Structural Reorganization Research Articles

Controlled reconstruction of metal-organic frameworks via coordination environment tuning as oxygen evolution electrocatalysts.

During the oxygen evolution reaction (OER), metal-organic framework (MOF) catalysts undergo structural reorganization, a phenomenon that is still not fully comprehended. Additionally, designing MOFs that undergo structural reconstruction to produce highly active OER catalysts continues to pose significant challenges. Herein, a bimetallic MOF (CoNi-MOF) with carboxylate oxygen and pyridine nitrogen coordination has been synthesized and its reconstruction behavior has been analyzed. The CoNi-MOF electrocatalyst attains a current density of 10 mA cm-2 with a minimal overpotential of just 250 mV, along with a Tafel slope of 91.57 mV dec-1, which is relatively low. After undergoing CV cycling tests, changes were observed in its catalytic activity, as well as in the microstructure and electrochemically active surface area, which are related to its activity. Importantly, in situ Raman analysis indicates that during the electrocatalytic process, the MOFs undergo a transition to MOOH, signifying the occurrence of reconstruction. Notably, compared to monometallic MOFs, bimetallic MOFs undergo reconstruction at lower voltage and with a faster reconstruction rate. Further analysis has revealed that the electrochemical reconstruction rate of the Co-N/O coordination mode at the active center is higher than that of Ni-N/O, playing a crucial role in enhancing OER activity. This study underscores the significance of the reconstruction strategy in enhancing the activity of MOF catalysts, providing new insights for the development of high-activity materials.

Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton

Although epigenetic modification has long been recognized as a vital force influencing gene regulation in plants, the dynamics of chromatin structure implicated in the intertwined transcriptional regulation of duplicated genes in polyploids have yet to be understood. Here, we document the dynamic organization of chromatin structure in two subgenomes of allotetraploid cotton (Gossypium hirsutum) by generating 3D genomic, epigenomic and transcriptomic datasets from 12 major tissues/developmental stages covering the life cycle. We systematically identify a subset of genes that are closely associated with specific tissue functions. Interestingly, these genes exhibit not only higher tissue specificity but also a more pronounced homoeologous bias. We comprehensively elucidate the intricate process of subgenomic collaboration and divergence across various tissues. A comparison among subgenomes in the 12 tissues reveals widespread differences in the reorganization of 3D genome structures, with the Dt subgenome exhibiting a higher extent of dynamic chromatin status than the At subgenome. Moreover, we construct a comprehensive atlas of putative functional genome elements and discover that 37 cis-regulatory elements (CREs) have selection signals acquired during domestication and improvement. These data and analyses are publicly available to the research community through a web portal. In summary, this study provides abundant resources and depicts the regulatory architecture of the genome, which thereby facilitates the understanding of biological processes and guides cotton breeding.

Effect of annealing on the structure and properties formation of a copper alloy alloyed with palladium and silver

A copper alloy with small additions of palladium and silver (Cu–1.5Pd–3Ag (at. %))—which has potential applications as a corrosionresistant conductor of weak electrical signals—was studied using X-ray diffraction analysis, microhardness measurements, specific electrical resistivity, and tensile mechanical properties tests. Samples were examined in several initial states: quenched (from 700 °C) and deformed at room and cryogenic temperatures (with a 90 % reduction in cross-sectional area in both cases). To study the processes of structural reorganization and property evolution, the initial samples were annealed in the temperature range from 150 to 450 °C (in 50 °C increments), followed by cooling in water or air. The duration of the heat treatments ranged from 1 to 48 hours. It was established that annealing the Cu–1.5Pd–3Ag alloy at temperatures below 450 °C leads to the precipitation of silver-based phase particles in the Cu matrix. Annealing of the initially quenched alloy was found to slightly increase its specific electrical resistivity (ρ) from 3.55·10–8 to 3.8·10–8 Ohm·m (after 48 h at 250 °C). It was revealed that alloying copper with 1.5 at. % palladium and 3 at. % silver enhances the strength properties (the yield strength of the alloy reaches 500 MPa) and raises the recrystallization temperature, while the electrical conductivity of the alloy remains around 50 % IACS. The optimal combination of properties (strength, ductility, and electrical conductivity) is observed after annealing the pre-cryodeformed alloy at 250 °C for less than 18 h. Extending the annealing time causes overaging, resulting in softening. The results of this study can be applied in the development of a new high-strength material with reduced electrical resistivity.

Beta Diversity Is Better—Microhabitat Diversity and Multiplet Diversity Offer Novel Insights into Plant Coexistence in Grassland Restoration

Quantifying within-community variability and understanding the related assembly rules are important in developing and assessing grassland restoration. Beta diversity has great potential, revealing mechanisms behind community-level changes in succession. Here, we introduce two simple beta diversity indices: Microhabitat Diversity is the Shannon diversity of patches formed by the locally dominant species, and Multiplet Diversity is the Shannon diversity of subordinate species richness categories detected at a fine scale. Using null models, we tested the biotic filtering effects of dominants on the distribution of subordinates. Based on long-term vegetation monitoring data, we tested the utility of these models in grassland restoration. Sites sown with seed mixture and developing spontaneously were compared and used as test data for exploring the proposed indices. Microhabitat Diversity was larger at spontaneously developing sites, and its local maxima reflected reorganization in the mosaic structure of the community. Species richness categories with zero or one subordinate species were typical in sown grassland, while small 5 cm × 5 cm microsites where 2, 3, or 4 subordinate species co-occured were more frequent in spontaneous succession. Contrary to expectation, a slight convergence of beta diversity measures was revealed after 15 years of succession between passive and active restorations. Microhabitat Diversity and Multiplet Diversity are simple indices that complement existing methods and provide new insights into grassland restoration.

Capturing Coupled Structural and Electronic Motions During Excited-State Intramolecular Proton Transfer via Computational Multiedge Resonant Inelastic X-ray Scattering.

Proton transfer processes form the foundation of many chemical processes. In excited-state intramolecular proton transfer (ESIPT) processes, ultrafast proton transfer is impulsively initiated through light. Here, we explore time-dependent coupled atomic and electronic motions during and following ESIPT through computational time-resolved resonant inelastic X-ray scattering (RIXS). Excited-state ab initio molecular dynamics simulations combined with time-dependent density functional theory calculations were performed for a model ESIPT system, 10-hydroxybenzo[h]quinoline, to obtain transient RIXS signatures. The RIXS spectra at both the nitrogen and oxygen K-edges were computed to resolve the electronic and atomic structural dynamics from both the proton donor and acceptor perspective. The results demonstrate that RIXS provides unprecedented details of the local electronic structure, the coupling between different core and valence excited electronic states, and the reorganization of the electronic structure coupled to the proton transfer process. We also develop a spectroscopic ruler correlating spectral shifts of a RIXS peak to the proton transfer distance during ESIPT. This work highlights the exciting potential of time-resolved RIXS experiments at newly commissioned soft X-ray free electron laser facilities for measuring coupled electronic and structural changes during ultrafast chemical processes.

Line-field confocal optical coherence tomography coupled with artificial intelligence algorithms as tool to investigate wound healing: A prospective, randomized, single-blinded pilot study.

Ablative fractional photothermolysis serves as an excellent invivo model for studying wound healing. The advent of non-invasive imaging devices, such as line-field confocal optical coherence tomography (LC-OCT), enhances this model by enabling detailed monitoring of skin wound healing over time. Additionally, artificial intelligence (AI)-based algorithms are revolutionizing the evaluation of clinical images by providing detailed analyses that are unfeasible manually. This study aims to assess the value of combining LC-OCT and AI for evaluating the acute wound healing process in the skin. The forearms of participating volunteers were ablated with a CO2 laser in a fractional pattern (7.5 mJ/MTZ) (ClinicalTrials.gov identifier: NCT05614557). To induce observable wound healing differences, two different approved silicone-based formulations were randomly assigned to two test sites, with a third site left untreated. Invivo LC-OCT images were obtained at predefined intervals post-laser treatment, ranging from 1 to 7 days. These images were further analysed using AI algorithms. LC-OCT visualization allows for the characterization of the structural reorganization of the skin during wound healing. The additional integration of AI algorithms significantly enhances the evaluation of the efficacy of wound care interventions by providing a deeper understanding of how these interventions improve wound healing. This is particularly valuable for primary care providers and dermatologists, as AI algorithms have proven useful in observing, characterizing and understanding keratinocyte behaviour. The combination of AI and high-resolution imaging represents a promising tool for better understanding wound healing, evaluating the efficacy of current wound care interventions and analysing keratinocyte behaviour in detail during the wound healing process. NCT05614557.

The Campylobacter jejuni BumS sensor phosphatase detects the branched short-chain fatty acids isobutyrate and isovalerate as direct cues for signal transduction.

Two-component signal transduction systems (TCSs) are nearly ubiquitous across bacterial species and enable bacteria to sense and respond to specific cues for environmental adaptation. The Campylobacter jejuni BumSR TCS is unusual in that the BumS sensor exclusively functions as a phosphatase rather than a kinase to control phosphorylated levels of its cognate BumR response regulator (P-BumR). We previously found that BumSR directs a response to the short-chain fatty acid butyrate generated by resident microbiota so that C. jejuni identifies ideal lower intestinal niches in avian and human hosts for colonization. However, butyrate is an indirect cue for BumS and did not inhibit in vitro BumS phosphatase activity for P-BumR. In this work, we expanded the repertoire of lower intestinal metabolites that are cues sensed by BumS that modulate the expression of genes required for colonization to include the branched short-chain fatty acids isobutyrate and isovalerate. Unlike butyrate, isobutyrate and isovalerate inhibited in vitro BumS phosphatase activity for P-BumR, indicating that these metabolites are direct cues for BumS. Isobutyrate and isovalerate reduced the thermostability of BumS and caused a reorganization of protein structure to suggest how sensing these cues inhibits phosphatase activity. We also identified residues in the BumS sensory domain required to detect isobutyrate, isovalerate, and butyrate and for optimal colonization of hosts to reveal how gut bacteria can recognize these intestinal metabolites. Our work reveals how this unusual bacterial sensor phosphatase senses a repertoire of intestinal metabolites and how cues alter BumSR signal transduction to influence C. jejuni colonization of hosts.IMPORTANCETCSs are prevalent in many bacteria, but the cues sensed by each are not actually known for many of these systems. Microbiota-generated butyrate in human and avian hosts is detected by the Campylobacter jejuni BumS sensor phosphatase so that the bacterium identifies ideal lower intestinal niches for colonization. However, BumS only indirectly senses butyrate to inhibit dephosphorylation of its cognate BumR response regulator. Here, we expanded the repertoire of cues sensed by BumS to the branched-short chain fatty acids isobutyrate and isovalerate that are also abundant in the lower intestines. Both isobutyrate and isovalerate are potent, direct cues for BumS, whereas butyrate is an indirect cue. Leveraging isobutyrate and isovalerate as direct cues, we reveal BumS structure is altered upon cue detection to inhibit its phosphatase activity. We provide an understanding of the mechanics of an unusual mode of signal transduction executed by BumSR and other bacterial sensor phosphatase-driven TCSs.

Progress Toward Epigenetic Targeted Therapies for Childhood Cancer.

Among the most significant discoveries from cancer genomics efforts has been the critical role of epigenetic dysregulation in cancer development and progression. Studies across diverse cancer types have revealed frequent mutations in genes encoding epigenetic regulators, alterations in DNA methylation and histone modifications, and a dramatic reorganization of chromatin structure. Epigenetic changes are especially relevant to pediatric cancers, which are often characterized by a low rate of genetic mutations. The inherent reversibility of epigenetic lesions has led to an intense interest in the development of epigenetic targeted therapies. Additionally, the recent appreciation of the interplay between the epigenome and immune regulation has sparked interest in combination therapies and synergistic immunotherapy approaches. Further, the recent appreciation of epigenetic variability as a driving force in cancer evolution has suggested new roles for epigenetic therapies in limiting plasticity and resistance. Here, we review recent progress and emerging directions in the development of epigenetic targeted therapeutics and their promise across the landscape of childhood cancers.

Metal Additive-Free Iodine-Promoted Reorganization of Ynamide-Ynes and Stereoselective 1,2-Diiodination.

We report a metal additive-free iodine-promoted one-step structural reorganization of ynamide-ynes and simultaneous stereoselective 1,2-diiodination of the migrated alkyne to form stereospecific tetrasubstituted alkenyl diiodo-tethered indoles (E-isomer). Molecular iodine is cost effective, user friendly, less toxic, commercially available, and easy to handle. The key features of the reaction include metal-and additive-free environment, selectivity, structural reorganization, mild reaction conditions, simple workup, and gram-scale synthesis. This transformation generates multiple bonds [nitrogen (N)-carbon (C)sp2, Csp2-Csp2, 2 Csp2-iodine (I)] via N-Csp bond cleavage in ynamide-ynes.

Impact of Geopolitical and Bilateral Trade Frictions on Global Supply Chain Resilience: Strategies for Multinational Corporations

In the context of the growing interconnectivity of the global economy, the resilience of global supply chains (GSCs) is increasingly contingent upon a range of external factors, including geopolitical developments and the implementation of bilateral trade policies. This study examines the vulnerabilities faced by GSCs in recent years, particularly the challenges they have shown in responding to geopolitical events and bilateral trade frictions. Taking the United Kingdom’s exit from the European Union and the trade war between the United States and China as examples, this study analyzes the significant impacts of these events on GSCs, including issues such as increased operating costs and structural reorganization. This study also proposes strategies for multinational corporations to cope with the complex international environment, such as supply chain diversification and localization of production. It is found that enhancing supply chain resilience is crucial to cope with geopolitical risks and safeguard business continuity, which helps to improve their market competitiveness and ability to cope with unexpected events.

Impacts of Post‐Fire Debris Flows on Fluvial Morphology and Sediment Transport in a California Central Coast Stream

AbstractPost‐fire debris flows alter impacted fluvial systems, but few studies quantify the magnitude and timing of reach‐scale channel response to these events. In August 2020, the Big Creek watershed along California's central coast burned in the Dolan Fire; in January 2021, an atmospheric river event triggered post‐fire debris flows in steep tributaries to the Big Creek. Here, we characterize the evolution of fluvial morphology and grain size in Big Creek, a cascade and step‐pool channel downstream of tributaries in which post‐fire debris flows initiated, using pre‐ and post‐fire structure from motion (SfM) and airborne lidar surveys. We also make comparisons to Devil's Creek, an adjacent basin which burned but did not experience post‐fire debris flows. We observe grain size fining following debris flows in Big Creek, but the coarsest 40% of the grain size distribution remained essentially unchanged despite reorganization of channel structure. Changes in grain size and elevated post‐fire peak flows account for approximately equal portions of a substantial increase in modeled bedload transport capacity one year post‐fire. In Big Creek, geomorphic recovery is well underway just two years post‐fire. A valley‐spanning log jam, which formed during debris flows, acts as a sediment trap upstream of our Big Creek study reach, and is partially responsible for accelerating recovery processes. In contrast, Devil's Creek exhibited little change in morphology or grain size despite elevated post‐fire peak flows. This period of geomorphic dynamism following the Dolan Fire has complex ecological impacts, notably for the threatened anadromous salmonid spawning habitat in Big Creek.

TTF2 promotes replisome eviction from stalled forks in mitosis.

When cells enter mitosis with under-replicated DNA, sister chromosome segregation is compromised, which can lead to massive genome instability. The replisome-associated E3 ubiquitin ligase TRAIP mitigates this threat by ubiquitylating the CMG helicase in mitosis, leading to disassembly of stalled replisomes, fork cleavage, and restoration of chromosome structure by alternative end-joining. Here, we show that replisome disassembly requires TRAIP phosphorylation by the mitotic Cyclin B-CDK1 kinase, as well as TTF2, a SWI/SNF ATPase previously implicated in the eviction of RNA polymerase from mitotic chromosomes. We find that TTF2 tethers TRAIP to replisomes using an N-terminal Zinc finger that binds to phosphorylated TRAIP and an adjacent TTF2 peptide that contacts the CMG-associated leading strand DNA polymerase ε. This TRAIP-TTF2-pol ε bridge, which forms independently of the TTF2 ATPase domain, is essential to promote CMG unloading and stalled fork breakage. Conversely, RNAPII eviction from mitotic chromosomes requires the ATPase activity of TTF2. We conclude that in mitosis, replisomes undergo a CDK- and TTF2-dependent structural reorganization that underlies the cellular response to incompletely replicated DNA.

Implications of Charge and Heteroatom Dopants on the Thermodynamics and Kinetics of Redox Reactions in Keggin-Type Polyoxometalates.

The utilization of polyoxometalate-based materials is largely dictated by their redox properties. Detailed understanding of the thermodynamic and kinetic efficiency of charge transfer is therefore essential to the development of polyoxometalate-based systems for target applications. Toward this end, we report electrochemical studies of a series of heteroatom-doped Keggin-type polyoxotungstate clusters [PW12O40]3- (PW 12 ), [VW12O40]3- (V in W 12 ), [P(VW11)O40]4- (PV out W 11 ), and [V(VW11)O40]4- (V in V out W 11 ) to elucidate the role of the identity and spatial location of heteroatoms and overall cluster charge on the rate constants of electron transfer and redox reaction entropies. Electrochemical analyses of the polyoxotungstates reveal that the kinetics of electron transfer for W-based redox processes change as a function of the redox activity of the heteroatom, whereas the spatial location of the heteroatom dopant does not significantly impact the electrokinetics. Variable temperature cyclic voltammetry measurements in organic solutions containing noncoordinating electrolyte ions establish that redox reaction entropies are primarily dictated by the overall charge of the clusters. Specifically, the redox entropy exhibits a good linear relationship with the dielectric continuum function Z ox 2 - Z red 2 (Z ox = charge of oxidized species, Z red = charge of reduced species). Finally, our experimental data do not show a prominent correlation between the kinetics of electron transfer and redox entropy, implying that the charge-transfer kinetics are not solely governed by structural reorganization. Taken together, these results highlight how structural and electronic parameters can influence the kinetics and thermodynamics of charge transfer in polyoxotungstates and provide insights into the design of polyoxometalate compounds with target redox properties.

Surface Speciation in Microwave-Assisted CO Oxidation over Perovskites─The Role of Water and Activation Pretreatment.

As a model for the energy-efficient aftertreatment of exhaust gas components, we studied microwave-assisted (MW) CO oxidation over a (La,Sr)CoO3-δ (LSC) perovskite oxide catalyst under dry and humidified conditions. We found that the use of a MW-based process can offer multiple advantages over traditional thermocatalysis in this scenario, as the nature of the MW-solid interaction offers quick, adaptive, and energy-efficient heating as well as improved yield and lower light-off temperatures. As found by combined CO and water MW-desorption experiments, the presence of technically relevant amounts of water leads to a competition for surface active sites and thus slows the reaction rate without indications for a fundamental change in the mechanism. Remarkably, the performance loss related to the presence of water was less pronounced in the MW-assisted process. Additionally, while we recorded a temperature-dependent degradation of the reaction rate in extended MW-catalysis experiments both in dry and humidified conditions, it quickly recovered after a short reactivation MW-treatment. Our study confirms that surface reaction can be driven by the use of MW-radiation in a similar magnitude that can be achieved by thermal activation at significantly higher temperatures. The nature of the effect of the MW-treatment on the structural and electronic surface properties of the LSC material was investigated by X-ray absorption (XAS) and X-ray photoelectron spectroscopy (XPS). We found evidence of a significant structural, chemical, and electronic reorganization of the oxide surface, possibly consistent with the occurrence of overheated surfaces or "hotspots" during MW-exposure, which may explain the increased catalytic and heating properties of the LSC after the MW-pretreatment. The good catalytic performance, quick response to MW-heating, and long-term stability of the catalyst all indicate the promising potential of a MW-based process for the energy-efficient exhaust aftertreatment using noble-metal-free oxide catalysts.

T-SRE: Transformer-based semantic Relation extraction for contextual paraphrased plagiarism detection

Plagiarism has become a pervasive issue in academics and professionals to safeguard academic integrity and intellectual property rights. The escalating sophistication of plagiarized content through semantic manipulation and structural reorganization poses significant challenges to existing detection systems that rely primarily on lexical similarity measures. The proposed T-SRE (Transformer-based Semantic Relation Extraction), a novel framework addresses the limitations of traditional n-gram and string-matching approaches by leveraging deep semantic analysis. The proposed framework combines Dependency Parsing (DP) for syntactic relationship mapping and Named Entity Recognition (NER) for contextual entity identification, augmented by a transformer-based neural network that captures long-range contextual dependencies. This learning methodology incorporates three key components: a position-aware word reordering algorithm, Levenshtein distance metric for structural similarity, and contextual word embeddings for semantic preservation detection. The proposed T-SRE enhances text structure recognition by combining position-aware reordering with semantic preservation through ensemble learning. The system implements a hierarchical classification scheme that quantifies plagiarism severity through a four-tier taxonomy: heavy, low, non-plagiarized and verbatim copy. The Udacity benchmark dataset showcases the model’s superior detection capabilities, achieving 92% precision, 89% recall, and an F1-score of 90.5%, particularly in lightweight textual modifications.The framework achieves a granularity score of 1.28, outperforming existing approaches.

Structural Reorganizations and Nanodomain Emergence in Lipid Membranes Driven by Ionic Liquids.

Ionic liquids (ILs) have promising applications in pharmaceuticals and green chemistry, but their use is limited by toxicity concerns, mainly due to their interactions with cell membranes. This study examines the effects of imidazolium-based ILs on the microscopic structure and phase behavior of a model cell membrane composed of zwitterionic dipalmitoylphosphatidylcholine (DPPC) lipids. Small-angle neutron scattering and dynamic light scattering reveal that the shorter-chain IL, 1-hexyl-3-methylimidazolium bromide (HMIM[Br]), induces the aggregation of DPPC unilamellar vesicles. In contrast, this aggregation is absent with the longer alkyl chain IL, 1-decyl-3-methylimidazolium bromide (DMIM[Br]). Instead, DMIM[Br] incorporation leads to the formation of distinct IL-poor and IL-rich nanodomains within the DPPC membrane, as evidenced by X-ray reflectivity, differential scanning calorimetry, and molecular dynamics simulations. The less evident nanodomain formation with HMIM[Br] underscores the role of hydrophobic interactions between lipid alkyl tails and ILs. Our findings demonstrate that longer alkyl chains in ILs significantly enhance their propensity to form membrane nanodomains, which is closely linked to enhanced membrane permeability, as shown by dye leakage measurements. This heightened permeability likely underlies the greater cytotoxicity of longer-chain ILs. This crucial link between nanodomains and toxicity provides valuable insights for designing safer, more environmentally friendly ILs, and promoting their use in biomedical applications and sustainable industrial processes.

A Mechanistic Way Triggering the Reversible Intercalation-Conversion Combined Chemistry for High Energy Density Lithium Ion Battery

The current status of lithium-ion battery technology has approached its theoretical capacity ceiling, necessitating a reevaluation of the cathode material design strategy. Over the past several decades, intercalation and conversion reactions have been recognized as the predominant chemistries governing lithium-ion battery cathode materials. While each of these charge storage mechanisms individually enables the development of high-energy-density cathode materials, integrating both mechanisms within a single-phase material presents significant challenges. Intercalation hosts demand facile lithium-ion diffusion kinetics facilitated by a well-defined crystal structure, whereas the repeated conversion reactions, accompanied by structural reorganization, can compromise intercalation capabilities. Recently, our research group demonstrated the reversible operation of intercalation-conversion combined chemistry within a single-phase material, specifically amorphous LiFeSO4F. To elucidate the underlying factors enabling the reversible utilization of intercalation and conversion reactions, we established a model system using the tavorite phase LiFeSO4F and systematically manipulated its degree of amorphization. The investigation of electrochemical properties across varying degrees of amorphization, along with first-principle computational simulations, elucidated the role of the amorphous structure in facilitating intercalation-conversion combined chemistry. The amorphous structure was found to promote an increase in conversion redox voltage and facilitate conversion kinetics, thereby enabling the reversible utilization of intercalation-conversion chemistry. Furthermore, our studies revealed that certain intercalation host materials can reversibly utilize conversion reactions through amorphization. These findings suggest a new paradigm for cathode design that integrates intercalation and conversion reactions, thereby expanding the possibilities within cathode chemistry.

Allosteric Communication Mediated by Protein Contact Clusters: ADynamical Model.

Describing the puzzling phenomenon of long-range communication between distant protein sites, allostery is of paramount importance in biomolecular regulation and signal transduction. It is commonly assumed to arise from a conformational rearrangement of the protein, although the underlying dynamical process has remained largely elusive. This study introduces a dynamical model of allosteric communication based on "contact clusters"─localized groups of highly correlated contacts that facilitate interactions between secondary structures. The model shows that allostery involves a multistep process with cooperative contact changes within clusters and communication between distant clusters mediated by rigid secondary structures. Considering time-dependent experiments on a photoswitchable PDZ3 domain, extensive (in total ∼500 μs) molecular dynamics simulations are conducted that directly monitor the photoinduced allosteric transition. The structural reorganization is illustrated by the time evolution of the contact clusters and the ligand, which effects the nonlocal coupling between distant clusters. A time scale analysis reveals dynamics from nano- to microseconds, which are in excellent agreement with the experimentally measured time scales. While the simulation of larger systems may require enhanced sampling techniques, it is expected that the general picture of allostery mediated by communicating contact clusters will still be applicable.

Voltage-Gated Switching of Moiré Patterns in Epitaxial Molecular Crystals.

Studying molecular materials at the nanoscale allows us to gain a deeper understanding of supramolecular structure formation and serves as the basis for rationally controlling the resulting interfacial properties. Here, we describe the formation of extended Moiré patterns resulting from the assembly of dipolar π-conjugated molecules on highly oriented pyrolytic graphite at the liquid-solid interface as characterized by scanning tunneling microscopy (STM). By switching the bias of the sample and thus the orientation of the external electric field in the vicinity of the STM junction, structural reorganization of the molecular building blocks and the resulting organic 2D crystal is induced and can conveniently be monitored in situ by the appearance and disappearance of the Moiré patterns. Importantly, the formation and loss of the Moiré patterns are fully reversible, providing exquisite control over epitaxial molecular crystals. Our approach provides fundamental insights into the supramolecular organization and resulting superstructure formation of incommensurable 2D lattices upon applying an electric field and enables the rational tuning of Moiré patterns as a key step toward the potential integration of organic 2D crystals in molecular nanodevices.

Guided Phase Transition in Host Formation Reaction for Designing Cathode Materials of Li-Ion Batteries

Conversion reaction-based cathode materials accompanying phase transition from transition metal compounds to lithium compounds and transition metal (MaXb + cLi → dLieX + aM, M: transition metal, X: anion) have been regarded as potential candidates for high-capacity cathodes due to multi-electron transfer reaction compared to intercalation cathode materials (LiMO2, M=Ni, Co, Mn) involving single electron transfer. Conversion reaction cathode materials also have received a lot of attention due to the high degree of freedom of designing the cathode materials according to the numerous combinations of transition metal (M) and anions (X). However, since the conversion reaction involves structural reorganization including phase separation, voltage hysteresis is inevitable due to the compositional inhomogeneity that occurs during the repeated lithiation/delithiation processes. These issues cause large irreversible capacity and progressive capacity degradation. Therefore, to utilize conversion reaction materials, it is desperately necessary to establish a reversible reaction path that can minimize voltage hysteresis and enable long-term cycle stability.The exploration of materials that separately store lithium ions and electrons has opened a new branch of cathode materials and design strategies through numerous combinations of lithium compounds and transition metal compounds. In certain combinations of these, the anions separated by the electrochemical decomposition of the lithium compound are incorporated into the transition metal compound, which enables to discover the new host of cathode materials polymorphs that can store the lithium and electrons reversibly. Herein, we introduce the mechanism of guided phase transition in host formation reactions inducing the phase transformation of transition metal compounds to a new metastable phase analogous to the original crystal structure. In the LiF-FeF2 composite system, the crystal structure of pristine tetragonal FeF2 successfully guides the phase transition route to reach metastable tetragonal FeF3 rather than the formation of thermodynamically stable rhombohedral FeF3. Induced tetragonal FeF3, due to its structural similarity to discharged FeF2, enables facile phase transitions even during insertion and conversion reactions, thereby reducing compositional inhomogeneity and providing low voltage hysteresis and high reversibility. We believe that guiding the reaction pathway to minimize changes in crystal structure during the charging and discharging processes is essential to evade the irreversible reaction pathway for the conversion reaction cathode materials. Therefore, a deeper understanding of the reaction mechanisms in the LiF-FeF2 nanocomposite provides valuable insights into designing cathode materials with enhanced performance and cycle stability by controlling the reaction pathway and crystal structure.