Journal of Molecular Modeling最新文献

{"title":"Molecular dynamics simulation of TNT/PYRN cocrystal PBXs","authors":"Yu-hang Han,&nbsp;Xin-yi Li,&nbsp;Zhong-liang Ma,&nbsp;Bao-guo Wang,&nbsp;Ji-hang Du,&nbsp;Yu Yang,&nbsp;Hong-wei Zhao,&nbsp;Qing-jun Jin,&nbsp;Peng-yu Bi","doi":"10.1007/s00894-025-06394-9","DOIUrl":"10.1007/s00894-025-06394-9","url":null,"abstract":"<div><h3>Context</h3><p>The ternary eutectic system comprising trinitrotoluene (TNT) and pyranidine (PYRN) exhibits potential as a moderate-energy explosive compound characterized by reduced sensitivity. Recently, this composition can be a suitable alternative to TNT in the development of low-vulnerability explosive formulations, thus providing a promising alternative for future applications in the field of energetic materials. However, the changes in the structure and properties of eutectic explosives and their intrinsic causes for these changes have been rarely explored. Here, we construct a theoretical model of the TNT/PYRN eutectic system and integrates a diverse array of polymer additives, including butadiene rubber (BR), ethylene–vinyl acetate copolymer (EVA), polyethylene glycol (PEG), fluorinated polymer (F2603), and polyvinylidene fluoride (PVDF), into five distinct cleavage planes ((1 0 0), (0 1 0), (0 1 − 1), (1 0 0), and (1 0 − 1)) within the eutectic matrix. We found that the synthesis of polymer-bonded explosives (PBXs) is achieved through the integration of the aforementioned polymers into the TNT/PYRN eutectic system. This investigation elucidated the influence of various polymer matrices on the structural integrity, critical bond distances for initiation, mechanical attributes, and detonative behavior of the resultant PBXs. Within the corpus of five PBX models examined, the TNT/PYRN/F2603 configuration showed the supremum in binding energetics and the infimum in critical bond lengths, which portends superior stability, interfacial harmony, and a minimized propensity for unintended initiation. Furthermore, the TNT/PYRN/F2603 system was delineated by its enhanced capability for explosive initiation. Note importantly that the TNT/PYRN/F2603 model exhibited pre-eminence in its aggregate performance metrics, corroborating the hypothesis that F2603 constitutes a preferential binder candidate for PBX formulations predicated on the TNT/PYRN eutectic composite.</p><h3>Methods</h3><p>Utilizing the Materials Studio computational platform, the physicochemical attributes of the TNT/PYRN eutectic-based polymer-bonded explosives (PBXs) were anticipated via molecular dynamics (MD) simulations. The MD protocol was executed with a temporal increment of 1 fs, encompassing an aggregate simulation span of 2 ns. An isothermal-isobaric (NPT) thermodynamic ensemble was employed for the duration of the 2 ns MD trajectory. The COMPASS empirical force field was utilized to model interatomic interactions, and the thermal parameter was maintained at a constant 295 K throughout the simulation campaign.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144090996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural dynamics of LDL receptor interactions with E498A and R499G variants of PCSK9","authors":"Nur Alya Amirah Azhar,&nbsp;Yung-An Chua,&nbsp;Hapizah Nawawi,&nbsp;Siti Azma Jusoh","doi":"10.1007/s00894-025-06380-1","DOIUrl":"10.1007/s00894-025-06380-1","url":null,"abstract":"<div><h3>Context</h3><p>The low-density lipoprotein receptor (LDLR) regulates cholesterol uptake by mediating the hepatic clearance of plasma low-density lipoprotein cholesterol (LDL-C). Proprotein convertase subtilisin/kexin type-9 (PCSK9) attenuates LDLR function by binding to the LDLR, leading to its lysosomal degradation and preventing the total depletion of circulating LDL-C. However, pathogenic PCSK9 variants can reduce LDLR availability, significantly increase plasma LDL-C levels. Despite this understanding, the detailed molecular mechanism of LDLR-PCSK9 interaction remains unclear due to the incomplete LDLR structure. This study uses molecular dynamics (MD) simulations to predict LDLR structural dynamics upon binding to PCSK9. Furthermore, PCSK9 variants, E498A and R499G, that were identified in Malaysian FH patients were investigated for their mutational effects. Throughout the simulations, PCSK9 remained stable, while LDLR explored a larger conformational space. The LDLR-PCSK9 wild-type (WT) complex showed minimal changes, while the LDLR-PCSK9(R499G) complex exhibited pronounced conformational rearrangement. The MM/GBSA analysis revealed that the LDLR-PCSK9(E498A) complex had the highest binding affinity (− 63.81 kcal/mol), followed by the WT complex (− 33.07 kcal/mol), and LDLR-PCSK9(R499G) (− 24.21 kcal/mol). These findings offer novel insights into the dynamic interactions between LDLR and PCSK9, highlighting the role of structural flexibility in their relationship. Further MD simulation studies with the complete LDLR structure as well as experimental validation are needed to elucidate the molecular mechanisms underlying LDLR-PCSK9-mediated cholesterol homeostasis.</p><h3>Methods</h3><p>The initial structure of the wild-type (WT) LDLR-PCSK9 complex was obtained from PDB ID 3P5C, and the PCSK9 mutant structures (E498A and R499G) were modeled using the SPDBV program. MD simulations for each complex—LDLR-PCSK9 WT, LDLR-PCSK9(E498A), and LDLR-PCSK9(R499G)—were conducted using the GROMACS package with the CHARMM36m force field. The simulations were performed at 310.15 K with 2-fs timesteps under the isothermal-isobaric (NPT) ensemble, with each run lasting 500 ns. Including triplicates, the total duration of MD simulation time for all complexes amounted to 3.5 μs.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144084897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new selenium nanomaterial: structural insights, nonlinear optical properties (DFT study), and biological potential","authors":"Rumyana Yankova,&nbsp;Tsvetelina Yotova,&nbsp;Mario Avramov,&nbsp;Daiana Benkova,&nbsp;Dimitar Dimov,&nbsp;Aneliya Kostadinova,&nbsp;Pavel Markov","doi":"10.1007/s00894-025-06387-8","DOIUrl":"10.1007/s00894-025-06387-8","url":null,"abstract":"<div><h3>Context</h3><p>This study investigates the synthesis, structural characteristics, thermal properties, and biological activity of the double selenate salt Na₂Cd(SeO₄)₂·2H₂O. The synthesis of this compound was driven by the need for novel materials with potential applications in medicinal chemistry and materials science. The structural integrity and physicochemical properties of Na₂Cd(SeO₄)₂·2H₂O were confirmed through a series of characterization techniques, including FT-IR spectroscopy, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), dynamic light scattering (DLS), and zeta potential measurements. The thermal behavior of the compound, exhibiting a multi-stage decomposition pattern, provides important insights into its stability and transformation mechanisms, essential for its potential use in various applications. Biological testing, conducted on the HepG2 liver cancer cell line, revealed a dose-dependent cytotoxic effect, with morphological changes and cytoskeletal disruption at higher concentrations, highlighting the compound’s anticancer potential. The compound also demonstrated a high zeta potential, indicating good colloidal stability and suggesting favorable bioavailability. These findings underscore the relevance of Na₂Cd(SeO₄)₂·2H₂O for biomedical applications, particularly in anticancer therapies, where its unique combination of properties may offer therapeutic advantages.</p><h3>Methods</h3><p>Quantum chemical calculations were performed using density functional theory (DFT) to gain insights into the electronic structure, molecular geometry, and nonlinear optical (NLO) properties of Na₂Cd(SeO₄)₂·2H₂O. Molecular electrostatic potential (MEP) mapping revealed nucleophilic and electrophilic activity regions, pointing to possible reactive sites. Frontier molecular orbital (FMO) analysis indicated a moderate HOMO–LUMO energy gap, suggesting a balance between stability and reactivity. Thermal decomposition stages were characterized using TGA and DSC, with identifiable mass loss steps corresponding to water release and selenium dioxide formation. In vitro biological evaluation was conducted on HepG2 cells using MTT assays, immunofluorescence staining, and morphological analysis. The IC₅₀ value was established at approximately 0.05 µg/ml. Zeta potential and DLS analyses were employed to assess colloidal behavior and particle distribution. Together, these methodologies support the promising physicochemical and biological profile of Na₂Cd(SeO₄)₂·2H₂O, justifying its further investigation for nanomedicine and drug delivery applications.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144084896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A constant pH molecular dynamics and experimental study on the effect of different pH on the structure of urease from Sporosarcina pasteurii","authors":"Yifei Zheng,&nbsp;Lingling Wu,&nbsp;Qiucai Zhang,&nbsp;Lin Hu,&nbsp;Yakun Tian,&nbsp;Min Wang,&nbsp;Huaimiao Zheng,&nbsp;Zhijun Zhang","doi":"10.1007/s00894-025-06369-w","DOIUrl":"10.1007/s00894-025-06369-w","url":null,"abstract":"<div><h3>Context</h3><p>Urease is pivotal in microbial-induced calcium carbonate precipitation (MICP), where its catalytic efficiency directly governs calcium carbonate formation. However, practical MICP applications in extreme environments (e.g., acidic mine drainage, industrial waste sites) are hindered by limited understanding of urease behavior under extreme pH conditions. This study combines laboratory experiments and constant pH molecular dynamics (CpHMD) simulations to investigate how pH variations (3–11) affect the structural stability of <i>Sporosarcina pasteurii</i> urease, focusing on its α-subunit (PDB: 4CEU). Experimental validation identified pH 7–8 as optimal for urease activity, aligning with molecular dynamics results showing minimal structural deviations (RMSD) and stable protonation states under neutral to mildly alkaline conditions. Extreme pH (3, 4, 11) disrupted active-site geometry and induced charge fluctuations, impairing catalytic function. CpHMD simulations revealed that the α-subunit retains structural integrity at pH 7–8, suggesting potential reassembly post-environmental stress. This work bridges gaps in enzymatic stability under harsh conditions, offering insights for optimizing MICP in geotechnical and environmental remediation applications.</p><h3>Methods</h3><p>The study combined experimental and computational approaches. <i>Sporosarcina pasteurii</i> urease activity was experimentally assessed across pH 3–11 by monitoring urea hydrolysis-induced conductivity changes. Computational analyses employed GROMACS constant pH with the CHARMM36 force field to perform pH-dependent molecular dynamics simulations. The urease structure was solvated, neutralized, energy-minimized, and subjected to constant pH simulations. Structural stability, active site dynamics, and protonation states of titratable residues were analyzed via RMSD, hydrogen bonds, solvent-accessible surface area (SASA), and Epock 1.0.5. Free energy landscapes and residue interactions were evaluated using principal component analysis (PCA) and λ-dynamics. Experimental data were processed with OriginPro 2024b and Python, linking pH-induced conformational shifts to enzymatic function.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144090997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Relativistic DFT investigation for reaction energies and electronic/bonding properties of Schiff-base polypyrrolic uranyl(V) complexes: effects of group 14-functionalized uranyl exo-oxo group","authors":"Xiu-Jun Zheng,&nbsp;Qing-Jiang Pan,&nbsp;Yan-Ping Dong","doi":"10.1007/s00894-025-06382-z","DOIUrl":"10.1007/s00894-025-06382-z","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;The safe immobilization of radionuclides and the removal of nuclear waste contamination from environment require a thorough understanding of the structures, reaction behaviour and bonding properties of uranium complexes. The cation-cation interaction (CCI), which is also known as the direct actinyl-actinyl bonding interaction, is common only for An(V). A series of binuclear uranyl compounds of Schiff-base polypyrrolic macrocycle (H&lt;sub&gt;4&lt;/sub&gt;L), [{(Me&lt;sub&gt;3&lt;/sub&gt;R)OU&lt;sup&gt;V&lt;/sup&gt;O}&lt;sub&gt;2&lt;/sub&gt;(L)] (R = C (&lt;b&gt;1&lt;/b&gt;), Si (&lt;b&gt;2&lt;/b&gt;), Ge (&lt;b&gt;3&lt;/b&gt;), Sn (&lt;b&gt;4&lt;/b&gt;) and Pb (&lt;b&gt;5&lt;/b&gt;)), featuring CCIs, were systematically investigated by relativistic density functional theory (DFT). Three electronic states of singlet (&lt;i&gt;f&lt;/i&gt;&lt;sup&gt;&lt;i&gt;αβ&lt;/i&gt;&lt;/sup&gt;), symmetry-broken (&lt;i&gt;f&lt;/i&gt;&lt;sup&gt;&lt;i&gt;α&lt;/i&gt;&lt;/sup&gt;&lt;i&gt;f&lt;/i&gt;&lt;sup&gt;&lt;i&gt;β&lt;/i&gt;&lt;/sup&gt;), and triplet (&lt;i&gt;f&lt;/i&gt;&lt;sup&gt;&lt;i&gt;α&lt;/i&gt;&lt;/sup&gt;&lt;i&gt;f&lt;/i&gt;&lt;sup&gt;&lt;i&gt;α&lt;/i&gt;&lt;/sup&gt;) were calculated, which are labeled as &lt;b&gt;s&lt;/b&gt;, &lt;b&gt;s′&lt;/b&gt; and &lt;b&gt;t&lt;/b&gt;, respectively. Calculations show that the latter two electronic states are energy-degenerate, and much lower in energy than the singlet state. Along compounds &lt;b&gt;1 t&lt;/b&gt; to &lt;b&gt;5 t&lt;/b&gt;, R − O&lt;sub&gt;exo&lt;/sub&gt; bonds gradually decrease in strength, while U − O&lt;sub&gt;exo&lt;/sub&gt; bond gradually increases. The quantum theory of atoms in molecule (QTAIM) analyses show that the R − O&lt;sub&gt;exo&lt;/sub&gt; bond is a covalent one for &lt;b&gt;1 t&lt;/b&gt;, and it turns a covalent/ionic mixed bond in &lt;b&gt;2 t&lt;/b&gt; and &lt;b&gt;3 t&lt;/b&gt;, and is attributed to a dative bond for &lt;b&gt;4 t&lt;/b&gt; and &lt;b&gt;5 t&lt;/b&gt;. From &lt;b&gt;1 t&lt;/b&gt; to &lt;b&gt;4 t&lt;/b&gt;, the HOMO and H-1 orbitals, as well as the π(R − O&lt;sub&gt;exo&lt;/sub&gt;) and π(U − O&lt;sub&gt;exo&lt;/sub&gt;) orbitals ascend to the higher energy level. In addition, the shortest bond distance, the maximum vibration wavenumber and the most negative interaction energy &lt;i&gt;E&lt;/i&gt;&lt;sub&gt;int&lt;/sub&gt; of R − O&lt;sub&gt;exo&lt;/sub&gt; bond result in the strongest CCI in &lt;b&gt;1 t&lt;/b&gt; among &lt;b&gt;1 t&lt;/b&gt; − &lt;b&gt;5 t&lt;/b&gt;, along with the corresponding lowest reaction free energy. Our calculations reveal that the CCIs are instrumental in enhancing the stability of &lt;b&gt;1 t&lt;/b&gt; − &lt;b&gt;5 t&lt;/b&gt;.&lt;/p&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;Structural optimizations of all compounds were performed in the gas phase using the Priroda code. A generalized gradient approximation (GGA) of the Perdew-Burke-Ernzerhoff (PBE) functional was used. All-electron correlation-consistent double-ς polarized quality basis sets were used in all calculations. Single point calculations have been performed by using the ADF 2012 code on the basis of optimized geometries from Priroda code. The scalar relativistic zero-order regular approximation (ZORA) method and Slater-type triple-zeta polarization (TZP) basis sets were employed. Solvation effects were considered with the Conductor-Like Screening Model (COSMO) and spin–orbit coupling (SOC) effects were explicitly included in the calculations. Single-point calculations were carried out using the Gaussian09 program. Stuttgart relativistic large-core eff","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143949447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thermal decomposition behaviors of an ultralow-density porous ice stored with H2","authors":"Jiajia Kong,&nbsp;Dezhen Li,&nbsp;Yuan Liu,&nbsp;Chang Liu","doi":"10.1007/s00894-025-06383-y","DOIUrl":"10.1007/s00894-025-06383-y","url":null,"abstract":"<div><h3>Context</h3><p>Porous ice with ultralow density has recently demonstrated remarkable hydrogen storage capacity. However, the thermal decomposition behavior of ultralow-density porous ice stored with H₂ had not been investigated. In this work, the decomposition behavior of an ultralow-density porous ice, known as EMT, filled with varying amounts of H₂ was studied using molecular dynamics (MD) simulations. It was found that hydrogen molecules can rapidly diffuse within the porous ice framework even at low temperatures. As the temperature increases, the diffusion of water molecules intensifies until the clathrate framework of H₂O breaks down. The decomposition temperature rises from 230 to 250 K at 1 bar as the number of H₂ molecules increases from 192 to 1632 in a supercell of EMT containing 2304 H₂O molecules. Notably, the decomposition temperature further increases to 270 K at 1 bar when each 4⁶6⁸ water cavity of EMT is occupied by a C₂H₆ molecule. This reveals the decomposition mechanism of EMT porous ice stored with H₂ and demonstrates that the stability of EMT porous ice can be significantly enhanced by encapsulating C₂H₆ within 4⁶6⁸ water cavities. These findings provide valuable insights into hydrogen storage in porous ice.</p><h3>Method</h3><p>Thermal decomposition behaviors of the ultralow-density porous ice EMT stored with H₂ were investigated by gradually increasing the temperature in steps of 10 K from 200 K at ambient pressure based on MD simulations. The consistent valence force field was employed to describe the intermolecular and intramolecular interactions of the system with <i>NPT</i> ensemble.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143938176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential molecular interactions between iberiotoxin and human SLO3 and SLO1 potassium channels","authors":"Jorge Arturo Torres Juárez,&nbsp;Ana Gabriela Hernández Puga,&nbsp;Ana Alicia Sánchez Tusie","doi":"10.1007/s00894-025-06379-8","DOIUrl":"10.1007/s00894-025-06379-8","url":null,"abstract":"<p>SLO1and SLO3 are similar voltage-gated K + channels. However, SLO3 expression is sperm specific and plays an important role in the hyperpolarization of the sperm membrane potential that is crucial for sperm fertilization. This makes SLO3 an excellent molecular target for the development of male contraceptives, and computational methods can facilitate structural insights for this drug development. Here, we evaluated the differential molecular interactions between the human SLO3 (hSLO3) and SLO1 (hSLO1) potassium channels and iberiotoxin (IbTX), a toxin that selectively blocks SLO channels. To do this, molecular docking and dynamics were implemented on the channel-toxin complexes to help elucidate atomistic details of their interaction and binding energy. Our analysis found that IbTX has a similar binding energy to both channels but interacts in a distinct manner with them. Particularly, Trp14 and Arg25 residues of IbTX diverges in their interaction with the residues Val283 and Asn260 residues of hSLO3 and the corresponding residues Tyr359 and Ala336 of hSLO1. Knowledge of key residues in the molecular interface of IbTX blockage can help guide and hasten non-hormonal contraceptive development. Our results encourage the use of toxins as scaffolds for specific SLO3 blockers.</p><p>Atomistic molecular dynamics were implemented on the channel-toxin complexes. To generate the complexes, IbTX was docked to the channels using HADDOCK. CHARMM-GUI was used to generate simulation systems. GROMACS v2023.1 was used to run the simulations for 500 ns in an NPT ensemble at 297.26 K employing the CHARMM36 force field. Binding energy was evaluated by molecular mechanics generalized born surface area (MM/GBSA) with gmxMMPBGBSA.py.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143938175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Formation pathways of hydrogen polysulfides in sulfur-bearing natural gas reservoirs from density functional theory calculations","authors":"Ying Qin,&nbsp;Shuangli Yue,&nbsp;Donghui Xu,&nbsp;Mingli Yang,&nbsp;Li Zhang","doi":"10.1007/s00894-025-06388-7","DOIUrl":"10.1007/s00894-025-06388-7","url":null,"abstract":"<div><h3>Context</h3><p>The interaction mechanisms between a sulfur atom (S) and hydrogen sulfide (H₂S), as well as the formation and stability of H₂S_n (<i>n</i> = 2–9), are fundamental to understanding sulfur chemistry in natural gas reservoirs. Despite their importance, the abiogenic origins and reaction pathways of H₂S_n in natural gas fields remain inadequately understood. Clarifying these mechanisms is essential for addressing sulfur deposition challenges, which have direct implications for extraction efficiency, operational safety, and reservoir management.</p><h3>Methods</h3><p>This study utilized quantum chemistry calculations to systematically investigate the reaction mechanisms between sulfur atoms and hydrogen sulfide, with a particular focus on the formation of H₂S_n. Transition state (TS) searches were conducted to identify energetically favorable reaction pathways, and intrinsic reaction coordinate (IRC) analyses were performed to validate the reaction trajectories. The kinetics and thermodynamics of H₂S₂ formation from elemental sulfur and H₂S were comprehensively evaluated. Additionally, stability analyses were carried out to assess the relative stability of H₂S_n under varying reservoir conditions, offering insights into their decomposition tendencies and subsequent formation of H₂S and elemental sulfur (S₈).</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143938480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First-principles calculations of structural, mechanical and electronic properties of erythritol tetranitrate, 2,4-dinitro- 1H-imidazole, 5-amino- 3,4-dinitro- 1H-pyrazole, 1,1'-dinitro- 3,3'-azo- 1,2,4-triazole, 1-(4-Nitro- 1H-pyrazol- 3-yl)- 1H-tetrazole and ammonium dinitroguanidine","authors":"Ruo-Tong Wu,&nbsp;Hong-Yan Li,&nbsp;Zheng-Tang Liu,&nbsp;Zhi-Xin Bai","doi":"10.1007/s00894-025-06371-2","DOIUrl":"10.1007/s00894-025-06371-2","url":null,"abstract":"<div><h3>Context</h3><p>This study investigates the structural, mechanical and electronic properties of erythritol tetranitrate, 2,4-dinitro-1H-imidazole, 5-amino-3,4-dinitro-1H-pyrazole, 1,1'-dinitro-3,3'-azo-1,2,4-triazole, 1-(4-Nitro-1H-pyrazol-3-yl)-1H-tetrazole and ammonium dinitroguanidine. The calculated structural parameters are in good agreement with the experimental values, indicating that the adopted calculation method and model are reasonable. Based on the obtained elastic constants, the Voigt-Reuss-Hill method is used to calculate the bulk modulus, shear modulus, Young's modulus, and Poisson's ratio for six energetic materials. Furthermore, the electronic properties are given and discussed.</p><h3>Methods</h3><p>All calculations in this study were performed using the CASTEP code. In the calculation, the Perdew-Burke-Ernzerhof (PBE) function in the framework of the generalized gradient approximation (GGA) was used as the exchange–correlation functional. Additionally, the Grimme dispersion correction method was utilized to address the weak intermoleculer interaction.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143938174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Axial compression–induced post-buckling of nanotube films on copper nanopillars: a molecular dynamics study","authors":"Jing Xu,&nbsp;Kang Li,&nbsp;Hang Yin","doi":"10.1007/s00894-025-06377-w","DOIUrl":"10.1007/s00894-025-06377-w","url":null,"abstract":"<div><h3>Context</h3><p>Understanding the mechanical behavior of nanoscale films on substrates, particularly under compression, is crucial for NEMS and flexible electronics. While theoretical models describe film buckling, complexities arise at the nanoscale due to specific structures (like nanotubes) and substrate interactions, including plasticity, which are often simplified in continuum approaches. This study investigates the axial compression–induced post-buckling mechanisms of carbon nanotube (CNT) and boron nitride nanotube (BNNT) films interacting with copper nanopillars. Key questions addressed via molecular dynamics include how nanotube chirality and material stiffness influence buckling thresholds and post-buckling transitions (e.g., wrinkling, ridging, sagging), and how substrate size and deformability affect these processes. Initial findings reveal distinct behaviors linked to structure: armchair CNTs require higher buckling strains than zigzag CNTs, while stiffer BNNTs show delayed, abrupt transitions. Substrate plasticity significantly alters these deformation pathways compared to rigid substrate models.</p><h3>Methods</h3><p>Molecular dynamics (MD) simulations were conducted using LAMMPS, employing the Tersoff potential for CNT/BNNT covalent bonds and the Embedded Atom Model (EAM) for copper nanopillars. Lennard–Jones potentials modeled nanotube-substrate interactions. Simulations compared armchair/zigzag CNTs and armchair BNNTs on both fixed and deformable copper pillars of varying sizes at 0.1 K and 300 K. Axial compression was applied incrementally, followed by relaxation and unloading, to analyze buckling behavior, energy dissipation, and substrate deformation.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143908670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}