The Journal of Physical Chemistry B最新文献

{"title":"Subcritical Determination of the Frenkel Line in Liquid Nitrogen, the Emergent Final Picture, and a Universal Equation for the Coordination Number of Real Fluids.","authors":"Ciprian G Pruteanu, Ayobami D Daramola, Marcin Kirsz, Cerian E A Robertson, Luke J Jones, Tianrui Wang, John S Loveday, Graeme J Ackland, Oliver L G Alderman, John E Proctor","doi":"10.1021/acs.jpcb.5c00018","DOIUrl":"10.1021/acs.jpcb.5c00018","url":null,"abstract":"<p><p>We performed a series of neutron scattering experiments on deeply subcritical liquid nitrogen at 90 K (0.7<i>T</i>_<i>C</i>). Our findings, when taken together with our previous results at 160 K (1.27<i>T</i>_<i>C</i>) and 300 K (2.4<i>T</i>_<i>C</i>), allow the Frenkel line phenomenon to be characterized in a reliable and consistent manner over an extremely broad temperature range, extending into the subcritical regime. Through an analysis of local order, we show how the fluid structure changes as the Frenkel line is crossed and present a new method for identifying the line. Our determination of coordination numbers shows a remarkable data collapse when plotted against density. This allows us to produce a universal relationship relating the coordination number to the density of a simple fluid, dictated by molecular/atomic size and its density on the melt line.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3420-3427"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707793","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":"Development of SAFT-Based Coarse-Grained Models of Carbon Dioxide and Nitrogen.","authors":"Alexandros Chremos, William P Krekelberg, Harold W Hatch, Daniel W Siderius, Nathan A Mahynski, Vincent K Shen","doi":"10.1021/acs.jpcb.5c00536","DOIUrl":"10.1021/acs.jpcb.5c00536","url":null,"abstract":"<p><p>We develop coarse-grained models for carbon dioxide (CO₂) and nitrogen (N₂) that capture the vapor-liquid equilibria of both their single components and their binary mixtures over a wide range of temperatures and pressures. To achieve this, we used an equation of state (EoS), namely Statistical Associating Fluid Theory (SAFT), which utilizes a molecular-based algebraic description of the free energy of chain fluids. This significantly accelerates the exploration of the parameter space, enabling the development of coarse-grained models that provide an optimal description of the macroscopic experimental data. SAFT creates models of fluids by chaining together spheres, which represent coarse-grained parts of a molecule. The result is a series of fitted parameters, such as bead size, bond length, and interaction strengths, that seem amenable to molecular simulation. However, only a limited set of models can be directly implemented in a particle-based simulation; this is predominantly due to how SAFT handles overlap between bonded monomers with parameters that do not translate to physical features, such as bond length. To translate such parameters to bond lengths in a coarse-grained force-field, we performed Wang-Landau transition-matrix Monte Carlo (WL-TMMC) simulations in the grand canonical ensemble on homonuclear fused two-segment Mie models and evaluated the phase behavior at different bond lengths. In the spirit of the law of corresponding states, we found that a force field, which matches SAFT predictions, can be derived by rescaling length and energy scales based on ratios of critical point properties of simulations and experiments. The phase behavior of CO₂ and N₂ mixtures was also investigated. Overall, we found excellent agreement over a wide range of temperatures and pressures in pure components and mixtures, similar to TraPPE CO₂ and N₂ models. Our proposed approach is the first step to establishing a more robust bridge between SAFT and molecular simulation modeling.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3443-3453"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143672884","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":"Decoding Anti-Amyloidogenic and Fibril Neutralizing Action of Gut Microbiota-Derived Indole 3-Acetic Acid on Insulin Fibrillation through Multispectroscopic, Machine Learning, and Hybrid Quantum Mechanics/Molecular Mechanics Approaches.","authors":"Saswati Soumya Mohapatra, Krishna Singh Bisht, Sakshi Suryawanshi, Shreshth Gupta, Viplov Kumar Biswas, Ayon Chakraborty, Sunil Kumar Raghav, Tushar Kanti Maiti, Rajiv K Kar, Ashis Biswas","doi":"10.1021/acs.jpcb.4c07325","DOIUrl":"10.1021/acs.jpcb.4c07325","url":null,"abstract":"<p><p>Insulin fibrillation inflicts both economic and clinical challenges by causing bioactivity loss, inflammation, and adverse effects during storage, transport, and injection. The present study explores antiamyloidogenic and fibril-disaggregating effects of a gut microbiota-derived indole metabolite, indole-3-acetic acid (IAA) on insulin fibrillation. According to Thioflavin T (ThT) fluorescence assays and transmission electron microscopy (TEM), IAA significantly inhibited both primary and seed-induced fibrillation of insulin. We note that IAA reduced insulin aggregate sizes as evident from the scattering profiles, while circular dichroism studies confirmed that IAA preserves native α-helical structure possibly minimizing the exposed surface hydrophobicity of insulin. Additionally, IAA showed effectiveness in breaking apart preformed fibrils, indicated by a time-dependent decrease in ThT fluorescence and further confirmed by TEM. Our biolayer interferometry interaction studies revealed a moderate 2:1 binding affinity between IAA and insulin. Two key binding sites on insulin were identified via machine-learning-based-docking and hybrid QM/MM studies, where IAA interacts. Site I (Leu13^A, Tyr14^A, Glu17^A, Phe1^B) showed more favorable interaction energetics than site II (Tyr19^A, Phe25^B, Thr27^B) based on SAPT0 residue-wise interaction energy analysis. IAA also protected cells from fibril-induced cytotoxicity and hemolysis, thereby offering a promising therapeutic option for amyloid-related disorders, with dual action in preventing fibril formation and promoting fibril disaggregation.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3281-3296"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661560","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":"ReaxFF-Guided Optimization of VIRIP-Based HIV-1 Entry Inhibitors.","authors":"Fabian Zech, Christoph Jung, Armando Alexei Rodríguez Alfonso, Janet Köhler, Ludger Ständker, Gilbert Weidinger, Timo Jacob, Frank Kirchhoff","doi":"10.1021/acs.jpcb.5c00440","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00440","url":null,"abstract":"<p><p>Peptides hold great promise for safe and effective treatment of viral infections. However, their use is often constrained by limited efficacy and high production costs, especially for long or complex peptide chains. Here, we used ReaxFF molecular dynamics (MD) simulations to optimize the size and activity of VIRIP (Virus Inhibitory Peptide), a naturally occurring 20-residue fragment of α1-antitrypsin that binds the HIV-1 GP41 fusion peptide (FP), thereby blocking viral fusion and entry into host cells. Specifically, we used the NMR structure of the complex between an optimized VIRIP derivative (VIR-165) and the HIV-1 gp41 FP for ReaxFF-guided in silico analysis, evaluating the contribution of each amino acid in the interaction of the inhibitor with its viral target. This approach allowed us to reduce the size of the HIV-1 FP inhibitor from 20 to 10 amino acids (2.28-1.11 kDa). HIV-1 infection assays showed that the size-optimized VIRIP derivative (soVIRIP) retains its broad-spectrum anti-HIV-1 capability and is nontoxic in the vertebrate zebrafish model. Compared to the original VIRIP, soVIRIP displayed more than 100-fold higher antiviral activity (IC₅₀ of ∼120 nM). Thus, it is more potent than a dimeric 20-residue VIRIP derivative (VIR-576) that was proven safe and effective in a phase I/II clinical trial. Our results show that ReaxFF-based MD simulations represent a suitable approach for the optimization of therapeutic peptides.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778534","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":"Ultrasensitive Differential Scanning Calorimetric (US-DSC) Study of the Thermal-Induced Dynamic Transition Behaviors of PEO-PPO-PEO in Aqueous Solution.","authors":"Lin Li, Kang Ni, Lvdan Liu, Yuxia Bai, Yanwei Ding","doi":"10.1021/acs.jpcb.4c08247","DOIUrl":"10.1021/acs.jpcb.4c08247","url":null,"abstract":"<p><p>Temperature-responsive macromolecules can provide insights into the mechanisms of the aggregation and precipitation processes of proteins. In this study, the PEO-PPO-PEO triblock copolymer, Pluronic P123, has been utilized as a protein model to investigate the thermally induced dynamic transition behavior by ultrasensitive differential scanning calorimetry (US-DSC). The results of US-DSC reveal hysteresis in the disaggregation process of P123 micelles. Combined with the particle size distribution, a stepwise disaggregation mechanism is proposed. The disaggregation of P123 micelles in the cooling process involved rod-to-sphere transition, fragmentation, and dissolution of micelles. Moreover, US-DSC results show that both the sphere-to-rod transition and micelle fragmentation are dependent on the scanning rate and reveal the relationship between the dynamic transition and thermodynamic properties of P123. These findings expand the understanding not only of aggregation and disaggregation of P123 in dilute aqueous systems but also of the thermal unfolding and aggregation of proteins.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3482-3491"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661595","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":"Exceptionally Strong Double-Layer Barriers Generated by Polyampholyte Salt.","authors":"David Ribar, Clifford E Woodward, Jan Forsman","doi":"10.1021/acs.jpcb.5c00012","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00012","url":null,"abstract":"<p><p>Experiments using the surface force apparatus have found anomalously long-range interactions between charged surfaces in concentrated salt solutions. Ion clustering has been suggested as a possible origin of this behavior. In this work, we demonstrate that if such stable clusters indeed form, they are able to induce remarkably strong free energy barriers under conditions where a corresponding solution of simple salt provides negligible forces. Our cluster model is based on connected ions producing a polyampholyte salt containing a symmetric mixture of monovalent cationic and anionic polyampholytes. Ion distributions and surface interactions are evaluated utilizing statistical-mechanical (<i>classical</i>) polymer density functional theory, cDFT. In the Supporting Information, we briefly investigate a range of different polymer architectures (connectivities), but in the main part of the work, a polyampholyte ion is modeled as a linear chain with alternating charges, in which the ends carry an identical charge (hence, a monovalent net charge). These salts are able to generate repulsions, between similarly charged surfaces, of a remarkable strength, exceeding those from simple salts by orders of magnitude. The underlying mechanism for this is the formation of brush-like layers at the surfaces, i.e., the repulsion is strongly related to excluded volume effects, in a manner similar to the interaction between surfaces carrying grafted polymers. We believe our results are relevant not only to possible mechanisms underlying anomalously long-ranged underscreening in concentrated simple salt solutions but also for the potential use of synthesized polyampholyte salt as extremely efficient stabilizers of colloidal dispersions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770752","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":"Plasticization Effects of PEG of Low Molar Fraction and Molar Mass on the Molecular Dynamics and Crystallization of PLA-<i>b</i>-PEG-<i>b</i>-PLA Triblock Copolymers Envisaged for Medical Applications.","authors":"Nikolaos D Bikiaris, Panagiotis A Klonos, Evi Christodoulou, Panagiotis Barmpalexis, Apostolos Kyritsis","doi":"10.1021/acs.jpcb.5c00171","DOIUrl":"10.1021/acs.jpcb.5c00171","url":null,"abstract":"<p><p>We prepared and studied a series of triblock copolymers based on poly(ethylene glycol) (PEG) and poly(lactic acid) (PLA). PLA blocks were <i>in situ</i> by ring-opening polymerization (ROP) of lactide (LA) onto the two sites of PEG. While in our recent work on similar copolymers with varying LA/PEG molar ratios and fixed PEG blocks [Bikiaris, N. D. <i>Mater. Today Commun.</i> 2024, 38, 107799], herein, we kept this ratio quite low, at 640/1, and employed different molecular weights, <i>M</i>_n, of the initial PEG at 1, 4, 6, and 8 kg/mol. The triblocks demonstrated high homogeneity, as manifested by the single thermal transition (glass transition, crystallization) with corresponding alternations in a systematic way with the <i>M</i>_n of PEG. With the increase of the latter <i>M</i>_n, accelerated segmental mobility and lowering of <i>T</i>_g by up to 15 K were recorded, accompanied by suppression in the chain fragility (cooperativity). Compared with linear PLAs of various <i>M</i>_ns [Klonos, P. A. <i>Polymer</i> 2024, 305, 127177] and other PLA-based copolymers prepared by similar ROPs, with the overall <i>M</i>_n of our copolymers, PEG here sees to play the role of plasticizer on PLA, leading to increased free volume. Due to these effects, in general, the low crystalline fraction of PLA (∼3%) was significantly enhanced in the copolymers (20-26%), and the formed spherulites were mainly enlarged. Contrary to these, nucleation was barely affected; thus, the copolymers exhibited altered semicrystalline morphologies as compared to that in neat PLA. Both aspects of molecular dynamics, free volume and crystallization, were connected to the processability as well as the performance of these systems, considering the envisaged biomedical applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3514-3528"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661581","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":"Theoretical Basis for Refractive Index Changes Resulting from Solution Phase Molecular Interaction.","authors":"Michael N Kammer, Amanda K Kussrow, Darryl J Bornhop","doi":"10.1021/acs.jpcb.4c07563","DOIUrl":"10.1021/acs.jpcb.4c07563","url":null,"abstract":"<p><p>Refractive index (RI) is a fundamental optical property widely used to investigate the physical and chemical characteristics of materials. Here, we build on our previous work to refine the framework for RI sensing in solution-phase chemical and biochemical interactions. Starting from the Clausius-Mossotti relation, we present a first-principles derivation of a relationship for the RI signal resulting from chemical binding. We then demonstrate how the binding-induced conformational and hydration changes of interacting species relate to their estimated change in dielectric and thus the solution-phase change in refractive index (ΔRI). By varying the model parameters, such as solvation shell size and polarizability, we investigate the RI changes for two interactions: Ca²⁺ with the protein Recoverin and benzenesulfonamide with carbonic anhydrase 2 (CAII). These examples show that our theory predicts that even for small changes in binding-induced <i>polarizability</i> (relative to previous literature values), a quantifiable RI change is produced within the detectable range of RI detectors operating at ca. 10^-6 RIU. Empirical observations confirm our theoretical predictions. Surprisingly, theory and experiment yield a <i>decrease</i> in ΔRI for the benzenesulfonamide-CAII interaction. We attribute this observation to shielding of charged residues and water molecule displacement during the binding event. Our approach is generalized, enabling it to be extended to other binding systems, as well as those undergoing nonbinding conformational changes, and facilitates the exploration of diverse biological and chemical processes by solution-phase RI sensing.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3297-3305"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699133","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":"Exciton Transfer Simulations in a Light-Harvesting 2 Complex Reveal the Transient Delocalization Mechanism.","authors":"David S Hoffmann, Philipp M Dohmen, Monja Sokolov, Ulrich Kleinekathöfer, Marcus Elstner","doi":"10.1021/acs.jpcb.5c00320","DOIUrl":"10.1021/acs.jpcb.5c00320","url":null,"abstract":"<p><p>The striking efficiency of exciton transfer in light-harvesting (LH) complexes has remained a topic of debate since the revision of the long-held role of electronic coherences. To address this issue, we have developed a neural network for the pigments in the LH2 complex of <i>Rhodospirillum molischianum</i> that allows nonadiabatic molecular dynamic (NAMD) simulations of exciton transfer in a coupled quantum mechanical/molecular mechanics (QM/MM) embedding. The calculated exciton occupations are averaged over hundreds of trajectories, each lasting several picoseconds. We have obtained transitions within the B800 and B850 rings that agree well with the experimental results, indicating an incoherent hopping process in the B800 ring and a more delocalized transfer in the B850 subsystem. The reorganization energies and excitonic couplings are comparable to each other, indicating that the \"transient delocalization\" transport model is the underlying cause of the highly efficient exciton transport in the B850 ring. This phenomenon can be attributed to a localized exciton that shows occasional large delocalization events. Our results indicate that the reason for the striking efficiency is the unusual electronic property of bacteriochlorophyll, manifested in minimal inner and outer sphere reorganization energies.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3345-3365"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699115","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":"Investigating the Impact of the Spatial Arrangement of the Terminal Methyl Group Relative to the Bridging Ethylene Group on the Properties of PMO Films.","authors":"Dmitry A Vorotyntsev, Alexey S Vishnevskiy, Dmitry S Seregin, Sergej Naumov, Konstantin A Vorotilov, Mikhail R Baklanov","doi":"10.1021/acs.jpcb.4c08605","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08605","url":null,"abstract":"<p><p>The impact of the spatial arrangement of the terminal methyl group in relation to the bridging ethylene group on the properties of PMO films has been studied using pairs of BTMSE-MTMS and TESDEMSE-MTMS precursors containing C-C bridging groups. TESDEMSE features a Si-attached CH₃ group within the same molecule, forming hydrophobic films independently of MTMS concentration. Pure BTMSE-based films are hydrophilic and exhibit an increased dielectric constant due to water adsorption. The addition of MTMS to BTMSE introduces CH₃ into the films, rendering them hydrophobic. The spatial arrangement of CH₃ relative to C-C significantly affects hydrophobicity, dielectric properties, thermal stability, and porosity. The mechanical properties of the films also depend on the location of CH₃ groups. TESDEMSE demonstrates potential as a single precursor for low-<i>k</i> film deposition. However, annealing (curing) at 430 °C reduces the concentration of C-C bonds, and this phenomenon is more pronounced in TESDEMSE-based films. Quantum chemical analysis indicates that the ethylene bridge is generally weaker than the terminal methyl group, with the presence of an adjacent methyl group further decreasing its stability. The low thermal stability of these films poses a challenge for certain practical applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778528","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}