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At least 145 records · Page 8

Elucidating the speciation of extracted lanthanides by diglycolamides

Many studies over the past few decades have been devoted to addressing the application of diglycolamides (DGAs) for hydrometallurgical-based, f-element separations. Work to date has shown the molecular structure of a DGA derivative can have a significant impact on intra-lanthanide partitioning patterns. More recent studies have pushed towards probing the structure function relationship of the lanthanide-DGA complex to enable the design of more efficient lanthanide separation systems. Spectroscopic techniques, such as UV–Visible, Fourier Transformed Infrared Spectroscopy (FT-IR), Nuclear Magnetic Resonance (NMR), and Extended X-ray Absorption Fine Structure (EXAFS), provide information regarding the inner-sphere coordination of a given lanthanide-DGA complex. Scattering techniques, such as Dynamic Light Scattering (DLS), Small-Angle X-ray Scattering (SAXS), and Small-Angle Neutron Scattering (SANS), address nanoscale structures including aggregate sizes and morphology. Here, this review assesses the current state-of-knowledge regarding lanthanide-DGA hydrometallurgical (i.e., solvent extraction systems) interrogated using spectroscopic and scattering techniques to characterize the extracted Ln 3+ DGA species. Of particular interest to this review is the impact of varied diluents, inclusion and variation of phase modifiers, and DGA derivatization on system characteristics. While there has been extensive literature on the application of DGAs for f-element separations, the literature lacks a collective assessment of the speciation of Ln 3+ in the organic phase. This review provides new insights into the field of DGA separations, explicitly with an application to intra-lanthanide separations. Specifically, this review illustrates the importance of both the co-extraction anion (Cl - , NO 3 - , or ClO 4 - ) as it pertains to both the aggregate size and Ln 3+ distribution coefficient. It is evident the ability of the anion to disrupt the hydrogen bonding network limits both aggregate size and distribution coefficients according to the Hoffmeister series. This suggests the importance of the large, softer anions with a low charge-to-surface area ratio on encouraging hydrogen bond interactions. In addition, the co-extracted cation (H + vs Na + ) is important for mitigating transfer of Ln 3+ from the aqueous to the organic phase through extensive hydrogen bonding networks. These networks are responsible for forming supramolecular aggregates where a change in morphology is observed with increasing concentrations of H + and/or Ln 3+ in the organic phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural characterization of HIV-1 matrix mutants implicated in envelope incorporation

During the late phase of HIV-1 infection, viral Gag polyproteins are targeted to the plasma membrane (PM) for assembly. Gag localization at the PM is a prerequisite for the incorporation of the envelope protein (Env) into budding particles. Gag assembly and Env incorporation are mediated by the N-terminal myristoylated matrix (MA) domain of Gag. Nonconservative mutations in the trimer interface of MA (A45E, T70R, and L75G) were found to impair Env incorporation and infectivity, leading to the hypothesis that MA trimerization is an obligatory step for Env incorporation. Conversely, Env incorporation can be rescued by a compensatory mutation in the MA trimer interface (Q63R). The impact of these MA mutations on the structure and trimerization properties of MA is not known. In this study, we employed NMR spectroscopy, X-ray crystallography, and sedimentation techniques to characterize the structure and trimerization properties of HIV-1 MA A45E, Q63R, T70R, and L75G mutant proteins. NMR data revealed that these point mutations did not alter the overall structure and folding of MA but caused minor structural perturbations in the trimer interface. Analytical ultracentrifugation data indicated that mutations had a minimal effect on the MA monomer–trimer equilibrium. The high-resolution X-ray structure of the unmyristoylated MA Q63R protein revealed hydrogen bonding between the side chains of adjacent Arg-63 and Ser-67 on neighboring MA molecules, providing the first structural evidence for an additional intermolecular interaction in the trimer interface. These findings advance our knowledge of the interplay of MA trimerization and Env incorporation into HIV-1 particles.

60 APPLIED LIFE SCIENCES↗

Influence of heterocyclic N-donors on the structural topologies and vibrational spectra of uranyl selenate phases

Uranyl (U(VI)O 2 2+ ) selenate compounds represent a well-studied family of structures with diverse structural arrays. Differences in the overall topology and bonding with the uranyl cation combined with additional intermolecular interactions can lead to variation in the resulting spectroscopic signals. Here, in the current study, we evaluated the structural chemistry and vibrational spectroscopy for uranyl selenates crystallized with heterocyclic N-donors. Five compounds ((C 4 H 12 N 2 )[(UO 2 )(SeO 4 ) 2 (H 2 O)]·H 2 O (USe_pip), (C 4 H 5 N 2 ) 2 [(UO 2 )(SeO 4 ) 2 (H 2 O)] (USe_pyrdz), (C 5 H 5 N) 2 [(UO 2 ) 2 (SeO 4 ) 3 (H 2 O)] ∙ 3H 2 O (USe_pyrmd), (H 3 O) 2 (C 4 H 5 N 2 ) 2 [(UO 2 ) 3 (SeO 4 ) 5 (H 2 O)]·H 2 O (USe_pyrz), and (C 5 H 6 N) 2 [(UO 2 ) 2 (SeO 4 ) 3 (H 2 O)] ∙ 3H 2 O (USe_pyr)) were characterized using X-ray diffraction (single-crystal and powder) and vibrational (Raman and IR) spectroscopy. Two one-dimensional (1-D) chain and three two-dimensional sheet (2-D) topologies were identified and classified based upon previous graphical representations. Overall, the arrangement of the heteroatoms could be linked to the hydrogen bonding network associated with the heterocycles and selenate anions. Vibrational spectra of the solid-state compounds were complex, with multiple bands associated with the uranyl cation, selenate anion, and heteroatoms. The ν 1 symmetric stretching band of the uranyl was relatively consistent across all compounds, whereas differences were observed for the ν 3 asymmetric band between the 1-D and 2-D structural topologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

3D-printing methacrylate/chitin nanowhiskers composites via stereolithography: Mechanical and thermal properties

We report on the mechanical and thermal properties of stereolithography (SLA) 3D-printed methacrylate (MA) resin reinforced by chitin nanowhiskers (CNWs). CNWs were synthesized by acid hydrolysis of crab shell chitin and nanocomposites with 0 wt%, 0.5 wt%, 1.0 wt%, and 1.5 wt% CNWs loading were prepared by slurry compounding method. The obtained CNWs (diameter = 23 ± 5 nm, length = 253 ± 100 nm, and aspect ratio = 11 ± 3) are well dispersed within the bulk of MA at 1.0 wt% loading, implying good interfacial adhesion between the nanofiller and the resin matrix possibly due to hydrogen bonding interactions. The addition of up to 1.0 wt% CNWs to neat MA enhances the tensile strength, strain at break, modulus, and maximum thermal degradation temperatures of the nanocomposites. Moreover, the incorporation of CNWs not only improves the mechanical and thermal properties, but also preserves the excellent resolution and accuracy of 3D-printed MA/CNWs nanocomposites.

36 MATERIALS SCIENCE↗

In situ friction and wear behavior of rubber materials incorporating various fillers and/or a plasticizer in high-pressure hydrogen

Polymers are used routinely for equipment and infrastructure in hydrogen vehicle refueling stations, but significant gaps remain in understanding their hydrogen compatibility. The tribological properties of these materials in a high-pressure hydrogen environment is important in preventing component failure and the need for frequent replacement. We present in situ tribological studies on model rubbers, which include common fillers and plasticizer, using an in situ tribometer developed previously. Results suggest a clear, yet complicated, combined effect of the high-pressure hydrogen and the additives on the tribological performance of the chosen materials, as compared to matching experiments performed in ambient air. We find that the additives improved wear resistance in EPDM but deteriorated that in NBR due to disparate additive-polymer interactions.

Kuang, Wenbin↗

PySIDT: Subgraph Isomorphic Decision Trees for Molecular Property Prediction

Accurate molecular property prediction is important across all fields of chemistry. Deep neural networks (DNNs) have become increasingly popular due to their ability to train automatically, avoiding the incredibly tedious process of constructing and extending traditional property estimation schemes. However, DNNs require large amounts of training data, are challenging to interpret, require large amounts of memory to load even during inference, and have severe difficulties incorporating qualitative chemical knowledge, which are often desired for molecular property prediction tasks. Here, in this study, we present PySIDT (https://github.com/zadorlab/PySIDT), a software for training and running inference on Subgraph Isomorphic Decision Trees (SIDTs). SIDTs are graph-based decision trees made of nodes associated with molecular substructures. Inference is done by descending target molecular structures down the decision tree to nodes with matching subgraph isomorphic substructures and making predictions based on the final (most specific) nodes matched. SIDTs scale down well to dataset sizes much smaller than is feasible for DNNs. As trees of molecular substructures, SIDTs are inherently readable and easy to visualize, making them easy to analyze. They are also straightforward to extend and retrain, facilitate uncertainty estimation, and enable easy integration of expert knowledge. We demonstrate the SIDT approach discussing its application to a diverse range of molecular prediction tasks: rate coefficient estimation, diffusion coefficient estimation, thermochemistry estimation, transition state bond stretch prediction, p K a prediction, stability of molecular structures, stability of surface structures, and prediction of surface lateral interaction energetics. Additionally, we demonstrate the power of the SIDT algorithms in two direct learning curve vanilla comparisons with the popular DNN-based software Chemprop and the popular gradient boosted trees-based software XGBoost on enthalpy of formation and rate coefficient prediction tasks. In particular, in the enthalpy of formation case, vanilla PySIDT is able to outperform vanilla Chemprop and XGBoost across the full range of training/validation set sizes out to 11,560 data points.

Johnson, Matthew Sean [Sandia National Laboratorie↗

Cyanine-Incorporated Amorphous Polymeric Carbon Dots for Optical Reactive Oxygen Species Sensing

Reactive oxygen species (ROS) are common cellular oxidants that when overproduced by cellular stressors cause harm to cells. Detection of ROS is of utmost importance to understanding a wide variety of cellular function and toxicity mechanisms. Conventional ROS fluorescence assays involve using a single dye to visualize the ROS quantity. Herein, we describe ROS-sensitive, fluorescent-dye-incorporated carbon dots with dual fluorescence capabilities and good biocompatibility. Carbon dots (CDs) made of citric acid and urea were synthesized with incorporated cyanine-3-amine (Cy3), a bright red fluorescent dye, to create Cy3-CDs. Additionally, to get Cy3 into the ROS-sensitive form, this work demonstrated that Cy3 alone and Cy3 within carbon dots can be electrochemically reduced to their colorless ROS-sensitive form. Cy3, CDs, and Cy3-CDs are all responsive to additions of superoxide, leading to an increase in the fluorescence. Overall, this work examines how O 2 •– and additional oxidizers interact with CDs, Cy3, and Cy3-CDs, and molecular-level hypotheses are explored that will inform the design of future carbon dot-based ROS sensors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Prediction of plant complex traits via integration of multi-omics data

The formation of complex traits is the consequence of genotype and activities at multiple molecular levels. However, connecting genotypes and these activities to complex traits remains challenging. Here, we investigate whether integrating genomic, transcriptomic, and methylomic data can improve prediction for six Arabidopsis traits. We find that transcriptome- and methylome-based models have performances comparable to those of genome-based models. However, models built for flowering time using different omics data identify different benchmark genes. Nine additional genes identified as important for flowering time from our models are experimentally validated as regulating flowering. Gene contributions to flowering time prediction are accession-dependent and distinct genes contribute to trait prediction in different genotypes. Models integrating multi-omics data perform best and reveal known and additional gene interactions, extending knowledge about existing regulatory networks underlying flowering time determination. These results demonstrate the feasibility of revealing molecular mechanisms underlying complex traits through multi-omics data integration.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis of tRNA recognition by the widespread OB fold

The widespread oligonucleotide/oligosaccharide-binding (OB)-fold recognizes diverse substrates from sugars to nucleic acids and proteins, and plays key roles in genome maintenance, transcription, translation, and tRNA metabolism. OB-containing bacterial Trbp and yeast Arc1p proteins are thought to recognize the tRNA elbow or anticodon regions. Here we report a 2.6 Å co-crystal structure of Aquifex aeolicus Trbp111 bound to tRNA Ile , which reveals that Trbp recognizes tRNAs solely by capturing their 3' ends. Structural, mutational, and biophysical analyses show that the Trbp/EMAPII-like OB fold precisely recognizes the single-stranded structure, 3' terminal location, and specific sequence of the 3' CA dinucleotide — a universal feature of mature tRNAs. Arc1p supplements its OB – tRNA 3' end interaction with additional contacts that involve an adjacent basic region and the tRNA body. This study uncovers a previously unrecognized mode of tRNA recognition by an ancient protein fold, and provides insights into protein-mediated tRNA aminoacylation, folding, localization, trafficking, and piracy.

59 BASIC BIOLOGICAL SCIENCES↗

Ramification of complex magnetism in Nd 2 Ir 2 O 7 observed by Raman scattering spectroscopy

Using Raman scattering spectroscopy, we uncover a complex magnetic behavior of Nd2Ir2O7, which stands out among magnetic pyrochlores by the lowest temperature of the all-in-all-out (AIAO) Ir moments ordering (${T}_{{\rm{Ir}}}^{{\rm{N}}} = 33$ K) and the highest temperature at which AIAO order of rare-earth Nd ions is detected (${T}_{{\rm{Nd}}}^{{\rm{* }}}$ = 15 K). Detected magnetic Raman scattering and calculations of expected response allow us to demonstrate that the ordering of Ir magnetic moments is accompanied by an appearance of one-magnon Raman modes at 26.3 and 29.6 meV compatible with the AIAO order and allowing to estimate the energies of Ir-Ir interactions. An additional two-magnon excitation of the AIAO Nd order at around 33 meV appears in the spectra below the ordering temperature of Nd moments ${T}_{{\rm{Nd}}}^{{\rm{* }}}$ = 15 K. In the temperature range between 15 K and 33 K we observe a broad mode, which demonstrates strong temperature dependence and shifts on cooling below 20 K from 14 meV to higher frequencies, and disappears at 5 K, when two-magnon excitation of Nd moments becomes prominent. We suggest an interpretation of this excitation in terms of continuum arising from collective fluctuations of Nd moments above the transition. This complex behavior emerges from the interplay of strong spin-orbit coupling, electronic correlations, and geometric frustration on two magnetic pyrochlore sublattices of Nd and Ir ions.

magnetic properties and materials↗

Unravelling the dynamics of the maturation protein in MS2 bacteriophage via molecular simulations

The MS2 bacteriophage capsid serves as a model system for studying viral structure and function. Mature MS2 virus consists of 178 capsid proteins and a single maturation protein (MP), which is essential for host receptor binding and infection initiation. Despite its critical role, the dynamic behavior of the capsid with the MP remains poorly understood. To address this, we conducted 0.5 µs all-atom molecular dynamics (MD) simulations of the MS2 capsid with and without the MP, revealing key insights into its structural dynamics. Our simulations showed that MP exhibits high flexibility, particularly in the “tip” and “side-loop” regions, which undergo significant motions that likely enhance its ability to engage with the F-pilus receptor. Detailed analysis of MP conformational states revealed that loop rearrangements around H357 enable transient switching between “semi-closed” and “open” conformations, suggesting a conformational selection mechanism for pilus binding. Additionally, ion interaction analyses revealed distinct sodium and chloride binding patterns, where sodium ions were mostly found at the outer capsid shell, while chloride ions interacted with the basic residues on the RNA-facing side. We also found that the presence of the MP enhances salt-bridge interactions, contributing to increased capsid stability, yet it does not significantly alter the pore sizes of pentameric and hexameric units. Together, these findings provide new insights into the functional role of the MP, highlighting its contribution to capsid stability and host receptor engagement. This study offers a foundation for understanding capsid dynamics relevant to viral infectivity and may guide future rational strategies aimed at disrupting host-virus interactions.

Capsid stability↗

Efficient generation and amplification of intense vortex and vector laser pulses via strongly-coupled stimulated Brillouin scattering in plasmas

The past decade has seen tremendous progress in the production and utilization of vortex and vector laser pulses. Although both are considered as structured light beams, the vortex lasers have helical phase fronts and phase singularities, while the vector lasers have spatially variable polarization states and polarization singularities. In contrast to the vortex pulses that carry orbital angular momentum (OAM), the vector laser pulses have a complex spin angular momentum (SAM) and OAM coupling. Despite many potential applications enabled by such pulses, the generation of high-power/-intensity vortex and vector beams remains challenging. Here, we demonstrate using theory and three-dimensional simulations that the strongly-coupled stimulated Brillouin scattering (SC-SBS) process in plasmas can be used as a promising amplification technique with up to 65% energy transfer efficiency from the pump beam to the seed beam for both vortex and vector pulses. We also show that SC-SBS is strongly polarization-dependent in plasmas, enabling an all-optical polarization control of the amplified seed beam. Additionally, the interaction of such structured lasers with plasmas leads to various angular momentum couplings and decouplings that produce intense new light structures with controllable OAM and SAM. This scheme paves the way for novel optical devices such as plasma-based amplifiers and light field manipulators.

Physics↗

Infrared-active phonon modes in single-crystal thorium dioxide and uranium dioxide

The infrared-active phonon modes, in single-crystal samples of thorium dioxide (ThO 2 ) and uranium dioxide (UO 2 ), were investigated using spectroscopic ellipsometry and compared with density functional theory. Both ThO 2 and UO 2 are found to have one infrared-active phonon mode pair [consisting of one transverse optic (TO) and one associated longitudinal optic (LO) mode], which is responsible for the dominant features in the ellipsometric data. Furthermore, at room temperature, our results for the mode pair’s resonant frequencies and broadening parameters are comparable with previous reflectance spectroscopy characterizations and density functional theory predictions. For ThO 2 , our ellipsometry and density function theory results both show that the LO mode broadening parameter is larger than the TO mode broadening. This signifies mode anharmonicity, which can be attributed to the intrinsic phonon–phonon interaction. In addition to the main mode pair, a broad low-amplitude impurity-like vibrational mode pair is detected within the reststrahlen band for both ThO 2 and UO 2 . Elevated temperature measurements were performed for ThO 2 in order to study the mechanisms by which the phonon parameters evolve with increased heat. The observed change in the TO resonant frequency is in excellent agreement with previous density functional calculations, which only consider volume expansion of the crystal lattice. This suggests that the temperature-dependent change in the TO frequency is primarily due to volume expansion. The change in the main mode pair’s broadening parameters is nearly linear within the temperature range of this study, which indicates the intrinsic anharmonic scattering (via cubic anharmonicities) as the main decay mechanism.

36 MATERIALS SCIENCE↗

Computing x-ray absorption spectra from linear-response particles atop optimized holes

State specific orbital optimized density functional theory (OO-DFT) methods, such as restricted open-shell Kohn–Sham (ROKS), can attain semiquantitative accuracy for predicting x-ray absorption spectra of closed-shell molecules. OO-DFT methods, however, require that each state be individually optimized. In this Communication, we present an approach to generate an approximate core-excited state density for use with the ROKS energy ansatz, which is capable of giving reasonable accuracy without requiring state-specific optimization. Herein, this is achieved by fully optimizing the core-hole through the core-ionized state, followed by the use of electron-addition configuration interaction singles to obtain the particle level. This hybrid approach can be viewed as a DFT generalization of the static-exchange (STEX) method and can attain ~0.6 eV rms error for the K-edges of C–F through the use of local functionals, such as PBE and OLYP. This ROKS(STEX) approach can also be used to identify important transitions for full OO ROKS treatment and can thus help reduce the computational cost of obtaining OO-DFT quality spectra. ROKS(STEX), therefore, appears to be a useful technique for the efficient prediction of x-ray absorption spectra.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Isotope study of the nonlinear pressure shifts of 85 Rb and 87 Rb hyperfine resonances in Ar, Kr, and Xe buffer gases

Measurements of the 0–0 hyperfine resonant frequencies of ground-state 85 Rb atoms show a nonlinear dependence on the pressure of the buffer gases Ar, Kr, and Xe. The nonlinearities are similar to those previously observed with 87 Rb and 133 Cs and presumed to come from alkali-metal–noble-gas van der Waals molecules. However, the shape of the nonlinearity observed for Xe conflicts with previous theory, and the nonlinearities for Ar and Kr disagree with the expected isotopic scaling of previous 87 Rb results. Improving the modeling alleviates most of these discrepancies by treating rotation quantum mechanically and considering additional spin interactions in the molecules. Including the dipolar-hyperfine interaction allows simultaneous fitting of the linear and nonlinear shifts of both 85 Rb and 87 Rb in either Ar, Kr, or Xe buffer gases with a minimal set of shared, isotope-independent parameters. To the limit of experimental accuracy, the shifts in He and N 2 were linear with pressure. Further, the results are of practical interest to vapor-cell atomic clocks and related devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Defects of perovskite semiconductor CsPbBr3 investigated via photoluminescence and thermally stimulated current spectroscopies

Halide perovskites are essential materials for hard radiation detectors at ambient temperature. To improve detector performance, charge transport must be investigated and optimized. Using photoluminescence (PL) and thermally stimulated current (TSC) spectroscopies, we investigate photogenerated charge carriers in Bridgman-grown CsPbBr3 single crystals to understand the nature of charge transport. PL spectroscopy of these halide perovskites revealed the presence of strong emission bands at the band edge, which were attributed to free or bound excitons. It is shown that a wide broadening of the excitonic linewidth in these halide perovskites arises from strong exciton–phonon coupling, which is substantially dominated by longitudinal optical phonons via Fröhlich interaction. An additional contribution due to the presence of ionized impurities was also observed. Crystals with a detectable sensitivity to high-energy gamma radiation are characterized by a higher intensity and a narrower linewidth of the principal PL peak at 2.326 eV. Defect states beyond 2.214 eV have a negative impact on detector sensitivity to high-energy gamma radiation. TSC spectroscopy reveals an array of trap levels spanning 0.15–0.70 eV, attributed to intrinsic point defects and multiple extrinsic defects involving dopants or impurities. Defects identified included Cs and Br vacancies, as well as Pb interstitials with concentrations in the 1011–1016 cm−3 range. Understanding how the synthesis process impacts the types and concentrations of the defects present is currently under investigation. Elimination or suppression of the defect/trap states should result in halide perovskite materials with longer carrier diffusion lengths and improved detector characteristics.

Physics↗

Relativistic Douglas–Kroll–Hess calculations of hyperfine interactions within first-principles multireference methods

A relativistic magnetic hyperfine interaction Hamiltonian based on the Douglas–Kroll–Hess (DKH) theory up to the second order is implemented within the ab initio multireference methods, including spin–orbit coupling in the Molcas/OpenMolcas package. This implementation is applied to calculate relativistic hyperfine coupling (HFC) parameters for atomic systems and diatomic radicals with valence s or d orbitals by systematically varying active space size in the restricted active space self-consistent field formalism with restricted active space state interaction for spin–orbit coupling. The DKH relativistic treatment of the hyperfine interaction reduces the Fermi contact contribution to the HFC due to the presence of kinetic factors that regularize the singularity of the Dirac delta function in the nonrelativistic Fermi contact operator. This effect is more prominent for heavier nuclei. As the active space size increases, the relativistic correction of the Fermi contact contribution converges well to the experimental data for light and moderately heavy nuclei. The relativistic correction, however, does not significantly affect the spin-dipole contribution to the hyperfine interaction. In addition to the atomic and molecular systems, the implementation is applied to calculate the relativistic HFC parameters for large trivalent and divalent Tb-based single-molecule magnets (SMMs), such as Tb(III)Pc2 and Tb(II)(CpiPr5)2 without ligand truncation using well-converged basis sets. In particular, for the divalent SMM, which has an unpaired valence 6s/5d hybrid orbital, the relativistic treatment of HFC is crucial for a proper description of the Fermi contact contribution. Even with the relativistic hyperfine Hamiltonian, the divalent SMM is shown to exhibit strong tunability of HFC via an external electric field (i.e., strong hyperfine Stark effect).

Chemistry↗