The Journal of Physical Chemistry B最新文献

{"title":"Interactions and Oscillatory Dynamics of Chemically Powered Soft Swimmers.","authors":"Suzanne Ahmed, Juan Perez-Mercader","doi":"10.1021/acs.jpcb.4c07069","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07069","url":null,"abstract":"<p><p>We report the interactions and dynamics of chemically powered soft swimmers that undergo autonomous oscillatory motion. The interaction of autonomous entities is the basis for the development of collective behaviors among biological organisms. Collective behaviors enable organisms to efficiently attain food and coordinate against threats. The basis of these behaviors is the interaction between nearest neighbors. Mimicking these interactions in artificial systems would enable their organization for the performance of complex tasks. Oscillatory phenomena are also ubiquitous in nature. Hence artificial oscillatory systems can serve as the most direct mimics and models of many biological systems. In this work, we report the interactions and dynamics of oscillatory swimmers propelled by the nonlinear oscillatory Belousov-Zhabotinsky (BZ) reaction. Individually, these swimmers displace by undergoing nonfully reciprocal oscillatory motion in conjunction with the BZ reaction. We find that, in addition to their individual oscillatory motion, multiple BZ swimmers exhibit successive oscillatory changes in their inter swimmer distance. This oscillatory attraction and repulsion between adjacent swimmers occurs in conjunction with the BZ waves and oxidation state of the catalyst. The effect of swimmer size and number on these dynamic interactions is interrogated. The level of chemical synchronization between multiple swimmers is determined. This work is a starting point for the design of collective behaviors utilizing autonomous chemically propelled soft swimmers.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875357","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":"Design and Synthesis of Novel Dual-Functional Protic Ionic Liquids with a Superior High CO₂ Absorption Efficiency.","authors":"Jing Ma, Yaxuan Du, Meizhe Liu, Yamei Zhou, Xiejun Wang, Baohe Wang, Jing Zhu, Mingxuan Zhu","doi":"10.1021/acs.jpcb.4c06299","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06299","url":null,"abstract":"<p><p>As a predictive tool, quantum chemical calculations can be used to design protic ionic liquids (PILs) and predict the result. By adding anionic negative potential sites, two dual-functional PILs diethylenetriamine-barbituric acid [C₄H₁₄N₃]₂[C₄H₂N₂O₃] and diethylenetriamine-ethylenolactonium [C₄H₁₄N₃]₂[C₃H₂N₂O₂] were designed. The simulation results indicated that multisite absorption of anions and cations resulted in an expected absorption ratio exceeding 3:1 (mol CO₂:mol ILs). Furthermore, the Gibbs free energy and enthalpy barrier were calculated. Based on this, the two PILs were synthesized in a controlled manner, and the experimental results demonstrated that 0.25 mol/L [C₄H₁₄N₃]₂[C₄H₂N₂O₃] and [C₄H₁₄N₃]₂[C₃H₂N₂O₂] exhibited a superior CO₂ absorption capacity of 3.152 and 3.466 mol CO₂/mol ILs, respectively. After five adsorption-desorption experiments, the regeneration rates of [C₄H₁₄N₃]₂[C₃H₂N₂O₂] were all higher than 90%. Finally, the reaction mechanism for CO₂ capture in these PILs was revealed that the significant increase in capacity could be attributed to the combined absorption of double negative potential N atoms on anions and primary and secondary amines on cations by using ¹³C NMR.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875353","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":"Fluctuating Spinodal-like Structure in the Glacial Phase of d-Mannitol.","authors":"Jianing Wang, Lijian Song, Xiao Chen, Xiao Jin, Meng Gao, Juntao Huo, Jun-Qiang Wang","doi":"10.1021/acs.jpcb.4c06398","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06398","url":null,"abstract":"<p><p>The glacial phase can be formed from supercooled liquid (SCL) in certain systems, which is called liquid-liquid transition (LLT). Revealing the nature of the glacial phase especially in a single-component system is crucial for understanding the LLT process. Here, by using flash differential scanning calorimetry and cold-field transmission electron microscopy, the structure of the d-mannitol glacial phase and the phase transition kinetics between the glacial phase and SCL were studied. We found that the glacial phase is a fluctuating spinodal-like structure. And the glacial phase displays a first-order melting characteristic when it transforms into the SCL. Furthermore, the LLT diagram in the enthalpy-temperature coordinate system is constructed based on the nucleation-growth and spinodal-decomposition transitions. Our findings provide new insight into the LLT process of the glass forming liquids.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875355","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":"Molecular Dynamics Simulations on Heat Transport of Nanoconfined Water under Electric Fields: Effect of Nanochannel Size.","authors":"Wen-Qing Guo, Jie-Wen Deng, Bing-Bing Wang","doi":"10.1021/acs.jpcb.4c06213","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06213","url":null,"abstract":"<p><p>When water is confined in a nanochannel, its thermodynamic and kinetic properties change dramatically compared to the macroscale. To investigate these phenomena, we conducted nonequilibrium molecular dynamics simulations on the heat transfer in copper-water nanochannels with lengths ranging from 12 to 20 nm in the absence and presence of an electric field. The results indicate that in the absence of an electric field (<i>L</i>_<i>z</i> = 12-20 nm), the binding force between water molecules in the 20 nm nanochannel is the weakest, facilitating thermal motion in the liquid phase. When compared to the 12 nm nanochannel, the enhancement rate of the thermal conductivity is 19.53%. In the presence of a uniform electric field in the positive <i>z</i>-direction (<i>L</i>_<i>z</i> = 12-16 nm), water molecules in the 16 nm nanochannel are more readily frozen into ice crystal structures. This change in the mode of heat transfer shifts from the thermal diffusion of water molecules to the vibrations between copper atoms and the ice crystal, resulting in a significant increase in the thermal conductivity of water.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875360","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":"Robust Method for Property Prediction via Artificial Neural Networks: Incorporating Key Structural Features for Carbon Dioxide-Ionic Liquid Mixtures.","authors":"Hugo Marques, José N Canongia Lopes, Adilson Alves de Freitas, Karina Shimizu, Pedro S F Mendes","doi":"10.1021/acs.jpcb.4c04432","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c04432","url":null,"abstract":"<p><p>This study addresses a critical gap in the existing literature on carbon dioxide and ionic liquid (IL) mixtures, where fragmented and incomplete data, particularly for flow properties, hinder practical applications. Therefore, this work aimed to establish a robust and efficient method for predicting the density of the CO₂-IL mixtures across diverse operating conditions and IL families using novel validation techniques. Both linear and symbolic regression models provided relevant insights but failed to accurately capture the IL-CO₂ interactions in a mixture that determine the molar volume of CO₂ at infinite dilution when solubilized by a given IL. Therefore, more mathematically flexible artificial neural networks (ANN) were trained based on three different sets of features: (1) IL critical properties, (2) IL structural descriptors, and (3) a selective combination of (1) and (2). While all models showed relative deviations consistently below 3% for the testing data, combining critical and structural data significantly improved accuracy (<i>R</i>² = 0.986, testing data set). A postprocessing outlier-handling method enhanced model performance, removing a minimal fraction (below 0.2%) of unphysical data points. Furthermore, molecular dynamics simulations validated the robust generalization of all ANN models, with the combined model exhibiting remarkable accuracy over operating conditions outside the training ranges for ILs in the training set and even for ILs that are not included in this data set. This computational approach provides a significantly faster and broader alternative to other thermodynamical tools, establishing a solid method for future machine learning (ML)-based property prediction augmented by external validation from cross-comparison tests and statistical thermodynamics models.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875373","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":"Ordered Aggregates of Fmoc-Diphenylalanine at Alkaline pH as a Precursor of Fibril Formation and Peptide Gelation.","authors":"Emily Hughes, Nichole S O'Neill, Reinhard Schweitzer-Stenner","doi":"10.1021/acs.jpcb.4c06796","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06796","url":null,"abstract":"<p><p>The ultrashort peptide <i>N</i>-fluorenylmethoxycarbonyl-phenylalanyl-phenylalanine (FmocFF) has been largely investigated due to its ability to self-assemble into fibrils (100 nm-μm scale) that can form a sample-spanning gel network. The initiation of the gelation process requires either a solvent switch (water added to dimethyl sulfoxide) or a pH-switch (alkaline to neutral) protocol, both of which ensure the solubility of the peptide as a necessary step preceding gelation. While the respective gel phases are well understood in structural and material characteristics terms the pregelation conditions are known to a lesser extent. The question we asked is to what extent the gel-forming fibrils are already partially formed, i.e., oligomers or protofibrils. Focusing on the pregelation conditions for the pH-switch method, we investigated the self-assembly of soluble FmocFF aggregates in alkaline pH by UV circular dichroism, IR, vibrational circular dichroism, and ¹H NMR spectroscopy for different peptide concentrations and more systematically as a function of temperature. The temperature dependence of the UVCD spectra of FmocFF in H₂O and D₂O revealed a complicated isotope effect that affects the peptide backbone and fluorene conformations in peptide aggregates differently. Moreover, we found that the melting of formed aggregates depends on peptide concentration in a nonmonotonic way. At 20 mM the UVCD data revealed the population of at least two different thermodynamic intermediate states, which seem to differ in terms of the relative arrangement of the fluorene moiety. The IR spectrum of this sample at room temperature indicates an antiparallel β-sheet arrangement, as suggested earlier in the literature. However, we show that this interpretation can only be valid if one invokes a nondispersive redshift of the two amide I' bands in a locally crystalline environment. The respective vibrational circular dichroism spectrum of the amide I' region is consistent with a left-handed helically twisted structure of the formed aggregates. A comparison of our data with spectra of the aqueous gel phase suggests that fibrils in the latter resemble the ones at alkaline pH probed by our experiments.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875362","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":"Photoisomerization Dynamics of Azo-Escitalopram Using Surface Hopping and a Semiempirical Method.","authors":"Hans Georg Gallmetzer, Eduarda Sangiogo Gil, Leticia González","doi":"10.1021/acs.jpcb.4c06924","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06924","url":null,"abstract":"<p><p>The photoisomerization dynamics of azo-escitalopram, a synthetic photoswitchable inhibitor of the human serotonin transporter, is investigated in both gas-phase and water. We use the trajectory surface hopping method─as implemented in SHARC─interfaced with the floating occupation molecular orbital-configuration interaction semiempirical method to calculate on-the-fly energies, forces, and couplings. The inclusion of explicit water molecules is enabled using an electrostatic quantum mechanics/molecular mechanics framework. We find that the photoisomerization quantum yield of trans-azo-escitalopram is wavelength- and environment-dependent, with <i>n</i> → π* excitation yielding higher quantum yields than π → π* excitation. Additionally, we observe the formation of two distinct cis-isomers in the photoisomerization from the most thermodynamically stable trans-isomer, with formation rates influenced by both the excitation window and the surrounding environment. We predict longer excited-state lifetimes than those reported for azobenzene, suggesting that the escitalopram moiety contributes to prolonged lifetimes and slower torsional motions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142870580","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":"Vulcanization Accelerators and Silica Coupling Agents in Polyisoprene Melts.","authors":"Nikolaos Patsalidis, George J Papakonstantopoulos, Jan Domurath, Patrycja Polińska, Craig Burkhart, Vagelis Harmandaris, Manolis Doxastakis","doi":"10.1021/acs.jpcb.4c07099","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07099","url":null,"abstract":"<p><p>The achievement of sufficient dispersion of vulcanization accelerators is critical to tailoring superior cross-linked elastomers. Modern recipes rely on multicomponent formulations with silica particles covered by coupling agents. We study the molecular properties of select accelerators in polyisoprene melts and their affinity for functionalized surfaces via extensive all-atom molecular dynamics simulations. We focus on the common (<i>N</i>-cyclohexyl)-2-benzothiazole sulfenamide (CBS), 1,6-bis(<i>N</i>,<i>N</i>-dibenzylthiocarbamoyldithio)hexane (DBTH), and diphenyl guanidine (DPG) molecules and their mixing characteristics at curing temperatures. Our results support a low self-association affinity for CBS and DBTH within polyisoprene, whereas DPG forms small hydrogen-bonded aggregates. Subsequently, we examine systems in contact with silica interfaces, bare or grafted with (3-mercaptopropyl)triethoxysilane (MPTES), (3-octanoylthio) 1-propyl-triethoxysilane (NXT), and bis[3-(triethoxysilyl)propyl]disulfide (TESPD). Accelerator-substrate affinity is first assessed at infinite dilution using free energy calculations and subsequently at finite concentrations. Accelerators exhibit high substrate affinity (DPG > CBS > DBTH) irrespective of functionalization. However, coupling agents are able to displace from the surface a significant amount that increases with the grafting density and the size of the coupling agent. Finally, we investigate the behavior of DPG in binary DPG-CBS formulations, where the former can act as a covering agent that solubilizes CBS into the bulk polymer.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142870582","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":"Computational Method for Determining the Excess Chemical Potential Using Liquid-Vapor Phase Coexistence Simulations.","authors":"Andrew M Fadgen, Nicholas A Pizzi, Rodney J Wigent, Preston B Moore","doi":"10.1021/acs.jpcb.4c07206","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07206","url":null,"abstract":"<p><p>Molecular dynamics simulations are a powerful tool for probing and understanding the theoretical aspects of chemical systems and solutions. Our research introduces a novel method for determining the excess chemical potential of non-ideal solutions by leveraging the equivalence between the chemical potential of the vapor phase and liquid phase. Traditional approaches have relied on bulk simulations and the integration of pair distribution functions (<i>g</i>(<i>r</i>)), which are computationally intensive to obtain accurate results. In contrast, our method utilizes a liquid-gas system, where determining the vapor pressure allows for a quick and accurate calculation of the excess chemical potential relative to a reference system, e.g., pure solvent. This approach significantly reduces computational effort while maintaining high accuracy and precision. We demonstrate the effectiveness of this method using a simplified Lennard-Jones model, although the method is broadly applicable to a wide range of systems, including those with complex interactions, varying concentrations, and different temperatures. The reduced computational demands and versatility of our approach make it a valuable tool for studying non-ideal solutions, including ionic solutions in molecular simulations.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862542","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":"Coarse-Grained Simulation Study of the Association of Selected Dipeptides.","authors":"Mateusz Leśniewski, Emilia Iłowska, Justyna Sawicka, Zihan Li, Chun Tang, Adam Liwo","doi":"10.1021/acs.jpcb.4c06305","DOIUrl":"10.1021/acs.jpcb.4c06305","url":null,"abstract":"<p><p>The association of 55 dipeptides extracted from aggregation-prone regions of selected proteins was studied by means of multiplexed replica-exchange molecular dynamics simulations with the coarse-grained UNRES model of polypeptide chains. Each simulation was carried out with 320 dipeptide molecules in a periodic box at 0.24 mol/dm³ concentration, in the 260-370 K temperature range. The temperature profiles of the degree of association, distributions of dipeptide cluster size, and structures of clusters were examined. It has been found that the dipeptides composed of strongly nonpolar (aromatic or aliphatic) residues associate nearly completely at all temperatures to form tight clusters, while those composed of charged or polar residues exhibited no or residual association. The dipeptides composed of nonpolar and small polar residues and those composed of less hydrophobic residues formed single clusters, gradually dissolving with increasing temperature, while those composed of phenylalanine or tryptophan and polar or charged residues formed multiple irregular clusters with room to accommodate water inside, suggesting the formation of liquid droplets or gels. The logarithms of the average degree of association and the free energy of aggregation per monomer were found to correlate with the dipeptide hydrophobicity.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12403-12415"},"PeriodicalIF":2.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142778799","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}