MLTB: Enhancing Transferability and Extensibility of Density Functional Tight-Binding Theory with Many-body Interaction Corrections
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Predicting Partial Atomic Charges in Metal–Organic Frameworks: An Extension to Ionic MOFs
Molecular simulation is an invaluable tool to predict and understand the usage of metal–organic frameworks (MOFs) for gas storage and separation applications. Accurate partial atomic charges, commonly obtained from density functional theory (DFT) calculations, are often required to model the electrostatic interactions between the MOF and adsorbates, especially when the adsorbates have dipole or quadrupole moments, such as water and CO 2 . Machine learning (ML) models have been previously employed to predict partial charges and avoid the computational cost associated with DFT calculations. However, previous ML models suffer from small training data sets, which limit their scope of application. In this work, we introduce two novel machine learning models, PACMOF2-neutral and PACMOF2-ionic, aimed at predicting the density-derived electrostatic and chemical (DDEC6) partial atomic charges for both neutral and ionic MOFs. These models not only yield DFT-level accuracy at a fraction of the computational cost but also demonstrate a remarkable improvement in prediction of adsorption, as validated with grand canonical Monte Carlo simulations. Furthermore, the robustness and fast computational time of the PACMOF2 models, along with their transferability to other porous materials such as covalent organic frameworks and zeolites, underscores their potential in high-throughput screening of MOFs for diverse applications.
36 MATERIALS SCIENCE↗
Extension of Solvent-Assisted Linker Exchange to Supported Metal–Organic Framework Thin Films
Solvent-assisted linker exchange (SALE) is a common postsynthetic approach used to accommodate metal–organic frameworks (MOFs) for targeted applications. As this technique is relatively untested in immobilized MOF structures, we repeated the generalized SALE approach with ZIF-8 deposited directly onto solid substrates and assessed the results with a variety of techniques, including time-of-flight secondary-ion mass spectrometry (ToF-SIMS). Our methods confirm that the supported films maintain their key structural properties while allowing for linker substitution with foreign species. Alongside experiments, we used computational modeling to quantify the relative energetics of SALE reactions with a variety of linkers. These techniques together reveal that SALE is translatable to immobilized MOFs. Additionally, we recognize how various aspects of the postsynthetic approach can bear consequences for the material’s final micro- and macroscopic properties. Furthermore, the results uncover basic yet critical details needed to inform future efforts to engineer MOF films with functional properties.
Ligands↗
Incorporation of Thioacetate Pendants on a Polyalkenamer Enables High Extensibility
This study focuses on functionalizing polycyclooctene (PCOE) with thioacetate groups using thiol–ene click chemistry. The ethylene thioacetate (EVSA) copolymers produced vary in thioacetate incorporation (4–25 mol %) via a controlled semibatch addition technique with AIBN dosing. Copolymers with 4–14 mol % thioacetate are semicrystalline, while those with 20–25 mol % are amorphous. Increased functionalization correlates with decreased crystallinity and increased stretchability, with the highest functionalization (25 mol %) showing a modulus of 0.045 MPa and 2000% elongation at break. Here, this behavior is due to the pseudoprecise functionalization of the thioacetate pendants and intrinsic cross-linking that occurs during melt processing. Broadband dielectric spectroscopy (BDS) indicates a low activation energy barrier (16 kJ/mol for the β process), suggesting potential self-healing applications.
36 MATERIALS SCIENCE↗
200-Fold Lifetime Extension of 2,6- Dihydroxyanthraquinone Electrolyte during Flow Battery Operation
Not provided.
Materials Science↗
Flexible and Extensive Platinum Ion Gel Condensers for Programmable Catalysis
Catalytic condensers composed of ion gels separating a metal electrode from a platinum-on-carbon active layer were fabricated and characterized to achieve more powerful, high surface area dynamic heterogeneous catalyst surfaces. Ion gels comprised of poly(vinylidene difluoride)/1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide were spin coated as a 3.8 μm film on a Au surface, after which carbon sputtering of a 1.8 nm carbon film and electron-beam evaporation of 2 nm Pt clusters created an active surface exposed to reactant gases. Electronic characterization indicated that most charge condensed within the Pt nanoclusters upon application of a potential bias, with the condenser device achieving a capacitance of ∼20 μF/cm 2 at applied frequencies of up to 120 Hz. The maximum charge of ∼10 14 |e – | cm –2 was condensed under stable device conditions at 200 °C on catalytic films with ∼10 15 sites cm –2 . Grazing incidence infrared spectroscopy measured carbon monoxide adsorption isobars, indicating a change in the CO* binding energy of ∼19 kJ mol –1 over an applied potential bias of only 1.25 V. Condensers were also fabricated on flexible, large area Kapton substrates allowing stacked or tubular form factors that facilitate high volumetric active site densities, ultimately enabling a fast and powerful catalytic condenser that can be fabricated for programmable catalysis applications.
Catalysis↗
Advancing Protein Display on Bacterial Spores through an Extensive Survey of Coat Components
The profound stability of bacterial spores makes them a promising platform for biotechnological applications like biocatalysis, bioremediation, drug delivery, etc. However, though the Bacillus subtilis spore is composed of >40 types of proteins, only ∼12 have been explored as fusion carriers for protein display. Here, we assessed the suitability of 33 spore proteins (SPs) as enzyme display carriers by direct allele tagging at native genomic loci. Of the 33 SPs investigated, 26 formed functional fusions with β-glucuronidase (GUS)─a ∼272 kDa homotetramer. This almost triples the number of SPs assessed for enzyme display and doubles the number of functional fusions documented in the literature. We quantitatively assessed 1) SP promoter activation dynamics, 2) GUS activity on spores, 3) surface availability, and 4) protection from thermal and proteolytic degradation. Multicopy expression and pairwise coexpression of the most promising SP-GUS fusions highlighted the complexity of spore structure/assembly and the difficulty in predicting compatibility between different SP fusions. We also assessed the suitability of engineered spores to degrade PET (polyethylene terephthalate) films and found that surface-exposed SPs were most effective. Beyond the broad survey, a key outcome of our work was the identification of SscA (small spore coat assembly protein A) as an effective spore display carrier. SscA supported enzyme activity at least 4-fold higher than any other SP, including the well-established anchor, CotY. We attribute this to its promoter, which demonstrated early and sustained activation relative to other SPs and its small size (∼3 kDa), which likely minimally interferes with enzyme folding, oligomerization, and activity. Labeling and genetic studies, its hydrophobic nature, and low surface availability suggest that SscA assembles within the inner spore coat, which makes it stabilizing and suitable for many biocatalytic applications. Overall, this work serves as a knowledge base to advance the biotechnological utility of B. subtilis spores.
Bacillus subtilis↗
Extensive Secondary Cratering From the InSight Sol 1034a Impact Event
Abstract Impact cratering is one of the fundamental processes throughout the history of the Solar System. The formation of new impact craters on planetary bodies has been observed with repeat images from orbiting satellites. However, the time gap between images is often large enough to preclude detailed analysis of smaller‐scale features such as secondary impact craters, which are often removed or buried over a short time period. Here we use a seismic event detected on Mars by the NASA InSight mission to investigate secondary cratering at a new impact crater. We strengthen the case that the seismic event that occurred on Sol 1034 (S1034a) is the result of a new impact cratering event. Using the exact timing of this event from InSight, we investigated the resulting new impact crater in orbital image data. The S1034a impact crater is approximately 9 m in diameter but is responsible for over 900 secondary impact events in the form of low albedo spots that are located at distances of up to almost 7 km from the primary crater. We suggest that the low albedo spots formed from relatively low energy ejecta, with individual ejecta block velocities less than 200 m s −1 . We estimate that the low albedo spots, the main evidence of secondary impact processes at this new impact event, fade within 200–300 days after formation.
Grindrod, P. M. [Natural History Museum London UK]↗
Extension of nature's NIR-I chromophore into the NIR-II region
Two annulated bacteriochlorin isomers exhibit profoundly different spectral and photophysical features, which are attributed to the absence or presence of electronic (and vibronic) mixing of x - and y -polarized transitions/states.
Chemistry↗
The impact of second coordination sphere functional group extension on product selectivity for manganese bipyridyl CO 2 reduction electrocatalysts
Utilizing the well established manganese bipyridyl class of homogeneous electrocatalyst, four new ligands are studied to probe the influence of distal, outer coordination sphere, H-bonding and steric effects on product selectivity for proton-coupled electrocatalytic CO 2 reduction. The presence of a simple acetate functional group in the second coordination sphere provides a high selectivy for CO 2 -to-CO conversion irrespective of proton source (H 2 O vs. PhOH) or applied potential. The o-(methoxybenzoate)phenyl second/outer coordination sphere at the bipyridyl 6,6′-positions imparts poor product selectivity. In contrast, upon conjugation of the acetate functional group with the N-Boc-alanine moiety, a CO : HCO 2 − product selectivity of ∼1 : 1 is observed at the high overpotential catalytic wave (for both H 2 O and PhOH acids). Computed enthalpy and free energy of activation parameters suggest that selective CO 2 insertion at the manganese hydride transition state is favored, over protonation, consistent with negligible hydrogen production during controlled potential electrolysis studies.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Central π-conjugated extension in quinoxaline-based small-molecule acceptors as guest components enabling high-performance ternary organic solar cells
Ternary strategies have critical roles in pursuing high efficiencies for organic solar cells (OSCs).
Kwok, Chung Hang [Department of Applied Biology an↗
Molecular beam epitaxy growth and optoelectronic properties of droplet-free lattice-matched GaInAsSbBi on GaSb with wavelength extension exceeding 5 μ m
GaInAsSbBi alloys are grown lattice-matched on GaSb by molecular beam epitaxy demonstrating smooth surface morphologies, >5 μm wavelength photoluminescence emission, and minority carrier lifetimes >1 μs. At a growth temperature of 400 °C, the Ga flux is systematically increased and the Bi flux systematically decreased to identify GaInAsSbBi growth conditions that yield smooth droplet-free surface morphologies. The minority carrier lifetime is evaluated using time-resolved photoluminescence, where it is observed that GaInAsSbBi samples exhibit minority carrier lifetimes comparable to their Bi-free GaInAsSb counterparts, on the order of 1.5–2 μs. The bandgap and Urbach energy are evaluated from steady-state photoluminescence to gain insight into the impact of the incorporated Bi. Coupled with Rutherford backscattering spectrometry measurements of the Bi mole fraction, bandgap reduction rates of 97 meV/% Bi in InAsSbBi and 150 meV/% Bi in GaInAsSbBi are observed, significantly higher than previous evaluations in InAsSbBi (35–55 meV/% Bi). Detailed comparisons of the Bi mole fraction, bandgap energy, and Urbach energy indicate that the bandgap reduction potential in this alloy system is inhibited by the formation of Bi clusters; however, the inclusion of Ga in the quinary alloy is effective in suppressing Bi's tendency to incorporate in clusters for Ga mole fractions >9%, maximizing the bandgap reduction per unit Bi and overall optoelectronic quality.
Atomic force microscopy↗
Extensive analysis of reconstruction algorithms for DESI 2024 baryon acoustic oscillations
Reconstruction of the baryon acoustic oscillation (BAO) signal has been a standard procedure in BAO analyses over the past decade and has helped to improve the BAO parameter precision by a factor of ∼2 on average. The Dark Energy Spectroscopic Instrument (DESI) BAO analysis for the first year (DR1) data uses the “standard” reconstruction framework, in which the displacement field is estimated from the observed density field by solving the linearized continuity equation in redshift space, and galaxy and random positions are shifted in order to partially remove non-linearities. There are several approaches to solving for the displacement field in real survey data, including the multigrid (MG), iterative Fast Fourier Transform (iFFT), and iterative Fast Fourier Transform particle (iFFTP) algorithms. In this work, we analyze these algorithms and compare them with various metrics including two-point statistics and the displacement itself using realistic DESI mocks. We focus on three representative DESI samples, the emission line galaxies (ELG), quasars (QSO), and the bright galaxy sample (BGS), which cover the extreme redshifts and number densities, and potential wide-angle effects. We conclude that the MG and iFFT algorithms agree within 0.4% in post-reconstruction power spectrum on BAO scales with the RecSym convention, which does not remove large-scale redshift space distortions (RSDs), in all three tracers. The RecSym convention appears to be less sensitive to displacement errors than the RecIso convention, which attempts to remove large-scale RSDs. However, iFFTP deviates from the first two; thus, we recommend against using iFFTP without further development. In addition, we provide the optimal settings for reconstruction for five years of DESI observation. The analyses presented in this work pave the way for DESI DR1 analysis as well as future BAO analyses.
79 ASTRONOMY AND ASTROPHYSICS↗
Development and extension of a monochromatic neutron beamline for neutron polarimetry device characterization at the Spallation Neutron Source
Explore the source record for details and available documents.
Physics - Nuclear physics and radiation physics↗
Quantitative proteomics reveals extensive lysine ubiquitination and transcription factor stability states in Arabidopsis
Abstract Protein activity, abundance, and stability can be regulated by post-translational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function; yet, we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich ubiquitinated peptides coupled with isobaric labeling to enable quantification of up to 18-multiplexed samples. This approach identified 17,940 ubiquitinated lysine sites arising from 6,453 proteins from Arabidopsis (Arabidopsis thaliana) primary roots, seedlings, and rosette leaves. Gene ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and metabolism. We determined ubiquitinated lysine residues that directly regulate the stability of three transcription factors, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1), CIB1 LIKE PROTEIN 2 (CIL2), and SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) using in vivo degradation assays. Furthermore, codon mutation of CIB1 to create a K166R conversion to prevent ubiquitination, via CRISPR/Cas9-derived adenosine base editing, led to an early flowering phenotype and increased expression of FLOWERING LOCUS T (FT). These comprehensive site-level ubiquitinome profiles provide a wealth of data for future functional studies related to modulation of biological processes mediated by this post-translational modification in plants.
Biochemistry & Molecular Biology↗
Nonparametric extensions of nuclear equations of state: Probing the breakdown scale of relativistic mean-field theory
Phenomenological calculations of the properties of dense matter, such as relativistic mean-field theories, represent a pathway to predicting the microscopic and macroscopic properties of neutron stars. However, such theories do not generically have well-controlled uncertainties and may break down within neutron stars. To faithfully represent the uncertainty in this breakdown scale, we develop a hybrid representation of the dense-matter equation of state, which assumes the form of a relativistic mean-field theory at low densities, while remaining agnostic to any nuclear theory at high densities. To achieve this, we use a nonparametric equation of state model to incorporate the correlations of the underlying relativistic mean-field theory equation of state at low pressures and transition to more flexible correlations above some chosen pressure scale. We perform astrophysical inference under various choices of the transition pressure between the theory-informed and theory-agnostic models. Here, we further study whether the chosen relativistic mean-field theory breaks down above some particular pressure and find no such evidence. Using simulated data for future astrophysical observations at about two-to-three times the precision of current constraints, we show that our method can identify the breakdown pressure associated with a potential strong phase transition.
Equations of state of nuclear matter↗
Competing ionization and dissociation: Extension of the energy-dependent frame transformation to the gerade symmetry of H 2
This article solves two major tasks that frequently arise in the theory of electron collisions with a target molecular cation. First, it extends the energy-dependent frame transformation (EDFT) treatment, which is needed to map fixed-nuclei electron-molecule scattering matrices into an energy-dependent laboratory-frame scattering matrix with vibrational channel indices. The EDFT mapping can now be carried out even when the target molecule possesses multiple low-energy potential curves, significantly transcending previous applications. Second, it implements a method to extract the rest of the full laboratory-frame scattering matrix, i.e., the columns and rows describing input and/or output dissociation channels. The treatment is benchmarked in this article against the essentially exact solution of a refined two-dimensional model of the singlet gerade Σ symmetry of H 2 . Our tests demonstrate that the theory accurately maps fixed-nuclei scattering information, of the type provided by existing electron-molecule computer codes, into a laboratory-frame scattering matrix that includes both ionization and dissociation. Furthermore, this treatment can provide a general framework applicable to a broad class of electron collision processes involving diatomic target ions, suitable for an accurate description of challenging processes such as dissociative recombination.
74 ATOMIC AND MOLECULAR PHYSICS↗