The Journal of Physical Chemistry B最新文献

{"title":"d-Limonene and 1-Pentanol Mixtures: Vapor–Liquid Equilibrium Analysis Using Molecular Dynamics","authors":"Suguru Nishikawa,&nbsp; and ,&nbsp;Hitoshi Washizu*,&nbsp;","doi":"10.1021/acs.jpcb.4c0747810.1021/acs.jpcb.4c07478","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07478https://doi.org/10.1021/acs.jpcb.4c07478","url":null,"abstract":"<p >Vapor–liquid equilibrium (VLE) data of fragrance components are crucial for product development and separation processes. However, experimentally obtaining these data can often be a high-cost and challenging task. In order to address this issue, simulations of VLE data using molecular dynamics (MD) methods have gained attention, though there are still relatively few studies about the vapor–liquid equilibrium calculations of fragrance components using MD. In this study, we focused on a mixture of <i>d</i>-limonene and 1-pentanol as representative components and conducted MD simulations. The VLE data obtained by varying the molar fraction of <i>d</i>-limonene, including x-y phase diagrams and activity coefficients, showed a high degree of agreement with the experimental data. Additionally, an analysis of the density profiles on a molecular level revealed a slight increase in the concentration of 1-pentanol at the vapor–liquid interface.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 12","pages":"3216–3223 3216–3223"},"PeriodicalIF":2.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143703876","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":"Microscopic Significance of Hydrophobic Residues for Protein Stability in Ionic Liquids","authors":"Guochao Sun,&nbsp;Bing Fang,&nbsp;Yanmei Yang,&nbsp;Yuanyuan Qu,&nbsp;Qingmeng Zhang* and Weifeng Li*,&nbsp;","doi":"10.1021/acs.jpcb.5c0023610.1021/acs.jpcb.5c00236","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00236https://doi.org/10.1021/acs.jpcb.5c00236","url":null,"abstract":"<p >It is well-known that ionic liquids (ILs) can alter the structural stability of proteins. The change in protein conformation is closely related to the interaction between the protein residue and ILs. To probe the impact of hydrophobic interactions on protein stability in ILs, we conducted molecular dynamic simulations and compared the unfolding process of two proteins, the wild-type villin headpiece protein HP35 and its doubly mutant form HP35NN which contains two hydrophobic norleucine (NLE) substitutions at Lys24/29, in hydrated 1-butyl-3-methylimidazolium chloride ([BMIM]Cl). By sampling at a long time scale, the denaturation ability of ILs was well captured. Specifically, HP35NN exhibits greater structural instability than HP35, characterized by the unfolding of helix-3 where the mutated hydrophobic residues are located. These findings highlight the thermodynamic instability of the protein caused by the mutation of two hydrophobic residues in the ILs. By evaluating the hydration kinetics of helix-3 with ILs, we found that the intramolecular hydrogen bonds of HP35NN were broken. At the same time, HP35NN binds to more ILs through hydrophobic interactions. Therefore, we propose that the hydrophobic interaction between ILs and the mutated hydrophobic residue plays a crucial role in the denaturation of HP35NN. The stability comparison and verification of the alkyl chain model of hydrophobic residues in ILs also further prove the instability of hydrophobic residue mutation in ILs. These findings may provide valuable basic information for understanding the effect of ILs on the conformational stability of proteins.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 12","pages":"3244–3252 3244–3252"},"PeriodicalIF":2.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143703877","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":"Understanding Anti-Polyelectrolyte Effect in Polyzwitterions Using Coarse-Grained Molecular Dynamics Simulations","authors":"Akshay Chauhan,&nbsp; and ,&nbsp;Srabanti Chaudhury*,&nbsp;","doi":"10.1021/acs.jpcb.4c0772810.1021/acs.jpcb.4c07728","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07728https://doi.org/10.1021/acs.jpcb.4c07728","url":null,"abstract":"<p >Polyzwitterions (PZs)─polymers bearing both positive and negative charges within each repeating unit─exhibit an unusual antipolyelectrolyte effect where their solubility and viscosity increase upon the addition of salt, contrary to typical polyelectrolytes. As model synthetic analogues of intrinsically disordered proteins, PZs in dilute aqueous solutions are expected to adopt either globular or random coil conformations, with salt addition influencing these structures. We employed coarse-grained Langevin dynamics simulations to investigate how structural parameters─specifically, the spacing between dipolar side chains (<i>d</i>), and the overall polymer chain length (<i>N</i>)─affect the conformational properties of polyzwitterions in salt solutions. Our simulations reveal that added salt leads to nonmonotonic changes in the polymer’s radius of gyration, exhibiting both antipolyelectrolyte and polyelectrolyte effects depending on the salt concentration. This behavior is attributed to charge regulation and screening of dipole–dipole interactions by ions. Understanding and controlling the conformations of PZs in aqueous solutions by adjusting salt concentration is of paramount interest for applications in antimicrobial materials, antifouling coatings, drug delivery, membranes, and polymer electrolytes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 12","pages":"3253–3262 3253–3262"},"PeriodicalIF":2.8,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143703870","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":"Water Droplet and Its Contact Line Characteristics on Hydrophobic and Hydrophilic Surfaces: A Molecular Dynamics Simulation Approach.","authors":"Zahra Shamsi, Masumeh Foroutan","doi":"10.1021/acs.jpcb.4c08403","DOIUrl":"10.1021/acs.jpcb.4c08403","url":null,"abstract":"<p><p>In literature, for a water droplet on a solid surface, the set of points at the intersection of the three phases, solid_ liquid_ gas, is referred to as the triple phase contact line (TPCL). However, recent studies indicate that the intersections of these phases form a region, which we refer to as the triple phase contact vicinity (TPCV). In the present work, the dimensions of the TPCV, including its width and cross-sectional area, have been calculated for a water droplet on a wide range of hydrophilic and hydrophobic surfaces, using molecular dynamics simulations. Additionally, the behavior of molecules, including their presence frequency, velocity, and displacement, has been studied. The results indicate that, as the surface becomes more hydrophobic, the width of the TPCV increases and its cross-sectional area decreases. The presence frequency of molecules located at the TPCV in equilibrium shows that the molecules are arranged in a Gaussian distribution and exhibit oscillatory movements around their average positions. It has also been shown that in equilibrium TPCV of hydrophobic surfaces, there are more molecules moving toward the center of the droplet relative to hydrophilic surfaces. Conversely, in equilibrium TPCV of hydrophilic surfaces, there are more molecules that move toward wetting the substrate relative to hydrophobic surfaces. Furthermore, for hydrophobic surfaces, the velocity of molecules moving toward the center of the droplet is greater than the velocity of molecules moving toward wetting the substrate. On hydrophilic surfaces, these two velocities are almost identical. Water molecules on hydrophobic surfaces move faster in all directions; however, on hydrophilic surfaces, they move slower in one direction. The density profile of the droplet on the surface shows that for hydrophobic surfaces, the highest density is reported at the center of the droplet. In contrast, for hydrophilic surfaces, due to the formation of layers of water molecules parallel to the substrate, the highest density is reported in the closest layer to the surface. At the end, considering the importance of graphene and its wettability behavior, which has recently attracted significant attention, the investigations related to the TPCV on the graphene surface are also reported.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"2708-2717"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497567","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":"Impacts of External Electric Fields on Structures and Alignments of Ring Molecules.","authors":"Jiang Wang, Zhiling Li, Wenli Zhang","doi":"10.1021/acs.jpcb.4c06923","DOIUrl":"10.1021/acs.jpcb.4c06923","url":null,"abstract":"<p><p>Ring molecules, which lack free ends, exhibit unique chemical and physical properties, making them promising candidates for nanodevice applications. Unlike their linear counterparts with two free ends, the behavior of ring molecules in water under external electric fields (EF) is not well understood. In this research, we employ molecular dynamics (MD) simulations to explore the structural and alignment behavior of two ring molecules of different sizes─C₃₀H₆₀ and C₆₀H₁₂₀─in water, under 300 K, 1 bar and various EF conditions, including direct current EF (DC EF), alternating current EF (AC EF), and circular polarized EF (CP EF) at different frequencies. Our findings reveal the following: (1) both large and small rings exhibit two free energy minima. For C₆₀H₁₂₀, these correspond to collapsed and stretched configurations, while for C₃₀H₆₀, they represent open and closed configurations. (2) The applied EF can regulate the depth of these free energy minima. For C₆₀H₁₂₀, no EF, AC EF, and high-frequency CP EF favor the collapsed state, while DC EF and low-frequency CP EF promote the stretched configuration. In the case of C₃₀H₆₀, no EF and high-frequency CP EF favor the open-ring state, whereas all other EF conditions tend to close the ring. (3) Both ring molecules align with the directional EF to minimize disruption of the hydrogen-bond network, with C₆₀H₁₂₀ showing a stronger alignment effect than C₃₀H₆₀ due to its longer structure. (4) Under CP EF, ring molecules exhibit rotation driven by the rotating EF, but there is a lag in the angle between the EF vector and the molecule's elongation. Higher frequency CP EF shows less ability to capture and align the molecule. This research enhances our understanding of how ring molecules behave in water under external EF and provides a theoretical foundation for future engineering applications involving controlled manipulation of these molecules.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"2746-2760"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514153","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 Structure Refinement of a ß-Heptapeptide Based on Residual Dipolar Couplings: The Challenge of Extracting Structural Information from Measured RDCs","authors":"Maria Pechlaner*,&nbsp;Wilfred F. van Gunsteren,&nbsp;Lorna J. Smith and Niels Hansen,&nbsp;","doi":"10.1021/acs.jpcb.4c0695510.1021/acs.jpcb.4c06955","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06955https://doi.org/10.1021/acs.jpcb.4c06955","url":null,"abstract":"<p >The experimental determination of residual dipolar couplings (RDCs) rests on sampling the rotational motion of a molecule in an environment that induces a slightly nonuniform, unfortunately immeasurable, orientation distribution of the molecule in solution. Averaging over this slightly nonuniform, anisotropic distribution reduces the size of the dipolar couplings (DCs) from the kHz range to the Hz range for the resulting RDCs by a factor of 10³ to 10⁴. These features hamper the use of measured RDCs to contribute to the structure determination or refinement of (bio)molecules. The commonly used alignment-tensor (<i>AT</i>) methodology assumes that the immeasurable, unknown orientation distribution of the molecule can be expressed in terms of five spherical harmonic functions of order 2. Staying close to experiment, RDCs can, alternatively, be calculated from a molecular simulation by sampling the rotational motion of the molecule (<i>MRS</i> method) or, instead, of a vector (<i>mfv</i>) representing the magnetic field (<i>HRS</i> method). The <i>AT</i> and <i>HRS</i> methods were applied to a β-heptapeptide solvated in methanol, for which 131 NOE atom–atom distance upper bounds and 21 ^<i>3</i><i>J</i>-couplings derived from NMR experiments are available and, in addition, 39 RDC values obtained for the molecule solvated in methanol with polyvinyl acetate added. In methanol at room temperature and pressure, the molecule adopts a relatively stable helical fold. It appears that MD simulation of the molecule in methanol using the GROMOS biomolecular force field already satisfies virtually all experimental data. Application of RDC restraining shows the limitations caused by the assumptions on which the <i>AT</i> and <i>HRS</i> methods rest and suggests that experimentally measured RDCs are less useful for molecular structure determination or refinement than other observable quantities that can be measured by NMR techniques. The results illustrate that in structure determination or refinement of a (bio)molecule based on experimentally measured data, it is mandatory (i) to refrain from the vacuum boundary condition and (ii) from torsional-angle restraints that do not account for the multiplicity of the inverse function of the Karplus relation expressing ³<i>J</i>-couplings in terms of molecular torsional angles, (iii) to allow for Boltzmann-weighted time- or molecule-averaging and, not the least, (iv) to use a force field that has an adequate basis in thermodynamic data of biomolecules.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 12","pages":"3131–3158 3131–3158"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpcb.4c06955","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143703783","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":"Phospholipid Bilayer Properties in pH-Responsive Hemoglobin-Based Oxygen Carriers.","authors":"John M Sansalone, Parikshit Moitra, Allan Doctor, Dipanjan Pan, N R Aluru","doi":"10.1021/acs.jpcb.4c07060","DOIUrl":"10.1021/acs.jpcb.4c07060","url":null,"abstract":"<p><p>Hemoglobin (Hb)-based oxygen carriers (HBOCs) are a potential solution to the growing shortage in the worldwide blood supply. Recent developments in HBOC design have shown that Polyethylene glycol surface-conjugated liposome-encapsulated Hb (PEG-LEH) has shown promising results in mimicking the oxygen uptake and release of human red blood cells. This study aims to use atomistic simulations to investigate the mechanical properties, gas-exchange properties, and pH responsiveness of a novel HBOC which introduces a pH-sensitive molecule (KC1003) to the phospholipid membrane to regulate the uptake and release of oxygen based on pH. Mechanical properties of KC1003 in a phospholipid membrane show that it is a stable phospholipid membrane, with slight structural differences from increasing the concentration of KC1003, where an increased concentration slightly increases lipid disorder. Gas diffusion through the membrane was not limited by the addition of KC1003, and the gas diffusion values were similar to those of red blood cells. Furthermore, the membrane proved to be pH responsive, allowing for the binding and release of 2,3-DPG (2,3-Diphosphoglyceric Acid) at high and low pHs, respectively. These results collectively show that the membrane is mechanically stable at physiological conditions at a molecular scale, allows for proper gas diffusion through the phospholipid membrane, and can act as a pH-sensitive lipid membrane that the concentration of KC1003 can modify. Collectively, these results can be used for tuning of the membrane of an HBOC to mimic the physiological oxygen intake and release of a red blood cell.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"2668-2677"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536204","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":"A Machine Learning Model for the Prediction of Water Contact Angles on Solid Polymers.","authors":"Jose Sena, Linus O Johannissen, Jonny J Blaker, Sam Hay","doi":"10.1021/acs.jpcb.4c06608","DOIUrl":"10.1021/acs.jpcb.4c06608","url":null,"abstract":"<p><p>The interaction between water and solid surfaces is an active area of research, and the interaction can be generally defined as hydrophobic or hydrophilic depending on the level of wetting of the surface. This wetting level can be modified, among other methods, by applying coatings, which often modify the chemistry of the surface. With the increase in available computing power and computational algorithms, methods to develop new materials and coatings have shifted from being heavily experimental to including more theoretical approaches. In this work, we use a range of experimental and computational features to develop a supervised machine learning (ML) model using the XGBoost algorithm that can predict the water contact angle (WCA) on the surface of a range of solid polymers. The mean absolute error (MAE) of the predictions is below 5.0°. Models composed of only computational features were also explored with good results (MAE < 5.0°), suggesting that this approach could be used for the \"bottom-up\" computational design of new polymers and coatings with specific water contact angles.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"2739-2745"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912489/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536200","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":"Probing the Secondary Structure of Membrane-Bound gp28 Using Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy.","authors":"Nancy C Rotich, Rasal H Khan, Andrew Morris, Robert McCarrick, Binaya Baral, Evelyn A Okorafor, Emily Faul, Luke Wardrip, Indra D Sahu, Gary A Lorigan","doi":"10.1021/acs.jpcb.4c08270","DOIUrl":"10.1021/acs.jpcb.4c08270","url":null,"abstract":"<p><p>Membrane proteins play a vital role in various cellular functions and are important targets for drug interactions. However, determining their local secondary structure is challenging due to their hydrophobic nature and limited experimental techniques. This study focuses on the use of electron spin echo envelope modulation (ESEEM) spectroscopy, in combination with site-directed spin labeling (SDSL) and ²H-labeled amino acid side chain (d₁₀-Leu), to study the local secondary structure of a recently discovered phage-encoded lytic protein, gp28. gp28 is a membrane protein with three predicted helices that plays a crucial role in the lysis process of bacteriophages that lack spanins. gp28 is an antimicrobial protein specifically involved in disrupting the outer membrane of the host cell. Through the synthesis of nine constructs of gp28 peptides, we systematically probed the three predicted helices. The local secondary structure of the gp28 protein in POPC/POPG vesicles was investigated using ESEEM spectroscopy. Additionally, the global secondary structure was verified using CD spectroscopy. Subsequently, the ESEEM technique allowed us to determine the local secondary structure within the three predicted alpha helices of gp28 in a membrane. This study revealed the presence of alpha helical structural components in all three predicted helices of gp28. These results not only enhance our comprehension of the local secondary structure of gp28 but also showcase the effectiveness of the ESEEM spectroscopic technique in studying membrane protein systems encoded by bacteriophages.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"2659-2667"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514164","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":"Recent Advances in Membrane Protein Simulations.","authors":"James C Gumbart, Sonya M Hanson","doi":"10.1021/acs.jpcb.5c00803","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00803","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 10","pages":"2657-2658"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612703","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}