The Journal of Physical Chemistry B最新文献_第6页

Topology-Dependent Dissociation Kinetics in DNA Tetrahedron Assemblies DNA四面体组合体的拓扑依赖解离动力学

IF 3.2 2区化学

The Journal of Physical Chemistry B Pub Date : 2026-10-08 Epub Date: 2026-09-28 DOI: 10.1021/acs.jpcb.6c03431

Reza Soheilifard, Marzieh Bagheripour

{"title":"Topology-Dependent Dissociation Kinetics in DNA Tetrahedron Assemblies","authors":"Reza Soheilifard, Marzieh Bagheripour","doi":"10.1021/acs.jpcb.6c03431","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03431","url":null,"abstract":"DNAtetrahedra are versatile programmable nanostructures that canassemble into higher-order architectures through sticky-end hybridization.Here, we use coarse-grained molecular dynamics simulations with theoxDNA model to examine dissociation of hybridized sticky-end linkersin finite linear (1D), looped (2D), and multiply connected (3D) tetrahedronassemblies containing 4–9-bp linkers at 300–330 K. Increasingsticky-end length systematically stabilized linker hybridization,increased hydrogen-bond occupancy, and generally increased the effectiveactivation energy for dissociation. Increasing connectivity suppressedglobal configurational fluctuations but did not monotonically delaythe first linker-opening event. Comparative simulations of isolatedhybridized duplexes further showed that incorporation into tetrahedralframeworks shifts opening times and effective activation energiesin a topology- and linker-length-dependent manner. In particular,the 3D assemblies displayed sequential opening times with the greatesttemporal separation between early and late dissociation events, indicatingthat the kinetic environment of the remaining linkers evolves as connectivityis progressively lost. Overall, the results demonstrate that networktopology regulates linker dissociation through an interplay betweenlocal hybridization energetics, configurational constraints, and topology-dependentstructural reorganization rather than through simple monotonic stabilizationwith increasing connectivity.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 40","pages":"10403–10417"},"PeriodicalIF":3.2,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149130635","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

Topological Engineering of Perylene Diimide-Based Metallacycles through Multicomponent Self-Assembly for Fluorescence Sensing of Picric Acid 基于苦味酸荧光传感的苝酰二亚胺基金属环的多组分自组装拓扑工程

IF 3.2 2区化学

The Journal of Physical Chemistry B Pub Date : 2026-10-08 Epub Date: 2026-09-10 DOI: 10.1021/acs.jpcb.6c04747

Yingjie Li, Yali Hou, Shijin Jian, Haonan Peng, Zhaohui Wang, Mingming Zhang

{"title":"Topological Engineering of Perylene Diimide-Based Metallacycles through Multicomponent Self-Assembly for Fluorescence Sensing of Picric Acid","authors":"Yingjie Li, Yali Hou, Shijin Jian, Haonan Peng, Zhaohui Wang, Mingming Zhang","doi":"10.1021/acs.jpcb.6c04747","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c04747","url":null,"abstract":"Therational construction of discrete supramolecular architectureswith controlled topological complexity remains a significant challengein coordination-driven self-assembly. Herein, we report a modularmulticomponent self-assembly strategy for the construction of a homologousseries of perylene diimide (PDI)-based fluorescent metallacycles withprogressively increasing structural complexity. By simply varyingthe geometry and connectivity of auxiliary carboxylate ligands, discretemonocyclic, bicyclic, and tricyclic metallacycles were successfullyassembled and characterized by nuclear magnetic resonance spectroscopy,electrospray ionization mass spectrometry, and single-crystal X-raydiffraction. Photophysical and frontier-orbital analyses reveal thatthese metallacycles retain strong PDI-centered absorption and highfluorescence quantum yields of 69.5–81.4%, while the tricyclicmetallacycle displays a distinct donor–acceptor-type orbitalseparation. Furthermore, these metallacycles exhibited efficient fluorescencesensing toward picric acid, with the tricyclic metallacycle showingthe highest sensitivity with a detection limit of 2.3 μmol/L.This work demonstrates that topological engineering through multicomponentcoordination-driven self-assembly provides an effective strategy fordeveloping structurally sophisticated fluorescent supramolecular sensors.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 40","pages":"10609–10618"},"PeriodicalIF":3.2,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149124691","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

High-Performance Prediction of Thermodynamic Property of NaNO3–NaCl–NaF Molten Salt by Deep Potential Molecular Dynamics Simulation for High-Temperature Thermal Application 高温热应用中NaNO3-NaCl-NaF熔盐热力学性质的深势分子动力学模拟

IF 3.2 2区化学

The Journal of Physical Chemistry B Pub Date : 2026-10-08 Epub Date: 2026-09-24 DOI: 10.1021/acs.jpcb.6c04441

Heqing Tian, Xianyou Lan, Tianyu Liu

{"title":"High-Performance Prediction of Thermodynamic Property of NaNO3–NaCl–NaF Molten Salt by Deep Potential Molecular Dynamics Simulation for High-Temperature Thermal Application","authors":"Heqing Tian, Xianyou Lan, Tianyu Liu","doi":"10.1021/acs.jpcb.6c04441","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c04441","url":null,"abstract":"Nitrate molten salts are widely appliedin concentratingsolarpower due to their excellent thermodynamic properties. However, conventionalexperimental methods struggle to accurately measure the thermodynamicproperties of molten salts and thoroughly analyze their microscopicstructures. The deep potential molecular dynamics (DPMD) method providesa novel approach for investigating the structures and thermodynamiccharacteristics of molten salts. By integrating machine learning (ML)with the deep potential GENerator (DP-GEN) active learning algorithm,we developed a high-fidelity interatomic potential function of NaNO3–NaCl–NaF molten salt. The structure and thermodynamicproperties of the molten salt were systematically explored, and theinfluence of temperature on these characteristics was elucidated.The results show that the elevated temperature changes the interionicdistances and the interionic forces. The increase in temperature leadsto a decrease in the coordination number and a reduction in the energybarrier, making it easier for ions to detach from the central ion,thereby enhancing the ion migration ability in molten salts. The simulateddensity and specific heat capacity show excellent consistency withthe experimental results, with relative errors of 2.11% and 0.45%,respectively. When the temperature rises from 573 to 773 K, the simulatedviscosity reduces from 2.803 to 1.526 mPa·s, while thermal conductivitydeclines from 0.576 to 0.504 W/(m·K). Combining deep potentialmolecular dynamics with the DP-GEN active learning algorithm, thisstudy provides an efficient approach to predict the thermodynamicproperties of molten salt thermal energy storage materials.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 40","pages":"10591–10600"},"PeriodicalIF":3.2,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149124927","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

Speed Limits on Biomolecular Processes from Fundamental Physical Constants 从基本物理常数看生物分子过程的速度限制

IF 3.2 2区化学

The Journal of Physical Chemistry B Pub Date : 2026-10-08 Epub Date: 2026-09-23 DOI: 10.1021/acs.jpcb.6c04792

Dmitrii E. Makarov

引用次数: 0

Transmembrane Coupling of Protein Condensates via Membrane-Mediated Interactions: A Simulation Study 蛋白质凝聚物通过膜介导的相互作用的跨膜偶联：模拟研究

IF 3.2 2区化学

The Journal of Physical Chemistry B Pub Date : 2026-10-08 Epub Date: 2026-09-29 DOI: 10.1021/acs.jpcb.6c04719

B. Rusen Argun, Jeanne Stachowiak, Pengyu Ren

{"title":"Transmembrane Coupling of Protein Condensates via Membrane-Mediated Interactions: A Simulation Study","authors":"B. Rusen Argun, Jeanne Stachowiak, Pengyu Ren","doi":"10.1021/acs.jpcb.6c04719","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c04719","url":null,"abstract":"Recent experimentsshow that protein condensates sitting on oppositesurfaces of a flat lipid membrane move together and prefer to overlap,even though they cannot touch each other. This points to an indirect,membrane-mediated interaction. Two mechanisms could be responsible:a curvature-induced interaction, which is energetic in origin, anda fluctuation-induced interaction, which is entropic. Here we studyboth with coarse-grained molecular dynamics simulations, using Cooke’simplicit-solvent lipid model together with a generic bead–springpolymer model for the condensate. We compute the potential of meanforce between two condensates across the membrane. For condensatesof the same size, full overlap is unfavorable, and the pair insteadsettles into a partially overlapping state that bends the membraneinto an S-like shape. When the two condensates differ strongly insize, full overlap becomes favorable. We explain this with a simplegeometric picture. The condensate wets the membrane as a thin filmand imposes curvature only along its rim, while membrane tension flattensthe membrane under its interior. The resulting ring of curvature cantrap a smaller condensate on the opposite side. We also compare thebending undulations and the effective bending modulus of a bare membrane,a membrane with one condensate, and a membrane with condensates onboth sides. A wetting condensate suppresses the undulation modes andstiffens the membrane, but whether this makes overlap entropicallyfavorable remains inconclusive. Our results indicate that the couplingis driven mainly by curvature, and that it depends on the wettingmechanism and on the membrane tension.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 40","pages":"10506–10518"},"PeriodicalIF":3.2,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149125001","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

Protein Breathing Induces Non-Markovian Buried Ring-Flip Dynamics in Cytochrome C 蛋白质呼吸诱导细胞色素C的非马尔可夫埋藏环翻转动力学

IF 3.2 2区化学

The Journal of Physical Chemistry B Pub Date : 2026-10-08 Epub Date: 2026-09-25 DOI: 10.1021/acs.jpcb.6c04066

Bikirna Roy, Arnab Mukherjee

引用次数: 0

Modified Ewald Summation Method for Slab Geometries: Application to Donnan Potentials, Confinement Electrostatics, and Titration Simulations 板状几何的修正Ewald求和法：在Donnan电位、约束静电学和滴定模拟中的应用

IF 3.2 2区化学

The Journal of Physical Chemistry B Pub Date : 2026-10-08 Epub Date: 2026-09-23 DOI: 10.1021/acs.jpcb.6c05163

Yan Levin, Amin Bakhshandeh

{"title":"Modified Ewald Summation Method for Slab Geometries: Application to Donnan Potentials, Confinement Electrostatics, and Titration Simulations","authors":"Yan Levin, Amin Bakhshandeh","doi":"10.1021/acs.jpcb.6c05163","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c05163","url":null,"abstract":"Simulating electrochemical systems confined within nanoscaleslabgeometries is a major challenge due to long-range electrostatic interactionsand the breakdown of global charge neutrality when the domain exchangesions with an external bulk electrolyte reservoir. In this work, wepresent a grand-canonical simulation framework designed for slab geometriesthat utilizes a regularized 3D periodic Ewald summation techniqueto systematically converge to the true 2D periodic Green’sfunction without unphysical cell-width (Lz) dependencies. Unlike traditional grand canonicalmethods that rely on neutral-pair insertions to maintain a zero netcharge, our framework allows the net cell charge to fluctuate by implementingdecoupled, single-ion trial moves. This approach bypasses the cooperativesampling bottlenecks that plague neutral-pair insertions inside dense,strongly charged nanopores. Crucially, the method allows us to calculatethe Donnan potential (φD) inside the cell, whichcannot be accessed directly by any other available simulation method.The Donnan potential acts as a direct microscopic analog to the electromotiveforce (emf) of a nanoscale electrochemical cell, making the methoduniquely suited for iontronic and nanofluidic applications where nonidealion–ion correlations and strong inhomogeneities modify devicepotentials. The methodology is validated against exact solutions ofthe nonlinear Poisson–Boltzmann equation, demonstrating excellentagreement for both local ionic density profiles and self-consistentpotentials. Finally, we demonstrate the utility of this frameworkby simulating charge regulation and surface titration of weak acidicgroups at the pore wall.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 40","pages":"10792–10803"},"PeriodicalIF":3.2,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149124848","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

Anomalous Increase of Sum-Frequency Signal from a Cationic Langmuir Monolayer upon Salt Addition 盐加入后阳离子Langmuir单层和频信号的异常增加

IF 3.2 2区化学

The Journal of Physical Chemistry B Pub Date : 2026-10-08 Epub Date: 2026-09-30 DOI: 10.1021/acs.jpcb.6c03423

Sokhuoy Sam, Sona Krem, Doseok Kim

{"title":"Anomalous Increase of Sum-Frequency Signal from a Cationic Langmuir Monolayer upon Salt Addition","authors":"Sokhuoy Sam, Sona Krem, Doseok Kim","doi":"10.1021/acs.jpcb.6c03423","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03423","url":null,"abstract":"Ions in water near the interface create an electricaldouble layer,in which counterions are attracted, while co-ions are repelled fromthe interface. Adding salt to the subphase water is always expectedto decrease the electric field in the electrical double layer as increasedcounterions screen the surface charge more effectively. We discovereda phenomenon contrary to this common belief in a cationic Langmuirmonolayer upon addition of fluoride salts. A Langmuir monolayer consistingof DPTAP (1,2-dipalmitoyl-3-trimethylammonium-propane chloride) atdifferent concentrations of alkali-metal fluoride salts (LiF, NaF,KF, RbF, and CsF) in the subphase water was investigated by sum-frequencyvibrational spectroscopy (SFVS). The OH signal from interfacial watermolecules increased upon addition of NaF and LiF, reached a maximumsignal (about twice that from pure water) at ∼100 μM,and decreased afterward. This phenomenon was explained by the actionof Li+ and Na+ co-cations that bind effectivelywith the ubiquitous bicarbonate (HCO3–) anions at neutral pH and remove these counterions that initiallyscreen the positively charged headgroups of the DPTAP molecules. Bycontrast, the sum-frequency signal decreased almost monotonicallywith KF addition, indicating that the K+ co-cation cannotcapture these bicarbonate counterions effectively, and this behavioris explained in terms of the higher solubility of KHCO3 as compared to LiHCO3 and NaHCO3. This trendtoward even heavier alkali cations did not continue as RbF and CsFalso showed an increase in the sum-frequency signal, in spite of themonotonic increase of the solubility from LiHCO3 to CsHCO3. This tendency demonstrates that the polarizability and resultingsurface excess of large alkali cations become important at the interface,making them more accessible to the bicarbonate counterions.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 40","pages":"10749–10757"},"PeriodicalIF":3.2,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149125004","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

Unveiling the Molecular Driving Forces of Pollutant Extraction by Hydrophobic Eutectic Solvents 揭示疏水共晶溶剂萃取污染物的分子驱动力

IF 3.2 2区化学

The Journal of Physical Chemistry B Pub Date : 2026-10-08 Epub Date: 2026-09-29 DOI: 10.1021/acs.jpcb.6c04088

Sara Gómez, Usman Ali, Alessia Muroni, Andrea Mele, Maria Enrica Di Pietro, Tommaso Giovannini

{"title":"Unveiling the Molecular Driving Forces of Pollutant Extraction by Hydrophobic Eutectic Solvents","authors":"Sara Gómez, Usman Ali, Alessia Muroni, Andrea Mele, Maria Enrica Di Pietro, Tommaso Giovannini","doi":"10.1021/acs.jpcb.6c04088","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c04088","url":null,"abstract":"Hydrophobic eutectic solvents (HES) are emerging as sustainablealternatives to conventional organic solvents for the extraction ofmolecular pollutants from water. Yet, their selectivity remains poorlyunderstood, hindering the predictive design of eutectic solvents beyondempirical success. Here, we present a multiscale strategy to rationalizeand predict solute partitioning in HES. Focusing on bisphenol A (BPA)in trioctylphosphine oxide (TOPO):menthol as a prototypical system,we combine monophasic and biphasic molecular dynamics with quantumenergy decomposition of dominant solvation motifs. Our methodologycaptures the experimentally measured spontaneous migration of BPAand its thermodynamic stabilization in the HES phase, and it identifiesthe microscopic origin of selectivity: cooperative hydrogen bondingcouples with strong dispersion and polarization in the hydrophobiceutectic microenvironment. The extension of the workflow to a secondexperimentally relevant HES provides additional evidence supportingthe transferability of the mechanistic interpretation and illustratesits potential as a computational framework for the rational screeningand design of HES formulations.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 40","pages":"10571–10581"},"PeriodicalIF":3.2,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149124958","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

Impact of Charge Distribution on the Membrane Binding and Antimicrobial Activity of Cationic Heptapeptides 电荷分布对阳离子七肽膜结合及抗菌活性的影响

IF 3.2 2区化学

The Journal of Physical Chemistry B Pub Date : 2026-10-01 Epub Date: 2026-09-17 DOI: 10.1021/acs.jpcb.6c02992

Jyoti Gangwar, Dipankar Roy, Vignesh Shanmugam Rajalakshmi, Priyadarshi Satpati, Sunanda Chatterjee

{"title":"Impact of Charge Distribution on the Membrane Binding and Antimicrobial Activity of Cationic Heptapeptides","authors":"Jyoti Gangwar, Dipankar Roy, Vignesh Shanmugam Rajalakshmi, Priyadarshi Satpati, Sunanda Chatterjee","doi":"10.1021/acs.jpcb.6c02992","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c02992","url":null,"abstract":"Antimicrobial peptides (AMPs) hold immense potentialin combatingcommunity-acquired and MDR infections. The therapeutic efficiencyof AMPs depends on their various physicochemical properties. We investigatedhow the hydrophobic–hydrophilic landscape of tryptophan-containingcationic heptapeptides (CAMPs) influenced their ability to bind tomicrobial membranes and their antimicrobial effectiveness againstseveral ESKAPE pathogens. We found that charge delocalization overthe peptide backbone enhanced antimicrobial activity, while chargelocalization at the C- and N-termini reduced efficacy (1.5-2.7 folds)for both the single and double tryptophan peptides. The double-tryptophanpeptide P32* had increased activity over the single tryptophan peptideP32 (∼2.3 fold), and alleviated the effect of charge segregationon activity. Using steered molecular dynamics umbrella sampling simulations,we evaluated the peptides based on their affinity (ΔG) for a membrane-mimetic bilayer model of Pseudomonas aeruginosa. Peptides with higher membrane-bindingaffinity exhibited greater antimicrobial potency. All peptides exhibitednegligible hemolytic activity (HC10% ≤ 10 μM)and retained membranolytic antibacterial activity. The calculatedbinding free energies of the peptide(s) and the bilayer exhibiteda strong linear correlation with the experimental minimum inhibitoryconcentration (MIC) values, with a negative slope. More favorablebinding free energies (i.e., more negative values) corresponded tolower MICs, as stronger interactions with the membrane enhanced themembranolytic properties of these peptides. We demonstrated that integratingmolecular simulations with experimental validation enables the useof membrane-binding free energy as a quantitative predictor of peptideactivity. This approach provides a rational framework for the futuredesign and optimization of membrane-active CAMPs.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 39","pages":"10244–10255"},"PeriodicalIF":3.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149093548","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