The Zika virus NS2B/NS3 protease is an important antiviral target, and macrocyclic peptide inhibitors represent promising scaffolds because they combine multibasic recognition motifs with conformational restriction. Here, we investigated two structurally related cyclic peptide inhibitors, referred to as CP1 and CP2, which share a conserved macrocyclic framework but differ in the chemical nature of their linker substituents. Molecular dynamics simulations showed that both peptides display broad intramolecular distance distributions in aqueous solution, indicating that key crystallographic contacts are not intrinsically maintained in the unbound state. Upon binding to the protease, CP2 adopted a more defined conformational ensemble and preserved a short intramolecular contact compatible with its crystallographic arrangement, whereas CP1 lost its crystallographic d2 contact and sampled a broader bound-state distribution. CP2 also showed a more focused interaction network involving residues from the catalytic and substrate-recognition regions and more favorable binding free-energy estimates.

Sodium-ion batteries (SIBs) are rich in resources and low in cost, exhibiting great potential for emergency energy storage in high-density public facilities such as subway stations. This study, based on density functional theory (DFT), systematically explores the theoretical performance of g-C3N6 and its sulfur-doped derivative (S-g-C3N6) as anode materials for SIBs. Electronic structure analysis revealed that pristine g-C3N6 is a direct-bandgap semiconductor with a bandgap of 2.601 eV, whereas S doping significantly reduced the bandgap to 0.326 eV. The most stable adsorption site for Na atoms on the g-C3N6 surface was found to be above the C atom, with an adsorption energy of -1.732 eV. Diffusion barrier calculations revealed that the minimum migration barriers for Na ions on the g-C3N6 and S-g-C3N6 surfaces are as low as 0.072 and 0.068 eV, respectively. The corresponding theoretical specific capacities reach 1339.2 and 1164.2 mAh/g, respectively. The average OCV was approximately 0.700 V, which is favorable for achieving a high energy density. In summary, g-C3N6-based materials, particularly after S doping modification, combine high specific capacity, excellent conductivity, and ultrafast ion diffusion kinetics, making them highly promising anode candidates intended for emergency energy storage in subway stations.

Bowman-Birk inhibitors (BBIs) are cysteine-rich proteins that inhibit trypsin and chymotrypsin proteases. Derived from soybeans, these natural BBIs have been identified as potential anticarcinogenic agents. Recent studies of the black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) demonstrated that peptides derived from the BBI family may retain their structure and inhibitory activity. Therefore, this study aimed to investigate the effects of solvent on BTCI-derived peptides and their inhibitory activity against trypsin. The results show that cyclic peptides exhibit reduced conformational flexibility, enhanced reactivity (narrower HOMO-LUMO gap), and LUMO localized at the disulfide bonds, in contrast to the linear peptide Ptry6. Non-covalent interactions were evaluated using the Independent Gradient Model based on Hirshfeld partitioning (IGMH). Molecular electrostatic potential maps and the IGMH confirmed that the cyclic architecture concentrates electropositive donor regions at key residues (Thr2, Lys3, Ser4, and Ile5), whereas Ptry6 displays only weak van der Waals contacts. Docking studies against trypsin showed strong hydrogen-bond and electrostatic interactions between cyclic peptides and residues involved in the catalytic mechanism. Predicted inhibition constants obtained from docking studies closely match experimental data. These findings suggest that electronic redistribution upon solvation governs peptide-trypsin affinity, highlighting Ptry9L as the most promising BTCI-derived inhibitor for further biotechnological development.

Hybrid organic-inorganic chalcogenides have emerged as promising multifunctional materials due to their structural flexibility and tunable physical properties, making them attractive candidates for energy-conversion, optoelectronic, environmental, and radiation-protection technologies. In this study, the structural, electronic, mechanical, optical, thermodynamic, radiation-shielding, and hydrogen-storage properties of CH3NH3MnS3 were comprehensively investigated. The optimized structure exhibits excellent stability, while mechanical analysis confirms elastic stability and anisotropic behavior. Optical calculations reveal strong absorption across the visible and ultraviolet regions, accompanied by a high dielectric response, moderate refractive index, and low reflectivity, indicating suitability for photovoltaic and photodetection applications. Dynamical and thermal stability are verified through phonon-dispersion and thermodynamic analyses. Radiation-shielding calculations demonstrate efficient attenuation of low-energy photons with small half-value and tenth-value layers. Furthermore, hydrogen-storage investigations predict favorable adsorption energetics, a gravimetric storage capacity of approximately 13.2 wt.%, and a low diffusion barrier of about 0.32 eV, facilitating rapid hydrogen transport. These findings identify CH3NH3MnS3 as a versatile multifunctional material with significant potential for next-generation energy, optoelectronic, hydrogen-storage, and radiation-shielding applications.

We theoretically study the excitonic properties in semiconductor transition metal dichalcogenide monolayers (ML-TMDs)(WSe 2 , WS 2 , MoSe 2 , MoS 2 , and MoTe 2) encapsulated in hexagonal boron nitride (hBN). Excitonic binding energies and full non-hydrogenic Rydberg series (s, p, and d states) are calculated. As a first validation, the binding energies of the 1s-5s states of WSe 2 /hBN are reproduced to less than 2 meV (< 1 %) over the entire range of thicknesses N ∈ [ 0 , ∞ [ , and the separation Δ 12 = 127.8 meV reproduces the experimental value without adjusted parameters. We further derive a generalized two-sided dielectric potential V (r , N top , N bot) that captures the asymmetric encapsulation geometry, and compute the two-dimensional map E b (N top , N bot) for WSe 2 . A new analysis of Coulomb engineering shows that E b (1s) varies by up to a factor of three across experimentally accessible dielectric environments, while the ratio E b (2 s) / E b (1 s) serves as a sensitive probe of the non-hydrogenic character. Moreover, Berry-curvature corrections lift the angular-momentum degeneracy of p-and d-type excitons by 2-8 meV, with M-based compounds showing larger effects. Finally, the quadratic Stark polarizability under an out-of-plane electric field is computed via exact s - p coupling, with results depending sensitively on N and the material parameters. These results provide a unified quantitative framework directly applicable to studies on van der Waals heterostructures.

The [H3O(H2O)3][+]Cl[-] ion-pair is the smallest cluster of ionized HCl in water. It has been demonstrated experimentally that it can be formed in conditions compatible with the interstellar medium (ISM). It is also a precursor of another ion-pair, H3O[+](MetOH)3Cl[-], suggested as an important prebiotic species in the ISM. Aiming to help the detection of the former ion-pair several properties of its n-3 s and n-3p singlet and triplet Rydberg states have been studied through a highly correlated ab-initio method. The vertical excitation energies (ΔEv), oscillator strengths (f), dipole moments (μ), diradical character, participation ratio of natural transition orbitals (PRNTO), single-excitation character (Ω), charge-transfer numbers and the singlet-triplet gaps (ΔEST) have been studied at the ground state (gs) geometry. The energies of the two lowest-lying dissociation channels have also been computed. Our highest-level results for ΔEv of the n-3 s singlet states are between 6.63 and 6.65 eV, while for n-3p one has 7.40 to 7.74 eV. Previous TD-DFT results are ~ 0.84 to 0.95 eV lower, but our results nicely agree with available CASPT2 results for the n-3 s states. The brighter state is the 2nd n-3 s state, with f = 0.172 at the highest-level. While the gs is essentially a closed-shell state, consistent with the [H3O(H2O)3][+]Cl[-] ion pair, all n-3 s and n-3p singlet states have high diradical characters, consistent with their small ΔEST values and with their nature as charge-recombination (CR) states. For most of the cases the CR characters are consistent with a decrease of μ. A possible deactivation pathway for the n-3 s states, involving their optimized geometries and a four-states conical intersection, is discussed. Our highest-level results yield the ionic channel 0.46 eV lower than the neutral channel. Ω indicates dominant single-excitation character for all Rydberg states, while PRNTO indicates multi-configurational character only for few n-3p states.

Organic light-emitting materials based on tris(8-hydroxyquinoline) aluminum (Alq₃) and gallium (Gaq₃) remain benchmark emitters in OLED research due to stable emission behaviors. The present work is concerned with the molecular and optical characteristics of these compounds by introducing CH/N substitutions at different positions. A series of derivatives was constructed to evaluate the impact of structural modifications on absorption, emission, and Stokes shift. The results reveal that substitution position apparently affects electronic transitions and spectral behavior. Modifications on the pyridyl side tend to induce red shifts, whereas those on the phenoxide side result in blue shifts. Molecular orbital analyses further indicate that parent complexes exhibit multi-orbital excitations, whereas the 5n₂p derivatives show localized HOMO to LUMO + 1 transitions, leading to higher excitation energies and narrower Stokes shifts.

The widespread application of crumb rubber modified asphalt is limited by its inadequate storage stability, which is largely governed by the compatibility between the asphalt binder and crumb rubber. This study investigated the influence of desulphurized crumb rubber with different solubility on the compatibility and storage stability of modified asphalt by combining molecular simulations with experimental validation. The results demonstrate that the compatibility between desulphurized crumb rubber and asphalt is strongly dependent on solubility when the difference in solubility parameter exceeds approximately 1.5 (J·cm[-][3])[1/2]. Desulphurized crumb rubber with a solubility of approximately 28.66 exhibited the highest interfacial binding energy, reduced phase separation, and improved storage stability, whereas excessive desulphurization decreased interfacial binding energy and increased the tendency for phase separation.

Monte Carlo (MC) simulations reveal that diblock copolymer nanoparticle morphology is dictated by the interplay between intermolecular attractions and soft confinement. Blocks with stronger cohesive interactions undergo local densification in the core, while blocks with weaker interactions localize at the surface. A key stabilizing mechanism is the expulsion of high-mobility end-monomers toward the interface to maximize cohesive energy in the bulk. This process is accompanied by a backbone gauche-to-trans conformational transition that enables polymer chains to flatten tangentially and adapt to nanoparticle curvature. By quantifying radial density profiles, structural anisotropy, and energetic oscillations, the methodology distinguishes morphologies ranging from surface-energy-driven mixing to frustrated core-shell segregation, providing molecular-level insight for the rational design of functional polymeric nanostructures.

Coumarin and its derivatives are privileged scaffolds in medicinal chemistry, yet their polymorphism poses significant challenges in pharmaceutical solid-form development. This work explores the crystal polymorphs and optoelectronic properties at ground state of coumarin. The crystal energy landscape of coumarin was constructed, identifying P43, Pccn, and P42bc as the dominant competing polymorphic structures. Electronic structure calculations reveal that the symmetry of crystal packing and intermolecular interactions significantly modulate the optical absorption edge and spectral response range, with the P43 phase exhibiting the smallest band gap (2.69 eV) due to its unique helical packing arrangement.

Chloride-containing species, H2O, and O2 are important environmental factors during the initial atmospheric corrosion of copper. In the present work, Cl[-] adsorption on Cu(111) was first investigated using a fully relaxed Cu model to characterize chloride-induced structural reconstruction and electronic activation. H2O and O2 were subsequently introduced to examine their additional co-adsorption effects on the chloride-affected Cu surface under simplified conditions representing humid and oxygen-containing environments. The introduction of Cl[-] induces pronounced local Cu-atom displacement, surface reconstruction, lattice distortion, and redistribution of the Cl-derived and Cu-derived electronic states. The subsequent addition of H2O and O2 further modifies the adsorption geometry and interfacial electronic environment. These results provide atomistic insight into chloride-induced surface activation relevant to the initial stage of copper corrosion, but they are not interpreted as direct proof of Cu dissolution or crystalline copper-chloride formation.

Cellulose nanocrystals (CNCs) are a type of cellulose with excellent mechanical performance and other advantageous attributes. According to previous reports, hydrogen bonds play a pivotal role in the anisotropic structure of the CNC. Understanding the structure and mechanical behavior of CNC on a mesoscopic scale is critical for the development and manufacture of cellulose materials. However, experimental observations and atomistic simulations are not appropriate on the mesoscopic scale. In this study, we introduce an analytical coarse-grained (CG) potential following an extended bottom-up approach that is directly parameterized using reinforcement learning (RL). RL is a powerful tool for industrial and academic applications in various fields. Nevertheless, the potential of RL has not yet been fully exploited in the field of molecular dynamics. The RL and Boltzmann inversion methods were employed to develop a novel CG model of cellulose to represent its anisotropy and polymer stiffness. The resulting approximate CG model is not limited to the specific properties used for training; it can reproduce the dynamic mechanical properties under various conditions without further optimization. This model confirms that RL can construct a CG potential that is both physically interpretable and powerful. The training code is available at https://github.com/EiPiFun/rl-cll-cg .

A theoretical investigation of 28 homoleptic Cu(I) complexes was conducted to assess their suitability as sensitizers in dye-sensitized solar cells (DSSCs). Two ligand families, triazolylpyridine (G1) and imidazopyridine-pyridine (G2), were systematically functionalized with heteroaromatic substituents derived from pyridine, furan, pyrrole, and thiophene. Pyridine- and thiophene-based spacers produced substantial bathochromic shifts in the absorption maxima, which reached 492 nm, and reduced the HOMO-LUMO energy gaps to values as low as 3.33 eV. These modifications also decreased the chemical hardness (η) and increased the electrophilicity (ω), thereby promoting intramolecular charge transfer and enhancing electron-accepting ability. In contrast, furan- and pyrrole-derived substituents induced only minor electronic changes but increased the propensity to form dual-bidentate or multidentate adsorption motifs on TiO2 surfaces, resulting in stronger interfacial binding. An integrated DSSC index (Di), combining structural, optoelectronic, reactivity, and photovoltaic parameters, identified the G2 family as the most favorable structural framework, with G2ANNC (Di = 0.6096) emerging as the leading sensitizer candidate. Overall, these results demonstrate the potential of these Cu(I) complexes for DSSC applications and provide a systematic framework for their rational design.

The tautomerization of thymine between its keto and enol forms is a key event for spontaneous mutagenesis. While the intrinsic enol-to-keto conversion is kinetically hindered in the gas phase, the presence of a discrete microhydration environment can drastically alter this landscape. Our M06-2X free energy calculations indicate that the cluster with two water molecules provides the lowest Gibbs free energy barrier among the investigated hydrated systems. However, benchmark electronic calculations show that the energetic differences between the mono-, bi-, and trihydrated clusters are small. HOMA index and QTAIM analyses confirm that the third water molecule induces an offset between aromaticity and intermolecular stabilization, providing a structural basis for the observed kinetic stabilization of the rare tautomer in a hydrated environment.

Using the density functional theory (DFT) method, we studied the adsorption behaviour of different toxic quinone molecules, including anthraquinone (AQ), naphthoquinone (NQ), and pyrenequinone (PQ), on β-antimonide phosphorus (β-SbP) nanosheet. Initially, we ascertained the geometrical stability of β-SbP with the support of formation energy, phonon band maps, and ab initio molecular dynamics (AIMD). The electronic attributes of β-SbP are investigated using band structure and projected density of states (PDOS) maps, and the energy gap is calculated to be 2.265 eV. The adsorption of quinone molecules induces a relative band gap variation of 33% to 60%. Among the studied quinone molecules, PQ exhibits the highest variation of 60.26% and 58.10% in parallel and perpendicular orientations, respectively. Furthermore, the sensing performance of quinone pollutants on β-SbP material is assessed using adsorption energy, Mulliken charge transfer, sensitivity, selectivity, and work function. The outcomes revealed that the nature of adsorption (chemisorption or physisorption) as well as the significant charge transfer observed in the ranges from 0.148 to 1.038 e, depending on the orientation of molecules adsorbed on β-SbP. A noticeable variation in the work function is observed for complex PQ1, which is recorded as 14.75%. Our findings reveal that β-SbP nanosheets are highly sensitive to these toxic quinones, indicating their suitability as an efficient sensing material.