Journal of Molecular Modeling最新文献

{"title":"Understanding the co-adsorption mechanism between nanoplastics and neonicotinoid insecticides from an atomistic perspective","authors":"Erwin García-Hernández,&nbsp;F. Javier Torres,&nbsp;Diego Cortés-Arriagada,&nbsp;Jorge Nochebuena","doi":"10.1007/s00894-025-06364-1","DOIUrl":"10.1007/s00894-025-06364-1","url":null,"abstract":"<div><h3>Context</h3><p>Density functional theory calculations were applied to elucidate the co-adsorption mechanism of different nanoplastic-neonicotinoid insecticides (NP-NEO) complexes where polyethylene terephthalate (PET), polyethylene (PE), and polystyrene (PS) are tested as adsorbents, and imidacloprid (IMI) and clothianidin (CLO) are considered adsorbates. HOMO energies indicate all nanoplastics (NPs) tend to donate electrons, while LUMO analysis shows PET and CLO favor electron acceptance, while PE, PS, and IMI are unstable, the last one due to resonance effects. Complex formation slightly increases HOMO energies but maintains trends, while LUMO energies improve only in PET due to its carbonyl groups. The LUMO–HOMO gap (G_LH) decreases significantly in PE-IMI and PE-CLO (~ 28%), reducing stability. Our results reveal that electrostatic and dispersion interactions dominate adsorption, contributing ~ 90% to the stabilization of NP-NEO complexes through physisorption onto the surface of all plastic matrices. Adsorption energies span the range from − 18.32 to − 32.56 kcal/mol, with the PE-IMI complex being the most stable. Our results provide molecular-level insights into the nature of pesticide-nanoplastic interactions, contributing to a better understanding of how these materials may influence the environmental fate of neonicotinoids.</p><h3>Methods</h3><p>Calculations of density functional theory at the wB97XD/def2-SVP level of theory in Gaussian16 were implemented. PCM, BSSE, and dispersion effects were considered. To gain insights into the nature of the interaction, ALMO-EDA and IGMH analyses were performed. Finally, the structures were visualized in the VMD program.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143830726","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":"Cl2 gas properties, temperature, and humidity effects on SnO2 sensor response: transition state theory study","authors":"Mudar Ahmed Abdulsattar,&nbsp;Hasan Mudar Almaroof,&nbsp;Wedyan Jawad Al-Saraf","doi":"10.1007/s00894-025-06368-x","DOIUrl":"10.1007/s00894-025-06368-x","url":null,"abstract":"<div><h3>Context</h3><p>Chlorine properties that affect its reaction with the SnO₂ sensor surface are discussed. This includes temperature variation and Cl₂ reaction with humidity. Transition state theory formalism evaluates related thermodynamic properties such as Gibbs free energy and its components, enthalpy, and entropy. Logistic functions determine the effective concentration of Cl₂ gas due to its reaction with humidity and sensor material. The Gibbs free energy of adsorption and transition or activation is evaluated as a function of temperature. Results include SnO₂ sensor response to Cl₂ gas as a function of temperature and Cl₂ concentration. Results also include response time and the effect of humidity. An optimum response temperature can be between room temperature and 200 °C. A comparison with available experimental results is performed, which shows a good agreement between theory and experiment. The present model is the only available model that can successfully compare the theory and experiment of response and response time, including temperature and humidity effects.</p><h3>Methods</h3><p>Gaussian 09 software package is used with B3LYP level of DFT since most previous successful gas sensor calculations are performed using this version of DFT. 6-311G** basis sets are used to represent oxygen and chlorine atoms, while SDD functionals are used to represent heavier Sn atoms.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143830727","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":"Electric field-induced modulation of VX nerve agent binding on h-BN nanotubes: a computational perspective","authors":"S. Prince Makarios Paul,&nbsp;Nancy S. Abisha,&nbsp;Parimaladevi Duraisamy,&nbsp;P. Selvarengan,&nbsp;A. Abiram","doi":"10.1007/s00894-025-06367-y","DOIUrl":"10.1007/s00894-025-06367-y","url":null,"abstract":"<div><h3>Context</h3><p>The interaction of toxic nerve agent VX with BN nanotube and nanocage is investigated in the presence of static electric field along perpendicular direction utilizing density functional theory (DFT). Accordingly, a static electric field (SEF) of strength 0.010 a.u and 0.020 a.u is passed along + <i>Y</i> and − <i>Y</i> axis and the effect on adsorption is analyzed. Upon interaction with VX, it was observed that the application of SEF in the + Y direction led to an increase interaction distance, whereas –Y SEF resulted in a decreased interaction distance between the nanotube and target gas. Among the observed complexations + Y SEF enhanced the sensing property of the nanotube by decreasing its E_ads and increasing its electronic responses. Moreover, the study also confirms that BN nanotube in + Y SEF has a short recovery time of 0.37 s in average and hence can perform as an effective sensor for the detection of VX.</p><h3>Methods</h3><p>The optimizations of the structures are performed out using B3LYP-D3 functional in conjunction with 6–31 +  + G(d,p) standard basis set. With the help of QTAIM analysis, parameters namely Laplacian (<span>({nabla }^{2}rho (r))</span>), energy density value (H(r)), bond energy (E_BE), and electron density ρ(r) are obtained. All the optimizations are carried out using the Gaussian 09 and visualized using gauss view and multiwfn software packages.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143826634","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 impact of (Ni, Cu) co-doping on the electronic, optical, magnetic, and I-V characteristics of GaP nanosheets","authors":"Moaaed Motlak,&nbsp;Sameer Nawaf,&nbsp;Alaa A. Al‑Jobory","doi":"10.1007/s00894-025-06359-y","DOIUrl":"10.1007/s00894-025-06359-y","url":null,"abstract":"<div><h3>Context</h3><p>The impact of the combination of transition metals on the electronic, optical, magnetic, and I-V characteristics of GaP nanosheet was carried out by first-principles density functional theory (DFT) with nonequilibrium green’s function calculations. The band energy results of the GaP structure showed a semiconductor feature with a direct band gap of 1.29 eV. The electronic structures and the density of Ni- and Cu-doped states and (Ni-Cu) co-doped GaP were investigated. It exhibited that the impurity states are crucial in their impact on modifying the electronic properties of the system as the electron transfer rate can be enhanced. On the other hand, a pristine and Cu-doped GaP nanosheet represents a nonmagnetic semiconductor due to the polarized DOS in both spins’ directions displaying similarity. At the same time, the polarized DOS of Ni-doped GaP nanosheet displays a ferromagnetic phase. For (Ni-Cu) Co-doped GaP nanosheet, the resulting material shows the total density of states for both spin states is different and implies the presence of magnetic moments. The optical results showed that the Cu-doped GaP displays a shift in the absorption edge compared to pristine GaP. Also, the co-doped system displays a smoother absorption spectrum with reduced intensity in the peak region, indicating a combined effect of both dopants. The Ni-doped GaP displays the highest conductivity with the current reaching around ± 100,000 nA. This suggests that Ni has a more significant effect in enhancing charge transport.</p><h3>Methods</h3><p>Density functional theory (DFT) with a nonequilibrium green’s function approach was utilized to calculate the electronic, optical, magnetic, and I-V characteristics of the GaP nanosheet. The results of the electronic, optical, and magnetic properties were evaluated by applying the SIESTA package. I-V characteristics were evaluated by using the quantum transport code “GOLLUM.”</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143826633","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":"Microstructure evolution and properties of liquid Fe–P with different phosphorus content: molecular dynamic investigation","authors":"Chunhe Jiang,&nbsp;Bo Liu,&nbsp;Wang Liang,&nbsp;Jianliang Zhang,&nbsp;Kejiang Li","doi":"10.1007/s00894-025-06350-7","DOIUrl":"10.1007/s00894-025-06350-7","url":null,"abstract":"<div><h3>Context</h3><p>With the scarcity of high-quality iron ore, high-phosphorus ores have become increasingly prevalent, posing challenges to maintaining the quality of steel. Phosphorus has emerged as a key factor affecting the fluidity of molten iron and the quality of steel products. Therefore, molecular dynamics method was conducted to analyze phosphorus’s impact on the microstructure and properties of liquid iron. The research examined phosphorus contents of 1 mol%, 3 mol%, 5 mol%, and 7 mol%, focusing on parameters like radial distribution functions, coordination numbers, and mean square displacements. Results showed that phosphorus decreases the viscosity, disrupts Fe–Fe bonds, and increases the self-diffusion coefficients of both Fe and P atoms. Microstructural analysis revealed phosphorus’s role in forming complex clusters, affecting the liquid iron’s local structural order. This research provides a deeper understanding of phosphorus behavior in liquid iron, offering insights for optimizing impurity control in ironmaking and enhancing the quality of steel products.</p><h3>Method</h3><p>Lammps software was conducted to do the molecular dynamics simulation using EAM potential with NVT ensemble at 1873 K. The research subject is Fe–P melts. The initial state model is created by randomly substituting Fe atoms in the iron crystal with P atoms based on the specific number of P atoms. The ISAACS software was used to analyze the trajectories of the Fe–P melt, including structural factors, radial distribution functions, coordination numbers, bond lengths, bond angles, and microscopic clusters. Additionally, mean square displacement and atomic diffusion coefficients are analyzed. The calculated viscosity is compared with experimental data from published literature.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143809362","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 on the structures and properties of neutral and anionic molecular clusters Y6Sn0/− (n = 1—12)","authors":"Xinchun Wu,&nbsp;Jucai Yang,&nbsp;Yaqing Chen,&nbsp;Caixia Dong","doi":"10.1007/s00894-025-06362-3","DOIUrl":"10.1007/s00894-025-06362-3","url":null,"abstract":"<div><h3>Context</h3><p>Transition metal (TM) doped sulfur clusters, because of their novel physicochemical properties, have significant applications in fields such as new energy and nanomaterials, and have thus received widespread attention from scientists. Theoretical studies on the structures and properties of TM doped sulfur clusters are essential for designing novel nanomaterials. Therefore, we deeply studied the ground state structures, evolutionary patterns, electronic and optical properties of molecular clusters Y₆S_<i>n</i>^0/− (<i>n</i> = 1—12). The relative stability, HOMO–LUMO gaps, and thermodynamic stability of the ground state structure Y₆S_<i>n</i>^0/− (<i>n</i> = 1—12) indicate that the Y₆S₈⁻ cluster not only has thermodynamic stability, but also possesses relative stability. The aforementioned findings suggest that the Y₆S₈⁻ cluster are the most suitable building block for further development into a potential optoelectronic material.</p><h3>Methods</h3><p>The ground state structures were studied using global search Artificial Bee Colony (ABC) algorithm combined with density functional theory (DFT) and implemented in Gaussian 09 software package. The photoelectron spectra as well as Infrared and Raman spectra were simulated using Multiwfn and Gaussian View software, respectively. The adaptive natural density partitioning (AdNDP) analysis was performed on the most stable configuration Y₆S₈⁻ using visual molecular dynamics (VMD) software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786468","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":"A study of asphaltene solubility and aggregation due to sulfur heteroatoms: molecular dynamics simulation","authors":"Ulviyya J. Yolchuyeva,&nbsp;Orhan R. Abbasov,&nbsp;Rena A. Jafarova,&nbsp;Gunay A. Hajiyeva,&nbsp;Ravan A. Rahimov,&nbsp;Nazli A. Mehdiyeva,&nbsp;Elnur E. Baloglanov","doi":"10.1007/s00894-025-06358-z","DOIUrl":"10.1007/s00894-025-06358-z","url":null,"abstract":"<div><h3>Context</h3><p>This study describes the molecular dynamics (MD) simulations to investigate the effects of sulfur atom position on the solubility and aggregation properties of asphaltenes extracted from Zaghli crude oil (East Azerbaijan). Two different asphaltene models were studied, i.e., A1 with sulfur in the aromatic ring and A2 with sulfur in the aliphatic side chain. The radial distribution function (RDF) analysis revealed significant differences in aggregation trends. A1 exhibited rapid aggregation in both solvents used in the experiments, as evidenced by a significant decrease in the radius of gyration from 0.6 to 0.4 Å in octane and from 0.8 to 0.5 Å in xylene. In contrast, A2 showed increased solubility; especially in xylene with a marked increase in the radius of gyration from 0.5 to 2 Å. Furthermore, the energy analysis confirmed these results, i.e., A2 exhibited a higher total energy (451.16 kcal/mol) than A1 (221.28 kcal/mol); indicating a more energetically favorable and less aggregated state of A2. These computational results open up new possibilities for understanding the critical role of the sulfur atom position in the asphaltene structure on its aggregation propensity, which can be used to prevent asphaltene-related problems in the petroleum industry. The work is very useful in the oil industry for enhancing oil production by studying asphaltene solubility and aggregation.</p><h3>Methods</h3><p>MD simulations were performed using the COMPASS force field and Material Studio V.6 2017 software to evaluate the solubility of asphaltenes in octane and xylene solvents. Geometric optimization was carried out to address unstable interactions, with periodic boundary conditions applied. Simulations were conducted in the NVT ensemble at 298 K and 1 atm pressure, using a time step of 1 fs, a Nose thermostat for temperature control, and a Berendsen thermostat for pressure control. RDF analysis was utilized to examine the behavior of two distinct asphaltene models, which differed in the positioning of the sulfur atom, in the solvents. The total energy contributions, including van der Waals and electrostatic interactions, were also analyzed.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786467","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 nature of σ-hole regium bond between CuX/AgX/AuX and pyridine","authors":"Junyong Wu,&nbsp;Hua Yan,&nbsp;Hao Chen,&nbsp;Guoliang Dai","doi":"10.1007/s00894-025-06360-5","DOIUrl":"10.1007/s00894-025-06360-5","url":null,"abstract":"<div><h3>Context</h3><p>The σ-hole regium bond complexes between coinage metal monohalide molecule CuX/AgX/AuX (X = F, Cl, and Br) and pyridine (C₅H₅N), which have linear orientation and perpendicular orientation, have been systematically probed at the MP2/aug-cc-pVTZ level. By comparing the calculated interaction energy, we can see that the linear orientation interactions are a little stronger than the corresponding perpendicular orientation interactions in C₅H₅N-CuX/AgX/AuX complexes. The binding energies for linear orientation regium bond complexes range from − 34 to − 60 kcal/mol, while those perpendicular orientation regium bond complexes are from − 24 to − 50 kcal/mol. Both types of interactions energies all tend to follow the Au &gt; Cu &gt; Ag order and reduced with the decrease in electronegativity F &gt; Cl &gt; Br in C₅H₅N-CuX/AgX/AuX complexes. The electrostatic energy is the major source of the attraction for the linear orientation regium bond interactions, while for the perpendicular orientation regium bond interactions are mainly due to electrostatic and induction energy.</p><h3>Methods</h3><p>All the complexes and respective monomers were optimized at the MP2/aug-cc-pVTZ level. Relativistic effects were considered for Cu, Ag, Au, and Br by using the aug-cc-pVTZ-PP basis set. The NBO population analysis and AIM and IRI analysis were carried out. The interaction energies of the σ-hole regium bonds complexes were decomposed by using the symmetric adaptive perturbation theory (SAPT).</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786482","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 docking of Cu(II) and Zn(II) complexes for tyrosinase inhibition and drug loading on boron nitride nanotube scaffolds using Monte Carlo simulations","authors":"Najeeb Ullah,&nbsp;Amir Karim,&nbsp;Muhammad Iqbal,&nbsp;Rahime Eshaghi Malekshah,&nbsp;Saqib Ali,&nbsp;Jebiti Haribabu,&nbsp;Sodio C. N. Hsu","doi":"10.1007/s00894-025-06355-2","DOIUrl":"10.1007/s00894-025-06355-2","url":null,"abstract":"<div><h3>Context</h3><p>Recent studies on drug delivery systems incorporating boron nitride nanostructures (BNNTs) highlight their excellent chemical stability and non-cytotoxic properties, positioning them as a promising platform for drug release in biomedical applications. This study aimed to optimize the mono-nuclear structures of Cu(II) and Zn(II) complexes and to functionalize zigzag (13, 13) boron nitride nanotubes with glutamic acid (GABNNTs). Based on Monte Carlo, the results revealed that complexes <b>6</b> and <b>19</b> exhibited stronger interactions with GABNNTs, attributed to π-π stacking between bipyridine/phenanthroline ligands and GABNNTs. This interaction suggests a greater challenge in their release compared to other compounds. The interaction energy analysis further revealed that complexes <b>1</b>, <b>4</b>, and <b>12</b>/GABNNTs exhibited the lowest stability, indicating weaker binding interactions between these complexes and the GABNNT surface. The adsorption of all complexes on GABNNTs was primarily found to be physisorption. Molecular docking with mushroom tyrosinase (2Y9X) identified complexes <b>5</b>, <b>10</b>, <b>11</b>, <b>15</b>, and <b>20</b> as having the strongest interactions, a trend that is partially supported by chemical hardness analysis. However, DFT-D results indicated that complexes <b>5</b>, <b>11</b>, and <b>20</b> exhibited the lowest chemical stability, suggesting a trade-off between strong interactions and lower stability in these complexes.</p><h3>Methods</h3><p>The energies of these systems were estimated using dispersion-corrected density functional theory (DFT-D) calculations performed in Materials Studio 2017. To evaluate the drug delivery potential of GABNNTs for Cu(II) and Zn(II) complexes, the Monte Carlo (MC) method was employed. The structural and electronic properties, as well as the relationship between biological activities and ΔE_g, were analyzed by calculating the HOMO–LUMO energy gap using the dispersion-corrected density functional theory (DFT-D) method. Molecular docking was used to interact with mushroom tyrosinase (2Y9X).</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786481","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":"Interaction of some phytochemical compounds with Er2O3 nanoparticle: First principle study","authors":"Mahmood Akbari","doi":"10.1007/s00894-025-06361-4","DOIUrl":"10.1007/s00894-025-06361-4","url":null,"abstract":"<div><h3>Context</h3><p>The interaction between phytochemicals and nanoparticles plays a crucial role in nanotechnology and biomedical applications. This study investigates the binding behavior and stability of six phytochemicals—Catechin, Limonene, Sabinene, Sinapic Acid, Vanillic Acid, and Luteolin 7-O-ß-glucuronide—with Er₂O₃ nanoparticles using Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations. The findings indicate that Luteolin, Catechin, and Sinapic Acid exhibit the strongest binding affinities and highest structural stability with Er₂O₃, attributed to their balanced hydrophilicity-lipophilicity and favorable electronic properties. These insights contribute to the design and functionalization of phytochemical-based nanomaterials, with potential applications in drug delivery, bioimaging, and photodynamic therapy.</p><h3>Methods</h3><p>DFT calculations were conducted using Gaussian 09 at the B3LYP/6–311 +  + G(d,p) level to determine HOMO–LUMO energy gaps, dipole moments, and polarizability of the phytochemicals. MD simulations, performed using GROMACS 2019 with the CHARMM36 force field and TIP3P water model, analyzed the dynamics of phytochemical adsorption on a 5 nm Er₂O₃ nanoparticle over 50 ns. Key parameters such as interaction energies, root mean square deviations (RMSD), radial distribution functions (RDF), and water solubility (logS) were evaluated using ALOPGPS 2.1 software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06361-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143761744","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}