Search Results (339)

Accessory proteins of SARS-CoV-2 play crucial roles in viral pathogenesis, yet their structural properties remain elusive. ORF7b, a small accessory protein comprising only 43 amino acids, is widely assumed to parallel the structure–function relationships of its SARS-CoV ortholog based solely on sequence homology. In this study, we challenge this paradigm through direct physicochemical and structural characterization. Sequence analysis and electrostatic profiling reveal that the SARS-CoV-2 protein is a macromolecular polyanion with a net charge of −4 at neutral pH, featuring a diffuse negative surface that is highly responsive to pH changes. Complete 3D structures generated via ab initio modeling display a helical core flanked by two highly fluctuating, disordered termini. Residue Interaction Network (RIN) topology and Normal Mode Analysis (NMA) identified specific hinges governing these flexible extremities. Furthermore, the calculated dipole moment vector is tilted outward by 24°, misaligning with the central axis. Molecular dynamics simulations suggest that while the soluble structure is highly stable in water, it undergoes severe distortions and insufficient solvation within a membrane-mimetic environment. Thermodynamic association profiles and verified interactomic data from BioGRID reveal a strong propensity for ORF7b to participate in liquid–liquid phase transitions alongside human and viral partners. Taken together, these unique properties suggest that ORF7b operates as a dynamic peripheral membrane protein rather than a sedentary transmembrane component, providing a fresh framework for future therapeutic targeting. Overall, these in silico findings shift the current paradigm on ORF7b2 topology and provide a robust, physically grounded framework that identifies specific molecular priorities for future in vitro and in vivo validation. Full article

High-entropy transition-metal diborides represent a promising class of ultra-high temperature ceramics. However, atomic insights into their high-temperature elastic response, anisotropic deformation, and fracture mechanisms remain elusive. Herein, we perform molecular dynamic simulations to study the thermomechanical behaviors of (Hf_0.2Zr_0.2Ta_0.2Ti_0.2Nb_0.2)B₂ from 900 to 3300 K by developing an ab initio accuracy deep-learning potential. The proposed potential accurately reproduces lattice parameters, equations of state, and elastic constants, in excellent agreement with density functional theory calculations and available experiments, and remains transferable under thermally expanded and compressed states. The simulations reveal anisotropic thermal expansion, with the out-of-plane expansion exceeding the in-plane expansion, together with progressive elastic softening while preserving C₁₁ > C₃₃ due to the dominant in-plane B-B bonding network. Furthermore, strain-rate- and temperature-dependent tensile and compressive responses show marked crystallographic anisotropy, tension–compression asymmetry, and severe thermomechanical degradation. Atomic structural evolution demonstrates that tensile fracture is dominated by bond stretching and progressive damage accumulation, whereas compressive failure is attributed to densification- and shear-mediated structural instability. These findings provide an atomistic understanding of the thermomechanical behavior and fracture mechanisms of the prototypical single-phase (Hf_0.2Zr_0.2Ta_0.2Ti_0.2Nb_0.2)B₂ high-entropy diboride, offering valuable insights into the design of ultra-high temperature ceramics under extreme service environments. Full article

Fluorinated carboxylate ester solvents are promising electrolyte components for lithium metal batteries because they can improve oxidative stability and promote LiF-rich solid electrolyte interphase (SEI) formation. However, how fluorination position and degree regulate their intrinsic decomposition behavior on lithium metal remains unclear. Herein, density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations were employed to systematically investigate six pure fluorinated ethyl acetate solvents on the Li(001) surface, including α-fluorinated ethyl fluoroacetate (EFA), ethyl difluoroacetate (EDFA), and ethyl trifluoroacetate (ETFA), as well as β-fluorinated 2-fluoroethyl acetate (FEA), 2,2-difluoroethyl acetate (DFEA), and 2,2,2-trifluoroethyl acetate (TFEA). Electronic-structure analysis shows that although the lowest unoccupied molecular orbitals (LUMOs) of all six solvents are mainly distributed around the carbonyl and adjacent regions, the dominant electron-accepting center strongly depends on the fluorination position. In α-fluorinated solvents, the LUMO is highly localized on the α-C atom directly bonded to fluorine, whereas in β-fluorinated solvents, it remains concentrated around the carbonyl C atom. Real-time Bader charge and bond-evolution analyses reveal that fluorination position is the primary factor governing the initial decomposition pathway. The α-fluorinated series preferentially undergoes C-F bond cleavage, and increasing fluorination degree induces deeper cascade decomposition; fully fluorinated ETFA even exhibits C=O double bond cleavage. In contrast, β-fluorinated solvents preferentially undergo carbonyl-side C-O bond cleavage, while C-F bond cleavage occurs only in subsequent steps or is completely suppressed. Notably, β-fluorinated solvents retain high chemical stability even with α-H atoms because the LUMO electron density on α-H is negligible. Meanwhile, limited deep decomposition can still provide F⁻ species for SEI formation. These findings establish an atomic-level structure–reactivity relationship for fluorinated carboxylate ester solvents and provide theoretical guidance for designing stable electrolyte solvents for lithium metal batteries. Full article

In this work, the structural, electronic, charge-transfer, thermal, and magnetic properties of pristine and Fe-doped silicon carbide nanosheets (SiCNShs) were systematically investigated using spin-polarized density functional theory (DFT) within the Local Spin Density Approximation including Hubbard correction (LSDA + U). A 4 × 4 SiCNSh supercell containing 80 atoms was considered, where Fe atoms were substitutionally introduced at carbon sites to evaluate dopant-induced modifications in the nanosheet. Structural optimization, energy convergence, force minimization, and stress evolution analyses confirm that Fe incorporation preserves the structural integrity of the SiCNSh and leads to energetically stable configurations. The calculated defect formation energy (−7.44 eV/atom) demonstrates the thermodynamic feasibility of Fe substitution, while ab initio molecular dynamics (AIMD) simulations at 300 K verify the thermal stability of the energetically favorable Fe-doped configuration. Electronic-structure calculations reveal that pristine SiCNSh exhibits a nonmagnetic semiconducting nature with a band gap of approximately 2.4 eV, whereas Fe incorporation significantly modifies the electronic structure through pronounced Fe–3d/C–2p/Si–3p orbital hybridization. The band gap is reduced to approximately 1.1 eV for the single-Fe-doped system and further decreases to 0.53/0.51 eV (spin-up/spin-down) in the double-Fe configuration, while preserving semiconducting behavior. Spin-polarized band structure and density of states analyses demonstrate clear spin asymmetry near the Fermi level, indicating strong dopant-induced spin polarization and exchange interactions. Charge-density difference and Bader charge analyses reveal substantial dopant-induced charge redistribution characterized by electron depletion around Fe atoms, enhanced electron accumulation on neighboring carbon atoms, and partial charge neutralization of nearby Si atoms, resulting in a more localized covalent Si–C–Fe bonding environment. Mulliken spin population analysis further demonstrates robust ferromagnetic ordering, where the Fe dopant acts as the dominant magnetic center with strong induced spin polarization extending into neighboring Si and C atoms. Comparison between ferromagnetic (FM) and antiferromagnetic (AFM) configurations confirms that the 2Fe@C-doped SiCNSh stabilizes in a ferromagnetic ground state, exhibiting a favorable FM–AFM energy difference of 0.216 eV. Based on the mean-field approximation, the Curie temperature was estimated to be approximately 837 K, indicating strong magnetic stability significantly above room temperature. The present findings collectively demonstrate that Fe incorporation effectively tailors the electronic and magnetic properties of SiCNSh through band-gap engineering, spin-symmetry breaking, and stabilization of high-temperature ferromagnetism. These combined characteristics establish Fe-doped SiCNShs as promising candidates for spintronic devices, magnetic semiconductors, spin injectors, spin filters, and non-volatile magnetic memory applications. Full article

Hydrogen is a clean and renewable energy carrier, but its reversible storage near ambient conditions remains a major challenge. Here, density functional theory (DFT) combined with ab initio molecular dynamics (AIMD) is employed to assess the newly predicted 2D orthorhombic diboron dinitride (o-B₂N₂) monolayer, in pristine and Li-functionalized forms, as a hydrogen storage medium. On the pristine surface, H₂ physisorbs with binding energies of −0.158 to −0.174 eV. Li atoms anchor strongly at the hexagonal hollow sites ($E_{\mathrm{bind}}$ from −0.979 to −1.321 eV, strongest at the B-rich H1 site), donate 0.65–0.84 $\left|e\right|$ to the substrate, and render the semiconducting monolayer metallic. A positive cluster formation energy ($+0.171$ eV per Li pair) and a 5 ps AIMD simulation at 400 K confirm that the Li adatoms remain dispersed, without clustering. Each ${\mathrm{Li}}^{+}$ center polarizes and binds up to five H₂ molecules, with average adsorption energies of −0.207 to −0.336 eV/H₂, within the optimal window for room-temperature reversible storage. The 4Li@o-B₂N₂(20H₂) system attains a theoretical gravimetric capacity of 15.12 wt% and a practical capacity of 10.99 wt% under realistic operating conditions (charging at 30 atm/25 °C; release at 3 atm/100 °C). These results establish Li-functionalized o-B₂N₂ as a promising hydrogen storage material that merits experimental exploration. Full article

The chemical evolution of simple molecules into higher-order structures, such as amino acids, is a fundamental process occurring throughout the cosmos. Methane (CH₄) serves as a key precursor in this evolutionary sequence and is prevalent on planetary bodies like Mars and Saturn. In these environments, CH₄ is frequently ionized by cosmic radiation, forming the methane radical cation (CH₄⁺). In this study, the ion-molecule reactions between CH₄⁺ and neutral CH₄ (CH₄⁺ + CH₄ → products) were investigated using direct ab initio molecular dynamics (AIMD) simulations to elucidate the underlying reaction mechanisms. Our calculations demonstrate that proton transfer (PT) occurs efficiently, yielding the methanium ion (CH₅⁺) and the highly reactive methyl radical (CH₃): CH₄⁺ + CH₄ → CH₅⁺ + CH₃. Furthermore, the reaction outcomes exhibit a strong dependence on the impact parameter (b). Collisions at very low impact parameters (b = 0–0.2 Å) resulted in non-reactive, billiard-ball-like scattering. Within the range of b = 0.2–3.0 Å, the formation of a long-lived complex, [CH₅-CH₃]⁺, was observed. In the intermediate range of b = 3.0–5.0 Å, a proton-stripping mechanism predominated in PT channel, while collisions at b > 5.0 Å were exclusively non-reactive. The reaction mechanism was qualitatively discussed. These findings provide a detailed atomistic picture of the collision dynamics governing methane-derived molecular evolution in celestial environments. Full article

The key to metallic fuel development is the fabrication of uranium metal and alloys into fuel forms. U-Nb alloys are one of the best candidates for a metallic fuel alloy with high-temperature strength sufficient to support the core, acceptable nuclear properties, good fabricability, and compatibility with usable coolant media. Melt processing has been a key component of the metallic fuel cycle, and process models require thermophysical parameters at elevated temperatures, particularly above the melting temperatures, regarding which experimental data are scarce, for accurate simulations and process development. By means of ab initio density-functional theory (DFT) quantum molecular dynamics (QMD), we have calculated the main thermophysical parameters—the density, thermal expansion coefficient, specific heat, thermal conductivity, melting temperature, latent heat of fusion, and viscosity—used in the modeling of the U-6 wt.% Nb alloy casting. The melting temperature of the U-6 wt.% Nb alloy at ambient pressure is obtained by means of QMD simulations using the Z-method. The ambient volume change and latent heat of melting of U-6 wt.% Nb are also derived from QMD simulations in conjunction with analytical fitting for the energy and pressure. The thermal conductivity for the solid U-Nb alloy is calculated from the semi-classical Boltzmann transport equation combined with an estimate of the electron relaxation time obtained from DFT simulations. Full article

The phase transformation characteristics of Sn-Pb-Bi ternary alloys with four representative Bi/Pb mass fraction ratios (0, 0.14, 0.33, and 0.60) were systematically investigated using the deep potential molecular dynamics (DeePMD) method over a temperature range of 300–600 K. A high-precision machine-learned interatomic potential was achieved using large-scale ab initio molecular dynamics (AIMD) datasets, reaching chemical accuracy (energy error <5 meV/atom, force error <100 meV/Å). Complete solid–liquid–solid heating–cooling cycle simulations were performed to accurately determine the melting temperature $T_m$, solidification temperature $T_s$, and undercooling $\Delta T$. The microscopic mechanisms through which Bi regulates phase transitions were revealed through radial distribution function (RDF), mean square displacement (MSD), self-diffusion coefficient, and viscosity analyses. Our results show that increasing the Bi/Pb ratio monotonically lowers $T_m$ from 475 K to 450 K, while $\Delta T$ reaches a maximum of ~48 K at Bi/Pb = 0.14. Bi addition disrupts short-range order, enhances chemical homogeneity, suppresses atomic diffusion, and optimizes liquid viscosity, with the optimal composition found to be Bi/Pb ≈ 0.14, balancing a low melting point, controlled undercooling, and improved flowability. This study provides an atomic-scale theoretical foundation for the precise composition design of low-melting-point Sn-Pb-Bi solders for photovoltaic and electronic packaging applications. Full article

Iron oxides, including hematite ($\alpha$-${\mathrm{Fe}}_2$${\mathrm{O}}_3$), magnetite (${\mathrm{Fe}}_3$${\mathrm{O}}_4$), and maghemite ($\gamma$-${\mathrm{Fe}}_2$${\mathrm{O}}_3$), play central roles in catalysis, corrosion, environmental remediation, magnetic nanotechnology, and energy storage. Molecular dynamics simulations have become an essential tool for understanding their structural, magnetic, and interfacial behavior at the atomic scale. This review provides a comprehensive overview of MD methodologies applied to these materials, spanning classical force fields, reactive force fields, ab initio molecular dynamics, and emerging machine learning interatomic potentials. Particular emphasis is placed on facet-dependent surface chemistry, especially the contrast between compact (111) and open (110) planes, and on adsorption processes involving water, nitrogen-containing molecules, and representative organic compounds. The review highlights recent advances in force field development, redox modeling, and multiscale simulation strategies while critically identifying limitations related to charge transfer, mixed valence, vacancy ordering, and magnetic–chemical coupling. Finally, future perspectives are outlined toward quantitatively predictive, facet-resolved, and magnetically aware simulations of iron oxide interfaces. These developments are expected to tightly link atomistic insights with experimental observations and guide the rational design of iron oxide-based functional materials. Full article

The structural, mechanical, electronic, and optical properties of cubic double perovskite oxides A₂TiSiO₆ (A = Ca, Sr, Ba) were systematically investigated using first-principles density functional theory calculations. Structural optimization within the GGA–PBE framework confirms that all compounds crystallize in a stable cubic phase. The negative formation energies indicate thermodynamic stability and potential experimental synthesizability. Ab initio molecular dynamics (AIMD) simulations performed at 300 K further confirm the dynamical stability of all compounds under finite-temperature conditions. The Born–Huang stability criteria performed elastic constant analysis establishes mechanical stability and the derived mechanical moduli indicate the presence of rigid but brittle behavior with moderate amounts of elastic anisotropy. Calculation of the electronic band structure reveals that all the compounds are direct wide-bandgap semiconductors, with the HSE06 bandgaps of Ca₂TiSiO₆, Sr₂TiSiO₆ as well as Ba₂TiSiO₆ being 2.61, 2.50 and 2.37 eV, respectively. The optical property analysis has shown that they are strong in terms of their absorption in the visible–ultraviolet region, with high dielectric constants and good refractive indices, which makes them appropriate in optoelectronics and photovoltaic applications. On the whole, A₂TiSiO₆ double perovskites are promising for use as wide-bandgap materials in the development of superior optoelectronic devices. Full article

Molten salt chlorination is a key industrial route for producing titanium tetrachloride (TiCl₄), yet the atomistic catalytic role of iron (Fe) in the carbothermic chlorination of titanium oxides remains unclear. Here, the chlorination behavior of the NaCl–C–Cl₂–FeTiO₃ system was investigated by combining thermodynamic calculations with Ab Initio Molecular Dynamics (AIMD) and Deep Potential Molecular Dynamics (DPMD) simulations. AIMD results show that carbon adjacent to Fe exhibits enhanced reactivity, and that Fe-C synergistic electron transfer promotes both titanium oxide reduction and subsequent titanium chlorination. DPMD results further reveal that Fe not only accelerates these transformations, but also improves interfacial contact among carbon, titanium oxides, and molten salt, thereby enhancing mass transfer and shortening the formation time of TiCl₄. Temperature-dependent analysis indicates that Fe-C and C-O coordination numbers remain high near 1073 K, where TiCl₄ formation is efficient and relatively stable. Although increasing temperature can further enhance diffusion, its effect on reaction acceleration is limited, while excessively high temperatures weaken Fe-C interactions and reduce catalytic efficiency. These findings clarify the catalytic mechanism of Fe in molten salt chlorination at the atomic scale and provide theoretical support for process optimization. Full article

Molecular dynamics simulations were performed on 27 deep eutectic solvents (DESs) composed of various hydrogen bond acceptors (HBAs)—tetrabutylammonium bromide (TBAB), tetrabutylammonium chloride (TBAC), and tetraethylammonium chloride (TEAC)—combined with different hydrogen bond donors (HBDs)—3-aminopropan-1-ol (AP), 2-(methyl-amino)ethanol (MAE), and 2-(n-butylamino)ethanol (BAE). Radial distribution functions (RDFs) were computed from the simulation trajectories to probe the microscopic structure of these DESs. The effects of HBA/HBD molar ratio, alkyl chain length, anion type, and the amine group’s substitution on the structural organization of the DESs were systematically investigated. Moreover, the influence of water addition on the structural properties of selected DESs (TBAB with AP, MAE, or BAE at a 1:6 molar ratio) was explored. These structural features were then correlated with previously reported experimental data. To complement the classical simulations, ab initio molecular dynamics simulations were conducted on the same TBAB-based systems, enabling the analysis of electronic structure phenomena, including RDFs, dipole moment distributions, and charge transfer. Furthermore, experimental large-angle X-ray scattering (LAXS) data collection and analysis were performed in terms of the simulated structural data. This multi-scale approach provides a detailed understanding of the structural and electronic characteristics governing the behavior of alkanolamine-based DES. Full article

Two-dimensional antimonene has recently emerged as a promising electrocatalytic platform; however, its oxygen reduction reaction (ORR) activity and modulation strategies remain largely unexplored. Herein, density functional theory (DFT) calculations are employed to systematically investigate ORR catalysis on antimonene co-doped with transition metal (TM) and nonmetal (C, P) dual atoms. The results reveal that Pd@C–Sb, Pt@C–Sb, and Pd@P–Sb exhibit remarkably enhanced ORR activity, delivering low overpotentials of 0.31 V, 0.32 V, and 0.38 V, respectively, significantly outperforming their single-atom-doped counterparts. Mechanistic analyses demonstrate that nonmetal dopants induce strong synergistic interactions with TM centers, leading to charge redistribution and effective regulation of the TM d-band center, which optimizes the adsorption energetics of key ORR intermediates. Notably, the number of d-electrons of TM atoms is identified as a reliable electronic descriptor governing intermediate binding strength and catalytic activity. Furthermore, ab initio molecular dynamics simulations confirm the excellent thermodynamic stability of the optimized dual-atom catalysts. This work elucidates the atomic-scale origin of synergistic enhancement in dual-atom-doped antimonene and provides a rational design strategy for high-performance ORR electrocatalysts based on two-dimensional main-group materials. Full article

Isosymmetric phase transitions driven by subtle hydrogen-bond rearrangements remain challenging for periodic density functional theory (DFT), particularly when energy differences between polymorphs are small. Resorcinol represents an interesting case in which the α and β polymorphs crystallize in the same space group and differ primarily in hydroxyl orientation and hydrogen-bond topology. In this work, the α–β phase transition was systematically investigated using periodic DFT calculations under ambient and elevated pressure. A broad set of exchange–correlation functionals combined with different dispersion corrections was benchmarked against experimental structural and energetic data. Dispersion-corrected methods were essential for reproducing lattice parameters and the pressure-induced inversion of stability. PBESOL with Tkatchenko–Scheffler dispersion provided the most consistent agreement with the experiment and was therefore used for phonon and ab initio molecular dynamics simulations. Phonon-derived thermodynamic analysis revealed a delicate enthalpy–entropy balance governing the transition, strongly affected by pressure. Dynamical simulations confirmed the instability of the α phase under compression, demonstrating the cooperative nature of this hydrogen-bond-driven isosymmetric transformation. Full article

Potassium superoxide (KO₂) can form during the oxidation of residual potassium in NaK-contaminated cold traps of sodium-cooled fast reactors. Its strong oxidizing nature, combined with limited thermal stability, raises safety concerns during shutdown and maintenance. Here, we integrate first-principles calculations with experiments to clarify the facet stability, temperature-driven surface evolution, and stepwise thermal decomposition of KO₂. Guided by the tetragonal I4/mmm crystal symmetry of bulk KO₂, symmetry-non-equivalent low-index facets and relevant surface terminations were systematically evaluated to identify physically meaningful exposed surfaces. Ab initio molecular dynamics (AIMD) simulations further show that heating induces progressive surface amorphization and enhanced oxygen mobility, accompanied by the emergence of shortened O-O bonds and outward migration of oxygen species. Kinetic analysis using the climbing-image nudged elastic band (CI-NEB) method indicates that oxygen evolution is preferentially mediated by O₂ release rather than atomic oxygen escape. Differential scanning calorimetry (DSC) reveals two endothermic events consistent with sequential decomposition, while X-ray diffraction (XRD) confirms the transformation of KO₂ into K₂O. Collectively, these results provide an atomistic-to-macroscopic understanding of KO₂ decomposition, offering practical guidance for defining safer preheating windows and handling strategies for NaK-contaminated components. Full article