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At least 1,333 records · Page 74

Direct Ab Initio Simulation of the Synthesis of BaZrO 3 and the Microstructure Impacts on Proton Transport

Controlling and predicting the processing-structure-performance relationship in functional materials is a grand challenge in materials science, with important implications for a wide range of emerging applications; a high fidelity understanding of the performance impact of microstructures formed under synthesis conditions is required to develop advanced materials, such as solid-state fuel cells and electrolyzers. Using the ceramic BaZrO 3 as a case study, we directly simulate the synthesis and investigate how proton transport is dictated by microstructures. We develop a framework that couples density functional theory (DFT), machine-learning interatomic potential (MLIP) driven molecular dynamics, and grand canonical Monte Carlo to perform large-scale, microstructure-resolved, atomistic simulations of proton transport in experimentally representative polycrystalline structures. Our fully ab initio approach, using a MLIP as a proxy for DFT, allows us to quantify the competition between two distinct diffusion mechanisms: one associated with grain-boundary regions and another within grains. When the impacts of grain boundaries are taken into account, proton transport exhibits substantial deviation from the bulk oxide limit. This addresses long-standing discrepancies between theory and experiments. Our integrated approach provides atomistic insight into microstructure-dependent proton pathways in BaZrO 3 and establishes a general protocol for predicting processing-structure-performance relationships.

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Assessment of TMT Labeling Efficiency in Large-Scale Quantitative Proteomics: The Critical Effect of Sample pH

Isobaric labeling via tandem mass tag (TMT) reagents enables sample multiplexing prior to LC–MS/MS, facilitating high-throughput large-scale quantitative proteomics. Consistent and efficient labeling reactions are essential to achieve robust quantification; therefore, embedded in our clinical proteomic protocol is a quality control (QC) sample that contains a small aliquot from each sample within a TMT set, referred to as “Mixing QC.” This Mixing QC enables the detection of TMT labeling issues by LC–MS/MS before combining the full samples to allow for salvaging of poor TMT labeling reactions. While TMT labeling is a valuable tool, factors leading to poor reactions are not fully studied. We observed that relabeling does not necessarily rescue TMT reactions and that peptide samples sometimes remained acidic after resuspending in 50 mM HEPES buffer (pH 8.5), which coincided with low labeling efficiency (LE) and relatively low median reporter ion intensities (MRIIs). To obtain a more resilient TMT labeling procedure, we investigated LE, reporter ion missingness, the ratio of mean TMT set MRII to individual channel MRII, and the distribution of log 2 reporter ion ratios of Mixing QC samples. We discovered that sample pH is a critical factor in LE, and increasing the buffer concentration in poorly labeled samples before relabeling resulted in the successful rescue of TMT labeling reactions. Moreover, resuspending peptides in 500 mM HEPES buffer for TMT labeling resulted in consistently higher LE and lower missing data. By better controlling the sample pH for labeling and implementing multiple methods for assessing labeling quality before combining samples, we demonstrate that robust TMT labeling for large-scale quantitative studies is achievable.

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Direct Recycling of Lithium-Ion Battery Cathodes: A Multi-Stage Annealing Process to Recover the Pristine Structure and Performance

Direct recycling is an alternative low-cost process that retains the structure of the lithium-ion battery cathode rather than going through materials dissolution and repurification. While the process shows promise, various steps need to be better understood and studied to identify possible roadblocks, cost intensive steps, and needed variations in protocol that may be necessary based on the feedstock of recycled cathodes available. In this study, we have evaluated the process of thermal relithiation as it applies to end-of-life cathode materials. For recovered end-of-life cathodes, approximately 20% of the useable lithium has been lost due to solid electrolyte interface formation, parasitic reactions, and particle isolation; this lost lithium contributes to higher cell impedance and a gradual shift in electrode potentials. As a first step in the direct recycling process, this lithium needs to be restored not only to recover capacity but also to eliminate surface vacancies and hinder surface reconstruction that may increase impedance and impact performance. Here, we have optimized a coating method followed by a two-stage annealing process that restores a model delithiated NMC333 material to pristine performance. Comparisons to single-stage processes are made, and new characterization tools have been used to better understand the processes.

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Not Cutting Corners: Bioderived Triggers Driving Oxidative Main Chain Scission of Poly(ethylene terephthalate)

About 20–34 billion poly(ethylene terephthalate) (PET) bottles from the beverage industry leak into aquatic ecosystems annually, necessitating the development of urgent strategies to treat waterborne plastic pollution. Inspired by the scalability of water disinfection infrastructure and protocols, we present a dual depolymerization approach relying on oxidation, followed by hydrolysis. Incorporating bioderived monounsaturated C18 diacid (C18:1-DA) counits at low dosages (2–5%) in the PET backbone overcomes the diffusional limitations of depolymerizing PET in the solid state by suppressing the glass transition temperature of the copolymer by 20 °C. Cryomilled C18:1-PET powder suspended in an oxidant-loaded alkaline slurry underwent bulk depolymerization to oligomers at 80–100 °C via oxidative scissions at the internally located unsaturations. In contrast, conventional PET undergoes only minor end-chain scission under mild alkaline conditions. These oligomers are suitable for low-energy repolymerization or facile solvolysis to monomers. A permanganate-periodate oxidant couple demonstrated successful oxidation through the bulk of the polymer, which subsequently was hydrolyzed to monomers. Furthermore, this model system serves as a proxy for ozonolysis, followed by mild hydrolysis to reduce the energetics of alkaline hydrolysis. This integrated oxidation–hydrolysis strategy paves the way for the industrial adoption of cleaner, advanced oxidation processes, such as ozonolysis for plastic pretreatment, further enabling commercialized chemical recycling of unsaturation-containing polyesters.

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Investigating and Optimizing the Lysate-Based Expression of Nonribosomal Peptide Synthetases Using a Reporter System

Lysate-based cell-free expression (CFE) systems are accessible platforms for expressing proteins that are difficult to synthesize in vivo, such as nonribosomal peptide synthetases (NRPSs). NRPSs are large (>100 kDa), modular enzyme complexes that synthesize bioactive peptide natural products. This synthetic process is analogous to transcription/translation (TX/TL) in lysates, resulting in potential resource competition between NRPS expression and NRPS activity in cell-free environments. Moreover, CFE conditions depend on the size and structure of the protein. Here, a reporter system for rapidly investigating and optimizing reaction environments for NRPS CFE is described. This strategy is demonstrated in E. coli lysate reactions using blue pigment synthetase A (BpsA), a model NRPS, carrying a C-terminal tetracysteine (TC) tag which forms a fluorescent complex with the biarsenical dye, FlAsH. A colorimetric assay was adapted for lysate reactions to detect the blue pigment product, indigoidine, of cell-free expressed BpsA-TC, confirming that the tagged enzyme is catalytically active. An optimized protocol for end point TC/FlAsH complex measurements in reactions enables quick comparisons of full-length BpsA-TC expressed under different reaction conditions, defining unique requirements for NRPS expression that are related to the protein’s catalytic activity and size. Importantly, these protein-dependent CFE conditions enable higher indigoidine titer and improve the expression of other monomodular NRPSs. Notably, these conditions differ from those used for the expression of superfolder GFP (sfGFP), a common reporter for optimizing lysate-based CFE systems, indicating the necessity for tailored reporters to optimize expression for specific enzyme classes. In conclusion, the reporter system is anticipated to advance lysate-based CFE systems for complex enzyme synthesis, enabling natural product discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Synthetic Biology Toolbox for Nitrogen-Fixing Soil Microbes

The soil environment adjacent to plant roots, termed the rhizosphere, is home to a wide variety of microorganisms that can significantly affect the physiology of nearby plants. Microbes in the rhizosphere can provide nutrients, secrete signaling compounds, and inhibit pathogens. These processes could be manipulated with synthetic biology to enhance the agricultural performance of crops grown for food, energy, or environmental remediation, if methods can be implemented in these nonmodel microbes. A common first step for domesticating nonmodel organisms is the development of a set of genetic engineering tools, termed a synthetic biology toolbox. A toolbox comprises transformation protocols, replicating vectors, genome engineering (e.g., CRISPR/Cas9), constitutive and inducible promoter systems, and other gene expression control elements. Furthermore, this work validated synthetic biology toolboxes in three nitrogen-fixing soil bacteria: Azotobacter vinelandii, Stutzerimonas stutzeri (Pseudomonas stutzeri), and a new isolate of Klebsiella variicola. All three organisms were amenable to transformation and reporter protein expression, with several functional inducible systems available for each organism. S. stutzeri and K. variicola showed more reliable plasmid-based expression, resulting in successful Cas9 recombineering to create scarless deletions and insertions. Using these tools, we generated mutants with inducible nitrogenase activity and introduced heterologous genes to produce resorcinol products with relevant biological activity in the rhizosphere.

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Automated Strain Construction for Biosynthetic Pathway Screening in Yeast

Automation accelerates the Design-Build-Test-Learn (DBTL) cycle for synthetic biology; however, most strain construction pipelines lack robotic integration. Here, in this study, we present the workflow design and source code for a modular, integrated protocol that automates the Build step in Saccharomyces cerevisiae. We programmed the Hamilton Microlab VANTAGE to integrate off-deck hardware via its central robotic arm, enabling automated steps that increased throughput to 2,000 transformations per week. We developed a user interface with the Hamilton VENUS software to support on-demand parameter customization. As a proof of concept, we screened a gene library in an engineered yeast strain producing verazine, a key intermediate in the biosynthesis of steroidal alkaloids. Our pipeline rapidly identified pathway bottlenecks and genes that enhanced verazine production by 2.0- to 5-fold. This technical note provides resources for synthetic biologists designing yeast workflows for biofoundries to screen libraries for pathway discovery/optimization, combinatorial biosynthesis, and protein engineering.

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Customized Chiral Colloids

This contribution describes a synthetic strategy for the fabrication of multicomponent colloidal “molecules” with controllable complex morphologies and compositionally distinct lobes. Using 3-(trimethoxysilyl)propyl methacry-late (TPM) as the building block, the methodology enables a scalable bulk synthesis of customized chiral colloidal particles with geometric and compositional chirality by sequential seeded growth method. Finally, the synthetic protocol presents a versatile platform for constructing colloidal molecules with multiple components having customized shapes and functionalities, with the potential to impact the design of chromatic patchy particles, colloidal swimmers and chiral optical materials, as well as informing programmable assembly.

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Node-Accessible Zirconium MOFs

High-stability, zirconium-based metal–organic frameworks are attractive as heterogeneous catalysts and as model supports for uniform arrays of subsequently constructed heterogeneous catalysts—for example, MOF-node-grafted metal–oxy and metal–sulfur clusters. For hexa-Zr(IV)-MOFs characterized by nodes that are less than 12-connected, sites not used for linkers are ideally occupied by reactive and displaceable OH/H 2 O pairs. Here, the desired pairs are ideal for grafting the aforementioned catalytic clusters, while aqua-ligand lability renders them effective for exposing highly Lewis-acidic Zr(IV) sites (catalytic sites) to candidate reactants. New single-crystal X-ray studies of an eight-connected Zr-MOF, NU-1000, reveal that conventional activation fully removes modulator ligands, but replaces them with three node-blocking formate ligands (from solvent decomposition) and only one OH/H 2 O pair, not four—a largely overlooked complication that now appears to be general for Zr-MOFs. Here we describe an alternative activation protocol that effectively removes modulators, avoids formate, and installs the full complement of terminal OH/H 2 O pairs. It does so via an unusual isolatable intermediate featuring eight aqua ligands and four non-ligated chlorides—again as supported by single-crystal X-ray data. We find that complete replacement of node-blocking modulators/formate with the originally envisioned OH/OH 2 pairs has striking consequences; here we touch upon just three. First, elimination of unrecognized formate renders aqua ligands much more thermally labile, enabling open Zr(IV) sites to be obtained at lower temperature. Second, in the absence of formate, which otherwise links and locks pairs of node Zr(IV) ions, reversible removal of aqua ligands engenders reversible contraction of MOF meso- and micropores, as evidenced by X-ray diffraction. Third, formate replacement with OH/OH 2 pairs renders NU-1000 ca.10× more active for catalytic hydrolytic degradation of a representative simulant of G-type chemical warfare agents.

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Optimizing Active Sites for High CO Selectivity during CO 2 Hydrogenation over Supported Nickel Catalysts

The undesired formation of CH 4 during the hydrogenation of CO 2 remains a great challenge with direct impact on selectivity towards CO or CH 3 OH. In this study, the selectivity of a supported Ni catalyst prepared by traditional impregnation method was found to change after a first CO 2 hydrogenation reaction cycle from 100 to 800 °C. The usually high CH 4 formation was suppressed leading to full selectivity towards CO. This behavior was also observed after the catalyst was treated under methane or propane atmospheres at elevated temperatures. In-situ spectroscopic studies revealed that the accumulation of carbon species on the catalyst surface at high temperature leads to a nickel carbide-like phase. The catalyst regains its high selectivity to CH 4 production after carbon depletion from the surface of the Ni particles by oxidation. However, the selectivity readily shifts back towards CO formation after a new temperature programmed CO 2 hydrogenation cycle. The fraction of weakly adsorbed CO species increases on the carbide-like surface when compared to a clean nickel surface, explaining the higher selectivity towards CO formation. This easy protocol of changing the surface of a common Ni catalyst to gain selectivity represents an important step for the commercial use of CO 2 hydrogenation to CO process together with Fischer-Tropsch applications.

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Quantum Machine-Learning for Eigenstate Filtration in Two-Dimensional Materials

Quantum machine-learning algorithms have emerged to be a promising alternative to their classical counterparts as they leverage the power of quantum computers. Such algorithms have been developed to solve problems like electronic structure calculations of molecular systems and spin models in magnetic systems. However, the discussion in all these recipes focuses specifically on targeting the ground state. Herein we demonstrate a quantum algorithm that can filter any energy eigenstate of the system based on either symmetry properties or a predefined choice of the user. The workhorse of our technique is a shallow neural network encoding the desired state of the system with the amplitude computed by sampling the Gibbs–Boltzmann distribution using a quantum circuit and the phase information obtained classically from the nonlinear activation of a separate set of neurons. We show that the resource requirements of our algorithm are strictly quadratic. To demonstrate its efficacy, we use state filtration in monolayer transition metal dichalcogenides which are hitherto unexplored in any flavor of quantum simulations. We implement our algorithm not only on quantum simulators but also on actual IBM-Q quantum devices and show good agreement with the results procured from conventional electronic structure calculations. We thus expect our protocol to provide a new alternative in exploring the band structures of exquisite materials to usual electronic structure methods or machine-learning techniques that are implementable solely on a classical computer.

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Covalent Organic Frameworks with Irreversible Linkages via Reductive Cyclization of Imines

Covalent organic frameworks (COFs) show great potential for many advanced applications on account of their structural uniqueness. To address the synthetic challenges, facile chemical routes to engineer the porosity, crystallinity, and functionality of COFs are highly sought after. Herein, we report a synthetic approach that employs the Cadogan reaction to introduce nitrogen-containing heterocycles as the linkages in the framework. Irreversible indazole and benzimidazolylidene (BIY) linkages are introduced into COFs for the first time via phosphine-induced reductive cyclization of the common imine linkages following either stepwise or one-pot reaction protocols. Further, the successful linkage transformation introduces new functionalities, as demonstrated in the case of BIY-COF, which displays excellent intrinsic proton conductivity without the need of impregnation with external proton transfer reagents. Such a general strategy will open the window to a broader class of functional porous crystalline materials.

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Understanding the Stability of Manganese Chromium Antimonate Electrocatalysts through Multimodal In Situ and Operando Measurements

Herein, we utilize an on-line electrochemical flow cell coupled with an inductively coupled plasma-mass spectrometer (ICP-MS) to characterize the impact of composition and reactant gas on the multielement dissolution of Mn(-Cr)-Sb-O electrocatalysts. Compared to Mn 2 O 3 and Cr 2 O 3 oxides, we find that the antimonate framework stabilizes Mn at OER potentials and Cr at both ORR and OER potentials. Furthermore, dissolution of Mn and Cr from Mn(-Cr)-Sb-O is found to be driven by ORR reaction rate, with minimal dissolution under N 2 . We observe preferential dissolution of Cr totaling 13% over 10 minutes at 0.3, 0.6, and 0.9 V vs RHE, with only 1.5% loss of Mn, indicating an enrichment of Mn at the surface of the particles. Despite this asymmetric dissolution, in situ X-ray absorption spectroscopy (XAS) showed no measurable changes in the Mn K-edge at comparable potentials. This lack of change could suggest that modification to the Mn oxidation state in the surface layer is too small or that layer is too thin to be measured with the bulk XAS measurement. Lastly, on-line ICP-MS was used to assess the effects of applied potential, scan rate, and current of Mn-Cr-Sb-O during cyclic voltammetry and accelerated stress tests. With this deeper understanding of the interplay between oxygen reduction and dissolution, testing procedures were identified to maximize both activity and stability. This work highlights the use of multi-modal in situ characterization techniques in tandem to build a more complete model of stability and develop protocols for optimizing catalyst performance.

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Investigating Fundamental Principles of Nonequilibrium Assembly Using Temperature-Sensitive Copolymers

Both natural biomaterials and synthetic materials benefit from complex energy landscapes that provide the foundation for structure–function relationships and environmental sensitivity. Understanding these nonequilibrium dynamics is important for the development of design principles to harness this behavior. Using a model system of poly(ethylene glycol) methacrylate-based thermoresponsive lower critical solution temperature (LCST) copolymers, we explored the impact of composition and stimulus path on nonequilibrium thermal hysteretic behavior. Through turbidimetry analysis of nonsuperimposable heat–cool cycles, we observe that LCST copolymers show clear hysteresis that varies as a function of pendent side chain length and hydrophobicity. Hysteresis is further impacted by the temperature ramp rate, as insoluble states can be kinetically trapped under optimized temperature protocols. As a result, this systematic study brings to light fundamental principles that can enable the harnessing of out-of-equilibrium effects in synthetic soft materials.

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Engineering Robust Metallic Zero-Mode States in Olympicene Graphene Nanoribbons

Metallic graphene nanoribbons (GNRs) represent a critical component in the toolbox of low-dimensional functional materials technology serving as 1D interconnects capable of both electronic and quantum information transport. The structural constraints imposed by on-surface bottom-up GNR synthesis protocols along with the limited control over orientation and sequence of asymmetric monomer building blocks during the radical step-growth polymerization have plagued the design and assembly of metallic GNRs. Here, we report the regioregular synthesis of GNRs hosting robust metallic states by embedding a symmetric zero-mode (ZM) superlattice along the backbone of a GNR. Tight-binding electronic structure models predict a strong nearest-neighbor electron hopping interaction between adjacent ZM states, resulting in a dispersive metallic band. First-principles density functional theory-local density approximation calculations confirm this prediction, and the robust, metallic ZM band of olympicene GNRs is experimentally corroborated by scanning tunneling spectroscopy.

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Photoinduced Magnetic Exchange-Jump Promotes Ground State Biradical Electron Spin Polarization

Photoinduced electron spin polarization (ESP) is reported in the electronic ground states of three Pt(II) complexes that are comprised of two S = ½ nitronyl nitroxide (NN) radicals attached through different length para-phenylethynyl bridges to the 3,6 positions of a catecholate (CAT, donor) and 4,4’-di-tert-butyl-2,2’-bipyridine (bpy, acceptor). Complexes 1-3 have from 17 to 41 bonds separating NN radicals, and display cw-EPR spectra consistent with |J NN-NN | >> |a N |, |J NN-NN | ≥ |a N |, and |J NN-NN | < |a N |, respectively, where J NN-NN is the magnetic exchange coupling between NN radicals in the electronic ground state, and a N is the isotropic 14 N hyperfine coupling constant. Light-induced transient EPR spectra characterized as enhanced ground-state absorption were observed for all three complexes using 532 nm pulsed laser excitation into the ligand-to-ligand charge transfer (LL’CT) band of the (CAT)Pt(bpy) chromophore. The magnitude of the observed ESP increases in the order 1 < 2 < 3 and is inversely correlated with the magnitude of ground-state J NN-NN . In addition to the experimental observation net absorptive polarization in 1-3, light excitation also produces multiplet polarization in 2. Since the weak dipolar coupling leads to strong spectral overlap of the absorptive and emissive components, the multiplet polarization is not observed in 1 and 3 and is very weak in 2. Here, the ability to spin polarize multiple radical spins with a single photon is anticipated to advance new photoinduced multi qubit/qudit ESP protocols for quantum information science applications.

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Aliovalent Substitution Tunes Physical Properties in a Conductive Bis(dithiolene) Two-Dimensional Metal–Organic Framework

Two-dimensional conductive metal–organic frameworks have emerged as promising electronic materials for applications in (opto)electronic, thermoelectric, magnetic, electrocatalytic, and energy storage devices. Many bottom-up or postsynthetic protocols have been developed to isolate these materials or further modulate their electronic properties. However, some methodologies commonly used in classic semiconductors, notably, aliovalent substitution, are conspicuously absent. Here, in this work, we demonstrate how aliovalent Fe(III) to Ni(II) substitution enables the isolation of a Ni bis(dithiolene) material from a previously reported Fe analogue. Detailed characterization supports the idea that aliovalent substitution of Fe(III) to Ni(II) results in an in situ oxidation of the organic dithiolene linker. This substitution-induced redox tuning modulates the electronic properties in the system, leading to higher electrical conductivity and Hall mobility but slightly lower carrier densities and weaker antiferromagnetic interactions. Moreover, this aliovalent substitution improves the material’s electrochemical stability and thus enables pseudocapacitive behavior in the Ni material. These results demonstrate how classic aliovalent substitution strategies in semiconductors can also be leveraged in conductive MOFs and add further support to this class of compounds as emerging electronic materials.

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Dynamic Bubbling Balanced Proactive CO 2 Capture and Reduction on a Triple-Phase Interface Nanoporous Electrocatalyst

The formation and preservation of the active phase of the catalysts at the triple-phase interface during CO 2 capture and reduction is essential for improving the conversion efficiency of CO 2 electroreduction toward value-added chemicals and fuels under operational conditions. Designing such ideal catalysts that can mitigate parasitic hydrogen generation and prevent active phase degradation during the CO 2 reduction reaction (CO 2 RR), however, remains a significant challenge. Herein, we developed an interfacial engineering strategy to build a new SnO x catalyst by invoking multiscale approaches. This catalyst features a hierarchically nanoporous structure coated with an organic F-monolayer that modifies the triple-phase interface in aqueous electrolytes, substantially reducing competing hydrogen generation (less than 5%) and enhancing CO 2 RR selectivity (~90%). This rationally designed triple-phase interface overcomes the issue of limited CO 2 solubility in aqueous electrolytes via proactive CO 2 capture and reduction. Concurrently, we utilized pulsed square-wave potentials to dynamically recover the active phase for the CO 2 RR to regulate the production of C1 products such as formate and carbon monoxide (CO). This protocol ensures profoundly enhanced CO 2 RR selectivity (~90%) compared with constant potential (~70%) applied at -0.8 V (V vs RHE). We further achieved a mechanistic understanding of the CO 2 capture and reduction processes under pulsed square-wave potentials via in situ Raman spectroscopy, thereby observing the potential-dependent intensity of Raman vibrational modes of the active phase and CO 2 RR intermediates. Finally, this work will inspire material design strategies by leveraging triple-phase interface engineering for emerging electrochemical processes, as technology moves toward electrification and decarbonization.

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