Experimental Testing of the Theoretically Predicted Magnetic Properties for Kagomé Compounds in the Li–Fe–Ge System
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Mantravadi, Aishwarya [Department of Chemistry; Io↗
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Catabolism of lignin-related methoxylated compounds in white-rot fungi utilizes non-canonical oxidoreductases
White-rot fungi (WRF) are the most effective lignin-degrading organisms in nature, making them essential to Earth’s carbon cycle. Lignin is a highly methoxylated, heterogeneous biopolymer derived from plants. However, the pathways WRF use to metabolize methoxylated aromatic monomericcompounds as carbon sources remain unidentified. Here, we employ a systems biology approach to elucidate the intracellular catabolism of vanillate – a monomethoxylated aromatic compound – in two white-rot fungi (WRF), Gelatoporia subvermispora and Trametes versicolor. We identified and biochemically validated a four-enzyme pathway that converts vanillate into ß-ketoadipate – a metabolite that enters central carbon metabolism. This pathway deviates from typical bacterial pathways, where vanillate is initially demethylated and ring-cleaved by intradiol dioxygenases; instead, oxidative decarboxylation occurs prior to ring cleavage by extradiol dioxygenases. Thus, we conducted an in-depth investigation of ring cleavage and further downstream catabolism by the identified fungal enzymes using biochemical and structural approaches. This revealed non-canonical enzymes, including a highly substrate-specific extradiol dioxygenase and a metal-free, promiscuous reductase, the latter capable of acting on catabolic intermediates derived from both methoxylated and non-methoxylated aromatic compounds. This work emphasizes the potential of WRF and their enzymes to advance lignin valorization and enhance our understanding of their role during wood decay.
dioxygenase↗
Volatile Organic Compounds in Bankhead National Forest (AMF3). August to September, 2025
The formation of atmospheric aerosols through the transformation of volatile organic compounds (VOCs) is a fundamental process in aerosol-climate interactions, as these particles serve as cloud condensation nuclei and ultimately influence Earth’s radiative balance. However, there remains a critical need to quantify the effects of multiple coexisting VOC precursors on aerosol formation beyond the limitations of laboratory-scale studies. This research aims to advance the mechanistic understanding of secondary organic aerosol formation in the southeastern United States by investigating interactions among coexisting VOC precursors observed at the third ARM Mobile Facility located in the Bankhead National Forest. The dataset was generated from the deployment of Oak Ridge National Laboratory’s PTR-TOF 6000 X2 Proton Transfer Reaction Time-of-Flight Mass Spectrometer (PTR-ToF-MS) for the real-time, continuous monitoring of VOCs from August 21 to September 15, 2025. To minimize sampling artifacts and compound losses, the PTR-ToF-MS inlet was connected to the cabin flow line by replacing the existing Tygon tubing with 1/2-inch outer diameter perfluoroalkoxy (PFA) tubing. The instrument operated on an hourly measurement cycle consisting of 8 minutes of zero-air measurements followed by 52 minutes of ambient air sampling, with a temporal resolution of 10 seconds. The dataset includes concentrations, reported in ppb, of methanol, acetone, acetonitrile, isoprene, methyl vinyl ketone and methacrolein (MVK + MACR), monoterpenes, benzene, toluene, and catechol.
Atmospheric concentration of volatile organic comp↗
NMR Database of Lignin and Cell Wall Model Compounds
This database was designed to provide a coherent, single source of NMR data of lignin and other plant cell wall model compounds. The database exists as an Adobe pdf cross-platform file for viewing and printing. This is the latest public version of the Database, version 2024/08 updated from the 2009 version.
cell wall↗
Ligand-Based Compound Activity Prediction via Few-Shot Learning
Predicting the activities of new compounds against biophysical or phenotypic assays based on the known activities of one or a few existing compounds is a common goal in early stage drug discovery. This problem can be cast as a “few-shot learning” challenge, and prior studies have developed few-shot learning methods to classify compounds as active versus inactive. However, the ability to go beyond classification and rank compounds by expected affinity is more valuable. We describe Few-Shot Compound Activity Prediction (FS-CAP), a novel neural architecture trained on a large bioactivity data set to predict compound activities against an assay outside the training set, based on only the activities of a few known compounds against the same assay. Our model aggregates encodings generated from the known compounds and their activities to capture assay information and uses a separate encoder for the new compound whose activity is to be predicted. The new method provides encouraging results relative to traditional chemical-similarity-based techniques as well as other state-of-the-art few-shot learning methods in tests on a variety of ligand-based drug discovery settings and data sets.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Structurally Diverse Compound Screening Library to Identify Substrates for Diamine, Polyamine, and Related Acetyltransferases
Spermidine/spermine N-acetyltransferases (SSATs) and other types of polyamine acetyltransferases (PAATs) acetylate diamines and/or polyamines. These enzymes are evolutionarily related and belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily, yet we lack a fundamental understanding of their substrate specificity and/or promiscuity toward different compounds. Many of these enzymes are known or are predicted to acetylate polyamines, but in the cell there are other types of compounds that contain moieties derived from polyamines that may be the native substrates for these enzymes. To learn more about the identity of substrates that are acetylated, we selected and screened 17 different GNAT enzymes for activity toward a set of structurally diverse compounds that contained different types of amine moieties (e.g., aminopropyl, aminobutyl, etc.). These compounds included diamines, triamines, and polyamines containing primary amino groups, and they had structural diversity with variation of the chain length and presence or absence of internal amino groups and other functional groups. We found 12 of the 17 enzymes acetylated at least one of the compounds. Some enzymes were selective toward acetylating only one compound while others exhibited substrate promiscuity toward numerous compounds. Our experimental results ultimately allowed us to pinpoint specific substrates that could be further investigated to more fully understand substrate specificity versus promiscuity of GNAT enzymes and the role of acetylated small molecules in cells.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Bacterial volatile organic compound specialists in the phycosphere
Abstract Labile dissolved organic carbon in the surface oceans accounts for about one-fourth of carbon produced through photosynthesis and turns over on average every 3 days, fueling one of the largest engines of microbial heterotrophic production on the planet. Volatile organic compounds are poorly constrained components of dissolved organic carbon. Here, we detected 72 m/z signals, corresponding to unique volatile organic compounds, including petroleum hydrocarbons, totaling ~18.5 nM in the culture medium of a model diatom. In five cocultures with bacteria adapted to grow with this diatom, 1–59 m/z signals were depleted. Two of the most active volatile organic compound consumers, Marinobacter and Roseibium, contained more genes encoding volatile organic compound oxidation proteins, and attached to the diatom, suggesting volatile organic compound specialism. With nanoscale secondary ion mass spectrometry and stable isotope labeling, we confirmed that Marinobacter incorporated carbon from benzene, one of the depleted m/z signals detected in the co-culture. Diatom gross carbon production increased by up to 29% in the presence of volatile organic compound consumers, indicating that volatile organic compound consumption by heterotrophic bacteria in the phycosphere—a region of rapid organic carbon oxidation that surrounds phytoplankton cells—could impact global rates of gross primary production.
Environmental Sciences & Ecology↗
In Vitro Antimicrobial Activity of Volatile Compounds from the Lichen Pseudevernia furfuracea (L.) Zopf. Against Multidrug-Resistant Bacteria and Fish Pathogens
Lichens are symbiotic organisms with unique secondary metabolism. Various metabolites from lichens have shown antimicrobial activity. Nevertheless, very few studies have investigated the antimicrobial potential of the volatile compounds they produce. This study investigates the chemical composition and antimicrobial properties of volatile compounds from Pseudevernia furfuracea collected in two regions of Morocco. Hydrodistillation was used to obtain volatile compounds from samples collected in the High Atlas and Middle Atlas. Gas chromatography–mass spectrometry (GC-MS) analysis identified phenolic cyclic compounds as the primary constituents, with atraric acid and chloroatranol being the most abundant. Additionally, eight compounds were detected in lichens for the first time. The antimicrobial activity of these compounds was assessed using disc diffusion and broth microdilution methods. Both samples demonstrated significant antimicrobial effects against multidrug-resistant human bacteria, reference microorganisms, fish pathogens, and Candida albicans, with minimum inhibitory concentrations (MICs) ranging from 1000 µg/mL to 31.25 µg/mL. This study provides the first report on the volatile compounds from Pseudevernia furfuracea and their antimicrobial effects, particularly against fish pathogens, suggesting their potential as novel antimicrobial agents for human and veterinary use. Further research is warranted to explore these findings in more detail.
Essadki, Yasser (ORCID:0009000648460075)↗
Disentangling atmospheric, hydrological, and coupling uncertainties in compound flood modeling within a coupled Earth system model
Compound riverine and coastal flooding is usually driven by complex interactions among meteorological, hydrological, and ocean extremes. However, existing efforts to model this phenomenon often do not integrate hydrological processes across atmosphere–land–river–ocean systems, leading to substantial uncertainties that have not been fully examined. To bridge this gap, we leverage the new capabilities of the Energy Exascale Earth System Model (E3SM) that enable a multi-component framework that integrates coastally refined atmospheric, terrestrial, and oceanic components. We evaluate compound uncertainties arising from two-way land–river–ocean coupling in E3SM and track the cascading meteorological and hydrological uncertainties through ensemble simulations over the Delaware River basin and estuary during Hurricane Irene (2011). Our findings highlight the importance of two-way river–ocean coupling to compound flood modeling and demonstrate E3SM's capability in capturing compound flood extent near the coast, with a hit rate over 0.75. Our study shows the growing uncertainties that transition from atmospheric forcings to flood distribution and severity. Furthermore, an analysis based on artificial neural networks is used to assess the roles of hydrological drivers, such as infiltration and soil moisture, in the generation of compound flooding. The response of compound floods to tropical cyclones (TCs) is found to be susceptible to these often overlooked drivers. For instance, the flooded area could increase more than 2-fold (∼2.4) if Hurricane Irene were preceded by an extreme antecedent soil moisture condition (AMC). The results not only support the use of a multi-component framework for interactive flooding processes, but also underscore the necessity of broader definitions of compound flooding that encompass the simultaneous occurrence of intense precipitation, storm surge, and high AMC during TCs.
Feng, Dongyu [Pacific Northwest National Laborator↗
Dual-Emitting Cyclometalated Platinum Compounds with Isocyanide Ligands
Cyclometalated platinum(II) compounds with both C^N chelating iminic ligands and isocyanide ligands were synthesized. Two sets of compounds from the reaction of two separate HC^N ligands (derived from thiophene or benzene) with [Pt2Me4(μ-SMe 2 ) 2 ] were obtained, resulting in square planar compounds with an anionic C^N ligand, a methyl ligand, and a dimethyl sulfide (dms) ligand completing the coordination sphere. Subsequently, the dms ligand was easily substituted by several isocyanide ligands (2-naphthyl, adamantyl, 2,6-dimethylphenyl, ptoluenesulfonylmethyl). The compounds were characterized by multinuclear NMR spectroscopy, IR spectroscopy, and singlecrystal X-ray diffraction (SCXRD). Their photophysical properties were explored using UV/vis, emission, and transient absorption (TA) spectroscopy. The emission spectra for the thiophene-derived compounds showed well-defined dual emission peaks, while the benzene-derived compounds’ bands appeared less resolved. DFT and TDDFT calculations were performed, and results were compared to the observed spectroscopic properties of the newly synthesized complexes.
Inorganic carbon compounds↗
Risk Assessment in a Chemical Laboratory Following an Explosive Incident Involving a Novel Diazonium Compound: Retrospective Analysis and Lessons Learned
Diazonium compounds are synthetically useful in the production of dyes and textiles, however they are highly explosive under dry conditions. Explosion prevention becomes more difficult when new diazonium compounds are synthesized, because while some syntheses include a counterion to increase their stability, this is not always a reliable method to prevent an explosive incident. Due to the uncertainty surrounding the explosiveness of different diazonium compounds, it is important to understand how to safely clean up after an incident and how to determine when it is safe to return a laboratory to typical operational use, particularly when the incident involves a novel compound where a standard does not exist for instrument calibration. Here, an explosive event is discussed involving the synthesis of 4-bromo-benzenediazonium-2-carboxylate. Following the explosive incident and 3-step cleanup, which involved a precautionary neutralization step, samples were collected from the fume hood where the incident occurred. Because the incident involved an unstable, novel compound that is not commercially available and was deemed unsafe to resynthesize for instrument calibration, we assessed the risk of further explosion by analyzing for the stable decomposition products. Mass spectrometry analysis confirmed that the residue in the fume hood contained 5-bromosalicylic acid, a decomposition product of 4-bromo-benzenediazonium-2-carboxylate. Samples were taken from multiple points in the fume hood and analyzed to estimate the spatial distribution of the decomposition product. Based on this analysis, we inferred that the primary decomposition product was far more abundant than residual energetic, indicating the energetic had been consumed or neutralized to a trace quantity where the risk of further explosion was low. Furthermore, the steps presented here─specifically, initial neutralization and then analyzing the spatial distribution of expected decomposition products to assess risk when a novel explosive material is detonated in a confined space─were our approach to assess further risk following an explosion due to a novel diazonium compound without the need for any further handling or resynthesis of the energetic. Here, we present our approach and critically analyze these steps by discussing retrospective lessons learned and alternative analytical approaches.
Computer simulations↗
Impacts of Precipitation Events on Concentrations of Oxygenated Gas- and Particle-Phase Compounds Observed in the Amazon
Removal of gases and particles by precipitation (wet deposition) is a critical process that significantly influences the transport and chemical transformation of atmospheric compounds. However, there are few studies that directly measure or constrain the rates of this process under real-world conditions. This work quantifies the net change in ambient concentrations during precipitation events (removal rates) of gas- and particle-phase organic compounds at a surface site near Manaus, Brazil, during the GoAmazon2014/5 campaign. Removal rates of identified and unknown compounds that have been previously classified into source-based clusters are measured during rain events and categorized based on estimated properties of compounds and clusters. Highly oxygenated gases, such as isoprene oxidation products, are removed during precipitation events with a median removal rate of 0.09 h –1 and the fastest analyte is removed at a rate of 0.22 h –1 . Removal rates of particle-phase compounds are observed at roughly this median rate, while less soluble gases, such as terpenes, exhibit low removal rates. These results are roughly in agreement with prior theoretical estimates of wet deposition rates for comparable compounds, providing an empirical point of comparison while noting that our metric reflects the net influence of precipitation events rather than wet deposition alone.
atmospheric chemistry↗
An idealized model for the crystal structure of intermetallic compounds isostructural with Mg 3 Cr 2 Al 18
Mg 3 Cr 2 Al 18 (abbreviated in this report as MCA) is the parent phase for a large class of intermetallic compounds that belong to the cubic crystal space group, $Fd\overline{3}m$. The purpose of this paper is to introduce an ideal, unrelaxed crystal structure for compounds isostructural with MCA. There are five distinct atomic sublattices in MCA compounds, which can be denoted, $A, B, C, D,$ and $E$. With this, a general description for MCA structures can be written as $A^{8a}_{1}B^{16c}_{2}C^{16d}_{2}D^{48f}_{6}E^{96g}_{12}$, where the superscripts represent the Wyckoff special equipoints associated with the various sublattices in MCA, and the subscripts indicate the contributions of each sublattice to the stoichiometry of one formula unit in an any given MCA structured compound. Sublattices D and E are where deviations from ideality occur in real, MCA-like compounds. This paper examines MCA bond lengths, nearest-neighbour polyhedral arrangements, 3-D sublattice crystal structures, 2-D atom tessellation patterns, and crystal chemical effects associated with atomic relaxations on the $D$ and $E$ sublattices. The ideal MCA crystal structure developed in this report provides an appropriate initial structure for use as input to crystal structure refinements of diffraction data for MCA-like phases being examined experimentally, or as input for computational, atomistic simulations of the structures of such compounds.
36 MATERIALS SCIENCE↗
Formation kinetics and thermodynamic stability of the Aurivillius compounds in Bi 4 Ti 3 O 12 –BiFeO 3 system
Abstract The Aurivillius compounds in the Bi 2 O 3 –Fe 2 O 3 –TiO 2 system, combining ferroelectric, semiconducting, and ferromagnetic properties, have attracted particular interest. Formation kinetics and thermodynamic stability are the fundamental knowledge needed for modeling and predicting the temporal microstructure and property evolution during materials processing but have not yet been addressed by quantitative experimental measurement. This article focuses on the Bi n +1 Fe n –3 Ti 3 O 3 n +3 Aurivillius compounds on the Bi 4 Ti 3 O 12 –BiFeO 3 tie‐line to elucidate the mechanisms and thermodynamic controls responsible for phase formation of compounds with various perovskite‐like layers. Five high‐purity Aurivillius compounds Bi 4 Ti 3 O 12 , Bi 5 FeTi 3 O 15 , Bi 6 Fe 2 Ti 3 O 18 , Bi 7 Fe 3 Ti 3 O 21 , and Bi 8 Fe 4 Ti 3 O 24 with integer n = 3–7 values were synthesized and their phase transformation properties and enthalpies of formation were studied by X‐ray diffraction in situ, high temperature differential scanning calorimetry, and high temperature oxide melt solution calorimetry. Thermodynamic stability of the compounds decreases with increasing n , and formation kinetics gradually slow down, demonstrating the inherent difficulty to synthesize pure Aurivillius compounds with n larger than 8. This difficulty was confirmed by an impurity phase coexisting with Bi 9 Fe 5 Ti 3 O 27 .
Gong, Weiping↗
Wide-ranging predictions of new stable compounds powered by recommendation engines
The computational search for new stable inorganic compounds is faster than ever, thanks to high-throughput density functional theory (DFT). However, stable compound searches remain highly expensive because of the enormous search space and the cost of DFT calculations. To aid these searches, recommendation engines have been developed. We conduct a systematic comparison of the performance of previously developed recommendation engines, specifically ones based on elemental substitution, data mining, and neural network prediction of formation enthalpy. After identifying ways to improve the recommendation engines, we find the neural network to be superior at recommending stable Heusler compounds. Armed with improved recommendation engines, we identify tens of thousands of compounds that are stable at zero temperature and pressure, now available in the Open Quantum Materials Database. We summarize this diverse pool of compounds, including the elusive mixed anion compounds, and two of their many applications: thermoelectricity and solar thermochemical fuel production.
Science & Technology - Other Topics↗
An expedited screening platform for the discovery of anti-ageing compounds in vitro and in vivo
Background: Restraining or slowing ageing hallmarks at the cellular level have been proposed as a route to increased organismal lifespan and healthspan. Consequently, there is great interest in anti-ageing drug discovery. However, this currently requires laborious and lengthy longevity analysis. Here, we present a novel screening readout for the expedited discovery of compounds that restrain ageing of cell populations in vitro and enable extension of in vivo lifespan. Methods: Using Illumina methylation arrays, we monitored DNA methylation changes accompanying long-term passaging of adult primary human cells in culture. This enabled us to develop, test, and validate the CellPopAge Clock, an epigenetic clock with underlying algorithm, unique among existing epigenetic clocks for its design to detect anti-ageing compounds in vitro. Additionally, we measured markers of senescence and performed longevity experiments in vivo in Drosophila, to further validate our approach to discover novel anti-ageing compounds. Finally, we bench mark our epigenetic clock with other available epigenetic clocks to consolidate its usefulness and specialisation for primary cells in culture. Results: We developed a novel epigenetic clock, the CellPopAge Clock, to accurately monitor the age of a population of adult human primary cells. We find that the CellPopAge Clock can detect decelerated passage-based ageing of human primary cells treated with rapamycin or trametinib, well-established longevity drugs. We then utilise the CellPopAge Clock as a screening tool for the identification of compounds which decelerate ageing of cell populations, uncovering novel anti-ageing drugs, torin2 and dactolisib (BEZ-235). We demonstrate that delayed epigenetic ageing in human primary cells treated with anti-ageing compounds is accompanied by a reduction in senescence and ageing biomarkers. Finally, we extend our screening platform in vivo by taking advantage of a specially formulated holidic medium for increased drug bioavailability in Drosophila. We show that the novel anti-ageing drugs, torin2 and dactolisib (BEZ-235), increase longevity in vivo. Conclusions: Our method expands the scope of CpG methylation profiling to accurately and rapidly detecting anti-ageing potential of drugs using human cells in vitro, and in vivo, providing a novel accelerated discovery platform to test sought after anti-ageing compounds and geroprotectors.
60 APPLIED LIFE SCIENCES↗
Final Technical Report on Investigation of Short-range Ordering in Transition Metal Compounds by Diffuse Scattering
Future energy needs and sustainability require new materials with novel properties for such applications as energy production, storage and transport and microelectronics. Quantum materials with several competing interactions at the electronic level offer tremendous opportunity to discover, design and tune properties for such applications. Although it has been recognized that small deviations in atomic positions, driven by the competing electronic interactions, in crystalline materials can have significant impact on properties, it remains a challenge to accurately characterize such deviations (short-range order) due to the lack of advanced instruments and analysis tools to characterize them. This project used the powerful neutron and x-ray scattering instruments recently developed at the DOE user facilities to address this challenge. New methods and efficient analysis tools were employed to uncover the hidden ordering that is behind the unique properties of transition metal compounds. One example of hidden order revealed by this project comes from vanadium (IV) oxide (VO 2 ) and related compounds. The project found that the chemical bonds in VO 2 compete against each other, unlike most crystalline compounds where the chemical bonds cooperate to yield the ordered structure. This helps explain why different measurements yielded different, competing pictures about the nature of VO 2 , which has led to disagreement about where its physical properties come from. Another example from this project of hidden ordering comes from a class of compounds known as condensed Chevrel phases, which are superconducting compounds that are generally believed to be non-magnetic. The neutron scattering methods used in this project revealed evidence of magnetism, which usually does not coexist with superconductivity. In this case, magnetism is believed to be one part of a special type of electronic behavior that can occur in compounds that have one-dimensional bonding character.
36 MATERIALS SCIENCE↗
Diverse organic carbon dynamics captured by radiocarbon analysis of distinct compound classes in a grassland soil
Soil organic carbon (SOC) is a large, dynamic reservoir composed of a complex mixture of plant- and microbe-derived compounds with a wide distribution of cycling timescales and mechanisms. The distinct residence times of individual carbon components within this reservoir depend on a combination of factors, including compound reactivity, mineral association, and climate conditions. To better constrain SOC dynamics, bulk radiocarbon measurements are commonly used to trace biosphere inputs into soils and to estimate timescales of SOC cycling. However, understanding the mechanisms driving the persistence of organic compounds in bulk soil requires analyses of SOC pools that can be linked to plant sources and microbial transformation processes. Here, we adapt approaches, previously developed for marine sediments, to isolate organic compound classes from soils for radiocarbon ( 14 C) analysis. We apply these methods to a soil profile from an annual grassland in Hopland, California (USA), to assess changes in SOC persistence with depth (down to 1 m). We measured the radiocarbon values of water-extractable organic carbon (WEOC), total lipid extracts (TLEs), total hydrolyzable amino acids (AAs), and an acid-insoluble (AI) fraction from bulk and physically separated size fractions (< 2 mm, 2 mm–63 µm, and < 63 µm). Our results show that Δ 14 C values of bulk soil, size fractions, and extracted compound classes became more depleted with depth, and individual SOC components have distinct age–depth distributions that suggest distinguishable cycling rates. We found that AAs and TLEs cycle faster than the bulk soils and the AI fraction. The AI was the most 14 C-depleted fraction, indicating that it is the most chemically inert in this soil. Our approach enables the isolation and measurement of SOC fractions that separate functionally distinct SOC pools that can cycle relatively quickly (e.g., plant and microbial residues) from more passive or inert SOC pools (associated with minerals or petrogenic) from bulk soils and soil physical fractions. With the effort to move beyond SOC bulk analysis, we find that compound class 14 C analysis can improve our understanding of SOC cycling and disentangle the physical and chemical factors driving OC cycling rates and persistence.
58 GEOSCIENCES↗