Journal of molecular graphics & modelling最新文献

{"title":"First-principles predictions of Co/V-doped MoS₂ for alkali metal ion storage: Electronic structure modulation and electrochemical performance.","authors":"Yuda Lin, Ziqing Lin, Huidan Lin, SuZhen He","doi":"10.1016/j.jmgm.2026.109621","DOIUrl":"https://doi.org/10.1016/j.jmgm.2026.109621","url":null,"abstract":"<p><p>This study systematically investigated the effects of Co- and V-doping on the structural stability, mechanical properties, electronic structure, and electrochemical performance of MoS₂ using first-principles calculations. Phonon dispersion spectrum analysis confirmed that both Co-MoS₂ and V-MoS₂ exhibit excellent dynamic stability. Mechanical property tests demonstrated that doping significantly enhances the Young's modulus (Co-MoS₂: 220 N/m; V-MoS₂: 238 N/m) and maintaining an appropriate Poisson's ratio, effectively mitigating stress concentration. DOS calculations revealed that Co- and V-doping markedly improve the intrinsic electronic conductivity of MoS₂, with band gaps reduced to 0.39 eV and 0.98 eV for Co-MoS₂ and V-MoS₂, respectively. In terms of electrochemical performance, the study yielded breakthrough findings: the doped systems significantly lowered the migration barriers for Li⁺/Na⁺/K⁺ (Co-MoS₂: 0.06 eV/0.09 eV/0.09 eV, V-MoS₂: 0.27 eV/0.24 eV/0.21 eV), achieving fast ion transport kinetics. Charge density difference and adsorption energy analyses showed that Co- and V-doping strengthens the interactions between MoS₂ and Li⁺/Na⁺/K⁺. Additionally, doped significantly increased the average open-circuit voltage of MoS₂ for Li⁺/Na⁺/K⁺ (Co-MoS₂: 0.76 V/0.68 V/0.44 V, V-MoS₂: 0.83 V/0.71 V/0.51 V), providing a crucial theoretical basis for designing electrode materials with high energy density. These findings provide new design strategies and theoretical guidance for developing high-performance MoS₂ materials for alkali metal-ion batteries.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"150 ","pages":"109621"},"PeriodicalIF":3.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149228072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Binding roles of major components and new inhibitor from Andrographis paniculata targeting SARS-CoV-2 main protease using molecular dynamics simulations, density functional theory, and in vitro study.","authors":"Aunlika Chimprasit, Nopawit Khamto, Sathid Aimjongjun, Supa Hannongbua, Patchreenart Saparpakorn","doi":"10.1016/j.jmgm.2026.109626","DOIUrl":"https://doi.org/10.1016/j.jmgm.2026.109626","url":null,"abstract":"<p><p>In a severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the main protease M^pro plays a crucial role in the viral replication process. Andrographis paniculata has been reported for anti-SARS-CoV-2 properties. This work aims to identify new SARS-CoV-2 M^pro inhibitors and investigate the binding roles of major diterpene lactones derived from Andrographis paniculata. Molecular docking and molecular dynamic (MD) simulations with the dimeric SARS-CoV-2 M^pro were performed to identify the potential compounds which are five major diterpene lactones and four selected compounds. Binding affinities, expressed as binding and interaction energies, were calculated using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method and the quantum mechanics/molecular mechanics (QM/MM) using density functional theory. Principal component analysis (PCA), along with free energy landscape (FEL) analysis, was performed to assess the stability of the ligand-protein binding interactions. The density functional theory in terms of residual interaction energies revealed that H-bond, H-pi and pi-pi interactions were key interactions during the binding. Andrographidine E from Andrographis paniculata was found to be a new SARS-CoV-2 M^pro inhibitor with the IC₅₀ of 158 μM. The results help explain the roles of binding of compounds against dimeric SARS-CoV-2M^pro which will be useful for the development of SARS-CoV-2 M^pro inhibitors.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"150 ","pages":"109626"},"PeriodicalIF":3.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149228051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative DFT and molecular dynamics investigation of PFAS adsorption on heteroatom-engineered metal-organic framework linker models.","authors":"Rahul Verma, Satvik Rastogi, Vanshika Mishra, Arvind Misra, Debabrata Ghosh, Satyakam Patnaik","doi":"10.1016/j.jmgm.2026.109616","DOIUrl":"https://doi.org/10.1016/j.jmgm.2026.109616","url":null,"abstract":"<p><p>Per- and polyfluoroalkyl substances (PFAS) represent persistent contaminants in aquatic environments, and developing effective absorbents for their removal is a major challenge. This study has been conducted for absorbent design using density functional theory (DFT) and molecular dynamics (MD) in order to understand the process of adsorption of the following PFAS species: PFBA^-, PFBS^-, PFOA^-, and PFOS^- on nitrogen-, oxygen-, and sulfur-containing linker models. For this, geometry optimizations were performed at ωB97XD/6-311++G(d, p) level under implicit aqueous solvation, and the adsorption energies were calculated using the counterpoise correction technique. The final results showed that four PFAS molecules exhibited appropriate counterpoise-corrected adsorption energies ranging from -0.700 to -20.047 kcal mol^-1, with the strongest interaction between the PFOS^- molecule and the sulfur-containing linker model (-20.047 kcal mol^-1). As for the effect of sulfur substitution on the mean energy of adsorption for various PFAS species, it was negative, but the identity of the heteroatom affected PFAS adsorption behavior. Conceptual DFT descriptors based on frontier orbitals showed weak and statistically insignificant linear relations with adsorption energies, indicating that a single comprehensive electronic descriptor is not sufficient to explain the trend in adsorption energy across the data set. The analyses based on ALIE, RDG and NCI showed that the electronic activity depends on the ligands and involves both dispersive and attractive non-covalent interactions. Hirshfeld analysis revealed the predominance of ligand-H contacts, while other analyses (ELF and DOS) indicated that electron localization and redistribution depend on the heteroatoms. Finally, the 100 ns aqueous MD simulations provided evidence of continuous interaction between PFOS and ligands, accompanied by significant conformational and interfacial alterations, as well as sampling of low-free-energy states. The conclusions drawn from these results indicate that PFAS adsorption at the linker level arises from the combined effects of molecular structure, the electronic environment influenced by heteroatoms, and noncovalent interactions.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"150 ","pages":"109616"},"PeriodicalIF":3.1,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PRAXIS-MD: a long-term brain-enhanced agent framework for end-to-end molecular dynamics research.","authors":"Zhenyu Ma, Chunyi Yang, Jingyi Zhu, Yuyang Song, Letian Yang, Limei Xu, Min Xiao, Xukai Jiang","doi":"10.1016/j.jmgm.2026.109623","DOIUrl":"https://doi.org/10.1016/j.jmgm.2026.109623","url":null,"abstract":"<p><p>Molecular dynamics (MD) simulation is widely used to investigate biomolecular stability, conformational transitions, molecular recognition and membrane transport, yet practical MD research still relies on many experience-driven decisions that are difficult to standardize and reproduce. Here, we present PRAXIS-MD, a case-guided problem-solving protocol that converts a natural-language biological question into an auditable MD workflow. The protocol couples an external long-term brain, comprising case memory, reusable skills and negative cases, with a brain-gated retrieve-plan-execute loop. This design grounds structure selection, system preparation, simulation planning, trajectory analysis and mechanistic interpretation in reusable prior experience rather than one-shot prompting. We distilled nine representative MD studies into reusable workflow knowledge and evaluated the protocol on nine unseen benchmark tasks under bare, memory-only, skill-only, rule-only and full PRAXIS-MD settings. Full PRAXIS-MD achieved the highest benchmark score, and integration with five additional LLM hosts improved performance across all hosts. In an independent membrane lipid transport case, PRAXIS-MD organized a coherent flippase/scramblase workflow without a predefined template. These results suggest that structured case learning can improve the reproducibility, transferability and biological interpretability of automated MD workflows.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"150 ","pages":"109623"},"PeriodicalIF":3.1,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the structural, Elastomechanical, and optoelectronic properties of HfHgX₂ (X = S, Se, Te) ternary Chalcogenides: A first-principles study.","authors":"Sadaf Bashir, Naif Almakayeel, Nadia Ayari, Farah Andleeb, Hira Iqbal, Muhammad Nasir Rasul","doi":"10.1016/j.jmgm.2026.109619","DOIUrl":"https://doi.org/10.1016/j.jmgm.2026.109619","url":null,"abstract":"<p><p>The present study aims to theoretically explore the physical properties of HfHgX₂ (X = S, Se, Te) compounds. The structural, electronic, bonding, elastic, and optical properties are investigated using density functional theory based VASP code. Structural analysis unveils that HfHgX₂ (X = S, Se, Te) compounds crystallize in the trigonal crystal system with the R 3‾ m (No. 166) space group. The calculated structural and lattice parameters are in good agreement with the available literature data. The calculated formation energy values are -1.195622 eV (HfHgS₂), -1.257295 eV (HfHgSe₂), and -0.615084 eV (HfHgTe₂) showing the thermodynamic stability. The electronic properties reveal that HfHgS₂ possesses a direct band gap, whereas HfHgSe₂ and HfHgTe₂ exhibit indirect band gaps via PBE-GGA potential. The absence of imaginary phonons modes indicates the lattice dynamical stability of these studied compounds. The partial charge density distribution indicates that the occupied electronic states are predominantly localized around the chalcogen atoms, whereas the unoccupied electronic states are mainly localized around the Hf atoms providing the electronic transition route from X → Hf. The examination of -COHP demonstrates that Hf-X bonding interactions are the primary contributors to the structural stability of these compounds with ICOHP values for Hf-X (X = S, Se, Te) bonds are -3.107, -2.808, and -2.383 and corresponding ICOBI values of 0.644, 0.643, and 0.646 respectively. The direction-dependent optical properties were calculated along the ab-plane, c-axis, and total, revealing substantial directional dependence and pronounced optical anisotropy via PBE-GGA and SCAN potentials. The elastic properties confirm the mechanical stability criterion, indicating that the HfHgS₂ compound is less brittle than HfHgSe₂ and HfHgTe₂. The mechanical properties show that the HfHgX₂ (X = S, Se, Te) compounds are highly anisotropic due to their distinct bonding environment and the different interactions within the layers of their layered crystal framework.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"150 ","pages":"109619"},"PeriodicalIF":3.1,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149228031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pharmacophore modelling-based screening of natural allosteric EGFR inhibitors using molecular docking, DFT, and molecular dynamics simulations.","authors":"Fatima Munir, Muhammad Bilal Amir, Kashif Hussain, Muhammad Zahid, Jian Zhang","doi":"10.1016/j.jmgm.2026.109594","DOIUrl":"https://doi.org/10.1016/j.jmgm.2026.109594","url":null,"abstract":"<p><p>The development of allosteric inhibitors is a promising strategy for targeting epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC), especially in cases where orthosteric inhibitors face resistance. However, despite their selective inhibition of EGFR mutations, fourth-generation allosteric inhibitors show limited antiproliferative efficacy without cetuximab. The present study aims to identify potent natural product-derived allosteric inhibitors for NSCLC using a comprehensive approach, including pharmacophore modelling, Lipinski's Rule of Five (Ro5), ADMET profiling, density functional theory, and molecular docking. Experimentally validated EGFR tyrosine kinase inhibitors (TKIs) were used to build a pharmacophore model. The validated pharmacophore model was used to screen the Natural Product Activity and Species Source database. Drug-likeness was assessed using Ro5 and ADMET to predict pharmacokinetic and toxicity profiles for further drug development. Molecular docking studies revealed that the identified natural compounds exhibited more favorable docking scores (-8.74 to -7.87 kcal/mol) than the co-crystallized ligand (-7.32 kcal/mol), indicating significant interactions with the receptor residues. Geometry optimization, electrostatic potential, and frontier molecular orbital analyses were performed to assess potential reactive sites and molecular stability. Molecular dynamics (MD) simulations, subsequent post-MD analyses, and binding free energy calculations provided additional support for these findings. The free-energy landscape revealed stable, favorable binding conformations, suggesting that they may act as allosteric inhibitors. These results highlight the potential of natural compounds to combat resistance to EGFR-TKIs in NSCLC. In particular, compounds 1 and 2 emerged as promising candidates targeting mutant EGFR and warrant further experimental validation as potential leads for NSCLC treatment.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"150 ","pages":"109594"},"PeriodicalIF":3.1,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GeoSeq-EGNN: A geometry-sequence fused equivariant graph neural network for predicting short linear motifs within intrinsically disordered regions.","authors":"Jun Zhang, Jinming Zhang, Liting Zheng, Huiqiong Ruan, Yuxiang Li, Yi Li, Guilan Luo","doi":"10.1016/j.jmgm.2026.109610","DOIUrl":"https://doi.org/10.1016/j.jmgm.2026.109610","url":null,"abstract":"<p><p>Short linear motifs (SLiMs) located within intrinsically disordered regions (IDRs) are essential for mediating dynamic protein-protein interactions. However, their short length, sequence degeneracy, and the conformational heterogeneity of IDRs pose significant challenges for accurate computational identification. Traditional methods that rely exclusively on one-dimensional sequences or static three-dimensional structures may not adequately capture the intricate interplay between structure and sequence, while severe class imbalance often results in unacceptably high false-positive rates. To address these challenges, we introduce GeoSeq-EGNN, a Geometry-Sequence Fused Equivariant Graph Neural Network designed for dual-modality SLiMs prediction. This architecture effectively integrates Global-Local Hybrid Equivariant Message Passing Layers (GLH-EMPL) to model the three-dimensional spatial folding dynamics of IDRs, alongside Multi-Scale Geometry-Sequence Fusion Network Layers (MSGS-FNL) that utilize Bidirectional LSTMs to extract critical one-dimensional primary sequence topologies. We also incorporate an adaptive coordinate update mechanism to improve geometric stability in deeper layers and dynamic gate feature fusion to reduce representation over-smoothing. To address class imbalance, we use a confidence-aware focal loss that penalizes overconfident erroneous predictions. On the evaluated SLiMs dataset, GeoSeq-EGNN achieved an accuracy of 92.94% and an AUPRC of 82.17% under the final F6 feature configuration and outperformed the evaluated baseline models in the controlled one-hot comparison, with higher Precision and Matthews Correlation Coefficient (MCC). These results support GeoSeq-EGNN as a computational framework for SLiM prediction and provide a basis for future studies of SLiM-mediated regulatory networks.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"150 ","pages":"109610"},"PeriodicalIF":3.1,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A first-principles study of hydrogen storage on MXene Mo2C monolayer","authors":"Mohamed Bakhit,&nbsp;Sina Karimzadeh,&nbsp;Tien-Chien Jen","doi":"10.1016/j.jmgm.2026.109283","DOIUrl":"10.1016/j.jmgm.2026.109283","url":null,"abstract":"<div><div>This study investigates the potential of Mo₂C MXene as a hydrogen storage material using density functional theory (DFT) and molecular dynamics (MD) simulations to examine its structural stability, electronic properties, and hydrogen adsorption behavior. The optimized Mo₂C structure exhibits a hexagonal lattice with favorable adsorption sites over Mo atoms and shows a surface area expansion of approximately 4 % after hydrogen loading while maintaining lattice symmetry. Thermodynamic stability is confirmed through adsorption energy calculations, which reveal a clear relationship between energy levels and hydrogen concentration. The results indicate that H₂ adsorption on Mo₂C is a thermodynamically favorable and exothermic process, with adsorption energies ranging from −0.184 to −0.528 eV, satisfying the criteria for practical hydrogen storage applications. Charge transfer analysis identifies Mo atoms as electron acceptors. Density of States (DOS) calculations reveal a near-zero band gap, confirming the metallic nature of Mo₂C, while Projected DOS (PDOS) and orbital maps show significant hybridization and electronic polarization among H, Mo, and C atoms. Charge density difference maps highlight effective charge redistribution with strong electric fields around Mo atoms. MD simulations further confirm the structural stability of the Mo₂C–H₂ system, showing minimal deformation during a 100 ps simulation and supporting efficient hydrogen adsorption. Overall, these findings establish Mo₂C MXene as a promising candidate for hydrogen storage applications and provide valuable insights for experimental validation and further development of sustainable energy storage technologies.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"144 ","pages":"Article 109283"},"PeriodicalIF":3.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145980546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico engineering of transaminase variants for enhanced biocatalytic conversion of an ACE inhibitor precursor","authors":"Mohammad Asad ,&nbsp;Mohamed Usman ,&nbsp;Anisha Ashokan,&nbsp;Naveen Kulkarni","doi":"10.1016/j.jmgm.2026.109308","DOIUrl":"10.1016/j.jmgm.2026.109308","url":null,"abstract":"<div><div>Angiotensin-converting enzyme (ACE) inhibitors are widely prescribed for cardiovascular disorders, yet their conventional chemical synthesis involves multiple steps, high energy consumption, and poor stereoselectivity. In this work, we present a fully <em>in</em> <em>silico</em> framework for the computational design and prediction of transaminase (TA) variants capable of catalyzing the asymmetric amination of ethyl 2-oxo-4-phenylbutanoate (OPBE) to yield L-homophenylalanine ethyl ester (L-HPE), a key chiral intermediate in ACE inhibitor synthesis. A homology model of the <em>Silicibacter</em> transaminase (62.7 % identity to 5KR6) was constructed in its dimeric form. Eleven active-site variants were designed and screened through molecular docking, followed by 100 ns molecular dynamics simulations. The top variants SbTA10, SbTA01, and SbTA11 exhibited reactive distances below 6 Å, binding energies between −17.7 and −20.8 kcal/mol, and substrate RMSD values under 2.0 Å, indicating stable enzyme–substrate complexes. A composite QZ-score integrating productive conformations, binding energy, pocket contacts, and structural stability ranked SbTA10 highest (0.89), followed by SbTA01 (0.88) and SbTA11 (0.85). Free-energy profiles derived from umbrella sampling revealed binding minima of −10.2 kcal/mol (SbTA10) and −8.1 kcal/mol (SbTA11), suggesting distinct substrate retention characteristics that may influence catalytic turnover. Collectively, these results identify plausible transaminase variants with favorable structural and energetic features for the proposed OPBE to L-HPE transformation. This study presents a computational framework for predicting transaminase variants, providing a basis for rational biocatalyst design that warrants future experimental validation to confirm catalytic efficiency and stereoselectivity.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"144 ","pages":"Article 109308"},"PeriodicalIF":3.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146079023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the potential of π-conjugated 2TT-R non-fullerene alternatives for multifunctional optoelectronic applications: A first-principles study","authors":"Sidra Manzoor ,&nbsp;Nadeem Raza ,&nbsp;Faheem Abbas","doi":"10.1016/j.jmgm.2026.109285","DOIUrl":"10.1016/j.jmgm.2026.109285","url":null,"abstract":"<div><div>Organic solar cells (OSCs) offer lightweight, flexible, and cost−effective energy solutions. However, fullerene−based systems face limitations in stability, tunability, and absorption, prompting the exploration of non−fullerene alternatives to enhance efficiency and scalability. In this work, five newly designed molecules <strong>(2</strong><strong>TT−1A to 2</strong><strong>TT−5A)</strong> were systematically studied using Density Functional Theory (DFT) and Time−Dependent DFT (TD−DFT) at the B3LYP/6−311G (d, p) level in both gas and solvent (chloroform) phases. Key optoelectronic properties, including HOMO−LUMO gaps, absorption spectra, dipole moments, and excitation energies, were analyzed to evaluate their photovoltaic performance. All compounds demonstrated strong light−harvesting abilities, with a notable redshift in the absorption spectra observed in the solvent phase. Among them, <strong>2</strong><strong>TT−5A</strong> stood out with the narrowest energy gap (1.35 eV), the longest absorption wavelength (861 nm), the highest dipole moment (12.17 D), and the lowest excitation energy (1.43 eV), indicating efficient charge transfer and exciton dissociation. Open−circuit voltages (<em>V</em>_oc) ranging from 0.54 to 1.38 V also suggest good photovoltaic potential. Additionally, the nonlinear optical (NLO) and organic light−emitting diodes (OLED) properties of <strong>2</strong><strong>TT−5A</strong> were explored, revealing significant hyperpolarizability and a favorable emission profile. These results suggested that <strong>2</strong><strong>TT−5A</strong> is an exceptional multifunctional candidate, encouraging experimental synthesis and validating this material's stability, potentially accelerating the development of multifunctional organic optoelectronic devices.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"144 ","pages":"Article 109285"},"PeriodicalIF":3.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146018703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}