The Journal of Physical Chemistry B最新文献_第10页

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-07-24

Tao Zhang, Zi Wang, Shuang Li and Jiaye Su*,

引用次数: 0

Ultrafast Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulations Reveal Slow Water Dynamics in Sulfobutylether-β-Cyclodextrin. 超快二维红外光谱和分子动力学模拟揭示了磺基丁醚-β-环糊精的慢水动力学。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-07-24 Epub Date: 2025-07-15 DOI: 10.1021/acs.jpcb.5c04390

Aruna K Mora, Dibyendu Bandyopadhyay, Niharendu Choudhury, Prabhat K Singh

{"title":"Ultrafast Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulations Reveal Slow Water Dynamics in Sulfobutylether-β-Cyclodextrin.","authors":"Aruna K Mora, Dibyendu Bandyopadhyay, Niharendu Choudhury, Prabhat K Singh","doi":"10.1021/acs.jpcb.5c04390","DOIUrl":"10.1021/acs.jpcb.5c04390","url":null,"abstract":"Despite the central role of cyclodextrins in supramolecular chemistry and biomedical formulations, their internal hydration dynamics have remained inaccessible to ultrafast vibrational spectroscopy due to the absence of a suitable vibrational reporter. Here, we present the first application of two-dimensional infrared (2DIR) spectroscopy to probe water dynamics inside a cyclodextrin cavity under thermal equilibrium. By employing azidoadamantane (AdN3)─an intelligently designed vibrational reporter that combines strong binding affinity for a cyclodextrin cavity with a spectrally isolated azide stretch─we investigate the host-guest complex of AdN3 and sulfobutylether-β-cyclodextrin (SBE-β-CD). The 2DIR spectra reveal minimal spectral diffusion, strong vibrational frequency correlation, and extended water residence times, indicative of a rigid, nanoconfined hydration environment. Frequency-frequency correlation function (FFCF) analysis and complementary molecular dynamics simulations show that restricted translational mobility governs these slow dynamics. This combined experimental-computational approach underscores the unique hydration dynamics within cyclodextrin cavities and highlights the potential of 2DIR spectroscopy for probing ultrafast hydration in nanoscale cavities and provides critical mechanistic insights with broad implications for drug delivery, molecular recognition, and confined water systems. Unlike previous reports attributing interfacial water slowdown to polar or ionic binding, we identify steric confinement by a host cavity as a distinct cause of retarded water dynamics.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"7686-7697"},"PeriodicalIF":2.8,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144641168","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

Calculations of the Absolute Free Energy, Enthalpy, and Entropy of Drug Binding Using Different Potential Models. 用不同电位模型计算药物结合的绝对自由能、焓和熵。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-07-24 Epub Date: 2025-07-09 DOI: 10.1021/acs.jpcb.4c07569

Steven W Rick, Christopher M Summa

引用次数: 0

H-O Bond Dynamics: Length, Energy, and Flexibility under Perturbation. 氢氧键动力学：微扰下的长度、能量和柔韧性。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-07-24 Epub Date: 2025-07-09 DOI: 10.1021/acs.jpcb.5c02544

Chang Q Sun, Chunyang Nie, Yongli Huang, Yong Zhou, Xuexian Yang, Lei Zhang, Biao Wang

引用次数: 0

Static and Dynamic Correlations in Binary and Ternary Mixtures of TMAO, Urea, and Water. 氧化三甲胺、尿素和水的二元和三元混合物的静态和动态相关性。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-07-24 DOI: 10.1021/acs.jpcb.5c03841

Christoph Hölzl, Dominik Horinek

引用次数: 0

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-07-24

Chang Q. Sun*, Chunyang Nie, Yongli Huang, Yong Zhou, Xuexian Yang, Lei Zhang* and Biao Wang*,

引用次数: 0

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-07-24

Arkaprava Chowdhury*, Sucheta Kundu, Souradip Dasgupta, Ayushi Chand and Anindya Datta*,

引用次数: 0

Arginine: II. Interactions of Its Salt Bridges with Branched Aliphatic Side Chains. 精氨酸:II。其盐桥与支链脂肪侧链的相互作用。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-07-24 Epub Date: 2025-07-09 DOI: 10.1021/acs.jpcb.5c02172

Christopher M Ng, Vivian Kui, Katherine Y Han, Eric R Kempson, Margaret Mandziuk

{"title":"Arginine: II. Interactions of Its Salt Bridges with Branched Aliphatic Side Chains.","authors":"Christopher M Ng, Vivian Kui, Katherine Y Han, Eric R Kempson, Margaret Mandziuk","doi":"10.1021/acs.jpcb.5c02172","DOIUrl":"10.1021/acs.jpcb.5c02172","url":null,"abstract":"Previous analyses of the structures deposited in the PDB revealed that arginine (Arg) side chains are often in close contact with leucine (Leu) side chains. In the previous paper, we studied interactions between Leu and Arg side chains alone [Ng et al. https://doi.org/10.1021/acs.jpcb.5c02168]. In this work, we have focused on the interactions between Leu side chains and salt bridges formed between Arg and acidic side chains. We inspected the trimer structures of the three side chains: Leu, Arg, and an acidic residue in the high-resolution files in the PDB. We also performed optimization of the model trimers with the ωB97X-D density functional and aug-cc-pVTZ basis set. We found that the salt bridges in a relatively low-polarity environment are most likely in a dynamic equilibrium between an ionic form and two neutral tautomers. That leads to the increased distances between Arg and the acidic residue as well as to the increased density of low-energy vibrational states, consequently increasing specific heat and entropy. The Leu residue controls the polarity of the environment. These findings explain why an increased number of salt bridges provides increased stability to the thermophilic enzymes and increases the fluctuations and mobility of psychrophilic proteins. Further studies are needed to find out whether methyl protons are scrambled with amino protons. We also performed calculations on the trimers with the doubly protonated Arg side chain. Energy of such trimers is lower than the energy of the monoprotonated trimers. Their lowest energy is obtained after a proton transfer to an acidic residue, and the guanidinium ion returns to the lowest energy planar structure. Such proton transfer may occur in membrane proteins where salt bridges are interspersed between nonpolar residues.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"7430-7441"},"PeriodicalIF":2.9,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12302201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590085","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

Aglycone, Glycoside, or Glucuronide? Experimental and Mechanistic Insights into the Antioxidative Potential of Gossypetin, Gossypin, and Hibifolin. 糖苷元、糖苷还是葡萄糖醛酸？Gossypetin， Gossypin和Hibifolin抗氧化潜能的实验和机理研究。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-07-24 Epub Date: 2025-07-16 DOI: 10.1021/acs.jpcb.5c03338

Maciej Spiegel, Adam Kowalczyk

{"title":"Aglycone, Glycoside, or Glucuronide? Experimental and Mechanistic Insights into the Antioxidative Potential of Gossypetin, Gossypin, and Hibifolin.","authors":"Maciej Spiegel, Adam Kowalczyk","doi":"10.1021/acs.jpcb.5c03338","DOIUrl":"10.1021/acs.jpcb.5c03338","url":null,"abstract":"Oxidative stress, caused by an imbalance between reactive oxygen species and antioxidants, drives chronic diseases such as cancer and neurodegeneration. This study investigates the antioxidant potential of three flavonoids from the Malvaceae family─gossypetin, gossypin, and hibifolin─using DPPH (radical scavenging) and FRAP (reducing power) assays, backed by quantum mechanical computations. Gossypetin displayed exceptional scavenging (TEAC: 111.53 mM/g) and reducing power (TEAC: 155.24 mM/g), thanks to its hydroxyl-rich structure, positioning it as a promising therapeutic option for oxidative stress-related conditions. Gossypin provided moderate scavenging (TEAC: 41.68 mM/g) but robust reducing capacity (TEAC: 126.28 mM/g), making it well-suited for food preservation. Hibifolin, with its stable glucuronyl group, showed balanced scavenging and reducing abilities (TEAC: 39.99 mM/g; 94.67 mM/g), ideal for nutraceuticals. Quantum mechanical analyses revealed the mechanisms behind these antioxidant effects, shedding light on their performance.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"7593-7601"},"PeriodicalIF":2.9,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12302068/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144641164","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

The Role of Electron Donating Ability of Pendant Groups in the Photophysics of Donor-Acceptor-Donor Diaminoterephthalate Derivatives. 垂坠基团给电子能力在给体-受体-给体二氨基对苯二甲酸酯衍生物光物理中的作用。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-07-24 Epub Date: 2025-06-30 DOI: 10.1021/acs.jpcb.5c02113

Arkaprava Chowdhury, Sucheta Kundu, Souradip Dasgupta, Ayushi Chand, Anindya Datta

引用次数: 0