The Journal of Physical Chemistry B最新文献

{"title":"Molecular Dynamics of Peptide Sequencing through MoS₂ Solid-State Nanopores for Binary Encoding Applications.","authors":"Andreina Urquiola Hernández, Christophe Guyeux, Adrien Nicolaï, Patrick Senet","doi":"10.1021/acs.jpcb.4c06277","DOIUrl":"10.1021/acs.jpcb.4c06277","url":null,"abstract":"<p><p>Biological peptides have emerged as promising candidates for data storage applications due to their versatility and programmability. Recent advances in peptide synthesis and sequencing technologies have enabled the development of peptide-based data storage systems for realizing novel information storage technologies with enhanced capacity, durability, and data access speeds. In this study, we performed coarse-grained peptide sequencing of 12 distinct sequences through single-layer MoS₂ solid-state nanopores (SSNs) using molecular dynamics (MD). Peptide sequences were composed of 1 positively charged, 1 negatively charged, and 4 neutral amino acids, with the position of amino acids in the sequence being shuffled to generate all possible configurations. From MD, the goal was to evaluate the efficiency of these peptide sequences to encode binary information based on ionic current traces monitored during their passage through the SSNs. Classification approaches using LightGBM were trained and tested to analyze different sequence factors such as the position of amino acids or the spacing between charged amino acids in the sequences. Our findings reveal the presence of two distinct groups of sequences determined by the relative position of the positively charged amino acid compared to the negatively charged amino acid. Furthermore, we observe a strong correlation between discrimination accuracy and the separation in the sequence between charged amino acids, depending on the number of adjacent neutral amino acids between them. Finally, MD allowed us to establish the nonlinear relationship between amino acid positions inside the pore (called sequence motifs) and fluctuations in ionic current traces to discriminate false positives and to enable effective training of machine learning classification algorithms. These very promising results emphasized the best approaches to design peptide sequences as building blocks for molecular data storage. Finally, this study highlights the potential of the proposed approach for designing peptide sequence combinations that could help the development of efficient, scalable, and reliable molecular data storage solutions, with future research focused on encoding longer binary chains to enhance storage capacity and support the goal of stable, energy-free biological systems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"96-110"},"PeriodicalIF":2.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142880720","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":"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":"417-422"},"PeriodicalIF":2.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726687/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Review of 2024 at <i>The Journal of Physical Chemistry</i>.","authors":"Joan-Emma Shea, T Daniel Crawford, Barbara Kirchner, Gregory V Hartland, Cary L Pint","doi":"10.1021/acs.jpcb.4c08544","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08544","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 1","pages":"1-2"},"PeriodicalIF":2.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941493","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":"Unlocking the Catalytic Potential of Anionic Micelles: Insights into the Ce(IV)-Directed Phenylalanine Oxidation Kinetics in Asymmetric Hydrophobic Environments.","authors":"Priya Karmakar, Mousumi Layek, Sk Mehebub Rahaman, Sandip Kundu, Kripasindhu Karmakar, Arnab Patra, Ujjwal Mandal, Pintu Sar, Bidyut Saha","doi":"10.1021/acs.jpcb.4c06663","DOIUrl":"10.1021/acs.jpcb.4c06663","url":null,"abstract":"<p><p>The oxidation kinetics of phenylalanine (Phe) by Ce(IV) have been examined in both the absence and presence of aqueous micellar media with asymmetric tails, specifically using sodium dodecyl sulfate (SDS) and sodium tetradecyl sulfate (STS) surfactants. The reaction progress was monitored by observing a decrease in absorbance using UV-vis spectroscopy. Interestingly, the kinetic profile revealed a consistent increase in the observed rate constant values as the concentration of the surfactant increased. The kinetic results have been analyzed by using numerous experimental studies, such as dynamic light scattering (DLS), zeta potential, ¹H NMR analysis, FT-IR spectroscopy, conductometry, scanning electron microscopy (SEM), fluorometry, time-correlated single-photon counting (TCSPC), and transmission electron microscopy (TEM). Micellar aggregates maintain their spherical shape in the presence of the substrate, even at higher surfactant concentrations, as revealed by microstructural analysis. The substrate molecules are encapsulated to a greater extent in the inner micellar core of STS micelles on account of the more hydrophobic nature of STS surfactants. Therefore, in STS micellar media, fewer substrate molecules diffuse to the Stern layer compared to the SDS micellar medium, resulting in fewer molecules participating in the oxidative transformation reaction. As a result, the rate enhancement of oxidation kinetics is less pronounced in STS micelles than in SDS micelles. A plausible mechanism that aligns with the kinetic results has been highlighted, along with the interpretation of the Piszkiewicz model, to explain the observed catalytic effect of both micellar mediums.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"238-249"},"PeriodicalIF":2.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142851673","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":"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":"385-397"},"PeriodicalIF":2.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726678/pdf/","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":"OA","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":"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":"563-578"},"PeriodicalIF":2.8,"publicationDate":"2025-01-09","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":"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":"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":"260-272"},"PeriodicalIF":2.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726616/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First-Principles Study on Formation Mechanism of Six-Coordinated Si in Silicophosphate Glass.","authors":"Arata Sakakibara, Tomoyuki Tamura, Kazuya Takada, Toshihiro Kasuga","doi":"10.1021/acs.jpcb.4c04427","DOIUrl":"10.1021/acs.jpcb.4c04427","url":null,"abstract":"<p><p>Six-coordinated Si (^[6]Si) structures are readily formed in silicophosphate glasses with high P₂O₅ contents. Although experiments and simulations have provided some information on the local configurations around ^[6]Si, further research on the formation mechanism of ^[6]Si at the atomic scale is needed. To investigate the formation mechanism of ^[6]Si, we performed dynamic and static analyses based on first-principles calculations. In first-principles molecular dynamics simulations with models in which all Si atoms are four-coordinated as the initial structure, we observed that the coordination number of Si increased, and the P-Q² (P-Q^<i>n</i>, where <i>n</i> represents the number of bridging oxygen atoms) changed to P-Q³. Atomic energy analysis revealed that the energy decreases with the structural change from P-Q² to P-Q³ exceeded the energy increase with an increase in the coordination number of Si, stabilizing of the entire system. We conclude that the key factor in the formation of ^[6]Si is the decrease in energy associated with the change from a nonbridging oxygen in a PO₄ tetrahedral structure to bridging oxygen.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"447-455"},"PeriodicalIF":2.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845321","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":"Supercritical Water: Density-Independent Angular Jumps.","authors":"Ashu Choudhary, Arpan Kundu, Chaitanya Singh, Abhiruchi Sharma, Kamal Kishore Pant, Amalendu Chandra","doi":"10.1021/acs.jpcb.4c05676","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c05676","url":null,"abstract":"<p><p>Molecular dynamics simulations were employed to investigate the reorientation dynamics of water molecules under supercritical conditions. Our findings indicate that supercritical water consists of a fluctuating assembly of water clusters of varying sizes. The reorientational motions are characterized by large angular displacements and occur on fast time scales. We found that the decreasing density of supercritical water correlates with a decrease in the number of angular jumps as more water molecules were found in isolated or small clustered states at lower densities. Notably, the amplitude of rotational jumps in relative coordinates does not depend much on the density of supercritical water at a given temperature.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 1","pages":"329-337"},"PeriodicalIF":2.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941495","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 Insights into Binary Ionic Melts of Protic Ionic Liquid 1,2,4-Triazolium Methanesulfonate and Methanesulfonic Acid Electrolytes.","authors":"Shweta Dagar, Shijie Liu, Jiangshui Luo, Anurag Prakash Sunda","doi":"10.1021/acs.jpcb.4c05867","DOIUrl":"10.1021/acs.jpcb.4c05867","url":null,"abstract":"<p><p>Binary ionic melts formed by a protic ionic liquid (PIL) 1,2,4-triazolium methanesulfonate ([TAZ][MS]) dissolved in methanesulfonic acid are studied as non-stoichiometric electrolytes. The composition-driven structure-property relationship of methanesulfonic acid is explored at varying molar fraction ratios from 0/100 to 10/90, 20/80, and 30/70 by the addition of 1,2,4-triazolium methanesulfonate [TAZ][MS] IL. To unveil molecular characteristics of these mixtures of [TAZ][MS] PIL and CH₃SO₃H, we performed classical molecular dynamics simulations at varying temperatures from 293 to 303, 363, and 423 K. Ion-pair interactions and ion-solvent interactions are captured through various atom-atom radial distribution functions, and hydrogen bonding is presented through N-H hydrogen atom interactions with the [MS]^- anion or CH₃SO₃H oxygen atoms. Apart from the temperature, the PIL ratio itself plays a critical role in hydrogen bonding interactions, and spatial density distribution maps show strengthening of ion-pair interactions with an increase in PIL concentration. The mobility of ions and CH₃SO₃H is also explored through mean square displacement plots and by calculating the diffusion coefficient. The diffusion coefficient is used to calculate Nernst-Einstein conductivity, which shows an excellent match with experimental conductivity at 363 and 423 K.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"338-347"},"PeriodicalIF":2.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142884836","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}