The Journal of Physical Chemistry B最新文献

{"title":"Can Electrostatic Solvation Entropy Predict Skin Irritation Potential from Surfactants?","authors":"Sundas Khan Farooq, Manori Jayasinghe","doi":"10.1021/acs.jpcb.5c04440","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04440","url":null,"abstract":"<p><p>Surfactants are essential in industrial and biological applications, but their interactions with biological systems, particularly skin, often lead to irritation. Understanding the molecular determinants of surfactant-induced skin irritation requires a detailed analysis of the solvation thermodynamics. In this study, we employ all-atom free energy perturbation molecular dynamics (FEP/MD) simulations to investigate the solvation free energy and entropy of sodium lauryl ether sulfate (SLES) surfactants with varying ethoxylate spacer lengths C₁₂H₂₅(OCH₂CH₂)_<i>x</i>OSO₃Na (where <i>x</i> = 1-3). The solvation free energy is partitioned into van der Waals (vdW) and electrostatic contributions, revealing that (1) vdW interactions become increasingly unfavorable with longer hydrophobic spacers due to entropic penalties for water ordering; (2) electrostatic contributions dominate solvation and grow more favorable with extended ethoxylation, driven by charge delocalization and reduced water structuring around headgroups. Temperature-dependent analyses show that electrostatic solvation entropy becomes less negative with longer spacers, indicating a chaotropic (water-structure-breaking) effect. This trend correlates with experimental observations of a reduced critical micelle concentration (CMC) and attenuated skin irritation, supporting the monomer penetration theory. Our results suggest that electrostatic entropy serves as a predictive descriptor for skin irritation potential, providing a molecular framework for designing milder surfactants. These insights bridge computational thermodynamics with practical applications in personal care and pharmaceutical formulations.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190457","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":"How Dissolved Gas and High-Intensity Ultrasound Are Coupled to Affect Bubble Cavitation.","authors":"Jiaohui Hu, Youbin Zhou, Baoyun Ye, Jing Li, Xianren Zhang","doi":"10.1021/acs.jpcb.5c05717","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c05717","url":null,"abstract":"<p><p>Bubble cavitation plays a pivotal role in various ultrasound applications, but ultrasound-induced cavitation poses a challenge to our present understanding. Here, we employ both theoretical analysis and molecular dynamics simulations to study the dissolved gas-enhanced cavitation and subsequent evolution of nanoscale cavitating bubbles under high-intensity ultrasound. The simulation results reveal that dissolved gas indeed promotes the formation of cavitating bubbles, which strongly interact with the applied ultrasound. First, the bubble formation causes a significant distortion of the surrounding acoustic field, especially weakening the negative pressure during the negative pressure phase of the ultrasound. Second, the ultrasonic amplitude and frequency, along with the type of dissolved gas, affect bubble evolution via interface-crossing gas transfer. Different responses of CO₂ and CH₄ bubbles to the exerted ultrasound are interpreted by the liquefaction of CO₂ molecules in nanoscale bubbles, the relatively low solubility of CH₄, and the lagging of gas molecule transfer behind the pressure variation.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197366","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":"Energy Barriers of Peptide Translocation in Nanopores: Insights from MD Simulations.","authors":"Jinyang Zhu, Jilong Zhang, Pengyin Zhang, Hao Zhang, Song Wang","doi":"10.1021/acs.jpcb.5c04924","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04924","url":null,"abstract":"<p><p>Solid-state nanopores offer label-free protein sensing potential, but rational design is hindered by limited quantitative understanding of pore geometry's impact on translocation energetics. To address this, the influence of Si₃N₄ nanopore thickness and radius on a model peptide's translocation free energy landscape was systematically examined via all-atom molecular dynamics simulations and potential of mean force calculations. Close matching between pore thickness and the peptide's maximum extended length was found to induce significant conformational entropy loss and desolvation energy barriers, yielding a peak free energy barrier. During peptide translocation, a critical pore radius was identified, at which an anomalous surge in the energy barrier was observed. This \"critical matching effect\" forces the peptide into a highly ordered, stretched conformation, triggering substantial entropy penalties, hydration shell stripping, and moderate electrostatic interactions, thereby forming a distinct \"most unfavorable conformation window\". The free energy barrier height is determined by the tripartite coupling of conformational freedom, solvent accessibility, and charge interactions. Consequently, a \"geometry-conformation matching\" nanopore design paradigm is proposed, enabling targeted free energy barrier enhancement through precise dimensional matching for intelligent protein sieving and signal modulation. This mechanism establishes a universal theoretical foundation for optimizing next-generation nanopore sensors and biomolecular separation membranes while pioneering new pathways for manipulating biomolecular transport in nanoconfined spaces, with significant implications for precision diagnostics and targeted drug delivery.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184299","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":"Insights from Void Volumes and Hydration Dynamics on Protein Spontaneous Rupture via Dynamic Internal Impact Forces: Protein Compressibility Changes Under External Piconewton Compressive Force.","authors":"Dedunu S Senarathne, Lalita Shahu, H Peter Lu","doi":"10.1021/acs.jpcb.5c04689","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04689","url":null,"abstract":"<p><p>Mechanical forces play a critical role in modulating the conformational landscape of protein-like biomolecules. Thermal force fluctuation and molecular interaction force fluctuation, under both ambient and physiological conditions, provide a fundamental background for the fluctuation of force vectors in the energy landscape of biomolecules within living cells. The nonlinear compressibility of proteins, a key biophysical property influenced by internal cavities and hydration dynamics, plays a critical role in determining their structural responses to mechanical stress. In this study, we employed all-atom steered molecular dynamics (SMD) simulations to investigate how the internal void volumes and hydration dynamics of the epidermal growth factor receptor (EGFR) change during compressive force-induced tertiary structural rupture, considering EGFR as a model system. Our SMD simulations revealed that the tertiary structure-ruptured state of EGFR exhibits reduced internal cavity volumes, increased surface hydrophobicity, and a more ordered hydration shell while retaining overall surface hydrophilicity, along with shifts in surface electrostatic potential compared to the native structure. Together, these changes suggest enhanced hydration and reduced structural flexibility, indicating that EGFR adopts a mechanically less compressible conformation upon rupture. The identified void volumes and hydration dynamics can contribute to the internal force time-dependent redistribution and internal dynamic impact force that can result in a much smaller static and external compressive force to rupture a protein from the inside-out. The mechanistic understanding obtained from studying EGFR is likely generally applicable to other proteins and protein complexes for their responses and spontaneous ruptures under the external pN compressive force. It is the dynamic and internal structural and force fluctuations under dynamic stress, stiffness, damping, nonlinearity of group displacements, and group velocity and acceleration that result in stochastic and spontaneous ruptures from the inside-out. These results shed light on the mechanical stability and structural responsiveness of proteins under compressive force, providing valuable insights into the development of biomaterials with tunable mechanical properties.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184240","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":"Influence of Co-Solutes and Solvents on Diffusion Interaction Parameters in Multicomponent Solutions: New Insights through the Kirkwood-Buff Theory.","authors":"Jiyoung Yang, Matthias Brosz, Niklas Adebar, Oliver Burkert, Moritz Schulze, Jens Smiatek","doi":"10.1021/acs.jpcb.5c03102","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c03102","url":null,"abstract":"<p><p>We introduce new mathematical expressions for the diffusion interaction parameter in liquid multicomponent solutions. Our theory, which incorporates Kirkwood-Buff integrals, expresses the diffusion interaction parameter as the derivative of the logarithmic solute thermodynamic activity coefficient with respect to solute concentration. Unlike previous approaches, our expressions do not rely on approximations or truncated Taylor series and are tailored differently for binary, ternary, and higher-order solutions. In binary solutions, the resulting expressions indicate that solvation properties primarily govern solute association. In ternary solutions, however, cross-interactions dominate, revealing mechanisms that can either suppress or induce aggregation effects. These findings are supported by experimental data from binary aqueous solutions containing urea and paracetamol, as well as from ternary solutions involving monoclonal antibodies (mAbs) in different formulations. Our results pave the way for the development of tailored formulations that mitigate protein aggregation and enhance shelf life. Overall, the proposed expressions offer a comprehensive framework that integrates diffusive and thermodynamic properties to deepen our understanding of solute behavior and stabilization in complex solution environments.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184274","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":"Insights into Ionic Diffusion in C-S-H Gel Pore from Molecular Dynamics Simulations: Spatial Distributions, Energy Barriers, and Structural Descriptor.","authors":"Weiqiang Chen, Kai Gong","doi":"10.1021/acs.jpcb.5c04534","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04534","url":null,"abstract":"<p><p>Understanding transport behavior in nanoconfined environments is critical to many natural and engineering systems, including cementitious materials, yet its molecular-level mechanisms remain poorly understood. Here, molecular dynamics (MD) simulations were used to investigate Na⁺, Cl^-, and water diffusion inside a 4 nm calcium-silicate-hydrate (C-S-H) pore channel over temperatures ranging from 300 to 360 K. Spatially resolved analysis revealed strong suppression of diffusivity near the solid-liquid interface and gradual recovery toward the pore center. Arrhenius analysis further quantified the spatial variation of activation energy barriers and intrinsic mobilities across the pore channel, showing distinct confinement effects. The spatially resolved structural analysis uncovers a mechanistic transition from structure-controlled to hydrodynamics-controlled transport regimes with increasing distance from the pore surface. A structural descriptor, total coordination strength (TCS), was introduced, providing a predictive link between local liquid structure and molecular mobility within ∼1 nm of the interface. Beyond ∼1 nm, suppressed diffusivities were well captured by an empirical model inspired by the Darcy-Brinkman framework. To the best of our knowledge, this is the first MD study to comprehensively resolve the spatial heterogeneity of transport, thermal kinetics, and structure within cementitious nanopores. These findings deepen the fundamental understanding of nanoscale transport phenomena and suggest that tailoring the nanochannel structure and interfacial chemistry of cementitious gels, e.g., surface coordination environments, pore size distributions, and adsorption sites, may offer a promising strategy to suppress ionic ingress and enhance the durability of cement-based materials.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190425","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":"Extension of Molecular Exchange Monte Carlo for the Prediction of Liquid-Liquid Equilibria in Gibbs Ensemble Monte Carlo Simulations.","authors":"Mohammad Soroush Barhaghi, Loren Schwiebert, Jeffrey J Potoff","doi":"10.1021/acs.jpcb.5c04156","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04156","url":null,"abstract":"<p><p>The Molecular Exchange Monte Carlo (MEMC) algorithm is extended to support the calculation of liquid-liquid equilibria with Gibbs ensemble Monte Carlo (GEMC). The utility of the method is demonstrated through the application of constant-pressure GEMC simulations, using the Transferable Potentials for Phase Equilibria, to predict liquid-liquid coexistence curves for mixtures of perfluoroalkanes + alkanes and dimethyl ether + water. Good qualitative agreement is achieved between the predictions of the simulation and experiment; however, improvements to the intermolecular potentials used are required to achieve quantitative accuracy. Relative acceptance rates for molecule transfers up to 50 times greater than those obtained with standard configurational-bias Monte Carlo are obtained.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184318","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":"Bottom-up Coarse-Grained Models of Asymmetric Membranes.","authors":"Ayan Majumder, Patrick G Sahrmann, Gregory A Voth","doi":"10.1021/acs.jpcb.5c04855","DOIUrl":"10.1021/acs.jpcb.5c04855","url":null,"abstract":"<p><p>Biological membranes are inherently asymmetric, consisting of various lipids and proteins that are heterogeneously distributed between membrane leaflets. The study of spatial heterogeneity in membrane bilayers is of fundamental importance in membrane biophysics. However, the accurate simulation of realistic membranes remains challenging. In all-atom (AA) modeling, the slow diffusion of lipids renders multicomponent bilayer simulations computationally demanding. In coarse-grained (CG) modeling, top-down models have been largely employed for the study of membranes; however, their implementation is not ideal due to the inaccuracies in modeling lipid-lipid and lipid-protein interactions from the point of view of statistical mechanics. In this study, we have constructed a \"bottom-up\" CG model of an asymmetric bilayer, in this case chosen to mimic the HIV-1 virion membrane, by following a systematic statistical mechanical route. The resulting CG model is also found to be transferable for simulating various membrane compositions, effectively capturing the cholesterol condensation effect in which higher cholesterol concentrations induce lipid tail ordering. Using this bottom-up CG model, we demonstrate that in an asymmetric bilayer, cholesterol rapidly moves from a compressed leaflet to an expanded leaflet to reduce membrane stress. The free energy landscape for interleaflet cholesterol movement was calculated in different membrane compositions. In a symmetric bilayer, the cholesterol is found to be equally stable in both leaflets. However, in an asymmetric bilayer, the stability of cholesterol depends on the overall lipid composition of the different leaflets. Overall, this study opens up a new paradigm for the systematic, bottom-up CG modeling of realistic membranes and offers insight into the nature of lipid interactions in an asymmetric bilayer.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12479098/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145172099","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":"Physicochemical Properties and Structure of FLiBeTh Salts: Insights from Machine Learning Accelerated Molecular Dynamics Simulations.","authors":"Yuan Yin, Wenshuo Liang, Shuaiyi Shui, Wentao Zhou, Dezhong Wang","doi":"10.1021/acs.jpcb.5c04764","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04764","url":null,"abstract":"<p><p>LiF-BeF₂-ThF₄ (FLiBeTh) is a promising fuel salt for thorium-based molten salt reactors due to its excellent neutron economy and adjustable properties. However, experiments on such systems remain challenging due to high temperature, corrosiveness, and toxicity. To address these challenges, this study employs molecular dynamics simulations based on a machine learning potential. Using data sets from ab initio calculations and an iterative workflow, a highly accurate machine-learning model was developed, achieving energy and force prediction errors below 1 meV/atom and 50 meV/Å, respectively. This model accurately reproduces the AIMD-predicted radial distribution functions, coordination numbers, and angular distributions. Furthermore, MLMD simulations enabled the exploration of larger-scale or long-term structural characteristics, including coordination shell lifetime, ionic network formation, and physicochemical properties such as density, ionic diffusion, shear viscosity, and thermal conductivity. Results show that increasing ThF₄ concentration promotes the formation of networks composed of Be²⁺, Th⁴⁺, and F^- ions, which significantly reduces ion mobility and changes the physicochemical properties of the molten salts.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147258","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":"Effects of Hydroxylation and Packing Geometry on Tropocollagen Stability: Insights from Molecular Dynamics Simulations.","authors":"Nesreen Alkanakri, Babak Minofar, Michael C Owen","doi":"10.1021/acs.jpcb.5c02935","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02935","url":null,"abstract":"<p><p>Collagen is the most prevalent protein in living organisms, playing diverse roles across multiple tissues. Its hierarchical structure relies on the assembly of tropocollagen, the fundamental building block of collagen fibrils. This assembly occurs in a predominantly random manner, allowing for variations in packing. This randomness can lead to regions of both tight and nontight packing within the fibrils. The mechanisms by which these regions influence collagen's packing configurations, structural organization, and functional properties remain poorly understood. This study provides a focused investigation by comparing tight packing (hexameric) and less tight (heptameric) tropocollagen configurations enriched with proline or hydroxyproline residues using molecular dynamics simulations. The results indicate that the hexameric structures are more stable and uniform because their strands fit together well. This close packing allows for better hydrogen bonding, strengthening their connections. In contrast, adding a seventh strand in the heptameric structures creates asymmetry. This disrupts the hydrogen bonding, leading to weaker connections and a less stable structure. We also found that hydroxyproline-rich systems exhibit greater global mobility due to enhanced water interactions while maintaining local structural rigidity through increased intermolecular hydrogen bonding. In contrast, proline-rich systems display greater flexibility at the residue level but reduced overall molecular movement, indicating a more rigid global structure. This distinction between tropocollagen assemblies and their composition offers invaluable insights into the molecular basis of collagen stability and functionality.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147104","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}