Journal of Molecular Modeling最新文献

Context: Lithium carbonate (Li₂CO₃) is a pivotal raw material in the lithium industry, where its crystal morphology and size critically influence performance in energy storage and optoelectronic applications. However, at present, there is a lack of research on the change of properties during the nucleation process of Li₂CO₃, especially the evolution of interface properties in the early stage of growth, which is crucial to realize the precise control of the size and morphology of Li₂CO₃.This study investigates the nucleation behavior and layer-dependent evolution of electronic and optical properties of Li₂CO₃ thin films. We determine the critical nucleation radius for the (100) surface and demonstrate that as the film thickness increases from 1 to 6 layers, the material transitions from an indirect bandgap semiconductor to a direct bandgap semiconductor and finally exhibits metallic characteristics. The optical properties, including dielectric function and absorption, show a systematic layer dependence. These findings provide a fundamental theoretical basis for optimizing the crystallization process of Li₂CO₃.

Methods: All calculations were performed using first-principles density functional theory (DFT) as implemented in the CASTEP code. The Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) functional was employed for exchange-correlation interactions. Ultrasoft pseudopotentials were used to describe core-valence electron interactions. A plane-wave cutoff energy of 600 eV was applied. Structural models of the (100) and (001) surfaces with 1-6 layers were constructed, and a vacuum layer of 15 Å was added to eliminate spurious interactions. The Brillouin zone was sampled using a 3 × 3 × 1 k-point mesh. Geometries were optimized using the BFGS algorithm until the convergence criteria for energy, force, stress, and displacement were met. Based on classical nucleation theory, the free energy change during nucleus formation was analyzed. Electronic properties (band structure, density of states) and optical properties (dielectric function, absorption coefficient, reflection coefficient) were subsequently calculated for the optimized structures.

Context: Surface defects, such as steps and ledges, significantly modify the local energy landscape of crystalline substrates, thereby affecting adsorption, diffusion, and mixing during alloy thin-film growth. However, the atomistic mechanisms of alloy deposition on stepped metallic surfaces, particularly for NiTi systems, remain poorly understood. In this work, molecular dynamics simulations are employed to investigate the growth behavior of Ni₅₅Ti₄₅ thin films deposited on Ni substrates with different step geometries. The effects of incident angle, step width, surface configuration, substrate temperature, and incident energy on surface morphology, interfacial mixing, and structural evolution were systematically analyzed. The results indicate that stepped substrates significantly enhance interfacial atomic mixing compared to flat surfaces, while step width has a limited effect on surface roughness but strongly influences intermixing at the upper terrace. Increasing the incident angle intensifies shadowing effects, leading to higher surface roughness. Radial distribution function and common neighbor analyses confirm that all deposited films remain predominantly amorphous. Elevated substrate temperature promotes surface relaxation, whereas higher incident energy enhances interfacial mixing. These findings provide atomistic insight into NiTi thin-film growth on defected substrates.

Methods: Classical molecular dynamics simulations were carried out using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). Structural evolution and atomistic mechanisms were analyzed with the Open Visualization Tool (OVITO). The surface mesh construction, radial distribution functions (RDF), common neighbor analysis (CNA), and atomic coordination analysis are used to elucidate interfacial mixing and structural evolution during thin-film growth.

Context: Spirooxindoles represent a distinguished category in medicinal chemistry. Their three-dimensional structure enhances interactions with many biological targets. They exhibit anticancer, antibacterial, antiviral, anti-inflammatory, antioxidant, and antidiabetic properties. Various methods were applied to synthesize spirooxindoles and their derivatives. This review focuses on different synthetic approaches, pharmacological activities, and molecular insights of spirooxindoles that have been published in the first quarter of the twenty-first century. Furthermore, research gaps were highlighted, such as the lack of in vivo validation, toxicity profiling, and standardized yield/replicability data. Twelve synthesis procedures were statistically compared. A total of 40 studies were pharmacologically summarized, and their molecular insights were highlighted.

Methods: The method of literature search engines and citation databases such as Google Scholar, PubMed, Web of Science, and Scopus was utilized for the present review and searching for specific research questions. Then each of the transformed queries has been processed by running the applied inclusion & exclusion criteria in order to retrieve a focused set of candidate papers, and 219 papers were retrieved. Out of the total retrieved papers, 99 of them were mostly relevant.

Context: Antibiotics are among the most commonly prescribed medications and are among the most widely used drugs, essential for treating various bacterial infections. However, these molecules adopt different tautomeric conformations in the cellular environment. Therefore, understanding tautomerism in antibiotics is crucial for their recognition by receptors and the design of more effective antibiotics. In this study, a systematic conformational analysis of 23 Food and Drug Administration (FDA)-approved antibiotics across five major classes is performed to identify their most stable and active tautomeric conformations in biological media. In doing so, 105 tautomers of different antibiotics were generated. It is found that Doxycycline favours three degenerate tautomeric conformations and therefore, all these conformers can influence the receptor binding. However, other antibiotics exhibited a single distinct energetically favourable tautomeric conformation. The second most stable tautomer of all antibiotics, except Doxycycline, is ~8-27 kcal/mol less stable than its most stable counterpart. Hence, they may rarely populate in cells. However, the docking scores of the two most stable tautomers bound to their protein and DNA receptors are comparable. It is therefore proposed that the two most stable tautomers of each antibiotic should be considered to explore their substrate-inhibitory activities.

Methods: Initially, the ωB97X-D dispersion-corrected density functional theoretic method and 6-31 + G* basis set were used to optimize all tautomers of different antibiotics in the implicit aqueous medium. Subsequently, the ωB97X-D/AUG-cc-pVDZ level of theory was used to refine total electronic energies in the aqueous medium. The SCRF and IEFPCM methods were used to model the aqueous medium. The Gaussian 09 program was used for geometry optimizations and binding energy calculations. Autodock 1.5.7 was used for the molecular docking of the two most stable tautomers of different antibiotics into the substrate active site of their receptors.

Context: The CL-20/1,4-DNI cocrystal is a novel high explosive with exceptional energy density and detonation parameters. However, in comparison with insensitive explosives including TNT and TATB, it still retains a relatively high level of sensitivity. To mitigate the sensitivity of the CL-20/1,4-DNI cocrystal explosive, this study constructed a molecular model of the CL-20/1,4-DNI cocrystal, and then separately incorporated five distinct classes of polymers-butadiene rubber (BR), ethylene-vinyl acetate copolymer (EVA), polyethylene glycol (PEG), fluoropolymer (F2603), and polyvinylidene fluoride (PVDF)-onto its four most probable crystal planes, namely (1 0 1), (0 0 2), (0 1 1), and (1 1 0), a series of polymer-bonded explosives (PBXs) were thereby fabricated, and the influence of varying polymer matrices on the resulting materials-including their stability, trigger bond length, mechanical properties, and detonation performance-was systematically predicted and evaluated. Among the five developed PBX models, the CL-20/1,4-DNI/PEG composite attained the highest binding energy and the shortest trigger bond length. These outcomes demonstrate that the CL-20/1,4-DNI/PEG system possesses optimal stability, compatibility, and minimal sensitivity. Additionally, while the CL-20/1,4-DNI/F2603 composite exhibited superior detonation initiation capability, of note is that the compatibility of this particular formulation was relatively low. Consequently, the CL-20/1,4-DNI/PEG composite, which demonstrates an optimal stability-performance balance, emerges as the definitive choice, highlighting PEG as the preferred binder for CL-20/1,4-DNI-derived PBXs.

Methods: Utilizing the molecular dynamics (MD) framework implemented in Materials Studio, the relevant functions embedded in the Forcite module were employed for the calculations; the performance of CL-20/1,4-DNI-based PBXs was evaluated. The simulation parameters were configured to a time step of 1 fs and a cumulative run time of 2 ns. The isothermal-isobaric (NPT) ensemble was employed for the 2-ns MD simulations. The COMPASS force field was adopted, and the simulation temperature was fixed at 295 Kelvin (K).

Context: The opioid overdose crisis, driven by synthetic opioids like fentanyl, demands a paradigm shift beyond conventional pharmacology. Fentanyl's lethality stems from its sub-nanomolar affinity and ultra-slow dissociation kinetics from the μ-opioid receptor (μOR), which render competitive antagonists like naloxone increasingly ineffective. This critical limitation necessitates a physics-based strategy capable of directly disrupting the molecular bonds anchoring fentanyl within the receptor's binding pocket.

Method: We develop a quantum-mechanical framework to achieve precise, nonthermal disruption of the native fentanyl-μOR complex. Our approach exploits resonant terahertz (THz) near-fields to deliver a Stark perturbation phase-locked to the dominant reaction coordinates: the Asp147 salt-bridge stretch and the His297 hydrogen-bond stretch. The model combines anharmonic Morse potentials for bond stretching with a quantum hindered rotor for ligand torsion, yielding a time-dependent Schrödinger equation with analytic matrix elements. This formalism captures the critical interplay between linear (dipolar) and quadratic (polarizability) Stark effects, which transiently lower the dissociation barrier. We predict dissociation kinetics as a function of field amplitude, frequency, orientation, and pulse duty cycle, establishing a scalable and testable platform for an electromagnetic antidote.

Context: Tandem sequential cycloaddition reactions (TSCARs) offer powerful strategies for constructing complex molecular frameworks, yet predicting the preferred chronological order of competing cycloaddition steps remains challenging. In this work, the mechanisms of tandem [4 + 2]/[3 + 2] versus [3 + 2]/[4 + 2] cycloaddition sequences involving functionalized acetylenes, cyclopentadienyl derivatives, and phenyl azide were systematically investigated to elucidate their kinetic preferences, selectivities, and product distributions. The results reveal that the reactions are thermodynamically feasible but kinetically controlled, with the [4 + 2] step identified as the rate-determining step in both sequences. Overall, the [4 + 2]/[3 + 2] sequence is kinetically favored and predominantly furnishes exo-norbornene 1,2,3-triazoline cycloadducts, while the competing sequence exhibits distinct stereochemical outcomes. Solvent effect analysis with toluene shows no contrary outcome to the overall kinetically preferred sequence, established energetic trends and stereoselectivities of the products in the reference reaction except for an observed increase in the magnitudes of the energies. Substituent and heteroatom effects significantly influence activation barriers and selectivity, and the findings highlight notable deviations from the classical exo-rule.

Methods: All calculations were performed using density functional theory with the M06 functional and the 6-311G(d,p) basis set. Geometry optimizations, frequency calculations, and intrinsic reaction coordinate analyses were carried out in the gas phase to characterize stationary points and reaction pathways. Global and local reactivity descriptors were evaluated within the framework of conceptual DFT to rationalize observed kinetic trends and selectivities.

Context: A series of triazole-oxadiazole nitro derivatives have been optimised and evaluated computationally. The heat of formation has been computed and compared to conventional energy materials like RDX, TNT and MTNI (1-methyl-2,4,5-trinitroimidazole). 4,5-dinitro-2-(4-nitro-1,2,5-oxadiazol-3-yl)-2H-1,2,3-triazole (M4) shows the highest heat of formation value of 370.79 kJ/mol along with all other compounds exhibiting positive heat of formation. All compounds exhibit oxygen balance of - 5.88%, indicating that these compounds are not oxygen deficient. The detonation performance has been evaluated by the Kamlet-Jacob's equation with density of 1.95 g/cm³. In addition, NBO, frontier molecular orbital, Fukui function, bond dissociation energy (BDE), and molecular electrostatic potential (MEP) studies have been performed to identify reactive sites and assess stability.

Method: All molecules were optimised and analysed by using DFT at the B3PW91 6-31G (d,p) in Gaussian 09 package. Multiwfn_3.8_dev was used to compute molecular surface properties. Fukui functions and local reactivity descriptors have been calculated by the UCA-FUKUI program.