The Journal of Physical Chemistry B最新文献

{"title":"Cation-π Interactions in Biomolecular Contexts by Neutron Scattering and Molecular Dynamics: A Case Study of the Tetramethylammonium Cation.","authors":"Matej Cervenka, Brennon L Shanks, Philip E Mason, Pavel Jungwirth","doi":"10.1021/acs.jpcb.5c02001","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02001","url":null,"abstract":"<p><p>Cation-π interactions involving the tetramethylammonium motif are prevalent in biological systems, playing crucial roles in membrane protein function, DNA expression regulation, and protein folding. However, accurately modeling cation-π interactions where electronic polarization plays a critical role is computationally challenging, especially in large biomolecular systems. This study implements a physically justified electronic continuum correction (ECC) to the CHARMM36 force field, scaling ionic charges by a factor of 0.75 to effectively account for electronic polarization without additional computational overhead. This approach, while not specifically designed for cation-π interactions, is shown here to significantly improve predictions of the structure of an aqueous tetramethylammonium-pyridine complex as compared to neutron diffraction data. This result, together with computational predictions for the structure of the aqueous tetramethylammonium-phenol complex, underscores the potential of ECC as a versatile method to improve the description of cation-π interactions in biomolecular simulations.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504226","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":"Relative Thermodynamic Stability of α and β PVDF Crystal Phases: A Molecular Simulation Methodology.","authors":"Shubham Mireja, Devang V Khakhar","doi":"10.1021/acs.jpcb.5c01058","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01058","url":null,"abstract":"<p><p>Poly(vinylidene fluoride) (PVDF) is a piezoelectric polymer, with the crystalline β-phase having the highest polarity among all its phases. A multistage transformation process is developed, using molecular dynamics simulations, to compute the free energy difference between α- and β-phases of PVDF. Methods of free energy perturbation and Jarzynski's equality were used to determine Helmholtz free energy change, Δ<i>F</i>, for the individual stages, from which the Gibbs free energy difference, Δ<i>G</i>, between the α- and β-phases was calculated. Infinitely large crystals modeled using periodic boundaries with 36 chains and 12 monomers in each chain were used for the study. All-atom simulations were performed with the force fields previously developed for PVDF. In concurrence with experimental observations, the α-phase was found to be thermodynamically more stable at normal temperature and pressure conditions. The β-phase was found to be more stable at high and low temperatures and high pressure.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144511330","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":"The String Method with Swarms of Trajectories: A Tutorial for Free-Energy Calculations Along a Zero-Drift Pathway.","authors":"Chenyu Tang, Haochuan Chen, Emad Tajkhorshid, Benoît Roux, Christophe Chipot","doi":"10.1021/acs.jpcb.5c02470","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02470","url":null,"abstract":"<p><p>The objective of this tutorial is to provide a comprehensive overview of the string method and its usage to determine a detailed transition pathway and the free-energy difference between two conformational states of a system. The computational protocol is illustrated in detail by setting out to calculate the free-energy difference between the C_7eq and C_7ax conformations of the short, terminally blocked peptide, <i>N</i>-acetyl-<i>N</i>'-methylalaninamide. Starting from a rectilinear transition pathway connecting the two conformations in the backbone-torsional subspace, an optimal zero-drift pathway (ZDP) is determined using the string method with a swarm of trajectories. The free-energy change along this path is then estimated using the path-collective variables (PCV) coordinate in the framework of the adaptive biasing force (ABF) importance-sampling algorithm.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504230","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":"","authors":"Ryo Miyashita,&nbsp;Ryo Kawakami,&nbsp;Kanata Kimura,&nbsp;Aoi Tokutake and Hiromasa Goto*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 25","pages":"XXX-XXX 2305–2315"},"PeriodicalIF":2.8,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c01578","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144479695","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":"","authors":"Allison Stettler,&nbsp;Gary A. Baker and G. J. Blanchard*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 25","pages":"XXX-XXX 2305–2315"},"PeriodicalIF":2.8,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c02468","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144479744","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":"","authors":"Chieh-Chih George Yeh,&nbsp;Harold W. Hatch,&nbsp;Adithya N Sreenivasan,&nbsp;Bhuvnesh Bharti,&nbsp;Vincent K. Shen,&nbsp;Zachary M. Sherman and Thomas M. Truskett*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 25","pages":"XXX-XXX 2305–2315"},"PeriodicalIF":2.8,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c02389","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480043","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":"","authors":"Florian Mast,&nbsp;Maximilian M. Hielscher,&nbsp;Eva Plut,&nbsp;Jürgen Gauss,&nbsp;Gregor Diezemann* and Siegfried R. Waldvogel,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 25","pages":"XXX-XXX 2305–2315"},"PeriodicalIF":2.8,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c00650","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480070","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":"","authors":"Andreas Steinhoff,&nbsp;Alexandra Höltzel and Ulrich Tallarek*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 25","pages":"XXX-XXX 2305–2315"},"PeriodicalIF":2.8,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c01697","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480076","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":"Energy Pathway of Lipid Monolayer Fusion: From Droplet Contact to Coalescence.","authors":"Rodion J Molotkovsky, Timur R Galimzyanov, Mariya M Minkevich, Konstantin V Pinigin, Peter I Kuzmin, Pavel V Bashkirov","doi":"10.1021/acs.jpcb.5c02054","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02054","url":null,"abstract":"<p><p>Neutral fats in living organisms are stored in lipid droplets, intracellular organelles enveloped by a phospholipid monolayer. The fusion of these lipid droplets is vital for numerous physiological functions and is regulated by specific proteins and lipids. Dysregulation of this process, leading to excessive droplet growth, is associated with various pathological conditions. Notably, changes in the lipid composition of the boundary monolayers can significantly influence the fusion rate, mirroring fusion dynamics of membranous compartments surrounded by lipid bilayers. In this study, we conducted a theoretical and computational analysis of monolayer fusion, extending the established bilayer fusion model to this context. We characterize the energy trajectory associated with monolayer fusion, tracing the process from the initial unperturbed state to the formation of physical contact between monolayers, and subsequently to the expansion of this structure, which we refer to as the monolayer stalk, analogous to bilayer fusion. Unlike bilayer fusion, monolayer fusion features a single energy barrier, determining the process efficiency. Once this barrier is overcome, further droplet merging occurs spontaneously, highlighting the dynamic nature of lipid droplet interactions. We analyze how lipid composition influences this energy barrier and explore the effects of factors such as Gaussian curvature and hydration-induced repulsion on the energy landscape. Our calculations reveal that Gaussian curvature energy significantly contributes to barrier height. An increase in the proportion of lipids exhibiting large negative spontaneous curvature, which enhances fusion likelihood, can substantially decrease this barrier. Our findings are consistent with existing experimental data and allow us to quantify the barrier height as a function of lipid composition. Specifically, we demonstrate that incorporating 50 mol % of dioleoylphosphatidylethanolamine (DOPE) into pure dioleoylphosphatidylcholine (DOPC) monolayers reduces the energy barrier height by approximately 16 <i>k</i>_B<i>T</i> - half of this reduction attributed to changes in spontaneous curvature, with the other half due to modification in hydration repulsion parameters. These findings provide quantitative insights into lipid droplet fusion mechanisms, advancing our understanding of lipid metabolism and its physiological regulation.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493119","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":"","authors":"Yi Zheng,&nbsp;Rongrong Shen,&nbsp;Yunuo Dai,&nbsp;Yile Xie,&nbsp;Chaojie Wang,&nbsp;Yuepiao Cai* and Kun Wang*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 25","pages":"XXX-XXX 2305–2315"},"PeriodicalIF":2.8,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c01232","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144479698","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}