Journal of molecular graphics & modelling最新文献

{"title":"Mechanical and thermoelectric properties of ZrX2 and HfX2 (X = S and Se) from Van der Waals density-functional theory","authors":"S. Ferahtia ,&nbsp;S. Benyettou ,&nbsp;S. Saib ,&nbsp;N. Bouarissa ,&nbsp;Kh Ouail","doi":"10.1016/j.jmgm.2024.108812","DOIUrl":"10.1016/j.jmgm.2024.108812","url":null,"abstract":"<div><p>The structural, mechanical, and thermoelectric characteristics of layered transition metal dichalcogenides MX₂ (M = Zr, Hf; X = S, Se) have been studied using density functional theory along with van der Waals correction. The exchange-correlation functional, enhanced with corrections for van der Waals interactions, has been evaluated for the hexagonal bulk structures of these materials. The analysis of elastic properties reveals that these compounds exhibit brittleness at zero pressure and conform to Born's criteria for mechanical stability. Examination of elastic constants and moduli suggests that the compounds possess reasonable machinability, moderate hardness, and anisotropy in terms of sound velocity. Transport properties, including the Seebeck coefficient, electrical conductivity, thermal conductivity, and power factor, have been computed using the semi-classical Boltzmann theory implemented in the BoltzTraP code. All investigated compounds exhibit excellent thermoelectric performance at high temperatures. This result suggests that our compounds are highly promising candidate for practical utilization in the thermoelectric scope.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"131 ","pages":"Article 108812"},"PeriodicalIF":2.9,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141413239","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":"Engineered nanoparticles as Selinexor drug delivery systems across the cell membrane and related signaling pathways in cancer cells","authors":"Alireza Nakhaei,&nbsp;Heidar Raissi,&nbsp;Farzaneh Farzad","doi":"10.1016/j.jmgm.2024.108809","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108809","url":null,"abstract":"<div><p>In the present work, molecular dynamics simulation is applied to evaluate the drug carrier efficiency of graphene oxide nanoflake (GONF) for loading of Selinexor (SXR) drug as well as the drug delivery by 2D material through the membrane in aqueous solution. In addition, to investigate the adsorption and penetration of drug-nanocarrier complex into the cell membrane, well-tempered metadynamics simulations and steered molecular dynamics (SMD) simulations were performed. Based on the obtained results, it is evident that intermolecular hydrogen bonds (HBs) and π-π interactions play a significant role in expediting the interaction between drug molecules and the graphene oxide (GO) nanosheet, ultimately resulting in the formation of a stable SXR-GO complex. The Lennard-Jones (L-J) energy value for the interaction of SXR with GONF is calculated to be approximately −98.85 kJ/mol. In the SXR-GONF complex system, the dominant interaction between SXR and GONF is attributed to the L-J term, resulting from the formation of a strong π−π interaction between the drug molecules and the substrate surface. Moreover, our simulations show by decreasing the distance of GONF with respect to cell membrane, the interaction energy of GONF-membrane significantly decrease to −1500 kJ/mol resulting in fast diffusion of SXR-GONF complex toward the bilayer surface that is favored opening the way to natural drug nanocapsule.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"131 ","pages":"Article 108809"},"PeriodicalIF":2.9,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141329345","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":"Dynamics of nucleoplasm in human leukemia cells: A thrust towards designing anti-leukemic agents","authors":"Hridoy R. Bairagya","doi":"10.1016/j.jmgm.2024.108807","DOIUrl":"10.1016/j.jmgm.2024.108807","url":null,"abstract":"<div><p>The human inosine monophosphate dehydrogenase (hIMPDH) is a metabolic enzyme that possesses a unique ability to self-assemble into higher-order structures, forming cytoophidia. The hIMPDH II isoform is more active in chronic myeloid leukemia (CML) cancer cells, making it a promising target for anti-leukemic therapy. However, the structural details and molecular mechanisms of the dynamics of hIMPDHcytoophidia assembly in vitro need to be better understood, and it is crucial to reconstitute the computational nucleoplasm model with cytophilic-like polymers in vitro to characterize their structure and function. Finally, a computational model and its dynamics of the nucleoplasm for CML cells have been proposed in this short review. This research on nucleoplasm aims to aid the scientific community's understanding of how metabolic enzymes like hIMPDH function in cancer and normal cells.</p><p>However, validating and justifying the computational results from modeling and simulation with experimental data is essential. The new insights gained from this research could explain the structure/topology, geometrical, and electronic consequences of hIMPDH inhibitors on leukemic and normal cells. They could lead to further advancements in the knowledge of nucleoplasmic chemical reaction dynamics.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"131 ","pages":"Article 108807"},"PeriodicalIF":2.7,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141415875","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":"Impact of mutations in SARS-CoV-2 recombinant sub-variant XBB.1.16 on the binding affinity with human ACE2 receptor","authors":"Syeda Sumayya Tariq ,&nbsp;Komal Zia ,&nbsp;Mohammad Nur-e-Alam ,&nbsp;Dmitry Nerukh ,&nbsp;Vladimir S. Farafonov ,&nbsp;Zaheer Ul-Haq","doi":"10.1016/j.jmgm.2024.108813","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108813","url":null,"abstract":"<div><p>Despite the waning threat of the COVID-19 pandemic, its detrimental impact on global health persists. Regardless of natural immunity or immunity obtained through vaccination, emerging variants of the virus continue to undergo mutations and propagate globally. The persistent mutations in SARS-CoV-2, along with the subsequent formation of recombinant sub-variants has become a challenge for researchers and health professionals, raising concerns about the efficacy of current vaccines. Gaining a better understanding of the biochemical interactions between the Spike Protein (RBD) of SARS-CoV-2 variants and the human ACE2 receptor can prove to be beneficial in designing and developing antiviral therapeutics that are equally effective against all strains and emerging variants. Our objective in this study was to investigate the interfacial binding pattern of the SARS-CoV-2 RBD-ACE2 complex of the Wild Type (WT), Omicron, and the Omicron recombinant sub-variant XBB.1.16. We aimed to examine the atomic level factors and observe how mutations influence the interaction between the virus and its host using Molecular Dynamics simulation, MM/GBSA energy calculations, and Principal Component Analysis. Our findings reveal a higher degree of structural deviation and flexibility in XBB.1.16 compared to WT and Omicron. PCA indicated a wider cluster and significant flexibility in the movements of XBB.1.16 which can also be observed in free energy landscapes, while the normal mode analysis revealed converging motions within the RBD-ACE2 complexes which can facilitate the interaction between them. A pattern of decreased binding affinity was observed in case of XBB.1.16 when compared to the WT and Omicron. These observed deviations in XBB.1.16 when compared to its parent lineage Omicron, and WT can be attributed to the mutations specific to it. Collectively, these results enhance our understanding of the impact of mutations on the interaction between this strain and the host, taking us one step closer to designing effective antiviral therapeutics against the continually mutating strains.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"131 ","pages":"Article 108813"},"PeriodicalIF":2.9,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141333068","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":"Prediction of binding affinity and enthalpy of CB7 with alkaloids by attach-pull-release molecular dynamics simulations study","authors":"Xiru Wu,&nbsp;Lingzhi Wang,&nbsp;Yuan Qin,&nbsp;Yalei Gao,&nbsp;Min Yang,&nbsp;Pei Cao,&nbsp;Kai Liu","doi":"10.1016/j.jmgm.2024.108810","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108810","url":null,"abstract":"<div><p>Host-guest complex has attracted much attention because of their fantastic capability. Accurate prediction of their binding affinity and enthalpy is essential to the rational design of guest molecules. The attach-pull-release (APR) method proposed by Henriksen et al. (J. Chem. Theory Comput., 2015, 11:4377.) shows good prediction capability of binding affinity especially for host-guest system. In order to further evaluate the performance of APR method in practice, we have conducted the calculations on the macrocycle cucurbit [7]urils (CB7) encapsulated with four structurally similar alkaloids (berberine, coptisine, epiberberine and palmatine) with two force fields (GAFF and GAFF2) and three water models (TIP3P, SPC/E and OPC). Compared to the experimental data, the calculation by the combination of GAFF2 and SPC/E force field presents the best performance, of which the Pearson correlation coefficients (R²) is 0.95, and the root-mean-square-deviation is 3.04 kcal/mol. While the predictions from GAFF force field all overestimated the binding affinity, suggesting a systematic error may be involved. Comparison of calculation also indicates that the accuracy of prediction was susceptible to the combination of force field. Therefore, it would be necessary to repeat the simulation with different combination of force fields in practice.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"131 ","pages":"Article 108810"},"PeriodicalIF":2.9,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141294934","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":"Thermal curing mechanisms and cross-linking network structure of a novel silicon-containing arylacetylene resin with 2,7-diethynylnaphthalene unit","authors":"Hui Li,&nbsp;Lei Yang,&nbsp;Zijian Sun,&nbsp;Weihua Zhu","doi":"10.1016/j.jmgm.2024.108811","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108811","url":null,"abstract":"<div><p>Silicon-containing arylacetylene resin and its composites have attracted great interest as emerging heat-resistant materials, but their curing mechanisms and products are still elusive. In this work, the influences of the terminal and inner acetylenes on the curing mechanisms of silicon-containing arylacetylene resin with 2,7-diethynylnaphthalene were first identified by density functional theory. Two reaction pathways were proposed and their products include polyenes, anthracene dimers, and benzene trimers. To gain a distinct observation of the cross-linking process, molecular dynamics simulations were used to construct a cross-linking polymerization model. The effects of the temperature on the cured structure were investigated by analyzing the characteristics of the cross-linked network. As expected, higher curing temperature will make the larger proportion of polyene chain and aromatic ring in the terminal alkyne−terminal alkyne route, meanwhile, for the inner alkyne−inner alkyne route, the short chains and a small amount of aromatic rings are major productions. Overall, our cross-linking method may provide an unique guidance for studying the cured structure of other thermosetting resins.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"131 ","pages":"Article 108811"},"PeriodicalIF":2.9,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141308458","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":"Computational evaluation of novel XCuH3 (X = Li, Na and K) perovskite-type hydrides for hydrogen storage applications using LDA and GGA approach","authors":"Muhammad Mubashir ,&nbsp;Mubashar Ali ,&nbsp;Zunaira Bibi ,&nbsp;Usama Afzal ,&nbsp;Munirah D. Albaqami ,&nbsp;Saikh Mohammad ,&nbsp;Muhammad Muzamil","doi":"10.1016/j.jmgm.2024.108808","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108808","url":null,"abstract":"<div><p>Hydrogen energy has attracted a lot of interest from researchers as a sustainable and renewable energy source, but there are some technical challenges related to its storage. Hydride materials demonstrate the ability to store hydrogen adequately and safely. In the current study, we have investigated the structural and optoelectronic properties of the XCuH₃ (where X = Li, Na and K) perovskite-type hydride using LDA and GGA formalisms for hydrogen storage application. Electronic properties such as band structure, density of states reveal the metallic character of the studied XCuH₃ hydrides. Various optical parameters such as the complex dielectric function, refractive index, extinction coefficient, absorption coefficient, reflectivity, optical conductivity, energy loss function, and joint density of states have been computed and compared. The gravimetric hydrogen storage capacity for LiCuH₃, NaCuH₃ and KCuH₃ are found to be 4.11, 3.37 and 2.86 wt%, respectively. The computed values of the gravimetric ratio manifest that XCuH₃ hydrides are potential candidates for hydrogen storage applications. These calculations are made for the first time for XCuH₃ hydrides and will be inspirational in the future for comparison and for hydrogen storage purposes.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"131 ","pages":"Article 108808"},"PeriodicalIF":2.9,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141290327","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":"Catalytic battle of activated carbon supported transition metal atom towards adsorption and dissociation of molecular hydrogen: Progress towards quantum chemical application on renewable energy resource","authors":"Abhijit Dutta ,&nbsp;Amit Kumar Pradhan ,&nbsp;Paritosh Mondal","doi":"10.1016/j.jmgm.2024.108804","DOIUrl":"10.1016/j.jmgm.2024.108804","url":null,"abstract":"<div><p>Density functional theory (DFT) investigation has been done to unravel the adsorption and dissociation nature of hydrogen molecule on 3<em>d</em>, 4<em>d</em> and 5<em>d</em> transition metal (M = Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Os, Ir, Pt or Au) atom doped activated carbon (AC) surface. Transition metal doped AC are found to be active catalyst for storage of hydrogen and also gives the stability of <em>M</em> − H bonds formed after bond breakage of H₂ molecule. Transition metals are found to occupy the position on the five member ring rather than six member ring of the AC. Five member ring of the AC is seen to be more deformed than the six-member ring on metal doping. Higher values of LUMO-HOMO gap and vertical ionization potential and lower electron affinity signify the higher stability of hydrogen molecule adsorbed metal doped AC. Bond length and vibrational analysis of the adsorbed hydrogen molecule suggest the higher activation of hydrogen molecule on AC, where 4<em>d</em> and 5<em>d</em> metal doped ACs are found to be more efficient in comparison to 3<em>d</em> metal. Adsorbed hydrogen molecule on metal doped AC follows dissociation either via spill-over or via normal process. DFT evaluated rate constant and the transition states suggest that Ru, Rh, Os and Ir doped AC are found to be efficient in the dissociation of hydrogen molecule, while, Cu doped AC is seen to be worst in the same reaction. Deformed electron density, HOMO-LUMO isosurface, and density of states confirms the redistribution of electrons among H₂ and metal doped AC surface. ΔG_H values of Hydrogen evolution reaction also signifies the greater catalytic activities of Ru and Os supported activated carbon towards HER.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"131 ","pages":"Article 108804"},"PeriodicalIF":2.9,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141275801","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 binding of diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes at DNA/RNA nucleobases: Computational evidences of an appreciable selectivity toward the AU base pairs","authors":"Iogann Tolbatov ,&nbsp;Paolo Umari ,&nbsp;Alessandro Marrone","doi":"10.1016/j.jmgm.2024.108806","DOIUrl":"10.1016/j.jmgm.2024.108806","url":null,"abstract":"<div><p>Multiple medicinal strategies involve modifications of the structure of DNA or RNA, which disrupt their correct functioning. Metal complexes with medicinal effects, also known as metallodrugs, are among the agents intended specifically for the attack onto nucleosides. The diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes constitute promising dual acting drugs due to their ability to release the therapeutically active bridging ligands upon their substitution by endogenous ligands. In this paper, we study the structure and the stability of the complexes formed by the diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes coordinated in axial positions with the DNA/RNA nucleobases or base pairs, assuming the attainable metalation at all the accessible pyridyl nitrogens. Dirhodium complexes coordinate at the pyridyl nitrogens more strongly than the diruthenium complexes. On the other hand, we found that the diruthenium scaffold binds more selectively to nucleobase targets. Furthermore, we reveal a tighter coordination of diruthenium complex at the adenine-uracil base pair, compared to adenine-thymine, hence constituting a scarce instance of RNA-selectivity. We envision that the here reported computational outcomes may pace future experiments addressing the binding of diruthenium and dirhodium paddlewheel complexes at either single nucleobases or DNA/RNA fragments.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"131 ","pages":"Article 108806"},"PeriodicalIF":2.9,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1093326324001062/pdfft?md5=b8d31fab85c9aebf7546ea342dbc40f5&pid=1-s2.0-S1093326324001062-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combined experimental and computational investigation of tetrabutylammonium bromide-carboxylic acid-based deep eutectic solvents","authors":"Sahar Shokri,&nbsp;Nosaibah Ebrahimi,&nbsp;Rahmat Sadeghi","doi":"10.1016/j.jmgm.2024.108805","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108805","url":null,"abstract":"<div><p>Aiming at shedding light on the molecular interactions in deep eutectic solvents (DESs), the DESs based on tetrabutylammonium bromide (TBAB) as hydrogen bond acceptor (HBA) and carboxylic acids (CAs) (formic acid (FA), oxalic acid (OA), and malonic acid (MA)) as hydrogen bond donor (HBD) were investigated by both experimental and theoretical techniques. The thermal behaviors of the prepared DESs were investigated by differential scanning calorimetry (DSC) method. In order to study the hydrogen bond formation between the DESs constituents, the FT-IR analysis was carried out. The large positive deviations of the iso solvent activity lines of ternary HBA + HBD + 2-propanol mixtures determined by the isopiestic technique from the semi-ideal behavior indicate that CAs interact strongly with TBAB and therefore they can form DESs. Molecular dynamics (MD) simulations were performed to present an atomic-scale image of the components and describe the microstructure of DESs. From the MD simulations, the radial distribution functions (RDFs), coordination numbers (CNs), combined distribution functions (CDFs), and spatial distribution functions (SDFs) were calculated to investigate the interaction between the components and three-dimensional visualization of the DESs. The obtained results confirmed the importance of hydrogen bonds in the formation of TBAB/CAs DESs.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"131 ","pages":"Article 108805"},"PeriodicalIF":2.9,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141242867","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}