The Journal of Physical Chemistry B最新文献

{"title":"Effects of Nanoplastics on Lipid Membranes and Vice Versa: Insights from All-Atom Molecular Dynamics Simulations.","authors":"Anderson D S Duraes, Elaine L Jiao, Wenlin Zhang","doi":"10.1021/acs.jpcb.4c08361","DOIUrl":"10.1021/acs.jpcb.4c08361","url":null,"abstract":"<p><p>We compute the potential of mean force (PMF) between semicrystalline polyethylene (PE) nanoplastics (NPLs) and model POPC and DPPC bilayers, which approximate in vivo membranes, using atomistic simulations. Our work shows that atomistic resolution is required to characterize the NPL and lipid interactions. By analyzing the PMF, we demonstrate that the mechanical properties of membranes, rather than NPL semicrystalline morphologies, govern NPL-membrane interactions. Resistance to NPL penetration arises from the elastic energy of the membrane deformation. The flexible POPC membranes resist NPL translocation, and the brittle DPPC membranes fracture under stress. Using an elastic free energy model, we approximate effective repulsions between lipid membranes and NPLs of various sizes. Our mean first-passage time analysis shows that even small, bare NPLs cannot easily penetrate brittle lipid membranes via passive diffusion, even at high concentrations. However, eco-coronas or other mechanisms, such as endocytosis, may still facilitate the cellular uptake of NPLs and MPLs. While semicrystalline morphologies do not directly impact NPL translocation, they do influence NPL behavior within lipid membranes upon translocation. Semicrystalline NPLs remain intact within lipid membranes, whereas amorphous NPLs can dissolve into the hydrophobic core and alter the elastic properties of the membrane.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3385-3395"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143404922","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":"Modulating the Charge Transfer Coupling in Boron-Dipyrromethene Homodimers by π-Bridge Units.","authors":"Li Ma, Zhuoran Kuang, Hao Zhang, Yan Wan, Yuanyuan Guo, Andong Xia, Yang Li","doi":"10.1021/acs.jpcb.5c00292","DOIUrl":"10.1021/acs.jpcb.5c00292","url":null,"abstract":"<p><p>To mimic the excitation energy conversion mechanisms observed in natural light-harvesting systems, we have extensively investigated photoinduced symmetry-breaking charge separations (SBCSs) in various multichromophoric model systems have been extensively investigated. However, designing multichromophoric model systems capable of simultaneously achieving ultrafast and complete SBCS remains a significant challenge. In this study, we employed benzene, thiophene, and furan as π-bridges to develop a series of boron dipyrromethene (BODIPY) homodimers. Spectral analysis, together with an estimation of the π-bridge-dependent charge transfer (CT) coupling using the fragment charge difference method, reveals that π-bridge units with different electron-donating abilities can effectively modulate the CT coupling between chromophores. Notably, the furan-based π-bridge, exhibiting the most pronounced electron-donating character, facilitates symmetry-breaking charge transfer (SBCT), i.e., excimer formation with a time constant of about 12 ps in weak polar toluene. Furthermore, a dramatic increase in the SBCS rate constant was observed in highly polar acetonitrile, improving from 60.4 ps for the benzene-bridged homodimer to 2.9 ps for the furan-bridged counterpart. These findings underscore the potential of π-bridge units in tuning the photophysical properties of covalent molecular aggregates by optimizing such systems for specific applications such as organic photovoltaics and photocatalysis.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3428-3435"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661575","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":"Isomerism and Solvent Interaction in Octamethyl Calix[4]pyrrole Complexed with Formate.","authors":"Lane M Terry, Madison M Foreman, J Mathias Weber","doi":"10.1021/acs.jpcb.5c00393","DOIUrl":"10.1021/acs.jpcb.5c00393","url":null,"abstract":"<p><p>We investigate the binding motifs of host-guest complexes of the anion receptor octamethyl calix[4]pyrrole (omC4P) with the formate anion using cryogenic ion vibrational spectroscopy in concert with density functional theory. The resulting infrared spectrum in vacuo is compared to that in deuterated acetonitrile and acetone solutions. The combination of the strong host-guest interaction and the charge distribution that the formate ion presents to the chemical environment results in complex behavior of the NH stretching features in the two solvents. The formate-omC4P complex has three low energy isomers in vacuo: (i) one with an oxygen atom of formate interacting with three of the NH groups of omC4P and the other oxygen atom interacting with the remaining NH group; (ii) one with a single oxygen atom of formate interacting with all four NH groups of omC4P; and (iii) one with each oxygen atom interacting with two NH groups. Each complex geometry lowers the C_4v symmetry of the receptor to C₁, C_s, or C_2v, respectively, and both symmetry breaking and isomerism are reflected in the pattern and broad line shapes of the NH stretching modes of omC4P.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3436-3442"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707790","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":"Resonant Soft X-ray Scattering for Organic Photovoltaics.","authors":"Dean M DeLongchamp","doi":"10.1021/acs.jpcb.5c00362","DOIUrl":"10.1021/acs.jpcb.5c00362","url":null,"abstract":"<p><p>Resonant Soft X-ray Scattering (RSoXS) has emerged as a powerful technique for probing the morphology in organic bulk heterojunction (BHJ) solar cells, frequently employed as a measurement of phase purity and compositional length scales. Here we use the National Institute of Standards and Technology RSoXS Simulation Suite to systematically examine how structural features common to BHJs would contribute to RSoXS patterns in the PM6:Y6 BHJ system. Starting from experimentally determined anisotropic optical constants, we simulate scattering from controlled morphological variations including compositional heterogeneity, interfacial sharpness, surface roughness, and molecular orientation. Our results demonstrate that noncompositional features can cause increases in scattering intensity exceeding those from compositional phase separation. Surface roughness of just a few nanometers produces substantial scattering due to the high contrast between organic materials and vacuum, and molecular orientation effects─whether random, interface-aligned, or independently correlated─can dramatically influence pattern intensity and shape. However, each structural feature exhibits a distinct energy-dependent scattering signature across the carbon K-edge, suggesting that careful analysis of the complete spectral response could enable deconvolution of multiple contributions. These findings provide a broader interpretation of the excellent correlations between RSoXS measurements and BHJ solar cell device performance, while highlighting the potential of forward simulation approaches to leverage the full information content of energy-dependent RSoXS measurements.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3529-3545"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707792","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":"Tuning Excited-State Charge Transfer Character in Cofacial Core-Substituted Perylenediimide Dimers.","authors":"Samuel B Tyndall, Jonathan R Palmer, Nikolai A Tcyrulnikov, Ryan M Young, Michael R Wasielewski","doi":"10.1021/acs.jpcb.5c00617","DOIUrl":"10.1021/acs.jpcb.5c00617","url":null,"abstract":"<p><p>Understanding the interplay between excimer formation and symmetry-breaking charge separation is important for optimizing charge separation in organic photovoltaic materials. To explore this connection, we synthesized four 1,6,7,12-tetrakis(<i>p</i>-X-phenoxy)perylene-(3,4:9,10)-bisdicarboximide cofacially stacked dimers, where X = MeO, <i>tert</i>-butyl, Br, and CF₃. Steady-state spectroscopy reveals H-type aggregation and excimer formation in all four dimers, while transient absorption spectroscopy shows relatively small changes in their excited-state absorptions. However, time-resolved fluorescence (TRF) spectroscopy shows that relaxation occurs from an initial Frenkel exciton-dominated excimer state to one in which charge transfer (CT) character contributes. Relaxation to the lower-lying state with CT character is attributed to a combination of structural and charge distribution changes elicited by varying the substituents. This study illustrates how subtle changes in charge distribution and structure can combine to influence the excited state dynamics that influence charge separation in molecular dimers.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3454-3463"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707795","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":"Cryo-Raman Observation on the Photocycle of a Light-Driven Cl^- Pump from <i>Mastigocladopsis repens</i> at High Cl^- Concentration.","authors":"Kana Miyazaki, Takashi Kikukawa, Masashi Unno, Tomotsumi Fujisawa","doi":"10.1021/acs.jpcb.4c08322","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08322","url":null,"abstract":"<p><p>A retinylidene photoreceptor from the cyanobacterium <i>Mastigocladopsis repens</i> (<i>Mr</i>HR) is a novel type of light-driven Cl^- pump that has a structural similarity to the archaeal H⁺ pumps but transports Cl^-. An open question regarding the photocycle of this photoreceptor involves the role of a late red-shifted photoproduct, the O intermediate, which is reportedly present at high Cl^- concentrations. In this study, we used cryo-Raman spectroscopy to examine the chromophore structures of the photointermediates at a high Cl^- concentration. When compared to the photointermediates formed as <i>Mr</i>HR + <i>hv</i> → K → L → N1 → N2 → <i>Mr</i>HR' at a low Cl^- concentration, we found that N2 kinetically disappears at a high Cl^- concentration. This indicated that N2 is the transient Cl^--unbound state of <i>Mr</i>HR. In addition, we found that no Raman signal of the O intermediate is observed at the high Cl^- concentration, while the signal from N1 is exclusively observed in the later stages of the photocycle. After confirming that N1's absorption spectrum displays an extending red edge, we concluded that the O intermediate is attributable to the red edge of the absorption band of N1. Here, we report a revised understanding of the photocycle for Cl^- transport of <i>Mr</i>HR.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770750","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":"Electrospun Fiber Mats with Metronidazole: Design, Evaluation, and Release Kinetics.","authors":"Olga Adamczyk, Aleksandra Deptuch, Tomasz R Tarnawski, Piotr M Zieliński, Anna Drzewicz, Ewa Juszyńska-Gałązka","doi":"10.1021/acs.jpcb.5c00873","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00873","url":null,"abstract":"<p><p>Novel drug delivery systems (DDSs) strive to eliminate or at least reduce the side effects and limitations associated with conventional medical products. Among the many potential candidates for DDSs, there are one-dimensional micro- and nanostructured materials such as electrospun fibers. In this study, two different polymers, i.e., amphiphilic block copolymer (poly(2-vinylpyridine-<i>co</i>-styrene)) and hydrophobic polymer (polycaprolactone), were utilized as base materials for fibers. Through the electrospinning and coaxial electrospinning techniques, fibers with diverse architectures were obtained, homogeneous or core/shell structures. An antibacterial drug (metronidazole) in varying concentrations was incorporated into the electrospun fibers. The potential application of the obtained electrospun fiber mats is as a dressing for wounds or the treatment of periodontitis. The average diameter of fibers fell within the range of 700-1300 nm, with a drug content of 7-27 wt %. The amorphization or decrease in crystallinity of metronidazole present in the fibers was achieved during the electrospinning process. In vitro drug release tests showed that burst effects can be successfully suppressed, and more sustained release can be accomplished for some formulations. Therefore, electrospun polymer fiber mats are promising candidates for the local delivery of active substances.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770751","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":"Ammonia Binding to the Oxygen-Evolving Complex Probed by High-Energy Resolution Fluorescence Detected X-Ray Absorption Spectroscopy.","authors":"Maria Chrysina, Maria Drosou, Dimitrios A Pantazis, Serena DeBeer","doi":"10.1021/acs.jpcb.5c00269","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00269","url":null,"abstract":"<p><p>The insertion pathways and binding sites of substrate water molecules at the catalytic Mn₄CaO₅ cluster of the oxygen-evolving complex (OEC) in photosystem II (PSII) remain a fundamentally unresolved question toward understanding biological water oxidation. To address this question, small molecules have been employed as \"water analogues\" to probe substrate binding to the OEC. In this context, the binding of ammonia has been extensively investigated and discussed using spectroscopic, structural, and quantum chemical methods, but a definitive answer regarding the ammonia binding site has not yet been achieved. Herein, we present high-energy resolution fluorescence detected (HERFD) Mn K-edge X-ray absorption spectroscopy (XAS) in ammonia-treated S₂ state samples of the OEC. Pre-edge features were correlated with possible structural models with the aid of quantum chemical calculations. The comparison of calculated and experimental difference spectra between the native and ammonia-treated samples allows us to evaluate different modes of ammonia interaction with the OEC. The combined spectroscopic and theoretical investigation suggests the substitution of the terminal water ligand W2 on Mn4 as the most plausible ammonia binding mode, followed closely by the substitution of the second terminal water ligand (W1), and the coordination of ammonia on Mn1 as a sixth ligand. Our results are in line with the leading interpretations of other spectroscopic and kinetic studies, converging on the conclusion that the Mn4 ion is either the most accessible or the strongest binding site for substrate analogues.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770749","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":"Molecular Dynamics Investigation into the Stability of KRas and CRaf Multimeric Complexes.","authors":"Chongli Geng, Juan Zeng, Xianming Deng, Fei Xia, Xin Xu","doi":"10.1021/acs.jpcb.4c08767","DOIUrl":"10.1021/acs.jpcb.4c08767","url":null,"abstract":"<p><p>In the Ras/Raf/MAPK signaling pathway, Ras and Raf proteins interact synergistically to form a tetrameric complex. NMR experiments have demonstrated that Ras dimerizes in solution and binds stably to Raf, forming Ras·Raf complexes. In this study, we constructed the ternary and quaternary complexes of KRas and CRaf based on crystal structures, denoted as (KRas)₂·CRaf and (KRas)₂·(CRaf)₂, respectively. Molecular dynamics (MD) simulations were performed to investigate the stability of these complexes, while hydrogen bonds as well as salt bridges formed at the protein-protein interaction interfaces were analyzed based on simulation trajectories. The results revealed that the KRas·CRaf complex is more stable in explicit solvent compared with the KRas dimer. Formation of the stable quaternary complex (KRas)₂·(CRaf)₂ might be attributed to the association of two binary KRas·CRaf complexes. Additionally, MD simulations of the KRasG12D·CRaf complex revealed a stable and extended binding site at the KRas-CRaf interaction interface. This binding site was identified as a potential therapeutic target to block abnormal signal transmission in the pathway.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3306-3316"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690515","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":"Electrostatic Work Causes Unexpected Reactivity in Ionic Photoredox Catalysts in Low Dielectric Constant Solvents.","authors":"Justin L Ratkovec, Justin D Earley, Max Kudisch, William P Kopcha, Eve Yuanwei Xu, Robert R Knowles, Garry Rumbles, Obadiah G Reid","doi":"10.1021/acs.jpcb.5c01038","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01038","url":null,"abstract":"<p><p>We show that in low dielectric constant (ε_<i>r</i>) solvents, the prototypical cationic photoredox catalyst [Ir(III)(dFCF₃ppy)₂-(5,5'-dCF₃bpy)]⁺ is capable of oxidizing its counterion in an unexpected photoinduced electron transfer (PET) process. Photoinduced oxidation of the tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (abbv. [BAr₄^F]^-) anion leads to its irreversible decomposition and a buildup of the neutral Ir(III)(dFCF₃ppy)₃-(5,5'-dCF₃ bpy^·-) (abbv. [Ir(dCF₃^·-)]⁰) species. The rate constant of the PET reaction, <i>k</i>_<i>rxn</i>, between the two oppositely charged ions was determined by monitoring the growth of absorption features associated with the singly reduced product molecule, [Ir(dCF₃^·-)]⁰, in various solvents with a range of ε_<i>r</i>. The PET reaction between the ions of [Ir(dCF₃) - BAr₄^F] is predicted to be nonspontaneous (Δ<i>G</i>_PET ≥ 0) in high ε_<i>r</i> solvents, such as acetonitrile, and we observe that <i>k</i>_<i>rxn</i> ≃ 0 under these circumstances. However, <i>k</i>_<i>rxn</i> increases as ε_<i>r</i> decreases. We attribute this change in spontaneity to the electrostatic work described by the Born (Δ<i>G</i>_<i>S</i>) and Coulomb (<math><mi>W</mi></math>) correction terms to the change in Gibbs free energy of a PET (Δ<i>G</i>_PET). The electrostatic work associated with these often-neglected corrections can be utilized to design novel and surprising photoredox chemistry. Our facile preparation of [Ir(dCF₃^·-)]⁰ is one example of a general rule: ion-paired reactants can result in energetic neutral products that chemically store photon energy without an associated Coulomb binding between them.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778520","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}