Research on novel co-crystals has long been a focal point in the field of high-energy material modification. In the present exploration, density functional theory (DFT) and molecular dynamics (MD) simulations were employed to investigate the properties of pentaerythritol tetranitrate (PETN)/3,4-dinitrofurazanofurazan (DNTF) mixtures across a molar fraction interval of 9:1 to 1:9. This study incorporated a comprehensive analysis of multiple key characteristics, encompassing the surface electrostatic potential of molecules, atomic interaction lines, binding energy values, trigger bond lengths, cohesive energy density, together with the mechanical behaviors of the designated assembly. Additionally, the detonation characteristics of pure PETN, pure DNTF, and the PETN/DNTF system were predicted using the EXPLO-5 software in conjunction with the nitrogen equivalent coefficient (NEC) method. The outcomes of the study uncovered significant divergences in the surface electrostatic potential of PETN versus DNTF molecules. These disparities indicate that intermolecular interactions across different molecular species are stronger than the interactions within homogeneous molecular groups, which in turn points to the viability of co-crystal synthesis between PETN and DNTF. A peak value of binding energy was ascertained at a molar ratio of 3:7, indicating the highest likelihood of co-crystal formation at this composition. The primary driving forces for co-crystallization were identified as electrostatic forces and van der Waals forces. The as-obtained co-crystal explosive demonstrated modest sensitivity and intermediate mechanical behavior. In a similar vein, the detonation behavior of the co-crystal at a molar ratio of 3:7 fell between that of pure PETN and pure DNTF, positioning it as a novel type of insensitive high-energy material. Materials Studio software was utilized to forecast the characteristics of PETN/DNTF co-crystals with varying molar ratios and crystal planes via molecular dynamics (MD) simulations. The MD simulations were performed with a time step of 1 femtosecond (fs) and a total simulation duration of 2 ns (ns). An isothermal-isobaric (NPT) ensemble was employed for the 2 ns MD simulations. The COMPASS force field was adopted, with the temperature set at 295 Kelvin (K). For the prediction of detonation characteristics, the EXPLO-5 software was combined with the nitrogen equivalent coefficient (NEC) method.
2,8-Bis (2,4,6-trinitrophenyl)-5,11-dioxo-2,4,6,8,10,12-hexacyclo[7.3.0.03,7]dodecane-1(12),3,6,9-tetraene (TNBP) is a new thermally stable explosive renowned for its exceptional detonation performance and thermal stability, making it highly valuable for applications in supersonic weapons, aerospace engineering, and ultra-deep well perforation. This study utilizes reactive molecular dynamics simulations to elucidate the thermal decomposition mechanism and kinetics of TNBP. Under both non-isothermal and isothermal conditions, the initial decomposition stages involve key reactions such as intermolecular oxygen transfer, dimerization, and NO dissociation. The primary decomposition products include small molecules like NO2, NO, N2, H2O, CO2, H2, HNO2, and HNO, alongside a range of clustered molecular species. Structural analysis indicates that TNBP's highly stable cyclic framework restricts cluster growth at lower temperatures. As the temperature rises, the rapid dissociation of H and N atoms from these clusters promotes a structural transition toward chain-like configurations. Furthermore, unlike RDX, TNBP pyrolysis generates a significant quantity of clusters, which effectively suppress the migration of atoms and retard heat transfer-this is identified as a crucial factor contributing to its superior thermal stability. Finally, kinetic parameters, including the activation energy (Ea) and pre-exponential factor (lnA), were determined for different stages of the pyrolysis process through reaction kinetics modeling. This work provides fundamental insights into TNBP's behavior under extreme high-temperature conditions, offering a theoretical basis for the design and synthesis of novel heat-resistant energetic materials. Molecular dynamics simulations of the thermal decomposition behavior of TNBP were conducted using the Large-scale Atomic/Molecular Parallel Simulator (LAMMPS) in conjunction with the ReaxFF/lg reaction force field. First, a 2 × 2 × 1 supercell model was constructed based on X-ray diffraction crystal data. To obtain a reasonable initial equilibrium configuration, the system underwent 5 ps of geometric optimization under NPT conditions (300 K, 1 atm) with a time step of 0.1 fs and a temperature damping coefficient of 10 fs. The applicability of the ReaxFF/lg force field in describing the TNBP system was verified by comparing crystal parameters with the interatomic radial distribution function. To investigate the impact of elevated temperatures on TNBP thermal decomposition, two heating simulation protocols were employed: First, the system was heated from 300 to 2700 K at a rate of 12 K·ps-1 under NVT conditions. Second, isothermal kinetic simulations of 200 ps were conducted at four temperatures: 2500 K, 2750 K, 3000 K, and 3250 K. During simulations, molecular species information and thermodynamic data were output every 10 fs, with bond-level evolution and atomic trajectories recorded synchronously.
Aflatoxin (AFT) is a toxic carcinogen and mutagen produced mainly by Aspergillus species. Dietary intake is the main route of exposure to AFT in humans, and DNA damage caused by AFT exposure receives wide concern as an endogenous factor in the pathogenesis of liver cancer. The systematic exploration on the toxicity mechanism of AFB1-the most toxic AFT subtype-is of great significance for the prevention and control of liver cancer. In this work, three adduct models, gap-AFT (GA), mispairing-AFT (MA), and insertion-AFT (IA), have been defined based on all the available three-dimensional structures of AFT in complex with DNA. In addition, their molecular recognition and conformational change features were investigated via comparative molecular dynamics (MD) simulations. Subsequently, the effects of six adduct models resulted from both AFB1-N7-dG and AFB1-Fapy on the recognition by DNA polymerase IV (Dpo4) were analyzed, with the possible toxicity mechanism of the destruction against DNA replication being given. Specifically, AFT partially destroyed the conservative structure including dATP and Ca2+ ion in the catalytic center of Dpo4. Moreover, the extent of disruption from AFB1-Fapy was slightly higher than that from AFB1-N7-dG. This work enriches the mechanism of AFT toxicity and provides clinical theoretical guidance for the control of human injuries caused by AFT exposure, making a contribution in the field of food and environmental safety. The experimental structure of 16 aflatoxin-containing DNA systems was obtained from the protein database ( http://www.rcsb.org/ ), and the relevant structural parameters of DNA were analyzed using the Curves program, revealing the effect of AFT binding on DNA structural deformability. The initial models of the AFB1-N7-dG and AFB1-Fapy adducts were structurally optimized at the B3LYP-D3/6-311G(d,p) level of theory using the Gaussian 09 software package. Molecular dynamics simulations were performed using the AMBER 20 software package. The following force-field combination was employed: the AMBER ff19SB force field for the protein, the OL15 force field for DNA, and specialized parameters for key system components. The catalytic Ca2⁺ ions were described using the 12-6 Lennard-Jones non-bonded parameters developed by Li and Merz. For the dATP substrate, parameters including the refined partial charges for the triphosphate moiety were adopted from the specialized nucleotide force-field set based on the work of Meagher, Redman, and Carlson. All-atom simulations were conducted, yielding stable and physically reasonable trajectories. RDG analysis of covalent binding regions of DNA and AFT using the Multiwfn 3.8 program to visualize the type, intensity, and variation of weak intermolecular interactions; the molecular mechanics/Poisson-Boltzmann solvent area (MM/PBSA) method was used to calculate the binding free energy between protein and DNA. Subsequently, the energy decomposition technology based on the MM/GBSA method was used to quantitatively analyze the key residues in dATP recognition in Dpo4.
To elucidate the performance mechanisms and limiting factors of UiO-66-NH₂ in catalyzing biodiesel production from waste oil at the molecular level, this study integrates experimental investigation with molecular dynamics (MD) simulations. Initially, UiO-66-NH₂ with high crystallinity and octahedral morphology was synthesized via an atmospheric solvothermal method. Single-factor experiments optimized the transesterification process parameters: alcohol-to-oil molar ratio of 15:1, catalyst loading of 3 wt%, reaction temperature of 50 °C, reaction time of 120 min, ultrasonic power of 90 W, and the addition of 50 wt% deep eutectic solvent (DES), achieving a biodiesel yield of 68.886%. The core analysis involved constructing a "waste oil-UiO-66-NH₂-ethanol" trilayer interface model for MD simulations, focusing explicitly on the diffusion behavior and adsorption mechanisms of reactants at the catalyst interface to elucidate their impact on yield. Analysis based on mean squared displacement (MSD) and radial distribution function (RDF) revealed that UiO-66-NH₂ exhibits mobility within the system and demonstrates dual adsorption towards both waste oil (represented by oleic acid) and ethanol. The catalytic advantage stems from the strong hydrogen-bonding interactions between the amino groups of UiO-66-NH₂ and ethanol molecules, which significantly enriches the local ethanol concentration at the interface, thereby promoting the reaction. However, the MD simulations critically identified the primary factor limiting yield enhancement: The inherently small pore size of UiO-66-NH₂ severely hinders the effective diffusion and mass transfer of large reactant molecules like oleic acid. This diffusion limitation induces significant steric hindrance near the interface, restricting sufficient contact between these molecules, the catalytically active sites, and the enriched ethanol. Consequently, by deciphering diffusion and adsorption behaviors, this study elucidates the concurrent molecular mechanisms in UiO-66-NH₂-catalyzed biodiesel synthesis: "interface reactant enrichment promotion" and "large-molecule diffusion limitation suppression." These findings provide crucial microscopic theoretical insights for understanding the experimental yield and guiding the future design and optimization of catalysts. Molecular dynamics (MD) simulations were performed using Materials Studio 2020. The COMPASS III force field was applied, and a representative model of the oil component was constructed based on molecular configurations identified through GC-MS analysis. The UIO-66-NH₂ model was derived by modifying the UIO-66 framework according to its synthetic rationale. A three-layer interfacial system was subsequently assembled to simulate the relevant environment. The simulation results yielded dynamical parameters, including the mean square displacement (MSD) and radial distribution function (RDF) of the constituent molecules. These results elucidate the promoting and limiting factors influencing biodiesel yield by UIO-66-NH₂ at the molecular level.
BRAF kinases are involved in cancer cell survival and metastasis. Mutations in BRAF are frequent in several types of cancer, occurring in more than 50% of melanomas, 50-70% of thyroid cancers, 15% of colorectal cancers, and 5-8% of non-small-cell lung cancers. The most prevalent mutation is V600E. Vemurafenib and dabrafenib are two selective BRAF inhibitors approved by the FDA for clinical use. However, due to the increasing resistance to current kinase inhibitors, there is an urgent need to identify new molecular scaffolds with potential BRAF inhibitory activity. In this work, molecular docking, molecular dynamics, and metadynamics simulations were performed on twelve triterpenes to identify the best ligands with potential binding to BRAFWT and BRAFV600E. The interaction profiles of the selected triterpenes revealed key contacts with residues ILE463, THR529, GLN530, TRP531, CYS532, and PHE583, which contribute to stabilizing the conformation of both inhibitors and triterpenes within the catalytic binding site of the proteins. The ΔG of betulinic acid (-57.46 kcal/mol) in complex with BRAFWT is comparable to the BRAF inhibitors vemurafenib-OMe and dabrafenib reported in previous work, the ΔG of β-amyrin (-51.83 kcal/mol) showed a ΔG comparable to the inhibitors with BRAFV600E; moreover, the ΔG of lupeol (-62.43 kcal/mol) and moronic acid (-61.05 kcal/mol) are more favorable with BRAFV600E than vemurafenib-OMe and dabrafenib. These computational calculations allow us to consider these triterpenes as potential candidates for drug design cycles and to optimize the binding profile for the development of new selective inhibitors for BRAFV600E to cancer treatments. Molecular docking calculations using AutoGrid 4.2.6, AutoDockGPU 1.5.3, and AutoDockTools 1.5.6 were performed. Molecular dynamics and metadynamics simulations were performed in the Desmond module of the academic version of the Schrödinger-Maestro 2021-4 program, utilizing the OPLS-2005 force field. Finally, all the protein figures presented in this article were made in the PyMOL program and the RMSD graphics were made in the statistical package R and RStudio 2025.05.1.
Polymer micelles have garnered extensive research interest and found widespread applications in drug delivery, targeted modification, and intelligent controlled release in recent years. Herein, the micelle molecule (FUC-VES) is theoretically designed by embedding fucoidan (FUC) and vitamin E succinate (VES) as a carrier for loading coenzyme Q10 (CoQ10), in which FUC and VES have excellent hydrophilic and hydrophobic properties, respectively. The molecular structures, frontier molecular orbital (FMO) energies, and solvent energies of FUC, VES, and FUC-VES were optimized and calculated using density functional theory (DFT) method. The lower molecular energy of FUC-VES (-5144.176294 a.u. in gas) comparing with that of FUC (-3554.359166 a.u. in gas) and VES (-1666.241224 a.u. in gas) implies that FUC-VES has stronger stability. In addition, the binding energy and global reactivity descriptors of FUC-VES@CoQ10 were also calculated. The results indicate FUC-VES would exhibit the higher molecular reactivity and water solubility in theory due to its lower energy gap and greater solvent energy. Besides, FUC-VES can spontaneously adsorb CoQ10 due to the negative binding energy (-1.456 kcal/mol). Interestingly, from the perspective of global reactivity descriptors, FUC-VES@CoQ10 exhibits better molecular activity compared with FUC-VES and CoQ10. Through the research of this work, the theoretical reference can be provided for the design of micelle molecules based on FUC and VES. All theoretical simulations in this work were performed using the Gaussian 16 software package. The ground-state structures of FUC, VES, FUC-VES, and CoQ10 were optimized using the DFT/B3LYP/6-31G(d) method. The molecular docking and IGMH diagram between FUC-VES and CoQ10 were carried out using AutoDock 4.2, Multiwfn 3.3.8, and VMD 1.9.4 software. The FMO energies containing the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) and energy gap (∆EH-L), and solvent energies of FUC, VES, and FUC-VES were optimized and calculated. Moreover, the binding energies and global reactivity descriptors, containing ionization potential (IP), electron affinity (EA), global hardness (η), global softness (σ), chemical potential (μ), electrophilicity (Ψ), and electronegativity (χ) of FUC-VES@CoQ10 were calculated.
II-VI semiconductor materials (CdSe belongs to this class of materials) exhibit unique electronic and optical properties arising from quantum confinement effects. The optical characteristics of these materials can be tuned by modulating the size of the constituent nanoparticles. CdSe is known for its narrow bulk band gap (~ 1.6 eV) and relatively large exciton Bohr radius (~ 5.4 nm). The clusters of CdSe hold significant potential for applications in novel light emitters, next-generation solar cells, sensor technologies, and biomedical diagnostics. Thus, the determination of energetic and quantum-chemical parameters for CdSe clusters with different geometries (linear, ring, and 3D) is highly valuable. Given the limited information regarding the impact of geometries change from linear (1D) to three-dimensional (3D) geometries on the energetic parameters and stability of CdmSem clusters, the present study is of relevance. The stoichiometric CdmSem (m = 1-6) clusters with linear, ring and spatial (3D) forms are studied. Structural properties, average bond length, and electronic properties like the highest-occupied-lowest-unoccupied molecular orbital (HOMO-LUMO gap (ΔE), binding energy (Eb), electronegativity (χ), chemical potential (π), chemical hardness (η), global softness (S), global electrophilicity (ω), and stability factor (SF) have been analysed. These parameters are calculated for the CdSe clusters in the solvent (ethanol). Based on the binding energy and relative stability values, the most favourable CdmSem (m < 6) cluster geometry was determined for the studied samples. Data regarding the most stable geometric configurations of CdSe clusters are constrained by the sample set presented in this study, the specific cluster sizes, and the structural limitations in their construction. All calculations including geometry optimization and energy spectra of the CdSe were made using density functional theory (DFT). The GGA + PBE approximation was used to describe the exchange-correlation energy of the electronic subsystem with Hubbard corrections (GGA + U). Initially, structural optimization and electronic band structure calculations were performed for bulk CdSe to estimate the appropriate Hubbard corrections (U). A plane-wave cut-off energy Ecut-off = 660 eV was employed. The valence electron states were defined by the 4d105s2 and 4s24p4 configurations for Cd and Se atoms, respectively. The self-consistent field convergence threshold for total energy was set to 5.0 10-6 eV/atom. Geometry optimization, including lattice parameters and internal atomic coordinates, was conducted using the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm. The convergence criteria were defined by a maximum Hellmann-Feynman force of 0.01 eV/Å, a maximum ionic displacement of 5.0 10-4 Å, and a maximum stress of 0.02 GPa. To ensure an accurate description of the electronic spectrum, Hubbard corrections were applied to the Cd d-orbitals (U4d = 5.80 eV) and Se p-orbitals (U4p = 4.00 eV). Based on the optimized bulk CdSe structure, stoichiometric CdmSem (m = 1-6) clusters were constructed with various geometries, including linear, ring, and spatial (3D) configurations. For all cluster calculations, the energy and force convergence criteria were established at approximately ~ 3 10-4 eV and ~ 5 10-2 eV/Å, respectively.
The accurate visualization and modeling of nanostructures, such as carbon nanotubes (CNTs) and graphene play a crucial role in advancing nanoscale research and applications. The versatile properties of graphene and CNTs make them fashionable among the scientific community. Modeling and simulation play an important role in understanding and predicting the behavior of these nanomaterials. Traditional modeling approaches often rely on specialized software and complex computational methods. However, the advent of versatile programming languages like Python has opened new avenues for simulating and visualizing nanostructures. Python's extensive libraries and user-friendly syntax make it an attractive tool for researchers aiming to model CNTs and graphene structures. The study demonstrated 3D visualization of graphene and two configurations of CNTs, namely single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs) marvelously using Python-based libraries. The Python codes of 3D nanostructure models advance the nanoscale research. The present study investigates the potential and limitations of Python-based libraries with a primary focus on Mayavi and PyVista for rendering and analyzing these nanostructures, while Mayavi offers a high-level 3D visualization interface built on visualization toolkit (VTK). The attempts to generate structurally accurate CNTs and graphene lattices revealed several critical challenges, including improper bonding representation, lattice distortions, and scaling inconsistencies. Moreover, the study presents the implementation strategies, code structure, and visual output limitations encountered during the modeling process. To provide a comparative landscape, additional tools such as Matplotlib (for 2D visualization), VPython (for quick atomic modeling), and atomic simulation environment (ASE) are briefly evaluated. The study also describes the role of NumPy, SciPy, and Pymatgen in computational geometry, structural logic, and periodic boundary condition (PBC) modeling.
Integrating municipal solid waste (MSW) treatment with chemical looping combustion technology offers a promising strategy for energy recovery and pollution/carbon reduction. While pyrolysis serves as the crucial first step in this process, its fundamental reaction mechanisms remain incompletely understood. This study employs ReaxFF molecular dynamics simulations to investigate early-stage pyrolysis behaviors of MSW, focusing on the effects of temperature and H2O/CO2 additives on pyrolysis characteristics and nitrogen transformation pathways. The results indicate that inorganic gas yields increase with temperature, while among organic gases, C2H4 demonstrates both the earliest formation and the highest yield. The maximum gas yield (60.4%) and light tar production (32.9%) occur at 2500 K. 10 wt% CO2 and 10 wt% H2O enhance organic gas production. The promoting effect of H2O is more pronounced, increasing the output of organic gases by 4.9% while promoting the decomposition of heavy oil and char. Nitrogen migration analysis reveals a progressive transformation from char-N to gas-N with increasing temperature. Under continuous high-temperature conditions, these N compounds further convert into NH3 and CH3N. This atomic-level investigation provides insights into the pyrolysis behavior of multi-component waste, offering theoretical support for further studies on the interaction between pyrolysis products and oxygen carriers. In the Forcite module of Materials Studio, the COMPASS II force field is employed to perform geometric optimization and annealing for the construction of the MSW models. ReaxFF MD calculations are conducted using the ReaxFF module within the Amsterdam Modeling Suite computational platform. Force field parameters for H/C/O/N/S/B are adopted, and temperature is controlled via the Berendsen thermostat.
Mitogen-activated protein kinase kinase kinase 7 (MAP3K7), also known as transforming growth factor-β-activated kinase 1 (TAK1), is a widely expressed kinase that plays a crucial role in various cellular processes variants in the MAP3K7 gene have been implicated in two distinct genetic disorders: frontometaphyseal dysplasia Type 2 (FMD2) and cardiofaciocutaneous syndrome (CSCF). To elucidate the consequences of the MAP3K7 variant, we investigated a Chinese family with CSCF harboring a novel heterozygous MAP3K7 variant and examined the genotype-phenotype correlation. Functional validation was performed using clinical evaluations, whole-exome sequencing (WES), and biochemical assays, including western blotting to assess TAK1 phosphorylation levels and downstream signaling pathways. Clinical data and genomic DNA were collected from the proband and family members. WES identified a novel heterozygous variant in MAP3K7 (NM_145331.3: c.149 T > C, p.Val50Ala) inherited from the affected mother. Sequence conservation analysis revealed that the Val50 residue is highly conserved among vertebrates and is critical for ATP binding. Protein 3D modeling predicted that the Val50Ala variant disrupts the kinase domain structure, potentially impairing TAK1 function. In vitro overexpression experiments in human embryonic kidney 293T (HEK293T) cells demonstrated that the Val50Ala variant significantly reduced TAK1 phosphorylation levels. Furthermore, this variant differentially affected downstream signaling molecules (p38, p65, and JNK) compared with variants causing FMD2. Notably, stimulation with transforming growth factor-β (TGF-β) partially restored the altered phosphorylation patterns, suggesting a potential compensatory mechanism. Our study provides novel insights into the molecular pathogenesis of MAP3K7 variants associated with CSCF and FMD2. We demonstrate that the p.Val50Ala variant impairs TAK1 kinase activity and differentially affects downstream signaling pathways. These findings highlight the distinct molecular fingerprints of MAP3K7 variants causing CSCF versus FMD2 and underscore the importance of considering MAP3K7 variants in the differential diagnosis of syndromic congenital cardiac defects, recurrent infections, and global developmental delays. Our results also suggest that TGF-β signaling may offer a potential therapeutic target for modulating the effects of MAP3K7 variants.
Chronic diabetic foot ulcers (DFUs) are associated with the collapse of endogenous bioelectric field gradients and redox-compromised wound microenvironments, conditions under which externally applied electroceutical stimulation and reactive oxygen species (ROS)-dominated photodynamic therapies become ineffective or deleterious. This limitation motivates the search for intrinsic, bias-free mechanisms capable of generating localized bioelectric-scale fields using benign external energy inputs. At photoactive organic-semiconductor interfaces, excited-state intramolecular proton transfer (ESIPT) offers a pathway by which molecular photophysics may be converted into interfacial electrostatic modulation, yet this transduction mechanism has not been formulated within a rigorous quantum-electrostatic framework. Here, we develop a first-principles quantum modeling framework establishing the Stokes-Induced Stark Effect (SISE) at quercetin-ZnO interfaces as a bias-free mechanism for interfacial electric field generation. Visible-light excitation of chemisorbed quercetin induces ultrafast ESIPT-driven Stokes relaxation, accompanied by excited-state dipole reconfiguration (Δµ ≈ 5-15 D, τ ≈ 100 fs). This time-dependent dipole couples electrostatically to ZnO surface states, generating localized interfacial Stark fields of order 105-106 V·m⁻1. Using a composite molecular-semiconductor Hamiltonian incorporating dielectric screening and surface-state quantization, we show that although instantaneous fields are strongly attenuated in physiological media (Debye length λ D ≈ 0.8 nm), spatiotemporal integration via dipole-density gradients and continuous low-intensity illumination yields effective quasi-static comparable in magnitude to endogenous bioelectric signals at the interface ( E eff ≈ 50 - 500 V · m - 1 ). The model explicitly avoids assumptions of static field penetration and instead delineates a defined operational window (coverage factor η ≈ 0.3-0.7; illumination < 10 mW·cm⁻2) in which electrostatic guidance dominates over ROS-driven photochemistry. The framework provides quantitative design constraints and experimentally testable predictions, establishing SISE as a physically plausible molecular photophysics-driven route for bias-free bioelectric modulation, with chronic wound repair serving as a representative application context.
The complex formation between peptides and nucleosides underlies the molecular recognition and regulation processes in biological systems. The present study focuses on the optimized structures of complexes formed between the glycyl-L-glutamate and four nucleosides-adenosine, guanosine, cytidine, and uridine. The most stable structures are found for complexes in which the preferred binding sites and the relative strength of hydrogen bonds are established. The terminal charged NH3+ and γ-COO- groups, as well as the amide fragment, can act as H-bonding sites in a peptide. The functional groups NH2, NH, CO, and N in nucleosides are potential H-bonding sites for the peptide. Unlike nucleobases, the hydroxyl groups of the ribose moiety in nucleoside molecules are additional H-bonding sites. The involvement of each of these groups depends on the complementarity of the peptide and nucleoside structures. The peptide affinity for nucleosides increases in the series: cytidine > guanosine > adenosine > uridine. The preference of each nucleoside depends on the balance of contribution from the structure rearrangement and intermolecular interaction, including electrostatic, orbital, dispersion interactions, and Pauli repulsion. The study combines DFT/B97-D/6-311++G(3d,3p) calculations with topological (QTAIM) and energy decomposition (EDA) analyses to investigate ion-molecular complexes between the tripolar anion of glycyl-glutamic acid and the neutral nucleosides. Solvation effects were taken into account within the PCM (water) model. Several initial structures with different coordination modes were generated according to the molecular electrostatic potential (MEP) distribution. Hydrogen bond parameters were obtained from the properties of bond critical points. The interaction energies and complex formation energies were determined to estimate the stability of the systems. Energy decomposition analysis (EDA) performed using the ORCA software allowed the contributions of electrostatic, polarization, dispersion, and Pauli repulsion components to the total interaction energy to be separated.
Boron clusters are of significant interest due to their inherent fluxionality and aromaticity. Among them, the B4 unit exhibits a unique dynamic behavior, interconverting between a square-shaped transition state (TS, D4h) and a diamond-shaped ground state (GS, D2h). This dynamic motif also plays a pivotal role within the cationic B13+ molecular rotor, where the B4 subunit acts as a driving element in the rotational motion of the outer B10 ring around the inner B3 core which are analogous to the rim and axle of a wheel. The present study aims to establish a dynamic correlation between the isolated B4 cluster and that of the B13+ cluster containing embedded B4 units within it, using Born-Oppenheimer Molecular Dynamics (BOMD) simulations. The key observation is a recurring diamond-square-diamond (DSD) to diamond-diamond (DD) transformation involving multiple B4 units, which governs the stepwise rotation of the B13+ cluster. By comparing the timescales and change in bonding pattern studied through AdNDP analysis, a direct correspondence between dynamics of isolated B4 cluster and that of B13+ cluster has been revealed. This study highlights the fundamental role of the intrinsic dynamics of the B4 unit in orchestrating the collective rotational behavior of the B13+ molecular rotor containing multiple B4 subunits. All quantum chemical calculations were carried out using Density Functional Theory (DFT) as implemented in Gaussian 09 (Revision D.01). Geometry optimizations and frequency analyses were performed using the PBE1PBE hybrid functional in conjunction with the 6-311+G(d) basis set. To ensure accurate determination of stationary points, a superfine integration grid and very tight convergence criteria were applied throughout. Minimum energy structures (NImag = 0) and transition states (NImag = 1) for both the B4 and B13+ clusters were identified based on vibrational frequency analysis. Born-Oppenheimer Molecular Dynamics (BOMD) simulations were also performed within Gaussian 09 to investigate the real-time structural dynamics of the clusters. Simulations were conducted under an NVE ensemble by coupling the system to a thermal reservoir at 150 K. Each cluster was propagated over a 5000-fs timescale to capture thermally driven transformations. To explore the bonding evolution during structural transitions, Adaptive Natural Density Partitioning (AdNDP) analysis was conducted using the Multiwfn3.8 program. Electron density distribution plots were also generated via Multiwfn to visualize bonding changes and electronic flux during dynamic processes.
The multiscale modeling of charge carrier dynamics in amorphous organic semiconductors is fundamentally challenged by the inherent sampling limitations of atomistic morphologies. This work provides a critical investigation into how finite-size artifacts in molecular dynamics (MD) supercells introduce spurious anisotropy in carrier transport, even in systems comprising as many as 2000 molecules. I demonstrate that off-lattice kinetic Monte Carlo (kMC) simulations based on Marcus transfer theory often yield directionally biased mobility values that lack physical consistency under low-field strengths due to these scale-dependent constraints. To address these limitations, I propose an on-lattice kMC framework that reconstructs the local molecular environment while preserving the essential statistical features of the disordered system. Compared to conventional off-lattice approaches, the presented method offers a more stable and representative description of the field-dependent mobility across varying MD cell sizes. This study highlights the necessity of accounting for finite-size effects in multiscale workflows and establishes lattice-based reconstruction as a practical alternative for achieving statistically reliable transport simulations. Amorphous morphologies of 4,4'-bis(N-carbazolyl)-1,1'-biphenyl (CBP) were generated for system sizes ranging from 250 to 2000 molecules using Desmond MD simulations with the OPLS4 force field. Marcus transfer parameters were calculated via density functional theory (DFT) using the Amsterdam Density Functional (ADF) package at the PW91/TZ2P level and Gaussian software at the B3LYP/6-311G** level. Charge carrier transport was then simulated via in-house kMC codes to investigate the resulting carrier dynamics. The proposed on-lattice framework was compared with the conventional off-lattice approach in terms of transport isotropy and sampling efficiency.
In this contribution, we investigate the stability of boron phosphide in various low dimensional forms ranging from the 3D bulk, the 2D slab model to the 1D single- and multi-walled zigzag nanotubes. A variety of energetic and geometric parameters including relaxation, cohesive and formation energies, polarisability, piezoelectric and elastic tensors components, and equilibrium lattice parameters have been reported. All arrangements are confirmed to exhibit a relatively wide band gap with properties dependent of geometric parameters. A connection between the 2D phonon modes and those of the 1D zigzag nanotubes has been established. Comparisons between IR and Raman of the single- and multi-walled nanotubes reveal that symmetry reduction leads to more active modes. By contrast, we found that angles and bond lengths only slightly deviate from those of the 1D single-walled nanotubes. By increasing the number of walls, the low frequency phonon modes become softer and shift toward lower wavelengths while high frequency phonon modes become harder with a blue shift owing to possible mechanical distortions that could occur between walls. These outcomes are expected to guide and motivate both experimentalists and theorists to design and optimize new emerging low dimensional inorganic materials for next generation nanodevices. All computational modeling has been performed based on the density functional theory methodology with the B3LYP hybrid functional as implemented in the CRYSTAL23 program. The electronic wave-functions of the periodic 3D, 2D and 1D boron phosphide ground state are expressed with Bloch functions which are constructed as linear combination of Gaussian local type functions. Let us recall that the mode frequencies at the center of the Brillouin zone are obtained from the diagonalization of the mass-weighted Hessian matrix of the second derivatives of the total energy per cell with respect to atomic displacements. Therefore, IR and Raman spectra of all arrangements are simulated using the Coupled Perturbed Hartree-Fock or Kohn-Sham CPHF/KS approach.
CL-20/BMDNP eutectic explosive is a late-model explosive with excellent energy density and detonation parameters, but it still has higher sensitivity than TATB and FOX-7. In an attempt to reduce the sensitivity of CL-20/BMDNP eutectic explosive, a CL20/BMDNP eutectic model was installed in the paper. Polymer-bonded explosives (PBXs) were obtained by adding five different types of polymers, such as butadiene rubber (BR), ethylene-vinyl acetate copolymer (EVA), polyethylene glycol (PEG), fluoropolymer (F2603), and polyvinylidene difluoride (PVDF), to six cleavage surfaces(1 0 0), (0 0 1),(0 1 1),(0 -1 1), (1 1 0), and (1 -1 0), respectively. The sways of various polymers on the stability, trigger bond length, mechanical properties, and detonation properties of PBXs were predicted. The CL-20/BMDNP/PEG model has maximum binding energy and minimum trigger bond length among the five PBX models, manifesting that the CL-20/BMDNP/PEG model has tip-top stability, compatibility, and lowest sensitivity. Besides, despite the CL-20/BMDNP/F2603 model exhibiting exceptional detonation competences, it is supposed to denote that this model revealed a low level of compatibility. In conclusion, the CL-20/BMDNP/PEG model showed better integrated capacities, indicating that PEG is a more appropriate binder choice for PBXs on the basis of the CL-20/BMDNP cocrystal. The molecular dynamics (MD) simulation method was used to investigate the properties of CL-20/BMDNP eutectic and its PBXs composites. All simulations were performed in the Materials Studio software platform. The COMPASS force field suitable for energetic materials was selected in the simulation process. The system was first equilibrated under the Isothermal-isobaric (NPT) ensemble at 295 K; the simulation duration was 2 ns, and the integration step was 1 fs.
Hexamethyldisilane (HMDS) serves as a critical single-source precursor for the chemical vapor deposition (CVD) of silicon carbide (SiC), yet its atomic-level pyrolysis mechanism and the kinetics of radical generation remain unclear. This study investigates the thermal decomposition behavior of HMDS to provide theoretical guidance for optimizing SiC deposition processes. The results demonstrate that HMDS pyrolysis follows first-order kinetics with an apparent activation energy of 44.47 kcal/mol, a value significantly lower than the theoretical dissociation energy of the Si-Si bond. By combining this kinetic data with reaction pathway analysis, it is concluded that the decomposition is governed by a multistep cooperative mechanism rather than simple homolytic bond cleavage. The reaction proceeds through three distinct stages: initial precursor decomposition dominated by C-Si bond dissociation, secondary reactions of intermediates involving cascading demethylation, and small-molecule formation accompanied by radical recombination. Methyl radicals (CH3) are identified as the primary chain carriers, which are ultimately converted into thermodynamically stable methane (CH4) via hydrogen abstraction. Furthermore, temperature is found to critically regulate the generation and accumulation behavior of CH3 radicals. Density functional theory (DFT) calculations were carried out with Gaussian 16 at the unrestricted ωB97XD/6-311G(d,p) level to optimize geometries and train the force field. A broken-symmetry strategy with guess = (mix,always) and nosymm was adopted to reliably describe bond dissociation and radical behaviors. Using the high-quality DFT data, the ReaxFF force field was further optimized. Reactive molecular dynamics simulations were then performed in LAMMPS with the optimized potential under the NVT ensemble at 2500-4000 K with a 0.1-fs time step. A cubic box with 100 HMDS molecules and periodic boundary conditions was adopted, and each condition was run three times for statistical reliability.
High-energy-density materials (HEDMs) with balanced energy, stability, and safety are central to modern defense and civilian energetic applications. Among nitrogen-rich heterocyclic frameworks, oxadiazole rings stand out for their high formation enthalpy, oxygen balance, and structural tunability-making them ideal building blocks for next-generation energetic materials. However, the isomeric effect on molecular structure, electron distribution, and response to external stimuli (e.g., electric fields) remains poorly understood, despite its critical role in predicting sensitivity, detonation behavior, and environmental stability. In this study, the structural response and electronic properties of PA-1~PA-3 under an electric field were studied by a theoretical calculation system. The results showed the following: First, in terms of molecular structure response, PA-1 showed significant nonlinear changes, PA-2 only mutated at a specific field strength (0.010 a.u.) due to amino modification, while PA-3 maintained optimal stability by virtue of azide groups; second, the polarization characteristic analysis showed that the linear polarizability of PA-1 reached the peak at 0.020 a.u. field strength, PA-2 showed nonlinear behavior, and PA-3 showed the lowest sensitivity; third, weak interaction studies show that the C1 atom dominates the interaction of molecular fragments, and different functional groups significantly affect the electric field adaptability of materials; fourth, the electronic structure analysis revealed that PA-3 had the strongest resistance to an electric field, and its HOMO-LUMO energy gap had the smallest change. This study clarified the molecular mechanism of functional groups regulating the electric field response of materials and provided theoretical guidance for the design of new electric field response materials. Using density functional theory, the B3LYP/6-311+G(d, p) method was employed for structural optimization. After optimizing convergence, ensure that there are no imaginary frequencies to obtain a stable structure. Wave function analysis was performed using Multiwfn 3.8 and VMD 1.9.3. The EEF strength ranged from 0 to 0.02 a.u., with a growth gradient of 0.005 a.u.
The behaviour of gas molecules in nanopore materials is essential for research in gas separation, catalytic reactions, and nanofluidic transport. However, controlling gas dynamics at the nanoscale, especially in charged nanopores, remains a significant challenge. Through molecular dynamics simulations, this study reveals that external electric fields can synergise with the surface properties of charged nanotubes to regulate the distribution and aggregation behaviour of gases inside the nanotubes. Increasing the wall charge density of the nanopore leads to gas aggregation and the formation of nanobubbles at the tube centre, thereby obstructing water flow. In contrast, applying an axial external electric field weakens the stability of nitrogen bubbles, causing collapse and reopening the liquid transport channel. The formation and distribution of ordered water layers on nanopore walls is a key influencing factor on the dynamic behaviour of gases within nanotubes. This interfacial structure enables regulating gas adsorption and desorption, as well as liquid flow blockage or activation, by the combined modulation of surface charge and external electric fields. These insights provide a reference for designing electrically controlled nanofluidic valves in electrically charged nanopore materials, a technology with strong relevance to applications such as gas storage, sensing, and integrated nanofluidic systems. Classical molecular dynamics simulations were performed using GROMACS 2021.5 in NVT ensemble at 300 K for the water-N₂ system in an uncapped (40,40) carbon nanotube. The nanotube wall was implemented by alternating ± q charges on diagonally adjacent sites of neighbouring hexagons (q = 0-1.4 e/atom in 0.2 e/atom increments), resulting in a net neutral nanotube. The GROMOS43a1 force field was employed for system interactions, and water molecules were modelled using the SPC/E model. Electrostatic interactions were handled using the Particle-Mesh Ewald (PME) method with a real-space cutoff of 10 Å; van der Waals forces were similarly truncated at 10 Å. A uniform static axial electric field in the + z direction was simultaneously applied, with magnitudes varying from 0.00 V/Å to 0.10 V/Å at an interval of 0.01 V/Å. Data, including density distribution, water flux, and water molecule orientation/hydrogen bond counts, were extracted via Python/C +  + scripts. Model Structure and trajectories were visualised using VMD 1.9.3 software.
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. 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.