Salt‐induced formation of DNA double helices from single stranded DNA investigated by analytical ultracentrifugation

The effect of monovalent and divalent cations on the ssDNA to dsDNA transformation was systematically examined. For salts containing monovalent cations (LiCl, NaC1, KCl, CsCl), the conversion of ssDNA to dsDNA increased with ionic strength up to a value of I = 0.01 M and then plateaued, confirming that all four of the monovalent cations behaved similarly and promoted the formation of dsDNA. The monovalent cation type influenced the equilibrium constant for the conversion of ssDNA to dsDNA, indicating a degree of ion‐specificity in dsDNA formation. In the case of salts containing divalent cations (e.g., MgCl₂), the conversion of ssDNA to dsDNA also increased with increasing ionic strength, though the plateau region was reached at a much lower ionic strength (I = 5.0 × 10⁻⁴ M), which can be attributed to the higher electrostatic screening efficiency of Mg²⁺ cations and thus their superior ability to link DNA chains. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 501–508     

How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes

The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺), and (post-)transition metal (Zn²⁺, Cd²⁺, Hg²⁺, and Pb²⁺) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K⁺). Importantly, we establish the nature of the cation-GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations’ unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.     

Reversed Cation Selectivity of G8‐Octamer and G16‐Hexadecamer towards Monovalent and Divalent Cations

A reverse‐binding‐selectivity between monovalent and divalent cations was observed for two different self‐assembly G₁₆‐hexadecamer and G₈‐octamer systems. The dissociation constant between G₄‐quadruplex and monomer was calculated via VT‐¹H NMR experiments. Quantitative energy profiles revealed entropy as the key factor for the weaker binding toward Ba²⁺ compared with K⁺ in the G₈‐octamer system despite stronger ion‐dipole interactions. This study is the first direct comparison of the G₄‐quartet binding affinity between mono and divalent cations and will benefit future applications of G‐quadruplex‐related research. Further competition experiments between the G₈‐octamer and 18‐crown‐6 with K⁺ demonstrated the potential of this G₈ system as a new potassium receptor.     

Affinity capillary electrophoresis employed for determination of stability constants of antamanide complexes with univalent and divalent cations in methanol

Affinity capillary electrophoresis (ACE) and pressure‐assisted ACE were employed to study the noncovalent molecular interactions of antamanide (AA), cyclic decapeptide from the deadly poisonous fungus Amanita phalloides, with univalent (Li⁺, Na⁺, K⁺, and NH₄⁺) and divalent (Mg²⁺ and Ca²⁺) cations in methanol. The strength of these interactions was quantified by the apparent stability constants of the appropriate AA‐cation complexes. The stability constants were calculated using the nonlinear regression analysis of the dependence of the effective electrophoretic mobility of AA on the concentration of the above ions in the BGE (methanolic solution of 20 mM chloroacetic acid, 10 mM Tris, pH_MeOH 7.8, containing 0–50 mM concentrations of the above ions added in the form of chlorides). Prior to stability constant calculation, the AA effective mobilities measured at actual temperature inside the capillary and at variable ionic strength of the BGEs were corrected to the values corresponding to the reference temperature of 25°C and to the constant ionic strength of 10 mM. From the above ions, sodium cation interacted with AA moderately strong with the stability constant 362 ± 16 L/mol. K⁺, Mg²⁺, and Ca²⁺ cations formed with AA weak complexes with stability constants in the range 37–31 L/mol decreasing in the order K⁺ > Ca²⁺ > Mg²⁺. No interactions were observed between AA and small Li⁺ and large NH₄⁺ cations.     

Electrostatic bonding models: A test on group 1 and 2 metal complexes with H2O,NH3, H2S,PH3, and related ligands

Electrostatic models frequently proposed to describe ion–molecule interactions have been tested on the adducts formed by Group 1 and 2 cations with H₂O, NH₃, H₂S, PH₃, their methyl analogs, and their anions. The results from the model calculations were compared with all-electron calculations (geometry optimized, MP2, TZP basis sets) carried out on adducts formed with Li⁺, Na⁺, K⁺, Ca²⁺, and Mg²⁺. The electrostatic potential model was utilized in two ways: The attraction of the point charge was calculated with and without relaxation of the ligand. A third model allowed relaxation of the ligand but treated the cation as a frozen core. The final model was the crude point charge/point dipole approximation. At long range, the models satisfactorily track the effects on energy of gross changes in the ion–ligand interaction (monovalent versus divalent ions, neutral ligands versus anions, parent ligands versus methyl derivatives), but correlation at close range is poor, especially for binding by divalent cations. The hypothesis that the calculated strength of cation–dipole binding is dependent on calculated dipole moment could not be verified. © 1995 by John Wiley & Sons, Inc.     

Affinity capillary electrophoresis and density functional theory study of noncovalent interactions of cyclic peptide [Gly6]‐antamanide with small cations

ACE and density functional theory were employed to study the noncovalent interactions of cyclic decapeptide glycine‐6‐antamanide ([Gly⁶]AA), synthetic derivative of native antamanide (AA) peptide from the deadly poisonous fungus Amanita phalloides , with small cations (Li⁺, Rb⁺, Cs⁺, NH₄⁺, and Ca²⁺) in methanol. The strength of these interactions was quantified by the apparent stability constants of the appropriate complexes determined by ACE. The stability constants were calculated using the nonlinear regression analysis of the dependence of the effective electrophoretic mobility of [Gly⁶]AA on the concentration of the above ions in the BGE (methanolic solution of 20 mM chloroacetic acid, 10 mM Tris, pH_MeOH 7.8, containing 0–70 mM concentrations of the above ions added in the form of chlorides). Prior to stability constant calculation, the effective mobilities measured at actual temperature inside the capillary and at variable ionic strength of the BGEs were corrected to the values corresponding to the reference temperature of 25°C and to the constant ionic strength of 10 mM. From the above ions, Rb⁺ and Cs⁺ cations interacted weakly with [Gly⁶]AA but no interactions of [Gly⁶]AA with univalent Li⁺ and NH₄⁺ ions and divalent Ca²⁺ ion were observed. The apparent stability constants of [Gly⁶]AA‐Rb⁺ and [Gly⁶]AA‐Cs⁺ complexes were found to be equal to 13 ± 4 and 22 ± 3 L/mol, respectively. The structural characteristics of these complexes, such as position of the Rb⁺ and Cs⁺ ions in the cavity of the [Gly⁶]AA molecule and the interatomic distances within these complexes, were obtained by the density functional theory calculations.     

A theoretical study of cation--π interactions: Li+, Na+, K+, Be2+, Mg2+ and Ca2+ complexation with mono- and bicyclic ring-fused benzene derivatives

DFT (B3LYP functional) and MP2 methods using 6-311+G(2d,2p) basis set have been employed to examine the effect of ring fusion to benzene on the cation--π interactions involving alkali metal ions (Li⁺, Na⁺, and K⁺) and alkaline earth metal ions (Be²⁺, Mg²⁺ and Ca²⁺). Our present study indicates that modification of benzene (π-electron source) by fusion of monocyclic or bicyclic (or mixture of these two kinds of rings) strengthens the binding affinity of both alkali and alkaline earth metal cations. The strength of interaction decreases in the following order: Be²⁺ > Mg²⁺ > Ca²⁺ > Li⁺ > Na⁺ > K⁺ for any considered aromatic ligand. The interaction energies for the complexes formed by divalent cations are 4–6 times larger than those for the complexes involving monovalent cations. The structural changes in the ring wherein metal ion binds are examined. The distance between ring centroid and the metal ion is calculated for all of the complexes. Strained bicyclo[2.1.1]hexene ring fusion has substantially larger effect on the strength of cation--π interactions than the monocyclic ring fusion for all of the cations due to the π-electron localization at the central benzene ring.     

Transport of N-CD and Pre-Sorbed Pb in Saturated Porous Media

Carbon dots (CDs) are a new type of nanomaterials of the carbon family with unique characteristics, such as their small size (e.g., <10 nm), high water solubility, low toxicity, and high metal affinity. Modification of CDs by Nitrogen functional groups (N-CDs) enhances their metal adsorption capacity. This study investigated the influences of pH (4, 6, and 9), ionic strength (1, 50, and 100 mM), and cation valency (Na⁺ and Ca²⁺) on the competitive adsorption of Pb to quartz and N-CD surfaces, the transport and retention of N-CDs in saturated porous media, and the capacity of N-CDs to mobilize pre-adsorbed Pb in quartz columns. Pb adsorption was higher on N-CDs than on quartz surfaces and decreased with increases in ionic strength (IS) and divalent cations (Ca²⁺) concentration. N-CD mobility in quartz columns was highest at pH of 9- and 1-mM monovalent cations (Na⁺) and decreased with decreases in pH and increases in ionic strength and ion valency. N-CDs mobilized pre-adsorbed Pb from quartz due to the higher adsorption affinity of Pb to N-CD than to quartz surfaces. These findings provide valuable insights into the transport, retention, and risk assessment of lead in the presence of carbon-based engineered nanoparticles.     

Abrupt Structural Changes in Polyanionic Gels Evoked by Na-Ca Ion Exchange: Their Biological Implications

Anionic polyelectrolyte gels, synthetic or natural, undergo abrupt structural changes when the monovalent counterions in the gel, e.g., Na⁺, are replaced with divalent cations, e.g., Ca²⁺. These structural changes are caused by the preferential binding of Ca²⁺ to the polyelectrolyte chains and the ability of Ca²⁺ to form crosslinks between two neighboring chains. Strong lyotropic (Hofmeister) effects of anions, such as fluoride, phosphate, aspartate and chloride, on the repetitiveness of abrupt structural changes in the gel strands are demonstrated. These findings have important biological implications.     

Effect of counterion condensation on the acid-base equilibrium of a pH-sensitive merocyanine dye covalently attached to polyelectrolytes

Effects of monovalent and divalent counterions on the acid-base equilibrium of a pH-sensitive merocyanine dye covalently attached to copolymers of acrylic acid and acrylamide with varying charge densities (0.28 < ξ < 2.8) were investigated. Added chloride salts of Li⁺, Na⁺, K⁺, and NH⁺₄ (< 0.2 mM) had essentially no effect on pK observed (pK^obs) for the equilibrium. By contrast, the salts of Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺ caused a significant decrease in pK^obs for the copolymers with larger ξ. With smaller ξ, most likely when ξ < 0.5, no decrease in pK^obs was observed upon addition of the salts of divalent cations. A competitive effect of Ca²⁺ and Na²⁺ ions on pK^obs in the presence of an excess of Na⁺ ions implied that Ca²⁺ ions at very low concentrations were preferentially, and therefore exhaustively, condensed on the polyanions with sufficiently large ξ probably until effective charge density was lowered to 0.5. The observed difference in the influence of the monovalent and divalent cations on pK^obs was discussed in terms of the difference in the microscopic behavior of the condensed monovalent and divalent cations. © 1993 John Wiley & Sons, Inc.     

Adsorption of trace elements or radionuclides on hydrous iron oxides

Factors that influence the adsorption of trace elements or radionuclides on hydrous iron oxides were investigated. The adsorption of monovalent cations (Cs⁺, Rb⁺) on hydrous iron oxides is not strongly pH-dependent and it can be regarded as nonspecific. On the other hand, the adsorption of Ag⁺, divalent cations (Zn²⁺, Cd²⁺, Mn²⁺, Sr²⁺) or trivalent cations (Cr³⁺, La³⁺, Ce³⁺, Eu³⁺, Gd³⁺, Er³⁺, Yb³⁺) is strongly pH-dependent. The regularities of the adsorption of these cations on hydrous iron oxides are discussed. Also, the differences in the adsorption behaviour of some divalent and trivalent cations are explained. Freshly precipitated iron(III) hydroxide can be used for the decontamination of radionuclides from low-level waste solutions. However, the efficacy of decontamination depends on the oxidation state and the chemical properties of radionuclides.     

Highly sensitive detection of human thrombin in serum by affinity capillary electrophoresis/laser-induced fluorescence polarization using aptamers as probes

The detection and quantification of disease-related proteins play critical roles in clinical practice and diagnostic assays. We present an affinity probe capillary electrophoresis/laser-induced fluorescence polarization (APCE/LIFP) assay for detection of human thrombin using a specific aptamer as probe. In the APCE/LIFP assay, the mobility and fluorescence polarization of complex are measured simultaneously during CE analysis. The affinity complex of human thrombin can be well separated from unbound aptamer on CE and clearly identified on the basis of its fluorescence polarization and migration. Because of the binding favorable G-quartet conformation potentially involved in the specific aptamer, it was assumed that monovalent and bivalent cations promoting the formation of a stable G quadruplex conformation in the aptamer may enhance the binding of the aptamer and thrombin. Therefore, we investigated the effects of various metal cations on the binding of human thrombin and the aptamer. Our results show that cations like K⁺ and Mg²⁺ could not stabilize the affinity complex. Without the use of typical cations, a highly sensitive assay of human thrombin was developed with the corresponding detection limits of 4.38 × 10⁻¹⁹ and 2.94 × 10⁻¹⁹ mol in mass for standard solution and human serum, respectively.     

Effect of metal cations [Li+, Na+, K+, Be2+, Mg2+, and Ca2+] on the structure of 2‐(3′‐hydroxy‐2′‐pyridyl)benzoxazole: A theoretical investigation

Density functional theory calculations were performed at the B3LYP/6‐311++G(d,p) level to systematically explore the geometrical multiplicity and binding strength for the complexes formed by alkaline and alkaline earth metal cations, viz. Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ (Mⁿ⁺, hereinafter), with 2‐(3′‐hydroxy‐2′‐pyridyl)benzoxazole. A total of 60 initial structures were designed and optimized, of which 51 optimized structures were found, which could be divided into two different types: monodentate complexes and bidentate complexes. In the cation‐heteroatom complex, bidentate binding is generally stronger than monodentate binding, and of which the bidentate binding with five‐membered ring structure has the strongest interaction. Energy decomposition revealed that the total binding energies mainly come from electrostatic interaction for alkaline metal ion complexes and orbital interaction energy for alkaline earth metal ion complex. In addition, the electron localization function analysis show that only the Be? O and Be? N bond are covalent character, and others are ionic character. © 2012 Wiley Periodicals, Inc.     

Competition between Monovalent and Divalent Counterions in Surfactant Systems

Competition between mono- and divalent ions in the association of counterions to the headgroups of amphiphiles was studied in one surfactant system with organic counterions (piperidine⁺/piperazine²⁺octanesulfonate) and one with inorganic counterions (Na⁺/Ca²⁺octyl sulfate). By conductivity and¹³C NMR chemical shift measurements the critical micelle concentration (CMC) was found to decrease drastically when small amounts of divalent counterions were present in the system. Self-diffusion coefficients of surfactant ions and organic counterions were measured in the micellar phase by the Fourier transform pulsed-gradient spin-echo (FT-PGSE) NMR method. The degree of counterion binding in the micellar system with piperidine⁺/piperazine²⁺counterions was obtained from FT-PGSE NMR measurements. It was observed that the divalent counterions were more strongly bound than the monovalent counterions. The experimental results were compared with theoretical Poisson–Boltzmann calculations. The cell model was used to study the electrostatic effects. Good agreement between electrostatic theory and experiment was observed; however, an attractive force exists between the monovalent piperidine counterions and the micelle, probably because of hydrophobic interactions.     

ACE applied to the quantitative characterization of benzo‐18‐crown‐6‐ether binding with alkali metal ions in a methanol–water solvent system

ACE was applied to the quantitative evaluation of noncovalent binding interactions between benzo‐18‐crown‐6‐ether (B18C6) and several alkali metal ions, Li⁺, Na⁺, K⁺, Rb⁺ and Cs⁺, in a mixed binary solvent system, methanol–water (50/50 v/v). The apparent binding (stability) constants (K_b) of B18C6–alkali metal ion complexes in the hydro‐organic medium above were determined from the dependence of the effective electrophoretic mobility of B18C6 on the concentration of alkali metal ions in the BGE using a nonlinear regression analysis. Before regression analysis, the mobilities measured by ACE at ambient temperature and variable ionic strength of the BGE were corrected by a new procedure to the reference temperature, 25°C, and the constant ionic strength, 10 mM . In the 50% v/v methanol–water solvent system, like in pure methanol, B18C6 formed the strongest complex with potassium ion (log K_b=2.89±0.17), the weakest complex with cesium ion (log K_b=2.04±0.20), and no complexation was observed between B18C6 and the lithium ion. In the mixed methanol–water solvent system, the binding constants of the complexes above were found to be about two orders lower than in methanol and about one order higher than in water.     

A model for cation adsorption to clays and membranes

A cation adsorption model is presented and its recent applications are discussed. The model combines electrostatic equations with specific binding, and considers neutral and positively charged complexes between the negative surface sites and organic cations in a closed system. Extensions in the model account for dye aggregation in solution, and for the formation of solution complexes of inorganic cations, such as [M⁺⁺ Cl^–]⁺. The amounts of 45Ca²⁺ adsorbed to vesicles extracted from the plasma membranes of melon root cells could be adequately simulated and predicted. The binding coefficients determined for Ca²⁺, Na⁺, and Mg²⁺ are in the range of values previously deduced for binding to phospholipid components. Model calculations were applied to the test of hypotheses on the effect of salt stress on the growth of roots. The adsorption of monovalent organic cations to montmorillonite is characterized by binding coefficients that are at least six orders of magnitude larger than those of Na⁺, Mg²⁺, Ca²⁺, and Cd²⁺, or those of CdCl⁺ or CaCl⁺. Monovalent organic cations were found to adsorb 140–200% of the cation exchange capacity of the clay and to cause charge reversal. Deductions from adsorption results of acriflavin are consistent with those drawn from the application of other experimental methods. Preliminary results on the adsorption of divalent organic cations are presented. Agro-environmental applications of organo-clays are discussed.     

Lead‐Free Silver‐Bismuth Halide Double Perovskite Nanocrystals

Lead‐free perovskite nanocrystals (NCs) were obtained mainly by substituting a Pb²⁺ cation with a divalent cation or substituting three Pb²⁺ cations with two trivalent cations. The substitution of two Pb²⁺ cations with one monovalent Ag⁺ and one trivalent Bi³⁺ cations was used to synthesize Cs₂AgBiX₆ (X=Cl, Br, I) double perovskite NCs. Using femtosecond transient absorption spectroscopy, the charge carrier relaxation mechanism was elucidated in the double perovskite NCs. The Cs₂AgBiBr₆ NCs exhibit ultrafast hot‐carrier cooling (<1 ps), which competes with the carrier trapping processes (mainly originate from the surface defects). Notably, the photoluminescence can be increased by 100 times with surfactant (oleic acid) added to passivate the defects in Cs₂AgBiCl₆ NCs. These results suggest that the double perovskite NCs could be potential materials for optoelectronic applications by better controlling the surface defects.     

Formability and properties of self-standing clay film by montmorillonite with different interlayer cations

Influences of exchangeable interlayer cations were investigated on self-standing film formability, film morphology, and properties of the clay films such as flexibility and gas barrier property. Ion-exchanged montmorillonite samples were prepared by a cation exchange from naturally bearing cation, mostly Na⁺, to Li⁺, Mg²⁺, Ca²⁺, Al³⁺, and Fe^{2+, 3+}. Self-standing films were prepared from aqueous colloidal dispersions of these montmorillonite samples with no additives. The montmorillonite samples with monovalent or divalent cation formed flat self-standing films while the Al-montmorillonite sample produced a distorted film. The Fe-montmorillonite sample formed many separated reddish-brown rod-shaped pieces. Clay film microstructures were different with interlayer cations. The films with monovalent interlayer cations were constructed by the stacking of units with delicately waved thin clay sheets in the whole film, but other films show different morphologies between the upper side and lower side; the upper side is laminated with thin sheets; the lower side is laminated with large thick sheets.The self-standing films’ flexibility and gas barrier property differed according to the interlayer cations. These properties were good in cases of samples with monovalent cations. The innumerable short wave and sheet thinness are considered to foster good flexibility and gas barrier properties. The differences in film formability and properties of the films are attributable to different swellability among samples with different interlayer cations. The montmorillonite samples with monovalent cations swell sufficiently by water, but those with polyvalent cations swell poorly. In the latter case, clay crystals aggregate in water, then the aggregate grows into large particles, creating a film with large particles.     

Interaction of divalent metal cations and nucleotides: A computational study

In this study, the anionic phosphate group of nucleotides was found to be the best site to bind the divalent metal cations Be²⁺, Mg²⁺, Zn²⁺, Cd²⁺, Hg²⁺ and Pb²⁺ to form the most stable complexes. Molecular orbital calculations at the semiempirical level were performed on nucleotidemetal cation complexes to report energies of complexation reactions, geometrical parameters of complexes and charge distributions on the complexes. In the discussion, complexational preferences of divalent metal cations, the charge transfer involved in the binding of the metal cations to the phosphate anion of the nucleotides and their conformational effects are included.     

Application of localized reactivity index in combination with periodic DFT calculation to rationalize the swelling mechanism of clay type inorganic material

Clays are layered alumino-silicates. Clays swell and expand in aqueous solution. This property governs the usage of these materials in synthesis of nano-composites and is a source of many of its catalytic applications. We used both localized and periodic calculations within the realm of density functional theory (DFT) on a series of monovalent (Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺), and divalent (Mg²⁺, Ca²⁺, Sr²⁺, Ba²⁺) cations, to monitor their effect on the swelling of clays. The activity order obtained for the exchangeable cations among all the monovalent and divalent series studied is: Mg²⁺ > Ca²⁺ > Sr²⁺ > Ba²⁺ > Cs⁺ > Rb⁺ > Na⁺ > Li⁺ > K⁺. We have studied two types of clays, montmorillonite and beidellite, with different surface structures and with/without water using periodic calculations. We have calculated the layer spacing at the first, second and third hydration shells of exchangeable cation, to compare with the experimentald-spacing values to correlate with humidity. A novel quantitative scale is proposed in terms of the intermolecular relative nucleophilicity of the active cation sites in their hydrated state through Fukui functions using hard-soft acid base (HSAB) principle. Finally, a swelling mechanism is proposed. This is a unique study where a combination of periodic and localized calculations has been performed to validate the capability of reactivity index calculations in material designing.