Excess Electron Localization in Solvated DNA Bases

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

MeV negative ion generation from ultra-intense laser interaction with a water spray

MeV negative oxygen ions are obtained from a water spray target irradiated by high intensity (5 x 10(19) W/cm(2)) and ultrashort (50 fs) laser pulses. Generation of negative ions is ascribed to electron-capture processes that the laser-accelerated high-energy positive ion experiences when it interacts with atoms in the spray. This mechanism implies the existence of a large number of MeV neutral oxygen atoms, which is consistent with indirect experimental evidence. (C) 2011 American Institute of Physics. [doi:10.1063/1.3622664]

Binding modes of diketo-acid inhibitors of HIV-1 integrase: A comparative molecular dynamics simulation study

HIV-1 integrase (IN) has become an attractive target since drug resistance against HIV-1 reverse transcriptase (RT) and protease (PR) has appeared. Diketo acid (DKA) inhibitors are potent and selective inhibitors of HIV-1 IN: however the action mechanism is not well understood. Here, to study the inhibition mechanism of DKAs we performed 10 ns comparative molecular dynamics simulations on HIV-1 IN bound with three most representative DMA inhibitors: Shionogi inhibitor, S-1360 and two Merck inhibitors L-731,988 and L-708,906. Our simulations show that the acidic part of S-1360 formed salt bridge and cation-pi interactions with Lys159. In addition, the catalytic Glu152 in S-1360 was pushed away from the active site to form an ion-pair interaction with Arg199. The Merck inhibitors can maintain either one or both of these ion-pair interaction features. The difference in potencies of the DMA inhibitors is thus attributed to the different binding modes at the catalytic site. Such structural information at atomic level, not only demonstrates the action modes of DMA inhibitors but also provides a novel starting point for structural-based design of HIV-1 IN inhibitors.

Alkynyl-Bridged Ruthenium(II) 4 '-Diferroceny1-2,2 ':6 ',2 ''-terpyridine Electron Transfer Complexes: Synthesis, Structures, and Electrochemical and Spectroscopic Studiese

The novel ligand 4'-diferrocenylallcyne-2,2':6',2 ''-terpyridine (7; Fc-C C-Fc-tpy; tpy = terpyridyl; Fc = ferrocenyl) and its Ru2+ complexes 8-10 have been synthesized and characterized by single-crystal X-ray diffraction, cyclic voltammetry, and UV-vis and luminescence spectroscopy. Electrochemical data and UV absorption and emission spectra indicate that the insertion of an ethynyl group causes delocalization of electrons in the extended pi* orbitals. Cyclic voltammetric measurements of 7 show two successive reversible one-electron-oxidation processes with half-wave potentials of 0.53 and 0.78 V. The small variations of the E-1/2 values for the Fe2+/Fe3+ redox couples after the coordination of the Ru2+ ion suggest a weak interaction between the Ru2+ and Fe2+ centers. After insertion of an ethynyl group, UV-vis absorption spectra show a red shift of the absorption peak of the (1)[(d(pi)(Fe))(6)]->(1)[(d(pi)(Fe))(5)(pi*(Ru)(tpy))(1)] MMLCT of the Ru2+ complexes. The Ru2+ complex 8 exhibits the strongest luminescence intensity (lambda(em)(max) 712 nm, Phi(em) = 2.63 x 10(-4), tau = 323 ns) relative to analogous ferrocene-based terpyridine Ru(II) complexes in H2O/CH3CN (4/1 v/v) solution.

Electron-impact excitation of CrII: A theoretical calculation of effective collision strengths for optically allowed transitions.

In this paper, we present electron-impact excitation collision strengths and Maxwellian averaged effective collision strengths for the complicated iron-peak ion Cr II. We consider specifically the allowed lines for transitions from the 3d(5) and 3d(4)4s even parity configuration states to the 3d(4)4p odd parity configuration levels. The parallel suite of R-Matrix packages, RMATRX II, which have recently been extended to allow for the inclusion of relativistic effects, were used to compute the collision cross sections. A total of 108 LS pi/280 J pi levels from the basis configurations 3d(5), 3d(4)4s, and 3d(4)4p were included in the wavefunction representation of the target including all doublet, quartet, and sextet terms. Configuration interaction and correlation effects were carefully considered by the inclusion of seven more configurations and a pseudo-corrector (4d) over bar type orbital. The 10 configurations incorporated into the Cr II model thus listed are 3d(5), 3d(4)4s, 3d(4)4p, 3d(3)4s(2), 3d(3)4p(2), 3d(3)4s4p, 3d(4)(4d) over bar, 3d(3)4s (4d) over bar, 3d(3)4p (4d) over bar, and 3d(3)(4d) over bar (2), constituting the largest Cr II target model considered to date in a scattering calculation. The Maxwellian averaged effective collision strengths are computed for a wide range of electron temperatures 2000-100,000 K which are astrophysically significant. Care has been taken to ensure that the partial wave contributions to the collision strengths for these allowed lines have converged with "top-up" from the Burgess-Tully sum rule incorporated. Comparisons are made with the results of Bautista et al. and significant differences are found for some of the optically allowed lines considered.

Ultra-fast spin dynamics in the 2s2p^2 configuration of C^+ studied by time-dependent R-matrix theory

We employ time-dependent R-matrix theory to study ultra-fast dynamics in the doublet 2s2p(2) configuration of C+ for a total magnetic quantum number M = 1. In contrast to the dynamics observed for M = 0, ultra-fast dynamics for M = 1 is governed by spin dynamics in which the 2s electron acts as a flag rather than a spectator electron. Under the assumption that m(S) = 1/2, m(2s) = 1/2 allows spin dynamics involving the two 2p electrons, whereas m(2s) = -1/2 prevents spin dynamics of the two 2p electrons. For a pump-probe pulse scheme with (h) over bar omega(pump) = 10.9 eV and (h) over bar omega(probe) = 16.3 eV and both pulses six cycles long, little sign of spin dynamics is observed in the total ionization probability. Signs of spin dynamics can be observed, however, in the ejected-electron momentum distributions. We demonstrate that the ejected-electron momentum distributions can be used for unaligned targets to separate the contributions of initial M = 0 and M = 1 levels. This would, in principle, allow unaligned target ions to be used to obtain information on the different dynamics in the 2s2p(2) configuration for the M = 0 and M = 1 levels from a single experime

Energy levels, radiative rates and electron impact excitation rates for transitions in He-like Li II, Be III, B IV and C V

We report calculations for energy levels, radiative rates and electron impact excitation rates for transitions in He-like Li II, Be III, B IV and C V. grasp (general-purpose relativistic atomic structure package) is adopted for calculating energy levels and radiative rates. For determining the collision strengths and subsequently the excitation rates, the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 49 levels of each ion. Collision strengths have been averaged over a Maxwellian velocity distribution and the effective collision strengths so obtained are reported over a wide temperature range up to 10(6) K. Comparisons have been made with similar data obtained from the flexible atomic code (FAC) to highlight the importance of resonances, included in calculations from darc, in the determination of effective collision strengths. Discrepancies between the collision strengths from darc and fac, particularly for weak transitions and at low energies, have also been discussed. Additionally, lifetimes are also listed for all calculated levels of the above four ions.

An analysis of VUV C (IV) emission from the JET divertor giving measurements of electron temperatures

A description of the radiation emitted by impurities from within a plasma is crucial if spectral line intensities are to be used in detailed studies, such as the analysis of impurity transport. The simplest and most direct check that can be made on measurements of line intensities is to analyse their ratios with other lines from the same ion. This avoids uncertainties in determining the volume of the emitting plasma and the absolute sensitivity calibration of the spectrometer and, in some cases, the need even for accurate measurements of parameters such as electron density. Consistency is required between the measured line intensity ratios and the theoretical values. The expected consistency has not been found for radiation emitted from the JET scrape-off layer (e.g. Lawson et al 2009a JINST 4 P04013), meaning that the description of the spectral line intensities of impurity emission from the plasma edge is incomplete. In order to gain further understanding of the discrepancies, an analysis has been carried out for emission from the JET divertor plasma and this is reported in this paper. Carbon was the main low Z intrinsic impurity in JET and an analysis of spectral line intensity ratios has been made for the C (IV) radiation emitted from the JET divertor. In this case, agreement is found between the measured and theoretical ratios to a very high accuracy, namely to within the experimental uncertainty of similar to +/- 10%. This confirms that the description of the line intensities for the present observations is complete. For some elements and ionization stages, an analysis of line intensity ratios can lead to the determination of parameters such as the electron temperature of the emitting plasma region and estimates of the contribution of recombination to the electron energy level populations. This applies to C (IV) and, to show the value and possibilities of the spectral measurements, these parameters have been calculated for a database of Ohmic and additionally heated phases of a large number of pulses. The importance of dielectronic, radiative and charge-exchange recombination as well as ionization has been investigated. In addition, the development of T-e throughout two example discharges is illustrated. The presented results indicate a number of areas for further investigation.

Energy levels, radiative rates and electron impact excitation rates for transitions in He-like Cl XVI, K XVIII, Ca XIX and Sc XX.

We report calculations of energy levels, radiative rates and electron impact excitation cross
sections and rates for transitions in He-like Cl XVI, K XVIII, Ca XIX and Sc XX. The grasp
(general-purpose relativistic atomic structure package) is adopted for calculating energy levels
and radiative rates. To determine the collision strengths and subsequently the excitation rates,
the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line
strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 49 levels of
each ion. Collision strengths are averaged over a Maxwellian velocity distribution and the
effective collision strengths obtained listed over a wide temperature range up to 107.4 K.
Comparisons are made with similar data obtained from the flexible atomic code (fac) to
highlight the importance of resonances, included in calculations with darc, in the
determination of effective collision strengths. Discrepancies between the collision strengths
from darc and fac, particularly for forbidden transitions, are also discussed. Additionally,
theoretical lifetimes are listed for all the 49 levels of the above four ions.

The photo-oxidation of water by sodium persulfate, and other electron acceptors, sensitised by TiO2

A number of different electron acceptors are tested for efficacy in the oxidation of water to oxygen, photocatalysed by titanium dioxide. The highly UV-absorbing metal ion electron acceptors, Ce4+ and Fe3+, appear ineffective at high concentration (10(-2) M), due to UV-screening, but more effective at lower concentrations (10(-3) M). The metal-depositing electron acceptor, Ag+, is initially effective, but loses activity upon prolonged irradiation due to metal deposition which promotes electron-hole recombination as well as UV-screening the titania particles. Most striking of the electron acceptors tested is persulfate, particularly in alkaline solution (0.1 M NaOH). The kinetics of the photo-oxidation of water by persulfate, photocatalysed by titania are studied as a function of pH, [S2O82-] and incident light intensity (I). The initial rate of water oxidation increases with pH, is directly proportional to the concentration of persulfate present and depends upon I-0.6. The TiO2/alkaline persulfate photosystem is robust and shows very little evidence of photochemical wear upon repeated irradiation. The results of this work are discussed with regard to previous work in this area and current mechanistic thinking. The formal quantum efficiency of the TiO2/alkaline persulfate photosystem was estimated as ca. 2%. (C) 2004 Elsevier B.V. All rights reserved.

Molecular Logic Gates and Luminescent Sensors Based on Photoinduced Electron Transfer

The competition between Photoinduced electron transfer (PET) and other de-excitation pathways such as fluorescence and phosphorescence can be controlled within designed molecular structures. Depending on the particular design, the resulting optical output is thus a function of various inputs such as ion concentration and excitation light dose. Once digitized into binary code, these input-output patterns can be interpreted according to Boolean logic. The single-input logic types of YES and NOT cover simple sensors and the double- (or higher-) input logic types represent other gates such as AND and OR. The logic-based arithmetic processors such as half-adders and half-subtractors are also featured. Naturally, a principal application of the more complex gates is in multi-sensing contexts.

Dynamics of nanometer-scale foil targets irradiated with relativistically intense laser pulses

In this paper we report on an experimental study of high harmonic radiation generated in nanometer-scale foil targets irradiated under normal incidence. The experiments constitute the first unambiguous observation of odd-numbered relativistic harmonics generated by the v x B component of the Lorentz force verifying a long predicted property of solid target harmonics. Simultaneously the observed harmonic spectra allow in-situ extraction of the target density in an experimental scenario which is of utmost interest for applications such as ion acceleration by the radiation pressure of an ultraintense laser.

Dynamics of charge-displacement channeling in intense laser-plasma interactions

The dynamics of transient electric fields generated by the interaction of high intensity laser pulses with underdense plasmas has been studied experimentally with the proton projection imaging technique. The formation of a charged channel, the propagation of its front edge and the late electric field evolution have been characterized with high temporal and spatial resolution. Particle-in-cell simulations and an electrostatic, ponderomotive model reproduce the experimental features and trace them back to the ponderomotive expulsion of electrons and the subsequent ion acceleration.

Sheath dynamics observed in a 13.56 MHz-driven plasma

We have established, through time correlated plasma emission and electrode and plasma potential measurements, that the near electrode emission observed in asymmetric capacitively coupled 13.56 MHz-driven hydrogen plasmas is caused by field reversal that leads to sheath collapse. Near-electrode emission has now been observed in Ar and He. The field reversal appears to be due to collision-induced electron drag. (C) 1997 American Institute of Physics.

ABSOLUTE DOUBLY DIFFERENTIAL CROSS-SECTIONS FOR ELECTRON-EMISSION IN COLLISIONS OF 3.5-MEV/U FE(17+) AND FE(22+) IONS WITH HE AND AR GAS TARGETS

Absolute doubly differential cross sections have been measured as a function of electron energy and angle of observation for electron emission in collisions of 3.5-MeV/u Fe17+ and Fe22+ ions with He and Ar gas targets under single-collision conditions. The measured electron emission cross sections are compared to theoretical and scaled cross sections based on the Born approximation. The results using intermediate-mass ions are discussed with reference to previously reported cross sections from collisions with highly charged lighter- and heavier-ion species at MeV/u projectile energies. The continuum-distorted-wave-eikonal-initial-state approximation shows good agreement with experiments except in the