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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Influence of Polymorphs and Local Defect Structures on NMR Parameters of Graphite Fluorides

In this study, the role of local molecular structure on calculated 13 C and 19 F NMR chemical shifts for graphite fluoride materials was explored by using gauge-including projector augmented wave (GIPAW) computational methods for different periodic crystal polymorphs and density functional theory (DFT) gauge-including atomic orbital (GIAO) computational methods for individual graphite fluoride platelets, i.e., fluorinated graphene (FG). The impact of stacking sequences, d -spacing, and ring conformations on fully fluorinated graphite fluoride structures was investigated. A range of different defects including Stone–Wales, F and C vacancies, void formation, and F inversion were also evaluated using FG structures. These calculations show that distinct chemical shift signatures exist for many of these polymorphs and defects, therefore providing a basis for spectral assignment and development of models describing the mean local CF structure in disordered graphite fluoride materials.

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

Design of a Structure for Assembly and Cooling the Magnet of the Next-Generation 45 GHz ECR Ion Source MARS-D

Here, the current Electron Cyclotron Resonance Ion Sources (ECRISs), constructed with Nb-Ti wires and the conventional racetrack-and-solenoid structure, have achieved operating frequencies up to 28 GHz and utilized about 90% of the critical current of the Nb-Ti wire. A Mixed Axial and Radial field System Demonstrator (MARS-D) is being developed at Lawrence Berkeley National Laboratory (LBNL). This system, which consists of an innovative hexagonal Closed-Loop Coil (CLC) and a set of solenoids, can generate higher magnetic fields (up to 150% ) while requiring only about 50% of the superconducting wire, enabling Nb-Ti wires to be used in the next-generation 45 GHz ECRIS. However, the assembly and cooling of such an efficient and compact magnet are particularly challenging due to the small radial gap between the CLC and solenoids, as well as the tight operating temperature margin. To address these challenges, a structure was developed that combines a three-section radially split solenoid mandrel with a series of shrink-fit reinforcement rings and cooling channels. This paper presents the detailed structure, manufacturing method, assembly procedure, impregnation method, mechanical Finite Element Analysis (FEA) comparison, and thermal FEA comparison.

ECR ion sources↗
DOE OSTI2022

Exploring the use of the pentaphenylcyclopentadienyl ligand in uranium chemistry: the crystal structure of (C

The reaction of UI3 with NaC5Ph5 in THF generated (η5-C5Ph5)UI2(THF)2 which was characterized by X-ray crystallography. The complex has a four-legged piano stool structure with a 2.539 Å U– (C5Ph5 ring centroid) distance that is slightly longer than the 2.504 Å distance in (η5-C5Me5)UI2(THF)3 which has a larger formal coordination number. Although the synthesis of the mono-cyclopentadienyl complex was facile, no bis-cyclopentadienyl complexes were isolated from reactions using two equivalents of the pentaphenylcyclopentadienyl ligand per uranium. In one UI3/2NaC5Ph5 synthesis, the X-ray crystal structure of (THF)3Na(η5-C5Ph5) was obtained. Attempts to reduce (η5-C5Ph5)UI2(THF)2 did not give evidence for a UII product. KC8 reductions of the in situ reaction of NdI3 and NaC5Ph5, analogous to the synthesis of (η5-C5Ph5)UI2(THF)2, yielded an X-ray crystal structure of a solvent-separated ion pair (SSIP), [K(18-crown-6)(THF)2][C5Ph5].

Chemistry↗
DOE OSTI2025

Epoxide Alcoholysis over M-BEA Zeolites: Effects of Alcohol Chain Length on Rates and Regioselectivities

The structures of nucleophilic reactants affect their coordination behavior among solvent molecules and kinetics of reactions with surface intermediates within the confines of fluidfilled pores of zeolites and other microporous materials. Consequently, rates and regioselectivities of diverse chemistries may depend sensitively on nucleophile identity in manners not observed for classic fluid phase reactions. Here, we examine the impact of varying the primary alcohol (ROH) chain length on the kinetics of 1,2-epoxybutane (C 4 H 8 O) ring-opening within Brønsted (Al-BEA) and Lewis acid (Zr-BEA) zeolites. Turnover rates increase by factors of ∼6 (Al-BEA) and 4-fold (Zr-BEA) between methanol and 1-hexanol, yet the reaction mechanisms remain comparable. Despite modest rate differences, apparent activation enthalpies calculated from rates and activities of solvated reactants decrease linearly by 12 (Al-BEA) to 33 kJ mol −1 (Zr- BEA) with increased proton affinity, which suggests bond formation energies for the nucleophile strongly influence rate increases. The molecular interpretation of these trends demonstrates, however, that the solvation of ring-opening transition states by zeolite pore structures and solvent molecules also governs rates. The impact of local solvating interactions appears most directly as changes in regioselectivities, which tend to enhance terminal alcohol formation with increasing ROH chain length. Regioselectivities largely do not vary with differences in fluid composition for a given ROH. The addition of H 2 O increases the number of hydrogen bonds among reactive species, and trends in regioselectivities imply that the decreased hydrogen bonding ability of longer chain ROH, and not the nucleophile strength or steric bulk, determines the regioselectivities of the resulting products. This work provides direct experimental evidence that nucleophilicity and hydrogen bonding influence reaction barriers and regioselectivities in zeolitecatalyzed epoxide ring-opening, offering pathways to better control reaction kinetics.

acidic zeolites↗
DOE OSTI2022

Formation and Evolution of Metallocene Single-Molecule Circuits with Direct Gold-π Links

Single molecule circuits with group 8 metallocenes are formed without additional linker groups in Scanning Tunnelling Microscope-based break junction (STMBJ) measurements at cryogenic and room temperature conditions with gold (Au) electrodes. We investigate the nature of this direct gold-π binding motif and its affect on molecular conductance and persistence characteristics during junction evolution. The measurement technique under cryogenic conditions tracks molecular plateaus through the full cycle of extension and compression. Analysis reveals that junction persistence when the metal electrodes are pushed together correlates with whether electrodes are locally sharp or blunt, suggesting distinct scenarios for metallocene junction formation and evolution. The top and bottom surfaces of the "barrel" shaped metallocenes present the electron-rich π system of cyclopentadienyl rings which interacts with the gold electrodes in two distinct ways. An undercoordinated gold atom on a sharp tip forms a donor-acceptor bond to a specific carbon atom in the ring. However, a small, flat patch on a dull tip can bind more strongly to the ring as a whole through Van der Waals interactions. Density functional theory (DFT) based calculations of model electrode structures provide an atomic-scale picture of these scenarios, demonstrating the role of these bonding motifs during junction evolution and showing that the conductance is relatively independent of tip atomic-scale structure. Furthermore, the non-specific interaction of the cyclopentadienyl rings with the electrodes enables extended conductance plateaus, a mechanism distinct from that identified for the more commonly studied, rod-shaped organic molecular wires.

25 ENERGY STORAGE↗
DOE OSTI2021

Influence of Al location on formation of silver clusters in mordenite

Formation of zeolite supported Ag 0 clusters depends on a combination of thermodynamically stable atomic configurations, charge balance considerations, and mobility of species on the surface and within pores. Periodic density functional theory (DFT) calculations were performed to evaluate how the location of Al in the mordenite (MOR) framework and humidity control Ag 0 nanocluster formation. Four Al framework sites were studied (T1-T4) and the Al positions in the framework were identified by the shifts in the differential Al…Al pair distribution function (PDF). Furthermore, structural information about the Ag 0 nanoclusters, such as dangling bonds, can be identified by Ag…Ag PDF data. For Ag 0 formation in vacuum MOR structures with a Si:Al ratio of 5:1 with Al in the T1 position resulted in the most framework flexibility and the lowest Ag 0 nanocluster charge, indicating the best result for formation of charge neutral nanoclusters. When water is present, Al in the T3 and T4 positions results in the formation of the smallest average Ag 0 nanoclusters plus greater expansion of the O-T-O bond angle than in vacuum, indicating easier diffusion of the Ag 0 nanoclusters to the surface. Here, the presence of Al in 4-membered rings and in pairs indicates favorable MOR structures for formation of single Ag atoms, despite the existence of synthesis challenges. Therefore, Al in the T2 position is the least favorable for Ag 0 nanocluster formation in both vacuum and in the presence of water. Al in the T1, T3, and T4 positions provides beneficial effects through framework flexibility and changes in nanocluster size or charge that can be leveraged for design of zeolites for formation of metallic nanoclusters.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Crystal structure of haloxon, C 14 H 14 C l3 O 6 P

The crystal structure of haloxon has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Haloxon crystallizes in space group P2 1 /n (#14) with a = 19.60382(6), b = 10.05473(3), c = 8.73591(2) Å, β = 92.6617(2)°, V = 1720.088(11) Å 3 , and Z = 4. The structure consists of discrete molecules. The mean planes of the fused ring systems are approximately 0–11 and 011. The rings form staggered stacks perpendicular to these planes. There are no traditional hydrogen bonds in the structure, but several C–H∙∙∙O and C–H∙∙∙Cl hydrogen bonds contribute to the crystal energy. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure and functional determinants of Rad6–Bre1 subunits in the histone H2B ubiquitin-conjugating complex

The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 ‘backside’. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6–Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6–Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6–Bre1 interaction through a novel interface that is important for their biochemical and biological responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP

Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli .

protofilaments↗
DOE OSTI2024

Structural Gating Enhances Long-Distance Light-Driven Interfacial Electron Transfer

Structural gating provides a molecular means to transfer electrons preferentially in one desired vectorial direction, a behavior needed for applications in artificial photosynthesis. At the interfaces utilized herein, visible-light absorption by a transition metal complex opens a “structural gate” by planarization of otherwise rotating phenyl rings in p-phenylene ethynylene (PE) bridge units. Planarization provides a conjugated pathway for electron flow toward a conductive oxide surface. Interfacial electron transfer to the oxide restores rotation and closes the gate to the unwanted recombination reaction. This structural gating results in nearly quantitative long-distance (>20 Å) interfacial electron transfer that occurs ~1000 times faster than transfer in the opposite direction. A comparative kinetic study of these complexes with those that contain ionic bridge units, without gating function, as a function of the applied potential and hence –ΔG° provided a physical basis for the structural gating. A small distance-dependent reorganization energy with weak electronic coupling underlies the success of this gate that enables efficient long-distance electron transfer and slow recombination.

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

First Observations of an Ion Vortex in a Magnetic Hole in the Solar Wind by MMS

The coronal heating region is able to generate mirror mode structures by ion mirror instabilities. Linear magnetic holes are believed to be the remnants of mirror mode structures, thus they are believed to be messengers from the coronal heating region. They can be convected to ∼9 au with the solar wind flow, indicating that a stabilizing mechanism is necessary to make the magnetic holes survive for such a long time. Here, we investigate a magnetic hole with a size of ∼6.7 ρ {sub i} in the solar wind based on observations by the Magnetospheric Multiscale mission. The unprecedented high-resolution data enable us to reveal the existence of the ion vortex inside the structure for the first time. Such an ion vortex forms a ring-like current, which is consistent with the magnetic field depression. The self-consistent structure of the magnetic hole contributed by the ion vortex can help to further shed light on the mechanism of the long-term survival of magnetic holes in the astrophysical plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Progressive evolutions of non-fused ring electron acceptors toward efficient organic solar cells with improved photocurrent and reduced energy loss

Resolving competitive counterbalance between high external quantum efficiency (EQE) response and low energy loss is critical for achieving efficient organic solar cells (OSCs), including those based on low-cost non-fused-ring electron acceptor (NFREA). In this work, we performed a comparable study by utilizing four NFREAs with progressive evolutions in molecular structures, energetic levels, spectral coverages, crystallinity, etc, to pair with polymer donor J52. By regulating the terminal and side chains of NFREAs, the enhanced intramolecular charge transfer (ICT) effect allows O-PC-EH possessing the broader spectral coverage for higher photocurrent, the reduced energetic offset enables O-PC-EH-based device owning higher luminescence property for lower energy loss, the strengthened crystallinity endows O-PC-EH-based blend better charge transport property for less charge recombination. With those comprehensive managements from molecule to blend properties, the J52:O-PC-EH-based OSCs achieved the best efficiency of 14.4% (certified: 14.1%) with benefits in all the three device parameters. Here, this work reveals the importance of fine-tuning molecular structures of NFREAs according to paired polymer donor for maximizing the device performances.

14 SOLAR ENERGY↗
DOE OSTI2022

Hydrogen bonds and dispersion forces serving as molecular locks for tailored Group 11 bis(amidine) complexes

A flexible polydentate bis(amidine) ligand LH 2 , LH 2 = {CH 2 NH( t Bu)C=N-2-(6-MePy)} 2 , operates as a molecular lock for various coinage metal fragments and forms the dinuclear complexes [LH 2 (MCl) 2 ], M = Cu (1), Au (2), the coordination polymer [{(LH 2 ) 2 (py) 2 (AgCl) 3 }(py) 3 ] n (3), and the dimesityl-digold complex [LH 2 (AuMes) 2 ] (4) by formal insertion of MR fragments (M = Cu, Ag, Au; R = Cl, Mes) into the N–H∙∙∙N hydrogen bonds of LH 2 in yields of 43–95%. Complexes 1, 2, and 4 adopt C 2 -symmetrical structures in the solid state featuring two interconnected 11-membered rings that are locked by two intramolecular N–H∙∙∙R–M hydrogen bonds. QTAIM analyses of the computational geometry-optimized structures 1a, 2a, and 4a reveal 13, 11, and 22 additional bond critical points, respectively, all of which are related to weak intramolecular attractive interactions, predominantly representing dispersion forces, contributing to the conformational stabilization of the C2-symmetrical stereoisomers in the solid state. Variable-temperature 1 H NMR spectroscopy in combination with DFT calculations indicate a dynamic conformational interconversion between two C 2 -symmetrical ground state structures in solution (ΔG ‡ c = 11.1–13.8 kcal mol –1 ), which is accompanied by the formation of an intermediate possessing C i symmetry that retains the hydrogen bonds.

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

Spatial Effect on the Performance of Carboxylate Anode Materials in Na-Ion Batteries

Developing low-voltage carboxylate anode materials is critical for achieving low-cost, high-performance, and sustainable Na-ion batteries (NIBs). However, the structure design rationale and structure-performance correlation for organic carboxylates in NIBs remains elusive. Herein, the spatial effect on the performance of carboxylate anode materials is studied by introducing heteroatoms in the conjugation structure and manipulating the positions of carboxylate groups in the aromatic rings. Planar and twisted organic carboxylates are designed and synthesized to gain insight into the impact of geometric structures to the electrochemical performance of carboxylate anodes in NIBs. Among the carboxylates, disodium 2,2’-bipyridine-5,5’-dicarboxylate (2255-Na) with a planar structure outperforms the others in terms of highest specific capacity (210 mAh g -1 ), longest cycle life (2000 cycles), and best rate capability (up to 5 A g -1 ). Further, the cyclic stability and redox mechanism of 2255-Na in NIBs are exploited by various characterization techniques. Moreover, high-temperature (up to 100 °C) and all-organic batteries based on a 2255-Na anode, a polyaniline (PANI) cathode, and an ether-based electrolyte are achieved and exhibited exceptional electrochemical performance. Therefore, this work demonstrates that designing organic carboxylates with extended planar conjugation structures is an effective strategy to achieve high-performance and sustainable NIBs.

25 ENERGY STORAGE↗
DOE OSTI2022

Biocatalytic system for comparatively assessing the functional association of monolignol cytochrome P450 monooxygenases with their redox partners

Lignin is a complex heterogenous polymer derived from oxidative radical polymerization of three monolignols, i.e., p-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol. These lignin monomeric precursors structurally differ in their methoxy groups of the benzene rings. In phenylpropanoid-monolignol biosynthetic pathway, the endoplasmic reticulum (ER)-resident cytochrome P450 monooxygenases, cinnamate 4-hydroxylase, coumaroyl ester 3´-hydroxylase and ferulate 5-hydroxylase, establish the key structural characteristics of monolignols. The catalysis of cytochrome P450 monooxygenase requires reducing power, which is supplied by the ER electron transfer chains, composed of cytochrome P450 oxidoreductase (CPR), cytochrome b5 reductase (CBR) and/or cytochrome b5 protein (CB5), from cofactor NADPH or NADH. While NADPH-dependent CPR serves as the typical electron donor for most P450 enzymes, in some cases, the CBR-CB5 or CPR-CB5 electron transfer system also transfers electrons to the terminal P450 enzymes. There are tremendous studies focusing on the discovery and characterization of cytochrome P450 monooxygenases. However, very limited attention has been paid to the versatility and the roles of electron transfer components in the P450 catalytic system. Due to the membrane-residence property of both P450 enzymes and electron transfer components, it is challenging to establish an effective experimental system to evaluate the functional association of P450s with their redox partners. This chapter describes a yeast cell biocatalytic system and the related experimental procedures for comparatively assessing the functional relationship of monolignol biosynthetic P450 enzymes and different redox partners in their catalysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Isopropyl 3-deoxy-α- D - ribo -hexopyranoside (isopropyl 3-deoxy-α-D-glucopyranoside): evaluating trends in structural parameters

Isopropyl 3-de­oxy-α-D-ribo-hexo­pyran­oside (isopropyl 3-de­oxy-α-D-gluco­py­ran­oside), C 9 H 18 O 5 , (I), crystallizes from a methanol–ethyl acetate solvent mixture at room temperature in a 4C1 chair con­form­ation that is slightly dis­torted towards the C5 S C1 twist-boat form. A com­parison of the structural parameters in (I), methyl α-D-gluco­pyran­oside, (II), α-D-gluco­pyranosyl-(1→4)-D-glucitol (maltitol), (III), and 3-de­oxy-α-D-ribo-hexo­pyran­ose (3-de­oxy-α-D-gluco­pyran­ose), (IV), shows that most endocyclic and exocyclic bond lengths, valence bond angles and torsion angles in the aldohexo­pyranosyl rings are more affected by anomeric configuration, aglycone structure and/or the con­form­ation of exocyclic substituents, such as hy­droxy­methyl groups, than by mono­deoxy­genation at C3. The structural effects observed in the crystal structures of (I)–(IV) were confirmed though density functional theory (DFT) calculations in com­puted structures (I) c –(IV) c . Exocyclic hy­droxy­methyl groups adopt the gauche–gauche (gg) con­form­ation (H5 anti to O6) in (I) and (III), and the gauche–trans (gt) con­form­ation (C4 anti to O6) in (II) and (IV). The O-glycoside linkage con­form­ations in (I) and (III) resemble those observed in disaccharides containing β-(1→4) linkages.

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

Vortex Structure of Head Bubble in Convective Cloud Starting Plume

Abstract A developing cumulus cloud (Cu) was modeled, and dynamic, thermodynamic, and microphysical properties of an ascending head bubble reproducing the upper part of a developing Cu were investigated. The data for analysis are taken from 10-m-resolution LES of trade wind Cu under BOMEX conditions. The detection of a rising bubble is carried out using wavelet filtering of the velocity fields and microphysical fields, while a low-frequency signal of the filtering is associated with the convective-scale structure of cloud. We substantiate and discuss the representation of the bubble as a vortex ring, and estimate the parameters of this vortex ring. The simplest Hill’s vortex was chosen as a model of a vortex ring inside cloud. Analytical approximations of the radial profiles of the vertical velocity and of conservative quantities (such as total water mixing ratio and liquid water potential temperature inside and outside the bubble) are obtained. The spatial structure of these quantities is investigated using analytical expressions. Analytical models for spatial distributions of liquid water content (LWC) and adiabatic fraction (AF) are also designed and analyzed. The results demonstrate the existence of a cloud core with high values of LWC and AF up to the height of 1800 m. The horizontally averaged value of the adiabatic fraction, calculated analytically using the Hill’s vortex concept, is evaluated as 0.39, which is the typical AF value in the upper parts of such Cu. The vertical profiles of different important quantities characterizing cloud structure are presented. The analysis performed in this study allows us to conclude that a rising vortex ring plays the dominating role in formation of the thermodynamic and microphysical structure of developing Cu. Significance Statement 1) Dynamic and thermodynamic fields of a developing cumulus cloud simulated by high-resolution LES with spectral bin microphysics are separated into convective and turbulent components by means of the wavelet technique. 2) The analysis of convective component of the cloud revealed the existence of a vortex ring at the developing stage of the cloud and evaluate its parameters. 3) The analysis performed in this study allows us to conclude that a rising vortex ring plays the important role in formation of the thermodynamic and microphysical structure of developing Cu. 4) The study provides a novel insight into the cloud–environment interaction. 5) The approximating equations describing the vortex ring can be usefully applied for developing new schemes of convective parameterization.

Meteorology & Atmospheric Sciences↗