Journal of Molecular Modeling最新文献

{"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":"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":"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":"Mechanism and kinetics of the reaction of atomic hydrogen with allene.","authors":"Tien V Pham","doi":"10.1007/s00894-025-06406-8","DOIUrl":"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":"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}

{"title":"Effect of gold slab layers relaxation on adsorption of alkanethiols on the (111) surface: a density functional theory study.","authors":"Walid Iken, Hayat El Ouafy, Loubna Halil, Soukaina Naciri, Mouad Boutkbout Nait Moudou, Mouna Aamor, Mohamed Reda Chriyaa, Tarik El Ouafy","doi":"10.1007/s00894-025-06404-w","DOIUrl":"10.1007/s00894-025-06404-w","url":null,"abstract":"<p><strong>Context: </strong>Despite numerous studies on alkanethiol adsorption on gold surfaces, this work uniquely investigates the impact of Au(111) surface layers relaxation on adsorption energy, electrical conductivity, and molecular geometry using density functional theory (DFT). We demonstrate that adsorption energy increases linearly with increasing relaxation layers. Notably, relaxing only the top layer yields a slope close to experimental data. Geometrically, molecules exhibit greater tilt on a fully frozen surface, except methanethiol. In terms of electrical conductivity, gap energy decreases upon adsorption when all layers are frozen. Furthermore, Fermi energy rises exponentially with adsorption energy for a frozen surface but follows a linear trend with relaxation. These insights offer a deeper understanding of surface effects on molecular adsorption.</p><p><strong>Methods: </strong>Adsorption energies and geometric parameters were calculated by DFT with QUANTUM ESPRESSO, using GGA-PBE and Grimme D3 for van der Waals corrections. Core-valence interactions were described by PAW and pseudopotentials. Au(111) slab, constructed with VESTA, contained 3 layers.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"182"},"PeriodicalIF":2.1,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214580","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 research on tricyclic-based as high-energy performance energetic materials.","authors":"Shaoqing Wang, Yan Huang, Qing Ma, Fu-Xue Chen","doi":"10.1007/s00894-025-06401-z","DOIUrl":"10.1007/s00894-025-06401-z","url":null,"abstract":"<p><strong>Context: </strong>A series of tricyclic high energy density materials (HEDMs) incorporating diazole, triazole, and tetrazole frameworks were systematically investigated through density functional theory (DFT) calculations at the B3LYP/6-31G +  + (d,p) and M06-2X/def2-SVP levels. Nitroform-based compounds and fluorodinitromethyl-substituted derivatives were found to exhibit superior densities compared to HMX. Notably, compound II-7 demonstrated the highest predicted density of 2.04 g cm⁻³, along with optimal detonation performance (D = 9451 m s⁻¹, P = 42.57 GPa), surpassing that of HMX. Regarding heat of formation, the tetrazole-based compound III-1 exhibited the highest value of 844.42 kJ mol⁻¹, suggesting enhanced energy content. While nitroform groups improve performance, fluorine substitution offers better stability and sensitivity, representing an effective optimization strategy for energetic materials. Comparative analysis of structures with identical substituents but different parent ring frameworks reveals clear structure property relationships. The incorporation of nitrogen oxygen bonds is shown to significantly enhance performance characteristics.</p><p><strong>Method: </strong>Based on the DFT, molecular optimization and performance metrics analysis were all calculated using the Gaussian 09 package at B3LYP/6-31G +  + (d,p) and M06-2X/def2-SVP levels. The electrostatic potential energy and other related calculations were computed using Multiwfn_3.8_dev software. The visualization of the weak interaction between dimers was accomplished using VMD 1.9.3 program.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"183"},"PeriodicalIF":2.1,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214584","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":"Fused pyrido[3,4-D]pyrimidine moiety with phthalazinone ring accelerate dual inhibition of PARP1 and CDK4 in triple-negative breast cancer: a hybrid design with computational investigation through molecular modeling and quantum mechanics.","authors":"Mahema Sivakumar, Jency Roshni, Sheikh F Ahmad, Sabry M Attia, Magesh Ramasamy, Shiek S S J Ahmed","doi":"10.1007/s00894-025-06393-w","DOIUrl":"10.1007/s00894-025-06393-w","url":null,"abstract":"<p><strong>Context: </strong>The PARP inhibitor olaparib is effective in breast cancer patients; however, its efficacy is reduced in triple-negative breast cancer (TNBC) due to mechanisms of drug resistance. Recent studies demonstrate that the CDK4 inhibitor palbociclib can enhance the sensitivity of cancer cells to PARP inhibitors. We designed 43 hybrid compounds by combining the pyrido[3,4-d]pyrimidine moiety from palbociclib with the phthalazinone ring from olaparib. Pharmacokinetic profiling and molecular docking revealed compound 17 as a promising candidate, demonstrating a binding affinity of - 8.42 kcal/mol with PARP1 and - 10.05 kcal/mol with CDK4, in contrast to the native inhibitors. Furthermore, the induced fit docking validated its superiority compared to the native inhibitors. Molecular dynamics simulations over 500 ns confirmed the structural stability of compound 17 with both targets. Moreover, the QM/MM, DFT, TD-DFT, and MEP analyses yielded significant insights into charge transfer and electronic transitions, augmenting our understanding of the electronic and bonding properties of the hybrid compound.</p><p><strong>Methods: </strong>To facilitate the design of 43 hybrid compounds, ChemSketch was utilized, and QikProp, a module of the Maestro Schrödinger suite (v13.5), was used to make predictions regarding the pharmacokinetic properties of these compounds. We checked the binding affinities using docking methods and the stability of the protein-ligand complex using molecular dynamics simulations with Desmond module in Maestro Schrödinger suite (v13.5). Quantum mechanical analyses at the B3LYP/6-31G** level were conducted to elucidate the DFT/TD-DFT, molecular electrostatic potential, Mulliken charges, chemical descriptors, NBO, and NLO properties.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"181"},"PeriodicalIF":2.1,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214582","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":"The K⁺/Y³⁺ cationic exchange in a C₅-symmetric metallamacrocyclic scaffold: DFT examination with QTAIM, ELF, MEP approaches and XRD study of the final alaninehydroximate complex.","authors":"Grigory Zhigulin, Galina Zabrodina, Evgeny Baranov, Marina Katkova, Sergey Ketkov","doi":"10.1007/s00894-025-06409-5","DOIUrl":"10.1007/s00894-025-06409-5","url":null,"abstract":"<p><strong>Context: </strong>Participation of the heterobimetallic potassium-copper metallamacrocycle in synthesis of the yttrium-copper C₅-symmetric complex based on the L-α-alaninehydroximate (Alaha) ligands was investigated by DFT. Two possible conformations of the K(I)-Cu(II) intermediate which can realize in solution were simulated. Theoretical estimations of an activation barrier for the conformational conversion, ∆G^≠_sol(298.15) = 2.7 and 1.0 kcal/mol, indicate a structural inversion of the encapsulated K⁺ ion relative to the copper-containing metallamacrocyclic environment (scaffold). The K(I)-Cu(II) intermediate is considered as a handy molecular platform for facile chelation of the Y³⁺ ions in water solutions that can be used in the nuclear medicine. Replacement of the K⁺ central ion by Y³⁺ is driven by the higher positive charge of the latter which makes it a stronger acceptor of the metallamacrocyclic electron density. Corresponding changes in the electron structure were revealed and quantified by the DFT calculations. Also, the theoretical thermodynamic estimations predict enhanced stability of the final Y(III)-Cu(II) metallamacrocycle. Accordingly, the water-soluble Y(III)-Cu(II) alaninehydroximate complex was prepared in the presence of K₂CO₃ as one of starting reagents.</p><p><strong>Methods: </strong>The quantum chemical calculations were performed at the M06/def2-TZVP and TPSS-D3/def2-TZVP levels of DFT with use of the polarizable continuum model. The differences in the electron structures were investigated in detail by the quantum theory of atoms in molecules, electron localization function, and molecular electrostatic potential. The final product of the Y(CO₃)(H₂O)[15-MC_Cu(II)Alaha-5](I)∙11H₂O composition was characterized by the X-ray diffraction.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"180"},"PeriodicalIF":2.1,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214583","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":"Geometrical and electronic structures, stability, and aromaticity of copper-doped boron clusters B_nCu^0/- (n = 1-13).","authors":"Nguyen Huu Tho, Ngo Huyen Tran, Pham Hong Cam, Nguyen Minh Tam","doi":"10.1007/s00894-025-06381-0","DOIUrl":"10.1007/s00894-025-06381-0","url":null,"abstract":"<p><strong>Context: </strong>Besides small pure boron clusters which have been well studied, doped boron clusters, in particular with transition metal dopants, are also increasingly investigated due to their unique geometrical structures accompanied by novel physical and chemical properties. However, studies on copper-doped boron clusters are still scarce despite copper being a transition metal with important properties. In this context, the geometry, stability, and electronic properties of copper-doped boron clusters B_nCu^0/- (n = 1-13) were systematically studied. The obtained results show that the geometries of neutral and anionic clusters are very similar only at sizes n = 2, 5, 6, 8, and 10. In the ground state, both neutral and anionic clusters tend to be in the low-spin state, except for B₂Cu^- and B₆Cu^-. The relative stability of these structures was evaluated using various energetic parameters. Moreover, the aromaticity of the B₈Cu^- anion along with its enhanced stability are also discussed and rationalized in detail.</p><p><strong>Method: </strong>In this work, the geometry optimization and the following molecular orbital analyses of B_nCu^0/- (n = 1-13) structures are performed using density functional theory (DFT), specifically the hybrid functional TPSSh combined with the 6-311+ G(d) basis set for boron atoms and the aug-cc-pVTZ-PP basis set for a copper atom. To obtain more reliable results, the single point energies of some lowest lying isomers whose relative energy values are close corresponding to geometries optimized at the TPSSh/6-311+ G(d) (B) / aug-cc-pVTZ-PP (Cu) level were determined with higher precision at the CCSD(T) level with the same basis sets. Based on the obtained results at the DFT level, the energetic parameters are determined to elucidate thermodynamic stability of B_nCu clusters. NICS and ELF indices, the density of states, and AdNDP bond analysis are then examined to rationalize the aromaticity of the anion B₈Cu^-. All calculations were performed using the Gaussian 09 and Multiwfn programs.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":"179"},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186192","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}