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At least 703 records · Page 39

Bridging Aromatic/Antiaromatic Units: Recent Advances in Aromaticity and Antiaromaticity in Main-group and Transition-Metal Clusters from Bonding and Magnetic Analyses

Synthetic exploration and theoretical characterization of metal clusters are actively developing branches of modern inorganic chemistry. Advances in these areas constantly expand the rich structural diversity of viable species, allowing a detailed study of the fundamental characteristics of bench-stable compounds. In this minireview, we summarize recent achievements in synthesis and computational analyses of main-group and heterometallic clusters containing multiple aromatic/antiaromatic units. These systems range from bare clusters to ligand-decorated aggregates, providing a fundamental understanding of the aromaticity and antiaromaticity concepts in species exhibiting unprecedented shapes and composition. The review gives a comprehensive summary of bonding and magnetic response properties of such systems deciphered from the Adaptive Natural Density Partitioning (AdNDP) approach and induced magnetic field analyses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transcriptome and metabolome integration in sugarcane through culm development

Abstract Sugarcane (Saccharum sp.) is a tropical and subtropical C4 plant with a high photosynthetic and carbon assimilation efficiency that stores sucrose. Culm biomass is also composed of bagasse fibre, a by‐product of the sugarcane industry. This high‐yielding grass, high in sucrose and lignocellulosic biomass, is considered an optimal feedstock as an alternative to fossil fuels and to produce a broad range of high‐value biomaterials. The ideal sugarcane production system would optimise the relative production of sugar and these new products. Multi‐omics correlation analysis was used to generate a global view of the essential metabolic pathways identifying critical genes involved in carbon partitioning during different stages of development. This research employed an unprecedented metabolic and transcriptomic dataset of 360 samples from a selection of 1440 culms of 24 genotypes at five different development stages. Chemical composition and metabolome analysis showed an increase through the culm development of lignin, sucrose, carbon, and amino acids such as aspartic acid, serine, alanine, methionine, threonine 3‐cyano‐L‐alanine, and citric acid. Transcriptome analysis revealed functionalities such as transcription, nucleotide transport and metabolism, and the biosynthesis of amino acids that are highly activated during the immature stage and highly down‐regulated during the most mature age.

Perlo, Virginie↗

Relating land surface, water table, and weathering fronts with a conceptual valve model for headwater catchments

Knowing little about how porosity and permeability are distributed at depth, we commonly develop models of groundwater by treating the subsurface as a homogeneous black box even though porosity and permeability vary with depth. One reason for this depth variation is that infiltrating meteoric water reacts with minerals to affect porosity in localized zones called reaction fronts. We are beginning to learn to map and model these fronts beneath headwater catchments and show how they are distributed. The subsurface landscapes defined by these fronts lie subparallel to the earth-air interface but with lower relief. They can be situated above, below, or at the water table. These subsurface landscapes of reaction are important because porosity developed from weathering can control subsurface water storage. In addition, porosity often changes at the weathering fronts, and when this affects permeability significantly, the front can act like a valve that re-orients water flowing through the subsurface. We explore controls on the positions of reaction fronts under headwater landscapes by accounting for the timescales of erosion, chemical equilibration, and solute transport. One strong control on the landscape of subsurface reaction is the land surface geometry, which is in turn a function of the erosion rate. In addition, the reaction fronts, like the water table, are strongly affected by the lithology and water infiltration rate. We hypothesize that relationships among the land surface, reaction fronts, and the water table are controlled by feedbacks that can push landscapes toward an “ideal hill”. In this steady state, reaction-front valves partition water volumes into shallow and deep flowpaths. Furthermore, these flows dissolve low- and high-solubility minerals, respectively, allowing their reaction fronts to advance at the erosion rate. This conceptualization could inform better models of subsurface porosity and permeability, replacing the black box.

54 ENVIRONMENTAL SCIENCES↗

The Colorado East River Community Observatory Data Collection

Abstract The U.S. Department of Energy's (DOE) Colorado East River Community Observatory (ER) in the Upper Colorado River Basin was established in 2015 as a representative mountainous, snow‐dominated watershed to study hydrobiogeochemical responses to hydrological perturbations in headwater systems. The ER is characterized by steep elevation, geologic, hydrologic and vegetation gradients along floodplain, montane, subalpine, and alpine life zones, which makes it an ideal location for researchers to understand how different mountain subsystems contribute to overall watershed behaviour. The ER has both long‐term and spatially‐extensive observations and experimental campaigns carried out by the Watershed Function Scientific Focus Area (SFA), led by Lawrence Berkeley National Laboratory, and researchers from over 30 organizations who conduct cross‐disciplinary process‐based investigations and modelling of watershed behaviour. The heterogeneous data generated at the ER include hydrological, genomic, biogeochemical, climate, vegetation, geological, and remote sensing data, which combined with model inputs and outputs comprise a collection of datasets and value‐added products within a mountainous watershed that span multiple spatiotemporal scales, compartments, and life zones. Within 5 years of collection, these datasets have revealed insights into numerous aspects of watershed function such as factors influencing snow accumulation and melt timing, water balance partitioning, and impacts of floodplain biogeochemistry and hillslope ecohydrology on riverine geochemical exports. Data generated by the SFA are managed and curated through its Data Management Framework. The SFA has an open data policy, and over 70 ER datasets are publicly available through relevant data repositories. A public interactive map of data collection sites run by the SFA is available to inform the broader community about SFA field activities. Here, we describe the ER and the SFA measurement network, present the public data collection generated by the SFA and partner institutions, and highlight the value of collecting multidisciplinary multiscale measurements in representative catchment observatories.

54 ENVIRONMENTAL SCIENCES↗

Increasing temperature and flow management alter mercury dynamics in East Fork Poplar Creek

East Fork Poplar Creek (EFPC) is a mercury (Hg) contaminated creek in east Tennessee, USA. Stream restoration activities included the initiation of a flow management programme in 1996 in which water from a nearby lake was pumped to the head of the creek. We conducted regular water sampling for 2 years along the length of EFPC during active flow management and for 5 years after flow management stopped. Total Hg and total monomethylmercury (MMHg) concentration and flux decreased in the uppermost reaches of EFPC that were closest to the point of water addition. Most water quality parameters, including DOC concentration, remained unchanged after flow management termination. Nevertheless, SUVA 254 , a measure of dissolved organic matter (DOM) composition, increased and coincided with increased dissolved Hg (Hg D ) concentration and flux and decreased Hg solid-water partitioning coefficients throughout EFPC. Higher SUVA 254 and Hg D concentration have potential implications for bioavailability and MMHg production. Total and dissolved MMHg concentrations increased in lower reaches of EFPC after the end of flow management and these increases were most pronounced during spring and early summer when biota are more susceptible to exposure and uptake. A general warming trend in the creek after active flow management ended likely acted in concert with higher Hg D concentration to promote higher MMHg concentration. Total and dissolved MMHg concentrations were positively correlated with water temperature above a threshold value of 10°C. Concentration changes for Hg and MMHg could not be accounted for by changes in creek discharge that accompanied the cessation of flow management. In addition to the changing DOM composition in-stream, other watershed-scale factors likely contributed to the observed patterns, as these changes occurred over months rather than instantaneously after flow management stopped. Nevertheless, similar changes in MMHg have not been observed in a tributary to EFPC.

54 ENVIRONMENTAL SCIENCES↗

Water Stable Isotopes in Precipitation, Rivers, and Groundwater Across an Elevation Gradient in the Sierra Nevada Mountains (USA) Reflect Source Elevation

Understanding watershed processes is critical to predict the impacts of climate change and forest management on water resources. However, collecting hydrological data in mountainous terrain is challenging. Precipitation, river water, and groundwater H and O stable isotope data can provide insights into processes occurring at the mountain range scale. Water δ 2 H and δ 18 O values in precipitation vary with terrain elevation; thus, the resulting isotopic lapse rates of precipitation, groundwater, and river water have the potential to elucidate watershed processes and source elevations of major rivers. We analysed H and O stable isotope data of precipitation, groundwater, and river water over the course of one Water Year (Oct 2016—Oct 2017) in the Sierra Nevada mountains of California, USA. We calculated elevation-dependent isotopic lapse rates of these waters to estimate the source elevation of major rivers draining the west flank of the Sierra Nevada mountains. We also investigated the Cosumnes River's watershed in more detail to determine how river flow may be more fully partitioned. Here, we found that H and O stable isotopes in precipitation are temporally variable, but isotopic lapse rates are generally consistent with prior studies. However, groundwater samples across an elevation gradient provide a more consistent and accessible isotopic lapse rate to predict river water source elevations.

54 ENVIRONMENTAL SCIENCES↗

Environmental life cycle of fentanyl: From the cradle to an unknown grave

The lack of available information on the presence and persistence of fentanyl in the environment is a significant gap in the technical literature. Although the origins of the opioid in the environment are well-known because they follow the same pathways of other drug-related environmental contaminants, the downstream effects of fentanyl in the water supply and its retention in soil are less understood. The characterization of fentanyl and its potential degradation products in complex environmental samples such as soil is severely understudied. Very few articles are available that work to identify fentanyl and its degradation products in complex samples or name the possible hazards that may result from environmental exposure and degradation. Therefore, the objectives were to identify available articles focused on environmental fentanyl and its pathways and highlight quantifiable research or results that included specific degradation products or downstream effects. Research articles focused on fentanyl between 2000 and 2024 were identified and reviewed and then filtered using Boolean search terms for environmental parameters. Various studies have determined that trace levels of fentanyl can be found in a variety of environments, and additional data suggest preferential partitioning into soils from water and long-term persistence. Despite this knowledge, very little data exists on the long-term downstream effects of fentanyl or its analogs. As the chronic effects from low-level fentanyl exposure are currently unknown, this lack of insight brings to the forefront the need for further research to improve our understanding of fentanyl persistence, degradation, and toxicity within the environment.

54 ENVIRONMENTAL SCIENCES↗

Climatic controls on soil and saprock nitrogen distribution and persistence in the Sierra Nevada

Nitrogen (N) is an essential nutrient in soil that regulates plant growth, terrestrial sequestration of atmospheric carbon dioxide, and persistence of organic compounds. However, major knowledge gaps remain about how climate change may impact N accumulation and persistence, especially in deep soil and saprock (friable weakly weathered bedrock). Our objective was to understand how climate impacts the accumulation of N in soil and saprock and how climate impacts soil N distribution, persistence, and mechanisms of N persistence. We investigated N concentration in bulk soil and density fractions. We estimated N persistence along a bio-climatic sequence—sites range from a low-elevation oak savannah, mid-elevation pine-oak/mixed-conifer forest, to a high-elevation subalpine forest—in the southern Sierra Nevada in California. A combination of radiocarbon and elemental composition measurements along with a first-order kinetic model was used. The N concentration in the bulk soil and density fractions declined with depth, and there was a relatively greater mineral-associated heavy fraction (HF) N in deeper samples. The cooler/wetter mixed conifer site held 37% of profile N in saprock, which was greater than that of the entire soil profile at the drier/hotter oak savannah. The majority of N in soil, which was in the HF, was not influenced by climate proxies tested. However, both unprotected and occluded fractions of N were strongly influenced by climate. Soil N mean residence time (MRT) showed that drier/hotter climates have a shorter MRT, compared to mid-elevation sites with cooler/wetter climates. The effect of climate on deep saprock N storage might be indirect, primarily through climatic influence on the thickness of saprock. Overall, our findings suggest the mineral-associated HF N pool will not be vulnerable to changes in climate and will continue to contribute to the persistent soil N pool. The amount of topsoil and subsoil unprotected and occluded N can be explained by gross primary productivity and mean annual precipitation indicating that changes in climate can influence N partitioning. N stored in deep soil and saprock may be less vulnerable to climate than N stored in drier/hotter climates with less deeply stored N. It is critical to dig deeper to understand terrestrial ecosystems’ response to climate.

58 GEOSCIENCES↗

Continuous Counter‐Current Microfluidic Liquid–Liquid Extraction Achieved Using a Pair of Wettable Screen Meshes

Continuous counter‐current microfluidic liquid–liquid extraction performs separations by flowing immiscible liquids in opposing directions within a single flow channel. In principle, this flow arrangement enables a large number of theoretical separation units in a small footprint, without using interstage valving, pumping, and phase separation. Despite its potential for excellent separation performance, this microfluidic scheme rarely appears in literature due to the requirement for capillary forces to be greater than hydrodynamic forces for stable flow. We present a novel microfluidic device and flow approaches that overcome this force‐balance challenge, enabling stable, long‐duration continuous counter‐current flow. Additionally, we cover a suite of methodologies for quantifying the performance of the microfluidic device, revealing the number of theoretical equilibrium stages achieved. The enabling technologies include a woven mesh screen‐based microfluidic device architecture that is easily fabricated outside of a clean room, surface functionalization strategies to promote conjugate (organic/aqueous) wettability, flow approaches to eliminate bubbles and carryover, and computer‐aided flow automation with optical measurement of extraction performance. The reported experiments lasted for over 36 h, terminated only at experiment conclusion, where the device still exhibited good performance. Automated Raman spectroscopy was used for solute quantitation of the ternary system tert‐butanol in a toluene/water matrix, a ternary system that was specifically chosen to analyze the device's performance with a small solute partition ratio and to enable in‐line Raman measurements of solute concentrations in both phases. The microfluidic device possessed a 55 mm contact length and a 38.5 µL internal volume. During counter‐current flow, we observed approximately 37 equilibrium stages (37 ± 13) based on a best‐fit of the solute fraction remaining in the aqueous phase using a Kremser Group Method analysis.

36 MATERIALS SCIENCE↗

Investigation of Corrosion Behavior of Carbide Phase Strengthened Nickel‐Based Alloy in Molten Fluoride Salt

The corrosion behavior of a high creep strength carbide-phase strengthened Ni-based alloy in molten FLiNaK (LiF-NaF-KF: 46.5-11.5-42 mol%) salt in the temperature range of 700°C–750°C has been investigated as a part of the development of structural alloys for fluoride salt-based molten salt reactors (MSRs). The alloy composition was designed based on Hastelloy-N, but with the goal of improving creep strength. Cr depletion depth, a measure of corrosion, was observed to be single micrometers after several hundred hours of corrosion testing. Sequential corrosion testing involving testing of pre-tested samples in fresh salt coupled with SEM-EDS, scanning transmission electron microscopy (STEM) examinations and thermodynamic and kinetic modeling, suggest that the corrosion rate at the alloy-salt interface is governed by diffusion of elements from the alloy bulk to the surface. The carbide phases in the corrosion-tested sample microstructure were identified to be largely M 6 C-type Mo-rich carbides and MC-type mixed carbides. Atom probe tomography (APT) showed some partitioning of Cr and Ti to the carbide phase and showed the carbide phases to be stable at the salt-facing surface.

Gordon, Ryan [Univ. of Wisconsin, Madison, WI (Uni↗

Building materials genome from ground‐state configuration to engineering advance

Individual phases are commonly considered as the building blocks of materials. However, the accurate theoretical prediction of properties of individual phases remains elusive. The top-down approach by decoding genomic building blocks of individual phases from experimental observations is nonunique. The density functional theory (DFT), as a state-of-the-art solution of quantum mechanics, prescribes the existence of a ground-state configuration at 0 K for a given system. It is self-evident that the ground-state configuration alone is insufficient to describe a phase at finite temperatures as symmetry-breaking non-ground-state configurations are excited statistically at temperatures above 0 K. Our multiscale entropy approach (recently terms as Zentropy theory) postulates that the entropy of a phase is composed of the sum of the entropy of each configuration weighted by its probability plus the configurational entropy among all configurations. Consequently, the partition function of each configuration in statistical mechanics needs to be evaluated by its free energy rather than total energy. The combination of the ground-state and symmetry-breaking non-ground-state configurations represents the building blocks of materials and can be used to quantitatively predict free energy of individual phases with the free energy of each configuration predicted from DFT as well as all properties derived from free energy of individual phases.

CALPHAD↗

Spectral deferred correction methods for high-order accuracy in poroelastic problems

In this work, we investigate high-order accuracy in time integration by examining two operator splitting methods for poroelastic problems: the two-pass and the spectral deferred correction (SDC) methods. To enhance the order of accuracy, the two-pass method partitions a coupled operator symmetrically, whereas the SDC method corrects truncation errors by establishing an error equation. These high-order methods are applied to underlying solution strategies, i.e., monolithic, fixed-stress sequential, and undrained sequential methods. We observe that semi-discretized systems from spatial discretization have forms similar to those of index-1 differential algebraic equations (DAEs), causing order reduction against the two-pass method when it is used in conjunction with either the monolithic or sequential method. On the other hand, the SDC in conjunction with the monolithic method exhibits the desired second-order accuracy in poroelastic problems while increasing the order of accuracy for index-1 DAEs. However, the SDC in conjunction with either of the two sequential methods does not achieve the desired order of accuracy, and maintains first order because the flow equation for poroelasticity has an additional approximation associated with the volumetric strain rate term, which does not yield exactly the same forms as those of conventional DAEs. Thus, the monolithic SDC method can achieve higher-order accuracy, but may require higher computational costs because it involves solving matrix systems larger than those for the sequential methods.

02 PETROLEUM↗

An optimized ChIP-Seq framework for profiling histone modifications in Chromochloris zofingiensis

The eukaryotic green alga Chromochloris zofingiensis is a reference organism for studying carbon partitioning and a promising candidate for the production of biofuel precursors. Recent transcriptome profiling transformed our understanding of its biology and generally algal biology, but epigenetic regulation remains understudied and represents a fundamental gap in our understanding of algal gene expression. Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a powerful tool for the discovery of such mechanisms, by identifying genome-wide histone modification patterns and transcription factor-binding sites alike. Here, we established a ChIP-Seq framework for Chr. zofingiensis yielding over 20 million high-quality reads per sample. The most critical steps in a ChIP experiment were optimized, including DNA shearing to obtain an average DNA fragment size of 250 bp and assessment of the recommended formaldehyde concentration for optimal DNA-protein cross-linking. We used this ChIP-Seq framework to generate a genome-wide map of the H3K4me3 distribution pattern and to integrate these data with matching RNA-Seq data. In line with observations from other organisms, H3K4me3 marks predominantly transcription start sites of genes. Our H3K4me3 ChIP-Seq data will pave the way for improved genome structural annotation in the emerging reference alga Chr. zofingiensis.

59 BASIC BIOLOGICAL SCIENCES↗

Ion separations with membranes

Ion separations are important for resource recovery, water treatment, and energy production and storage. Techniques such as chemical precipitation, selective adsorption, and solvent extraction are effective, but membranes may separate ions continuously with less waste and lower energy costs. Separation of monovalent and multivalent ions with nanofiltration or electrodialysis membranes already enables water softening and edible salt purification. Similar membranes are attractive as separators in vanadium redox flow batteries. Selective partitioning of divalent counter-ions into ion-exchange membranes even allows transport of these ions against their concentration gradients in salt mixtures. However, separations of ions with the same charge is more challenging. Recent research demonstrated highly selective ion “sieving” at small scales. Here, separations using electrical potentials and differences in ion electrophoretic mobilities are promising, but relatively unexplored. Carrier-mediated transport affords high selectivity in liquid membranes, but these systems are not very stable, and selective transport via hopping between anchored carriers has proven elusive. Finally, this paper discusses how concentration polarization decreases selectivities in many membrane processes. Although development of selective, inexpensive ion-separation membranes is a work in progress, successes in water softening and edible salt purification suggests that future selective membranes will serve as complementary methods to traditional purification techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nonlinear Logistic Regression Mixture Experiment Modeling for Binary Data Using Dimensionally Reduced Components

This article presents and illustrates an approach using nonlinear logistic regression for modeling binary response data from a mixture experiment when the components can be partitioned into groups used to form dimensionally-reduced pseudocomponents (DRPs). A DRP is a linear combination of the components in a group, where the linear combinations over all groups are normalized so that the DRP proportions sum to unity. Nonlinear logistic regression is required because, after normalization of the linear combinations, the model expressed in terms of the DRPs is nonlinear in the parameters that specify the linear combinations. A method for obtaining nonparametric tolerance limits on the probability of a “success” for the binary response variable using a bootstrap approach is also presented. Having three DRPs enables viewing data and modeling results on a ternary plot even though there may be many more than three mixture components. A real database, involving whether or not nepheline crystals form in simulated nuclear waste glass after cooling, is used to illustrate the nonlinear logistic regression modeling and nonparametric tolerance limit approaches when there are three DRPs.

Waste glass, Nepheline, Mixture experiment, Logist↗

Deriving Stable Peak Models to Fit Complex XPS Data From Cu Contaminated Pt Electrocatalysts

X-ray Photoelectron Spectroscopy spectra peak models, designed to partition photoemission signals emanating from different elements or chemical states within an atom, are fitted to data limited to an energy interval over which inelastically scattered photoemission signal can be estimated. While the choice of background approximation and line shapes of components to the peak model requires careful consideration, the energy interval used to define the data to which the peak model is optimized has a significant impact on the final peak model. The relationship between the background intensity and data intensity at the start and end of the energy interval dictates the line shapes used in the peak model. In this work, we devise a method to peak fit a complex overlapping Cu 3p and Pt 4f XPS peak structure to perform the elemental quantification. We first use an Al 2s peak to illustrate how background curves approach data at the limits of the energy interval over which the background is defined, influencing the analysis of XPS spectra. Next, we demonstrate the nature of interactions between specific line shapes (Voigt and pseudo-Voigt profiles) suitable for photoemission peaks and a specific background curve (Shirley) and a peak model is presented that includes components to the peak model that accommodates background intensity during fitting of the peak model to data. The peak model allowed for quantification of the contributions of Pt 4f peaks emanating from the substrate that exhibits strong asymmetry in the presence of the inhomogeneously distributed Cu species, mostly of Lorentzian character.

XPS↗

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Substrate, temperature, and geographical patterns among nearly 2000 natural yeast isolates

Yeasts have broad importance as industrially and clinically relevant microbes and as powerful models for fundamental research, but we are only beginning to understand the roles yeasts play in natural ecosystems. Yeast ecology is often more difficult to study compared to other, more abundant microbes, but growing collections of natural yeast isolates are beginning to shed light on fundamental ecological questions. In this work, we used environmental sampling and isolation to assemble a dataset of 1962 isolates collected from throughout the contiguous United States of America (USA) and Alaska, which were then used to uncover geographic patterns, along with substrate and temperature associations among yeast taxa. We found some taxa, including the common yeasts Torulaspora delbrueckii and Saccharomyces paradoxus, to be repeatedly isolated from multiple sampled regions of the USA, and we classify these as broadly distributed cosmopolitan yeasts. A number of yeast taxon-substrate associations were identified, some of which were novel and some of which support previously reported associations. Further, we found a strong effect of isolation temperature on the phyla of yeasts recovered, as well as for many species. We speculate that substrate and isolation temperature associations reflect the ecological diversity of and niche partitioning by yeast taxa.

59 BASIC BIOLOGICAL SCIENCES↗