The Journal of Physical Chemistry B最新文献

{"title":"Ozone–Persulfate Coupled Oxidation Mechanism of Asphaltene and Resin in Heavy Petroleum Components Based on Reactive Force Field Potential","authors":"Xinxin Liang,&nbsp;, ,&nbsp;Jin Li*,&nbsp;, and ,&nbsp;Zongkuan Liu*,&nbsp;","doi":"10.1021/acs.jpcb.5c03143","DOIUrl":"10.1021/acs.jpcb.5c03143","url":null,"abstract":"<p >Asphaltene and resin are the most structurally complex and recalcitrant compounds in petroleum, causing them to form persistent pollutants when they enter the environment. In this study, the degradation mechanisms of asphaltene and resin in heavy petroleum components under ozone–persulfate coupled oxidation systems were investigated using reactive force field molecular dynamics simulations. The oxidation process consisted of a rapid reaction phase and a slow reaction phase, wherein components with a higher molecular weight and more ring structures exhibited faster radical consumption rates. The coupled oxidation system demonstrated superior efficiency compared to single-oxidant systems. Hydroxyl radicals demonstrated superior degradation efficiency for macromolecules compared to sulfate radicals. Asphaltene degradation primarily involved the sequential cleavage of side chains around condensed rings, followed by ring-opening and reorganization. Resin degradation preferentially targeted alkyl chains and heterocycles, among which sulfur-containing heterocycles were more readily degraded than oxygen-containing structures. This study provides the reaction network of heavy petroleum components under coupled oxidation, as well as a theoretical foundation for remediating petroleum-contaminated soils.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"10035–10048"},"PeriodicalIF":2.9,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hub Occupancy by Competitively Interacting Proteins Obeys a Simple Queuing Law","authors":"Yuming Jiang,&nbsp;, ,&nbsp;Antun Skanata*,&nbsp;, and ,&nbsp;Liviu Movileanu*,&nbsp;","doi":"10.1021/acs.jpcb.5c04305","DOIUrl":"10.1021/acs.jpcb.5c04305","url":null,"abstract":"<p >Coordinated interactions between a protein hub, or receptor, and its cognate protein ligands are at the heart of cell signaling. Any significant perturbations in their kinetic and dynamic complexities result in major alterations in biochemical traffic at the subcellular and extracellular levels. The coexistence of multiple ligands with varying local concentrations and affinity constants, as well as the transient nature of their underlying protein–protein interactions (PPIs), makes predicting hub occupancy a challenging task. Here, we develop models of PPIs anchored in queuing theory to determine hub occupancy as a function of the kinetic rate constants and concentrations in complex mixtures of protein ligands. We find that in a ternary mixture of protein ligands spanning a range of kinetic rate constants, the concentration of one ligand can significantly influence the competitive PPIs between the other two ligands and the protein receptor, thereby impacting its overall occupancy. Further, for more complex mixtures, we developed a coarse-graining approach to compartmentalize large numbers of ligands competing for the same binding site of the receptor. Our analytical strategy provides a mechanistic and quantitative understanding of competitive PPIs, with broad applicability to biochemical processes, protein analytics, and drug development.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"9904–9912"},"PeriodicalIF":2.9,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c04305","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Specific Binding Modes of the SIRT6 C-Terminal Domain to the Nucleosome Core Particle Influence DNA Unwrapping and H3K27 Accessibility","authors":"Yuya Qiu,&nbsp;, ,&nbsp;Gabor Papai,&nbsp;, ,&nbsp;Adam Ben Shem,&nbsp;, and ,&nbsp;Emmanuelle Bignon*,&nbsp;","doi":"10.1021/acs.jpcb.5c02221","DOIUrl":"10.1021/acs.jpcb.5c02221","url":null,"abstract":"<p >Sirtuins are a class of NAD-dependent histone deacetylases that regulate important biological pathways in prokaryotes and eukaryotes. This enzyme family comprises seven members, named SIRT1 to SIRT7. Among them, Sirtuin 6 (SIRT6) is a human sirtuin that deacetylates histones and plays a key role in DNA repair, telomere maintenance, carbohydrate and lipid metabolism, and lifespan. SIRT6’s structure consists of a zinc finger domain, a Rossmann fold domain containing the NAD⁺ binding site, and disordered N-terminal and C-terminal (CTD) extensions. The specific role of the CTD in SIRT6’s interaction with nucleosomes for histone deacetylation remains unclear. Here, we resort to extended molecular dynamics simulations to uncover the dynamical behavior of the full-length SIRT6 bound to a nucleosome core particle. Our simulations reveal that the CTD preferentially interacts with DNA at the entry/exit near the enzyme’s docking site, exhibiting a variety of different binding modes. In specific cases, the CTD contributes to the promotion of DNA unwrapping and enhances H3K27 accessibility to SIRT6’s active site, suggesting a pivotal role of this domain for H3K27 deacetylation. This work provides new structural insights into the binding process of the full-length SIRT6 to a nucleosome core particle, shedding light on the conformational behavior and functional role of its CTD. It constitutes an important step toward understanding of SIRT6 deacetylation mechanisms and specificity.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"9855–9861"},"PeriodicalIF":2.9,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Benchmark of Available Explicit Solvent Models in CHARMM36m to Characterize Glycosaminoglycans","authors":"P. A. Wesołowski*,&nbsp;, ,&nbsp;D. J. Wales,&nbsp;, and ,&nbsp;K. K. Bojarski*,&nbsp;","doi":"10.1021/acs.jpcb.5c04919","DOIUrl":"10.1021/acs.jpcb.5c04919","url":null,"abstract":"<p >Heparin is a highly sulfated glycosaminoglycan (GAG) with essential roles in anticoagulation, angiogenesis, cell signaling, and host–pathogen interactions, mediated largely through electrostatic binding to diverse protein targets. While the TIP3P water model is commonly used in molecular simulations of GAGs, the influence of solvent representation on HP structure within the CHARMM36m force field remains poorly understood. Here, we report 5 μs molecular dynamics simulations of an HP dodecamer in five explicit solvent models: TIP3P, TIP4P, TIP5P, SPC/E, and OPC. TIP3P and SPC/E yield stable HP conformations, whereas TIP4P, TIP5P, and OPC introduce greater structural variability. Comparison with GLYCAM06 reveals that CHARMM36m preserves global HP architecture but differs in sampling specific glycosidic linkages. These findings highlight the critical impact of water model choice on GAG conformational dynamics and offer practical guidance for the accurate simulation of sulfated carbohydrates.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"9953–9964"},"PeriodicalIF":2.9,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c04919","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Superionic Transition in Mixed Conducting Graphite Intercalation Compounds CsC8 and RbC8","authors":"Mengyuan Zhu,&nbsp;, ,&nbsp;Jianfu Li*,&nbsp;, ,&nbsp;Mengxin Lu,&nbsp;, ,&nbsp;Yong Liu,&nbsp;, ,&nbsp;Jianan Yuan,&nbsp;, ,&nbsp;Jiani Lin,&nbsp;, and ,&nbsp;Xiaoli Wang*,&nbsp;","doi":"10.1021/acs.jpcb.5c05805","DOIUrl":"10.1021/acs.jpcb.5c05805","url":null,"abstract":"<p >Mixed ionic-electronic conductors (MIECs) have attracted considerable interest in electrode/interface materials for solid-state batteries. Here, we investigate the ionic diffusion behavior of graphite intercalation compounds XC₈ (X = Cs, Rb) through first-principles calculations combined with ab initio molecular dynamics simulations. The results show that CsC₈ and RbC₈ undergo superionic transitions near 500 and 600 K, respectively, with corresponding ionic conductivities of 0.0127 and 0.0787 S/cm. Their electrical conductivities reached up to 10⁷ S/m. Notably, RbC₈ exhibits a stacking sequence transition from ΑαAβAγAδ to ΑαAβ at 500 K. The introduction of defects further reduces the superionic transition temperature to 400 K. Cs⁺ and Rb⁺ ions migrate via a vacancy mechanism along two pathways: crossing C–C bonds or diffusing from above carbon atoms to nearby hexagon centers. Additionally, both compounds show good thermal stability and mechanical properties. These findings offer new insights into the design of high-performance MIEC materials.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 40","pages":"10595–10602"},"PeriodicalIF":2.9,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145135957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Calculating Free-Energy Differences Using an Average Force: A Tutorial for Adaptive Biasing Force Simulations","authors":"Radu A. Talmazan,&nbsp;, ,&nbsp;Haohao Fu,&nbsp;, ,&nbsp;Mengchen Zhou,&nbsp;, ,&nbsp;Jérôme Hénin,&nbsp;, ,&nbsp;James C. Gumbart,&nbsp;, and ,&nbsp;Christophe Chipot*,&nbsp;","doi":"10.1021/acs.jpcb.5c04333","DOIUrl":"10.1021/acs.jpcb.5c04333","url":null,"abstract":"<p >The purpose of this tutorial is to get the reader familiarized with the calculation of a free-energy change along a reaction-coordinate (RC) model through a number of applications of variants of the importance-sampling adaptive biasing force algorithm. The reversible sodium-chloride ion pairing in aqueous solution serves as an introductory example, wherein the RC model is defined as the distance separating the ions. For the reversible folding of the short peptide deca-alanine, alternative collective variables are considered to map the conformational free-energy landscape. The importance-sampling algorithm is then applied to the transfer of an ethanol molecule across the water liquid–vapor interface to estimate its hydration free energy. The results are compared to those of an alchemical transformation using free-energy perturbation calculations. In the final application, the Ramachandran free-energy surface underlying the conformational equilibrium of <i>N</i>-methyl-<i>N</i>′-acetylalanylamide is determined in two dimensions, comparing single- and multiple-walker strategies.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"9913–9928"},"PeriodicalIF":2.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating the Accelerated Aging of Water-in-Salt Electrolytes: A Focus on Magnesium Perchlorates via Radiolysis","authors":"Caroline Keller,&nbsp;, ,&nbsp;Malaurie Paillot,&nbsp;, ,&nbsp;Zhiwen Jiang,&nbsp;, ,&nbsp;Solène Legand,&nbsp;, ,&nbsp;Mehran Mostafavi,&nbsp;, ,&nbsp;Jean-Pierre Dognon,&nbsp;, ,&nbsp;Magali Gauthier*,&nbsp;, and ,&nbsp;Sophie Le Caër*,&nbsp;","doi":"10.1021/acs.jpcb.5c05353","DOIUrl":"10.1021/acs.jpcb.5c05353","url":null,"abstract":"<p >Magnesium-based batteries hold great promise for energy storage, owing to the abundance of magnesium and its theoretical high energy densities. However, the use of organic electrolytes in these batteries presents significant safety concerns, particularly regarding corrosion, flammability and toxic degradation products. Water-in-salt electrolytes (WiSE) offer a safer solution, expanding the electrochemical stability window of conventional aqueous solutions through high salt concentrations. Among the various salts, magnesium perchlorate stands out due to its good solubility, low cost, and chaotropic properties, which modify the water network significantly. To investigate the aging mechanisms of Mg(ClO₄)₂ WiSE electrolytes, radiolysis-induced degradation processes were studied using picosecond pulse radiolysis experiments, with a focus on the effects of salt molality on the formation of reactive species. These experiments, in conjunction with quantum chemical calculations, provide insights into the formation of transient species and their evolution during electrolyte degradation. Moreover, the radiolytic yields of stable species, including dihydrogen (H₂), dioxygen (O₂), chlorate (ClO₃^–), and chloride (Cl^–), were measured. O₂ is exclusively derived from perchlorate anions, while H₂ originates from water. As the concentration of Mg(ClO₄)₂ increases, the radiolytic yields of chlorinated species rise, in particular for ClO₃^–. The results obtained highlight that excited perchlorate anions in concentrated solutions generate a range of reactive species, namely ClO₃^–, ClO₂^–, as well as ClO₄^• and ClO₃^• radicals. Notably, ClO₃^– anions are formed from excited perchlorate anions. On the other hand, ClO₄^•, also directly generated through ionizing radiation/matter interaction, leads to the formation of O₂ and ClO₂^•. The ClO₂^• radical quickly loses O₂, resulting in the formation of the chlorine radical, and eventually of the chloride anion. The study also reveals that hydrogen peroxide formation is consistent across varying molalities, indicating a balance between contributions from both water and perchlorate anions. These findings provide critical insights into the radiolysis processes in Mg(ClO₄)₂ electrolytes, contributing to the understanding of electrolytes aging to further develop more efficient magnesium-ion batteries.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"10109–10121"},"PeriodicalIF":2.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidating the Impact of Red Blood Cell Membrane Components on Melittin-Induced Pore Formation with Molecular Dynamics Simulations","authors":"Joshua D. Richardson,&nbsp; and ,&nbsp;Reid C. Van Lehn*,&nbsp;","doi":"10.1021/acs.jpcb.5c04289","DOIUrl":"10.1021/acs.jpcb.5c04289","url":null,"abstract":"<p >Understanding the membrane-disrupting mode of action of antimicrobial peptides (AMPs) in complex biological membranes is critical for the design of therapeutically viable AMPs that are both active against microbial pathogens and nontoxic to human cells. To assess human toxicity in AMP design studies, melittin (MEL) (a highly charged 26-amino acid AMP sourced from bee venom) is often used as the positive control in experimental human red blood cell (RBC) hemolysis assays. Molecular dynamics (MD) simulations have proven invaluable in elucidating the pore-formation mechanism of MEL in single-lipid zwitterionic membranes. However, modeling pore formation in lipid bilayers containing multiple lipid species, like RBC membranes, has been limited due to the challenges of using atomistic MD simulations to capture long-time-scale membrane restructuring events that depend on lipid heterogeneity, leaflet asymmetry, and cholesterol content. To address these challenges and access larger time scales, in this work, we utilize the coarse-grained MARTINI force field to model four lipid membranes of increasing complexity, ranging from single-lipid POPC membranes to asymmetric RBC-mimetic membranes containing cholesterol. Through the application of a nucleation collective variable (ξ) to create transmembrane pores and a coarse-grained-to-atomistic backmapping strategy, we studied MEL pore-lining affinity and pore nucleation free energies to assess the effect of lipid complexity and cholesterol on MEL pore formation. We find that although cholesterol strongly inhibits MEL-induced pore formation regardless of lipid content, pore nucleation is more favorable in RBC versus single-lipid POPC membranes when cholesterol is absent due to the enrichment of anionic POPS lipids near the pore that permits increased conformational flexibility for MEL. These results provide new physical insight into factors that affect pore formation in compositionally complex membranes and are a step toward understanding how AMPs can be designed to selectively induce pores in membranes with different compositions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"9983–9997"},"PeriodicalIF":2.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Defect-Engineered Graphene Nanoribbons for Enhanced DNA Sequencing: A Study of Structural Defects and Their Impact on Nucleobase Interaction and Quantum Transport","authors":"Rameshwar L. Kumawat*,&nbsp;, ,&nbsp;Sanjiv K. Jha*,&nbsp;, ,&nbsp;Benjamin O. Tayo,&nbsp;, and ,&nbsp;C. David Sherrill*,&nbsp;","doi":"10.1021/acs.jpcb.5c03247","DOIUrl":"10.1021/acs.jpcb.5c03247","url":null,"abstract":"<p >Graphene, a low-dimensional material, has shown significant promise in bioelectronics over the past two decades. Most research in this field has focused on pristine graphene. However, experimentally fabricated two-dimensional (2D) graphene and one-dimensional (1D) graphene nanoribbons (GNRs) often contain impurities, such as Stone–Wales (sw) and divacancy (dv) defects. In this study, we conducted a comparative analysis of the adsorption behavior of DNA nucleobases–adenine (A), guanine (G), thymine (T), and cytosine (C)─on three types of graphene nanoribbon (GNR) surfaces: pristine (prGNR), divacancy-defected (dvGNR), and Stone–Wales-defected (swGNR). Using semilocal (PBE) and van der Waals-corrected density functional theory methods (vdW-DF2 and PBE-D2), we evaluated the binding energies of the nucleobases on the different GNR surfaces. Our results show that defected GNRs exhibit less negative binding energies for all nucleobases compared to prGNR when dispersion interactions are taken into account. The binding energies calculated using PBE, PBE-D2, and vdW-DF2 methods range from −0.06 to −0.10, −0.55 to −0.80 and −0.59 to −0.78 eV, respectively. The vdW-DF2 method effectively captures vdW interactions, with binding energies following the order G &gt; A &gt; T &gt; C. These interactions result in weak binding between nucleobase and the π-states of the GNR surfaces, inducing a small interfacial dipole and a shift in the energy bandgap. Quantum transport analysis reveals that while pristine GNRs exhibit distinct conduction channels, defects─such as dv and sw configurations─introduce localized states that interact with delocalized ones, generating pronounced <i>Fano resonances</i> characterized by sharp dips in the transmission spectra. Physisorption of DNA nucleobases on different GNR surfaces induces unique resonance peaks in the transmission function, influenced by the type and position of defects. Conductance sensitivity analysis indicates prGNR as a promising candidate for nucleobase detection, leveraging <i>Fano resonances</i> for precise electronic measurements. However, defected GNRs also exhibit significant sensitivity. Furthermore, Current–Voltage (<i>I</i>–<i>V</i>) analysis identifies dvGNR devices as the most effective for nucleobase detection due to their high current sensitivity and distinct responses across nucleobases. While prGNR devices detect certain nucleobases, they show less consistent performance due to uniform current trends at higher biases. In contrast, swGNR devices effectively differentiate all four nucleobases through distinct current signals in the 0.6–0.8 V range. These findings underscore the potential of defect-engineered GNRs for the next-generation DNA sequencing applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"9862–9879"},"PeriodicalIF":2.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c03247","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anisotropic Crystallization Growth of 4H-SiC: Insights from Molecular Dynamics","authors":"Qi Li,&nbsp;, ,&nbsp;Tinghong Gao*,&nbsp;, ,&nbsp;Kejun Dong,&nbsp;, ,&nbsp;Guiyang Liu,&nbsp;, ,&nbsp;Wanjun Yan,&nbsp;, ,&nbsp;Jin Huang,&nbsp;, and ,&nbsp;Han Song,&nbsp;","doi":"10.1021/acs.jpcb.5c05183","DOIUrl":"10.1021/acs.jpcb.5c05183","url":null,"abstract":"<p >Silicon carbide (SiC) exhibits outstanding physical and chemical properties, making it highly promising for applications in power electronics and high-temperature sensors. Among its polytypes, 4H-SiC has attracted significant attention due to its superior electrical properties and high thermal conductivity. However, structural defects arising during the growth of SiC crystals hinder their practical application, and the conventional physical vapor transport (PVT) method lacks effective in situ monitoring capabilities. In this study, molecular dynamics (MD) simulations were conducted using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to model the solid–liquid growth of 4H-SiC with various crystal orientations under the NPT ensemble. The effect of temperature on crystallization was analyzed, and 1900 K was determined to be the optimal simulation temperature. The impact of crystal orientation on crystallization quality and defect distribution was systematically investigated by analyzing the radial distribution function, growth rate, morphology, and defect characteristics. The results indicate that the F1 and F2 orientations exhibit high crystallization efficiency and low defect densities. In contrast, the F3 and F4 orientations exhibit higher defect concentrations, although some self-healing behavior is observed. These findings provide theoretical guidance for optimizing 4H-SiC synthesis and improving its performance, thereby facilitating the broader application of high-quality SiC crystals in next-generation electronic devices.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"10084–10095"},"PeriodicalIF":2.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}