Journal of Molecular Modeling最新文献

Context: The structural stability, ground state magnetic order, electronic, elastic and thermoelectric properties of NdMn₂ in the C15, C14 and C36 polytypic phases is investigated. The magnetic phase optimization and magnetic susceptibility reveal that NdMn₂ is antiferromagnetic (AFM) in C36 phase; and paramagnetic (PM) in C14 and C15 phases respectively. The band profiles and electrical resistivity show the metallic nature in all these polytypic phases and reveal that the C36 phase possesses smaller resistivity. The presence of covalent bonds among Nd-Nd and Nd-Mn has been verified from the electron charge densities plots. The elastic constants calculated in different phases confirm the mechanical stability and are elastically anisotropic and incompressible in all phases. Due to large enough value of Young and Bulk moduli in C14 phase NdMn₂ would be suitable candidate for applications that require high strength, stiffness and durability, as well as the ability to withstand extreme environments.

Method: The density functional theory (DFT) is used to investigate the physical properties of understudy binary intermetallic compounds NdMn₂ in the C15, C14 and C36 polytypic phases. BoltzTraP code based on Boltzmann semi-classical transport theory is used to investigate magnetic susceptibility and electrical resistivities of the understudy compounds. The elastic constants are calculated with the help of IRELAST code embedded in WIEN2k software. Linux based xmgrace and origin software are used for plotting.

Context: The flow equations are derived for describing the two-dimensional hybrid molecular-scale and continuum flows in the very small surface separation with inhomogeneous solid surfaces and they can be applied for designing the specific bearings. The aim of the present study is to solve this specific flow problem in engineering with normal computational cost. The flow factor approach model describes the flow of the molecule layer adjacent to the solid surface and the Newtonian fluid model describes the flow of the intermediate continuum fluid. By using these flow equations, the simulation results show that designing the inhomogeneous stationary surface can very significantly improve the load-carrying capacity of the hydrodynamic thrust bearing with low clearances.

Method: The flow of the physically adsorbed layer is treated as non-continuum and it is modeled by the equivalent non-continuum flow model by considering the fluid molecules orientated normal to the solid surface. The fluid between the two adsorbed layers is treated as continuum and Newtonian. The slippage can occur between the adsorbed layer-solid surface interface. It is assumed as absent on the adsorbed layer-continuum fluid interface. The flow equations are derived according to the equilibrium of the momentum transfer in the surface clearance. The film pressures and carried load of the thrust bearing with low clearance and inhomogeneous surfaces are derived by applying the obtained flow equations.

Context: This study systematically investigated the effects of single S-atom vacancy defects and composite defects (vacancy combined with doping) on the properties of MoS₂ using density functional theory. The results revealed that N-doped S-vacancy MoS₂ has the smallest composite defect formation energy, indicating its highest stability. Doping maintained the direct band gap characteristic, with shifts in the valence band top. The Fermi level slightly shifted down in N- and P-doped systems, with N-doped MoS₂ showing a larger increase in valence band top energy. Doping also significantly altered the density of states at the Fermi level and weakened the dielectric properties of MoS₂. The maximum dielectric peaks of doped systems appeared near 2.7 eV with reduced intensities and red-shifted energies. Optical properties were significantly changed, with decreased reflectance, narrower reflectance spectra, and blue-shifted absorption spectra. These findings suggest that introducing composite defects can effectively reduce the forbidden bandwidth of MoS₂, enhancing electrical conductivity. This research provides theoretical guidance for novel material design and offers insights into composite defect behavior in other two-dimensional materials.

Methods: The Materials-Studio CASTEP module was used to calculate density functional theory (DFT). A plane wave ultrasoft pseudopotential is used to optimize the crystal structure, and the generalized gradient approximation (GGA) in the form of Perdew-Burke-Ernzerhof (PBE) is used to characterize the exchange correlation energy. After the convergence test, the truncation energy and dot settings were finally selected to be 450 eV and 3 × 3 × 1, respectively, the convergence accuracy was set to 1.0e-5eV/atom, and the convergence criterion for the interatomic interaction force was 0.02 eV/Å. The parameters were all at or better than the accuracy settings. The vacuum layer between the layers was set to 18 Å to avoid interactions caused by the periodic calculation method.

Context: The study of the influence of solvent on 1-bromo adamantane (BAD) exposes prominent solvatochromatic shifts in the optical absorbance and substantial solvent effects on the electronic structure. This facilitates the molecular probe abilities for the BAD with respect to the surrounding environments such as dielectric constant and polarity. BAD exhibits positive solvatochromism for nonpolar solvents and negative solvatochromatic shifts for polar and aromatic solvents. In accordance with this, significant energy changes are obtained on the orbital occupancies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), resulting in a large difference in energy among the various solvation environments. According to this, the HOMO-LUMO gap decreases in nonpolar solvents, and it increases with respect to polarity in the case of polar and aromatic solvents. Computed thermodynamic parameters and noncovalent interaction analysis also demonstrate the noticeable changes for different solvent dielectric continuums with more changes for solvent continuums with large dielectric constants.

Methods: Experimentally recorded UV-Vis absorption spectra of the solvents exhibit positive and negative solvatochromism for the n to σ* electronic transition. Computational investigations carried out with equation-of-motion coupled-cluster with single and double excitations and configuration interaction singles calculations by means of the solvent model density implicit solvation model clearly demonstrate the strong influence of solvents on the electronic structure of the BAD molecule.

Context: SiGe nanotubes (SiGeNTs) hold significant promise for applications in nanosolar cells, optoelectronic systems, and interconnects, where thermal conductivity is critical to performance. This study investigates the effects of length, diameter, temperature, and axial strain on the thermal conductivity of armchair and zigzag SiGeNTs through molecular dynamics simulations. Results indicate that thermal conductivity increases with sample length due to ballistic heat transport and decreases with temperature as phonon scattering intensifies. Axial strain transitions from compression to tension enhance phonon propagation, improving conductivity. Chirality affects conductivity, with zigzag SiGeNTs consistently outperforming armchair structures, while diameter exhibits negligible impact.

Methods: Non-equilibrium molecular dynamics simulations were conducted using the LAMMPS package with the Tersoff potential to model Si-Ge interactions. Thermal conductivity was computed via Fourier's law, with the system divided into regions for controlled heat input and dissipation. Lengths, diameters, temperatures (100-500 K), and axial strains (- 6% to + 9%) were varied systematically. Phonon spectrum analysis was performed using Fourier transforms of velocity autocorrelation functions to compute.

Context: Holey nanographene, an allotrope of carbon arranged in two dimensions, has gained remarkable attention as a nanomaterial with several potential uses in numerous industries, such as electronics, energy storage, healthcare, and environmental cleanup, because of its high carrier mobility, flexibility, transparency, high surface area, conductivity, and chemical stability. The fundamental holey nanographene is assembled in a linear form to create the holey nanographene chain (HNC) that is being discussed. To fully utilize it in various applications, it is essential to comprehend the basic ideas guiding its behavior at the nanoscale; for that, we find various topological indices for this holey nanographene chain using the cut method. Because topological indices are a robust mathematical tool that links molecular structure with chemical, physical, and biological properties, they are essential in diverse areas, namely chemistry, pharmaceutical research, environmental science, and materials science METHODS: The cut method is essential for calculating topological indices in large structures as standard definitions become increasingly complex for such computations. In this study, we apply the cut method to compute each topological index for holey nanographene structures, which involves extensive summations. MATLAB software is employed to simplify these calculations. To generate the DDSV (Distance Degree Sequence Vector) for each vertex within any dimension of holey nanographene, we utilize the NEWGRAPH interface. Python code is then used to analyze the DDSVs assigned to each vertex. Additionally, MATLAB code is applied to validate the numerical results derived from analytical formulae for the topological indices of the HNCs under consideration.

Context: Natural fluorapatite (FAP) has been investigated as an adsorbent for the removal of dyes such as methylene blue (MB) and crystal violet (CV) from aqueous solutions. Effective dye removal is crucial for water treatment, particularly for industrial wastewater containing toxic dyes. FAP, a naturally abundant material, was characterized using XRD, FTIR, and SEM analysis. The maximum adsorption efficiency achieved was 97% (23 mg/g) for CV and 95% (13 mg/g) for MB under optimal conditions within an equilibrium time of 50 min. The adsorption capacity increased with the ionic strength of the dye solution, reaching 35 mg/g for CV and 28 mg/g for MB. The kinetic study showed that the adsorption of CV and MB is well described by the pseudo-second-order kinetic model (R² = 0.999) and fits the Freundlich model significantly, with an R² = 0.99 for both studied molecules. The thermodynamic analysis (ΔH° = 22.647 and 14.907 kJ.mol^-1, ΔS° = 88.627 and 47.330 J.mol^-1.K^-1 for CV and MB, respectively) revealed that the adsorption process is spontaneous and endothermic, with significant randomness at the adsorbent-adsorbate interface. However, desorption and regeneration tests showed that the efficiency of FAP decreases upon reuse. Despite this, the abundance of natural FAP balances its drawbacks. MD simulations confirmed that adsorption is exothermic and spontaneous, especially in basic conditions, where Van der Waals interactions dominate. These findings suggest that natural FAP has significant potential for dye removal in wastewater treatment applications.

Methods: The effects of various parameters, including dye concentration, temperature, adsorbent mass, and pH, on the adsorption capacity of FAP were studied. Experimental conditions included an initial dye concentration of 20 mg/L, adsorbent mass of 1 g/L, pH of 12, and temperature of 298 K. The Freundlich model was used to describe the adsorption process, while MD simulations provided insights into the adsorption mechanism.

Context: The medications for metabolic syndromes are very minimal and the available are not effective and show adverse effects. There is a huge need for the development of effective and safe drugs to battle metabolic syndromes. In this context, our study aimed to decipher the key molecules from Artocarpus communis seed hexane fraction and their possible mechanism of action against metabolic syndrome. Network pharmacology and hub gene analysis revealed that STAT3 displayed the highest number of interactions with 56 genes compared to its counterparts HSP90AA1 (51 interactions) and EP300 (42 interactions). The molecular docking analysis revealed a suitable phytochemical with a higher binding affinity towards the three target genes (STAT3, HSP90AA1, and EP300), which were taken further for the molecular dynamic simulations. Overall, the simulation results depict that all the phytochemicals were stably bound within the cavity of the respective target proteins. Therefore, Artocarpus communis seed hexane fraction can potentially alleviate metabolic syndrome in humans.

Methods: Solvent-based extraction was performed in this study to extract the phytochemicals in Artocarpus communis seed powder. The hexane fraction was subjected to GCMS analysis to identify the constituents. ADMETlab 3.0 was used in ADME predictions. Gene databases (GeneCards, Pharos, NCBI-gene, and DisGe NET) were used to identify the genes for the study. STRING, DAVID, and KEGG pathways were utilized in this study. PubChem and Protein Databank were used to retrieve the structures of phytochemicals and protein structures. Schrodinger Suite was used for the molecular docking and Desmond 2021-4 was used to simulate the ligand-bound complexes.