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Open Access Publications from the University of California

Femtosecond Photoelectron Spectroscopy of the Dynamics of Electron Attachment and Photodissociation in Iodide-Nucleobase Clusters

  • Author(s): Kunin, Alice
  • Advisor(s): Neumark, Daniel M
  • et al.

DNA and RNA photodamage mechanisms are of significant importance but remain relatively poorly understood. The attachment of low-energy electrons to nucleic acid constituents has been shown to induce single and double strand breaks, although the mechanism of electron attachment and subsequent fragmentation remains debated. Nucleobases have been suggested to be the most likely target for attachment. The transient negative ions (TNIs) that form as a result of attachment have been implicated as important species in the damage mechanism. In addition, nucleobases exhibit strong photoabsorption cross-sections for UV light that may create a photoexcited species vulnerable to electron attachment. In vivo, local water molecules may stabilize TNIs and affect dissociation barriers, among other effects.

Time-resolved photoelectron spectroscopy (TRPES) of gas phase iodide-nucleobase clusters is a powerful tool to probe ultrafast reductive damage pathways in nucleic acid constituents. This femtosecond pump-probe technique employs an ultraviolet (UV) pump pulse to either initiate charge transfer from the iodide to the nucleobase or directly photoexcite the nucleobase species. A UV or infrared (IR) probe pulse can photodetach nascent transient negative ions (TNIs) or anionic photofragments to trace the ultrafast dynamics of TNI formation, decay, and cluster dissociation. In this thesis, we employ TRPES in conjunction with excited state calculations and photofragment action spectroscopy to probe the dynamics of electron attachment and photodissociation in a variety of iodide-nucleobase clusters, including iodide-uracil, iodide-uracil-water, and the simpler model system iodide-nitromethane.

Photofragment action spectroscopy and excited state calculations have revealed two distinct regimes of UV photoabsorption in iodide-nucleobase clusters: near the cluster vertical detachment energy (VDE) and near 4.8 eV. Near-VDE photoexcitation corresponds to optical excitation from an I(5p) orbital to form a dipole-bound (DB) anion, in which the excess electron is bound by the large dipole moment of the base. Photoexcitation from 4.6 - 5.2 eV is expected to correspond to base-centered pi-pi* photoexcitation of the nucleobase. In addition to DB anions, the canonical nucleobases are known to support conventional, valence-bound (VB) anionic states.

Like the canonical nucleobases, nitromethane (CH3NO2) also possesses a large dipole moment and is known to support both DB and VB anion states and thus serves as a valuable small molecule model for the dynamics in larger nucleobase species. TRPES of iodide-nitromethane clusters with a near-VDE photon energy UV pump pulse yields instantaneous formation of the iodide-nitromethane DB anion with complete or nearly complete conversion to form a VB state in 400 - 500 fs. The VB state exhibits bi-exponential decay in 2 ps and 1200 ps. A UV probe pulse measures the formation of iodide as the major dissociation channel of the cluster, with mono-exponential formation in approximately 20 ps. Rice-Ramsperger-Kassel-Marcus (RRKM) calculations to model the statistical unimolecular dissociation of the cluster predict dissociation to form iodide in only 300 fs. The lack of a charged intermediate decay state suggests that intramolecular vibrational energy redistribution (IVR) in the cluster is the rate-limiting step in the nonstatistical dissociation of the cluster.

TRPES of iodide-uracil binary clusters shows some similarities to iodide-nitromethane, with only partial DB to VB anion conversion following near-VDE photoexcitation likely due to the reversed energetic ordering of the two TNI states. In this pump energy regime, bi-exponential formation of iodide in 15 ps and 150 ps is measured and is expected to correspond to internal conversion and dissociation from each of the two relatively long-lived TNIs. Based on our TRPES results for iodide-nitromethane, we expect the long dissociation time constant to correspond to decay of the VB anion, with delayed dissociation due to inefficient IVR from vibrationally excited ring modes to the iodide---uracil stretch coordinate.

In the pi-pi* photoexcitation regime, the VB anion of the iodide-uracil complex is found to form instantaneously despite the lack of a direct optical excitation to form this state. No DB anion is detected in this pump regime. We have suggested that VB anion formation occurs by charge transfer from iodide to fill the empty hole in the pi orbital following base-centered excitation. Autodetachment decay signal is measured in this photoexcitation regime to be approximately commensurate with the prompt formation and decay of the VB state. Thus, we expect that the decay of the nascent VB state is by autodetachment. Iodide formation is measured to occur in 10s of ps, and we expect that cluster dissociation to form iodide likely occurs as a result of internal conversion of the pi-pi* photoexcited base.

The addition of a single water molecule to iodide-uracil is found to have two major effects: near-VDE photoexcitation yields a somewhat more pronounced DB to VB anion conversion in iodide-uracil-water than in iodide-uracil, and pi-pi* photoexcitation yields bi-exponential formation of iodide. In the near-VDE photoexcitation regime, the nascent DB anion may undergo relatively prompt water binding site reorientation to reach a conformer with a lower DB to VB anion conversion barrier resulting in delayed VB anion formation and thus more prominent conversion. Pi-pi* photoexcited iodide-uracil-water clusters may have other decay channels that can contribute to the bi-exponential formation of iodide such as the formation of iodide-water.

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