Journal of Molecular Modeling最新文献

{"title":"Theoretical study on fused 1,2,3,4-tetrazine-1,3-dinitroxide derivatives under external electric field","authors":"Zhihui Gu,&nbsp;Mengjie Bo,&nbsp;Zikai Gao,&nbsp;Congming Ma,&nbsp;Peng Ma","doi":"10.1007/s00894-025-06289-9","DOIUrl":"10.1007/s00894-025-06289-9","url":null,"abstract":"<div><h3>Context</h3><p>Considering the excellent properties of 1,2,3,4-tetrazine-1,3-dinitroxides, several types of energetic derivatives have been synthesized from them. Among them, [1,2,5] oxadiazolo [3,4-e] [1,2,3,4]-tetrazine-4,6-Di-N-dioxide (FTDO), 5,7-dinitrobenzo-1,2,3,4-tetrazine-1,3-nitrogen dioxide (DTND), and [1,2,3,4] tetrazino [5,6-e] [1,2,3,4] tetrazine-1,3,8-tetraoxide (TTTO) are considered excellent energetic materials. However, there is limited research on their behavior under electric fields. The effect of electric fields was studied using density functional theory to calculate trigger bond changes, strain energy, chemical reactivity, and surface electrostatic potential. The results indicate that the planar structure of FTDO is more unique than that of DTND and TTTO, and its trigger bond is located at special position. Increased electric field strength can lengthen the trigger bond, increase sensitivity, and reduce strain energy of FTDO. Under a positive electric field, DTND and TTTO have longer trigger bond lengths, increased sensitivity, and increased strain energy, while exhibiting the opposite behavior under a negative electric field. Electric fields can affect the chemical reactivity of the all three derivatives. FTDO is less active under positive electric fields, DTND is more active under both electric fields, and TTTO becomes more active under negative electric fields. Finally, the electric field can expand their absorption spectrum range, affecting electron transfer between fragments.</p><h3>Methods</h3><p>All calculations in this article were completed on Gaussian 16 software. The calculation levels are B3LYP/6-311G**, B3LYP/Def2-TZVPP, and PBE1PBE/6-311G**. Multiwfn and VMD were used for wave function analysis. Electric fields have a strength range of − 0.02 to 0.02 a.u., with a growth gradient of 0.01 a.u.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078393","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":"Plasma-driven synthesis of nitrogen-doped graphene: unveiling the reaction mechanism and kinetic insights","authors":"Chuanhao Dong,&nbsp;Minglin Li,&nbsp;Hai Yang,&nbsp;Yanyi Huang,&nbsp;Bo Wu,&nbsp;Ruoyu Hong","doi":"10.1007/s00894-025-06297-9","DOIUrl":"10.1007/s00894-025-06297-9","url":null,"abstract":"<div><h3>Context</h3><p>The rotating arc plasma technique for the synthesis of nitrogen-doped graphene capitalizes on the distinctive attributes of plasma, presenting a straightforward, efficient, and catalyst-free strategy for the production of nitrogen-doped graphene. However, experimental outcomes generally fail to elucidate the atomic-level mechanism behind this process. Our research utilizes molecular dynamics simulations to explore theoretically the formation of radicals during the plasma-driven reaction between methane (CH₄) and nitrogen (N₂). The simulations present a complex reaction system comprising nine principal species: CH₄, CH₃, CN, CH₂, HCN, CH, N₂, H₂ and H. Notably, HCN and CN emerge as pivotal precursors for nitrogen doping. Optimal nitrogen concentrations enhance the synthesis of these precursors, whereas excessive nitrogen suppresses the formation of C₂ species, impacting the yield of nitrogen-doped graphene. Conversely, higher methane concentrations stimulate the generation of carbon radicals, augmenting the production of HCN and CN and thus, influencing the properties of the synthesized material. This work is expected to lay a theoretical foundation for the refinement of nitrogen-doped graphene synthesis processes.</p><h3>Methods</h3><p>In this investigation, we employed the LAMMPS software package to explore the formation of free radicals during the methane–nitrogen reaction via molecular dynamics (MD) simulations. These simulations were conducted under an NVT ensemble, maintaining a constant temperature of 3500 K with a time step of 0.1 fs over a duration of 1000 ps. To reduce the variability and enhance the reliability of the simulation outcomes, each simulation was meticulously conducted three times under identical parameters for subsequent statistical analysis.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063003","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 composition, temperature, and grain size on mechanical behavior and deformation mechanism of lightweight magnesium alloy","authors":"Thi-Xuyen Bui,&nbsp;Yu-Sheng Lu,&nbsp;Sheng-Hsiang Tsai,&nbsp;Te-Hua Fang","doi":"10.1007/s00894-025-06292-0","DOIUrl":"10.1007/s00894-025-06292-0","url":null,"abstract":"<div><h3>Context</h3><p>To address the severe fuel crisis and environmental pollution, the use of lightweight metal materials, such as AZ alloy, represents an optimal solution. This study investigates the mechanical behavior and deformation mechanism of AZ alloys under uniaxial compressive using molecular dynamics (MD) simulations. The influence of various compositions, grain sizes (GSs), and temperatures on the compressive stress, the ultimate compressive strength (UCS), compressive yield stress (CYS), Young’s modulus (<i>E</i>), shear strain, phase transformation, dislocation distribution, and total deformation length is thoroughly examined. The results show that although AZ91 has the highest Al content, it exhibits the lowest UCS, CYS, and fraction atoms with shear strain larger than 0.2 (FSS0.2) compared to AZ31 and AZ61. At the same time, the total dislocation length of AZ31 is the largest. The effect of GS and temperature on the mechanical response and deformation mechanism of AZ31 alloy indicates that a GS of 7.6 nm is the critical value to determine the mechanical properties and deformation intensity of AZ31 alloy. Moreover, the <i>E</i>, UCS, and CYS values decrease gradually as temperature increases. The compressive stress, <i>E</i>, UCS, CYS, and FSS0.2 of single crystalline AZ31 are higher than those of polycrystalline AZ31 with all GSs. The MD simulation results show that the sample experiences the formation of stacking faults at both single crystalline and polycrystalline AZ31 while forming the shear band at the single crystalline, leading to strong oscillations in compressive stress. In contrast, polycrystalline AZ31, across all GSs, exhibits high shear strain zones, causing oscillations in compressive stress.</p><h3>Methods</h3><p>The ATOMSK program is used to create the polycrystalline AZ structures. The MD method is employed to investigate the influence of various compositions, GSs, and temperatures on the mechanical properties and deformation mechanism of AZ alloys. All the simulations are performed by LAMMPS software. The visualization tool (OVITO) is used to inspect, analyze, and illustrate the simulation results. The EAM potential is applied to the interactions between Al-Zn, Al–Mg, and Zn-Mg.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063002","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 theoretical study on the mechanism and rate constants of luteolin and selenium dioxide","authors":"Zhi Chen,&nbsp;Cai Hua Zhou,&nbsp;Ya Rong Wei,&nbsp;Zhi Hui Sun,&nbsp;Ling Juan Deng","doi":"10.1007/s00894-025-06291-1","DOIUrl":"10.1007/s00894-025-06291-1","url":null,"abstract":"<div><h3>Context</h3><p>This study investigates the reaction mechanism of luteolin with selenium dioxide in ethanol. Through a detailed search for transition states and thermodynamic energy calculations, it was found that the reaction proceeds via two possible pathways, leading to the formation of products P1 and P2, respectively. A common feature of both pathways is that the first elementary step results in the formation of the intermediate INT1. Kinetic calculations indicate that, within the temperature range of 273 to 340 K, the apparent rate constant (<i>k</i>2) for the formation of intermediate INT1 is significantly larger than those of <i>k</i>3 and <i>k</i>4, and all three rate constants increase substantially with temperature. Interestingly, the product P1 from the first pathway is thermodynamically and kinetically feasible, and is in complete agreement with experimental results. In contrast, the product P2 from the second pathway contains a Se-O-Se ether bond, which exhibits dynamic stability in its molecular structure. In conclusion, this study not only validates the experimental findings but also provides theoretical guidance for the synthesis of novel organoselenium compounds.</p><h3>Methods</h3><p>All calculations were performed using the DFT/M06-2X/6-31G(d,p) method. The solvent effect was considered by applying the IEFPCM model in all calculations. The free energy (∆<i>G</i>) of each compound at 298.15 K was obtained with a correction factor of 0.967. The apparent rate constants for each step were calculated over a temperature range from 273.15 to 373.15 K using transition state theory.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063001","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 chemical studies of carbon-based graphene-like nanostructures: from benzene to coronene","authors":"Alberto Soares Vanny,&nbsp;Arlan da Silva Gonçalves","doi":"10.1007/s00894-025-06285-z","DOIUrl":"10.1007/s00894-025-06285-z","url":null,"abstract":"<div><h3>Context</h3><p>This study presents quantum chemical analysis of 14 distinct carbon-based nanostructures (CBN), ranging from simple molecules, like benzene, to more complex structures, such as coronene, which serves as an exemplary graphene-like model. The investigation focuses on elucidating the relationships between molecular orbital (MO) energies, the energy band gaps, electron occupation numbers (eON), electronic conduction, and the compound topologies, seeking to find the one that approaches most of a graphene-like structure for <i>in silico</i> studies. Through detailed examination of molecular properties including chemical hardness and chemical potential, we demonstrate that the electronic exchange between orbitals is directly influenced by the structural topology of the carbon-based nanostructures, as the electron occupation numbers and the molecular orbital energies. Raman theoretical analysis was performed, ensuring the approximation to a graphene structure by its experimental fingerprint comparison. The correlations presented here offer an approach for anticipating electronic conductivity in graphene-like materials, as well as the confirmation of coronene as a graphene nanostructure for theoretical analyses.</p><h3>Method</h3><p>The models were designed at Ghemical software optimized at Tripos5.2 force field and properly protonated on the peripheral carbons. The models were then optimized by PM7 semiempirical method using MOPAC2016 to minimize the gradient energy before applying the DFT calculations. After that, the model’s geometry was finally optimized at ab initio B3LYP hybrid functional and 6-31 G* basis, using ORCA5.0.4. The eON, the MO energies and the Raman spectrum were obtained with the same methods, making possible the spectrum extraction without the interference of H atoms, approaching the analyses to graphene-like topologies.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063004","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":"DFT study of the binary intermetallic compound NdMn2 in different polytypic phases","authors":"Murad Murad,&nbsp;Zahid Ali,&nbsp;Shahid Mehmood","doi":"10.1007/s00894-025-06286-y","DOIUrl":"10.1007/s00894-025-06286-y","url":null,"abstract":"<div><h3>Context</h3><p>The structural stability, ground state magnetic order, electronic, elastic and thermoelectric properties of NdMn₂ in the C15, C14 and C36 polytypic phases is investigated. The magnetic phase optimization and magnetic susceptibility reveal that NdMn₂ is antiferromagnetic (AFM) in C36 phase; and paramagnetic (PM) in C14 and C15 phases respectively. The band profiles and electrical resistivity show the metallic nature in all these polytypic phases and reveal that the C36 phase possesses smaller resistivity. The presence of covalent bonds among Nd–Nd and Nd-Mn has been verified from the electron charge densities plots. The elastic constants calculated in different phases confirm the mechanical stability and are elastically anisotropic and incompressible in all phases. Due to large enough value of Young and Bulk moduli in C14 phase NdMn₂ would be suitable candidate for applications that require high strength, stiffness and durability, as well as the ability to withstand extreme environments.</p><h3>Method</h3><p>The density functional theory (DFT) is used to investigate the physical properties of understudy binary intermetallic compounds NdMn₂ in the C15, C14 and C36 polytypic phases.</p><p>BoltzTraP code based on Boltzmann semi-classical transport theory is used to investigate magnetic susceptibility and electrical resistivities of the understudy compounds. The elastic constants are calculated with the help of IRELAST code embedded in WIEN2k software. Linux based xmgrace and origin software are used for plotting.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045340","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":"Hybrid molecular-scale and continuum modeling of two-dimensional flow between inhomogeneous solid surfaces and its application to the thrust bearing","authors":"Xiaoying Shao,&nbsp;Chen Huang,&nbsp;Yongbin Zhang","doi":"10.1007/s00894-024-06258-8","DOIUrl":"10.1007/s00894-024-06258-8","url":null,"abstract":"<div><h3>Context</h3><p>The flow equations are derived for describing the two-dimensional hybrid molecular-scale and continuum flows in the very small surface separation with inhomogeneous solid surfaces and they can be applied for designing the specific bearings. The aim of the present study is to solve this specific flow problem in engineering with normal computational cost. The flow factor approach model describes the flow of the molecule layer adjacent to the solid surface and the Newtonian fluid model describes the flow of the intermediate continuum fluid. By using these flow equations, the simulation results show that designing the inhomogeneous stationary surface can very significantly improve the load-carrying capacity of the hydrodynamic thrust bearing with low clearances.</p><h3>Method</h3><p>The flow of the physically adsorbed layer is treated as non-continuum and it is modeled by the equivalent non-continuum flow model by considering the fluid molecules orientated normal to the solid surface. The fluid between the two adsorbed layers is treated as continuum and Newtonian. The slippage can occur between the adsorbed layer-solid surface interface. It is assumed as absent on the adsorbed layer-continuum fluid interface. The flow equations are derived according to the equilibrium of the momentum transfer in the surface clearance. The film pressures and carried load of the thrust bearing with low clearance and inhomogeneous surfaces are derived by applying the obtained flow equations.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045363","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":"Monolayer MoS2 with S vacancy defects doped with Group V non-metallic elements (N, P, As): a first-principles study","authors":"Junxiang Zhang,&nbsp;Xia Zhao,&nbsp;Yan Yang,&nbsp;Jiayu Cui","doi":"10.1007/s00894-025-06290-2","DOIUrl":"10.1007/s00894-025-06290-2","url":null,"abstract":"<div><h3>Context</h3><p>This study systematically investigated the effects of single S-atom vacancy defects and composite defects (vacancy combined with doping) on the properties of MoS₂ using density functional theory. The results revealed that N-doped S-vacancy MoS₂ has the smallest composite defect formation energy, indicating its highest stability. Doping maintained the direct band gap characteristic, with shifts in the valence band top. The Fermi level slightly shifted down in N- and P-doped systems, with N-doped MoS₂ showing a larger increase in valence band top energy. Doping also significantly altered the density of states at the Fermi level and weakened the dielectric properties of MoS₂. The maximum dielectric peaks of doped systems appeared near 2.7 eV with reduced intensities and red-shifted energies. Optical properties were significantly changed, with decreased reflectance, narrower reflectance spectra, and blue-shifted absorption spectra. These findings suggest that introducing composite defects can effectively reduce the forbidden bandwidth of MoS₂, enhancing electrical conductivity. This research provides theoretical guidance for novel material design and offers insights into composite defect behavior in other two-dimensional materials.</p><h3>Methods</h3><p>The Materials-Studio CASTEP module was used to calculate density functional theory (DFT). A plane wave ultrasoft pseudopotential is used to optimize the crystal structure, and the generalized gradient approximation (GGA) in the form of Perdew-Burke-Ernzerhof (PBE) is used to characterize the exchange correlation energy. After the convergence test, the truncation energy and dot settings were finally selected to be 450 eV and 3 × 3 × 1, respectively, the convergence accuracy was set to 1.0e-5eV/atom, and the convergence criterion for the interatomic interaction force was 0.02 eV/Å. The parameters were all at or better than the accuracy settings. The vacuum layer between the layers was set to 18 Å to avoid interactions caused by the periodic calculation method.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045367","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":"Solvent influence on the optical absorption, frontier molecular orbitals, and electronic structure of 1-bromo adamantane","authors":"R. Aravindhan,&nbsp;M. Ummal Momeen,&nbsp;Jianping Hu","doi":"10.1007/s00894-025-06284-0","DOIUrl":"10.1007/s00894-025-06284-0","url":null,"abstract":"<div><h3>Context</h3><p>The study of the influence of solvent on 1-bromo adamantane (BAD) exposes prominent solvatochromatic shifts in the optical absorbance and substantial solvent effects on the electronic structure. This facilitates the molecular probe abilities for the BAD with respect to the surrounding environments such as dielectric constant and polarity. BAD exhibits positive solvatochromism for nonpolar solvents and negative solvatochromatic shifts for polar and aromatic solvents. In accordance with this, significant energy changes are obtained on the orbital occupancies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), resulting in a large difference in energy among the various solvation environments. According to this, the HOMO–LUMO gap decreases in nonpolar solvents, and it increases with respect to polarity in the case of polar and aromatic solvents. Computed thermodynamic parameters and noncovalent interaction analysis also demonstrate the noticeable changes for different solvent dielectric continuums with more changes for solvent continuums with large dielectric constants.</p><h3>Methods</h3><p>Experimentally recorded UV–Vis absorption spectra of the solvents exhibit positive and negative solvatochromism for the n to σ* electronic transition. Computational investigations carried out with equation-of-motion coupled-cluster with single and double excitations and configuration interaction singles calculations by means of the solvent model density implicit solvation model clearly demonstrate the strong influence of solvents on the electronic structure of the BAD molecule.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045368","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":"Molecular dynamics work on thermal conductivity of SiGe nanotubes","authors":"Yao Huang,&nbsp;Cong Tan,&nbsp;Jing Wan,&nbsp;Lan Zhang,&nbsp;Yan Rong","doi":"10.1007/s00894-025-06293-z","DOIUrl":"10.1007/s00894-025-06293-z","url":null,"abstract":"<div><h3>Context</h3><p>SiGe nanotubes (SiGeNTs) hold significant promise for applications in nanosolar cells, optoelectronic systems, and interconnects, where thermal conductivity is critical to performance. This study investigates the effects of length, diameter, temperature, and axial strain on the thermal conductivity of armchair and zigzag SiGeNTs through molecular dynamics simulations. Results indicate that thermal conductivity increases with sample length due to ballistic heat transport and decreases with temperature as phonon scattering intensifies. Axial strain transitions from compression to tension enhance phonon propagation, improving conductivity. Chirality affects conductivity, with zigzag SiGeNTs consistently outperforming armchair structures, while diameter exhibits negligible impact.</p><h3>Methods</h3><p>Non-equilibrium molecular dynamics simulations were conducted using the LAMMPS package with the Tersoff potential to model Si-Ge interactions. Thermal conductivity was computed via Fourier’s law, with the system divided into regions for controlled heat input and dissipation. Lengths, diameters, temperatures (100–500 K), and axial strains (− 6% to + 9%) were varied systematically. Phonon spectrum analysis was performed using Fourier transforms of velocity autocorrelation functions to compute.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045365","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}