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We study the counterion condensation on a two-dimensional charged disk in the limit of infinite dilution, and compare the energy-temperature relation obtained from the canonical free energy and microcanonical entropy. The microcanonical entropy is piecewise linear in energy, and is shown to be concave for all energies. As a result, even though the interactions are long-ranged, the energy-temperature relation and hence the counterion condensation transition points are identical in both the ensembles.
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http://dx.doi.org/10.1103/PhysRevE.85.011119 | DOI Listing |
J Phys Chem B
September 2025
Department of Physics and Mathematics, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, São Paulo 14800-060, Brazil.
Magnesium ions (Mg) play a crucial role in stabilizing various RNA tertiary motifs, such as pseudoknots, G-quadruplexes, kissing loops, and A-minor motifs, to name a few. Despite their importance, the precise location and role of Mg ions in RNA folding are challenging to characterize both experimentally and computationally. In this study, we employ an all-atom structure-based model integrated with the dynamic counterion condensation (DCC) model to investigate the folding and unfolding transitions of apo SAM-II riboswitch RNA at physiological concentrations of Mg.
View Article and Find Full Text PDFElife
September 2025
Department of Biology, Graduate School of Science, Osaka Metropolitan University, Sumiyoshi ku, Osaka, Japan.
Animal opsins are G protein-coupled receptors that have evolved to sense light by covalently binding a retinal chromophore via a protonated (positively charged) Schiff base. A negatively charged amino acid in the opsin, acting as a counterion, stabilizes the proton on the Schiff base, which is essential for sensitivity to visible light. In this study, we investigate the spectroscopic properties of a unique class of opsins from a reef-building coral belonging to the anthozoan-specific opsin II group (ASO-II opsins), which intriguingly lack a counterion residue at any of established sites.
View Article and Find Full Text PDFJ Mol Biol
July 2025
Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA. Electronic address:
Dimerization, liquid-liquid condensate formation, and amyloid deposition are all examples of macromolecular assembly and phase transitions essential for healthy cellular function but that become dysregulated in disease. A common underlying mechanism in these transitions is the dehydration of macromolecule surfaces. Through this lens, a deeper understanding emerges of how changing solvent conditions (e.
View Article and Find Full Text PDFDalton Trans
August 2025
School of Chemical Sciences, Indian Institute of Technology Mandi, Kamand - 175005, Himachal Pradesh, India.
Introducing task-specific catalytic sites through rational design is paramount while developing a multifunctional catalyst for organic transformation reactions. In this work, we utilized rarely explored quinolinium counterions to build a new class of quinolinium-polyoxometalate (POM) hybrids and test their catalytic activities in various organic transformation reactions. We introduced a task-specific '-NH' functional group onto the quinolinium moiety to enhance basic and hydrogen bonding sites towards the catalytic reactions and developed a series of POM-hybrids (ACMQ)[HVO] (hybrid 1), (ACMQ)[SiMoO] (hybrid 2) and (ACMQ)[SiWO] (hybrid 3) (where ACMQ = 4-amino-7-chloro-1-methylquinolin-1-ium) starting from common POM precursors.
View Article and Find Full Text PDFJ Am Chem Soc
August 2025
Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China.
Biomolecular condensates formed by liquid-liquid phase separation (LLPS) establish gradients of biomolecules and ions across the dilute-dense interface, giving rise to interfacial electric fields (IEFs) that can drive redox reactions. Here, we demonstrate that such electrochemical behavior is not exclusive to biological systems. By using polyelectrolyte-counterion interactions to induce phase separation, we formed synthetic coacervates that exhibit surface electrical potentials.
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