The Journal of Physical Chemistry B最新文献_第4页

Phase Diagram of Polyelectrolyte Solutions in Ice and Water 冰与水中聚电解质溶液的相图

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-07 DOI: 10.1021/acs.jpcb.5c0064410.1021/acs.jpcb.5c00644

George Mallinos, and , Ali Dhinojwala*,

{"title":"Phase Diagram of Polyelectrolyte Solutions in Ice and Water","authors":"George Mallinos,  and , Ali Dhinojwala*, ","doi":"10.1021/acs.jpcb.5c0064410.1021/acs.jpcb.5c00644","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00644https://doi.org/10.1021/acs.jpcb.5c00644","url":null,"abstract":"Strong interactions of polyelectrolytes (PEs) with water have been used to control many technological applications of PEs in cryopreservation as well as in anti-icing or lubricating coatings. In all of these cases, knowledge of the phase diagrams of PE with water is important, particularly at low temperatures, where the ice phase is more stable. In this work, we study the phase diagrams of negatively and positively-charged PEs by using infrared spectroscopy (IR) and differential scanning calorimetry (DSC). The results show a coexistence curve of the ice phase in equilibrium with the PE-rich phase in water. The phase diagrams for positively- and negatively-charged PEs were similar, and a nearly 40% volume fraction of water to polymer remains unfrozen. Comparison of the collected data with the predictions from a theoretical model based on the Gibbs–Thomson and Flory–Huggins models reveals that the concentrated PE-water phase has closely associated counterions, and the entropy of the counterions does not play a dominant role. This finding is surprising since PEs are expected to have strongly dissociated charges under these conditions. Interestingly, we also found evidence of a stable unfrozen water PE phase that does not change upon further cooling to −100 °C. These observations are important for applications where controlling the formation of ice is critical.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 15","pages":"3918–3927 3918–3927"},"PeriodicalIF":2.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143837745","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

Unraveling the Tether: Exploring Representative Protein Linkers and Their Structural and Thermodynamical Properties. 解开绳索：探索具有代表性的蛋白质连接体及其结构和热力学性质。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-06 DOI: 10.1021/acs.jpcb.4c04194

Josef Šulc, Jiří Vondrášek

{"title":"Unraveling the Tether: Exploring Representative Protein Linkers and Their Structural and Thermodynamical Properties.","authors":"Josef Šulc, Jiří Vondrášek","doi":"10.1021/acs.jpcb.4c04194","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c04194","url":null,"abstract":"This study explores the thermodynamic and structural behaviors of linker peptides, short polypeptide segments that often bridge protein domains. We are focusing on three prototypical classes─glycine-serine (GS), glycine-glycine (GG), and alanine-proline (AP)─and exploring their conformational dynamics as isolated entities outside a multidomain protein context. Using extensive molecular dynamics (MD) simulations and free energy perturbation (FEP) analyses, we characterize the free energy landscapes, entropic properties, and solvation energetics of 20 representative linkers. Our results reveal a pronounced linear relationship between linker length and key thermodynamic contributions, including zero-point vibrational energy (ZPVE), potential energy, and entropy. Notably, vibrational entropy emerges as a dominant stabilizing term. We also found that AP linkers display more rigid, yet extended conformations compared to the highly flexible GS and moderately flexible GG linkers. These findings underscore the nuanced role of linker composition in contributing to multidomain protein architecture and dynamics, and highlight how thermodynamic forces shape linker conformational behavior. Collectively, our work enhances the mechanistic understanding of protein linkers, offering valuable insights for the rational design of peptide-based systems and informing future efforts to modulate interdomain flexibility and stability in multidomain proteins.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794148","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

Unraveling the Tether: Exploring Representative Protein Linkers and Their Structural and Thermodynamical Properties 解开绳索：探索具有代表性的蛋白质连接体及其结构和热力学性质

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-06 DOI: 10.1021/acs.jpcb.4c0419410.1021/acs.jpcb.4c04194

Josef Šulc, and , Jiří Vondrášek*,

{"title":"Unraveling the Tether: Exploring Representative Protein Linkers and Their Structural and Thermodynamical Properties","authors":"Josef Šulc,  and , Jiří Vondrášek*, ","doi":"10.1021/acs.jpcb.4c0419410.1021/acs.jpcb.4c04194","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c04194https://doi.org/10.1021/acs.jpcb.4c04194","url":null,"abstract":"This study explores the thermodynamic and structural behaviors of linker peptides, short polypeptide segments that often bridge protein domains. We are focusing on three prototypical classes─glycine-serine (GS), glycine–glycine (GG), and alanine-proline (AP)─and exploring their conformational dynamics as isolated entities outside a multidomain protein context. Using extensive molecular dynamics (MD) simulations and free energy perturbation (FEP) analyses, we characterize the free energy landscapes, entropic properties, and solvation energetics of 20 representative linkers. Our results reveal a pronounced linear relationship between linker length and key thermodynamic contributions, including zero-point vibrational energy (ZPVE), potential energy, and entropy. Notably, vibrational entropy emerges as a dominant stabilizing term. We also found that AP linkers display more rigid, yet extended conformations compared to the highly flexible GS and moderately flexible GG linkers. These findings underscore the nuanced role of linker composition in contributing to multidomain protein architecture and dynamics, and highlight how thermodynamic forces shape linker conformational behavior. Collectively, our work enhances the mechanistic understanding of protein linkers, offering valuable insights for the rational design of peptide-based systems and informing future efforts to modulate interdomain flexibility and stability in multidomain proteins.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 15","pages":"3720–3730 3720–3730"},"PeriodicalIF":2.8,"publicationDate":"2025-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpcb.4c04194","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143837706","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

Dynamics of a von Willebrand Factor A1 Autoinhibitory Module with O-Linked Glycans and Its Roles in Regulation of GPIbα Binding 带有o链聚糖的血管性血友病因子A1自抑制模块的动力学及其在调节GPIbα结合中的作用

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-04 DOI: 10.1021/acs.jpcb.5c0092510.1021/acs.jpcb.5c00925

Yiwei Cao, X. Frank Zhang and Wonpil Im*,

{"title":"Dynamics of a von Willebrand Factor A1 Autoinhibitory Module with O-Linked Glycans and Its Roles in Regulation of GPIbα Binding","authors":"Yiwei Cao, X. Frank Zhang and Wonpil Im*, ","doi":"10.1021/acs.jpcb.5c0092510.1021/acs.jpcb.5c00925","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00925https://doi.org/10.1021/acs.jpcb.5c00925","url":null,"abstract":"The von Willebrand factor (VWF), a multimeric plasma glycoprotein, binds to the platelet glycoprotein (GPIbα) to initiate the process of primary hemostasis as a response to blood flow alteration in the site of vascular injury. The GPIbα binding site located on the A1 domain of VWF is exposed during the activation of the VWF multimer when it changes from a coiled form to a thread-like, extended form. Though experimental studies have demonstrated that the autoinhibitory module (AIM) connected to the N-/C-termini of the A1 domain is a regulator of VWF activity, the molecular mechanism underlying the regulation of A1–GPIbα binding remains unclear. We modeled the structures of the A1 domain having full-length N-terminal AIM (NAIM) and C-terminal AIM (CAIM) with different types of O-linked glycans. The conventional and steered molecular dynamics simulations were conducted to investigate the dynamics of the AIM and O-glycans under different conditions and elucidate how they affect the binding of GPIbα. Our results indicate that the NAIM alone with no glycan is sufficient to shield the GPIbα binding site under static conditions. However, when the AIM is unfolded with external forces applied, the O-glycans on both NAIM and CAIM increase the shielding of the binding site. These findings suggest a potential mechanism by which the AIM and O-glycans regulate the interaction of the VWF A1 domain and GPIbα.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 15","pages":"3796–3806 3796–3806"},"PeriodicalIF":2.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpcb.5c00925","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143837777","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

Study on the Promotion of Gas Hydrate Generation by Three Different Electric Field Waveform Signals in Synergy with Surfactants. 三种不同电场波形信号与表面活性剂协同促进天然气水合物生成的研究。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-04 DOI: 10.1021/acs.jpcb.5c00510

Junhui Li, Lingli Shi, Qi Zhang, Xuebing Zhou, Xiaoya Zang, Dongliang Li, Deqing Liang

{"title":"Study on the Promotion of Gas Hydrate Generation by Three Different Electric Field Waveform Signals in Synergy with Surfactants.","authors":"Junhui Li, Lingli Shi, Qi Zhang, Xuebing Zhou, Xiaoya Zang, Dongliang Li, Deqing Liang","doi":"10.1021/acs.jpcb.5c00510","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00510","url":null,"abstract":"The rapid development of the natural gas hydrate industry has put forward higher requirements for hydrate promotion technology. The exploration of methods that can simultaneously enhance both the hydrate formation rate and the final gas and water conversion efficiency has become a critical research focus. This study systematically investigated the synergistic effects of electric field (EF) signals, including three distinct waveforms (square, sine, ramp wave) at six different voltage levels, combined with four concentration gradients of the cationic surfactant called hexadecyl trimethylammonium bromide (CTAB) on the CH4 hydrate formation process. Experimental results demonstrated that the application of external EF significantly enhanced the gas storage capacity of hydrate, with different waveforms exhibiting varying degrees of promotional effects. Notably, square wave and ramp wave, which allow for instantaneous changes in the EF direction, exhibited superior performance in improving hydrate formation rates and gas and water conversion efficiency and enhancing hydrate fluidity. Furthermore, a kinetic model for hydrate formation was developed, which showed excellent agreement with the observed results. These findings not only advance the theoretical framework of EF-assisted hydrate formation but also provide valuable insights and practical guidance for the development of natural gas hydrate technologies.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787416","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

Study on the Promotion of Gas Hydrate Generation by Three Different Electric Field Waveform Signals in Synergy with Surfactants 三种不同电场波形信号与表面活性剂协同促进天然气水合物生成的研究

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-04 DOI: 10.1021/acs.jpcb.5c0051010.1021/acs.jpcb.5c00510

Junhui Li, Lingli Shi*, Qi Zhang, Xuebing Zhou, Xiaoya Zang, Dongliang Li and Deqing Liang*,

{"title":"Study on the Promotion of Gas Hydrate Generation by Three Different Electric Field Waveform Signals in Synergy with Surfactants","authors":"Junhui Li, Lingli Shi*, Qi Zhang, Xuebing Zhou, Xiaoya Zang, Dongliang Li and Deqing Liang*, ","doi":"10.1021/acs.jpcb.5c0051010.1021/acs.jpcb.5c00510","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00510https://doi.org/10.1021/acs.jpcb.5c00510","url":null,"abstract":"The rapid development of the natural gas hydrate industry has put forward higher requirements for hydrate promotion technology. The exploration of methods that can simultaneously enhance both the hydrate formation rate and the final gas and water conversion efficiency has become a critical research focus. This study systematically investigated the synergistic effects of electric field (EF) signals, including three distinct waveforms (square, sine, ramp wave) at six different voltage levels, combined with four concentration gradients of the cationic surfactant called hexadecyl trimethylammonium bromide (CTAB) on the CH4 hydrate formation process. Experimental results demonstrated that the application of external EF significantly enhanced the gas storage capacity of hydrate, with different waveforms exhibiting varying degrees of promotional effects. Notably, square wave and ramp wave, which allow for instantaneous changes in the EF direction, exhibited superior performance in improving hydrate formation rates and gas and water conversion efficiency and enhancing hydrate fluidity. Furthermore, a kinetic model for hydrate formation was developed, which showed excellent agreement with the observed results. These findings not only advance the theoretical framework of EF-assisted hydrate formation but also provide valuable insights and practical guidance for the development of natural gas hydrate technologies.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 15","pages":"3879–3894 3879–3894"},"PeriodicalIF":2.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143837819","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

Dynamics of a von Willebrand Factor A1 Autoinhibitory Module with O-Linked Glycans and Its Roles in Regulation of GPIbα Binding. 带有o链聚糖的血管性血友病因子A1自抑制模块的动力学及其在调节GPIbα结合中的作用。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-04 DOI: 10.1021/acs.jpcb.5c00925

Yiwei Cao, X Frank Zhang, Wonpil Im

{"title":"Dynamics of a von Willebrand Factor A1 Autoinhibitory Module with O-Linked Glycans and Its Roles in Regulation of GPIbα Binding.","authors":"Yiwei Cao, X Frank Zhang, Wonpil Im","doi":"10.1021/acs.jpcb.5c00925","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00925","url":null,"abstract":"The von Willebrand factor (VWF), a multimeric plasma glycoprotein, binds to the platelet glycoprotein (GPIbα) to initiate the process of primary hemostasis as a response to blood flow alteration in the site of vascular injury. The GPIbα binding site located on the A1 domain of VWF is exposed during the activation of the VWF multimer when it changes from a coiled form to a thread-like, extended form. Though experimental studies have demonstrated that the autoinhibitory module (AIM) connected to the N-/C-termini of the A1 domain is a regulator of VWF activity, the molecular mechanism underlying the regulation of A1-GPIbα binding remains unclear. We modeled the structures of the A1 domain having full-length N-terminal AIM (NAIM) and C-terminal AIM (CAIM) with different types of O-linked glycans. The conventional and steered molecular dynamics simulations were conducted to investigate the dynamics of the AIM and O-glycans under different conditions and elucidate how they affect the binding of GPIbα. Our results indicate that the NAIM alone with no glycan is sufficient to shield the GPIbα binding site under static conditions. However, when the AIM is unfolded with external forces applied, the O-glycans on both NAIM and CAIM increase the shielding of the binding site. These findings suggest a potential mechanism by which the AIM and O-glycans regulate the interaction of the VWF A1 domain and GPIbα.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778517","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

Catalytic Effects of Water-Solvated Metal Cations in Epoxy-Amine Curing through Hydrogen Bonds and Metal-Ligand Interactions. 水溶剂化金属阳离子通过氢键和金属配体相互作用对环氧胺固化的催化作用。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-03 Epub Date: 2025-03-25 DOI: 10.1021/acs.jpcb.4c05874

Dipak Prasad, Nilanjan Mitra

引用次数: 0

The Enhanced Proton-Accepting Ability of Bound Water in Poly(vinyl alcohol) Films. 聚乙烯醇膜中结合水接受质子能力的增强。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-03 Epub Date: 2025-03-25 DOI: 10.1021/acs.jpcb.5c00861

Qin Yu, Siyu Hou, Mengrong Hu, Zheng Li, Jian Luo

引用次数: 0

Molecular-Level Understanding of Water Transport Mechanisms in Functionalized Ti₃C₂T_X MXene Membrane-Combined Experimental Approaches. 功能化Ti3C2TX MXene膜中水传输机制的分子水平理解-结合实验方法。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-03 Epub Date: 2025-03-25 DOI: 10.1021/acs.jpcb.4c08655

Yang He, Guowei Chen, Yiping Zhao, Li Chen

{"title":"Molecular-Level Understanding of Water Transport Mechanisms in Functionalized Ti3C2TX MXene Membrane-Combined Experimental Approaches.","authors":"Yang He, Guowei Chen, Yiping Zhao, Li Chen","doi":"10.1021/acs.jpcb.4c08655","DOIUrl":"10.1021/acs.jpcb.4c08655","url":null,"abstract":"The hydrophilicity of two-dimensional (2D) transition-metal carbides, carbonitrides, and nitrides (MXene) nanochannels plays a critical role in water transport during filtration, yet its specific effects on MXene membranes remain inadequately understood. Herein, we systematically investigated water transport through Ti3C2TX MXene nanochannels using molecular dynamics simulations coupled with experimental validation, addressing a significant knowledge gap in MXene-based separation membranes. Our simulations demonstrated that strong interactions between water molecules and hydrophilic nanochannel MXene surfaces (Ti3C2(OH)2 MXene or Ti3C2(NH)2 MXene) facilitated the formation of ordered molecular arrangements, substantially improving water permeability. Conversely, hydrophobic nanochannels (Ti3C2O2 MXene or Ti3C2F2 MXene) exhibited disordered water molecule distributions, leading to reduced permeability. Experimental validation corroborated these simulation results, demonstrating a direct correlation between the hydrophilicity of the Ti3C2TX surface and the water flux. The highly hydrophilic Ti3C2(OH)2 MXenes exhibited water flux maximum, whereas the more hydrophobic Ti3C2F2 MXenes had the lowest water flux. By integrating molecular dynamics simulations with experimental analyses, we gained comprehensive insights into the influence of nanochannel hydrophilicity on water transport mechanisms in MXene membranes. These findings provide critical guidelines for designing high-performance MXene-based membranes for advanced water treatment and separation applications.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3396-3407"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707791","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