Combining Scattering Experiments and Colloid Theory to Characterize Charge Effects in Concentrated Antibody Solutions

Charges and their contribution to protein-protein interactions are essential for the key structural and dynamic properties of monoclonal antibody (mAb) solutions. In fact, they influence the apparent molecular weight, the static structure factor, the collective diffusion coefficient, or the relative viscosity, and their concentration dependence. Further, charges play an important role in the colloidal stability of mAbs. There exist standard experimental tools to characterize mAb net charges, such as the measurement of the electrophoretic mobility, the second virial coefficient, or the diffusion interaction parameter. However, the resulting values are difficult to directly relate to the actual overall net charge of the antibody and to theoretical predictions based on its known molecular structure. Here, we report the results of a systematic investigation of the solution properties of a charged IgG1 mAb as a function of concentration and ionic strength using a combination of electrophoretic measurements, static and dynamic light scattering, small-angle X-ray scattering, and tracer particle-based microrheology. We analyze and interpret the experimental results using established colloid theory and coarse-grained computer simulations. We discuss the potential and limits of colloidal models for the description of the interaction effects of charged mAbs, in particular pointing out the importance of incorporating shape and charge anisotropy when attempting to predict structural and dynamic solution properties at high concentrations.

Ingenious Architecture and Coloration Generation in Enamel of Rodent Teeth

Teeth exemplify architectures comprising an interplay of inorganic and organic constituents, resulting in sophisticated natural composites. Rodents (Rodentia) showcase extraordinary adaptations, with their continuously growing incisors surpassing human teeth in functional and structural optimizations. In this study, employing state-of-the-art direct atomic-scale imaging and nanoscale spectroscopies, we present compelling evidence that the release of material from ameloblasts and the subsequent formation of iron-rich enamel and surface layers in the constantly growing incisors of rodents are complex orchestrated processes, intricately regulated and independent of environmental factors. The synergistic fusion of three-dimensional tomography and imaging techniques of etched rodent́s enamel unveils a direct correlation between the presence of pockets infused with ferrihydrite-like material and the acid resistant properties exhibited by the iron-rich enamel, fortifying it as an efficient protective shield. Moreover, observations using optical microscopy shed light on the role of iron-rich enamel as a microstructural element that acts as a path for color transmission, although the native color remains indistinguishable from that of regular enamel, challenging the prevailing paradigms. The redefinition of "pigmented enamel" to encompass ferrihydrite-like infusion in rodent incisors reshapes our perception of incisor microstructure and color generation. The functional significance of acid-resistant iron-rich enamel and the understanding of the underlying coloration mechanism in rodent incisors have far-reaching implications for human health, development of potentially groundbreaking dental materials, and restorative dentistry. These findings enable the creation of an entirely different class of dental biomaterials with enhanced properties, inspired by the ingenious designs found in nature.

Sterically Selective [3 + 3] Cycloaromatization in the On-Surface Synthesis of Nanographenes

Surface-catalyzed reactions have been used to synthesize carbon nanomaterials with atomically predefined structures. The recent discovery of a gold surface-catalyzed [3 + 3] cycloaromatization of isopropyl substituted arenes has enabled the on-surface synthesis of arylene-phenylene copolymers, where the surface activates the isopropyl substituents to form phenylene rings by intermolecular coupling. However, the resulting polymers suffered from undesired cross-linking when more than two molecules reacted at a single site. Here we show that such cross-links can be prevented through steric protection by attaching the isopropyl groups to larger arene cores. Upon thermal activation of isopropyl-substituted 8,9-dioxa-8a-borabenzo[fg]tetracene on Au(111), cycloaromatization is observed to occur exclusively between the two molecules. The cycloaromatization intermediate formed by the covalent linking of two molecules is prevented from reacting with further molecules by the wide benzotetracene core, resulting in highly selective one-to-one coupling. Our findings extend the versatility of the [3 + 3] cycloaromatization of isopropyl substituents and point toward steric protection as a powerful concept for suppressing competing reaction pathways in on-surface synthesis.

Some plasma biomarkers of residual feed intake in beef cattle remain consistent regardless of intake level

This study investigated whether plasma biomarkers of residual feed intake (RFI), identified under ad libitum feeding conditions in beef cattle, remained consistent during feed restriction. Sixty Charolais crossbred young bulls were divided into two groups for a crossover study. Group A was initially fed ad libitum (first test) and then restricted (second test) on the same diet, while Group B experienced the opposite sequence. Blood samples were collected from the 12 most divergent RFI animals in each group at the end of the first test and again after the second test. 12 plasma variables consistently increased, while three consistently decreased during feed restriction (FDR < 0.05). Only two metabolites, α-aminoadipic acid for Group A and 5-aminovaleric acid for Group B, were associated with RFI independent of feed intake level (FDR < 0.05), demonstrating moderate-to-high repeatability across feeding levels (intraclass correlation coefficient ≥ 0.59). Notably, both metabolites belong to the same metabolic pathway: lysine degradation. These metabolites consistently correlated with RFI, irrespective of fluctuations in feed intake, indicating a connection to individual metabolic processes influencing feed efficiency. These findings suggest that a portion of RFI phenotypic variance is inherent to an individual's metabolic efficiency beyond variations in feed intake.

Chemical Fingerprinting of Biomass Burning Organic Aerosols from Sugar Cane Combustion: Complementary Findings from Field and Laboratory Studies

Agricultural fires are a major source of biomass-burning organic aerosols (BBOAs) with impacts on health, the environment, and climate. In this study, globally relevant BBOA emissions from the combustion of sugar cane in both field and laboratory experiments were analyzed using comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. The derived chemical fingerprints of fresh emissions were evaluated using targeted and nontargeted evaluation approaches. The open-field sugar cane burning experiments revealed the high chemical complexity of combustion emissions, including compounds derived from the pyrolysis of (hemi)cellulose, lignin, and further biomass, such as pyridine and oxime derivatives, methoxyphenols, and methoxybenzenes, as well as triterpenoids. In comparison, laboratory experiments could only partially model the complexity of real combustion events. Our results showed high variability between the conducted field and laboratory experiments, which we, among others, discuss in terms of differences in combustion conditions, fuel composition, and atmospheric processing. We conclude that both field and laboratory studies have their merits and should be applied complementarily. While field studies under real-world conditions are essential to assess the general impact on air quality, climate, and environment, laboratory studies are better suited to investigate specific emissions of different biomass types under controlled conditions.

High-Resolution Mass Spectrometry-Based Chemical Fingerprinting of Baijiu, a Traditional Chinese Liquor

Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry, coupled with electrospray ionization (ESI) or atmospheric-pressure photoionization (APPI), was employed for chemical fingerprinting of baijiu, a traditional Chinese liquor. Baijiu is the most consumed distilled alcoholic beverage globally, with over 10 billion liters sold annually. It is a white (transparent) spirit that exhibits similarities to dark spirits such as whisky or rum in terms of aroma and mouthfeel. In this study, direct-infusion FT-ICR mass spectrometry was used to analyze 10 commercially available baijiu liquors, enabling the examination of both volatile and nonvolatile constituents without the need for tedious sample extractions or compound derivatizations. The chemical fingerprints obtained by FT-ICR MS revealed substantial compositional diversity among different baijiu liquors, reflecting variations in the raw materials and production methods. The main compounds identified included a variety of acids, esters, aldehydes, lactones, terpenes, and phenolic compounds. The use of ESI and APPI provided complementary compositional information; while ESI demonstrated greater selectivity toward polar, aliphatic sample constituents, APPI also ionized semipolar and nonpolar (aromatic) ones.

Targeting the Main Protease (Mpro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies

The main protease Mpro, nsp5, of SARS-CoV-2 (SCoV2) is one of its most attractive drug targets. Here, we report primary screening data using nuclear magnetic resonance spectroscopy (NMR) of four different libraries and detailed follow-up synthesis on the promising uracil-containing fragment Z604 derived from these libraries. Z604 shows time-dependent binding. Its inhibitory effect is sensitive to reducing conditions. Starting with Z604, we synthesized and characterized 13 compounds designed by fragment growth strategies. Each compound was characterized by NMR and/or activity assays to investigate their interaction with Mpro. These investigations resulted in the four-armed compound 35b that binds directly to Mpro. 35b could be cocrystallized with Mpro revealing its noncovalent binding mode, which fills all four active site subpockets. Herein, we describe the NMR-derived fragment-to-hit pipeline and its application for the development of promising starting points for inhibitors of the main protease of SCoV2.

Do Not Waste Time─Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin

Cross-linking mass spectrometry (XL-MS) has become a very useful tool for studying protein complexes and interactions in living systems. It enables the investigation of many large and dynamic assemblies in their native state, providing an unbiased view of their protein interactions and restraints for integrative modeling. More researchers are turning toward trying XL-MS to probe their complexes of interest, especially in their native environments. However, due to the presence of other potentially higher abundant proteins, sufficient cross-links on a system of interest may not be reached to achieve satisfactory structural and interaction information. There are currently no rules for predicting whether XL-MS experiments are likely to work or not; in other words, if a protein complex of interest will lead to useful XL-MS data. Here, we show that a simple iBAQ (intensity-based absolute quantification) analysis performed from trypsin digest data can provide a good understanding of whether proteins of interest are abundant enough to achieve successful cross-linking data. Comparing our findings to large-scale data on diverse systems from several other groups, we show that proteins of interest should be at least in the top 20% abundance range to expect more than one cross-link found per protein. We foresee that this guideline is a good starting point for researchers who would like to use XL-MS to study their protein of interest and help ensure a successful cross-linking experiment from the beginning. Data are available via ProteomeXchange with identifier PXD045792.

Gas-to-Particle Partitioning of Products from Ozonolysis of Δ3-Carene and the Effect of Temperature and Relative Humidity

Formation of oxidized products from Δ3-carene (C10H16) ozonolysis and their gas-to-particle partitioning at three temperatures (0, 10, and 20 °C) under dry conditions (<2% RH) and also at 10 °C under humid (78% RH) conditions were studied using a time-of-flight chemical ionization mass spectrometer (ToF-CIMS) combined with a filter inlet for gases and aerosols (FIGAERO). The Δ3-carene ozonolysis products detected by the FIGAERO-ToF-CIMS were dominated by semivolatile organic compounds (SVOCs). The main effect of increasing temperature or RH on the product distribution was an increase in fragmentation of monomer compounds (from C10 to C7 compounds), potentially via alkoxy scission losing a C3 group. The equilibrium partitioning coefficient estimated according to equilibrium partitioning theory shows that the measured SVOC products distribute more into the SOA phase as the temperature decreases from 20 to 10 and 0 °C and for most products as the RH increases from <2 to 78%. The temperature dependency of the saturation vapor pressure (above an assumed liquid state), derived from the partitioning method, also allows for a direct way to obtain enthalpy of vaporization for the detected species without accessibility of authentic standards of the pure substances. This method can provide physical properties, beneficial for, e.g., atmospheric modeling, of complex multifunctional oxidation products.

A New Eyeless Species of Micranops Cameron 1913 from Bolivia (Coleoptera: Staphylinidae: Paederinae)

This work adds a new eyeless species of the genus Micranops Cameron, 1913 (Staphylinidae, Paederinae, Scopaeina) to the endogean Coleoptera of the Bolivian fauna. The loss of eyes is usually associated with adaptations to subterranean habitats, although M. bolivianus Guzman & Żyła sp. nov. was collected from leaf litter. We also report new occurrences for the genus west of the Andes mountain range. Our work increases the number of known Neotropical Micranops species to seven and extends the known distribution range for the genus in South America.

Monitoring mAb proteoforms in mouse plasma using an automated immunocapture combined with top-down and middle-down mass spectrometry

Monoclonal antibodies (mAbs) have established themselves as the leading biopharmaceutical therapeutic modality. Once the developability of a mAb drug candidate has been assessed, an important step is to check its in vivo stability through pharmacokinetics (PK) studies. The gold standard is ligand-binding assay (LBA) and liquid chromatography-mass spectrometry (LC-MS) performed at the peptide level (bottom-up approach). However, these analytical techniques do not allow to address the different mAb proteoforms that can arise from biotransformation. In recent years, top-down and middle-down mass spectrometry approaches have gained popularity to characterize proteins at the proteoform level but are not yet widely used for PK studies. We propose here a workflow based on an automated immunocapture followed by top-down and middle-down liquid chromatography-tandem mass spectrometry (LC-MS/MS) approaches to characterize mAb proteoforms spiked in mouse plasma. We demonstrate the applicability of our workflow on a large concentration range using pembrolizumab as a model. We also compare the performance of two state-of-the-art Orbitrap platforms (Tribrid Eclipse and Exploris 480) for these studies. The added value of our workflow for an accurate and sensitive characterization of mAb proteoforms in mouse plasma is highlighted.

Isotopic Depletion Increases the Spatial Resolution of FPOP Top-Down Mass Spectrometry Analysis

Protein radical labeling, like fast photochemical oxidation of proteins (FPOP), coupled to a top-down mass spectrometry (MS) analysis offers an alternative analytical method for probing protein structure or protein interaction with other biomolecules, for instance, proteins and DNA. However, with the increasing mass of studied analytes, the MS/MS spectra become complex and exhibit a low signal-to-noise ratio. Nevertheless, these difficulties may be overcome by protein isotope depletion. Thus, we aimed to use protein isotope depletion to analyze FPOP-oxidized samples by top-down MS analysis. For this purpose, we prepared isotopically natural (IN) and depleted (ID) forms of the FOXO4 DNA binding domain (FOXO4-DBD) and studied the protein-DNA interaction interface with double-stranded DNA, the insulin response element (IRE), after exposing the complex to hydroxyl radicals. As shown by comparing tandem mass spectra of natural and depleted proteins, the ID form increased the signal-to-noise ratio of useful fragment ions, thereby enhancing the sequence coverage by more than 19%. This improvement in the detection of fragment ions enabled us to detect 22 more oxidized residues in the ID samples than in the IN sample. Moreover, less common modifications were detected in the ID sample, including the formation of ketones and lysine carbonylation. Given the higher quality of ID top-down MSMS data set, these results provide more detailed information on the complex formation between transcription factors and DNA-response elements. Therefore, our study highlights the benefits of isotopic depletion for quantitative top-down proteomics. Data are available via ProteomeXchange with the identifier PXD044447.

Ligand-Based Competition Binding by Real-Time 19F NMR in Human Cells

The development of more effective drugs requires knowledge of their bioavailability and binding efficacy directly in the native cellular environment. In-cell nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for investigating ligand-target interactions directly in living cells. However, the target molecule may be NMR-invisible due to interactions with cellular components, while observing the ligand by 1H NMR is impractical due to the cellular background. Such limitations can be overcome by observing fluorinated ligands by 19F in-cell NMR as they bind to the intracellular target. Here we report a novel approach based on real-time in-cell 19F NMR that allows measuring ligand binding affinities in human cells by competition binding, using a fluorinated compound as a reference. The binding of a set of compounds toward Hsp90α was investigated. In principle, this approach could be applied to other pharmacologically relevant targets, thus aiding the design of more effective compounds in the early stages of drug development.

Guidelines for Free-Energy Calculations Involving Charge Changes

The Coulomb interactions in molecular simulations are inherently approximated due to the finite size of the molecular box sizes amenable to current-day compute power. Several methods exist for treating long-range electrostatic interactions, yet these approaches are subject to various finite-size-related artifacts. Lattice-sum methods are frequently used to approximate long-range interactions; however, these approaches also suffer from artifacts which become particularly pronounced for free-energy calculations that involve charge changes. The artifacts, however, also affect the sampling when plain simulations are performed, leading to a biased ensemble. Here, we investigate two previously described model systems to determine if artifacts continue to play a role when overall neutral boxes are considered, in the context of both free-energy calculations and sampling. We find that ensuring that no net-charge changes take place, while maintaining a neutral simulation box, may be sufficient provided that the simulation boxes are large enough. Addition of salt to the solution (when appropriate) can further alleviate the remaining artifacts in the sampling or the calculated free-energy differences. We provide practical guidelines to avoid finite-size artifacts.

Dinitrogen Activation Mediated by the (P2PPh)Fe Complex: Electronic Structure, Dimerization Mechanism, and Magnetic Coupling

Herein, we report the estimation of the extent of dinitrogen activation by different charged and structural forms of (P2PPh)Fe biomimetic catalysts, which, in the presence of light, exhibit significant yield in the N2-to-NH3 conversion. Complete active space self-consistent field (CASSCF) calculations have been used to determine the electronic structure of different reduced forms of the mononuclear complexes: the neutral (P2PPh)Fe(N2)2 adduct and the anionic [(P2PPh)Fe(N2)]- and [(P2PPh)Fe(N2)]2- complexes. These calculations also revealed that the extent of reduction of a dinitrogen molecule reaches up to one electron (N21-) due to the back-bonding from the Fe center, in agreement with the changes observed in the vibration frequency of the N-N bond in these complexes. In addition, the energy profile of the dimerization of the mononuclear (P2PPh)Fe(N2)2 complex to the dinuclear mono-N2-bridged [(P2PPh)Fe]2(μ-N2) complex has been determined by means of density functional theory (DFT) calculations. A three-step mechanism has been proposed for the dimerization, favored by both kinetics and thermodynamics criteria. Finally, the magnetic coupling constant in the diiron (μ-N2) complex is estimated from CASSCF/NEVPT2 calculations. Such a dinuclear complex presents a strong antiferromagnetic coupling resulting from the interaction between two S = 1 d6 Fe2+ ions, bridged by a highly activated dinitrogen molecule (N22-) with two electrons on the π* orbitals.

Electron Beam Induced Circularly Polarized Light Emission of Chiral Gold Nanohelices

Chiral plasmonic nanostructures possess a chiroptical response orders of magnitude stronger than that of natural biomolecular systems, making them highly promising for a wide range of biochemical, medical, and physical applications. Despite extensive efforts to artificially create and tune the chiroptical properties of chiral nanostructures through compositional and geometrical modifications, a fundamental understanding of their underlying mechanisms remains limited. In this study, we present a comprehensive investigation of individual gold nanohelices by using advanced analytical electron microscopy techniques. Our results, as determined by angle-resolved cathodoluminescence polarimetry measurements, reveal a strong correlation between the circular polarization state of the emitted far-field radiation and the handedness of the chiral nanostructure in terms of both its dominant circularity and directional intensity distribution. Further analyses, including electron energy-loss measurements and numerical simulations, demonstrate that this correlation is driven by longitudinal plasmonic modes that oscillate along the helical windings, much like straight nanorods of equal strength and length. However, due to the three-dimensional shape of the structures, these longitudinal modes induce dipolar transverse modes with charge oscillations along the short axis of the helices for certain resonance energies. Their radiative decay leads to observed emission in the visible range. Our findings provide insight into the radiative properties and underlying mechanisms of chiral plasmonic nanostructures and enable their future development and application in a wide range of fields, such as nano-optics, metamaterials, molecular physics, biochemistry, and, most promising, chiral sensing via plasmonically enhanced chiral optical spectroscopy techniques.

Cavity Lasing Characteristics of Thioflavin T and Thioflavin X in Different Solvents and Their Interaction with DNA for the Controlled Reduction of a Light Amplification Threshold in Solid-State Biofilms

The lasing characteristics of Thioflavin T (ThT) and Thioflavin X (ThX) dyes were investigated in solvents with increasing viscosity: water, ethanol, butanol, ethylene glycol, and glycerol and three forms of DNA (double-helix natural, fragmented, and aggregated). The results identified that lasing thresholds and photostability depend on three critical factors: the solvation shell surrounding dye molecules, the organization of their dipole moments, which is driven by the DNA structure, and the molecules diffusion coefficient in the excitation focal spot. The research highlights that dye doped to DNA accumulated in binding sites fosters long-range dye orientation, facilitating a marked reduction of lasing thresholds in the liquid phase as well as amplified spontaneous emission (ASE) thresholds in the solid state. Leveraging insights from lasing characteristics obtained in liquid, ASE in the solid state was optimized in a controlled way by changing the parameters influencing the DNA structure, i.e., magnesium salt addition, heating, and sonication. The modifications led to a large decrease in the ASE thresholds in the dye-doped DNA films. It was shown that the examination of lasing in cavities can be useful for preparing optical materials with improved architectures and functionalities for solid-state lasers.

Hybrid Metrology for Nanostructured Optical Metasurfaces

Metasurfaces have garnered increasing research interest in recent years due to their remarkable advantages, such as efficient miniaturization and novel functionalities compared to traditional optical elements such as lenses and filters. These advantages have facilitated their rapid commercial deployment. Recent advancements in nanofabrication have enabled the reduction of optical metasurface dimensions to the nanometer scale, expanding their capabilities to cover visible wavelengths. However, the pursuit of large-scale manufacturing of metasurfaces with customizable functions presents challenges in controlling the dimensions and composition of the constituent dielectric materials. To address these challenges, the combination of block copolymer (BCP) self-assembly and sequential infiltration synthesis (SIS), offers an alternative for fabrication of high-resolution dielectric nanostructures with tailored composition and optical functionalities. However, the absence of metrological techniques capable of providing precise and reliable characterization of the refractive index of dielectric nanostructures persists. This study introduces a hybrid metrology strategy that integrates complementary synchrotron-based traceable X-ray techniques to achieve comprehensive material characterization for the determination of the refractive index on the nanoscale. To establish correlations between material functionality and their underlying chemical, compositional and dimensional properties, TiO2 nanostructures model systems were fabricated by SIS of BCPs. The results from synchrotron-based analyses were integrated into physical models, serving as a validation scheme for laboratory-scale measurements to determine effective refractive indices of the nanoscale dielectric materials.

Atomic Structure of Hardening Precipitates in Al-Mg-Si Alloys: Influence of Minor Additions of Cu and Zn

Shifting toward sustainability and low carbon emission necessitates recycling. Aluminum alloys can be recycled from postconsumer scrap with approximately 5% of the energy needed to produce the same amount of primary alloys. However, the presence of certain alloying elements, such as copper and zinc, as impurities in recycled Al-Mg-Si alloys is difficult to avoid. This work has investigated the influence of tiny concentrations of Cu (0.05 wt %) and Zn (0.06 wt %), individually and in combination, on the precipitate crystal structures in Al-Mg-Si alloys in peak aged and overaged conditions. To assess whether such concentrations can affect the hardening precipitate structures, atomic resolution high-angle annular dark-field scanning transmission electron microscopy and atom probe tomography were adopted. The results indicate that low levels of Cu or Zn have a significant influence. Both elements showed a relatively high tendency to incorporate into precipitate structures, where Cu occupies specific atomic sites, creating its own local atomic configurations. However, Zn exhibited distinct behavior through the formation of extended local areas with 2-fold symmetry and mirror planes, not previously observed in precipitates in Al-Mg-Si alloys. Incorporation of Cu and/or Zn will influence the precipitates' electrochemical potential relative to matrix- and precipitate-free zones and thus the corrosion resistance. Furthermore, the presence of Cu/Zn structures (e.g., β'Cu, Q'/C) enhances the thermal stability of these precipitates and, accordingly, the mechanical properties of the material. The results obtained from this work are highly relevant to the topic of recycling of aluminum alloys, where accumulation of certain alloying elements is almost unavoidable; thus, tight compositional control might be critical to avoid quality degradation.

Whole-brain modeling of the differential influences of amyloid-beta and tau in Alzheimer's disease

BACKGROUND

Alzheimer's disease is a neurodegenerative condition associated with the accumulation of two misfolded proteins, amyloid-beta (A[Formula: see text]) and tau. We study their effect on neuronal activity, with the aim of assessing their individual and combined impact.

METHODS

We use a whole-brain dynamic model to find the optimal parameters that best describe the effects of A[Formula: see text] and tau on the excitation-inhibition balance of the local nodes.

RESULTS

We found a clear dominance of A[Formula: see text] over tau in the early disease stages (MCI), while tau dominates over A[Formula: see text] in the latest stages (AD). We identify crucial roles for A[Formula: see text] and tau in complex neuronal dynamics and demonstrate the viability of using regional distributions to define models of large-scale brain function in AD.

CONCLUSIONS

Our study provides further insight into the dynamics and complex interplay between these two proteins, opening the path for further investigations on biomarkers and candidate therapeutic targets in-silico.

Ensemble-Based Approaches Ensure Reliability and Reproducibility

It is increasingly widely recognized that ensemble-based approaches are required to achieve reliability, accuracy, and precision in molecular dynamics calculations. The purpose of the present article is to address a frequently raised question: what is the optimal way to perform ensemble simulation to calculate quantities of interest?

Impact of the Current on Reverse Bias Degradation of Perovskite Solar Cells

Nonequal current generation in the cells of a photovoltaic module, e.g., due to partial shading, leads to operation in reverse bias. This quickly causes a significant efficiency loss in perovskite solar cells. We report a more quantitative investigation of the reverse bias degradation. Various small reverse biases (negative voltages) were applied for different durations. After normalizing the applied voltages with the breakdown voltages, we found similar dependences of the reverse bias current and the degradation rate. We draw conclusions regarding possible degradation mechanisms and propose a way to increase the comparability of degradation rates for comparing different perovskite solar cells.

Amino Acids as Chelating Ligands for Platinum: Enhanced Stability in an Aqueous Environment Promoted by Biocompatible Molecules

Platinum-based chemotherapeutics are a cornerstone in the treatment of many malignancies. However, their dose-limiting side effects have rooted efforts to develop new drug candidates with higher selectivity for tumor tissues and less problematic side effects. Here, we developed a cytotoxic platinum(II) complex based on Zeise's salt, containing the nonsteroidal anti-inflammatory drug acetylsalicylic acid and alanine as ligands (4). The previously developed complex (5) displayed high reactivity against sulfur-containing biomolecules; therefore, we put the focus on the optimization of the structure regarding its stability. Different amino acids were used as biocompatible chelating ligands to achieve this aim. Differences in the coordination sphere caused pronounced changes in the stability of Zeise-type precursors 1-3. Coordination with l-Ala through N in the trans position to ethylene showed the most promising results and was employed to stabilize 5. As a result, complex 4 showed improved stability and cytotoxicity, outperforming both 5 and 1.

Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions

Alchemical relative binding free energy calculations have recently found important applications in drug optimization. A series of congeneric compounds are generated from a preidentified lead compound, and their relative binding affinities to a protein are assessed in order to optimize candidate drugs. While methods based on equilibrium thermodynamics have been extensively studied, an approach based on nonequilibrium methods has recently been reported together with claims of its superiority. However, these claims pay insufficient attention to the basis and reliability of both methods. Here we report a comparative study of the two approaches across a large data set, comprising more than 500 ligand transformations spanning in excess of 300 ligands binding to a set of 14 diverse protein targets. Ensemble methods are essential to quantify the uncertainty in these calculations, not only for the reasons already established in the equilibrium approach but also to ensure that the nonequilibrium calculations reside within their domain of validity. If and only if ensemble methods are applied, we find that the nonequilibrium method can achieve accuracy and precision comparable to those of the equilibrium approach. Compared to the equilibrium method, the nonequilibrium approach can reduce computational costs but introduces higher computational complexity and longer wall clock times. There are, however, cases where the standard length of a nonequilibrium transition is not sufficient, necessitating a complete rerun of the entire set of transitions. This significantly increases the computational cost and proves to be highly inconvenient during large-scale applications. Our findings provide a key set of recommendations that should be adopted for the reliable implementation of nonequilibrium approaches to relative binding free energy calculations in ligand-protein systems.

Limits to Hole Mobility and Doping in Copper Iodide

Over one hundred years have passed since the discovery of the p-type transparent conducting material copper iodide, predating the concept of the "electron-hole" itself. Supercentenarian status notwithstanding, little is understood about the charge transport mechanisms in CuI. Herein, a variety of modeling techniques are used to investigate the charge transport properties of CuI, and limitations to the hole mobility over experimentally achievable carrier concentrations are discussed. Poor dielectric response is responsible for extensive scattering from ionized impurities at degenerately doped carrier concentrations, while phonon scattering is found to dominate at lower carrier concentrations. A phonon-limited hole mobility of 162 cm2 V-1 s-1 is predicted at room temperature. The simulated charge transport properties for CuI are compared to existing experimental data, and the implications for future device performance are discussed. In addition to charge transport calculations, the defect chemistry of CuI is investigated with hybrid functionals, revealing that reasonably localized holes from the copper vacancy are the predominant source of charge carriers. The chalcogens S and Se are investigated as extrinsic dopants, where it is found that despite relatively low defect formation energies, they are unlikely to act as efficient electron acceptors due to the strong localization of holes and subsequent deep transition levels.

Site-Selective Functionalized PD-1 Mutant for a Modular Immunological Activity against Cancer Cells

Targeting immune checkpoints is a well-established strategy in cancer therapy, and antibodies blocking PD-1/PD-L1 interactions to restore the immunological activity against cancer cells have been clinically validated. High-affinity mutants of the PD-1 ectodomain have recently been proposed as an alternative to antibodies to target PD-L1 on cancer cells, shedding new light on this research area. In this dynamic scenario, the PD-1 mutant, here reported, largely expands the chemical space of nonantibody and nonsmall-molecule inhibitor therapeutics that can be used to target cancer cells overexpressing PD-L1 receptors. The polyethylene glycol moieties and the immune response-stimulating carbohydrates, used as site-selective tags, represent the proof of concept for future applications.

Unraveling Excited State Dynamics of a Single-Stranded DNA-Assembled Conjugated Polyelectrolyte

Conformational templating of conjugated polyelectrolytes with single-stranded DNAs (ssDNAs) has the prospect of tailoring excited state dynamics for specific optoelectronic applications. We use ultrafast time-resolved infrared spectroscopy to study the photophysics of a cationic polythiophene assembled with different ssDNAs, inducing distinct conformations (flexible disordered structures vs more rigid complexes with increased backbone planarity). Intrachain polarons are always produced upon selective excitation of the polymer, the extent being dependent on backbone torsional order. Polaron formation and decay were monitored through evolution of IR-active vibrational modes that interfere with mid-IR polaron electronic absorption giving rise to Fano-antiresonances. Selective UV excitation of ssDNAs revealed that stacking interactions between thiophene rings and nucleic acid bases can promote the formation of an intermolecular charge transfer complex. The findings inform designers of functional conjugated polymers by identifying that involvement of the scaffold in the photophysics needs to be considered when developing such structures for optoelectronic applications.

Top-Down Proteoform Analysis by 2D MS with Quadrupolar Detection

Two-dimensional mass spectrometry (2D MS) is a multiplexed tandem mass spectrometry method that does not rely on ion isolation to correlate the precursor and fragment ions. On a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), 2D MS instead uses the modulation of precursor ion radii inside the ICR cell before fragmentation and yields 2D mass spectra that show the fragmentation patterns of all the analytes. In this study, we perform 2D MS for the first time with quadrupolar detection in a dynamically harmonized ICR cell. We discuss the advantages of quadrupolar detection in 2D MS and how we adapted existing data processing techniques for accurate frequency-to-mass conversion. We apply 2D MS with quadrupolar detection to the top-down analysis of covalently labeled ubiquitin with ECD fragmentation, and we develop a workflow for label-free relative quantification of biomolecule isoforms in 2D MS.

Effect of forest management choices on carbon sequestration and biodiversity at national scale

Forest management methods and harvest intensities influence wood production, carbon sequestration and biodiversity. We devised different management scenarios by means of stakeholder analysis and incorporated them in the forest growth simulator PREBAS. To analyse impacts of harvest intensity, we used constraints on total harvest: business as usual, low harvest, intensive harvest and no harvest. We carried out simulations on a wall-to-wall grid in Finland until 2050. Our objectives were to (1) test how the management scenarios differed in their projections, (2) analyse the potential wood production, carbon sequestration and biodiversity under the different harvest levels, and (3) compare different options of allocating the scenarios and protected areas. Harvest level was key to carbon stocks and fluxes regardless of management actions and moderate changes in proportion of strictly protected forest. In contrast, biodiversity was more dependent on other management variables than harvesting levels, and relatively independent of carbon stocks and fluxes.

Low-Cost, High-Yield Zinc Oxide-Based Nanostars for Alkaline Overall Water Splitting

The investigation of high-efficiency and sustainable electrocatalysts for hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) in alkaline media is critical for renewable energy technologies. Here, we report a low-cost and high-yield method to obtain ZnOHF-ZnO-based 2D nanostars (NSs) by means of chemical bath deposition (CBD). The obtained NSs, cast onto graphene paper substrates, were used as active materials for the development of a full water splitting cell. For the HER, NSs were decorated with an ultralow amount of Pt nanoparticles (11.2 μg cm-2), demonstrating an overpotential of 181 mV at a current density of 10 mA cm-2. The intrinsic activity of Pt was optimized, thanks to the ZnO supporting nanostructures, as outlined by the mass activity of Pt (0.9 mA mgPt-1) and its turnover frequency (0.27 s-1 for a Pt loading of 11.2 μg cm-2). For the OER, bare NSs showed a remarkable result of 355 mV at 10 mA cm-2 in alkaline media. Pt-decorated and bare NSs were used as the cathode and anode, respectively, for alkaline electrochemical water splitting, assessing a stable overpotential of 1.7 V at a current density of 10 mA cm-2. The reported data pave the way toward large-scale production of low-cost electrocatalysts for green hydrogen production.

Tailoring Interlayer Charge Transfer Dynamics in 2D Perovskites with Electroactive Spacer Molecules

The family of hybrid organic-inorganic lead-halide perovskites are the subject of intense interest for optoelectronic applications, from light-emitting diodes to photovoltaics to X-ray detectors. Due to the inert nature of most organic molecules, the inorganic sublattice generally dominates the electronic structure and therefore the optoelectronic properties of perovskites. Here, we use optically and electronically active carbazole-based Cz-Ci molecules, where Ci indicates an alkylammonium chain and i indicates the number of CH2 units in the chain, varying from 3 to 5, as cations in the two-dimensional (2D) perovskite structure. By investigating the photophysics and charge transport characteristics of (Cz-Ci)2PbI4, we demonstrate a tunable electronic coupling between the inorganic lead-halide and organic layers. The strongest interlayer electronic coupling was found for (Cz-C3)2PbI4, where photothermal deflection spectroscopy results remarkably reveal an organic-inorganic charge transfer state. Ultrafast transient absorption spectroscopy measurements demonstrate ultrafast hole transfer from the photoexcited lead-halide layer to the Cz-Ci molecules, the efficiency of which increases by varying the chain length from i = 5 to i = 3. The charge transfer results in long-lived carriers (10-100 ns) and quenched emission, in stark contrast to the fast (sub-ns) and efficient radiative decay of bound excitons in the more conventional 2D perovskite (PEA)2PbI4, in which phenylethylammonium (PEA) acts as an inert spacer. Electrical charge transport measurements further support enhanced interlayer coupling, showing increased out-of-plane carrier mobility from i = 5 to i = 3. This study paves the way for the rational design of 2D perovskites with combined inorganic-organic electronic properties through the wide range of functionalities available in the world of organics.

Sensitivity Constraints of Extractive Electrospray for a Model System and Secondary Organic Aerosol

The quantification of an aerosol chemical composition is complicated by the uncertainty in the sensitivity of each species detected. Soft-ionization response factors can vary widely from molecule to molecule. Here, we have employed a method to separate molecules by their volatility through systematic evaporation with a thermal denuder (TD). The fraction remaining after evaporation is compared between an extractive electrospray ionization time-of-flight mass spectrometer (EESI-TOF) and a scanning mobility particle sizer (SMPS), which provides a comparison between a quantified mass loss by the SMPS and the signal loss in the EESI-TOF. The sensitivity of the EESI-TOF is determined for both a simplified complex mixture (PEG-300) and also for a complex mixture of α-pinene secondary organic aerosol (SOA). For PEG-300, separation is possible on a molecule-by-molecule level with the TD and provides insights into the molecule-dependent sensitivity of the EESI-TOF, showing a higher sensitivity toward the most volatile molecule. For α-pinene SOA, sensitivity determination for specific classes is possible because of the number of molecular formula observed by the EESI-TOF. These classes are separated by their volatility and are broken down into monomers (O3-5,6-7,8+), dimers (O4-7,8+), and higher order oligomers (e.g., trimers and tetramers). Here, we show that the EESI-TOF initially measures 60.1% monomers, 32.7% dimers, and 7.2% trimers and tetramers in α-pinene SOA, but after sensitivity correction, the distribution of SOA is 37.4% monomers, 56.1% dimers, and 6.4% trimers and tetramers. These results provide a path forward for the quantification of aerosol components with the EESI-TOF in other applications and potentially for atmospheric measurements.

Aperiodic Modulation of Graphene Driven by Oxygen-Induced Reconstruction of Rh(110)

Artificial nanostructuring of graphene has served as a platform to induce variations in its structural and electronic properties, fostering the experimental observation of a wide and fascinating phenomenology. Here, we present an approach to graphene tuning, based on Rh(110) surface reconstruction induced by oxygen atoms intercalation. The resulting nanostructured graphene has been characterized by scanning tunneling microscopy (STM) complemented by low-energy electron microscopy (LEEM), micro low-energy electron diffraction (μ-LEED), micro angle-resolved photoemission spectroscopy (μ-ARPES), and micro X-ray photoelectron spectroscopy (μ-XPS) measurements under ultrahigh vacuum (UHV) conditions at room temperature (RT). It is found that by fine-tuning the O2 exposure amount, a mixture of missing row surface reconstructions of the metal surface below the graphene layer can be induced. This atomic rearrangement under the graphene layer results in aperiodic patterning of the two-dimensional (2D) material. The electronic structure of the resulting nanostructured graphene is dominated by a linear dispersion of the Dirac quasiparticles, characteristic of its free-standing state but with a p-doping character. The local effects of the underlying missing rows on the interfacial chemistry and on the quasiparticle scattering processes in graphene are studied using atomically resolved STM images. The possibilities offered by this nanostructuring approach, which consists in inducing surface reconstructions under graphene, could provide a novel tuning strategy for this 2D material.

Equivariant Graph Neural Networks for Toxicity Prediction

Predictive modeling of toxicity is a crucial step in the drug discovery pipeline. It can help filter out molecules with a high probability of failing in the early stages of de novo drug design. Thus, several machine learning (ML) models have been developed to predict the toxicity of molecules by combining classical ML techniques or deep neural networks with well-known molecular representations such as fingerprints or 2D graphs. But the more natural, accurate representation of molecules is expected to be defined in physical 3D space like in ab initio methods. Recent studies successfully used equivariant graph neural networks (EGNNs) for representation learning based on 3D structures to predict quantum-mechanical properties of molecules. Inspired by this, we investigated the performance of EGNNs to construct reliable ML models for toxicity prediction. We used the equivariant transformer (ET) model in TorchMD-NET for this. Eleven toxicity data sets taken from MoleculeNet, TDCommons, and ToxBenchmark have been considered to evaluate the capability of ET for toxicity prediction. Our results show that ET adequately learns 3D representations of molecules that can successfully correlate with toxicity activity, achieving good accuracies on most data sets comparable to state-of-the-art models. We also test a physicochemical property, namely, the total energy of a molecule, to inform the toxicity prediction with a physical prior. However, our work suggests that these two properties can not be related. We also provide an attention weight analysis for helping to understand the toxicity prediction in 3D space and thus increase the explainability of the ML model. In summary, our findings offer promising insights considering 3D geometry information via EGNNs and provide a straightforward way to integrate molecular conformers into ML-based pipelines for predicting and investigating toxicity prediction in physical space. We expect that in the future, especially for larger, more diverse data sets, EGNNs will be an essential tool in this domain.

Influence of nuclear dynamics on molecular attosecond photoelectron interferometry

In extreme ultraviolet spectroscopy, the photoionization process occurring in a molecule due to the absorption of a single photon can trigger an ultrafast nuclear motion in the cation. Taking advantage of attosecond photoelectron interferometry, where the absorption of the extreme ultraviolet photon is accompanied by the exchange of an additional infrared quantum of light, one can investigate the influence of nuclear dynamics by monitoring the characteristics of the photoelectron spectra generated by the two-color field. Here, we show that attosecond photoelectron interferometry is sensitive to the nuclear response by measuring the two-color photoionization spectra in a mixture of methane (CH4) and deuteromethane (CD4). The effect of the different nuclear evolution in the two isotopologues manifests itself in the modification of the amplitude and contrast of the oscillations of the photoelectron peaks. Our work indicates that nuclear dynamics can affect the coherence properties of the electronic wave packet emitted by photoionization on a time scale as short as a few femtoseconds.

MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity

Cross-linking mass spectrometry has become a powerful tool for the identification of protein-protein interactions and for gaining insight into the structures of proteins. We previously published MS Annika, a cross-linking search engine which can accurately identify cross-linked peptides in MS2 spectra from a variety of different MS-cleavable cross-linkers. In this publication, we present MS Annika 2.0, an updated version implementing a new search algorithm that, in addition to MS2 level, only supports the processing of data from MS2-MS3-based approaches for the identification of peptides from MS3 spectra, and introduces a novel scoring function for peptides identified across multiple MS stages. Detected cross-links are validated by estimating the false discovery rate (FDR) using a target-decoy approach. We evaluated the MS3-search-capabilities of MS Annika 2.0 on five different datasets covering a variety of experimental approaches and compared it to XlinkX and MaXLinker, two other cross-linking search engines. We show that MS Annika detects up to 4 times more true unique cross-links while simultaneously yielding less false positive hits and therefore a more accurate FDR estimation than the other two search engines. All mass spectrometry proteomics data along with result files have been deposited to the ProteomeXchange consortium via the PRIDE partner repository with the dataset identifier PXD041955.

Molecular and Crystal Structure, Spectroscopy, and Photochemistry of a Dispiro Compound Bearing the Tetraoxane Pharmacophore

The molecular structure and photochemistry of dispiro[cyclohexane-1,3'-[1,2,4,5]tetraoxane-6',2''-tricyclo[3.3.1.13,7 ]decan]-4-one (TX), an antiparasitic 1,2,4,5-tetraoxane was investigated using matrix isolation IR and EPR spectroscopies, together with quantum chemical calculations undertaken at the DFT(B3LYP)/6-311++G(3df,3pd) level of theory, with and without Grimme's dispersion correction. Photolysis of the matrix-isolated TX, induced by in situ broadband (λ>235 nm) or narrowband (λ in the range 220-263 nm) irradiation, led to new bands in the infrared spectrum that could be ascribed to two distinct photoproducts, oxepane-2,5-dione, and 4-oxohomoadamantan-5-one. Our studies show that these photoproducts result from initial photoinduced cleavage of an O-O bond, with the formation of an oxygen-centered diradical that regioselectivity rearranges to a more stable (secondary carbon-centered)/(oxygen-centered) diradical, yielding the final products. Formation of the diradical species was confirmed by EPR measurements, upon photolysis of the compound at λ=266 nm, in acetonitrile ice (T=10-80 K). Single-crystal X-ray diffraction (XRD) studies demonstrated that the TX molecule adopts nearly the same conformation in the crystal and matrix-isolation conditions, revealing that the intermolecular interactions in the TX crystal are weak. This result is in keeping with observed similarities between the infrared spectrum of the crystalline material and that of matrix-isolated TX. The detailed structural, vibrational, and photochemical data reported here appear relevant to the practical uses of TX in medicinal chemistry, considering its efficient and broad parasiticidal properties.

Lithium-Induced Reorientation of Few-Layer MoS2 Films

Molybdenum disulfide (MoS2) few-layer films have gained considerable attention for their possible applications in electronics and optics and also as a promising material for energy conversion and storage. Intercalating alkali metals, such as lithium, offers the opportunity to engineer the electronic properties of MoS2. However, the influence of lithium on the growth of MoS2 layers has not been fully explored. Here, we have studied how lithium affects the structural and optical properties of the MoS2 few-layer films prepared using a new method based on one-zone sulfurization with Li2S as a source of lithium. This method enables incorporation of Li into octahedral and tetrahedral sites of the already prepared MoS2 films or during MoS2 formation. Our results discover an important effect of lithium promoting the epitaxial growth and horizontal alignment of the films. Moreover, we have observed a vertical-to-horizontal reorientation in vertically aligned MoS2 films upon lithiation. The measurements show long-term stability and preserved chemical composition of the horizontally aligned Li-doped MoS2.

Time-Resolved X-ray Photoelectron Spectroscopy: Ultrafast Dynamics in CS2 Probed at the S 2p Edge

Recent developments in X-ray free-electron lasers have enabled a novel site-selective probe of coupled nuclear and electronic dynamics in photoexcited molecules, time-resolved X-ray photoelectron spectroscopy (TRXPS). We present results from a joint experimental and theoretical TRXPS study of the well-characterized ultraviolet photodissociation of CS2, a prototypical system for understanding non-adiabatic dynamics. These results demonstrate that the sulfur 2p binding energy is sensitive to changes in the nuclear structure following photoexcitation, which ultimately leads to dissociation into CS and S photoproducts. We are able to assign the main X-ray spectroscopic features to the CS and S products via comparison to a first-principles determination of the TRXPS based on ab initio multiple-spawning simulations. Our results demonstrate the use of TRXPS as a local probe of complex ultrafast photodissociation dynamics involving multimodal vibrational coupling, nonradiative transitions between electronic states, and multiple final product channels.

Time-Resolved Molecular Characterization of Secondary Organic Aerosol Formed from OH and NO3 Radical Initiated Oxidation of a Mixture of Aromatic Precursors

Aromatic hydrocarbons (ArHCs) and oxygenated aromatic hydrocarbons (ArHC-OHs) are emitted from a variety of anthropogenic activities and are important precursors of secondary organic aerosol (SOA) in urban areas. Here, we analyzed and compared the composition of SOA formed from the oxidation of a mixture of aromatic VOCs by OH and NO3 radicals. The VOC mixture was composed of toluene (C7H8), p-xylene + ethylbenzene (C8H10), 1,3,5-trimethylbenzene (C9H12), phenol (C6H6O), cresol (C7H8O), 2,6-dimethylphenol (C8H10O), and 2,4,6-trimethylphenol (C9H12O) in a proportion where the aromatic VOCs were chosen to approximate day-time traffic-related emissions in Delhi, and the aromatic alcohols make up 20% of the mixture. These VOCs are prominent in other cities as well, including those influenced by biomass combustion. In the NO3 experiments, large contributions from CxHyOzN dimers (C15-C18) were observed, corresponding to fast SOA formation within 15-20 min after the start of chemistry. Additionally, the dimers were a mixture of different combinations of the initial VOCs, highlighting the importance of exploring SOAs from mixed VOC systems. In contrast, the experiments with OH radicals yielded gradual SOA mass formation, with CxHyOz monomers (C6-C9) being the dominant constituents. The evolution of SOA composition with time was tracked and a fast degradation of dimers was observed in the NO3 experiments, with concurrent formation of monomer species. The rates of dimer decomposition in NO3 SOA were ∼2-3 times higher compared to those previously determined for α-pinene + O3 SOA, highlighting the dependence of particle-phase reactions on VOC precursors and oxidants. In contrast, the SOA produced in the OH experiments did not dramatically change over the same time frame. No measurable effects of humidity were observed on the composition and evolution of SOA.

Strongly Modified Mechanical Properties and Phase Transition in AlPO4-17 Due to Insertion of Guest Species at High Pressure

The porous aluminophosphate AlPO₄-17 with a hexagonal erionite structure, exhibiting very strong negative thermal expansion, anomalous compressibility, and pressure-induced amorphization, was studied at high pressure by single-crystal and powder X-ray diffraction in the penetrating pressure transmitting media N₂, O₂, and Ar. Under pressure, these guest species were confirmed to enter the pores of AlPO₄-17, thus completely modifying its behavior. Pressure-induced collapse in the xy plane of AlPO₄-17 no longer occurred, and this plane exhibited close to zero area compressibility. Pressure-induced amorphization was also suppressed as the elastic instability in the xy plane was removed. Crystal structure refinements at a pressure of 5.5 GPa indicate that up to 28 guest molecules are inserted per unit cell and that this insertion is responsible for the reduced compressibility observed at high pressure. A phase transition to a new hexagonal structure with cell doubling along the a direction was observed above 4.4 GPa in fluid O₂.

Mobility constraints in segregation models

Since the development of the original Schelling model of urban segregation, several enhancements have been proposed, but none have considered the impact of mobility constraints on model dynamics. Recent studies have shown that human mobility follows specific patterns, such as a preference for short distances and dense locations. This paper proposes a segregation model incorporating mobility constraints to make agents select their location based on distance and location relevance. Our findings indicate that the mobility-constrained model produces lower segregation levels but takes longer to converge than the original Schelling model. We identified a few persistently unhappy agents from the minority group who cause this prolonged convergence time and lower segregation level as they move around the grid centre. Our study presents a more realistic representation of how agents move in urban areas and provides a novel and insightful approach to analyzing the impact of mobility constraints on segregation models. We highlight the significance of incorporating mobility constraints when policymakers design interventions to address urban segregation.

Binding-and-Folding Recognition of an Intrinsically Disordered Protein Using Online Learning Molecular Dynamics

Intrinsically disordered proteins participate in many biological processes by folding upon binding to other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main questions is whether folding occurs prior to or after binding. Here we use a novel, unbiased, high-throughput adaptive sampling approach to reconstruct the binding and folding between the disordered transactivation domain of c-Myb and the KIX domain of the CREB-binding protein. The reconstructed long-term dynamical process highlights the binding of a short stretch of amino acids on c-Myb as a folded α-helix. Leucine residues, especially Leu298-Leu302, establish initial native contacts that prime the binding and folding of the rest of the peptide, with a mixture of conformational selection on the N-terminal region with an induced fit of the C-terminal.

Optimized Suspension Trapping Method for Phosphoproteomics Sample Preparation

A successful mass spectrometry-based phosphoproteomics analysis relies on effective sample preparation strategies. Suspension trapping (S-Trap) is a novel, rapid, and universal method of sample preparation that is increasingly applied in bottom-up proteomics studies. However, the performance of the S-Trap protocol for phosphoproteomics studies is unclear. In the existing S-Trap protocol, the addition of phosphoric acid (PA) and methanol buffer creates a fine protein suspension to capture proteins on a filter and is a critical step for subsequent protein digestion. Herein, we demonstrate that this addition of PA is detrimental to downstream phosphopeptide enrichment, rendering the standard S-Trap protocol suboptimal for phosphoproteomics. In this study, the performance of the S-Trap digestion for proteomics and phosphoproteomics is systematically evaluated in large-scale and small-scale samples. The results of this comparative analysis show that an optimized S-Trap approach, where trifluoroacetic acid is substituted for PA, is a simple and effective method to prepare samples for phosphoproteomics. Our optimized S-Trap protocol is applied to extracellular vesicles to demonstrate superior sample preparation workflow for low-abundance, membrane-rich samples.

Photo-elasticity of silk fibroin harnessing whispering gallery modes

Silk fibroin is an important biomaterial for photonic devices in wearable systems. The functionality of such devices is inherently influenced by the stimulation from elastic deformations, which are mutually coupled through photo-elasticity. Here, we investigate the photo-elasticity of silk fibroin employing optical whispering gallery mode resonation of light at the wavelength of 1550 nm. The fabricated amorphous (Silk I) and thermally-annealed semi-crystalline structure (Silk II) silk fibroin thin film cavities display typical Q-factors of about 1.6 × 10⁴. Photo-elastic experiments are performed tracing the TE and TM shifts of the whispering gallery mode resonances upon application of an axial strain. The strain optical coefficient K' for Silk I fibroin is found to be 0.059 ± 0.004, with the corresponding value for Silk II being 0.129 ± 0.004. Remarkably, the elastic Young's modulus, measured by Brillouin light spectroscopy, is only about 4% higher in the Silk II phase. However, differences between the two structures are pronounced regarding the photo-elastic properties due to the onset of β-sheets that dominates the Silk II structure.

Correction to Brown Carbon from Photo-Oxidation of Glyoxal and SO2 in Aqueous Aerosol

[This corrects the article DOI: 10.1021/acsearthspacechem.3c00035.].

Tannic acid-functionalized 3D porous nanofiber sponge for antibiotic-free wound healing with enhanced hemostasis, antibacterial, and antioxidant properties

Developing an antibiotic-free wound dressing with effective hemostasis and antibacterial and antioxidant capacity is highly desirable. In this work, a three-dimensional (3D) chitosan/polyvinyl alcohol-tannic acid porous nanofiber sponge (3D-TA) was prepared via electrospinning. Compared with two-dimensional (2D) fiber membrane, the unique fluffy 3D-TA nanofiber sponge had high porosity, water absorption and retention ability, hemostatic capacity. Furthermore, the 3D sponge functionalized by tannic acid (TA) endow the sponge with high antibacterial and antioxidant capacity without loading antibiotics. In addition, 3D-TA composite sponges have shown highly biocompatibility against L929 cells. The in vivo experiment shows the 3D-TA is enable to accelerate wound healing. This newly 3D-TA sponges hold great potential as wound dressings for future clinical application.

Stable Sn-Based Hybrid Perovskite-Related Structures with Tunable Color Coordinates via Organic Cations in Low-Temperature Synthesis

Organic-inorganic Pb-free layered perovskites are efficient broadband emitters and thus are promising materials for lighting applications. However, their synthetic protocols require a controlled atmosphere, high temperature, and long preparation time. This hinders the potential tunability of their emission through organic cations, as is instead common practice in Pb-based structures. Here, we present a set of Sn-Br layered perovskite-related structures that display different chromaticity coordinates and photoluminescence quantum yield (PLQY) up to 80%, depending on the choice of the organic monocation. We first develop a synthetic protocol that is performed under air and at 4 °C, requiring only a few steps. X-ray and 3D electron diffraction analyses show that the structures exhibit diverse octahedra connectivity (disconnected and face-sharing) and thus optical properties, while preserving the organic-inorganic layer intercalation. These results provide key insight into a previously underexplored strategy to tune the color coordinates of Pb-free layered perovskites through organic cations with complex molecular configurations.

Characterizing the visualization design space of distant and close reading of poetic rhythm

Metrical and rhythmical poetry analysis is founded on the systematic statistical analysis and comparison of sonic devices (e.g., rhythmic patterns) that emerge from a combination of pre-established aesthetic and structural rules and the poet's abilities and creative genius to convey a given message adhering to the said constraints. These rhythmical patterns, which have been traditionally obtained by means of a careful close reading of the poems, in a process known as "scansion," can now be obtained and made visible by automatic means. However, the visualization literature is still scarce on approaches that allow an insightful close and distant reading of the rhythmical patterns in a poetry corpus. In this work, we report our initial efforts in characterizing of the visualization design space of distant and close reading of poetic rhythm. By employing a digital version of a corpus of 11,268 verses originally written by the Spanish poet and playwright Federico García-Lorca (1898-1936), we could craft several prototypical visualizations representative of the inherent complexity of the problem which we expect to employ in future user studies and that we share here with the rest of the community to foster further discussion around this interesting topic.