Recent lbnl_es_es items

Native Chemical Ligation of Peptoid Oligomers

Wed, 27 May 2026 00:00:00 +0000

Bioorganic chemists are inspired by natural biopolymers to design peptidomimetic oligomers that can exhibit sequence-structure-function relationships. Biomimetic polymers can be synthesized to incorporate a specific sequence of nonbiological monomer units using a variety of iterative solution-phase or solid-phase reaction schemes. These protocols generally provide access to a vast diversity of oligomeric compounds but are limited with respect to their ability to attain protein-like chain lengths. This constraint can preclude access to sequence-defined synthetic macromolecules with sufficient sizes required to exhibit tertiary structure and other protein-mimetic attributes. In contrast, peptide chemists have overcome this limitation by developing convergent synthetic methods, such as native chemical ligation, to join individual, smaller peptide chains together to make larger peptides or full proteins. A similar convergent approach is needed to establish efficient synthetic routes...

Atomic-Scale Imaging Reveals Polar‑π Interactions in Two-Dimensional Molecular Superlattices

Wed, 25 Mar 2026 00:00:00 +0000

Controlling coassembly of synthetic oligomers into binary superlattices at the atomic level is challenging. We report a strategy for programming polar-π interactions in oligomeric peptoids, a class of sequence-defined peptidomimetics, facilitating the formation of homogeneous two-dimensional (2D) superlattices. N-2-phenylethyl and N-(2-perfluorophenyl)ethyl side chains, similar in size, but with contrasting electrostatic characteristics, were introduced at defined sequence positions to generate favorable dipolar aromatic interactions. The resulting nanosheets exhibit different crystal motifs depending on the side chain interactions: systems containing only one type of aromatic side chain form a parallel V-shaped motif driven by π-π interactions, whereas a combination of both types of aromatic side chains, either within one backbone or through the coassembly of two distinct peptoids, adopt an antiparallel V-shaped superlattice with higher thermal stability, driven...

Curvilinear Magnonic Crystal Based on 3D Hierarchical Nanotemplates

Tue, 17 Feb 2026 00:00:00 +0000

Curvilinear magnetic nanostructures enable control of magnetization dynamics through geometry-induced anisotropy and chiral interactions, as well as magnetic field modulation. In this work, we report a curvilinear magnonic crystal based on large-area square arrays of truncated nanospikes fabricated by conformal coating of 3D hierarchical templates with permalloy thin films. Brillouin light scattering spectroscopy reveals an anisotropic band structure with multiple dispersive and folded Bloch-type dispersive spin-wave modes as well as nondispersive modes exhibiting direction-dependent frequency shifts and intensity asymmetries along lattice principal axes. Finite element micromagnetic simulations indicate that curvature-induced variations of the demagnetizing field govern the magnonic response, enabling the identification of modes propagating in nanochannels and others localized on nanospike apexes or along the ridges connecting adjacent nanospikes. The combination of geometric...

Bioactive peptoids against vector-borne parasitic diseases

Tue, 16 Dec 2025 00:00:00 +0000

Protozoan parasites represent a severe threat to global human health as they are responsible for infection in Malaria, and a range of Neglected Tropical Diseases (NTDs) including Chagas disease, leishmaniasis and African sleeping sickness. Often treatments for protozan parasites are limited in their efficacy and drug resistance is an emerging problem. The current efforts to develop new treatments for the aforementioned diseases have been met with limited success and as such novel compound classes for development are being actively sought. Peptoids are peptidomimetics that have showed promise as antimicrobial agents but their application in the field of vector-borne parasitic diseases is highly underdeveloped. Herein, a library of over 50 peptoids containing a wide variety of chemical functionalities has been prepared and biologically evaluated against a range of protozoan parasitic targets. Selected members of the peptoid library were found to have potent anti-parasitic activity...

Curvature Induced Modifications of Chirality and Magnetic Configuration in Perpendicular Films

Mon, 8 Sep 2025 00:00:00 +0000

Designing curvature in three-dimensional (3D) magnetic nanostructures enables controlled manipulation of local energy landscapes, allowing for the modification of noncollinear spin textures relevant for next-generation spintronic devices. In this study, we experimentally investigate 3D magnetization textures in a Co/Pd multilayer film, exhibiting strong perpendicular magnetic anisotropy (PMA), deposited onto curved Cu nanowire meshes with diameters as small as 50 nm and lengths of several microns. Utilizing magnetic soft X-ray nanotomography, we achieve reconstructions of 3D magnetic domain patterns at approximately 30 nm spatial resolution. This approach provides detailed information on both the orientation and magnitude of magnetization within the film. Our results reveal that interfacial anisotropy in the Co/Pd multilayers drives the magnetization toward the local surface normal. In contrast to typical labyrinth domains observed in planar films, the presence of curved nanowires...

Three-Dimensional Crystals Assembled by Linear Oligopeptoids

Thu, 28 Aug 2025 00:00:00 +0000

The rational construction of three-dimensional (3D) crystalline lattices from synthetic short-chain polymers remains a significant challenge due to the lack of inherent driving forces to enable crystal growth in all three dimensions. Here, we report the design of 3D peptoid crystals from linear peptoid hexamers, derived from amphiphilic diblock sequences that typically form crystalline two-dimensional (2D) nanosheets. By removing the amorphous domains and tuning the chain termini, crystalline lamellae up to 500 nm thick were achieved, far exceeding the thickness of typical nanosheets (on the order of a few nanometers). These 3D crystals form via the stacking of unit cells with lattice parameters similar to those in 2D nanosheets, where terminal groups, particularly compact C-terminal moieties, facilitate vertical growth and enhance crystallinity. This study highlights the importance of atomic precision in terminus chemistry for achieving long-range ordering and isotropic crystal...

On ultrafast x-ray scattering methods for magnetism

Tue, 22 Jul 2025 00:00:00 +0000

With the introduction of x-ray free electron laser sources around the world, new scientific approaches for visualizing matter at fundamental length and time-scales have become possible. As it relates to magnetism and ‘magnetic-type’ systems, advanced scattering methods are being developed for studying ultrafast magnetic responses on the time-scales at which they occur. We describe three capabilities which have the potential to seed new directions in this area and present original results from each: pump-probe x-ray scattering with low energy excitation, x-ray photon fluctuation spectroscopy, and ultrafast diffuse x-ray scattering. By combining these experimental techniques with advanced modeling together with machine learning, we describe how the combination of these domains allows for a new understanding in the field of magnetism. Finally, we give an outlook for future areas of investigation and the newly developed instruments which will take us there.

Thermodynamic phase transitions of nematic order in magnetic helices

Mon, 21 Jul 2025 00:00:00 +0000

A nematic phase lacks translation order but has orientational order. Nematic phases have been discovered in a variety of systems, including liquid crystals, correlated materials, and superconductors. Here, we report on a magnetic nematic phase, where the basis components are composed of magnetic helices. We directly probed the order parameters associated with the magnetic helices using resonant soft x-ray scattering and find two distinct nematic phases with complex spatiotemporal signatures. Using x-ray correlation spectroscopy, we find that near the phase boundary between the two nematic phases, fluctuations coexist on multiple disparate timescales. Our micromagnetic simulations and density functional theory calculations show that the fluctuations occur concomitantly with a reorientation of the magnetic helices, indicating spontaneous symmetry breaking and the emergence of additional degrees of freedom. Our results provide a framework for characterizing exotic phases that can...

Crystalline Peptoid Nanofibers with a Single-Unit Cell Cross Section

Mon, 21 Jul 2025 00:00:00 +0000

Ultranarrow crystalline one-dimensional nanostructures formed from soft materials facilitate precise structural control in nanomaterial design, which is essential for biomedicine and nanotechnology applications. Systematic control of their hierarchical structure is challenging due to the complexities of simultaneously manipulating multiple noncovalent interactions at such small scales. We employed a polypeptoid crystal motif as a supramolecular synthon to engineer ultranarrow crystalline nanofibers constrained to a single lattice axis by incorporating a single ionizable side chain into the hydrophobic core of a nanosheet-forming peptoid. Cryogenic transmission electron microscopy of the nanofibers revealed detailed molecular arrangements of a unit-cell cross-section and the presence of distinct pH-dependent lattice isoforms that resulted in morphological transformations. Molecular dynamics simulations demonstrated that the ionizable side chain plays a critical role in changing...

Cooperative Role of Mixed Solvent in the Evaporation-Induced Self-Assembly of Polypeptoid Nanocrystals

Wed, 25 Jun 2025 00:00:00 +0000

Peptoids, or polypeptoids, are biomimetic polymers that can self-assemble into nanocrystals for biomedical and biotechnological applications. Polypeptoid nanocrystals can be prepared by evaporation-induced self-assembly, but the roles of solvent components for this process have long been overlooked at the molecular level, leaving a tunable parameter for improving self-assembly protocols. This work utilized molecular dynamics simulations to study the effects of water and the commonly used tetrahydrofuran (THF) on the assembly of nanosheets from molecules of acetylated diblock polypeptoid, poly-(N-decylglycine)-b-poly-(N-2-(2-(2-methoxyethoxy)-ethoxy) ethylglycine), abbreviated as Ac-Ndc₁₀-Nte₁₀. To probe the stages of self-assembly, isolated molecules and preassembled nanofibers/nanosheets were simulated in pure THF, water, and their mixtures, respectively. The assembly energies show that the THF/water mixture has a greater tendency to...

Multimodal correlative study of Hall transport and magnetic phases in Fe/Gd multilayer systems

Tue, 17 Jun 2025 00:00:00 +0000

The Fe/Gd multilayer system hosts a number of magnetic phases, such as stripe, mixed stripe and skyrmion, skyrmion lattice, and isolated skyrmions for a wide range of temperature and magnetic field. We report different Hall transport signals in a Fe/Gd system through multimodal correlative resonant soft x-ray scattering (RSXS), Hall effect, magneto-optic Kerr effect, and transmission x-ray microscopy measurements. The simultaneous nature of the RSXS and Hall transport measurements allowed us to accurately connect various features in the transport data with the specific magnetic phases. We found that the topological Hall effect (THE) shows peaks with opposite signs, which we attribute to two different mechanisms. Our multimodal correlative study indicates that the sign reversal in THE occurs when the system transforms to and from a skyrmion lattice and low density isolated skyrmion phases. We propose that the skyrmion lattice contributes to the THE through a Berry phase induced...

Science and technology of 3D magnetic nanostructures

Thu, 22 May 2025 00:00:00 +0000

Science and technology of 3D magnetic nanostructures

2025 roadmap on 3D nanomagnetism

Thu, 22 May 2025 00:00:00 +0000

The transition from planar to three-dimensional (3D) magnetic nanostructures represents a significant advancement in both fundamental research and practical applications, offering vast potential for next-generation technologies like ultrahigh-density storage, memory, logic, and neuromorphic computing. Despite being a relatively new field, the emergence of 3D nanomagnetism presents numerous opportunities for innovation, prompting the creation of a comprehensive roadmap by leading international researchers. This roadmap aims to facilitate collaboration and interdisciplinary dialogue to address challenges in materials science, physics, engineering, and computing. The roadmap comprises eighteen sections, roughly divided into three blocks. The first block explores the fundamentals of 3D nanomagnetism, focusing on recent trends in fabrication techniques and imaging methods crucial for understanding complex spin textures, curved surfaces, and small-scale interactions. Techniques such...

The road to 3-dim nanomagnetism: Steep curves and architectured crosswalks

Thu, 22 May 2025 00:00:00 +0000

Nanoscience and its associated nanotechnology started several decades ago to discover and harness properties and behavior of materials that occur due to lowering their dimensionality. Nanomagnetism, which is the branch of nanoscience to investigate magnetic properties of materials down to fundamental length and time scales led to the discovery of a plethora of novel nanoscale spin phenomena and has further laid the groundwork for spintronics, which has become the primary enabler for the most advanced information technologies, including magnetic storage and sensor devices. So far, low-dimensional magnetic systems have been confined to zero (quantum dots), one (nanowires), and two (thin films) dimensions, however, recently research with artificially designed three-dimensional magnetic systems is emerging as it opens the path to novel scientifically exciting phenomena with enormous technological potential to advance spintronics further towards ultrasmall, ultrafast and most importantly...

Screening and Development of Sacrificial Cathode Additives for Lithium‐Ion Batteries

Tue, 22 Apr 2025 00:00:00 +0000

Abstract This work presents a computational screening approach to identify Li‐rich transition‐metal oxide sacrificial cathode additives and provides experimental validation of antifluorite‐structured Li 6 MnO 4 as a potential candidate. Initial attempts to synthesize this compound result in low purity (≤40% by weight) owing to close thermodynamic competition with Li 2 O and MnO at low temperature. However, it is shown that a much higher purity of 85% by weight can be achieved by combining Li excess with rapid cooling from high temperature, which effectively stabilizes the Li 6 MnO 4 phase. The synthesized product delivers a high irreversible Li release capacity that exceeds 700 mAh g −1 by utilizing combined Mn oxidation (Mn 2+/3+ and Mn 3+/4+ ) and O oxidation. These results demonstrate that Li 6 MnO 4 may therefore be useful as a potential sacrificial cathode additive in Li‐ion batteries and motivate further investigation of other structurally‐related compounds. While attempts...

Key Intermediate Nanostructures in the Self-Assembly of Amphiphilic Polypeptoids Revealed by Cryo-TEM

Tue, 22 Apr 2025 00:00:00 +0000

Amphiphilic copolypeptoids are known to form a variety of nanostructures (fibers, tubes, sheets, etc.), but the assembly mechanisms and key intermediates remain underexplored. This study investigates the intermediate structures formed during the early stages of self-assembly in diblock copolypeptoids using cryo-transmission electron microscopy (cryo-TEM). We focused on two diblock copolypeptoids, one with a free N-terminus and the other with a capped N-terminus, which ultimately form less-ordered nanofibers and well-ordered nanosheets, respectively. Through cryo-TEM imaging of vitrified solutions at various time points during the self-assembly process, the study identified micelles and vesicles as key intermediate structures. Notably, the formation of vesicles as intermediates is unusual in crystallization-driven self-assembly and suggests a unique pathway in polypeptoid self-assembly. The study provides direct imaging evidence of key intermediates in polypeptoid self-assembly,...

Thermodynamic Driving Forces for the Self-Assembly of Diblock Polypeptoids

Tue, 25 Mar 2025 00:00:00 +0000

Peptoid polymers with sequence-defined side chains are observed to self-assemble into a variety of structures spanning nanometer and micron scales. We explored a diblock copolypeptoid, poly(N-decylglycine)₁₀-block-poly(N-2-(2-(2-methoxyethoxy)ethoxy)-ethylglycine)₁₀ (abbreviated as Ndc₁₀-Nte₁₀), which forms crystalline nanofibers and nanosheets as evidenced by recent cryo-transmission electron microscopy, atomic force microscopy, X-ray diffraction, and calorimetry. Using all-atom molecular dynamics simulations, we examined the thermodynamic forces driving such self-assembly and how nanoscale morphology is tailored through modification of the N-terminus or via the addition of small molecules (urea). We have found that the hydrophobic Ndc domain alignment is key to the formation of molecular stacks whose growth is limited by electrostatic repulsion between protonated N-termini. These stacks are the building blocks...

Systematic softening in universal machine learning interatomic potentials

Thu, 6 Mar 2025 00:00:00 +0000

Machine learning interatomic potentials (MLIPs) have introduced a new paradigm for atomic simulations. Recent advancements have led to universal MLIPs (uMLIPs) that are pre-trained on diverse datasets, providing opportunities for universal force fields and foundational machine learning models. However, their performance in extrapolating to out-of-distribution complex atomic environments remains unclear. In this study, we highlight a consistent potential energy surface (PES) softening effect in three uMLIPs: M3GNet, CHGNet, and MACE-MP-0, which is characterized by energy and force underprediction in atomic-modeling benchmarks including surfaces, defects, solid-solution energetics, ion migration barriers, phonon vibration modes, and general high-energy states. The PES softening behavior originates primarily from the systematically underpredicted PES curvature, which derives from the biased sampling of near-equilibrium atomic arrangements in uMLIP pre-training datasets. Our findings...

Magnetic Solitons in Hierarchical 3D Magnetic Nanoarchitectures of Nanoflower Shape

Wed, 8 Jan 2025 00:00:00 +0000

Curvilinear magnetism emerged as a new route to tailor properties of magnetic solitons by the choice of geometry and topology of a magnetic architecture. Here, we develop an anodized aluminum oxide template-based approach to realize hierarchical 3D magnetic nanoarchitectures of nanoflower shape. The technique provides defect-free regular arrays of magnetic nanoflowers of tunable shape with a period of 400 nm over cm² areas. We combined advanced magnetic imaging methods with micromagnetic simulations to study complex magnetic states in nanoflowers originating due to magnetostatics-driven symmetry break in curvilinear nanomembranes. An interaction between surface and volume magnetostatic charges in 3D curved nanoflowers leads to the stabilization of asymmetric and shifted vortices as well as states with two Bloch lines. Ordered large area arrays of complex-shaped magnetic nanoarchitectures developed in this work are relevant for prospective research on 3D magnonics and...

Concurrent measurement of strain and chemical reaction rates in a calcite grain pack undergoing pressure solution: Evidence for surface-reaction controlled dissolution

Fri, 20 Dec 2024 00:00:00 +0000

Pressure solution is inferred to be a significant contributor to sediment compaction and lithification, especially in carbonate sediments. For a sediment deforming primarily by pressure solution, the compaction rate should be directly related to the rate of calcite dissolution, transport along grain contacts, and calcite reprecipitation. Previous experimental work has shown that there is evidence that deformation in wet calcite grain packs is consistent with control by pressure solution, but considerable ambiguity remains regarding the rate limiting mechanism. We present the results of laboratory compaction experiments designed to directly measure calcite dissolution and precipitation rates (recrystallization rates) concurrently with strain rate to test whether measured rates are consistent with predicted rates both in absolute magnitude and time evolution. Recrystallization rates are measured using trace element chemistry (Sr/Ca, Mg/Ca) and isotopes (87Sr/86Sr) of fluids flowing...

2024 roadmap on magnetic microscopy techniques and their applications in materials science

Mon, 9 Dec 2024 00:00:00 +0000

Considering the growing interest in magnetic materials for unconventional computing, data storage, and sensor applications, there is active research not only on material synthesis but also characterisation of their properties. In addition to structural and integral magnetic characterisations, imaging of magnetisation patterns, current distributions and magnetic fields at nano- and microscale is of major importance to understand the material responses and qualify them for specific applications. In this roadmap, we aim to cover a broad portfolio of techniques to perform nano- and microscale magnetic imaging using superconducting quantum interference devices, spin centre and Hall effect magnetometries, scanning probe microscopies, x-ray- and electron-based methods as well as magnetooptics and nanoscale magnetic resonance imaging. The roadmap is aimed as a single access point of information for experts in the field as well as the young generation of students outlining prospects of...

Modeling Intercalation Chemistry with Multiredox Reactions by Sparse Lattice Models in Disordered Rocksalt Cathodes

Mon, 9 Dec 2024 00:00:00 +0000

Modern battery materials can contain many elements with substantial site disorder, and their configurational state has been shown to be critical for their performance. The intercalation voltage profile is a critical parameter to evaluate the performance of energy storage. The application of commonly used cluster expansion techniques to model the intercalation thermodynamics of such systems ab initio is challenged by the combinatorial increase in configurational degrees of freedom as the number of species grows. Such challenges necessitate the efficient generation of lattice models without overfitting and proper sampling of the configurational space under the requirement of charge balance in ionic systems. In this work, we introduce a combined approach that addresses these challenges by (1) constructing a robust cluster expansion Hamiltonian using the sparse regression technique, including ℓ0ℓ2-norm regularization and structural hierarchy; and (2) implementing semigrand-canonical...

From Design to Device: Challenges and Opportunities in Computational Discovery of p-Type Transparent Conductors

Mon, 9 Dec 2024 00:00:00 +0000

A high-performance -type transparent conductor (TC) does not yet exist but could lead to advances in a wide range of optoelectronic applications and enable new architectures for, e.g., next-generation photovoltaic (PV) devices. High-throughput computational material screenings have been a promising approach to filter databases and identify new -type TC candidates and some of these predictions have been experimentally validated. However, most of these predicted candidates do not have experimentally achieved properties on par with -type TCs used in solar cells and therefore have not yet been used in commercial devices. Thus, there is still a significant divide between transforming predictions into results that are actually achievable in the laboratory and an even greater lag in scaling predicted materials into functional devices. In this perspective, we outline some of the major disconnects in this materials discovery process—from scaling computational predictions into synthesizable...

Quantifying the topology of magnetic skyrmions in three dimensions

Mon, 11 Nov 2024 00:00:00 +0000

Magnetic skyrmions have so far been treated as two-dimensional spin structures characterized by a topological winding number. However, in real systems with the finite thickness of the device material being larger than the magnetic exchange length, the skyrmion spin texture extends into the third dimension and cannot be assumed as homogeneous. Using soft x-ray laminography, we reconstruct with about 20-nanometer spatial (voxel) size the full three-dimensional spin texture of a skyrmion in an 800-nanometer-diameter and 95-nanometer-thin disk patterned into a 30× [iridium/cobalt/platinum] multilayered film. A quantitative analysis finds that the evolution of the radial profile of the topological skyrmion number is nonuniform across the thickness of the disk. Estimates of the micromagnetic energy densities suggest that the changes in topological profile are related to nonuniform competing energetic interactions. Our results provide a foundation for nanoscale metrology for spintronics...

Atomic-Scale Imaging of Condensed Counterions

Tue, 5 Nov 2024 00:00:00 +0000

The functioning of a wide variety of charged macromolecules, from DNA to fuel cell membranes, is dependent on how the counterions surrounding them are arranged. In order to decrease Coulombic repulsion, some of the fixed charges on these molecules are neutralized by a fraction of the counterionsthis phenomenon is called counterion condensation. The nature of counterion condensation can be only be inferred indirectly from traditional experiments such as X-ray scattering and modern experiments such as single molecule electrometry. The prevalent conclusion in the literature, based on both theory and experiment, is that the distribution of counterions is peaked right next to the macromolecule, i.e., condensation results in the formation of contact ion pairs. In this study, cryogenic electron microscopy (cryo-EM) was used to study the arrangement of condensed halide counterions near a positively charged polypeptoid nanofiber. The locations of both condensed and fixed charges were...

Evaluating Cryo‐TEM Reconstruction Accuracy of Self‐Assembled Polymer Nanostructures

Tue, 24 Sep 2024 00:00:00 +0000

Cryogenic transmission electron microscopy (cryo-TEM) combined with single particle analysis (SPA) is an emerging imaging approach for soft materials. However, the accuracy of SPA-reconstructed nanostructures, particularly those formed by synthetic polymers, remains uncertain due to potential packing heterogeneity of the nanostructures. In this study, the combination of molecular dynamics (MD) simulations and image simulations is utilized to validate the accuracy of cryo-TEM 3D reconstructions of self-assembled polypeptoid fibril nanostructures. Using CryoSPARC software, image simulations, 2D classifications, ab initio reconstructions, and homogenous refinements are performed. By comparing the results with atomic models, the recovery of molecular details is assessed, heterogeneous structures are identified, and the influence of extraction location on the reconstructions is evaluated. These findings confirm the fidelity of single particle analysis in accurately resolving complex...

Discovery of a Peptoid-Based Nanoparticle Platform for Therapeutic mRNA Delivery via Diverse Library Clustering and Structural Parametrization

Fri, 30 Aug 2024 00:00:00 +0000

Nanoparticle-mediated mRNA delivery has emerged as a promising therapeutic modality, but its growth is still limited by the discovery and optimization of effective and well-tolerated delivery strategies. Lipid nanoparticles containing charged or ionizable lipids are an emerging standard for in vivo mRNA delivery, so creating facile, tunable strategies to synthesize these key lipid-like molecules is essential to advance the field. Here, we generate a library of N-substituted glycine oligomers, peptoids, and undertake a multistage down-selection process to identify lead candidate peptoids as the ionizable component in our Nutshell nanoparticle platform. First, we identify a promising peptoid structural motif by clustering a library of >200 molecules based on predicted physical properties and evaluate members of each cluster for reporter gene expression in vivo. Then, the lead peptoid motif is optimized using design of experiments methodology to explore variations on the charged...

Atomic-scale cryogenic electron microscopy imaging of self-assembled peptoid nanostructures

Thu, 22 Aug 2024 00:00:00 +0000

Amphiphilic polypeptoids with defined sequences, versatile in forming various nanostructures, are ideal for mimicking biomacromolecular structures. The predictive design of nanostructures depends on our understanding of the relationship between molecular structure and the locations of atoms in the nanostructure. Factors of importance include chain conformation, crystal motifs, and the arrangement of the molecules within the nanostructure. This review introduces the cryogenic transmission electron microscopy (cryo-TEM) method, sorting and averaging unit cells in nanosheets for resolution enhancement and identifying structural heterogeneity. The resulting atomic-scale images reveal the presence of two types of crystal motifs. The impact of processing conditions, capping group chemistry, and side chain chemistry on structural heterogeneity and crystal motifs can be quantified. The 3D reconstruction of nanosheets, wherein atomic-scale corrugations were revealed, is introduced in this...

Imaging the magnetic nanowire cross section and magnetic ordering within a suspended 3D artificial spin-ice

Wed, 21 Aug 2024 00:00:00 +0000

Artificial spin-ice systems are patterned arrays of magnetic nanoislands arranged into frustrated geometries and provide insight into the physics of ordering and emergence. The majority of these systems have been realized in two-dimensions, mainly due to the ease of fabrication, but with recent developments in advanced nanolithography, three-dimensional artificial spin ice (ASI) structures have become possible, providing a new paradigm in their study. Such artificially engineered 3D systems provide new opportunities in realizing tunable ground states, new domain wall topologies, monopole propagation, and advanced device concepts, such as magnetic racetrack memory. Direct imaging of 3DASI structures with magnetic force microscopy has thus far been key to probing the physics of these systems but is limited in both the depth of measurement and resolution, ultimately restricting measurement to the uppermost layers of the system. In this work, a method is developed to fabricate 3DASI...

Relationship between molecular structure and corrugations in self-assembled polypeptoid nanosheets revealed by cryogenic electron microscopy

Tue, 20 Aug 2024 00:00:00 +0000

Designing conformationally dynamic molecules that self-assemble into predictable nanostructures remains an important unmet challenge. This paper describes how atomic-scale cryogenic transmission electron microscopy (cryo-TEM) can be used to explore the relationship between molecular structure and self-assembly of block copolymers. We examined sheetlike micelles formed in water using a series of diblock copolypeptoids with the same hydrophilic block and three distinct crystalline hydrophobic blocks. Our cryo-TEM images revealed all the structures share nansoscale features, but differ in their intermolecular packing geometries. Different molecular arrangements, parallel and antiparallel V-shaped crystal motifs, were revealed by two-dimensional atomic-scale through-plane images. However, images from tilted samples revealed an unexpected feature when the hydrophobic polypeptoid block comprised phenyl rings with substituted bromine atoms at the para position. The nanosheets contained...

Solubilities of Ethylene and Carbon Dioxide Gases in Lithium-Ion Battery Electrolyte

Wed, 10 Jul 2024 00:00:00 +0000

During Li-ion battery operation, (electro)chemical side reactions occur within the cell that can promote or degrade performance. These complex reactions produce byproducts in the solid, liquid, and gas phases. Studying byproducts in these three phases can help optimize battery lifetimes. To relate the measured gas-phase byproducts to species dissolved in the liquid-phase, equilibrium proprieties such as the Henry's law constants are required. The present work implements a pressure decay experiment to determine the thermodynamic equilibrium concentrations between the gas and liquid phases for ethylene (C₂H₄) and carbon dioxide (CO₂), which are two gases commonly produced in Li-ion batteries, with an electrolyte of 1.2 M LiPF₆ in 3:7 wt/wt ethylene carbonate/ethyl methyl carbonate and 3 wt % fluoroethylene carbonate (15:25:57:3 wt % total composition). The experimentally measured pressure decay curve is fit to an analytical dissolution...

α-Phenylthioaldehydes for the effective generation of acyl azolium and azolium enolate intermediates

Sat, 6 Jul 2024 00:00:00 +0000

α-Phenylthioaldehydes are readily prepared using a simple multi-step procedure and herein are introduced as a new precursor for the NHC-catalysed generation of acyl azolium and azolium enolate intermediates that are of widespread synthetic interest and utility. Treatment of α-phenylthioaldehydes with an NHC precatalyst and base produces an efficient redox rearrangement via a Breslow intermediate, elimination of thiophenolate, and subsequent rebound addition to the generated acyl azolium to give the corresponding thiol ester. In the presence of an external alcohol, competition between redox rearrangement and redox esterification can be controlled through judicious choice of the N-aryl substituent within the NHC precatalyst and the base used in the reaction. With NEt₃ as base, NHCs bearing electron-withdrawing (N-C₆F₅ or N-C₆H₂Cl₃) substituents favour redox rearrangement, while triazolium...

Designed Metal-Containing Peptoid Membranes as Enzyme Mimetics for Catalytic Organophosphate Degradation

Mon, 1 Jul 2024 00:00:00 +0000

The detoxification of lethal organophosphate (OP) residues in the environment is crucial to prevent human exposure and protect modern society. Despite serving as excellent catalysts for OP degradation, natural enzymes require costly preparation and readily deactivate upon exposure to environmental conditions. Herein, we designed and prepared a series of phosphotriesterase mimics based on stable, self-assembled peptoid membranes to overcome these limitations of the enzymes and effectively catalyze the hydrolysis of dimethyl p-nitrophenyl phosphate (DMNP)─a nerve agent simulant. By covalently attaching metal-binding ligands to peptoid N-termini, we attained enzyme mimetics in the form of surface-functionalized crystalline nanomembranes. These nanomembranes display a precisely controlled arrangement of coordinated metal ions, which resemble the active sites found in phosphotriesterases to promote DMNP hydrolysis. Moreover, using these highly programmable peptoid nanomembranes...

The Limited Incorporation and Role of Fluorine in Mn-rich Disordered Rocksalt Cathodes

Sat, 29 Jun 2024 00:00:00 +0000

Disordered rocksalt oxide (DRX) cathodes are promising candidates for next-generation Co- and Ni-free Li-ion batteries. While fluorine substitution for oxygen has been explored as an avenue to enhance their performance, the amount of fluorine incorporated into the DRX structure is particularly challenging to quantify and impedes our ability to relate fluorination to electrochemical performance. Herein, an experimental-computational method combining ⁷Li and ¹⁹F solid-state nuclear magnetic resonance, and ab initio cluster expansion Monte Carlo simulations, is developed to determine the composition of DRX oxyfluorides. Using this method, the synthesis of Mn- and Ti-containing DRX via standard high temperature sintering and microwave heating is optimized. Further, the upper fluorination limit attainable using each of these two synthesis routes is established for various Mn-rich DRX compounds. A comparison of their electrochemical performance reveals that...

Exploiting Saturation Regimes and Surface Effects to Tune Composite Design: Single Platelet Nanocomposites of Peptoid Nanosheets and CaCO3

Tue, 18 Jun 2024 00:00:00 +0000

Mineral-polymer composites found in nature exhibit exceptional structural properties essential to their function, and transferring these attributes to the synthetic design of functional materials holds promise across various sectors. Biomimetic fabrication of nanocomposites introduces new pathways for advanced material design and explores biomineralization strategies. This study presents a novel approach for producing single platelet nanocomposites composed of CaCO₃ and biomimetic peptoid (N-substituted glycines) polymers, akin to the bricks found in the brick-and-mortar structure of nacre, the inner layer of certain mollusc shells. The significant aspect of the proposed strategy is the use of organic peptoid nanosheets as the scaffolds for brick formation, along with their controlled mineralization in solution. Here, we employ the B28 peptoid nanosheet as a scaffold, which readily forms free-floating zwitterionic bilayers in aqueous solution. The peptoid nanosheets...

The effect of ancillary ligands on hydrocarbon C–H bond functionalization by uranyl photocatalysts

Mon, 27 May 2024 00:00:00 +0000

The aqueous uranyl dication has long been known to facilitate the UV light-induced decomposition of aqueous VOCs (volatile organic compounds), via the long-lived highly efficient, uranyl excited state. The lower-energy visible light excited uranyl ion is also able to cleave unactivated hydrocarbon C-H bonds, yet the development of this reactivity into controlled and catalytic C-H bond functionalization is still in its infancy, with almost all studies still focused on uranyl nitrate as the precatalyst. Here, hydrocarbon-soluble uranyl nitrate and chloride complexes supported by substituted phenanthroline (Ph₂phen) ligands are compared to each other, and to the parent salts, as photocatalysts for the functionalization of cyclooctane by H atom abstraction. Analysis of the absorption and emission spectra, and emission lifetimes of Ph₂phen-coordinated uranyl complexes demonstrate the utility of the ligand in light absorption in the photocatalysis, which...

A new era is emerging at scientific user facilities

Wed, 24 Apr 2024 00:00:00 +0000

Global scientific exchange has been profoundly perturbed by the COVID-19 pandemic, altering user travel behaviours and accelerating the use of remote access. Combined with the advent of artificial intelligence (AI), these trends together can change how large-scale user scientific facilities are used by the community and managed by operators.

Oxygen Transport through Amorphous Cathode Coatings in Solid-State Batteries

Sat, 20 Apr 2024 00:00:00 +0000

All solid-state batteries (SSBs) are considered the most promising path to enabling higher energy-density portable energy, while concurrently improving safety as compared to current liquid electrolyte solutions. However, the desire for high energy necessitates the choice of high-voltage cathodes, such as nickel-rich layered oxides, where degradation phenomena related to oxygen loss and structural densification at the cathode surface are known to significantly compromise the cycle and thermal stability. In this work, we show, for the first time, that even in an SSB, and when protected by an intact amorphous coating, the LiNi_0.5Mn_0.3Co_0.2O₂ (NMC⁵³²) surface transforms from a layered structure into a rocksalt-like structure after electrochemical cycling. The transformation of the surface structure of the Li₃B₁₁O₁₈ (LBO)-coated NMC⁵³² cathode in a thiophosphate-based solid-state cell...

Switching the spin cycloid in BiFeO3 with an electric field

Sat, 20 Apr 2024 00:00:00 +0000

Bismuth ferrite (BiFeO3) is a multiferroic material that exhibits both ferroelectricity and canted antiferromagnetism at room temperature, making it a unique candidate in the development of electric-field controllable magnetic devices. The magnetic moments in BiFeO3 are arranged into a spin cycloid, resulting in unique magnetic properties which are tied to the ferroelectric order. Previous understanding of this coupling has relied on average, mesoscale measurements. Using nitrogen vacancy-based diamond magnetometry, we observe the magnetic spin cycloid structure of BiFeO3 in real space. This structure is magnetoelectrically coupled through symmetry to the ferroelectric polarization and this relationship is maintained through electric field switching. Through a combination of in-plane and out-of-plane electrical switching, coupled with ab initio studies, we have discovered that the epitaxy from the substrate imposes a magnetoelastic anisotropy on the spin cycloid, which establishes...

Periodicity staircase in a centrosymmetric Fe/Gd magnetic thin film system

Wed, 17 Apr 2024 00:00:00 +0000

The presence of multiple competing periodicities may result in a system to go through states with modulated periodicities, an example of which is the self-similar staircase-like structure called the Devil’s Staircase. Herein we report on a novel staircase structure of domain periodicity in an amorphous and centrosymmetric Fe/Gd magnetic thin film system wherein the reciprocal space wavevector Q due to the ordered stripe domains does not evolve continuously, rather exhibits a staircase structure. Resonant X-ray scattering experiments show jumps in the periodicity of the stripe domains as a function of an external magnetic field. When resolved in components, the length-scale step change along Qx was found to be an integral multiple of a minimum step height of 7 nm, which resembles closely to the exchange length of the system. Modeling the magnetic texture in the Fe/Gd system as an achiral spin arrangement, we have been able to reproduce the steps in the magnetization using a Landau-Lifshitz...

High-throughput determination of Hubbard U and Hund J values for transition metal oxides via the linear response formalism

Fri, 12 Apr 2024 00:00:00 +0000

DFT+U provides a convenient, cost-effective correction for the self-interaction error (SIE) that arises when describing correlated electronic states using conventional approximate density functional theory (DFT). The success of a DFT+U(+J) calculation hinges on the accurate determination of its Hubbard U and Hund J parameters, and the linear response (LR) methodology has proven to be computationally effective and accurate for calculating these parameters. This study provides a high-throughput computational analysis of the U and J values for transition metal d-electron states in a representative set of over 1000 magnetic transition metal oxides (TMOs), providing a frame of reference for researchers who use DFT+U to study transition metal oxides. In order to perform this high-throughput study, an atomate workflow is developed for calculating U and J values automatically on massively parallel supercomputing architectures. To demonstrate an application of this workflow, the spin-canting...

Extracting structured seed-mediated gold nanorod growth procedures from scientific text with LLMs

Fri, 29 Mar 2024 00:00:00 +0000

Although gold nanorods have been the subject of much research, the pathways for controlling their shape and thereby their optical properties remain largely heuristically understood. Although it is apparent that the simultaneous presence of and interaction between various reagents during synthesis control these properties, computational and experimental approaches for exploring the synthesis space can be either intractable or too time-consuming in practice. This motivates an alternative approach leveraging the wealth of synthesis information already embedded in the body of scientific literature by developing tools to extract relevant structured data in an automated, high-throughput manner. To that end, we present an approach using the powerful GPT-3 language model to extract structured multi-step seed-mediated growth procedures and outcomes for gold nanorods from unstructured scientific text. GPT-3 prompt completions are fine-tuned to predict synthesis templates in the form of...

Photocatalytic dechlorination of unactivated chlorocarbons including PVC using organolanthanide complexes

Mon, 25 Mar 2024 00:00:00 +0000

Simple lanthanide cyclopentadienyl (Cp) complexes can photochemically cleave the sp³ carbon-chlorine bond of unactivated chlorinated hydrocarbons including polyvinyl chloride (PVC). The excited state lifetimes of these simple complexes are among the longest observed for cerium complexes (175 ns for [(Cp^Me4)₂Ce(μ-Cl)]₂) and the light absorption by the Cp ligand is efficient, so photocatalytic reactivity is enhanced for cerium and now also made possible for neighboring, normally photoinactive, lanthanide congeners.

Corrigendum to “Isotopic fractionation accompanying CO2 hydroxylation and carbonate precipitation from high pH waters at the Cedars, California, USA” [Geochim. Cosmochim. Acta 301 (2021) 91–115]

Thu, 21 Mar 2024 00:00:00 +0000

The authors regret that in the original article, the kinetic fractionation factors (KFFs) related to the CO2 hydroxylation reaction (CO2(aq) + OH– → HCO3–) were calculated using atmospheric δ18OCO2 values of 0.0 ± 0.5 ‰ (VPDB) while the correct values are 10.25 ± 0.5 ‰ (VPDB). We erroneously employed the atmospheric δ18OCO2 values from the NOAA CO2 global network (Trolier et al., 1996) by not converting atmospheric δ18OCO2 from the VPDB-CO2 scale to the VPDB scale through the following expression (e.g. Srivastava and Verkouteren, 2018): [Formula presented] This correction affects the reported oxygen isotope KFFs for CO2 hydroxylation to form HCO3– prior to CaCO3 precipitation. We have corrected Table 7 and Fig. 13 accordingly (see below). The composition of atmospheric CO2 was also incorrectly plotted on the VPDB scale in Figs. 1, 8 and 15 of our original manuscript based on previous works (Fig. 8 in Clark and Fontes, 1990; Fig. 2 in Clark et al., 1992). Importantly, the modelling...

Atomic-Scale Corrugations in Crystalline Polypeptoid Nanosheets Revealed by Three-Dimensional Cryogenic Electron Microscopy

Thu, 21 Mar 2024 00:00:00 +0000

Amphiphilic molecules that can crystallize often form molecularly thin nanosheets in aqueous solutions. The possibility of atomic-scale corrugations in these structures has not yet been recognized. We have studied the self-assembly of amphiphilic polypeptoids, a family of bio-inspired polymers that can self-assemble into various crystalline nanostructures. Atomic-scale structure of the crystals in these systems has been inferred using both X-ray diffraction and electron microscopy. Here we use cryogenic electron microscopy to determine the in-plane and out-of-plane structures of a crystalline nanosheet. Data were collected as a function of tilt angle and analyzed using a hybrid single-particle crystallographic approach. The analysis reveals that adjacent rows of peptoid chains, which are separated by 4.5 Å in the plane of the nanosheet, are offset by 6 Å in the direction perpendicular to the plane of the nanosheet. These atomic-scale corrugations lead to a doubling of the unit...

Tin Metal Improves the Lithiation Kinetics of High-Capacity Silicon Anodes

Wed, 20 Mar 2024 00:00:00 +0000

Si-based anodes present a great promise for high energy density lithium-ion batteries. However, its commercialization is largely hindered by a grand challenge of a rapid capacity fade. Here, we demonstrate excellent cycling stability on a Si–Sn thin film electrode that outperforms pure Si or Sn counterpart under the similar conditions. Combined with the first-principles calculations, in situ transmission electron microscopy studies reveal a reduced volume expansion, increased conductivity, as well as dynamic rearrangement upon lithiation of the Si–Sn film. We attribute the improved lithiation kinetics to the formation of a conductive matrix that comprises a mosaic of nanostructured Sn, Li y Sn (specifically, Li7Sn2 develops around the lithiation potential of Si), and Li x Si. This work provides an important advance in understanding the lithiation mechanism of Si-based anodes for next-generation lithium-ion batteries.

Direct Transformation of SiH4 to a Molecular L(H)2CoSiCo(H)2L Silicide Complex

Tue, 19 Mar 2024 00:00:00 +0000

The synthesis of bimetallic molecular silicide complexes is reported, based on the use of multiple Si-H bond activations in SiH₄ at the metal centers of 14-electron LCo^I fragments (L = Tp″, HB(3,5-diisopropylpyrazolyl)₃^-; [BP₂^tBuPz], PhB(CH₂P^tBu₂)₂(pyrazolyl)). Upon exposure of (Tp″Co)₂(μ-N₂) (1) to SiH₄, a mixture of (Tp″Co)₂(μ-H) (2) and (Tp″Co)₂(μ-H)₂ (3) was formed and no evidence for Si-H oxidative addition products was observed. In contrast, [BP₂^tBuPz]-supported Co complexes led to Si-H oxidative additions with the generation of silylene and silicide complexes as products. Notably, the reaction of ([BP₂^tBuPz]Co)₂(μ-N₂) (5) with SiH₄ gave the dicobalt silicide complex...

Nanopatterned Monolayers of Bioinspired, Sequence-Defined Polypeptoid Brushes for Semiconductor/Bio Interfaces

Tue, 12 Mar 2024 00:00:00 +0000

The ability to control and manipulate semiconductor/bio interfaces is essential to enable biological nanofabrication pathways and bioelectronic devices. Traditional surface functionalization methods, such as self-assembled monolayers (SAMs), provide limited customization for these interfaces. Polymer brushes offer a wider range of chemistries, but choices that maintain compatibility with both lithographic patterning and biological systems are scarce. Here, we developed a class of bioinspired, sequence-defined polymers, i.e., polypeptoids, as tailored polymer brushes for surface modification of semiconductor substrates. Polypeptoids featuring a terminal hydroxyl (-OH) group are designed and synthesized for efficient melt grafting onto the native oxide layer of Si substrates, forming ultrathin (∼1 nm) monolayers. By programming monomer chemistry, our polypeptoid brush platform offers versatile surface modification, including adjustments to surface energy, passivation, preferential...

CoeffNet : predicting activation barriers through a chemically-interpretable, equivariant and physically constrained graph neural network

Mon, 4 Mar 2024 00:00:00 +0000

Activation barriers of elementary reactions are essential to predict molecular reaction mechanisms and kinetics. However, computing these energy barriers by identifying transition states with electronic structure methods (e.g., density functional theory) can be time-consuming and computationally expensive. In this work, we introduce CoeffNet, an equivariant graph neural network that predicts activation barriers using coefficients of any frontier molecular orbital (such as the highest occupied molecular orbital) of reactant and product complexes as graph node features. We show that using coefficients as features offer several advantages, such as chemical interpretability and physical constraints on the network's behaviour and numerical range. Model outputs are either activation barriers or coefficients of the chosen molecular orbital of the transition state; the latter quantity allows us to interpret the results of the neural network through chemical intuition. We...

Structured information extraction from scientific text with large language models

Mon, 26 Feb 2024 00:00:00 +0000

Extracting structured knowledge from scientific text remains a challenging task for machine learning models. Here, we present a simple approach to joint named entity recognition and relation extraction and demonstrate how pretrained large language models (GPT-3, Llama-2) can be fine-tuned to extract useful records of complex scientific knowledge. We test three representative tasks in materials chemistry: linking dopants and host materials, cataloging metal-organic frameworks, and general composition/phase/morphology/application information extraction. Records are extracted from single sentences or entire paragraphs, and the output can be returned as simple English sentences or a more structured format such as a list of JSON objects. This approach represents a simple, accessible, and highly flexible route to obtaining large databases of structured specialized scientific knowledge extracted from research papers.

A Critical Analysis of Chemical and Electrochemical Oxidation Mechanisms in Li-Ion Batteries

Wed, 7 Feb 2024 00:00:00 +0000

Electrolyte decomposition limits the lifetime of commercial lithium-ion batteries (LIBs) and slows the adoption of next-generation energy storage technologies. A fundamental understanding of electrolyte degradation is critical to rationally design stable and energy-dense LIBs. To date, most explanations for electrolyte decomposition at LIB positive electrodes have relied on ethylene carbonate (EC) being chemically oxidized by evolved singlet oxygen (¹O₂) or electrochemically oxidized. In this work, we apply density functional theory to assess the feasibility of these mechanisms. We find that electrochemical oxidation is unfavorable at any potential reached during normal LIB operation, and we predict that previously reported reactions between the EC and ¹O₂ are kinetically limited at room temperature. Our calculations suggest an alternative mechanism in which EC reacts with superoxide (O₂^-) and/or peroxide (O₂^2-)...

Circular Polydiketoenamine Elastomers with Exceptional Creep Resistance via Multivalent Cross-Linker Design

Tue, 16 Jan 2024 00:00:00 +0000

Elastomers are widely used in textiles, foam, and rubber, yet they are rarely recycled due to the difficulty in deconstructing polymer chains to reusable monomers. Introducing reversible bonds in these materials offers prospects for improving their circularity; however, concomitant bond exchange permits creep, which is undesirable. Here, we show how to architect dynamic covalent polydiketoenamine (PDK) elastomers prepared from polyetheramine and triketone monomers, not only for energy-efficient circularity, but also for outstanding creep resistance at high temperature. By appending polytopic cross-linking functionality at the chain ends of flexible polyetheramines, we reduced creep from >200% to less than 1%, relative to monotopic controls, producing mechanically robust and stable elastomers and carbon-reinforced rubbers that are readily depolymerized to pure monomer in high yield. We also found that the multivalent chain end was essential for ensuring complete PDK deconstruction....

CHGNet as a pretrained universal neural network potential for charge-informed atomistic modelling

Fri, 12 Jan 2024 00:00:00 +0000

Large-scale simulations with complex electron interactions remain one of the greatest challenges for atomistic modelling. Although classical force fields often fail to describe the coupling between electronic states and ionic rearrangements, the more accurate ab initio molecular dynamics suffers from computational complexity that prevents long-time and large-scale simulations, which are essential to study technologically relevant phenomena. Here we present the Crystal Hamiltonian Graph Neural Network (CHGNet), a graph neural network-based machine-learning interatomic potential (MLIP) that models the universal potential energy surface. CHGNet is pretrained on the energies, forces, stresses and magnetic moments from the Materials Project Trajectory Dataset, which consists of over 10 years of density functional theory calculations of more than 1.5 million inorganic structures. The explicit inclusion of magnetic moments enables CHGNet to learn and accurately represent the orbital...

Designing transparent conductors using forbidden optical transitions

Fri, 12 Jan 2024 00:00:00 +0000

Many semiconductors present weak or forbidden transitions at their fundamental band gaps, inducing a widened region of transparency. This occurs in high-performing n-type transparent conductors (TCs) such as Sn-doped In 2 O 3 (ITO); however, thus far, the presence of forbidden transitions has been neglected in the search for new p-type TCs. To address this, we first compute high-throughput absorption spectra across ∼ 18,000 semiconductors, showing that over half exhibit forbidden or weak optical transitions at their band edges. Next, we demonstrate that compounds with highly localized band-edge states are more likely to present forbidden transitions. Lastly, we search this set for p-type and n-type TCs with forbidden transitions and, by performing defect calculations, propose unexplored TC candidates such as ambipolar BeSiP 2 , p-type wurtzite BAs , and n-type Ba 2 InGaO 5 , among others. We share our dataset and recommend that future screenings for optical properties consider...

Importance of nonuniform Brillouin zone sampling for ab initio Bethe-Salpeter equation calculations of exciton binding energies in crystalline solids

Mon, 8 Jan 2024 00:00:00 +0000

Excitons are prevalent in semiconductors and insulators, and their binding energies are critical for optoelectronic applications. The state-of-the-art method for first-principles calculations of excitons in extended systems is the ab initio GW-Bethe-Salpeter equation (BSE) approach, which can require a fine sampling of reciprocal space to accurately resolve solid-state exciton properties. Here we show, for a range of semiconductors and insulators, that the commonly employed approach of uniformly sampling the Brillouin zone can lead to underconverged exciton binding energies, as impractical grid sizes are required to achieve adequate convergence. We further show that nonuniform sampling of the Brillouin zone, focused on the region of reciprocal space where the exciton wave function resides, enables efficient rapid numerical convergence of exciton binding energies at a given level of theory. We propose a well-defined convergence procedure, which can be carried out at relatively...

Density functional theory assessment of the lithiation thermodynamics and phase evolution in si-based amorphous binary alloys

Wed, 3 Jan 2024 00:00:00 +0000

Development of novel alloy-based anodes has the potential to increase the energy storage capacity of current Li-ion based energy storage technology. In particular, Si-based anodes are of interest due to their high theoretical capacity, but suffer from poor cycle and calendar life stemming from large volumetric expansion and a non-passivating solid-electrolyte interface. The addition of amorphous components to the Si anode has been shown to improve the mechanical and chemical stability during lithiation. In this study, we use density functional theory (DFT) to probe the thermodynamics of amorphous alloy formation in a range of binary Si-X alloy systems, where X constitutes any element from periodic table groups 1–17. The alloying elements are classified as active or inactive components based on the reactivity with Li, where active elements form stable binary compounds with Li and inactive elements do not. We find that when alloying inactive elements, most inactive components do...

Oxygen Loss on Disordered Li-Excess, Mn-Rich Li-Ion Cathode Li2MnO2F through First-Principles Modeling

Mon, 18 Dec 2023 00:00:00 +0000

Oxygen evolution energies were calculated for the {100}, {110}, {111}, and {112} type facets of the rock-salt-structured cation-disordered Li-excess, Mn-rich Li-ion (DRX) cathode Li₂MnO₂F at the fully lithiated, 25% delithiation, and 50% delithiation states. Our calculations showed that Li₂MnO₂F remains much more robust to O loss than its nonfluorinated counterparts, as has been shown in experimental work. In particular, the {110} and {112} facets are the most resilient against O loss. Focusing on the {100} type facet, which previous work has shown to be the most likely exposed facet of Li₂MnO₂F, it was found that higher proportions of Li in an O coordination shell lead to lower O evolution energy (Ẽ_O) and facilitate O loss. It was also found that at higher states of delithiation, surface fluorine had a weaker effect in increasing Ẽ_O, meaning the protective effect of F against...

Solvation Effects on the Dielectric Constant of 1 M LiPF6 in Ethylene Carbonate: Ethyl Methyl Carbonate 3:7

Fri, 8 Dec 2023 00:00:00 +0000

We report the dielectric constant of 1 M LiPF 6 in EC:EMC 3:7 w/w (ethylene carbonate/ethyl methyl carbonate) in addition to neat EC:EMC 3:7 w/w. Using three Debye relaxations, the static permittivity value, or dielectric constant, is extrapolated to 18.5, which is compared to 18.7 for the neat solvent mixture. The EC solvent is found to strongly coordinate with the Li + cations of the salt, which results in a loss of dielectric contribution to the electrolyte. However, the small amplitude and large uncertainty in relaxation frequency for EMC cloud definitive identification of the Li + solvation shell. Importantly, the loss of the free EC permittivity contribution due to Li + solvation is almost completely balanced by the positive contribution of the associated LiPF 6 salt, demonstrating that a significant quantity of dipolar ion pairs exists in 1 M LiPF 6 in EC:EMC 3:7.

Rational Design of Fluorinated Electrolytes for Low Temperature Lithium‐Ion Batteries

Fri, 1 Dec 2023 00:00:00 +0000

Abstract Nonaqueous carbonate electrolytes are commonly used in commercial lithium‐ion battery (LIB). However, the sluggish Li + diffusivity and high interfacial charge transfer resistance at low temperature (LT) limit their wide adoption among geographical areas with high latitudes and altitudes. Herein, a rational design of new electrolytes is demonstrated, which can significantly improve the low temperature performance below −20 °C. This electrolyte is achieved by tailoring the chemical structure, i.e., altering the fluorination position and the degree of fluorination, of ethyl acetate solvent. It is found that fluorination adjacent to the carbonyl group or high degree of fluorination leads to a stronger electron‐withdrawing effect, resulting in low atomic charge on the carbonyl oxygen solvating sites, and thus low binding energies with Li + ions at LT. The optimal electrolyte 2,2,2‐trifluoroethyl acetate (EA‐f) shows significantly improved cycle life and C‐rate of a...

High-throughput calculations of charged point defect properties with semi-local density functional theory—performance benchmarks for materials screening applications

Tue, 28 Nov 2023 00:00:00 +0000

Calculations of point defect energetics with Density Functional Theory (DFT) can provide valuable insight into several optoelectronic, thermodynamic, and kinetic properties. These calculations commonly use methods ranging from semi-local functionals with a-posteriori corrections to more computationally intensive hybrid functional approaches. For applications of DFT-based high-throughput computation for data-driven materials discovery, point defect properties are of interest, yet are currently excluded from available materials databases. This work presents a benchmark analysis of automated, semi-local point defect calculations with a-posteriori corrections, compared to 245 “gold standard” hybrid calculations previously published. We consider three different a-posteriori correction sets implemented in an automated workflow, and evaluate the qualitative and quantitative differences among four different categories of defect information: thermodynamic transition levels, formation energies,...

Assessing Thermodynamic Selectivity of Solid-State Reactions for the Predictive Synthesis of Inorganic Materials

Wed, 15 Nov 2023 00:00:00 +0000

Synthesis is a major challenge in the discovery of new inorganic materials. Currently, there is limited theoretical guidance for identifying optimal solid-state synthesis procedures. We introduce two selectivity metrics, primary and secondary competition, to assess the favorability of target/impurity phase formation in solid-state reactions. We used these metrics to analyze 3520 solid-state reactions in the literature, ranking existing approaches to popular target materials. Additionally, we implemented these metrics in a data-driven synthesis planning workflow and demonstrated its application in the synthesis of barium titanate (BaTiO₃). Using an 18-element chemical reaction network with first-principles thermodynamic data from the Materials Project, we identified 82985 possible BaTiO₃ synthesis reactions and selected 9 for experimental testing. Characterization of reaction pathways via synchrotron powder X-ray diffraction reveals that our selectivity metrics...

Modernist materials synthesis: Finding thermodynamic shortcuts with hyperdimensional chemistry

Tue, 14 Nov 2023 00:00:00 +0000

Synthesis remains a challenge for advancing materials science. A key focus of this challenge is how to enable selective synthesis, particularly as it pertains to metastable materials. This perspective addresses the question: how can “spectator” elements, such as those found in double ion exchange (metathesis) reactions, enable selective materials synthesis? By observing reaction pathways as they happen (in situ) and calculating their energetics using modern computational thermodynamics, we observe transient, crystalline intermediates that suggest that many reactions attain a local thermodynamic equilibrium dictated by local chemical potentials far before achieving a global equilibrium set by the average composition. Using this knowledge, one can thermodynamically “shortcut” unfavorable intermediates by including additional elements beyond those of the desired target, providing access to a greater number of intermediates with advantageous energetics and selective phase nucleation....

Topological graph-based analysis of solid-state ion migration

Wed, 8 Nov 2023 00:00:00 +0000

To accelerate the development of ion conducting materials, we present a general graph-theoretic analysis framework for ion migration in any crystalline structure. The nodes of the graph represent metastable sites of the migrating ion and the edges represent discrete migration events between adjacent sites. Starting from a collection of possible metastable migration sites, the framework assigns a weight to the edges by calculating the individual migration energy barriers between those sites. Connected pathways in the periodic simulation cell corresponding to macroscopic ion migration are identified by searching for the lowest-cost cycle in the periodic migration graph. To exemplify the utility of the framework, we present the automatic analyses of Li migration in different polymorphs of VO(PO4), with the resulting identification of two distinct crystal structures with simple migration pathways demonstrating overall <300 meV migration barriers.

Discovery of Stable and Selective Antibody Mimetics from Combinatorial Libraries of Polyvalent, Loop-Functionalized Peptoid Nanosheets

Sun, 22 Oct 2023 00:00:00 +0000

The ability of antibodies to bind a wide variety of analytes with high specificity and high affinity makes them ideal candidates for therapeutic and diagnostic applications. However, the poor stability and high production cost of antibodies have prompted exploration of a variety of synthetic materials capable of specific molecular recognition. Unfortunately, it remains a fundamental challenge to create a chemically diverse population of protein-like, folded synthetic nanostructures with defined molecular conformations in water. Here we report the synthesis and screening of combinatorial libraries of sequence-defined peptoid polymers engineered to fold into ordered, supramolecular nanosheets displaying a high spatial density of diverse, conformationally constrained peptoid loops on their surface. These polyvalent, loop-functionalized nanosheets were screened using a homogeneous Förster resonance energy transfer (FRET) assay for binding to a variety of protein targets. Peptoid sequences...

Isolation and Study of Ruthenium–Cobalt Oxo Cubanes Bearing a High-Valent, Terminal RuV–Oxo with Significant Oxyl Radical Character

Sun, 22 Oct 2023 00:00:00 +0000

High-valent Ru^V-oxo intermediates have long been proposed in catalytic oxidation chemistry, but investigations into their electronic and chemical properties have been limited due to their reactive nature and rarity. The incorporation of Ru into the [Co₃O₄] subcluster via the single-step assembly reaction of Co^II(OAc)₂(H₂O)₄ (OAc = acetate), perruthenate (RuO₄^-), and pyridine (py) yielded an unprecedented Ru(O)Co₃(μ₃-O)₄(OAc)₄(py)₃ cubane featuring an isolable, yet reactive, Ru^V-oxo moiety. EPR, ENDOR, and DFT studies reveal a valence-localized [Ru^V(S = 1/2)Co^III₃(S = 0)O₄] configuration and non-negligible covalency in the cubane core. Significant oxyl radical character in the Ru^V-oxo unit is experimentally demonstrated by radical coupling reactions...

Trapping and Electron Paramagnetic Resonance Characterization of the 5′dAdo• Radical in a Radical S‑Adenosyl Methionine Enzyme Reaction with a Non-Native Substrate

Sun, 22 Oct 2023 00:00:00 +0000

S-Adenosyl methionine (SAM) is employed as a [4Fe-4S]-bound cofactor in the superfamily of radical SAM (rSAM) enzymes, in which one-electron reduction of the [4Fe-4S]-SAM moiety leads to homolytic cleavage of the S-adenosyl methionine to generate the 5'-deoxyadenosyl radical (5'dAdo^•), a potent H-atom abstractor. HydG, a member of this rSAM family, uses the 5'dAdo^• radical to lyse its substrate, tyrosine, producing CO and CN that bind to a unique Fe site of a second HydG Fe-S cluster, ultimately producing a mononuclear organometallic Fe-l-cysteine-(CO)₂CN complex as an intermediate in the bioassembly of the catalytic H-cluster of [Fe-Fe] hydrogenase. Here we report the use of non-native tyrosine substrate analogues to further probe the initial radical chemistry of HydG. One such non-native substrate is 4-hydroxy phenyl propanoic acid (HPPA) which lacks the amino group of tyrosine, replacing the C_αH-NH₂ with a...

Tris(carbene)borates; alternatives to cyclopentadienyls in organolanthanide chemistry

Tue, 10 Oct 2023 00:00:00 +0000

The chemistry of the tris-carbene anion phenyltris(3-alkyl-imidazoline-2-yliden-1-yl)borate, [C3Me]- ligand, is initiated for f-block metal cations. Neutral, molecular complexes of the form Ln(C3)₂I are formed for cerium(III), while a separated ion pair [Ln(C3)₂]I forms for ytterbium(III). DFT/QTAIM computational analyses of the complexes and related tridentate tris(pyrazolyl)borate (Tp) - supported analogs demonstrates the anticipated strength of the σ donation and confirms greater covalency in the metal-carbon bonds of the [C3Me]- complexes in comparison with those in the TpMe,Me complexes. The DFT calculations demonstrate the crucial role of THF solvent in accurately reproducing the contrasting molecular and ion-pair geometries observed experimentally for the Ce and Yb complexes.

2DMatPedia, an open computational database of two-dimensional materials from top-down and bottom-up approaches

Wed, 20 Sep 2023 00:00:00 +0000

Two-dimensional (2D) materials have been a hot research topic in the last decade, due to novel fundamental physics in the reduced dimension and appealing applications. Systematic discovery of functional 2D materials has been the focus of many studies. Here, we present a large dataset of 2D materials, with more than 6,000 monolayer structures, obtained from both top-down and bottom-up discovery procedures. First, we screened all bulk materials in the database of Materials Project for layered structures by a topology-based algorithm and theoretically exfoliated them into monolayers. Then, we generated new 2D materials by chemical substitution of elements in known 2D materials by others from the same group in the periodic table. The structural, electronic and energetic properties of these 2D materials are consistently calculated, to provide a starting point for further material screening, data mining, data analysis and artificial intelligence applications. We present the details...

Paramagnetic Intermediates Generated by Radical S‑Adenosylmethionine (SAM) Enzymes

Mon, 18 Sep 2023 00:00:00 +0000

A [4Fe-4S](+) cluster reduces a bound S-adenosylmethionine (SAM) molecule, cleaving it into methionine and a 5'-deoxyadenosyl radical (5'-dA(•)). This step initiates the varied chemistry catalyzed by each of the so-called radical SAM enzymes. The strongly oxidizing 5'-dA(•) is quenched by abstracting a H-atom from a target species. In some cases, this species is an exogenous molecule of substrate, for example, L-tyrosine in the [FeFe] hydrogenase maturase, HydG. In other cases, the target is a proteinaceous residue as in all the glycyl radical forming enzymes. The generation of this initial radical species and the subsequent chemistry involving downstream radical intermediates is meticulously controlled by the enzyme so as to prevent unwanted reactions. But the manner in which this control is exerted is unknown. Electron paramagnetic resonance (EPR) spectroscopy has proven to be a valuable tool used to gain insight into these mechanisms. In this Account, we summarize efforts to...

The Cyanide Ligands of [FeFe] Hydrogenase: Pulse EPR Studies of 13C and 15N‑Labeled H‑Cluster

Mon, 18 Sep 2023 00:00:00 +0000

The two cyanide ligands in the assembled cluster of [FeFe] hydrogenase originate from exogenous l-tyrosine. Using selectively labeled tyrosine substrates, the cyanides were isotopically labeled via a recently developed in vitro maturation procedure allowing advanced electron paramagnetic resonance techniques to probe the electronic structure of the catalytic core of the enzyme. The ratio of the isotropic (13)C hyperfine interactions for the two CN(-) ligands-a reporter of spin density on their respective coordinating iron ions-collapses from ≈5.8 for the Hox form of hydrogenase to <2 for the CO-inhibited form. Additionally, when the maturation was carried out using [(15)N]-tyrosine, no features previously ascribed to the nitrogen of the bridging dithiolate ligand were observed suggesting that this bridge is not sourced from tyrosine.

Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example

Mon, 18 Sep 2023 00:00:00 +0000

Fluorinated tyrosines (FnY's, n = 2 and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the recently evolved M. jannaschii Y-tRNA synthetase/tRNA pair. Class Ia RNRs require four redox active Y's, a stable Y radical (Y·) in the β subunit (position 122 in E. coli), and three transiently oxidized Y's (356 in β and 731 and 730 in α) to initiate the radical-dependent nucleotide reduction process. FnY (3,5; 2,3; 2,3,5; and 2,3,6) incorporation in place of Y122-β and the X-ray structures of each resulting β with a diferric cluster are reported and compared with wt-β2 crystallized under the same conditions. The essential diferric-FnY· cofactor is self-assembled from apo FnY-β2, Fe(2+), and O2 to produce ∼1 Y·/β2 and ∼3 Fe(3+)/β2. The FnY· are stable and active in nucleotide reduction with activities that vary from 5% to 85% that of wt-β2. Each FnY·-β2 has been characterized by 9 and 130 GHz electron paramagnetic resonance and high-field...

Thionitrite (SNO−) and Perthionitrite (SSNO−) are Simple Synthons for Nitrosylated Iron Sulfur Clusters

Sat, 9 Sep 2023 00:00:00 +0000

S/N crosstalk species derived from the interconnected reactivity of H₂ S and NO facilitate the transport of reactive sulfur and nitrogen species in signaling, transport, and regulatory processes. We report here that simple Fe²⁺ ions, such as those that are bioavailable in the labile iron pool (LIP), react with thionitrite (SNO^- ) and perthionitrite (SSNO^- ) to yield the dinitrosyl iron complex [Fe(NO)₂ (S₅ )]^- . In the reaction of FeCl₂ with SNO^- we were able to isolate the unstable intermediate hydrosulfido mononitrosyl iron complex [FeCl₂ (NO)(SH)]^- , which was characterized by X-ray crystallography. We also show that [Fe(NO)₂ (S₅ )]^- is a simple synthon for nitrosylated Fe-S clusters via its reduction with PPh₃ to yield Roussin's Red Salt ([Fe₂ S₂ (NO)₄ ]^2- ), which highlights...

A protein fold switch joins the circadian oscillator to clock output in cyanobacteria

Sat, 9 Sep 2023 00:00:00 +0000

Organisms are adapted to the relentless cycles of day and night, because they evolved timekeeping systems called circadian clocks, which regulate biological activities with ~24-hour rhythms. The clock of cyanobacteria is driven by a three-protein oscillator composed of KaiA, KaiB, and KaiC, which together generate a circadian rhythm of KaiC phosphorylation. We show that KaiB flips between two distinct three-dimensional folds, and its rare transition to an active state provides a time delay that is required to match the timing of the oscillator to that of Earth's rotation. Once KaiB switches folds, it binds phosphorylated KaiC and captures KaiA, which initiates a phase transition of the circadian cycle, and it regulates components of the clock-output pathway, which provides the link that joins the timekeeping and signaling functions of the oscillator.

Novel Structural Motif To Promote Mg-Ion Mobility: Investigating ABO4 Zircons as Magnesium Intercalation Cathodes

Thu, 17 Aug 2023 00:00:00 +0000

There is an increasing need for sustainable energy storage solutions as fossil fuels are replaced by renewable energy sources. Multivalent batteries, specifically Mg batteries, are one energy storage technology that researchers continue to develop with hopes to surpass the performance of Li-ion batteries. However, the limited energy density and transport properties of Mg cathodes remain critical challenges preventing the realization of high-performance multivalent batteries. In this work, ABO₄ zircon materials (A = Y, Eu and B = V, Cr) are computationally and experimentally evaluated as Mg intercalation cathodes. Remarkably good Mg-ion transport properties were predicted and Mg-ion intercalation was experimentally verified in sol-gel synthesized zircon YVO₄, EuVO₄, and EuCrO₄. Among them, EuVO₄ exhibited the best electrochemical performance and demonstrated repeated reversible cycling. While we believe that the one-dimensional...

Materials design principles of amorphous cathode coatings for lithium-ion battery applications

Wed, 9 Aug 2023 00:00:00 +0000

We propose the general selection guidelines of amorphous cathode coatings for lithium-ion batteries based on an extensive high-throughput computational study and detailed ionic diffusion analysis. Cathode surface coatings present one of the most popular and effective solutions to suppress cathode degradation and improve cycling performance of lithium-ion batteries (LIBs). In this work, we carry out an extensive high-throughput computational study to develop materials design principles governing amorphous cathode coating selections for LIBs. Our high-throughput screening includes descriptors to evaluate the thermodynamic stability, electrochemical stability, chemical reactivity with electrolytes and cathodes, and ionic diffusion of the cathode coatings. In the ionic diffusion analysis, we mainly focus on Li-containing compounds. From the 20 selected materials, we highlight the formidable challenge of mitigating oxygen diffusion when selecting an ideal cathode coating, and suggest...

New insights into Mn2+ and Mg2+ inhibition of calcite growth

Wed, 9 Aug 2023 00:00:00 +0000

Impurity ion and isotope partitioning into carbonate minerals provide a window into the molecular processes occurring at the fluid-mineral interface during crystal growth. Here, we employ calcium isotope fractionation together with process-based modeling to elucidate the mechanisms by which two divalent cations with starkly contrasting compatibility, magnesium and manganese, inhibit calcite growth and incorporate into the mineral lattice. Calcite growth inhibition by Mg2+ is log-linear and KMg is on the order of 0.02–0.03 throughout the range of {Mg2+}/{Ca2+} studied here (0.01–2.6). Mn2+ exhibits much stronger log-linear growth rate inhibition at low Mn2+ concentrations (fluid {Mn2+}/{Ca2+} = 0.001–0.02). Mn2+ is readily incorporated into the calcite lattice to form a calcite-rhodochrosite solid solution, with large partition coefficients (KMn 4.6–15.6) inversely correlated to growth rate. For both Mn2+ and Mg2+, calcium isotope fractionation is found to be invariant...

Cluster expansions of multicomponent ionic materials: Formalism and methodology

Tue, 8 Aug 2023 00:00:00 +0000

The cluster expansion (CE) method has seen continuous and increasing use in the study of configuration-dependent properties of crystalline materials. The original development of the CE method along with the underlying mathematical formalism and assumptions was focused on the study of metallic alloys. Since then the methodology has been actively and successfully used in the study of ionic materials as well. In this work, we present a cohesive reformulation of the mathematical formalism underlying the CE method based on a synthesis of its original formulation, several additions and extensions that have been proposed since, and a revised representation of its constituent mathematical objects. We then proceed to describe some of the formal implications of using the methodology for charge-neutral configurations in ionic systems. In particular, we discuss the reduction of the size of configuration spaces and the resulting linear dependencies that arise among correlation functions that...

A representation-independent electronic charge density database for crystalline materials

Tue, 25 Jul 2023 00:00:00 +0000

In addition to being the core quantity in density-functional theory, the charge density can be used in many tertiary analyses in materials sciences from bonding to assigning charge to specific atoms. The charge density is data-rich since it contains information about all the electrons in the system. With the increasing prevalence of machine-learning tools in materials sciences, a data-rich object like the charge density can be utilized in a wide range of applications. The database presented here provides a modern and user-friendly interface for a large and continuously updated collection of charge densities as part of the Materials Project. In addition to the charge density data, we provide the theory and code for changing the representation of the charge density which should enable more advanced machine-learning studies for the broader community.

Ordering of room-temperature magnetic skyrmions in a polar van der Waals magnet

Wed, 19 Jul 2023 00:00:00 +0000

Control and understanding of ensembles of skyrmions is important for realization of future technologies. In particular, the order-disorder transition associated with the 2D lattice of magnetic skyrmions can have significant implications for transport and other dynamic functionalities. To date, skyrmion ensembles have been primarily studied in bulk crystals, or as isolated skyrmions in thin film devices. Here, we investigate the condensation of the skyrmion phase at room temperature and zero field in a polar, van der Waals magnet. We demonstrate that we can engineer an ordered skyrmion crystal through structural confinement on the μm scale, showing control over this order-disorder transition on scales relevant for device applications.

Chemical Reaction Networks Explain Gas Evolution Mechanisms in Mg-Ion Batteries

Tue, 18 Jul 2023 00:00:00 +0000

Out-of-equilibrium electrochemical reaction mechanisms are notoriously difficult to characterize. However, such reactions are critical for a range of technological applications. For instance, in metal-ion batteries, spontaneous electrolyte degradation controls electrode passivation and battery cycle life. Here, to improve our ability to elucidate electrochemical reactivity, we for the first time combine computational chemical reaction network (CRN) analysis based on density functional theory (DFT) and differential electrochemical mass spectroscopy (DEMS) to study gas evolution from a model Mg-ion battery electrolyte─magnesium bistriflimide (Mg(TFSI)₂) dissolved in diglyme (G2). Automated CRN analysis allows for the facile interpretation of DEMS data, revealing H₂O, C₂H₄, and CH₃OH as major products of G2 decomposition. These findings are further explained by identifying elementary mechanisms using DFT. While TFSI^-...

Enabling selective zinc-ion intercalation by a eutectic electrolyte for practical anodeless zinc batteries

Tue, 18 Jul 2023 00:00:00 +0000

Two major challenges hinder the advance of aqueous zinc metal batteries for sustainable stationary storage: (1) achieving predominant Zn-ion (de)intercalation at the oxide cathode by suppressing adventitious proton co-intercalation and dissolution, and (2) simultaneously overcoming Zn dendrite growth at the anode that triggers parasitic electrolyte reactions. Here, we reveal the competition between Zn2+vs proton intercalation chemistry of a typical oxide cathode using ex-situ/operando techniques, and alleviate side reactions by developing a cost-effective and non-flammable hybrid eutectic electrolyte. A fully hydrated Zn2+ solvation structure facilitates fast charge transfer at the solid/electrolyte interface, enabling dendrite-free Zn plating/stripping with a remarkably high average coulombic efficiency of 99.8% at commercially relevant areal capacities of 4 mAh cm−2 and function up to 1600 h at 8 mAh cm−2. By concurrently stabilizing Zn redox at both electrodes, we achieve a...

Structural Elucidation of a Polypeptoid Chain in a Crystalline Lattice Reveals Key Morphology-Directing Role of the N‑Terminus

Wed, 12 Jul 2023 00:00:00 +0000

The ability to engineer synthetic polymers with the same structural precision as biomacromolecules is crucial to enable the de novo design of robust nanomaterials with biomimetic function. Peptoids, poly(N-substituted) glycines, are a highly controllable bio-inspired polymer family that can assemble into a variety of functional, crystalline nanostructures over a wide range of sequences. Extensive investigation on the molecular packing in these lattices has been reported; however, many key atomic-level details of the molecular structure remain underexplored. Here, we use cryo-TEM 3D reconstruction to directly visualize the conformation of an individual polymer chain within a peptoid nanofiber lattice in real space at 3.6 Å resolution. The backbone in the N-decylglycine hydrophobic core is shown to clearly adopt an extended, all-cis-sigma strand conformation, as previously suggested in many peptoid lattice models. We also show that packing interactions...

Machine Learning Full NMR Chemical Shift Tensors of Silicon Oxides with Equivariant Graph Neural Networks

Wed, 12 Jul 2023 00:00:00 +0000

The nuclear magnetic resonance (NMR) chemical shift tensor is a highly sensitive probe of the electronic structure of an atom and furthermore its local structure. Recently, machine learning has been applied to NMR in the prediction of isotropic chemical shifts from a structure. Current machine learning models, however, often ignore the full chemical shift tensor for the easier-to-predict isotropic chemical shift, effectively ignoring a multitude of structural information available in the NMR chemical shift tensor. Here we use an equivariant graph neural network (GNN) to predict full ²⁹Si chemical shift tensors in silicate materials. The equivariant GNN model predicts full tensors to a mean absolute error of 1.05 ppm and is able to accurately determine the magnitude, anisotropy, and tensor orientation in a diverse set of silicon oxide local structures. When compared with other models, the equivariant GNN model outperforms the state-of-the-art machine learning models...

COVIDScholar: An automated COVID-19 research aggregation and analysis platform

Tue, 11 Jul 2023 00:00:00 +0000

The ongoing COVID-19 pandemic produced far-reaching effects throughout society, and science is no exception. The scale, speed, and breadth of the scientific community's COVID-19 response lead to the emergence of new research at the remarkable rate of more than 250 papers published per day. This posed a challenge for the scientific community as traditional methods of engagement with the literature were strained by the volume of new research being produced. Meanwhile, the urgency of response lead to an increasingly prominent role for preprint servers and a diffusion of relevant research through many channels simultaneously. These factors created a need for new tools to change the way scientific literature is organized and found by researchers. With this challenge in mind, we present an overview of COVIDScholar https://covidscholar.org, an automated knowledge portal which utilizes natural language processing (NLP) that was built to meet these urgent needs. The search interface for...

Free-atom-like d states beyond the dilute limit of single-atom alloys

Mon, 10 Jul 2023 00:00:00 +0000

Through a data-mining and high-throughput density functional theory approach, we identify a diverse range of metallic compounds that are predicted to have transition metals with "free-atom-like" d states that are highly localized in terms of their energetic distribution. Design principles that favor the formation of localized d states are uncovered, among which we note that site isolation is often necessary but that the dilute limit, as in most single-atom alloys, is not a pre-requisite. Additionally, the majority of localized d state transition metals identified from the computational screening study exhibit partial anionic character due to charge transfer from neighboring metal species. Using CO as a representative probe molecule, we show that localized d states for Rh, Ir, Pd, and Pt tend to reduce the binding strength of CO compared to their pure elemental analogues, whereas this does not occur as consistently for the Cu binding sites. These trends are rationalized through...

Controlled monodefluorination and alkylation of C(sp 3 )–F bonds by lanthanide photocatalysts: importance of metal–ligand cooperativity

Sat, 8 Jul 2023 00:00:00 +0000

The controlled functionalization of a single fluorine in a CF₃ group is difficult and rare. Photochemical C-F bond functionalization of the sp³-C-H bond in trifluorotoluene, PhCF₃, is achieved using catalysts made from earth-abundant lanthanides, (Cp^Me4)₂Ln(2-O-3,5- ^t Bu₂-C₆H₂)(1-C{N(CH)₂N(ⁱPr)}) (Ln = La, Ce, Nd and Sm, Cp^Me4 = C₅Me₄H). The Ce complex is the most effective at mediating hydrodefluorination and defluoroalkylative coupling of PhCF₃ with alkenes; addition of magnesium dialkyls enables catalytic C-F bond cleavage and C-C bond formation by all the complexes. Mechanistic experiments confirm the essential role of the Lewis acidic metal and support an inner-sphere mechanism of C-F activation. Computational studies agree that coordination of the C-F substrate is essential for C-F bond cleavage....

Covalent bond shortening and distortion induced by pressurization of thorium, uranium, and neptunium tetrakis aryloxides

Thu, 6 Jul 2023 00:00:00 +0000

Covalency involving the 5f orbitals is regularly invoked to explain the reactivity, structure and spectroscopic properties of the actinides, but the ionic versus covalent nature of metal-ligand bonding in actinide complexes remains controversial. The tetrakis 2,6-di-tert-butylphenoxide complexes of Th, U and Np form an isostructural series of crystal structures containing approximately tetrahedral MO4 cores. We show that up to 3 GPa the Th and U crystal structures show negative linear compressibility as the OMO angles distort. At 3 GPa the angles snap back to their original values, reverting to a tetrahedral geometry with an abrupt shortening of the M-O distances by up to 0.1 Å. The Np complex shows similar but smaller effects, transforming above 2.4 GPa. Electronic structure calculations associate the M-O bond shortening with a change in covalency resulting from increased contributions to the M-O bonding by the metal 6d and 5f orbitals, the combination promoting MO4 flexibility...

Tryptophan Can Promote Oxygen Reduction to Water in a Biosynthetic Model of Heme Copper Oxidases

Thu, 6 Jul 2023 00:00:00 +0000

Heme-copper oxidases (HCOs) utilize tyrosine (Tyr) to donate one of the four electrons required for the reduction of O₂ to water in biological respiration, while tryptophan (Trp) is speculated to fulfill the same role in cyt bd oxidases. We previously engineered myoglobin into a biosynthetic model of HCOs and demonstrated the critical role that Tyr serves in the oxygen reduction reaction (ORR). To address the roles of Tyr and Trp in these oxidases, we herein report the preparation of the same biosynthetic model with the Tyr replaced by Trp and further demonstrate that Trp can also promote the ORR, albeit with lower activity. An X-ray crystal structure of the Trp variant shows a hydrogen-bonding network involving two water molecules that are organized by Trp, similar to that in the Tyr variant, which is absent in the crystal structure with the native Phe residue. Additional electron paramagnetic resonance measurements are consistent with the formation of a Trp...

Organometallic Fe2(μ-SH)2(CO)4(CN)2 Cluster Allows the Biosynthesis of the [FeFe]-Hydrogenase with Only the HydF Maturase

Wed, 28 Jun 2023 00:00:00 +0000

The biosynthesis of the active site of the [FeFe]-hydrogenases (HydA1), the H-cluster, is of interest because these enzymes are highly efficient catalysts for the oxidation and production of H₂. The biosynthesis of the [2Fe]_H subcluster of the H-cluster proceeds from simple precursors, which are processed by three maturases: HydG, HydE, and HydF. Previous studies established that HydG produces an Fe(CO)₂(CN) adduct of cysteine, which is the substrate for HydE. In this work, we show that by using the synthetic cluster [Fe₂(μ-SH)₂(CN)₂(CO)₄]^2- active HydA1 can be biosynthesized without maturases HydG and HydE.

Big Data in a Nano World: A Review on Computational, Data-Driven Design of Nanomaterials Structures, Properties, and Synthesis

Tue, 27 Jun 2023 00:00:00 +0000

The recent rise of computational, data-driven research has significant potential to accelerate materials discovery. Automated workflows and materials databases are being rapidly developed, contributing to high-throughput data of bulk materials that are growing in quantity and complexity, allowing for correlation between structural-chemical features and functional properties. In contrast, computational data-driven approaches are still relatively rare for nanomaterials discovery due to the rapid scaling of computational cost for finite systems. However, the distinct behaviors at the nanoscale as compared to the parent bulk materials and the vast tunability space with respect to dimensionality and morphology motivate the development of data sets for nanometric materials. In this review, we discuss the recent progress in data-driven research in two aspects: functional materials design and guided synthesis, including commonly used metrics and approaches for designing materials properties...

Biosynthesis of fluopsin C, a copper-containing antibiotic from Pseudomonas aeruginosa

Tue, 27 Jun 2023 00:00:00 +0000

Metal-binding natural products contribute to metal acquisition and bacterial virulence, but their roles in metal stress response are underexplored. We show that a five-enzyme pathway in Pseudomonas aeruginosa synthesizes a small-molecule copper complex, fluopsin C, in response to elevated copper concentrations. Fluopsin C is a broad-spectrum antibiotic that contains a copper ion chelated by two minimal thiohydroxamates. Biosynthesis of the thiohydroxamate begins with cysteine and requires two lyases, two iron-dependent enzymes, and a methyltransferase. The iron-dependent enzymes remove the carboxyl group and the α carbon from cysteine through decarboxylation, N-hydroxylation, and methylene excision. Conservation of the pathway in P. aeruginosa and other bacteria suggests a common role for fluopsin C in the copper stress response, which involves fusing copper into an antibiotic against other microbes.

Biosynthesis of the [FeFe] hydrogenase H-cluster via a synthetic [Fe( ii )(CN)(CO) 2 (cysteinate)] − complex

Sat, 24 Jun 2023 00:00:00 +0000

The H-cluster of [Fe-Fe] hydrogenase consists of a [4Fe]_H subcluster linked by the sulfur of a cysteine residue to an organometallic [2Fe]_H subcluster that utilizes terminal CO and CN ligands to each Fe along with a bridging CO and a bridging SCH₂NHCH₂S azadithiolate (adt) to catalyze proton reduction or hydrogen oxidation. Three Fe-S "maturase" proteins, HydE, HydF, and HydG, are responsible for the biosynthesis of the [2Fe]_H subcluster and its incorporation into the hydrogenase enzyme to form this catalytically active H-cluster. We have proposed that HydG is a bifunctional enzyme that uses S-adenosylmethione (SAM) bound to a [4Fe-4S] cluster to lyse tyrosine via a transient 5'-deoxyadenosyl radical to produce CO and CN ligands to a unique cysteine-chelated Fe(II) that is linked to a second [4Fe-4S] cluster via the cysteine sulfur. In this "synthon model", after two cycles of tyrosine...

Quantum Chemical Study of a Radical Relay Mechanism for the HydG-Catalyzed Synthesis of a Fe(II)(CO)2(CN)cysteine Precursor to the H‑Cluster of [FeFe] Hydrogenase

Sat, 24 Jun 2023 00:00:00 +0000

The [FeFe] hydrogenase catalyzes the redox interconversion of protons and H₂ with a Fe-S "H-cluster" employing CO, CN, and azadithiolate ligands to two Fe centers. The biosynthesis of the H-cluster is a highly interesting reaction carried out by a set of Fe-S maturase enzymes called HydE, HydF, and HydG. HydG, a member of the radical S-adenosylmethionine (rSAM) family, converts tyrosine, cysteine, and Fe(II) into an organometallic Fe(II)(CO)₂(CN)cysteine "synthon", which serves as the substrate for HydE. Although key aspects of the HydG mechanism have been experimentally determined via isotope-sensitive spectroscopic methods, other important mechanistic questions have eluded experimental determination. Here, we use computational quantum chemistry to refine the mechanism of the HydG catalytic reaction. We utilize quantum mechanics/molecular mechanics simulations to investigate the reactions at the canonical Fe-S cluster, where a radical cleavage of...

Reductive Decomposition Kinetics and Thermodynamics That Govern the Design of Fluorinated Alkoxyaluminate/Borate Salts for Mg-Ion and Ca-Ion Batteries

Thu, 22 Jun 2023 00:00:00 +0000

The rational design of electrolytes has been a long-standing challenge in chemistry and materials science. In this work, we demonstrate a computational rationale for improving the performance of weakly coordinating electrolytes in currently challenging multivalent-ion battery applications, based on enhanced thermodynamic and kinetic stability against reductive decomposition. A series of fluorinated alkoxyborate and alkoxyaluminate salts are systematically examined based on their reduction and oxidation potentials and, motivated by NMR spectroscopy, detailed reductive decomposition pathways involving the breaking of Al/B–O, C–O, or C–F bonds are obtained. Based on the decomposition kinetics, the hexafluoro-tert-isopropoxy (hfip) ligand for borates and the trifluoro-tert-butoxy (tftb) ligand for aluminates are identified as promising ligands for constructing the salt anions. This borate prediction corroborates previous experimental work on Mg[B(hfip)4]2 and Ca[B(hfip)4]2, in...

CaMn3IVO4 Cubane Models of the Oxygen‐Evolving Complex: Spin Ground States S<9/2 and the Effect of Oxo Protonation

Wed, 21 Jun 2023 00:00:00 +0000

We report the single crystal XRD and MicroED structure, magnetic susceptibility, and EPR data of a series of CaMn₃^IV O₄ and YMn₃^IV O₄ complexes as structural and spectroscopic models of the cuboidal subunit of the oxygen-evolving complex (OEC). The effect of changes in heterometal identity, cluster geometry, and bridging oxo protonation on the spin-state structure was investigated. In contrast to previous computational models, we show that the spin ground state of CaMn₃^IV O₄ complexes and variants with protonated oxo moieties need not be S=9/2. Desymmetrization of the pseudo-C₃ -symmetric Ca(Y)Mn₃^IV O₄ core leads to a lower S=5/2 spin ground state. The magnitude of the magnetic exchange coupling is attenuated upon oxo protonation, and an S=3/2 spin ground state is observed in CaMn₃^IV O₃ (OH). Our studies...

Trapping a cross-linked lysine–tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB

Wed, 21 Jun 2023 00:00:00 +0000

The radical S-adenosylmethionine (rSAM) enzyme SuiB catalyzes the formation of an unusual carbon-carbon bond between the sidechains of lysine (Lys) and tryptophan (Trp) in the biosynthesis of a ribosomal peptide natural product. Prior work on SuiB has suggested that the Lys-Trp cross-link is formed via radical electrophilic aromatic substitution (rEAS), in which an auxiliary [4Fe-4S] cluster (AuxI), bound in the SPASM domain of SuiB, carries out an essential oxidation reaction during turnover. Despite the prevalence of auxiliary clusters in over 165,000 rSAM enzymes, direct evidence for their catalytic role has not been reported. Here, we have used electron paramagnetic resonance (EPR) spectroscopy to dissect the SuiB mechanism. Our studies reveal substrate-dependent redox potential tuning of the AuxI cluster, constraining it to the oxidized [4Fe-4S]²⁺ state, which is active in catalysis. We further report the trapping and characterization of an unprecedented...

Crystal Structure of the [FeFe]-Hydrogenase Maturase HydE Bound to Complex‑B

Wed, 21 Jun 2023 00:00:00 +0000

[FeFe]-hydrogenases use a unique organometallic complex, termed the H cluster, to reversibly convert H₂ into protons and low-potential electrons. It can be best described as a [Fe₄S₄] cluster coupled to a unique [2Fe]_H center where the reaction actually takes place. The latter corresponds to two iron atoms, each of which is bound by one CN^- ligand and one CO ligand. The two iron atoms are connected by a unique azadithiolate molecule (^-S-CH₂-NH-CH₂-S^-) and an additional bridging CO. This [2Fe]_H center is built stepwise thanks to the well-orchestrated action of maturating enzymes that belong to the Hyd machinery. Among them, HydG converts l-tyrosine into CO and CN^- to produce a unique l-cysteine-Fe(CO)₂CN species termed complex-B. Very recently, HydE was shown to perform radical-based chemistry using synthetic complex-B as a substrate. Here we report...

Thermo‐Hydro‐Chemical Simulation of Mid‐Ocean Ridge Hydrothermal Systems: Static 2D Models and Effects of Paleo‐Seawater Chemistry

Wed, 21 Jun 2023 00:00:00 +0000

Abstract Decades of research have resulted in characterization of the ocean floor manifestations of mid‐ocean ridge (MOR) hydrothermal systems, yet numerical models accounting for the connections between heat transfer, hydrology and geochemistry have been slow to develop. The Thermo‐hydro‐chemical code ToughReact can be used to describe the coupled effects of fluid flow, heat transfer, and fluid‐rock chemical interactions that occur in MOR systems. We describe the results of 2‐dimensional simulations of steady state flow in fractured diabase with mineral‐fluid chemical reactions. Basal heating and specified permeability yield maximum temperature of 400°C. Total fluid flux and high fracture flow velocities are in accord with observations. Fluid chemistry, mineralogical changes and 87 Sr/ 86 Sr ratios can be compared to observations to assess and calibrate models. Simulated high temperature fracture fluids have Mg and SO 4 near zero, elevated Ca and 87 Sr/ 86 Sr of about 0.7040....

Facile Synthesis of (C6F5)2BBr and (C6F5)2BX(OEt2) (X=Cl, Br) using Hydrogen Halides and Piers’ Borane

Tue, 20 Jun 2023 00:00:00 +0000

We report the facile and efficient synthesis of common electrophilic haloboranes via a protonolysis reaction between Piers’ borane, HB(C6F5)2, and H−X (X=Cl, Br). This route benefits from fast reaction times, easy setup, and minimal workup to yield the analytically pure etherates, (C6F5)2BCl(OEt2) (1) and (C6F5)2BBr(OEt2) (2), as well as the ether-free tri-coordinate species, (C6F5)2BBr (3).

Cover Feature: Facile Synthesis of (C6F5)2BBr and (C6F5)2BX(OEt2) (X=Cl, Br) using Hydrogen Halides and Piers’ Borane (Z. Anorg. Allg. Chem. 8/2023)

Tue, 20 Jun 2023 00:00:00 +0000

Cover Feature: Facile Synthesis of (C6F5)2BBr and (C6F5)2BX(OEt2) (X=Cl, Br) using Hydrogen Halides and Piers’ Borane (Z. Anorg. Allg. Chem. 8/2023)