The Journal of Physical Chemistry B最新文献_第2页

Effect of a Knot on the Thermal Stability of Protein MJ0366: Insights into Molecular Dynamics and Monte Carlo Simulations

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-10 DOI: 10.1021/acs.jpcb.4c0791010.1021/acs.jpcb.4c07910

A. M. Begun*, A. A. Korneev and A. V. Zorina,

引用次数: 0

Nuclear Magnetic Resonance- and Electron Paramagnetic Resonance Spectroscopic Characterization of S4N4 and (SN)x Dissolved in [EMIm][OAc]

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-10 DOI: 10.1021/acs.jpcb.5c0029410.1021/acs.jpcb.5c00294

Julian Radicke, Vanessa Jerschabek, Haleh Hashemi Haeri, Muhammad Abu Bakar, Dariush Hinderberger, Jörg Kressler and Karsten Busse*,

{"title":"Nuclear Magnetic Resonance- and Electron Paramagnetic Resonance Spectroscopic Characterization of S4N4 and (SN)x Dissolved in [EMIm][OAc]","authors":"Julian Radicke, Vanessa Jerschabek, Haleh Hashemi Haeri, Muhammad Abu Bakar, Dariush Hinderberger, Jörg Kressler and Karsten Busse*, ","doi":"10.1021/acs.jpcb.5c0029410.1021/acs.jpcb.5c00294","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00294https://doi.org/10.1021/acs.jpcb.5c00294","url":null,"abstract":"This work focuses on the reaction mechanism of poly(sulfur nitride) ((SN)x, (S15N)x), with the ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate [EMIm][OAc]. We compare this with the reaction of the IL with S4N4 or its 15N-labeled form S415N4, a precursor for the synthesis of (SN)x and (S15N)x. After purification of the S4N4–IL- and S415N4–IL systems via column chromatography, we characterized the reaction products with 1H, 13C, and 15N nuclear magnetic resonance spectroscopy and with electron spray ionization time-of-flight mass spectrometry. Furthermore, time-resolved electron paramagnetic resonance spectroscopy and time-resolved ultraviolet–visible spectroscopy were carried out. Thus, radical intermediates were detected, which were consumed with reaction time. Finally, we postulate a reaction mechanism for the S4N4–IL- and S415N4–IL systems and compare this with the respective data for the (SN)x −IL- and (S15N)x–IL-systems.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 16","pages":"4063–4077 4063–4077"},"PeriodicalIF":2.8,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpcb.5c00294","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143863136","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}

引用次数: 0

Interaction of Polystyrene Nanoplastic with Lipid Membranes

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-09 DOI: 10.1021/acs.jpcb.5c0073810.1021/acs.jpcb.5c00738

Grzegorz Łazarski, Natan Rajtar, Marek Romek, Dorota Jamróz, Michał Rawski and Mariusz Kepczynski*,

{"title":"Interaction of Polystyrene Nanoplastic with Lipid Membranes","authors":"Grzegorz Łazarski, Natan Rajtar, Marek Romek, Dorota Jamróz, Michał Rawski and Mariusz Kepczynski*, ","doi":"10.1021/acs.jpcb.5c0073810.1021/acs.jpcb.5c00738","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00738https://doi.org/10.1021/acs.jpcb.5c00738","url":null,"abstract":"As demonstrated in in vitro studies, polystyrene nanoplastics (PSNPs) are effectively internalized by various cells. All known mechanisms of PSNP internalization involve the initial step of their interaction with the cell membrane, highlighting the importance of understanding such interactions at the molecular level. Here we consider the effects of PSNPs obtained from disposable food packaging on zwitterionic lipid membranes, used as a model system for protein-free cell membranes. We combined microscopic imaging and unbiased atomistic molecular dynamics (MD) to investigate the behavior of PSNPs on the surface and inside the lipid membrane. Our results show that PSNPs are hydrated and have a high negative surface charge when dispersed in an aqueous media. The penetration of PS nanoparticles into the lipid bilayer requires the removal of water molecules at the nanoparticle–membrane interface, which is an effective barrier to the entry of PSNPs into its hydrophobic region. Overcoming this energy barrier by slightly inserting the PS nanoparticle into the polar region of the membrane leads to its rapid penetration into the center of the bilayer and coating its surface with lipid molecules. PS nanoplastics do not disaggregate after penetrating the lipid membrane, which affects the molecular structure of the bilayer. In addition, our MD simulations demonstrated that small-molecule additives (e.g., unreacted monomers) present in nanoplastics can be released into lipid membranes if they are located close to the nanoparticle surface. The outcomes of this study are important for understanding the passive uptake of nanoplastics by cells.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 16","pages":"4110–4122 4110–4122"},"PeriodicalIF":2.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpcb.5c00738","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143863113","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}

引用次数: 0

Shear Viscosity of Quasi-Two-Dimensional Ionic Liquids.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-09 DOI: 10.1021/acs.jpcb.4c07573

J D Hernández Velázquez, A Gama Goicochea

引用次数: 0

Intermolecular Vibrational and Orientational Dynamics of Deep Eutectic Solvents Composed of Lithium Bis(trifluoromethylsulfonyl)amide and Organic Amides Revealed by Dynamic Kerr Effect Spectroscopy

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-09 DOI: 10.1021/acs.jpcb.4c0862310.1021/acs.jpcb.4c08623

Maharoof Koyakkat, and , Hideaki Shirota*,

{"title":"Intermolecular Vibrational and Orientational Dynamics of Deep Eutectic Solvents Composed of Lithium Bis(trifluoromethylsulfonyl)amide and Organic Amides Revealed by Dynamic Kerr Effect Spectroscopy","authors":"Maharoof Koyakkat,  and , Hideaki Shirota*, ","doi":"10.1021/acs.jpcb.4c0862310.1021/acs.jpcb.4c08623","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08623https://doi.org/10.1021/acs.jpcb.4c08623","url":null,"abstract":"In this study, we investigated the intermolecular dynamics, including intermolecular vibration and orientational dynamics, of five deep eutectic solvents (DESs) consisting of lithium bis(trifluoromethylsulfonyl)amide and organic amides, such as acetamide, propanamide, N-methylacetamide, butyramide, and urea, at a mole ratio of 1:3 using femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES) and subpicosecond optical Kerr effect spectroscopy (ps-OKES). The fs-RIKES results showed that the line shape of the low-frequency band of the N-methylacetamide was trapezoidal, while that of the other organic amide-based DESs was bimodal. The peak and first moment of the intermolecular vibrational band appearing in the frequency range less than 250 cm–1 for the acetamide- and urea-based DESs were in a higher-frequency region compared to the other three DESs, indicating stronger intermolecular interactions. Furthermore, analysis of the intramolecular vibrational bands of the bis(trifluoromethylsulfonyl)amide anion showed that the population of the transoid conformer of the anion was slightly higher in the urea-based DES than in the other organic amide-based DESs, suggesting that urea solvate lithium cations more than the other organic amides. The slow relaxation dynamics of all five DESs were captured for up to 1 ns using ps-OKES. The slow relaxation dynamics also depended on the organic amide species. However, the slow relaxation time constant did not show a clear correlation with the viscosity; therefore, the relaxation dynamics of the DESs did not follow the Stokes–Einstein–Debye hydrodynamic model. The densities, viscosities, surface tensions, and electrical conductivities of the DESs were also measured for comparison with spectroscopic results.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 16","pages":"4023–4036 4023–4036"},"PeriodicalIF":2.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143863114","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}

引用次数: 0

Shear Viscosity of Quasi-Two-Dimensional Ionic Liquids

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-09 DOI: 10.1021/acs.jpcb.4c0757310.1021/acs.jpcb.4c07573

J. D. Hernández Velázquez, and , A. Gama Goicochea*,

引用次数: 0

Coupling of Charge Regulation and Geometry in Soft Ionizable Molecular Assemblies.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-08 DOI: 10.1021/acs.jpcb.5c00162

Joseph M McCourt, Leticia Lopez-Flores, Sumit Kewalramani, Noah B Welke, Monica Olvera de la Cruz, Michael J Bedzyk

{"title":"Coupling of Charge Regulation and Geometry in Soft Ionizable Molecular Assemblies.","authors":"Joseph M McCourt, Leticia Lopez-Flores, Sumit Kewalramani, Noah B Welke, Monica Olvera de la Cruz, Michael J Bedzyk","doi":"10.1021/acs.jpcb.5c00162","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00162","url":null,"abstract":"The size, shape, and charge of structures, such as proteins and amphiphile assemblies, respond in an interconnected manner to solution ionic conditions. We analyze assemblies of an amphiphile (C16K2), with two ionizable amino acids [lysine (K)] coupled to a 16-carbon alkyl tail, via small-angle X-ray scattering (SAXS), nonlinear Poisson-Boltzmann theory (nl-PB), and hybrid Monte Carlo-molecular dynamics (MC-MD) simulations. SAXS revealed structural transitions from spherical micelles to cylindrical micelles to bilayers with increasing pH. By combining SAXS-determined structural information and nl-PB, we derived the molecular degree of ionization as a function of pH. The back-calculated titration curves matched the experimental data over an extended pH range, without adjustable parameters. Similarly, the SAXS data on the evolution of spherical micelle structure with ionic strength were combined with nl-PB and MC-MD to derive the bare and effective charges. MC-MD, which considered finite ion sizes, showed that bare and effective charges saturate quickly with increasing salt concentration. Furthermore, the calculated effective charges closely matched results from Zeta-potential measurements. The presented approach has advantages over customary methods for charge regulation, such as the Henderson-Hasselbalch (HH) or Hill models, where molecular ionization/deionization in assemblies is described by effective pKs that are distinct from the pK for isolated molecules. However, these models lack a physical explanation for these pK shifts. By contrast, our approach of combining structural details with an electrostatic model and simulations provides a more intuitive understanding of structure-charge coupling and a framework for understanding charge regulation in many synthetic and biological systems.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802072","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}

引用次数: 0

Photophysical and Photochemical Features of Lysine Derivatives Bearing Two Triphenylaminocinnamic-Based Fluorophores

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-08 DOI: 10.1021/acs.jpcb.5c0103210.1021/acs.jpcb.5c01032

Mario Saletti, Marco Paolino, Jacopo Venditti, Gianluca Giorgi, Claudia Bonechi, Alessandro Donati, Claudio Rossi, Germano Giuliani, Antonella Caterina Boccia, Chiara Botta, Lluís Blancafort and Andrea Cappelli*,

{"title":"Photophysical and Photochemical Features of Lysine Derivatives Bearing Two Triphenylaminocinnamic-Based Fluorophores","authors":"Mario Saletti, Marco Paolino, Jacopo Venditti, Gianluca Giorgi, Claudia Bonechi, Alessandro Donati, Claudio Rossi, Germano Giuliani, Antonella Caterina Boccia, Chiara Botta, Lluís Blancafort and Andrea Cappelli*, ","doi":"10.1021/acs.jpcb.5c0103210.1021/acs.jpcb.5c01032","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01032https://doi.org/10.1021/acs.jpcb.5c01032","url":null,"abstract":"A Morita–Baylis–Hillman adduct (MBHA) derivative bearing a triphenylamine (TPA) moiety was previously found to react with Nα-acetyl-l-lysine methyl ester with the formation of the corresponding diadduct derivative as the major reaction product and a monoadduct as the minor one. The characterization of photochemical features of the diadduct bearing two triphenylaminocinnamic (TPAC) fluorophores suggested that this compound shows the tendency to undergo the [2 + 2] photocycloaddition reaction. This hypothesis was evaluated in the present study in both the diadduct derivatives obtained with Nα-acetyl-l-lysine methyl ester and Nα-acetyl-l-lysine. The hypothesis was confirmed in the case of the diadduct derivative obtained from Nα-acetyl-l-lysine methyl ester, whereas the UV-A irradiation of the diadduct derivative obtained from Nα-acetyl-l-lysine led to the formation of a strongly emissive (QY = 69%, λem = 460 nm) symmetric dimer.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 15","pages":"3928–3937 3928–3937"},"PeriodicalIF":2.8,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143837805","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}

引用次数: 0

Coupling of Charge Regulation and Geometry in Soft Ionizable Molecular Assemblies

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-08 DOI: 10.1021/acs.jpcb.5c0016210.1021/acs.jpcb.5c00162

Joseph M. McCourt, Leticia Lopez-Flores, Sumit Kewalramani, Noah B. Welke, Monica Olvera de la Cruz* and Michael J. Bedzyk*,

{"title":"Coupling of Charge Regulation and Geometry in Soft Ionizable Molecular Assemblies","authors":"Joseph M. McCourt, Leticia Lopez-Flores, Sumit Kewalramani, Noah B. Welke, Monica Olvera de la Cruz* and Michael J. Bedzyk*, ","doi":"10.1021/acs.jpcb.5c0016210.1021/acs.jpcb.5c00162","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00162https://doi.org/10.1021/acs.jpcb.5c00162","url":null,"abstract":"The size, shape, and charge of structures, such as proteins and amphiphile assemblies, respond in an interconnected manner to solution ionic conditions. We analyze assemblies of an amphiphile (C16K2), with two ionizable amino acids [lysine (K)] coupled to a 16-carbon alkyl tail, via small-angle X-ray scattering (SAXS), nonlinear Poisson–Boltzmann theory (nl-PB), and hybrid Monte Carlo-molecular dynamics (MC-MD) simulations. SAXS revealed structural transitions from spherical micelles to cylindrical micelles to bilayers with increasing pH. By combining SAXS-determined structural information and nl-PB, we derived the molecular degree of ionization as a function of pH. The back-calculated titration curves matched the experimental data over an extended pH range, without adjustable parameters. Similarly, the SAXS data on the evolution of spherical micelle structure with ionic strength were combined with nl-PB and MC-MD to derive the bare and effective charges. MC-MD, which considered finite ion sizes, showed that bare and effective charges saturate quickly with increasing salt concentration. Furthermore, the calculated effective charges closely matched results from Zeta-potential measurements. The presented approach has advantages over customary methods for charge regulation, such as the Henderson–Hasselbalch (HH) or Hill models, where molecular ionization/deionization in assemblies is described by effective pKs that are distinct from the pK for isolated molecules. However, these models lack a physical explanation for these pK shifts. By contrast, our approach of combining structural details with an electrostatic model and simulations provides a more intuitive understanding of structure-charge coupling and a framework for understanding charge regulation in many synthetic and biological systems.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 15","pages":"3814–3828 3814–3828"},"PeriodicalIF":2.8,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143837713","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}

引用次数: 0

Ultrafast Dynamics in Flavocytochrome C by Using Transient Absorption and Femtosecond Fluorescence Lifetime Spectroscopy

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-08 DOI: 10.1021/acs.jpcb.4c0549610.1021/acs.jpcb.4c05496

Krishna P. Khakurel*, Gustavo Fuertes, Aron Sipos, Gábor Paragi, Jakub Dostal, Miroslav Kloz, Gabriel Žoldák, Jakob Andreasson and András Tóth*,

{"title":"Ultrafast Dynamics in Flavocytochrome C by Using Transient Absorption and Femtosecond Fluorescence Lifetime Spectroscopy","authors":"Krishna P. Khakurel*, Gustavo Fuertes, Aron Sipos, Gábor Paragi, Jakub Dostal, Miroslav Kloz, Gabriel Žoldák, Jakob Andreasson and András Tóth*, ","doi":"10.1021/acs.jpcb.4c0549610.1021/acs.jpcb.4c05496","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c05496https://doi.org/10.1021/acs.jpcb.4c05496","url":null,"abstract":"Flavocytochrome c sulfide dehydrogenase (FCC) is an important enzyme of sulfur metabolism in sulfur-oxidizing bacteria, and its catalytic properties have been extensively studied. However, the ultrafast dynamics of FCC is not well understood. We present ultrafast transient absorption and fluorescence spectroscopy measurements to unravel the early events upon excitation of the heme and flavin chromophores embedded in the flavocytochrome c (FccAB) from the bacterium Thiocapsa roseopersicina. The fluorescence kinetics of FccAB suggests that the majority of the photoexcited species decay nonradiatively within the first few picoseconds. Transient absorption spectroscopy supports these findings by suggesting two major dynamic processes in FccAB, internal conversion occurring in about 400 fs and the vibrational cooling occurring in about 4 ps, mostly affecting the heme moiety.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 15","pages":"3731–3739 3731–3739"},"PeriodicalIF":2.8,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpcb.4c05496","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143837806","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}

引用次数: 0