Intensities of DNA ion-phosphate modes in the low-frequency Raman spectra

The Raman intensities of counterion vibrations with respect to the phosphate groups of the double-helix backbone (ion-phosphate modes) in the low-frequency spectra (< 200 cm^-1) of B -DNA with different alkali metal counterions have been calculated using the model for DNA conformational vibrations and the valence-optic approach. The results have showed that the spectra of DNA with heavy counterions ( Rb⁺ and Cs⁺ differ from the spectra of DNA with light counterions ( Na⁺ and K⁺ . The calculated spectra of DNA with heavy counterions are characterized by intensive modes of ion-phosphate vibrations that form one united band near 115cm^-1. Ion-phosphate modes in the spectra of DNA with light counterions are characterized by higher frequencies (near 180cm^-1) and much lower intensity. Our calculations explain why the modes of ion-phosphate vibrations are observed in Cs-DNA spectra rather than in Na-DNA. The determined sensitivity of the intensities of DNA low-frequency spectra to the counterion type proves the existence of the ion-phosphate modes.     

How water and counterions diffuse into the hydrated montmorillonite

Molecular dynamics simulations have been performed to study the diffusive transport properties of water and counterions in 1-, 2- and 3-layer hydrated Wyoming-type montmorillonite (MMT). The considered counterions included in the clay are monovalent cations, such as Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺, and divalent cations, such as Ca²⁺, Ni²⁺, Zn²⁺ and Pb²⁺. The diffusion simulation results of Li-, Na-, K-, Cs-MMT, based on NVE ensemble and SPC/E water model, compared well to available experimental quantities and previous simulations, which permit us to study the diffusion behaviour of heavy metal counterion including in the different hydrated montmorillonite. Our simulation results show that the diffusion coefficients of both water molecule and counterions increase versus the quantity of water content. At the same hydrated state, the diffusion of cations strongly depends on their size, weight and capacity of attracting water. Monovalent cations diffuse always much faster than divalent ones. Although the increasing of hydrate degree can raise the diffusion coefficient of divalent heavy cations, the activity of these heavy counterions is still very weak. The diffusion of cations in the interlayer space of clay is much weaker than that in bulk water. That means the presence of charged clay has great influence on the diffusion of cations, which change totally the diffusion behaviour of cations.     

Understanding the mechanism of DNA deactivation in ion therapy of cancer cells: hydrogen peroxide action*

Changes in the medium of biological cells under ion beam irradiation has been considered as a possible cause of cell function disruption in the living body. The interaction of hydrogen peroxide, a long-lived molecular product of water radiolysis, with active sites of DNA macromolecule was studied, and the formation of stable DNA-peroxide complexes was considered. The phosphate groups of the macromolecule backbone were picked out among the atomic groups of DNA double helix as a probable target for interaction with hydrogen peroxide molecules. Complexes consisting of combinations including: the DNA phosphate group, H₂O₂ and H₂O molecules, and Na⁺ counterion, were considered. The counterions have been taken into consideration insofar as under the natural conditions they neutralise DNA sugar-phosphate backbone. The energy of the complexes have been determined by considering the electrostatic and the Van der Waals interactions within the framework of atom-atom potential functions. As a result, the stability of various configurations of molecular complexes was estimated. It was shown that DNA phosphate groups and counterions can form stable complexes with hydrogen peroxide molecules, which are as stable as the complexes with water molecules. It has been demonstrated that the formation of stable complexes of H₂O₂-Na⁺-PO₄ ^- may be detected experimentally by observing specific vibrations in the low-frequency Raman spectra. The interaction of H₂O₂ molecule with phosphate group of the double helix backbone can disrupt DNA biological function and induce the deactivation of the cell genetic apparatus. Thus, the production of hydrogen peroxide molecules in the nucleus of living cells can be considered as an additional mechanism by which high-energy ion beams destroy tumour cells during ion beam therapy.     

Synthesis and Spectral Study of Several Solid M3[Eu(2,6-Pyridinedicarboxylate)3] Salts (M=Li+, Na+, K+, Rb+, Cs+, NH4 +, and Pyridinium+)

Abstract

Salts of the [Eu(2,6-pyridinedicarboxylate)₃]^3- complex anion and various monovalent inorganic and organic counterions (Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺, NH₄ ⁺, and pyridinium⁺) have been synthesized and studied by emission spectroscopy. The Eu³⁺ ion emission spectra exhibited by these salts have been observed with high resolution (less than 1.0 cm^?1) and at low temperature (77 K). The emission spectra of these compounds indicate that changing the attached counterion does not affect the site symmetry observed by the europium ion beyond slight distortions indicated by small shifts in the energies of the Eu³⁺ electronic levels.     

Hofmeister series and ionic effects of alkali metal ions on DNA conformation transition in normal and less polarised water solvent

Normal and less polarised water models are used as the solvent to investigate Hofmeister effects and alkali metal ionic effects on dodecamer d(CGCGAATTCGCG) B-DNA with atomic dynamics simulations. As normal water solvent is replaced by less polarised water, the Hofmeister series of alkali metal ions is changed from Li⁺ > Na⁺ ? K⁺ ? Cs⁺ ? Rb⁺ to Li⁺ > Na⁺ > K⁺ > Rb⁺ > Cs⁺. In less polarised water, DNA experiences the B→A conformational transition for the lighter alkali metal counterions (Li⁺, Na⁺ and K⁺). However, it keeps B form for the heavier ions (Rb⁺ and Cs⁺). We find that the underlying cause of the conformation transition for these alkali metal ions except K⁺ is the competition between water molecules and counterions coupling to the free oxygen atoms of the phosphate groups. For K⁺ ions, the ‘economics’ of phosphate hydration and ‘spine of hydration’ are both concerned with the DNA helixes changing.     

Interaction between guest AgI and host zeolite FAU studied by optical spectra and EXAFS

AgI molecules were dilutely adsorbed into nano-cages of Na⁺, K⁺ and Cs⁺ type FAU zeolites in order to understand the interaction between host zeolite and guest AgI. This interaction was investigated using optical absorption spectroscopy and extended X-ray absorption fine structure (EXAFS). The optical spectra strongly depend on the type of the alkali cations. Compared with the lowest absorption band of AgI molecules in gas phase, the spectra of AgI molecules adsorbed in the zeolite cages shifts to higher energy in the order of Cs⁺, K⁺, and Na⁺. On the contrary, Ag-I bond lengths of adsorbed AgI molecules obtained from EXAFS were independent of the type of the alkali-cations. The bond length was very close to gas phase AgI molecules. Therefore, the interaction between AgI molecules and the zeolite, whose magnitude is Na⁺ > K⁺ > Cs⁺, is important in the photo-excited electronic state.     

Cation disorder in NaW2O6+δ·nH2−zO post-ion exchange with K, Rb, Sr, and Cs

The structure of the defect pyrochlore NaW₂O_6+δ·nH_2−zO after ion exchange with K, Rb, Sr or Cs for Na has been investigated using thermal analysis, solid-state nuclear magnetic resonance, laboratory X-ray and neutron diffraction methods. Neutron diffraction studies show that both the A-type cations (Na⁺, K⁺, Rb⁺, and/or Cs⁺) and the water molecules reside within the channels that form in the 111 direction of the W₂O₆ framework and that these strongly interact. The analytical results suggest that the water and A-type cations compete for space in the tunnels within the W₂O₆ pyrochlore framework, with the total number of water molecules and cations being approximately constant in the six samples investigated. The interplay between the cations and water explains the non-linear dependence of the a lattice parameter on the choice of cation. It appears that the ion-exchange capacity of the material will be controlled by the amount of water initially present in the sample.     

Europium ion as a probe for binding sites to carrageenans

Carrageenans, sulfated polysaccharides extracted from red algae, present a coil-helix transition and helix aggregation dependence on the type and concentration of counterions. In this study, we focus attention on a mixed valence counterion system: Eu³⁺/Na⁺ or K⁺ with different gel-forming carrageenans: kappa, iota, and kappa-2. Results of stationary and time-dependent luminescence showed to be a suitable tool to probe ion binding to both the negatively charged sulfate group and the hydroxyl groups present in the biopolymer. For lower europium ion concentrations, a single longer decay emission lifetime was detected, which was attributed to the binding of europium ion to the carrageenan sulfate groups. An additional decay ascribed to europium binding to hydroxyl groups was observed above a threshold concentration, and this decay was dependent on the carrageenan charge density. Symmetry of the europium ion microenvironment was estimated by the ratio between the intensities of its emission bands, which has been shown to depend on the concentration of europium ions and on the specificity of the monovalent counterion bound to the carrageenan.     

Density functional theory study of the bis‐3‐benzo‐crown ethers and their complexes with alkali metal cations Na+, K+, Rb+ and Cs+

The binding interactions of bis‐3‐benzo‐15‐crown‐5 ethers and bis‐3‐benzo‐18‐crown‐6 ethers (neutral hosts) with a series of alkali metal cations Na⁺, K⁺, Rb⁺ and Cs⁺ (charged guests) were investigated using quantum chemical density functional theory. Different optimized structures, binding energies and various thermodynamic parameters of free crown ethers and their metal cation complexes were obtained based on the Becke, three‐parameter, Lee–Yang–Parr functional using mixed basis set (C, H, O, Na⁺ and K⁺ using 6‐31 g, and the heavier cation Rb⁺ and Cs⁺ using effective core potentials). Natural bond orbital analysis is conducted on the optimized geometric structures. The main types of driving force host–guest interactions are investigated. The electron donating O offers a lone pair of electrons to the contacting LP* (1‐center valence antibond lone pair) orbitals of metal cations. The bis‐3‐benzocrown ethers are assumed to have sandwich‐like conformations, considering the binding energies to gauge the exact interactions with alkali cations. It is found that there are two different types of complexes: one is a tight ion pair and the other is a separated ion pair. Copyright © 2011 John Wiley & Sons, Ltd.     

Temperature effects on the diffusion of water and monovalent counterions in the hydrated montmorillonite

We investigate here the effect of temperature on the diffusion of water and cations in the Wyoming-type montmorillonite clay. The considered cations are monovalent compensating ions, such as Li⁺, Na⁺, K⁺, Rb⁺ and Cs⁺ in one-, two- and three-hydration states. For this purpose, molecular dynamics simulations have been performed to obtain the dynamic behaviour regarding the interlayer ions and water molecules under a temperature range between 260 and 400 K. The diffusion coefficient of water and cations in different hydrated clays increases with temperature. The influence of temperature on the diffusion of water is much greater than that of cations in one-, two- or three-hydrated clay. The degree of hydration plays an important role on the diffusion behaviour of water and counterions. We found that the effect of temperature is negligible in weakly hydrated clay, whereas it became significant in highly hydrated one. Besides, the size and mass of cations’ hydrate also affect the diffusion behaviour of water and cations in the interlayer space of hydrated clay.     

Temperature effect in a montmorillonite clay at low hydration—microscopic simulation

The effect of temperature in the range 0–150°C was studied for homo-ionic montmorillonite clays with Na⁺ and Cs⁺ compensating ions in low hydration states. Monte Carlo and molecular dynamics simulations were employed to provide both static and dynamic information concerning the interlayer ions and water molecules, and emphasis was laid on the temperature activation of the diffusion coefficients. Principal structural changes were limited to the interlayer water phase. In the monohydrated systems, neither of the cations was seen to enter into the hexagonal cavities of the clay. Cs⁺ exhibited clear site-to-site diffusion between sites allowing coordination to six oxygen atoms of the clay sheets, this behaviour persisting to high temperatures. Preferential sites for the Na⁺ counterion were much less well-defined, even at low temperatures. The behaviour of the water phase in the monohydrated states was similar for the two ions. A rapid approach to bulk dynamics was seen in the transition from monohydrated to bihydrated Na-montmorillonite. A detailed quantitative comparison of the temperature activation of diffusion for a two-dimensional water phase and three-dimensional bulk water is presented for the first time.     

Poly(ethylene glycol) cationization with alkali metals in matrix-assisted laser desorption ionization investigated with the solvent-free method

Matrix-assisted laser desorption ionization (MALDI) was applied to determine the relative efficiencies for attachment of alkali cations to poly(ethylene glycol) polymers. The solvent-free sample preparation method was employed in order to discriminate the gas-phase polymer-cation complex formation mechanism from solubility and co-crystallization effects. We show that the cohesion energy of the cation precursor has a strong influence on the outcome of the MALDI measurements. This potential drawback is circumvented by the simultaneous use of alkali salts of similar lattice energy. The experiments include chain polymers of different length (PEG600 and PEG1000) and alkali cations of different size (Na⁺, K⁺, Cs⁺). We found that the attachment efficiencies decrease with growing cation size. This decrease is significantly more rapid for the shorter PEG600 polymers. These results corroborate the general trends observed in earlier studies, but correct the dependence on alkali cation size assessed in previous MALDI experiments with the conventional dried-droplet sample preparation method.     

Hydration states and metallic intercalation effects in dry DNA

Temperature dependence of the complex dielectric constant at 16.3 GHz has been measured on dry poly(dA)-poly(dT) DNA with Na⁺ counterions under different relative humidity (RH). The rotational motion of sole water dipoles hydrated in PO₂⁻ is detected at low RH, and the collective motion due to water network in major groove is successfully observed at high RH. From the infrared (IR) spectroscopy in dry DNA introducing metallic ions (M-DNA), the symmetric and antisymmetric stretching bands of PO₂⁻ distinctly depend on RH and type of metallic ions. The IR spectral change indicates that the monovalent ions (Li and Na) are arranged in PO₂⁻ though the divalent and trivalent ions connect to the base molecules.     

Effect of solvent on the cation-sensitive fluorescence of polyanions bearing 4′-acryloylbenzo-18-crown-6 Units

Changes in the fluorescence intensity of polyanions bearing 4-acryloylbenzo-18-crown-6 units on the addition of cations were studied in a mixed solvent of methanol and water at 30°C. The sensitivity of the change in fluorescence intensities of the polymers toward cations was strongly enhanced compared to that of the corresponding model compound. When alkali metal cations were added, the fluorescence intensity of the polymers decreased in the orders Li⁺>Na⁺>Cs⁺>Rb⁺>K⁺ in a methanol-water (19) mixture and Li⁺>Na⁺>Rb⁺>K⁺Cs⁺ in a methanol-water (91) mixture. Alkaline earth metal cations and alkylamine hydrochlorides decreased the fluorescence intensity of the polymers in a methanol-water (19) mixture. The cation-dependent decrease in the fluorescence intensity of the polymers was affected by the water fraction in a mixed solvent of methanol and water.     

Rietveld refinements and vibrational spectroscopic studies of Na1−xKxPb4(PO4)3 lacunar apatites (0≤x≤1)

Synthesis of apatites, Na_1−xK_xPb₄(PO₄)₃ 0≤x≤1, with anion vacancy was carried out using solid state reactions. The solid solution of apatite-type structure crystallizes in the hexagonal system, space group P6₃/m (No 176). Rietveld refinements showed that 75% of Pb²⁺ cations are located in the (6h) sites; the ninefold coordination sites (4f) are equally occupied by the other 25% lead cations and the K⁺ and Na⁺ monovalent ions.The structure can be described as built up from [PO₄]³⁻ tetrahedra and Pb²⁺ of sixfold coordination cavities (6h positions), which delimit void hexagonal tunnels running along [0 0 1]. These tunnels are connected by cations of mixed sites (4f) half occupied by Pb²⁺ and half by Na⁺/K⁺ mixed cations. The assignment of the observed frequencies in the Raman and infrared spectra is discussed on the basis of a unit cell group analysis and by comparison with other apatites. The Raman modes of all the compositions show some linear shifts of the frequencies as a function of the composition toward lower values due the substitutions of Na⁺ by K⁺ with a larger radius.     

Type I FA (Rb, Cs) and II FA (Li, Na) tunable laser activities and donor-acceptor properties of O and O at KCl (001) surface: first principle calculations

Type I F_A (Rb⁺, Cs⁺) and II F_A (Li⁺, Na⁺) tunable laser activities, adsorptivity and donor-acceptor properties of O and O⁻ adsorbates at the flat surface of KCl crystal were investigated using an embedded cluster model and ab initio methods of molecular electronic structure calculations. Ion clusters were embedded in a simulated Coulomb field that closely approximates the Madelung field of the host surface, and the nearest neighbor ions to the defect site were allowed to relax to equilibrium. Based on the calculated Stokes shifted optical transition bands, F_A tunable laser activities were found to be inversely proportional to the size of the dopant cation (Li⁺, Na⁺, Rb⁺, Cs⁺) relative to the host cation (K⁺). This relation was explained in terms of the axial perturbation of the impurity cation. The probability of orientational bleaching attributed to the RES saddle point ion configuration along the 〈110〉 axis was found to be inversely proportional to the size of the dopant cation, with activation energy barriers of ca. 0.44-3.34 eV. Surface relaxation energies of type II F_A centers were more important than those of type I F_A centers. In terms of defect formation energies, the products of type II F_A center imperfection were more stable than those of type I F_A. The difference between F or F_A band energies and exciton bands depended almost exclusively on the size of the positive ion species. As far as the adsorptivity of O and O⁻ is concerned, the results confirm that surface imperfection enhances the adsorption energies by ca. 4.38-16.37 eV. O and O⁻ penetrate through the defect-containing surface. The energy gap between the adsorbate and the defect containing surface and the donor-acceptor property of adsorbate play the dominant role in the course of adsorbate substrate interactions and the results were explained in terms of electrostatic potential curves and Mulliken population analysis.     

An Analysis of the Trigonal Center Structure of Yb3+ Ion in CsCaF3

The crystal field parameters determined from interpretation of optical spectra are used to analyze distortions of a crystal lattice in the vicinity of an impurity ion and vacancy at a Cs⁺ site compensating the excess positive charge in the trigonal centers of Yb³⁺ ions in CsCaF₃ crystal. Interactions of the impurity ion with the nearest neighbors (an octahedron of F^? ions) and the next nearest neighbors (a cube of Cs⁺ ions) are considered within the superposition model. It is established that, at formation of the trigonal center, three F^? ions of the nearest octahedron, placed symmetrically along the threefold axis on the side of the vacancy, move away from the impurity ion a little and significantly deviate from this axis. The second triangle of F^? ions, on the contrary, comes nearer to the impurity ion and nestles on the axis of the center a little. The three Cs⁺ ions, the second neighbors on the side of the vacancy, slightly come nearer to Yb³⁺ ion and considerably nestle on the center axis. The second triangle of Cs⁺ ions, from the opposite side of vacancy, also comes nearer to the paramagnetic ion and also nestles on the center axis a little. The Cs⁺ ion, lying on the center axis, comes considerably nearer to the impurity ion.     

Low-frequency dielectric relaxation of Cs+-ions in single-crystals of mica-type layer-silicates

Measurements of the permittivity ?′ and of the dielectric loss ?″ have been made on oriented single-crystals of mica-type layer silicates (vermiculites) in the frequency range 30 Hz–10 MHz. A low-frequency region of dielectric absorption has been observed which has been assigned to the migration of Cs⁺-interlayer cations on free cation sites. In a close relation to this migration we have to assume the reorientation of large electric dipoles—originated in interstitial cation and negative layer charges. Applying the BAUER equation there results an activation enthalpy of diffusion across the lattice of 11.21 $\text{kcal}\text{mol}$. Estimates of an effective dipole moment and of the number of cations contributing to the process agree well with the structural and our experimental data.     

Infrared intensities of ion-water interactions in aqueous electrolyte solutions

The i.r. absorption intensities have been measured of the fundamental vibrations of water molecules in metal halide aqueous solutions. Pseudo-isosbestic points were observed in the regions of both the stretching and bending vibrations and interpreted in terms of two states of water molecules in the solutions. The intensities of the stretching vibrations of water molecules coordinated to the dissolved ions have been estimated. The intensities become stronger in the order, Li⁺ > Na⁺ > K⁺ for the cations and F^- > Cl^- > Br^- > I^- for the anions. These orders are consistent with the strengths of the ion-water interactions, which are related to the dynamical behavior of the water molecules in the primary hydration shell.     

Electronic polarisabilities of ions in alkali halide crystals

Tessman, Kahn and Shockley calculated the electronic polarisabilities of ions in alkali halide crystals using the long wavelength limiting values of the visible light dielectric constants. We have recalculated these widely used polarisabilities using the more accurate room-temperature dielectric constant data of Lowndes and Martin and a better minimisation procedure of Pirenne and Kartheuser. We have also calculated for the first time the low temperature values of these polarisabilities. The computed values of the polarisability in ų are Li⁺ 0·029, Na⁺ 0·285, K⁺ 1·149, Rb⁺ 1·707, Cs⁺ 2·789, F^? 0·876, Cl^? 3·005, Br^? 4·168, I^? 6·294 at 300°K and Li⁺ 0·029, Na⁺ 0·290, K⁺ 1·133, Rb⁺ 1·679, Cs⁺ 2·743, F^? 0·858, Cl^? 2·947, Br^? 4·091, I^? 6·116 at 4°K. The relative standard deviations for all the alkali halides are 1·20 and 1·43 per cent at 300°K and 4°K respectively justifying the additive nature of the individual ion polarisabilities.