nitrogen. Thermolysis of the cobalt–imido compound induced selective insertion of the imido group into a Co−P bond and yielded a three‐coordinate cobalt complex with a distorted T‐shaped geometry. Transition state analysis conducted with DFT calculations established the thermodynamic stability of the P–N coupled product and provided insight into the exclusive selectivity.

Park, Yoonsu↗
DOE OSTI2021

Correlating 3D Surface Atomic Structure and Catalytic Activities of Pt Nanocrystals

Active sites and catalytic activity of heterogeneous catalysts is determined by their surface atomic structures. However, probing the surface structure at an atomic resolution is difficult, especially for solution ensembles of catalytic nanocrystals, which consist of heterogeneous particles with irregular shapes and surfaces. In this study, we constructed 3D maps of the coordination number (CN) and generalized CN ($\bar{C}\bar{N}$) for individual surface atoms of sub-3 nm Pt nanocrystals. Our results reveal that the synthesized Pt nanocrystals are enclosed by islands of atoms with nonuniform shapes that lead to complex surface structures, including a high ratio of low-coordination surface atoms, reduced domain size of low-index facets, and various types of exposed high-index facets. 3D maps of $\bar{C}\bar{N}$ are directly correlated to catalytic activities assigned to individual surface atoms with distinct local coordination structures, which explains the origin of high catalytic performance of small Pt nanocrystals in important reactions such as oxygen reduction reactions and CO electro-oxidation.

3D atomic structure↗
DOE OSTI2023

Binding of carboxylate and water to monovalent cations

The interactions of carboxylate anions with water and cations are important for a wide variety of systems, both biological and synthetic. Here, in order to gain insight on properties of the local complexes, we apply density functional theory, to treat the complex electrostatic interactions, and investigate mixtures with varied numbers of carboxylate anions (acetate) and waters binding to monovalent cations, Li + , Na + and K + . The optimal structure with overall lowest free energy contains two acetates and two waters such that the cation is four-fold coordinated, similar to structures found earlier for pure water or pure carboxylate ligands. More generally, the complexes with two acetates have the lowest free energy. In transitioning from the overall optimal state, exchanging an acetate for water has a lower free energy barrier than exchanging water for an acetate. In most cases, the carboxylates are monodentate and in the first solvation shell. As water is added to the system, hydrogen bonding between waters and carboxylate O atoms further stabilizes monodentate structures. These structures, which have strong electrostatic interactions that involve hydrogen bonds of varying strength, are significantly polarized, with ChelpG partial charges that vary substantially as the bonding geometry varies. Overall, these results emphasize the increasing importance of water as a component of binding sites as the number of ligands increases, thus affecting the preferential solvation of specific metal ions and clarifying Hofmeister effects. Finally, structural analysis correlated with free energy analysis supports the idea that binding to more than the preferred number of carboxylates under architectural constraints are a key to ion transport.

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

Plutonium and Cerium Perrhenate/Pertechnetate Coordination Polymers and Frameworks

Spent nuclear fuel (SNF) contains transuranic and lanthanide species, which are sometimes recovered and repurposed. One particularly problematic fission product, 99 TcO 4 – , hampers this recovery via coextraction with high valence metals, perhaps by complexation during aqueous reprocessing of SNF. There is limited molecular-level knowledge concerning the coordination chemistry between TcO 4 – or its well-known surrogate ReO 4 – and transuranic/lanthanide species. In the current study, we investigated the coordination of ReO 4 – /TcO 4 – with plutonium and cerium cations by structural and chemical characterization of a series of isolated extended solids. In this study, Ce represents both trivalent lanthanides and is considered a surrogate for Pu, respectively, in its common trivalent and tetravalent oxidation states. The structural elucidation of the seven isolated crystalline solids revealed that ReO 4 – /TcO 4 – directly connects to Pu IV , Pu VI O 2 2 + , Ce III , and Ce IV in the terminal and bridging coordination modes, leading to 1-, 2-, and 3-dimensional frameworks. For example, ReO 4 – coordination to Pu(IV) formed a 1D chain or 2D framework, isostructural with previously isolated Th(IV) compounds. However, Pu VI O 2 2 + alternating with ReO 4 – led to a unique 1D chain, different from the prior-reported U(VI)/Np(VI)-ReO 4 – /TcO 4 – structures. Coordination of ReO 4 – /TcO 4 – with Ce(III) promotes the assembly of 3D frameworks. Finally, attempted synthesis of a Ce(IV)-ReO 4 – compound resulted in a 2D framework with a mixed-valence Ce III/IV . The highly acidic reaction conditions supported the reduction of both Ce IV and Tc VII , challenging isolation of compounds featuring these species. Only one TcO 4 -containing structure was obtained in this study (Ce III –TcO 4 3D framework), vs the six total Ce/Pu-ReO 4 compounds. Furthermore, our three Pu-ReO 4 crystal structures are the first reported and translated to atomic-level information about Pu-TcO 4 coordination in nuclear fuel reprocessing scenarios, in addition to broadening our knowledge of bonding trends in the early, high-valence actinides.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2022

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

Abstract As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

Burley, Stephen K. (ORCID:0000000224879713)↗
DOE OSTI2020

Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations

Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG gene ERCC5 lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG’s role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Effects on Human Non-Small Lung Cancer Cell growth of Cu(II), Au(III) and Re(I) Complexes Containing N-donor Pyridyl Ligands: A Senior Undergraduate Research Project

Hands-on synthetic laboratory experiences are critically important for undergraduate chemistry majors. A senior undergraduate research experience at the College of Wooster is presented in the current work. The inorganic complexes [Cu(phenan) 2 (NO 3 ) 2 ] (1; phenan = phenanthridine) and [Au(phenan)Cl 3 ](2) were prepared by metallation of the phenan ligand in a 1:1 CH 3 OH/CH 2 Cl 2 mixture at room temperature. Complex 1 is a new inorganic coordination compound. The structures were confirmed by X-ray crystallography. Complex 1 reveals a distorted octahedral geometry around the central Cu (II) metal ion. In complex 2, the Au(III) atom exhibits a square planar geometry. In addition, we investigated [Cu(dmeobpy)(H 2 O) 2 ][NO 3 ] 2 (3; dmeobpy = 4,4’-dimethoxy-2,2’-bipyridine), [Cu(bap)(NO 3 ) 2 ](4; bap = 2,6-bis(azaindole)pyridine) and [Re(CO) 3 (dmeobpy)Cl] (5). The cytoxocities of 1-5, phenan, dmeobpy, bap and cisplatin were evaluated against several human non-small cell lung cancer cell lines (NCI-H1975, HCC827, NCI-H460, and NCI-A549). Compound 1 exhibited modest antitumor activity against the HCC827 cell line, with an IC 50 value of 19 µM. Compound 3 exhibits lower cytotoxic activity than 1. Finally, the cytotoxic activity of complex 5 (IC 50 < 11 µM) is significantly greater than 1 and 3 against the H1975 cancer cell line.

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

Entropic control of the free-energy landscape of an archetypal biomolecular machine

Biomolecular machines are complex macromolecular assemblies that utilize thermal and chemical energy to perform essential, multistep, cellular processes. Despite possessing different architectures and functions, an essential feature of the mechanisms of action of all such machines is that they require dynamic rearrangements of structural components. Surprisingly, biomolecular machines generally possess only a limited set of such motions, suggesting that these dynamics must be repurposed to drive different mechanistic steps. Although ligands that interact with these machines are known to drive such repurposing, the physical and structural mechanisms through which ligands achieve this remain unknown. Using temperature-dependent, single-molecule measurements analyzed with a time-resolution-enhancing algorithm, here, we dissect the free-energy landscape of an archetypal biomolecular machine, the bacterial ribosome, to reveal how its dynamics are repurposed to drive distinct steps during ribosome-catalyzed protein synthesis. Specifically, we show that the free-energy landscape of the ribosome encompasses a network of allosterically coupled structural elements that coordinates the motions of these elements. Moreover, we reveal that ribosomal ligands which participate in disparate steps of the protein synthesis pathway repurpose this network by differentially modulating the structural flexibility of the ribosomal complex (i.e., the entropic component of the free-energy landscape). Here, we propose that such ligand-dependent entropic control of free-energy landscapes has evolved as a general strategy through which ligands may regulate the functions of all biomolecular machines. Such entropic control is therefore an important driver in the evolution of naturally occurring biomolecular machines and a critical consideration for the design of synthetic molecular machines.

Science & Technology - Other Topics↗
DOE OSTI2021

Structural Manipulation of a Zirconocene-Based Porous Coordination Cage Using External and Host–Guest Stimuli

Porous coordination cages (PCCs) constructed from a zirconocene-based cluster have drawn great attention for their high stability and structural tunability. These features have enabled these cages to be utilized for a wide array of applications. Here this work demonstrates the structural flexibility and stimulus-responsive features of two interconvertible zirconocene-based PCCs. The subjects, PCC-20c (capsular) and PCC-20t (tetrahedral), are constructed from the same cluster and ligand but exhibit different shapes and properties. In the synthetic study of the cages, it is found that higher temperatures of synthesis yield PCC-20c in several different crystalline phases while lower temperatures of synthesis yield pure phase PCC-20t. Thermodynamic studies on the interconversion of the two cages show that the conversion from PCC-20t into PCC-20c is an entropically driven process and can be largely affected by the solvent environment. Additionally, the process of PCC-20t/c conversion can be mediated by the counter anions and light irradiation as evidenced by the change in equilibrium constants under these influences. The current studies are conducted to decipher how the PCC-20t/c phase can be controllably synthesized, interconverted, and their properties can be modified under the use of external stimuli: heat, light, and guest molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Solution-processable copper(I) iodide-based inorganic-organic hybrid semiconductors composed of both coordinate and ionic bonds

Three new one-dimensional (1D) All-In-One (AIO) type CuI-based hybrid semiconductors with both dative and ionic bonds between the inorganic and organic components have been successfully designed and synthesized by using the ligands containing both cationic center and coordination available sites. Structural analysis confirms that all compounds share the same formula of Cu 4 I 6 (L) 2 (L = ligand) and are composed of 1D-Cu 4 I 6 2- anionic chains that coordinate to cationic ligands. Additionally, these materials demonstrate high stability towards heat and moisture and excellent solution processability due to their unique bonding nature. They emit low energy light ranging from green to orange color (530-590 nm). The origin and mechanism of their emissions were studied by both experimental and theoretical methods. More importantly, all compounds can be easily fabricated into films by solution process, a desired but rare feature for most of CuI-based hybrids built of extended networks.

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

Hydration of divalent lanthanides, Sm 2+ and Eu 2+ : A molecular dynamics study with polarizable AMOEBA force field

The chemistry of divalent lanthanides, Ln 2+ , is a growing sub-field of heavy element chemistry owing to new synthetic approaches. However, some theoretical aspects of these unusual cations are currently underdeveloped, especially as they relate to their dynamic properties in solution. In this study, we address the hydration of two of the classical Ln 2+ cations, Sm 2+ and Eu 2+ , using atomic multipole optimized energetic for biomolecular applications (AMOEBA) force fields. These cations have not been parameterized to date with AMOEBA, and few studies are available because of their instability with respect to oxidation in aqueous media. Coordination numbers (CN's) of 8.2 and 8.1 respectively for Sm 2+ and Eu 2+ , and 8.8 for both Sm 3+ and Eu 3+ have been obtained and are in good agreement with the few available AIMD and X-ray absorption fine structures studies. The decreased CN of Ln 2+ compared with Ln 3+ arises from progressive water exchange events that indicates the gradual stabilization of 8-coordinate structures with respect to 9-coordinate geometries. Moreover, the effects of the chloride counter anions on the coordination of Ln 2+ cations have been studied at different chloride concentrations in this work. Lastly, water exchange times of Ln 2+ cations have been calculated to provide a comprehensive understanding of the behavior of Eu 2+ and Sm 2+ in aqueous chloride media.

AMOEBA force field parameterization↗
DOE OSTI2025

Image-Driven Hybrid Structural Analysis Based on Continuum Point Cloud Method with Boundary Capturing Technique

Conventional approaches for the structural health monitoring of infrastructures often rely on physical sensors or targets attached to structural members, which require considerable preparation, maintenance, and operational effort, including continuous on-site adjustments. This paper presents an image-driven hybrid structural analysis technique that combines digital image processing (DIP) and regression analysis with a continuum point cloud method (CPCM) built on a particle-based strong formulation. Polynomial regressions capture the boundary shape change due to the structural loading and precisely identify the edge and corner coordinates of the deformed structure. The captured edge profiles are transformed into essential boundary conditions. This allows the construction of a strongly formulated boundary value problem (BVP), classified as the Dirichlet problem. Capturing boundary conditions from the digital image is novel, although a similar approach was applied to the point cloud data. It was shown that the CPCM is more efficient in this hybrid simulation framework than the weak-form-based numerical schemes. Unlike the finite element method (FEM), it can avoid aligning boundary nodes with regression points. A three-point bending test of a rubber beam was simulated to validate the developed technique. The simulation results were benchmarked against numerical results by ANSYS and various relevant numerical schemes. The technique can effectively solve the Dirichlet-type BVP, yielding accurate deformation, stress, and strain values across the entire problem domain when employing a linear strain model and increasing the number of CPCM nodes. In addition, comparative analysis with conventional displacement tracking techniques verifies the developed technique’s robustness. The proposed technique effectively circumvents the inherent limitations of traditional monitoring methods resulting from the reliance on physical gauges or target markers so that a robust and non-contact solution for remote structural health monitoring in real-scale infrastructures can be provided, even in unfavorable experimental environments.

Chemistry↗
DOE OSTI2025

Molecular insights into Yb(III) speciation in sulfate-bearing hydrothermal fluids from X-ray absorption spectra informed by ab initio molecular dynamics

Rare earth elements (REEs) are critical for advanced technologies, yet in hydrothermal aqueous solutions the molecular level details of their interaction with ligands that control their geochemical transport and deposition remain poorly understood. Here, this study elucidates the coordination behavior of Yb 3+ in sulfate-rich hydrothermal fluids using in situ extended X-ray absorption fine structure (EXAFS) spectroscopy and ab initio molecular dynamics (AIMD) simulations. By integrating multi-angle EXAFS with AIMD-derived constraints, we precisely resolve Yb 3+ coordination structures and ligand interactions under hydrothermal conditions. At room temperature, Yb 3+ is coordinated by five water molecules and two sulfate ligands (coordination number, CN = 8), forming a distorted square antiprism geometry. Increasing temperature induces progressive dehydration, reducing the hydration shell and favoring stronger sulfate complexation. At 200°C, sulfate ligands reorganize around Yb 3+ , shifting its geometry to a capped octahedron (CN = 7). At 300 °C, sulfate binding dominates, leading to structural reorganization that parallels the onset of sulfate mineral precipitation, consistent with the retrograde solubility of REE sulfates. These findings provide direct molecular-scale evidence that sulfate acts as both a transport and deposition ligand, critically influencing REE mobility in geochemical environments. Our results can also help to refine thermodynamic models of REE speciation in high-temperature hydrothermal fluids and improve our understanding of REE ore formation processes in nature.

AIMD↗
DOE OSTI2021

Moving beyond the constraints of chemistry via crystal structure discovery with isotropic multiwell pair potentials

The rigid constraints of chemistry-dictated by quantum mechanics and the discrete nature of the atom-limit the set of observable atomic crystal structures. What structures are possible in the absence of these constraints? Here, we systematically crystallize one-component systems of particles interacting with isotropic multiwell pair potentials. We investigate two tunable families of pairwise interaction potentials. Our simulations self-assemble a multitude of crystal structures ranging from basic lattices to complex networks. Sixteen of the structures have natural analogs spanning all coordination numbers found in inorganic chemistry. Fifteen more are hitherto unknown and occupy the space between covalent and metallic coordination environments. The discovered crystal structures constitute targets for self-assembly and expand our understanding of what a crystal structure can look like.

crystal structures↗
DOE OSTI2022

The Synthesis and Structure of a Scandium Nitrate Hydroxy-Bridged Dimeric Complex Supported by Bipyridyl Ligands

The current discussion on whether scandium, yttrium and lanthanum should represent Group 3 in the Periodic Table or whether lutetium should replace lanthanum in the group has prompted us to further explore the structural chemistry of the Group 3 elements and compare the coordination numbers and coordination geometries adopted. The steric and electronic properties of the coordinated ligands have a major influence on the structures adopted. We report the synthesis and crystal structure determination of an unusual dinuclear scandium complex [(bipy)(NO 3 ) 2 Sc(µ-OH) 2 Sc(NO 3 ) 2 (bipy)] obtained by the reaction of hydrated scandium nitrate with 2,2'-bipyridyl (bipy) in either ethanol or nitromethane. The crystal structure of the complex shows that the scandium centers are eight coordinate, and the structure obtained contrasts with related complexes found in the lanthanide series [Ln(bipy) 2 (NO 3 ) 3 ] and [Ln(phen) 2 (NO 3 ) 3 ] (phen = phenanthroline) and in [M(terpy)(NO 3 ) 3 ] (M = Sc, Er–Lu), where these complexes are all mononuclear.

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

Probing Distinctive Redox Mechanism in Ni-Rich Cathode Via Real-Time Quick X-Ray Absorption Spectroscopy

X-ray radiation damage on the measuring system has been a critical issue regularly for a long-time exposure to X-ray beam during the in operando characterizations, which is particularly severe when the applied X-ray energy is near the absorption edges (M, L, K, etc.) of the interest element. Here, to minimize the negative effects raised by beam radiation, we employ quick X-ray absorption spectroscopy (QXAS) to study the electrochemical reaction mechanism of a Ni-rich layered structure cathode for lithium-ion batteries. With the advanced QXAS technique, the electronic structure and local coordination environment of the transition metals (TMs) are monitored in-operando with limited radiation damage. Compared to the conventional step-mode X-ray absorption spectroscopy, the QXAS can provide more reliable oxidation state change and more detailed local structure evolutions surrounding TMs (Ni and Co) in Ni-rich layered oxides. By leveraging these advantages of QXAS, we demonstrated that the Ni dominates the electrochemical process with the Co being almost electrochemically inactive. Reversible Ni ions movement between TMs sites and Li sites is also revealed by the time-resolved QXAS technique.

25 ENERGY STORAGE↗