Journal of Molecular Modeling最新文献

Context

Semiempirical computational methods based on the MNDO approximation have a long history. Since its release in 1977, the original MNDO method has evolved steadily, passing through several forms (AM1, PM3, etc.) up to the present. Each new form represented an improvement, and it is anticipated that the evolution will continue for many more years.

Methods

A summary of the history of MNDO-based methods will be given, followed by a description of the mechanisms involved in developing some of the current methods. To assist in this, a set of files illustrating the steps and procedures involved is provided in Supporting Material; hopefully these will be useful in facilitating the development of future methods.

Context

This study aims to clarify the linear response excitation mechanisms and characteristics of the explosive 1-methyl-3,5-dinitro-1,2,4-triazole (MDNT) in the implicit solvent dimethyl sulfoxide (DMSO) when transitioning from the ground state to the 20 lowest-energy excited states. In the ground state MDNT molecule, there exists a steric hindrance effect within the triazole ring and between the nitro oxygen (O) and the azole ring nitrogen (N). Ahydrogen bond dominated by dispersion interaction is formed between the nitro O and the methyl hydrogen (H). Among the 20 low-energy excited states, S5, S7, S9, S10, S11, and S12 are significant bright states (with an oscillator strength of 0.01), and the remaining 14 are dark states (weakly allowed transitions, not observable in conventional UV-vis spectra). Note that this differs from the d–d transitions in transition metal complexes, where an f of 0.001 may still be weakly observable. The lifetimes of the six bright states are all in the nanosecond ranges (S10 is the longest, reaching 4.93 ns; S11 is the shortest, only 0.7 ns). S11 requires an excitation energy of 6.47 eV and corresponds to the maximum absorption peak. In terms of the excitation mechanism, S0 → S5/S7/S12 is a C–N π → N–O π charge transfer excitation (CT), S0 → S11 is a C–N π → N–O π local excitation (LE), and S0 → S9/S10 is a local excitation (LE) of the lonepair electrons n → N–O π* of the nitro O. This study provides a theoretical reference for the research on the electronic excitation mechanism and decomposition behavior of energetic materials.

Method

The Gaussian16 software is used for optimization and calculation, and the Multiwfn and VMD programs are applied for further processing and visualization. Using the time-dependent density functional theory (TDDFT) at the M06-2X/6-311G(d) level, the linear response electron excitation of MDNT in implicit solvent DMSO was investigated.

Context

MoNbTaW-based refractory high-entropy alloys exhibit excellent high-temperature mechanical properties, but their poor room-temperature ductility severely restricts engineering applications. Compositional optimization is an effective strategy for enhancing the mechanical properties of these alloys. However, the composition-dependent synergistic effects of group VB/VIB elements on elastic properties, along with the coupled regulatory mechanisms between the valence electron concentration (VEC) and the degree of atomic size mismatch (δ), remain unclear. These unresolved issues represent critical bottlenecks that hinder the compositional design of MoNbTaVW RHEAs with balanced strength and toughness.

Methods

First-principle calculations based on density functional theory (DFT) were performed with the CASTEP code to investigate the MoNbTaVW RHEA system. A BCC solid-solution model was established via a virtual crystal approximation (VCA) and fully relaxed via the BFGS algorithm. The PBE generalized gradient approximation and norm-conserving pseudopotentials are employed for total energy and elastic constant calculations. Lattice constants, elastic constants, VEC, and δ are computed for 21 alloy compositions spanning variations in Mo, Nb, Ta, V, and W. Polycrystalline bulk, shear, and Young’s moduli are derived via the Voigt–Reuss–Hill averaging scheme, and mechanical stability is verified against the Born criteria for cubic crystals. The calculated properties are further correlated with VEC and δ to establish quantitative composition–property relationships.

Context

Lead-free double perovskites are actively explored as environmentally benign alternatives to lead-based halide perovskites for optoelectronic applications. In this work, the influence of halide substitution (X = I, Br, Cl) on the structural, mechanical, electronic, and optical properties of cubic K₂AgSbX₆ double perovskites is systematically investigated. Halide replacement induces a monotonic reduction in lattice parameters and a widening of the electronic band gap, increasing from the iodide to the chloride compound. Hybrid-functional calculations predict indirect band gaps ranging from 0.60 eV for K₂AgSbI₆ to 1.73 eV for K₂AgSbCl₆. Mechanical analysis reveals ductile behavior for the iodide and bromide phases, while the chloride phase is significantly stiffer and brittle. Optical calculations indicate strong absorption across the visible range, with K₂AgSbBr₆ exhibiting an optimal balance between band gap, absorption strength, and mechanical flexibility, making it particularly promising for optoelectronic and photovoltaic applications.

Methods

First-principles density functional theory calculations were performed using the CASTEP code. Structural optimization and ground-state properties were obtained using the rSCAN meta-GGA functional, while electronic band structures were refined using the HSE06 hybrid functional. Ultrasoft pseudopotentials generated within the on-the-fly scheme were employed with a plane-wave cutoff energy of 500 eV and a Γ-centered 4 × 4 × 4 Monkhorst–Pack k-point mesh. Elastic properties were evaluated via the Voigt–Reuss–Hill approach, phonon dispersions were calculated using density-functional perturbation theory, and frequency-dependent optical properties were derived from the complex dielectric function.

Context

Orally disintegrating tablets (ODTs) are highly sensitive to environmental humidity due to their hydrophilic excipients, which impact critical quality attributes like hardness, friability, and disintegration time. This study integrates molecular simulation with experimental analysis to investigate how excipient composition governs the moisture affinity and physicochemical stability of two ondansetron ODT formulations (gelatin-based vs. microcrystalline cellulose (MCC)-based) under varying humidity conditions. Molecular dynamics simulations predicted higher hygroscopicity for the MCC-based formulation, which correlated with experimental observations of increased friability and faster disintegration at elevated humidity. The gelatin-based formulation exhibited greater stability across humidity levels. These findings validate MD simulation as a predictive tool for screening excipient interactions with moisture during ODT pre-formulation.

Methods

Molecular dynamics simulations were performed using Materials Studio 6.0.0 (BIOVIA, 2012) with the COMPASS force field. All molecular structures were energy-minimized, and amorphous cells for both formulations were constructed using the Amorphous Cell module with the COMPASS force field. Henry’s constants and isosteric heats of adsorption were calculated using the Sorption module via Grand Canonical Monte Carlo simulations at 298 K. Experimental evaluations included hardness, friability, loss on drying, and disintegration time tests conducted according to USP 43–NF 38 guidelines at 29% and 57% relative humidity. Statistical analysis was performed using one-way ANOVA in JMP 13.2.0.

Context

This study examines how spin multiplicity governs the structure, electronic states, magnetism, and optics of Er-doped ZnO nanostructures. Substitutional Er³⁺ at Zn sites slightly elongates Er–O bonds while preserving the Zn–O framework, consistent with prior experiments. Energetically, the triplet and quintet states are nearly degenerate and substantially more stable than the singlet, identifying both magnetic states as relevant. Spin polarization reorganizes frontier levels and introduces Er-centered localized states; in the magnetic states, the Kohn–Sham HOMO–LUMO separation is  ~1.8 eV. The Er-4f moment couples mainly through O-2p, with assistance from Zn(s + p), yielding weakened net ferromagnetism in the triplet and stronger parallel alignment in the quintet. Simulated spectra show a blue-shifted UV edge near ~3.9 eV relative to pristine ZnO and weak visible shoulders at ~2.1 and ~2.8 eV, consistent with partially allowed Er³⁺ intra-4f transitions.

Methods

Finite ZnO clusters were treated with spin-polarized hybrid DFT using the range-separated CAM-B3LYP functional. Geometry optimizations were performed without symmetry constraints, followed by electronic-structure analyses for singlet (S = 0), triplet (S = 1), and quintet (S = 2) states. Optical properties were obtained from time-dependent DFT on the optimized spin states. Standard ultrafine integration grids and tight SCF thresholds were used to ensure numerical stability; wavefunction stability checks were applied to open-shell solutions. Calculations were carried out with the Gaussian suite, and postprocessing/visualization employed common electronic-structure analysis tools (molecular orbitals, PDOS, and spin-density mapping).

Graphical abstract

Context

Boron nitride nanosheets (BNNS) possess high thermal stability and large surface area; however, their inherently wide band gap and weak adsorption capability limit their effectiveness in gas-sensing and gas-storage applications. This study investigates the adsorption and sensing behavior of H₂, CH₄, and C₂H₅OH on pristine and doped BNNS, including Al-doped, P-doped, and AlP co-doped B₃₉N₃₉ systems, in order to evaluate how doping modification can overcome these intrinsic limitations. The results show that doping significantly narrows the energy gap of BNNS from 5.940 to 5.481, 5.771, and 5.242 eV for Al-, P-, and AlP-doped systems, respectively, thereby enhancing their sensing sensitivity. Pristine BNNS exhibits weak adsorption toward H₂, CH₄, and C₂H₅OH (−0.04, −0.27, and −2.95 kcal/mol), whereas Al-doped BNNS demonstrates markedly stronger interactions, especially for C₂H₅OH (−30.35 kcal/mol), indicating substantially improved sensing performance. Moreover, adsorption induces pronounced electronic structure changes in Al-doped and AlP co-doped BNNS, particularly in the presence of C₂H₅OH. These findings identify Al-doped BNNS as a highly promising material for H₂, CH₄, and C₂H₅OH sensing, while AlP co-doped BNNS is especially suitable for selective C₂H₅OH detection.

Methods

All DFT calculations were performed using the GAUSSIAN 09 program package. The structural, electronic, and adsorption properties were examined at the B3LYP/6-31G(d,p) level of theory. Natural Bond Orbital (NBO) analysis (version 3.1), as implemented in GAUSSIAN 09, was employed to examine the electronic structures and natural population analysis (NPA) charges, while the density of states (DOS) plots and molecular electrostatic potential (MEP) maps were generated using GaussSum 2.1.4 and MOLEKEL 4.3, respectively.

Context

A thermo-reversible sol–gel transition of titanium butoxide–based materials was recently reported. Experimentally, the gel formation was attributed to the direct interaction between the nitrate ions and titanium atoms forming bridging and chelates nitrates. The exposed oxygen atoms of the nitrate groups, bonded to titanium, form hydrogen bonds with water and alcohol molecules of the circulant medium to build up the gel molecular structure. In this work, DFT-QTAIM computer calculations confirm the experimentally predicted oligomer formation mechanism. According to our DFT-QTAIM calculations, water and/or alcohol molecules link, upon weak bond formation, two titanium butoxide–based neighboring monomers stabilizing the oligomer structure. The QTAIM hydrogen-bonding topology shows an elaborate network of relatively short and long “weak bonds” including interactions not only with nitrates but with other functional groups.

Method

We have performed DFT computer simulations on a series of monomers and dimers of titanium butoxide–based thermoreversible sol–gel systems. Stable structures were obtained through a geometry optimization procedure using the PBE exchange–correlation functional along with a Slater DZP basis set, considering a convergence criterion of 1 × 10⁻⁶ hartree/Å. QTAIM properties and IR spectra were obtained as a single-point calculation at the stable structure of the corresponding system.