Pub Date : 2025-12-12DOI: 10.1016/j.jmgm.2025.109254
G. Dodero , E. Noseda Grau , A. Díaz Compañy , G. Román , S. Simonetti
The adsorption of hydrochlorothiazide and aspirin drugs onto a phosphorus (P) -magnesium (Mg) -doped (5,3) single-walled carbon nanotube (SWCNT) is investigated by density-functional theory (DFT) calculations using the Vienna Ab initio Simulation Package (VASP). The optimization of different structures indicates that the hydrochlorothiazide drug is stronger adsorbed than aspirin onto (5,3) SWCNT-P-Mg, affecting de release kinetics of the drugs. The results manifest the importance of the selected dopant atoms on the modification of the material surface in order to change the adsorption properties and the release conditions. We corroborate the results by means of electronic structure, density of states (DOS), frontier orbitals, and molecular electrostatic potential analysis.
利用维也纳从头算模拟包（VASP），通过密度泛函理论（DFT）计算，研究了磷(P) -镁（Mg）掺杂（5,3）单壁碳纳米管（SWCNT）对氢氯噻嗪和阿司匹林药物的吸附。不同结构的优化表明，氢氯噻嗪类药物比阿司匹林更强地吸附在（5,3）swcnts - p - mg上，影响药物的释放动力学。结果表明，掺杂原子的选择对于改变材料表面的吸附性能和释放条件具有重要意义。我们通过电子结构、态密度（DOS）、前沿轨道和分子静电势分析证实了结果。
{"title":"(5,3) SWCNT-doping phosphorus-magnesium: Difference in adsorption of cardiovascular drugs","authors":"G. Dodero , E. Noseda Grau , A. Díaz Compañy , G. Román , S. Simonetti","doi":"10.1016/j.jmgm.2025.109254","DOIUrl":"10.1016/j.jmgm.2025.109254","url":null,"abstract":"<div><div>The adsorption of hydrochlorothiazide and aspirin drugs onto a phosphorus (P) -magnesium (Mg) -doped (5,3) single-walled carbon nanotube (SWCNT) is investigated by density-functional theory (DFT) calculations using the Vienna Ab initio Simulation Package (VASP). The optimization of different structures indicates that the hydrochlorothiazide drug is stronger adsorbed than aspirin onto (5,3) SWCNT-P-Mg, affecting de release kinetics of the drugs. The results manifest the importance of the selected dopant atoms on the modification of the material surface in order to change the adsorption properties and the release conditions. We corroborate the results by means of electronic structure, density of states (DOS), frontier orbitals, and molecular electrostatic potential analysis.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109254"},"PeriodicalIF":3.0,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145756839","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}
The research highlights the impact of pH on the structural stability of insulin amyloid fibrils, linked to clinical complications such as insulin-derived amyloidosis and potential insulin resistance. Using molecular dynamics (MD) simulations, we demonstrate that at neutral pH (pH 7), deprotonated glutamate residues create electrostatic repulsion within the fibril core. This reduces inter-protomer hydrogen bonding and leads to partial destabilization. In contrast, at acidic pH (pH 2), protonation of acidic residues diminishes repulsion, facilitating tighter packing and a more organized hydrogen-bond network. Further analyses, including hydration shell characterization and principal component analysis (PCA), underscore structural differences between fibrils under different pH conditions. At pH 7, the fibrils exhibit a more hydrated shell and greater collective motions, revealing reduced compactness and stability. Residues such as Leu, Glu, and Gln are crucial for fibril stability, with their hydrogen bonding participation notably reduced at neutral pH. These findings provide critical insights into the molecular mechanisms underlying the pH-dependent destabilization of insulin fibrils. Such a mechanistic understanding holds significant potential for guiding the development of therapeutic strategies aimed at preventing fibril formation or promoting controlled fibril disassembly. These advancements could help address the challenges posed by insulin-derived amyloidosis, thereby improving clinical outcomes for patients requiring recurrent insulin therapy.
{"title":"Investigating the pH influence on insulin fibril stability: Molecular dynamics insights","authors":"Yasaman Mahmoodi , Shirin Jalali , Shirin Shahabadi, Hamed Emami, Faramarz Mehrnejad","doi":"10.1016/j.jmgm.2025.109255","DOIUrl":"10.1016/j.jmgm.2025.109255","url":null,"abstract":"<div><div>The research highlights the impact of pH on the structural stability of insulin amyloid fibrils, linked to clinical complications such as insulin-derived amyloidosis and potential insulin resistance. Using molecular dynamics (MD) simulations, we demonstrate that at neutral pH (pH 7), deprotonated glutamate residues create electrostatic repulsion within the fibril core. This reduces inter-protomer hydrogen bonding and leads to partial destabilization. In contrast, at acidic pH (pH 2), protonation of acidic residues diminishes repulsion, facilitating tighter packing and a more organized hydrogen-bond network. Further analyses, including hydration shell characterization and principal component analysis (PCA), underscore structural differences between fibrils under different pH conditions. At pH 7, the fibrils exhibit a more hydrated shell and greater collective motions, revealing reduced compactness and stability. Residues such as Leu, Glu, and Gln are crucial for fibril stability, with their hydrogen bonding participation notably reduced at neutral pH. These findings provide critical insights into the molecular mechanisms underlying the pH-dependent destabilization of insulin fibrils. Such a mechanistic understanding holds significant potential for guiding the development of therapeutic strategies aimed at preventing fibril formation or promoting controlled fibril disassembly. These advancements could help address the challenges posed by insulin-derived amyloidosis, thereby improving clinical outcomes for patients requiring recurrent insulin therapy.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109255"},"PeriodicalIF":3.0,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145734022","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}
Pub Date : 2025-12-09DOI: 10.1016/j.jmgm.2025.109251
Elena Ermakova, Yuriy Zuev
The molecular mechanisms of fish gelatin (FG)-polysaccharide interactions are crucial for designing of advanced biomaterials. While experimental studies have demonstrated that polysaccharides can enhance the FG's functional properties, the atomic-level details of these interactions remain poorly characterized. In this study, we employ molecular docking to identify preferential binding sites of gelatin and the all-atom molecular dynamics (MD) simulations to quantify the interaction energetics and complex stability, with particular focus on the role of local charge distribution along gelatin molecule. We modeled four FG fragments with varying charge distribution and analyzed their interactions with anionic and cationic polysaccharides ι-carrageenan, alginate and chitosan. The MD simulations revealed that the charge density patterns of both interacting molecules critically determine gelatin-polysaccharide binding affinity and complex stability. This work provides first 3D-structural models of FG-polysaccharide complexes, offering fundamental insight for biomaterial design.
{"title":"Charge distribution defines the mechanism of fish gelatin-polysaccharide interactions","authors":"Elena Ermakova, Yuriy Zuev","doi":"10.1016/j.jmgm.2025.109251","DOIUrl":"10.1016/j.jmgm.2025.109251","url":null,"abstract":"<div><div>The molecular mechanisms of fish gelatin (FG)-polysaccharide interactions are crucial for designing of advanced biomaterials. While experimental studies have demonstrated that polysaccharides can enhance the FG's functional properties, the atomic-level details of these interactions remain poorly characterized. In this study, we employ molecular docking to identify preferential binding sites of gelatin and the all-atom molecular dynamics (MD) simulations to quantify the interaction energetics and complex stability, with particular focus on the role of local charge distribution along gelatin molecule. We modeled four FG fragments with varying charge distribution and analyzed their interactions with anionic and cationic polysaccharides ι-carrageenan, alginate and chitosan. The MD simulations revealed that the charge density patterns of both interacting molecules critically determine gelatin-polysaccharide binding affinity and complex stability. This work provides first 3D-structural models of FG-polysaccharide complexes, offering fundamental insight for biomaterial design.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109251"},"PeriodicalIF":3.0,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145734083","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}
Pub Date : 2025-12-09DOI: 10.1016/j.jmgm.2025.109253
A. El Aiboudi , A. Sibari , Y. Kaddar , N. Masaif , H. Ez-Zahraouy
The development of high-performance gas sensors for detecting inorganic pollutants is vital for environmental protection. Using first-principles calculations, this study reveals that hydrogen boride (HB) monolayers exhibit remarkable sensitivity toward CO2, CO, and NO, which is further enhanced by Fe and Li decoration. Li-decorated HB shows strong NO adsorption (Eads = −1.53 eV, charge transfer = 0.52 e), while Fe decoration greatly improves CO (Eads = −2.56 eV) and CO2 (Eads = −2.74 eV) adsorption. Compared with other 2D materials such as graphene (−0.12 eV) and MoS2 (−0.35 eV), Fe–HB displays adsorption strengths nearly one order of magnitude higher, highlighting its superior sensitivity and selectivity. Li–HB offers fast recovery suitable for CO2 detection, whereas Fe–HB shows long desorption times favorable for capture. These results identify Li- and Fe-decorated HB monolayers as promising candidates for next-generation CO2 sensing and capture technologies.
{"title":"Fe- and Li-decorated hydrogen boride as a gas sensor for CO, NO, and CO2 detection: A DFT study","authors":"A. El Aiboudi , A. Sibari , Y. Kaddar , N. Masaif , H. Ez-Zahraouy","doi":"10.1016/j.jmgm.2025.109253","DOIUrl":"10.1016/j.jmgm.2025.109253","url":null,"abstract":"<div><div>The development of high-performance gas sensors for detecting inorganic pollutants is vital for environmental protection. Using first-principles calculations, this study reveals that hydrogen boride (HB) monolayers exhibit remarkable sensitivity toward CO<sub>2</sub>, CO, and NO, which is further enhanced by Fe and Li decoration. Li-decorated HB shows strong NO adsorption (Eads = −1.53 eV, charge transfer = 0.52 e), while Fe decoration greatly improves CO (Eads = −2.56 eV) and CO<sub>2</sub> (Eads = −2.74 eV) adsorption. Compared with other 2D materials such as graphene (−0.12 eV) and MoS<sub>2</sub> (−0.35 eV), Fe–HB displays adsorption strengths nearly one order of magnitude higher, highlighting its superior sensitivity and selectivity. Li–HB offers fast recovery suitable for CO<sub>2</sub> detection, whereas Fe–HB shows long desorption times favorable for capture. These results identify Li- and Fe-decorated HB monolayers as promising candidates for next-generation CO<sub>2</sub> sensing and capture technologies.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109253"},"PeriodicalIF":3.0,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145734020","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}
Pub Date : 2025-12-08DOI: 10.1016/j.jmgm.2025.109252
Loknath Patro, B.L. Bhargava
Surfactin, a highly effective biosurfactant synthesized by various strains of Bacillus subtilis, exhibits remarkable biological and physicochemical properties. Molecular dynamics simulations highlight the influence of hydrocarbon chain length on the micellar structure, aggregation behavior, hydrogen bonding patterns, and secondary structure of surfactin molecules. The findings reveal that the aggregates adopt an increasingly spherical shape as the hydrocarbon chain length increases. The aggregation number of surfactin molecules also increases with longer chain lengths, indicating enhanced clustering tendencies. In the peptide ring, the occurrence of -turn, identified by the intramolecular hydrogen bond between Leu2 – Val4 residues, decreases with increasing chain length. The -turn, identified by hydrogen bond between Leu2–Asp5 does not exhibit a clear trend, though the maximum occurrence probability is observed in systems with surfactin having longer alkyl tail. The surface tension of surfactin solutions increases with chain length due to lower coverage of the surface in case of surfactins with longer tails due to the tilted orientation of their hydrophobic tails, which limits efficient packing.
{"title":"Effect of chain length on the structure of aqueous surfactin solutions: Molecular dynamics studies","authors":"Loknath Patro, B.L. Bhargava","doi":"10.1016/j.jmgm.2025.109252","DOIUrl":"10.1016/j.jmgm.2025.109252","url":null,"abstract":"<div><div>Surfactin, a highly effective biosurfactant synthesized by various strains of Bacillus subtilis, exhibits remarkable biological and physicochemical properties. Molecular dynamics simulations highlight the influence of hydrocarbon chain length on the micellar structure, aggregation behavior, hydrogen bonding patterns, and secondary structure of surfactin molecules. The findings reveal that the aggregates adopt an increasingly spherical shape as the hydrocarbon chain length increases. The aggregation number of surfactin molecules also increases with longer chain lengths, indicating enhanced clustering tendencies. In the peptide ring, the occurrence of <span><math><mi>γ</mi></math></span>-turn, identified by the intramolecular hydrogen bond between Leu2 – Val4 residues, decreases with increasing chain length. The <span><math><mi>β</mi></math></span>-turn, identified by hydrogen bond between Leu2–Asp5 does not exhibit a clear trend, though the maximum occurrence probability is observed in systems with surfactin having longer alkyl tail. The surface tension of surfactin solutions increases with chain length due to lower coverage of the surface in case of surfactins with longer tails due to the tilted orientation of their hydrophobic tails, which limits efficient packing.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109252"},"PeriodicalIF":3.0,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145734019","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}
Pub Date : 2025-12-05DOI: 10.1016/j.jmgm.2025.109249
Tarik Boutadghart, Rachida Ghailane
The [4 + 2] cycloaddition reaction catalyzed by the Lewis acids AlCl3 and TiBr4 was systematically explored within the framework of Molecular Electron Density Theory (MEDT). The complete reaction pathway including reactants, transition states, and products was optimized and characterized using density functional theory (DFT) calculations at the SDD/M06/6–311++G (d,p) level. Conceptual DFT descriptors, combined with frontier molecular orbital (FMO) analysis, confirmed the nucleophilic role of isoprene and the electrophilic character of acrylic acid. Mechanistic insights revealed a one-step, concerted yet asynchronous process. The inclusion of Lewis acid catalysts markedly reshaped the reaction profile, enhancing both kinetic and thermodynamic features as well as regioselectivity. Notably, TiBr4 decreased the activation barrier of the para transition state by 15.242 kcal mol−1, whereas AlCl3 increased the exothermic stabilization of the para adduct by 7.489 kcal mol−1, thereby favoring the para pathway over the competing meta channel. Noncovalent interaction (NCI) analysis further highlighted stabilizing contacts, particularly through amino group interactions with protein residues, suggesting potential biological significance and bioactivity of the cycloadducts. Moreover, electron localization function (ELF) analysis underscored the decisive influence of steric effects, reinforcing that both catalyzed and uncatalyzed reactions proceed through an intrinsically asynchronous bond-formation mechanism.
{"title":"Mechanistic study of the steric effect of Lewis acids AlCl3 and TiBr4 on the asynchronous [4+2] cycloaddition reaction of isoprene with Aryl acid: MEDT study","authors":"Tarik Boutadghart, Rachida Ghailane","doi":"10.1016/j.jmgm.2025.109249","DOIUrl":"10.1016/j.jmgm.2025.109249","url":null,"abstract":"<div><div>The [4 + 2] cycloaddition reaction catalyzed by the Lewis acids AlCl3 and TiBr4 was systematically explored within the framework of Molecular Electron Density Theory (MEDT). The complete reaction pathway including reactants, transition states, and products was optimized and characterized using density functional theory (DFT) calculations at the SDD/M06/6–311++G (d,p) level. Conceptual DFT descriptors, combined with frontier molecular orbital (FMO) analysis, confirmed the nucleophilic role of isoprene and the electrophilic character of acrylic acid. Mechanistic insights revealed a one-step, concerted yet asynchronous process. The inclusion of Lewis acid catalysts markedly reshaped the reaction profile, enhancing both kinetic and thermodynamic features as well as regioselectivity. Notably, TiBr<sub>4</sub> decreased the activation barrier of the para transition state by 15.242 kcal mol<sup>−1</sup>, whereas AlCl<sub>3</sub> increased the exothermic stabilization of the para adduct by 7.489 kcal mol<sup>−1</sup>, thereby favoring the para pathway over the competing meta channel. Noncovalent interaction (NCI) analysis further highlighted stabilizing contacts, particularly through amino group interactions with protein residues, suggesting potential biological significance and bioactivity of the cycloadducts. Moreover, electron localization function (ELF) analysis underscored the decisive influence of steric effects, reinforcing that both catalyzed and uncatalyzed reactions proceed through an intrinsically asynchronous bond-formation mechanism.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109249"},"PeriodicalIF":3.0,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145708462","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}
Pub Date : 2025-12-04DOI: 10.1016/j.jmgm.2025.109246
Saurabh Gupta, Yogita Bansal
Dysregulation of p38α MAP kinase (MAPK14) increases the production of pro-inflammatory cytokines, causing pathogenesis of inflammatory, oncological, and neurodegenerative diseases. Till date, no orally effective p38α MAPK inhibitor exists in clinics, which may be due to poor selectivity and off-target effects. This emphasizes the urgent need for the design of potential p38α MAPK inhibitors. In this study, SMILES-based 2D-QSAR and field-point-based 3D QSAR models were developed to guide the design of novel p38α MAPK inhibitors. A dataset of 207 molecules was used to developed 2D-QSAR models via Monte Carlo optimization. Among fifteen models, Split-3 of model 14 exhibited highest statistical performance and was identified as the best model. Structural fragments that either enhance or hinder activity were identified. Subsequently for 3D-QSAR approach, a pharmacophoric template was generated and employed to align dataset. This aligned dataset was utilized to developed 3D-QSAR and a 5-component model showed superior predictivity and provided SAR insights. Based on these insights, a virtual library of 14,040 compounds was designed and screened using in silico workflow such as Lipinski's Rule of Five, predicted pIC50, molecular docking, electrostatic complementarity, molecular dynamics simulations, MM/GBSA, WaterSwap, and ADMET predictions. From this virtual screening, compound P38S002073 emerged as the most promising lead candidate. Overall, this integrative approach provides important structural insights, field-based insights, and SAR for the development of potent and orally bioavailable p38α MAPK inhibitors.
{"title":"Identification of structural fragments and field point-based design of novel p38α MAPK inhibitor: Integrating 2D and 3D-QSAR models with advanced in-silico techniques","authors":"Saurabh Gupta, Yogita Bansal","doi":"10.1016/j.jmgm.2025.109246","DOIUrl":"10.1016/j.jmgm.2025.109246","url":null,"abstract":"<div><div>Dysregulation of p38α MAP kinase (MAPK14) increases the production of pro-inflammatory cytokines, causing pathogenesis of inflammatory, oncological, and neurodegenerative diseases. Till date, no orally effective p38α MAPK inhibitor exists in clinics, which may be due to poor selectivity and off-target effects. This emphasizes the urgent need for the design of potential p38α MAPK inhibitors. In this study, SMILES-based 2D-QSAR and field-point-based 3D QSAR models were developed to guide the design of novel p38α MAPK inhibitors. A dataset of 207 molecules was used to developed 2D-QSAR models via Monte Carlo optimization. Among fifteen models, Split-3 of model 14 exhibited highest statistical performance and was identified as the best model. Structural fragments that either enhance or hinder activity were identified. Subsequently for 3D-QSAR approach, a pharmacophoric template was generated and employed to align dataset. This aligned dataset was utilized to developed 3D-QSAR and a 5-component model showed superior predictivity and provided SAR insights. Based on these insights, a virtual library of 14,040 compounds was designed and screened using in silico workflow such as Lipinski's Rule of Five, predicted pIC<sub>50</sub>, molecular docking, electrostatic complementarity, molecular dynamics simulations, MM/GBSA, WaterSwap, and ADMET predictions. From this virtual screening, compound P38S002073 emerged as the most promising lead candidate. Overall, this integrative approach provides important structural insights, field-based insights, and SAR for the development of potent and orally bioavailable p38α MAPK inhibitors.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109246"},"PeriodicalIF":3.0,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145714606","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}
Pub Date : 2025-12-03DOI: 10.1016/j.jmgm.2025.109250
Selvaraj Immanuel , S. Manivarman , Akhil K. Sivan , Jisha Mary Thomas , Velankanni Nandhakumar , Francisxavier Paularokiadoss , Thayalaraj Christopher Jeyakumar
Density Functional Theory (DFT) calculations at the B3LYP level were performed to investigate the structural and electronic properties of axial and equatorial isomers of [Fe(CO)4(PbX)] complexes, where X = O, S, Se, and Te. Total energy evaluations indicate that equatorial isomers are generally more stable than their axial counterparts. Detailed bonding analysis was carried out using Natural Population Analysis (NPA) and Energy Decomposition Analysis (EDA), providing insight into the nature of the Fe–PbX interactions. The Fe–PbX bond strengths were further assessed through Wiberg Bond Index (WBI) calculations. Frontier Molecular Orbital (FMO) analysis revealed HOMO–LUMO gaps ranging from 3.04 to 3.97 eV, all of which are narrower than the corresponding gap in Fe(CO)5, suggesting enhanced electronic reactivity due to PbX substitution. Natural Bond Orbital (NBO) analysis indicated a greater electron density contribution from the Pb atom to the Fe–Pb bond, whereas for Fe–C bonds, carbon atoms contributed more significantly than Pb. These results collectively highlight the influence of terminal lead chalcogenide ligands on both the geometric and electronic structure of iron carbonyl complexes.
采用B3LYP水平的密度泛函理论（DFT）计算研究了X = O， S， Se和Te的[Fe(CO)4(PbX)]配合物的轴向和赤道异构体的结构和电子性质。总能量评价表明，赤道同分异构体通常比轴向同分异构体更稳定。利用自然种群分析（NPA）和能量分解分析（EDA）进行了详细的键合分析，从而深入了解了Fe-PbX相互作用的性质。通过Wiberg bond Index （WBI）计算进一步评估Fe-PbX的结合强度。前沿分子轨道（FMO）分析显示，HOMO-LUMO的间隙范围为3.04 ~ 3.97 eV，均比Fe(CO)5中的相应间隙窄，表明PbX取代增强了电子反应性。自然键轨道（NBO）分析表明，Pb原子对Fe-Pb键的电子密度贡献较大，而碳原子对Fe-C键的电子密度贡献大于Pb原子。这些结果共同强调了末端硫系铅配体对铁羰基配合物几何结构和电子结构的影响。
{"title":"DFT study of structural and electronic properties of [Fe(CO)4(PbX)] complexes (X = O, S, Se and Te): Influence of terminal lead chalcogenide ligands on bonding and stability","authors":"Selvaraj Immanuel , S. Manivarman , Akhil K. Sivan , Jisha Mary Thomas , Velankanni Nandhakumar , Francisxavier Paularokiadoss , Thayalaraj Christopher Jeyakumar","doi":"10.1016/j.jmgm.2025.109250","DOIUrl":"10.1016/j.jmgm.2025.109250","url":null,"abstract":"<div><div>Density Functional Theory (DFT) calculations at the B3LYP level were performed to investigate the structural and electronic properties of axial and equatorial isomers of [Fe(CO)<sub>4</sub>(PbX)] complexes, where X = O, S, Se, and Te. Total energy evaluations indicate that equatorial isomers are generally more stable than their axial counterparts. Detailed bonding analysis was carried out using Natural Population Analysis (NPA) and Energy Decomposition Analysis (EDA), providing insight into the nature of the Fe–PbX interactions. The Fe–PbX bond strengths were further assessed through Wiberg Bond Index (WBI) calculations. Frontier Molecular Orbital (FMO) analysis revealed HOMO–LUMO gaps ranging from 3.04 to 3.97 eV, all of which are narrower than the corresponding gap in Fe(CO)<sub>5</sub>, suggesting enhanced electronic reactivity due to PbX substitution. Natural Bond Orbital (NBO) analysis indicated a greater electron density contribution from the Pb atom to the Fe–Pb bond, whereas for Fe–C bonds, carbon atoms contributed more significantly than Pb. These results collectively highlight the influence of terminal lead chalcogenide ligands on both the geometric and electronic structure of iron carbonyl complexes.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109250"},"PeriodicalIF":3.0,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145734021","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}
Pub Date : 2025-12-02DOI: 10.1016/j.jmgm.2025.109248
R. Rajeswara Palanichamy , A. Amudhavalli , R. Meenakshi , T.M. Chithresh , M. Manikandan , K. Iyakutti , Y. Kawazoe
First-principles calculations based on the density functional theory (DFT) are employed to study the structural, electronic, magnetic, optical, and thermal properties of new Zr based half- Heusler compounds with α, β and γ phases. The most stable state is predicted as ferromagnetic α-phase. Electronic structure predicted the half metallic property and indirect band gap nature of the compounds. The magnetic moment around 1μB obeys the Slater-Pauling rule. The spin polarization at the Fermi level is 100 % which also supports the half metallic behavior. The high Curie temperature values 342.7 K, 1082.7 K and 835.3 K of these half-Heusler alloys make them strong ferromagnets. The high value of dielectric function leads to better polarization, stability and energy storage. The dielectric constant values of ZrFeAs, ZrFeSb and ZrFeBi are found to be 19.4, 18.6 and 18.1 respectively. The absence of negative frequency modes in phonon dispersion curve suggests that these alloys are dynamically stable. The zero-point energy values of ZrFeAs, ZrFeSb and ZrFeBi are 8.4 kJ/mol, 8.06 kJ/mol and 6.79 kJ/mol respectively.
{"title":"Computational investigation of high Curie temperature, magnetic anisotropy and optical properties of new Zr based half-Heusler compounds","authors":"R. Rajeswara Palanichamy , A. Amudhavalli , R. Meenakshi , T.M. Chithresh , M. Manikandan , K. Iyakutti , Y. Kawazoe","doi":"10.1016/j.jmgm.2025.109248","DOIUrl":"10.1016/j.jmgm.2025.109248","url":null,"abstract":"<div><div>First-principles calculations based on the density functional theory (DFT) are employed to study the structural, electronic, magnetic, optical, and thermal properties of new Zr based half- Heusler compounds with α, β and γ phases. The most stable state is predicted as ferromagnetic α-phase. Electronic structure predicted the half metallic property and indirect band gap nature of the compounds. The magnetic moment around 1μ<sub>B</sub> obeys the Slater-Pauling rule. The spin polarization at the Fermi level is 100 % which also supports the half metallic behavior. The high Curie temperature values 342.7 K, 1082.7 K and 835.3 K of these half-Heusler alloys make them strong ferromagnets. The high value of dielectric function leads to better polarization, stability and energy storage. The dielectric constant values of ZrFeAs, ZrFeSb and ZrFeBi are found to be 19.4, 18.6 and 18.1 respectively. The absence of negative frequency modes in phonon dispersion curve suggests that these alloys are dynamically stable. The zero-point energy values of ZrFeAs, ZrFeSb and ZrFeBi are 8.4 kJ/mol, 8.06 kJ/mol and 6.79 kJ/mol respectively.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109248"},"PeriodicalIF":3.0,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145682694","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}
Pub Date : 2025-12-01Epub Date: 2025-08-05DOI: 10.1016/j.jmgm.2025.109130
Mohamed J Saadh, Faris Anad Muhammad, Rafid Jihad Albadr, Suhas Ballal, Abhayveer Singh, Anita Devi, Kamal Kant Joshi, Saida Saidkhodjaeva, Waam Mohammed Taher, Mariem Alwan, Mahmood Jasem Jawad, Ali M Ali Al-Nuaimi
The Marburg virus, a close relative of the Ebola virus, is a menacing Filovirus known for its devastating outbreaks in Germany and recent outbreaks in Guinea and Tanzania. This deadly pathogen triggers severe hemorrhagic fever, posing a grave threat to public health and demanding urgent attention from the global medical community. The amino acid sequence and PDB of the Envelope glycoprotein (GP) were extracted from RCSB for use in predicting epitopes (IEDB server). The construction of the multi-epitope vaccine included an adjuvant and linkers (AAY, EAAAK, GPGPG), which were assessed with the ProtParam tool to characterize their physico-chemical properties. Additionally, modeling was carried out with the Robetta server, and the modeled vaccine was docked with Toll-like receptor 4 (TLR4). Finally, immune and molecular dynamic simulations were implemented using the C-ImmSim and GROMACS packages. The final multi-epitope vaccine consists of 211 amino acids, created with 5 CTL and 4 HTL epitopes that were validated and passed assessments for antigenicity, allergenicity, and toxicity. The modeled multi-epitope vaccine was evaluated and demonstrated high model quality. The best molecular docking candidate was selected and evaluated using PDBsum. Subsequently, by assessing RMSD, RMSF, and Gyration, the molecular dynamic simulation revealed considerable binding with TLR4, and the complex remained stable throughout the simulation. Ultimately, the multi-epitope vaccine can stimulate both humoral and cell-mediated immune responses, validated computationally. The overall implication of this investigation shows the potency of the multi-epitope construct as an efficient protective vaccine against the Marburg virus.
{"title":"Structure-based design of a multi-epitope vaccine candidate against marburg virus using immunoinformatics and dynamics simulations.","authors":"Mohamed J Saadh, Faris Anad Muhammad, Rafid Jihad Albadr, Suhas Ballal, Abhayveer Singh, Anita Devi, Kamal Kant Joshi, Saida Saidkhodjaeva, Waam Mohammed Taher, Mariem Alwan, Mahmood Jasem Jawad, Ali M Ali Al-Nuaimi","doi":"10.1016/j.jmgm.2025.109130","DOIUrl":"10.1016/j.jmgm.2025.109130","url":null,"abstract":"<p><p>The Marburg virus, a close relative of the Ebola virus, is a menacing Filovirus known for its devastating outbreaks in Germany and recent outbreaks in Guinea and Tanzania. This deadly pathogen triggers severe hemorrhagic fever, posing a grave threat to public health and demanding urgent attention from the global medical community. The amino acid sequence and PDB of the Envelope glycoprotein (GP) were extracted from RCSB for use in predicting epitopes (IEDB server). The construction of the multi-epitope vaccine included an adjuvant and linkers (AAY, EAAAK, GPGPG), which were assessed with the ProtParam tool to characterize their physico-chemical properties. Additionally, modeling was carried out with the Robetta server, and the modeled vaccine was docked with Toll-like receptor 4 (TLR4). Finally, immune and molecular dynamic simulations were implemented using the C-ImmSim and GROMACS packages. The final multi-epitope vaccine consists of 211 amino acids, created with 5 CTL and 4 HTL epitopes that were validated and passed assessments for antigenicity, allergenicity, and toxicity. The modeled multi-epitope vaccine was evaluated and demonstrated high model quality. The best molecular docking candidate was selected and evaluated using PDBsum. Subsequently, by assessing RMSD, RMSF, and Gyration, the molecular dynamic simulation revealed considerable binding with TLR4, and the complex remained stable throughout the simulation. Ultimately, the multi-epitope vaccine can stimulate both humoral and cell-mediated immune responses, validated computationally. The overall implication of this investigation shows the potency of the multi-epitope construct as an efficient protective vaccine against the Marburg virus.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"141 ","pages":"109130"},"PeriodicalIF":3.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812116","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号