Journal of Molecular Modeling最新文献

{"title":"Electronic excitation behavior and anharmonic IR spectrum characteristics of RDX","authors":"Xinrui Zhang,&nbsp;Zhiyue Han","doi":"10.1007/s00894-025-06398-5","DOIUrl":"10.1007/s00894-025-06398-5","url":null,"abstract":"<div><h3>Context</h3><p>RDX, a typical nitro-based energetic material, has a wide range of applications. In recent years, the frequent occurrence of production accidents has created an urgent need for effective early detection technologies, which rely heavily on its spectral characteristics. This research systematically discusses the ultraviolet spectrum and electronic excitation behavior of RDX using charge transfer spectrum, hole-electron analysis, and NBO analysis methods. It also conducts anharmonic calculations to systematically explore various vibrational forms related to the -NO₂ characteristic bands in the infrared spectrum of RDX. Additionally, considering the requirements of actual production scenarios, the impact of solvents on spectral changes is examined. The findings can provide a theoretical basis for the safe production detection methods of energetic materials.</p><h3>Method</h3><p>All calculations on the structures and NBO analysis were conducted using Gaussian 16 software. Additionally, further calculations on electronic excitations were performed using Multiwfn, while VMD was employed for visualization.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140161","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 comprehensive review on structural insights through molecular visualization: tools, applications, and limitations","authors":"Ved Vrat Verma,&nbsp;Swapnil Vimal,&nbsp;Manoj Kumar Mishra,&nbsp;Varun Kumar Sharma","doi":"10.1007/s00894-025-06402-y","DOIUrl":"10.1007/s00894-025-06402-y","url":null,"abstract":"<div><h3>Context</h3><p>Biomolecules serve as intrinsic repositories of information related to function, binding interactions, molecular motion, and structural conformations. With the rapid accumulation of structural data from fields such as structural biology and cheminformatics, the ability to visualize biomolecular architecture has become essential for researchers in biology, pharmacology, and related disciplines. Molecular visualization represents a foundational step in accessing and interpreting this data, enabling its application in diverse scientific and therapeutic contexts. Recent advancements in computational algorithms and web-based visualization platforms have provided powerful resources for structural biologists, chemists, and crystallographers, facilitating efficient analysis and reproducibility of experimental outcomes. This review offers a comprehensive overview of contemporary molecular visualization tools, emphasizing their practical applications. Particular attention is given to PyMOL and NGL Viewer, with detailed guidance for their implementation in visualizing proteins, DNA, protein–ligand complexes, protein–protein interactions, protein-DNA assemblies, and small molecule ligands. Challenges frequently encountered in structural biology and cheminformatics, such as the identification of lead compounds for therapeutic development, are also addressed. Molecular dynamics simulations, including binding free energy calculations, are discussed as cost- and time-effective strategies to enhance drug discovery pipelines. In response to the increasing complexity of data-driven research, this review aims to serve as a valuable resource for professionals seeking efficient, reliable visualization tools to support structure-based research and drug design.</p><h3>Methods</h3><p>This review article provides a comprehensive comparative analysis of biomolecular visualization features integrated into standalone and web-based molecular visualization tools. PyMOL (standalone) and NGL (web-based) were systematically employed to visualize proteins, ligands, protein–ligand complexes, protein–protein complexes, and protein-DNA complexes. The methodological framework outlined in this study establishes standardized guidelines for the effective utilization of molecular visualization tools, offering valuable insights for structural biologists and researchers engaged in molecular modeling and structural analysis.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140087","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":"Quantum chemistry studies on the cationic polymerization of p-methylstyrene in ionic liquid [BMIM][NTf2]","authors":"Wei Li,&nbsp;Chuansong Qi,&nbsp;Hao Wang","doi":"10.1007/s00894-025-06397-6","DOIUrl":"10.1007/s00894-025-06397-6","url":null,"abstract":"<div><h3>Context</h3><p>Ionic liquids (ILs) have garnered significant attention as eco-friendly media for living/controlled cationic polymerization due to their tunable solvation properties and enhanced reaction control. However, the fundamental principles governing cationic polymerization and the specific role of ionic liquids in these reactions remain poorly understood, leading to the continued reliance on a trial-and-error approach for ILs selection. To address this fundamental challenge, we conducted computational investigations of the CumOH/BF₃OEt₂-initiated living cationic polymerization of p-methylstyrene within the prototypical hydrophobic ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([BMIM][NTf₂]). Additionally, a comparative analysis of solvent effects was conducted, contrasting the performance of [BMIM][NTf₂] with the conventional organic solvent dichloromethane (CH₂Cl₂). Quantum chemical calculations revealed that both the BMIM⁺ cation and CH₂Cl₂ significantly lower the activation barrier of the initiation step. More importantly, the NTf₂⁻ anion was found to play a dual catalytic role by stabilizing key cationic intermediates and modulating the transition state geometry during chain initiation and dimerization. These mechanistic insights quantitatively account for the the observed differences in reaction rates and yields of p-MeSt polymerization in [BMIM][NTf₂] compared to CH₂Cl₂.</p><h3>Methods</h3><p>Employing density functional theory (DFT) at the B3LYP/6–311 +  + G(d,p) level of theory using Gaussian-03, we conducted a comprehensive mechanistic investigation of three pivotal elementary steps governing the early-stage polymerization: (i) initiator activation, (ii) monomer chain initiation, and (iii) dimer formation.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140160","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":"Influence of wetted micro/nano-structures on bubble nucleation in flow boiling: a molecular dynamics study","authors":"Chengdi Xiao,&nbsp;Dalin Yu,&nbsp;Jiaxun Huang,&nbsp;Haitao Zhang,&nbsp;Xixin Rao","doi":"10.1007/s00894-025-06389-6","DOIUrl":"10.1007/s00894-025-06389-6","url":null,"abstract":"<div><h3>Context</h3><p>Ongoing advancements in microelectronic device integration and performance have intensified thermal management challenges. Surface roughness and wettability are key parameters for bubble nucleation during flow boiling, yet their nano-scale effects are not fully understood. This study uses molecular dynamics simulations to explore how wetted micro/nano-structured surfaces affect flow boiling, focusing on roughness, alignment, and driving forces. Results show that applying a force and optimizing wettability can boost heat transfer efficiency and accelerate heterogeneous bubble nucleation. Specifically, liquid film detachment time was reduced by 1888 ps on hydrophobic and 1370 ps on hydrophilic surfaces. The study also shows a subtle relationship between roughness and boiling performance. On different wettable surfaces, the average heat flux of hydrophobic surfaces can increase by up to 9.21% and that of hydrophilic surfaces by up to 7.90% with increasing roughness. Surface B2 (hydrophilic, roughness = 1.13), despite being rougher than B1 (hydrophilic, roughness = 1.09), has a delayed detachment time, highlighting the complex interdependence of surface morphology and fluid dynamics. In addition, the parallel flow arrangement promotes bubble nucleation by adjusting the flow field distribution while slowing bubble growth. The explosive boiling time is delayed by 6.5% compared to the staggered arrangement. These findings offer insights for designing more efficient thermal management systems in high-performance microelectronics.</p><h3>Methods</h3><p>In this study, the synergistic effect of the roughness of different wettabilities micro/nano-structures and their arrangement on the flow boiling was systematically analyzed by molecular dynamics simulation method based on the open-source software LAMMPS. The wall material is modelled as an L-J solid with a face-centered cubic (FCC) lattice structure, with a lattice constant of 3.5 Å. The structure was divided into three parts: the fixed layer, the thermostatic layer, and the heat-conducting layer. The L-J fluid system was composed of a FCC lattice arrangement, with a lattice constant of 5.8 Å in the liquid region and 32 Å in the vapor region. All interatomic interactions are described by the Lennard–Jones (L-J) potential function.</p><h3>Graphical Abstract</h3><p>Boiling nucleation for different operating conditions. <b>a</b> Roughness average. <b>b</b> Parallel flow and staggered arrangement</p>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140162","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":"Corrosion inhibition of aluminum alloy in HCl by SDS: experimental, SEM/AFM imaging, and computational insights (DFT and MD simulations)","authors":"Krishna G. Prajapati,&nbsp;P. S. Desai","doi":"10.1007/s00894-025-06391-y","DOIUrl":"10.1007/s00894-025-06391-y","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;The surfactant sodium dodecyl sulfate (SDS) has been investigated for aluminum (Al) corrosion inhibition in 0.2–0.4 M hydrochloric acid (HCl) employing mass loss (ML), electrochemical impedance spectroscopy (EIS), and potentiodynamic polarization (PDP) techniques. The inhibition efficiency (IE) of SDS was found to be concentration-dependent, with a maximum of 97% at 8 mM, which was attributed to the presence of long-chain groups. Notably, the highest inhibition efficiencies were recorded at an inhibitor concentration of 8 mM in a 0.2 M HCl solution at 303 K, achieving 97.76% via the gravimetric method, 97.30% through PDP, and 93.72% using EIS analysis. The temperature variation from 303 to 333 K showed that higher SDS concentrations improved the degree of inhibition, whereas higher temperatures reduced the degree of effectiveness. Polarization measurements indicated that SDS exhibited a cathodic inhibition mechanism. A double-layer capacitance (&lt;i&gt;C&lt;/i&gt;&lt;sub&gt;dl&lt;/sub&gt;) was added to an equivalent circuit model for evaluating the electrochemical impedance spectroscopy data. SDS adsorption behaviour followed the Langmuir and Freundlich isotherms as well as the kinetic thermodynamic model. SEM (scanning electron microscopy), EDX (energy-dispersive X-ray spectroscopy), and AFM (atomic force microscopy) proved the protective adsorbed layer of the Al surface.&lt;/p&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;Corrosion resistance of aluminum in SDS-acidic environments was investigated using PDP and EIS methods. Experiments utilized a three-electrode system in which only a 1-mm&lt;sup&gt;2&lt;/sup&gt; area of the aluminum sample was exposed, with measurements carried out in 0.2 M HCl solutions (with and without SDS) under controlled conditions, including OCP stabilization, PDP, and EIS with repeated trials to ensure data reliability. The study assessed Al corrosion by measuring weight loss under varying SDS concentrations, immersion times, and temperatures, using precise weighing and standardized calculation methods for inhibition efficiency. Additionally, surface analysis after immersion in corrosive media was carried out using SEM, EDX, and AFM to observe morphological and elemental changes. The Gaussian 09 W software utilizes density functional theory (DFT) for computational studies in this research, applying the B3LYP functional with the 6–311 +  + G (d,p) basis set and conducting a natural bond orbital analysis of sodium dodecyl sulfate (SDS) in both gas and aqueous environments. To enhance the precision, the polarizable continuum model (PCM) was employed, using water as the solvent. The computational tasks were run on a PC with results visualized through Gaussian View 5.0.9, with a focus on parameters such as the HOMO energy, LUMO energy, band gap, and electrophilicity. For the Monte Carlo (MC) and molecular dynamics (MD) simulations, Material Studio 7.0 was used to model interactions between the aluminum surface and an inhibitor molecule in corrosion simulations. Th","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140137","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":"Study on efficient seawater desalination of Ti3C2 MXene nanochannels","authors":"Yixuan Zhang,&nbsp;Jiaxin Liu,&nbsp;Xiaohong Yang,&nbsp;Fanhang Yuan,&nbsp;Xinyu Zhang","doi":"10.1007/s00894-025-06386-9","DOIUrl":"10.1007/s00894-025-06386-9","url":null,"abstract":"<p>In the context of materials, novel two-dimensional nanomaterials with exceptional chemical and thermal stability and smooth capillary pore structures facilitate efficient water transport and are widely utilized in interfacial evaporation. This study employs molecular dynamics simulations to evaluate the seawater desalination performance of MXene Ti₃C₂ and MoS₂, offering key insights into the mechanisms of water evaporation and ion exclusion in nanochannels and providing a theoretical foundation for their efficient seawater desalination applications.</p><p>Molecular dynamics simulations using LAMMPS systematically examined seawater evaporation through layered Ti₃C₂ membranes, focusing on the effects of slit width on water flux and salt rejection. Surface properties and functional groups (-O, -OH, -F) were analyzed using OVITO and VMD to assess their impact on desalination efficiency. Key parameters such as water molecule distribution, energy barriers, and hydrogen bond networks were studied to elucidate the underlying mechanisms driving Ti₃C₂ membrane desalination performance.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144125756","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":"Mechanism of wetting by anionic surfactants with different polar groups on hydrophilic and hydrophobic nano-silica","authors":"Jiangshi Zhang,&nbsp;Yanan Wang,&nbsp;Hongfu Jia,&nbsp;Kai Wang,&nbsp;Yulu Jia,&nbsp;Xiaofeng Ren,&nbsp;Yongtun Li,&nbsp;Linquan Tong","doi":"10.1007/s00894-025-06384-x","DOIUrl":"10.1007/s00894-025-06384-x","url":null,"abstract":"<div><h3>Context</h3><p>With advancing technology, the hazards of hydrophilic and hydrophobic nano-silica dust have become increasingly apparent. Surfactants are widely used in dust control; however, their performance is primarily determined by their polar groups. To investigate the effect of various polar groups of anionic surfactants on the wettability of hydrophilic and hydrophobic nanosilica. The results indicate that the electronegativity of the electrostatic potential on the hydroxylated silica surface is relatively strong, the larger the electrostatic potential difference (ΔESP) between the surface binding sites and the polar groups of the surfactant, the less favorable the surface is for hydrophobic modification. Additionally, C and O atoms tend to form smaller negative electrostatic potentials compared to S and O atoms, with polar group activity ranked as carboxylate &gt; sulfonate &gt; benzene sulfonate &gt; sulfate. The interaction between SiO2-OH surfaces and water molecules is approximately 3.4 times stronger than that of SiO2-CH3 surfaces. The interaction between water molecules and the SiO2-OH surface is primarily governed by van der Waals forces, whereas the interaction between water molecules and the SiO2-CH3 surface is mainly driven by electrostatic forces. The polar groups of the surfactant are distributed in the aqueous phase, while the nonpolar groups interact with the surface through electrostatic interactions. The hydration layer surrounding the polar groups of hydrophilic surfaces is primarily stabilized by strong hydrogen bonding with water molecules. In contrast, for hydrophobic nano-silica surfaces, the hydration layer is influenced by both van der Waals forces and weaker hydrogen bonding interactions. The SiO2-CH3 surface cannot form hydrogen bonds, while the SiO2-OH surface has a strong capacity to stably form hydrogen bonds with carboxylate and sulfate groups. Hydrogen bonding is an essential factor in wetting. The polar group COO- is suitable for controlling hydrophilic and hydrophobic nano-silica dust. These findings provide theoretical and technical references for the selection, application, and design of surfactants in nano-silica dust control.</p><h3>Methods</h3><p>To elucidate the effects of various polar groups of anionic surfactants on the wetting of hydrophilic and hydrophobic nano-silica, quantum chemical calculations and molecular dynamics simulations were used to investigate the interfacial adsorption and wetting behavior of anionic surfactants with identical chain lengths but different polar groups on these surfaces.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144125755","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":"QTAIM view of Ru–Ru bonding in a series of tri-ruthenium hydride clusters: [{CpRu(μ-H)}3(μ3-BH)], [{CpRu(μ-H)}3(μ3-H)2], [{CpRu(CO)}3(μ-BO)(μ-H)2], and [{CpRu(μ-H)}3(μ3-AlEt)]","authors":"Noorhan Ali Hamza,&nbsp;Haider Ali Hamza,&nbsp;Muhsen Abood Muhsen Al-Ibadi,&nbsp;Emad Salaam Abood,&nbsp;Ali R. Khudhair","doi":"10.1007/s00894-025-06395-8","DOIUrl":"10.1007/s00894-025-06395-8","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;The ruthenium–ruthenium and ruthenium-ligand bonding interactions in the [{CpRu(μ-H)} &lt;sub&gt;3&lt;/sub&gt;(μ&lt;sup&gt;3&lt;/sup&gt;-BH)](&lt;b&gt;1&lt;/b&gt;), [{CpRu(μ-H)}&lt;sub&gt;3&lt;/sub&gt;(μ&lt;sup&gt;3&lt;/sup&gt;-H)&lt;sub&gt;2&lt;/sub&gt;](&lt;b&gt;2&lt;/b&gt;), [{CpRu(CO)}&lt;sub&gt;3&lt;/sub&gt;(μ-BO)(μ-H)&lt;sub&gt;2&lt;/sub&gt;](&lt;b&gt;3&lt;/b&gt;), and [{CpRu(μ-H)}&lt;sub&gt;3&lt;/sub&gt;(μ&lt;sup&gt;3&lt;/sup&gt;-AlEt)](&lt;b&gt;4&lt;/b&gt;) clusters were examined using density functional theory (DFT). Various parameters related to electron density, including the electron density &lt;i&gt;ρ&lt;/i&gt;(b), Laplacian ∇&lt;sup&gt;2&lt;/sup&gt;&lt;i&gt;ρ&lt;/i&gt;(b), local energy density H(b), local kinetic energy density G(b), potential energy density V(b), and bond delocalization index (A, B), were calculated using the quantum theory of atoms in a molecule (QTAIM). Other QTAIM indicators, such as the electron localization function (ELF) and source function (SF) were computed. According to the transition metal complexes referenced in the academic literature, the computed topological parameters are consistent. The calculated data have made it possible to compare the topological characteristics of related but distinct atom-to-atom interactions, including Ru–H interactions against Ru-BH, Ru-BO, and Ru-Al interactions, as well as H-bridged Ru–Ru interactions versus BH-, BO-, and Al-bridged interactions. The electron density distribution of the Ru–Ru interactions is influenced by different bridging ligands. Despite the presence of bridged hydride and boron in clusters &lt;b&gt;1&lt;/b&gt; and &lt;b&gt;3&lt;/b&gt;, H in cluster &lt;b&gt;2&lt;/b&gt;, and H and Al in the Ru–Ru interactions of &lt;b&gt;4&lt;/b&gt;, no localized bond, bond critical, or bond path was observed. However, the large delocalization indices &lt;i&gt;δ&lt;/i&gt;(Ru, Ru) indicate that significant indirect Ru–Ru interactions are mediated through bridging ligands. For clusters &lt;b&gt;1&lt;/b&gt;, &lt;b&gt;2&lt;/b&gt;, &lt;b&gt;3&lt;/b&gt;, and &lt;b&gt;4&lt;/b&gt;, we propose the following interactions for their core components: H&lt;sub&gt;3&lt;/sub&gt;-Ru–B (7c–14e), H&lt;sub&gt;5&lt;/sub&gt;-Ru (8c–12e), H&lt;sub&gt;2&lt;/sub&gt;-Ru&lt;sub&gt;3&lt;/sub&gt;-B (6c–8e), and H&lt;sub&gt;3&lt;/sub&gt;-Ru&lt;sub&gt;3&lt;/sub&gt;-Al (7c–14e). The AdNDP analysis confirms the presence of 4c–2e multicenter bonds in several Ru₃-based clusters, emphasizing the critical role of electron delocalization in stabilizing their core structures. The BO ligand has a higher delocalization index of 1.023, indicating that it shares a pair of electrons. Moreover, the delocalization index for cluster &lt;b&gt;3&lt;/b&gt;, &lt;i&gt;δ&lt;/i&gt;(Ru…O&lt;sub&gt;CO&lt;/sub&gt;), is very large at 0.576. This suggests that CO ligands play a significant role in M π-back-donation.&lt;/p&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;Using the PBE1PBE hybrid functional and an effective core potential LanL2DZ basis set for the atoms of Ru as well as the all-electron 6-31G(d) basis set for the other atoms (Al, B, H, C and O), the optimizations were performed using the Gaussian 09 program. The geometries were verified as a local minimum by examining if imaginary vibrational frequencies were present after unrestricted optimization was carried out. Utilizing AIM2000 and Multiwfn software, we conducted QTA","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144100363","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":"The α/β3 complex of human voltage-gated sodium channel hNav1.7 to study mechanistic differences in presence and absence of auxiliary subunit β3","authors":"Jordan Edilberto Ruiz-Castelan,&nbsp;Fernando Villa-Díaz,&nbsp;María Eugenia Castro,&nbsp;Francisco J. Melendez,&nbsp;Thomas Scior","doi":"10.1007/s00894-025-06378-9","DOIUrl":"10.1007/s00894-025-06378-9","url":null,"abstract":"<div><h3>Context</h3><p>In the context of structural interactomics, we generated a 3D model between α and β3 subunits for the hitherto unknown human voltage-gated sodium channel complex (hNa 1.7α/β3). We embedded our 3D model in a membrane lipid bilayer for molecular dynamics (MD) simulations of the sodium cation passage from the outer vestibule through the inner pore segment of our hNa 1.7 complex in presence and absence of auxiliary subunit β3 with remarkable changes close to electrophysiological study results. A complete passage could not be expected due to because the inactivated state of the underlying 3D template. A complete sodium ion passage would require an open state of the channel. The computed observations concerning side chain rearrangements for favorable cooperativity under evolutionary neighborhood conditions, favorable and unfavorable amino acid interactions, proline kink, loop, and helix displacements were all found in excellent keeping with the extant literature without any exception nor contradiction. Complex-stabilizing pairs of interacting amino acids with evolutionary neighborhood complementary were identified.</p><h3>Methods</h3><p>The following tools were used: sequence search and alignment by FASTA and Clustal Omega; 3D model visualization and homology modeling by Vega ZZ, SPDBV, Chimera and Modeller, respectively; missing sections (loops) by Alphafold; geometry optimization prior to MD runs by GROMACS 2021.4 under the CHARMM 36 force field; local healing of bad contacts by SPDBV based on its Ramachandran plots; protein-protein docking by HDOCK 2.4; membrane insertion assisted by OPM; Berendsen V-rescaling for NVT; Parrinello-Rahman and Nose-Hoover for MPT; MD analyses by VMD and XMGRACE</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06378-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144100440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the influence mechanisms of different substituents on the chemical activity of N-heterocyclic phosphines via theoretical calculations","authors":"Yilei Chen","doi":"10.1007/s00894-025-06390-z","DOIUrl":"10.1007/s00894-025-06390-z","url":null,"abstract":"<div><h3>Context</h3><p>N-Heterocyclic phosphines (NHP-H) represent a distinctive class of phosphorus-containing heterocycles characterized by “polarity-inverted” P–H bonds. These unique bonds facilitate a wide array of P–H reactions, rendering NHP-H compounds promising candidates for applications in organocatalysis. Although significant advancements have been made in NHP-H research, the experimental quantification of their reactivity parameters poses considerable challenges due to their high reactivity. Furthermore, the influence of various substituents on the chemical activity of NHP-H compounds remains insufficiently understood. This study examines eight NHP-H compounds with varying substituents. The findings indicate that electron-donating substituents decrease the P–H bond order, increase the negative charge on the phosphorus atom, and enhance nucleophilicity. Conversely, electron-withdrawing substituents exhibit opposite effects. Furthermore, substituents influence the local electron attachment energy of the phosphorus atom, thereby affecting reactivity in proton-transfer reactions. According to conceptual density functional theory, electron-donating substituents are associated with lower electrophilicity and higher nucleophilicity indices, whereas electron-withdrawing substituents demonstrate the opposite trend. Charge-transfer spectra suggest that electron-donating substituents reduce the excitation energy of NHP-H, thereby increasing its reactivity. Additionally, IRI analysis indicates that electron-donating substituents weaken the P–H bond, while electron-withdrawing substituents strengthen it, along with alterations in other intramolecular interactions.</p><h3>Methods</h3><p>The study utilized the M06-2X functional in conjunction with the def2-TZVP basis set within the SMD model, employing acetonitrile as the solvent, to perform structural optimization and frequency analysis of NHP-H compounds. Computational analyses were conducted using Gaussian 09 software, with 30 excited states calculated for each compound. Multiwfn software facilitated the determination of atomic dipole moment-corrected Hirshfeld population, local electron attachment energy, the Interaction Region Indicator, and charge-transfer spectrum, which were subsequently visualized using VMD 1.9.3. Additionally, GaussView 6.0.16 software was employed to generate three-dimensional molecular configurations and prepare input files.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06390-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144100361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}