ACS Publications最新文献

{"title":"Correction to \"High-Level Calculation for Assessing the Atmospheric Reactivity of Pentachlorophenol with Hydroxyl Radical: Mechanism and Kinetics\".","authors":"Nissrin Alharzali, Ivan Černušák, Hisham K Al Rawas, Sonia Taamalli, Abderrahman El Bakali, Florent Louis, Duy Quang Dao","doi":"10.1021/acs.jpca.5c02803","DOIUrl":"10.1021/acs.jpca.5c02803","url":null,"abstract":"","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"4968"},"PeriodicalIF":2.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118337","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":"Low-Energy Isomers of the Magic Number H⁺(H₂O)₂₁ Cluster.","authors":"T-H Choi, E V Henderson, K D Jordan","doi":"10.1021/acs.jpca.5c01977","DOIUrl":"10.1021/acs.jpca.5c01977","url":null,"abstract":"<p><p>Electronic structure calculations are used to characterize low-energy isomers of H⁺(H₂O)₂₁. Eleven different classes of isomers, based on the (H₂O)₂₀ pentagonal dodecahedron with the excess proton localized on the surface (as a hydrated hydronium ion) and the \"extra\" water molecule located in the interior of the cluster, are characterized. In 10 of these classes, the internal water molecule is engaged in six 5-membered rings, but in the remaining class, which is predicted to start at only 0.6 kcal/mol above the global minimum, the internal water is engaged in a 4-membered ring, an additional 6-membered ring, and four 5-membered rings. In addition, isomers with two 4-membered rings and two 6-membered rings on the cluster surface are predicted to start at only ∼1.3 kcal/mol above the lowest-energy dodecahedral-based structure.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"4927-4935"},"PeriodicalIF":2.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118339","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":"Oxygen Dependence on Hydrated Electron Yields: Pulsed Radiolysis Studies Using Proton Beams.","authors":"Sarra Terfas, Guillaume Blain, Emeline Craff, Charbel Koumeir, Ferid Haddad, Freddy Poirier, Gregory Delpon, Johan Vandenborre","doi":"10.1021/acs.jpca.5c00629","DOIUrl":"10.1021/acs.jpca.5c00629","url":null,"abstract":"<p><p>Understanding the yield and kinetics of the hydrated electron (e^-_aq) is critical for applications in both biological and chemical systems, especially in the context of innovative FLASH radiation therapy. Most studies have employed chemical scavenging methods to measure radical yields. Although these techniques have undeniable advantages, such as probing early processes down to nanosecond time scale, and are easy to implement, they also have significant limitations. The main one is that they are not appropriate to longer time scales, especially the microsecond one, which is a key part of the homogeneous chemistry stage. Direct measurements of hydrated electron using pulsed ion beams are rare, especially with lighter particles such as protons used in radiotherapy, mainly due to instrumental complexity. This study addresses this gap by employing a dedicated time-resolved UV-visible absorption spectrometer coupled to a pulsed ion beam to measure transient hydrated electron radiolytic yield (<i>G</i>-value) in pure water, under both aerated and deaerated conditions. Pulsed radiolysis experiments were conducted at the Arronax cyclotron facility (Nantes, France) with a 68 MeV extracted H⁺ ion beam under ultra-high-dose rate (UHDR) conditions. The pulsed proton beam provides a radiolytic yield at <i>t</i> = 2 μs as well as e^-_aq formation and decay times. The results present the following track segment (TS) yields <b><i>G</i></b>_{<b>TS_2μ<i>s</i></b>}(e^-_aq) = (1.00 ± 0.17) × 10^-7 mol·J^-1 under deaerated conditions (≤0.04% O₂) with a half-life of 8.8 ± 1.5 μs, and <b><i>G</i></b>_{<b>TS_2μ<i>s</i></b>}(e^-_aq) = (0.90 ± 0.20) × 10^-7 mol·J^-1, <b><i>G</i></b>_{<b>TS_2μ<i>s</i></b>}(e^-_aq) = (0.62 ± 0.24)×10^-7 mol·J^-1, and <b><i>G</i></b>_{<b>TS_2μ<i>s</i></b>}(e^-_aq) = (0.13 ± 0.04) × 10^-7 mol·J^-1 under oxygen concentrations of 0.4, 1, and 21% O₂, respectively. These results represent the yields measured directly at the homogeneous chemistry stage, without the use of scavengers, and offer new data within several oxygen contents, allowing a better understanding of the dependence of oxygen on <i>G</i>_TS(e^-_aq). They are essential to explore UHDR chemistry dedicated to FLASH radiation therapy and to produce reliable data to validate Monte Carlo codes, such as Geant4-DNA and Topas-nBio.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"4861-4869"},"PeriodicalIF":2.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118341","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":"Formation and Disruption of Hydrogen Bond in 1-Ethyl-3-methylimidazolium Ethylsulfate and Glycerol Binary Mixtures: A Molecular Perspective.","authors":"Md Ahad Ali, Md Abu Bin Hasan Susan","doi":"10.1021/acs.jpcb.5c01519","DOIUrl":"10.1021/acs.jpcb.5c01519","url":null,"abstract":"<p><p>This study focuses on the hydrogen bonding interactions that govern the physicochemical properties of the binary mixtures of 1-ethyl-3-methylimidazolium ethylsulfate ([C₂mim]C₂H₅SO₄) and glycerol. Various thermodynamic properties of [C₂mim]C₂H₅SO₄ and glycerol mixtures were investigated by using density and viscosity across a range of compositions and temperatures, while structural properties were explored by using temperature-dependent near-infrared (NIR) spectroscopy, two-dimensional (2D) correlation spectroscopy, and principal component analyses (PCA). In order to better understand hydrogen bonding interactions, both analyses were employed. The NIR spectroscopic analysis shows the presence of various types of hydrogen-bonded clusters in the structure of glycerol and a strong hydrogen bond between the hydrogen of the imidazole ring and the oxygen of ethylsulfate anions. In the binary mixtures, hydrogen-bonded clusters of glycerol were sustained upon addition of [C₂mim]C₂H₅SO₄ up to a mole fraction of 0.6. Further addition of [C₂mim]C₂H₅SO₄ causes breakdown of the cluster of glycerol and forms solvated ions of [C₂mim]C₂H₅SO_4. The variation of excess molar volume, dynamic viscosity deviation, excess molar Gibbs free energy of activation, and thermodynamic activation parameters also show transitions at this particular composition. Hence, the dynamic interaction between the formation and disruption of hydrogen bonds in these compounds controls the thermodynamic properties, which is the key factor to apply this binary system in various fields.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5541-5549"},"PeriodicalIF":2.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126234","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":"Diverging and Converging Propagation of the Polymerization Front of Cyclooctadiene for Tunable Front Velocity and Patterning.","authors":"Lily J Shan, Yuqun Feng, Yuan Gao","doi":"10.1021/acs.jpcb.5c01387","DOIUrl":"10.1021/acs.jpcb.5c01387","url":null,"abstract":"<p><p>Frontal polymerization (FP) with thermochemical instabilities provides a morphogenic manufacturing method for polymeric parts by autonomously forming patterned domains with different phases, leading to mechanical properties surpassing the homogeneous counterpart. The mechanical properties largely depend on the characteristics of the patterns. Understanding and controlling the pattern features are of vital importance to FP-based manufacturing processes. In the present study, we demonstrate that the geometry and propagating route of FP in cyclooctadiene have significant impacts on the front velocity and the pattern formed by the instability. By varying the diverging angle of the propagating route, the front velocity and the wavelength of the pattern can be typically adjusted by 25% and 50%, respectively. The tuning range on the wavelength of patterns is almost twice that with controlling merely the thermal condition. The tuning effects on the front velocity and pattern features are further validated with a parametric study. The mechanism of energy balance between the reaction and diffusion and the geometry-dependent cure kinetics are elucidated with detailed finite-element analyses. The current results and findings provide a fundamental understanding of unstable FP in various geometries and can theoretically guide the development of FP-based morphogenic manufacturing methods with adjustable material properties.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5621-5629"},"PeriodicalIF":2.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109133","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":"Probing the Epidermal Growth Factor Receptor under Piconewton Mechanical Compressive Force Manipulations.","authors":"Dedunu S Senarathne, Lalita Shahu, H Peter Lu","doi":"10.1021/acs.jpcb.5c00800","DOIUrl":"10.1021/acs.jpcb.5c00800","url":null,"abstract":"<p><p>Studying the relationship among protein structure, dynamics, and function under external compressive forces offers valuable insights. While extensive research has focused on manipulating protein dynamics and ligand-receptor interactions under pulling forces, the exploration of protein conformational changes under compressive forces has been limited. In this study, we investigate the response of unliganded epidermal growth factor receptor (EGFR) monomers, liganded EGF-EGFR monomers, and dimers when exposed to external compressive forces using a home-modified AFM setup with an ultrasoft AFM tip. We observed that both ligand-bound and unbound EGFR proteins can undergo spontaneous tertiary structural rupture under piconewton-level compressive forces, a previously hidden protein behavior that may play a significant role in protein cell signaling. The magnitudes of the threshold compressive forces obtained in our study lie in the range of tens and hundreds of piconewtons (pN), which is accessible within a live biological system. Moreover, we developed a kinetic model to exhibit that only a fraction of the uniaxial compressive force exerted by the AFM tip affects the internal tension that causes a pseudopulling force within the protein before it undergoes the tertiary structural rupture. This calculated fraction ranged from 0.45 to 0.65, depending on the protein type and the approach velocity of the AFM tip. Additionally, we employed molecular dynamics (MD) simulations, particularly Steered MD (SMD) simulations along with Umbrella Sampling (US), to investigate the dynamics of unliganded and liganded EGFR in the presence of external compressive forces. These MD simulation results offer valuable insights into the flexibilities and unfolding behaviors of both liganded and unliganded EGFR proteins when subjected to external compressive forces.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5411-5422"},"PeriodicalIF":2.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144148679","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":"Controllable Skyrmion Nucleation and Transition in a Confined Nanodisk for the Binarized Neuron Network of 2D Ferromagnet Fe₅GeTe₂.","authors":"Chengfang Che, Juan Hou, Chendi Yang","doi":"10.1021/acsami.5c04834","DOIUrl":"https://doi.org/10.1021/acsami.5c04834","url":null,"abstract":"<p><p>The integration of skyrmions in 2D ferromagnetic materials and advanced spintronic devices enables energy-efficient computing for artificial synapses in neuromorphic architecture. Nucleation of skyrmions plays a critical role in ensuring high reliability and low energy consumption. However, the key challenge lies in selectively generating skyrmions, excluded from trivial bubbles and their controllable transition. Here, as a concept example of 2D ferromagnets, we demonstrate the evolution of the skyrmion in Fe₅GeTe₂ excluded from the trivial bubbles within the geometrically confined 1 μm nanodisk. The skyrmions selectively nucleate from stripe domains, driven by the competition between dipolar-dipolar interactions and Zeeman energy, captured in real-time/space using in situ Lorentz TEM. Furthermore, we reveal a reversible skyrmion-to-trivial bubble transition in the 500 nm nanodisk induced by an in-plane magnetic field, confirmed by the micromagnetic simulation. The reversible switching of skyrmions and trivial bubbles enables the implementation of a binary-state neuromorphic computing framework. The skyrmion-based artificial synapses demonstrate over 85% handwriting recognition accuracy. The findings bridging fundamental skyrmion physics with practical applications offer key insights for designing next-generation 2D materials-based devices.</p>","PeriodicalId":5,"journal":{"name":"ACS Applied Materials & Interfaces","volume":" ","pages":""},"PeriodicalIF":8.3,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144223696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retrieval of Genuine Ultraviolet Liquid-Microjet Photoelectron Spectra.","authors":"Edoardo Simonetti, Helen H Fielding","doi":"10.1021/acs.jpca.5c02024","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c02024","url":null,"abstract":"<p><p>Ultraviolet liquid-microjet photoelectron spectroscopy is a powerful technique for the determination of electron binding energies of molecules in aqueous solution and for exploring their photochemical dynamics. However, our poor understanding of inelastic scattering of low energy electrons (<10 eV) in water has hindered the determination of accurate vertical ionization energies; although several algorithms have been implemented to retrieve genuine binding energies from experimental spectra, a consensus on the parameters employed is yet to be reached. Here, we investigate the effect of these parameters on the retrieval of true photoelectron spectra of water, phenol, and phenolate. We show that the scattering cross sections, obtained by extrapolating the cross sections in amorphous ice to zero electron kinetic energy, describe the distortion observed in our spectra accurately and that the description of the transmission of electrons at the liquid-vacuum interface is crucial to infer a value for the electron affinity of water at the surface, and we emphasize the importance of considering concentration depth profiles when retrieving true photoelectron spectra of surface-active solutes. Our work highlights the potential for accurate ultraviolet photoelectron spectroscopy of aqueous solutions of organic molecules.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144223742","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":"Proximity-Induced Fluorescence Quenching in Rhodamine Systems <i>In Vacuo</i>: Effect of Charges and Aromatic Moieties.","authors":"Thomas Toft Lindkvist, Lukas Raphael Benzenberg, Steen Brøndsted Nielsen, Renato Zenobi","doi":"10.1021/acs.jpca.5c03150","DOIUrl":"10.1021/acs.jpca.5c03150","url":null,"abstract":"<p><p>FRET is a valuable technique for exploring conformations of macromolecules in solution and in the gas phase. Donor fluorescence quenching is often identified from shortened excited-state lifetimes. However, when dyes are incorporated into proteins, the local microenvironment can affect the photophysics and energy transfer. To examine the effect of nearby charges and aromatic moieties on lifetimes, we investigated different cationic rhodamine-575 model systems <i>in vacuo</i>. In homodimers, the internal Coulomb repulsion induces a distance-dependent increase in lifetime, ranging from 5.90 ns (single dye) to 6.78 ns (shortest interdye linker), which we attribute to reduced oscillator strengths as corroborated by TD-DFT calculations. Our findings highlight that excited-state lifetimes are not necessarily directly correlated with fluorescence quantum yields, contrasting typical intuition. We discuss different quenching mechanisms and compare with results obtained in solution, as the opposite effect is observed in methanol, where excited-state lifetimes decrease upon bringing the dyes closer together. In the case of homotrimers in the gas phase, lifetimes systematically decrease with the number of nonprotonated (neutral) dyes. This suggests enhanced nonradiative decay rates driven by strong interactions between dyes and nearby aromatic moieties.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"4936-4943"},"PeriodicalIF":2.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109132","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":"Computing the pH-Dependent Thermodynamics of the Allostery between Dimerization and Palmitate Binding in β-Lactoglobulin.","authors":"Lucie da Rocha, Sara R R Campos, António M Baptista","doi":"10.1021/acs.jpcb.5c01119","DOIUrl":"10.1021/acs.jpcb.5c01119","url":null,"abstract":"<p><p>The study of pH-dependent allosteric processes presents a significant challenge, both experimentally and computationally. In this work, we apply the constant-pH molecular dynamics method to explore an interesting case of allostery involving protein-ligand binding and dimerization. As a model system, we use β-lactoglobulin (BLG), a small protein from bovine milk known to dimerize and bind palmitic acid in a hydrophobic pocket─both processes sensitive to pH. This study focuses on the holo form of BLG, and, when combined with our previous study of the apo form (da Rocha et al. <i>J. Chem. Theory Comput.</i> <b>2022</b> 18, 1982), completes the thermodynamic cycle of the allosteric process. The corresponding pH-dependent free energy profiles are obtained through the use of a thermodynamic linkage relation, avoiding the need of performing heavy computational calculations. Dimerization is found to be more favorable near the isoionic point, as observed in the apo form. Palmitate binding is found to be more favorable around pH 6-7, a biologically relevant pH range at which the gate covering the binding site is known to open. A pH-dependent measure of allosteric coupling is computed, showing that ligand binding and dimerization exhibit an antagonist relationship within the studied pH range of 3-8, with binding destabilizing dimerization and vice versa.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5423-5437"},"PeriodicalIF":2.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126229","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}