Multireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron–Sulfur Clusters
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SEARCH · Engineering Papers
Results for “cluster structure”
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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A structural underpinning of the lower critical solution temperature (LCST) behavior behind temperature-switchable liquids
In this work, we use state-of-the-art X-ray scattering and molecular dynamics to analyze amine-water mixtures that show the unusual lower critical solution temperature (LCST) behavior. The goal is to provide direct experimental evidence for the entropy-lowering molecular cluster formation hypothesized as necessary for LCST behavior. Differential wide-angle X-ray scattering and pair distribution analysis and small-angle X-ray scattering measurements were combined with molecular modeling and liquid-liquid equilibrium measurements, revealing direct experimental evidence for the hypothesis. However, the response of the amine phase to accommodating water is even more subtle than the simple hypothesis suggests, with the formation of robust nanoscale reverse micelles. The techniques developed in this paper can be expected to yield insights in the use of temperature-switchable liquids in solvent extraction and other separations, and the stabilization of organelles in living cells that do not have physical membranes but do require compositional gradients to operate.
36 MATERIALS SCIENCE↗
Cluster model of C 12 in the density functional theory framework
We employ the constrained density functional theory to investigate cluster phenomena for the 12 C nucleus. The proton and neutron densities are generated from the placement of three 4 He nuclei (α particles) geometrically. These densities are then used in a density constrained Hartree-Fock calculation that produces an antisymmetrized state with the same densities through energy minimization. In the calculations no a priori analytic form for the single-particle states is assumed and the full energy density functional is utilized. The geometrical scan of the energy landscape provides the ground state of 12 C as an equilateral triangular configuration of three αs with molecular bond like structures. The use of the nucleon localization function provides further insight to these configurations. One can conclude that these configurations are a hybrid between a pure mean-field and a pure α particle condensate. Furthermore, this development could facilitate density functional theory based fusion calculations with a more realistic 12 C ground state.
6 ≤ A ≤ 19↗
Fetch-trap Pairs: Exploring definition of carbon storage prospects to increase capacity and flexibility in areas with competing uses
As CCS grows beyond isolated first-mover projects, the question of how to identify potential storage sites (prospects) is key to siting projects amidst the constraints of neighboring storage projects, hydrocarbon fields and other considerations. To date, prospects have been defined either by the extent of a buoyant trap or by the predicted maximum extent of the CO 2 or pressure plume. Both approaches have worked, but they may struggle in places like the Gulf of Mexico where complex geologic structure can invalidate simple assumptions of radial plume spread and buoyant traps are commonly unattractive due to numerous legacy well penetrations. Here, we propose identifying prospective storage sites by fetch area (drainage cell) rather than by buoyant closure alone. Doing so offers 1) greater freedom in siting injectors to avoid surface and subsurface constraints, including legacy wells that tend to cluster on structural high; and 2) a coherent flow regime in which buoyancy drives all injected CO 2 toward a common high. This strategy gives space to dissipate injection pressure and minimize the number of legacy wells needing review. It may also offer 1) better injectivity by bringing synclines and associated channel axes into play; and 2) potentially improved capacity by tapping a larger rock volume and taking advantage of migration losses.
58 GEOSCIENCES↗
Nature of Zirconia on a Copper Inverse Catalyst Under CO 2 Hydrogenation Conditions
The growing concern over the escalating levels of anthropogenic CO 2 emissions necessitates effective strategies for its conversion to valuable chemicals and fuels. In this research, we embark on a comprehensive investigation of the nature of zirconia on a copper inverse catalyst under the conditions of CO 2 hydrogenation to methanol. We employ density functional theory calculations in combination with the Grand Canonical Basin Hopping method, enabling an exploration of the free energy surface including a variable amount of adsorbates within the relevant reaction conditions. Our focus centers on a model three-atom Zr cluster on a Cu(111) surface decorated with various OH, O, and formate ligands, noted Zr 3 O x (OH) y (HCOO) z /Cu(111), revealing major changes in the active site induced by various reaction parameters such as the gas pressure, temperature, conversion levels, and CO 2 /H 2 feed ratios. Further, through our analysis, we have unveiled insights into the dynamic behavior of the catalyst. Specifically, under reaction conditions, we observe a large number of composition and structures with similar free energy for the catalyst, with respect to changing the type, number, and binding sites of adsorbates, suggesting that the active site should be regarded as a statistical ensemble of diverse structures that interconvert.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
BCG alignment with the locations of cluster members and the large-scale structure out to 10 R 200
Using a sample of >200 clusters, each with typically 100–200 spectroscopically confirmed cluster members, we search for a signal of alignment between the position angle (PA) of the Brightest Cluster Galaxy (BCG) and the distribution of cluster members on the sky about the cluster centre out to projected distances of 3 R 200 . The deep spectroscopy, combined with corrections for spectroscopic incompleteness, makes our sample ideal to determine alignment signal strengths. We also use an SDSS based skeleton of the filamentary large-scale structure (LSS), and measure BCG alignment with the location of the LSS skeleton segments on the sky out to projected distances of 10 R 200 . The alignment signal is measured using three separate statistical measures; Rao’s spacing test (U), Kuiper’s V parameter (V), and the Binomial probability test (P). The significance of the BCG alignment signal with both cluster members and LSS segments is extremely high (1 in a million chance or less to be drawn randomly from a uniform distribution). We investigate a wide set of parameters that may influence the strength of the alignment signal. Clusters with more elliptical-shaped BCGs show stronger alignment with both their cluster members and LSS segments. Also, selecting clusters with closely connected filaments, or using a luminosity-weighted LSS skeleton, increases the alignment signal significantly. Alignment strength decreases with increasing projected distance. Combined, these results provide strong evidence for the growth of clusters and their BCGs by preferential feeding along the direction of the filaments in which they are embedded.
79 ASTRONOMY AND ASTROPHYSICS↗
Theory-Guided Inelastic Neutron Scattering of Crystalline Alkaline Aluminate Salts Bearing Principal Motifs of Solution-State Species
Aluminate salts precipitated from caustic alkaline solutions exhibit a correlation between the anionic speciation and the identity of the alkali cation in the precipitate, with the aluminate ions occurring either in monomeric (Al(OH) 4 – ) or dimeric (Al 2 O(OH) 6 2– ) forms. The origin of this correlation is poorly understood as are the roles that oligomeric aluminate species play in determining the solution structure, prenucleation clusters, and precipitation pathways. Characterization of aluminate solution speciation with vibrational spectroscopy results in spectra that are difficult to interpret because the ions access a diverse and dynamic configurational space. To investigate the Al(OH) 4 – and Al 2 O(OH) 6 2– anions within a well-defined crystal lattice, inelastic neutron scattering (INS) and Raman spectroscopic data were collected and simulated by density functional theory for K 2 [Al 2 O(OH) 6 ], Rb 2 [Al 2 O(OH) 6 ], and Cs[Al(OH) 4 ]·2H 2 O. These structures capture archetypal solution aluminate species: the first two salts contain dimeric Al 2 O(OH) 6 2– anions, while the third contains the monomeric Al(OH) 4 – anion. Here, comparisons were made to the INS and Raman spectra of sodium aluminate solutions frozen in a glassy state. In contrast to solution systems, the crystal lattice of the salts results in well-defined vibrations and associated resolved bands in the INS spectra. The use of a theory-guided analysis of the INS of this solid alkaline aluminate series revealed that differences were related to the nature of the hydrogen-bonding network and showed that INS is a sensitive probe of the degree of completeness and strength of the bond network in hydrogen-bonded materials. Results suggest that the ionic size may explain cation-specific differences in crystallization pathways in alkaline aluminate salts.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Trapping an Unexpected/Unprecedented Hexanuclear Ce(III) Hydrolysis Product with Neutral 4‐Amino‐1,2,4‐triazole
Using Ce(III) as both a representative lanthanide and actinide analog, the ability of mixtures of acidic and basic azoles to allow direct access to homoleptic N-donor f-element complexes in one pot reactions from hydrated salts as starting materials was examined by reacting mixtures of 4-amino-1,2,4-triazole (4-NH 2 -1,2,4-Triaz), 5-amino-tetrazole (5-NH 2 -HTetaz), and 1,2,3-triazole (1,2,3-HTriaz) in 1 : 1 and 1 : 3 ratios with CeCl 3 ⋅ 7H 2 O, [C 2 mim] 3 [CeCl 6 ] ([C 2 mim] + =1-ethyl-2-methylimidazolium), and Ce(NO 3 ) 3 ⋅ 6H 2 O. Although unsuccessful in our goal, structural analysis revealed that neutral 4-NH 2 -1,2,4-Triaz is structure directing via η 2 μ 2 κ 2 bridging, with the formation of the dinuclear complexes [Ce 2 Cl 2 (μ 2 -4-NH 2 -1,2,4-Triaz) 4 (H 2 O) 8 ]Cl 4 ⋅ 4H 2 O, [Ce 2 (μ 2 -4-NH 2 -1,2,4-Triaz) 4 (4-NH 2 -1,2,4-Triaz) 2 (Cl) 6 ], and [4-NH 2 -1,2,4-HTriaz][Ce 2 (μ 2 -4-NH 2 -1,2,4-Triaz) 2 (μ 2 -NO 3 )(NO 3 ) 6 (H 2 O) 2 ]. When the synthetic conditions favored hydrolysis, the hexanuclear Ce(III) complex [Ce 6 (μ 3 -O) 4 (μ 3 -OH) 2 (μ 3 -Cl) 2 (Cl) 6 (μ 2 -4-NH 2 -1,2,4-Triaz) 12 ] ⋅ 7H 2 O was isolated. This unexpected hydrolysis product represents the first example of a high nuclearity lanthanide complex where all Ln atoms are pairwise connected through 12 N-donor ligands or 12 neutral bridging ligands of any type, a rare example of incorporation of non-oxo coordinating anions in the M 6 X 8 core, and the first reported Ce(III) hexanuclear complex of this type.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Facile and dynamic cleavage of every iron–sulfide bond in cuboidal iron–sulfur clusters
Nature employs weak-field metalloclusters to support a wide range of biological processes. The most ubiquitous metalloclusters are the cuboidal Fe–S clusters, which are comprised of Fe sites with locally high-spin electronic configurations. Such configurations enhance rates of ligand exchange and imbue the clusters with a degree of structural plasticity that is increasingly thought to be functionally relevant. Here, we examine this phenomenon using isotope tracing experiments. Specifically, we demonstrate that synthetic [Fe 4 S 4 ] and [MoFe 3 S 4 ] clusters exchange their Fe atoms with Fe 2+ ions dissolved in solution, a process that involves the reversible cleavage and reformation of every Fe–S bond in the cluster core. This exchange is facile—in most cases occurring at room temperature on the timescale of minutes—and documented over a range of cluster core oxidation states and terminal ligation patterns. In addition to suggesting a highly dynamic picture of cluster structure, these results provide a method for isotopically labeling pre-formed clusters with spin-active nuclei, such as 57 Fe. Such a protocol is demonstrated for the radical S -adenosyl- l -methionine enzyme, RlmN.
Science & Technology - Other Topics↗
Investigating the influence of particle distribution on force and torque statistics using hierarchical machine learning
An accurate representation of hydrodynamic force and torque experienced by every particle in a distribution can be obtained from particle resolved (PR) simulations. These unique quantities are influenced by the deterministic position of surrounding particles. However, systems simulated with this methodology are typically limited to particles due to the involved computational cost. This resource requirement is a major bottleneck in analyzing the effect of variations in particle distribution. Here, this article attempts to address this bottleneck by availing relatively inexpensive deep learning models. The surrogate models that we employ in this article use a physics‐based hierarchical framework and symmetry‐preserving neural networks to achieve robustness with limited training data. This article first performs additional generalizability tests on PR data of distinct distributions that are not involved in the training process. The models are then deployed on several different particle distributions. Impact of clustering and structure on the observed statistics are investigated.
42 ENGINEERING↗
Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks
Abstract Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss .
59 BASIC BIOLOGICAL SCIENCES↗
Structural Properties of Nanometer‐Sized Gold Nanoparticles on a Silicon Substrate
Properties of gold nanoparticles (Au NPs) supported on Si substrates, which have been the focus of recent attention, depend sensitively on the size, structure, and coordination of Au NPs as well as on the processes of interdiffusion and chemical bonding at the Au–Si interface. There is a great need, therefore, for developing structural techniques capable of imaging such nanosystems in atomic detail. Here, it is discussed how the atomic structure of nanometer‐sized Au NPs deposited on a silicon surface can be determined by using high‐energy X‐ray diffraction measurements in combination with an analysis based on atomic‐pair‐distribution functions and advanced reverse Monte Carlo methods. This approach delivers simple and incisive pictures of the structure of Au clusters on Si and reveals direct structural evidence for the emergence of a Au‐silicide interface following room temperature deposition of Au NPs on Si. This study will contribute to designing Au/Si nanostructures with desirable properties.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Evaluating lightweight unsupervised online IDS for masquerade attacks in CAN
Vehicular controller area networks (CANs) are susceptible to masquerade attacks by malicious adversaries. In masquerade attacks, adversaries silence a targeted ID and then send malicious frames with forged content at the expected timing of benign frames. As masquerade attacks could seriously harm vehicle functionality and are the stealthiest attacks to detect in CAN, recent work has devoted attention to compare frameworks for detecting masquerade attacks in CAN. However, most existing works report offline evaluations using CAN logs already collected using simulations that do not comply with the domain’s real-time constraints. Here we contribute to advance the state of the art by presenting a comparative evaluation of four different non-deep learning (DL)-based unsupervised online intrusion detection systems (IDS) for masquerade attacks in CAN. Our approach differs from existing comparative evaluations in that we analyze the effect of controlling streaming data conditions in a sliding window setting. In doing so, we use realistic masquerade attacks being replayed from the ROAD dataset. We show that although evaluated IDS are not effective at detecting every attack type, the method that relies on detecting changes in the hierarchical structure of clusters of time series produces the best results at the expense of higher computational overhead. We discuss limitations, open challenges, and how the evaluated methods can be used for practical unsupervised online CAN IDS for masquerade attacks.
Anomaly detection↗
Electron Counting and High-Pressure Phase Transformations in Metal Hexaborides
Pressure-induced structural transitions of the alkaline earth hexaborides, CaB 6 , SrB 6 , and BaB 6 , are studied theoretically using electron counting rules and density functional theory calculations. Here, we demonstrate the applicability of gas-phase borane electron counting methods to solid-state metal borides under pressure and validate the assumptions of the rules by density functional theory (DFT) calculations. All three compounds share ambient-pressure and high-pressure structures, but BaB 6 differs from CaB 6 and SrB 6 at intermediate pressures. The unique BaB 6 phase is shown to break electron counting rules, while all other phases obey them. This anomaly is resolved by DFT, which reveals B–Ba covalency and unusual B–B π bonding under pressure. The relationships between structure and bonding can help us to understand the exotic behavior of lanthanide hexaborides and design new borides with desirable properties. Developing electron counting procedures for solids will enhance materials discovery efforts with chemical intuition.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Monte Carlo Explicitly Correlated Second-Order Many-Body Green’s Function Calculations of Semiconductor Band Gaps
A systematically converging series of ab initio, post-density-functional, size-consistent, electron-correlated approximations is desired for predictive computing of felectronic band structures of insulating, semiconducting, and metallic solids. A series that meets all of these desiderata (except the applicability to metals) is ab initio many-body Green's function theory based on Gaussian-type-orbital (GTO) basis sets. Here, its leading-order approximation, the second-order Green's function (GF2) method in the diagonal and frequency-independent approximations with the aug-cc-pVDZ basis set, is applied to the fundamental band gaps of three semiconductors (diamond, silicon, and silicon carbide in the zincblende structure) using cluster models. Corrections are made to the basis-set-incompleteness errors by the explicit-correlation (F12) ansatz (GF2-F12) for the valence band edges. The crystals are modeled as surface-passivated clusters of increasing sizes, whose wave functions are expanded by up to 2709 GTO basis functions. Immense computational costs of these calculations are overcome by the highly scalable stochastic algorithm of the Monte Carlo GF2-F12 method, whose operation cost per state increases only as a cubic power of system size, which has a tiny memory footprint and easily achieves near-perfect parallel efficiency on thousands of CPUs or on hundreds of GPUs. The correlated, F12-corrected highest-occupied and lowest-unoccupied molecular-orbital energy (HOMO-LUMO) gap is 5.78 ± 0.07 eV for C 87 H 76 as compared with the experimental value of the fundamental (indirect) band gap of bulk diamond at 5.48 eV. The correlated, F12-corrected HOMO-LUMO gaps for Si 75 H 76 and Si 32 C 43 H 76 are 2.56 ± 0.15 eV and 3.50 ± 0.12 eV, respectively, which are expected to decrease further with increasing cluster sizes. As a result, the experimental fundamental (indirect) band gaps of bulk silicon and silicon carbide are 1.17 eV and 2.42 eV, respectively.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Bismuth-Polyoxocation Coordination Networks: Controlling Nuclearity and Dimension-Dependent Photocatalysis
Bismuth-oxocluster nodes for metal–organic frameworks (MOFs) and coordination networks/polymers are less prolific than other families featuring zinc, zirconium, titanium, lanthanides, etc. However, Bi 3+ is non-toxic, it readily forms polyoxocations, and its oxides are exploited in photocatalysis. This family of compounds provides opportunity in medicinal and energy applications. Here, we show that Bi node nuclearity depends on solvent polarity, leading to a family of Bi x -sulfonate/carboxylate coordination networks with x = 1–38. Larger nuclearity-node networks were obtained from polar and strongly coordinating solvents, and we attribute the solvent’s ability to stabilize larger species in solution. Here, the strong role of the solvent and the lesser role of the linker in defining node topologies differ from other MOF syntheses, and this is due to the Bi 3+ intrinsic lone pair that leads to weak node–linker interactions. We describe this family by single-crystal X-ray diffraction (eleven structures), obtained in pure forms and high yields. Ditopic linkers include NDS (1,5-naphthalenedisulfonate), DDBS (2,2'-[biphenyl-4,4'-diylchethane-2,1-diyl] dibenzenesulphonate), and NH 2 -benzendicarboxylate (BDC). While the BDC and NDS linkers yield more open-framework topologies that resemble those obtained by carboxylate linkers, topologies with DDBS linkers appear to be in part driven by association between DDBS molecules. An in situ small-angle X-ray scattering study of Bi 38 -DDBS reveals stepwise formation, including Bi 38 -assembly, pre-organization in solution, followed by crystallization, confirming the less important role of the linker. We demonstrate photocatalytic hydrogen (H 2 ) generation with select members of the synthesized materials without the benefit of a co-catalyst. Band gap determination from X-ray photoelectron spectroscopy (XPS) and UV–vis data suggest the DDBS linker effectively absorbs in the visible range with ligand-to-Bi-node charge transfer. In addition, materials containing more Bi (larger Bi 38 -nodes or Bi 6 inorganic chains) exhibit strong UV absorption, also contributing to effective photocatalysis by a different mechanism. All tested materials became black with extensive UV–vis exposure, and XPS, transmission electron microscopy, and X-ray scattering of the black Bi 38 -framework suggest that Bi o is formed in situ, without phase segregation. This evolution leads to enhanced photocatalytic performance, perhaps due to increased light absorption.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Cobalamin-Dependent Radical S -Adenosylmethionine Enzymes: Capitalizing on Old Motifs for New Functions
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Shear Response of Ionizable Polymer Melts at the Crossover from Ionomers to Polyelectrolytes
Nonlinear shear response of polymers is affected by inherent barriers for diffusive motion, including entanglements and topology. In ionizable polymers, ionic clusters further constrain the intrinsic dynamics of the polymers, significantly enhancing their viscosity. Here, using fully atomistic molecular dynamics simulations, the nonlinear shear response of ionizable polymers is presented, across the transition from the ionomer regime where distinctive clusters dominate the structure to the polyelectrolyte regime where clusters percolate, in polystyrene randomly sulfonated with fractions of SO 3 − groups of f = 0.20 and 0.35, in pristine and tetrahydrofuran (THF) swollen polyelectrolyte melts. For f = 0.20, the ionic clusters first fracture into smaller clusters followed by splitting into individual ionic groups and eventually reform. At higher f, the clusters morph in shape but do not break under high shear. At very high shear rates, all of the chains stretch and recoil rapidly. As the shear rate is reduced, some chains stretch and recoil, while others remain largely unaffected by the shear. Macroscopically, for all systems, the shear viscosity displays initially an elastic response, followed by nonlinear shear stress overshoot and, eventually, a steady state. The evolution of viscosity with time and shear reflects that of the ionizable domains.
cluster chemistry↗