The Journal of Physical Chemistry B最新文献

{"title":"Solvation Free Energies of Ion Dissociations in Dichloromethane: En Route to Accurate Computations.","authors":"Adélaïde Savoy, Eno Paenurk, Robert Pollice, Philippe H Hünenberger, Peter Chen","doi":"10.1021/acs.jpcb.5c01446","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01446","url":null,"abstract":"<p><p>Calculating accurate free energies for solution-phase reactions is notoriously difficult. In our previous joint experimental and computational studies, we observed a striking failure of quantum mechanical calculations with popular implicit solvent models to even qualitatively reproduce the experimental trends of dissociation free energies of numerous proton-bound pyridine dimers in organic solvents [Pollice, R. . <i>J. Am. Chem. Soc.</i> 2017, 139(37), 13126-13140]; [Pollice, R. . <i>Angew. Chem., Int. Ed.</i> 2019, 58(40), 14281-14288]. In this article, we expand the computational study of the dissociation of proton-bound pyridine dimers in the gas phase and in dichloromethane (DCM). In an effort to determine the prerequisites for reproducing the experimental trends and magnitudes of the dissociation free energies (Δ<i>G</i>_diss) in solvent, we investigated the impact of accounting for the ensemble free energy, umbrella sampling, thermodynamic integration, and explicit solvation using semiempirical quantum mechanics and molecular mechanics. We estimated the effect of conformational free energy contributions with semiempirical quantum mechanics (SE). Molecular dynamics (MD) with explicit solvation and classical molecular mechanics (MM) was used as a method to treat not only the solute but also the solvent configurational entropy. We found that explicit solvation with MM is indeed capable of reproducing Δ<i>G</i>_diss in DCM for our test system within an acceptable error margin. We analyze and discuss the results and limitations of our approach for calculating the solvation free energy.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281646","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":"Exciton Coupling and Charge Transfer Dynamics in Zn(II) Complexes of π-Extended Dipyrrins.","authors":"Dabin Kim, Luca Ravotto, April Bialas, Thomas Troxler, Zhongping Ou, Karl M Kadish, Andrei V Cheprakov, Frank C Spano, Sergei A Vinogradov, Jessica M Anna","doi":"10.1021/acs.jpcb.5c03312","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c03312","url":null,"abstract":"<p><p>Dipyrrins form a group of versatile chromophores, which find use as laser dyes as well as in light harvesting and bioimaging applications. The mode of the central ion coordination and the ensuing molecular geometry play a key role in the photophysics of dipyrrins, whereby some complexes are brightly fluorescent and some completely lack emissivity. However, the relationship between the structure and excitation dynamics in dipyrrins is still poorly understood. Here, we used a range of spectroscopic methods to investigate the photophysics of Zn(II) complexes of <i>meso</i>-Ar-2,2'-di-<i>tert</i>-butoxycarbonyl-dibenzodipyrrins (BDP; Ar = 4-MeO₂C-C₆H₄). In particular, two-dimensional electronic spectroscopy (2DES) was used to characterize the initial excited states in a homoleptic <i>bis</i>-dipyrrinate Zn(BDP)₂, in which two dipyrrin ligands are oriented in a nonorthogonal geometry. From the position of the peaks in the 2DES spectra and spectral modeling, the initial excited states of Zn(BDP)₂ were assigned to excitonic states. The low oscillator strength, associated with excitation to the lower excitonic state, is responsible in part for the weak emissivity of Zn(BDP)₂, contrasting the bright fluorescence of <i>mono</i>-dippyrinate Zn(BDP)X. Femtosecond (fs-), nanosecond (ns-) transient absorption (TA), and time-resolved fluorescence spectroscopies were used to monitor the solvent-dependent evolution of the excitonic states, which appear to evolve into an intermediate state possibly with charge transfer character. Taken together, our findings reveal a significant impact of both structural and environmental factors on the photophysics of dipyrrins and present the first example of the application of 2DES to investigate excitonic states in a system where the interacting chromophores are held together via coordination of an optically neutral metal ion. On a broader scale, we demonstrate that nonorthogonal <i>bis</i>-dipyrrin complexes constitute a versatile model for studying exciton coupling and associated energy and charge dynamics.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144289356","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":"Thermally Invertible Helical PEDOTs Synthesized by Asymmetric Electrochemical Polymerization in Temperature-Responsive Chiral Liquid Crystals.","authors":"Yoshinori Okada, Keita Horie, Kazuo Akagi","doi":"10.1021/acs.jpcb.5c02914","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02914","url":null,"abstract":"<p><p>A thermal stimulus-responsive chiral nematic liquid crystal (N*-LC) is prepared by adding a chiral dopant with a thermally switchable helical sense into a host nematic liquid crystal. The helical sense of the N*-LC is reversibly controlled with a temperature difference of just 20 °C. Helical poly(3,4-ethylenedioxythiophene)s (H-PEDOTs) are synthesized through the asymmetric electrochemical polymerization of <i>ter</i>-ethylenedioxythiophene (EDOT) in N*-LCs containing an electrolyte. The helical senses of the H-PEDOTs are rigorously controlled by modulating the polymerization temperature. Changes in the chiroptical and electrochemical properties of H-PEDOTs upon electrochemical doping and dedoping were investigated. The circular dichroism (CD) spectra measured from the visible to near-infrared regions indicate that the helically π-stacked structure formed in neutral H-PEDOT is preserved even in oxidized H-PEDOT after electrochemical doping. This is the first example revealing that a helically π-stacked structure exists in the polaron and bipolaron states of conjugated polymers. The relationships between the helical sense of the N*-LC and those of the helically π-stacked structure, screwed fibril bundles and spiral morphology of the H-PEDOT were elucidated using a newly proposed mechanism for electrochemical polymerization in the N*-LC.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281647","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":"Hydrogen Bonds Mediating the Structural and Dynamic Behaviors in Choline-Phenolic Acid Ionic Liquids: A Computational Investigation.","authors":"Yi Zheng, Rongrong Shen, Yunuo Dai, Yile Xie, Chaojie Wang, Yuepiao Cai, Kun Wang","doi":"10.1021/acs.jpcb.5c01232","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01232","url":null,"abstract":"<p><p>The impact of hydrogen bonds (HBs) on the structural and dynamic behaviors of choline-phenolic acid ionic liquids ([Cho][PA] ILs) was explored by using density functional theory (DFT) calculations and molecular dynamics (MD) simulations. The most stable conformation of individual [Cho][PA] ion pairs was determined, and the interactions between charged entities were characterized, indicating the existence of robust HBs between [Cho]⁺ and [PA]^-. The bulk phase MD simulations of [Cho][PA] ILs showed that ion aggregation becomes more pronounced as more phenolic hydroxyl groups are present on [PA]^-. The results further indicated that the carboxylate oxygen of [PA]^- forms strong HBs with both the hydroxyl hydrogen of [Cho]⁺ and the phenolic hydroxyl hydrogen of [PA]^-. The former type of HBs remains robust even with more phenolic hydroxyl groups attached to [PA]^-, whereas the latter type increases in quantity with more phenolic hydroxyl groups, potentially driving ion aggregation and reducing the self-diffusion coefficients of both [Cho]⁺ and [PA]^-. Our findings are expected to contribute to a fundamental understanding of how HBs affect the structural and dynamic properties of [Cho][PA] ILs, thereby facilitating their broader applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144289357","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":"Mobile-Phase Contributions to Analyte Retention and Selectivity in Reversed-Phase Liquid Chromatography: 1. General Effects.","authors":"Andreas Steinhoff, Alexandra Höltzel, Ulrich Tallarek","doi":"10.1021/acs.jpcb.5c01695","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01695","url":null,"abstract":"<p><p>Analyte retention in reversed-phase liquid chromatography is manipulated via the elution strength of the water-organic solvent (W-OS) mobile phase, whereby raising the OS volume fraction or eluent strength (methanol < acetonitrile) lowers retention. We investigated this effect at the molecular level through molecular dynamics simulations in a slit-pore model of a C₁₈ stationary phase, using the solute benzene to trace the composition and occupation of the immediate analyte environments involved in solute partitioning into the bonded-phase region and solute adsorption to the interfacial region. Spatially resolved contact analysis revealed that the number of bonded-phase contacts per analyte molecule decreases from the bonded-phase region over the extension of the interfacial region while the number of solvent contacts increases. The analyte density distribution in the stationary phase is sensitive to the local W density, which is controlled by the mobile-phase parameters. With increasing mobile-phase elution strength, the W density recedes from the interfacial region, favoring the occupation of analyte environments closer to the bulk liquid region. The ensuing redistribution of analyte density within the stationary phase results in an overall loss of bonded-phase contacts, tantamount to loss of retention. The retentivity of the stationary phase therefore depends on its solvation by the mobile phase.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144289358","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":"CO₂ Capture by Porous Polymeric Sorbents: From New <i>cis-</i>/<i>trans</i>-Oxovanadium(IV) Catalyst to Functional Materials.","authors":"Kacper Pobłocki, Marzena Białek, Katarzyna N Jarzembska, Mateusz A Baluk, Radosław Kamiński, Przemysław Rybiński, Krzysztof Matus, Joanna Drzeżdżon, Barbara Gawdzik, Dagmara Jacewicz","doi":"10.1021/acs.jpcb.5c01060","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01060","url":null,"abstract":"<p><p>The challenge of ever-increasing greenhouse gas emissions correlates with intensive research into the development of new CO₂ sorbents. The research aimed to propose a new generation of porous polymer sorbents that contribute to decarbonization. Among all oligomers and (co)polymers, the 3-buten-2-ol oligomer showed the highest CO₂ sorption properties (0.82 mmol g^-1). The heat of adsorption of CO₂ by oligo(3-buten-2-ol) was equal to 8.51 kJ mol^-1. Polyolefins and polar oligomers were synthesized using a new, innovative, and highly active oxovanadium(IV) precatalyst. An easy, one-step method for the synthesis of <i>cis</i>/<i>trans</i>-[VO(acac)₂(3-ppy)] provides a unique coordination compound containing two molecules that are reciprocal geometric isomers with a spatial arrangement of acetylacetonate ligands (<i>cis</i> and <i>trans</i>). The complex shows very active catalytic properties in the polymerization reactions of olefins (83,400 kg_PE mol_V^-1 h^-1) and polar monomers, for example, 2-propen-1-ol (1060 kg mol_V^-1 h^-1). A physicochemical study was also conducted to determine the stability constant of the complex formation, log β₁₂₁₀ = 27.82.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281642","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 Imaging of an Amphotericin B Potentiator in Single-Cell <i>Saccharomyces cerevisiae</i>.","authors":"Ryosuke Miyake, Masahiro Ando, Keisuke Kobayashi, Kenichiro Nagai, Taichi Ohshiro, Hiroshi Tomoda, Haruko Takeyama","doi":"10.1021/acs.jpcb.5c02477","DOIUrl":"10.1021/acs.jpcb.5c02477","url":null,"abstract":"<p><p>Nectriatide, a fungal cyclotetrapeptide, was previously found to enhance the antifungal activity of amphotericin B (AmB), with nectriatide linear derivatives (NLDs) exhibiting even stronger potentiation. Although we showed that NLDs have an affinity for ergosterol <i>in vitro</i>, the precise mechanism underlying these interactions within living fungal cells remained elusive. Here, we demonstrate for the first time a label-free, single-cell Raman microspectroscopic imaging approach to visualize how NLD-1 colocalizes with ergosterol in <i>Saccharomyces cerevisiae</i>. Our results revealed clear evidence of NLD-1 localization in ergosterol-rich regions, indicating direct interaction. Furthermore, antifungal-enhancing effect of NLD-1 was markedly reduced in <i>ERG4</i>-deficient <i>S. cerevisiae</i>─supporting its specific recognition of ergosterol. This unprecedented real-time, <i>in situ</i> visualization of an AmB potentiator in living yeast cells not only provides new insights into the mechanism of AmB enhancement but also sets the stage for broader applications in understanding other antifungal synergies at the molecular level.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5720-5727"},"PeriodicalIF":2.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186080","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":"Implicit Solvent Sample-Based Quantum Diagonalization.","authors":"Danil Kaliakin, Akhil Shajan, Fangchun Liang, Kenneth M Merz","doi":"10.1021/acs.jpcb.5c01030","DOIUrl":"10.1021/acs.jpcb.5c01030","url":null,"abstract":"<p><p>The sample-based quantum diagonalization (SQD) method shows great promise in quantum-centric simulations of ground state energies in molecular systems. Inclusion of solute-solvent interactions in simulations of electronic structure is critical for biochemical and medical applications. However, all of the previous applications of the SQD method were shown for gas-phase simulations of the electronic structure. The present work aims to bridge this gap by introducing the integral equation formalism polarizable continuum model (IEF-PCM) of solvent into the SQD calculations. We perform SQD/cc-pVDZ IEF-PCM simulations of methanol, methylamine, ethanol, and water in aqueous solution using quantum hardware and compare our results to CASCI/cc-pVDZ IEF-PCM simulations. Our simulations on ibm_cleveland, ibm_kyiv, and ibm_marrakesh quantum devices are performed with 27, 30, 41, and 52 qubits demonstrating the scalability of SQD IEF-PCM simulations.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5788-5796"},"PeriodicalIF":2.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074941","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":"Insights into Formation of Bicontinuous Emulsion Gels via In Situ (Ultra-)Small Angle X-Ray Scattering.","authors":"Meyer T Alting, Dominique M E Thies-Weesie, Alexander M van Silfhout, Mariska de Ruiter, Theyencheri Narayanan, Martin F Haase, Andrei V Petukhov","doi":"10.1021/acs.jpcb.5c02375","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02375","url":null,"abstract":"<p><p>Nanostructured materials formed via kinetically controlled self-assembly processes gather more interest nowadays. In particular, bicontinuous emulsion gels stabilized by colloidal particles, called bijels, are attractive materials as they combine bulk properties of two immiscible liquids into an interwoven network structure. The limited understanding of the complex formation phenomena of bijels restricts the control over the synthesis, and so its applicability. In this work, in situ (ultra-) small-angle X-ray scattering is applied to gain insight into the phase separation and self-assembly kinetics of bijels formed via solvent transfer induced phase separation. An X-ray compatible microfluidic setup allows accessing the kinetics of the extrusion process with a millisecond resolution. The formation of such bijels out of a liquid precursor mixture is shown to occur via three consecutive steps. The first 7 ms of the extrusion are dominated by fluid dynamics. Then, the precursor mixture remains in an induction phase for 50 ms where nanoparticles start to self-assemble without structural development on the (sub)micron scale. From 50 ms on, an inward propagation of a liquid-liquid phase separation front occurs, besides the proceeding nanoparticle self-assembly obtaining (sub)micron-sized structures. This time-resolved monitoring technique offers valuable insights into the structural evolution of kinetically controlled materials and enhances our understanding of the formation of bicontinuous emulsion gels.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281645","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":"Fluorescence Gratings from Chromophore-Functionalized Azo Molecule Migration.","authors":"Feng Liu, Bobbara Sanyasi Rao, Agnieszka Pawlicka, Jean-Michel Nunzi","doi":"10.1021/acs.jpcb.5c01544","DOIUrl":"10.1021/acs.jpcb.5c01544","url":null,"abstract":"<p><p>A Nile blue (NB) chromophore functionalized with disperse red 1 (DR1) was synthesized in three steps. NB-DR1-guest host-poly(methyl methacrylate) films were deposited on glass substrates and used to produce rewritable surface relief gratings (SRGs). These SRGs were observed by fluorescence microscopy after exposition of the films to an interference pattern from a laser, revealing the fluorescence pattern that mapped the angle-dependent SRG. The SRG formation was due to the azo-hauling chromophore migration under moderate irradiation conditions. Experiments with different host-guest concentrations showed that low doping of the host-guest system provides better contrast and a higher sensitivity of the fluorescence imaging to detect the surface grating. Finally, the chromophore-functionalized azo polymer material offers rewritable properties, which make it a potential candidate for applications in the field of data storage and holography.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5880-5886"},"PeriodicalIF":2.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207215","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}