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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

A Nitroxide Containing Organic Molecule in a Deep Eutectic Solvent for Flow Battery Applications

The nitroxide radical redox organic molecule, 2-phenyl-4,4,5,5-tetrame- thylimidazoline-1-oxyl-3-oxide (PTIO), was investigated for the first time in a deep eutectic solvent (DES)-like system consisting of a 1:4 molar ratio of choline chloride and ethylene glycol(Ch1EG4) as a redox flow battery electrolyte. PTIO is a single molecule with three oxidation states, and can provide both positive and negative redox couples for a flow battery. A flow battery using the PTIO/Ch1EG4 electrolyte demonstrated nearly 50% roundtrip efficiency with an approximately 1 V open circuit potential. Inefficiencies were primarily due to membrane resistance which can be significantly lowered with increased temperature. While PTIO appears stable over short periods (hours), the oxidized form is not stable in the DES-like electrolyte over longer times. Molecular modeling was performed to investigate the relative stability of PTIO in DES as compared to the previously studied 4-hydroxy-TEMPO (4HT). It was found that the oxoammonium cation 4HT + exhibits a noticeably larger nucleophilic reactive cloud as compared to PTIO + , indicating a higher reactivity. This method to predict stability of the oxoammonium cation shows promise to inform the design and synthesis of promising redox systems based on nitroxide radicals in DES electrolytes to identify new chemistries for large scale energy storage.

25 ENERGY STORAGE↗
DOE OSTI2021

Light–matter interaction of a molecule in a dissipative cavity from first principles

Cavity-mediated light–matter coupling can dramatically alter opto-electronic and physico-chemical properties of a molecule. Ab initio theoretical predictions of these systems need to combine non-perturbative, many-body electronic structure theory-based methods with cavity quantum electrodynamics and theories of open-quantum systems. Here, we generalize quantum-electrodynamical density functional theory to account for dissipative dynamics of the cavity and describe coupled cavity–single molecule interactions in the weak-to-strong-coupling regimes. Specifically, to establish this generalized technique, we study excited-state dynamics and spectral responses of benzene and toluene under weak-to-strong light–matter coupling. By tuning the coupling, we achieve cavity-mediated energy transfer between electronically excited states. This generalized ab initio quantum-electrodynamical density functional theory treatment can be naturally extended to describe cavity-mediated interactions in arbitrary electromagnetic environments, accessing correlated light–matter observables and thereby closing the gap between electronic structure theory, quantum optics, and nanophotonics.

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

Long-term super-resolution inner mitochondrial membrane imaging with a lipid probe

The inner mitochondrial membrane (IMM) generates power to drive cell function, and its dynamics control mitochondrial health and cellular homeostasis. Here, we describe the cell-permeant, lipid-like small molecule MAO-N 3 and use it to assemble high-density environmentally sensitive (HIDE) probes that selectively label and image the IMM in live cells and multiple cell states. MAO-N 3 pairs with strain-promoted azide–alkyne click chemistry-reactive fluorophores to support HIDE imaging using confocal, structured illumination, single-molecule localization and stimulated emission depletion microscopy, all with significantly improved resistance to photobleaching. These probes generate images with excellent spatial and temporal resolution, require no genetic manipulations, are non-toxic in model cell lines and primary cardiomyocytes (even under conditions that amplify the effects of mitochondrial toxins) and can visualize mitochondrial dynamics for 12.5 h. This probe will enable comprehensive studies of IMM dynamics with high temporal and spatial resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Extremely Bright, Near-IR Emitting Spontaneously Blinking Fluorophores Enable Ratiometric Multicolor Nanoscopy in Live Cells

New bright, photostable, emission-orthogonal fluorophores that blink without toxic additives are needed to enable multicolor, live-cell, single-molecule localization microscopy (SMLM). Here we report the design, synthesis, and biological evaluation of Yale676sb, a photostable, near-IR-emitting fluorophore that achieves these goals in the context of an exceptional quantum yield (0.59). When used alongside HMSiR, Yale676sb enables simultaneous, live-cell, two-color SMLM of two intracellular organelles (ER + mitochondria) with only a single laser and no chemical additives.

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

Theory of Photoluminescence Spectral Line Shapes of Semiconductor Nanocrystals

Single-molecule photoluminescence (PL) spectroscopy of semiconductor nanocrystals (NCs) reveals the nature of exciton–phonon interactions in NCs. Understanding the homogeneous spectral line shapes and their temperature dependence remains an open problem. Here, we develop an atomistic model to describe the PL spectrum of NCs, accounting for excitonic effects, phonon dispersion relations, and exciton–phonon couplings. We validate our model using single-NC measurements on CdSe/CdS NCs from T = 4 to 290 K, and we find that the slightly asymmetric main peak at low temperatures is comprised of a narrow zero-phonon line (ZPL) and acoustic phonon sidebands. Furthermore, we identify the specific phonon modes that give rise to the optical phonon sidebands. At temperatures above 200 K, the spectral line width shows a stronger dependence upon the temperature, which we demonstrate to be correlated with higher order exciton–phonon couplings. We also identify the line width dependence upon reorganization energy, NC core sizes, and shell thicknesses.

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

A Generalized Transformer-Based Pulse Detection Algorithm

Pulse-like signals are ubiquitous in the field of single molecule analysis, e.g., electrical or optical pulses caused by analyte translocations in nanopores. The primary challenge in processing pulse-like signals is to capture the pulses in noisy backgrounds, but current methods are subjectively based on a user-defined threshold for pulse recognition. Here, we propose a generalized machine-learning based method, named pulse detection transformer (PETR), for pulse detection. PETR determines the start and end time points of individual pulses, thereby singling out pulse segments in a time-sequential trace. It is objective without needing to specify any threshold. It provides a generalized interface for downstream algorithms for specific application scenarios. PETR is validated using both simulated and experimental nanopore translocation data. It returns a competitive performance in detecting pulses through assessing them with several standard metrics. Finally, the generalization nature of the PETR output is demonstrated using two representative algorithms for feature extraction.

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

Charge Transport Characteristics of Molecular Electronic Junctions Studied by Transition Voltage Spectroscopy

The field of molecular electronics is prompted by tremendous opportunities for using a single-molecule and molecular monolayers as active components in integrated circuits. Until now, a wide range of molecular devices exhibiting characteristic functions, such as diodes, transistors, switches, and memory, have been demonstrated. However, a full understanding of the crucial factors that affect charge transport through molecular electronic junctions should yet be accomplished. Remarkably, recent advances in transition voltage spectroscopy (TVS) elucidate that it can provide key quantities for probing the transport characteristics of the junctions, including, for example, the position of the frontier molecular orbital energy relative to the electrode Fermi level and the strength of the molecule–electrode interactions. These parameters are known to be highly associated with charge transport behaviors in molecular systems and can then be used in the design of molecule-based devices with rationally tuned electronic properties. This article highlights the fundamental principle of TVS and then demonstrates its major applications to study the charge transport properties of molecular electronic junctions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

SISGR: The regulation of carbon fixation in plant and green algae: Rubisco activase and the origin of heat inactivation of CO 2 assimilation

Rubisco activase (Rca) is a critical AAA+ ATPase protein complex that remodels and promotes the Rubisco enzyme, a key player in photosynthetic performance and carbon fixation. The assembly and function of the Rca protein complex are regulated by a range of factors, including subunit concentration, nucleotide-binding states, thermal conditions, metal-ion coordination, and post-translational modifications, such as phosphorylation. Despite its importance in photosynthesis, the detailed molecular mechanisms underlying the regulation of plant Rca and how it activates Rubisco remain elusive. This project aims to bridge this knowledge gap by integrating sophisticated enzymology tools with single-molecule methods and high-resolution electron microscopy to elucidate the structure and function of plant Rca. Through these multiple approaches, we have systematically investigated how the activity of plant Rca is impacted by various factors, such as phosphorylation and metal-ion coordination. The Rca complex assembly/disassembly dynamics were captured using anti-Brownian electrokinetic (ABEL) trap-based measurements, providing unprecedented insight into its structural flexibility and diverse assembly states. Furthermore, the structural analysis of Rca through electron crystallography and single-particle cryogenic electron microscopy (cryo-EM) reveals novel assembly states of the spinach Rca, providing insight into the mechanistic action for Rubisco remodeling. By combining cutting-edge tools and approaches, this work uncovers critical aspects of Rca’s regulation and assembly, paving the way for a deeper understanding of its role in photosynthetic efficiency and the potential for enhancing carbon fixation in crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Long-Range Resonant Charge Transport through Open-Shell Donor–Acceptor Macromolecules

A grand challenge in molecular electronics is the development of molecular materials that can facilitate efficient longrange charge transport. Research spanning more than two decades has been fueled by the prospects of creating a new generation of miniaturized electronic technologies based on molecules whose synthetic tunability offers tailored electronic properties and functions unattainable with conventional electronic materials. However, current design paradigms produce molecules that exhibit off-resonant transport under low bias, which limits the conductance of molecular materials to unsatisfactorily low levels several orders of magnitude below the conductance quantum 1 G 0 and often results in an exponential decay in conductance with length. Here, we demonstrate a chemically robust, air-stable, and highly tunable molecular wire platform comprised of open-shell donor−acceptor macromolecules that exhibit remarkably high conductance close to 1 G 0 over a length surpassing 20 nm under low bias, with no discernible decay with length. Single-molecule transport measurements and ab initio calculations show that the ultralong-range resonant transport arises from extended π-conjugation, a narrow bandgap, and diradical character, which synergistically enables excellent alignment of frontier molecular orbitals with the electrode Fermi energy. The implementation of this long-sought-after transport regime within molecular materials offers new opportunities for the integration of manifold properties within emerging nanoelectronic technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Ultraintense, ultrashort pulse X-ray scattering in small molecules

In this work, we examine X-ray scattering from an isolated organic molecule from the linear to nonlinear absorptive regime. In the nonlinear regime, we explore the importance of both the coherent and incoherent channels and observe the onset of nonlinear behavior as a function of pulse duration and energy. In the linear regime, we test the sensitivity of the scattering signal to molecular bonding and electronic correlation via calculations using the independent atom model (IAM), Hartree–Fock (HF) and density functional theory (DFT). Finally, we describe how coherent X-ray scattering can be used to directly visualize femtosecond charge transfer and dissociation within a single molecule undergoing X-ray multiphoton absorption.

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

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

Background: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. Results: We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark. Conclusions: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Porous Membranes for Moisture Probe Protection (SR18024)

In the presence of contaminants, moisture probes can give false moisture readings and have shorter lifetimes. Absolute humidity probes are composed of porous, hygroscopic metallic oxide thin films (Al 2 O 3 ) coupled to electrodes (e.g. Au and Al). While these materials provide absolute humidity readings at low water levels at a relatively low cost, they are sensitive to the presence of contaminants, especially ammonia, due to its high hygroscopicity and ability to bind to the probe. Without frequent recalibration, especially in the presence of contaminants, the humidity levels are inaccurately reported due to measurement drift that occurs when the pores close, changing the impedance of the probe. The goal of this project was to improve the stability and reliability of these moisture probes by incorporating a molecular sieve into the probe to allow only the water to reach the sensor. Molecular sieves contain pores that allow molecule specific permeation. Two dimensional inorganic nanosheets (e.g. BN, MoO 2 , MoS 2 ) have recently been shown to behave as molecular sieves for water. Compared to zeolites, nanoporous materials have higher flux rates through the pores, leading to faster water permeation. Graphene oxide sheets have also been successfully employed for unimpeded water permeation; however, at lower humidity levels, the structure is unstable and the pores shrink, preventing the sieving of molecules. Compared to graphene oxide, sheets based off of inorganic materials, such as molybdenum, have been found to be more stable at lower humidity levels and have faster permeation rates. By creating a barrier in before the Al 2 O 3 sensor chip to prevent the permeation of contaminants into the probe, the lifetime of the probe will be extended. While the molybdenum sheets are a promising material for this application, their performance against ammonia and tritiated compounds have not yet been evaluated. This technology can be applied to other applications, including gas and liquid purification for environmental remediation, single molecule sensors, field effect transistors, and catalysts.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments

mRNA translation is the ubiquitous cellular process of reading messenger-RNA strands into functional proteins. Over the past decade, large strides in microscopy techniques have allowed observation of mRNA translation at a single-molecule resolution for self-consistent time-series measurements in live cells. Dubbed Nascent chain tracking (NCT), these methods have explored many temporal dynamics in mRNA translation uncaptured by other experimental methods such as ribosomal profiling, smFISH, pSILAC, BONCAT, or FUNCAT-PLA. However, NCT is currently restricted to the observation of one or two mRNA species at a time due to limits in the number of resolvable fluorescent tags. In this work, we propose a hybrid computational pipeline, where detailed mechanistic simulations produce realistic NCT videos, and machine learning is used to assess potential experimental designs for their ability to resolve multiple mRNA species using a single fluorescent color for all species. Our simulation results show that with careful application this hybrid design strategy could in principle be used to extend the number of mRNA species that could be watched simultaneously within the same cell. We present a simulated example NCT experiment with seven different mRNA species within the same simulated cell and use our ML labeling to identify these spots with 90% accuracy using only two distinct fluorescent tags. We conclude that the proposed extension to the NCT color palette should allow experimentalists to access a plethora of new experimental design possibilities, especially for cell Signaling applications requiring simultaneous study of multiple mRNAs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Increased Crystal Field Drives Intermediate Coupling and Minimizes Decoherence in Tetravalent Praseodymium Qubits

Crystal field (CF) control of rare-earth (RE) ions has been employed to minimize decoherence in qubits and to enhance the effective barrier of single-molecule magnets. The CF approach has been focused on the effects of symmetry on dynamic magnetic properties. Herein, the magnitude of the CF is increased via control of the RE oxidation state. The enhanced 4f metal-ligand covalency in Pr 4+ gives rise to CF energy scales that compete with the spin-orbit coupling of Pr 4+ and thereby shifts the paradigm from the ionic ζ SOC >> V CF limit, used to describe trivalent RE-ion, to an intermediate coupling (IC) regime. We examine Pr 4+ -doped perovskite oxide lattices (BaSnO 3 and BaZrO 3 ). These systems are defined by IC which quenches orbital angular momentum. Therefore, the single-ion spin-orbit coupled states in Pr 4+ can be chemically tuned. We demonstrate a relatively large hyperfine interaction of A iso = 1800 MHz for Pr 4+ , coherent manipulation of the spin with Q M = 2Ω R $T$ m reaching up to ~400 for 0.1Pr:BSO at $T$ = 5 K, and significant improvement of the temperature at which $T$ m is limited by $T$ 1 ($T$* = 60 K) compared to other RE ion qubits.

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

Magnetic Blocking in Fluoflavine Radical-Bridged Dilanthanide Complexes

Magnetic exchange coupling is difficult to foster in polynuclear lanthanide (Ln) complexes and poorly understood. While coupling Ln ions through closed-shell ligands is inherently weak due to the contracted 4f orbitals, placing open-shell ligands instead has proven to promote orders of magnitude stronger coupling, giving rise to single-molecule magnets (SMMs) innate to real magnetic memory effect in the case of the anisotropic Ln ions. Notably, the impact of radical bridges with differing oxidation states on magnetic blocking remains unexplored due to lack of Ln SMMs with radicals in two distinct charge states. Herein, the first dilanthanide complexes (Ln = Gd, Dy) containing fluoflavine (flv) bridges, [(Cp* 2 Ln) 2 (μ-flv z )]X, (where X = [Al(OC{CF 3 } 3 ) 4 ] − (z = 1−•), 1-Ln; X = 0 (z = 2−), 2-Ln; X =[K(crypt-222)] + (z = 3−•), 3-Ln) are reported. 1-Ln and 3-Ln, comprising the flv 1−• and flv 3−• radical bridges, were investigated via single-crystal X-ray diffraction (SCXRD), ultraviolet−visible (UV−vis) spectroscopy, Superconducting Quantum Interference Device (SQUID) magnetometry, high-field electron paramagnetic resonance (HF-EPR) spectroscopy and broken-symmetry density functional theory (BS-DFT) calculations. 1-Dy and 3-Dy constitute the first SMMs innate to radicals in two differing oxidation states. 1-Dy exhibits a spin-reversal barrier U eff of 28.36 cm −1 and open magnetic hysteresis loops below 3 K. By contrast, 3-Dy displays a much higher U eff of 143(2) cm −1 and open hysteresis loops until 9.5 K, representing a record for dilanthanide SMMs containing an organic radical bridge. The boost in SMM properties in 3-Dy is attributed to spin-phonon coupling and improved frontier orbital structure. This study paves the way for advanced design strategies of polynuclear Ln SMMs.

Benner, Florian [Michigan State Univ., East Lansin↗
DOE OSTI2023

Identification of small-molecule protein–protein interaction inhibitors for NKG2D

NKG2D (natural-killer group 2, member D) is a homodimeric transmembrane receptor that plays an important role in NK, γδ + , and CD8 + T cell-mediated immune responses to environmental stressors such as viral or bacterial infections and oxidative stress. However, aberrant NKG2D signaling has also been associated with chronic inflammatory and autoimmune diseases, and as such NKG2D is thought to be an attractive target for immune intervention. Here, in this study, we describe a comprehensive small-molecule hit identification strategy and two distinct series of protein–protein interaction inhibitors of NKG2D. Although the hits are chemically distinct, they share a unique allosteric mechanism of disrupting ligand binding by accessing a cryptic pocket and causing the two monomers of the NKG2D dimer to open apart and twist relative to one another. Leveraging a suite of biochemical and cell-based assays coupled with structure-based drug design, we established tractable structure–activity relationships with one of the chemical series and successfully improved both the potency and physicochemical properties. Together, we demonstrate that it is possible, albeit challenging, to disrupt the interaction between NKG2D and multiple protein ligands with a single molecule through allosteric modulation of the NKG2D receptor dimer/ligand interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Substituent Effects in Mechanochemical Allowed and Forbidden Cyclobutene Ring-Opening Reactions

Woodward and Hoffman once jested that a very powerful Maxwell demon could seize a molecule of cyclobutene at its methylene groups and tear it open in a disrotatory fashion to obtain butadiene (Woodward, R. B.; Hoffmann, R. The Conservation of Orbital Symmetry. Angew. Chem., Int. Ed. 1969, 8, 781–853). Nearly 40 years later, that demon was discovered, and the field of covalent polymer mechanochemistry was born. In the decade since our demon was befriended, many fundamental investigations have been undertaken to build up our understanding of force-modified pathways for electrocyclic ring-opening reactions. In this work, we seek to extend that fundamental understanding by exploring substituent effects in allowed and forbidden ring-opening reactions of cyclobutene (CBE) and benzocyclobutene (BCB) using a combination of single-molecule force spectroscopy (SMFS) and computation. We show that, while the forbidden ring-opening of cis-BCB occurs at a lower force than the allowed ring-opening of trans-BCB on the time scale of the SMFS experiment, the opposite is true for cis- and trans-CBE. Such a reactivity flip is explained through computational analysis and discussion of the so-called allowed/forbidden gap.

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

Polyelectrolyte Surface Diffusion in a Nanoslit Geometry

The surface diffusion of poly-l-lysine (PLL) in a planar nanoslit was studied using convex lens-induced confinement (CLiC) single-molecule tracking microscopy. Here, three surface chemistries were employed to understand the interplay of electrostatic and short-range interactions: an amine-functionalized silica surface, an oligo(ethylene oxide) (OEG)-modified surface, and a 1:1 mixture of the two ligands. Effective surface diffusion coefficients increased rapidly with slit height until saturating for slit heights <30 nm. While diffusion at a semi-infinite interface was significantly faster for OEG surfaces, the diffusion coefficient increased most rapidly with slit height for amine-functionalized surfaces, resulting in surface diffusion within very thin slits being nearly independent of surface chemistry. Intermittent random walks were simulated within a planar slit geometry, using experimentally measured parameters obtained from diffusion at a single interface to account for the characteristic short-range interactions between PLL and each surface chemistry, and were in good agreement with experimental measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗