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At least 505 records · Page 28

Structural Conservation of the A 1 Binding Site in Photosystem I across Cyanobacteria and Green Algae

Time-resolved step-scan Fourier transform infrared (FTIR) difference spectroscopy was used to obtain (A 1 − − A 1 ) FTIR difference spectra from photosystem I (PSI) samples isolated from eight phylogenetically diverse cyanobacterial strains and one green alga, totaling 13 PSI preparations. These included samples from cells grown under farred light and PSI in monomeric, dimeric, trimeric, and tetrameric states. Spectral profiles were shown to be independent of oligomeric state. Remarkably, all (A 1 − − A 1 ) FTIR difference spectra exhibited high similarity, underscoring the robustness of the technique and indicating minimal experimental variability. This congruence reveals a highly conserved environment for the phylloquinone cofactor at the A 1 binding site across diverse taxa. Conserved bands associated with the A 0 pigment further suggest structural continuity from A 0 to A 1 . To leverage this consistency, we constructed a composite (A 1 − − A 1 ) FTIR difference spectrum by averaging all 13 spectra. This composite spectrum provides enhanced resolution, enabling unambiguous identification of previously unresolved bands. The fact that a highly resolved composite spectrum can be obtained by averaging demonstrates the similarity in the spectra from the different types of samples. Band assignments were refined using prior studies, yielding an improved spectral framework for future investigations of PSI electron transfer cofactors.

Charge transfer↗

Roadmap for Optical Metasurfaces

Metasurfaces have recently risen to prominence in optical research, providing unique functionalities that can be used for imaging, beam forming, holography, polarimetry, and many more, while keeping device dimensions small. Despite the fact that a vast range of basic metasurface designs has already been thoroughly studied in the literature, the number of metasurface-related papers is still growing at a rapid pace, as metasurface research is now spreading to adjacent fields, including computational imaging, augmented and virtual reality, automotive, display, biosensing, nonlinear, quantum and topological optics, optical computing, and more. At the same time, the ability of metasurfaces to perform optical functions in much more compact optical systems has triggered strong and constantly growing interest from various industries that greatly benefit from the availability of miniaturized, highly functional, and efficient optical components that can be integrated in optoelectronic systems at low cost. This creates a truly unique opportunity for the field of metasurfaces to make both a scientific and an industrial impact. Furthermore, the goal of this Roadmap is to mark this “golden age” of metasurface research and define future directions to encourage scientists and engineers to drive research and development in the field of metasurfaces toward both scientific excellence and broad industrial adoption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

evSeq: Cost-Effective Amplicon Sequencing of Every Variant in a Protein Library

Widespread availability of protein sequence-fitness data would revolutionize both our biochemical understanding of proteins and our ability to engineer them. Unfortunately, even though thousands of protein variants are generated and evaluated for fitness during a typical protein engineering campaign, most are never sequenced, leaving a wealth of potential sequence-fitness information untapped. Primarily, this is because sequencing is unnecessary for many protein engineering strategies; the added cost and effort of sequencing is thus unjustified. It also results from the fact that, even though many lower cost sequencing strategies have been developed, they often require at least some sequencing or computational resources, both of which can be barriers to access. In this work, we present every variant sequencing (evSeq), a method and collection of tools/standardized components for sequencing a variable region within every variant gene produced during a protein engineering campaign at a cost of cents per variant. evSeq was designed to democratize low-cost sequencing for protein engineers and, indeed, anyone interested in engineering biological systems. Execution of its wet-lab component is simple, requires no sequencing experience to perform, relies only on resources and services typically available to biology labs, and slots neatly into existing protein engineering workflows. Analysis of evSeq data is likewise made simple by its accompanying software (found at github.com/fhalab/evSeq, documentation at fhalab.github.io/evSeq), which can be run on a personal laptop and was designed to be accessible to users with no computational experience. Here, low-cost and easy to use, evSeq makes collection of extensive protein variant sequence-fitness data practical.

59 BASIC BIOLOGICAL SCIENCES↗

Carbon Negative Synthesis of Amino Acids Using a Cell-Free-Based Biocatalyst

Biological systems can directly upgrade carbon dioxide (CO 2 ) into chemicals. The CO 2 fixation rate of autotrophic organisms, however, is too slow for industrial utility, and the breadth of engineered metabolic pathways for the synthesis of value-added chemicals is too limited. Biotechnology workhorse organisms with extensively engineered metabolic pathways have recently been engineered for CO 2 fixation. Yet, their low carbon fixation rate, compounded by the fact that living organisms split their carbon between cell growth and chemical synthesis, has led to only cell growth with no chemical synthesis achieved to date. Here, we engineer a lysate-based cell-free expression (CFE)-based multienzyme biocatalyst for the carbon negative synthesis of the industrially relevant amino acids glycine and serine from CO 2 equivalents–formate and bicarbonate–and ammonia. The formate-to-serine biocatalyst leverages tetrahydrofolate (THF)-dependent formate fixation, reductive glycine synthesis, serine synthesis, and phosphite dehydrogenase-dependent NAD(P)H regeneration to convert 30% of formate into serine and glycine, surpassing the previous 22% conversion using a purified enzyme system. We find that (1) the CFE-based biocatalyst is active even after 200-fold dilution, enabling higher substrate loading and product synthesis without incurring additional cell lysate cost, (2) NAD(P)H regeneration is pivotal to driving forward reactions close to thermodynamic equilibrium, (3) balancing the ratio of the formate-to-serine pathway genes added to the CFE is key to improving amino acid synthesis, and (4) efficient THF recycling enables lowering the loading of this cofactor, reducing the cost of the CFE-based biocatalyst. To our knowledge, this is the first synthesis of amino acids that can capture CO 2 equivalents for the carbon negative synthesis of amino acids using a CFE-based biocatalyst. Looking ahead, the CFE-based biocatalyst process could be extended beyond serine to pyruvate, a key intermediate, to access a variety of chemicals from aromatics and terpenes to alcohols and polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanistic Origin of Photoredox Catalysis Involving Iron(II) Polypyridyl Chromophores

Photoredox catalysis employing ruthenium- and iridium-based chromophores have been the subject of considerable research. However, the natural abundance of these elements are among the lowest on the periodic table, a fact that has led to an interest in developing chromophores based on earth-abundant transition metals that can perform the same function. There have been reports of using Fe II -based polypyridyl complexes as photocatalysts, but there is limited mechanistic information pertaining to the nature of their reactivity in the context of photoredox chemistry. Herein, we report the results of bimolecular quenching studies between [Fe(tren(py) 3 )] 2+ (where tren(py) 3 = tris(2-pyridyl-methylimino-ethyl)amine) and a series of benzoquinoid acceptors. The data provide direct evidence of electron transfer involving the lowest-energy ligand-field excited state of the Fe(II)-based photosensitizer, definitively establishing that Fe(II) polypyridyl complexes can engage in photoinduced redox reactions but by a mechanism that is fundamentally different than the MLCT-based chemistry endemic to their second- and third-row congeners.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Resonant Tender X-ray Diffraction for Disclosing the Molecular Packing of Paracrystalline Conjugated Polymer Films

The performance of optoelectronic devices based on conjugated polymers is critically dependent upon molecular packing; however, the paracrystalline nature of these materials limits the amount of information that can be extracted from conventional X-ray diffraction. Resonant diffraction (also known as anomalous diffraction) occurs when the X-ray energy used coincides with an X-ray absorption edge in one of the constituent elements in the sample. The rapid changes in diffraction intensity that occur as the X-ray energy is varied across an absorption edge provide additional information that is lost in a conventional nonresonant experiment. Taking advantage of the fact that many conjugated polymers contain sulfur as heteroatoms, here we reveal pronounced resonant diffraction effects at the sulfur K-edge with a particular focus on the well-studied electron transporting polymer poly([N,N'-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-5,5'-(2,2'-bithiophene)), P(NDI2OD-T2). The observed behavior is found to be consistent with the theory of resonant diffraction, and by simulating the energy-dependent peak intensity based on proposed crystal structures for P(NDI2OD-T2), we find that resonant diffraction can discriminate between different crystalline packing structures. The utilization of resonant diffraction opens up a new way to unlock important microstructural information about conjugated polymers for which only a handful of diffraction peaks are typically available.

36 MATERIALS SCIENCE↗

Modes of Disorder in Poly(carbon monofluoride)

Poly(carbon monofluoride), or (CF) n , is a layered fluorinated graphite material consisting of nanosized platelets. In this work, we present experimental multidimensional solid-state NMR spectra of (CF)n, supported by density functional theory (DFT) calculations of NMR parameters, which overhauls our understanding of structure and bonding in the material by elucidating many ways in which disorder manifests. We observe strong 19 F NMR signals conventionally assigned to elongated or “semi-ionic” C–F bonds and find that these signals are in fact due to domains where the framework locally adopts boat-like cyclohexane conformations. We calculate that C–F bonds are weakened but are not elongated by this conformational disorder. Exchange NMR suggests that conformational disorder avoids platelet edges. We also use a new J-resolved NMR method for disordered solids which provides molecular-level resolution of highly fluorinated edge states. Strings of consecutive difluoromethylene groups at edges are relatively mobile. Topologically distinct edge features, including zigzag edges, crenellated edges, and coves are resolved in our samples by solid-state NMR. Disorder should be controllable in a manner dependent on synthesis, affording new opportunities for tuning the properties of graphite fluorides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Au and Pt Remain Unoxidized on a CeO 2 -Based Catalyst during the Water–Gas Shift Reaction

The active form of Au and Pt in CeO 2 based catalysts for the WGS reaction is an issue that although it has been widely studied remains unclear. On one hand, ionic species might be responsible of weakening the Ce-O bonds increasing the oxygen mobility and WGS activity. On the other hand, the close contact of Au or Pt atoms with CeO 2 oxygen vacancies at the metal/CeO 2 interface might provide the active sites for an efficient reaction. In this work, by using in-situ X-ray absorption spectroscopy, we demonstrate that both Au and Pt remain unoxidized during the reaction. Here, remarkable differences involving the dynamics established by both species under WGS atmospheres were recognized. For the pre-reduced Pt catalyst, an increase of the conversion coincided with a re-structuration of the Pt atoms into cuboctahedrical metallic particles without significant variations on the overall particle size. Contrary to the relatively static behavior of Pt 0 , Au 0 nanoparticles exhibited a sequence of particle splitting and agglomeration whilst maintaining a zero oxidation state, even though not being located in a metallic environment during the process. High WGS activity was obtained when Au atoms were surrounded by oxygen. The fact that Au preserves its unoxidized state indicates that the chemical interaction between Au and oxygen must be necessarily electrostatic being such electrostatic interaction fundamental for a top performance in the WGS process.

36 MATERIALS SCIENCE↗

Hydride-Containing Eight-Electron Pt/Ag Superatoms: Structure, Bonding, and Multi-NMR Studies

Recent reports on hydride-doped noble metal nanoclusters strongly suggest that the encapsulated hydride is a part of the superatom core, but no accurate location of the hydride could be experimentally proved, so far. Here, we report herein a hydride-doped eight-electron platinum/silver alloy nanocluster in which the position of four-coordinated hydride was determined by neutron diffraction for the first time. X-ray structures of [PtHAg 19 (dtp/desp) 12 ] (dtp = S 2 P(O n Pr) 2 , 1; dsep = Se 2 P(O i Pr) 2 , 2) describe a central platinum hydride (PtH) unit encapsulated within a distorted Ag 12 icosahedron, the resulting (PtH)@Ag 12 core being stabilized by an outer sphere made up of 7 capping silver atoms and 12 dichalcogenolates. Solid-state structures of 1 and 2 differ somewhat in the spatial configuration of their outer spheres, resulting in overall different symmetries, C 1 and C 3 , respectively. Whereas the multi-NMR spectra of 2 in solution at 173 K reveal that the structure of C 3 symmetry is the predominant one, 1 H and 195 Pt NMR spectra of 1 at the same temperature disclose the presence of isomers of both C 1 and C 3 symmetry. DFT calculations found both isomers to be very close in energy, supporting the fact that they co-exist in solution. They also show that the [PtH@Ag 12 ] 5+ kernel can be viewed as a closed-shell superatomic core, the μ4-hydride electron contributing to its eight-electron count. On the other hand, the 1s(H) orbital contributes only moderately to the superatomic orbitals, being mainly involved in the building of a Pt–H bonding electron pair with the 5d z 2 (Pt) orbital.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of Gas Phase Monohydrated Nicotine: Implications for Nicotine’s Native Structure in the Acetylcholine Binding Protein

In this work, we report a joint experimental–theoretical study of the never reported before structure and infrared spectra of gas phase monohydrated nicotine (NIC) and nornicotine (NOR) and use them to assign their protonation sites. NIC’s biological activity is strongly affected by its protonation site, namely, the pyrrolidine (Pyrro-NICH + , anticipated active form) and pyridine (Pyri-NICH + ) forms; however, these have yet to be directly experimentally determined in either the nicotinic acetylcholine receptor (nAChR, no water present) or the acetylcholine-binding protein (AChBP, a single water molecule is present) but can only be inferred to be Pyrro-NICH + from the intermolecular distance to the neighboring residues (i.e., tryptophan). Our temperature-controlled double ion trap infrared spectroscopic experiments assisted by the collisional stripping method and high-level theoretical calculations yield the protonation ratio of Pyri:Pyrro = 8:2 at 240 K for the gas phase NICH + ···(H 2 O) complex, which resembles the molecular cluster present in the AChBP. Therefore, a single water molecule in the gas phase enhances this ratio in NICH + relative to the 3:2 for the nonhydrated gas phase NICH + in a trend that contrasts with the almost exclusive presence of Pyrro-NICH + in aqueous solution. In contrast, the Pyri-NORH + protomer is exclusively observed, a fact that may correlate with its weaker biological activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Surface Hydration of Porous Nickel Hydroxides Facilitates the Reversible Adsorption of CO 2 from Ambient Air

Direct air capture (DAC) under humid ambient conditions typically requires the use of organic components, with sorbents that are purely inorganic in composition for the most part operating hundreds of degrees above room temperature. In this work, we report porous metal hydroxides as a novel class of water-tolerant, oxidatively and hydrothermally stable low-temperature sorbents that exhibit competitive DAC working capacities of 1.25 mmol/g over 5 consecutive temperature swing adsorption–desorption cycles in the presence of steam and oxygen. Aqueous miscible organic solvent treatments are used to create highly porous structures with surface areas exceeding 700 m 2 /g that capture CO 2 in the form of bicarbonates under dry conditions, and carbonates under wet conditions. Water exerts a facilitative rather than an inhibiting effect on CO 2 binding, and the presence of hydrating multilayers serves to stabilize carbonate species akin to moisture swing adsorbents except for the fact that solvation results in a remarkable (upto 10-fold) increase, not decrease, in DAC capacity. High-valent doping with cerium is used to improve DAC capacities by amplifying surface basicity, evidencing porous nickel hydroxides specifically (and porous metal hydroxides more generally) as a novel class of robust, earth-abundant DAC sorbents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CMIP6 Models Predict Significant 21st Century Decline of the Atlantic Meridional Overturning Circulation

We explore the representation of the Atlantic Meridional Overturning Circulation (AMOC) in 27 models from the CMIP6 multi-model ensemble. Comparison with RAPID and SAMBA observations suggests that the ensemble mean represents the AMOC strength and vertical profile reasonably well. Linear trends over the entire historical period (1850-2014) are generally neutral, but many models exhibit an AMOC peak around the 1980’s. Ensemble-mean AMOC decline in future (SSP) scenarios is stronger in CMIP6 than CMIP5 models. In fact, AMOC decline in CMIP6 is surprisingly insensitive to the scenario at least up to 2060. We find an emergent relationship among a majority of models between AMOC strength and 21st century AMOC decline. Constraining this relationship with RAPID observations suggests that the AMOC might decline between 6 and 8 Sv (34-45%) by 2100. A smaller group of models projects much less AMOC weakening of only up to 30%.

58 GEOSCIENCES↗

Analysis of the Beaufort Gyre Freshwater Content in 2003–2018

Abstract Hydrographic data collected from research cruises, bottom‐anchored moorings, drifting Ice‐Tethered Profilers, and satellite altimetry in the Beaufort Gyre region of the Arctic Ocean document an increase of more than 6,400 km 3 of liquid freshwater content from 2003 to 2018: a 40% growth relative to the climatology of the 1970s. This fresh water accumulation is shown to result from persistent anticyclonic atmospheric wind forcing (1997–2018) accompanied by sea ice melt, a wind‐forced redirection of Mackenzie River discharge from predominantly eastward to westward flow, and a contribution of low salinity waters of Pacific Ocean origin via Bering Strait. Despite significant uncertainties in the different observations, this study has demonstrated the synergistic value of having multiple diverse datasets to obtain a more comprehensive understanding of Beaufort Gyre freshwater content variability. For example, Beaufort Gyre Observational System (BGOS) surveys clearly show the interannual increase in freshwater content, but without satellite or Ice‐Tethered Profiler measurements, it is not possible to resolve the seasonal cycle of freshwater content, which in fact is larger than the year‐to‐year variability, or the more subtle interannual variations.

Arctic Ocean↗

River Regulation Alleviates the Impacts of Climate Change on US Thermoelectricity Production

Climate change and anthropogenic activities can both influence stream temperature, which is a critical indicator of thermoelectric power generation potential. Previous studies emphasized the vulnerability of power-generation systems to climate warming (ref 1, 2). Despite the fact that two-thirds of the global rivers are regulated by dams (ref 3), the relative impacts of water management and climate change on stream temperature and thermoelectric production have not yet been evaluated. Using an integrated modeling system applied to the conterminous United States, simulations confirm the dominant role of climate change in shaping the future trends of stream temperature. However, water management, reservoir regulation in particular, can mitigate the stream temperature warming and reduce the frequency and magnitude of extreme high stream temperatures through redistribution of the seasonal streamflow. Moreover, water management can alleviate the loss of power plant usable capacity from climate change to the level of reduced warming from emission mitigation. By regulating the flow and temperature regimes, water management is a promising adaptation measure to alleviate climate change induced effects in the water-energy nexus.

Zhang, Xiao↗

The Contributions of Shear and Turbulence to Cloud Overlap for Cumulus Clouds

The causes of vertical cloud overlap, the ratio between the cloud fraction by area and the cloud fraction by volume, are studied for fields of cumulus convection. Using large-eddy simulations, the structure of individual clouds within the cloud field is inspected and connected to the overall cloud cover of the entire cloud field. First, it is shown that the cloud overlap of the entire field can be well approximated by the total cloud overlap of the individual clouds. It is then shown that a simple maximum overlap assumption, which is commonly used for cloud fields with small layer depth, can only account for roughly half of the overlap inefficiency. This is due to the fact that maximum overlap only represents variations in cloud width as a function of depth but does not take other factors into account, most notably shear or turbulence. The effects of turbulence and wind shear on the overlap of individual clouds are first estimated as a function of cloud depth, which closes the discrepancy between observed cloud overlap and the maximum overlap assumption. Then, an empirical model is developed for the shear and turbulence contributions on overlap as a function of cloud depth and of synoptic conditions. Finally, it is shown that our model is capable of accurately predicting overlap for a large number of cloud fields and under a variety of meteorological conditions.

54 ENVIRONMENTAL SCIENCES↗

A Model for Turbulence Spectra in the Equilibrium Range of the Stable Atmospheric Boundary Layer

Stratification can cause turbulence spectra to deviate from Kolmogorov's isotropic -5/3 power law scaling in the universal equilibrium range at high Reynolds numbers. However, a consensus has not been reached with regard to the exact shape of the spectra. Here we propose a shape of the turbulent kinetic energy and temperature spectra in horizontal wavenumber for the equilibrium range that consists of three regimes at small Froude number: the buoyancy subrange, a transition region, and the isotropic inertial subrange through dimensional analysis and substantial revision of previous theoretical approximation. These spectral regimes are confirmed by various observations in the atmospheric boundary layer. The representation of the transition region in direct numerical simulations will require large-scale separation between the Dougherty-Ozmidov scale and the Kolmogorov scale for strongly stratified turbulence at high Reynolds numbers, which is still challenging computationally. In addition, we suggest that the failure of Monin-Obukhov similarity theory in the very stable atmospheric boundary layer is due to the fact that it does not consider the buoyancy scale that characterizes the transition region.

54 ENVIRONMENTAL SCIENCES↗

Toward Understanding the Simulated Phase Partitioning of Arctic Single-Layer Mixed-Phase Clouds in E3SM

21 Mixed-phase clouds are widespread in the Arctic and have substantial impacts on the 22 surface energy budget, sea ice extent, and regional climate. Significant changes are found in the 23 modeled phase partitioning of Arctic mixed-phase clouds in the newly developed U.S. 24 Department of Energy (DOE) Energy Exascale Earth System Model (E3SM) Atmosphere Model 25 version 1 (EAMv1) compared to its predecessor (CAM5/EAMv0). The mixed-phase clouds 26 simulated by EAMv1 is overly dominated by super-cool liquid which is often underestimated by 27 CAM5. Compared to CAM5, EAMv1 has made several important changes in its cloud physical 28 parameterizations, including using CLUBB to unify shallow convection, PBL turbulence, and 29 cloud macrophysics, as well as updating the MG two-moment cloud microphysics scheme and 30 using the CNT heterogeneous ice nucleation scheme to replace the Meyers scheme for mixed- 31 phase clouds. To understand which of the newly-implemented physical parameterizations is 32 responsible for the change of modeled mixed-phase cloud phase partitioning in EAMv1, 33 sensitivity tests are conducted by utilizing the short-term hindcast approach and results are 34 compared to the observations from the ARM Mixed-Phase Arctic Cloud Experiment (M-PACE) 35 field campaign. 36 It is found that although each scheme contributes to the decrease of cloud ice water 37 content (IWC) and increase of cloud liquid water content (LWC), only the combined effect of 38 CLUBB and CNT can explain the significant underestimation of IWC. By examining the budgets 39 of cloud microphysical processes, CLUBB is found to play a dominant role due to the fact that 40 CLUBB does not diagnoses cloud ice phase water in its assumed joint PDF method and thus may 41 not provide sufficient cloud ice to initialize ice phase microphysical processes such as the growth 42 of ice crystals through vapor deposition. Although a more effective heterogeneous ice nucleation 43 may alleviate the underestimation of IWC, the ice phase process in CLUBB requires urgent 44 attention in the future model development.

Zhang, Meng↗

Where Are White Roofs More Effective in Cooling the Surface?

Solar reflective roofs (also called white or cool roofs) are a common heat mitigation strategy. By reflecting more sunlight than regular roofs, cool roofs experience lower surface temperatures and produce less heating of the surrounding air. The effectiveness of cool roofs, quantified by the surface temperature difference between cool roofs and regular roofs ??????, is known to vary spatially. A common perception is that ?????? is controlled by solar radiation that reaches the roof surface. Here we use an Earth System Model and a surface energy balance model to show that the spatial variability of ??????, when normalized by the albedo difference between cool roofs and regular roofs (????), is in fact more controlled by an energy distribution factor that encodes the efficiencies of surface energy balance components in dissipating heat. Our results suggest that painting the roof white is more effective in reducing the roof surface temperature when the roof has less water holding capacity and smaller thermal admittance and is located in places with more solar radiation, less precipitation, and lower wind speed.

Wang, Linying↗