Journal of molecular graphics & modelling最新文献

{"title":"Investigating the multifaceted characteristics of Ba2FeWO6 double perovskite: Insights from density functional theory","authors":"","doi":"10.1016/j.jmgm.2024.108834","DOIUrl":"10.1016/j.jmgm.2024.108834","url":null,"abstract":"<div><p>This study undertook a comprehensive examination of the double perovskite complex Ba₂FeWO₆, investigating its structural, electrical, magnetic, thermal and elastic characteristics. The study used density functional theory (DFT), specifically the full potential linearized augmented plane wave (FP-LAPW) method. It also used different approximations, including the generalized gradient approximation (GGA) and the modified Trans-Blaha (TB-mBJ) approach, to improve the accuracy of the band gap estimation more accurate. Additionlly, the GGA + U approach, incorporating the Hubbard correction term (U), was utilized. Our findings indicate that Ba₂FeWO₆ exhibits indirect half-metallic band gaps in the (L-X) direction, with value of 0.91 eV and a net magnetic moment of 4 <em>μ</em>_B, predominatly influenced by the iron atom. The compound demonstrated exceptional characteristics suitable for thermoelectric applications, particularly at lower temperatures. Furthermore, the elasticity analysis revealed low brittleness, facilitates its manipulation in manufacturing procedures.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141843759","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":"BC6NA monolayer as an ideal anode material for high-performance sodium-ion batteries","authors":"","doi":"10.1016/j.jmgm.2024.108832","DOIUrl":"10.1016/j.jmgm.2024.108832","url":null,"abstract":"<div><p>Selecting an appropriate anode material (AM) has been considered to be a crucial initial step in advancing high-performance batteries. Within this piece of research, we examine the suitability of the BC₆NA monolayer (referred to as BC₆NAML) as an AM by first-principles calculations. The BC₆NAML exhibits metallic behavior consistently, even with varying concentrations of Na atoms, making it an ideal choice for battery usages. Our findings revealed that the theoretical storage capacity for Na-adhered BC₆NAML was 406.36 mAhg⁻¹, surpassing graphite, TiO₂, BC₆NA, and numerous other 2D materials. The BC₆NAML also demonstrates a diffusion barrier of 0.39 eV and favorable diffusivity of Na-ions. Although the open-circuit voltage (OCV) of BC6NAML was temperate and lower compared to the OCV of other AMs like TiO₂, our results suggested that it is possible to utilize BC₆NAML as one of the encouraging host materials for sodium-ion batteries (SIBs). Consequently, this investigation into the potential anodic application of BC₆NAML proves valuable for future experimental studies into sodium storage for SIBs.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141766312","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":"Research on the formation and evolution mechanism of cracks in laser stealth dicing of silicon carbide crystals","authors":"","doi":"10.1016/j.jmgm.2024.108830","DOIUrl":"10.1016/j.jmgm.2024.108830","url":null,"abstract":"<div><p>In this study, to enhance the cutting efficiency and precision of the chip while minimizing waste from cutting damage, molecular dynamics simulation is used to investigate the formation mechanism of defects and cracks of silicon carbide crystals during the laser stealth dicing. The results showed that the high thermal stress generated by the laser scanning induced the production and expansion of cracks. Thus, the crack propagates in the direction of <span><math><mrow><mo>[</mo><mn>100</mn><mo>]</mo></mrow></math></span>, and subsequently forms branches in the directions of <span><math><mrow><mo>[</mo><mn>101</mn><mo>]</mo></mrow></math></span> and <span><math><mrow><mo>[</mo><mn>10</mn><mover><mn>1</mn><mo>‾</mo></mover><mo>]</mo></mrow></math></span>. It also can be found that the silicon carbide crystals produced dislocation slip, and the dislocation lines moved along the slip surface, which impeded the crack extension in the directions of <span><math><mrow><mo>[</mo><mn>10</mn><mover><mn>1</mn><mo>‾</mo></mover><mo>]</mo></mrow></math></span> and <span><math><mrow><mo>[</mo><mover><mn>1</mn><mo>‾</mo></mover><mn>0</mn><mover><mn>1</mn><mo>‾</mo></mover><mo>]</mo></mrow></math></span>. In addition, atomic phase transformation and loss is occurred under the high-temperature environment of the laser heating process. Cubic diamond crystal structure atoms are partially transformed into amorphous structure, while a small portion transformed into hexagonal diamond structure. The crystal structural arranged orderliness temporarily increased and then rapidly decreased due to prefabrication defects, and new unknown crystal structures are produced.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141728778","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":"Robust superhydrophobic self-cleaning coating prepared by silane modified multi-walled carbon nanotubes: A combined experimental and molecular dynamics study","authors":"","doi":"10.1016/j.jmgm.2024.108831","DOIUrl":"10.1016/j.jmgm.2024.108831","url":null,"abstract":"<div><p>As a functional material, superhydrophobic coating has been widely studied in the field of self-cleaning. However, obtaining superhydrophobic coatings with robustness through simple preparation processes remains a challenge. In this paper, a robust superhydrophobic coating is prepared based on multi-walled carbon nanotubes modified by octyltrimethoxysilane, and its performance and hydrophobic mechanism are studied by experiments and molecular dynamics simulation. The superhydrophobic coating is prepared by one-step spraying method. The coating is characterized and analyzed by scanning electron microscopy and Fourier transform infrared spectroscopy, and the properties of the coating are tested by experiments. Molecular dynamics simulation is used in the study to construct a molecular model system, and the molecular modification mechanism and coating wettability are simulated under the COMPASSII force field. The results show that octyltrimethoxysilane successfully modified carbon nanotubes, and the hydroxyl groups at the head of the molecular chain are bound to the surface of the carbon nanotubes in the form of hydrogen bonds, while the tail of the molecular chain is far away from the surface. After modification, the surface of carbon nanotubes changed from hydrophilic to hydrophobic. The prepared superhydrophobic coating not only has excellent self-cleaning properties, but also exhibits corrosion resistance to acid and alkali solutions. The coating still has superhydrophobic when the wear length is in the range of 400 cm. It can be seen that a robust superhydrophobic self-cleaning coating is successfully prepared by a simple one-step spraying method. The modification mechanism and the hydrophobic mechanism of the coating were obtained by the combination of experiment and molecular dynamics simulation, which provided theoretical support for the superhydrophobic of the coating at the micro level.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141732063","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":"Atomistic understanding on desalination performance of pristine graphenylene nanosheet membrane at high applied pressures","authors":"","doi":"10.1016/j.jmgm.2024.108833","DOIUrl":"10.1016/j.jmgm.2024.108833","url":null,"abstract":"<div><p>Molecular dynamics (MD) simulations are conducted to assess pristine graphenylene membranes' effectiveness in seawater desalination, explicitly focusing on their salt rejection and water permeability capabilities. This study investigates the potential of the graphenylene for separation of the Na⁺ as monovalent cation, in order to evaluate its further application for separation of the other type of contaminants. To this end, the pristine graphenylene nanosheet is introduced into the simulation box which included the water molecules, sodium and chlorine ions. Subsequently, MD simulations were conducted by applying different amounts of external pressures in which the temperature changes are investigated as another effective parameter in water permeability and salt rejection properties. Furthermore, the water density map, radial distribution functions, and water density elucidate the performance of the considered membrane in the presence of water molecules, Na⁺ ions, and Cl⁻ ions. The optimum performance of the pristine graphenylene for seawater desalination is achieved at <em>P</em> = 400 MPa and <em>T</em> = 298 K that results in the water flux of 2920 L/m² h bar and 98.8 % salt rejection. The pristine graphenylene nanosheet shows significant potential in effectively separating salt ions, which has elucidated its importance and subsequently, the functionalized membrane for this application.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141751927","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":"Water dissociation and COOH formation on Fe modified Cu(100) surface: A density functional theory study","authors":"","doi":"10.1016/j.jmgm.2024.108829","DOIUrl":"10.1016/j.jmgm.2024.108829","url":null,"abstract":"<div><p>Water splitting has emerged as a promising route for sustainable hydrogen production. In this research paper, adsorption and dissociation of H₂O accompanied with dissociated constituents reactions with CO₂ and CO have been investigated on Fe modified Cu(100) surface employing density functional theory (DFT) at GGA-PW91 level. The adsorption and other reactions carried out on Fe2–Cu(100) surfaces gave very promising results. The adsorption of H₂O on Fe top of this surface occurs yielding E_ads −1.73 eV, which highlights a favorable adsorption on the Fe-modified Cu(100) surface. The activation energy for the water splitting reaction is found to be 0.65 eV, suggesting a feasible pathway for hydrogen evolution. The process also accompanies reaction energy of −0.54 eV. Furthermore, the interaction between carbon dioxide (CO₂) and the H-atom on the surface lead to the formation of COOH through surmounting an activation barrier of 1.09 eV. The final position of COOH gets further stabilization having exothermicity of −0.43 eV. Another route for COOH formation from CO + OH operates on the Cu(100) part of the surface with a small activation barrier of 0.14 eV through exothermic process of −0.29 eV, however, diffusion of CO and OH from Fe to Cu is energetically expensive. This study signifies the consumption of CO and CO₂ in addition to water splitting giving birth to useful products.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141732061","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":"Insights into the mechanism, selectivity, and substituent effects in the Diels-Alder reaction of azatrienes with electron-rich dienophiles: An MEDT study","authors":"","doi":"10.1016/j.jmgm.2024.108819","DOIUrl":"10.1016/j.jmgm.2024.108819","url":null,"abstract":"<div><p>The reactivity and mechanistic intricacies of azatrienes in Diels-Alder reactions have been relatively unexplored despite their intriguing potential applications. In this study, we employ Molecular Electron Density Theory to theoretically investigate the hetero-Diels–Alder reaction involving azatrienes with ethyl vinyl ether and allenyl methyl ether. Analysis of Conceptual Density Functional Theory, energetic profiles, and the topological characteristics is conducted to elucidate the reactions. The revealed mechanism manifests as a polar one-step two-stages process under kinetic control. We establish a clear relationship of between the periselectivity, regioselectivity, and stereoselectivity on one hand and the characteristics of the reactions mechanism on the other hand. The influence of weak interactions on reaction activation barriers and bonding evolution are discussed in detail. We demonstrate that substituents enhancing the reverse electron density flux facilitate the feasibility of the reactions. The results lay ground for a meticulous control of the reaction of azatriene in similar synthetic scenarios.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141689385","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":"Uncovering substrate specificity determinants of class IIb aminoacyl-tRNA synthetases with machine learning","authors":"","doi":"10.1016/j.jmgm.2024.108818","DOIUrl":"10.1016/j.jmgm.2024.108818","url":null,"abstract":"<div><p>Specific amino acid (AA) binding by aminoacyl-tRNA synthetases (aaRSs) is necessary for correct translation of the genetic code. Sequence and structure analyses have revealed the main specificity determinants and allowed a partitioning of aaRSs into two classes and several subclasses. However, the information contributed by each determinant has not been precisely quantified, and other, minor determinants may still be unidentified. Growth of genomic data and development of machine learning classification methods allow us to revisit these questions. This work considered the subclass IIb, formed by the three enzymes aspartyl-, asparaginyl-, and lysyl-tRNA synthetase (LysRS). Over 35,000 sequences from the Pfam database were considered, and used to train a machine-learning model based on ensembles of decision trees. The model was trained to reproduce the existing classification of each sequence as AspRS, AsnRS, or LysRS, and to identify which sequence positions were most important for the classification. A few positions (5–8 depending on the AA substrate) sufficed for accurate classification. Most but not all of them were well-known specificity determinants. The machine learning models thus identified sets of mutations that distinguish the three subclass members, which might be targeted in engineering efforts to alter or swap the AA specificities for biotechnology applications.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141699041","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":"A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of E. coli ribosome","authors":"Merve Yuce ,&nbsp;Beril Ates ,&nbsp;Nesrin Isil Yasar ,&nbsp;Fethiye Aylin Sungur ,&nbsp;Ozge Kurkcuoglu","doi":"10.1016/j.jmgm.2024.108817","DOIUrl":"10.1016/j.jmgm.2024.108817","url":null,"abstract":"<div><p>The global antibiotic resistance problem necessitates fast and effective approaches to finding novel inhibitors to treat bacterial infections. In this study, we propose a computational workflow to identify plausible high-affinity compounds from FDA-approved, investigational, and experimental libraries for the decoding center on the small subunit 30S of the <em>E. coli</em> ribosome. The workflow basically consists of two molecular docking calculations on the intact 30S, followed by molecular dynamics (MD) simulations coupled with MM-GBSA calculations on a truncated ribosome structure. The parameters used in the molecular docking suits, Glide and AutoDock Vina, as well as in the MD simulations with Desmond were carefully adjusted to obtain expected interactions for the ligand-rRNA complexes. A filtering procedure was followed, considering a fingerprint based on aminoglycoside's binding site on the 30S to obtain seven hit compounds either with different clinical usages or aminoglycoside derivatives under investigation, suggested for <em>in vitro</em> studies. The detailed workflow developed in this study promises an effective and fast approach for the estimation of binding free energies of large protein-RNA and ligand complexes.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141558900","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":"Structural, magnetic, electronic, optical and mechanical properties of actinide perovskite oxides XAnO3 [X = Cs+, Ba2+; An = Np5+, Np4+]: GGA, GGA+U and GGA+U+mBJ investigations","authors":"M. Musa Saad H.-E. ,&nbsp;B.O. Alsobhi","doi":"10.1016/j.jmgm.2024.108815","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108815","url":null,"abstract":"<div><p>First-principles density functional theory (DFT)-based calculations were performed to investigate the structural, magnetic, electronic, optical and mechanical properties of two actinide perovskite oxides XAnO₃, where [X = Cs⁺, Ba²⁺; An = Np⁵⁺, Np⁴⁺]. Wien2k software is utilized with GGA, GGA + U and GGA + U + mBJ potentials. The unit cell volumes for cubic (Pm-3m) structure of XAnO₃ are optimized to achieve the ground state energy and equilibrium parameters. Substitution of X- and An-sites increases the lattice constant, <span><math><mrow><msub><mi>a</mi><mn>0</mn></msub></mrow></math></span> = 4.3998 Å (X = Cs⁺) and <span><math><mrow><msub><mi>a</mi><mn>0</mn></msub></mrow></math></span> = 4.4378 Å (X = Ba²⁺). The calculated band structure plus total and partial density of states using these methods confirm the 100 % spin-polarization and half-metallic (HM) nature of XAnO₃ with <span><math><mrow><msubsup><mi>E</mi><mi>g</mi><mo>↓</mo></msubsup></mrow></math></span> = 2.731, 3.896 and 3.787 eV (X = Cs⁺); 3.891, 3.929 and 4.329 eV (X = Cs⁺). Total magnetic moment per unit cell of XAnO₃ is respectively <span><math><mrow><msup><mi>M</mi><mrow><mi>T</mi><mi>o</mi><mi>t</mi></mrow></msup></mrow></math></span> = 2.0 and 3.0 μ_B revealing their ferromagnetic (FM) behavior with high Curie temperature (<span><math><mrow><msub><mi>T</mi><mi>C</mi></msub></mrow></math></span>) within GGA, GGA + U and GGA + U + mBJ. Mechanical and thermodynamic stability of XAnO₃ have been proved via the elastic parameters, sound velocity, Debye and melting temperatures, and enthalpy of formation. In addition, XAnO₃ show amazing optical responses include high absorption, conductivity, refractivity, and reflectivity. These investigated properties confirm that XAnO₃ materials have FM-HM and high optical characteristics and they perfectly suitable for many spintronics and optoelectronics applications such as sensors, storage devices and photodiodes.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141439056","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}