Interaction of some phytochemical compounds with Er2O3 nanoparticle: First principle study

IF 2.5 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Modeling Pub Date : 2025-04-03 DOI:10.1007/s00894-025-06361-4
Mahmood Akbari
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Abstract

Context

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.

Methods

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.

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一些植物化学物质与 Er2O3 纳米粒子的相互作用:第一原理研究
植物化学物质与纳米粒子之间的相互作用在纳米技术和生物医学应用中起着至关重要的作用。本研究利用密度泛函数理论(DFT)和分子动力学(MD)模拟研究了六种植物化学物质——儿茶素、柠檬烯、沙木烯、辛酸、香草酸和木犀草素7-O-ß-葡萄糖醛酸盐——与Er₂O₃纳米颗粒的结合行为和稳定性。研究结果表明,木犀草素、儿茶素和Sinapic酸与Er2O3的结合亲和力最强,结构稳定性最高,这是由于它们的亲水性和亲脂性平衡以及良好的电子性能。这些见解有助于基于植物化学的纳米材料的设计和功能化,在药物输送、生物成像和光动力治疗方面具有潜在的应用。方法采用Gaussian 09在B3LYP/ 6-311 + + G(d,p)水平上进行sdft计算,确定植物化学物质的HOMO-LUMO能隙、偶极矩和极化率。利用GROMACS 2019、CHARMM36力场和TIP3P水模型进行MD模拟,分析了5 nm Er2O3纳米颗粒在50 ns内的植物化学吸附动力学。采用ALOPGPS 2.1软件对主要参数如相互作用能、均方根偏差(RMSD)、径向分布函数(RDF)和水溶性(log)进行评价。
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来源期刊
Journal of Molecular Modeling
Journal of Molecular Modeling 化学-化学综合
CiteScore
3.50
自引率
4.50%
发文量
362
审稿时长
2.9 months
期刊介绍: The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling. Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry. Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.
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