Barrier-free proton transfer in the valence anion of 2′-deoxyadenosine-5′-monophosphate. II. A computational study

Abstract

The propensity of four representative conformations of 2(')-deoxyadenosine-5(')-monophosphate (5(')-dAMPH) to bind an excess electron has been studied at the B3LYP6-31++G(d,p) level. While isolated canonical adenine does not support stable valence anions in the gas phase, all considered neutral conformations of 5(')-dAMPH form adiabatically stable anions. The type of an anionic 5(')-dAMPH state, i.e., the valence, dipole bound, or mixed (valence/dipole bound), depends on the internal hydrogen bond(s) pattern exhibited by a particular tautomer. The most stable anion results from an electron attachment to the neutral syn-south conformer. The formation of this anion is associated with a barrier-free proton transfer triggered by electron attachment and the internal rotation around the C4(')-C5(') bond. The adiabatic electron affinity of the a_south-syn anion is 1.19 eV, while its vertical detachment energy is 1.89 eV. Our results are compared with the photoelectron spectrum (PES) of 5(')-dAMPH(-) measured recently by Stokes et al., [J. Chem. Phys. 128, 044314 (2008)]. The computational VDE obtained for the most stable anionic structure matches well with the experimental electron binding energy region of maximum intensity. A further understanding of DNA damage might require experimental and computational studies on the systems in which purine nucleotides are engaged in hydrogen bonding.

Importance of Time Scale and Local Environment in Electron-Driven Proton Transfer. The Anion of Acetoacetic Acid

“…20 For example, the anion photoelectron spectrum of 2′-deoxyadenosine-5′-monophosphate 20 has been interpreted through intramolecular proton transfer from a hydroxyl group of the phosphate to the N3 position of the adenine. 21 Here, we present computational and experimental results on neutral and anionic acetoacetic acid (AA), see Figure 1 (bottom row). Acetoacetic acid is the simplest beta-keto acid and is thermodynamically unstable with respect to the decomposition to acetone and CO 2 .…”

Communication: Remarkable electrophilicity of the oxalic acid monomer: An anion photoelectron spectroscopy and theoretical study

“…The electrophilicity of these molecules is typically enhanced upon specific geometric distortions, including tautomerizations. 5,6 In consequence, valence anionic states are frequently characterized by positive values of electron vertical detachment energies (VDE), while adiabatic electron affinities (AEA) of the corresponding neutrals might remain negative (CO 2 5 ), approach zero (canonical uracil 7 ), or settle at positive values (unconventional tautomers of guanine 8,9 and adenine, 10 nucleotides 11,12 ). Here, we report a significant electrophilicity of the oxalic acid (OA) monomer.…”

Valence Anions of DNA-Related Systems in the Gas Phase: Computational and Anion Photoelectron Spectroscopy Studies

“…As a result, the feature observed in the photoelectron spectrum was attributed to the structure denoted as a_south-syn_VI (see Fig. 11.37) [92]. The a_south-syn_VI nucleotide is stabilized by two intramolecular hydrogen bonds, that is, (base)N3···HO(phosphate) and (sugar)3 0 OH···O(phosphate) bonds, the former featuring proton transfer from phosphate hydroxyl group to the N3 site of adenine.…”

“…•À was provided by Kobyłecka et al who employed the DFT model at the B3LYP/6-31++G(d,p) level [92]. The authors demonstrated that the four representative neutral conformations of dAMPH are able to bind electron forming adiabatically stable radical anions with AEAs within a range of 0.13-0.73 eV and of 0.2-0.9 eV in terms of AEA E and AEA G , respectively.…”

“…The anionic geometries and their singly occupied molecular orbital plots are presented in Fig. 11.36 [92]. It can be noted that the type of anionic state (the valence, dipole bound or mixed) depends on the internal hydrogen bonds arrangement.…”