Journal of molecular graphics & modelling最新文献

{"title":"Electronic analysis of 1-ethyl-3-methyl imidazolium halide adsorption on AlN nanoflakes","authors":"Jabir H. Al-Fahemi ,&nbsp;Kamal A. Soliman","doi":"10.1016/j.jmgm.2025.109041","DOIUrl":"10.1016/j.jmgm.2025.109041","url":null,"abstract":"<div><div>This study explores the interaction of AlN nanoflakes with ionic liquids (ILs) consisting of 1-ethyl-3-methylimidazolium cations and halide anions (fluoride, chloride, bromide), aiming to enhance AlN nanoflake performance in energy applications. ILs adsorb onto the nanoflake surface, with halide ions attaching to aluminum atoms, indicating strong interactions that improve the material's electronic properties. Adsorption energy is the highest for fluoride and lowest for chloride, reflecting the strength and proximity of interaction. Thermodynamic analysis shows the adsorption is exothermic, with fluoride exhibiting the most substantial interaction due to its small size and high electronegativity. This significantly alters the electronic properties of the nanoflake, increasing dipole moment, redistributing charge, and reducing the HOMO-LUMO gap. Additionally, the enhanced nonlinear optical (NLO) properties make these IL-modified AlN nanoflakes promising candidates for energy storage and optical applications. These changes suggest improved conductivity and potential for enhanced supercapacitor performance, offering valuable insights for optimizing AlN nanoflakes in energy storage.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109041"},"PeriodicalIF":2.7,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143760966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The influence of π-conjugated bridge on photoabsorption and charge transfer characteristics of Diketo-Pyrrolo-Pyrrole derivatives","authors":"Haoran Ni,&nbsp;Yaochuan Wang,&nbsp;Ding Zhang,&nbsp;Xue Sun,&nbsp;Yizhuo Wang,&nbsp;Yu Li,&nbsp;Dajun Liu,&nbsp;Xuesong Xu","doi":"10.1016/j.jmgm.2025.109037","DOIUrl":"10.1016/j.jmgm.2025.109037","url":null,"abstract":"<div><div>In this work, three D-π-A-π-D structural Diketo-Pyrrolo-Pyrrole (DPP) derivatives have been designed and simulated, which have the same electron acceptor and donor connected by different π-conjugated bridges. The intramolecular charge transfer (ICT) effects of different electron transport structures on the nonlinear optical response as well as the mechanism have been explored. The results show that a suitable electronic transport structure can enhance the nonlinear optical response of the molecules and expand the absorption spectrum to the long wavelength range, which is of great significance for the practical applications. Impressively, the TDM and CDD maps of molecule constructed with thiophene as π-conjugated bridge exhibit striking excitation response, intense ICT effect as well as a minimal band gap value. The results in this work provide valuable references for the design and synthesis of novel nonlinear optical materials by modifying the electron channel structures.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109037"},"PeriodicalIF":2.7,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143739318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tailoring functionalized 2,3-diaza-1,3-butadienes for high-energy and insensitive applications","authors":"Hridya Rajan ,&nbsp;Prakash Chandran R. ,&nbsp;Sobha Vijayan Nair ,&nbsp;Renjith Raveendran Pillai ,&nbsp;Rahana Ameen","doi":"10.1016/j.jmgm.2025.109024","DOIUrl":"10.1016/j.jmgm.2025.109024","url":null,"abstract":"<div><div>The heat of formation (HOF), detonation performance, electronic properties, thermal stability, impact energy and explosive power of a series of highly functionalized 2,3-diaza-1,3-butadienes were studied using density functional theory. HOF values of all the designed compounds were positive. Among the 100 compounds, more than 50 % exhibited a density equal to or greater than 1.9 g cm^-3. There was close agreement in the calculated value of density, detonation performance and impact energy of traditional explosive RDX, HMX and CL-20 with the experimental value. The predicted values of detonation velocity and pressure indicated that about 45 compounds possessed values higher than that of 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX), among which 20 compounds had higher impact energy than HMX. Five compounds were identified as potential front-runners with superior detonation performance greater than CL-20, together with impact energy higher than HMX. Thus compounds with improved properties were designed by the adoption of strategies that involved the incorporation of diverse explosophores and nitrogen atoms in the ring and the framework. Our study proves that this work holds immense potential in the development of high-energetic density materials with promising properties.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109024"},"PeriodicalIF":2.7,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143746940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of donor units in band gap engineering of donor–acceptor conjugated polymers","authors":"Tugba Haciefendioglu ,&nbsp;Erol Yildirim","doi":"10.1016/j.jmgm.2025.109033","DOIUrl":"10.1016/j.jmgm.2025.109033","url":null,"abstract":"<div><div>Most used 60 distinct electron-donating units have been modelled, analyzed, and compared using density functional theory (DFT) for tetramer structures in the form (D–B–A–B)₄ with fixed acceptor and bridge units, where D, A and B represents donor, acceptor and bridge, respectively. The frontier orbitals and reorganization energy of tetramers with alternating donor units were analyzed to assess their potential applicability in organic electronic applications. Key structural properties including dihedral angles between the acceptor, donor, and bridge units, bond order, and bond length alternation were found to significantly influence the frontier electronic energy levels affecting the planarity, conjugation and electron delocalization of polymer backbone. While extended conjugation and planar structures generally lower the band gap; the specific electronic impact of substituents, such as methoxy or fluorine groups, depend on their position and interaction within the conjugated system. Similarly, the incorporation of heavier heteroatoms, such as selenium, germanium or silicon, introduces steric and electronic effects that can either enhance or disrupt π-conjugation due to the change in the strength of donor unit. Additionally, substitution effects and morphological variations in donor units play a crucial role in defining the physical properties of D-A conjugated polymers. This study establishes a benchmark by providing essential insights into the band gap engineering and the molecular design of D-A copolymers by alternating donor units, thereby supporting significant advancements in organic electronic applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109033"},"PeriodicalIF":2.7,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143725478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Probing the antibacterial mechanism of Aloe vera based on network pharmacology and computational analysis","authors":"Qian Tang ,&nbsp;Jingle Chu ,&nbsp;Peiqi Peng ,&nbsp;Yinjie Zou ,&nbsp;Yaguang Wu ,&nbsp;Yuanqiang Wang","doi":"10.1016/j.jmgm.2025.109034","DOIUrl":"10.1016/j.jmgm.2025.109034","url":null,"abstract":"<div><div>Bacterial resistance has emerged as a major clinical challenge globally. Natural products, such as Aloe vera, offer promising antimicrobial potential due to their diverse active components. However, the explicit molecular mechanisms remain unknown. In this study, we employed a multidisciplinary approach integrating network pharmacology, molecular docking, and molecular dynamics simulation to explore the antibacterial mechanism of Aloe vera. We screened the eight major active components of Aloe vera and their targets using multi-source bioinformatics platforms, identifying 55 targets closely associated with the antibacterial effects of Aloe vera. Protein-protein interaction network analysis, revealed potential crucial targets, including cysteine-aspartic acid protease-3 (CASP3) and matrix metalloproteinase-9 (MMP-9). Gene ontology functional enrichment analysis revealed that these targets play critical roles in several essential biological processes, such as “response to xenobiotic stimulus”, “positive regulation of gene expression”, and “collagen catabolism”. The Kyoto Encyclopedia of Genes and Genomes signal pathway analysis indicated that these targets are primarily involved in pathways associated with cancer, lipid metabolism, atherosclerosis, and the AGE/RAGE signaling pathway in diabetes. This finding suggests that Aloe vera may exert its antibacterial effects by regulating the host's immune response and metabolism. Molecular docking and molecular dynamics simulations demonstrated that active ingredients of Aloe vera, such as quercetin and aloe-emodin, can form stable complexes with CASP3 and MMP-9, exhibiting vigorous binding affinity to the active sites of the target. Further antibacterial activity assays and reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis demonstrated that aloe-emodin exerts antibacterial effects against gram-positive bacteria and inhibits the expression of the MMP-9 gene. This study provided insight into the antibacterial mechanisms of Aloe vera, highlighting MMP-9 as a key target. These findings lay a foundation for further studies on natural antibacterial agents.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109034"},"PeriodicalIF":2.7,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143714505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring phytochemicals and marine natural products as alternative therapeutic agents targeting phosphotransacetylase (PTA) in Mycobacterium tuberculosis: An underexplored drug target","authors":"Sneha Subramaniyan,&nbsp;Manikandan Jayaraman,&nbsp;Jeyakanthan Jeyaraman","doi":"10.1016/j.jmgm.2025.109025","DOIUrl":"10.1016/j.jmgm.2025.109025","url":null,"abstract":"<div><div>Tuberculosis (TB), caused by <em>Mycobacterium tuberculosis</em> (MTB), remains a significant global health threat due to its widespread prevalence and increasing drug resistance. This study targets phosphotransacetylase (PTA), an essential enzyme in acetate metabolism, as a potential therapeutic target. A comprehensive multi-tiered virtual screening approach was employed to identify potent phytochemicals and marine natural products (MNPs) from five databases (AMMPDB, CMNPD, MNPD, Seaweed and SPECS). Five promising bioactive molecules (AMMPDB10473, CMNPD23347, CMNPD5918, MNPD6660, and SPECS-AK-693) were identified, showing high docking scores (−8.17 to −10.83 kcal/mol) and MM-GBSA binding energy scores (−47.51 to −59.14 kcal/mol). These molecules adhered to Lipinski's rule of five (Ro5) and demonstrated acceptable pharmacokinetic profiles. Density functional theory (DFT) calculations further validated the interaction potential of these molecules through HOMO and LUMO analysis. Long-range molecular dynamics simulations (MDS) over 300 ns confirmed the structural stability and enhanced hydrogen-bonding potential of the natural products-PTA complexes. Principal component analysis (PCA) and free energy landscape (FEL) contour plots revealed a single dominant energy basin, indicating structural stability and limited conformational flexibility of the complexes. Additionally, MMPBSA analysis corroborated the strong binding affinities of the identified hit molecules with PTA. Critical <strong>'hot spot'</strong> residues (Phe516, Cys530, Ala531, and Tyr639) were identified, contributing significantly to the structural stability and binding energy of the complexes. This computational study offers valuable insights into the potential of these lead molecules for combating TB, providing a foundation for experimental validation and innovative therapeutic development, and paving the way for future research and breakthroughs in TB treatment.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109025"},"PeriodicalIF":2.7,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143680349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Noncovalent guest-host interactions unlock the potential of MOFs for anesthetic xenon recovery: GCMC and DFT insights into real anesthetic conditions","authors":"Tuğçe Gökdemir,&nbsp;Yeliz Gurdal","doi":"10.1016/j.jmgm.2025.109015","DOIUrl":"10.1016/j.jmgm.2025.109015","url":null,"abstract":"<div><div>Innovative designs offering cost-effective and highly efficient methods for xenon (Xe) recovery are becoming important for developing sustainable applications. Recently, the use of metal–organic frameworks (MOFs) has shown promise as candidates for separating Xe from anesthetic gas mixtures, however, there are limited studies available. We conducted combined Grand Canonical Monte Carlo (GCMC) and Density Functional Theory (DFT) simulations to determine the Xe recovery capacities of 19 MOFs from the exhaled anesthetic gas mixture, Xe/CO<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span>/O<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span>/N<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span>. COCMUE, GUHMIH, MAHCOQ, and PADKOK have demonstrated overall larger volumetric and gravimetric Xe uptake, demonstrating how ligand types can enhance selective Xe adsorption in MOFs. At low pressures, Xe atoms mainly adsorbed in close vicinity to the ligands, with tetrazole, phenyl, pyridyl, carboxamide, dicarboxylic acid, phenoxazine, and triazole ligands in the MOF structures acting as Xe trapping locations. Electronic structure analyses reveal that Xe-host interactions are primarily driven by charge-induced dipole and aerogen–<span><math><mi>π</mi></math></span> interactions. Our combined GCMC and DFT study shows that a relatively high amount of anesthetic Xe can be captured from real anesthetic exhale gas mixtures using MOFs with the proper chemical and geometrical characteristics. These characteristics maximize noncovalent Xe-host interactions and ultimately enable the utilization of Xe as an anesthetic gas in clinical applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109015"},"PeriodicalIF":2.7,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143680354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative in silico analysis to explore the potential of Zingiberaceae compounds to inhibit estrogen receptor alpha activity in breast cancer","authors":"Amit Dubey ,&nbsp;Hamad A. Al-Lohedan ,&nbsp;Mohd Sajid Ali ,&nbsp;Andrea Ragusa","doi":"10.1016/j.jmgm.2025.109023","DOIUrl":"10.1016/j.jmgm.2025.109023","url":null,"abstract":"<div><div>The estrogen receptor alpha (ERα) is a critical player in breast cancer progression, making it a key target for therapeutic development. This study employed an advanced computational method to discover potential inhibitors of ERα from a library of compounds from the Zingiberaceae family. The workflow includes virtual screening, re-docking, molecular dynamics (MD) simulations, radius of gyration (RG), and root mean-square deviation (RMSD)-based free energy landscape (FEL) analysis. This multifaceted strategy led to the selection of four compounds with superior docking scores compared to established control molecules. The MD simulation assessments confirmed that these selected compounds exhibited robust stability and favorable binding interactions within the ERα binding pocket. Notably, the pocket volume analysis of the minimum energy structures obtained from FEL analysis indicated a significant reduction in volume compared to the initial docking poses, suggesting a more compact and potentially more effective binding conformation. These findings highlight the potential of Zingiberaceae family-derived compounds as promising candidates for ERα inhibition. The stability of these interactions and the observed compactness of the binding pocket, as demonstrated by our comprehensive computational analysis, underscore the potential of these compounds for further preclinical evaluation.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109023"},"PeriodicalIF":2.7,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143705180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the catalytic performance of ligand-functionalized Cu-BTC paddlewheels in carboxylative cyclization of propargyl alcohol with CO2: DFT and SISSO insights","authors":"Jakkapan Sirijaraensre","doi":"10.1016/j.jmgm.2025.109022","DOIUrl":"10.1016/j.jmgm.2025.109022","url":null,"abstract":"<div><div>The M06-L functional with the 6-31G(d,p) and SDD ECP basis sets, was used to investigate the structure and electronic properties of defective linker-coordinated paddlewheel complexes (Cu-BTC(L1–L4)) in the catalytic conversion of propargyl alcohol (PA) and CO₂ into cyclic carbonate. Two catalytic processes are proposed based on the different PA adsorption modes at the Cu center. The reaction proceeds via adsorption by the hydroxyl group in two sequential steps: PA/CO₂ activation and cyclization. This pathway is proposed as the dominant process in the Cu-BTC and Cu-BTC(L1–L3) systems. However, only Cu-BTC(L3) and Cu-BTC(L4), which exhibit stronger electron back-donation compared to the other systems, effectively promote the catalytic process via PA adsorption through its alkyne bond. In this latter mode, the reaction proceeds through three consecutive steps: PA/CO₂ activation, ring closure, and H-transfer. Compared to pristine Cu-BTC, Cu-BTC(L3) and Cu-BTC(L4) are proposed as more efficient catalysts for the carboxylative cycloaddition of CO₂ with PA. The rate-determining step for the reaction on these two systems is the PA/CO₂ activation via the latter mechanism. This step has an activation free energy of 16.7 kcal/mol and 15.0 kcal/mol for the Cu-BTC(L3) and Cu-BTC(L4). The SISSO model reveals the role of the Cu center in activating PA and stabilizing the generated intermediate, thereby lowering the activation free energy for PA/CO₂ activation.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109022"},"PeriodicalIF":2.7,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143680353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular property prediction based on graph contrastive learning with partial feature masking","authors":"Kunjie Dong,&nbsp;Xiaohui Lin,&nbsp;Yanhui Zhang","doi":"10.1016/j.jmgm.2025.109014","DOIUrl":"10.1016/j.jmgm.2025.109014","url":null,"abstract":"<div><div>Molecular representation learning facilitates multiple downstream tasks such as molecular property prediction (MPP) and drug design. Recent studies have shown great promise in applying self-supervised learning (SSL) to cope with the data scarcity in MPP. Contrastive learning (CL) is a typical SSL method used to learn prior knowledge so that the trained model has better generalization performance on various downstream tasks. One important issue of CL is how to generate enhanced samples that preserve the molecular core semantics for each training sample, which may significantly impact the earnings of the CL strategy. To address this issue, we propose the partial <u>F</u>eature <u>M</u>asking-based molecular <u>G</u>raph <u>C</u>ontrastive <u>L</u>earning model (FMGCL). FMGCL constructs the masked molecular graph by masking partial features of each atom and bond in the featured molecular graph. Since the masking molecular graphs preserve the chemical structure of the molecules, they do not violate the chemical semantics of molecules, which is beneficial for capturing valuable prior knowledge of molecules during pre-training. Then, FMGCL fine-tunes the well-trained encoder on the featured molecular graph for downstream tasks. Moreover, we propose using the relative distance between samples within a batch to enhance the performance in regression tasks. Experiments on the 12 benchmark datasets from MoleculeNet and ChEMBL showed the superiority of FMGCL.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109014"},"PeriodicalIF":2.7,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143680351","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}