The Journal of Physical Chemistry B最新文献_第8页

Ultrasensitive Differential Scanning Calorimetric (US-DSC) Study of the Thermal-Induced Dynamic Transition Behaviors of PEO-PPO-PEO in Aqueous Solution.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-20 DOI: 10.1021/acs.jpcb.4c08247

Lin Li, Kang Ni, Lvdan Liu, Yuxia Bai, Yanwei Ding

{"title":"Ultrasensitive Differential Scanning Calorimetric (US-DSC) Study of the Thermal-Induced Dynamic Transition Behaviors of PEO-PPO-PEO in Aqueous Solution.","authors":"Lin Li, Kang Ni, Lvdan Liu, Yuxia Bai, Yanwei Ding","doi":"10.1021/acs.jpcb.4c08247","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08247","url":null,"abstract":"Temperature-responsive macromolecules can provide insights into the mechanisms of the aggregation and precipitation processes of proteins. In this study, the PEO-PPO-PEO triblock copolymer, Pluronic P123, has been utilized as a protein model to investigate the thermally induced dynamic transition behavior by ultrasensitive differential scanning calorimetry (US-DSC). The results of US-DSC reveal hysteresis in the disaggregation process of P123 micelles. Combined with the particle size distribution, a stepwise disaggregation mechanism is proposed. The disaggregation of P123 micelles in the cooling process involved rod-to-sphere transition, fragmentation, and dissolution of micelles. Moreover, US-DSC results show that both the sphere-to-rod transition and micelle fragmentation are dependent on the scanning rate and reveal the relationship between the dynamic transition and thermodynamic properties of P123. These findings expand the understanding not only of aggregation and disaggregation of P123 in dilute aqueous systems but also of the thermal unfolding and aggregation of proteins.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661595","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

Biochemical Nanotubes Containing Heterocycles as Artificial Strands for Pseudo Duplex and Triplex DNA Formation.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-20 Epub Date: 2025-03-11 DOI: 10.1021/acs.jpcb.4c08079

Jih Ru Hwu, Deepa Rohidas Landge, Wen-Chieh Huang, Jia-Cherng Horng, Yu-Chen Hu, Kuo Chu Hwang, Chun-Cheng Lin, Shwu-Chen Tsay

{"title":"Biochemical Nanotubes Containing Heterocycles as Artificial Strands for Pseudo Duplex and Triplex DNA Formation.","authors":"Jih Ru Hwu, Deepa Rohidas Landge, Wen-Chieh Huang, Jia-Cherng Horng, Yu-Chen Hu, Kuo Chu Hwang, Chun-Cheng Lin, Shwu-Chen Tsay","doi":"10.1021/acs.jpcb.4c08079","DOIUrl":"10.1021/acs.jpcb.4c08079","url":null,"abstract":"This report presents our discoveries that include the successful hybridization of grafted single-walled carbon nanotubes (SWCNTs) with dsDNA to form pseudo triplex-DNA. These tubes are attached with distinctive five-membered N-containing heterocycles (i.e., imidazolidinone and triazolidindione) on their surface. In this study, the heterocycles play a crucial role as DNA binders. Consequently, three functionalized SWCNTs (f-SWCNTs) are synthesized, which are incorporated with multiple-phenoxy-triazole-(ethylene glycol)-(heterocycle) ligands. These f-SWCNTs are entwined with dsDNA to form \"pseudo triplex\". Notably, the dsDNA disengages from the f-SWCNTs at 85 °C and then is able to revert to triplex-DNA upon temperature reduction. Additionally, these f-SWCNTs act as a complementary strand for ssDNA to form pseudo duplex-DNA, in which the base pairings therein dissociate at 55 °C. Comprehensive analysis by use of CD spectrometer, SEM, TEM, and AFM microscopy provides substantive evidence for these phenomena. The demonstrated ability to manipulate DNA liberation from pseudo duplexes and triplexes indicates the potential versatility of f-SWCNTs as effective delivery vehicles for drugs and biomaterials in gene therapy and biotechnology.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"2903-2914"},"PeriodicalIF":2.8,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603027","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

Achievable Information-Energy Exchange in a Brownian Information Engine through Potential Profiling.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-20 Epub Date: 2025-03-05 DOI: 10.1021/acs.jpcb.5c00036

Rafna Rafeek, Debasish Mondal

{"title":"Achievable Information-Energy Exchange in a Brownian Information Engine through Potential Profiling.","authors":"Rafna Rafeek, Debasish Mondal","doi":"10.1021/acs.jpcb.5c00036","DOIUrl":"10.1021/acs.jpcb.5c00036","url":null,"abstract":"The information engine extracts work from a single heat bath using mutual information obtained during the operation cycle. This study investigates the influence of potential shaping in a Brownian information engine (BIE) in harnessing the information from thermal fluctuations. We designed a BIE by considering an overdamped Brownian particle inside a confined potential and introducing an appropriate symmetric feedback cycle. We find that the upper bound of the extractable work for a BIE with a monostable centrosymmetric confining potential, with a stable state at the potential center, depends on the bath temperature and the convexity of the confinement. A concave confinement is more efficient than a convex one for an information-energy exchange. For a bistable confinement with an unstable center and two symmetric stable basins, one can find an engine-to-refrigeration transition beyond a certain barrier height related to the energy difference between the energy barrier and the stable basins. Finally, we use the concavity-induced gain in information harnessing to device a BIE in the presence of a multistable potential that can harvest even more energy than monostable confinement.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"2971-2977"},"PeriodicalIF":2.8,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143565516","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

Unveiling the Interaction Mechanism of siRNA with Lipid Bilayers of Different Types for siRNA-Based Therapy.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-20 Epub Date: 2025-03-07 DOI: 10.1021/acs.jpcb.4c07520

Dongfang Zheng, Zhi Guo Lu, Jing Li, Junjun Dong, Xianren Zhang, Xin Zhang, Dapeng Cao

{"title":"Unveiling the Interaction Mechanism of siRNA with Lipid Bilayers of Different Types for siRNA-Based Therapy.","authors":"Dongfang Zheng, Zhi Guo Lu, Jing Li, Junjun Dong, Xianren Zhang, Xin Zhang, Dapeng Cao","doi":"10.1021/acs.jpcb.4c07520","DOIUrl":"10.1021/acs.jpcb.4c07520","url":null,"abstract":"siRNA-based therapy is a new approach for the treatment of diseases, including cancer, viral infections, and so forth. When liposomes serve as an effective siRNA carrier, unveiling the siRNA-liposome interaction mechanism becomes extremely significant for siRNA-based therapy. Here, we investigate the interactions between siRNA and liposomes with different types of lipid molecules and find that the stable adsorption of siRNA on the phosphoethanolamine (PE) bilayer liposome mainly relies on hydrogen bonding between the siRNA phosphate groups and the ethanolamine structure of PE lipid molecules. On the contrary, the stability of the adsorption of siRNA on the phosphorylcholine (PC) bilayer liposome is often determined by electrostatic interactions, and the adsorption stability can be modulated by calcium ions. The concept of \"bridging\" is also invoked to reveal the adsorption mechanism of siRNA on the lipid bilayer after adding calcium ions. We found that adding divalent calcium ions can better regulate the stability of siRNA adsorption on the PC lipid bilayer, but calcium ions cannot regulate the adsorption of siRNA on the PE lipid bilayer, which is determined by H-bonds. In short, this work reveals the different adsorption mechanisms of siRNA on liposomes, which provides a physical insight into siRNA-based therapy at the molecular level.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"2872-2881"},"PeriodicalIF":2.8,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571572","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

Weak Organic Acid Effect of Bacterial Light-Driven Proton-Pumping Rhodopsin

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-19 DOI: 10.1021/acs.jpcb.4c0689110.1021/acs.jpcb.4c06891

Zikun Lyu, Shunki Takaramoto and Keiichi Inoue*,

{"title":"Weak Organic Acid Effect of Bacterial Light-Driven Proton-Pumping Rhodopsin","authors":"Zikun Lyu, Shunki Takaramoto and Keiichi Inoue*, ","doi":"10.1021/acs.jpcb.4c0689110.1021/acs.jpcb.4c06891","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06891https://doi.org/10.1021/acs.jpcb.4c06891","url":null,"abstract":"Microbial rhodopsins are photoreceptor proteins that utilize light to elicit various biological functions. The best-studied microbial rhodopsins are outward proton (H+)-pumping rhodopsins, which transport H+ from the cytoplasmic to the extracellular side. Recently, the weak organic acid (WOA) effect, specifically the enhancement of pumping activity by WOAs such as acetic acid and indole-3-acetic acid (IAA), was discovered in outward H+-pumping rhodopsins from fungi. However, it remains unclear whether the WOA effect exists in nonfungal H+-pumping rhodopsins. Here, we revealed that the H+-pumping activity of a bacterial outward H+ pump rhodopsin, PspR, from the rhizobacterium Pseudomonas putida, is also enhanced by extracellular acetic acid and IAA. Using transient absorption measurements on purified PspR protein, we found that extracellular WOAs accelerate cytoplasmic H+ uptake and extracellular H+ release from a protonated counterion during its photocycle. Furthermore, acetic acid applied on the cytoplasmic side has an inhibitory effect on the H+ pump activity of PspR, which is less significant for IAA and can be mitigated by increasing the H+ concentration or introducing a cytoplasmic donor residue. These findings on the WOA effect in a bacterial rhodopsin provide new insights into the physiological function of outward H+-pumping rhodopsins in bacteria, particularly in their interaction with plants.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 12","pages":"3198–3206 3198–3206"},"PeriodicalIF":2.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143703810","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

Modulating the Charge Transfer Coupling in Boron-Dipyrromethene Homodimers by π-Bridge Units.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-19 DOI: 10.1021/acs.jpcb.5c00292

Li Ma, Zhuoran Kuang, Hao Zhang, Yan Wan, Yuanyuan Guo, Andong Xia, Yang Li

{"title":"Modulating the Charge Transfer Coupling in Boron-Dipyrromethene Homodimers by π-Bridge Units.","authors":"Li Ma, Zhuoran Kuang, Hao Zhang, Yan Wan, Yuanyuan Guo, Andong Xia, Yang Li","doi":"10.1021/acs.jpcb.5c00292","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00292","url":null,"abstract":"To mimic the excitation energy conversion mechanisms observed in natural light-harvesting systems, we have extensively investigated photoinduced symmetry-breaking charge separations (SBCSs) in various multichromophoric model systems have been extensively investigated. However, designing multichromophoric model systems capable of simultaneously achieving ultrafast and complete SBCS remains a significant challenge. In this study, we employed benzene, thiophene, and furan as π-bridges to develop a series of boron dipyrromethene (BODIPY) homodimers. Spectral analysis, together with an estimation of the π-bridge-dependent charge transfer (CT) coupling using the fragment charge difference method, reveals that π-bridge units with different electron-donating abilities can effectively modulate the CT coupling between chromophores. Notably, the furan-based π-bridge, exhibiting the most pronounced electron-donating character, facilitates symmetry-breaking charge transfer (SBCT), i.e., excimer formation with a time constant of about 12 ps in weak polar toluene. Furthermore, a dramatic increase in the SBCS rate constant was observed in highly polar acetonitrile, improving from 60.4 ps for the benzene-bridged homodimer to 2.9 ps for the furan-bridged counterpart. These findings underscore the potential of π-bridge units in tuning the photophysical properties of covalent molecular aggregates by optimizing such systems for specific applications such as organic photovoltaics and photocatalysis.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661575","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

Plasticization Effects of PEG of Low Molar Fraction and Molar Mass on the Molecular Dynamics and Crystallization of PLA-b-PEG-b-PLA Triblock Copolymers Envisaged for Medical Applications.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-19 DOI: 10.1021/acs.jpcb.5c00171

Nikolaos D Bikiaris, Panagiotis A Klonos, Evi Christodoulou, Panagiotis Barmpalexis, Apostolos Kyritsis

{"title":"Plasticization Effects of PEG of Low Molar Fraction and Molar Mass on the Molecular Dynamics and Crystallization of PLA-b-PEG-b-PLA Triblock Copolymers Envisaged for Medical Applications.","authors":"Nikolaos D Bikiaris, Panagiotis A Klonos, Evi Christodoulou, Panagiotis Barmpalexis, Apostolos Kyritsis","doi":"10.1021/acs.jpcb.5c00171","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00171","url":null,"abstract":"We prepared and studied a series of triblock copolymers based on poly(ethylene glycol) (PEG) and poly(lactic acid) (PLA). PLA blocks were in situ by ring-opening polymerization (ROP) of lactide (LA) onto the two sites of PEG. While in our recent work on similar copolymers with varying LA/PEG molar ratios and fixed PEG blocks [Bikiaris, N. D. Mater. Today Commun. 2024, 38, 107799], herein, we kept this ratio quite low, at 640/1, and employed different molecular weights, Mn, of the initial PEG at 1, 4, 6, and 8 kg/mol. The triblocks demonstrated high homogeneity, as manifested by the single thermal transition (glass transition, crystallization) with corresponding alternations in a systematic way with the Mn of PEG. With the increase of the latter Mn, accelerated segmental mobility and lowering of Tg by up to 15 K were recorded, accompanied by suppression in the chain fragility (cooperativity). Compared with linear PLAs of various Mns [Klonos, P. A. Polymer 2024, 305, 127177] and other PLA-based copolymers prepared by similar ROPs, with the overall Mn of our copolymers, PEG here sees to play the role of plasticizer on PLA, leading to increased free volume. Due to these effects, in general, the low crystalline fraction of PLA (∼3%) was significantly enhanced in the copolymers (20-26%), and the formed spherulites were mainly enlarged. Contrary to these, nucleation was barely affected; thus, the copolymers exhibited altered semicrystalline morphologies as compared to that in neat PLA. Both aspects of molecular dynamics, free volume and crystallization, were connected to the processability as well as the performance of these systems, considering the envisaged biomedical applications.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661581","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

The Role of Fluorine Substituents on the Physical Properties of 4-Pentyl-4″-propyl-1,1':4',1″-terphenyl Liquid Crystals.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-18 DOI: 10.1021/acs.jpcb.5c00140

Anna Drzewicz, Przemysław Kula, Ewa Juszyńska-Gałązka

引用次数: 0

Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-18 DOI: 10.1021/acs.jpcb.5c00104

Shashank Pant, Sepehr Dehghani-Ghahnaviyeh, Noah Trebesch, Ali Rasouli, Tianle Chen, Karan Kapoor, Po-Chao Wen, Emad Tajkhorshid

引用次数: 0

rCGMM: A Coarse-Grained Force Field Embedding Elastic Network for Studying Small Noncoding RNA Dynamics

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-18 DOI: 10.1021/acs.jpcb.4c0728610.1021/acs.jpcb.4c07286

Subhasree Majumder, and , Debnath Pal*,

{"title":"rCGMM: A Coarse-Grained Force Field Embedding Elastic Network for Studying Small Noncoding RNA Dynamics","authors":"Subhasree Majumder,  and , Debnath Pal*, ","doi":"10.1021/acs.jpcb.4c0728610.1021/acs.jpcb.4c07286","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07286https://doi.org/10.1021/acs.jpcb.4c07286","url":null,"abstract":"Short noncoding RNA molecules play significant roles in catalysis, biological regulation, and disease pathways. Their assessment through sequence-based approaches has been a challenge, compounded by the significant structural flexibility accrued from six free backbone torsions per nucleotide. To efficiently study the structure and dynamics of an extensive repertoire of these molecules in a high throughput mode, we have built a coarse-grained force field using one, two, three, and four pseudoatoms to represent the phosphate, sugar, pyrimidines, and purines, respectively. The Boltzmann inversion method was applied to structures of 5 piRNA, 8 miRNA, and 13 siRNA from the Nucleic Acid Database (NDB) to estimate the initial force field parameters and iteratively optimized through 1 μs molecular dynamics run by comparing against an equivalent all-atom simulation using the CHARMM36 force field. We applied an elastic net to model the hydrogen bond network stabilizing the local structure for double-stranded cases. A spine using pseudoatoms was calculated for the same from the coarse-grain beads, and all beads within a threshold radial distance were constrained using soft distance potentials. Lennard-Jones and Coulomb’s potential function modeled the nonbonded interaction. Benchmarks on 26 molecules compared through root-mean-square deviation graphs against all-atom simulation show close concurrence for single- and double-stranded small noncoding RNA molecules. The rCGMM force field is available for download at https://github.com/majumderS/rCGMM.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 12","pages":"3159–3170 3159–3170"},"PeriodicalIF":2.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143703703","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