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At least 541 records · Page 30

Mixed Valence {Ni 2+ Ni 1+ } Clusters as Models of Acetyl Coenzyme A Synthase Intermediates

Acetyl coenzyme A synthase (ACS) catalyzes the formation and deconstruction of the key biological metabolite, acetyl coenzyme A (acetyl-CoA). The active site of ACS features a {NiNi} cluster bridged to a [Fe4S4] n+ cubane known as the A-cluster. The mechanism by which the A-cluster functions is debated, with few model complexes able to replicate the oxidation states, coordination features, or reactivity proposed in the catalytic cycle. In this work, we isolate the first bimetallic models of two hypothesized intermediates on the paramagnetic pathway of the ACS function. The heteroligated {Ni 2+ Ni 1+ } cluster, [K(12-crown-4) 2 ][1], effectively replicates the coordination number and oxidation state of the proposed “A red ” state of the A-cluster. Addition of carbon monoxide to [1] - allows for isolation of a dinuclear {Ni 2+ Ni 1+ (CO)} complex, [K(12-crown-2) n ][2] (n = 1–2), which bears similarity to the “A NiFeC ” enzyme intermediate. Structural and electronic properties of each cluster are elucidated by X-ray diffraction, nuclear magnetic resonance, cyclic voltammetry, and UV/vis and electron paramagnetic resonance spectroscopies, which are supplemented by density functional theory (DFT) calculations. Calculations indicate that the pseudo-T-shaped geometry of the three-coordinate nickel in [1] – is more stable than the Y-conformation by 22 kcal mol –1 , and that binding of CO to Ni 1+ is barrierless and exergonic by 6 kcal mol –1 . UV/vis absorption spectroscopy on [2] - in conjunction with time-dependent DFT calculations indicates that the square-planar nickel site is involved in electron transfer to the CO π*-orbital. Further, we demonstrate that [2] - promotes thioester synthesis in a reaction analogous to the production of acetyl coenzyme A by ACS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

De Novo Design of Proteins That Bind Naphthalenediimides, Powerful Photooxidants with Tunable Photophysical Properties

De novo protein design provides a framework to test our understanding of protein function and build proteins with cofactors and functions not found in nature. Here, we report the design of proteins designed to bind powerful photooxidants and the evaluation of the use of these proteins to generate diffusible small-molecule reactive species. Because excited-state dynamics are influenced by the dynamics and hydration of a photooxidant’s environment, it was important to not only design a binding site but also to evaluate its dynamic properties. Thus, we used computational design in conjunction with molecular dynamics (MD) simulations to design a protein, designated NBP (NDI Binding Protein), that held a naphthalenediimide (NDI), a powerful photooxidant, in a programmable molecular environment. Solution NMR confirmed the structure of the complex. We evaluated two NDI cofactors in this de novo protein using ultrafast pump–probe spectroscopy to evaluate light-triggered intra- and intermolecular electron transfer function. Moreover, we demonstrated the utility of this platform to activate multiple molecular probes for protein labeling.

carbonyls↗

Photoluminescent Cu(I) HETPHENs Featuring Bulky Alkyl-Substituted Phenanthrolines

Successful excited-state-enhancing substituent effect strategies applied in homoleptic Cu(I) metal-to-ligand charge transfer (MLCT) chromophores have been adapted to the heteroleptic phenanthroline (HETPHEN) platform, leveraging 2,9-mesityl-1,10-phenanthroline (mesPhen) in conjunction with a series of seven distinct 2,9- and 2,3,4,7,8,9-substituted phenanthrolines. The newly conceived CuHETPHEN complexes feature MLCT lifetimes ranging from 62 to 443 ns, all of which exhibit unprecedented room-temperature photoluminescence and demonstrate quantitative adherence to the energy gap law. TD-DFT calculations successfully modeled the systematic variation in electronic transition intensities, accounting for the experimentally observed UV–vis absorption bands across the entire series of molecules while providing detailed structural explanations for the variations in spectral profiles. These heteroleptic Cu(I) diimine chromophores exhibit thermally activated delayed fluorescence (TADF), with delayed fluorescence occurring between closely spaced 1 MLCT and 3 MLCT excited manifolds, having energetic separations of ΔE = 713–1009 cm –1 , as demonstrated here for the first time. Nanosecond and ultrafast transient absorption spectroscopy verified the MLCT nature of these excited states and extracted the time constants for the initial pseudo-Jahn–Teller distortion and intersystem crossing throughout the entire series of molecules. Lastly, the triplet photosensitization properties of these Cu(I) HETPHENs are demonstrated in a number of model photochemical transformations.

Chromophores↗

Ion Mobility Separations Using Cocentric Architecture

Ion mobility separations are usually performed in linear channels, which, when extended, can have a large footprint. In this work, we explored the performance of an ion mobility device with a curved architecture which can have a more compact form. The Co-centric Ion Mobility Spectrometer (CIMS) works by manipulating ions between two co-centric surfaces, each containing a serpentine track. The mobility separation inside CIMS is achieved using traveling waveforms (TWs). We initially evaluated the device using ion trajectory simulations using SIMION, which indicated that when ions traveled circularly inside CIMS, they resulted in similar resolving powers and transmitted m/z range as traveling in a straight path in structures for lossless ion manipulations (SLIM). We then performed experimental validation of CIMS in conjunction with a TOF MS. The CIMS was made of 2 flexible printed circuit board materials folded into concentric cylinders separated by a gap of 2.8 mm. The device was about 50 mm diameter × 152 mm long and provided 1.846 m of serpentine path length. Three sets of mixtures (Agilent tune mixture, tetraalkylammonium salts, and 8 peptide mixture) and four traveling waveform profiles (square, sine, triangle, and sawtooth) were used. The sawtooth TW profile produced a slightly higher resolving power for the Agilent tuning mixture and tetraalkylammonium ions. The average resolving power for Agilent tune mixture ions ranged from 37 (using sawtooth TW) to 27 (using square TW). For tetraalkylammonium ions, the average resolving powers ranged from 45 (sawtooth TW) to 31 (square TW). For the peptide mixture ions, the resolving power was similar among the four TW profiles and ranged from 51 to 56. The average percent error in TW CCS for the peptide mixture ions ranged was about 0.4%. In conclusion, the new device showed promising results for a device made of a flexible printed circuit board material, but improvements are needed to further increase the resolving power.

59 BASIC BIOLOGICAL SCIENCES↗

Expanded Understanding of the Western Antarctic Peninsula Sea‐Ice Environment Through Local and Regional Observations at Palmer Station

Abstract The Western Antarctic Peninsula (WAP) has been experiencing rapid regional warming since at least the 1950s, however, the impacts of this warming at the local scale are variable and nuanced. Previous studies that have linked sea‐ice variability to biogeochemical cycles and food web dynamics often combine local‐scale biogeochemical data with coarse‐resolution regional satellite sea‐ice data, which may not adequately capture local sea‐ice conditions. In this study, we analyzed local‐scale in situ sea‐ice observations collected as part of a 28‐year record (1992–2020) from the Palmer Long‐Term Ecological Research site at Anvers Island, mid‐WAP, in conjunction with isotopically‐derived sea‐ice meltwater (SIM) fractions and satellite‐derived sea‐ice motion and concentration, to quantify the variability and long‐term trends in local sea‐ice behavior. In situ sea ice observations at Palmer Station displayed higher variability than satellite observations and showed no significant declines over this time, despite region‐wide declines identified in prior studies. Higher spring SIM fractions were attributed to strong northward sea‐ice motion throughout the winter. Applying these local‐scale sea‐ice insights to similarly scaled stratification and chlorophyll‐ a measurements, we found that a longer‐lasting, more consistent sea‐ice pack led to greater water column stratification following the spring sea‐ice retreat. Greater sea‐ice persistence and stronger stratification led to larger peaks in chlorophyll‐ a , though sea‐ice metrics did not explain the positive temporal trends in either stratification strength or chlorophyll‐ a . Through this study, we identify how local sea‐ice observations and meltwater data can enhance satellite data to build an understanding of the intricate connections between ice, water column dynamics, and phytoplankton.

Goodell, E.↗

Relationship Between Tropical Cloud Feedback and Climatological Bias in Clouds

Abstract Global climate model (GCM) projections of future climate are uncertain largely due to a persistent spread in cloud feedback. This is despite efforts to reduce this model uncertainty through a variety of emergent constraints (ECs); with several studies suggesting an important role for present‐day biases in clouds. Here, we use three generations of GCMs to assess the value of climatological cloud metrics for constraining uncertainty in cloud feedback. We find that shortwave cloud radiative properties across the Southern Hemisphere extratropics are most robustly correlated with tropical cloud feedback (TCF). Using this relationship in conjunction with observations, we produce an EC that yields a TCF value of 0.52 ± 0.34 W/m 2 /K, which equates to a 34% reduction in uncertainty. Thus, we show that climatological cloud properties can be used to reduce uncertainty in how clouds will respond to future warming.

54 ENVIRONMENTAL SCIENCES↗

Measured air quality impacts after teaching parents about cooking ventilation with a video: a pilot study

BackgroundCooking-related emissions contribute to air pollutants in the home and may influence children’s health outcomes.ObjectiveIn this pilot study, we investigate the effects of a cooking ventilation intervention in homes with gas stoves, including a video-based educational intervention and range hood replacement (when needed) in children’s homes.MethodsThis was a pilot (n = 14), before-after trial (clinicaltrials.gov #NCT04464720) in homes in the San Francisco Bay Area that had a school-aged child, a gas stove, and either a venting range hood or over-the-range microwave/hood. Cooking events, ventilation use, and indoor air pollution were measured in homes for 2–4 weeks, and children completed respiratory assessments. Midway, families received this intervention: (1) education about the hazards of cooking-related pollutants and benefits of both switching to back burners and using the range hood whenever cooking and (2) ensuring the range hood met airflow and sound performance standards. The educational intervention was delivered via a video developed in conjunction with local youth.ResultsWe found substantially increased use of back burners and slight increases in range hood use during cooking after intervening. Even though there was no change in cooking frequency or duration, these behavior changes resulted in decreases in nitrogen dioxide (NO2), including significant decreases in the total integrated concentration of NO2 over all cooking events from 1230 ppb*min (IQR 336, 7861) to 756 (IQR 84.0, 4210; p < 0.05) and NO2 collected on samplers over the entire pre- and post-intervention intervals from 10.4 ppb (IQR 3.5, 47.5) to 9.4 (IQR 3.0, 36.1; p < 0.005). There were smaller changes in PM2.5, and no changes were seen in respiratory outcomes.ImpactThis pilot before-after trial evaluated the use of a four-minute educational video to improve cooking ventilation in homes with gas stoves and one or more school-aged children. Participant behavior changed after watching the video, and there were decreases in indoor air pollutant concentrations in the home, some of which were significant. This brief video is now publicly available in English and Spanish (wspehsu.ucsf.edu/projects/indoor-air-quality), and this provides suggestive evidence of the utility of this simple intervention, which could be particularly beneficial for households that have children with asthma.

Holm, Stephanie M↗

Advancing simulations of coupled electron and phonon nonequilibrium dynamics using adaptive and multirate time integration

Electronic structure calculations in the time domain provide a deeper understanding of nonequilibrium dynamics in materials. The real-time Boltzmann equation (rt-BTE), used in conjunction with accurate interactions computed from first principles, has enabled reliable predictions of coupled electron and lattice dynamics. However, the timescales and system sizes accessible with this approach are still limited, with two main challenges being the different timescales of electron and phonon interactions and the cost of computing collision integrals. As a result, only a few examples of these calculations exist, mainly for two-dimensional (2D) materials. Here we leverage adaptive and multirate time integration methods to achieve a major step forward in solving the coupled rt-BTEs for electrons and phonons. Relative to conventional (non-adaptive) time-stepping, our approach achieves a 10x speedup for a target accuracy, or greater accuracy by 3–6 orders of magnitude for the same computational cost, enabling efficient calculations in both 2D and bulk materials. This efficiency is showcased by computing the coupled electron and lattice dynamics in graphene up to ~100 ps, as well as modeling ultrafast lattice dynamics and thermal diffuse scattering maps in bulk materials (silicon and gallium arsenide). In addition to improved efficiency, our adaptive method can resolve the characteristic rates of different physical processes, thus naturally bridging different timescales. This enables simulations of longer timescales and provides a framework for modeling multiscale dynamics of coupled degrees of freedom in matter. Our work opens new opportunities for quantitative studies of nonequilibrium physics in materials, including driven lattice dynamics with phonons coupled to electrons, spin, and other degrees of freedom.

Yao, Jia [California Institute of Technology (CalT↗

Electronic response of a Mott insulator at a current-induced insulator-to-metal transition

The Mott insulator Ca 2 RuO 4 exhibits an insulator-to-metal transition induced by d.c. current. Despite the thorough examination of the structural changes associated with this transition, a comprehensive knowledge of the response of electronic degrees of freedom is still lacking. Here we demonstrate current-induced modifications of the electronic states of Ca 2 RuO 4 . Angle-resolved photoemission spectroscopy in conjunction with four-probe electrical transport (transport-ARPES) measurements reveal a clear reduction of the Mott gap and a modification in the dispersion of the Ru bands. Based on a free-energy analysis, we show that the current-induced phase is electronically distinct from the high-temperature zero-current metallic phase. Our results highlight strong interplay of lattice- and orbital-dependent electronic responses in the current-driven insulator-to-metal transition.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Digital image correlation and infrared thermography data for seven unique geometries of 304L stainless steel

Material Testing 2.0 (MT2.0) is a paradigm that advocates for the use of rich, full-field data, such as from digital image correlation and infrared thermography, for material identification. By employing heterogeneous, multi-axial data in conjunction with sophisticated inverse calibration techniques such as finite element model updating and the virtual fields method, MT2.0 aims to reduce the number of specimens needed for material identification and to increase confidence in the calibration results. To support continued development, improvement, and validation of such inverse methods—specifically for rate-dependent, temperature-dependent, and anisotropic metal plasticity models—we provide here a thorough experimental data set for 304L stainless steel sheet metal. The data set includes full-field displacement, strain, and temperature data for seven unique specimen geometries tested at different strain rates and in different material orientations. Commensurate extensometer strain data from tensile dog bones is provided as well for comparison. We believe this complete data set will be a valuable contribution to the experimental and computational mechanics communities, supporting continued advances in material identification methods.

36 MATERIALS SCIENCE↗

Belowground plant allocation regulates rice methane emissions from degraded peat soils

Carbon-rich peat soils have been drained and used extensively for agriculture throughout human history, leading to significant losses of their soil carbon. One solution for rewetting degraded peat is wet crop cultivation. Crops such as rice, which can grow in water-saturated conditions, could enable agricultural production to be maintained whilst reducing CO 2 and N 2 O emissions from peat. However, wet rice cultivation can release considerable methane (CH 4 ). Water table and soil management strategies may enhance rice yield and minimize CH 4 emissions, but they also influence plant biomass allocation strategies. It remains unclear how water and soil management influences rice allocation strategies and how changing plant allocation and associated traits, particularly belowground, influence CH 4 -related processes. We examined belowground biomass (BGB), aboveground biomass (AGB), belowground:aboveground ratio (BGB:ABG), and a range of root traits (root length, root diameter, root volume, root area, and specific root length) under different soil and water treatments; and evaluated plant trait linkages to CH 4 . Rice (Oryza sativa L.) was grown for six months in field mesocosms under high (saturated) or low water table treatments, and in either degraded peat soil or degraded peat covered with mineral soil. We found that BGB and BGB:AGB were lowest in water saturated conditions where mineral soil had been added to the peat, and highest in low-water table peat soils. Furthermore, CH 4 and BGB were positively related, with BGB explaining 60% of the variation in CH 4 but only under low water table conditions. Our results suggest that a mix of low water table and mineral soil addition could minimize belowground plant allocation in rice, which could further lower CH 4 likely because root-derived carbon is a key substrate for methanogenesis. Minimizing root allocation, in conjunction with water and soil management, could be explored as a strategy for lowering CH 4 emissions from wet rice cultivation in degraded peatlands.

54 ENVIRONMENTAL SCIENCES↗

Quantifying motion blur by imaging shock front propagation with broadband and narrowband X-ray sources

Time-integrated radiography using MeV Bremsstrahlung X-ray sources is the norm for imaging during system-level testing of components and structures under dynamic condition. One source of error in the analysis of the time-integrated radiography data sets stems from motion blur which smears out sharp interfaces to a greater degree with longer exposure times, which become necessary to provide sufficient signal-to-noise with low X-ray penetration of objects of interest. To quantify motion blur, a 1D shock wave through PMMA was investigated experimentally at The Dynamic Compression Sector at The Advanced Photon Source (DCS@APS) with tapered broadband and 25.46 ± 1.06 keV narrowband X-rays. Four cameras with different exposure times were used for each experiment to compare the effect that exposure time has on motion blur. In addition, our methodology to accurately simulate motion blur in terms of transmission and shape is presented and compared to our experimental results and quantified. There is a high level of agreement between the experimental and simulation results across the range of data sets investigated in this study with a percent difference range of 0.29–1.31% for the four shots. The methodology of this work serves as a steppingstone towards a physically validated model that could be used in conjunction with experimental results to deconvolve physical parameters, densities, and interfaces of interest in a way that would not be possible with experimental results alone.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Neural network representations of multiphase Equations of State

Abstract Equations of State model relations between thermodynamic variables and are ubiquitous in scientific modelling, appearing in modern day applications ranging from Astrophysics to Climate Science. The three desired properties of a general Equation of State model are adherence to the Laws of Thermodynamics, incorporation of phase transitions, and multiscale accuracy. Analytic models that adhere to all three are hard to develop and cumbersome to work with, often resulting in sacrificing one of these elements for the sake of efficiency. In this work, two deep-learning methods are proposed that provably satisfy the first and second conditions on a large-enough region of thermodynamic variable space. The first is based on learning the generating function (thermodynamic potential) while the second is based on structure-preserving, symplectic neural networks, respectively allowing modifications near or on phase transition regions. They can be used either “from scratch” to learn a full Equation of State, or in conjunction with a pre-existing consistent model, functioning as a modification that better adheres to experimental data. We formulate the theory and provide several computational examples to justify both approaches, highlighting their advantages and shortcomings.

Science & Technology - Other Topics↗

Historical sensible-heat-flux variations key to predicting future hydrologic sensitivity

Under anthropogenic climate change (CC), the global hydrological cycle intensifies at a rate known as hydrologic sensitivity (HS). Global climate models (GCMs) exhibit substantial uncertainty in HS. Past work suggests that another form of HS, derived from internal climate variability (IV), is useful for constraining this uncertainty. However, these two forms of HS are weakly related. Here we show that decomposing HS under both CC and IV, based on the global energy budget, provides insight into the likely range of future HS. We find that sensible heat exchange between the atmosphere and ocean is not accounted for in the atmospheric energy budget under IV, masking the connection between HS under IV and CC. Removing this term, a closer relationship emerges. We use observations in conjunction with this relationship to suggest an upward shift in the likely range of future HS (66% confidence interval: 2.00–2.36 W m -2 K -1

54 ENVIRONMENTAL SCIENCES↗

Observation of early events in the photoactivation of Myxobacterial phytochrome using time-resolved serial femtosecond crystallography

Myxobacteria are non-photosynthetic, soil-dwelling bacteria distinguished by a multicellular stage in their life cycle known as fruiting bodies that are stimulated by light. Myxobacterial phytochromes are candidates for the perception of red-light. The mechanism how light is perceived and converted to a physiological response is unknown. Here, time-resolved serial femtosecond crystallographic (TR-SFX) experiments were conducted on microcrystals of the photosensory core module of the Stigmatella aurantiaca bacteriophytochrome 2 (SaBphP2). Initial events of the Z to E isomerization reaction of the covalently bound, open-chain tetrapyrrole biliverdin (BV) chromophore were determined. At 3 ps after light activation, the BV ring-D assumes a configuration needed for the isomerization. At 100 ps, a mixture of BV in the Z or E configuration is observed in subunit A, while in the other subunit the chromophore remains in the Z configuration. In conjunction with prior results, these structures reveal the molecular mechanism of phytochrome activation in the photomorphogenesis of the myxobacteria and provide the molecular foundation for physiological responses to red light in other bacteria.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Stress-dependent χ phase transformation in a Ni-based superalloy

The ongoing push to elevate operating temperatures in aerospace gas turbine engines – driven by goals of enhanced fuel efficiency and reduced CO 2 emissions – mandates advancements in the creep resistance of Ni- and Co-based superalloys, which are integral for critical engine components. This study elucidates the role of stress assisted localized phase transformations in the creep properties of these alloys. By leveraging chemo-mechanical coupling, self-healing γ′ precipitates are designed to immobilize planar defects, thereby increasing creep resistance. Employing advanced characterization techniques such as high-resolution Scanning Transmission Electron Microscopy (HR-STEM), in conjunction with atomistic simulations and thermodynamic calculations, novel deformation pathways facilitated by χ local phase transformation (LPT) strengthening have been uncovered; notably, the formation of χ nano-laths through microtwinning and superlattice intrinsic stacking fault (SISF) shearing. This study highlights critical insights into the compositional boundaries necessary for optimizing LPT strengthening while avoiding deleterious bulk formation of η/χ phases. These advancements will guide the design of new alloys maximizing high-temperature creep strength for advanced aerospace applications.

Egan, Ashton J. [Friedrich-Alexander University Er↗

Signatures of Kramers-Weyl fermions in the charge density wave material (TaSe 4 ) 2 I

The quasi-one-dimensional charge density wave (CDW) material (TaSe 4 ) 2 I has been recently predicted to host Kramers-Weyl (KW) fermions which should exist in the vicinity of high symmetry points in the Brillouin zone in chiral materials with strong spin-orbit coupling. However, direct spectroscopic evidence of KW fermions is limited. Here we use helicity-dependent laser-based angle-resolved photoemission spectroscopy (ARPES) in conjunction with tight-binding and first-principles calculations to identify KW fermions in (TaSe 4 ) 2 I. We find that topological and symmetry considerations place distinct constraints on the (pseudo-) spin texture and the observed spectra around a KW node. Our findings highlight the unique topological nature of (TaSe 4 ) 2 I and provide a pathway for identifying KW fermions in other chiral materials.

36 MATERIALS SCIENCE↗

Targeting transcription factors through an IMiD independent zinc finger domain

Abstract Immunomodulatory imide drugs (IMiDs) degrade specific C2H2 zinc finger degrons in transcription factors, making them effective against certain cancers. SALL4, a cancer driver, contains seven C2H2 zinc fingers in three clusters, including an IMiD degron in zinc finger cluster one (ZFC1). Surprisingly, IMiDs do not inhibit the growth of SALL4-expressing cancer cells. To overcome this limit, we focused on a non-IMiD domain, SALL4 zinc finger cluster four (ZFC4). By combining ZFC4-DNA crystal structure and an in silico docking algorithm, in conjunction with cell viability assays, we screened several chemical libraries against a potentially druggable binding pocket, leading to the discovery of SH6, a compound that selectively targets SALL4-expressing cancer cells. Mechanistic studies revealed that SH6 degrades SALL4 protein through the CUL4A/CRBN pathway, while deletion of ZFC4 abolished this activity. Moreover, SH6 treatment led to a significant 87% tumor growth inhibition of SALL4+ patient-derived xenografts and demonstrated good bioavailability in pharmacokinetic studies. In summary, these studies represent a new approach for IMiD independent drug discovery targeting C2H2 transcription factors such as SALL4 in cancer.

Liu, Bee Hui↗