The Journal of Physical Chemistry B最新文献

{"title":"Tribute to Massimo Olivucci","authors":"Nicolas Ferré*,  and , Laura Pedraza-González*, ","doi":"10.1021/acs.jpcb.5c04287","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04287","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 32","pages":"8075–8076"},"PeriodicalIF":2.9,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144826261","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":"Polystyrene-Induced Dehydration of Lipid Membranes: Insights from Atomistic Simulations","authors":"Zeke A. Piskulich,&nbsp;Zeev Rosenzweig and Qiang Cui*,&nbsp;","doi":"10.1021/acs.jpcb.5c03171","DOIUrl":"10.1021/acs.jpcb.5c03171","url":null,"abstract":"<p >Nanoplastics, small plastic particles smaller than microplastics, have been suggested to have a wide-range of unique interactions when they encounter lipid membranes. Recent studies have demonstrated that the smaller size of nanoplastic particles may allow them to penetrate and dissolve in lipid membranes. Following this penetration, however, there is not yet a clear picture of how such particles impact the local lipid environment. A recent study by the present authors found that when lipid vesicles that included laurdan, a fluorescent dye molecule typically thought to report on the membrane phase, were exposed to polystyrene nanoparticles, they exhibited a concentration-dependent blue shift consistent with a fluid-to-gel phase transition. However, coarse-grained simulations suggested that no such transition was taking place; instead, the simulations observed that polymer chains from the polystyrene nanoparticles penetrated into the liposome membrane. In the present work, we use all-atom molecular dynamics simulations to demonstrate that the inclusion of polystyrene within a lipid membrane causes significant changes to the local hydration and structure of that membrane while maintaining the membrane phase. Specifically, through the explicit incorporation of laurdan within the present simulations, we demonstrate that the local hydration environment of the dye molecule changes significantly but continuously as membranes are exposed to polystyrene, thus suggesting a possible explanation for the previously reported experimental observation. The present results provide a picture of the complex heterogeneity generated within polymer-containing membranes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 34","pages":"8724–8731"},"PeriodicalIF":2.9,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144853953","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":"Transition and Regulation of MicroRNA Let-7a Conformation at the Membrane Interface by Different Ionic Solutions","authors":"Yulu Du,&nbsp;Chao Zhu,&nbsp;Haoyu Xiao,&nbsp;Dongqi Liu,&nbsp;Jiawei Zhang,&nbsp;Wenhui Li,&nbsp;Wangting Lu,&nbsp;Hongjuan Zhang and Feng Wei*,&nbsp;","doi":"10.1021/acs.jpcb.5c01379","DOIUrl":"10.1021/acs.jpcb.5c01379","url":null,"abstract":"<p >The Lethal 7 (Let-7) miRNA family is attracting more and more attention in recent decades due to its capability in post-transcriptional regulation and the modulation of various physiological and pathological processes. Yet, the underlying mechanism that controls the conformation and biofunctions of Let-7 molecules during their translocation in and out of the cell membrane is still elusive. In the present study, the sum frequency generation vibrational spectroscopy (SFG-VS), a second-order nonlinear spectroscopic technique, was applied to examine the interfacial behavior of Let-7a at the lipid membrane interface. By creating the lamellar membrane environment <i>in vitro</i> with different ionic solutions, we were able to capture conformational changes in the Let-7a molecule based on the SFG spectra collected from the membrane interface after the miRNA-membrane interaction. Our results indicate that the ribose guanosine (rG) residues and ribose uridine (rU) residues of the Let-7a molecule show versatile changes as the concentration of ionic solutions increases. The analysis results also indicate that the hydrogen-bonding networks around the Let-7a molecules are greatly changed by the salt as the concentration of the NaCl and CaCl₂ solutions increases. As NaCl and CaCl₂ solution concentrations rose during experiments, we noted a marked reconfiguration of the hydrogen-bonding network around Let-7a molecules, driven by strengthened interactions between salt ions, water molecules, and Let-7a’s functional groups, disrupting the original network and altering its connectivity/stability. This research offers valuable molecular-level insights into the salt-dependent conformation and behavior changes of miRNA at the lamellar lipid membrane interface. These findings also provide new perspectives for miRNA-related therapy and may help researchers in the improvement of innovative and pertinent drug delivery systems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 34","pages":"8712–8723"},"PeriodicalIF":2.9,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144853955","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":"Massimo Olivucci: A Scientific Autobiography","authors":"Massimo Olivucci*,&nbsp;","doi":"10.1021/acs.jpcb.5c04288","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04288","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 32","pages":"8077–8086"},"PeriodicalIF":2.9,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144826260","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 Simulations of Supercooled Aqueous Solutions of Calcium Perchlorate: Thermodynamics and Structure of Martian Solutes in TIP4P/2005 Water","authors":"Paolo La Francesca,&nbsp; and ,&nbsp;Paola Gallo*,&nbsp;","doi":"10.1021/acs.jpcb.5c03712","DOIUrl":"10.1021/acs.jpcb.5c03712","url":null,"abstract":"<p >We employ molecular dynamics simulations to determine how calcium perchlorate modifies the phase diagram and structure of supercooled TIP4P/2005 water. These solutions are particularly relevant in light of recent experimental evidence of liquid water in perchlorate solutions underneath Martian soil. We focus on the interplay between its low-density liquid (LDL) and high-density liquid (HDL) phases, simulating solutions at concentrations of 3.15 and 25.7 wt%. Thermodynamic analysis confirms the persistence of several water anomalies, albeit shifted by the solutes. A second-order liquid–liquid critical point (LLCP) is observed at a concentration of 3.15 wt%. Structurally, radial distribution functions demonstrate that upon increasing the solute concentration, the HDL-like behavior is enhanced, as the thermodynamic LDL-like region appears to be shrinking. Calcium ions with perchlorate ions in water appear to be particularly effective at favoring supercooling.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 34","pages":"8776–8787"},"PeriodicalIF":2.9,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c03712","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144853952","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":"A Unilamellar Crystalline Haze-Forming Phase of Methyl-Branched Isomerized High-Molecular-Weight Alkanes","authors":"Eric B. Sirota*,&nbsp;","doi":"10.1021/acs.jpcb.5c03166","DOIUrl":"10.1021/acs.jpcb.5c03166","url":null,"abstract":"<p >A new phase of wax is reported, formed from long randomly methyl-branched alkyl-chain molecules with sufficiently long unbranched runs. These are unilamellar monomolecular thin crystalline sheets, which stack into layered structures but are not laterally correlated between layers and will swell in the presence of a solvent. The structures are related to crystalline lamellae in semicrystalline polymers. The molecules were formed by isomerization of the heavy fraction of <i>n</i>-alkanes derived from Fischer–Tropsch synthesis. This wax comes out of solution as a kinetically slow-forming haze at temperatures well above the cloud-point. X-ray, neutron, and light scattering studies, along with compositional analysis and calorimetry, characterized its properties. Solution theory using a variable pseudocomponent method was employed to explain its equilibrium and kinetic crystallization behavior. Observations of some other waxes that swell are also reported.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 34","pages":"8806–8820"},"PeriodicalIF":2.9,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843866","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":"Conformation-Dependent Binding Affinity of Small Molecules to Aβ42 Fibrils: Mechanistic Insights into Tracer Design","authors":"Mengke Jia,&nbsp;Zijian Liu,&nbsp;Xiang Fan,&nbsp;Sajjad Ahmad,&nbsp;Zhi Wang,&nbsp;Xueying Zhu* and Hongqi Ai*,&nbsp;","doi":"10.1021/acs.jpcb.5c04444","DOIUrl":"10.1021/acs.jpcb.5c04444","url":null,"abstract":"<p >The β-amyloid (Aβ) deposits in Alzheimer’s disease (AD) are primarily composed of Aβ42-derived fibrils, and Aβ42 fibrils exhibit polymorphism with diverse molecular structures. While small-molecule-based targeting strategies have achieved phased progress in AD diagnosis and treatment, the distribution and quantity of binding sites on Aβ42 fibrils, as well as the dynamic interaction mechanisms between these sites and different tracers, remain unclear. Additionally, the binding efficacy of small molecules to Aβ42 fibrils with distinct structures and their conformational dependence have not yet been elucidated. In this study, five novel ligands were selected as tracers to investigate their interactions with four representative Aβ42 fibril conformations. The results demonstrated significant differences in the capacities of these molecules to bind Aβ fibrils with varying conformations, revealing a pronounced conformation-dependent relationship. Notably, small molecule <b>1</b> (<b>SM1</b>) and <b>SM3</b> exhibited robust binding affinities across all four Aβ fibril conformations, highlighting their potential as tracers. Furthermore, the binding sites of the υ-type (8EZE) Aβ fibril accommodating small molecules were first identified, and U-type (2BEG), S-type (2NAO), and LS-type (5OQV) Aβ fibrils were found to align with the ones reported previously for other ligands. Notably, strongly bound molecules induce structural deformation of the fibril. These findings provide critical insights for the rational design and modification of existing Aβ42 fibril-targeting ligands, facilitating the development of tracers with enhanced specificity and selectivity.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 34","pages":"8700–8711"},"PeriodicalIF":2.9,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843810","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":"Photobasicity-Triggered Twisted Intramolecular Charge Transfer of Push–Pull Chromophores","authors":"Austin Pounder,&nbsp;Matteo Pavlovic,&nbsp;Darren Chow,&nbsp;Keenan T. Regan,&nbsp;Aicheng Chen*,&nbsp;Stacey D. Wetmore* and Richard A. Manderville*,&nbsp;","doi":"10.1021/acs.jpcb.5c03367","DOIUrl":"10.1021/acs.jpcb.5c03367","url":null,"abstract":"<p >Fluorogenic probes that undergo excited-state proton transfer (ESPT) and twisted intramolecular charge transfer (TICT) offer tunable fluorescence properties for bioimaging and sensing applications. However, the relationship between ESPT and TICT remains poorly understood in push–pull chromophores. Despite extensive research on photoacids, photobases remain underutilized as fluorescence modulators, and the roles of solvent polarity, acidity, and donor–acceptor strength in governing photobasicity and TICT activation are not well established. We conducted photophysical experiments and (TD)-DFT calculations to explore how protonation and solvent interactions influence fluorescence behavior. Our findings reveal that while protonation consistently induces red-shifted absorption and emission, ESPT efficiency and TICT formation vary widely depending on molecular structure and solvent environment. This work provides new insights into photobasicity-driven fluorescence modulation, offering a foundation for designing next-generation probes with enhanced sensitivity to local acidity, viscosity, and microenvironmental factors.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 33","pages":"8485–8493"},"PeriodicalIF":2.9,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833503","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":"Thermal Behavior and Local Structural Organization in Curcumin Polymorphs’ Bulk Phase: A Molecular Dynamics Simulation Analysis","authors":"Artem Shagurin,&nbsp;Michael G. Kiselev,&nbsp;Pal Jedlovszky,&nbsp;Natalia T. Correia,&nbsp;Frederic Affouard and Abdenacer Idrissi*,&nbsp;","doi":"10.1021/acs.jpcb.5c04240","DOIUrl":"10.1021/acs.jpcb.5c04240","url":null,"abstract":"<p >Curcumin (CUR), a bioactive compound with known polymorphism, exhibits distinct conformational and thermophysical properties across its three crystalline forms. In this study, we employ molecular dynamics simulations to investigate the thermal behavior, local structural organization, and polymorph-specific stability of CUR in the bulk phase. We first evaluate four widely used classical force fields (OPLS-AA, CGENFF, GAFF2, and GROMOS) against experimental melting points, densities, and conformational preferences, identifying OPLS-AA as the most suitable one. Through targeted reparametrization of intramolecular dihedral angles based on DFT benchmarks, we significantly improve the ability of this force field to reproduce conformational distributions and melting transitions. Using the refined model, we characterize the temperature dependence of several structural observables, including local density (via Voronoi tessellation), nearest-neighbor distributions, pair interaction energies, hydrogen bonding, and molecular orientation. Our results reveal that conformational transitions, packing rearrangements, and fluctuations occur cooperatively near polymorph-specific temperatures, often beginning with disrupted π–π stacking and propagating through the lattice. Notably, cooling simulations fail to induce recrystallization, resulting in amorphous states. This comprehensive analysis highlights the critical interplay between molecular conformation, packing, and directional interactions in determining CUR’s polymorphic behavior, providing a mechanistic foundation for controlling phase transitions in flexible molecular solids.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 33","pages":"8615–8625"},"PeriodicalIF":2.9,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833504","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":"Systematic Investigation of the Liquid–Liquid Phase Separation Propensity of Intrinsically Disordered Proteins by Molecular Simulations","authors":"Zixin Hu,&nbsp;Tiedong Sun,&nbsp;Lars Nordenskiöld and Lanyuan Lu*,&nbsp;","doi":"10.1021/acs.jpcb.5c02419","DOIUrl":"10.1021/acs.jpcb.5c02419","url":null,"abstract":"<p >Liquid–liquid phase separation (LLPS) has been intensively studied since P-granules in <i>Caenorhabditis elegans</i> drew the attention of researchers. Decades of studies have revealed that intrinsically disordered proteins or regions (IDP/Rs) are closely related to phase-separating (PS) proteins, and their multivalency is instrumental to the LLPS propensity. Here, we constructed a comprehensive database of PS and non-PS IDPs and introduced a framework to calculate the exact value of multivalence with molecular dynamics (MD) simulations. Also, we examined the correlation of the calculated multivalence to LLPS. Results show that the simulation-based classification of the LLPS propensity can achieve high consistency with experimental observations despite varying experimental conditions. Besides, inspired by a graph theoretical approach, we determined a recommended cutoff of multivalence for effectively differentiating IDPs with a high LLPS propensity. Last, studies on the role of amino acid types in the fused in sarcoma (FUS) protein and its mutants reveal context-dependent interactions in prion-like and RNA-binding domains. Our work deepens the understanding of LLPS and provides a cost-effective computational framework for studying LLPS for IDPs.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 33","pages":"8299–8317"},"PeriodicalIF":2.9,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820168","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}