The Journal of Physical Chemistry B最新文献

{"title":"Correction to “Predictive Thermodynamics for Isochoric (Constant-Volume) Cryopreservation Systems”","authors":"Julia H. Grenke,  and , Janet A. W. Elliott*, ","doi":"10.1021/acs.jpcb.5c05935","DOIUrl":"10.1021/acs.jpcb.5c05935","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"10206–10212"},"PeriodicalIF":2.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111552","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 Classical Density Functional Theory for Predicting Energy and Orientation Properties of Chain-Like Molecules on Structured Interfaces","authors":"Chaolong Zhang,&nbsp; and ,&nbsp;Yu Liu*,&nbsp;","doi":"10.1021/acs.jpcb.5c04037","DOIUrl":"10.1021/acs.jpcb.5c04037","url":null,"abstract":"<p >The orientation of chain-like molecules is an important issue in many fields, but the theoretical understanding remains limited. In this work, we introduce a classical density functional theory (CDFT) to investigate the orientation and energy properties of chain-like molecules on structured interfaces. The interface is represented by a face of a body-centered cubic (BCC) crystal, and the theory is implemented by a 3-dimensional algorithm. The predictions for potential mean force (PMF), density profile and orientation order parameter are consistent with molecular simulations. The orientation distribution function suggests a bimodal orientation distribution and a vertical–horizontal transition governed by surface separation. The interfacial structure exerts a significant influence on PMF, density profile and orientation. The (111) face generates a repulsive PMF and a flat density profile, which is in contrast to the (100) and (110) faces. We also examine the roles of molecular interaction, surface attraction, chain length and packing fractions, which may provide an insight into the design of nanoparticles and porous adsorbents.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"10162–10173"},"PeriodicalIF":2.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111614","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":"Structural Dynamics and Topology of Human KCNE3 in Lipid Bilayers Studied by Site-Directed Spin Labeling and Electron Paramagnetic Resonance Spectroscopy","authors":"Draven Blade Reynolds,&nbsp;, ,&nbsp;Conner Campbell,&nbsp;, ,&nbsp;Matthew W. Scheyer,&nbsp;, ,&nbsp;Patrick L. Williams,&nbsp;, ,&nbsp;Patricia Loka,&nbsp;, ,&nbsp;Kayla Hamilton,&nbsp;, ,&nbsp;Ogechi Oriaku,&nbsp;, ,&nbsp;Ihsanne Damoh,&nbsp;, ,&nbsp;Alejandro Guerra Diaz,&nbsp;, ,&nbsp;Gabriel Mbey-Ogbonnaya,&nbsp;, ,&nbsp;Puspa K. Shah,&nbsp;, ,&nbsp;Charles R. Sanders,&nbsp;, ,&nbsp;Gary A. Lorigan,&nbsp;, and ,&nbsp;Indra D. Sahu*,&nbsp;","doi":"10.1021/acs.jpcb.5c03377","DOIUrl":"10.1021/acs.jpcb.5c03377","url":null,"abstract":"<p >KCNE3 is a member of the KCNE family and consists of a single-pass transmembrane segment that is vital for cellular function. It plays a role in modulating both activities and the function of voltage-gated potassium ion channels, including KCNQ1. KCNE3 interacts with voltage-gated potassium channels to form a complex that regulates the channel’s biophysical and physiological properties. KCNE3 is found in the colon, small intestine, and certain stomach cell types. Dysfunction and hereditary mutations in KCNE3 have been linked to a number of human disorders. The structural dynamics of KCNE3 in a native membrane environment are not yet fully understood. Here, we employed electron paramagnetic resonance (EPR) spectroscopy in connection with site-directed spin labeling to study the structural dynamics of KCNE3 in a lipid bilayer membrane. Fifty residue sites of the KCNE3 amino acid sequence were scanned using spin-labeling and CW-EPR spectral line shape analysis to determine the site-specific motions of KCNE3. The sites included 19 predicted transmembrane domain (TMD) sites and 31 residue sites of the N- and C-termini of KCNE3. The analysis of CW-EPR spectra revealed that sites residing within the predicted transmembrane domain (TMD) of KCNE3 exhibit reduced mobility in comparison to those of the KCNE3 N- and C-termini sites. Power saturation EPR measurements were then performed to obtain the topology of KCNE3 with respect to the POPC/POPG lipid bilayers. The results mapped the location of the membrane-spanning domain of the protein to residues 57–82. Power saturation EPR data further showed that the KCNE3 extracellular N-terminus is largely solvent-exposed, with some segments weakly or partially associated with the surface of the membrane. These results are in good agreement with the earlier solution NMR structure of KCNE3 in isotropic bicelles.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"9880–9892"},"PeriodicalIF":2.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111525","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":"pH Response of Weak Polyampholyte Brushes with Random Charge-Asymmetric Monomer Sequences","authors":"Rahatun Akter,&nbsp;, ,&nbsp;Xin Yuan,&nbsp;, ,&nbsp;Amanda B. Marciel*,&nbsp;, ,&nbsp;Jacinta C. Conrad*,&nbsp;, and ,&nbsp;Jeremy C. Palmer*,&nbsp;","doi":"10.1021/acs.jpcb.5c04431","DOIUrl":"10.1021/acs.jpcb.5c04431","url":null,"abstract":"<p >We perform simulations using the grand reaction method to investigate the pH response of polyampholyte brushes (PABs) with random sequences of weakly acidic and basic monomers. Titration curves, brush height, and chain conformations are shown to depend sensitively on the charge or compositional asymmetry, defined as the difference in numbers of weakly acidic and basic monomers on each chain. For asymmetric systems, the brush height response is a superposition of those for compositionally symmetric PABs and polyelectrolyte brushes. Further, we show that the pH response of PABs with random monomer sequences is distinct from those with ordered blocky sequences, even when parameters such as monomer composition and mean block size are similar. By contrast, we find that the sequence charge decoration parameter collapses structural data characterizing the brush height, lateral fluctuations, and chain conformations for all PABs examined, except for those with ordered sequences where large charge blocks result in strong inter- and intrachain electrostatic interactions. These results support the growing body of work highlighting the importance of charge separation on polyampholyte behavior.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"10174–10183"},"PeriodicalIF":2.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111478","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":"Raman, Dilatometric, and Dielectric Insights into Pr3+-Doped Pb–Sb Silicate Glasses toward Ion-Conducting Glass Electrolytes","authors":"Yeti Dana Rao,&nbsp;, ,&nbsp;Vandana Ravi Kumar*,&nbsp;, ,&nbsp;Luka Pavić*,&nbsp;, ,&nbsp;Arijeta Bafti,&nbsp;, ,&nbsp;José A. Jiménez*,&nbsp;, ,&nbsp;Ayyagari Venkata Sekhar,&nbsp;, ,&nbsp;Paulina Kapuśniak,&nbsp;, ,&nbsp;Piotr Brągiel,&nbsp;, ,&nbsp;Michal Piasecki,&nbsp;, and ,&nbsp;Nalluri Veeraiah,&nbsp;","doi":"10.1021/acs.jpcb.5c05304","DOIUrl":"10.1021/acs.jpcb.5c05304","url":null,"abstract":"<p >This work reports new physical insights concerning the effect of red lead (Pb₃O₄) addition (10–35 mol %) on the structural, dilatometric, dielectric, and conductivity properties of Sb₂O₃–SiO₂:Pr₂O₃ glasses for potential solid-state electrolyte applications. The melt-quenched glasses were scrutinized via Raman spectroscopy including a temperature-dependent evaluation revealing progressive polymerization of the glass network up to 30 mol % Pb₃O₄, followed by depolymerization at 35 mol %. Harmonizing with the structural evolution, thermal analysis by dilatometry showed that the thermal expansion coefficients/softening temperatures first decreased/increased from 10 to 30 mol % Pb₃O₄ and then increased/decreased for 35 mol % Pb₃O₄. The dielectric properties and ac conductivity were measured over 0.02–1 MHz and 20–240 °C. An increase in Pb₃O₄ from 10 to 30 mol % led to reduced dielectric constant and conductivity, which is attributed to a more compact and polymerized structure that limits ion mobility. Here, conduction is primarily polaronic, supported by mixed-valence Pb²⁺/Pb⁴⁺ and Sb³⁺/Sb⁵⁺ ions. At 35 mol % Pb₃O₄, network depolymerization introduced nonbridging oxygens and structural disorder, enhancing the free volume and ion migration pathways. Consequently, ionic conduction, particularly of Pb²⁺, becomes dominant, significantly boosting the conductivity. Although Pb²⁺ ions are relatively immobile compared to Li⁺ or Na⁺, the insights gained offer a foundational understanding and guide the development of similar glass systems doped with lighter and more mobile alkali ions for practical battery applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"10193–10205"},"PeriodicalIF":2.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c05304","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145123804","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":"Atomistic Insights into Lithium–Glyme Solvate Ionic Liquids: Effects of Chain Length and Anion Coordination","authors":"Orlando Carrillo-Bohórquez,&nbsp;, ,&nbsp;Daniel G. Kuroda*,&nbsp;, and ,&nbsp;Revati Kumar*,&nbsp;","doi":"10.1021/acs.jpcb.5c04265","DOIUrl":"10.1021/acs.jpcb.5c04265","url":null,"abstract":"<p >Mixtures of lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) in diglyme (G2), triglyme (G3) and tetraglyme (G4) at solvate ionic liquid (SIL) concentrations were investigated using classical molecular dynamics (cMD) simulations with a physically motivated force-field specifically developed for modeling these systems. The structural and dynamical properties of the mixtures were computed and analyzed. Lithium solvation shells, radial distribution functions, and X-ray structure factors were studied across the different SIL systems. Translational diffusion and rotational relaxation times were also evaluated, exhibiting similar trends with increasing glyme chain length. The results are consistent with experimental data and in good agreement with previous computational studies on G3 and G4. These findings validate the accuracy of the force field in modeling glyme systems and its use for describing the [Li(G2)_4/3][TFSI] mixture. Additionally, the thermal and electrochemical stability of these electrolytes were systematically examined. The thermal stability appears to be governed by cooperative interactions among glyme molecules, while the electrochemical stability is primarily influenced by Li⁺-anion interactions, which vary significantly with glyme chain length. Overall, the study sheds light on the crucial role of the anion in these glyme-based SILs and offers valuable insights into Li⁺-glyme systems at SIL concentrations, highlighting their promise as potential Li-ion battery electrolytes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"10072–10083"},"PeriodicalIF":2.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145123825","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 Basis of Calcium-Induced Acidic Shift in Antimicrobial Zinc Sequestration by S100A12","authors":"Mahil Kothalawala,&nbsp;, ,&nbsp;Shaan Shirazi,&nbsp;, ,&nbsp;Qian Wang,&nbsp;, ,&nbsp;Ahava Collado,&nbsp;, ,&nbsp;Angelo Bongiorno*,&nbsp;, and ,&nbsp;Rupal Gupta*,&nbsp;","doi":"10.1021/acs.jpcb.5c04464","DOIUrl":"10.1021/acs.jpcb.5c04464","url":null,"abstract":"<p >Antimicrobial protein S100A12 sequesters Zn(II) via a His₃Asp motif to inhibit pathogens during infection. Here, UV–vis and NMR spectroscopies and molecular dynamics (MD) simulations are used to gain molecular insight into the Zn(II) chelation properties of S100A12 under pH conditions relevant to infection and inflammation. UV–vis measurements show that binding of Zn(II) to apo S100A12 exhibits a sigmoidal dependence with pH, beginning its decline at pH 7.0 and vanishing at pH 4.0. In the Ca(II)-bound protein, a similar sigmoidal curve is found to exhibit an acidic shift, an effect not attributed to a Ca(II)-induced p<i>K</i>_a suppression of the His₃Asp scaffold. NMR measurements show that upon lowering the pH, resonances exhibit nonlinear migration trends with pH, suggesting the occurrence of several proton binding events, consistent with the sigmoidal pH dependence of Zn(II) binding. Analysis of the NMR chemical shifts versus pH shows that both apo- and Ca(II)-bound protein undergo conformational changes exhibiting spatial correlations, which are dispersed across the polypeptide in the apo protein and confined to discrete regions in Ca(II)-S100A12. MD simulations show the formation of a strong salt bridge within the His₃Asp scaffold of the apo protein upon protonation of Zn(II)-ligating histidines. Geometric constraints imposed by Ca(II) in the Ca(II)-bound protein hinder the formation of similar salt bridges until protonation of a histidine residue external to the His₃Asp and near Ca(II) takes place. Overall, our experimental and computational results support a scenario where protonation of the His₃Asp motif triggers the loss of Zn(II) binding and yields protonated histidine residues prone to form stable salt bridges. In Ca(II)-S100A12, formation of stable salt bridges at pH 7 is hindered compared to the apo form, thus extending Zn(II)-binding affinity to lower pH.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"9929–9938"},"PeriodicalIF":2.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c04464","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084540","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":"Twin Supercoil Domain Couples the Dynamics of Molecular Motors and Plectonemes during Bacterial DNA Transcription and Replication","authors":"Marc Joyeux*,&nbsp;","doi":"10.1021/acs.jpcb.5c04512","DOIUrl":"10.1021/acs.jpcb.5c04512","url":null,"abstract":"<p >The genomic DNA of most bacteria is significantly underwound, which constrains the DNA molecule to adopt a branched plectoneme geometry. Moreover, biological functions like replication and transcription require that the two DNA strands be transiently opened, which generates waves of positive (respectively, negative) supercoiling downstream (respectively, upstream) of the molecular motor, a feature known as Twin Supercoiled Domain (TSD). In this work, we used coarse-grained modeling and Brownian dynamics simulations to investigate the interactions between a TSD and the plectonemes of bacterial DNA. Simulations indicate that the slithering dynamics of short plasmids is not significantly affected by a TSD. In contrast, the TSD potently stimulates the spontaneous displacement modes (diffusion and growth/shrinkage) of the plectonemes of longer DNA molecules. This results in the motor trailing a growing plectoneme behind itself if it translocates more slowly than the maximum slithering speed of plectonemes. In contrast, if the motor translocates more rapidly than this limit, then quasi-immobile plectonemes nucleate almost periodically upstream of the motor, grow up to several kbp, detach from the motor, shrink, and disappear. The effect of an eventual static bend imposed by the motor and of the topological barriers was also investigated.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"9939–9952"},"PeriodicalIF":2.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084515","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":"¹²⁹Xe Nuclear Magnetic Resonance in Polymeric Membranes: A Computational Study of the Effect of Pore Size and Void Distribution on the Xenon Chemical Shift.","authors":"Valerio Mazzilli, Carmen Rizzuto, Elena Tocci, Giacomo Saielli","doi":"10.1021/acs.jpcb.5c05500","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c05500","url":null,"abstract":"<p><p>We present the results of a computational investigation of the structure and distribution of pore size in a polymer of intrinsic microporosity (PIM), a class of compounds with applications as sensors and membranes for gas separation. The high performance of PIMs, in our case PIM-EA-TB, meaning a PIM based on ethanoanthracene (EA) units linked by a Tröger's base (TB, i.e., methanodiazocene), is largely due to the presence of interconnected micropores within the rigid polymer matrix. We have applied a computational NMR protocol based on a combination of MD simulations to generate several trajectories of xenon within the polymeric matrix and DFT calculations of the ¹²⁹Xe chemical shift using clusters extracted from the MD trajectories. The comparison of experimental NMR data previously obtained and the results of the calculations allows to validate the bulk structure resulting from the MD simulations and to obtain a quantitative dependence of the ¹²⁹Xe chemical shift on the distance of xenon from the pores' internal walls. Such dependence is in very good agreement with the results reported in the literature concerning small model systems of Xe-alkane pairs and hints at a more general law that can be expected to hold for many different systems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090816","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":"Raman Dissection of Water-Interaction Coupling in Condensate-Relevant Peptides","authors":"Yu-Kai Tong,&nbsp;, ,&nbsp;Rui Shi,&nbsp;, and ,&nbsp;Hai Lei*,&nbsp;","doi":"10.1021/acs.jpcb.5c05547","DOIUrl":"10.1021/acs.jpcb.5c05547","url":null,"abstract":"<p >Biomolecular condensates formed through liquid–liquid phase separation are primarily driven by noncovalent interactions among intrinsically disordered proteins and nucleic acids. Despite water constituting the majority of the condensate volume, its role in modulating these molecular interactions remains poorly understood. Here, we employ time-resolved Raman spectroscopy to investigate amino acids and IDP-derived peptides, each designed to be dominated by a single type of noncovalent interaction. By simulating molecular crowding through controlled solution evaporation, we track changes in molecular vibrational modes and the water structure. Distinct responses were observed depending on the interaction type, with differences in backbone and side-chain behaviors as well as in the retention and loss of tetrahedral versus distorted water populations. Peptides driven by hydrogen bonding retained more tetrahedral water, while hydrophobic peptides showed stepwise water depletion. Our findings offer direct molecular-level insight into how hydration influences the behavior of condensate-relevant molecules and provide a framework for understanding the physicochemical basis of biomolecular condensate formation.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 39","pages":"10122–10130"},"PeriodicalIF":2.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084529","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}