Structural Rearrangements Research Articles

Molecular insights into substrate translocation in an elevator-type metal transporter

The Zrt/Irt-like protein (ZIP) metal transporters are key players in maintaining the homeostasis of a panel of essential microelements. The prototypical ZIP from Bordetella bronchiseptica (BbZIP) is an elevator transporter, but how the metal substrate moves along the transport pathway and how the transporter changes conformation to allow alternating access remain to be elucidated. Here, we combine structural, biochemical, and computational approaches to investigate the process of metal substrate translocation along with the global structural rearrangement. Our study reveals an upward hinge motion of the transport domain in a high-resolution crystal structure of a cross-linked variant, elucidates the mechanisms of metal release from the transport site into the cytoplasm and activity regulation by a cytoplasmic metal-binding loop, and unravels an unusual elevator mode in enhanced sampling simulations that distinguishes BbZIP from other elevator transporters. This work provides important insights into the metal transport mechanism of the ZIP family.

Photosystem rearrangements, photosynthetic efficiency, and plant growth in far red-enriched light.

Arabidopsis plants were grown in white light (400-700 nm) or in white light supplemented with far-red (FR) light peaking at 730 nm. FR-enriched light induced the typical shade avoidance syndrome characterized by enhanced length of seedling hypocotyl and leaf petiole. FR supplementation also caused a noticeable decrease in the carotenoid and chlorophyll content that was attributable to a block of pigment accumulation during plant development. The carotenoid decrease resulted from a downregulation of their biosynthesis pathway rather than carotenoid degradation. The losses of photosynthetic pigments are part of structural and functional rearrangements of the photosynthetic apparatus. The plastoquinone pool was chronically more oxidized in plants acclimated to white + FR light compared to white light-grown plants. Growth in FR-enriched light was associated with a higher photochemical efficiency of PSII compared to growth in white light and with a substantial increase in root and shoot biomass production. Light distribution between the photosystems was modified in favor of PSII by an increase in the PSII/PSI ratio and an inhibition of state transitions. Neither LHCII abundance nor nonphotochemical energy dissipation in the PSII chlorophyll antennae were modified significantly by the addition of FR light. A PSI supercomplex, not previously observed in Arabidopsis, was specifically found in plants grown in FR-enriched light. This large PSI complex contains a supplementary Lhca1-4 dimer, leading to a total of 6 LHCI antennae instead of 4 in the canonical PSI. Through those photosystem rearrangements and the synergistic interaction with white light, FR light is photosynthetically active and can boost photosynthesis and plant growth.

Monitoring C–C coupling in catalytic reactions via machine-learned infrared spectroscopy

Abstract Tracking atomic structural evolution along chemical transformation pathways is essential for optimizing chemical transitions and enhancing control. However, molecule-level knowledge of structural rearrangements during chemical processes remains a great challenge. Here, we couple infrared spectroscopy as a non-invasive method to probe molecular transformations, with a machine-learned protocol to immediately map the spectroscopic fingerprints to atomistic structures. From the theoretical perspective, we demonstrate it here with the example of C–C coupling in catalytic reactions, elucidating various structural conformations along dynamic trajectories. Within the transferable application to the specific CO–CO dimerization reaction, the structural and energetic variations of the critical chemical species could be identified via infrared spectroscopy. This approach extends the power of spectroscopy from fingerprinting chemical configurations to using them for assigning dynamic structural information.

Multiscale Analyses of Strain-Enhanced Charge Transport in Conjugated Polymers.

The advancement of flexible and wearable electronics relies on semiconducting polymers that can endure mechanical deformation while maintaining high electrical performance under strain. In this study, we demonstrate that fine-tuning backbone rigidity through the molecular design of donor moieties significantly enhances both the mechanical and charge transport properties of diketopyrrolopyrrole (DPP)-based polymers. Specifically, the flexible DPP-4T (quaterthiophene) exhibited a persistence length of 20.4 nm in solution, while DPP-DTT (dithienothiophene) showed a longer persistence length of 32.8 nm due to its stiff backbone, as confirmed by small-angle neutron scattering and Monte Carlo simulations. This flexibility enabled DPP-4T to achieve a crack-onset strain exceeding 100% via the film-on-elastomer method and a fracture strain of over 30% in quasi-free-standing films. Additionally, DPP-4T demonstrated a 180% increase in hole mobility at 80% strain, driven by strain-induced chain alignment and backbone planarization. Utilizing a range of characterization techniques, including ultraviolet-visible (UV-vis) spectroscopy, grazing incidence X-ray diffraction (XRD), and Raman spectroscopy, we characterized structural changes at multiple length scales under applied tensile strain. Notably, strain induced a transformation in chain conformation from a twisted to a flat structure, reducing the hopping energy barrier and enhancing charge transport. These structural rearrangements are crucial for sustaining efficient charge transport and ensuring the reliability of electronic performance under mechanical stress.

Effect of the critical melting treatment on the short/long-term retrogradation behaviour of maize starch

The shortand long-term retrogradation properties in normal maize starch (N-S) by critical melting treatment (CMT; including TO (onset temperature) melting (OM), TP (peak temperature) melting (PM), and TC (conclusion temperature) melting (CM)) were studied. Results indicated that CMT promoted short-term (1 day) and long-term (7 days) retrogradation of N-S in the following order: PM > CM > OM. After storage for 7 days, following the PM treatment, the gel hardness, the retrogradation degree, and relative crystallinity increased to 4.67 N, 13.191%, 8.58% from 2.87 N, 9.972%, and 6.20%, respectively. PM treatment resulted in harder starch granules, promoting the rearrangement of the starch crystalline structure during cold storage. This was confirmed by the increased storage modulus, decreased iodine blue value, reduced gap in the gel network, and compact aggregate formation. Results indicated that CMT can promote the retrogradation properties of N-S.

A triplicated wheat-rye chromosome segment including several 12-OXOPHYTODIENOATE REDUCTASE III genes influences magnesium partitioning and impacts wheat performance at low magnesium supply

We previously reported a structural rearrangement between wheat (Triticum aestivum) and rye (Secale cereale) chromosomes 1BS/1RS that increased the dosage of 12-OXOPHYTODIENOATE REDUCTASE III (OPRIII) genes involved in jasmonate biosynthesis (henceforth, 1RW line), and that drastically reduced primary root growth relative to a control line with the intact 1RS chromosome (henceforth, 1RS). In this study, we show that the increased gene-dosage of this region is associated with increases in the shoot-root partitioning of magnesium (Mg). Moreover, both a CRISPR-edited 1RW line with reduced OPRIII dosage and the 1RW line treated with the jasmonate biosynthesis inhibitor ibuprofen showed reduced differences in shoot-root Mg partitioning than 1RW. The observed differences in Mg partitioning between 1RS and 1RW plants occur over a wide range of external Mg supplies and imply opposite trends of Mg accumulation in roots and shoots. Furthermore, we show an association between the increase of shoot-root Mg partitioning and increased tolerance of the 1RW line to low levels of Mg supply. In summary, our results provide evidence of the role of the jasmonate pathway on the dynamics of Mg accumulation in roots and shoots, which correlates with the performance of wheat plants under conditions of Mg scarcity.

ZnFe-LDH synthesized by seed-induced method to simultaneous enhance arsenic removal, stabilization and sludge reduction

To simultaneously enhance arsenic removal, stabilization and sludge reduction, a seed-induced method was applied to in-stiu synthesize ZnFe-LDH containing arsenic (ZnFe-As-LDH). The optimal seed was determined to be ZnFe-LDH by analyzing the effects of the unseeded system and seed-induced system (FeⅡFeⅢ-LDH, ferrihydrite and ZnFe-LDH). In the ZnFe-LDH seed system, the arsenic removal efficiency increased and the arsenic leaching concentration were drastically reduced by 91.33% under the optimal conditions as the seeds dosage of 2.5g/L, pH 10 and Zn/Fe ratio of 1.5. The addition of seed crystals promoted crystal growth and aggregation and finally regulated the formation of dense bulk LDH with fewer pores and smaller pore sizes. The arsenic removal and stabilization were achieved by converting active arsenic into more stable crystalline bound arsenic through coprecipitation, ion exchange and complexation. The SV30 was reduced by 73.68% and it was due to reduction of unstable surface water and interspace and crystallinity enhancement. The formation pathway of ZnFe-As-LDH by seed-induced was elucidated. The seed-induced method promoted the formation of arsenic-containing ferrihydrite and Zn(OH)2 coprecipitations on the surface of ZnFe-LDH seed, and led to a structural rearrangement to generate ZnFe-As-LDH.

Durable Organic Coating-Free Superhydrophobic Metal Surface by Paracrystalline State Formation.

The chemical instability of traditional organically-decorated superhydrophobic metal surfaces is a significant issue, severely limiting practical applications. This is due to the susceptibility of low surface energy coatings to ion permeation, decomposition, and exfoliation, especially in harsh environments. Here, organic coating-free, durable superhydrophobic surfaces on Al alloys by developing the paracrystalline state of a bionic anthill tribe structure is successfully achieved, using femtosecond laser element-doping microstructuring followed by repetitive annealing processes. Remarkably, the inherent superhydrophobic properties of the sample are maintained for ≈2000 h in a corrosive 3.5 wt.% NaCl aqueous solution, significantly surpassing the performance of traditional organic coatings. Moreover, this inherent superhydrophobicity remains nearly unchanged, even after rigorous electrochemical reaction measurements. Additional tests involving UV irradiation (>100 h), freezing cycles (>100 cycles), and acid/alkali resistance (>65 h) further demonstrate that the environmental adaptability of the surface far exceeds that of silane-coated surfaces. Ab initio calculations reveal that the formation of the paracrystalline state reduces surface energy and enhances chemical stability, thereby extending the durability of the superhydrophobic metal. These findings offer a powerful strategy for utilizing atomic-level structural rearrangements to design inherent superhydrophobic surfaces without the need for organic coatings.

Understanding and simulating mechanochromism in dye-dispersed polymer blends: from atomistic insights to macroscopic properties.

In this work, we propose a computational protocol enabling the simulation of mechanochromic responses in dye-dispersed polymer blends. The main objective is the modeling of the molecular-level structural changes responsible for the modulation of the photophysical properties that lead to the mechanochromic phenomenon. In this demonstrative study, we focus on predicting the changes in optical absorption displayed by a model system consisting of a dimer of a tetraphenylethylene derivative dispersed in a polyethylene matrix. The blend is subjected to an external stimulus that causes a modulation of the polymer matrix density that translates, in turn, into the emergence of specific mechanical constraints on the optically active dimers. The accurate description of this phenomenon requires the reliable sampling of the dimer configurations induced by the interaction with the matrix under stress. These molecular geometries are associated with modified electronic structures that confer novel absorption responses to the dispersed dyes. In the present contribution, the sampling of these structures is achieved through classical molecular dynamics (MD) simulations including a model element to apply an anisotropic mechanical force. This element allows the microscopic modeling of the chains' and dyes' structural rearrangements under stress. After the sampling, we compare the results of two approaches for the prediction of the optical response: (i) the calculation of a mean response from a statistical average over quantum chemical calculations on the sampled MD structures and (ii) a prediction via a more expensive hybrid scheme allowing the relaxation of the sampled molecular geometries in the presence of the matrix constraints.

On the thermal dissipation in the thermomechanical treatment of metal materials

The results of plastic compression of steels and alloys of different chemical compositions at temperatures and rates of plastic deformation corresponding to common thermomechanical treatment (TMT) regimes are considered. The features of the diagrams σ (ε, έ, Т) are revealed. The processes of strain accumulation and thermal dissipation are accompanied by structural rearrangements. Depending on the chemical composition and hot compression modes, structural transformations occur self-organized, with the possibility of excitation of oscillations and the formation of dissipative solitons.

Fabrication of Ripple Structured Silicon Carbide (SiC) Films for Nano‐Grating and Solar Cell Applications

AbstractIn the present study, we aim to investigate the self‐organization of unexplored silicon carbide (SiC) film surfaces under 30 keV oblique Ar+ ions irradiation and hence unprecedented tailoring of optical and electrical characteristics with view of their uses in solar cells, gratings and nano‐ to micro‐scale devices. The surface morphology mainly consisted of triangular shaped nanoparticles which evolves into nanoscale ripple structures with an alignment parallel to the projection of ion beam direction. For the first time, we have demonstrated the fabrication of highly‐ordered ripple patterns with wavelength in visible region over SiC films and applicable as nano‐gratings. The underlying mechanism relies on the structural rearrangement due to transition of film microstructure from amorphous to mixed phase (crystalline, nano‐crystalline and amorphous) and lowering of C=C and C−C vibration modes by the heavier Si atoms. These nanostructured silicon carbide film shows unparalleled optical (energy gap decreases from 4.60±0.4 eV to 3.16±0.2 eV) & electrical characteristics (conductivity increases from 6.6×10−11 to 1.12×10−3 S/m with linear I−V behavior). Thus, we propose that ripple structured SiC films with wide band gap, high refractive index and high electrical conductivity with ohmic behaviour are promising candidates for application as window layer in solar cells and opto‐electronics.

Redox Properties of Structural Fe in Clay Minerals: 4. Reinterpreting Redox Curves by Accounting for Electron Transfer and Structural Rearrangement Kinetics.

Iron-bearing smectite clay minerals can act as electron sources and sinks in the environment. Previous studies using mediated electrochemical analyses to determine the reduction potential (EH) values of smectites observed that the relationship between the structural Fe2+(s)/FeTotal ratio in the smectite and EH varied based on the redox history of the smectite. We hypothesize that this behavior, referred to as redox hysteresis, results from the smectite particles not equilibrating with the applied EH over the course of the experiment (∼30 min). To test this hypothesis, we developed a model incorporating interfacial electron transfer kinetics and charge redistribution within the particle to simulate the mediated electrochemical experiments from previous studies. The simulated redox curves accurately matched the previously reported experimental redox curves of the smectite SWa-1, demonstrating that longer equilibration periods led to a decrease in redox hysteresis. We validated this experimentally by measuring the redox curve of SWa-1 after an equilibration period of at least 12 h. Furthermore, we extended the simulations to three other smectites (NAu-1, NAu-2, and SWy-2) and extracted their respective thermodynamic and kinetic parameters. This work offers a framework for interpreting and modeling redox reactions on clay surfaces, along with key parameters for four commonly studied smectites.

Crystal Evolution of Amorphous Poly(lactic acid) During Simultaneous Multi‐step Tensile Deformation and Annealing

ABSTRACTThe cold‐crystallization and crystal evolution of amorphous poly(lactic acid) (PLA) are analyzed during multistep tensile deformation and annealing at 70°C using in situ synchrotron wide‐angle X‐ray scattering (WAXS) measurements. The 2D‐WAXS diffraction pattern reveals that the PLA crystalline structure forms perpendicular to the draw direction. The annealing process lets to a rearrangement of the crystalline structure, while the stretching causes crystal contraction. Both WAXS and FTIR analyses confirm that the crystals developed through stretching and annealing are in the α′‐form. The crystallinity of PLA increases with higher deformation strains and longer annealing times. The orientation degree of both crystalline and amorphous phases of PLA, as indicated by the Hermans orientation factor and dichroic ratio of 956 cm−1 band (evaluated by WAXS and polarized FTIR analysis, respectively) also increase. The enhanced cold‐crystallization ability of PLA is attributed to the synergistic effect of tensile deformation and annealing, rather than either technique alone. The unusual crystallization phenomenon observed during multistep tensile deformation coupled with annealing provides valuable insights into the crystallization and crystal evolution of PLA.

Pressure-induced structural variations and mechanical behavior of silicate glasses: Role of aluminum and sodium

This study investigates the effects of pressure-induced densification on the structural and mechanical properties of albite-like (12.5 % Na2O·12.5 % Al2O3·75 % SiO2) and sodium silicate (12.5 % Na2O·87.5 % SiO2) glasses using Molecular Dynamics simulations. Densification increased the coordination numbers of Al and Na, facilitated Al-O-Al clustering and formation of three-bridging oxygens, reduced T-O-T angles, and packed sodium ions in albite glass. Sodium silicate glass exhibited densification primarily through increased Na coordination, reduction of Si-O-Si angle and reduced Na-Na distances. Elastic modulus calculations revealed increased stiffness with densification due to enhanced atomic packing and glass reticulation. Uniaxial tensile tests showed densified glasses had higher ductility and strength than undensified counterparts, highlighting the positive effects of pressure-induced structural rearrangements. Hydrostatic compression tests demonstrated reversible densification under varying pressure loads, with pre-treatment conditions significantly affecting residual densification.

Low PD-L1 expression, MAP2K2 alterations, and enriched HPV gene signatures characterize brain metastases in head and neck squamous cell carcinoma

BackgroundBrain metastasis (BM) is a rare but severe complication of head and neck squamous cell carcinoma (HNSCC), with limited knowledge of molecular characteristics and immunogenicity.MethodsWe analyzed 61 cases of HNSCC-BM from three academic institutions (n = 24) and Foundation Medicine Inc (FMI, n = 37). A subset of cases underwent next-generation sequencing, multiple immunofluorescence, and proximity ligation sequencing. Gene enrichment analysis compared alterations in FMI BM samples (n = 37) with local samples (n = 4082).ResultsDemographics included: median age of 59 years, 75% male, 55% current/former smokers, 75% oropharyngeal primary, and 67% human papillomavirus (HPV) +. ATM (54%), KMT2A (54%), PTEN (46%), RB1 (46%), and TP53 (46%) were frequently altered in BM samples from academic centers (62% HPV/p16+). Structural rearrangements ranged from 9 to 90 variants by proximity ligation sequencing. BMs had low densities of CD8+, PD-1+, PD-L1+, and FOXP3 + cells, and 92% had PD-L1 combined positive scores < 1%. CDKN2A (40.5%), TP53 (37.8%), and PIK3CA (27.0%) alterations were common in the FMI BMs (51% HPV+). MAP2K2 alterations and HPV + signature were enriched in FMI BMs compared to local tumors (11.8% vs. 6.4%, P = 0.005 and 51.25% vs. 26.11%, P = 0.001 respectively), and pathogenic TSC1 inactivating mutations were enriched in local tumors (67.3% vs. 37.8%, P = 0.008). Median overall survival from BM diagnosis was 9 months (range 0–27).ConclusionsHNSCC patients with BM frequently have oropharyngeal primary sites and are HPV+. Common molecular alterations in BM samples, including targetable PIK3CA and ATM, were identified. MAP2K2 alterations were enriched and densities of immune cells were low, highlighting potential targets for further research and immunotherapy considerations.

Cascade CO2 Insertion in Carbanion Ionic Liquids Driven by Structure Rearrangement.

The CO2 chemisorption in state-of-the-art sorbents based on oxide/hydroxide/amine moieties is driven by strong chemical bonding formation in the carbonate/bicarbonate/carbamate products, which in turn leads to high energy input in sorbent regeneration. In addition, the CO2 uptake capacity was limited by the active sites' utilization efficiency, with each active site incorporating one CO2 molecule or less. In this work, a new concept and generation of sorbent was developed to achieve cascade insertion of multiple CO2 molecules by leveraging structure rearrangement as the driving force, leading to in situ generation of extra CO2-binding sites and significantly reduced energy input for CO2 release. The designed ionic liquids (ILs) containing carbanions with conjugated and asymmetric structure, deprotonated (methylsulfonyl)acetonitrile ([MSA]) anion, allowed the cascade insertion of two CO2 molecules via consecutive C-C and O-C bond formations. The proton transfer and structure rearrangement of the carboxylic acid intermediates played critical roles in stabilizing the first integrated CO2 and generating extra electron-rich oxygen sites for the insertion of the second CO2. The structure variation and reaction pathway were confirmed by operando spectroscopy, magnetic resonance spectroscopy (NMR), mass spectroscopy, and computational chemistry. The energy input in sorbent regeneration could be further reduced by harnessing the phase-changing behavior of the carbanion salts in ether solutions upon reacting with CO2, avoiding the energy consumption in heating the solvent. The fundamental insights obtained herein provide a promising approach to greatly improve the CO2 sorption performance via sophisticated molecular-scale structural engineering of the sorbents.

Highly Diffusive Nonluminescent Carriers in Hybrid Phase Lead Triiodide Perovskite Nanowires

AbstractCrystal structural rearrangements unavoidably introduce defects into materials, where even these small changes in local lattice structure could arouse a prominent impact on the overall nature of crystals. Contrary to the traditional notion that defects obstruct carrier transport, herein, we report a promoted transport mechanism of nonluminescent carriers in single‐crystalline CH3NH3PbI3 nanowires (1345.2 cm2 V−1 s−1, about a 14‐fold improvement), enabled by the phase transition induced defects (PTIDs). Carriers captured by PTIDs evade both the radiative and non‐radiative recombinations during the incomplete tetragonal‐to‐orthorhombic phase transition at low temperatures, forming a specific nonluminescent state that exhibits an efficient long‐distance transport and thereby realize a prominent enhancement of photocurrent responsivity for photodetector applications. The findings provide broader insights into the carrier transport mechanism in perovskite semiconductors and have significant implications for their rational design for photoelectronic applications at varied operating temperatures.

Highly Diffusive Nonluminescent Carriers in Hybrid Phase Lead Triiodide Perovskite Nanowires.

Crystal structural rearrangements unavoidably introduce defects into materials, where even these small changes in local lattice structure could arouse a prominent impact on the overall nature of crystals. Contrary to the traditional notion that defects obstruct carrier transport, herein, we report a promoted transport mechanism of nonluminescent carriers in single-crystalline CH3NH3PbI3 nanowires (1345.2 cm2 V-1 s-1, about a 14-fold improvement), enabled by the phase transition induced defects (PTIDs). Carriers captured by PTIDs evade both the radiative and non-radiative recombinations during the incomplete tetragonal-to-orthorhombic phase transition at low temperatures, forming a specific nonluminescent state that exhibits an efficient long-distance transport and thereby realize a prominent enhancement of photocurrent responsivity for photodetector applications. The findings provide broader insights into the carrier transport mechanism in perovskite semiconductors and have significant implications for their rational design for photoelectronic applications at varied operating temperatures.

Developing Rapid-Charging Li-S Batteries via "Target Catalysis" of Cations and Anions Modified Electrocatalyst.

The shuttle effect and sluggish sulfur reduction reaction have resulted in significantly low efficiency and poor high current cycling stability in lithium-sulfur batteries, impeding their practical applications. To address these challenges, the introduction of Ni cations into MoS2 grown on reduced graphene oxide (MoS2/rGO) induces the formation of impurity energy levels between the conduction and valence bands of MoS2. Additionally, the introduction of anionic Se expands the interlayer spacing, enhances intrinsic conductivity, and improves ion diffusion rates. Simultaneously introducing anionic and cationic species into the MoS2/rGO causes the center of the d-band to shift upward, reducing the occupancy of electrons in antibonding orbitals. This modification leads to a rearrangement of the electronic structure of Mo, accelerating the redox reactions of lithium polysulfides. It particularly enhances the binding energy and lowers the conversion energy barrier of Li2S4. Consequently, the Li||S coin cell with the Ni-MoSSe/rGO cathode demonstrates an initial capacity of 446 mAh g-1 at 20 C, with a remarkable capacity retention of ≈96.7% after 200 cycles. Moreover, even under high sulfur loading conditions (6.45 mg cm-2) and a low electrolyte/sulfur ratio (5.4 µL mg-2), it maintains a high areal capacity of 6.42 mAh cm-2.

Sequential structure probing of cotranscriptional RNA folding intermediates.

Cotranscriptional RNA folding pathways typically involve the sequential formation of folding intermediates. Existing methods for cotranscriptional RNA structure probing map the structure of nascent RNA in the context of a terminally arrested transcription elongation complex. Consequently, the rearrangement of RNA structures as nucleotides are added to the transcript can be inferred but is not assessed directly. To address this limitation, we have developed linked- m ultipoint T ranscription E longation C omplex RNA structure prob ing (TECprobe-LM), which assesses the cotranscriptional rearrangement of RNA structures by sequentially positioning E. coli RNAP at two or more points within a DNA template so that nascent RNA can be chemically probed. We validated TECprobe-LM by measuring known folding events that occur within the E. coli signal recognition particle RNA, Clostridium beijerinckii pfl ZTP riboswitch, and Bacillus cereus crcB fluoride riboswitch folding pathways. Our findings establish TECprobe-LM as a strategy for detecting cotranscriptional RNA folding events directly using chemical probing.