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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Direct Monitoring of Conical Intersection Passage via Electronic Coherences in Twisted X-Ray Diffraction

Quantum coherences in electronic motions play a critical role in determining the pathways and outcomes of virtually all photophysical and photochemical molecular processes. However, the direct observation of electronic coherences in the vicinity of conical intersections remains a formidable challenge. Here we propose a novel time-resolved twisted x-ray diffraction technique that can directly monitor the electronic coherences created as the molecule passes through a conical intersection. We show that the contribution of electronic populations to this signal is canceled out when using twisted x-ray beams that carry a light orbital angular momentum, providing a direct measurement of transient electronic coherences in gas-phase molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Small-molecule modulation of β-arrestins

β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily. Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein–receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin–receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.

Kahsai, Alem W. [Duke University, Durham, NC (Unit↗
DOE OSTI2025

Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6

Human Interleukin-6 (hIL-6) is a pro inflammatory cytokine that binds to its receptor, IL-6Rα followed by binding to gp130 and subsequent dimerization to form a hexamer signaling complex. As a critical inflammation mediator, hIL-6 is associated with a diverse range of diseases and monoclonal antibodies in clinical use that either target IL-6Rα or hIL-6 to inhibit signaling. Here, we perform high-throughput structure-based computational screening using ensemble docking for small-molecule antagonists for which the target conformations were taken from 600 ns long molecular dynamics simulations of the apo protein. Prior knowledge of the contact sites from binary complex studies and experimental work was incorporated into the docking studies. The top 20 scoring ligands from the in silico studies after post analysis were subjected to in vitro functional assays. Among these compounds, the ligand with the second-highest calculated binding affinity experimentally showed an ~84% inhibitory effect on IL6-induced STAT3 reporter activity at 10 μM concentration. This finding may pave the way for designing small-molecule inhibitors of hIL-6 of therapeutic significance.

Human Interleukin-6↗
DOE OSTI2021

Signatures of electronic and nuclear coherences in ultrafast molecular x-ray and electron diffraction

Femtosecond x-ray and electron diffraction hold promise to image the evolving structures of single molecules. We present a unified quantum-electrodynamical formulation of diffraction signals, based on the exact many-body nuclear + electronic wavefunction that can be extracted from quantum chemistry simulations. This gives a framework for analyzing various approximate molecular dynamics simulations. We show that the complete description of ultrafast diffraction signals contains interesting contributions involving mixed elastic and inelastic scattered photons that are usually masked by other larger contributions and are neglected. These terms include overlaps of nuclear wavepackets between different electronic states that provide an electronic decoherence mechanism and are important for the time-resolved imaging of conical intersections.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Ultrafast disruptive probing: Simultaneously keeping track of tens of reaction pathways

Ultrafast science depends on different implementations of the well-known pump–probe method. Here, we provide a formal description of ultrafast disruptive probing, a method in which the probe pulse disrupts a transient species that may be a metastable ion or a transient state of matter. Disruptive probing has the advantage of allowing for simultaneous tracking of the yield of tens of different processes. Our presentation includes a numerical model and experimental data on multiple products resulting from the strong-field ionization of two different molecules, partially deuterated methanol and norbornene. The correlated enhancement and depletion signals between all the different fragmentation channels offer comprehensive information on photochemical reaction pathways. In combination with ion imaging and/or coincidence momentum imaging or as complementary to atom-specific probing or ultrafast diffraction methods, disruptive probing is a particularly powerful tool for the study of strong-field laser–matter interactions.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Decoding ultrafast polarization responses in lead halide perovskites by the two-dimensional optical Kerr effect

Significance Optoelectronic devices, such as photovoltaics or light-emitting diodes, are based on the interaction of light with charges in the active material. Lead halide perovskites (LHPs) have emerged as excellent materials for optoelectronics, but mysteries remain as to how these materials interact with light. Here, we develop a spectroscopic method to observe the nearly instantaneous responses of LHPs to propagating light fields. This method has allowed us to precisely trace a nonlinear material response resulting from the mixing of different light components overtaking each other during propagation. The resulting oscillatory signals could be easily confused with collective motions of ions or molecules, but are quantitatively accounted by strong nonlinear mixing and polarization-dressed light propagation in single-crystal LHPs.

14 SOLAR ENERGY↗
DOE OSTI2021

Molecular structure retrieval directly from laboratory-frame photoelectron spectra in laser-induced electron diffraction

Ubiquitous to most molecular scattering methods is the challenge to retrieve bond distance and angle from the scattering signals since this requires convergence of pattern matching algorithms or fitting methods. This problem is typically exacerbated when imaging larger molecules or for dynamic systems with little a priori knowledge. Here, we employ laser-induced electron diffraction (LIED) which is a powerful means to determine the precise atomic configuration of an isolated gas-phase molecule with picometre spatial and attosecond temporal precision. We introduce a simple molecular retrieval method, which is based only on the identification of critical points in the oscillating molecular interference scattering signal that is extracted directly from the laboratory-frame photoelectron spectrum. The method is compared with a Fourier-based retrieval method, and we show that both methods correctly retrieve the asymmetrically stretched and bent field-dressed configuration of the asymmetric top molecule carbonyl sulfide (OCS), which is confirmed by our quantum-classical calculations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Pump-probe spectroscopy of chiral vibrational dynamics

A planar molecule may become chiral upon excitation of an out-of-plane vibration, changing its handedness during half a vibrational period. When exciting such a vibration in an ensemble of randomly oriented molecules with an infrared laser, half of the molecules will undergo the vibration phase-shifted by π compared to the other half, and no net chiral signal is observed. This symmetry can be broken by exciting the vibrational motion with a Raman transition in the presence of a static electric field. Subsequent ionization of the vibrating molecules by an extreme ultraviolet pulse probes the time-dependent net handedness via the photoelectron circular dichroism. Our proposal for pump-probe spectroscopy of molecular chirality, based on quantum-chemical theory and discussed for the example of the carbonyl chlorofluoride molecule, is feasible with current experimental technology.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination

To understand the dynamic structure–function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.

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

Electron Sextets as Optically Addressable Molecular Qubits: Triplet Carbenes

There is a growing demand in quantum information science and sensing for electron spin purification and readout via a spin-optical interface. This technique, known as optically detected magnetic resonance (ODMR), has been applied to diamond-NV centers and transition-metal complexes. Metal-free counterparts of these optically addressable spin qubits promise to be cheaper, more sustainable color centers with prolonged polarization lifetimes. However, progress has been hindered by the low ODMR signals of carbon-based π-diradicals, partly due to the lack of a ground singlet-to-triplet intersystem crossing (ISC). In this work, we propose exploring organic systems that are even more electron-deficient: electron sextets. Using triplet carbenes as an example, we illustrate how the ground singlet-triplet gap can be widened beyond thermal energy with the associated singlet-to-triplet ISC made available by vibronic effects. Through careful molecular engineering, this ISC can occur at a rate similar to and with an opposite spin selectivity from the excited-state ISC well-established in π-diradicals, unlocking a new ODMR pathway with potential signal gains. Persistent triplet carbenes are a renascent field, with multiple stable molecules being isolated in the past five years. To motivate further development of its emissive properties, we illustrate our design in three realistic carbene candidates that incorporate existing strategies for carbene stabilization. Furthermore, we believe that a new realm of quantum materials can be uncovered by expanding our scope toward stable electron sextets.

Carbene compounds↗
DOE OSTI2025

Surface structure of water from soft X-ray second harmonic generation

The microscopic structure of water’s surface is crucial to many natural and industrial processes, but studying its hydrogen bond (H-bond) network directly remains challenging due to the required interfacial sensitivity of experimental techniques. By leveraging advances in flat liquid sheet microjets and terawatt-scale attosecond soft X-ray pulses from the LCLS X-ray free electron laser, we employed soft X-ray second harmonic generation (SXSHG) spectroscopy to examine the liquid water/vapor interface. SXSHG combines the elemental selectivity of X-ray spectroscopies with the surface selectivity of SHG and gives access to the electronic structure of interfacial species. Here, we show the SXSHG spectrum differs from bulk water’s X-ray absorption, with its peak shifted several eV, indicating a vastly different electronic environment at the interface as compared to the bulk. First-principles electronic structure calculations show the signal is highly sensitive to H-bond interactions, such as water molecules accepting a single H-bond, which are surface abundant.

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

Defining the S-Glutathionylation Proteome by Biochemical and Mass Spectrometric Approaches

Protein S-glutathionylation (SSG) is a reversible post-translational modification (PTM) featuring the conjugation of glutathione to a protein cysteine thiol. SSG can alter protein structure, activity, subcellular localization, and interaction with small molecules and other proteins. Thus, it plays a critical role in redox signaling and regulation in various physiological activities and pathological events. In this review, we summarize current biochemical and analytical approaches for characterizing SSG at both the proteome level and at individual protein levels. To illustrate the mechanism underlying SSG-mediated redox regulation, we highlight recent examples of functional and structural consequences of SSG modifications. Finally, we discuss the analytical challenges in characterizing SSG and the thiol PTM landscape, future directions for understanding of the role of SSG in redox signaling and regulation and its interplay with other PTMs, and the potential role of computational approaches to accelerate functional discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A conspicuous 27 Al-NMR signal at 72 ppm during isomerization of Keggin Al 13 ions

A sharp signal at 72 ppm was recently observed in 27 Al-NMR spectra during the isomerization of Keggin-Al 13 ions in the presence of calcium and glycine [1]. It has been proposed that this signal corresponds to one of the Keggin isomers. Conversion of the most common ε-isomer of the Keggin series of molecules, having the stoichiometry [AlO 4 Al 12 (OH) 24 (OH 2 ) 12 ] 7+ , is enhanced by the addition of calcium and glycine [2,3]. Here we show that a 72 ppm signal can also be observed in the absence of calcium or glycine; the magnitude of which depends on aluminum concentration and temperature. Additionally, isomerization of the ε-Keggin-Al 13 to the γ-Keggin-Al 13 isomer was observed in the absence of calcium and glycine at elevated temperatures after several days. Furthermore, calcium and glycine were previously shown to enhance rates of γ-Keggin-Al 13 formation. 2.

27Al-NMR↗
DOE OSTI2022

Light Dark Matter Detection with Hydrogen-Rich Targets and Low-$T_c$ TES Detectors

Direct detection of nuclear scatterings of sub-GeV dark matter (DM) particles favors low-Z nuclei. Hydrogen nucleus, which has a single proton, provides the best kinematic match. The characteristic nuclear recoil energy is boosted by a factor of a few tens from those for larger nuclei used in traditional Weakly Interacting Massive Particles searches. Furthermore, hydrogen is optimal for detecting spin-dependent nuclear scatterings of sub-GeV DM, where large parameter space still remains unconstrained yet. In this paper, we first introduce several hydrogen-rich targets, which emit two classes of signals under kinetic excitations. One class of the signals is infrared photons, which are from fundamental vibrational and rotational modes of molecules and at several characteristic wavelengths. Another is acoustic phonons and optical phonons that decay into acoustic phonons. Then we discuss the technical status and future researches of low-T c transition-edge sensor (TES) detectors, which measure the infrared photons and acoustic phonons with desirable sensitivities. Utilization of hydrogen-rich targets and ultra-sensitive low-T c TES detectors for light DM detection requires both theoretical modeling and experimental prototyping.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Visualization and modeling of inhibition of IL-1β and TNF-α mRNA transcription at the single-cell level

Abstract IL-1β and TNF-α are canonical immune response mediators that play key regulatory roles in a wide range of inflammatory responses to both chronic and acute conditions. Here we employ an automated microscopy platform for the analysis of messenger RNA (mRNA) expression of IL-1β and TNF-α at the single-cell level. The amount of IL-1β and TNF-α mRNA expressed in a human monocytic leukemia cell line (THP-1) is visualized and counted using single-molecule fluorescent in-situ hybridization (smFISH) following exposure of the cells to lipopolysaccharide (LPS), an outer-membrane component of Gram-negative bacteria. We show that the small molecule inhibitors MG132 (a 26S proteasome inhibitor used to block NF-κB signaling) and U0126 (a MAPK Kinase inhibitor used to block CCAAT-enhancer-binding proteins C/EBP) successfully block IL-1β and TNF-α mRNA expression. Based upon this single-cell mRNA expression data, we screened 36 different mathematical models of gene expression, and found two similar models that capture the effects by which the drugs U0126 and MG132 affect the rates at which the genes transition into highly activated states. When their parameters were informed by the action of each drug independently, both models were able to predict the effects of the combined drug treatment. From our data and models, we postulate that IL-1β is activated by both NF-κB and C/EBP, while TNF-α is predominantly activated by NF-κB. Our combined single-cell experimental and modeling efforts show the interconnection between these two genes and demonstrates how the single-cell responses, including the distribution shapes, mean expression, and kinetics of gene expression, change with inhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Conformational Control of DNA Origami by DNA Oligomers, Intercalators and UV Light

DNA origami has garnered great attention due to its excellent programmability and precision. It offers a powerful means to create complex nanostructures which may not be possible by other methods. The macromolecular structures may be used as static templates for arranging proteins and other molecules. They are also capable of undergoing structural transformation in response to external signals, which may be exploited for sensing and actuation at the nanoscale. Such on-demand reconfigurations are executed mostly by DNA oligomers through base-pairing and/or strand displacement, demonstrating drastic shape changes between two different states, for example, open and close. Recent studies have developed new mechanisms to modulate the origami conformation in a controllable, progressive manner. Here we present several methods for conformational control of DNA origami nanostructures including chemical adducts and UV light as well as widely applied DNA oligomers. The detailed methods should be useful for beginners in the field of DNA nanotechnology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The APOGEE Data Release 16 Spectral Line List

The updated H-band spectral-line list (from λ15000–17000) adopted by the Apache Point Observatory Galactic Evolution Experiment (APOGEE) for the SDSS-IV Data Release 16 (DR16) is presented in this work. The APOGEE line list is a combination of atomic and molecular lines, with data drawn from laboratory, theoretical, and astrophysical sources. Oscillator strengths and damping constants are adjusted using high signal-to-noise, high-resolution spectra of the Sun, and α Boo (Arcturus), as “standard stars.” Updates to the DR16 line list, as compared to the previous DR14 version, include the addition of molecular H{sub 2}O and FeH lines, as well as a much larger (by a factor of ∼4) atomic line list, including a significantly greater number of transitions with hyperfine splitting. More recent references and line lists for the crucial molecules, CO and OH, as well as for C{sub 2} and SiH, are also included. In contrast to DR14, DR16 contains measurable lines from the heavy neutron-capture elements cerium (as Ce ii), neodymium (as Nd ii), and ytterbium (as Yb ii), as well as one line from rubidium (as Rb i), which may be detectable in a small fraction of APOGEE red giants.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Monitoring aromatic ring-currents in Mg-porphyrin by time-resolved circular dichroism

We report time-resolved circular dichroism signals (TRCD) in the X-ray regime can directly probe the magnitude and the direction of ring currents in molecules. The electronic ring currents in Mg-porphyrin, generated by a coherent superposition of electronic states induced by a circularly polarized UV pulse, are tracked by a time-delayed circularly polarized attosecond X-ray pulse. The signals are calculated using the minimal coupling Hamiltonian, which directly makes use of transition current densities. The TRCD signals obtained from the left and right circularly polarized light pump have opposite signs, revealing the direction of the ring current. Molecular aromaticity and its role in photochemical reactions such as ring opening or closure can be studied using this technique.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗