Recent Publications

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  1. Title: Electron-induced hydrogen loss in uracil in a water cluster environment

    Author(s): Smyth M., Kohanoff J., Fabrikant I.I.

    Journal of Chemical Physics, 140, pp. 184313- (12 May 2014)

    doi: 10.1063/1.4874841

    Low-energy electron-impact hydrogen loss due to dissociative electron attachment (DEA) to the uracil and thymine molecules in a water cluster environment is investigated theoretically. Only the A′-resonance contribution, describing the near-threshold behavior of DEA, is incorporated. Calculations are based on the nonlocal complex potential theory and the multiple scattering theory, and are performed for a model target with basic properties of uracil and thymine, surrounded by five water molecules. The DEA cross section is strongly enhanced when the attaching molecule is embedded in a water cluster. This growth is due to two effects: the increase of the resonance lifetime and the negative shift in the resonance position due to interaction of the intermediate negative ion with the surrounding water molecules. A similar effect was earlier found in DEA to chlorofluorocarbons.

  2. Title: Protection of DNA against low-energy electrons by amino acids: a first-principles molecular dynamics study

    Author(s): Gu B., Smyth M., Kohanoff J.

    Physical Chemistry Chemical Physics, 16, pp. 24350-24358 (2014)

    doi: 10.1039/C4CP03906H

  3. Title: Excess Electron Interactions with Solvated DNA Nucleotides: Strand Breaks Possible at Room Temperature

    Author(s): Smyth M., Kohanoff J.J.,

    Journal of the American Chemical Society, 134, pp. 9122-9125 (18 May 2012)

    doi: 10.1021/ja303776r

    When biological matter is subjected to ionizing radiation, a wealth of secondary low-energy (<20 eV) electrons are produced. These electrons propagate inelastically, losing energy to the medium until they reach energies low enough to localize in regions of high electron affinity. We have recently shown that in fully solvated DNA fragments, nucleobases are particularly attractive for such excess electrons. The next question is what is their longer-term effect on DNA. It has been advocated that they can lead to strand breaks by cleavage of the phosphodiester C3′–O3′ bond. Here we present a first-principles study of free energy barriers for the cleavage of this bond in fully solvated nucleotides. We have found that except for dAMP, the barriers are on the order of 6 kcal/mol, suggesting that bond cleavage is a regular feature at 300 K. Such low barriers are possible only as a result of solvent and thermal fluctuations. These findings support the notion that low-energy electrons can indeed lead to strand breaks in DNA.

  4. Title: Excess Electron Localization in Solvated DNA Bases

    Author(s): Smyth M., Kohanoff J.J,

    Physical Review Letters, 106, pp. 238108- (June 10 2011)

    doi: 10.1103/PhysRevLett.106.238108

    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.

  5. Title: Electron detachment from negative ions in a short laser pulse

    Author(s): Shearer S. F. C. , Smyth M., and Gribakin G. F.

    Physical Review A, 84, pp. 033409- (12 September 2011)

    doi: 10.1103/PhysRevA.84.033409

    We present an efficient and accurate method to study electron detachment from negative ions by a few-cycle linearly polarized laser pulse. The adiabatic saddle-point method of Gribakin and Kuchiev [ Phys. Rev. A 55 3760 (1997)] is adapted to calculate the transition amplitude for a short laser pulse. Its application to a pulse with N optical cycles produces 2(N+1) saddle points in complex time, which form a characteristic “smile.” Numerical calculations are performed for H− in a 5-cycle pulse with frequency 0.0043 a.u. and intensities of 1010, 5×1010, and 1011 W/cm2, and for various carrier-envelope phases. We determine the spectrum of the photoelectrons as a function of both energy and emission angle, as well as the angle-integrated energy spectra and total detachment probabilities. Our calculations show that the dominant contribution to the transition amplitude is given by 5–6 central saddle points, which correspond to the strongest part of the pulse. We examine the dependence of the photoelectron angular distributions on the carrier-envelope phase and show that measuring such distributions can provide a way of determining this phase.