The Journal of Physical Chemistry B最新文献

{"title":"Concentration-Dependent Evolution of the Belousov–Zhabotinsky Reaction as Determined by X-ray Absorption and UV–Vis Spectroscopies","authors":"Francesco Tavani*,&nbsp;, ,&nbsp;Giorgio Capocasa,&nbsp;, ,&nbsp;Marika Di Berto Mancini,&nbsp;, ,&nbsp;Federico Frateloreto,&nbsp;, ,&nbsp;Daniele Del Giudice,&nbsp;, ,&nbsp;Osvaldo Lanzalunga,&nbsp;, ,&nbsp;Stefano Di Stefano,&nbsp;, and ,&nbsp;Paola D’Angelo*,&nbsp;","doi":"10.1021/acs.jpcb.5c04472","DOIUrl":"10.1021/acs.jpcb.5c04472","url":null,"abstract":"<p >Although the Belousov–Zhabotinsky (BZ) chemical reaction has been the object of intense research efforts for almost a century, many aspects of the BZ complex oscillatory behavior still remain to be clarified, also due to difficulties in experimentally monitoring the speciation of the main brominated compounds during the reaction cycles. Herein, we describe an integrated approach based on Br K-edge X-ray absorption and ultraviolet–visible (UV–vis) spectroscopies to identify the onset and evolution of concentration-dependent collective bromine oscillations in the classical BZ reaction. Principal component analysis, multivariate curve resolution, and theoretical X-ray spectroscopy simulations were combined to identify the number, nature, and concentration time evolution of the key reaction brominated species during the chaotic and periodic BZ regimes. Our integrated approach enabled real-time monitoring of how variations in metal catalyst concentration influence both the metal center and key brominated BZ species throughout the different stages of the complex reaction pathway. The multidisciplinary experimental and theoretical approach, sensitive to both the brominated and metal portions of the BZ system, overcomes the challenges in detecting the spectroscopically silent BZ reaction species and may be applied to rationalize a wide range of BZ and non-BZ oscillatory reactions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 41","pages":"10838–10845"},"PeriodicalIF":2.9,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c04472","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211102","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":"Probing Passive Permeation of Tetracycline: Are Simulations Ready for beyond-Rule-of-Five Drug Permeability Calculation?","authors":"Yajing Qi,&nbsp;, ,&nbsp;Christophe Chipot*,&nbsp;, and ,&nbsp;Yi Wang*,&nbsp;","doi":"10.1021/acs.jpcb.5c05445","DOIUrl":"10.1021/acs.jpcb.5c05445","url":null,"abstract":"<p >Passive permeation across lipid membranes is a key determinant of drug bioavailability and efficacy. Accurate computational estimation of drug permeability is essential for rational drug design, yet remains challenging, particularly for ionizable and beyond-Rule-of-Five (bRo5) compounds. In this study, we employ advanced molecular simulations and the inhomogeneous solubility-diffusion model to calculate the effective permeability and elucidate the membrane permeation mechanism of the antibiotic tetracycline (TC), the six hydrogen-bond donors of which violates one of Lipinski’s Rule-of-Five. By integrating the pH-partitioning and Boltzmann-weighted average potential schemes and accounting for both its neutral (TC_N) and zwitterionic (TC_Z) tautomers, we show that the dominant contribution to the effective permeability of TC arises from TC_N, despite its low abundance. This result is attributed to the relatively small permeation barrier of TC_N, explaining why the antibiotic exhibits moderate effective permeability even though it predominantly exists in the zwitterionic form at neutral pH. A further systematic investigation reveals that membrane patch size significantly impacts permeability estimates for TC, in contrast to the relative insensitivity observed for three other permeants. This unique sensitivity can be attributed to the hydrogen-bond network formed between TC and its lipid environment, with the smallest 32-POPC patch artificially raising the drug molecule’s permeation barrier and the largest 256-POPC patch exhibiting significant hysteresis that compromises the quality of the one-dimensional free-energy calculation. Overall, our results suggest that while probing the passive permeation of bRo5 drugs by molecular simulations appears increasingly feasible, the protonation and tautomeric states of the permeants, the uncertainty in their microscopic acid dissociation constants, as well as the potential impact of membrane patch-size effects need to be fully considered in permeability predictions for these complex molecules.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 41","pages":"10810–10823"},"PeriodicalIF":2.9,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c05445","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224683","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":"Photodynamics of Microbial Rhodopsin Mimic M1-L121E: Insights from Computational Modeling","authors":"Yongnan Hu,&nbsp;, ,&nbsp;Yunyu Wang,&nbsp;, ,&nbsp;Siteng Zhao,&nbsp;, ,&nbsp;Jin Dai*,&nbsp;, ,&nbsp;Xubiao Peng*,&nbsp;, and ,&nbsp;Qing Zhao*,&nbsp;","doi":"10.1021/acs.jpcb.5c03243","DOIUrl":"10.1021/acs.jpcb.5c03243","url":null,"abstract":"<p >Understanding the photodynamics of rhodopsin is crucial for elucidating light-induced biological processes. This study investigates the excited-state properties and isomerization dynamics of the microbial rhodopsin mimic protein, focusing on its all-trans (AT) and 13-cis (13C) conformations. By scanning the C13═C14 dihedral angle, we revealed distinct isomerization pathways for the two conformations. In the all-trans conformation, the crossing of S1 and S2 energy levels results in significant electronic state mixing, slowing the isomerization rate and extending the excited-state lifetime. Furthermore, the interaction between the chromophore and the protein varies markedly between the conformations, it is attractive in the 13-cis conformations, but repulsive near the mutation site in the all-trans conformations. These findings suggest that the repulsive force in the all-trans conformations may influence ground-state stability, indirectly affecting the excited-state isomerization process.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 41","pages":"10631–10643"},"PeriodicalIF":2.9,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224710","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":"Bridging Quantum Chemical Predictions of Excitation Energies with Experimental Data for Voltage-Sensitive Fluorescent Dyes","authors":"Patrik Bitó,&nbsp;, ,&nbsp;Zsófia Borbála Rózsa,&nbsp;, ,&nbsp;Zsófia Horváth,&nbsp;, ,&nbsp;Zoltán Mucsi,&nbsp;, ,&nbsp;Levente Cseri,&nbsp;, ,&nbsp;Béla Fiser,&nbsp;, and ,&nbsp;Milán Szőri*,&nbsp;","doi":"10.1021/acs.jpcb.5c03526","DOIUrl":"10.1021/acs.jpcb.5c03526","url":null,"abstract":"<p >Voltage-sensitive dyes (VSDs) are fluorescent molecules that detect changes in the membrane potential, making them invaluable for studying electrical activity in neurons, cardiac cells, and other excitable tissues. They are widely used in neuroscience and physiology to visualize and measure real-time voltage dynamics in cellular networks and whole tissues. VSDs exhibit a high sensitivity to their surrounding environment, which leads to notable solvation relaxation and a substantial Stokes shift upon excitation. Accurate prediction of their fluorescence spectra requires an advanced solvation model that captures these dynamic effects. In this work, we extend the Similarity Transformed Equation-of-Motion Domain-Based Local Pair Natural Orbital Coupled Cluster with Singles and Doubles (STEOM-DLPNO-CCSD) method, a computationally efficient approach for vertical excitation energies, to predict fluorescence spectra for VSDs. While the default perturbative solvation correction at the Hartree–Fock level has proven effective for some excited state calculations, it fails to account for the electron correlation effects that are crucial for accurate fluorescence spectra predictions. To address this, we incorporate a time-dependent density functional theory-based perturbative solvation correction, which improves the accuracy of the methods by better capturing the necessary correlation effects. The methodology is validated through studies of two carefully selected VSDs, (<i>E</i>)-3-(4-(2-(6-(dibutylamino)naphthalen-2-yl)vinyl)pyridin-1-ium-1-yl)propane-1-sulfonate (di-4-ANEPPS) and 4-((<i>E</i>)-4-((<i>E</i>)-4-(diethylamino)-2-methoxystyryl)styryl)-2-(6-(dimethylamino)-3-(dimethyliminio)-3<i>H</i>-xanthen-9-yl)benzenesulfonate (sRhoVR-1). The developed quantum chemical protocol allows for accurate prediction of fluorescence maxima for dyes with a predominant excited state and can accommodate computational constraints without greatly compromising precision. However, the study also highlights the need for further improvements for the prediction of peak intensity, suggesting that explicit solvent models or hybrid quantum mechanics/molecular mechanics (QM/MM) approaches could be valuable for future work. The proposed method provides a powerful tool for the design of VSDs optimized for specific environments and applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 41","pages":"10666–10677"},"PeriodicalIF":2.9,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224726","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":"DNA Conformational Regulation in PDMS Chambers under Low-Concentration Monovalent Ionic Solutions","authors":"Xia Wang,&nbsp;, ,&nbsp;Mingyan Gao,&nbsp;, ,&nbsp;Ying Wang,&nbsp;, ,&nbsp;Fengyan Hou,&nbsp;, ,&nbsp;Jianjun Dong,&nbsp;, ,&nbsp;Jingyu Wang,&nbsp;, ,&nbsp;Ye Li*,&nbsp;, and ,&nbsp;Zuobin Wang*,&nbsp;","doi":"10.1021/acs.jpcb.5c05708","DOIUrl":"10.1021/acs.jpcb.5c05708","url":null,"abstract":"<p >Low concentrations of monovalent alkali metal ions fail to effectively shield the strong electrostatic repulsion between DNA strands, preventing them from approaching and forming entangled structures. This concentration dilemma limits the application of DNA entanglement-dependent programmable assembly strategies in physiologically relevant low-salt environments. To address this challenge, a PDMS chamber with spatiotemporal regulation capabilities was designed, featuring the following. (1) Spatial regulation: The PDMS evaporation chamber suppressed excessive lateral spreading behavior of droplets, thereby preventing nonuniform dispersion and rapid deposition of DNA and ions. Raman results indicated about 18-fold Na⁺ concentration enhancement in evaporation-driven droplets within PDMS chambers before liquid film rupture. (2) Temporal regulation: The liquid phase retention time of a 10 μL droplet was extended to 55–60 min under controlled conditions (22 °C, 55% RH), providing a temporal window for ion-mediated DNA conformational regulation. (3) DNA conformational regulation: Raman analysis revealed that the high-salt microenvironment formed by evaporative concentration in PDMS chambers drove the entanglement of DNA molecules. Atomic force microscopy (AFM) topographies further confirmed denser DNA entanglement networks in PDMS-chambered droplets, with higher surface coverage than those in open-surface droplets. This work presents a strategy for low-concentration monovalent-ion-mediated DNA morphological regulation, with potential applications in microfluidics, biosensing, and programmable nanomaterials.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 41","pages":"10786–10796"},"PeriodicalIF":2.9,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211077","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":"Diffusion of Submicron Particles on Biological Surfactant Monolayers Governed by the Viscoelasticity and Interfacial Dynamics","authors":"Yang Liu*,&nbsp;, ,&nbsp;Xu Zheng*,&nbsp;, ,&nbsp;Weiguo Liang,&nbsp;, ,&nbsp;Feng Gao,&nbsp;, and ,&nbsp;Yinghao Wang,&nbsp;","doi":"10.1021/acs.jpcb.5c04851","DOIUrl":"10.1021/acs.jpcb.5c04851","url":null,"abstract":"<p >The diffusion of microscale and nanoscale particles on biological membranes plays a critical role in understanding various physiologic processes and optimizing drug delivery. In this study, we investigate the diffusive motion of submicron particles on in vitro porcine pulmonary surfactant monolayers at the air–water interface using single-particle tracking. The viscoelastic response of the monolayer becomes apparent only when particle sizes fall below the Saffman and Delbrück length. Hydrodynamic and nonhydrodynamic interfacial dynamics induce distinct anomalous diffusion behaviors for small and large particles, respectively. For smaller particles, their thermal velocities approach the minimum phase velocity of interfacial capillary waves, causing a hydrodynamic wave drag, whose magnitude can be approximately modeled using the sudden accelerated/decelerated rectilinear motion of an object at the interface. In contrast, larger particles do not exhibit wave drag due to their lower thermal velocities. Instead, their displacement correlation functions reveal unusually slow-decaying oscillations─a phenomenon fundamentally stemmed from nanoscale contact-line interfacial dynamics. These oscillations are linked to the diffusion coefficient that varies instantaneously with the particle’s immersion depth. By performing Langevin dynamics simulations of the particle’s perpendicular motion, we confirmed that the oscillation period precisely coincides with the cyclic time of the particle’s motion along the interfacial normal direction. These simulations explicitly account for subtle contact-line perturbations to the interfacial free energy, which arise from nanoscale surface heterogeneity of the particle. This behavior demonstrates strong dynamic coupling between in-plane and out-of-plane particle motions. Crucially, the oscillation amplitude becomes magnified when the particle’s transverse displacement per unit time decreases, explaining why these oscillations are exclusively observable in larger particles. The displacement probability distributions (DPDs) remain non-Gaussian even at long elapsed times when the diffusion becomes linear. This non-Gaussianity stems from variations in the diffusion coefficients of individual particles, which originate from the heterogeneity of the monolayer’s structure.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 41","pages":"10891–10902"},"PeriodicalIF":2.9,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145205208","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":"Lever Arm Flexibility Controls the Extent of (Un)Coupling to the Motor Domain in Myosin Motors","authors":"Mauro L. Mugnai*,&nbsp;, ,&nbsp;Yonathan Goldtzvik,&nbsp;, and ,&nbsp;D. Thirumalai*,&nbsp;","doi":"10.1021/acs.jpcb.5c05554","DOIUrl":"10.1021/acs.jpcb.5c05554","url":null,"abstract":"<p >Dimeric myosin motors, with both heads simultaneously bound to filamentous actin, are in a frustrated conformation. The lever arm of each head would prefer to orient forward, but the interhead tension hinders the relaxation to the state favored by a myosin monomer. Here, we investigate theoretically the impact of lever arm stiffness and coupling to the head domain by using a polymer model. The theory for myosin V and myosin VI qualitatively reproduces the salient experimental observations. Furthermore, we construct chimeras in which the lever arm and head domains are swapped and predict that the fluctuations of the leading head lever arm of myosin VI are strongly impacted by the stiffness of the lever arm. Finally, by continuously and independently varying the lever arm persistence length and the strength of its coupling to the head domain, we predict their roles in altering the average geometry and conformational flexibility of the dimer. We explore conditions under which LH lever arm flexibility and coupling to the motor domain affect the angle it makes with respect to F-actin.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 41","pages":"10775–10785"},"PeriodicalIF":2.9,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211164","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":"Analyzing the Solvation and Electrochemical Behavior of Triethylmethylammonium Tetrafluoroborate in Pure and Aqueous Ethaline Deep Eutectic Solvent: Experimental and Computational Approaches","authors":"Renuka Sharma,&nbsp;, ,&nbsp;Akshay Sharma,&nbsp;, and ,&nbsp;Ramesh Chand Thakur*,&nbsp;","doi":"10.1021/acs.jpcb.5c05019","DOIUrl":"10.1021/acs.jpcb.5c05019","url":null,"abstract":"<p >The growing population has led to an increase in global energy demands. Efficient energy storage methods and devices are the need of the hour. Deep eutectic solvents (DESs) being only two decades old have presented themselves as suitable candidates for electrolytes in energy storage devices. These solvents are cost-effective and environmentally friendly and can be designed in numerous ways to meet the targeted applications. In order to make these solvents more environmentally friendly and cheap, water as an additive can be explored. In this regard, electrochemical and thermophysical properties like apparent and partial molal volumes, isentropic compressibility, and apparent and partial molal isentropic compressibility of solutions comprising triethylmethylammonium tetrafluoroborate (TEMABF₄) in pure and aqueous DES (ethaline) were determined using experimental and computational techniques. The tetra-alkyl salt was found to act as a structure breaker after the analysis of thermophysical parameters in all of the solvent systems under consideration. Upon moving from pure to aqueous DES systems, substantial rise in the ionic conductivity and drop in the viscosity values were observed while maintaining an electrochemical window of 2.3 and 1.7 V for pure DES and aq. DES, respectively. Computational studies (RDG, MEP, and NCI) and FTIR findings complemented the experimental results and showed increased kinetic stability upon addition of water, confirming significant H-bonding between water and DES and increased solvation of ionic components in water.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 41","pages":"10873–10890"},"PeriodicalIF":2.9,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211089","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":"Vibrational Spectroscopic Analysis of Water Absorption in Polyimides and the Correlation with Dielectric Properties at 10 GHz","authors":"Ririka Sawada,&nbsp;, ,&nbsp;Haonan Liu,&nbsp;, and ,&nbsp;Shinji Ando*,&nbsp;","doi":"10.1021/acs.jpcb.5c05709","DOIUrl":"10.1021/acs.jpcb.5c05709","url":null,"abstract":"&lt;p &gt;Unveiling the mechanism behind the relative humidity (RH) dependence of the dielectric properties of polyimides (PIs) in the high-frequency (GHz) range is a crucial challenge in the development of novel low-dielectric thermally stable polymers. Herein, the correlations among the dielectric constant (&lt;i&gt;D&lt;/i&gt;&lt;sub&gt;k&lt;/sub&gt;), dissipation factor (&lt;i&gt;D&lt;/i&gt;&lt;sub&gt;f&lt;/sub&gt;), water absorption content, and hydrogen-bonding structures of sorbed H&lt;sub&gt;2&lt;/sub&gt;O molecules were precisely analyzed for 15 types of aromatic and semiaromatic PIs based on variable-RH Fourier transform infrared (FT-IR) vibrational spectroscopy. The absorbance of the IR bands assignable to the O–H stretching (ν(OH)) and H–O–H bending (δ(HOH)) vibrations of H&lt;sub&gt;2&lt;/sub&gt;O molecules sorbed in PI films gradually increased with an increase in the RH of the atmosphere. Notably, the slopes of the increase in &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;k&lt;/sub&gt; and &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;f&lt;/sub&gt; against the integrated area of the δ(HOH) IR band (&lt;i&gt;A&lt;/i&gt;&lt;sub&gt;δ(HOH)&lt;/sub&gt;), which can be used as a measure of the concentration of sorbed H&lt;sub&gt;2&lt;/sub&gt;O, were nearly constant and independent of the chemical structure of PIs. However, the slopes of the RH dependences of &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;k&lt;/sub&gt; and &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;f&lt;/sub&gt;, that is, &lt;i&gt;h&lt;/i&gt;&lt;sub&gt;Dk&lt;/sub&gt; and &lt;i&gt;h&lt;/i&gt;&lt;sub&gt;Df&lt;/sub&gt;, were strongly dependent on the structure of PIs and proportional to each other. This confirms that the amount of water absorbed is a crucial factor in the RH dependence of &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;k&lt;/sub&gt; and &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;f&lt;/sub&gt;. The &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;k&lt;/sub&gt; values of the PIs increased linearly with an increase in &lt;i&gt;A&lt;/i&gt;&lt;sub&gt;δ(HOH)&lt;/sub&gt;, whereas the &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;f&lt;/sub&gt; values increased linearly with &lt;i&gt;A&lt;/i&gt;&lt;sub&gt;δ(HOH)&lt;/sub&gt; at a lower RH but gradually showed a concave-up increase at a higher RH. In addition, the relationship between &lt;i&gt;A&lt;/i&gt;&lt;sub&gt;δ(HOH)&lt;/sub&gt; and &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;f&lt;/sub&gt; for all PIs was nearly aligned along a single master curve. This unified and marked increase in &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;f&lt;/sub&gt; could be induced by both the large &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;f&lt;/sub&gt; of water (∼0.5) and the plasticization effect of the H&lt;sub&gt;2&lt;/sub&gt;O molecules sorbed in the PI films. This water-induced plasticization activates the local relaxation motions of the moieties with large dipole moments, i.e., the imide and ester groups, in the PI chains, resonating at 10 GHz. Furthermore, the spectral decomposition of the IR ν(OH) band enables the classification and characterization of the structures of sorbed and hydrogen bonded H&lt;sub&gt;2&lt;/sub&gt;O molecules at the molecular level, namely 1) H&lt;sub&gt;2&lt;/sub&gt;O molecules directly form hydrogen bonds (HBs) with imide carbonyl (C═O) groups, called “bound water,” and 2) H&lt;sub&gt;2&lt;/sub&gt;O molecules form HBs with bound water, called “self-associated water.” Notably, with an increase in &lt;i&gt;A&lt;/i&gt;&lt;sub&gt;δ(HOH)&lt;/sub&gt;, the total amount of the spectral components of self-associated water (&lt;i&gt;A&lt;/i&gt;&lt;sub&gt;assoc&lt;/sub&gt;) increased curvilinearly and simultaneously with &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;f&lt;/sub&gt;. The quas","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 41","pages":"10928–10943"},"PeriodicalIF":2.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c05709","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145205211","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":"Tunable Conformational Properties of POSS-Peptide Conjugate Molecule in Selective Solvents: An Atomistic Molecular Dynamics Simulation Study","authors":"Junhao Dai,&nbsp;, ,&nbsp;Wen Tang,&nbsp;, ,&nbsp;Xianbo Huang*,&nbsp;, and ,&nbsp;Rui Zhang*,&nbsp;","doi":"10.1021/acs.jpcb.5c05243","DOIUrl":"10.1021/acs.jpcb.5c05243","url":null,"abstract":"<p >Giant molecules with precisely defined modular architectures hold promise to generate distinct structure-dynamics-property relationships in solution-phase materials. Recently, a novel class of hybrid macromolecules that combine structural rigidity of polyhedral oligomeric silsesquioxanes (POSS) with flexibility of peptide sequences (POSS-peptide conjugate molecules) have been established experimentally. To elucidate their detailed microscopic structural and dynamic features, high-precision atomistic modeling and simulation are in demand. In this study, we develop a standardized and extensible all-atom force field parametrization workflow for POSS-peptide molecules, integrating quantum chemical calculations to derive accurate force field parameters for the rigid POSS units, including bond, angle, and dihedral terms, as well as atomic charges for the whole molecule. Upon applying the parametrization framework to five representative POSS-peptide molecules with varied POSS functionality and peptide composition in water or DMF solvent, all-atom molecular dynamics simulations are performed for the ten systems to investigate the highly tunable conformational properties of POSS-peptides. We construct detailed conformational free energy landscapes that provide insight into the role of different factors in shaping the molecule’s solution-phase behavior. Our analysis reveals that molecular structure and solvent polarity co-regulate the conformational preferences of POSS-peptide molecules. Of particular interest is the finding of some unusual structure-dynamics correlation behaviors driven by close-distance interactions between the POSS and peptide unit. This work expands our understanding of the conformational richness of POSS-peptides in solution and provides a methodology foundation for exploring larger-scale supramolecular structures achievable by this emergent family of giant molecules in future research.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 41","pages":"10903–10913"},"PeriodicalIF":2.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145205193","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}