Molecular Fingerprints of Ice Surfaces in Sum Frequency Generation Spectra: A First-Principles Machine Learning Study
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36 MATERIALS SCIENCE↗
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Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2
Abstract PROTAC® (proteolysis-targeting chimera) molecules induce proximity between an E3 ligase and protein-of-interest (POI) to target the POI for ubiquitin-mediated degradation. Cooperative E3-PROTAC-POI complexes have potential to achieve neo-substrate selectivity beyond that established by POI binding to the ligand alone. Here, we extend the collection of ubiquitin ligases employable for cooperative ternary complex formation to include the C-degron E3 KLHDC2. Ligands were identified that engage the C-degron binding site in KLHDC2, subjected to structure-based improvement, and linked to JQ1 for BET-family neo-substrate recruitment. Consideration of the exit vector emanating from the ligand engaged in KLHDC2’s U-shaped degron-binding pocket enabled generation of SJ46421, which drives formation of a remarkably cooperative, paralog-selective ternary complex with BRD3 BD2 . Meanwhile, screening pro-drug variants enabled surmounting cell permeability limitations imposed by acidic moieties resembling the KLHDC2-binding C-degron. Selectivity for BRD3 compared to other BET-family members is further manifested in ubiquitylation in vitro, and prodrug version SJ46420-mediated degradation in cells. Selectivity is also achieved for the ubiquitin ligase, overcoming E3 auto-inhibition to engage KLHDC2, but not the related KLHDC1, KLHDC3, or KLHDC10 E3s. In sum, our study establishes neo-substrate-specific targeted protein degradation via KLHDC2, and provides a framework for developing selective PROTAC protein degraders employing C-degron E3 ligases.
Science & Technology - Other Topics↗
Ab initio mechanisms and design principles for photodesorption from TiO2
Not Available
36 MATERIALS SCIENCE↗
A single-cell atlas of the bobtail squid visual and nervous system highlights molecular principles of convergent evolution
Abstract The cephalopod and vertebrate visual systems are a textbook example of convergent evolution with unknown molecular underpinnings. Here we characterize 98,537 single-cell transcriptomes in the bobtail squidEuprymna berryito understand how the cephalopod retina and optic lobes relate to the vertebrate retina. We confirm the overall relative simplicity of the cephalopod retina but identify two related photoreceptor cell subtypes expressing distinct r-opsins. By contrast, the adult optic lobe contains a diverse repertoire of neuronal and glial cell types, with a predominance of dopaminergic neurons. We show that cephalopod-specific gene duplicates probably contributed to this cell type diversification. Comparing neuronal cell population in the optic lobes of hatchlings and adults, we reveal a switch towards dopaminergic neurotransmitter usage with age, indicative of a maturation process. We further identify an FMRF-amide-based retrograde signal from the optic lobe towards the retina that supports the functional analogy of the cephalopod optic lobe cortex and the vertebrate inner retina in visual signal processing from a molecular standpoint. Finally, comparative analyses with vertebrate and arthropod cells suggest a scenario in which two photoreceptor types and two neuronal populations may have already been present in the eye of the bilaterian ancestor.
Environmental Sciences & Ecology↗
First-principles data for solid solution niobium-tantalum-vanadium alloys with body-centered-cubic structures
Not Available
36 MATERIALS SCIENCE↗
First-Principles insights into group-V impurities and their impact on germanium detector performance
The outstanding properties of high-purity germanium (HPGe) detectors, such as excellent energy resolution, high energy sensitivity, and a low background-to-signal ratio, make them essential and ideal candidates for detecting particle signatures in nuclear processes such as neutrino-less double beta decay (0νββ). However, the presence of defects and impurities in HPGe crystals can lead to charge trapping, which affects carrier mobility and results in significant energy resolution degradation. In this work, we employ density functional theory with a hybrid functional to study the energetics of possible point defects in Ge. Our findings indicate that group-V impurities form more readily in Ge compared to vacancy and interstitial of Ge. Unlike N dopants, which yield deep trap states, P, As, and Sb create shallow traps close to the conduction band edge of Ge. Furthermore, we predict that group-V defects can condense into defect complexes with Ge vacancies. These vacancy-impurity complexes form deep traps in Ge, similar to Ge vacancies, suggesting that both vacancies and vacancy-impurity complexes contribute to charge trapping in these detectors, thereby diminishing their performance.
36 MATERIALS SCIENCE↗
Vibrational and electronic properties of Np 2 O 5 from experimental spectroscopy and first principles calculations
High-valence actinide oxides are critical to understanding the behavior of 5f-electrons, yet their structural and electronic properties remain poorly understood due to challenges in synthesis and handling. We report the first Raman spectroscopic study of single-crystalline Np 2 O 5 and the first scanning tunneling spectroscopy (STS) measurement on any neptunium-containing material. Hydrothermally synthesized crystals were structurally verified by X-ray diffraction. Raman spectra revealed sharply resolved vibrational features, including previously unreported low-frequency modes. STS measurements revealed a band gap of 1.5 eV. Density functional theory (DFT) enables vibrational mode assignments, reveals neptunium-dominated low-frequency phonons, oxygen-dominated high-frequency modes, and predicts an indirect band gap of 1.68 eV. This predicted value is in excellent agreement with the experimentally measured STS gap. This combined Raman, DFT, and STS approach provides a robust framework for correlating lattice dynamics and electronic structure in actinide materials, providing benchmark data for Np 2 O 5 , and opening new avenues for probing structure–property relationships in complex f-electron materials.
36 - MATERIALS SCIENCE↗
First-principles evaluation of dopant impact on structural deformability and processability of Li 7 La 3 Zr 2 O 12
Li 7 La 3 Zr 2 O 12 (LLZO) and related ceramic solid electrolytes feature excellent stability and reasonable ionic conductivity, but processing remains challenging.
36 MATERIALS SCIENCE↗
First principles density functional theory study of tritium species adsorption on Ni(111) surface and diffusion in nickel-sublayer for tritium storage
The nickel-plated zircaloy-4 is used as a tritium ( 3 H) getter in the tritium-producing burnable absorber rods (TPBARs) to capture 3 H produced in the 6 Li-riched annular γ-LiAlO 2 pellet under neutron irradiation. The experimental data and our previous theoretical results showed that the 3 H species produced from the γ-LiAlO 2 pellet were mainly 3 H 2 and 3 H 2 O. These 3 H species diffuse from the surface of the LiAlO 2 pellet across vacuum to the nickel-plated zircaloy-4 getter and then further diffuse into the getter to chemically form metal hydrides. While a number of studies show that oxygen binds strongly as compared to 3 H on the nickel (Ni) layer, the detailed mechanism of 3 H species absorption and diffusion across the Ni plate and Ni/Zr interface are still unclear. By employing density functional theory calculations, here we explored the 3 H 2 and 3 H 2 O species adsorption and dissociation on the Ni(111) surface and diffusion into the Ni sublayer. Our results indicated that the 3 H 2 and 3 H 2 O dissociate on the Ni(111) surface. The NiO x and Ni(O 3 H) x could be formed in the Ni layer due to the higher oxygen (O) diffusion energy barrier and formation of Ni vacancy defects. The oxygen was found to be retained in the Ni layer from diffusing across the Ni–Zr interface. This was revealed by comparing the diffusion barriers for 3 H with O. 3 H was found to have nearly three times smaller diffusion barrier than for O, making 3 H comparatively easier to diffuse through the Ni layer. In conclusion, the obtained results provide guidelines for experimental measurements on 3 H retention behavior in TPBARs and may open further avenues to explore the impurity effects on 3 H diffusion and storage at the Ni/zircaloy interfaces.
Tafen, De Nyago [National Energy Technology Lab. (↗
Design principle of disordered rocksalt type overlithiated anode for high energy density batteries
Li 3+ x M 2 O 5 with M being V, Cr, Nb, Mn, and Fe are identified among 23 potential redox centers as promising overlithiated DRX anodes with high energy density, good stability, good electronic conductivity, small volumetric change, and low cost.
He, Yufang↗
Design principles for anode stable solid-state electrolytes
This work presents a comparative study of six types of oxide and halide solid-state electrolytes. It has been demonstrated that the electrochemical stability not only depends on metal species, but alsk the Li content and other factors.
Chemistry↗
Unveiling the photocatalytic potential of two-dimensional ferroelastic LuSX monolayers for efficient water splitting: a first-principles discovery
Two-dimensional ferroelastic materials can be utilized to enhance photocatalytic applications.
Ma, Fengxian [College of Physics, Hebei Key Labora↗
Iron Cluster Encapsulated N-Doped Single-Walled Carbon Nanotubes as ORR Electrocatalyst: A First-Principles Study
The ORR electrocatalytic activities of N-doped single-walled nanotubes infused with Fe7 clusters are assessed with DFT calculations. The incorporation of Fe7 leads to enhanced activity and stability via electron donation. The models presented in this work propose a promising strategy for designing non-precious metal ORR catalysts.
Fu, Yuqing [UC Riverside]↗
Bandgap engineering of SrZrS 3 chalcogenide perovskite via substitutional doping for photovoltaic applications: a first-principles DFT study
Strontium zirconium sulfide (SrZrS 3 ) has garnered significant attention for photovoltaic (PV) applications due to its excellent optoelectronic properties, high chemical and moisture stability, and non-toxicity. However, the bandgaps of both the α- and β-phases lie outside the optimum ranges for both single-junction solar cells (SJSCs) and tandem solar cells (TSCs), thereby limiting their applications in PV technologies. In this study, we employed hybrid density functional theory to engineer the band gaps of α- and β-SrZrS 3 through substitutional doping. We considered three dopants (Hf, Sn, and Ti) at the Zr site of SrZrS 3 with varying doping concentrations and investigated their effects on the structural, electronic, and optical properties of the materials. We found that Sn and Ti doping effectively lowers the band gaps of both α- and β-SrZrS 3 , whereas Hf doping increases them. For x values up to 0.25, the band gaps of the α-SrZr 1−x Sn x S 3 and α-SrZr 1−x Ti x S 3 are within the optimum range for SJSCs, and those of β-SrZr 1−x Sn x S 3 and β-SrZr 1−x Ti x S 3 lie within the optimum range for Si/perovskite as well as perovskite/perovskite TSCs. The three dopants exhibited significant effects on the optical properties of both α- and β-SrZrS 3 , including the absorption coefficient, energy-loss functions, reflectivity, and refractivity spectra. Thermodynamic stability analysis revealed that for both phases, SrZr 1−x Hf x S 3 can be synthesized via exothermic processes, whereas the formation of SrZr 1−x Ti x S 3 and SrZr1−xSn x S 3 is endothermic and hence, not thermodynamically favorable. Further analysis showed that SrZr 1−x Ti x S 3 in both α- and β-phases are stable under thermodynamic equilibrium conditions, whereas SrZr 1−x Sn x S 3 is prone to dissociation into ternary phases (SrZrS 3 and SrSnS 3 ), especially at higher doping concentrations. These results show that Ti doping is effective in tuning the band gaps of α- and β-SrZrS 3 toward the optimal values for PV applications.
14 SOLAR ENERGY↗
Investigating trends in actinide covalency and magnetism with 35/37 Cl SSNMR spectroscopy and first-principles calculations
Solid-state NMR (SSNMR) spectroscopy is a powerful technique for studying actinide chemistry but has been significantly limited due to the complex paramagnetism, and radiological hazards presented by these materials. Lanthanide and actinide salts often feature magnetic ordering and can be paramagnetic, ferromagnetic, or antiferromagnetic depending on temperature and electronic structure. Paramagnetic interactions can manifest in SSNMR both as secular spectral shifts and/or couplings as well as contributions from non-secular relaxation. Both effects can be directly measured with NMR and used to extrapolate rich chemical information such as coordination environments, bonding characteristics, local molecular dynamics, and correlation times. Typically, these studies are carried out on high-γ and highly abundant NMR-active isotopes (e.g., 1 H, 6/7 Li, 19 F, 23 Na, etc.) or on enriched rare isotopes (e.g., 2 H and 17 O), which can be expensive. Herein, we present a facile methodology to measure the 35/37 Cl electric-field gradient (EFG) and paramagnetic shift anisotropy (SA) tensor components using static wideline SSNMR measurements of LaCl 3 , NdCl 3 , UCl 3 , and UCl 4 . The static powder spectra were measured with both 35 Cl and 37 Cl SSNMR to increase the fidelity of the extracted tensor parameters. Variable temperature NMR of a select case confirms the Curie–Weiss paramagnetism. Relaxation measurements of both nuclei further corroborate observations owing to the paramagnetic relaxation enhancement and reveal simultaneous quadrupolar relaxation mechanisms. Density functional theory (DFT) calculations using Hubbard U corrections to the uranium valence orbitals show excellent agreement with experimental EFG tensor parameters and help describe the bonding characteristics in these lanthanide and actinide systems.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
First-principles insights into chromium-induced oxide phases in NiO
The high-temperature oxidation of Ni–Cr alloys leads to complex oxide scales comprising Ni(Cr)O solid solutions, NiCr 2 O 4 spinel, and Cr 2 O 3 corundum within the NiO matrix. Understanding the atomic-scale mechanisms of Cr segregation and precipitate formation is crucial for enhancing oxidation resistance. Here, we employ density functional theory calculations to investigate Cr behavior on NiO(100), (110), and (111) surfaces and in the bulk. Our results reveal that isolated Cr atoms preferentially segregate to the surfaces, stabilizing Ni(Cr)O solid solutions via strong Cr–O bonding, whereas Cr pairs and clusters favor subsurface migration and bulk aggregation, promoting nucleation of NiCr 2 O 4 and Cr 2 O 3 phases. These findings elucidate a size-dependent segregation mechanism linking Cr coordination environments to oxide phase evolution. This atomic-scale insight informs strategies to tailor oxide microstructures and enhance the high-temperature oxidation resistance of Ni–Cr alloys.
Chromium Segregation↗
Insights from designing an artificial cascade catalysis system using principles from substrate channeling in enzymes
Generalizing the key requirements of highly-selective, multi-step chemical conversions involving spatially separated reaction centers remains one of the grand challenges of chemistry. Much work towards this effort has focused on decomposing multi-step conversions into their constituent reactions, whose intermediates are successively upgraded in a chemical cascade via diffusion from center to center. This approach for synthesizing more complex molecules takes its cues from biochemical networks, where near-unit conversion of even complex carbohydrates is achieved by upgrading chemical precursors via enzymatic cascades. In this computational study we examine a simple cascade involving coupled Ag and Cu catalysts that sequentially converts CO2 to CO and then CO2 and CO to reduced products, generically named CO2Product and COProduct. The system architecture is inspired by the phenomenon of biological substrate channeling, and components are examined to evaluate their effects on conversion efficiency in the cascade. Aside from a substrate channel linking two reaction centers, we find efficient cascades must also incorporate directional substrate diffusion, compartmentalization of the reaction centers, and proper timing of substrate arrival at the active center. We make explicit linkages between these requirements and chemical conversion in known biological systems, revealing additional control elements that could be incorporated.
CO 2 reduction↗
Design principles of spacer cations for suppressing phase segregation in 2D halide perovskites
Suppression of photoinduced halide segregation in mixed halide perovskites remains a significant challenge for their application as wide bandgap semiconductors in solar cells. In addition to stability issues, halide segregation leads to a loss in power conversion efficiency in solar cells and a shift in emission wavelength in light-emitting devices. However, employing low-dimensional halide perovskites, such as two-dimensional (2D) or quasi-2D structures, offers a strategy to mitigate this segregation. Here, we have systematically studied how the molecular structure and binding configuration of spacer cations, ranging from linear alkyl chains to aromatic structures, affect photoinduced halide segregation across both Ruddlesden–Popper (RP) and Dion–Jacobson (DJ) frameworks in 2D mixed halide perovskites (Br : I = 50 : 50). Aromatic spacer cations within the DJ perovskite configuration were found to suppress segregation most effectively. For example, the halide segregation rate in a 2D mixed halide perovskite film with the DJ phase using the aromatic spacer cation 1,4-phenylenedimethanammonium (PDMA) was 9.3 × 10 −4 s −1 —an order of magnitude lower than that observed with linear 2D RP perovskites employing butylammonium (BA) as the spacer cation (6.1 × 10 −3 s −1 ). Spectroscopic studies detailing the influence of spacer cation selection in mixed halide perovskites for suppressing phase segregation are discussed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗