The Journal of Physical Chemistry B最新文献

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Phase-State-Dependent Silica Nanoparticle Uptake of Giant Unilamellar Vesicles. 相态依赖性硅纳米粒子对巨型单拉米小泡的吸收。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2024-07-12 DOI: 10.1021/acs.jpcb.4c02383
Manuel M Sirch, Andrej Kamenac, Simon V Neidinger, Achim Wixforth, Christoph Westerhausen
{"title":"Phase-State-Dependent Silica Nanoparticle Uptake of Giant Unilamellar Vesicles.","authors":"Manuel M Sirch, Andrej Kamenac, Simon V Neidinger, Achim Wixforth, Christoph Westerhausen","doi":"10.1021/acs.jpcb.4c02383","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c02383","url":null,"abstract":"<p><p>We quantify endocytosis-like nanoparticle (NP) uptake of model membranes as a function of temperature and, therefore, phase state. As model membranes, we use giant unilamellar vesicles (GUV) consisting of 1,2-dipentadecanoyl-sn-glycero-3-phosphocholine (15:0 PC). Time-series micrographs of the vesicle shrinkage show uptake rates that are a highly nonlinear function of temperature. A global maximum appears close to the main structural phase transition at <i>T</i> = <i>T</i><sub>m</sub> + 3 K = 37 °C and a minor peak at the pretransition <i>T</i> = <i>T</i><sub>p</sub> = 22 °C. The quality of linear fits to the shrinkage, and thus uptake kinetics, reveals a deviation from the linear trend at the vesicle shrinkage peaks. Taking values for the bending modulus as a function of temperature from literature and Helfrich's model allows us to draw qualitative conclusions on the membrane tension and the adhesion of the NP to the membrane as a function of temperature. These findings provide valuable insights into the dynamic interplay between temperature, membrane phase transitions, and NP uptake, shedding light on the complex behavior of biological membranes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589029","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}
引用次数: 0
Protonation State of a Bioactive Compound Regulates Its Release from Lamellar Gel-Phase Bilayers. 生物活性化合物的质子化状态可调节其从胶状双分子层的释放
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2024-07-12 DOI: 10.1021/acs.jpcb.4c02442
Choon-Peng Chng, Shikhar Gupta, Changjin Huang
{"title":"Protonation State of a Bioactive Compound Regulates Its Release from Lamellar Gel-Phase Bilayers.","authors":"Choon-Peng Chng, Shikhar Gupta, Changjin Huang","doi":"10.1021/acs.jpcb.4c02442","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c02442","url":null,"abstract":"<p><p>Lamellar gel networks (LGNs) in personal care or pharmaceutical lotions and creams provide an opaque cream appearance and a creamy texture to these products. Within the LGNs, the lamellar gel (L<sub>β</sub>) phase composed of regularly spaced bilayers of surfactants and long-chain fatty alcohols is predominately responsible for the unique rheological properties of the LGNs. To extend the shelf life of LGN-containing products, bioactive compounds with antimicrobial properties are often incorporated into the formulation. However, how the protonation state of the bioactive compounds regulates their release from the L<sub>β</sub>-phase bilayers is currently unknown. Using molecular dynamics simulations, we found that the protonated (neutral) form of cinnamic acid, a common antimicrobial food additive, has a retention ratio higher than that of its deprotonated (charged) counterpart in the L<sub>β</sub>-phase bilayer. From free energy calculations, we determined that not only is the protonated molecule more stable in the hydrophobic interior of the bilayer but also the formation of hydrogen-bonded dimers significantly enhances its stability within the bilayer. Thus, the protonation state has a profound impact on bioavailability of the compounds. Our results also highlight the importance of considering possible oligomeric states of molecules when performing calculations to estimate the permeability of molecules within various bilayers.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589030","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}
引用次数: 0
Fracture of Epoxy Networks Using Atomistic Simulations. 利用原子模拟研究环氧树脂网络的断裂。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c02350
Iakovos Delasoudas, Spyros V Kallivokas, Vassilis Kostopoulos
{"title":"Fracture of Epoxy Networks Using Atomistic Simulations.","authors":"Iakovos Delasoudas, Spyros V Kallivokas, Vassilis Kostopoulos","doi":"10.1021/acs.jpcb.4c02350","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c02350","url":null,"abstract":"<p><p>Predicting fracture properties through all-atomistic simulations poses challenges due to classical force field limitations in breaking covalent bonds and the computational demands of reactive force fields like ReaxFF. In addressing this, we propose a scale-bridging method for forecasting the fracture behavior of highly cross-linked epoxy combining classical force fields, the LAMMPS package REACTER, and for bond breaking a parameter based on experimental distance criterion. In our analysis, we anticipate the macroscopic fracture energy <i>G</i><sub>C</sub> of the epoxy network through the application of a continuum fracture mechanics model developed for fibrils. In addition, we extract the value of the stress intensity factor <i>K</i><sub>I</sub>. This modeling approach is specifically implemented for a frequently used epoxy system that consists of bisphenol F and DETDA hardener. Notably, our results demonstrate a robust correlation with existing literature and experimental studies. Moreover, our approach boasts a substantial computational time advantage, facilitating calculations that are significantly faster compared to those performed using reactive force fields.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578302","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}
引用次数: 0
60 Years of Betaine 30─From Solvatochromic Discovery to Future Frontiers. 甜菜碱 30 的 60 年--从 Solvatochromic 发现到未来前沿。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c02813
Rathiesh Pandian, Henrik Burda, Ibrahim Alfurayj, Christian Reichardt, Clemens Burda
{"title":"60 Years of Betaine 30─From Solvatochromic Discovery to Future Frontiers.","authors":"Rathiesh Pandian, Henrik Burda, Ibrahim Alfurayj, Christian Reichardt, Clemens Burda","doi":"10.1021/acs.jpcb.4c02813","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c02813","url":null,"abstract":"<p><p>Betaine-30 (B30) was reported by Karl Dimroth and Christian Reichardt et al. in 1963 as a solvatochromic probe that can be easily synthesized, shows good solubility, and remains stable in various organic solvents and solutions. Its strongly negatively solvatochromic behavior arises from differential solvation between its electronic ground and excited states, making it a valuable tool for assessing solvent polarity using the <i>E</i><sub>T</sub>(30) polarity scale, also devised by Dimroth and Reichardt. In addition, advancements in femtosecond laser spectroscopy in the 1990s greatly improved the understanding of B30's relaxation dynamics following photoexcitation. In solvents capable of hydrogen bonding, such as alcohols, intermolecular hydrogen-bond rearrangement contributes to the multiple relaxation components observed. Since the 1990s, the applications of B30 have expanded beyond simple organic solvents to include complex solvent mixtures, such as electrolyte solutions for battery technologies and eutectic solvent mixtures. Given the growing importance of these complex solvent mixtures, B30 is becoming an increasingly valuable tool for studying previously unexplored solvation properties.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578297","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}
引用次数: 0
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. 开放力场计划:分子建模的开放软件和开放科学。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c01558
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley
{"title":"The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling.","authors":"Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley","doi":"10.1021/acs.jpcb.4c01558","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c01558","url":null,"abstract":"<p><p>Force fields are a key component of physics-based molecular modeling, describing the energies and forces in a molecular system as a function of the positions of the atoms and molecules involved. Here, we provide a review and scientific status report on the work of the Open Force Field (OpenFF) Initiative, which focuses on the science, infrastructure and data required to build the next generation of biomolecular force fields. We introduce the OpenFF Initiative and the related OpenFF Consortium, describe its approach to force field development and software, and discuss accomplishments to date as well as future plans. OpenFF releases both software and data under open and permissive licensing agreements to enable rapid application, validation, extension, and modification of its force fields and software tools. We discuss lessons learned to date in this new approach to force field development. We also highlight ways that other force field researchers can get involved, as well as some recent successes of outside researchers taking advantage of OpenFF tools and data.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578305","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}
引用次数: 0
Virtual Special Issue on Machine Learning in Physical Chemistry Volume 2 物理化学中的机器学习》虚拟特刊第 2 卷。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c03823
Andrew L. Ferguson*,  and , Jim Pfaendtner*, 
{"title":"Virtual Special Issue on Machine Learning in Physical Chemistry Volume 2","authors":"Andrew L. Ferguson*,&nbsp; and ,&nbsp;Jim Pfaendtner*,&nbsp;","doi":"10.1021/acs.jpcb.4c03823","DOIUrl":"10.1021/acs.jpcb.4c03823","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578307","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}
引用次数: 0
Quantitative Optical Imaging of Oxygen in Brain Vasculature. 脑血管中氧的定量光学成像。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c01277
Emily Rathbone, Dan Fu
{"title":"Quantitative Optical Imaging of Oxygen in Brain Vasculature.","authors":"Emily Rathbone, Dan Fu","doi":"10.1021/acs.jpcb.4c01277","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c01277","url":null,"abstract":"<p><p>The intimate relationship between neuronal activity and cerebral oxygenation underpins fundamental brain functions like cognition, sensation, and motor control. Optical imaging offers a noninvasive approach to assess brain oxygenation and often serves as an indirect proxy for neuronal activity. However, deciphering neurovascular coupling─the intricate interplay between neuronal activity, blood flow, and oxygen delivery─necessitates independent, high spatial resolution, and high temporal resolution measurements of both microvasculature oxygenation and neuronal activation. This Perspective examines the established optical techniques employed for brain oxygen imaging, specifically functional near-infrared spectroscopy, photoacoustic imaging, optical coherence tomography, and two-photon phosphorescent lifetime microscopy, highlighting their fundamental principles, strengths, and limitations. Several other emerging optical techniques are also introduced. Finally, we discuss key technological challenges and future directions for quantitative optical oxygen imaging, paving the way for a deeper understanding of oxygen metabolism in the brain.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589031","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}
引用次数: 0
Modulating Weak Protein-Protein Cross-Interactions by the Addition of Free Amino Acids at Millimolar Concentrations. 通过添加毫摩尔浓度的游离氨基酸调节弱蛋白质-蛋白质交叉相互作用
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c01086
Pamina M Winkler, Cécilia Siri, Johann Buczkowski, Juliana V C Silva, Lionel Bovetto, Christophe Schmitt, Francesco Stellacci
{"title":"Modulating Weak Protein-Protein Cross-Interactions by the Addition of Free Amino Acids at Millimolar Concentrations.","authors":"Pamina M Winkler, Cécilia Siri, Johann Buczkowski, Juliana V C Silva, Lionel Bovetto, Christophe Schmitt, Francesco Stellacci","doi":"10.1021/acs.jpcb.4c01086","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c01086","url":null,"abstract":"<p><p>In this paper, we quantify weak protein-protein interactions in solution using cross-interaction chromatography (CIC) and surface plasmon resonance (SPR) and demonstrate that they can be modulated by the addition of millimolar concentrations of free amino acids. With CIC, we determined the second osmotic virial cross-interaction coefficient (<i>B</i><sub>23</sub>) as a proxy for the interaction strength between two different proteins. We perform SPR experiments to establish the binding affinity between the same proteins. With CIC, we show that the amino acids proline, glutamine, and arginine render the protein cross-interactions more repulsive or equivalently less attractive. Specifically, we measured <i>B</i><sub>23</sub> between lysozyme (Lys) and bovine serum albumin (BSA) and between Lys and protein isolates (whey and canola). We find that <i>B</i><sub>23</sub> increases when amino acids are added to the solution even at millimolar concentrations, corresponding to protein/ligand stoichiometric ratios as low as 1:1. With SPR, we show that the binding affinity between proteins can change by 1 order of magnitude when 10 mM glutamine is added. In the case of Lys and one whey protein isolate (WPI), it changes from the mM to the M range, thus by 3 orders of magnitude. Interestingly, this efficient modulation of the protein cross-interactions does not alter the protein's secondary structure. The capacity of amino acids to modulate protein cross-interactions at mM concentrations is remarkable and may have an impact across fields in particular for specific applications in the food or pharmaceutical industries.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589028","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}
引用次数: 0
Polarizing Perspectives: Ion- and Dipole-Induced Dipole Interactions Dictate Bulk Nanobubble Stability. 极化视角:离子和偶极子引发的偶极子相互作用决定了纳米气泡的稳定性。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c03973
Mohammadjavad Karimi, Gholamabbas Parsafar, Hamidreza Samouei
{"title":"Polarizing Perspectives: Ion- and Dipole-Induced Dipole Interactions Dictate Bulk Nanobubble Stability.","authors":"Mohammadjavad Karimi, Gholamabbas Parsafar, Hamidreza Samouei","doi":"10.1021/acs.jpcb.4c03973","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c03973","url":null,"abstract":"<p><p>The origin of the stability of bulk Nanobubbles (NBs) has been the object of scrutiny in recent years. The interplay between the surface charge on the NBs and the Laplace pressure resulting from the surface tension at the solvent-NB interface has often been evoked to explain the stability of the dispersed NBs. While the Laplace pressure is well understood in the community, the nature of the surface charge on the NBs has remained obscure. In this work, we aim to show that the solvent and the present ions can effectively polarize the NB surface by inducing a dipole moment, which in turn controls the NB stability. We show that the polarizability of the dispersed gas and the polarity of the dispersing solvent control the dipole-induced dipole interactions between the solvent and the NBs, and that, in turn, determines their stability in solution.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578303","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}
引用次数: 0
The Dissociation Process of NADP+ from NADPH-Cytochrome P450 Reductase Studied by Molecular Dynamics Simulation. 分子动力学模拟研究 NADP+ 与 NADPH-Cytochrome P450 还原酶的解离过程。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c03329
Songyan Xia, Hajime Hirao
{"title":"The Dissociation Process of NADP<sup>+</sup> from NADPH-Cytochrome P450 Reductase Studied by Molecular Dynamics Simulation.","authors":"Songyan Xia, Hajime Hirao","doi":"10.1021/acs.jpcb.4c03329","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c03329","url":null,"abstract":"<p><p>NADPH-cytochrome P450 reductase (CPR) plays a vital role as a redox partner for mammalian cytochrome P450 enzymes (P450s), facilitating the transfer of two electrons from NADPH to the P450 heme center in a sequential manner. Previous experimental studies revealed substantial domain movements of CPR, transitioning between closed and open states during the electron transfer (ET) cycle. These transitions are essential and are influenced by the binding of NADPH or the release of NADP<sup>+</sup>. However, the intricate molecular mechanisms governing the CPR-mediated ET cycle have largely remained elusive. This study employed molecular dynamics (MD) simulation techniques to explore the dissociation of NADP<sup>+</sup> from CPR, a crucial step preceding the initial ET from CPR to a P450. Alongside the binding structure of NADP<sup>+</sup> observed in a crystal structure (pose I), our MD simulations identified an alternative binding structure (pose II). Although pose II exhibits slightly lower stability than pose I, it can be formed through an approximate 210° counterclockwise rotation of the adenine group, with a free energy barrier of only 2.76 kcal/mol. The simulation results further suggest that NADP<sup>+</sup> dissociation involves a tentative formation of pose II from pose I before complete dissociation, and that the binding of NADP<sup>+</sup> to CPR is primarily governed by nonbonded interactions within the adenosine binding pocket.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589032","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}
引用次数: 0
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