ion atmosphere - PMC

Jasper Kirkby, Jonathan Duplissy, Kamalika Sengupta, Carla Frege, Hamish Gordon, Christina Williamson, Martin Heinritzi, Mario Simon, Chao Yan, João Almeida, Jasmin Tröstl, Tuomo Nieminen, Ismael K. Ortega, Robert Wagner, Alexey Adamov, Antonio Amorim, Anne-Kathrin Bernhammer, Federico Bianchi, Martin Breitenlechner, Sophia Brilke, Xuemeng Chen, Jill Craven, Antonio Dias, Sebastian Ehrhart, Richard C. Flagan, Alessandro Franchin, Claudia Fuchs, Roberto Guida, Jani Hakala, Christopher R. Hoyle, Tuija Jokinen, Heikki Junninen, Juha Kangasluoma, Jaeseok Kim, Manuel Krapf, Andreas Kürten, Ari Laaksonen, Katrianne Lehtipalo, Vladimir Makhmutov, Serge Mathot, Ugo Molteni, Antti Onnela, Otso Peräkylä, Felix Piel, Tuukka Petäjä, Arnaud P. Praplan, Kirsty Pringle, Alexandru Rap, Nigel A. D. Richards, Ilona Riipinen, Matti P. Rissanen, Linda Rondo, Nina Sarnela, Siegfried Schobesberger, Catherine E. Scott, John H. Seinfeld, Mikko Sipilä, Gerhard Steiner, Yuri Stozhkov, Frank Stratmann, Antonio Tomé, Annele Virtanen, Alexander L. Vogel, Andrea C. Wagner, Paul E. Wagner, Ernest Weingartner, Daniela Wimmer, Paul M. Winkler, Penglin Ye, Xuan Zhang, Armin Hansel, Josef Dommen, Neil M. Donahue, Douglas R. Worsnop, Urs Baltensperger, Markku Kulmala, Kenneth S. Carslaw, Joachim Curtius

Nature. 2016; 533(7604): 521–526. Published online 2016 May 25. doi: 10.1038/nature17953

PMCID:: PMC8384037

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Dynamics of Cations around DNA and Protein as Revealed by ²³Na Diffusion NMR Spectroscopy

Binhan Yu, Karina G. Bien, Channing C. Pletka, Junji Iwahara

Anal Chem. 2022 Feb 8; 94(5): 2444–2452. Published online 2022 Jan 26. doi: 10.1021/acs.analchem.1c04197

PMCID:: PMC8829827

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Compositional and Structural Modifications by Ion Beam in Graphene Oxide for Radiation Detection Studies

Mariapompea Cutroneo, Lorenzo Torrisi, Letteria Silipigni, Alena Michalcova, Vladimir Havranek, Anna Mackova, Petr Malinsky, Vasily Lavrentiev, Pavol Noga, Jozef Dobrovodsky, Petr Slepicka, Dominik Fajstavr, Lucio Andò, Vaclav Holy

Int J Mol Sci. 2022 Oct; 23(20): 12563. Published online 2022 Oct 19. doi: 10.3390/ijms232012563

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Observations of biogenic ion-induced cluster formation in the atmosphere

Clémence Rose, Qiaozhi Zha, Lubna Dada, Chao Yan, Katrianne Lehtipalo, Heikki Junninen, Stephany Buenrostro Mazon, Tuija Jokinen, Nina Sarnela, Mikko Sipilä, Tuukka Petäjä, Veli-Matti Kerminen, Federico Bianchi, Markku Kulmala

Sci Adv. 2018 Apr; 4(4): eaar5218. Published online 2018 Apr 25. doi: 10.1126/sciadv.aar5218

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Ten Years Progress of Electrical Detection of Heavy Metal Ions (HMIs) Using Various Field-Effect Transistor (FET) Nanosensors: A Review

Shaili Falina, Mohd Syamsul, Nuha Abd Rhaffor, Sofiyah Sal Hamid, Khairu Anuar Mohamed Zain, Asrulnizam Abd Manaf, Hiroshi Kawarada

Biosensors (Basel) 2021 Dec; 11(12): 478. Published online 2021 Nov 25. doi: 10.3390/bios11120478

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Biomimetic KcsA channels with ultra-selective K⁺ transport for monovalent ion sieving

Weiwen Xin, Jingru Fu, Yongchao Qian, Lin Fu, Xiang-Yu Kong, Teng Ben, Lei Jiang, Liping Wen

Nat Commun. 2022; 13: 1701. Published online 2022 Mar 31. doi: 10.1038/s41467-022-29382-6

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A Review on Polyacrylonitrile as an Effective and Economic Constituent of Adsorbents for Wastewater Treatment

Archana Gupta, Vishal Sharma, Pawan Kumar Mishra, Adam Ekielski

Molecules. 2022 Dec; 27(24): 8689. Published online 2022 Dec 8. doi: 10.3390/molecules27248689

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Dynamics of Ionic Interactions at Protein–Nucleic Acid Interfaces

Binhan Yu, B. Montgomery Pettitt, Junji Iwahara

Acc Chem Res. 2020 Sep 15; 53(9): 1802–1810. Published online 2020 Aug 26. doi: 10.1021/acs.accounts.0c00212

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The Composition and Chemistry of Titan’s Atmosphere

Conor A. Nixon

ACS Earth Space Chem. 2024 Mar 21; 8(3): 406–456. Published online 2024 Feb 29. doi: 10.1021/acsearthspacechem.2c00041

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PMC Images search for ion atmosphere

Figure 1

Nucleic acid ion atmosphere. (A) Schematic representation of the cation excess surrounding a nucleic acid. (B) Schematic representation of ion concentrations as a function of distance from a nucleic acid estimated by Poisson–Boltzmann (PB) theory; PB predictions adapted from . The cation concentration is the highest near to the nucleic acid and equal to the bulk concentration far from the nucleic acid; the anion concentration is lower near the nucleic acid relative to the bulk concentration. The number of ions associated with the ion atmosphere is calculated by integrating the excess ion density around the nucleic acid; ).

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

J Am Chem Soc. ;137(46):14705-14715.
Figure 2.Experimental characterization of the ion atmosphere around macromolecules by ‘ion counting’.

(A) Schematic of an ‘ion counting’ experiment to quantify the composition of the ion atmosphere around dsDNA, nucleosomes, histones or the histone octamer (; ; ). A detailed description of the ion counting method can be found in the Materials and methods section. Adapted from reference (). (B): i) Schematic representation of the cation excess surrounding a nucleic acid. ii) Schematic representation of ion density as a function of distance from a nucleic acid estimated by Poisson-Boltzmann (PB) theory; PB predictions adapted from (). Counterions and coions are radially distributed within the ion atmosphere around charged molecules. The highest density of counterions localizes near to the surface of the molecule, where the highest electrostatic potential resides; far from the molecule the density equals that of the bulk solution. Coions give the opposite behavior, with the lowest density near the molecule’s surface due to electrostatic repulsion. iii) Computationally, the number of ions associated (the excess number, (N) with the ion atmosphere is calculated by integrating the excess ion density around the nucleic acid ( in Material and methods).

Ion counting demonstrates a high electrostatic field generated by the nucleosome

eLife. 2019;8:e44993.
Figure 5

In an atmosphere of ¹⁸O₂, ¹⁸O is incorporated into the substrate loaded onto DdaD and N_βFmmDAP is converted to N_β-trans-EpSmDAP. (A) Under normal reaction conditions (an atmosphere of ¹⁶O₂), in the presence of α-KG and the absence of DdaC, the only Ppant ejection ion observed (blue) during Ppant ejection analysis (using NSD) of N_βFmmDAP-S-DdaD corresponds to the unoxidized starting substrate. (B) Under normal reaction conditions (an atmosphere of ¹⁶O₂), in the presence of both α-KG and DdaC, Ppant ejection ions corresponding to both N_βFmmDAP-S-DdaD and N_βEpSmDAP-S-DdaD (orange) are observed. (C) Under an atmosphere of ¹⁸O₂, in the presence of α-KG but the absence of DdaC, the only Ppant ejection ion observed corresponds to N_βFmmDAP-S-DdaD. (D) Under an atmosphere of ¹⁸O₂, in the presence of both α-KG and DdaC, Ppant ejection ions are observed for both N_βFmmDAP-S-DdaD and N_βEpSmDAP-S-DdaD. A +2 Da mass shift (from the N_βEpSmDAP-S-DdaD Ppant ejection ion in (B)) is observed in the Ppant ejection ion corresponding to N_βEpSmDAP-S-DdaD (purple), indicating that the oxygen in the epoxide originates from molecular oxygen. For the predicted structures of the Ppant ejection ions see .

The NRPS Enzyme DdaD Tethers Nβ-fumaramoyl-DAP for Fe(II)/α-ketoglutarate-Dependent Epoxidation by DdaC During Dapdiamide Antibiotic Biosynthesis

J Am Chem Soc. ;132(44):15773-15781.
Figure 4

Quantifying the total composition of the ion atmosphere. (a) Excess ion density as a function of distance from a nucleic acid, approximated here as a cylinder of radius 10 Å, determined from Poisson–Boltzmann theory. The ion atmosphere does not penetrate into the cylinder; the ion density is highest close to the nucleic acid and equals the bulk concentration far away from the nucleic acid. (b) The excess numbers of ions determined from a molecular dynamics simulation and the total charge of these ions around a 24-bp DNA duplex. The total charge of the ion atmosphere is equal and opposite to the charge of the DNA of −46e (dashed line). The example shown is for 5 mM MgCl₂ and 40 mM NaCl. Data were taken from Reference . (c) Scheme of the buffer equilibration–atomic emission spectroscopy (BE-AES) approach that enables complete quantification of the total ion atmosphere (, ). (d) The number of associated excess Na⁺ ions (blue circles), depleted Cl⁻ ions (orange triangles), and their total charge (green squares) around a 24-bp DNA duplex determined by BE-AES. The total charge of the ion atmosphere is equal, to within experimental error, to the inverse of the DNA charge (dashed line). Data are from Reference .

Understanding Nucleic Acid–Ion Interactions

Annu Rev Biochem. ;83:813-841.