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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Molecular-Scale Insights into the Heterogeneous Interactions between an m -Terphenyl Isocyanide Ligand and Noble Metal Nanoparticles

The structural and chemical properties of metal nanoparticles are often dictated by their interactions with molecular ligand shells. These interactions are highly material-specific and can vary significantly even among elements within the same group or materials with similar crystal structure. In this study, we surveyed the heterogeneous interactions between an m-terphenyl isocyanide ligand and Au and Ag nanoparticles (NPs) at the single-molecule limit. Specifically, we found that the ligation behavior with this molecule differs significantly between that of Au and AgNPs. Surface-enhanced Raman spectroscopy measurements revealed unique enhancement factors for two molecular vibrational modes between two metal surfaces, indicating different ligand binding geometries. Molecular-level characterization using scanning tunneling microscopy allowed us to directly visualize these variations between Ag and Au surfaces, which we assign as two distinct binding mechanisms. This molecular-scale visualization provides clear insights into the different ligand–metal interactions as well as the chemical behavior and spectroscopic characteristics of isocyanide-functionalized NPs.

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

Metal–Carbodithioate-Based 3D Semiconducting Metal–Organic Framework: Porous Optoelectronic Material for Energy Conversion

Solar energy conversion requires the working compositions to generate photoinduced charges with high potential and the ability to deliver charges to the catalytic sites and/or external electrode. These two properties are typically at odds with each other and call for new molecular materials with sufficient conjugation to improve charge conductivity but not as much conjugation as to overly compromise the optical band gap. In this work, we developed a semiconducting metal-organic framework (MOF) prepared explicitly through metal-carbodithioate"(-CS 2 ) n M" linkage chemistry, entailing augmented metal-linker electronic communication. The stronger ligand field and higher covalent character of metal-carbodithioate linkages-when combined with spirofluorene-derived organic struts and nickel-(II) ion-based nodes-provided a stable, semiconducting 3D-porous MOF, Spiro-CS 2 Ni. This MOF lacks long-range ordering and is defined by a flexible structure with non-aggregated building units, as suggested by reverse Monte Carlo simulations of the pair distribution function obtained from total scattering experiments. The solvent-removed "closed pore"material recorded a Brunauer-Emmett-Teller area of similar to 400m 2 /g, where the "open pore" form possesses90 wt % solvent-accessible porosity. Electrochemical measurements suggest that Spiro-CS 2 Ni possesses a band gap of 1.57 eV(sigma = 10 -7 S/cm at -1.3 V bias potential),which can be further improved by manipulating the d-electron configuration through an axial coordination (ligand/substrate), the latter of which indicates usefulness as an electrocatalyst and/or a photoelectrocatalyst(upon substrate binding). Transient-absorption spectroscopy reveals a long-lived photo-generated charge-transfer state (τ CR = 6.5 mu s) capable of chemical transformation under a biased voltage. Spiro-CS 2 Ni can endure a compelling range of pH(1-12 for weeks) and hours of electrochemical and photoelectrochemical conditions in the presence of water and organic acids. We believe this work provides crucial design principles for low-density, porous,light-energy-conversion materials.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Defect‐Mediated Ordering of Condensed Water Structures in Microporous Zeolites

Abstract Ab‐initio molecular dynamics simulations and transmission infrared spectroscopy are employed to characterize the structure of water networks in defect‐functionalized microporous zeolites. Thermodynamically stable phases of clustered water molecules are localized at some of the defects in zeolite Beta, which include catalytic sites such as framework Lewis acidic Sn atoms in closed and hydrolyzed‐open forms, as well as silanol nests. These water clusters compete with ideal gas‐like structures at low water densities and pore‐filling phases at higher water densities, with the equilibrium phase determined by the water chemical potential. The physical characteristics of these phases are determined by the defect identity, with the local binding and orientation of hydroxyl moieties around the defects playing a central role. The results suggest general principles for how the structure of polar solvents in microporous solid acids is influenced by local defect functionalization, and the thermodynamic stability of the condensed phases surrounding such sites, in turn, implies that the catalysis of Lewis acids will be influenced by local water ordering.

Bukowski, Brandon C.↗
DOE OSTI2019

Defect‐Mediated Ordering of Condensed Water Structures in Microporous Zeolites

Abstract Ab‐initio molecular dynamics simulations and transmission infrared spectroscopy are employed to characterize the structure of water networks in defect‐functionalized microporous zeolites. Thermodynamically stable phases of clustered water molecules are localized at some of the defects in zeolite Beta, which include catalytic sites such as framework Lewis acidic Sn atoms in closed and hydrolyzed‐open forms, as well as silanol nests. These water clusters compete with ideal gas‐like structures at low water densities and pore‐filling phases at higher water densities, with the equilibrium phase determined by the water chemical potential. The physical characteristics of these phases are determined by the defect identity, with the local binding and orientation of hydroxyl moieties around the defects playing a central role. The results suggest general principles for how the structure of polar solvents in microporous solid acids is influenced by local defect functionalization, and the thermodynamic stability of the condensed phases surrounding such sites, in turn, implies that the catalysis of Lewis acids will be influenced by local water ordering.

Bukowski, Brandon C.↗
DOE OSTI2025

Subnanometer Thick Native sp 2 Carbon on Oxidized Diamond Surfaces

Oxygen-terminated diamond has a wide breadth of applications, which include stabilizing near-surface color centers, semiconductor devices, and biological sensors. Despite the vast literature on characterizing functionalization groups on diamond, the chemical composition of the shallowest portion of the surface (<1 nm) is challenging to probe with conventional techniques like XPS and FTIR. In this work, we demonstrate the use of angleresolved XPS to probe the first ten nanometers of both oxygen and hydrogen terminated (100) single-crystalline diamond grown via chemical vapor deposition (CVD). With the use of consistent peakfitting methods, the peak identities and relative peak binding energies were identified for sp 2 carbon, ether, hydroxyl, carbonyl, and C−H groups for both of these diamond surface terminations. For the oxygen-terminated sample, we also quantified the thickness of the sp 2 carbon layer situated on top of the bulk sp 3 diamond bonded carbon to be 0.3 ± 0.1 nm, based on the analysis of the Auger electron spectra and D-parameter calculations. These results indicate that the majority of the oxygen is bonded to the sp 2 carbon layer on the diamond, and not directly to the sp 3 diamond bonded carbon.

Carbon↗
DOE OSTI2023

Architector for high-throughput cross-periodic table 3D complex building

Abstract Rare-earth and actinide complexes are critical for a wealth of clean-energy applications. Three-dimensional (3D) structural generation and prediction for these organometallic systems remains a challenge, limiting opportunities for computational chemical discovery. Here, we introduce Architector , a high-throughput in-silico synthesis code for s-, p-, d-, and f-block mononuclear organometallic complexes capable of capturing nearly the full diversity of the known experimental chemical space. Beyond known chemical space, Architector performs in-silico design of new complexes including any chemically accessible metal-ligand combinations. Architector leverages metal-center symmetry, interatomic force fields, and tight binding methods to build many possible 3D conformers from minimal 2D inputs including metal oxidation and spin state. Over a set of more than 6,000 x-ray diffraction (XRD)-determined complexes spanning the periodic table, we demonstrate quantitative agreement between Architector-predicted and experimentally observed structures. Further, we demonstrate out-of-the box conformer generation and energetic rankings of non-minimum energy conformers produced from Architector , which are critical for exploring potential energy surfaces and training force fields. Overall, Architector represents a transformative step towards cross-periodic table computational design of metal complex chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Discovery of dual-activity small-molecule ligands of Pseudomonas aeruginosa LpxA and LpxD using SPR and X-ray crystallography

The lipid A biosynthesis pathway is essential in Pseudomonas aeruginosa. LpxA and LpxD are the first and third enzymes in this pathway respectively, and are regarded as promising antibiotic targets. The unique structural similarities between these two enzymes make them suitable targets for dual-binding inhibitors, a characteristic that would decrease the likelihood of mutational resistance and increase cell-based activity. We report the discovery of multiple small molecule ligands that bind to P. aeruginosa LpxA and LpxD, including dual-binding ligands. Binding poses were determined for select compounds by X-ray crystallography. The new structures reveal a previously uncharacterized magnesium ion residing at the core of the LpxD trimer. In addition, ligand binding in the LpxD active site resulted in conformational changes in the distal C-terminal helix-bundle, which forms extensive contacts with acyl carrier protein (ACP) during catalysis. These ligand-dependent conformational changes suggest a potential allosteric influence of reaction intermediates on ACP binding, and vice versa. Taken together, the novel small molecule ligands and their crystal structures provide new chemical scaffolds for ligand discovery targeting lipid A biosynthesis, while revealing structural features of interest for future investigation of LpxD function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Analysis of the Fe 2p XPS for hematite α Fe2O3: Consequences of covalent bonding and orbital splittings on multiplet splittings

The origins of the complex Fe 2p X-Ray Photoelectron Spectra (XPS) of hematite (α-Fe2O3) are analyzed and related to the character of the bonding in this compound. This analysis provides a new and novel view of the reasons for XPS binding energies (BEs) and BE shifts, which deepens the current understanding and interpretation of the physical and chemical significance of the XPS. In particular, many-body effects are considered for the initial and the final, 2p-hole configuration wavefunctions. It is shown that a one-body or one-configuration analysis is not sufficient and that the many-body, many-determinantal, and many-configurational character of the wavefunctions must be taken into account to describe and understand why the XPS intensity is spread over an extremely large number of final 2p-hole multiplets. The focus is on the consequences of angular momentum coupling of the core and valence open shell electrons, the ligand field splittings of the valence shell orbitals, and the degree of covalent mixing of the Fe(3d) electrons with the O(2p) electrons. Novel theoretical methods are used to estimate the importance of these various terms. An important consequence of covalency is a reduction in the energy separation of the multiplets. Although shake satellites are not considered explicitly, the total losses of intensity from the angular momentum multiplets to shake satellites is determined and related to the covalent character of the Fe-O interaction. The losses are found to be the same for Fe 2p1/2 and 2p3/2 ionization.

Bagus, Paul S. (ORCID:0000000349315217)↗
DOE OSTI2020

Structural basis for substrate recognition and chemical inhibition of oncogenic MAGE ubiquitin ligases

Testis-restricted melanoma antigen (MAGE) proteins are frequently hijacked in cancer and play a critical role in tumorigenesis. MAGEs assemble with E3 ubiquitin ligases and function as substrate adaptors that direct the ubiquitination of novel targets, including key tumor suppressors. However, how MAGEs recognize their targets is unknown and has impeded the development of MAGE-directed therapeutics. Here, we report the structural basis for substrate recognition by MAGE ubiquitin ligases. Biochemical analysis of the degron motif recognized by MAGE-A11 and the crystal structure of MAGE-A11 bound to the PCF11 substrate uncovered a conserved substrate binding cleft (SBC) in MAGEs. Mutation of the SBC disrupted substrate recognition by MAGEs and blocked MAGE-A11 oncogenic activity. A chemical screen for inhibitors of MAGE-A11:substrate interaction identified 4-Aminoquinolines as potent inhibitors of MAGE-A11 that show selective cytotoxicity. These findings provide important insights into the large family of MAGE ubiquitin ligases and identify approaches for developing cancer-specific therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Core-level binding energy shifts between interior, terrace and edge atoms in MnO(001) thin films

Understanding the physical origin of core-level photoemission line shapes can offer valuable information about the chemical and physical properties of surfaces. For instance, in a large number of transition metals oxides, changes in the line shape allow the accurate determination of their oxidation states and cation site symmetry. Yet, despite this importance, experimental investigations on core-level shifts have been much neglected in recent years. In order to provide further evidence of the physical relevance, we have, in this contribution, introduced a new aspect of interior-, terrace- and edge- atom core-level binding energy shifts to describe monolayers of MnO(001) films grown on an Au(111) substrate. By this means we were able to distinguish the line shape contributions related to different types of atomic sites. Here we show that their relative intensities and energy shifts are able to provide information about the relative amount of under coordinated atoms on the surface and, thus give insights into their catalytic properties. Our findings reveal the importance of a detailed surface science characterization to provide the correct interpretation of distinct photoemission line shapes when considering thin film samples as well as nanostructures in general.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Water-polyamide chemical interplay in desalination membranes explored by ambient pressure X-ray photoelectron spectroscopy

Reverse osmosis using aromatic polyamide membranes is currently the most important technology for seawater desalination. The performance of reverse osmosis membranes is highly dependent on the interplay of their surface chemical groups with water and water contaminants. In order to better understand the underlying mechanisms of these membranes, we study ultrathin polyamide films that chemically resemble reverse osmosis membranes, using ambient pressure X-ray photoelectron spectroscopy. This technique can identify the functional groups at the membrane–water interface and allows monitoring of small shifts in the electron binding energy that indicate interaction with water. We observe deprotonation of free acid groups and formation of a ‘water complex’ with nitrogen groups in the polymer upon exposure of the membrane to water vapour. The chemical changes are reversed when water is removed from the membrane. While the correlation between functional groups and water uptake is an established one, this experiment serves to understand the nature of their chemical interaction, and opens up possibilities for tailoring future materials to specific requirements.

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

Harnessing biomimetic cryptic bonds to form self-reinforcing gels

Cryptic sites, which lay hidden in folded biomolecules, become exposed by applied force and form new bonds that reinforce the biomaterial. While these binding interactions effectively inhibit mechanical deformation, there are few synthetic materials that harness mechano-responsive cryptic sites to forestall damage. Here, we develop a computational model to design polymer gels encompassing cryptic sites and a lower critical solution temperature (LCST). LCST gels swell with a decrease in temperature, thereby generating internal stresses within the sample. The gels also encompass loops held together by the cryptic sites, as well as dangling chains with chemically reactive ends. A decrease in temperature or an applied force causes the loops to unfold and expose the cryptic sites, which then bind to the dangling chains. We show that these binding interactions act as “struts” that reinforce the network, as indicated by a significant decrease in the volume of the gel (from 44% to 80%) and shifts in the volume phase transition temperature. Once the temperature is increased or the deformation is removed, the latter “cryptic bonds” are broken, allowing the loops to refold and the gel to return to its original state. These findings provide guidelines for designing polymer networks with reversible, mechano-responsive bonds, which allow gels to undergo a self-stiffening behavior in response to a temperature-induced internal stress or external force. When applied as a coating, these gels can prevent the underlying materials from undergoing damage and thus, extend the lifetime of the system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Selective Adsorption of Thiol-Containing Molecules on Copper Sulfide Surfaces via Molecule–Surface Disulfide Bridges

Recent results in the fields of nanoenhanced agriculture and expanding interest in prebiotic chemistry have placed increased emphasis on understanding the chemically selective interaction of small molecules with the surfaces of metal sulfides. Here, we present an integrated experimental and computational study of the interaction of thiol-containing molecules with copper sulfide (covellite) surfaces in aqueous media. In situ Fourier-transform infrared (FTIR) measurements and ex situ X-ray photoelectron spectroscopy (XPS) measurements show that molecules bearing free thiol groups, including glutathione and cysteine, bind strongly to CuS (covellite) nanoparticles and to CuS (001) single crystals, while control studies show that similar molecules lacking the free thiol group exhibit much less binding. Additional experiments show that these thiol-containing molecules interact transiently with CuO nanoparticle surfaces but are readily removed by rinsing. The FTIR and XPS experiments demonstrate that adsorption of molecular thiols to CuS surfaces occurs in a chemically selective manner. Further experimental studies and density functional calculations show that the preferred mode of binding is through the surface S atoms, forming a Solid–S–S–Molecule disulfide linkage. While the role of disulfide linkages in controlling structure and function of proteins and other biomolecules is widely known, the formation of surface disulfide linkages as a motif for covalent molecular binding at surfaces has not been established previously.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Analysis of Bis(trifluoromethylsulfonyl)imide Interactions with Metal Cations Through a Chemical Informatics Approach

Nominally weakly coordinating anions are useful for modulating the solubility and chemical properties of metal complexes, but identification and analysis of the systematics of the interactions of anions with cationic metal complexes has not received the attention it deserves. Here, a chemical informatics approach is demonstrated for identifying and quantitatively analyzing the ways that the bis(trifluoromethylsulfonyl)imide anion (TFSI) can interact with metal-containing species. An open access computer program (PyCIFTer) was developed to facilitate large-scale structural analysis of TFSI-containing species by utilization of experimental atomic coordinate data from single-crystal X-ray diffraction (XRD) studies obtained from the Cambridge Structural Database (CSD). PyCIFTer establishes a three-dimensional vector space from the raw atomic coordinates, generating acyclic, undirected graphs that are used to rapidly analyze the structural properties (bond lengths and angles) of TFSI in individual structures in sequential/batch fashion. The structures are sorted by PyCIFTer into groups based on pre-set and chemically sensible criteria, affording a comprehensive and systematic view of TFSI structural chemistry. This approach avoids tedious one-at-a-time interrogation of structures, a prospect unreasonable in this case, and many others of contemporary chemical relevance; there were over 1500 structures in the CSD containing TFSI as of November 2024. The results demonstrate that TFSI only rarely binds to cations in the solid state, favoring the formation of species in which TFSI is found in cations’ outer coordination spheres. The prospect of applying PyCIFTer to other moieties is also discussed. PyCIFTer is also schematically compared to the commercial CSD Python application programming interface (API). Taken together, this work demonstrates the usefulness of modular workflows for sequential/batch analysis of structural data from XRD, an approach that appears poised to accelerate the translation of legacy structural results into new chemical insights and hypotheses.

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

High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules

Flaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae. The flavivirus genome contains a 5’ end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5’ guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small-molecule inhibitors to disrupt the promoter function. To facilitate identification of small molecule binding sites in flavivirus SLA, we determined high-resolution structures of bottom and top stems of ZIKV SLA, which contain a single U- or G-bulge, respectively. Both bulge nucleotides exhibit multiple orientations, from folded back on the adjacent nucleotide to flipped out of the helix, and are stabilized by stacking or base triple interactions. These structures suggest that even a single unpaired nucleotide can provide flexibility to RNA structures and its conformation is mainly determined by the stabilizing chemical environment. To facilitate discovery of small molecule inhibitors that interfere with the functions of ZIKV SLA, we screened and identified compounds that bind to the bottom and top stems of ZIKV SLA.

Biochemistry & Molecular Biology↗
DOE OSTI2021

A General Strategy to Immobilize Single‐Atom Catalysts in Metal–Organic Frameworks for Enhanced Photocatalysis

Abstract Single‐atom catalysts (SACs) are witnessing rapid development due to their high activity and selectivity toward diverse reactions. However, it remains a grand challenge in the general synthesis of SACs, particularly featuring an identical chemical microenvironment and on the same support. Herein, a universal synthetic protocol is developed to immobilize SACs in metal–organic frameworks (MOFs). Significantly, by means of SnO 2 as a mediator or adaptor, not only different single‐atom metal sites, such as Pt, Cu, and Ni, etc., can be installed, but also the MOF supports can be changed (for example, UiO‐66‐NH 2 , PCN‐222, and DUT‐67) to afford M 1 /SnO 2 /MOF architecture. Taking UiO‐66‐NH 2 as a representative, the Pt 1 /SnO 2 /MOF exhibits approximately five times higher activity toward photocatalytic H 2 production than the corresponding Pt nanoparticles (≈2.5 nm) stabilized by SnO 2 /UiO‐66‐NH 2 . Remarkably, despite featuring identical parameters in the chemical microenvironment and support in M 1 /SnO 2 /UiO‐66‐NH 2 , the Pt 1 catalyst possesses a hydrogen evolution rate of 2167 µmol g –1 h –1 , superior to the Cu 1 and Ni 1 counterparts, which is attributed to the differentiated hydrogen binding free energies, as supported by density‐functional theory (DFT) calculations. This is thought to be the first report on a universal approach toward the stabilization of SACs with identical chemical microenvironment on an identical support.

Sui, Jianfei↗
DOE OSTI2020

Manipulating the Geometric and Electronic Structures of Manganese Nitrides for Ammonia Synthesis

Abstract Manganese (Mn) nitrides are important nitrogen (N) carriers for small‐scale intermittent ammonia (NH 3 ) synthesis. However, only 3∼8 % of lattice N are converted into NH 3 . In this study, the geometric and electronic structures of well‐defined Mn 4 N and Mn 2 N lattices were altered using transition metal heteroatoms (Cr, Fe, Co, Ni, Mo) to understand the driving force behind lattice N diffusion and extraction. Density Functional Theory (DFT) revealed that the binding of early hydrogenation product (NH) follows a linear relationship with lattice N over a wide range of close‐packed surfaces. But, the binding of NH 2 and NH 3 are more sensitive to the geometric and electronic structures. Further, the chemical bonding can be quantitatively characterized with the covalency derived from Crystal Orbital Hamiltonian Population (COHP). In the Eley Rideal‐Mars van Krevelan pathway, the overall NH 3 formation free energy ( ) and lattice N diffusion barrier ( ) are the respective thermodynamic and kinetic determining factors. Aided by a rate‐determining step (RDS) model, Mn 4 N modified with Fe, Co, Ni single‐atom dopants all show enhanced rates for NH 3 formation.

Shan, Nannan↗