Journal of Molecular Modeling最新文献

{"title":"Porosity dependence of mechanical properties of titanium nanofoams.","authors":"Thi-Thuy Binh Ngo, Van-Thuc Nguyen, Te-Hua Fang","doi":"10.1007/s00894-025-06416-6","DOIUrl":"https://doi.org/10.1007/s00894-025-06416-6","url":null,"abstract":"<p><strong>Context: </strong>This study employs molecular dynamics (MD) simulations to investigate the mechanical properties and deformation mechanisms of titanium (Ti) nanofoam under uniaxial tensile loading. The effects of porosity (ranging from 20 to 50%), strain rate (from 5 × 10⁸ to 5 × 10⁹ s⁻¹), and temperature (from 300 to 900 K) on the tensile response are systematically examined. The results reveal that increasing porosity significantly reduces the ultimate tensile strength (UTS) and elastic modulus, while intensifying localized shear strain and stress concentration. These conditions facilitate the formation of amorphous phases and grain structures, and substantially influence dislocation behavior. Furthermore, higher strain rates are found to enhance strength by increasing both UTS and elastic modulus. In contrast, elevated temperatures induce phase transformations that improve ductility but compromise strength. Overall, this work provides valuable insights into tailoring the mechanical performance of Ti nanofoams, with implications for their use in biomedical, structural, and functional applications.</p><p><strong>Methods: </strong>The simulations were performed using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) package. The results were analyzed using the Open Visualization Tool (OVITO). Structural analysis was conducted using common neighbor analysis (CNA) and polyhedral template matching (PTM), while dislocation behavior was studied with dislocation analysis (DXA). Surface meshes for volume and surface computations were generated using the construct surface mesh method.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"193"},"PeriodicalIF":2.1,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324106","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":"Shedding light on main-group dithiolene chemistry: electronic and geometrical perspectives of tris(dmit) complexes.","authors":"Heloisa N S Menezes, Henrique C S Junior, Glaucio B Ferreira","doi":"10.1007/s00894-025-06417-5","DOIUrl":"https://doi.org/10.1007/s00894-025-06417-5","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Context: &lt;/strong&gt;1,3-Dithiola-2-thiona-4,5-dithiolate is a versatile noninnocent ligand with applications in superconductivity, magnetism, and nonlinear optical materials. This study evaluated the tris(dmit) antimony(V) and tin(IV) complexes via modern computational methods. A local energy decomposition analysis of metal‒sulfur bond formation revealed that the distorted geometry of the tris(dmit) complexes in acetonitrile is the most stable conformation for both systems, whereas other conformations remain energetically accessible. The geometrical stability arises from the ionic and soft acid‒base interactions between the highly oxidized cations and thiolated sulfur atoms. State-averaged complete active-space self-consistent field with N-electron valence second-order perturbation theory correction calculations indicated that while the ground states are dominated by a single configuration, the excited state manifold in both systems shows multiconfigurational character, which is relevant for understanding systems with potentially non-innocent ligands. Finally, similarity-transformed equations of motion coupled-cluster calculations successfully reproduced the experimental UV‒Vis spectra of the two complexes in acetonitrile, highlighting the low-energy ligand-to-metal charge-transfer excitations in the tris(dmit) antimony(V) complex. These findings increase the understanding of the electronic structure and stability of tris(dmit) complexes, which can help in understanding potential applications.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;The tris(dmit) complexes were computationally investigated via two solvation models: implicit and explicit solvation. All ab initio and DFT wave function calculations were performed via ORCA software version 5.0.3. Model implicit solvation were optimized via the TPSSh/Def2-TZVP level of theory with CPCM used to simulate an acetonitrile medium. AIMD calculations for explicit solvation of the dmit salts were conducted using the GFN2-xTB method with 40 explicit acetonitrile molecules as the solvent at 300 K for a total simulation time of 35.0 ps, a timestep of 0.2 fs and data dumps every 10.0 fs. The final geometries were optimized via an ONIOM approach, with the high-level region set at the R2SCAN-3C method, which included the complexes and the first solvation shell. The low-level region utilized the extended tight-binding (xTB) method to encapsulate the explicitly solvated models, which comprised the remaining solvent molecules. Local energy decomposition (LED) analysis at the DLPNO-CCSD(T)/Def2-TZVP level of theory was utilized to investigate the stability of the complex geometries identified by AIMD. The electronic structures of the complexes were assessed using the SA-CASSCF/NEVPT2/Def2-TZVP method to confirm the multiconfigurational and multireference nature of their electronic structures. Electronic spectra were analyzed using the STEOM-DLPNO-CCSD/Def2-TZVP method, with CPCM used to simulate an acetonitrile mediu","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"192"},"PeriodicalIF":2.1,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144300919","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":"Chiral generation in achiral lower diamondoid triamantane through prochiral halogen substitution.","authors":"Aravindhan R, Jianping Hu, Ummal Momeen M","doi":"10.1007/s00894-025-06407-7","DOIUrl":"https://doi.org/10.1007/s00894-025-06407-7","url":null,"abstract":"<p><strong>Context: </strong>Our work demonstrates the chiral and chiroptical behavior of lower diamondoid molecules such as triamantane. Through the halogen substitution prochirality process, chirality was attained from the achiral triamantane molecule. The chiroptical behavior of chiral triamantane obtained from VCD, ROA, and ORD analysis evidences the significant chiral activity for all halogen substitutions ranging from fluorine to iodine for both S and R enantiomers. These chiral and chiroptical characteristics of the triamantane enantiomers can be tuned well through various halogen substitutions. The absolute configurations for chiral triamantane molecules are identified through the Cahn-Ingold-Prelog rule together with VCD analysis. The optical rotatory dispersion (ORD) of chiral triamantane molecules is dominant for chlorine, bromine, and iodine substitutions. Chiral triamantane molecules with various halogen substitutions also find a prominent role in pharmacology through their anisotropic charge distribution and binding abilities, tunable lipophilicity, nominal synthetic accessibility, and good bioavailability score.</p><p><strong>Methods: </strong>The absolute configurations for chiral triamantane molecules are identified through the Cahn-Ingold-Prelog rule. To study the chiroptical behavior of chiral triamantane molecules, wB97XD and M06-2X DFT functionals are employed, and for the initial guesses, 6-311G(d,p) and MidiX basis sets are used.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"190"},"PeriodicalIF":2.1,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293079","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":"Novel push-pull dyes with cyclic ring spacers (titanol, chromol, ferrol, nickelol, and zinkol): a DFT study for optoelectronic optimization in DSSCs.","authors":"Mourad Zouaoui-Rabah, Abdelkader M Elhorri, Madani Hedidi, Hicham Mahdjoub-Araibi, Laib Assia, Mahammed Zenati","doi":"10.1007/s00894-025-06414-8","DOIUrl":"https://doi.org/10.1007/s00894-025-06414-8","url":null,"abstract":"<p><strong>Context: </strong>This computational investigation delves into the strategic design of bimetallic Zn/M organometallic D-π-A dyes for dye-sensitized solar cells (DSSCs), with a focus on how transition metals (Ti, Cr, Fe, Ni) modulate optoelectronic behavior and photovoltaic performance. Employing density functional theory (DFT) and time-dependent DFT (TD-DFT) simulations, four dyes (Dye1-Dye4) were systematically evaluated for their light-harvesting efficiency (LHE), charge transfer kinetics, and stability under vacuum and tetrahydrofuran (THF) solvation. The results underscore distinct metal-dependent trade-offs: the chromium-based dye (Dye2) demonstrates outstanding visible-light absorption (λ_max = 570 nm) with a high LHE (85%) and oscillator strength (f = 0.830), whereas the nickel-based dye (Dye4) exhibits redshifted absorption (λ_max = 609 nm) and an extended excited-state lifetime (τ = 1.55 ns), advantageous for charge separation. Titanium (Dye1) and iron (Dye3) variants emerge as economical alternatives, offering moderate efficiency and stability. THF solvation induces pronounced bathochromic shifts (+ 138 nm for Dye1) and thermodynamically favorable interactions (ΔG_solv <  - 61 kcal·mol⁻¹), enhancing light absorption and stability. Critical metrics such as electron injection energy (ΔG_inj), open-circuit voltage (V_oc), and regeneration energy (ΔG_reg) emphasize the need to harmonize optical performance with charge management. The study advocates co-sensitization of Dye2 and Dye4 to synergistically broaden spectral response and boost power conversion efficiency. These findings pave the way for sustainable DSSCs leveraging earth-abundant metals, aligning with global initiatives for green energy innovation.</p><p><strong>Method: </strong>All calculations were performed with Gaussian 16. Ground state geometries were optimized by DFT with the B3LYP functional. The LanL2DZ basis set was used for transition metals, while 6-31 +  + G(d,p) was used for non-metallic atoms. The solvation models studied are the CPCM (Conductor Polarizable Continuum) model and the SMD (Solvation Model Density) model. Excited state properties have been calculated using TD-DFT with the CAM-B3LYP functional to evaluate electronic transitions.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"191"},"PeriodicalIF":2.1,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293080","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":"Coherent electron transport in poly(p-phenylene).","authors":"Yukihito Matsuura","doi":"10.1007/s00894-025-06413-9","DOIUrl":"https://doi.org/10.1007/s00894-025-06413-9","url":null,"abstract":"<p><strong>Context: </strong>Conductive polymers like poly(p-phenylene) (PPP) exhibit polarons and bipolarons (radical cations/dications) in bulk. While individual π-conjugated molecules are generally conductive, the role of these charged states in single-molecule junctions, where deviations from bulk behavior are suggested, remains unclear. This study employs first-principles calculations to examine the relationship between charge state (neutral, radical cation, dication) and conductance in single oligo(p-phenylene) junctions. My results demonstrate significant conductance enhancement upon doping, yet reveal that the single-molecule charge transport mechanism deviates substantially from bulk expectations, highlighting differences between molecular and bulk electronic properties.</p><p><strong>Methods: </strong>Geometry optimizations for mercapto-terminated octa(p-phenylene) (neutral, radical cation, and dication states) used Density Functional Theory (B3LYP functional, 6-31G(d,p) basis set, RHF/ROHF methods) via Gaussian 16. Coherent electron transport calculations for molecules bridging Au(111) electrodes employed the Non-Equilibrium Green's Function (NEGF)-DFT method with QuantumATK. These transport calculations utilized norm-conserving Troullier-Martin pseudopotentials, double-zeta plus polarization (DZP) basis sets for C, H, S, single-zeta plus polarization (SZP) for Au, and the Perdew-Burke-Ernzerhof (PBE) functional with the spin-polarized Generalized Gradient Approximation (SGGA).</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"187"},"PeriodicalIF":2.1,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281900","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":"Quantum-inspired computational drug design for phytopharmaceuticals: a herbal holography analysis.","authors":"Yashwanth S, Prasiddhi Naik, Darshan B R, Chethan Patil, Prakash Goudanavar","doi":"10.1007/s00894-025-06412-w","DOIUrl":"https://doi.org/10.1007/s00894-025-06412-w","url":null,"abstract":"<p><strong>Context: </strong>Modern medication discovery is undergoing a paradigm change at the junction of herbal pharmacology with computational modeling informed by quantum theory. Herbal compounds, which have often been considered as complex and poorly understood entities, have historically been investigated using linear screening approaches and reductionist bioactivity models. A novel paradigm being presented in this work is herbal holography. Herbal molecules are seen by it as multi-dimensional systems best understood using holographic and quantum theories. As the pharmacological potential of plant-based compounds is under expanding research, more intricate integrated approaches are needed to grasp their bioactivities, predict their pharmacokinetics, and maximize drug lead optimization. The aim is to ascertain whether using quantum-driven methods results in a real revolution in herbal medicine or if it is really a pipe dream.</p><p><strong>Methods: </strong>This paper conducts a thorough examination of herbal remedies, focusing on how algorithms powered by hybrid quantum-classical simulations, deep learning models, and quantum mechanics can address the shortcomings of traditional methods. The advanced computational approaches explored in this research provide scalable models for modeling herbal compounds and assessing their pharmacological effects. Integrating views from systems biology, photochemistry, and quantum mechanics helps one to evaluate the translational usefulness of these technologies. The methodological approach using computational approaches for electronic structure prediction, network pharmacology, and bioactivity modeling draws from quantum physics, systems biology, and phytochemistry. We examine these early quantum technologies' scalable, usable benefits for interpreting herbal therapy complexity from a multidisciplinary perspective to include them into present drug development projects.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"188"},"PeriodicalIF":2.1,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281902","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":"Identification of potential human targets for epigallocatechin gallate through a novel protein binding site screening approach.","authors":"Jernej Hirci, Sandra Škufca, Tanja Kunej, Dušanka Janežič, Janez Konc","doi":"10.1007/s00894-025-06410-y","DOIUrl":"10.1007/s00894-025-06410-y","url":null,"abstract":"<p><strong>Context: </strong>Epigallocatechin-3-gallate (EGCG), a compound found in green tea, is known for its anticancer properties, although its specific protein targets remain largely undefined. In this study, we identified EGCG targets across the human proteome using a novel protein binding site screening approach. Among the 20 most likely predicted targets, six proteins-KRAS, FXa, MMP1, PLA2G2A, Hb, and CDK2-had been experimentally validated in previous studies. Fourteen additional proteins, including five kinases, were newly predicted as potential targets, all of which are implicated in cancer development and may mediate EGCG's anticancer effects. Enrichment analysis revealed KEGG pathways associated with cancer, with KRAS and PIM1 appearing as key nodes. These findings, which align with previous experimental research, offer new insights into the molecular mechanisms of EGCG and its potential role in modulating cancer-related pathways.</p><p><strong>Methods: </strong>An approach was devised to screen EGCG with 36,532 human protein binding sites using the ProBiS-Dock algorithm and the ProBiS-Dock database. Network and enrichment analyses with Cytoscape and StringApp identified protein interactions and KEGG pathways, revealing potential anticancer mechanisms of EGCG.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"189"},"PeriodicalIF":2.1,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12165993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281901","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":"Mechanism and kinetics of the reaction of atomic hydrogen with allene.","authors":"Tien V Pham","doi":"10.1007/s00894-025-06406-8","DOIUrl":"https://doi.org/10.1007/s00894-025-06406-8","url":null,"abstract":"<p><strong>Context: </strong>In the present work, mechanism and kinetics of the H + allene reaction have been carefully conducted. The computed results reveal that the abstraction mechanism can lead to the formation of propargyl radical (C₃H₃), an important precursor for the formation of aromatic hydrocarbons, with the energy barrier of about 10.3 kcal/mol. In contrast, the addition mechanism can easily overcome the energy barriers of only 2.1 and 3.8 kcal/mol to form two adducts IS1 (CH₃CCH₂, 2-propenyl) and IS2 (CH₂CHCH₂, allyl), respectively. These two adducts can then decomepose to various bimolecular products such as (C₂H₂ + CH₃) and (H + propyne). Kinetic analysis shows IS1 dominates product formation at T ≤ 600 K (yield 41-70%), while the (H + propyne) channel becomes predominant above 900 K (branching ratio 50-70%). The calculated rate constants for the abstraction channel are consistent with literature values, and the overall rate constants agree well with experimental data from Whytock, Brown, Michael, and Bentz. These results highlight the reliability of the computational approach and provide essential parameters for modeling C₃H₅-related systems.</p><p><strong>Methods: </strong>All species involved in the H + allene reaction were optimized using the DFT/M06-2X method with the aug-cc-pVTZ basis set. Single-point energies were calculated at the CCSD(T) level and extrapolated to the complete basis set (CBS) limit using aug-cc-pVTZ, aug-cc-pVQZ, and aug-cc-pV5Z. Rate constants were computed using transition state theory (TST) with the ChemRate program for the abstraction pathway, and RRKM/master equation calculations with the MESMER software for the addition-dissociation network. All quantum chemical calculations were performed using the Gaussian software package.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"185"},"PeriodicalIF":2.1,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257067","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 the role of density functional theory in the design of gold nanoparticles for targeted drug delivery: a systematic review.","authors":"Obiekezie C Obijiofor, Alexander S Novikov","doi":"10.1007/s00894-025-06405-9","DOIUrl":"10.1007/s00894-025-06405-9","url":null,"abstract":"<p><strong>Context: </strong>Targeted drug delivery systems leveraging gold nanoparticles (AuNPs) demand precise atomic-level design to overcome current limitations in drug-loading efficiency and controlled release. Unlike previous focused reviews, this systematic analysis compares density functional theory's (DFT) performance across multiple AuNP design challenges, including drug interactions, surface functionalization, and stimuli-responsive behaviors. DFT predicts binding energies with ~ 0.1 eV accuracy and elucidates electronic properties of AuNP-drug complexes, critical for optimizing drug delivery. For example, B3LYP-D3/LANL2DZ calculations predict a - 0.58 eV binding energy for thioabiraterone, ensuring stable chemisorption via sulfur-Au bonds, as validated by experimental binding assays. However, high computational costs restrict its application to large biomolecular systems. Emerging hybrid machine learning (ML)/DFT approaches address scalability while preserving quantum-mechanical accuracy, reducing computational costs from ~ 10⁶ to ~ 10³ CPU h for a 50 nm AuNP, positioning hybrid ML/DFT as a transformative approach for next-generation nanomedicine.</p><p><strong>Methods: </strong>This systematic evaluation covers DFT approaches including gradient-corrected (PBE), hybrid (B3LYP), and meta-GGA (M06-L) functionals, using relativistic basis sets (e.g., LANL2DZ) for Au atoms and polarized sets (e.g., 6-31G(d)) for organic ligands. Solvent effects are modeled via implicit (SMD) or explicit approaches. Time-dependent DFT (TD-DFT) analyzes localized surface plasmon resonance and frontier molecular orbitals. Multiscale approaches integrate DFT with molecular dynamics (MD) and machine learning interatomic potentials (MLIPs) to model extended systems, enabling simulations of AuNP-protein interactions for systems up to 10⁵ atoms with ~ 0.2 eV accuracy.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"186"},"PeriodicalIF":2.1,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257066","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":"Evaluation of antioxidant properties of lycopene isomers using density functional theory.","authors":"Baggya Sharmali Wickramanayaka Karunarathna, Thashini Kavindiyani Gunawardhana, G M Supun Tharaka Gajasinghe, Ranga Srinath Jayakody, Jayamal Damsith Wanniarachchi, Krishna Kuben Govender","doi":"10.1007/s00894-025-06399-4","DOIUrl":"https://doi.org/10.1007/s00894-025-06399-4","url":null,"abstract":"<p><strong>Context: </strong>Lycopene, a naturally occurring carotenoid found in all-trans configuration in various fruits and vegetables, is recognized for its potential antioxidant properties. This study employed the Density Functional Theory (DFT) to investigate and compare lycopene isomers' antioxidant properties through the radical scavenging mechanism. The antioxidant capacity of the isomers is quantified using global descriptive parameters, ranking their potential from highest to lowest as 5-cis > all-trans > 9-cis > 13-cis. The study identifies the Hydrogen Atom Transfer (HAT) mechanism as the predominant mode of antioxidant action, evidenced by the lowest bond dissociation energies when compared to other mechanisms such as Sequential Electron Transfer Proton Transfer (SETPT) and Sequential Proton Loss Electron Transfer (SPLET). The 5-cis isomer exhibits the lowest bond dissociation energy, indicating a superior thermodynamic potential for antioxidant activity relative to the other isomers. Additionally, activation energy assessments reveal that the 5-cis and 13-cis isomers are the most kinetically favourable under the HAT radical scavenging mechanism, surpassing the 9-cis and all-trans configurations. This investigation highlights the 5-cis isomer as both thermodynamically and kinetically the most favourable antioxidant among the lycopene isomers studied.</p><p><strong>Methods: </strong>The antioxidant potential and radical scavenging mechanism were computed using the ωB97X-D/6-31 + G (d,p) level of theory and the Gaussian 16 software package. The frontier molecular analysis and the global descriptive parameters were performed to compare the antioxidant properties of all-trans, 5-cis, 9-cis, and 13-cis isomers. Hydrogen atom abstraction (HAA), sequential electron transfer proton transfer (SETPT), and sequential proton loss electron transfer (SPLET) mechanisms were studied. The radical scavenging mechanism of isomers was performed using the QST3 (synchronization transition Quasi-Newton Searching) calculation, followed by the IRC (Intrinsic Reaction Coordinate) calculation.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"184"},"PeriodicalIF":2.1,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214581","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}