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At least 577 records · Page 32

Top-down proteomics

Proteoforms arising from posttranslational modifications, genetic polymorphisms, and RNA splice variants, play a pivotal role as the key drivers in biology. Thus, a comprehensive understanding of proteoforms is essential for unraveling the intricacies of biological systems and bridging the gap between genotype and phenotype. By analyzing whole proteins without digestion, top-down proteomics (TDP) provides a holistic view of the proteome and presents a next-generation approach for deciphering protein function, uncovering disease mechanisms, and advancing precision medicine. This Primer embarks on a journey into the world of TDP by encapsulating its historical context, underlying principles, recent advances, and an outlook on the future of TDP. The experimental section navigates instrumentation, sample preparation, intact protein separation, tandem mass spectrometry techniques, and data collection. Results decipher raw data, visualize intact protein spectra, unravel data analysis, and explain proteoform identification, characterization, and quantitation, as well as statistical analysis. Various applications of TDP spanning the human proteoform project, biomedical, biopharmaceutical, and clinical applications are described. These are complemented by discussions on measurement reproducibility, limitations, and a forward-looking perspective outlining uncharted waters where the field can advance, and potential exciting future applications of TDP.

Roberts, David S.↗

Selective electrified polyethylene upcycling by pore-modulated pyrolysis

Plastic waste is a increasing problem, accumulating in landfills and the environment. Pyrolysis is a promising and industrially relevant approach for transforming plastic waste into value-added chemicals. However, the selectivity and yield of traditional plastic pyrolysis are poor, with products featuring broad molar mass distributions. Here we report a highly selective, energy-efficient and catalyst-free pyrolysis method that can upcycle plastic into value-added chemicals via pore-modulated pyrolysis. Using a Joule-heated carbon column, we demonstrate the pivotal role of the reactor’s graded porous structure in decreasing the polydispersity of the reaction intermediates, enabling high product selectivity and yield. The decreasing pore size of the reactor modulates the mass transport in an apparent gating effect—preventing high-molar-mass species from exiting the reactor before sufficient pyrolysis has occurred. Using polyethylene as a model reactant, we demonstrate a high yield of 65.9 ± 5.2% and up to 80.8% selectivity toward value-added aviation fuel precursor (C8–C18 hydrocarbons) without the use of any catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Advances in soft X-ray RIXS for studying redox reaction states in batteries

Redox (reduction and oxidation) chemistry provides the fundamental basis for numerous energy-related electrochemical devices. Detecting the electrochemical redox chemistry is pivotal but challenging because it requires independent probes of the cationic and anionic redox states at different electrochemical states. Here, the synchrotron-based soft X-ray mapping of resonant inelastic X-ray scattering (mRIXS) has recently emerged as a powerful tool for exploring such states in electrochemical devices, especially batteries. High-efficiency mRIXS covers the energy range of the absorption edge with the extra dimension of information on the emitted photon energies. In this frontier article, we review recent representative demonstrations of utilizing soft X-ray mRIXS for detecting the novel chemical state during electrochemical operation and for quantifying the cationic redox reactions through inverse partial fluorescence yield analysis (mRIXS-iPFY). More importantly, the non-divalent states of oxygen in electrodes involving oxygen redox reactions could be reliably captured by mRIXS, with its reversibility quantified by the intensity variation of the characteristic mRIXS feature through a super-partial fluorescence yield analysis (mRIXS-sPFY). These recent demonstrations inspire future perspectives on using mRIXS for studying the complex phenomena in energy materials, with both technical and scientific challenges in RIXS theory, in situ/operando experiments, and spatially resolved RIXS imaging.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transition metal-based bimetallic MOFs and MOF-derived catalysts for electrochemical oxygen evolution reaction

The oxygen evolution reaction (OER) is a critical electrochemical reaction in water splitting and rechargeable metal–air batteries. It plays a pivotal role in achieving high-efficiency clean-energy production and energy storage in these devices. Transition metal-based bimetallic MOFs (TMB MOFs) with two different metal ions possess specific synergistic effects, which could exhibit OER performance and stability superior to those of the corresponding monometallic MOFs for water oxidation. Benefiting from the diversity of chemical composition and structural type, TMB MOFs can also serve as precursors and templates to obtain alloy-particle-decorated carbon materials with high surface area, or metal compounds such as bimetallic sulfides, phosphides, and hydroxides with atomic-level mixing of heterometallic elements. These materials with high-density active sites exhibit much improved catalytic activity in the water oxidation reaction. Furthermore, this article aims to review the recent progress with TMB MOFs and their derivatives in relation to applications as electrocatalysts in OER, including analysis of the mechanism of the OER process with the assistance of DFT calculations and in situ or operando techniques.

36 MATERIALS SCIENCE↗

Amino acid interacting network in the receptor-binding domain of SARS-CoV-2 spike protein

The relation between amino acid (AA) sequence and biologically active conformation controls the process of polypeptide chains folding into three-dimensional (3d) protein structures. The recent achievements in the resolution achieved in cryo-electron microscopy coupled with improvements in computational methodologies have accelerated the analysis of structures and properties of proteins. However, the detailed interaction between AAs has not been fully elucidated. Herein, we present a de novo method to evaluate inter-amino acid interactions based on the concept of accurately evaluating the amino acid bond pairs (AABP). The results obtained enabled the identification of complex 3d long-range interconnected AA interacting network in proteins. The method is applied to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. We show that although nearest-neighbor AAs in the primary sequence have large AABP, other nonlocal AAs make substantial contribution to AABP with significant participation of both covalent and hydrogen bonding. Detailed analysis of AABP in RBD reveals the pivotal role they play in sequence conservation with profound implications on residue mutations and for therapeutic drug design. This approach could be easily applied to many other proteins of biomedical interest in life sciences.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Local orientation of chains at crystal/amorphous interfaces buried in isotactic polypropylene thin films

A better understanding of the aggregation states of polymer chains in thin films is of pivotal importance for developing thin film polymer devices in addition to its inherent scientific interest. Here we report the preferential orientation of the crystalline lamellae for isotactic polypropylene (iPP) in spin-coated films by grazing incidence of wide-angle X-ray diffraction in conjunction with sum frequency generation vibrational spectroscopy, which provides information on the local conformation of chains at crystal/amorphous interfaces buried in a thin film. The crystalline orientation of iPP, which formed cross-hatched lamellae induced by lamellar branching, altered from a mixture of edge-on and face-on mother lamellae to preferential face-on mother lamellae with decreasing thickness. Here, the orientation of methyl groups at the crystal/amorphous interfaces in the interior region of the iPP films changed, accompanied by a change in the lamellar orientation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adsorption of ethylenediamine on Cu surfaces: attributes of a successful capping molecule using first-principles calculations

The shape-controlled synthesis of Cu nanocrystals can benefit a wide range of applications, though challenges exist in achieving high and selective yields to a particular shape. Capping agents play a pivotal role in controlling shape, but their exact role remains ambiguous. In this study, the adsorption of ethylenediamine (EDA) on Cu(100) and Cu(111) was investigated with quantum density functional theory (DFT) to reveal the complex roles of EDA in promoting penta-twinned Cu nanowire growth. We find EDA has stronger binding on Cu(100) than on Cu(111), which agrees the general expectation that penta-twinned Cu nanowires express facets with stronger capping-molecule binding. Despite this stronger binding, ab initio thermodynamics reveals the surface energy of EDA-covered Cu(111) is lower than that EDA-covered Cu(100) at all solution-phase EDA chemical potentials, so there is no thermodynamic driving force for penta-twinned nanowires. We also investigated the capability of EDA to protect Cu surfaces from oxidation in water by quantifying energy barriers for a water molecule to diffuse through EDA layers on Cu(100) and Cu(111). The energy barrier on Cu(100) is significantly lower, which supports observations of faster oxidation of Cu(100) in electrochemical experiments. Thus, we elucidate another possible function of a capping agent – to enable selective oxidation of crystal facets. This finding adds to the general understanding of successful attributes of capping agents for shape-selective nanocrystal growth.

36 MATERIALS SCIENCE↗

Refining the thermochemical properties of CF, SiF, and their cations by combining photoelectron spectroscopy, quantum chemical calculations, and the Active Thermochemical Tables approach

Fluorinated species have a pivotal role in semiconductor material chemistry and some of them have been detected beyond the Earth's atmosphere. Achieving good energy accuracy on fluorinated species using quantum chemical calculations has long been a challenge. In addition, obtaining direct experimental thermochemical quantities has also proved difficult. Here, we report the threshold photoelectron and photoion yield spectra of SiF and CF radicals generated with a fluorine reactor. The spectra were analysed with the support of ab initio calculations, resulting in new experimental values for the adiabatic ionisation energies of both CF (9.128 ± 0.006 eV) and SiF (7.379 ± 0.009 eV). Using these values, the underlying thermochemical network of Active Thermochemical Tables was updated, providing further refined enthalpies of formation and dissociation energies of CF, SiF, and their cationic counterparts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bond clusters control rupture force limit in shear loaded histidine-Ni 2+ metal-coordinated proteins

Dynamic noncovalent interactions are pivotal to the structure and function of biological proteins and have been used in bioinspired materials for similar roles. Metal-coordination bonds, in particular, are especially tunable and enable control over static and dynamic properties when incorporated into synthetic materials. Despite growing efforts to engineer metal-coordination bonds to produce strong, tough, and self-healing materials, the systematic characterization of the exact contribution of these bonds towards mechanical strength and the effect of geometric arrangements is missing, limiting the full design potential of these bonds. In this work, we engineer the cooperative rupture of metal-coordination bonds to increase the rupture strength of metal-coordinated peptide dimers. Utilizing all-atom steered molecular dynamics simulations on idealized bidentate histidine-Ni 2+ coordinated peptides, we show that histidine-Ni 2+ bonds can rupture cooperatively in groups of two to three bonds. We find that there is a strength limit, where adding additional coordination bonds does not contribute to the additional increase in the protein rupture strength, likely due to the highly heterogeneous rupture behavior exhibited by the coordination bonds. Further, we show that this coordination bond limit is also found natural metal-coordinated biological proteins. Using these insights, we quantitatively suggest how other proteins can be rationally designed with dynamic noncovalent interactions to exhibit cooperative bond breaking behavior. Altogether, this work provides a quantitative analysis of the cooperativity and intrinsic strength limit for metal-coordination bonds with the aim of advancing clear guiding molecular principles for the mechanical design of metal-coordinated materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Boosting the performance of reversible solid oxide electrochemical cells with a novel hybrid oxygen electrode, Pr 1.39 Ba 0.14 Sr 0.53 Co 1.48 Fe 0.76 O 6- δ -Ba 0.66 Sr 0.34 CoO 3- δ

Solid oxide electrochemical cells (SOECs) stand out as a highly promising clean energy technology that offers several benefits, showing significant potential to play a pivotal role in the transition towards a sustainable and low-carbon energy future. SOECs can efficiently convert the chemical energy stored in fuels to electricity in fuel cell mode, and produce various chemicals from abundant feedstocks (e.g., CO 2 , H 2 O) and intermittent solar/wind-based renewable electricity. Despite extensive efforts that have been devoted to designing novel materials and optimizing SOEC manufacturing processes, aiming to achieve enhanced energy efficiency, the current SOECs still suffer from poor performance, which is mainly due to the sluggish oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) kinetics. To address this challenge, in this work, we have successfully designed an in situ formed hybrid oxygen electrode material (Pr 1.39 Ba 0.14 Sr 0.53 Co 1.48 Fe 0.76 O 6- δ -Ba 0.66 Sr 0.34 CoO 3- δ ), which significantly improves the surface oxygen exchange coefficient and bulk oxygen-ion diffusion coefficient, enhancing the OER and ORR electrocatalytic activities. Further, the SOECs equipped with this newly developed oxygen electrode achieved exceptional performance for power generation using both hydrogen and propane as the fuels. At 750 °C, a peak power density of 2.4 W cm -2 was obtained with H 2 as the fuel. Additionally, the SOECs attain unprecedented performance in steam electrolysis mode. A current density of 4.4 A cm -2 was achieved at 1.3 V and 750 °C, which represents the highest performance among all yttria-stabilized zirconia (YSZ) electrolyte-based SOECs. The SOECs also deliver remarkable stability during the accelerated stability testing, highlighting the great potential of Pr 1.39 Ba 0.14 Sr 0.53 Co 1.48 Fe 0.76 O 6- δ -Ba 0.66 Sr 0.34 CoO 3- δ as a high-performance oxygen electrode for next generation SOECs.

08 HYDROGEN↗

The role of oxygen in automotive grade lithium-ion battery cathodes: an atomistic survey of ageing

The rising demand for high-performance lithium-ion batteries, pivotal to electric transportation, hinges on key materials like the Ni-rich layered oxide LiNi x Co y Al z O 2 (NCA) used in cathodes. The present study investigates the redox mechanisms, with particular focus on the role of oxygen in commercial NCA electrodes, both fresh and aged under various conditions (aged cells have performed >900 cycles until a cathode capacity retention of ~80%). Our findings reveal that oxygen participates in charge compensation during NCA delithiation, both through changes in transition metal (TM)–O bond hybridization and formation of partially reversible O 2 , the latter occurs already below 3.8 V vs. Li/Li + . Aged NCA material undergoes more significant changes in TM–O bond hybridization when cycling above 50% SoC, while reversible O 2 formation is maintained. Nickel is found to be redox active throughout the entire delithiation and shows a more classical oxidation state change during cycling with smaller changes in the Ni–O hybridization. By contrast, Co redox activity relies on a stronger change in Co–O hybridization, with only smaller Co oxidation state changes. The Ni–O bond displays an almost twice as large change in its bond length on cycling as the Co–O bond. The Ni–O 6 octahedra are similar in size to the Co–O 6 octahedra in the delithiated state, but are larger in the lithiated state, a size difference that increases with battery ageing. These contrasting redox activities are reflected directly in structural changes. The NCA material exhibits the formation of nanopores upon ageing, and a possible connection to oxygen redox activity is discussed. The difference in interaction of Ni and Co with oxygen provides a key understanding of the mechanism and the electrochemical instability of Ni-rich layered transition metal oxide electrodes. Our research specifically highlights the significance of the role of oxygen in the electrochemical performance of electric-vehicle-grade NCA electrodes, offering important insights for the creation of next-generation long-lived lithium-ion batteries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unifying thermochemistry concepts in computational heterogeneous catalysis

Thermophysical properties of adsorbates and gas-phase species define the free energy landscape of heterogeneously catalyzed processes and are pivotal for an atomistic understanding of the catalyst performance. These thermophysical properties, such as the free energy or the enthalpy, are typically derived from density functional theory (DFT) calculations. Enthalpies are species-interdependent properties that are only meaningful when referenced to other species. The widespread use of DFT has led to a proliferation of new energetic data in the literature and databases. However, there is a lack of consistency in how DFT data is referenced and how the associated enthalpies or free energies are stored and reported, leading to challenges in reproducing or utilizing the results of prior work. Additionally, DFT suffers from exchange–correlation errors that often require corrections to align the data with other global thermochemical networks, which are not always clearly documented or explained. In this review, we introduce a set of consistent terminology and definitions, review existing approaches, and unify the techniques using the framework of linear algebra. This set of terminology and tools facilitates the correction and alignment of energies between different data formats and sources, promoting the sharing and reuse of ab initio data. Standardization of thermochemistry concepts in computational heterogeneous catalysis reduces computational cost and enhances fundamental understanding of catalytic processes, which will accelerate the computational design of optimally performing catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unlocking the potential: machine learning applications in electrocatalyst design for electrochemical hydrogen energy transformation

Machine learning (ML) is rapidly emerging as a pivotal tool in the hydrogen energy industry for the creation and optimization of electrocatalysts, which enhance key electrochemical reactions like the hydrogen evolution reaction (HER), the oxygen evolution reaction (OER), the hydrogen oxidation reaction (HOR), and the oxygen reduction reaction (ORR). This comprehensive review demonstrates how cutting-edge ML techniques are being leveraged in electrocatalyst design to overcome the time-consuming limitations of traditional approaches. ML methods, using experimental data from high-throughput experiments and computational data from simulations such as density functional theory (DFT), readily identify complex correlations between electrocatalyst performance and key material descriptors. Leveraging its unparalleled speed and accuracy, ML has facilitated the discovery of novel candidates and the improvement of known products through its pattern recognition capabilities. This review aims to provide a tailored breakdown of ML applications in a format that is readily accessible to materials scientists. Hence, we comprehensively organize ML-driven research by commonly studied material types for different electrochemical reactions to illustrate how ML adeptly navigates the complex landscape of descriptors for these scenarios. We further highlight ML's critical role in the future discovery and development of electrocatalysts for hydrogen energy transformation. Potential challenges and gaps to fill within this focused domain are also discussed. As a practical guide, we hope this work will bridge the gap between communities and encourage novel paradigms in electrocatalysis research, aiming for more effective and sustainable energy solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

rNets: a standalone package to visualize reaction networks

In the study of chemical processes, visualizing reaction networks is pivotal for identifying crucial compounds and transformations. Traditional methods, such as network schematics and reaction path linear plots, often struggle to effectively represent complex reaction networks due to their size and intricate connectivity. Alternatives capable of leading with complexity include graph methods, but they are not user-friendly, lacking simplicity and modularity, which hinders their integration with widely-used research software. This work introduces rNets an innovative tool designed for the efficient visualization of reaction networks with a user-friendly interface, modularity, and seamless integration with existing software packages. The effectiveness of rNets is demonstrated through its application in analyzing three catalytic reactions, showcasing its potential to significantly enhance research both in homogeneous and heterogeneous catalysis fields. This tool not only simplifies the visualization process but also opens new avenues for exploring complex reaction networks in diverse research contexts.

Pablo-García, Sergio↗

Structural regulation-induced Li-electron disentanglement for stabilized oxygen redox of Li-excess disordered rock-salt cathode materials

Since the discovery of its electrochemical activity, Li-excess disordered rock-salt (DRX) cathode material has received worldwide attention as it sets up a new way to exploit oxygen redox beyond the conventional layered structure with late-3d transition metals. However, the intricate structure-function relationship in the disordered lattice of the DRX material fogs the researcher's lens on the underlying redox mechanisms. Here, in this study, we employ a synergistic approach combining neutron total scattering with reverse Monte Carlo modeling and density functional theory calculations to unravel the landscape of oxygen redox reactions in DRX. Redox activities are evaluated in diverse oxygen clusters (OLi x TM 6-x ) and the spatial distribution of these clusters in the model DRX structure (Li 1.16 Ti 0.37 Ni 0.37 Nb 0.1 O 2 and Li 1.2 Ti 0.35 Ni 0.35 Nb 0.1 O 1.8 F 0.2 ) is explicitly determined. The results unveil that by regulating the short-range ordering between cations, fluorine atoms can effectively decouple the location of Li extraction and electron depletion. Such disentanglement between the Li reservoir and electron reservoir in the DRX lattice could play a pivotal role in protecting the oxidized oxygen and preserving the lattice framework during cycling. Through a tentatively designed non-fluorinated DRX oxide realizing similar Li-electron decoupling, an obvious enhancement of the cycling capability can be achieved without compromising the capacity release.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Finding a needle in a haystack: quantitative HERFD-XRF imaging and HERFD-XANES characterization of trace platinum in gold solidi from the Late Roman and Byzantine Empires

High-Energy Resolution Fluorescence Detection X-Ray Fluorescence (HERFD-XRF) imaging and HERFD X-ray Absorption Near Edge Structure (XANES) spectroscopy are used to quantify and characterize trace platinum (Pt) in gold solidi from the Late Roman and Byzantine Empires. Historically, the elemental analysis of coins has been pivotal in distinguishing authentic artifacts from forgeries, elucidating minting practices, and understanding economic shifts. Notably, a new gold source with high platinum content appeared in the fourth century CE, transforming the Roman economy. Traditional methods struggled to detect platinum due to the overwhelming gold matrix. Here, this study demonstrates the effectiveness of HERFD techniques in resolving this challenge. Three gold solidi, minted between 654 and 659 CE, were analyzed alongside reference gold materials with known Pt concentrations. The HERFD-XRF imaging revealed spatial distributions of platinum, highlighting non-uniformities within the coins. Additionally, HERFD-XANES spectroscopy identified the oxidation states and chemical speciation of platinum. Results demonstrate that platinum in the solidi primarily exists as metallic Pt, with some surface oxidation. The findings align with previous measurements but reveal higher Pt concentrations and significant inhomogeneities. This research confirms the reliability of HERFD methods for quantifying trace elements and provides new insights into the raw material sources and minting techniques of ancient gold coins. The non-destructive nature of this approach allows for extensive analyses, offering valuable data for historical, economic, and archaeological studies. This innovative application of HERFD-XRF imaging and XANES in cultural heritage research underscores the potential for detailed material characterization and conservation, enhancing our understanding of ancient economies and trade patterns.

Van Loon, Lisa L.↗