Stable Structure Research Articles

Toward quantitative characterization of simulated earthquake-cycle complexities

Earthquake cycle simulations based on the rate-and-state friction formulation are evolutions of nonlinear dynamical systems (NDS). The term “cycle” implies an overall stable structure that is a phase-space attractor naturally traced out by trajectories of NDS as it evolves. Quantitatively characterizing these attractors should be a basis for measuring complexities of the simulated earthquake cycles, i.e. to determine if and how regular or chaotic they are. I first revisit the textbook-standard quasi-dynamic spring-slider system from an NDS perspective, explicitly showing the attractors, their relationship with the parameters of the NDS, and how they can be characterized taken advantage of their low-dimensionality while aiming to extend the analysis to high-dimensionality. I evaluate two approaches, computing the Lyapunov exponents (LEs) and measuring correlation dimensions, with the simple spring-slider and earthquake-cycle examples whose phase-space attractors can be visually verified. I conclude LEs are too inconvenient and computationally expensive to use whereas measuring correlation dimensions is an easy and effective approach even with highly non-uniform time sampling present in all simulations. For earthquake-cycle simulations, an attractor reconstruction is performed based on Taken’s theorem to corroborate my correlation-dimension results. The current method is limited in its ability to detect chaos in a dichotomous manner, which illuminates the direction for future study. An improving ability to quantitatively characterize earthquake-cycle simulations as an overall stable structure offers new opportunities to understand exotic seismic observations such as slow-slip events and enables more informative comparison with real data, particularly from paleoseismology, which could have far-reaching implications in earthquake forecasting.

Theoretical study of metal contacts to the monolayer ferroelectric material CuInP2S6 and its device applications

Two-dimensional (2D) ferroelectric materials exhibit significant potential for applications in nonvolatile memory and device miniaturization. In the device design stage, it is essential to consider the compatibility between 2D ferroelectric materials and three-dimensional (3D) metal. However, the interface between them introduces complex interactions that could impact the device's performance. In this work, based on the first-principles method, we simulate several 3D metal–2D ferroelectric material contact systems by utilizing different 3D metals in contact with the 2D ferroelectric monolayer CuInP2S6 (CIPS). By calculating the electronic structures of the systems, we find that the Cd(001)–CIPS configuration is the most stable structure, followed by the Ag(111)–CIPS and Au(111)–CIPS systems. Both the Cd(001)–CIPS and Ag(111)–CIPS systems undergo a transition from Schottky to Ohmic contact. Finally, we theoretically design a ferroelectric tunnel junction (FTJ) based on the Cd(001)–CIPS contact system, achieving a tunneling electroresistance ratio of 2.394×105% and a remarkably low resistance–area product of 0.78 Ω·μm2, which makes the proposed FTJ superior to the conventional 3D FTJ. This work provides some insights for the design of nonvolatile storage devices.

Halogen-Bonded Organic Frameworks (XOFs) Based on N⋅⋅⋅Br+⋅⋅⋅N Bonds: Robust Organic Networks Constructed by Fragile Bonds.

Organic frameworks face a trade-off between the framework stability and the bond dynamics, which necessitates the development of innovative linkages that can generate stable frameworks without hindering efficient synthesis. Although iodine(I)-based halogen-bonded organic frameworks (XOFs) have been developed, constructing XOFs based on bromine(I) is desirable yet challenging due to the high sensitivity of bromine(I) species. In this work, we present the inaugural construction of stable bromine(I)-bridged two-dimensional (2D) halogen-bonded organic frameworks, XOF(Br)-TPy-BF4/OTf, based on sensitive [N⋅⋅⋅Br⋅⋅⋅N]+ halogen bonds. The formation of XOF(Br)-TPy-BF4/OTf was monitored by 1H NMR, XPS, IR, SEM, TEM, HR-TEM, SEAD. Their framework structures were established by the results from PXRD, theoretical simulations and SAXS. More importantly, XOF(Br) displayed excellent chemical and thermal stabilities. They exhibited stable two-dimensional framework structures in various organic solvents and aqueous media, even over a wide pH range (pH 3-12), while the corresponding model compounds BrPy2BF4/OTf decomposed quickly even in the presence of minimal water. Furthermore, the influence of the counterions were investigated by replacing BF4 with OTf, which improved the stability of XOF(Br). This characteristic enabled XOF(Br) to serve as an efficient oxidizing reagent in aqueous environments, in contrast with the sensitivity of BrPy2BF4/OTf, which performed well only in organic media. This study not only deepens our fundamental understanding of organic frameworks but also opens new avenues for the development and application of multifunctional XOFs.

Crystal Structure Prediction and Performance Assessment of Hydrogen Storage Materials: Insights from Computational Materials Science

Hydrogen storage materials play a pivotal role in the development of a sustainable hydrogen economy. However, the discovery and optimization of high-performance storage materials remain a significant challenge due to the complex interplay of structural, thermodynamic and kinetic factors. Computational materials science has emerged as a powerful tool to accelerate the design and development of novel hydrogen storage materials by providing atomic-level insights into the storage mechanisms and guiding experimental efforts. In this comprehensive review, we discuss the recent advances in crystal structure prediction and performance assessment of hydrogen storage materials from a computational perspective. We highlight the applications of state-of-the-art computational methods, including density functional theory (DFT), molecular dynamics (MD) simulations, and machine learning (ML) techniques, in screening, evaluating, and optimizing storage materials. Special emphasis is placed on the prediction of stable crystal structures, assessment of thermodynamic and kinetic properties, and high-throughput screening of material space. Furthermore, we discuss the importance of multiscale modeling approaches that bridge different length and time scales, providing a holistic understanding of the storage processes. The synergistic integration of computational and experimental studies is also highlighted, with a focus on experimental validation and collaborative material discovery. Finally, we present an outlook on the future directions of computationally driven materials design for hydrogen storage applications, discussing the challenges, opportunities, and strategies for accelerating the development of high-performance storage materials. This review aims to provide a comprehensive and up-to-date account of the field, stimulating further research efforts to leverage computational methods to unlock the full potential of hydrogen storage materials.

Observations of Cu-Granules-coated graphite particles for characteristics of Cu-Graphite sintered composite

Cu-graphite sintered composites synthesized by flake powder metallurgy process are evaluated according to microstructure characteristics and mechanical properties. Impact of processing parameters and correlation between the reinforcement for the synthesized composite are discussed in detail. Obtained results showed an effect of un-melted Cu granules, which develop better stable and organized composite structure. The metallization graphite surface significantly improves the wettability between Cu and graphite.

THE QUEST FOR STABLE BOROZENE CORE IN MAIN-GROUP CAPPED INVERSE SANDWICH COMPLEXES, [(HE)2B6H6]2- (E=B, Al, Ga, In, and Tl).

The ubiquitous chemistry of benzene led us to explore ways to stabiliseanalogous borozene, by capping them with appropriate groups. The mismatch in overlap of ring-cap fragment molecular orbitals in [(HB)2B6H6]2-is overcome by replacing the two BH caps withhigher congeners of boron. We calculated the relative energies of all the polyhedral structural candidates for[(HE)2B6H6]2-(E = Al-Tl)and found hexagonal bipyramid(HBP) to be more stable with Al-H caps. A global minimum search also gives HBP as the most stable structure for [Al2B6H8]2-. The capped B6H6ring in[(HAl)2B6H6]2-has aromaticity comparable to that of benzene.

A Novel Spinel High-Entropy Oxide (Cr0.2Mn0.2Co0.2Ni0.2Zn0.2)3O4 as Anode Material for Lithium-Ion Batteries

In this study, we synthesized spinel high-entropy oxide (HEO) (Cr0.2Mn0.2Co0.2Ni0.2Zn0.2)3O4 nanoparticles by a simple solution combustion method. These particles were investigated for their performance as anodes in lithium-ion batteries. The reversible capacity is 132 mAh·g−1 after 100 cycles at a current density of 100 mA·g−1, 107 mAh·g−1 after 1000 cycles at a current density of 1 A g−1, and 96 mAh·g−1 rate capacity at a high current density of 2 A g−1. The outstanding cycle stability under high current densities and remarkable rate performance can be attributed to the stable structure originating from the high entropy of the material.

Theoretical perspectives on the electronic, optical, mechanical, magnetic, and anisotropic behaviors of the quaternary Heusler alloys RhFeMnZ and IrMnCrZ (where Z = Si, Ge)

High-spin-polarised materials are the most promising candidates for spintronic devices. Here, the spin-polarised electronic structure, magnetism, mechanical, and optical properties of RhFeMnZ and IrMnCrZ (where Z = Si, Ge) Quaternary Heusler alloys were calculated by first-principles calculations. The calculations show that type III for the RhFeMnSi, RhFeMnGe, and IrMnCrSi and type I for the IrMnCrGe compound configuration is the most stable crystal structure for the studied alloys. The four alloys were found to have a half-metallic ferromagnetic structure with indirect band gaps in the majority spin channels of 0.957, 0.66, 0.745, and 0.891 eV for RhFeMnSi, RhFeMnGe, IrMnCrSi, and IrMnCrGe, respectively. They exhibit an appreciable total magnetic moment of 4 μB for RhFeMnZ (Z = Si, Ge) and 2 μB for IrMnCrZ (Z = Si, Ge). The results show that RhFeMnZ and IrMnCrZ (where Z = Si, Ge) are ferromagnetic half-metals with 100 % spin polarisation. The results of the elastic constants demonstrate the mechanical stability of RhFeMnZ and IrMnCrZ (where Z = Si, Ge) alloys. Optical properties such as dielectric function, absorption, reflectance, optical conductivity, and other optical properties were also probed. In the ultraviolet region, RhFeMnZ and IrMnCrZ (where Z = Si, Ge) are effective absorbers and have a high refractive index. Alloys are promising candidates for potential applications in spintronic devices.

Deep learning guided design of dynamic proteins.

Deep learning has greatly advanced design of highly stable static protein structures, but the controlled conformational dynamics that are hallmarks of natural switch-like signaling proteins have remained inaccessible to de novo design. Here, we describe a general deep-learning-guided approach for de novo design of dynamic changes between intra-domain geometries of proteins, similar to switch mechanisms prevalent in nature, with atom-level precision. We solve 4 structures validating the designed conformations, show microsecond transitions between them, and demonstrate that the conformational landscape can be modulated by orthosteric ligands and allosteric mutations. Physics-based simulations are in remarkable agreement with deep-learning predictions and experimental data, reveal distinct state-dependent residue interaction networks, and predict mutations that tune the designed conformational landscape. Our approach demonstrates that new modes of motion can now be realized through de novo design and provides a framework for constructing biology-inspired, tunable and controllable protein signaling behavior de novo.

Eukaryotic Pif1 helicase unwinds G-quadruplex and dsDNA using a conserved wedge

G-quadruplexes (G4s) formed by guanine-rich nucleic acids induce genome instability through impeding DNA replication fork progression. G4s are stable DNA structures, the unfolding of which require the functions of DNA helicases. Pif1 helicase binds preferentially to G4 DNA and plays multiple roles in maintaining genome stability, but the mechanism by which Pif1 unfolds G4s is poorly understood. Here we report the co-crystal structure of Saccharomyces cerevisiae Pif1 (ScPif1) bound to a G4 DNA with a 5′ single-stranded DNA (ssDNA) segment. Unlike the Thermus oshimai Pif1-G4 structure, in which the 1B and 2B domains confer G4 recognition, ScPif1 recognizes G4 mainly through the wedge region in the 1A domain that contacts the 5′ most G-tetrad directly. A conserved Arg residue in the wedge is required for Okazaki fragment processing but not for mitochondrial function or for suppression of gross chromosomal rearrangements. Multiple substitutions at this position have similar effects on resolution of DNA duplexes and G4s, suggesting that ScPif1 may use the same wedge to unwind G4 and dsDNA. Our results reveal the mechanism governing dsDNA unwinding and G4 unfolding by ScPif1 helicase that can potentially be generalized to other eukaryotic Pif1 helicases and beyond.

An Artificial Light-Harvesting System based on Supramolecular AIEgen Assembly.

Photosynthesis is a complex multi-step process in which light collection is the initial step of photosynthesis and plays an important role in the efficiency of solar energy utilization. In order to improve the utilization of sunlight, researchers have developed a variety of artificial light-harvesting system to simulate photosynthesis in nature. Here, we report a supramolecular self-assembly artificial light-harvesting system in aqueous solution. We modified β-CD with the donor molecule naphthalimide and adamantane with the tetraphenylethylene molecule which has aggregation-induced emission effects (AIE). By using fluorescent molecules with AIE, the self-quenching effect caused by aggregation in aqueous solution can be effectively avoided. Due to the host-guest interaction of β-CD and adamantane, nanoparticles with stable structure and uniform size can be spontaneously assembled in water. Because of the close distance and strong spectral overlap between naphthalimide and tetraphenylethylene, Förster resonance energy transfer (FRET) was realized, and artificial light-harvesting system was successfully constructed in aqueous solution. The light-harvesting system has a high energy transfer efficiency (ΦET). Therefore, this study provides a new strategy for constructing artificial light-harvesting system.

Quantum mechanical, spectroscopic, docking studies (Dementia & breast cancer) and in-vitro assays of phytochemical compound Dehydrozingerone by DFT

Density functional theory (DFT) based quantum computing techniques were used to study the phytochemical compound Dehydrozingerone (DHZ), which originated from the ginger plant Zingiber officinale. Structural analyses, of the title compound such as FTIR, FTR, and Ultraviolet-Visible (UV-Vis) are performed both theoretically and experimentally. DHZ was optimized for the most stable molecular structure. Vibrational frequencies were scaled using a scaling factor, and prominent peaks were identified. Potential energy distribution (%PED) assignments were also examined to determine the percentage of vibrational transitions. Four different solvents were quantitatively analyzed using TD-DFT from UV-Vis spectra. HOMO-LUMO calculations were performed to forecast Dehydrozingerone's stability and non-toxicity. The Natural Bond Orbital (NBO) method was used to study inter- and intra-molecular interactions. DOS spectra were convoluted to analyse the overlapping interactions of the various bonds present in DHZ. Population analysis, such as Mulliken and Natural, was conducted to determine the charge distribution within the compound. Topological analyses such as ELF, LOL and reactive site of DHZ were identified using MEP. Non-linear optical (NLO) behaviour was further studied and compared to urea, a prototype substrate. Drug likeness and Ramachandran plot were determined. Using the Autodock tools for molecular docking studies, the pharmaceutical importance of DHZ was analysed for targeted proteins 4MS4 (anticonvulsant), 7AIX (dementia syndrome), 7E9B (anti-brain cancer) and 7C00 (anti-breast cancer). The biological activity of breast cancer was analysed both theoretically (protein) and experimentally (MCF7). The standard drug was theoretically studied for the four proteins, and binding energies are comparable, implying that DHZ could be a suitable drug for the control and treatment of anti-convulsant, dementia, brain tumours and breast cancer. To better understand the toxicity and bioavailability of the title compound, cytotoxicity assays were also performed.

Investigating the Stable Structures and Topological Insulator Characteristics of Honeycomb AuTe Monolayer Through Decorating with Alkali Metal Atoms, as well as the Effects of Strain and Layering: a First‐Principle Study

Investigating the Stable Structures and Topological Insulator Characteristics of Honeycomb AuTe Monolayer Through Decorating with Alkali Metal Atoms, as well as the Effects of Strain and Layering: a First‐Principle Study

High-Value and Environmentally Friendly Recycling Method for Coal-Based Solid Waste Based on Polyurethane Composite Materials.

This study aims to provide a high-value and environmentally friendly method for the application of coal-based solid waste. Modified fly ash/polyurethane (MFA/PU) and modified coal gangue powder/polyurethane (MCG/PU) composites were prepared by adding different contents of MFA and MCG (10%, 20%, 30%, 40%). At the filler content of 30%, the compressive strengths of MFA/PU and MCG/PU are 84.1 MPa and 46.3 MPa, respectively, likely due to an improvement in interface compatibility, as indicated by scanning electron microscopy (SEM). The MFA/PU and MCG/PU composites present their highest limiting oxygen index (LOI) values of 29% and 23.5%, respectively, when their filler content is 30%. MFA has advantages in improving the LOIs of composites. Cone calorimetry (CCT) and SEM demonstrate that the two composites exhibit similar condensed-phase flame-retardant behaviors during combustion, which releases CO2 in advance and accelerates the formation of a dense barrier layer. Compared with the MFA/PU composites, the MCG/PU composites could produce a more stable and dense barrier structure. Water quality tests show that heavy metals do not leak from FA and CG embedded in PU. This work provided a new strategy for the safe and high-value recycling of coal-based solid waste.

Superoxide Photoproduction from Wetland Plant-Derived Dissolved Organic Matter: Implications for Biogeochemical Impacts of Plant Invasion.

Although the impacts of exotic wetland plant invasions on native biodiversity, landscape features, and carbon-nitrogen cycles are well appreciated, biogeochemical consequences posed by ecological competition, such as the heterogeneity of dissolved organic matter (DOM) from plant detritus and its impact on the formation of reactive oxygen species, are poorly understood. Thus, this study delves into O2•- photogeneration potential of DOM derived from three different parts (stem, leaf, and panicle) of invasive Spartina alterniflora (SA) and native Phragmites australis (PA). It is found that DOM from the leaves of SA and the panicles of PA has a superior ability to produce O2•-. With more stable aromatic structures and a higher proportion of sulfur-containing organic compounds, SA-derived DOM generally yields more O2•- than that derived from PA. UVA exposure enhances the leaching of diverse DOM molecules from plant detritus. Based on the reported monitoring data and our findings, the invasion of SA is estimated to approximately double the concentration of O2•- in the surrounding water bodies. This study can help to predict the underlying biogeochemical impacts from the perspective of aquatic photochemistry in future scenarios of plant invasion, seawater intrusion, wetland degradation, and elevated solar UV radiation.

Theoretical Study of Structural and Electronic Trends of the Sulfonylurea Herbicides Family.

The sulfonylurea herbicide family has been extensively studied using computational techniques. The most stable conformer structures of the 34 molecules analyzed in gaseous, aqueous, and octanol phases have been determined. The study employed CREST conformational search methods along with the CENSO script to explore all possible conformational structures. Additional evaluations conducted at the B3LYP-D3/6-311+G(d,p) level have enabled the identification of intramolecular stability patterns across the various compounds. It has been discovered that stability is primarily determined by two factors: intramolecular hydrogen bonding involving an NH group adjacent to the sulfonyl group with either N donors or the nearby carbonyl group and potential π-π interactions between the aromatic rings of the molecules. These have been characterized through QTAIM and NCI population analyses. Furthermore, with the goal of developing predictive models for the physicochemical properties of pesticides that include the sulfonylurea family, a statistical analysis among the different properties of the studied molecules has been conducted. Significant correlations have been found between various properties, predicting a promising future for the prediction of characteristics that could assist laboratories in selecting among different pesticides.

Theoretical study on the synergistic mechanism of Fe–Mn in sodium-ion batteries

This article conducts first-principles calculations to initially explore the construction of two configurations, NaFeO2 (NFO) and NaMnO2 (NMO), and studies the mixing enthalpies under different Fe–Mn ratios. The results indicate that NaFe3/8Mn5/8O2 (NFMO) exhibits the most thermodynamically stable structure. Subsequent calculations on the mixing enthalpies and volume changes during the sodium extraction process for NFO, NMO, and NFMO configurations are presented, along with the partial density of states (PDOS) and Bader charges of transition metals (TM) and oxygen. These calculations reveal the synergistic mechanism of Fe and Mn. Fe and Mn can engage in more complex electron exchanges during sodium extraction, optimizing the internal electron density distribution and overall charge balance, thereby stabilizing the crystal structure and reducing the migration of Fe3+ to the sodium layers during deep sodium extraction. The interaction between Fe’s 3d electrons and Mn’s 3d electrons through the shared oxygen atoms’ 2p orbitals occurs in the Fe–Mn–O network. This interaction can lead to a rebalancing of the electron density around Mn³⁺ atoms, mitigating the asymmetric electron density distribution caused by the d4 configuration of the lone Mn³⁺ and suppressing the Jahn-Teller effect of Mn3+. Moreover, the synergistic effects between Fe and Mn can provide a more balanced charge distribution, reducing extreme changes to the charge state of oxygen atoms and decreasing the irreversible oxygen release caused by anionic redox reactions during deep sodium extraction, thereby enhancing the material’s stability. This in-depth study of the interaction mechanism at the microscopic level when co-doping Fe and Mn offers valuable insights for the rational design and development of high-performance cathode materials.

Stability of Cs2NaBiBr6 and Cs2NaBiCl6.

Bismuth-based halide perovskites are nontoxic alternatives to widely studied lead-based perovskites for optoelectronic applications. Here, we synthesized Cs2NaBiCl6 thin films and attempted to synthesize Cs2NaBiBr6 using physical vapor deposition. While Cs2NaBiCl6 forms a stable cubic structure with a 3.4 eV band gap and could be synthesized successfully, Cs2NaBiBr6 does not form and is unstable with respect to dissociation into Cs3-xNaxBi2Br9 and Cs3-xNaxBiBr6. Furthermore, the close X-ray diffraction patterns of Cs3-xNaxBi2Br9 and Cs2NaBiBr6 raise doubts about the previous reports of the latter's formation based on X-ray diffraction alone.

Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a.

CRISPR-Cas12a binds and processes a single pre-crRNA during maturation, providing a simple tool for genome editing applications. Here, we constructed a kinetic and thermodynamic framework for pre-crRNA processing by Cas12a in vitro, and we measured the contributions of distinct regions of the pre-crRNA to this reaction. We find that the pre-crRNA binds rapidly and extraordinarily tightly to Cas12a (Kd = 0.6 pM), such that pre-crRNA binding is fully rate limiting for processing and therefore determines the specificity of Cas12a for different pre-crRNAs. The guide sequence contributes 10-fold to the binding affinity of the pre-crRNA, while deletion of an upstream sequence has no significant effect. After processing, the mature crRNA remains very tightly bound to Cas12a with a comparable affinity. Strikingly, the affinity contribution of the guide region increases to 600-fold after processing, suggesting that additional contacts are formed and may pre-order the crRNA for efficient DNA target recognition. Using a direct competition assay, we find that pre-crRNA binding specificity is robust to changes in the guide sequence, addition of a 3' extension, and secondary structure within the guide region. However, stable secondary structure in the guide region can strongly inhibit DNA targeting, indicating that care should be taken in crRNA design. Together our results provide a quantitative framework for pre-crRNA binding and processing by Cas12a and suggest strategies for optimizing crRNA design in genome editing applications.

A Novel Shape Memory Alloy Modular Robot with Spatially Stable Structure

Soft robots exhibit significant flexibility but normally lack stability owing to their inherent low stiffness. Current solutions for achieving variable stiffness or implementing lock mechanisms tend to involve complex structures. Additionally, passive solutions like bistable and multistate mechanisms lack spatial stable characteristics. This study presents a novel shape memory alloy (SMA) modular robot with spatially stable structure, by utilizing gooseneck as the backbone. This is the first time that a concept of spatially stable structure is proposed. When the power is off, the robot can still maintain its current posture in three‐dimensional space and resist external disturbance. The SMA spring and gooseneck are characterized, elucidating the mechanism behind achieving spatial stability. Then, a controller based on the inverse kinematics is designed, and validated by experiments. The results demonstrate the structural stability of the robot. Specifically, it can withstand a maximum external force of 2.5 N (0.0875 Nm) when bent at an angle of 20° without consuming energy. Moreover, with the assistance of the SMA spring, this resistance capacity surpasses 5 N (0.175 Nm).