The Journal of Physical Chemistry B最新文献

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Cooperative Dynamics and Hydration of Aqueous D-Mannitol and myo-Inositol. d -甘露醇和肌醇水溶液的协同动力学和水合作用。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-01-16 Epub Date: 2025-01-03 DOI: 10.1021/acs.jpcb.4c07344
Iwona Płowaś-Korus, Paweł Korus, Richard Buchner
{"title":"Cooperative Dynamics and Hydration of Aqueous D-Mannitol and <i>myo</i>-Inositol.","authors":"Iwona Płowaś-Korus, Paweł Korus, Richard Buchner","doi":"10.1021/acs.jpcb.4c07344","DOIUrl":"10.1021/acs.jpcb.4c07344","url":null,"abstract":"<p><p>The cooperative dynamics and hydration of D-mannitol and <i>m</i>yo-inositol in aqueous solution at 25 °C were investigated by broad-band dielectric relaxation spectroscopy (DRS) for solute concentrations <i>c</i> < 0.9M. The recorded spectra, covering the frequency range 0.05 ≤ ν/GHz ≤ 50, can be described as a superposition of three Debye-type relaxation processes. The determined total effective hydration numbers, <i>Z</i><sub>t</sub>, as well as the effective dipole moments, μ<sub>eff</sub>, of D-mannitol and <i>m</i>yo-inositol do not depend on solute concentration. The <i>Z</i><sub>t</sub> values obtained for both sugar alcohols are significantly smaller than that of the previously studied xylitol. In contrast to aqueous xylitol, the dielectric spectra also showed no indication of the formation of D-mannitol or <i>m</i>yo-inositol aggregates.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"712-718"},"PeriodicalIF":2.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142925858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reactive Brownian Dynamics of Chemically Fueled Droplets: Roles of Attraction and Deactivation Modes. 化学燃料液滴的反应布朗动力学:吸引和失活模式的作用。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-01-16 Epub Date: 2025-01-06 DOI: 10.1021/acs.jpcb.4c06205
Lennard Holschuh, Joachim Dzubiella
{"title":"Reactive Brownian Dynamics of Chemically Fueled Droplets: Roles of Attraction and Deactivation Modes.","authors":"Lennard Holschuh, Joachim Dzubiella","doi":"10.1021/acs.jpcb.4c06205","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06205","url":null,"abstract":"<p><p>The self-assembly of biological membraneless organelles can be mimicked by active droplets resulting from chemically fueled microphase separation. However, how the nonequilibrium, transient structure of these active droplets can be controlled through the physicochemical input parameters is not yet well understood. In our work, a chemically fueled two-state chemical reaction and subsequent droplet growth and decay are modeled with a reactive Brownian dynamics simulation in two spatial dimensions. In our model, particles that are activated via the consumption of fuel become attractive and can accumulate into droplets. A local-density-dependent distinction of the droplet's 'internal' and 'external' particles allows for structural feedback by giving further control over the deactivation process. The simulation shows that the deactivation of only external particles slows down the decay and stabilizes the droplets, whereas the deactivation of only internal particles can lead to a temporary encapsulation of deactivated particles (in nonequilibrium 'core-shell' structures) where the chemically active particles serve as an outer shell. Additionally, the role of hydrophobicity resembled by the attraction energy ε and the dependency of the nonequilibrium droplet formation on the various parameters of the chemical reaction are investigated. For example, a high attraction energy can lead to transient finite-size crystalline droplets, while other parameter choices indicate bimodal droplet size distributions at specific times. Similarities and differences to related experiments are discussed.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 2","pages":"626-636"},"PeriodicalIF":2.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Side-Chain and Ring-Size Effects on Permeability in Artificial Water Channels. 侧链和环尺寸对人工水道渗透性的影响。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-01-16 Epub Date: 2025-01-02 DOI: 10.1021/acs.jpcb.4c05244
Tyler J Duncan, Harekrushna Behera, Michael F Meng, Zidan Zhang, Nico Marioni, Meron Tadesse, Manish Kumar, Venkat Ganesan
{"title":"Side-Chain and Ring-Size Effects on Permeability in Artificial Water Channels.","authors":"Tyler J Duncan, Harekrushna Behera, Michael F Meng, Zidan Zhang, Nico Marioni, Meron Tadesse, Manish Kumar, Venkat Ganesan","doi":"10.1021/acs.jpcb.4c05244","DOIUrl":"10.1021/acs.jpcb.4c05244","url":null,"abstract":"<p><p>Artificial water channels (AWCs) have emerged as a promising framework for stable water permeation, with water transport rates comparable to aquaporins (3.4-40.3 × 10<sup>8</sup> H<sub>2</sub>O/channel/s). In this study, we probe the influence of ring-size and side-chain length on the water permeability observed within a class of AWCs termed ligand-appended pillar[n]arenes (LAPs) that have an adjustable ring-size (<i>m</i>) and side-chain length (<i>n</i>). Through all-atom molecular dynamics simulations, we calculate the permeability of these channels using the collective diffusion model and find their permeabilities. We characterize the mechanistic influence of pillar[n]arene ring-size and side-chain length on the channel water permeability by analyzing the characteristics of the internal permeating water-wire and the surrounding channel structure. We observe that water permeability decreases as a function of increasing ring-size due to increases in hydrophilic contacts between the permeating water-wire and the oxygen groups on the channel wall. Further, we observe an increase in water permeability as a function of side-chain length due to increased partitioning of the channel terminal groups into the hydrophilic blocks of the surrounding bilayer. For the LAP6 channel, with increase in side-chain length, the distance between terminal groups increases and leads to an increase in pore size, thereby enhancing water permeability. In the case of LAP5, as side-chain length increases, the channel displays a compensatory effect between tilt and bend angle due to the flexible side-chains. Such flexibility leads to higher terminal group partitioning in the hydrophilic blocks of the bilayer and extends the permeating water-wire. This increase in water-wire length and hydrophilic block access overcomes the nonmonotonic pore size trend in pillar[5]arene channels.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"659-670"},"PeriodicalIF":2.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Interaction of a Novel Dihydroxy Dibenzoazacrown with Different Surfactants: A Physicochemical and Spectroscopic Investigation. 一种新型二羟基二苯并氮杂冠与不同表面活性剂的相互作用:理化和光谱研究。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-01-16 Epub Date: 2025-01-06 DOI: 10.1021/acs.jpcb.4c05919
Sourav Das, Pravat Ghorai, Rosa M Gomila, Antonio Frontera, Amrita Saha, Soumen Ghosh
{"title":"Interaction of a Novel Dihydroxy Dibenzoazacrown with Different Surfactants: A Physicochemical and Spectroscopic Investigation.","authors":"Sourav Das, Pravat Ghorai, Rosa M Gomila, Antonio Frontera, Amrita Saha, Soumen Ghosh","doi":"10.1021/acs.jpcb.4c05919","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c05919","url":null,"abstract":"<p><p>Interaction of a novel dihydroxy dibenzoazacrown (H<sub>2</sub>DTC) with various surfactants of different charges, for example, anionic (sodium dodecylsulfate, SDS), cationic (dodecyl trimethylammonium bromide, DTAB), cationic gemini (butanediyl-1,4-bis(dimethylcetylammonium bromide), 16-4-16), ionic liquid (1-hexadecyl-3-methylimidazolium chloride, C<sub>16</sub>MImCl), and nonionic (polyoxyethylene sorbitan monostearate, Tween-60), has been investigated at a widespread range of surfactant concentrations (including premicellar, micellar, and postmicellar regime) in 15% (v/v) EtOH medium at room temperature. Several experimental techniques, viz., tensiometry, UV-vis spectroscopy, and steady-state fluorimetry, are implemented to explicate these interactions. Incorporation of H<sub>2</sub>DTC with surfactants having several inflections in surface tension, steady-state fluorimetry, and absorption profiles at different [surfactant] varying from low to high is found, apart from the conventional critical micelle concentration (cmc) of surfactants itself. This present study assesses equilibrium binding constant (<i>K</i><sub>b</sub>), Gibbs free energies of binding (<math><mi>Δ</mi><msubsup><mi>G</mi><mi>b</mi><mn>0</mn></msubsup></math>) of H<sub>2</sub>DTC with micelles of different surfactants, partition coefficient for H<sub>2</sub>DTC (<i>K</i><sub>x</sub>) in the micellar phase to solvent, molar absorptivity of H<sub>2</sub>DTC in the absence (ε<sub>0</sub>) and presence (ε) of micelles, and Gibbs free energy of partition of H<sub>2</sub>DTC (<math><mi>Δ</mi><msubsup><mi>G</mi><mi>p</mi><mn>0</mn></msubsup></math>) in the micellar to solvent phase. It has been observed that H<sub>2</sub>DTC strongly binds with the micelles of Tween-60 than the micelles of other surfactants investigated here and the corresponding <i>K</i><sub>x</sub> values are also found higher in micellar medium of Tween-60. On the other hand, the ε value of H<sub>2</sub>DTC is found lower in micellar Tween-60 medium, whereas it shows little rise in other cationic and anionic micellar medium, especially in cationic, compared with the H<sub>2</sub>DTC free solvent. Negative values of <math><mi>Δ</mi><msubsup><mi>G</mi><mi>b</mi><mn>0</mn></msubsup></math> and <math><mi>Δ</mi><msubsup><mi>G</mi><mi>p</mi><mn>0</mn></msubsup></math> strongly suggest that the binding and partitioning of H<sub>2</sub>DTC with micelles are feasible in solution medium. DFT calculations have been used to predict the geometries of the assemblies of the surfactants in monomeric form with H<sub>2</sub>DTC and the interaction energies.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 2","pages":"736-749"},"PeriodicalIF":2.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Therapeutic Advantages of Nanoparticle-Impregnated Lysozyme Conjugates toward Amyloid-β Fibrillation and Antimicrobial Activity. 纳米粒子浸渍溶菌酶共轭物对淀粉样β纤维化和抗菌活性的治疗优势
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-01-15 DOI: 10.1021/acs.jpcb.4c07261
Jahnabi Upadhyaya, Imocha Rajkumar Singh, Bishal Pun, Hirak Jyoti Baishya, Sugam Kumar, S R Joshi, Sivaprasad Mitra
{"title":"Therapeutic Advantages of Nanoparticle-Impregnated Lysozyme Conjugates toward Amyloid-β Fibrillation and Antimicrobial Activity.","authors":"Jahnabi Upadhyaya, Imocha Rajkumar Singh, Bishal Pun, Hirak Jyoti Baishya, Sugam Kumar, S R Joshi, Sivaprasad Mitra","doi":"10.1021/acs.jpcb.4c07261","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07261","url":null,"abstract":"<p><p>The interaction of protein with nanoparticles (NPs) of varying shape and/or size boosts our understanding on their bioreactivity and establishes a comprehensive database for use in medicine, diagnosis, and therapeutic applications. The present study explores the interaction between lysozyme (LYZ) and different NPs like graphene oxide (GO) and zinc oxide (ZnO) having various shapes (spherical, 's', and rod-shaped, 'r') and sizes, focusing on their binding dynamics and subsequent effects on both the protein fibrillation and antimicrobial properties. Typically, GO is considered a promising medium due to its apparent inhibition and prolonged lag phase for LYZ fibrillation. However, the present results showed that spherical ZnO NPs (sZnO) offer superior efficacy in modulating fibrillation with an extended lag time of about 158.70 h, further emphasizing the importance of detailed investigation on the nanomaterial characteristics and fibril formation kinetics beyond initial observations. The experimental findings further confirmed a strong correlation between the binding affinity of NPs to the native protein and their effective inhibition of protein denaturation, ultimately preventing fibril formation. Interestingly, the lysozyme nanoconjugates showed intriguing bactericidal effects, as confirmed through the agar plate assay and SEM imaging, over the native protein. Overall, this study shows that appropriate bionanomaterials can exhibit multifunctional properties, which paves the way for a deeper investigation of NP characteristics, ultimately benefiting a wide array of intriguing research.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deciphering the Photophysical Properties of Nonplanar Heterocyclic Compounds in Different Polarity Environments. 解密非平面杂环化合物在不同极性环境中的光物理特性。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-01-15 DOI: 10.1021/acs.jpcb.4c06300
Rajeswari Kainda, Santosh Kumar Behera, Asish K Dehury, Yatendra S Chaudhary
{"title":"Deciphering the Photophysical Properties of Nonplanar Heterocyclic Compounds in Different Polarity Environments.","authors":"Rajeswari Kainda, Santosh Kumar Behera, Asish K Dehury, Yatendra S Chaudhary","doi":"10.1021/acs.jpcb.4c06300","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06300","url":null,"abstract":"<p><p>Nonplanar (butterfly-shaped) phenothiazine (<b>PTZ</b>) and its derivative's (<b>M-PTZ</b>) photophysical and spectral properties have been tuned by varying the solvents and their polarity and investigated employing spectroscopic techniques such as UV-Vis, steady-state and time-resolved fluorescence, and TDDFT calculations. The UV-Vis absorption studies and TDDFT calculations reveal two distinct bands for both compounds: a strong π-π* transition at shorter wavelengths and a weaker <i>n</i>-π* transition, which displays a little bathochromic shift in polar solvents. The detailed emission studies reveal that such dual emission is a result of the photoinduced excited-state conjugation enhancement (ESCE) process. The band at a shorter wavelength corresponds to the locally excited (LE) state, while the longer wavelength band arises from the planarized excited state resulting from ESCE. With the increase in solvent polarity, the LE band is less affected, whereas strong positive solvatochromism is observed for the ESCE band. As the solvent polarity increases, the ESCE band demonstrates significant positive solvatochromism, while emission intensity decreases with higher solvent polarity, suggesting stabilization of the excited state. The biexponential decay of fluorescence lifetimes further corroborates the dual emission behavior of <b>PTZ</b> and <b>M-PTZ</b>. <b>PTZ</b> exhibits a higher photoluminescence quantum yield (PLQY) than that observed for <b>M-PTZ</b>, and the solvent viscosity influences the PLQY, indicating that nonradiative decay is activated during the planarization of the excited state, also known as excited-state conjugation enhancement. Furthermore, the (time-dependent) density functional theory (TD) DFT calculations performed to understand the geometrical parameters and the electronic transitions of these model molecules further corroborate experimental findings. These findings underscore the significant influence of solvent polarity and molecular structure on the dual emission and excited-state dynamics of <b>PTZ</b> and <b>M-PTZ</b>, which eventually hold substantial implications for advanced photophysical applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Investigating the Restricted Dynamical Environment in and Around Aβ Peptide Oligomers in Aqueous Ionic Liquid Solutions. 离子液体中Aβ肽低聚物及其周围受限动力环境的研究。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-01-15 DOI: 10.1021/acs.jpcb.4c07336
Subhadip Sahoo, Sanjoy Bandyopadhyay
{"title":"Investigating the Restricted Dynamical Environment in and Around Aβ Peptide Oligomers in Aqueous Ionic Liquid Solutions.","authors":"Subhadip Sahoo, Sanjoy Bandyopadhyay","doi":"10.1021/acs.jpcb.4c07336","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07336","url":null,"abstract":"<p><p>It is widely believed that the aggregation of amyloid β (Aβ) peptides into soluble oligomers is the root cause behind Alzheimer's disease. In this study, we have performed room-temperature molecular dynamics (MD) simulations of aggregated Aβ oligomers of different sizes (pentamer (O(5)), decamer (O(10)), and hexadecamer (O(16))) in binary aqueous solutions containing 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF<sub>4</sub>]) ionic liquid (IL). Investigations have been carried out to obtain a microscopic understanding of the effects of the IL on the dynamic environment around the exterior surfaces and within the confined nanocores of the oligomers. The calculations revealed that in contrast to nearly uniform dynamics near the exterior surface, heterogeneous structural distortions of oligomers of varying sizes and nonuniform distributions of water and IL components within their core volumes modify the core dynamics in a differential manner. It is demonstrated that increasingly restricted mobility of water and IL components is the origin behind the longer time scale of dynamic heterogeneity in and around the oligomers. Importantly, due to the equivalent nondirectional nature of the B-F bonds, BF<sub>4</sub><sup>-</sup> anions are found to reorient on a time scale faster than that of water molecules. Further, the structural relaxation of protein-anion (PA) hydrogen bonds around the oligomers has been found to be correlated with sluggish translational motions of the anions but anticorrelated with their reorientational time scale. In addition, it is quantified that compared to the pure aqueous medium, strengthening of protein-water (PW) hydrogen bonds in the presence of the IL leads to their longer lifetimes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Laser Flash Photolysis of Carbazole in Solution: Cation Radical as a Source of Carbazolyl Radical. 溶液中咔唑的激光光解:阳离子自由基是咔唑基自由基的来源。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-01-15 DOI: 10.1021/acs.jpcb.4c04401
Malgorzata Bayda-Smykaj, Gotard Burdzinski, Jacek Koput, Magdalena Grzelak, Gordon L Hug, Bronislaw Marciniak
{"title":"Laser Flash Photolysis of Carbazole in Solution: Cation Radical as a Source of Carbazolyl Radical.","authors":"Malgorzata Bayda-Smykaj, Gotard Burdzinski, Jacek Koput, Magdalena Grzelak, Gordon L Hug, Bronislaw Marciniak","doi":"10.1021/acs.jpcb.4c04401","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c04401","url":null,"abstract":"<p><p>In the course of 266 nm nanosecond laser flash photolysis of carbazole (CBL) in acetonitrile, we discovered a new transient absorption band centered at 360 nm that has been heretofore unreported despite numerous reports on similar topics. To put some limits on possible transients responsible for this absorption band and thus to solve the mechanism of CBL photolysis, we employed the strategy of selectively blocking the CBL active sites by various modifications in the structure. This strategy was supported by the use of the solvent effect and triplet quenching by molecular oxygen. As a result, the mechanism of carbazole photolysis has been elucidated, part of which was our new discovery that the carbazolyl radical can be formed by the deprotonation of the cation radical. The proposed mechanism has been supported by the reaction with TEMPO, theoretical calculations, and also LC-MS/UV analysis of the stable photoproducts. Given the high impact of CBL-based compounds as one of the key compounds in material science (e.g., OLEDs, TADF, and other light-emitting materials), the understanding of the observed radical-driven processes that occur in the photolysis of carbazole seems to be of great interest.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural and Dynamic Heterogeneity of Deep Eutectic Solvents Composed of Choline Chloride and Ortho-Phenol Derivatives. 由氯化胆碱和正苯酚衍生物组成的深共晶溶剂的结构和动态异质性。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-01-14 DOI: 10.1021/acs.jpcb.4c06787
Derrick Poe, Dinis O Abranches, Xiaoyu Wang, Jeffrey Klein, William Dean, Benworth B Hansen, Brian Doherty, Carla Fraenza, Burcu Gurkan, Joshua R Sangoro, Mark Tuckerman, Steven G Greenbaum, Edward J Maginn
{"title":"Structural and Dynamic Heterogeneity of Deep Eutectic Solvents Composed of Choline Chloride and Ortho-Phenol Derivatives.","authors":"Derrick Poe, Dinis O Abranches, Xiaoyu Wang, Jeffrey Klein, William Dean, Benworth B Hansen, Brian Doherty, Carla Fraenza, Burcu Gurkan, Joshua R Sangoro, Mark Tuckerman, Steven G Greenbaum, Edward J Maginn","doi":"10.1021/acs.jpcb.4c06787","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06787","url":null,"abstract":"<p><p>Structural, thermal, and dynamic properties of four deep eutectic solvents comprising choline chloride paired with <i>ortho-</i>phenolic derivative hydrogen-bond donors were probed using experiments and molecular simulations. The hydrogen-bond donors include phenol, catechol, <i>o</i>-chlorophenol, and o-cresol, in a 3:1 mixture with the hydrogen-bond acceptor choline chloride. Density, viscosity, and pulsed-field gradient NMR diffusivity measurements were conducted over a range of temperatures. Classical and ab initio molecular dynamics simulation results match experimental data reasonably well. The simulation results were then used to perform a more detailed analysis of the local structure and dynamics of these systems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pretrained Deep Neural Network Kin-SiM for Single-Molecule FRET Trace Idealization. 用于单分子FRET跟踪理想化的预训练深度神经网络Kin-SiM。
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-01-14 DOI: 10.1021/acs.jpcb.4c05276
Leyou Zhang, Jieming Li, Nils G Walter
{"title":"Pretrained Deep Neural Network Kin-SiM for Single-Molecule FRET Trace Idealization.","authors":"Leyou Zhang, Jieming Li, Nils G Walter","doi":"10.1021/acs.jpcb.4c05276","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c05276","url":null,"abstract":"<p><p>Single-molecule fluorescence resonance energy transfer (smFRET) has emerged as a pivotal technique for probing biomolecular dynamics over time at nanometer scales. Quantitative analyses of smFRET time traces remain challenging due to confounding factors such as low signal-to-noise ratios, photophysical effects such as bleaching and blinking, and the complexity of modeling the underlying biomolecular states and kinetics. The dynamic distance information shaping the smFRET trace powerfully uncovers even transient conformational changes in single biomolecules both at or far from equilibrium, relying on trace idealization to identify specific interconverting states. Conventional trace idealization methods based on hidden Markov models (HMMs) require substantial a priori knowledge of the system under study, manual intervention, and assumptions about the number of states and transition probabilities. Here, we present a deep learning framework using long short-term memory (LSTM) to automate the trace idealization, termed Kin-SiM. Our approach employs neural networks pretrained on simulated data to learn high-order correlations in the multidimensional FRET trajectories. Without user input of Markovian assumptions, the trained LSTM networks directly idealize the FRET traces to extract the number of underlying biomolecular states, their interstate dynamics, and associated kinetic parameters. On benchmark smFRET data sets, Kin-SiM achieves a performance similar to conventional HMM-based methods but with less hands-on time and lower risk of bias. We further systematically evaluate the key training factors that affect network performance to define the correct hyperparameter tuning for applying deep neural networks to smFRET data analyses.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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