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At least 829 records · Page 46

Dehydrogenation vs Apparent Hydrogenation: Unraveling the Mechanisms of He and O 2 Plasma Etching on Colloidal Nanocrystal Films

Removing organic ligands from colloidal nanoparticles is critical for fabricating solid-state devices, yet accurately quantifying this removal remains a significant analytical challenge. Here, we establish a robust and accessible method for this quantification by calibrating Raman spectroscopy against precise ion beam analysis (IBA) for nanoparticle assemblies (CNAs) processed by helium (He) and oxygen (O 2 ) plasmas. We demonstrate that the calibration curves are remarkably independent of plasma power and pressure, depending critically only on the choice of feed gas. He plasma induces rapid dehydrogenation and cross-linking, evidenced by a much faster decrease in the C–H Raman signal relative to the actual carbon loss. Conversely, O 2 plasma leads to a surprising “apparent hydrogenation”, where the carbon backbone is removed significantly faster than the C–H signal diminishes. This counterintuitive effect is explained by a serial mechanism of oxidative fragmentation; β-scission cleaves the alkyl chains, and subsequent stabilization steps enrich the remaining film with hydrogen-rich methyl-terminated fragments, while carbon is efficiently removed as volatile CO. This work provides calibrated functions that enable the rapid determination of absolute carbon content in processed CNAs using simple Raman spectroscopy with uncertainties of ∼8% for O 2 and ∼12% for He plasma, offering a vital tool for both process diagnostics and fundamental studies of plasma–matter interactions in colloidal nanocrystal films.

Animal feed↗

Unraveling the Interfacial Structure–Performance Correlation of Flexible Metal–Organic Framework Membranes on Polymeric Substrates

Pure metal–organic framework (MOF) layers deposited on porous supports are important candidates for molecular sieving membranes, but their performance usually deviates from theoretical estimations. Here, we combine stepwise scanning electron microscopy imaging, time-resolved synchrotron X-ray scattering, terahertz infrared spectroscopy, and density functional theory calculation to investigate the ZIF-8 membrane formation on two types (polydopamine and TiO2) of functionalized porous supports. Though molecular sieving of ZIF-8 membranes for smaller gases (He, H 2 , and CO 2 ) can be achieved with both types of functionalized supports, we unravel that the strong interaction between MOF and polydopamine can disrupt the formation of “perfect” MOF crystals at the interface, leading to a “contracted” MOF structure with partially uncoordinated imidazolate ligands. This further affects the low-frequency dynamical parameters of the framework and inhibits the effective seeded growth. Eventually, it leads to an unexpected loss of selectivity for the bulkier gases (N 2 and CH 4 ) for ZIF-8 on polydopamine-functionalized supports. This work links the dynamical aspects of MOFs with their gas transport behavior and highlights the importance of regulating the interfacial weak forces to preserve the ideal molecular sieving efficiency of MOF membranes, which a

36 MATERIALS SCIENCE↗

Mechanistic Insights into Co and Fe Quaterpyridine-Based CO 2 Reduction Catalysts: Metal–Ligand Orbital Interaction as the Key Driving Force for Distinct Pathways

Both [Co II (qpy)(H 2 O) 2 ] 2+ and [Fe II (qpy)(H 2 O) 2 ] 2+ (with qpy = 2,2':6',2'':6'',2'''-quaterpyridine) are efficient homogeneous electrocatalysts and photoelectrocatalysts for the reduction of CO 2 to CO. The Co catalyst is more efficient in the electrochemical reduction, while the Fe catalyst is an excellent photoelectrocatalyst. This work uses density functional theory to shed light on the contrasting catalytic pathways. While both catalysts experience primarily ligand-based reductions, the second reduction in the Co catalyst is delocalized onto the metal via a metal-ligand bonding interaction, causing a spin transition and a distorted ligand framework. This orbital interaction explains the experimentally observed mild reduction potential and slow kinetics of the second reduction. The decreased hardness and doubly occupied d z 2 -orbital facilitate a σ-bond with the CO 2 -π* in an η 1 - κC binding mode. CO 2 binding is only possible after two reductions resulting in an EEC mechanism (E = electron transfer, C = chemical reaction), and the second protonation is rate-limiting. In contrast, the Fe catalyst maintains a Lewis acidic metal center throughout the reduction process because the metal orbitals do not strongly mix with the qpy-π* orbitals. Further, this allows binding of the activated CO 2 in an η 2 -binding mode. This interaction stabilizes the activated CO 2 via a π-type interaction of a Fe-t 2g orbital and the CO 2 -π* and a dative bond of the oxygen lone pair. This facilitates CO 2 binding to a singly reduced catalyst resulting in an ECE mechanism. The barrier for CO 2 addition and the second protonation are higher than those for the Co catalyst and rate-limiting.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reticular Structural Diversification of Zirconium Metal–Organic Frameworks Through Angular Ligand Configuration Control

Reticular chemistry offers practical guidelines for enlarging and enriching the arsenal of metal–organic frameworks (MOFs). However, reticular expansion to access mesoporous structures remains challenging due to limitations in achieving precise control over both the size and configuration during building units’ extension. Herein, we combine ligand isomerization and functionalization strategies to regulate the ligand configuration by systematically replacing aryl C–H groups with N atoms, resulting in angular dicarboxylate ligands with various symmetries. The assembly between a 4,4′-(pyridine-2,6-diyl)dibenzoic acid ligand (1N, C 2 symmetry) and 12-connected Zr 6 cluster leads to the formation of a pseudo ftw topology framework (NU-2611), where one pair of nose-to-nose 1N ligands resembles a tetra-topic ligand. When a 6,6′-(1,3-phenylene)dinicotinic acid ligand (2N, C S symmetry) was used, another pseudo ftw network NU-2612 was obtained with a 2-fold framework interpenetration. Interestingly, the planar [2,2′:6′,2″-terpyridine]-5,5″-dicarboxylic acid ligand (3N, C 2V symmetry) yielded an intriguing mesoporous Zr-MOF with kag topology. NU-2613 represents the first example of kag Zr-MOF designed to include large, well-defined mesopores. The diversity of these MOFs was further enhanced through post-synthetic metalation of linkers. Particularly, metalation of the chelating 3N ligand with Fe 3+ in NU-2613 enables efficient catalytic transformation within the functionalized channels. This work contributes insight into the reticular expansion of Zr-MOFs by finely-tuning the ligand planarity, advancing the structure diversification of mesoporous frameworks for specific applications.

Cluster chemistry↗

Probing plexciton emission from 2D materials on gold nanotrenches

Probing strongly coupled quasiparticle excitations at their intrinsic length scales offers unique insights into their properties and facilitates the design of devices with novel functionalities. In this work, we investigate the formation and emission characteristics of plexcitons, arising from the interaction between surface plasmons in narrow gold nanotrenches and excitons in monolayer WSe 2 . We study this strong plasmon–exciton coupling in both the far-field and the near-field. Specifically, we observe a Rabi splitting in the far-field reflection spectra of about 80 meV under ambient conditions, consistent with our theoretical modeling. Using a custom-designed near-field probe, we find that plexciton emission originates predominantly from the lower-frequency branch, which we can directly probe and map its local field distribution. We precisely determine the plexciton's spatial extension, similar to the trench width, with nanometric precision by collecting spectra at controlled probe locations. Our work opens exciting prospects for nanoscale mapping and engineering of plexcitons in complex nanostructures with potential applications in nanophotonic devices, optoelectronics, and quantum electrodynamics in nanoscale cavities.

36 MATERIALS SCIENCE↗

The molecular basis of Human FN3K mediated phosphorylation of glycated substrates

Abstract Glycation, a non-enzymatic post-translational modification occurring on proteins, can be actively reversed via site-specific phosphorylation of the fructose-lysine moiety by FN3K kinase, to impact the cellular function of the target protein. A regulatory axis between FN3K and glycated protein targets has been associated with conditions like diabetes and cancer. However, the molecular basis of this relationship has not been explored so far. Here, we determined a series of crystal structures of HsFN3K in the apo-state, and in complex with different nucleotide analogs together with a sugar substrate mimic to reveal the features important for its kinase activity and substrate recognition. Additionally, the dynamics in sugar substrate binding during the kinase catalytic cycle provide important mechanistic insights into HsFN3K function. Our structural work provides the molecular basis for rational small molecule design targeting FN3K.

Science & Technology - Other Topics↗

Impact of ion fluxes across thylakoid membranes on photosynthetic electron transport and photoprotection

In photosynthetic thylakoid membranes the proton motive force (pmf) not only drives ATP synthesis, in addition it is central to controlling and regulating energy conversion. As a consequence, dynamic fine-tuning of the two pmf components, electrical (Δψ) and chemical (ΔpH), is an essential element for adjusting photosynthetic light reactions to changing environmental conditions. Good evidence exists that the Δψ/ΔpH partitioning is controlled by thylakoid potassium and chloride ion transporters and channels. However, a detailed mechanistic understanding of how these thylakoid ion transporter/channels control pmf partitioning is lacking. In this work, we combined functional measurements on potassium and chloride ion transporter and channel loss-of-function mutants with extended mathematical simulations of photosynthetic light reactions in thylakoid membranes to obtain detailed kinetic insights into the complex interrelationship between membrane energization and ion fluxes across thylakoid membranes. The data reveal that potassium and chloride fluxes in the thylakoid lumen determined by the K + /H + antiporter KEA3 and the voltage-gated Cl – channel VCCN1/Best1 have distinct kinetic responses that lead to characteristic and light-intensity-dependent Δψ/ΔpH oscillations. These oscillations fine-tune photoprotective mechanisms and electron transport which are particularly important during the first minutes of illumination and under fluctuating light conditions. By employing the predictive power of the model, we unravelled the functional consequences of changes in KEA3 and VCCN1 abundance and regulatory/enzymatic parameters on membrane energization and photoprotection.

59 BASIC BIOLOGICAL SCIENCES↗

Pressure-induced structural phase transitions in CrSBr

There is growing interest in combining chemical complexity with external stimuli like pressure, field, and light for property control in van der Waals solids. This is because extreme conditions trigger the development of new states of matter and functionality. In this work, we bring together synchrotron-based infrared absorption, Raman scattering, and diamond anvil cell techniques with first-principles calculations of the lattice dynamics and energy landscape to reveal the series of structural phase transitions in CrSBr. By tracking how the phonons change under pressure, we uncover a remarkable chain of complex symmetry modifications, interlayer interactions, and chemical reactions. A group-subgroup analysis suggests that CrSBr undergoes an orthorhombic Pmmn → monoclinic P2/m transition at 7.6 GPa, and based upon a comparison with model oxychlorides like FeOCl and CrOCl, we propose that changes in the pendant halide groups drive the system to a P2 1 /m-like space group above 15.3 GPa. Compression above 20.2 GPa is irreversible, resulting in the formation of an entirely new compound that is metastable for months. This work opens the door to the use of pressure and possibly strain to control the properties of CrSBr.

Microscopy↗

Warming response of peatland CO 2 sink is sensitive to seasonality in warming trends

Peatlands have acted as net CO 2 sinks over millennia, exerting a global climate cooling effect. Rapid warming at northern latitudes, where peatlands are abundant, can disturb their CO 2 sink function. In this work, we show that sensitivity of peatland net CO 2 exchange to warming changes in sign and magnitude across seasons, resulting in complex net CO 2 sink responses. We use multiannual net CO 2 exchange observations from 20 northern peatlands to show that warmer early summers are linked to increased net CO 2 uptake, while warmer late summers lead to decreased net CO 2 uptake. Thus, net CO 2 sinks of peatlands in regions experiencing early summer warming, such as central Siberia, are more likely to persist under warmer climate conditions than are those in other regions. Our results will be useful to improve the design of future warming experiments and to better interpret large-scale trends in peatland net CO 2 uptake over the coming few decades.

54 ENVIRONMENTAL SCIENCES↗

Climatic controls of decomposition drive the global biogeography of forest-tree symbioses

The identity of the dominant microbial symbionts in a forest determines the ability of trees to access limiting nutrients from atmospheric or soil pools, sequester carbon and withstand the impacts of climate change. Characterizing the global distribution of symbioses, and identifying the factors that control it, are thus integral to understanding present and future forest ecosystem functioning. In this work we generate the first spatially explicit global map of forest symbiotic status using a database of over 1.1 million forest inventory plots with over 28,000 tree species. Our analyses indicate that climatic variables, and in particular climatically-controlled variation in decomposition rate, are the primary drivers of the global distribution of major symbioses. We estimate that ectomycorrhizal (EM) trees, which represent only 2% of all plant species, constitute approximately 60% of tree stems on Earth. EM symbiosis dominates forests where seasonally cold and dry climates inhibit decomposition, and are the predominant symbiosis at high latitudes and elevation. On the other hand, arbuscular mycorrhizal (AM) trees dominate aseasonally warm tropical forests and occur with EM trees in temperate biomes where seasonally warm-and-wet climates enhance decomposition. Continental transitions between AM and EM dominated forests occur relatively abruptly along climate driven decomposition gradients, which is likely caused by positive plant-microbe feedbacks. Symbiotic N-fixers, which are insensitive to climatic controls on decomposition compared with mycorrhizal fungi, are most abundant in arid biomes with alkaline soils and high maximum temperatures. The climatically driven global symbiosis gradient we document represents the first spatially-explicit, quantitative understanding of microbial symbioses at the global scale and demonstrates the critical role of microbial mutualisms in shaping the distribution of plant species.

59 BASIC BIOLOGICAL SCIENCES↗

Nanocomplex made up of antimicrobial metallo-supramolecules and model biomembranes – characterization and enhanced fluorescence

Antimicrobial pentatopic 2,2':6',2"-terpyridines that form 3-D supramolecular hexagonal prisms with Cd 2+ through coordination driven self-assembly can be entrapped by lipid discoidal bicelles, composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 1,2-dihexanoyl-sn-glycero-3-phosphocholine and 1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) lipid, forming a well-defined nanocomplex. Structural characterization performed by very small angle neutron scattering, small angle X-ray scattering and transmission electron microscopy suggests that the hexagonal prisms are preferably located at the rim of bicellar discs with the hexagonal face in parallel with the bilayers, instead of face-to-face stacking. Such a configuration reduces the π–π interaction and consequently enhances the fluorescence emission. Since novel supramolecules were reported to have antibiotic functions, in this work we provide insight into the interactions of antimicrobial supermolecules with lipid membranes, leading to potential theranostic applications.

36 MATERIALS SCIENCE↗

Water adsorption on olivine(010) surfaces: Effect of alkali and transition metal cation doping

Dopants have the potential to locally modify water-olivine interactions, which can impact geological processes, such as weathering, CO 2 sequestration, and abiotic hydrocarbon generation. As a first step in understanding the role of dopants on the water structure and chemistry at water-olivine interfaces, water monomer adsorption on alkaline earth (AE) and transition metal (TM) doped forsterite(010) [Mg 2 SiO 4 (010)] surfaces was studied in this work using density functional theory (DFT). Dopants that occur in olivine minerals were considered and consisted of Ca, Sr, and Ba for the AE dopants and Cr, Mn, Fe, Co, and Ni for the TM dopants. The water molecule adsorbs on the olivine surface through a metal-water bond (Me–Ow) and a hydrogen bond with an adjacent surface lattice oxygen (Ox–Hw). A frontier orbital analysis reveals that the 1b 2 , 3a 1 , and 1b 1 (HOMO) of the water molecule are involved in the bonding. All of the TM dopants show strong net Me–Ow covalent bonding between 3a 1 and 1b 1 water orbitals and TM d states, while the AE dopants except for Mg 2 SiO 4 (010) show negligible Me–Ow covalent bonding. Both the AE and TM dopants show similar hydrogen bonding features involving both the 1b 2 and 3a 1 orbitals. While the AE cations show an overall lower Me–Ow covalent interaction, the AE dopants have strong electrostatic interactions between the positive metal cation and the negatively charged water dipole. A bonding model incorporating a linear combination of the covalent Me–Ow bond, the Ox–Hw hydrogen bond, the electrostatic interaction between the dopant cation and the H 2 O molecule, and the surface distortion energy is needed to capture the variation in the DFT adsorption energies on the olivine surfaces. The bonding analysis is able to identify the dominant contributions to water-dopant interactions and can serve as a basis for future studies of more realistic water-olivine interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ionization wave propagation in a He plasma jet in a controlled gas environment

Characterizing ionization wave propagation in low temperature plasma jets is critical to predicting production of reactive species and plasma–surface interactions for biomedical applications and surface functionalization. In this work, results from optical emission and laser induced fluorescence measurements of the ionization wave in a He plasma jet operating in a controlled gas environment are discussed and used for comparison with numerical modeling. Additionally, the ionization wave was observed using ICCD (Intensified Charge Coupled Device) imaging and characterized by time and spatially resolved electron density measurements using laser-collision-induced fluorescence. The plasma jet was initially characterized using pure He (nominally at 200 Torr), while varying pressure and voltage. When operating in pure He, the ionization wave broadly expands exiting the plasma tube. Increasing the operating pressure reduces the speed and isotropic expansion of the ionization wave. Furthermore, the jet operated with a humid He shroud was also studied. The humid He shroud results in the electron density increasing and having an annular profile due to the lower ionization potential of H2O compared to He and localized photoionization in the mixing region. Numerical modeling highlighted the importance of resonance radiation emitted by excited states of He, photoelectron emission from the quartz tube, and the kinetic behavior of the electrons produced by photoionization ahead of the ionization front.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Role of ripples in altering the electronic and chemical properties of graphene

Ripples of graphene are known to manipulate electronic and hydrogenation properties of graphitic materials. More detailed work is needed to elucidate the structure–property relationship of these systems. In this work, the density functional theory is used to compute the energy and electronic structure of the graphene models with respect to variable curvatures and hydrogen adsorption sites. The magnitude of finite bandgap opening depends on the orientation of ripples, and the hydrogen adsorption energy depends on the local curvature of graphene. An adsorbed hydrogen alters the local curvature, resulting in relatively weakened adsorption on the neighboring three sites, which gives a rationale to experimentally observed dynamic equilibrium stoichiometry (H:C = 1:4) of hydrogenated graphene. The surface diffusion transition state energy of adsorbed hydrogen is computed, which indicates that the Eley–Rideal surface recombination mechanism may be important to establish the dynamic equilibrium, instead of the commonly assumed Langmuir–Hinshelwood mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hierarchical Ion Interactions in the Direct Air Capture of CO 2 at Air/Aqueous Interfaces

The direct air capture (DAC) of CO 2 using aqueous solvents is plagued by slow kinetics and interfacial barriers that limit effectiveness in combating climate change. Functionalizing air/aqueous surfaces with charged amphiphiles shows promise in accelerating DAC; however, insight into these interfaces and how they evolve in time remains poorly understood. Specifically, competitive ion interactions between DAC reagents and reaction products feedback onto the interfacial structure, thereby modulating interfacial chemical composition and overall function. In this work, we probe the role of glycine amino acid anions (Gly - ), an effective CO 2 capture reagent, that promotes the organization of cationic oligomers at air/aqueous interfaces. These surfaces are probed with vibrational sum frequency generation spectroscopy and molecular dynamics simulations. Our findings demonstrate that the competition for surface sites between Gly - and captured carbonaceous anions (HCO 3 - , CO 3 2 -, carbamates) drives changes in surface hydration, which in turn tunes oligomer ordering. This phenomenon is related to a hierarchical ordering of anions at the surface that are electrostatically attracted to the surface and their ability to compete for interfacial water. These results point to new ways to tune interfaces for DAC via stratification of ions based on relative surface propensities and specific ion effects.

54 ENVIRONMENTAL SCIENCES↗

A combinatorially complete epistatic fitness landscape in an enzyme active site

Protein engineering often targets binding pockets or active sites which are enriched in epistasis—nonadditive interactions between amino acid substitutions—and where the combined effects of multiple single substitutions are difficult to predict. Few existing sequence-fitness datasets capture epistasis at large scale, especially for enzyme catalysis, limiting the development and assessment of model-guided enzyme engineering approaches. We present here a combinatorially complete, 160,000-variant fitness landscape across four residues in the active site of an enzyme. Assaying the native reaction of a thermostable β-subunit of tryptophan synthase (TrpB) in a nonnative environment yielded a landscape characterized by significant epistasis and many local optima. These effects prevent simulated directed evolution approaches from efficiently reaching the global optimum. There is nonetheless wide variability in the effectiveness of different directed evolution approaches, which together provide experimental benchmarks for computational and machine learning workflows. The most-fit TrpB variants contain a substitution that is nearly absent in natural TrpB sequences—a result that conservation-based predictions would not capture. Thus, although fitness prediction using evolutionary data can enrich in more-active variants, these approaches struggle to identify and differentiate among the most-active variants, even for this near-native function. Overall, this work presents a large-scale testing ground for model-guided enzyme engineering and suggests that efficient navigation of epistatic fitness landscapes can be improved by advances in both machine learning and physical modeling.

biocatalysis↗

The Random Ray Method Versus Multigroup Monte Carlo: The Method of Characteristics in OpenMC and SCONE

The Random Ray Method (TRRM) is a recently developed approach to solving neutral particle transport problems based on the Method of Characteristics. While the method previously has been implemented only in closed-source or limited-functionality codes, this work describes its implementation in two open-source Monte Carlo codes: OpenMC and SCONE. The random ray implementations required small modifications to the existing Multigroup Monte Carlo (MGMC) solvers, offering a rare venue for redundant, fine-grained, "apples-to-apples" speed and accuracy comparisons between transport methods. To this end, TRRM and MGMC solvers are evaluated against each other using each code's native capabilities on reactor eigenvalue problems with different degrees of energy discretization. On the C5G7 benchmark (featuring only seven energy groups), TRRM achieves a maximum pin power error comparable to or lower than that of MGMC for a given run time. On a problem with 69 energy groups, MGMC is found to scale more efficiently, obtaining a lower pin power error for a given run time. However, the defining difference between the two transport methods is found to be their vastly different uncertainty distributions. Specifically, TRRM is found to maintain similar levels of accuracy and uncertainty throughout the simulation domain whereas MGMC can exhibit orders-of-magnitude greater errors in areas of the problem that feature low neutron flux. For instance, TRRM provided an up to 373 times speed advantage compared with MGMC for computing the flux in low-flux regions in the moderator surrounding the C5G7 core.

42 ENGINEERING↗

First-principles calculation of gate-tunable ferromagnetism in magic-angle twisted bilayer graphene under pressure

Magic-angle twisted bilayer graphene (MATBG) is notable as a highly tunable platform for investigating strongly correlated phenomena such as unconventional superconductivity and quantum spin liquids, due to easy control of doping level through gating and sensitive dependence of the magic angle on hydrostatic pressure. Experimental observations of correlated insulating states, unconventional superconductivity and ferromagnetism in MATBG indicate that this system exhibits rich exotic phases. In this work, using density functional theory calculations in conjunction with the effective screening medium method, we find the MATBG under pressure at a twisting angle of 2.88 °and simulate how its electronic states evolve when doping level and electric field perpendicular to plane are tuned by gating. Our calculations show that, at doping levels between two electrons and four holes per moiré unit cell, a ferromagnetic (FM) solution with spin density localized at AA stacking sites is lower in energy than the nonmagnetic solution. The magnetic moment of this FM state decreases with both electron and hole doping and vanishes at four electrons/holes doped per moiré unit cell. Hybridization between the flat bands at the Fermi level and the surrounding dispersive bands can take place at finite doping. On increasing the out-of-plane electric field at zero doping, a transition from the FM state to the nonmagnetic one is seen. An investigation of impurity effects shows that both absorption of O 2 molecules and occurrence of Stone–Wales impurities suppress the FM state, and the mechanisms are understood from our calculations. We also analyze the interlayer bonding character due to flat bands via Wannier functions. Finally, we report trivial band topology of the flat bands in the FM state at a certain doping level.

Physics↗