Journal of Molecular Modeling最新文献

{"title":"Theoretical study of the nature of σ-hole regium bond between CuX/AgX/AuX and pyridine","authors":"Junyong Wu,&nbsp;Hua Yan,&nbsp;Hao Chen,&nbsp;Guoliang Dai","doi":"10.1007/s00894-025-06360-5","DOIUrl":"10.1007/s00894-025-06360-5","url":null,"abstract":"<div><h3>Context</h3><p>The σ-hole regium bond complexes between coinage metal monohalide molecule CuX/AgX/AuX (X = F, Cl, and Br) and pyridine (C₅H₅N), which have linear orientation and perpendicular orientation, have been systematically probed at the MP2/aug-cc-pVTZ level. By comparing the calculated interaction energy, we can see that the linear orientation interactions are a little stronger than the corresponding perpendicular orientation interactions in C₅H₅N-CuX/AgX/AuX complexes. The binding energies for linear orientation regium bond complexes range from − 34 to − 60 kcal/mol, while those perpendicular orientation regium bond complexes are from − 24 to − 50 kcal/mol. Both types of interactions energies all tend to follow the Au &gt; Cu &gt; Ag order and reduced with the decrease in electronegativity F &gt; Cl &gt; Br in C₅H₅N-CuX/AgX/AuX complexes. The electrostatic energy is the major source of the attraction for the linear orientation regium bond interactions, while for the perpendicular orientation regium bond interactions are mainly due to electrostatic and induction energy.</p><h3>Methods</h3><p>All the complexes and respective monomers were optimized at the MP2/aug-cc-pVTZ level. Relativistic effects were considered for Cu, Ag, Au, and Br by using the aug-cc-pVTZ-PP basis set. The NBO population analysis and AIM and IRI analysis were carried out. The interaction energies of the σ-hole regium bonds complexes were decomposed by using the symmetric adaptive perturbation theory (SAPT).</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786482","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 docking of Cu(II) and Zn(II) complexes for tyrosinase inhibition and drug loading on boron nitride nanotube scaffolds using Monte Carlo simulations","authors":"Najeeb Ullah,&nbsp;Amir Karim,&nbsp;Muhammad Iqbal,&nbsp;Rahime Eshaghi Malekshah,&nbsp;Saqib Ali,&nbsp;Jebiti Haribabu,&nbsp;Sodio C. N. Hsu","doi":"10.1007/s00894-025-06355-2","DOIUrl":"10.1007/s00894-025-06355-2","url":null,"abstract":"<div><h3>Context</h3><p>Recent studies on drug delivery systems incorporating boron nitride nanostructures (BNNTs) highlight their excellent chemical stability and non-cytotoxic properties, positioning them as a promising platform for drug release in biomedical applications. This study aimed to optimize the mono-nuclear structures of Cu(II) and Zn(II) complexes and to functionalize zigzag (13, 13) boron nitride nanotubes with glutamic acid (GABNNTs). Based on Monte Carlo, the results revealed that complexes <b>6</b> and <b>19</b> exhibited stronger interactions with GABNNTs, attributed to π-π stacking between bipyridine/phenanthroline ligands and GABNNTs. This interaction suggests a greater challenge in their release compared to other compounds. The interaction energy analysis further revealed that complexes <b>1</b>, <b>4</b>, and <b>12</b>/GABNNTs exhibited the lowest stability, indicating weaker binding interactions between these complexes and the GABNNT surface. The adsorption of all complexes on GABNNTs was primarily found to be physisorption. Molecular docking with mushroom tyrosinase (2Y9X) identified complexes <b>5</b>, <b>10</b>, <b>11</b>, <b>15</b>, and <b>20</b> as having the strongest interactions, a trend that is partially supported by chemical hardness analysis. However, DFT-D results indicated that complexes <b>5</b>, <b>11</b>, and <b>20</b> exhibited the lowest chemical stability, suggesting a trade-off between strong interactions and lower stability in these complexes.</p><h3>Methods</h3><p>The energies of these systems were estimated using dispersion-corrected density functional theory (DFT-D) calculations performed in Materials Studio 2017. To evaluate the drug delivery potential of GABNNTs for Cu(II) and Zn(II) complexes, the Monte Carlo (MC) method was employed. The structural and electronic properties, as well as the relationship between biological activities and ΔE_g, were analyzed by calculating the HOMO–LUMO energy gap using the dispersion-corrected density functional theory (DFT-D) method. Molecular docking was used to interact with mushroom tyrosinase (2Y9X).</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786481","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":"Interaction of some phytochemical compounds with Er2O3 nanoparticle: First principle study","authors":"Mahmood Akbari","doi":"10.1007/s00894-025-06361-4","DOIUrl":"10.1007/s00894-025-06361-4","url":null,"abstract":"<div><h3>Context</h3><p>The interaction between phytochemicals and nanoparticles plays a crucial role in nanotechnology and biomedical applications. This study investigates the binding behavior and stability of six phytochemicals—Catechin, Limonene, Sabinene, Sinapic Acid, Vanillic Acid, and Luteolin 7-O-ß-glucuronide—with Er₂O₃ nanoparticles using Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations. The findings indicate that Luteolin, Catechin, and Sinapic Acid exhibit the strongest binding affinities and highest structural stability with Er₂O₃, attributed to their balanced hydrophilicity-lipophilicity and favorable electronic properties. These insights contribute to the design and functionalization of phytochemical-based nanomaterials, with potential applications in drug delivery, bioimaging, and photodynamic therapy.</p><h3>Methods</h3><p>DFT calculations were conducted using Gaussian 09 at the B3LYP/6–311 +  + G(d,p) level to determine HOMO–LUMO energy gaps, dipole moments, and polarizability of the phytochemicals. MD simulations, performed using GROMACS 2019 with the CHARMM36 force field and TIP3P water model, analyzed the dynamics of phytochemical adsorption on a 5 nm Er₂O₃ nanoparticle over 50 ns. Key parameters such as interaction energies, root mean square deviations (RMSD), radial distribution functions (RDF), and water solubility (logS) were evaluated using ALOPGPS 2.1 software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06361-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143761744","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":"Adsorption attributes of β-phosphoborophane nanosheets towards some vapors emitted from cosmetics—a first-principles study","authors":"V. Nagarajan,&nbsp;Lakshitaa B.,&nbsp;R. Chandiramouli","doi":"10.1007/s00894-025-06352-5","DOIUrl":"10.1007/s00894-025-06352-5","url":null,"abstract":"<div><h3>Context</h3><p>Recently, new two-dimensional (2D) materials have emerged and are used for various engineering applications. One such new 2D material is beta (β-)phosphoborophane. Initially, we ensured the structural and dynamic stability of β-phosphoborophane. The semiconducting behavior of β-phosphoborophane with an energy band of 1.252 eV reveals that it is a suitable material for chemical nanosensors. We used β-phosphoborophane as adsorbing material for some of the molecules emitted from cosmetics such as hydroxycitronellal and alpha isomethyl ionone. The adsorption of target molecules changes the energy band gap of β-phosphoborophane, inferred based on the results of band structure and projected density of states. Furthermore, the changes in the electronic properties of β-phosphoborophane upon adsorption of target molecules are observed with regard to charge transfer and electron density difference results. The chemo-resistive nature of β-phosphoborophane is revealed from the relative energy gap changes owing to hydroxycitronellal and alpha isomethyl ionone adsorption.</p><h3>Methods</h3><p>The structural stability, dynamical firmness, electronic properties, and interaction behavior of hydroxycitronellal and alpha isomethyl ionone on β-phosphoborophane are explored within the framework of the DFT method. The hybrid GGA/B3LYP functional is used for optimizing the base material β-phosphoborophane. All the calculation in the research study is carried out by the QuantumATK simulation package. The result of the proposed work supports that β-phosphoborophane can be a suitable sensing material for hydroxycitronellal and alpha isomethyl ionone, which are found in cosmetics.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143761745","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":"Excited-state proton transfer in the rare isoguanine-isocytosine base pair in water solution","authors":"Tsvetina D. Cherneva,&nbsp;Mina M. Todorova,&nbsp;Rumyana I. Bakalska,&nbsp;Ernst Horkel,&nbsp;Vassil B. Delchev","doi":"10.1007/s00894-025-06351-6","DOIUrl":"10.1007/s00894-025-06351-6","url":null,"abstract":"<div><h3>Context</h3><p>With the current research, we aim to study the mechanism of the excites state proton transfer (ESPT) between the nucleobases isoguanine (iG) and isocytosine (iC) in their Watson–Crick model. Such research is proposed for the first time and it can partially reveal the question why the nature “has chosen” guanine and cytosine for pairing in the DNA duplex and not their analogs (isoforms). The UV irradiation of the water solution of equimolar mixture of iG and iC implies a tautomeric conversion between the nucleobases. In the research, the mechanism of the ESPT was followed and clarified for the first time. All this reflects to the photostability of the iG-iC base pair in water solution.</p><h3>Methods</h3><p>For the purposes of the current research, we chose to use the TD DFT with the hybrid functional B3LYP in combination with the aug-cc-pVDZ basis set. The water surroundings are modeled according to the polarizable continuum model (PCM) modeling the solvation effects on the studying systems. Linear interpolation and intrinsic reaction coordinate approach were applied for the reaction path follow of the ESPT.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143749172","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 fabrication process parameters and graphene reinforcement on mechanical behaviour of additively manufactured AlSi10Mg alloy: A molecular dynamics simulation study","authors":"Sunita K. Srivastava,&nbsp;N. Rajesh Mathivanan","doi":"10.1007/s00894-025-06354-3","DOIUrl":"10.1007/s00894-025-06354-3","url":null,"abstract":"<div><h3>Context</h3><p>AlSi10Mg alloy is among the most widely recognised aluminium alloys due to its dimensional stability and exceptional properties for additive manufacturing. However, the alloy’s performance can be improved and optimized through appropriate reinforcement and control of the manufacturing process parameters. This work focuses on the impact of process parameters (laser power, scan speed and layer thickness) and graphene reinforcement on the mechanical properties of SLM-fabricated AlSi10Mg alloy. The results indicate that, increasing the laser power within the studied range enhances both tensile and compressive strength. Furthermore, reducing the laser scanning speed improved these properties, although further reduction beyond a threshold value minimizes the impact. However, increasing the layer thickness while maintaining the same laser power reduces the material properties, the effect can be mitigated by supplying more laser energy. The addition of graphene as reinforcement has markedly improved the composite properties, improving its elastic and plastic behaviour. The graphene reinforcement also improved the stiffness, yield strength, toughness, and ultimate strength making it a highly effective way to enhance the AlSi10Mg alloy performance.</p><h3>Methods</h3><p>In this study, molecular dynamics (MD) was performed to model the selective laser melting (SLM) process using LAMMPS (large-scale atomic/molecular massively parallel simulator) software. The simulation setup was programmed to analyse the impact of process parameters, including laser power (500, 600, and 700 μW), scanning speed (1, 1.5, and 2 nm/ps) and layer thickness (two and three-particle layer system) on the mechanical properties (tensile and compressive strength) of AlSi10Mg alloy. Additionally, the impact of graphene reinforcement was also examined using nano-scale simulation. The simulation provides insights into both the SLM process and the mechanical behaviour of the alloy and its composite under different processing conditions.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143749171","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":"In silico study of a new class of DNA fluorescent probes: docking, molecular dynamics and quantum chemistry calculations","authors":"Guilherme Saldanha Henkin,&nbsp;Simone Cristina Baggio Gnoatto,&nbsp;Diego Defferrari,&nbsp;Bruno Bercini de Araújo,&nbsp;Paulo Fernando Bruno Gonçalves,&nbsp;Paulo Augusto Netz","doi":"10.1007/s00894-025-06342-7","DOIUrl":"10.1007/s00894-025-06342-7","url":null,"abstract":"<div><h3>Context</h3><p>Natural fluorescence in biochemical structures can result in unsatisfactory outcomes in cell imaging. This drawback can be addressed by using probe molecules that fluoresce via Excited State Intramolecular Proton Transfer (ESIPT), thereby improving resolution and the signal-to-noise ratio. A docking study was conducted to estimate the binding free energy of 132 benzazoles and to determine their binding modes (minor groove (MG) or intercalation (INT)) to DNA, comparing them with the commercial probes 4’,6-Diamidino-2-phenylindole dihydrochloride (DAPI) and acridine orange (AO). Atomistic molecular dynamics simulations under physiological conditions were performed for the five top-ranked ligands, as well as for AO and DAPI. Three of the investigated ligands exhibited stronger binding energy than both commercial probes, while the other two showed stronger binding energy than AO, but not than DAPI. The proposed benzazoles acted as intercalators and MG binders. Using molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations to estimate the binding free energy of the ligand-receptor complexes, we could confirm the strong interaction of these molecules with DNA. Quantum Chemical Calculations were performed to estimate the emission energies upon excitation of the selected ligands, which showed large Stokes shift values and, for some molecules, favorable ESIPT processes. Benzazoles 1–5 demonstrated strong interactions with DNA, surpassing the commercial probes in binding strength and displaying promising photophysical properties. Consequently, these ligands are promising fluorescent DNA probes, suitable for various diagnostic techniques.</p><h3>Methods</h3><p>132 Benzazole ligands were constructed and optimized using Gabedit and docked to a B-DNA oligomer using AutoDock. Molecular dynamics simulations were run in GROMACS, using AMBER-parmbsc0 and GAFF force fields. Quantum chemical calculations (TD-DFT) in Gaussian 16 provided excited-state properties, optimized at the CAM-B3LYP/cc-pVDZ level of theory.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143740690","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":"Structure and properties of pentazole ionic salts","authors":"Yang Zhu,&nbsp;Peng Zhang,&nbsp;YuQin Chu,&nbsp;Zhihui Gu,&nbsp;Zikai Gao,&nbsp;Mengjie Bo,&nbsp;CongMing Ma,&nbsp;Peng Ma","doi":"10.1007/s00894-025-06348-1","DOIUrl":"10.1007/s00894-025-06348-1","url":null,"abstract":"<div><h3>Context</h3><p>Based on the periodic density functional theory, we systematically studied 13 kinds of anhydrous pentazole non-metallic ionic salts synthesized by other scientists (<b>PA-1 ~ PA-13</b>)[Chem-An Asian J, 13(8):924-928 6, J Am Chem Soc 140(48):16488-16494 7, J Mater Chem A 7(20):12468-12479 8, Chem-An Asian J 14(16):2877-2882 9]. The results show the following: first, the heat of formation of <b>PA-1 ~ PA-13</b> exceeds that of TNT and RDX. The heat of formation of PA-9 reaches 1357.56 kJ/mol, and it has excellent detonation performance (<i>D</i> = 9.41 km/s, <i>P</i> = 34.79 GPa, <i>Q</i> = 7.78 kJ/g), demonstrating the potential of high-energy ionic salts. Second, in cations, the introduction of -NH₂ or -OH substituents is beneficial to improving the heat of formation and detonation performance, while the introduction of -COOH substituents is unfavorable for the improvement of the heat of formation and detonation performance. Third, replacing -NH₂ with -OH can improve the chemical reactivity of pentazole ionic salts, while increasing the number of -NH₂ or introducing carbonyl groups will reduce the reactivity. Forth, the introduction of -NH₂ can enhance the hydrogen bonding and increase the electron density of pentazole ionic salts, and the introduction of -COOH can enhance the van der Waals interaction and the steric hindrance effect. Fifth, with other conditions remaining unchanged, the larger the volume of the cation, the greater the impact sensitivity and friction sensitivity of the ionic salt as actually measured, and the more stable the ionic salt is.</p><h3>Method</h3><p>All calculations in this paper are performed using Gaussian 16 based on density functional theory. Firstly, the structures of the derivatives were optimized at the level of B3LYP-D3/6-311G**, and then single-site energy calculations were carried out at the level of M06-2X-D3/def2-TZVPP, in order to explore the influence of different cation structures on various properties of pentazole ionic salts.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143740691","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 influence of external electric field on the structure of pentazole ionic salt","authors":"Peng Zhang,&nbsp;YuQin Chu,&nbsp;Yang Zhu,&nbsp;CongMing Ma,&nbsp;Peng Ma","doi":"10.1007/s00894-025-06353-4","DOIUrl":"10.1007/s00894-025-06353-4","url":null,"abstract":"<div><h3>Context</h3><p>Pentazole ion salt is a cutting-edge new type of all-nitrogen ion high-energy material. When subjected to an external electric field (EEF), the structure and various properties of pentazole ion salts are altered. This article studied six types of pentazole ion salts (PA-1 ~ PA-6) under an external electric field (intensity 0 ~ 0.008 a.u.). GGA/PBE method was used to calculate and analyze the lattice constants, cell volume, density, bond length, bond angle, dihedral angle, energy bands, and density of states of pentazole ion salts. The results showed that six types of pentazole ion salts exhibited good crystal and geometric stability under the action of an external electric field. The band gap exhibits different levels of decrease, and electrons are more prone to transition, resulting in a continuous weakening of the stability of pentazole ion salts. The dense attitudes of PA-1, PA-3, PA-4, and PA-6 gradually shift towards the low-energy region, with an increase in peak width and a splitting phenomenon. The peak values show a gradually decreasing trend. The electronic structures of PA-2 and PA-5 exhibit high stability. PA-3 and PA-6 are more sensitive to the applied electric field.</p><h3>Methods</h3><p>The Materials Studio software has been chosen for simulation and computation in this study. The GGA/PBE method has been utilized for the calculation and simulation of external electric fields, with the strength ranging from 0 to 0.008 a.u. and an increment gradient of 0.001 a.u.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143740688","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":"Deformation and phase transformation of dual-phase Ti under tension and compression process","authors":"Thi-Thuy Binh Ngo,&nbsp;Van-Thuc Nguyen,&nbsp;Te-Hua Fang","doi":"10.1007/s00894-025-06349-0","DOIUrl":"10.1007/s00894-025-06349-0","url":null,"abstract":"<div><h3>Context</h3><p>This study utilizes molecular dynamics (MD) simulation to investigate polycrystalline dual-phase titanium (DP Ti) deformation behavior and phase transformation under tensile and compressive loading. The analysis focuses on the influence of hexagonal close-packed (HCP) phase fraction, strain rate, and temperature on the mechanical properties and microstructural evolution. The results indicate that increasing the HCP phase fraction enhances the elastic modulus (36.5%), yield strength, and strain hardening while maintaining acceptable ductility. The optimal mechanical performance is achieved at 75.4% HCP phase fraction. Strain rate has significantly influenced mechanical response, with higher rates promoting increased yield strength, elastic modulus, dislocation activity, and phase transformations to body-centered cubic (BCC) and amorphous phases. In contrast, raising the temperature from 300 to 900 K results in thermal softening, reduced strength, and diminished dislocation activity, alongside pronounced HCP-to-BCC phase transformation. Interphase boundaries are critical in shaping the deformation mechanisms, influencing dislocation evolution and strain hardening. During deformation, Shockley, Hirth, and other partial dislocations appear. These findings offer valuable insights into the deformation mechanisms and phase behavior of DP Ti, emphasizing its potential for applications requiring a balance between strength and ductility.</p><h3>Methods</h3><p>The simulations utilized the open-source software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) for modeling atomic-scale interactions. Visualization of the evolving atomic structures was performed using OVITO (Open Visualization Tool). To analyze microstructural changes, the Dislocation Extraction Algorithm (DXA) and Common Neighbor Analysis (CNA) methods were employed.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676432","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}