Journal of Molecular Modeling最新文献

{"title":"Compatibility between twin-screw desulphurized crumb rubber and asphalt binder based on molecular dynamics simulation","authors":"Bo Li,&nbsp;Wenli Liu,&nbsp;Hui Dou,&nbsp;Jingzhuo Zhao,&nbsp;Jihong Han,&nbsp;Liangying Li","doi":"10.1007/s00894-026-06907-0","DOIUrl":"10.1007/s00894-026-06907-0","url":null,"abstract":"<div><h3>Context</h3><p>The widespread application of crumb rubber modified asphalt is limited by its inadequate storage stability, which is largely governed by the compatibility between the asphalt binder and crumb rubber. This study investigated the influence of desulphurized crumb rubber with different solubility on the compatibility and storage stability of modified asphalt by combining molecular simulations with experimental validation. The results demonstrate that the compatibility between desulphurized crumb rubber and asphalt is strongly dependent on solubility when the difference in solubility parameter exceeds approximately 1.5 (J·cm⁻³)^1/2. Desulphurized crumb rubber with a solubility of approximately 28.66 exhibited the highest interfacial binding energy, reduced phase separation, and improved storage stability, whereas excessive desulphurization decreased interfacial binding energy and increased the tendency for phase separation.</p><h3>Methods</h3><p>Molecular dynamics (MD) simulations and density functional theory (DFT) calculations were performed using Materials Studio 2023. MD simulations were carried out with the Forcite module using the COMPASS III force field. Following geometry optimization and annealing, the systems were equilibrated under the NPT and NVT ensembles, and the solubility parameter, interaction energy, mean square displacement, and fractional free volume were calculated. DFT calculations were performed using the DMol³ module with the BLYP functional within the generalized gradient approximation (GGA) to investigate the intermolecular interactions. Desulphurized crumb rubber with different solubility was prepared by a twin-screw extrusion process, and the simulation results were validated using the separation softening point difference and multi-stress creep recovery (MSCR) tests.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 9","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148872621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the polymorphism and optoelectronic properties of coumarin via high-throughput computational screening","authors":"Yanshuang Zhao,&nbsp;Zhenyu Liu,&nbsp;Yan Lv","doi":"10.1007/s00894-026-06928-9","DOIUrl":"10.1007/s00894-026-06928-9","url":null,"abstract":"<div><h3>Context</h3><p>Coumarin and its derivatives are privileged scaffolds in medicinal chemistry, yet their polymorphism poses significant challenges in pharmaceutical solid-form development. This work explores the crystal polymorphs and optoelectronic properties at ground state of coumarin. The crystal energy landscape of coumarin was constructed, identifying P4₃, Pccn, and P4₂bc as the dominant competing polymorphic structures. Electronic structure calculations reveal that the symmetry of crystal packing and intermolecular interactions significantly modulate the optical absorption edge and spectral response range, with the P4₃ phase exhibiting the smallest band gap (2.69 eV) due to its unique helical packing arrangement.</p><h3>Methods</h3><p>Crystal structures were generated using the PyXtal library across 230 space groups. High-throughput geometric optimization was performed using the universal machine learning interatomic potential DPA-3. Low-energy candidate structures were further refined via density functional theory (DFT) calculations using the Quantum ESPRESSO package with the PBE functional and DFT-D3 dispersion correction. Optical properties were derived from the complex dielectric function computed from first principles.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 9","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148872543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular insights into conformational and structural properties of diblock copolymer nanoparticles: a high-resolution RIS-based Monte Carlo study on a high-coordination lattice","authors":"Krisana Monklang,&nbsp;Visit Vao-soongnern","doi":"10.1007/s00894-026-06918-x","DOIUrl":"10.1007/s00894-026-06918-x","url":null,"abstract":"<div><h3>Context</h3><p>Monte Carlo (MC) simulations reveal that diblock copolymer nanoparticle morphology is dictated by the interplay between intermolecular attractions and soft confinement. Blocks with stronger cohesive interactions undergo local densification in the core, while blocks with weaker interactions localize at the surface. A key stabilizing mechanism is the expulsion of high-mobility end-monomers toward the interface to maximize cohesive energy in the bulk. This process is accompanied by a backbone <i>gauche</i>-to-<i>trans</i> conformational transition that enables polymer chains to flatten tangentially and adapt to nanoparticle curvature. By quantifying radial density profiles, structural anisotropy, and energetic oscillations, the methodology distinguishes morphologies ranging from surface-energy-driven mixing to frustrated core–shell segregation, providing molecular-level insight for the rational design of functional polymeric nanostructures.</p><h3>Methods</h3><p>MC simulation of the coarse-grained (CG) models based on “polyethylene-like” chains mapped onto the second nearest neighbor diamond (<i>2nnd</i>) lattice was employed to investigate conformational and structural properties of diblock copolymer nanoparticles. The model integrates a revised Rotational Isomeric State (RIS) model to define backbone bond conformations and discretized Lennard–Jones (LJ) potential energy settings to systematically vary intermolecular interaction parameters. Free-standing nanoparticles were equilibrated using single bead moves and the Metropolis criterion over 40 million Monte Carlo steps, and data analysis was based on snapshots collected at intervals of 10,000 MCS. All simulations and data analysis were performed using in-house FORTRAN codes with the gfortran compiler.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 9","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148872558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analytical coarse grained potential parameterization by reinforcement learning for anisotropic cellulose","authors":"Xu Dong","doi":"10.1007/s00894-026-06909-y","DOIUrl":"10.1007/s00894-026-06909-y","url":null,"abstract":"<div><h3>Context</h3><p>Cellulose nanocrystals (CNCs) are a type of cellulose with excellent mechanical performance and other advantageous attributes. According to previous reports, hydrogen bonds play a pivotal role in the anisotropic structure of the CNC. Understanding the structure and mechanical behavior of CNC on a mesoscopic scale is critical for the development and manufacture of cellulose materials. However, experimental observations and atomistic simulations are not appropriate on the mesoscopic scale. In this study, we introduce an analytical coarse-grained (CG) potential following an extended bottom-up approach that is directly parameterized using reinforcement learning (RL). RL is a powerful tool for industrial and academic applications in various fields. Nevertheless, the potential of RL has not yet been fully exploited in the field of molecular dynamics. The RL and Boltzmann inversion methods were employed to develop a novel CG model of cellulose to represent its anisotropy and polymer stiffness. The resulting approximate CG model is not limited to the specific properties used for training; it can reproduce the dynamic mechanical properties under various conditions without further optimization. This model confirms that RL can construct a CG potential that is both physically interpretable and powerful. The training code is available at https://github.com/EiPiFun/rl-cll-cg.</p><h3>Methods</h3><p>All atom (AA) reference molecular dynamics simulations were conducted using GROMACS with CHARMM36 force field, utilizing CHARMM-GUI tools to generate the necessary force field files. Coarse-grained (CG) simulations were performed using LAMMPS, employing a custom-defined explicit analytical force field. This potential consists of harmonic bonded interactions, 12–6 Lennard–Jones nonbonded interactions, and a modified 12–10 potential to account for directional hydrogen bonding. Initial estimates for bonded force constants were derived using the Boltzmann inversion method. The CG potential parameters were parameterized via a degenerate reinforcement learning (RL) approach employing the soft actor-critic (SAC) algorithm, implemented through the OpenAI Stable-Baselines3. To assess mechanical performance and model generalization, steered molecular dynamics techniques were utilized to simulate in-plane and out-of-plane fractures. For benchmarking purposes, baseline CG models were generated using the iterative Boltzmann inversion (IBI), relative entropy (RE), and force matching (FM) approaches via VOTCA, while the MARTINI 3 model was prepared using Polyply. Further validation of the optimization strategy was performed by comparing the RL approach against Tree-structured Parzen Estimator (TPE) and Covariance Matrix Adaptation Evolution Strategy (CMAES) algorithms using OPTUNA. All molecular structures were visualized using Open-Source PyMOL.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 9","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148863200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adsorption characteristics of Cl, H2O, and O2 on Cu(111) and their implications for initial corrosion susceptibility: a density functional theory study","authors":"Yanxun Wu,&nbsp;Ting Gao,&nbsp;Lei Niu,&nbsp;Jianyi Xue,&nbsp;Qinwen Ye","doi":"10.1007/s00894-026-06895-1","DOIUrl":"10.1007/s00894-026-06895-1","url":null,"abstract":"<div><h3>Context</h3><p>Chloride-containing species, H₂O, and O₂ are important environmental factors during the initial atmospheric corrosion of copper. In the present work, Cl⁻ adsorption on Cu(111) was first investigated using a fully relaxed Cu model to characterize chloride-induced structural reconstruction and electronic activation. H₂O and O₂ were subsequently introduced to examine their additional co-adsorption effects on the chloride-affected Cu surface under simplified conditions representing humid and oxygen-containing environments. The introduction of Cl⁻ induces pronounced local Cu-atom displacement, surface reconstruction, lattice distortion, and redistribution of the Cl-derived and Cu-derived electronic states. The subsequent addition of H₂O and O₂ further modifies the adsorption geometry and interfacial electronic environment. These results provide atomistic insight into chloride-induced surface activation relevant to the initial stage of copper corrosion, but they are not interpreted as direct proof of Cu dissolution or crystalline copper-chloride formation.</p><h3>Methods</h3><p>Density functional theory calculations were performed using a three-layer, nonuniform Cu(111)-derived model containing 121 Cu atoms. Two structural-relaxation protocols were adopted according to the purposes of the calculations. For the initial Cl⁻/Cu(111) systems used to examine chloride-induced reconstruction, all Cu atoms and the Cl⁻ species were allowed to relax without positional constraints. After the optimized Cl/Cu(111) configuration had been obtained, H₂O and O₂ were introduced sequentially. In the subsequent co-adsorption calculations, all adsorbates and the Cu atoms in the outermost layer were allowed to relax, whereas the lower two Cu layers were fixed. Optimized structures, relaxation-inclusive adsorption energies, Hirshfeld charge redistribution, work-function changes, interlayer displacements, total density of states, and projected density of states were analyzed to characterize the structural and electronic responses of the investigated systems.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 9","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148863230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical study of the effect of the inclusion of aromatic heterocyclic compounds in Cu(I) complexes: structure, optoelectronics, and adsorption properties, and their evaluation as dyes in DSSCs","authors":"Ricardo Moreno-Inzunza,&nbsp;Juan Pedro Palomares-Báez,&nbsp;Rody Soto-Rojo,&nbsp;Tomás Delgado-Montiel,&nbsp;Samuel Soto-Acosta,&nbsp;Manuel Luque-Román,&nbsp;Nora Aydee Sánchez-Bojorge,&nbsp;Daniel Glossman-Mitnik,&nbsp;Jesús Baldenebro-López","doi":"10.1007/s00894-026-06932-z","DOIUrl":"10.1007/s00894-026-06932-z","url":null,"abstract":"<div><h3>Context</h3><p>A theoretical investigation of 28 homoleptic Cu(I) complexes was conducted to assess their suitability as sensitizers in dye-sensitized solar cells (DSSCs). Two ligand families, triazolylpyridine (G1) and imidazopyridine–pyridine (G2), were systematically functionalized with heteroaromatic substituents derived from pyridine, furan, pyrrole, and thiophene. Pyridine- and thiophene-based spacers produced substantial bathochromic shifts in the absorption maxima, which reached 492 nm, and reduced the HOMO–LUMO energy gaps to values as low as 3.33 eV. These modifications also decreased the chemical hardness (η) and increased the electrophilicity (ω), thereby promoting intramolecular charge transfer and enhancing electron-accepting ability. In contrast, furan- and pyrrole-derived substituents induced only minor electronic changes but increased the propensity to form dual-bidentate or multidentate adsorption motifs on TiO₂ surfaces, resulting in stronger interfacial binding. An integrated DSSC index (D_i), combining structural, optoelectronic, reactivity, and photovoltaic parameters, identified the G2 family as the most favorable structural framework, with G2ANNC (D_i = 0.6096) emerging as the leading sensitizer candidate. Overall, these results demonstrate the potential of these Cu(I) complexes for DSSC applications and provide a systematic framework for their rational design.</p><h3>Methods</h3><p>Minimum-energy geometries were determined in ethanol using the M06 functional, with the 6-31G(d) basis set for nonmetal atoms, the DZVP basis set for Cu, and the IEF-PCM solvation model as implemented in Gaussian 16. UV–Vis transitions and excited-state energies were calculated by TD-DFT at the same level of theory for 20 excited states. Electronic transitions were analyzed using AOMix, whereas hole − electron distributions and natural transition orbitals were evaluated using Multiwfn. Photovoltaic parameters, including the light-harvesting efficiency (LHE), excited-state lifetimes, and thermodynamic driving forces for electron injection, dye regeneration, and recombination, were quantified. Bulk anatase TiO₂ and an expanded (TiO₂)₉₆ slab were optimized using the <i>tiorg-0–1</i> and <i>mio</i> parameter sets in DFTB + 24.1. Slab reoptimization and dye–surface interactions were evaluated using GFN1-xTB at the Γ point. The candidates were globally evaluated and ranked using a custom Python script. Molecular and crystal structures were visualized using VESTA 3.90.5a.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 9","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148863187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Car–Parrinello molecular dynamics of QMAP-DMSO microsolvation: first-shell structure and solvent-induced polarization","authors":"Renato Medeiros,&nbsp;Francisco A. P. Osório,&nbsp;Clodoaldo Valverde,&nbsp;Ademir J. Camargo","doi":"10.1007/s00894-026-06920-3","DOIUrl":"10.1007/s00894-026-06920-3","url":null,"abstract":"<div><h3>Context</h3><p>Directional solute–solvent contacts can influence the electrostatic response of donor–acceptor chromophores, although such local effects are often represented only as averaged contributions in continuum solvent models. Quinolinylaminophenol (QMAP) in dimethyl sulfoxide (DMSO) was examined as an explicit first-shell microsolvation model to clarify how local solvent organization couples to QMAP conformation and dipolar response. The Car–Parrinello molecular dynamics trajectory indicates a geometric reorganization around 12–13 ps, accompanied by changes in the first-shell DMSO dipolar arrangement. Within the limitations of the finite microsolvated model, these results suggest that transient first-shell solvent organization contributes to the modulation of the local electrostatic environment of QMAP, rather than acting only as a static dielectric background.</p><h3>Methods</h3><p>The gas-phase QMAP geometry was optimized at the CAM-B3LYP/6–311 + + G(d,p) level using Gaussian 16. The explicit QMAP–DMSO model contained one QMAP molecule and 21 DMSO molecules in a periodic cubic cell and was propagated by Car–Parrinello molecular dynamics using the CPMD code. The production trajectory was obtained with the PBE exchange–correlation functional, Troullier–Martins norm-conserving pseudopotentials, a plane-wave basis set, NVT equilibration at 300 K, and a restarted thermostatted CPMD production protocol, with a total analyzed trajectory length of approximately 32 ps. Structural, hydrogen-bond, dipole-moment, IR-like, and orientational-correlation analyses were carried out using in-house Python scripts.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 9","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06920-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DFT study of selective hydrogenation of non-conjugated dienes on a Pd surface: the case of 2,5-norbornadiene","authors":"Ravshan S. Shamsiev,&nbsp;Varvara A. Gomonyuk,&nbsp;Vitaly R. Flid","doi":"10.1007/s00894-026-06905-2","DOIUrl":"10.1007/s00894-026-06905-2","url":null,"abstract":"<div><h3>Context</h3><p>In this work a DFT modeling of various routes of hydrogenation of a non-conjugated bicyclic diene—norbornadiene (NBD)—was carried out using the all-electron scalar-relativistic approximation. According to calculations, the determining role in selective hydrogenation of NBD to norbornene (NBE) belongs to the type of palladium surface and adsorption configuration (exo or endo) of NBD and NBE molecules. Pd(111) surface shows selectivity in NBD adsorption, as well as activity in selective hydrogenation of NBD to NBE. Gibbs activation energies of hydrogenation of NBD to NBE and NBE to NB on Pd(111) differ by 4.3 kcal/mol in favor of the former route, which determines the selectivity of NBD hydrogenation. Formation of byproduct nortricyclane (NTC) involves overcoming a large Gibbs activation energy (29.2 kcal/mol), explaining its experimental trace amounts. Despite the high selectivity of Pd(100) surface in NBD adsorption, it is almost inactive in its hydrogenation. Notably, Gibbs activation energy of hydrogenation route of NBD to NBE on Pd(100) is 5.2 kcal/mol higher than that of NBE to NB on Pd(100) and 9.2 kcal/mol higher than that of NBD to NBE on Pd(111). Despite the significant increase in the adsorption energies of NBD and NBE, that was calculated with Grimme’s D3 dispersion corrections, most of this difference is compensated when calculating activation energy.</p><h3>Methods</h3><p>Main DFT calculations were carried out using the scalar-relativistic approximation. The PBE exchange–correlation functional and all-electron basis sets L2 for C and H atoms and L11 for Pd atoms were used. The Pd(111) and Pd(100) surfaces were modeled as 3-layered flat clusters Pd₇₀ and Pd₇₃, respectively. Geometry optimization for key intermediates and TSs using the PBE-D3(BJ) functional, def2-TZVP basis sets, and def2-ECP pseudopotentials was performed in ORCA 6.1.1 software. For the most energetically favorable adsorption configurations of NBD and NBE molecules, DFT-PBE and PBE-D3(BJ) calculations were performed under periodic boundary conditions in CP2K software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 9","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functionalized carbon nanotubes as nanoinhibitors of asphaltene aggregation: a molecular dynamics approach for enhanced oil recovery","authors":"Mohamed El Amine Boumeftah,&nbsp;Boumediene Bounaceur,&nbsp;Ali Rahmouni","doi":"10.1007/s00894-026-06910-5","DOIUrl":"10.1007/s00894-026-06910-5","url":null,"abstract":"<div><h3>Context</h3><p>Asphaltene aggregation and deposition pose major challenges in crude oil transport and processing. While extensive experimental studies have explored mitigation strategies, nanomaterials—particularly carbon nanotubes (CNTs)—have emerged as promising inhibitors due to their ability to adsorb asphaltenes and limit their clustering. However, experimental approaches provide limited insight into molecular-scale mechanisms. To address this, molecular dynamics (MD) simulations were performed to investigate interactions between model asphaltenes and CNTs in a toluene/heptane solvent. Five systems were studied: pristine CNTs and CNTs functionalized with carbamoyl (CONH₂), methylcarbamoyl (CONHCH₃), hydroxymethyl (CH₂OH), and carboxylate (COO⁻) groups. Intermolecular interactions and aggregation behavior were analyzed using radial distribution functions (RDF), solvent-accessible surface area (SASA), cluster analysis, hydrogen bonding, and interaction energy decomposition (van der Waals and electrostatic contributions). Results show that CNTs significantly modify asphaltene aggregation, with carboxyl-functionalized CNTs exhibiting the strongest inhibition effect. This performance correlates with enhanced specific interactions between functional groups and asphaltene molecules, leading to reduced aggregation.</p><h3>Methods</h3><p>Geometry optimizations and vibrational frequency calculations of toluene, heptane, the model asphaltene molecule, and the pristine carbon nanotube were performed using the Gaussian software package. These calculations were carried out within the framework of density functional theory (DFT) using the B3LYP functional and the 6-31G(d,p) basis set. The optimized structures obtained were subsequently used to construct the initial configurations for the molecular dynamics simulations and to derive Mulliken atomic charges for force-field parameterization. All-atom molecular dynamics simulations were performed using GROMACS 2023.3 and the OPLS-AA force field. After energy minimization using the steepest descent algorithm, the systems were equilibrated under NVT and NPT ensembles at 298.15 K and 1 bar. Production simulations were subsequently carried out for 150 ns using periodic boundary conditions and a 2 fs integration time step. Temperature and pressure were controlled using the velocity-rescaling thermostat and the Berendsen barostat, respectively. Long-range electrostatic interactions were treated using the Particle Mesh Ewald (PME) method, while bond constraints were maintained using the LINCS algorithm.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 9","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"β-antimonide phosphorus nanosheets as a sensing medium for quinone molecules—a first-principles study","authors":"V. M. Haripriyaa,&nbsp;V. Nagarajan,&nbsp;R. Chandiramouli","doi":"10.1007/s00894-026-06911-4","DOIUrl":"10.1007/s00894-026-06911-4","url":null,"abstract":"<div><h3>Context</h3><p>Using the density functional theory (DFT) method, we studied the adsorption behaviour of different toxic quinone molecules, including anthraquinone (AQ), naphthoquinone (NQ), and pyrenequinone (PQ), on β-antimonide phosphorus (β-SbP) nanosheet. Initially, we ascertained the geometrical stability of β-SbP with the support of formation energy, phonon band maps, and ab initio molecular dynamics (AIMD). The electronic attributes of β-SbP are investigated using band structure and projected density of states (PDOS) maps, and the energy gap is calculated to be 2.265 eV. The adsorption of quinone molecules induces a relative band gap variation of 33% to 60%. Among the studied quinone molecules, PQ exhibits the highest variation of 60.26% and 58.10% in parallel and perpendicular orientations, respectively. Furthermore, the sensing performance of quinone pollutants on β-SbP material is assessed using adsorption energy, Mulliken charge transfer, sensitivity, selectivity, and work function. The outcomes revealed that the nature of adsorption (chemisorption or physisorption) as well as the significant charge transfer observed in the ranges from 0.148 to 1.038 e, depending on the orientation of molecules adsorbed on β-SbP. A noticeable variation in the work function is observed for complex PQ1, which is recorded as 14.75%. Our findings reveal that β-SbP nanosheets are highly sensitive to these toxic quinones, indicating their suitability as an efficient sensing material.</p><h3>Methods</h3><p>In this work, all the simulations were carried out using the Quantum ATK package within the framework of the linear combination of atomic orbitals (LCAO) method with norm-conserving PseudoDojo pseudopotentials. We used hybrid GGA with the Heyd–Scuseria–Ernzerhof (HSE06) functional to study the structural, electronic, and adsorption properties of β-SbP nanosheet towards quinone pollutants. The energy and force convergence criteria were set to 10^–6 eV and 0.01 eV/Å, respectively. The vacuum distance was adjusted to <span>(20 mathrm{mathring{A}})</span> in order to eliminate the field effect of neighbouring layers. Also, the thermal stability of β-SbP nanosheet under ambient conditions and at elevated temperatures of 400 K and 500 K is explored using ab initio molecular dynamics (AIMD) simulations.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 9","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}