Journal of Molecular Modeling最新文献

{"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}

{"title":"Hydrogen storage, optoelectronic, and structural properties of novel osmium hydrides","authors":"Shahid Mehmood,&nbsp;Zahid Ali,&nbsp;Shah Rukh Khan,&nbsp;Ashfaq Ahmad,&nbsp;Nasar Khan,&nbsp;Mohamed Mousa","doi":"10.1007/s00894-025-06346-3","DOIUrl":"10.1007/s00894-025-06346-3","url":null,"abstract":"<div><h3>Context</h3><p>In present study, the density functional theory (DFT) is employed to analyze the structural, electronic, optical, and hydrogen storage characteristics of double perovskite-type hydrides A₂OsH₆ (A = Mg-Ba). The reported findings related to the structural aspects are in good agreement with the experimental results. All these compounds exhibit the FCC structure and formation enthalpy <i>H</i>_<i>f</i> which demonstrate their thermodynamic stability. The estimated band gap values for these compounds are 3.4, 3.0, 2.43, and 1.86 eV respectively by using perovskite-modified Becke-Johnson potential (P-mBJ) plus U parameter. According to the results, as going from Mg to Ba, the band gap decreases because of the increase in atomic radii. Furthermore, all the understudy compounds hold direct band gap nature, and their tuned band gap values show significant agreement with available results on isotropic compounds. The Mg₂OsH₆ is ultraviolet sensitive, and Ca₂OsH₆, Sr₂OsH₆, and Ba₂OsH₆ possess excellent optical behavior in the visible region. The characteristic dielectric function, oscillator strength, energy loss function, excitation coefficient, refractive index, reflectivity, and optical conductivity of these double perovskites type hydride indicate that they are highly suitable for optoelectronic applications. However, in terms of hydrogen storage performance, the gravimetric storage capacity of Mg₂OsH₆ is 2.77 wt%, for Ca₂OsH₆ is 2.59 wt%, for Sr₂OsH₆ is 2.15 wt%, and for Ba₂OsH₆ is 1.22 wt% while the favorable desorption temperature for these compounds is 189.46, 220.76, 311.19, and 356.37 K respectively with the formation energy of 24.76, 28.85, 40.67, and 46.58 kJ/mol, which is feasible in actual application.</p><h3>Method</h3><p>In the current investigation, the FP-LAPW method is used which is executed in WEIN2k simulation code. The generalized gradient approximation and mBJ with Hubbard U are used to address the exchange and correlation potentials. The Kramar-Kroning relation is used for optical properties assessment. The analytical technique is used to find out the gravimetric hydrogen storage capacity for these compounds while all the plotting was performed using Xmgrace and Origen software.</p><h3>Graphical Abstract</h3>\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 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143896687","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 mini review on revolutionizing hydrogenation catalysis: unleashing transformative power of artificial intelligence","authors":"Adarsh Sushil Mishra,&nbsp;Vikesh Gurudas Lade,&nbsp;Jyoti Ramesh Barmar,&nbsp;Ankush Babarao Bindwal,&nbsp;Ramesh Pandharinath Birmod","doi":"10.1007/s00894-025-06376-x","DOIUrl":"10.1007/s00894-025-06376-x","url":null,"abstract":"<div><h3>Context</h3><p>The field of hydrogenation catalysis has undergone a revolution due to the application of artificial intelligence (AI) and machine learning (ML), which have opened up new avenues for improving catalyst design, reaction efficiency, and pathway optimization. Trial-and-error techniques are a major component of traditional catalyst discovery methods, and they can be resource and time-intensive when it comes to real-world applications. On the other hand, real-time reaction condition optimization, predictive modelling, and quicker catalyst screening are made possible by AI-based techniques. Using methods like neural networks, Bayesian optimization, and generative models, this paper emphasizes how artificial intelligence has been revolutionizing catalyst creation along with mechanistic knowledge and process intensification. AI has the ability to completely transform catalytic research, as demonstrated by a number of case studies that demonstrate its use in CO₂ hydrogenation, biomass upgrading, and metal catalyzed reactions.</p><h3>Methods</h3><p>This review synthesizes recent developments in AI-enhanced catalytic modelling, kinetic parameter estimation, and multi-scale reaction simulations and explores machine learning models such as Random Forest, Gradient Boosting, Artificial Neural Networks, and Gaussian Processes to predict key catalytic performance indicators. Additionally, high-throughput simulated screening and computational methods such as Density Functional Theory simulations and molecular descriptor-based modelling have been used to improve catalyst design tactics. Summary of the ML models which were trained and validated using open source frameworks such as scikit-learn, TensorFlow, and PyTorch is also presented in this paper. Most of the research studies datasets were using the resource data from Catalysis Hub and the materials project. Techniques for data processing and pre-processing include methods for choosing the component features, such as d-band center analysis, adsorption energy calculations, and algorithm normalization. This review study consists of an in-depth analysis of how data-driven modelling improves catalyst performance, and its prediction and optimization in hydrogenation catalysis reactions by artificial intelligence and machine learning driven approaches.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143888560","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":"Simulation study of chemical looping with oxygen uncoupling of municipal solid waste tar model compounds by ReaxFF molecular dynamics","authors":"Zhihan Lu,&nbsp;Yousheng Lin,&nbsp;Runhua Ye,&nbsp;Ya Ge,&nbsp;Qing He","doi":"10.1007/s00894-025-06373-0","DOIUrl":"10.1007/s00894-025-06373-0","url":null,"abstract":"<div><h3>Context</h3><p>The chemical looping with oxygen uncoupling (CLOU) technology offers a low-carbon approach for municipal solid waste (MSW) management. However, tar generated from MSW pyrolytic-gasification can impair the cyclic reactivity of oxygen carriers (OCs). This study uses reactive force field molecular dynamics (ReaxFF MD) simulations to examine the interactions between three tar model compounds (toluene, phenol, and naphthalene) and CuO OCs during CLOU. The results indicate that tar initially undergoes thermal cracking, while CuO releases small amounts of O radicals that facilitate the reaction. The oxygen release rate and capacity of CuO are strongly influenced by temperature. All three tar compounds produce intermediate C₂H₂, which is further oxidized to C₂O₂ in the cases of phenol and naphthalene. CuO can nearly completely oxidize these tar compounds to CO₂ and H₂O at stoichiometric ratio, with only minor CO and H₂ byproducts. The research provides guidance for promoting CLOU technology in the efficient and clean energy utilization of MSW.</p><h3>Methods</h3><p>The models of MSW tar compounds and CuO are constructed using Materials Studio (MS) and are preliminarily optimized with the Forcite module. ReaxFF MD calculations are conducted using the ReaxFF module within the Amsterdam Modeling Suite (AMS) computational platform, employing force field parameters of C/H/O/N/S/Mg/P/Na/Cu/Cl. The temperature control is maintained using the Nose–Hoover chain (NHC) thermostat. The first-order Arrhenius equation is utilized to calculate the activation energy of the reaction process.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143883714","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":"Theoretical study of complexes based on lithium tetraamine and its fluorinated derivatives in interaction with Li−, Na−, and K− anions: study of static and dynamic NLO parameters by DFT","authors":"Mourad Zouaoui-Rabah,&nbsp;Madani Hedidi,&nbsp;Abdelkader M. Elhorri,&nbsp;Hicham Mahdjoub–Araibi","doi":"10.1007/s00894-025-06370-3","DOIUrl":"10.1007/s00894-025-06370-3","url":null,"abstract":"<div><h3>Context</h3><p>This study explores the impact of fluorine substitution on the structural, electronic, and nonlinear optical (NLO) properties of metallic complexes featuring the tetraamine lithium (TALi⁺) motif. Twelve complexes were designed by combining TALi⁺ with anions (Li⁻, Na⁻, K⁻), forming three categories (TALi-Li, TALi-Na, TALi-K), and analyzed using quantum chemical calculations. The results reveal exceptionally high static and dynamic first hyperpolarizabilities (∆<i>β</i>_tot × 10⁻³⁰ esu), with the largest gap (834.69 × 10⁻³⁰ esu) observed in the (TALi-K) series. Dynamic (<i>β</i>_tot) values reached (~ 60 million × 10⁻³⁰ esu) at 1064 nm, while second hyperpolarizabilities (<i>γ</i>ₐ_v) followed similar trends, though (TALi-K) complexes exhibited deviations in ranking. Notably, push–pull behavior was identified, with anions acting as donors and fluorinated ammonias as acceptors, bridged by (NH₃ ligands). Absorption maxima (600–900 nm) in both vacuum and solvent environments suggest tunable optoelectronic responses. Crucially, the (TALi-K) category demonstrated the highest nonlinear refractive indices (<i>n</i>₂), highlighting its potential for photonic applications such as optical switching. This work provides a roadmap for designing high-performance NLO materials through strategic anion selection and fluorination, advancing the development of functional materials for light-based technologies.</p><h3>Method</h3><p>All calculations were performed using Gaussian 16 software. Molecular geometries were optimized at the B3LYP-D3/6–31 +  + G(d,p) level in the gas phase without symmetry constraints for a series of tetraamine lithium complexes with various alkali metals (TAL-M). Nonlinear optical properties were extensively characterized through first hyperpolarizability (<i>β</i>_tot) calculations using seven different functionals (CAM-B3LYP, LC-wPBE, LC-BLYP, M11, wB97X, HSEh1PBE, and M06-2X) as well as MP2 theory, all with the 6–31 +  + G(d,p) basis set. Additional basis set dependence studies were conducted using CAM-B3LYP with eight different basis sets ranging from 6-31G(d,p) to augmented triple-zeta sets. Second harmonic generation properties were evaluated through (<i>β</i>_tot) and <i>γ</i>_av calculations at the CAM-B3LYP/6–31 +  + G(d,p) level. Electronic delocalization was analyzed via NBO calculations (E(2) energies) using the same theoretical approaches. Solvent effects were incorporated using the SMD model for solvation free energies (Δ<i>G</i>_solv) and the CPCM model for TD-DFT calculations of absorption maxima (<i>λ</i>_max) and oscillator strengths at the TD-CAM-B3LYP/6–31 +  + G(d,p) level. This multi-method approach ensures robust characterization of both molecular structures and NLO properties.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143883715","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":"Evolution of B13n (n = + 3 to − 3) wheel with electron injection/abstraction: an insight from electronic structure analysis","authors":"Sourav Ranjan Ghosh,&nbsp;Sasthi Charan Halder,&nbsp;Atish Dipankar Jana","doi":"10.1007/s00894-025-06375-y","DOIUrl":"10.1007/s00894-025-06375-y","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;The planar B&lt;sub&gt;13&lt;/sub&gt;&lt;sup&gt;+1&lt;/sup&gt; cluster, a prototypical molecular ‘Wankel motor’, has captivated the scientific community with its exceptional stability as well as rotor action. The present study is an exploration of how incremental electron injection/abstraction influences the electronic structure of B&lt;sub&gt;13&lt;/sub&gt; clusters with B&lt;sub&gt;13&lt;/sub&gt;&lt;sup&gt;+1&lt;/sup&gt; as a reference one. It has been found that seven different charge states (from + 3 to − 3) of B&lt;sub&gt;13&lt;/sub&gt; cluster are possible, among which B&lt;sub&gt;13&lt;/sub&gt;&lt;sup&gt;−1&lt;/sup&gt; triplet is the lowest energy cluster. For B&lt;sub&gt;13&lt;/sub&gt;&lt;sup&gt;&lt;i&gt;n&lt;/i&gt;&lt;/sup&gt; clusters, &lt;i&gt;n&lt;/i&gt; =  + 3 to − 2, the clusters are planar and possess C&lt;sub&gt;2v&lt;/sub&gt; symmetry and their relative atomic arrangement is similar to B&lt;sub&gt;13&lt;/sub&gt;&lt;sup&gt;+1&lt;/sup&gt; ground state (GS) structure in which a triangular boron core is encircled by ten peripheral boron atoms. B&lt;sub&gt;13&lt;/sub&gt;&lt;sup&gt;−3&lt;/sup&gt; cluster has a different geometric arrangement of atoms like that of the B&lt;sub&gt;13&lt;/sub&gt;&lt;sup&gt;+1&lt;/sup&gt; transition state (TS) structure; remains planar, possesses C&lt;sub&gt;2v&lt;/sub&gt; symmetry. The different atomic arrangement of B&lt;sub&gt;13&lt;/sub&gt;&lt;sup&gt;−3&lt;/sup&gt; can be assigned to the electronic structural relaxation to reduce the electronic stress arising from high negative charge. B&lt;sub&gt;13&lt;/sub&gt;&lt;sup&gt;+1&lt;/sup&gt; cluster is characterized by a unique electron density distribution in the cluster plane which is analogous to a ‘tri-spoke wheel’ configuration. In it, three spokes of electron dense lines connect the triangular core to the nearly circular periphery. The present study unveils how the injection or abstraction of electrons modifies the electronic topology in the cluster plane and how the spoke-wheel geometry evolves. It has been found that, in the + 3 and + 2 charge states, the wheel consists of four and five spokes respectively. On the other hand, for all other clusters, the overall electronic topology resembles that of the tri-spoke wheel-like B&lt;sub&gt;13&lt;/sub&gt;&lt;sup&gt;+1&lt;/sup&gt; cluster. AIM analysis helped to trace out and characterize the evolution of the spoke-wheel topology with electron density at ring critical points and the bond paths.&lt;/p&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;Density Functional Theory (DFT), utilizing the 6–311 + G(d) basis set and the PBE1PBE hybrid density functional, has been employed to determine the minimum energy structures of B&lt;sub&gt;13&lt;/sub&gt; clusters with different charged states. The calculations have been performed using a superfine integration grid and very tight optimization settings, as implemented in GAUSSIAN 09 Revision D.01. To address potential instabilities in SCF calculations, wavefunction stability has been thoroughly analysed. AIM analysis and various real-space functions, including electron density, Localized Orbital Locator (LOL), Phase-Space defined Fisher Information Density (PS-FID), and Electron Localization Function (ELF), have been investigated. Multiwfn 3.8 was utilized for plotting these functions.&lt;/p&gt;&lt;","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143883713","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":"Theoretical investigation of naphthodithiophene diimide derivatives as fluorescent sensors for 2,4,6-trinitrophenol detection","authors":"Leixing Luo,&nbsp;Mingxuan Dang,&nbsp;Xiaoming Song,&nbsp;Qingxia Zhao,&nbsp;Shuo Yang,&nbsp;Xiufang Hou,&nbsp;Shuai Liu,&nbsp;Yixia Ren","doi":"10.1007/s00894-025-06366-z","DOIUrl":"10.1007/s00894-025-06366-z","url":null,"abstract":"<div><h3>Context</h3><p>This study explored the geometry, aromaticity, electrostatic potential, and fluorescence sensing capability of N,N′-dimethyl naphthodithiophene diimide (C₁-NDTI-S) and its derivatives (C₁-NDFI-O and C₁-NDPI-N), where thiophene rings were substituted with furan and pyrrole, respectively. Theoretical calculations revealed that C₁-NDTI-S had the most negative adsorption energy for 2,4,6-trinitrophenol (TNP), and its electronic absorption spectrum and fluorescence spectrum decreased considerably upon TNP adsorption. Through FMO, hole–electron, independent gradient model, and energy decomposition analysis, it was revealed that the essence of fluorescence quenching is the intermolecular weak π–π interaction driving photo-induced electron transfer. Furthermore, C₁-NDFI-O and C₁-NDPI-N generated by modifying the structure of C₁-NDTI-S have the potential to serve as more efficient fluorescent sensors for TNP detection. The fluorescence recovery times confirmed the suitability of the three compounds as fluorescence probes.</p><h3>Methods</h3><p>In this study, the Gaussian 09 software package at B3LYP-D3(BJ)/6–311 +  + G** level was applied to optimize the structure, energy, and fluorescence recovery time. Multiwfn combined with VMD software package was used to analyze the aromaticity of compounds using LOL-π and HOMA, with a focus on the differences in aromaticity after thiophene was substituted with different rings. Using AMBER force field for energy decomposition analysis based on force field (EDA-FF), the weak intermolecular interaction components are decomposed. The independent gradient model analysis based on Hirshfeld partition analysis clearly demonstrates the π–π interactions between molecules, with the δ_g^inter parameter set to 0.005 a.u. Electron absorption spectroscopy, charge-transfer spectra spectroscopy, molecular interactions, and hole electron interactions were all completed with the help of Multifwn software.</p><h3>Graphical Abstract</h3>\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 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143883712","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":"Theoretical study of 2D cancer drug nanocarriers based on calcium chloride","authors":"Walid Iken,&nbsp;Hayat EL Ouafy,&nbsp;Mouna Aamor,&nbsp;Loubna Halil,&nbsp;Mouad Boutkbout Nait Moudou,&nbsp;Soukaina Naciri,&nbsp;Mohamed Reda Chriyaa,&nbsp;Tarik EL Ouafy","doi":"10.1007/s00894-025-06345-4","DOIUrl":"10.1007/s00894-025-06345-4","url":null,"abstract":"<div><h3>Context</h3><p>This study aims to use two-dimensional nanocarriers composed of cisplatin and fluorouracil molecules adsorbed on the surface of calcium chloride crystals. We found that cisplatin molecules release an alkaline ammonia molecule, neutralizing the acidic environment of cancerous tumors through acid–base interactions. This behavior is similar to the enzyme urease, which has shown good results in cancer treatment. The compounds cisplatin/CaCl₂(100), fluorouracil/CaCl₂(100), and cisplatin/CaCl₂(110) exhibited a wavy geometric structure, enhancing their efficiency as promising nanocarriers for drug delivery. This work allows future studies to focus on the experimental validation of these results and on the evaluation of their biological interactions for clinical applications.</p><h3>Methods</h3><p>The calculations were performed using the Quantum ESPRESSO software and density functional theory (DFT). The model compounds were optimized using the PBE functional combined with the vdw-DF3 functional to correct for dispersion forces in van der Waals interactions. The calcium chloride crystal was cut using VESTA software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143879636","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":"Effect of temperature and velocity on deformation behavior and frictional properties of rough surface at the nanoscale","authors":"Po-Han Tseng,&nbsp;Thi-Xuyen Bui,&nbsp;Sao-Kai Tsai,&nbsp;Te-Hua Fang","doi":"10.1007/s00894-025-06374-z","DOIUrl":"10.1007/s00894-025-06374-z","url":null,"abstract":"<div><h3>Context</h3><p>Soft materials, such as gold, play a crucial role in solid-state devices for the electronics industry, biochemical sensors, and miniaturized medical machinery. This study investigates the abrasive behavior and friction properties of the rough surface of polycrystalline Au material through a shearing process using molecular dynamics (MD). The effects of friction velocity and temperature are explored by analyzing the force–time curve, crystal evolution, shear strain distribution, differential distribution, and atomic flow direction. Temperature affects polycrystalline Au more deeply; almost crescent-peak regions of Au transform into an amorphous structure upon contact with abrasive Ni at shearing temperatures of 450 and 600 K, while atoms vibrate around their equilibrium positions. The compress simulation shows the different behavior of the Au material under various potentials. At lower abrasive velocities, atomic movement and the deformation region are more pronounced. The normal force increases with an increase in abrasive velocity from 20 to 100 m/s or a temperature rise from 150 to 450 K; however, it decreases as the abrasive velocity reaches 150 m/s or when the temperature increases to 600 K.</p><h3>Methods</h3><p>The ATOMSK program is applied to create the polycrystalline Au and Ni structures. The MD method is employed to investigate the influence of various friction velocities and temperatures on the force–time curve, crystal evolution, shear strain distribution, differential distribution, and atomic flow direction of polycrystalline Au alloys. The simulation process is performed via LAMMPS software. The visualization tool (OVITO) is borrowed to examine, evaluate, and demonstrate the simulation results. The Morse potential is used to describe the interaction forces between Ni–Ni, Au–Au, and Ni-Au.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143861318","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":"Pyrolysis of bioethanol and biobutanol: A thermodynamic and kinetic study","authors":"Christian Tshikala Mukeba,&nbsp;Mireille Kabuyi Bilonda,&nbsp;Haddy Mbuyi Katshiatshia,&nbsp;Jules Tshishimbi Muya","doi":"10.1007/s00894-025-06357-0","DOIUrl":"10.1007/s00894-025-06357-0","url":null,"abstract":"<div><h3>Context</h3><p>Bioethanol and biobutanol are renewable oxygenated fuels derived from biomass, commonly blended with gasoline for use in gasoline engines. These alcohol-based fuels have high oxygen content, promoting more complete combustion and reducing carbon dioxide emissions compared to petroleum fuels. However, during combustion, oxygenated radicals can interact and lead to the formation of formaldehyde, a highly toxic compound. This study delves into the thermodynamic and kinetic study of biofuel pyrolysis using quantum chemical methods. Our results identify C–C bond as the weakest in the initiation step, with bond dissociation enthalpy around 86 kcal/mol. Notably, ethanol exhibits higher bond dissociation energies than butanol. While the initiation step predominantly involves C–C bond breaking, the propagation step reveals a competition between H abstraction and C–C bond cleavage. Analyzing the computed rate constants and Gibbs free energies for radical reactions in the propagation steps indicates the likelihood formation of acetaldehyde, formaldehydes, methane, and ethylene. These products indeed present significant risks to both human health and the environment. This emphasizes the importance of carefully controlling macroscopic thermodynamic variables, such as temperature and pressure, during the pyrolysis of alcohol. Proper regulation of these factors is crucial in minimizing the formation of harmful aldehydes and ensuring a safer and more sustainable process.</p><h3>Methods</h3><p>The reaction mechanisms of thermal decomposition are analyzed using UωB97XD/6–311 + G(3 df,2p), G4MP2, and G4 computational methods. The latter offers highly accurate enthalpies of formation, with a deviation from experiment values approximately 1 kcal/mol, though it is computationally expensive compared to DFT. To evaluate the diradical character of certain open-shell intermediate species, CASSCF and MP2-CASSCF methods, which effectively account for static correlation effects, are employed with the cc-pVDZ basis set. Thermodynamic and kinetic analyses are carried out using both ab initio and semi-empirical approaches through Gaussian 09 and OpenSMOKE + + 0.21.0 programs.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143861317","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}