Journal of molecular graphics & modelling最新文献_第3页

The role of protonation and solvation in modulating the electronic structure in α- and β-D-glucosamine: A density functional theory study 质子化和溶剂化在调节α-和β- d -氨基葡萄糖电子结构中的作用：密度泛函理论研究。

IF 3 4区生物学

Journal of molecular graphics & modelling Pub Date : 2025-09-14 DOI: 10.1016/j.jmgm.2025.109175

Rodolfo Daniel Ávila-Avilés

{"title":"The role of protonation and solvation in modulating the electronic structure in α- and β-D-glucosamine: A density functional theory study","authors":"Rodolfo Daniel Ávila-Avilés","doi":"10.1016/j.jmgm.2025.109175","DOIUrl":"10.1016/j.jmgm.2025.109175","url":null,"abstract":"<div><div>Glucosamine is a biologically relevant amino sugar that plays a key role in glycoproteins and polysaccharides such as chitin and chitosan. Despite its importance, a detailed quantum-level understanding of the electronic and conformational behavior of its α- and β-anomers under varying protonation and hydration conditions remains limited. Herein, we present a comprehensive DFT study at the B3LYP/6-31+G(d,p) level, modeling α- and β-D-glucosamine in both neutral and protonated forms with explicit hydration (1–5 water molecules). Our results show that neutral β-glucosamine is energetically more stable than its α-counterpart by 0.61 kcal/mol, consistent with its predominance in aqueous solution. Protonation induces significant electronic redistribution, with the LUMO localizing around the NH<sub>3</sub><sup>+</sup> group and the HOMO shifting away from it. This leads to a marked increase in the HOMO–LUMO energy gap, from 6.37 kcal/mol (neutral α-form) to a maximum of 7.32 kcal/mol (protonated β-form with 4H<sub>2</sub>O), indicating enhanced electronic stability and decreased reactivity. Explicit solvation stabilizes key hydrogen bond networks, with H-bond lengths as short as 1.51 Å in protonated systems. These findings offer new insight into how solvation and protonation shape the electronic landscape of glucosamine, with implications for its behavior in biological systems, material design, and protonation-dependent reactivity. The novelty of this study lies in combining explicit microsolvation with frontier orbital and MEP analysis across protonation states of both anomers—a previously unexplored approach.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109175"},"PeriodicalIF":3.0,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145080785","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}

引用次数: 0

MolContraCLIP: Structurally similar molecule retrieval algorithm based on graph neural network and CLIP model MolContraCLIP：基于图神经网络和CLIP模型的结构相似分子检索算法。

IF 3 4区生物学

Journal of molecular graphics & modelling Pub Date : 2025-09-13 DOI: 10.1016/j.jmgm.2025.109172

Huiwen Long, Yongquan Jiang, Yan Yang, Kuanping Gong

{"title":"MolContraCLIP: Structurally similar molecule retrieval algorithm based on graph neural network and CLIP model","authors":"Huiwen Long, Yongquan Jiang, Yan Yang, Kuanping Gong","doi":"10.1016/j.jmgm.2025.109172","DOIUrl":"10.1016/j.jmgm.2025.109172","url":null,"abstract":"<div><div>Molecular similarity assessment is pivotal in drug discovery and materials science, yet conventional methods often fail to integrate complementary 2D topological and 3D geometric information effectively. Inspired by Radford et al. (2021) the cross-modal alignment capability of Contrastive Language-Image Pretraining (CLIP), this study proposes a novel graph neural network (GNN) framework that unifies 2D and 3D molecular representations through a CLIP-inspired contrastive learning strategy. Our dual-channel architecture employs a Graph Isomorphism Network (GIN) for 2D topology encoding and a Graph Attention Network (GAT) for 3D spatial feature extraction. These modality-specific embeddings are aligned in a shared latent space via the InfoNCE loss, emulating CLIP’s paradigm to maximize mutual information between 2D and 3D molecular structures. Extensive experiments on the QM9 dataset demonstrate that our model significantly outperforms traditional fingerprint-based methods and pure GNN baselines in molecular similarity assessment. Ablation studies further validate the critical role of cross-modal contrastive learning in bridging structural information. The framework exhibits robust generalizability across diverse molecular types, offering a pioneering adaptation of CLIP’s principles to non-visual domains. This work advances multimodal representation learning in cheminformatics and opens avenues for future applications in molecular-text retrieval and drug design.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109172"},"PeriodicalIF":3.0,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145092150","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}

引用次数: 0

Ricci-GraphDTA: A graph neural network integrating discrete Ricci curvature for drug–target affinity prediction Ricci- graphdta：一种集成离散Ricci曲率的图神经网络，用于药物靶点亲和力预测。

IF 3 4区生物学

Journal of molecular graphics & modelling Pub Date : 2025-09-13 DOI: 10.1016/j.jmgm.2025.109170

Xiangxiang Zheng , Zhongrong Zhang , Xiaona Zhang , Nengzhi Jin , Yunyun Zhang

{"title":"Ricci-GraphDTA: A graph neural network integrating discrete Ricci curvature for drug–target affinity prediction","authors":"Xiangxiang Zheng , Zhongrong Zhang , Xiaona Zhang , Nengzhi Jin , Yunyun Zhang","doi":"10.1016/j.jmgm.2025.109170","DOIUrl":"10.1016/j.jmgm.2025.109170","url":null,"abstract":"<div><div>Drug–target affinity (DTA) prediction facilitates accelerated drug screening and reduces development costs. To enhance prediction performance and generalization capability, this paper proposes a DTA prediction model based on discrete curvature, named Ricci-GraphDTA, which integrates molecular graph and protein sequence modeling for efficient and accurate DTA prediction. The model consists of three parts: feature encoding, input representation learning, and affinity prediction. In the feature encoding stage, drug molecules are modeled as graphs, where Forman curvature is introduced to adjust the weights of neighbor information aggregation. A GIN residual network is then used to capture the local geometric and topological features of molecules. Protein sequences are modeled using BiLSTM to extract global dependency features, enhanced by an attention mechanism to capture long-range dependencies and key residue interactions—overcoming the limitations of traditional CNNs in handling long-range dependencies. In the input representation learning stage, the high-level representations of drugs and proteins are concatenated and passed through multiple nonlinear transformations to extract cross-modal interaction features, which are then used for affinity prediction. Experimental results demonstrate that Ricci-GraphDTA exhibits significant performance across various evaluation metrics on the Davis and KIBA datasets. Further cold-start experiments demonstrate the strong generalization ability of Ricci-GraphDTA in scenarios involving unseen drugs or targets, highlighting its potential in real-world drug discovery applications. On average, it achieves a 22.5% reduction in MSE across three cold-start tasks, with over 42% reduction in the dual cold-start setting, showcasing excellent structural modeling capability and robustness.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109170"},"PeriodicalIF":3.0,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086332","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}

引用次数: 0

Aminopeptidase and carboxypeptidase activity of DPP-4 on the example of peptides LPQNIPPL and LPβ3hQNIPPL 以肽LPQNIPPL和LPβ3hQNIPPL为例，分析了DPP-4的氨基肽酶和羧基肽酶活性。

IF 3 4区生物学

Journal of molecular graphics & modelling Pub Date : 2025-09-11 DOI: 10.1016/j.jmgm.2025.109173

Amila Turalić , Amar Osmanović , Črtomir Podlipnik , Elma Omeragić , Selma Špirtović-Halilović , Jasmina Đeđibegović

{"title":"Aminopeptidase and carboxypeptidase activity of DPP-4 on the example of peptides LPQNIPPL and LPβ3hQNIPPL","authors":"Amila Turalić , Amar Osmanović , Črtomir Podlipnik , Elma Omeragić , Selma Špirtović-Halilović , Jasmina Đeđibegović","doi":"10.1016/j.jmgm.2025.109173","DOIUrl":"10.1016/j.jmgm.2025.109173","url":null,"abstract":"<div><div>Our previous research demonstrated that LPQNIPPL and LPβ<sup>3</sup><em>h</em>QNIPPL peptides are degraded <em>in vitro</em> by DPP-4 enzyme. Besides the expected degradation products, additional degradation products were observed on HPLC-MS chromatograms, suggesting cleavage of both the C- and N-terminal amino acids. Molecular docking provided a model for the observed carboxypeptidase, but not for aminopeptidase activity. Compared to conventional N-terminal binding at the active site, the obtained carboxypeptidase model suggested the α-amino group interaction with S2 subsite, C-terminal amino acid side chain interaction with the S1 subsite, reversed peptide backbone order and P1′ proline in a secondary peptide bond. The scissile bond position and distance relative to the active Ser630 seems to remain similar compared to conventional binding. Efficient C-terminal binding to the DPP-4 active site is reinforced by molecular dynamics results, but with altered interactions compared to molecular docking after ligand adaptation phase. Although peptide interactions and distance of scissile bond from the DPP-4 nucleophile Ser630 appears to support the cleavage model, the required nucleophilic attack angles are not confirmed. The proposed model does not allow final conclusions on nucleophilic attack stereochemistry but opens the discussion on possible DPP-4 carboxypeptidase cleavage of peptides, as well as retro/retro-inverso peptides with C-terminal Leu-NH<sub>2</sub>.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109173"},"PeriodicalIF":3.0,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145075445","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}

引用次数: 0

Synthesis, characterization and biological evaluation of a novel chalcone derivative: Spectroscopic, DFT, docking, ADMET and MD Studies 一种新型查尔酮衍生物的合成、表征和生物学评价：光谱、DFT、对接、ADMET和MD研究

IF 3 4区生物学

Journal of molecular graphics & modelling Pub Date : 2025-09-09 DOI: 10.1016/j.jmgm.2025.109161

Manikandan Anandhan , Vijayaraj Venkatachalam , D. Karthikeyan , Sebastian Anand , A.R. Prabakaran , Mysoon M. Al-Ansari , Sandhanasamy Devanesan

{"title":"Synthesis, characterization and biological evaluation of a novel chalcone derivative: Spectroscopic, DFT, docking, ADMET and MD Studies","authors":"Manikandan Anandhan , Vijayaraj Venkatachalam , D. Karthikeyan , Sebastian Anand , A.R. Prabakaran , Mysoon M. Al-Ansari , Sandhanasamy Devanesan","doi":"10.1016/j.jmgm.2025.109161","DOIUrl":"10.1016/j.jmgm.2025.109161","url":null,"abstract":"<div><div>E)-3-(2-hydroxy-6-methoxyphenyl)-1-(1OH-Pheno thiazin-2-yl) prop 2-en-1-one (3HM1P) was synthesized by condensing 2-acetyl phenothiazine and 2-hydroxy-3-methoxy benzaldehyde. The molecular structure of 3HM1P was confirmed by analysis and well supported by FT-IR spectrum. The compound's geometry was optimized using the B3LYP method at the 6–311++G(d,p) level, and theoretical calculations were compared to experimental data. Linear optical absorption spectra were analyzed to study solvent effects on 3HM1P, with HOMO-LUMO analysis revealing a highest energy gap of 3.27 eV in hexane. Molecular electrostatic potential (MEP) analysis identified electron-rich and electron-deficient regions, crucial for enzyme interactions. Natural bond orbital (NBO) analysis indicated a maximum stabilization energy of 392.59 kJ/mol from π→π∗ orbital overlap. Antibacterial potential was assessed through molecular docking studies against the 2JIU protein, supported by early drug-likeness evaluations and ADMET virtual screening. Molecular dynamics simulations confirmed successful docking of 3HM1P-3JUV, while normal mode analysis indicated stable and flexible molecular mobility at the binding site, with a low eigenvalue of 2.6383 × 10<sup>−04</sup>.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109161"},"PeriodicalIF":3.0,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145106255","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}

引用次数: 0

Structural, electronic, and thermodynamic characterization with spectroscopic, topological, reactivity, and molecular docking studies of diallyl sulfide 结构，电子和热力学表征与光谱，拓扑，反应性，和分子对接研究二烯丙基硫化

IF 3 4区生物学

Journal of molecular graphics & modelling Pub Date : 2025-09-04 DOI: 10.1016/j.jmgm.2025.109159

Bhijan Neupane , Khakendra Basnet , Raj Kumar Rai

{"title":"Structural, electronic, and thermodynamic characterization with spectroscopic, topological, reactivity, and molecular docking studies of diallyl sulfide","authors":"Bhijan Neupane , Khakendra Basnet , Raj Kumar Rai","doi":"10.1016/j.jmgm.2025.109159","DOIUrl":"10.1016/j.jmgm.2025.109159","url":null,"abstract":"<div><div>The bioactive organosulfur compound diallyl sulfide (DAS), found in garlic and onions, was analyzed using density functional theory (DFT). DAS exhibits antimicrobial and anticancer properties, making it a potential candidate for drug discovery. Geometry optimization revealed bond lengths and angles consistent with electron delocalization. Frontier molecular orbital analysis showed increased HOMO–LUMO gaps and stability in polar solvents. Natural bond orbital analysis confirmed significant charge delocalization via sulfur-centered interactions, explaining the partial S–C double-bond character and weakened adjacent C<img>H bonds, thus supporting electrophilicity trends. Thermodynamic properties displayed temperature-dependent changes, while UV–Vis spectra showed reduced <span><math><msub><mrow><mi>λ</mi></mrow><mrow><mtext>max</mtext></mrow></msub></math></span> in polar solvents owing to excited-state destabilization. The density of states indicates the excess electron density near the conduction band. The reduced density gradient plots identified the stabilizing van der Waals interactions. Molecular electrostatic potential mapping of electrophilic (sulfur) and nucleophilic (allyl H) sites was validated by Fukui function analysis. Druglikeness evaluation indicated that DAS satisfies Lipinski’s and Veber’s rules for oral bioavailability, but requires structural refinement to enhance complexity. Molecular docking with proteins 3IAI, 3E4E, and 4EY7 revealed hydrophobic and <span><math><mi>π</mi></math></span>–sulfur interactions, confirming their biological relevance.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109159"},"PeriodicalIF":3.0,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145020453","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}

引用次数: 0

Evaluation of AlphaFold3 prediction for post-translational modification, oligomeric assembly, and quenchable metal binding of fluorescent proteins 评价AlphaFold3对荧光蛋白翻译后修饰、寡聚物组装和可淬灭金属结合的预测

IF 3 4区生物学

Journal of molecular graphics & modelling Pub Date : 2025-09-03 DOI: 10.1016/j.jmgm.2025.109169

Ki Hyun Nam

{"title":"Evaluation of AlphaFold3 prediction for post-translational modification, oligomeric assembly, and quenchable metal binding of fluorescent proteins","authors":"Ki Hyun Nam","doi":"10.1016/j.jmgm.2025.109169","DOIUrl":"10.1016/j.jmgm.2025.109169","url":null,"abstract":"<div><div>Green fluorescent proteins (GFPs) are optical markers that are widely used in molecular and cell biology studies to track the location and function of biomolecules. Elucidating their structures will facilitate further engineering of these fluorescent proteins (FPs) to enhance their properties. AlphaFold3 (AF3) is a recently developed prediction tool that exhibits higher accuracy compared with other prediction tools, particularly in predicting protein–ligand interactions with state-of-the-art docking tools. However, studies on the use of AF3 to analyze the structure of FPs have not been fully conducted. To determine the accuracy of FP prediction using AF3, chromophore formation, oligomeric states, and metal ion binding of FPs were analyzed and compared with those of experimentally determined FPs. AF3 could not generate a chromophore comprising the two-ring structure by post-translational modification. Moreover, the oligomeric assembly formation of the FPs was similar to that of experimental oligomeric FPs; however, the detailed residue interactions between FP monomers were different. Quenchable metal ion docking to FPs using AF3 revealed a similar metal-binding site; however, metal coordination was significantly different between AF3 and the experimental structure. These results provide insight into the potential and limitations of using AF3 for FPs.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109169"},"PeriodicalIF":3.0,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144989842","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}

引用次数: 0

Diosgenin reduces β-sheet content in mutated α-syn aggregation: Insights from conformational dynamics at intracellular and extracellular neuronal salt concentrations 薯蓣皂苷元降低突变α-syn聚集中β-薄片的含量：来自细胞内和细胞外神经元盐浓度构象动力学的见解

IF 3 4区生物学

Journal of molecular graphics & modelling Pub Date : 2025-09-01 DOI: 10.1016/j.jmgm.2025.109160

Nandeshwar, Umakanta Tripathy

{"title":"Diosgenin reduces β-sheet content in mutated α-syn aggregation: Insights from conformational dynamics at intracellular and extracellular neuronal salt concentrations","authors":"Nandeshwar, Umakanta Tripathy","doi":"10.1016/j.jmgm.2025.109160","DOIUrl":"10.1016/j.jmgm.2025.109160","url":null,"abstract":"<div><div>Parkinson's disease (PD) is marked by the aggregation of α-syn protein and its mutant forms, such as A30P, A53T, and E46K, which make the protein more prone to misfolding and aggregation, leading to neuronal cell death. This study explores the potential of Diosgenin, a phytoconstituent identified through ADMET predictions, to inhibit α-syn aggregation at both extracellular (0.145 M) and intracellular (0.015 M) salt concentrations. Molecular dynamics (MD) simulation revealed that Diosgenin stabilizes α-syn mutants by inducing conformational changes that reduce β-sheet content, a key factor in aggregation. The salt concentration influenced the structural dynamics, with higher salt levels generally promoting more compact and stable conformations. Principal component analysis (PCA) and free energy landscapes further confirmed the enhanced stability of the Diosgenin-bound α-syn mutants. The outcomes of the study suggest that Diosgenin could serve as a promising therapeutic agent for mitigating PD progression by targeting the aggregation of α-syn mutants and reducing its β-sheet content at intracellular and extracellular neuronal salt concentration.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109160"},"PeriodicalIF":3.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144989843","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}

引用次数: 0

Identification of potential alternatives for isoniazid: An in silico molecular dynamics study 异烟肼潜在替代品的鉴定：硅分子动力学研究

IF 3 4区生物学

Journal of molecular graphics & modelling Pub Date : 2025-08-28 DOI: 10.1016/j.jmgm.2025.109158

Aman Yadav, Yasha Hasija

{"title":"Identification of potential alternatives for isoniazid: An in silico molecular dynamics study","authors":"Aman Yadav, Yasha Hasija","doi":"10.1016/j.jmgm.2025.109158","DOIUrl":"10.1016/j.jmgm.2025.109158","url":null,"abstract":"<div><div>Tuberculosis (TB) remains a major global health concern that affects millions and results in several casualties and these numbers are further increased because of the drug-resistant strains of <em>Mycobacterium tuberculosis (M. tb)</em>. Current treatments, such as Isoniazid (INH), while effective, are increasingly compromised by resistance and associated side effects, emphasizing the urgent need for new therapeutic options. This study focuses on identifying novel inhibitors for the Enoyl-Acyl Carrier Protein Reductase (InhA), a crucial enzyme in mycobacterium cell wall biosynthesis. Using a combination of ligand-based and structure-based virtual screening, we screened a library of FDA-approved drugs to find potential alternatives to INH. Several promising compounds with superior binding affinities to the INH-NAD adduct were identified. These compounds underwent further refinement and analysis through molecular dynamics simulations, where their stability, binding interactions, and free energy profiles were thoroughly evaluated. Our simulations revealed that Bictegravir and Vibegron demonstrated strong electrostatic interactions and favourable binding energies, making them a potential candidate for TB treatment. This computational approach provides a foundation for discovering safer and more effective therapies against both drug-sensitive and drug-resistant TB strains.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109158"},"PeriodicalIF":3.0,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144989844","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}

引用次数: 0

First-principles study of lead-free Na2TmAgCl6 and Na2TmCuCl6 double halide perovskites for photovoltaic and thermoelectric applications 无铅Na2TmAgCl6和Na2TmCuCl6双卤化物钙钛矿的第一性原理研究

IF 3 4区生物学

Journal of molecular graphics & modelling Pub Date : 2025-08-23 DOI: 10.1016/j.jmgm.2025.109157

Ayesha Awais , Zia ur Rehman , Maleeha Shafiq , A.F. Abd El-Rehim , M Qasim Shah , Alina Jaffar , Heba Y. Zahran , Hafiz Abdul Rahman

{"title":"First-principles study of lead-free Na2TmAgCl6 and Na2TmCuCl6 double halide perovskites for photovoltaic and thermoelectric applications","authors":"Ayesha Awais , Zia ur Rehman , Maleeha Shafiq , A.F. Abd El-Rehim , M Qasim Shah , Alina Jaffar , Heba Y. Zahran , Hafiz Abdul Rahman","doi":"10.1016/j.jmgm.2025.109157","DOIUrl":"10.1016/j.jmgm.2025.109157","url":null,"abstract":"<div><div>This study thoroughly investigates the lead-free halide double perovskites Na<sub>2</sub>TmAeCl<sub>6</sub> (Ae = Ag, Cu) using first-principles density functional theory (DFT) within the CASTEP framework. The formation energies are −3.987 eV for Na<sub>2</sub>TmAgCl<sub>6</sub> and −3.453 eV for Na<sub>2</sub>TmCuCl<sub>6</sub>. Additionally, phonon spectra without imaginary frequencies confirm their thermodynamic and dynamic stability. Both compounds adopt a cubic Fm-3m structure with tolerance factors of 0.76 and 0.83, placing them within the stable perovskite range. The elastic constants meet the Born-Huang stability criteria, and Pugh's ratios of 3.48 for Ag and 3.23 for Cu indicate they are ductile. Moreover, Debye temperatures of 124.48 K for Ag and 91.53 K for Cu suggest good lattice thermal stability. Electronic structure analysis shows Na<sub>2</sub>TmAgCl<sub>6</sub> has a direct bandgap of 2.51 eV, while Na<sub>2</sub>TmCuCl<sub>6</sub> features a direct bandgap of 2.32 eV. Their optical properties reveal high absorption coefficients of approximately 16 × 10<sup>4</sup> cm<sup>−1</sup> in the UV region. The calculated SLME efficiencies are 11 % for the Ag compound and 16.5 % for the Cu compound, with ZT values of 0.91 and 1.20, respectively, indicating strong thermoelectric potential. These findings suggest that both Na<sub>2</sub>TmAgCl<sub>6</sub> and Na<sub>2</sub>TmCuCl<sub>6</sub> are promising candidates for advanced optoelectronic, photovoltaic, and thermoelectric applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"141 ","pages":"Article 109157"},"PeriodicalIF":3.0,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144906928","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}

引用次数: 0