1
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Radwan EK, Omar RA, Moursy AS. Rapid adsorption of benzotriazole onto oxidized carbon cloth as an easily separable adsorbent. Sci Rep 2023; 13:17030. [PMID: 37813910 PMCID: PMC10562377 DOI: 10.1038/s41598-023-44067-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/03/2023] [Indexed: 10/11/2023] Open
Abstract
A commercial carbon cloth (CC) was oxidized by HNO3 acid and the features of the plain and oxidized CC were evaluated. The results of characterization illustrated that HNO3 oxidization duplicated the oxygen-containing functional groups and the surface area of the CC. The adsorption performance of the plain and oxidized CC (Oxi-CC) toward benzotriazole (BTR) was compared. The results disclosed that the uptake of BTR by oxidized CC was greater than the plain CC. Thence, the affinity of oxidized CC toward BTR was assessed at different conditions. It was found that the adsorption was quick, occurred at pH 9 and improved by adding NaCl or CaCl2 to the BTR solution. The kinetic and isotherm studies revealed that the surface of Oxi-CC is heterogeneous and the adsorption of BTR follows a physical process and forms multilayer over the Oxi-CC surface. The regenerability and reusability study illustrated that only deionized water can completely regenerate the Oxi-CC and that the Oxi-CC can be reused for five cycles without any loss of performance. The high maximum adsorption capacity of Dubinin-Radushkevich isotherm model (252 mg/g), ease of separation and regeneration, and maintaining the adsorption capacity for several cycles revealed the high efficiency and economical and environmental feasibility of Oxi-CC as an adsorbent for BTR.
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Affiliation(s)
- Emad K Radwan
- Water Pollution Research Department, National Research Centre, 33 El Buhouth St, Dokki, Giza, 12622, Egypt.
| | - Rehab A Omar
- Water Pollution Research Department, National Research Centre, 33 El Buhouth St, Dokki, Giza, 12622, Egypt
| | - Ahmed S Moursy
- Water Pollution Research Department, National Research Centre, 33 El Buhouth St, Dokki, Giza, 12622, Egypt
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2
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Water-Mediated attraction between Like-charged species involved in calcium phosphate nucleation. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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3
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Kruchinin SE, Fedotova MV. Ion Pairing of the Neurotransmitters Acetylcholine and Glutamate in Aqueous Solutions. J Phys Chem B 2021; 125:11219-11231. [PMID: 34597044 DOI: 10.1021/acs.jpcb.1c05117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neurotransmitters (NTs) play an important role in neural communication, regulating a variety of functions such as motivation, learning, memory, and muscle contraction. Their intermolecular interactions in biological media are an important factor affecting their biological activity. However, the available information on the features of these interactions is scarce and contradictory, especially, in an estimation of possible ion binding. In this paper, we present the results of a study for two well-known NTs, acetylcholine (ACh) and glutamate (Glu), with relation to the NT-inorganic ion and the NT-NT binding in a water environment. The features of NT pairing are investigated in aqueous AChCl and NaGlu solutions over a wide concentration range using the integral equation method in 1D- and 3D- reference interaction site model (RISM) approaches. The data for ACh are given for its two bioactive TG (trans, gauche) and TT (trans, trans) conformers. As was found, for both NTs, the results indicate the NT-inorganic counterion contact pair to be the predominant associate type in the concentrated solutions. In this case, the counterions occupy the vacated "water" space in the hydration shell of the onium moiety (ACh) or carboxylate groups (Glu). For ACh, the "unfolded" TT conformer demonstrates a slightly greater possibility for counterion pairing in comparison with the "folded" TG conformer. For Glu, the probability of its binding with a counterion is slightly stronger for the "side-chain" carboxylate group than for the "backbone" group. The obtained results also revealed an insignificant probability of Glu--Glu- pairing. Namely, the RISM data indicate Glu--Glu- binding by NH3+-COO- interactions. A link between the ion binding of NTs and their biological activity is discussed. This contribution adds new knowledge to our understanding of the interactions between the NTs and their molecular environment, providing further insights into the behavior of these compounds in biological media.
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Affiliation(s)
- Sergey E Kruchinin
- G.A. Krestov Institute of Solution Chemistry, the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia
| | - Marina V Fedotova
- G.A. Krestov Institute of Solution Chemistry, the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia
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4
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Wysokiński R, Zierkiewicz W, Michalczyk M, Scheiner S. Crystallographic and Theoretical Evidences of Anion⋅⋅⋅Anion Interaction. Chemphyschem 2021; 22:818-821. [PMID: 33719162 DOI: 10.1002/cphc.202100132] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/08/2021] [Indexed: 11/10/2022]
Abstract
Planar (HgCl3 )- anions are stacked fairly closely together in a slipped parallel arrangement within several crystal structures. Quantum chemical analysis shows evidence of strong noncovalent spodium bonds between the Hg π-hole of one unit and the Cl atom of an adjacent unit. Anion⋅⋅⋅anion spodium bonds work in tandem with crystal packing forces.
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Affiliation(s)
- Rafał Wysokiński
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah, 84322-0300, United States
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5
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Wysokiński R, Zierkiewicz W, Michalczyk M, Scheiner S. Anionanion (MX 3-) 2 dimers (M = Zn, Cd, Hg; X = Cl, Br, I) in different environments. Phys Chem Chem Phys 2021; 23:13853-13861. [PMID: 34156052 DOI: 10.1039/d1cp01502h] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibility that MX3- anions can interact with one another is assessed via ab initio calculations in gas phase as well as in aqueous and ethanol solution. A pair of such anions can engage in two different dimer types. In the bridged configuration, two X atoms engage with two M atoms in a rhomboid structure with four equal M-X bond lengths. The two monomers retain their identity in the stacked geometry which contains a pair of noncovalent MX interactions. The relative stabilities of these two structures depend on the nature of the central M atom, the halogen substituent, and the presence of solvent. The interaction and binding energies are fairly small, generally no more than 10 kcal mol-1. The large electrostatic repulsion is balanced by a strong attractive polarization energy.
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Affiliation(s)
- Rafał Wysokiński
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, USA.
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6
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Oh MI, Gupta M, Weaver DF. Understanding Water Structure in an Ion-Pair Solvation Shell in the Vicinity of a Water/Membrane Interface. J Phys Chem B 2019; 123:3945-3954. [DOI: 10.1021/acs.jpcb.9b01331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Myong In Oh
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Mayuri Gupta
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Donald F. Weaver
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario M5G 2C4, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
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7
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Dash SG, Thakur TS. Cation⋯cation hydrogen bonds in synephrine salts: a typical interaction in an unusual environment. Phys Chem Chem Phys 2019; 21:20647-20660. [DOI: 10.1039/c9cp03164b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Computational studies of hydrogen-bonded cationic species observed in the synephrine salts point towards the stabilizing nature of hydrogen bonds and highlights their contribution in reducing destabilization caused by coulombic repulsion.
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Affiliation(s)
- Sibananda G. Dash
- Academy of Scientific and Innovative Research (AcSIR)
- CSIR-Central Drug Research Institute (CSIR-CDRI) campus
- Lucknow 226 031
- India
- Molecular and Structural Biology Division
| | - Tejender S. Thakur
- Academy of Scientific and Innovative Research (AcSIR)
- CSIR-Central Drug Research Institute (CSIR-CDRI) campus
- Lucknow 226 031
- India
- Molecular and Structural Biology Division
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8
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Vazdar M, Heyda J, Mason PE, Tesei G, Allolio C, Lund M, Jungwirth P. Arginine "Magic": Guanidinium Like-Charge Ion Pairing from Aqueous Salts to Cell Penetrating Peptides. Acc Chem Res 2018; 51:1455-1464. [PMID: 29799185 DOI: 10.1021/acs.accounts.8b00098] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
It is a textbook knowledge that charges of the same polarity repel each other. For two monovalent ions in the gas phase at a close contact this repulsive interaction amounts to hundreds of kilojoules per mole. In aqueous solutions, however, this Coulomb repulsion is strongly attenuated by a factor equal to the dielectric constant of the medium. The residual repulsion, which now amounts only to units of kilojoules per mole, may be in principle offset by attractive interactions. Probably the smallest cationic pair, where a combination of dispersion and cavitation forces overwhelms the Coulomb repulsion, consists of two guanidinium ions in water. Indeed, by a combination of molecular dynamics with electronic structure calculations and electrophoretic, as well as spectroscopic, experiments, we have demonstrated that aqueous guanidinium cations form (weakly) thermodynamically stable like-charge ion pairs. The importance of pairing of guanidinium cations in aqueous solutions goes beyond a mere physical curiosity, since it has significant biochemical implications. Guanidinium chloride is known to be an efficient and flexible protein denaturant. This is due to the ability of the orientationally amphiphilic guanidinium cations to disrupt various secondary structural motifs of proteins by pairing promiscuously with both hydrophobic and hydrophilic groups, including guanidinium-containing side chains of arginines. The fact that the cationic guanidinium moiety forms the dominant part of the arginine side chain implies that the like-charge ion pairing may also play a role for interactions between peptides and proteins. Indeed, arginine-arginine pairing has been frequently found in structural protein databases. In particular, when strengthened by a presence of negatively charged glutamate, aspartate, or C-terminal carboxylic groups, this binding motif helps to stabilize peptide or protein dimers and is also found in or near active sites of several enzymes. The like-charge pairing of the guanidinium side-chain groups may also hold the key to the understanding of the arginine "magic", that is, the extraordinary ability of arginine-rich polypeptides to passively penetrate across cellular membranes. Unlike polylysines, which are also highly cationic but lack the ease in crossing membranes, polyarginines do not exhibit mutual repulsion. Instead, they accumulate at the membrane, weaken it, and might eventually cross in a concerted, "train-like" manner. This behavior of arginine-rich cell penetrating peptides can be exploited when devising smart strategies how to deliver in a targeted way molecular cargos into the cell.
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Affiliation(s)
- Mario Vazdar
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628 Prague, Czech Republic
| | - Philip E. Mason
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Giulio Tesei
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Christoph Allolio
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Giv’at Ram, Jerusalem 9190401, Israel
| | - Mikael Lund
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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9
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Chremos A, Douglas JF. Communication: Counter-ion solvation and anomalous low-angle scattering in salt-free polyelectrolyte solutions. J Chem Phys 2017; 147:241103. [PMID: 29289148 PMCID: PMC5839105 DOI: 10.1063/1.5010784] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the influence of counter-ion solvation on the homogeneity of salt-free polyelectrolyte solutions based on a coarse-grained model that includes an explicit solvent. We show that the solvation of the counter-ions can cause a transformation between a nearly homogeneous to a non-uniform polymer solution, in which there is both a chain clustering and the formation of large charge-free domains, i.e., "voids." The emergence of these heterogeneous structures induced by counter-ion solvation is accompanied by the localization and formation of counter-ion rich domains that are symptomatic of emergent effective long-range attractive interchain interactions.
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Affiliation(s)
- Alexandros Chremos
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Jack F. Douglas
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
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10
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Ghosh MK, Choi TH, Choi CH. Like-charge ion pairs of hydronium and hydroxide in aqueous solution? Phys Chem Chem Phys 2015; 17:16233-7. [DOI: 10.1039/c5cp02182k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydroxide can form stronger like-ion pairs than hydronium in aqueous solution mostly due to its versatile coordination ability with solvents.
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Affiliation(s)
- Manik Kumer Ghosh
- Department of Chemistry and Green-Nano Materials Research Center
- College of Natural Sciences
- Kyungpook National University
- Daegu 702-701
- South Korea
| | - Tae Hoon Choi
- Department of Chemical Engineering Education
- Chungnam National University
- Daejeon 305-764
- Republic of Korea
| | - Cheol Ho Choi
- Department of Chemistry and Green-Nano Materials Research Center
- College of Natural Sciences
- Kyungpook National University
- Daegu 702-701
- South Korea
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11
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van Duijnen PT, de Gier HD, Broer R, Havenith RW. The behaviour of charge distributions in dielectric media. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Water-mediated ion-ion interactions are enhanced at the water vapor-liquid interface. Proc Natl Acad Sci U S A 2014; 111:8729-34. [PMID: 24889634 DOI: 10.1073/pnas.1403294111] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There is overwhelming evidence that ions are present near the vapor-liquid interface of aqueous salt solutions. Charged groups can also be driven to interfaces by attaching them to hydrophobic moieties. Despite their importance in many self-assembly phenomena, how ion-ion interactions are affected by interfaces is not understood. We use molecular simulations to show that the effective forces between small ions change character dramatically near the water vapor-liquid interface. Specifically, the water-mediated attraction between oppositely charged ions is enhanced relative to that in bulk water. Further, the repulsion between like-charged ions is weaker than that expected from a continuum dielectric description and can even become attractive as the ions are drawn to the vapor side. We show that thermodynamics of ion association are governed by a delicate balance of ion hydration, interfacial tension, and restriction of capillary fluctuations at the interface, leading to nonintuitive phenomena, such as water-mediated like charge attraction. "Sticky" electrostatic interactions may have important consequences on biomolecular structure, assembly, and aggregation at soft liquid interfaces. We demonstrate this by studying an interfacially active model peptide that changes its structure from α-helical to a hairpin-turn-like one in response to charging of its ends.
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13
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Inagaki T, Aono S, Nakano H, Yamamoto T. Like-Charge Attraction of Molecular Cations in Water: Subtle Balance between Interionic Interactions and Ionic Solvation Effect. J Phys Chem B 2014; 118:5499-508. [DOI: 10.1021/jp501212y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Taichi Inagaki
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shinji Aono
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Hiroshi Nakano
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Takeshi Yamamoto
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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14
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Lukšič M, Fennell CJ, Dill KA. Using interpolation for fast and accurate calculation of ion-ion interactions. J Phys Chem B 2014; 118:8017-25. [PMID: 24625086 PMCID: PMC4142335 DOI: 10.1021/jp501141j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We perform extensive molecular dynamics (MD) simulations between pairs of ions of various diameters (2-5.5 Å in increments of 0.5 Å) and charge (+1 or -1) interacting in explicit water (TIP3P) under ambient conditions. We extract their potentials of mean force (PMFs). We develop an interpolation scheme, called i-PMF, that is capable of capturing the full set of PMFs for arbitrary combinations of ion sizes ranging from 2 to 5.5 Å. The advantage of the interpolation process is computational cost. Whereas it can take 100 h to simulate each PMF by MD, we can compute an equivalently accurate i-PMF in seconds. This process may be useful for rapid and accurate calculation of the strengths of salt bridges and the effects of bridging waters in biomolecular simulations. We also find that our data is consistent with Collins' "law of matching affinities" of ion solubilities: small-small or large-large ion pairs are poorly soluble in water, whereas small-large are highly soluble.
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Affiliation(s)
- Miha Lukšič
- Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794-5252, United States
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15
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Shokri A, Ramezani M, Fattahi A, Kass SR. Electrostatically defying cation-cation clusters: can likes attract in a low-polarity environment? J Phys Chem A 2013; 117:9252-8. [PMID: 24011262 DOI: 10.1021/jp405063h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Like-charge ion pairing is commonly observed in protein structures and plays a significant role in biochemical processes. Density functional calculations combined with the conductor-like polarizable continuum model were employed to study the formation possibilities of doubly charged noncovalently linked complexes of a series of model compounds and amino acids in the gas phase and in solution. Hydrogen bond interactions were found to offset the Coulombic repulsion such that cation-cation clusters are minima on the potential energy surfaces and neither counterions nor solvent molecules are needed to hold them together. In the gas phase the dissociation energies are exothermic, and the separation barriers span from 1.7 to 15.6 kcal mol(-1). Liquid-phase computations indicate that the separation enthalpies of the cation-cation complexes become endothermic in water and nonpolar solvents with dielectric constants of ≥7 (i.e., the value for THF). These results reveal that electrostatically defying noncovalent complexes of like-charged ions can overcome their Coulombic repulsion even in low-polarity environments.
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Affiliation(s)
- Alireza Shokri
- Department of Chemistry, University of Minnesota , Minneapolis, Minnesota55455, United States
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16
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Choi CH, Re S, Rashid MHO, Li H, Feig M, Sugita Y. Solvent Electronic Polarization Effects on Na+–Na+ and Cl––Cl– Pair Associations in Aqueous Solution. J Phys Chem B 2013; 117:9273-9. [DOI: 10.1021/jp4049346] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cheol Ho Choi
- Department of Chemistry and
Green-Nano Materials Research Center, College of Natural Sciences, Kyungpook National University, Taegu 702-701, Korea
| | - Suyong Re
- Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama
351-0198, Japan
| | - Mohammad H. O. Rashid
- Department of Chemistry and
Green-Nano Materials Research Center, College of Natural Sciences, Kyungpook National University, Taegu 702-701, Korea
| | - Hui Li
- Department of
Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska
68588, United States
| | - Michael Feig
- Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama
351-0198, Japan
- Chemistry and Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
- RIKEN Quantitative Biology Center, 7-1-26 minatojima-minamimachi, Chuo-ku,
Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama
351-0198, Japan
- RIKEN Quantitative Biology Center, 7-1-26 minatojima-minamimachi, Chuo-ku,
Kobe, Hyogo 650-0047, Japan
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17
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Lee D, Lee J, Seok C. What stabilizes close arginine pairing in proteins? Phys Chem Chem Phys 2013; 15:5844-53. [PMID: 23486862 DOI: 10.1039/c3cp00160a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Close stacking of arginine residues are often observed in protein structures despite the highly repulsive nature of the close like-charged groups. Physical factors stabilizing the close guanidinium ions of arginine side-chains have been previously studied in water and in protein-like environments, and the hydration free energy has been emphasized to be an important factor. However, how close arginine pairs are stabilized in real proteins has not been fully understood yet. In this paper, we show that arginine pairs are more frequently found in the protein interior than expected from the frequency of unpaired arginines buried inside protein through a statistical analysis of the protein structure database. We then confirm that 4 selected arginine pairs buried in the protein are indeed positively charged rather than neutralized, by molecular dynamics simulations and pKa estimation with molecular mechanics-Poisson-Boltzmann calculations. Further energy decomposition analysis shows that the hydration free energy may not be strong enough to overcome the repulsive Coulomb interaction between the positively charged arginine residues buried inside the protein. Instead, a highly polar interaction network is identified around each buried arginine pair, and the electrostatic interactions within such network are strong enough to stabilize the repulsive interaction of the buried arginine pair for the 4 selected cases. The polar interaction network is highly conserved evolutionarily in some proteins, implicating their roles in protein stabilization or biochemical function.
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Affiliation(s)
- Dongseon Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea
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18
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Harsányi I, Pusztai L. Hydration structure in concentrated aqueous lithium chloride solutions: A reverse Monte Carlo based combination of molecular dynamics simulations and diffraction data. J Chem Phys 2012. [DOI: 10.1063/1.4767437] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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19
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Chaumont A, Wipff G. Interactions between Keggin Anions in Water: The Higher Their Charge, the Higher Their Condensation? A Simulation Study. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200883] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Temelso B, Phan TN, Shields GC. Computational Study of the Hydration of Sulfuric Acid Dimers: Implications for Acid Dissociation and Aerosol Formation. J Phys Chem A 2012; 116:9745-58. [DOI: 10.1021/jp3054394] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Berhane Temelso
- Dean’s Office, College of Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837,
United States
| | - Thuong Ngoc Phan
- Dean’s Office, College of Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837,
United States
| | - George C. Shields
- Dean’s Office, College of Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837,
United States
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