Journal of molecular graphics & modelling最新文献

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First-principles insight into the multifunctional properties of tetragonal Zintl-phase CsCd4As3: From dynamical stability to thermoelectric performance. 四边形zintl相CsCd4As3多功能性质的第一性原理研究:从动态稳定性到热电性能。
IF 3 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2026-05-05 DOI: 10.1016/j.jmgm.2026.109433
A Jabar, Z Fadil, S Idrissi, L Bahmad, M Naziruddin Khan, Chaitany Jayprakash Raorane, Seong-Cheol Kim
{"title":"First-principles insight into the multifunctional properties of tetragonal Zintl-phase CsCd<sub>4</sub>As<sub>3</sub>: From dynamical stability to thermoelectric performance.","authors":"A Jabar, Z Fadil, S Idrissi, L Bahmad, M Naziruddin Khan, Chaitany Jayprakash Raorane, Seong-Cheol Kim","doi":"10.1016/j.jmgm.2026.109433","DOIUrl":"https://doi.org/10.1016/j.jmgm.2026.109433","url":null,"abstract":"<p><p>This paper provides a theoretical analysis of the structure, electronic structure, optical, and thermoelectric properties of the tetragonal CsCd<sub>4</sub>As<sub>3</sub> using first-principle calculations based on density functional theory. The stability of CsCd<sub>4</sub>As<sub>3</sub> is validated through phonon dispersions. The electronic structure calculation shows that there exists a direct bandgap of 1.120 eV in CsCd<sub>4</sub>As<sub>3</sub>, indicating its promising potential in optoelectronics. In the analysis of optical properties, it is seen that this material exhibits absorption over visible to near-infrared wavelengths. The calculation of thermoelectric transport properties within the framework of Boltzmann transport shows that a ZT value of 0.74 is achievable under high temperature conditions. Although the above results suggest multifunctionality in CsCd<sub>4</sub>As<sub>3</sub>, further studies such as those related to transport properties and defects are necessary.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"146 ","pages":"109433"},"PeriodicalIF":3.0,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856410","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
Regulation of charge transfer and photophysical properties of porphyrin-based hole transport materials by functional group substitution: DFT and TD-DFT investigations. 官能团取代对卟啉基空穴输运材料的电荷转移和光物理性质的调控:DFT和TD-DFT研究。
IF 3 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2026-05-03 DOI: 10.1016/j.jmgm.2026.109432
Xueling Zhang, Ying Yu, Peng Song, Fengcai Ma, Yuanzuo Li
{"title":"Regulation of charge transfer and photophysical properties of porphyrin-based hole transport materials by functional group substitution: DFT and TD-DFT investigations.","authors":"Xueling Zhang, Ying Yu, Peng Song, Fengcai Ma, Yuanzuo Li","doi":"10.1016/j.jmgm.2026.109432","DOIUrl":"https://doi.org/10.1016/j.jmgm.2026.109432","url":null,"abstract":"<p><p>Hole transport materials (HTMs), which are integral constituents of perovskite solar cells (PSCs), play a crucial role in determining their photovoltaic efficiency and long-term stability. This study used quantum chemistry methods to theoretically investigate the promising chlorophyll derivative molecule ZnChl-2 and its designed molecules (ZnChl-Z1∼ZnChl-Z3). The findings indicated that the substitution of diverse functional groups exerted a significant impact on the electronic and optical characteristics of the molecule. The data showed that three new molecules' energy levels were found to be inferior to that of ZnChl, and their energy levels matched well with perovskite. Three new molecules' solubility have been markedly enhanced compared with that of molecule ZnChl. Moreover, the wavelength of maximum absorption of the molecule ZnChl-Z1 is blue-shifted as compared to ZnChl. The new molecules ZnChl-Z1 and ZnChl-Z3 demonstrate a marked enhancement in hole mobility in comparison with the ZnChl, with ZnChl-Z1 exhibiting the superior level of hole mobility among them. Consequently, the molecule ZnChl-Z1 demonstrates superior overall performance compared to the other three molecules, thereby positioning it as a prospective optimal candidate for HTMs.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"146 ","pages":"109432"},"PeriodicalIF":3.0,"publicationDate":"2026-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838956","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
Glycation induced active site disruption of Biliverdin IXβ reductase: A molecular dynamics approach. 糖基化诱导胆绿素IXβ还原酶活性位点破坏:分子动力学方法。
IF 3 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2026-05-03 DOI: 10.1016/j.jmgm.2026.109431
Jayanth Jeevanandam, P Esackimuthu, K Bhuvana, A S Ruupha Shree, V R Harshini, Srikanth Raghavendran, N T Saraswathi
{"title":"Glycation induced active site disruption of Biliverdin IXβ reductase: A molecular dynamics approach.","authors":"Jayanth Jeevanandam, P Esackimuthu, K Bhuvana, A S Ruupha Shree, V R Harshini, Srikanth Raghavendran, N T Saraswathi","doi":"10.1016/j.jmgm.2026.109431","DOIUrl":"https://doi.org/10.1016/j.jmgm.2026.109431","url":null,"abstract":"<p><p>Flavin reductase (FR), also known as Biliverdin IXβ Reductase (BLVRB), is a monomeric enzyme belonging to the short-chain dehydrogenase/reductase (SDR) protein family, characterized by its NADPH-dependent catalytic conversion of biliverdin to bilirubin, a key antioxidant in fetal heme catabolism and cellular defense. Structurally, BLVRB features a Rossmann-fold domain with dynamic loop regions (Loop80 and Loop120) and coenzyme clamps (Arg14, Arg78) critical for substrate and cofactor binding. Under hyperglycemic conditions, BLVRB undergoes glycation by methylglyoxal (MG), further enhancing the diabetic complications due to advanced glycation end-products (AGEs) production. Here, molecular dynamics simulations were employed to examine glycation-induced structural changes. Results reveal a transition from open to closed loop conformations, tighter Thr12-Arg78 clamp association, narrowed NADPH binding pocket, reduced solvent accessibility, and altered interhelical orientations. Principal Component Analysis (PCA) and Free Energy Landscape (FEL) analyses confirmed significant shifts in conformational space and stability. These findings suggest glycation disrupts BLVRB dynamics, potentially impairing activity and its antioxidant function.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"146 ","pages":"109431"},"PeriodicalIF":3.0,"publicationDate":"2026-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147839141","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
A first-principles study of hydrogen storage on MXene Mo2C monolayer MXene Mo2C单层储氢的第一性原理研究
IF 3 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2026-05-01 Epub Date: 2026-01-12 DOI: 10.1016/j.jmgm.2026.109283
Mohamed Bakhit, Sina Karimzadeh, Tien-Chien Jen
{"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 Mo<sub>2</sub>C 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 Mo<sub>2</sub>C 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 H<sub>2</sub> adsorption on Mo<sub>2</sub>C 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 Mo<sub>2</sub>C, 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 Mo<sub>2</sub>C–H<sub>2</sub> system, showing minimal deformation during a 100 ps simulation and supporting efficient hydrogen adsorption. Overall, these findings establish Mo<sub>2</sub>C 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}
引用次数: 0
In silico engineering of transaminase variants for enhanced biocatalytic conversion of an ACE inhibitor precursor 转氨酶变异体的硅工程以增强ACE抑制剂前体的生物催化转化
IF 3 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2026-05-01 Epub Date: 2026-01-27 DOI: 10.1016/j.jmgm.2026.109308
Mohammad Asad , Mohamed Usman , Anisha Ashokan, Naveen Kulkarni
{"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}
引用次数: 0
Unveiling the potential of π-conjugated 2TT-R non-fullerene alternatives for multifunctional optoelectronic applications: A first-principles study 揭示π共轭2TT-R非富勒烯替代品在多功能光电应用中的潜力:第一性原理研究。
IF 3 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2026-05-01 Epub Date: 2026-01-12 DOI: 10.1016/j.jmgm.2026.109285
Sidra Manzoor , Nadeem Raza , Faheem Abbas
{"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><sub>oc</sub>) 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}
引用次数: 0
ClathPLM: Deep multi-view feature extraction with CNN and attention enhances clathrin protein identification ClathPLM:基于CNN和注意力的深度多视图特征提取增强了网格蛋白的识别。
IF 3 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2026-05-01 Epub Date: 2026-01-21 DOI: 10.1016/j.jmgm.2026.109307
Shuxin Song, Yusen Su, Qingyang Guo, Taigang Liu
{"title":"ClathPLM: Deep multi-view feature extraction with CNN and attention enhances clathrin protein identification","authors":"Shuxin Song,&nbsp;Yusen Su,&nbsp;Qingyang Guo,&nbsp;Taigang Liu","doi":"10.1016/j.jmgm.2026.109307","DOIUrl":"10.1016/j.jmgm.2026.109307","url":null,"abstract":"<div><div>Clathrin is a key structural protein in intracellular vesicle transport, mainly mediating clathrin-mediated endocytosis (CME) through trimeric assembly. Its functional abnormalities are closely associated with various diseases, including neurodegenerative disorders, tumor metastasis, and immune system dysregulation. Traditional experimental methods for identifying the presence of Clathrin have limitations such as high cost and time consumption. Therefore, it is particularly urgent to develop efficient and reliable computational methods to assist in Clathrin recognition. In this study, we propose a model named ClathPLM, which integrates sequence embeddings from three pre-trained protein language models (PPLMs), i.e., ProtT5, ProtBert, and ESM-3, and performs deep representation learning on each feature through an independent branch composed of a convolutional neural network (CNN) and a multi-head Attention (MHA) mechanism, finally fusing the representations of the three views to accomplish the classification task. To validate the effectiveness of this design, we further examined variants of the fusion strategy and attention mechanism. Evaluation results show that ClathPLM demonstrates excellent overall classification performance and robustness, surpassing current state-of-the-art methods. Moreover, the model performs strongly on an additional case-study dataset and shows good scalability on an extra vesicular transport proteins (VTPs) dataset. We anticipate that ClathPLM may contribute to a deeper understanding of the role of Clathrin in cellular regulation and disease mechanisms, and facilitate future biological studies as well as potential clinical applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"144 ","pages":"Article 109307"},"PeriodicalIF":3.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146046802","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
Exploring traditional Chinese medicine for antiviral drug discovery: A computational approach to combat human metapneumovirus (HMPV) 利用中药开发抗病毒药物:一种对抗人偏肺病毒(HMPV)的计算方法
IF 3 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2026-05-01 Epub Date: 2026-01-12 DOI: 10.1016/j.jmgm.2026.109290
Amit Dubey , Manish Kumar , Aisha Tufail , Vivek Dhar Dwivedi
{"title":"Exploring traditional Chinese medicine for antiviral drug discovery: A computational approach to combat human metapneumovirus (HMPV)","authors":"Amit Dubey ,&nbsp;Manish Kumar ,&nbsp;Aisha Tufail ,&nbsp;Vivek Dhar Dwivedi","doi":"10.1016/j.jmgm.2026.109290","DOIUrl":"10.1016/j.jmgm.2026.109290","url":null,"abstract":"<div><div>Human metapneumovirus (HMPV) remains a major respiratory pathogen without approved antivirals, highlighting the urgent need for novel therapeutics. This study implemented an integrative computational pipeline combining virtual screening, molecular docking, 2 μs molecular dynamics (MD) simulations, density functional theory (DFT), pharmacophore modeling, and ADMET profiling to identify potent HMPV inhibitors from Traditional Chinese Medicine. Among 180 screened phytoconstituents, <strong>glycyrrhizin (–9.3 kcal mol<sup>−1</sup>)</strong>, <strong>hesperidin (–9.1 kcal mol<sup>−1</sup>)</strong>, and <strong>saikosaponins (–9.0 kcal mol<sup>−1</sup>)</strong> exhibited strong binding affinities toward the HMPV matrix protein (<strong>PDB ID: 5WB0</strong>). Extended MD simulations confirmed complex stability with <strong>RMSD 0.17</strong>–<strong>0.22 nm</strong>, average of <strong>3</strong>–<strong>5 persistent H-bonds</strong>, and <strong>DCCM correlation coefficient = 0.86</strong> for glycyrrhizin. <strong>MM-PBSA</strong> binding free energies (ΔG_bind) of <strong>–46.2 ± 2.5</strong>, <strong>–44.7 ± 2.8</strong>, and <strong>–43.9 ± 2.2 kJ mol<sup>−1</sup></strong> for glycyrrhizin, hesperidin, and oseltamivir respectively, validated strong and stable interactions. <strong>DFT</strong> results indicated favorable electronic reactivity (HOMO–LUMO gap = 3.86 eV; electrophilicity = 2.74 eV), enhancing ligand-target complementarity. <strong>ADMET</strong> analysis predicted low systemic toxicity (<strong>LD<sub>50</sub></strong> <strong>= 380</strong>–<strong>530 mg kg<sup>−1</sup></strong>) but revealed moderate <strong>CYP3A4/CYP2C9 inhibition</strong>, suggesting the need for metabolic stability evaluation. Compared with reported fusion inhibitors such as EGCG and rutin, this <strong>matrix-targeted strategy</strong> introduces a distinct therapeutic mechanism. Overall, these findings establish a robust computational foundation for developing and experimentally validating potent natural inhibitors against HMPV.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"144 ","pages":"Article 109290"},"PeriodicalIF":3.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145980434","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
Y- and Zr-modified boron nitride nanosheets as efficient sensors for formamide: A first-principles approach Y和zr修饰的氮化硼纳米片作为甲酰胺的高效传感器:第一性原理方法
IF 3 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2026-05-01 Epub Date: 2026-01-12 DOI: 10.1016/j.jmgm.2026.109278
Meryem Derdare, Abdel-Ghani Boudjahem, Nedjoua Cheghib
{"title":"Y- and Zr-modified boron nitride nanosheets as efficient sensors for formamide: A first-principles approach","authors":"Meryem Derdare,&nbsp;Abdel-Ghani Boudjahem,&nbsp;Nedjoua Cheghib","doi":"10.1016/j.jmgm.2026.109278","DOIUrl":"10.1016/j.jmgm.2026.109278","url":null,"abstract":"<div><div>This study employs DFT calculations to investigate the structural stability and electronic properties of pristine and transition-metal-doped boron nitride (BN) nanosheets, using yttrium (Y) and zirconium (Zr) as dopants, as well as their gas-sensing response toward formamide (FO). The findings show that introducing Y or Zr atoms leads to notable modifications in the electronic structure of the BN nanosheet, substantially improving its chemical reactivity and adsorption performance. In the aqueous phase, the interaction between FO and Y/Zr-doped BN nanosheets becomes moderately weaker, with adsorption energies decreasing to – 4.23 to – 24.97 kcal mol<sup>−1</sup>; however, the most stable complexes still exhibit comparatively strong binding. Solvation also alters the electronic structure of the nanosheets, leading to noticeable variations in their energy gaps. Despite this reduction in interaction strength, both doped materials retain high sensitivity toward FO in water, with ZrBN reaching 99.9 %/1.43 × 10<sub>3</sub> % and YBN achieving 55.9 %/86.5 %. Moreover, the nanosheets exhibit extremely short recovery times in the liquid phase, with values of 1.27 × 10<sup>−15</sup> s for ZrBN and 2.06 s for YBN, enabling rapid FO desorption and efficient restoration of active metal sites. These combined features confirm the strong potential of Y- and Zr-doped BN nanosheets as reusable and high-performance sensors for formamide detection in aqueous environments.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"144 ","pages":"Article 109278"},"PeriodicalIF":3.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145980542","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
Evaluating the interactions of L-DOPA and droxidopa toward D3 dopamine receptor through computational study: A comparison with dopamine 通过计算研究评估左旋多巴和羟多巴对D3多巴胺受体的相互作用:与多巴胺的比较
IF 3 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2026-05-01 Epub Date: 2026-01-02 DOI: 10.1016/j.jmgm.2025.109270
Bhabesh Baro, Biplab Sarkar
{"title":"Evaluating the interactions of L-DOPA and droxidopa toward D3 dopamine receptor through computational study: A comparison with dopamine","authors":"Bhabesh Baro,&nbsp;Biplab Sarkar","doi":"10.1016/j.jmgm.2025.109270","DOIUrl":"10.1016/j.jmgm.2025.109270","url":null,"abstract":"<div><div>The D<span><math><msub><mrow></mrow><mrow><mn>3</mn></mrow></msub></math></span> dopamine receptor (D<span><math><msub><mrow></mrow><mrow><mn>3</mn></mrow></msub></math></span>R), a member of the G protein-coupled receptor family, plays a critical role in neurophysiological processes and has emerged as a potential target for treating neurological disorders such as Parkinson’s disease. In this study, we employed computational approaches to investigate the molecular interactions of D<span><math><msub><mrow></mrow><mrow><mn>3</mn></mrow></msub></math></span>R with dopamine and two key dopamine precursors: L-DOPA and droxidopa. Molecular docking was conducted to evaluate binding affinities and identify key receptor–ligand interactions, followed by molecular dynamics simulations to assess the stability and dynamic behavior of the complexes in a biological environment. MM-PBSA binding free energy calculations were used to further quantify the strength of ligand binding to D<span><math><msub><mrow></mrow><mrow><mn>3</mn></mrow></msub></math></span>R.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"144 ","pages":"Article 109270"},"PeriodicalIF":3.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928866","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
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