Journal of Molecular Modeling最新文献

{"title":"Boron-modified phenolic resin: thermal stability and decomposition mechanisms via experiments and simulations","authors":"Xiao-Feng Qing,&nbsp;Xiao Liu,&nbsp;Qing Han,&nbsp;Jia-Jun Ma,&nbsp;Li-Juan Ran,&nbsp;Fei Zhou,&nbsp;Hongli Wang,&nbsp;Bo Dai,&nbsp;Ni-Na Ge","doi":"10.1007/s00894-025-06602-6","DOIUrl":"10.1007/s00894-025-06602-6","url":null,"abstract":"<div><h3>Context</h3><p>Currently, boron modification represents a significant strategy for enhancing the thermal stability of phenolic resins. However, existing boron modification methods generally suffer from synthetic complexity, and the mechanism of boron’s effect on phenolic resins at the molecular level remains incompletely understood. This study investigated how 4-hydroxyphenylboronic acid pinacol ester (4-HPBAPE) doping regulates the glass transition temperature (<i>T</i>_g), thermal conductivity, and pyrolysis behavior of phenolic resin. Results showed that 4-HPBAPE doping increased the glass transition temperature (162 → 187 ℃), while thermal conductivity testing revealed a 10% reduction (0.2154 → 0.1920 W/(m·K)). The errors between the results obtained from MD simulation and the experimental results were all less than 10%. The char yield decreased with increasing 4-HPBAPE doping ratio. ReaxFF MD simulations demonstrated that boron modification of phenolic resins enhanced the production of light hydrocarbons (C₁–C₅) during pyrolysis, resulting in higher mass loss. This occurred via boron-mediated ring-opening and suppression of large aromatic cluster formation. Future efforts could focus on controlling the bonding form of boron to suppress ring-opening reactions, thereby enhancing the char yield.</p><h3>Methods</h3><p>The materials were characterized using Fourier transform infrared spectrometer (FTIR) and nuclear magnetic resonance spectroscopy (NMR). Thermal conductivity was measured using a DRE-2C thermal conductivity meter. Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) were performed using a synchronous thermal analyzer. Simulations were carried out with the LAMMPS and Materials Studio software package. Classical molecular dynamics (MD) simulations employed the COMPASS force field, while the reaction force field files containing C, H, O and B element were used. The post-processing of the results was implemented using OVITO and self-programmed Python scripts.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761560","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":"Enhanced quantum capacitance of near valence doped stanene nanosheets for asymmetric supercapacitors","authors":"Akash Moi,&nbsp;Md. Shahzad Khan,&nbsp;Anurag Srivastava,&nbsp;Boddepalli SanthiBhushan","doi":"10.1007/s00894-025-06600-8","DOIUrl":"10.1007/s00894-025-06600-8","url":null,"abstract":"<div><h3>Context</h3><p>Ever since the experimental realization of the first free-standing layers of stanene by researchers in 2016, this potential wonder material is widely being explored for various applications. This work analyzes the implication of this novel 2D material for supercapacitor electrodes and ways to enhance its quantum capacitance and charge storage capacity via first principles simulations. The stanene nanosheet is subjected to single vacancy (SV) defect and near valence (In and Sb) doping (direct doping at the SV site, independent doping at the SV edges, and co-doping at the SV edges). The results reveal the zero band gap nature of pristine stanene similar to graphene, yet at least 7 times enhancement in quantum capacitance in comparison to pristine graphene. The incorporation of a single vacancy (SV) defect in stanene has improved its quantum capacitance and charge storage capacity by 1.54 times, at the expense of compromised thermodynamic stability. Thus, to preserve the thermodynamic stability with minimal lattice distortions and enhance the quantum capacitance as well as charge storage of SV stanene, near valence dopants are introduced at the SV site and SV edges. Our results confirm that antimony doping in stanene offers better thermodynamic stability than Indium. Moreover, the independent doping of 3 antimony atoms at SV edges offers the highest quantum capacitance of 134.21 μF/cm² at 0.6 V, which is about 1.47 times higher than the maximum value (91 μF/cm² for N and Ni co-doping) reported in the literature for any doping. All the SV and near valence doped stanene configurations are observed to be better suitable for the anode electrode of asymmetric supercapacitors owing to their quantum capacitance and charge storage peaks on the positive side of the electrochemical window, except for one particular configuration, i.e., the direct antimony doping at the SV site, which is better suitable for the cathode electrode of the asymmetric supercapacitor.</p><h3>Methods</h3><p>The DFT-based first principle simulations combined with MATLAB programming are performed to study the capacitive behavior of the electrodes. A <i>k-point</i> sampling of 7 × 7 × 1 is found to be sufficient for sampling the Brillouin zone in reciprocal space, and a density mesh cutoff of 80 Hartree is used to define the fineness of real space effective potential and electron density grids for solving Poisson’s equation. The Generalized Gradient Approximation (GGA) with Perdew-Burke-Ernzerhof parameterization is used as the exchange correlation functional.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761783","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":"Investigation into the performance characteristics of N,N′-bonded bis-triazole derivatives","authors":"Die Gao,&nbsp;Qi Gao,&nbsp;Jianguo Zhang,&nbsp;Jinting Wu,&nbsp;Tingxing Zhao,&nbsp;Hongbo Li","doi":"10.1007/s00894-025-06604-4","DOIUrl":"10.1007/s00894-025-06604-4","url":null,"abstract":"<div><h3>Context</h3><p>Substituents including -NH₂, -NO₂, -NHNO₂, and -CH(NO₂)₂ were introduced into the <i>N,N</i>′-linked bis-triazole scaffold to design 72 derivatives. Density functional theory (DFT) calculations at the B3LYP/6-311+G(d, p) level were performed using the Gaussian 09 software package to evaluate critical parameters such as density, heat of formation (HOF), detonation pressure (<i>P</i>), detonation velocity (<i>D</i>), explosive energy release (<i>Q</i>), sensitivity, and molecular orbital energies (HOMO–LUMO) for all 72 derivatives. The results indicate that compound C3 (<i>ρ</i> = 1.86 g.cm⁻³, <i>D</i> = 8.77 km.s⁻¹, <i>P</i> = 34.83 GPa, <i>h</i>_50% = 39.27 cm), C12 (<i>ρ</i> = 1.86 g.cm⁻³, <i>D</i> = 9.11 km.s⁻¹, <i>P</i> = 37.45 GPa, <i>h</i>_50% = 29.97 cm), and D15 (<i>ρ</i> = 1.80 g.cm⁻³, <i>D</i> = 9.03 km.s⁻¹, <i>P</i> = 36.11 GPa, <i>h</i>_50% = 31.47 cm) exhibit potential as substitute explosive candidates for 1,3,5-trinitro-1,3,5-triazinane (RDX) (<i>ρ</i> = 1.80 g.cm⁻³, <i>D</i> = 8.75 km.s⁻¹, <i>P</i> = 34 GPa, <i>h</i>_50% = 26 cm).</p><h3>Methods</h3><p>The structural optimization, volume calculations, and electrostatic potential energy analyses were conducted using the Gaussian 09 and Multiwfn 3.8 software packages, employing the B3LYP method within density functional theory (DFT). The structures of 72 derivatives were optimized at the 6-311+G(d, p) basis set level, followed by an investigation into their detonation performance and stability characteristics.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761763","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":"Effects of Si-doped and shear strain on the optoelectronic properties of WSe2: A first principles study","authors":"Zilian Tian,&nbsp;Lu Yang,&nbsp;Jianlin He","doi":"10.1007/s00894-025-06608-0","DOIUrl":"10.1007/s00894-025-06608-0","url":null,"abstract":"<div><h3>Context</h3><p>Two-dimensional transition-metal dichalcogenides such as WSe₂ are promising platforms for tunable optoelectronic devices. Here, first-principles molecular modeling is used to examine how substitutional Si doping combined with shear strain tunes the electronic and optical properties of monolayer WSe₂. Si dopants introduce localized states that reduce the band gap from 1.599 to 1.029 eV and enhance low-energy absorption. Shear strain applied along orthogonal in-plane directions (xy and yx) further induces direction-dependent electronic localization and band-gap renormalization, giving rise to anisotropic optical absorption. These results provide mechanistic insight and a simple strategy for tailoring the optoelectronic response of WSe₂-based materials.</p><h3>Methods</h3><p>Density functional theory calculations within the generalized-gradient approximation are performed using the Perdew–Burke–Ernzerhof functional and Gaussian-type basis sets as implemented in the Materials Studio package. Substitutional Si doping is modeled in a WSe₂ supercell, and shear strain is introduced by distorting the in-plane lattice vectors along the xy and yx directions. For each configuration, fully relaxed geometries are used to evaluate the electronic band structures, charge redistribution, and complex dielectric function. Optical absorption spectra are obtained from the frequency-dependent dielectric tensor within the independent-particle approximation.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761553","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":"Competitive adsorption mechanisms of CO2 in hydrous silica-alumina clay shale nanopores: a comprehensive exploration","authors":"Zhichao Zhang,&nbsp;Liehui Zhang,&nbsp;Yulong Zhao,&nbsp;Peiming Bian,&nbsp;Xin Chen","doi":"10.1007/s00894-025-06597-0","DOIUrl":"10.1007/s00894-025-06597-0","url":null,"abstract":"<div><h3>Context</h3><p>High carbon emissions have become a major problem perplexing human society, and the use of shale for CO₂ storage has a broad application prospect and significance. In this paper, a SiO₂- Al₂O₃ heterostructure model representing clay shale is established, and the adsorption mechanisms of CO₂ in clay shale are studied systematically by means of grand canonical Monte Carlo (GCMC), molecular dynamics (MD) and density functional theory (DFT). The findings indicate that the system's equilibrium shifts toward adsorption as pressure increases, enhancing gas uptake. Conversely, rising temperature favors the desorption equilibrium, thereby reducing the overall adsorption capacity. Higher water content reduces CO₂ adsorption capacity in hydrous SiO₂-Al₂O₃ nanopores. For every 5 wt% increment in water content, the CO₂ adsorption amount decreases by approximately 18.6%. The density profiles show that the interaction between H₂O and adsorption sites on the shale surface is stronger than that of CO₂. The radial distribution functions indicate the difference of CO₂ distribution between SiO₂ region and Al₂O₃ region and reveal the effect of water on Al₂O₃ region is greater than that of SiO₂ region. This study has an in-depth exploration of the adsorption rule and migration mechanism of CO₂ in clay shale, which may contribute preliminary theoretical insights for optimizing CO₂ adsorption and storage.</p><h3>Method</h3><p>The simulation software employed in this study is Materials Studio, and the associated force field utilized is COMPASS III. The adsorption configurations are obtained from the Sorption module and molecular dynamics simulations are performed on it by using the Forcite module with the NVT ensemble. Based on the DFT, molecular optimization and performance metrics analysis are all calculated using the DMol³ module.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761569","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 enhancement of the photoconversion eficiency on zinc porphyrin dyes by combining electron donor–acceptor theory with the Barrera-Crivelli-Loeb (BCL) model","authors":"Mauricio Barrera,&nbsp;Irma Crivelli","doi":"10.1007/s00894-025-06591-6","DOIUrl":"10.1007/s00894-025-06591-6","url":null,"abstract":"<div><h3>Context</h3><p>In order to increase the efficiency of dye-sensitized solar cells (DSSC), we propose to study the influence of maximizing the push–pull effect by quantifying the donor force (Ds) and the acceptor capacity (Ap) calculated as functions of the Electrophilicity, Orbital Hardness, and Polarizability. The sum of the donor force and the acceptor capacity is the inductive force, which allows the push–pull effect to be maximized. With this approach, we applied the Barrera-Crivelli-Loeb (BCL) model to a series of eleven Zinc Porphyrins to correlate the Global Efficiency Index (GEI) with the experimental measurement of Photo Conversion Efficiency (PCE). The use of this strategy together with the use of siloles and siloxanes allows the design of two new dyes, BCL 516 and BCL 520, with theoretically calculated efficiencies of 10.64% and 10.61%.</p><h3>Methods</h3><p>In this work, all calculations were performed with the Amsterdam Density Functional 2023 package. For geometry optimization (ground state and first singlet), the optimized Perdew-Becke-Ernzerhof exchange correlation functional was employed with a DZP basis set for H, C, N, O, S, and a Zeroth Order Regular Approximation (ZORA) – TZP basis set for Ti and Zn. Time-Dependent Density Functional Theory (TDDFT) calculations were achieved with the Statistical Average Orbital model exchange correlation potential (SAOP), including solvent effects with the Conductor-like Screening Model (COSMO). Calculations of molecular properties like electrophilicity, orbital hardness, and polarizability were carried out in the gas phase with the SAOP potential model after optimization of the target molecule with the OPBE exchange correlation functional. To determine the orbital hardness of the HOMO and LUMO, the occupation number of the frontier orbital was modified by 0.3 units.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761562","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":"Chain rigidity of 3D-ladder polymers quantified by molecular simulations","authors":"Chaofu Wu","doi":"10.1007/s00894-025-06609-z","DOIUrl":"10.1007/s00894-025-06609-z","url":null,"abstract":"<div><h3>Context</h3><p>Due to the versatile properties, the hydrocarbon ladder polymers developed recently represent a class of promising materials for membrane separations of industrially relevant gas mixtures. The excellent thermomechanical properties and ultrahigh permselectivity are generally attributed to the chain rigidity of the three-dimensional (3D) ladder structures, which are not readily accessible via experiments. Therefore, this work takes advantage of molecular simulations to quantify the chain rigidity of such polymers, which exhibit quite different behaviors from the conventional polymers. It is first identified that the characteristic segments and repeating units behave like bows that are easy to press but difficult to pull. Furthermore, it is demonstrated that the subtle influences of side groups and temperature on the end-to-end distance (Re) can be well captured by these all-atomistic (AA) simulations. As suggested by the fluctuation in Re, the configuration provides an effective way to tune overall chain morphology and thus its rigidity, resulting from both the rigidity and shape of characteristic segments. These results highlight the unique rigidity of such polymers, which should inspire further development of new robust polymer membranes of gas separations.</p><h3> Methods</h3><p>The software named Materials Studio 4.0 was employed to construct the all-atomistic structures of model systems and to perform all the energy minimizations and molecular dynamics simulations with the Deriding force field and QEq charges, and to analyze the structural and energetic properties.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761563","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":"Aqueous-phase DFT insights into ciprofloxacin adsorption on COOH-functionalized carbon nanotubes: energetics, electronic structure, and sesign principles","authors":"Khaldoun A. Al-Sou’od","doi":"10.1007/s00894-025-06605-3","DOIUrl":"10.1007/s00894-025-06605-3","url":null,"abstract":"<div><h3>Context</h3><p>Pharmaceutical residues such as ciprofloxacin (CIP) are increasingly recognized as persistent aquatic contaminants with adverse ecological impacts. Understanding their interactions with functionalized nanomaterials is essential for designing efficient adsorbents. Here, we explore the adsorption mechanism of CIP on carboxyl-functionalized carbon nanotubes (CNT–COOH) under aqueous conditions. The study reveals favorable binding energetics, significant stabilization through solvation effects, and electronic structure changes that highlight CNT–COOH as an effective platform for pharmaceutical pollutant removal.</p><h3>Methods</h3><p>All calculations were carried out using density functional theory (DFT). Geometry optimizations, harmonic vibrational frequency analyses, and solvation modeling were performed within the polarizable continuum model (PCM, water). Electronic structure calculations were conducted with B3LYP, M06-2X, and ωB97X-D functionals in combination with the 6-311++G(d,p) basis set. The Gaussian 09W package was employed for all computations, and GaussView 6 was used for molecular visualization and analysis.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761596","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":"Coumarin benzamide scaffold as potential 5-HT2C inhibitors: a multiparametric investigation and molecular simulation","authors":"Akenaton Onassis Cardoso Viana Gomes,&nbsp;Francisco Nithael Melo Lúcio,&nbsp;Matheus Nunes da Rocha,&nbsp;Victor Moreira de Oliveira,&nbsp;Caio Henrique Alexandre Roberto,&nbsp;Márcia Machado Marinho,&nbsp;Hélcio Silva dos Santos,&nbsp;Pedro de Lima-Neto,&nbsp;Emmanuel Silva Marinho","doi":"10.1007/s00894-025-06590-7","DOIUrl":"10.1007/s00894-025-06590-7","url":null,"abstract":"<div><h3> Context</h3><p> This study investigates the interaction of synthetic coumarin benzamides (<b>CmB1</b>-<b>10</b>) obtained from the literature with the 5-HT2CR serotonergic receptor and the carbonic anhydrase II (CA-II) enzyme, with potential pharmacological applications in anxiety disorders. CmB is a type of drug that has been shown to affect the 5-HT2CR receptor. This receptor is involved in mood, thinking, and muscle control. CmB has similar effects to other known antagonists. In addition, the dimethylated derivatives (3,4-CH3 and 3,5-CH3)—<b>CmB2</b> and <b>CmB4</b>—were more effective as enzyme inhibitors, according to the literature. Structural analyses revealed that the <b>CmB2</b> and <b>CmB4</b> derivatives exhibit a higher nucleophilic character due to the electron-donating properties of the dimethyl substituents. The dimethylated derivatives exhibited ideal pharmacokinetic properties, including an apparent permeability (Papp, A→B 1.1 × 10⁻⁵ cm/s) and metabolic stability. The virtual screening revealed the structural specificity of the compounds for CA-II and 5-HT2CR, with affinity energy for 5-HT2CR – 10 kcal/mol. Molecular dynamics simulations estimated a low binding free energy (ΔG) of the lead compounds to about 5-HT2CR, indicating that they were energetically more stable complexes. This research provides a basis for future experimental studies that corroborate the neuromodulatory action of CmB derivatives.</p><h3> Methods</h3><p> This study utilized the integration of molecular modeling techniques at quantum levels (DFT/B3LYP/6-311++G(d,p)) using the Gaussian 09 program to investigate structural/electronic properties and classical levels such as molecular docking and molecular dynamics, using the AutoDockVina™ and GROMACS® programs respectively, to investigate the interaction between meanings and biological targets (5-HT2CR and CA-II). DMPK was used to investigate the bioavailability and metabolism of the drugs from the results.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145730313","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":"Investigation into the temperature resistance of saturated cardanol surfactants in crude oil–water systems: a molecular dynamics simulation","authors":"Congying Lu,&nbsp;Yue Zhao,&nbsp;Zhenyu Yuan,&nbsp;Xinyi Xu,&nbsp;Limin Li,&nbsp;Huijuan Qian,&nbsp;Qinghe Gao","doi":"10.1007/s00894-025-06587-2","DOIUrl":"10.1007/s00894-025-06587-2","url":null,"abstract":"<div><h3>Context</h3><p>Surfactant flooding represents one of the critical methods in chemical enhanced oil recovery (EOR) technology. However, under high-temperature and high-salinity conditions, the interfacial properties of surfactants are prone to alteration, leading to reduced interfacial activity. In this study, three distinct types of surfactants derived from saturated cardanol were selected: 8EO8POH (nonionic surfactant), 8EO8POC2SO₃ (sulfonate surfactant), and 8EO8POSO₃ (sulfate surfactant). A high-temperature (30 ~ 180 ℃) and high-salinity (NaCl + CaCl₂ concentration of 1.0 mol/L) system model was constructed through molecular dynamics simulations to evaluate their thermal resistance. The results indicate that an increase in temperature enhances the aggregation of water molecules and crude oil components around the surfactant molecules, thereby strengthening weak interactions. Under these conditions, the balance between hydrophilic and lipophilic effects becomes the predominant factor determining the superior interfacial performance of the surfactants. Consequently, the order of heat resistance is as follows: 8EO8POC2SO₃ &gt; 8EO8POSO₃ &gt; 8EO8POH.</p><h3>Method</h3><p>In this study, Packmol was employed to construct the model, and Gromacs was used to perform molecular dynamics simulations under the GAFF force field. The simulated pressure was set to 1115.0 kPa. The temperatures were set at 303.15 K, 333.15 K, 363.15 K, 393.15 K, 423.15 K, and 453.15 K, respectively. The time step for all simulations was set to 2 fs. In the 1 ns and 15 ns NPT simulations, the Berendsen and Parrinello-Rahman methods were employed to maintain system pressure, and the temperature control was achieved through velocity-rescale. The LINCS algorithm was utilized to constrain molecular bond lengths. Short-range and long-range were used Lennard–Jones potential and Particle-Mesh Ewald (PME) summation method.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145720239","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}