Ionization Energies of Aqueous Nucleic Acids: Photoelectron Spectroscopy of Pyrimidine Nucleosides and ab Initio Calculations

Abstract

Vertical ionization energies of the nucleosides cytidine and deoxythymidine in water, the lowest ones amounting in both cases to 8.3 eV, are obtained from photoelectron spectroscopy measurements in aqueous microjets. Ab initio calculations employing a nonequilibrium polarizable continuum model quantitatively reproduce the experimental spectra and provide molecular interpretation of the individual peaks of the photoelectron spectrum, showing also that lowest ionization originates from the base. Comparison of calculated vertical ionization potentials of pyrimidine bases, nucleosides, and nucleotides in water and in the gas phase underlines the dramatic effect of bulk hydration on the electronic structure. In the gas phase, the presence of sugar and, in particular, of phosphate has a strong effect on the energetics of ionization of the base. Upon bulk hydration, the ionization potential of the base in contrast becomes rather insensitive to the presence of the sugar and phosphate, which indicates a remarkable screening ability of the aqueous solvent. Accurate aqueous-phase vertical ionization potentials provide a significant improvement to the corrected gas-phase values used in the literature and represent important information in assessing the threshold energies for photooxidation and oxidation free energies of solvent-exposed DNA components. Likewise, such energetic data should allow improved assessment of delocalization and charge-hopping mechanisms in DNA ionized by radiation.

Exploring the Aqueous Vertical Ionization of Organic Molecules by Molecular Simulation and Liquid Microjet Photoelectron Spectroscopy

“…The data in the present manuscript is based on a single conformer that does not exhibit an intramolecular H-bond from the sugar to thymine, in analogy to a previous study on the photoelectron spectra of thymidine. 26 H-bonding to the thymine unit is expected to raise the VIE (see Figure 10 and related discussion), and the VIE gas reported here represents a lower bound. Considering the proximity in energy of conformations with and without intramolecular H-bond, 88 the true VIE gas may be as much as ≈0.15 eV higher in energy than the 8.74 eV reported in Table 1.…”

Base-Specific Ionization of Deprotonated Nucleotides by Resonance Enhanced Two-Photon Detachment

“…31 In aqueous solution the adiabatic ionization energy of the base in the two nucleosides studied decreases by ~2 eV relative to that of the gas phase base. 26 This shift arises almost entirely from solvent reorganzition following base ionization, both locally 29,[62][63][64][65] and due to a more extensive rearrangement. 26,30 Our measurements indicate that the charged phosphate decreases the ionization energy of the base by ~3 eV (see Table 1) through strong Coulomb interactions with the base.…”

“…Coulombic interaction is completely screened 26,30 such that the adiabatic ionization energy of that in solution is effectively that of the base only.…”

“…[20][21][22][23][24][25] In the solution phase, ionization potentials have been determined using PE spectroscopy on liquid microjets 26 and with ab initio [27][28][29][30] or semiempirical calculations. 31,32 Building on the gas phase work, the PE spectroscopy of isolated nucleotides and oligonucleotides has recently been studied by the Wang group with the aim of understanding how the ionization energy changes with the introduction of the sugar and phosphate backbone.…”

A VUV Photoionization and Ab Initio Determination of the Ionization Energy of a Gas-Phase Sugar (Deoxyribose)

“…There is one report in the literature of a 10.5 eV ionization energy measured using electron ionization, 4 and a few theoretical calculations present numbers around this value. [5][6][7][8] This is a surprisingly high value for a molecule that contains oxygen in a ring structure. Similar molecules such as tetrahydrofuran have ionization energies much lower, and there is near perfect agreement between theory and experiment for that molecule.…”