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At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Gas-phase preparation of the dibenzo[ e,l ]pyrene (C 24 H 14 ) butterfly molecule via a phenyl radical-mediated ring annulation

A high temperature phenyl-mediated addition–cyclization–dehydrogenation mechanism to form peri-fused polycyclic aromatic hydrocarbon (PAH) derivatives—illustrated through the formation of dibenzo[e,l]pyrene (C 24 H 14 )—is explored through a gas-phase reaction of the phenyl radical (C 6 H 5 ˙) with triphenylene (C 18 H 12 ) utilizing photoelectron photoion coincidence spectroscopy (PEPICO) combined with electronic structure calculations. Low-lying vibrational modes of dibenzo[e,l]pyrene exhibit out-of-plane bending and are easily populated in high temperature environments such as combustion flames and circumstellar envelopes of carbon stars, thus stressing dibenzo[e,l]pyrene as a strong target for far-IR astronomical surveys.

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

Random Knotting in Fractal Ring Polymers

Many ring polymer systems of physical and biological interest exhibit both pronounced topological effects and nontrivial self-similarity, but the relationship between these two phenomena has not yet been clearly established. Here, we use theory and simulation to formulate such a connection by studying a fundamental topological property—the random knotting probability—for ring polymers with varying fractal dimension, d f . Using straightforward scaling arguments, we generalize a classic mathematical result, showing that the probability of a trivial knot decays exponentially with chain size, N, for all fractal dimensions: P 0 (N) ∝ exp(–N/N 0 ). However, no such simple considerations can account for the dependence of the knotting length, N 0 , on d f , necessitating a more involved analytical calculation. This analysis reveals a complicated double-exponential dependence, which is well supported by numerical data. By contrast, functional forms typical of simple scaling theories fail to adequately describe the observations. These findings are equally valid for two-dimensional ring polymer systems, where “knotting” is defined as the intersection of any two segments.

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

Gas-Phase Formation of Fulvenallene (C 7 H 6 ) via the Jahn–Teller Distorted Tropyl (C 7 H 7 ) Radical Intermediate under Single-Collision Conditions

The fulvenallene molecule (C 7 H 6 ) has been synthesized via the elementary gas-phase reaction of the methylidyne radical (CH) with the benzene molecule (C 6 H 6 ) on the doublet C 7 H 7 surface under single collision conditions. The barrier-less route to the cyclic fulvenallene molecule involves the addition of the methylidyne radical to the π-electron density of benzene leading eventually to a Jahn–Teller distorted tropyl (C 7 H 7 ) radical intermediate and exotic ring opening–ring contraction sequences terminated by atomic hydrogen elimination. The methylidyne-benzene system represents a benchmark to probe the outcome of the elementary reaction of the simplest hydrocarbon radical—methylidyne—with the prototype of a closed-shell aromatic molecule—benzene—yielding nonbenzenoid fulvenallene. Combined with electronic structure and statistical calculations, this bimolecular reaction sheds light on the unusual reaction dynamics of Hückel aromatic systems and remarkable (polycyclic) reaction intermediates, which cannot be studied via classical organic, synthetic methods, thus opening up a versatile path to access this previously largely obscure class of fulvenallenes.

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

Magnetization orientation-dependent Shubnikov-de Haas oscillations in ferromagnetic Weyl semimetal Co 3 Sn 2 S 2

We report a study of Shubnikov–de Haas oscillations in high-quality single crystals of ferromagnetic Weyl semimetal Co 3 Sn 2 S 2 . The Fermi surfaces resolved in our experiments are three-dimensional and reflect an underlying trigonal crystallographic symmetry. Combined with density functional calculations, we identify that multiple Fermi surfaces in the system—of both electron and hole nature—arise from the energy dispersion of the (spin-orbit gapped) mirror-protected nodal rings. We observe an evolution of the Fermi surfaces with in-plane magnetic fields, in contrast to field perpendicular to the kagome lattice planes, which has little effect. Viewed alongside the easy-axis anisotropy of the system, our observation reveals an evolution of the electronic structure of Co 3 Sn 2 S 2 —including the Weyl points—with the ferromagnetic moment orientation. Through the case study of Co 3 Sn 2 S 2 , our results provide concrete experimental evidence of an anisotropic interplay via spin-orbit coupling between the magnetic degrees of freedom and electronic band singularities, which has long been expected in semimetallic and metallic magnetic systems.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Hub stability in the calcium calmodulin-dependent protein kinase II

The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within CaMKII isoforms, but the link between polymorphism and subunit exchange has not been resolved. Here, we present near-atomic resolution cryogenic electron microscopy (cryo-EM) structures revealing that hubs from the α and β isoforms, either standalone or within an β holoenzyme, coexist as 12 and 14 subunit assemblies. Single-molecule fluorescence microscopy of Venus-tagged holoenzymes detects intermediate assemblies and progressive dimer loss due to intrinsic holoenzyme lability, and holoenzyme disassembly into dimers upon mutagenesis of a conserved inter-domain contact. Molecular dynamics (MD) simulations show the flexibility of 4-subunit precursors, extracted in-silico from the β hub polymorphs, encompassing the curvature of both polymorphs. The MD explains how an open hub structure also obtained from the β holoenzyme sample could be created by dimer loss and analysis of its cryo-EM dataset reveals how the gap could open further. An assembly model, considering dimer concentration dependence and strain differences between polymorphs, proposes a mechanism for intrinsic hub lability to fine-tune the stoichiometry of αβ heterooligomers for their dynamic localization within synapses in neurons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Aromatic heterobicycle-fused porphyrins: impact on aromaticity and excited state electron transfer leading to long-lived charge separation

A new synthetic method to fuse benzo[4,5]imidazo[2,1-a]isoindole to the porphyrin periphery at the β,β-positions has been developed, and its impact on the aromaticity and electronic structures is investigated. Reactivity investigation of the fused benzoimidazo-isoindole component reveals fluorescence quenching of a zinc porphyrin (AMIm-2) upon treatment with a Brønsted acid. The reaction of the zinc porphyrin (AMIm-2) with methyl iodide initiated a new organic transformation, resulting in the ring-opening of isoindole with the formation of an aldehyde and dimethylation of the benzoimidazo component. The fused benzoimidazo-isoindole component acted as a good ligand to bind platinum(II), forming novel homobimetallic and heterobimetallic porphyrin complexes. The fusion of benzoimidazo-isoindole on the porphyrin ring resulted in bathochromically shifted absorptions and emissions, reflecting the extended conjugation of the porphyrin π-system. Time-resolved emission and transient absorption spectroscopy revealed stable excited state species of the benzoimidazo-isoindole fused porphyrins. Zinc porphyrin AMIm-2 promoted excited state electron transfer upon coordinating with an electron acceptor, C60, generating a long-lived charge-separated state, in the order of 37.4 μs. The formation of the exceptionally long-lived charge-separated state is attributed to the involvement of both singlet and triplet excited states of AMIm-2, which is rarely reported in porphyrins.

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

Simultaneous ambient pressure x-ray photoelectron spectroscopy and grazing incidence x-ray scattering in gas environments

We have developed an experimental system to simultaneously measure surface structure, morphology, composition, chemical state, and chemical activity for samples in gas phase environments. This is accomplished by simultaneously measuring x-ray photoelectron spectroscopy (XPS) and grazing incidence x-ray scattering in gas pressures as high as the multi-Torr regime while also recording mass spectrometry. Scattering patterns reflect near-surface sample structures from the nano-scale to the meso-scale, and the grazing incidence geometry provides tunable depth sensitivity of structural measurements. Scattered x rays are detected across a broad range of angles using a newly designed pivoting-UHV-manipulator for detector positioning. At the same time, XPS and mass spectrometry can be measured, all from the same sample spot and under ambient conditions. To demonstrate the capabilities of this system, we measured the chemical state, composition, and structure of Ag-behenate on a Si(001) wafer in vacuum and in O 2 atmosphere at various temperatures. These simultaneous structural, chemical, and gas phase product probes enable detailed insights into the interplay between the structure and chemical state for samples in gas phase environments. The compact size of our pivoting-UHV-manipulator makes it possible to retrofit this technique into existing spectroscopic instruments installed at synchrotron beamlines. Because many synchrotron facilities are planning or undergoing upgrades to diffraction limited storage rings with transversely coherent beams, a newly emerging set of coherent x-ray scattering experiments can greatly benefit from the concepts we present here.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Magnetic Field Optimization of an In-Vacuum Undulator at NSLS-II Transactions on Applied Superconductivity

A 3.0 m long In-Vacuum Undulator (IVU) is employed at the National Synchrotron Light Source II (NSLS-II) for the Hard X-ray Nanoprobe (HXN) beamline providing structural and X-ray fluorescence imaging with world-leading spatial resolution. On July 1 st 2018 a gearbox shaft in the gap drive train assembly sheared due to corrosion fatigue caused by stress due to mechanical misalignment. Furthermore, the device was extracted from the storage ring and measured. The magnetic field measurements detected a degradation of the magnetic performance as well as a localized demagnetization of the magnetic modules of the first 3 upstream periods. We describe here the mechanical repairs and the magnetic phase shimming optimization implemented to restore the spectral performance of the device.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

4D-STEM of Beam-Sensitive Materials

We report that a scanning electron nanobeam diffraction, or 4D-STEM (four-dimensional scanning transmission electron microscopy), is a flexible and powerful approach to elucidate structure from "soft" materials that are challenging to image in the transmission electron microscope because their structure is easily damaged by the electron beam. In a 4D-STEM experiment, a converged electron beam is scanned across the sample, and a pixelated camera records a diffraction pattern at each scan position. This four-dimensional data set can be mined for various analyses, producing maps of local crystal orientation, structural distortions, crystallinity, or different structural classes. Holding the sample at cryogenic temperatures minimizes diffusion of radicals and the resulting damage and disorder caused by the electron beam. The total fluence of incident electrons can easily be controlled during 4D-STEM experiments by careful use of the beam blanker, steering of the localized electron dose, and by minimizing the fluence in the convergent beam thus minimizing beam damage. This technique can be applied to both organic and inorganic materials that are known to be beam-sensitive; they can be highly crystalline, semicrystalline, mixed phase, or amorphous. One common example is the case for many organic materials that have a π-π stacking of polymer chains or rings on the order of 3.4-4.2 Å separation. If these chains or rings are aligned in some regions, they will produce distinct diffraction spots (as would other crystalline spacings in this range), though they may be weak or diffuse for disordered or weakly scattering materials. We can reconstruct the orientation of the π-π stacking, the degree of π-π stacking in the sample, and the domain size of the aligned regions. This Account summarizes illumination conditions and experimental parameters for 4D-STEM experiments with the goal of producing images of structural features for materials that are beam-sensitive. We will discuss experimental parameters including sample cooling, probe size and shape, fluence, and cameras. 4D-STEM has been applied to a variety of materials, not only as an advanced technique for model systems, but as a technique for the beginning microscopist to answer materials science questions. It is noteworthy that the experimental data acquisition does not require an aberration-corrected TEM but can be produced on a variety of instruments with the right attention to experimental parameters.

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

Behavior of Water Near Multimodal Chromatography Ligands and Its Consequences for Modulating Protein–Ligand Interactions

Multimodal chromatography is a powerful approach for purifying proteins that uses ligands containing multiple modes of interaction. Recent studies have shown that selectivity in multimodal chromatographic separations is a function of the ligand structure and geometry. Here, we performed molecular dynamics simulations to explore how the ligand structure and geometry affect ligand–water interactions and how these differences in solution affect the nature of protein–ligand interactions. Our investigation focused on three chromatography ligands: Capto MMC, Nuvia cPrime, and Prototype 4, a structural variant of Nuvia cPrime. First, the solvation characteristics of each ligand were quantified via three metrics: average water density, fluctuations, and residence time. We then explored how solvation was perturbed when the ligand was bound to the protein surface and found that the probability of the phenyl ring dewetting followed the order: Capto MMC > Prototype 4 > Nuvia cPrime. To explore how these differences in dewetting affect protein–ligand interactions, we calculated the probability of each ligand binding to different types of residues on the protein surface and found that the probability of binding to a hydrophobic residue followed the same order as the dewetting behavior. This study illustrates the role that wetting and dewetting play in modulating protein–ligand interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

All solid hybrid arrow fiber

An all solid hybrid waveguiding structure provides large mode area, acceptable losses of the desired core mode and very high losses of the undesired next higher order mode in the core. Embodiments of the waveguide include a hybrid of low index barriers providing confinement by total internal reflection, and further include high index rings that support guided modes only at effective indices different from that of the desired core mode.

Pax, Paul H.↗
DOE OSTI2023

Use of latent metathesis polymerization systems for photopolymerization-based additive manufacturing

Photolatent olefin metathesis catalysts can be used in combination with metathesis-active monomers or resins for photopolymerization-based additive manufacturing via ring-opening metathesis polymerization (ROMP). A variety of alternative catalysts and photosensitizers are commercially available that allows for tuning of thermomechanical properties, potlifes, activation rates, and irradiation wavelengths. As an example, two optimized catalyst/photosensitizer systems were demonstrated in the rapid stereolithographic printing of complex, multidimensional poly-dicyclopentadiene structures with microscale features under ambient conditions.

Leguizamon, Samuel↗
DOE OSTI2020

Formation of Phenanthrene via Recombination of Indenyl and Cyclopentadienyl Radicals: A Theoretical Study

This work presents quantum chemical G3(MP2,CC)//B2PLYPD3/6-311G(d,p) calculations of the potential energy surface for the indenyl (C 9 H 7 ) + cyclopentadienyl (C 5 H 5 ) reaction followed by unimolecular decomposition of the C 14 H 11 radicals formed as the primary products, as well as the Rice–Ramsperger–Kassel–Marcus master equation (RRKM-ME) calculations to predict temperature- and pressure-dependent reaction rate constants and product branching ratios. The reaction begins with the barrierless recombination of indenyl and cyclopentadienyl forming a C 14 H 12 molecule with a new C–C bond connecting two five-membered rings, which subsequently dissociates to C 14 H 11 radicals by H losses. The primary products of the C 9 H 7 + C 5 H 5 → C 14 H 11 + H reaction can directly decompose by another H loss to benzofulvalene, and this pathway is most favorable in terms of the entropy factor and hence is preferable at higher temperatures. Otherwise, the initial C 14 H 11 isomers can undergo significant structural rearrangements before eliminating an H atom and producing phenanthrene, anthracene, or benzoazulenes, among which the formation of phenanthrene via the “spiran” pathway is clearly preferred. The calculated barriers along the computed favorable dissociation pathways are relatively low, in the ~30–40 kcal/mol range, making the C 14 H 11 radicals unstable at temperatures above 1000–1250 K at 1 atm. The results of RRKM-ME calculations show that, under typical combustion conditions, the decomposition of the C 14 H 11 radicals predominantly leads to benzofulvalene. However, the latter can be rapidly converted to phenanthrene via H-assisted isomerization with the rate constant for the benzofulvalene + H → phenanthrene + H reaction being close to 10 –11 cm 3 molecule –1 s –1 at 1000–1500 K and 1 atm. Here, the results provide further support for the hypothesis that recombination of two π radicals containing five-membered rings can lead to a growth of PAH with the formation of two fused six-membered rings, but the reaction mechanism may not be direct and is likely to involve two consecutive H atom losses leading to a fulvalene-like product, with subsequent H-assisted isomerization of the latter to a benzenoid PAH.

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

Directed Gas-Phase Formation of The Propargyl Family of Resonance-Stabilized Radicals in The Reactions of Ground-State Carbon Atoms (C; 3 P j ) with Butene Isomers (C 4 H 8 ): Dimethylpropargyl and Ethylpropargyl

The propargyl radical (C 3 H 3 ) is the simplest resonance-stabilized free radical (RSFR), but how does stepwise methyl substitution in the alkene reactant affect its dynamics of their formation? We report a crossed molecular beam study of the reactions of atomic carbon (C, 3 P j ) with four butene isomers (C 4 H 8 ) under single collision conditions at a collision energy of 28 ± 2 kJ mol −1 . Barrierless addition of atomic carbon to the alkene C=C bond triggers ring opening to triplet substituted allenes—a de facto insertion mechanism—followed by unimolecular decomposition via atomic hydrogen (H), methyl (CH 3 ) or ethyl (C 2 H 5 ) loss, yielding a family of propargyl‑type RSFRs. RRKM calculations reveal that the branching ratios are highly sensitive to the alkene structure. While the methyl loss channel, affording 1‑methylpropargyl, dominates for 2 butenes (80–90%), the predicted hydrogen atom loss channel (≈10%) leading to 1,3 dimethylpropargyl is identified in the experiment by comparison with theoretical energetics. For isobutene, a near‑equal competition is seen, with the reaction producing 3‑methylpropargyl (≈50%) and 1,1‑dimethylpropargyl (≈40%), along with 2‑vinylallyl (≈5%), whose formation is supported by the experimental data. Most notably, the reaction with 1 butene uniquely favors an enthalpically driven hydrogen shift, eventually producing 1 vinylallyl (≈38%), which is assigned based on the excellent agreement between the measured and calculated reaction exothermicity. Rapid entropically favored fragmentation channels yield ≈40% of propargyl type species (propargyl, 1- and 3-ethylpropargyls), slightly outcompeting the allyl type product. Furthermore, these results establish a systematic progression from C 2 H 4 to C 4 H 8 , where the increasing alkyl substitution unlocks new fragmentation channels, providing a versatile gas phase route to alkylated RSFRs—key intermediates in the growth of methylated and ethylated PAHs and aliphatic chains in combustion and cold interstellar environments (molecular clouds).

Alkyls↗
DOE OSTI2024

Janus bottlebrush compatibilizers

Bottlebrush random copolymers (BRCPs), consisting of a random distribution of two homopolymer chains along a backbone, can segregate to the interface between two immiscible homopolymers. BRCPs undergo a reconfiguration, where each block segregates to one of the homopolymer phases, adopting a Janus-type structure, reducing the interfacial tension and promoting adhesion between the two homopolymers, thereby serving as a Janus bottlebrush copolymer (JBCP) compatibilizer. Here, we synthesized a series of JBCPs by copolymerizing deuterated or hydrogenated polystyrene (DPS/PS) and poly(tert-butyl acrylate) (PtBA) macromonomers using ruthenium benzylidene-initiated ring-opening metathesis polymerization (ROMP). Subsequent acid-catalyzed hydrolysis converted the PtBA brushes to poly(acrylic acid) (PAA). The JBCPs were then placed at the interface between DPS/PS homopolymers and poly(2-vinyl pyridine) (P2VP) homopolymers, where the degree of polymerization of the backbone (N BB ) and the grafting density (GD) of the JBCPs were varied. Neutron reflectivity (NR) was used to determine the interfacial width and segmental density distributions (including PS homopolymer, PS block, PAA block and P2VP homopolymer) across the polymer-polymer interface. Our findings indicate that the star-like JBCP with N BB = 6 produces the largest interfacial broadening. Increasing N BB to 100 (rod-like shape) and 250 (worm-like shape) reduced the interfacial broadening due to a decrease in the interactions between blocks and homopolymers by stretching of blocks. Decreasing the GD from 100% to 80% at N BB = 100 caused an increase the interfacial width, yet further decreasing the GD to 50% and 20% reduced the interfacial width, as 80% of GD may efficiently increase the flexibility of blocks and promote interactions between homopolymers, while maintaining relatively high number of blocks attached to one molecule. The interfacial conformation of JBCPs was further translated into compatibilization efficiency. Thin film morphology studies showed that only the lower N BB values (N BB = 6 and N BB = 24) and the 80% GD of N BB = 100 had bicontinuous morphologies, due to a sufficient binding energy that arrested phase separation, supported by mechanical testing using asymmetric double cantilever beam (ADCB) tests. These provide fundamental insights into the assembly behavior of JBCPs compatibilizers at homopolymer interfaces, opening strategies for the design of new BCP compatibilizers.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V o complex

Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a Vo proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo–electron microscopy (cryo-EM) structure of yeast V o proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of V o that shows the c-ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with c-ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free V o that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

This dataset contains a subset of raw diffraction images for the serial femtosecond crystallography data of S1P5-ONO-5430608 complex. The diffraction data contain a strong systematic background as described in Lyapina et al. No additional background subtraction was applied to the data. In order to avoid its effects, the background subtraction implemented in CrystFEL, was applied (--rings-grad subtraction). The final stream, supplemented with this dataset, was obtained with: indexamajig 0.8.0 Respectively, the hkl file was obtained with: partialator 0.8.0

Human sphingosine-1-phosphate receptor 5 (S1P5) in↗
DOE OSTI2025

Photon-magnon coupling using gain-assisted spoof-localized surface plasmons

Improving the photon-magnon coupling strength can be done by tuning the structure of microwave resonators to better interact with the magnon counterpart. Planar resonators accommodating unconventional photon modes beyond the half- and quarter-wavelength designs have been explored due to their optimized mode profiles and potentials for on-chip integration. Here, we designed and fabricated an actively controlled ring resonator supporting the spoof localized surface plasmons (LSPs), and implemented it in the investigation of photon-magnon coupling for hybrid magnonic applications. We demonstrated gain-assisted photon-magnon coupling with the YIG magnon mode under several different sample geometries. The achieved coupling amplification largely benefits from the high quality factor (Q-factor) due to the additional gain provided by a semiconductor amplifier, which effectively increases the Q-factor from a nearly null state (passive resonance) to more than 1000 for a quadrupole LSP mode. Our results suggest an additional control knob for manipulating photon-magnon coupled systems exploiting external controls of gain and loss.

47 OTHER INSTRUMENTATION↗