Journal of Molecular Modeling最新文献

{"title":"Diffusion mechanism of dissolved gases in transformer mineral oil under furfural effect","authors":"Jia Tao,&nbsp;Xiongying Duan,&nbsp;Peng Yu,&nbsp;Xubin Li,&nbsp;Minfu Liao,&nbsp;Jinjin Li","doi":"10.1007/s00894-025-06475-9","DOIUrl":"10.1007/s00894-025-06475-9","url":null,"abstract":"<div><h3>Context</h3><p>Dissolved gas analysis (DGA) technology is a crucial technique for evaluating the operational state of transformers by detecting characteristic gases dissolved in insulating oil. Notably, the aging of insulation paper generates both characteristic gases and furfural, which also dissolves into the oil. However, the influence of furfural on gas diffusion behavior remains unclear. This study systematically investigates the effects of different furfural concentrations (0%, 1%, 3%, and 5% by mass) on the diffusion behavior of characteristic gases in insulating oil using molecular dynamics (MD) simulations. By calculating diffusion coefficients, free volume, and interaction energies, the underlying microscopic mechanisms were revealed. The results indicate that increasing furfural content slightly raises the free volume of gas molecules, thereby facilitating gas diffusion. Furthermore, the binding energies between furfural and insulating oil, as well as between furfural and gas molecules, increase with furfural concentration—mainly due to van der Waals interactions between polar and non-polar molecules. This study provides theoretical insight into the diffusion behavior of characteristic gases in insulating oil containing furfural.</p><h3>Methods</h3><p>The MD simulations were conducted using Materials Studio 2023. The amorphous cell module was employed to construct insulating oil mixture models incorporating varying concentrations of furfural molecules, utilizing the COMPASS III force field. Simulation results yielded key parameters including the mean square displacement (MSD) of characteristic gas molecules and the fractional free volume (FFV) of the system. Intermolecular interaction energies were computed using a self-developed Perl script. The simulation results demonstrate that increasing furfural concentration in insulating oil significantly enhances the diffusion characteristics of dissolved gases at the molecular level.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144861534","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":"Influence of SiO2 nanoparticles grafted with surfactant on coal wetting properties and microscopic mechanism of action","authors":"Xiangjun Chen,&nbsp;Jiahui Xu,&nbsp;Peiqi Zuo,&nbsp;Yibo Li,&nbsp;Liyang Li,&nbsp;San Zhao","doi":"10.1007/s00894-025-06466-w","DOIUrl":"10.1007/s00894-025-06466-w","url":null,"abstract":"<div><h3>Context</h3><p>In coal mine spray dust suppression, conventional studies on individual surfactants or surfactant mixtures often fail to achieve optimal coal wettability enhancement. This study innovatively introduces SiO₂ nanoparticles and demonstrates through simulations that the nanoparticle-surfactant composite system substantially enhances coal wettability. Electrostatic potential analysis indicates that the modified nanoparticle molecules formed by surfactant-grafted nanoparticles are more likely to form stable structures with coal molecules, enabling the nanoparticles to be better fixed on the coal molecules and establish a stable adsorption configuration. When the surfactant-grafted composite structure adsorbs onto the coal surface, it significantly enhances water molecular diffusivity, facilitates increased hydrogen bond formation with the composite surface, and substantially strengthens the interaction energy between coal and surfactants. Moreover, nanoparticle incorporation leads to noticeable thickening of the coal wetting layer and a marked increase in water molecule density at the interface. The results conclusively demonstrate that this composite structure enhances coal wettability through three synergistic mechanisms: interface optimization, hydrogen bond reinforcement, and water molecule diffusion enhancement.</p><h3>Methods</h3><p>This study innovatively employed molecular dynamics simulation methods to construct two adsorption systems—“water-surfactant-coal” and “water-nanoparticle-grafted surfactant-coal”—based on the Wiser coal molecular model. Through comprehensive analysis of key parameters including adsorption configurations, interaction energies, relative concentration profiles, hydrogen bond counts, water molecule diffusion behaviors, and detailed examination of surface electrostatic potentials of various components, we conducted comparative studies on the wetting behaviors of sodium dodecyl sulfate (SDS), alcohol ethoxylate (AEO₉), and their nanoparticle-composite systems on coal. This investigation successfully revealed the microscopic mechanism by which composite structures enhance coal wettability at the molecular level.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144861533","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":"Simulation of the trimeric globular head of C1q reveals temperature-sensitive network: implications for inflammation","authors":"Nicole Rodgers,&nbsp;Christophe Lalaurie,&nbsp;Thomas Christopher Richard McDonnell","doi":"10.1007/s00894-025-06464-y","DOIUrl":"10.1007/s00894-025-06464-y","url":null,"abstract":"<div><h3>Context</h3><p>C1q is an important protein in immune processes, driving complement activation through the classical pathway. Further to this, alterations in C1q either through SNPs or through autoantibodies can lead to systemic lupus erythematosus. Beyond these functions, C1q can also bind to other inflammatory proteins such as C-reactive protein (CRP) via its globular domain, when CRP is in the pentameric form. These interactions require specific structures to facilitate binding. Using molecular dynamics simulations, it is possible to measure the movements of proteins over time, with increasing temperatures allowing them to explore most of their available conformational space. Here, we describe using an increasing temperature simulation of C1q to identify potential structures generated during states of increased energy such as inflammation. Increasing temperature yielded significantly more movement of the monomeric and trimeric protein forms. Monomer A drove most movement within the molecule regardless of temperature, within the monomer and trimer. Further to this, novel structures were generated at higher temperatures, with significant movement of the CRP binding site. The altered movement in the CRP binding amino acids was correlative with increased temperature driving a loss of correlation between the different amino acids involved. Increased temperature and energy in the system leads to an alteration of C1q’s structure, which may leave it unable to bind to CRP in solution. This could have implications for the activity of the C1q/CRP complex as well as both proteins individually.</p><h3>Methods</h3><p>Models were generated using PDB:1PK6 and prepared using Charmm-GUI’s online platform. Protein simulations were run using NAMD on the UCL HPC facility (ARC). Trajectories were combined and aligned for analysis and visualised using Visual Molecular Dynamics (VMD). Analysis was carried out using VMD, R Studio, and Excel to identify novel structures of C1q, areas of increased flexibility, and potential protein networks.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06464-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144832224","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":"A genetic algorithm search for the global minima of sodium nanoclusters using a tailored DFTB approach","authors":"Nelson R. C. Junior,&nbsp;Maicon Pierre Lourenço,&nbsp;Breno R. L. Galvão","doi":"10.1007/s00894-025-06457-x","DOIUrl":"10.1007/s00894-025-06457-x","url":null,"abstract":"<div><h3>Context</h3><p>Obtaining the global minimum in the potential energy hypersurface of nanoclusters is a very difficult task, due to the large number of degrees of freedom and the vast number of local minima. However, the discovery of such minima provides the geometrical arrangement that is more likely to occur, which is a key step in computing the properties of such particles. Here we developed a genetic algorithm (GA) including a gradient adjustment in each local optimization, to obtain an efficient GA, which is particularly useful when the algorithm is coupled with electronic structure methods. The idea is first validated, and then used to predict the minima of large sodium nanoclusters up to one hundred atoms.</p><h3>Methods</h3><p>To validate the algorithm, we analyzed its efficiency in obtaining the global minima of Lennard–Jones clusters, whose solutions are well known and can be used as benchmark. The new GA is compared to a random search and a standard GA. For exploring the potential energy surface of sodium clusters, we employ the Density-Functional Tight-Binding (DFTB) method, with parameters that have been tuned specifically to such clusters, thus enhancing its reliability for this specific application.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144832226","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 calculations of Janus SiC/MoTeS and SiC/MoSTe nanoceramics: improving the performance of ceramic jewelry","authors":"Wenxiu Yu,&nbsp;Xiaomeng Zhu","doi":"10.1007/s00894-025-06471-z","DOIUrl":"10.1007/s00894-025-06471-z","url":null,"abstract":"<div><h3>Context</h3><p>The development of novel nano-ceramic composite materials significantly enhances the design quality and performance of ceramic jewelry. This research utilizes density functional theory to create innovative nano-ceramic materials, specifically Janus SiC/MoTeS and SiC/MoSTe, and examines their structural and electronic characteristics. The study explores the influence of biaxial and vertical strain on the modulation of the band gap in Janus heterojunctions. Findings reveal that both of Janus heterojunctions exhibit notable structural stability. The SiC/MoTeS and SiC/MoSTe configurations are identified as indirect band gap semiconductors, with band gaps measuring 0.658 eV and 0.447 eV, respectively. Electron transfer within the heterojunction occurs from SiC to MoTeS, which contributes to enhanced structural stability. Furthermore, strain is shown to effectively modulate both the band gap values and optical absorption properties of the Janus heterojunctions. The superior properties of these Janus ceramic heterojunctions suggest their promising applications in ceramic products.</p><h3>Methods</h3><p>The CASTEP software package is used for related calculations. The generalized gradient approximation with the Perdew-Burke-Ernzerhof functional was employed to describe the exchange–correlation functional and the electron–ion interactions. A more accurate hybrid functional, HSE06, was also used to correct the band gap results, as the PBE functional tends to underestimate the width of the band gap. The DFT-D3 scheme was used to describe the van der Waals interactions between layers.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144832223","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":"First-principles study of the electronic, elastic, and optical properties of ternary LiAlTe2","authors":"Gui-Zhu Ran,&nbsp;Mi Zhong,&nbsp;Zheng-Tang Liu,&nbsp;Qi-Jun Liu","doi":"10.1007/s00894-025-06467-9","DOIUrl":"10.1007/s00894-025-06467-9","url":null,"abstract":"<div><h3>Context and results</h3><p>This study utilizes a first-principles computational approach to examine the elastic, electronic, and optical properties of LiAlTe₂, a ternary A^IB^IIIC₂^VI compound. The findings, in close agreement with experimental data, demonstrate the material’s strong potential as a p-type transparent conductive material. LiAlTe₂ crystallizes in a tetragonal structure, featuring a tetrahedral arrangement that forms a stable three-dimensional framework. The material’s elastic properties reveal a favorable balance between ductility and rigidity, with notable stretchability and resistance to fracture. With a direct bandgap of 2.42 eV, LiAlTe₂ exhibits a low absorption coefficient in the visible light range (&lt; 2 × 10⁴ cm⁻¹), indicating high transparency. Additionally, the reduced hole effective mass of 0.82 m₀ at the valence band maximum enhances its electronic transport properties, making it an ideal candidate for applications that require high carrier mobility and transparent conductivity.</p><h3>Computational methods</h3><p>The calculations were carried out using density functional theory (DFT) within the Cambridge Sequential Total Energy Package (CASTEP). This study employs both GGA-PBE and PBE0 methods to analyze the material properties. </p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144832225","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":"Grand canonical Monte Carlo simulation on the metal-doped zeolite for enhancing separation of organic sulfur","authors":"Bin Sun,&nbsp;Dalong Zheng,&nbsp;Xin Song","doi":"10.1007/s00894-025-06472-y","DOIUrl":"10.1007/s00894-025-06472-y","url":null,"abstract":"<div><h3>Content</h3><p>In this study, the effects of metal doping (Al, Cu, Fe) on the performance of MFI for adsorption and removal of organic sulfur (carbonyl sulfide (COS), methyl sulfide (CH₃SH), carbon disulfide (CS₂), and ethyl mercaptan (C₂H₅SH)) were systematically investigated. The mechanisms of metal doping on the adsorption sites and the competing adsorption behaviors were revealed. Under the independent adsorption conditions, Al doping resulted in an enhancement in the adsorption of COS and CS₂. Cu doping led to a preferential enhancement in the adsorption of COS, while concurrently inhibiting the adsorption of other molecules. Fe doping results in a slight reduction in the amount of adsorption. However, it concomitantly leads to a decrease in the stable adsorption escape from 607.43 to 470.32 kPa. Under the simultaneous adsorption conditions, Fe-MFI demonstrated optimal industrial adaptability, characterized by a low adsorption fugacity demand (130.87 kPa) and effective separation of the four molecules through a variable pressure process. Furthermore, the variation of organic sulfur concentration exerts a significant effect on the migration of the respective adsorption sites and the alteration of the adsorption configurations. The present study provides a theoretical basis for the application of metal-modified MFI zeolites in the field of organic sulfur removal and variable pressure adsorption separation.</p><h3>Methods</h3><p>The theoretical study is based on the density functional theory (DFT) method for geometric structure optimization and the grand canonical Monte Carlo (GCMC) method for simulation of adsorption properties. This geometric structure (MFI, metal-doped MFI, COS, CS₂, CH₃SH, and C₂H₅SH) optimization is carried out using the Dmol³ module in the Material Studio 2017. In this study, the GGA/PBE method was employed in conjunction with the DNP basis set, a spin-polarized set, and a DFT-D correction. The translational and rotational partition functions of the gas-phase molecules have been taken into account. This sorption behaviors of COS, CS₂, CH₃SH, and C₂H₅SH on MFI and metal-doped MFI are carried out using the Sorption module in the Material Studio 2017. The fugacity range is from 101.33 to 1013.25 kPa, and the temperature is 298 K.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144832227","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":"Exploring negative linear compressibility in the orthorhombic polymorph of ScF3 space group C222 under high pressure","authors":"Houda El Hyani,&nbsp;Haris Habib,&nbsp;Li Gong","doi":"10.1007/s00894-025-06468-8","DOIUrl":"10.1007/s00894-025-06468-8","url":null,"abstract":"<p>This study investigates the orthorhombic polymorph of ScF₃ (<i>C222</i>) under hydrostatic pressure, revealing negative linear compressibility (NLC) along the <i>b</i>-axis. First-principles calculations show anisotropic expansion (<i>b</i>-axis) and contraction (<i>a</i>-, <i>c</i>-axes), with compressibility coefficients quantified up to 40 GPa. The findings advance the understanding of pressure-induced behaviors in ScF₃ and its potential for functional materials design.</p><p>First-principles calculations were performed using density functional theory (DFT) within the generalized gradient approximation (GGA) framework as implemented in CASTEP. Lattice parameters and elastic properties were computed under varying pressure conditions. The Pascal program was used to determine compressibility coefficients and analyze NLC behavior. Computational settings, including energy cutoffs, k-point sampling, and convergence criteria, were optimized for accuracy and stability.\u0000</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144814377","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":"[N2H7+][B2H7–] supersalt as an alternative of [NH4+][BH4–] for efficient hydrogen storage","authors":"Ambrish Kumar Srivastava","doi":"10.1007/s00894-025-06463-z","DOIUrl":"10.1007/s00894-025-06463-z","url":null,"abstract":"<div><h3>Context</h3><p>Supersalts are charge transfer salts, which differ from traditional salts due to preferred dissociation into ionic fragments. These can be formed by the interaction of superalkalis with superhalogens. The inherent instability of [NH₄⁺][BH₄^–] against dissociation to ammonia borane restricts its practical application in hydrogen storage. In this work, we design [N₂H₇⁺][B₂H₇^–] by using binuclear superalkali cation (N₂H₇⁺) and superhalogen anion (B₂H₇^–) using DFT and MP2 methods. Although its gravimetric hydrogen density (22%) is slightly smaller than that of [NH₄⁺][BH₄^–] (24%), its dissociation energy and enthalpy are large enough to confirm its stability. The enhanced stability of [N₂H₇⁺][B₂H₇^–] can be attributed to its supersalt behavior, which makes it a possible candidate for chemical hydrogen storage.</p><h3>Methods</h3><p>DFT calculations were performed using a long-range dispersion corrected ωB97xD functional with a 6–311 +  + G(d,p) basis set in the Gaussian 16 program. The results were recalculated using the second-order Moller–Plesset perturbation theory (MP2) with the same basis set.\u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144810952","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":"Pressure effect on the atomic structure of amorphous silicon","authors":"Nicolás Amigo","doi":"10.1007/s00894-025-06470-0","DOIUrl":"10.1007/s00894-025-06470-0","url":null,"abstract":"<div><h3>Context</h3><p>This study explores how hydrostatic pressure influences the atomic structure of amorphous silicon. As pressure increases, the material undergoes densification, reflected in the shift of radial distribution functions and bond angle distributions. While the short-range order undergoes relatively small structural variations, the medium-range order exhibits significant structural rearrangements, including changes in coordination numbers and atomic connectivity. These pressure-induced transformations favor simpler, more compact atomic configurations. The resulting structural reorganization leads to increased internal energy and reduced atomic volume, revealing the energetic cost of compression. Overall, the findings offer insights into the fundamental behavior of amorphous silicon under extreme conditions.</p><h3>Methods</h3><p>Molecular dynamics simulations were conducted using the Tersoff potential for LAMMPS to study amorphous silicon. The samples were prepared using a cooling rate of 10<span>(^{11})</span> K/s and then relaxed at 100 K at six different pressures: 0, 2, 4, 6, 8, 10 GPa. Structural properties were calculated using radial distribution functions, bond angle distribution, Voronoi analysis, and atomic volumes, and network analysis was conducted to quantify connectivity among four-coordinated atoms. Calculations were performed using the OVITO software and Python programming language.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144810954","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}