Atomically Dispersed Dual-Metal Site Catalysts for Enhanced CO[subscsript 2] Reduction: Mechanistic
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Li, Yi↗
SEARCH · Engineering Papers
Results for “Structure Determination”
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Probing of Local Structure in Laves Compound TbFe 2
Abstract The Laves compounds Tb 1‐x Dy x Fe 2 have attracted much interest due to the giant magnetostriction effect appearing at their morphotropic phase boundary compositions. Although previous studies have established the relationship between the average structure and magnetostrictive properties in these compounds, there is a lack of characterization of their local structures. In this paper, as a first step toward this goal, the evolution of the local structure of the terminal compound (TbFe 2 ) of this system is reported, in an attempt to provide useful information about interatomic bonding in this system. The pair distribution function (PDF) results suggest that the compound presents the rhombohedral local crystal symmetry. The lattice at the local scale shows abnormal thermal expansion which is different from the long scale structure. The different role of the Tb─Fe bond and Fe─Fe bond in affecting the crystal lattice is revealed. These findings highlight the important role of local structure in determining the magnetostrictive properties of the Laves compounds.
Kou, Ronghui↗
PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions
Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.
59 BASIC BIOLOGICAL SCIENCES↗
HSV ‐1 ICP0 dimer domain adopts a novel β‐barrel fold
Abstract Infected cell protein 0 (ICP0) is an immediate‐early regulatory protein of herpes simplex virus 1 (HSV‐1) that possesses E3 ubiquitin ligase activity. ICP0 transactivates viral genes, in part, through its C‐terminal dimer domain (residues 555–767). Deletion of this dimer domain results in reduced viral gene expression, lytic infection, and reactivation from latency. Since ICP0's dimer domain is associated with its transactivation activity and efficient viral replication, we wanted to determine the structure of this specific domain. The C‐terminus of ICP0 was purified from bacteria and analyzed by X‐ray crystallography to solve its structure. Each subunit or monomer in the ICP0 dimer is composed of nine β‐strands and two α‐helices. Interestingly, two adjacent β‐strands from one monomer “reach” into the adjacent subunit during dimer formation, generating two β‐barrel‐like structures. Additionally, crystallographic analyses indicate a tetramer structure is formed from two β‐strands of each dimer, creating a “stacking” of the β‐barrels. The structural protein database searches indicate the fold or structure adopted by the ICP0 dimer is novel. The dimer is held together by an extensive network of hydrogen bonds. Computational analyses reveal that ICP0 can either form a dimer or bind to SUMO1 via its C‐terminal SUMO‐interacting motifs but not both. Understanding the structure of the dimer domain will provide insights into the activities of ICP0 and, ultimately, the HSV‐1 life cycle.
Biochemistry & Molecular Biology↗
Nanosized Zirconium Porphyrinic Metal–Organic Frameworks that Catalyze the Oxygen Reduction Reaction in Acid
Porphyrinic metal–organic frameworks (PMOFs) are very appealing electrocatalytic materials, in part, due to their highly porous backbone, well-defined and dispersed metal active sites, and their long-range order. Herein a series of (Co)PCN222 (PCN: porous coordination network) (nano)particles with different sizes are successfully prepared by coordination modulation synthesis. These particles exhibit stability in 0.1 M HClO 4 electrolyte with no obvious particle size or compositional changes observed after being soaked for 3 days in the electrolyte or during electrocatalysis. This long-term stability enables the in-depth investigation into the electrocatalytic oxygen reduction, and it is further demonstrated that the (Co)PCN222 particle size correlates with its catalytic activity. Of the three particle sizes evaluated (characteristic length scales of 200, 500, and 1000 nm), the smallest size demonstrates the highest mass activity while the largest size has the highest surface area normalized activity. Together these results highlight the importance of determining the structural stability of framework catalysts and provide insights into the important roles of particle size, opening new avenues to investigate and improve the electrocatalytic performance of this class of framework material.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Fed-batch production of deuterated protein in Escherichia coli for neutron scattering experimentation
Neutron scattering is a powerful technique for determining the structure and dynamics of biological materials in a variety of environmental conditions. A distinguishing property of the neutron is its sensitivity to detecting hydrogen and distinguishing it from its isotope deuterium. This enables unique types of experiments that take advantage of this differential sensitivity called isotopic contrast variation. Using this approach, the chemistry of the system is not changed, but the visibility of individual sample components can be tuned by varying the deuterium content of the system under investigation. Deuterated proteins are commonly produced in bacterial systems that are adapted to growth in D2O minimal media. To maximize the yield of deuterium-labeled protein and efficiently utilize D2O and occasionally the deuterated substrate, fed-batch processes are routinely used to maximize biomass production without compromising cell viability. A step-by-step procedure will be described along with a case study of the production of deuterated green fluorescent protein. Limitations of the process will also be discussed.
Weiss, Kevin L.↗
Ion-selective conformational stabilization of a disordered repeats-in-toxin protein domain
Ion-binding intrinsically disordered proteins (IDPs) recruit and bind to specific metal ions to perform critical biological functions. In proteins where ion binding and structural transitions are coupled, interactions with off-target toxic metals can dramatically disrupt protein structure and function, exemplified by lead and mercury poisoning. Understanding the complex mechanisms underlying how IDPs exclude or allow binding to different ionic species is crucial for addressing the origins of metal toxicity in biological systems. Here, we elucidate mechanisms of ion selectivity in an IDP that adopts a structure upon Ca 2+ binding. We probed ion-induced conformational changes of a repeats-in-toxin (RTX) protein domain in the presence of different ion ligands—Mg 2+ , Ca 2+ , Sr 2+ , and Ba 2+ —with chemical similarities but drastically different ionic radii. RTX adopts ion-selective conformations measured by x-ray crystallography, small-angle x-ray scattering, and circular dichroism. High-resolution x-ray structures reveal that Sr 2+ induces a nearly identical RTX structure as natively binding Ca 2+ , enabled by the intrinsic flexibility and disorder of the protein. Small-angle x-ray scattering and circular dichroism indicate that smaller Mg 2+ does not induce a significant conformational change in RTX, whereas larger Ba 2+ induces a partially folded structure. These results highlight the importance of geometric constraints imposed by protein structure in determining metal ion selectivity, yielding insights into how off-target ion binding may result in protein misfolding and malfunction.
Gudinas, Alana P. [Stanford Univ., CA (United Stat↗
Selective adsorption of arsenic over phosphate by transition metal cross-linked chitosan
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Pincus, Lauren N.↗
Order-disorder behavior at thin film oxide interfaces
Order-disorder processes fundamentally determine the structure and properties of many important oxide systems for energy and computing applications. While these processes have been intensively studied in bulk materials, they are less investigated and understood for nanostructured oxides in highly non-equilibrium conditions. These systems can now be realized through a range of deposition techniques and probed at exceptional spatial and chemical resolution, leading to a greater focus on interface dynamics. In this work, we survey a selection of recent studies of order-disorder behavior at thin film oxide interfaces, with a particular emphasis on the emergence of order during synthesis and disorder in extreme irradiation environments. We summarize key trends and identify directions for future study in this growing research area.
36 MATERIALS SCIENCE↗
Steady state thermo-mechanics and material property definition framework for analyzing DCLL blanket in the fusion nuclear science facility
In this work, a thermo-mechanics model that relies on creating the material property definition framework (MPDF) and multiphysics coupling of the heat transfer and the solid mechanics modules is developed to determine the structural integrity of the recently designed dual cooled lead lithium (DCLL) inboard blanket (IB) for the Fusion Nuclear Science Facility under steady state loads. The MPDF is called to supply fusion relevant neutron irradiation and temperature induced changes in material properties during multiphysics finite element runs, and PbLi temperature profiles are used to approximate Magnetohydrodynamics effect and the nuclear volumetric heating on the PbLi. Neutron irradiation and temperature induced reduction of the yield and ultimate strengths of F82H steel at the first wall (FW) are quantified for one year. A blanket in an assembly with gaps between blanket sectors and another blanket in an assembly with no gaps between blanket sectors, both exposed to radiation damage that lasted for one year are analyzed. Analysis using the elastic ITER structural design criteria for in-vessel components (ITER SDC-IC) design rules and a linear isotropic-hardening-type elastoplastic material model are used where most appropriate. The IB blanket with gaps between blanket sectors will withstand the steady state combined thermal and coolant loads for one year operational period but will fail if no gaps are allowed between blanket sectors. It is recommended that a gap of about 7.62 mm should be provided between IB blanket sectors during assembly which would close up during service, stop neutron streaming, reduce stresses and reduce bending of the FW into the scrape-off layer.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Surface energetics of wurtzite and sphalerite polymorphs of zinc sulfide and implications for their formation in nature
Surface energetics of zinc sulfide nanoparticles determines their structure, properties, and occurrence. Using a combination of experimental techniques, we investigated the thermodynamics of the two polymorphs, sphalerite and wurtzite at bulk and nanoscale to understand their occurrence. Calorimetric measurements confirmed that wurtzite has a lower surface energy than sphalerite, which causes a reversal in phase stability at the nanoscale, with wurtzite energetically stable for particle size below 10 nm. Taking these surface energies into account, a simple model of the thermodynamics of the sphalerite - wurtzite transformation as a function of particle size and temperature can explain the occurrence of the zinc sulfide polymorphs in environments as diverse as ore bodies and planetary atmospheres.
58 GEOSCIENCES↗
High entropy alloys with hexagonal close-packed structure derived from thin film combinatorial approach
A thin film combinatorial synthesis approach was utilized to develop a compositional and structural library for the OsRuWCo alloy system. The survey of this alloy space produced 24 unique compositions and their corresponding crystal structures, which represent a phase map where amorphous and single-phase hexagonal close-packed alloys were identified. Based on the identification of a promising candidate film region, a new high entropy alloy based on OsRuWCo, but with non-equiatomic composition, was synthesized in bulk form. The alloy exhibited a single-phase hexagonal close-packed structure in the as-cast state. Three derivatives from this system were also developed by considering the heat of mixing, atomic size, and binary solubility. These new alloys are based on OsRuWCoIr and OsRuWCoFe, both of which exhibit single-phase hexagonal close-packed as-cast structures, as determined by X-ray diffraction and electron microscopy. Additionally, this large compositional space was utilized to evaluate conventional parameters that describe high entropy alloys (ΔS mix , ΔH mix , Ω, δ, and VEC), and these were found to elucidate the criteria for solid solution formation in this system. Additionally, trends illustrating the evolution from amorphous to crystalline phases are demonstrated and discussed. It is concluded that in this particular case, the dominant factors promoting crystallinity are thermodynamic or electronic, rather than geometric.
36 MATERIALS SCIENCE↗
Unraveling transition-metal-mediated stability of spinel oxide via in situ neutron scattering
The energy materials performance is intrinsically determined by structures from the average lattice structure to the atom arrangement, valence, and distribution of the containing transition metal (TM) elements. Understanding the mechanism of the structure transition and atom rearrangement via synthesis or processing is key to expediting the exploration of excellent energy materials. In this work, in situ neutron scattering is employed to reveal the real-time structure evolution, including the TM-O bonds, lattice, TM valence and the migration of the high-voltage spinel cathode LiNi 0.5 Mn 1.5 O 4 . The transition-metal-mediated spinel destabilization under the annealing at the oxygen-deficient atmosphere is pinpointed. Additionally, the formation of Mn 3+ is correlated to the TM migration activation, TM disordered rearrangement in the spinel, and the transition to a layered-rocksalt phase. The further TM interdiffusion and Mn 2+ reduction are also revealed with multi-stage thermodynamics and kinetics. The mechanisms of phase transition and atom migrations as functions of temperature, time and atmosphere present important guidance on the synthesis in various-valence element containing oxides.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Proton-detected solid-state NMR spectroscopy of spin-1/2 nuclei with large chemical shift anisotropy
Constant-time (CT) dipolar heteronuclear multiple quantum coherence (D-HMQC) has previously been demonstrated as a method for proton detection of high-resolution wideline NMR spectra of spin-1/2 nuclei with large chemical shift anisotropy (CSA). However, 1 H transverse relaxation and t 1 -noise often reduce the sensitivity of D-HMQC experiments, preventing the theoretical gains in sensitivity provided by 1 H detection from being realized. In this paper, we demonstrate a series of improved pulse sequences for 1 H detection of spin-1/2 nuclei under fast MAS, with 195 Pt SSNMR experiments on cisplatin as an example. First, a t 1 -incrementation protocol for D-HMQC dubbed Arbitrary Indirect Dwell (AID) is demonstrated. AID allows the use of arbitrary, rotor asynchronous t 1 -increments, but removes the constant time period from CT D-HMQC, resulting in improved sensitivity by reducing transverse relaxation losses. Next, we show that short high-power adiabatic pulses (SHAPs), which efficiently invert broad MAS sideband manifolds, can be effectively incorporated into 1 H detected symmetry-based resonance echo double resonance (S-REDOR) and t 1 -noise eliminated (TONE) D-HMQC experiments. The S-REDOR experiments with SHAPs provide approximately double the dipolar dephasing, as compared to experiments with rectangular inversion pulses. We lastly show that sensitivity and resolution can be further enhanced with the use of swept excitation pulses as well as adiabatic magic angle turning (aMAT).
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Biosynthesis of polycyclopropanated high energy biofuels
Cyclopropane-functionalized hydrocarbons are excellent fuels due their high energy density. However, the organic synthesis of these molecules is challenging and harmful to the environment. In this work we produced polycyclopropanated fatty acids in bacteria. These molecules can be easily converted into renewable fuels for high energy applications such as shipping, long-haul transport, aviation, and rocketry. We explored the chemical diversity encoded in the genome of thousands of bacteria to identify and repurpose naturally occurring cyclopropanated molecules. We identified a set of candidate iterative polyketide synthases (iPKSs) predicted to produce polycyclopropanated fatty acids (POP-FAs), expressed these PKSs in Streptomyces coelicolor and produced the POP-FAs. We determined the structure of the molecules and increased their production 22-fold. Polycyclopropanated fatty acid methyl esters (POP-FAMEs) were obtained by methyl esterifying the POP-FAs. Finally, we calculated that our POP fuel candidates can have energy densities of more than 50 MJ/L. Our research shows that POP-FAMEs and other polyketide derived POPs have the energetic properties for energy-demanding applications for which sustainable alternatives are scarce.
09 BIOMASS FUELS↗
Net lithium deposition and dominant self-sputtering in lithium tokamak experiment-β with a liquid lithium wall
We observed enhanced net lithium deposition and lithium erosion, possibly dominated by physical sputtering of lithium by lithium-ion bombardment, on the outer plasma-facing surface in the Lithium Tokamak eXperiment-β (LTX-β) during liquid lithium wall operations. Silicon crystal samples with micro-trenches (30 μm × 30 μm × 2–7 μm deep) were exposed to hydrogen plasmas in LTX-β for solid and liquid lithium wall operations. Post-mortem analysis using X-ray photoelectron spectroscopy combined with argon ion sputtering measured net lithium deposition of 8.2 or 21 nm on the silicon crystal surface exposed for ~ 50 repeated shots of ~ 50-ms hydrogen plasma discharges during the liquid lithium wall operations at a vessel temperature of 475 K. Energy dispersive X-ray spectroscopy measured oxygen concentration patterns on the micro-trench floors, which were due to oxidized lithium deposition. Using the inhomogeneous oxygen concentration pattern caused by an ion-shadowing effect associated with the micro-trench’s geometric structure, we determined a polar incident ion direction of 68.4 ± 1.6° referenced to the surface normal direction. This observation was well-explained by the hypothesis that self-sputtering of Li was a dominant lithium erosion source in addition to lithium sputtering by hydrogen bombardment.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Current challenges in the physics of white dwarf stars
White dwarfs are a class of stars with unique physical properties. They present many challenging problems whose solution requires advanced theories of dense matter, state-of-the-art experimental techniques, and extensive computing efforts. New ground- and space-based observatories will soon provide an increasingly detailed view of white dwarf stars and reveal new phenomena that will challenge our models. This review is an introduction to the nature of white dwarfs, the physical processes that determine their structure and evolution, and the physical conditions they span. Here we discuss a wide variety of currently unsolved or partially resolved problems in their constitutive physics that are broadly related to equations of state, transport processes and opacities.
79 ASTRONOMY AND ASTROPHYSICS↗
Learning From User Behavior: A Survey-Assist Algorithm for Longitudinal Mobility Data Collection
GPS-based travel surveys are widely used in mobility studies to gather crucial qualitative data, like purpose, transportation mode and replaced mode. However, survey response still poses a burden to users, especially in long-term mobility studies, leading to response fatigue. We explore a survey-assist strategy to ease this burden by a novel, user-level modeling approach that leverages past responses from each user to predict responses for new trips, without relying on external data sources like GIS data. We investigate three main algorithms for predicting responses: (i) clustering trips and extrapolating responses for similar trips, (ii) using random forest classification, and (iii) clustering that uses a hybrid algorithm to determine spatial structure, which is then fed as input to a classic random forest classifier. The clustering approach can flexibly predict responses for even complex qualitative survey questions; it achieved F-scores of 65%. The random forest pipeline uses architecture that restricts it to predicting three predetermined survey questions: trip purpose, mode, and replaced mode. However, it achieved F-scores of 78%. While the survey-assist approach has been implemented by several proprietary systems, to our knowledge, this is the first exploration in the academic literature. It follows that this is also the first rigorous evaluation of multiple algorithms that can implement the approach. The evaluation uses a large scale, publicly available, longitudinal dataset consisting of ~ 92k trips from 235 users over a period of roughly one and a half years. With this approach, travel surveys can be pre-filled with the predicted responses for each trip, thus streamlining the survey process for users. Combined with an active learning system that requests user input on low-confidence predictions, models can be updated and improved over time to better support the long-term collection of longitudinal qualitative data.
clustering↗