{"title":"Interaction of some phytochemical compounds with Er2O3 nanoparticle: First principle study","authors":"Mahmood Akbari","doi":"10.1007/s00894-025-06361-4","DOIUrl":null,"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 Er<sub>2</sub>O<sub>3</sub>, 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 Er<sub>2</sub>O<sub>3</sub> 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":2.5000,"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":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Molecular Modeling","FirstCategoryId":"92","ListUrlMain":"https://link.springer.com/article/10.1007/s00894-025-06361-4","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
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.
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.