Conformational and hydration effects of site-selective sodium, calcium and strontium ion binding to the DNA Holliday junction structure d(TCGGTACCGA)(4)

The role of metal ions in determining the solution conformation of the Holliday junction is well established, but to date the picture of metal ion binding from structural studies of the four-way DNA junction is very incomplete. Here we present two refined structures of the Holliday junction formed by the sequence d(TCGGTACCGA) in the presence of Na+ and Ca2+, and separately with Sr2+ to resolutions of 1.85 Angstrom and 1.65 Angstrom, respectively. This sequence includes the ACC core found to promote spontaneous junction formation, but its structure has not previously been reported. Almost complete hydration spheres can be defined for each metal cation. The Na+ sites, the most convincing observation of such sites in junctions to date, are one on either face of the junction crossover region, and stabilise the ordered hydration inside the junction arms. The four Ca2+ sites in the same structure are at the CG/CG steps in the minor groove. The Sr2+ ions occupy the TC/AG, GG/CC, and TA/TA sites in the minor groove, giving ten positions forming two spines of ions, spiralling through the minor grooves within each arm of the stacked-X structure. The two structures were solved in the two different C2 lattices previously observed, with the Sr2+ derivative crystallising in the more highly symmetrical form with two-fold symmetry at its centre. Both structures show an opening of the minor groove face of the junction of 8.4degrees in the Ca2+ and Na+ containing structure, and 13.4degrees in the Sr2+ containing structure. The crossover angles at the junction are 39.3degrees and 43.3degrees, respectively. In addition to this, a relative shift in the base pair stack alignment of the arms of 2.3 Angstrom is observed for the Sr2+ containing structure only. Overall these results provide an insight into the so-far elusive stabilising ion structure for the DNA Holliday junction. (C) 2003 Elsevier Science Ltd. All rights reserved.

Steric effects on uranyl complexation: synthetic, structural, and theoretical studies of carbamoyl pyrazole compounds of the uranyl(VI) ion

New bifunctional pyrazole based ligands of the type [C3HR2N2CONR'] (where R = H or CH3; R' = CH3, C2H5, or (C3H7)-C-i) were prepared and characterized. The coordination chemistry of these ligands with uranyl nitrate and uranyl bis(dibenzoyl methanate) was studied with infrared (IR), H-1 NMR, electrospray-mass spectrometry (ES-MS), elemental analysis, and single crystal X-ray diffraction methods. The structure of compound [UO2(NO3)(2)(C3H3N2CON{C2H5}(2))] (2) shows that the uranium(VI) ion is surrounded by one nitrogen atom and seven oxygen atoms in a hexagonal bipyramidal geometry with the ligand acting as a bidentate chelating ligand and bonds through both the carbamoyl oxygen and pyrazolyl nitrogen atoms. In the structure of [UO2(NO3)(2)(H2O)(2)(C5H7N2CON {C2H5}(2))(2)], (5) the pyrazole figand acts as a second sphere ligand and hydrogen bonds to the water molecules through carbamoyl oxygen and pyrazolyl nitrogen atoms. The structure of [UO2(DBM)(2)C3H3N2CON{C2H5}(2)] (8) (where DBM = C6H5COCHCOC6H5) shows that the pyrazole ligand acts as a monodentate ligand and bonds through the carbamoyl oxygen to the uranyl group. The ES-MS spectra of 2 and 8 show that the ligand is similarly bonded to the metal ion in solution. Ab initio quantum chemical studies show that the steric effect plays the key role in complexation behavior.

Thermal ion flows in the topside auroral ionosphere and the effects of low-altitude, transverse acceleration

Topside ionospheric profiles are used to study the upward field-aligned flow of thermal O+ at high latitudes. On the majority of the field lines outside the plasmasphere, the mean flux is approximately equal to the mean polar wind measured by spacecraft at greater altitudes. This is consistent with the theory of thermal light ion escape supported, via charge exchange, by upward O+ flow at lower heights. Events of larger O+ flow are detected at auroral latitudes and their occurrence is found to agree with that of transversely accelerated ions within the topside ionosphere and the magnetosphere. The effects of low altitude heating of O+ by oxygen cyclotron waves, driven by downward field-aligned currents, are considered as a possible common cause of these two types of event.

A simple model of the effects of the mid-latitude total ion trough in the bottomsideFlayer on HF radiowave propagation

Observations of the amplitudes and Doppler shifts of received HF radio waves are compared with model predictions made using a two-dimensional ray-tracing program. The signals are propagated over a sub-auroral path, which is shown to lie along the latitudes of the mid-latitude trough at times of low geomagnetic activity. Generalizing the predictions to include a simple model of the trough in the density and height of the F2 peak enables the explanation of the anomalous observed diurnal variations. The behavior of received amplitude, Doppler shift, and signal-to-noise ratio as a function of the Kp index value, the time of day, and the season (in 17 months of continuous recording) is found to agree closely with that predicted using the statistical position of the trough as deduced from 8 years of Alouette satellite soundings. The variation in the times of the observation of large signal amplitudes with the Kp value and the complete absence of such amplitudes when it exceeds 2.75 are two features that implicate the trough in these effects.

Could saturation effects be visible in a future electron-ion collider?

We expect to observe parton saturation in a future electron-ion collider. In this Letter we discuss this expectation in more detail considering two different models which are in good agreement with the existing experimental data on nuclear structure functions. In particular, we study the predictions of saturation effects in electron-ion collisions at high energies, using a generalization for nuclear targets of the b-CGC model, which describes the ep HERA quite well. We estimate the total. longitudinal and charm structure functions in the dipole picture and compare them with the predictions obtained using collinear factorization and modern sets of nuclear parton distributions. Our results show that inclusive observables are not very useful in the search for saturation effects. In the small x region they are very difficult to disentangle from the predictions of the collinear approaches. This happens mainly because of the large uncertainties in the determination of the nuclear parton distribution functions. On the other hand, our results indicate that the contribution of diffractive processes to the total cross section is about 20% at large A and small Q(2), allowing for a detailed study of diffractive observables. The study of diffractive processes becomes essential to observe parton Saturation. (C) 2008 Elsevier B.V. All rights reserved.

Photoassociative ionization of cold Na atoms: repulsive levels effects on the ion production rate

We have revisited photoassociative ionization (PAI) in a cold sample of Na atmos. A two-color experiment was performed ina magneto-optical trap through the addition of aprobe laser. The observation of a marked change in the PAI rate for a definite frequency range can be attributed to the influence of repuisive levels and a possible avoided crossing between long-range molecular levels. (c) 2009 by Astro Ltd. Published exclusively by WLLEY-VCH Verlag GmbH & Co. KGaA

Ion pair stabilization effects on a series of procaine structural analogs

In this work, a series of 10 structural procaine analogs have been synthesized in order to investigate the structural features affecting the stability of ion pair formation and its influence on the lipophilicity of ionizable compounds. The structural variation within this series was focused on the terminal nitrogen substituents and on the intermediate chain linkage nature. The hydrophobic parameters log P(n) and log P(i) (partition coefficient of the neutral and ionic species, respectively), as well as the ionization constants pK(a) and pK(a)(oct), were obtained from log D-pH profiles measured at pH values ranging from 2 to 12. The difference between log P(i) and log P(n) values (i.e. difflog P) of each prepared compound was considered a measure of the stability of ion pair formation. In this set, the difflog P values varied nearly over one log unit, ranging from -2.40 to -3.37. It has been observed that the presence of hydrogen bonding groups (especially donor) and low steric hindrance around the terminal amine ionizable group increases the relative lipophilicity of the ionic species as compared to the corresponding neutral species. These results were interpreted as due to the increased stability of ion pairs of the compounds bearing these structural features. (C) 2010 Elsevier B.V. All rights reserved.

Effects of ion beam on nanoindentation characteristics of glassy polymeric carbon surface

Glassy polymeric carbon (GPC) is a useful material for medical applications due to its chemical inertness and biocompatible characteristics. Mitral and aortic and hydrocephalic valves are examples of GPC prosthetic devices that have been fabricated and commercialized in Brazil. In this work, ion beam was used to improve the mechanical characteristics of GPC surface and therefore to avoid the propagation of microcracks where the cardiac valves are more fragile. A control group of phenolic resin samples heat-treated at 300, 400, 700, 1000, 1500, and 2500 degrees C was characterized by measuring their hardness and Young's reduced elastic modulus with the depth of indentation. The control group was compared to results obtained with samples heat-treated at 700, 1000, and 1500 degrees C and bombarded with energetic ions of silicon, carbon, oxygen, and gold at energies of 5, 6, 8, and 10 MeV, respectively, with fluences between 10x10(13) and 10x10(16) ions/cm(2). GPC nonbombarded samples showed that hardness depends on the heat treatment temperature (HTT), with a maximum hardness for heat treatment at 1000 degrees C. The comparison between the control group and bombarded group also showed that hardness, after bombardment, had a greater increase for samples prepared at 700 degrees C than for samples prepared at higher temperatures. The Young's elastic modulus presents an exponential relationship with depth. The parameters obtained by fitting depend on the HTT and on the ion used in the bombardment more than on energy and fluence. The hardness results show clearly that bombardment can promote carbonization, increase the linkage between the chains of the polymeric material, and promote recombination of broken bonds in lateral groups that are more numerous for samples heat-treated at 700 degrees C. (c) 2004 Elsevier B.V. All rights reserved.

Effects of nitrogen ion irradiation on plasma polymerized films produced from titanium tetraiso pro poxide-oxygen-helium mixtures

In this work films were produced by the plasma enhanced chemical vapor deposition (PECVD) of titanium tetraisopropoxide-oxygen-helium mixtures and irradiated with 150 keV singly-charged nitrogen ions (N(+)) at fluences, phi, between 10(14) and 10(16) cm(-2). Irradiation resulted in compaction, which reached about 40% (measured via the film thickness) at the highest fluence. Infrared reflection-absorption spectroscopy (IRRAS) revealed the presence of Ti-O bonds in all films. Both O-H and C-H groups were present in the as-deposited films, but the density of each of these decreased with increasing phi and was absent at high phi, indicating a loss of hydrogen. X-ray photoelectron spectroscopy (XPS) analyses revealed an increase in the C to Ti atomic ratio as phi increased, while the O to Ti ratio hardly altered, remaining at around 2.8. The optical gap of the films, derived from data obtained by ultraviolet-visible spectroscopy (UVS), remained at about 3.6 eV for all fluences except the highest, for which an abrupt fall to around 1.0 eV was observed. For the irradiated films, the electrical conductivity, measured using the two-point method, showed a systematic increase with increasing phi. (c) 2008 Elsevier B.V. All rights reserved.

Comparative study of ion beam-irradiation effects on silica and α-quartz: evidences for excitonic mechanisms

Introduction - SiO 2 •Simple composition and structure; Crystalline and amorphous phases •Adequate for atomistic simulations •Abundant in nature. Relevant for many technologies -Irradiation with swift heavy ions: •They provide EXTREME physical conditions •Very high excitation densities similar to high power lasers •Very high local temperatures •By playing with high energy and heavy mass (SHI) : •One can go from low electronic excitations (collisions regime) to high electronic excitations (electronic regime

A molecular dynamics study of swift heavy ion irradiation of amorphous silica: the role of thermal effects

Irradiation with swift heavy ions (SHI), roughly defined as those having atomic masses larger than 15 and energies exceeding 1 MeV/amu, may lead to significant modification of the irradiated material in a nanometric region around the (straight) ion trajectory (latent tracks). In the case of amorphous silica, SHI irradiation originates nano-tracks of higher density than the virgin material (densification). As a result, the refractive index is increased with respect to that of the surroundings. Moreover, track overlapping leads to continuous amorphous layers that present a significant contrast with respect to the pristine substrate. We have recently demonstrated that SHI irradiation produces a large number of point defects, easily detectable by a number of experimental techniques (work presented in the parallel conference ICDIM). The mechanisms of energy transfer from SHI to the target material have their origin in the high electronic excitation induced in the solid. A number of phenomenological approaches have been employed to describe these mechanisms: coulomb explosion, thermal spike, non-radiative exciton decay, bond weakening. However, a detailed microscopic description is missing due to the difficulty of modeling the time evolution of the electronic excitation. In this work we have employed molecular dynamics (MD) calculations to determine whether the irradiation effects are related to the thermal phenomena described by MD (in the ps domain) or to electronic phenomena (sub-ps domain), e.g., exciton localization. We have carried out simulations of up to 100 ps with large boxes (30x30x8 nm3) using a home-modified version of MDCASK that allows us to define a central hot cylinder (ion track) from which heat flows to the surrounding cold bath (unirradiated sample). We observed that once the cylinder has cooled down, the Si and O coordination numbers are 4 and 2, respectively, as in virgin silica. On the other hand, the density of the (cold) cylinder increases with respect to that of silica and, furthermore, the silica network ring size decreases. Both effects are in agreement with the observed densification. In conclusion, purely thermal effects do not explain the generation of point defects upon irradiation, but they do account for the silica densification.

Ion charge number and flux saturation effects in the corona of a laser-irradiated pellet

The quasisteady structure of the corona of a laser-irradiated pellet is completely determined for arbitrary Z, (ion charge number} and re/ra (ratio of critical and ablation radii), and for heat-flux saturation factor/above approximately 0.04. The ion-to-electron temperature ratio at rc grows sensibly with Z,; all other quantities depend weakly and nonmonotonically on Z,. For rc /ra close to unity, and all Z, of interest (Z, < 47}, the flow is subsonic at rc. For a given laser power W, flux saturation may decrease (low/) or increase (high/) the ablation pressure Pa relative to the value obtained when saturation is not considered; in some cases a decrease in/with W fixed increases Pa. For intermediate^ ~0.1), Pa cc (W/r* )2/3 p\n\pc = critical density), independently of rc/ra; for/~0.6, Pa «s larger by a factor of about [rc/raf13. For rjra > 1.2 roughly, the mass ablation rate is C{Z,) [{m/kZ.f^Kr^Pl) l,\ independent of pc and/, and barely dependent on Z,(m, is ion mass; k, Boltzmann's constant; K, conductivity coefficient; and C, a tabulated function).

Distinguishing surface effects of calcium ion from pore-occupancy effects in Na+ channels

The effects of calcium ion on the Na+ activation gate were studied in squid giant axons. Saxitoxin (STX) was used to block ion entry into Na+ channels without hindering access to the membrane surface, making it possible to distinguish surface effects of calcium from pore-occupancy effects. In the presence of STX, gating kinetics were measured from gating current (Ig). The kinetic effects of external calcium concentration changes were small when STX was present. In the absence of STX, lowering the calcium concentration (from 100 to 10 mM) slowed the closing of Na+ channels (measured from INa tails) by more than a factor of 2. Surprisingly, the voltage sensitivity of closing kinetics changed with calcium concentration, and it was modified by STX. Voltage sensitivity apparently depends in part on the ability of calcium to enter and block the channels as voltage is driven negative. In external medium with no added calcium, INa tail current initially increases in amplitude severalfold with the relief of calcium block, then progressively slows and gets smaller, as calcium diffuses out of the layers investing the axon. INa tails seen just before the current disappears suggest that closing in the absence of channel block is very slow or does not occur. INa amplitude and kinetics are completely restored when calcium is returned. The results strongly suggest that calcium occupancy is a requirement for channel closing and that nonoccupied channels fold reversibly into a nonfunctional conformation.