Journal of Molecular Modeling最新文献

Context

Nanomaterial-based drug delivery systems offer an effective approach for treating nephropathy. In this study, first-principle calculations were employed to systematically investigate the electronic properties of SiC/TiS₂, SiC/TiS₂/SiC, and TiS₂/SiC/TiS₂ heterojunctions, as well as to evaluate their potential as carriers for the anti-nephropathy drug mycophenolic acid (MPA). The results show that all three heterojunctions exhibit excellent kinetic and thermal stability, with adsorption energies for MPA reaching −3.221 eV, −3.732 eV, and −3.703 eV, respectively. The band gaps of the heterojunctions (1.092 to 1.201 eV) are significantly reduced compared to monolayer SiC (3.361 eV) and TiS₂ (0.807 eV). A charge transfer of 0.22 to 0.28 |e| occurs from MPA to the substrate. After adsorption of MPA on the heterojunction, the optical absorption coefficient reaches 2.35 × 10⁵ cm⁻¹ and can be modulated by strain. These characteristics make the SiC/TiS₂ heterojunction an ideal candidate material for drug delivery carriers.

Methods

All computational analyses conducted in this study were grounded in DFT and executed utilizing the CASTEP software package integrated within the Materials Studio software suite. The interactions between ionic cores and valence electrons were modeled employing norm-conserving pseudopotentials. The exchange–correlation effects were treated using the Perdew–Burke–Ernzerhof functional within the framework of the generalized gradient approximation.

Context

Amino acid–based ionic liquids (AAILs) have emerged as promising materials for CO₂ capture. In this work, we present a combined molecular dynamics (MD) and density functional theory (DFT) study of the CO₂ sorption behaviour in three piperidinium AAILs. DFT calculations were employed to investigate the chemisorption of CO₂ through two intramolecular proton transfer pathways leading to the formation of carbamate or carbamic acid. The results indicate that [Pip][Lys] and [Pip][Arg] proceed through the carbamate pathway, while [Pip][His] proceeds through the carbamic acid pathway. MD simulations were carried out to study the physicochemical properties and dynamics of CO₂ absorption in AAILs. The CO₂ molecules tend to accumulate at the AAIL/CO₂ interface prior to diffusing into the AAIL phase, following the order [Pip][His] > [Pip][Arg] > [Pip][Lys]. Upon CO₂ sorption, the lifetimes of hydrogen bonds between cation and anion decrease, leading to enhanced ion mobility and increased self-diffusion coefficients. The strongest anion-CO₂ interaction was found for the [Pip][His] system, while the fastest dynamics was observed for the [Pip][Lys] system.

Method

Density functional theory calculations at the M06-2X/6-311++G(d,p) level were employed to examine interaction energy and CO₂ chemisorption mechanisms supported by Atoms-In-Molecules (AIM) analysis. Classical molecular dynamics simulations using the OPLS-AA force field were performed to investigate the physicochemical properties as well as the dynamics of CO₂ absorption in AAILs.

Graphical abstract

Context

The chemical effect of carbon dioxide (CO₂) addition on soot formation in flames is significant for developing cleaner combustion technologies, but its atomistic mechanisms remain elusive. This work investigates the formation and evolution of soot nanoparticles from polycyclic aromatic hydrocarbons (PAHs) in ethylene flames under different CO₂ additions using ReaxFF molecular dynamics (MD) simulations. The simulation reveals a three-stage process from PAHs to curved fullerene-like soot particles: nucleation, surface growth/coagulation, and graphitization. The results demonstrate that CO₂ effectively suppresses soot mass growth and nucleation primarily by consuming H radicals to reduce the reactivity of PAH precursors, while enhanced concentrations of oxidizers (OH and CO₂) promote the oxidation of soot nanoparticles.

Methods

The initial atomic configurations were constructed and energy-minimized using Materials Studio. All molecular dynamics simulations were performed using the LAMMPS software package with the ReaxFF reactive force field which parameters were optimized for large hydrocarbon interactions. The initial system comprised a mixture of PAH molecules, small species (C₂H₂, H, OH), and varying amounts of CO₂, based on compositions derived from chemical kinetic calculations. Simulations were conducted in the NVT ensemble at 3000 K for 1 ns. To ensure statistical reliability, each simulation case was run with three independent repetitions, and the results reported for analysis (e.g., carbon atom counts, radical populations) represent the average values. Chemical reaction pathways were analyzed using the ChemTraYzer program, and visualization was performed with VMD.

Context

In perovskite solar cells (PSCs), hole transport materials (HTMs) are crucial for charge extraction and transport. Therefore, molecular design of HTMs is an effective method to enhance PSCs performance. Considering that triphenylamine is a common group for constructing HTMs, molecules PD-Cz and MD-Cz were designed based on a carbazole-diphenylamine backbone with isomeric triphenylamine. Density functional theory (DFT), molecular dynamics (MD) simulations, and Marcus theory were employed to study the geometric structures, photoelectric properties, and hole transport properties of the designed HTMs. Simulated results indicate that differences in intermolecular interactions lead to a higher hole mobility in PD-Cz than that of MD-Cz. After synthesizing PD-Cz and MD-Cz and applying them to PSCs, it was found that PD-Cz exhibits higher hole mobility, good film-forming ability, and excellent capability to inhibit electron–hole recombination. Consequently, under the same conditions, the PCE of PSC devices based on PD-Cz reached 23.05%, which is higher than the PCE of MD-Cz (19.50%). The mutual confirmation of experimental results and theoretical models demonstrates that model by employing a side-chain triphenylamine isomerization strategy in this work is expected to provide guidance for designing novel HTMs.

Methods

DFT and TD-DFT calculations were carried out by the Gaussian 09. The ground-state geometry for the investigated molecules were optimized using the B3P86/6-311G(d, p) functional and basis set. The optical properties of the investigated molecules were calculated by TD-PBE0/6-31G(d) functional and basis set in dichloromethane solution with a polarizable continuum model (PCM). The MD simulations for the investigated molecules were conducted using the Gromacs program. Throughout the entire simulation process, the General Amber Force Field (GAFF) for HTMs and Universal Force Field (UFF) for perovskite was employed. The site energies, charge transfer integrals and overlap integrals were simulated at the PW91/TZP level using the ADF program.

Context

Polymer nanocomposites gain functionality from nanoscale fillers, yet the magnitude of structural and transport changes imparted by an isolated graphene sheet to dilute atactic polystyrene (aPS) chains in a good solvent remains unclear. We probe how chain dimensions, conformational statistics, cohesive energy density, and diffusivity respond to graphene when the matrix is dominated by toluene, a processing-relevant solvent. The results provide quantitative guidance for the rational design of dilute polymer nanocomposites in which graphene predominantly modulates the local structure without significantly altering the global chain statistics.

Methods

All-atom molecular dynamics simulations with the COMPASS II force field were performed for aPS oligomers containing 30 and 50 repeat units at 298 K. Each system (1, 3, or 5 chains) was equilibrated and sampled for 10 ns with 2 fs timestep in Materials Studio, both with and without a 2.46 nm graphene sheet. Ensemble analyses covered end-to-end distances, radii of gyration, probability densities, mean-squared displacements, diffusivities, cohesive energy density, and interaction-energy traces, providing statistically converged comparisons across compositions.

Context

The synergistic enhancement of both energy and safety in energetic materials is importance. Conventional polynitroaromatics like (e.g., HNS, TATB) offer high thermal stability but limited energy density, while nitrogen‑rich heterocycles (e.g., diazoles, triazoles) possess high energy density yet suffer from high sensitivity and poor thermal stability. In this research, five polycyclic energetic structures were designed by combining thermally stable polynitrophenyl units with high‑energy five‑membered nitrogen‑rich heterocycles via imine bridges. Density functional theory (DFT) calculations systematically correlated their electronic/molecular microstructures (e.g., electron density distribution, geometry) with macroscopic properties including detonation velocity and density. All designed compounds exhibited outstanding explosive performance, with detonation velocities (D_v) of 7892–8618 m·s⁻¹, detonation pressures (P) of 27.9–34.4 GPa, and high enthalpies of formation (380.82–719.52 kJ·mol⁻¹). Compounds 2 and 3 performed particularly well, surpassing HNS (7612 m·s⁻¹) and TATB (8144 m·s⁻¹) in detonation velocity. Moreover, all compounds showed excellent impact resistance (h₅₀, 26–37 cm), comparable to HMX and RDX. Overall, this work provides theoretical guidance and candidate structures for developing high‑energy, low‑sensitivity energetic materials with promising application potential.

Method

Theoretical calculations were performed using the Gaussian 09 software package. Structural geometric optimization and frequency analysis were all calculated using the DFT-B3LYP3 method with a 6-31G(d,p) basis set. Subsequently, the single-point energy of the pre-optimized structures was evaluated at DFT/B3LYP3/6-31G(d,p) levels. Electrostatic potential energy and other related calculations were performed using the spectrum analysis software Multiwfn_3.8_dev. Regional visualization was achieved through the VMD 1.9.3 program.

Context

Cu/Zr multilayers have important applications in high-strength structural materials, wear-resistant coatings, and microelectronic devices. This study presents a molecular dynamics model to simulate the diamond scratching process of Cu/Zr multilayers, examining the effects of parameters such as scratching speed and depth on this process. The simulations were conducted at different scratching speeds and scratching depths. The results indicate that scratching speed significantly influences the location of chip formation on the surface of the Cu/Zr multilayers. Moreover, increasing scratching depth results in larger chip volumes and higher scratching forces. This study enhances our understanding of how scratching parameters influence the behavior of Cu/Zr multilayers, providing valuable insights for their applications.

Methods

In this study, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used to simulate the entire scratching process, and EAM potential function is used to describe the interaction forces between atoms during the scratching process. After the simulation is completed, use the open visualization software OVITO to process the simulation results and obtain images.

Context

The protozoan parasite Leishmania donovani is a major causative agent of visceral leishmaniasis (VL), a lethal disease posing significant public health challenges globally. Existing anti-VL drugs have become increasingly ineffective due to rising drug resistance, underscoring the urgent need for novel and effective therapeutic candidates. Computational approaches offer rapid and systematic methods for identifying potential drug targets and supporting rational drug design. This review discusses in silico molecular docking studies targeting various Leishmania proteins and their inhibitors, alongside the in vitro and in vivo validation of selected compounds, emphasizing their crucial roles in advancing antileishmanial drug discovery.

Methods

In the review, we have focused on a molecular docking study and explored potential compounds with high binding energy toward protein targets of Leishmania. Following the in silico screening, our review highlights compounds that exhibit both in vitro and in vivo antileishmanial properties, allowing for an assessment of their therapeutic efficacy. Different Software is available for molecular docking, has been mentioned in the review. Overall conclusion of this review supports the computational approach in drug discovery before the in vitro and in vivo study, which can save cost and time efficiency as well.

Graphical Abstract

Context

Carbon nanotubes (CNTs) possess remarkable properties, fundamentally governed by the transition between curvature-induced structural distortions (partial (text {sp}^3)) and planar ((text {sp}^2)) hybridization. We present a detailed computational investigation into the atomic structure of armchair single-walled carbon nanotubes (SWCNTs) with chiral indices (n, n) ranging from (3,3) to (11,11). Using ab initio Hartree-Fock calculations, we precisely quantify a direct, quasi-linear structural transition from increased (text {sp}^3) character to (text {sp}^2) character that is quantitatively dictated by the relief of nanotube curvature (i.e., increasing radius). Our results demonstrate how average bond lengths, bond angles, and dihedral angles regularly evolve as the radius increases, revealing how diminishing curvature drives the progressive convergence toward ideal planar (text {sp}^2) geometry. Crucially, we uncover a noticeable odd-even pattern in the incremental change of radius across the series, indicating precise, localized bond relaxations under strain. These findings provide unprecedented quantitative insights into how fundamental bond parameters dictate hybridization shifts in curved carbon systems, establishing a clearer understanding of the intrinsic flexibility of CNTs for advanced quantum electronics, spintronics, and next-generation materials science.

Methods

The initial geometries of armchair SWCNTs with chiral indices (n, n) from (3,3) to (11,11) were generated using the Avogadro molecular builder. Subsequently, ab initio Hartree-Fock (HF) calculations were performed to fully optimize the geometries using the Gaussian09 software with the 6–31 G basis set. Structural parameters like average bond lengths, bond angles, and dihedral angles were extracted from the optimized structures to quantify the curvature-induced deviations from ideal (text {sp}^2) geometry.

Context

Nanoporous graphene has emerged as a promising platform for desalination because its atomic thickness and tunable pore chemistry can, in principle, overcome the conventional permeability–selectivity trade-off of polymeric reverse osmosis membranes. Here, we investigate water and ion transport through a single-layer pyridinic-N-doped nanoporous graphene membrane containing sub-nanometer pores with an effective diameter of ~ 2.75 Å, separating a saline feed from a pure permeate reservoir under an axial electric field of 0.05 V Å⁻¹. Non-equilibrium molecular dynamics simulations reveal that this functionalized membrane supports very high-water throughput while maintaining complete Na⁺/Cl⁻ rejection over multi-nanosecond trajectories. The inferred water permeance is on the hundreds of LMH bar⁻¹, and potential of mean force calculations show ion translocation barriers, dominated by steric confinement and dehydration. Structural analysis indicates strong hydrogen bonding between water and pyridinic N at the pore rim, together with field-induced alignment of water dipoles along the transport direction. These synergistic effects enable rapid, selective water transport through sub-nanometer pores, highlighting pyridinic N-doping and modest electric fields as a viable design strategy for next-generation high-flux desalination membranes.

Methods

We performed non‑equilibrium classical molecular dynamics simulations of a slit‑pore desalination cell containing a pyridinic‑N‑doped nanoporous graphene membrane, explicit water, and NaCl electrolyte. Water was represented by a rigid four‑site TIP4P‑family model, and Na⁺/Cl⁻ parameters were chosen to be compatible with this water model. The N‑doped graphene sheet, patterned with ~ 2.75 Å pores and decorated at the rims by pyridinic-N, was modeled using an AIREBO/REBO‑type potential for C–C and C–N bonding. Electrostatics were treated with a particle–particle particle–mesh (PPPM) method under three‑dimensional periodic boundary conditions and van der Waals interactions were described by Lennard–Jones potentials with Lorentz–Berthelot mixing and an appropriate real‑space cutoff. A uniform external electric field of 0.05 V Å⁻¹ was applied along the membrane normal, and a pressure‑like driving force was imposed via rigid carbon pistons at the cell ends. Water geometry was constrained using SHAKE/SETTLE, and the equations of motion were integrated with a velocity–Verlet scheme in the NVT ensemble at 300 K, controlled by a Nosé–Hoover thermostat. Trajectories on the order of a few nanoseconds were generated using the LAMMPS package and analyzed with in‑house Python tools to obtain fluxes, permeances, z‑resolved densities, mean‑squared displacements, radial distribution functions, orientational order parameters, and accessible‑area‑corrected potentials of mean force.