Photoelectron Spectroscopy and Theoretical Investigations of Gaseous Doubly Deprotonated 2′-Deoxynucleoside 5′-Monophosphate Dianions

Abstract

A better understanding of the mechanism of oxidative DNA damage requires obtaining a molecular level description of nucleotides in various charge states. Herein, we report a systematic photoelectron spectroscopy and theoretical investigation of the electronic and geometric structures of four doubly deprotonated 2′-deoxynucleoside 5′-monophosphate dianions, the smallest quintessential DNA building block. These dianions are intrinsically stable with their adiabatic/vertical detachment energies (ADE/VDE) ranging from 0.85/1.07 (A) and 1.05/1.30 (G) to 1.20/1.50 (C) and 1.80/2.10 eV (T). The repulsive Coulomb barrier against electron detachment is 2.0 eV for purines and 2.5 eV for pyrimidines. Dianions are deprotonated at the phosphate group and the amino group of a nucleobase. The πtype HOMO orbital resides on the nucleobase moiety for each dianion. This spatial distribution of HOMO suggests that the most loosely bound electron is detached along the direction perpendicular to the nucleobase. When combined with the previous results, this work makes complete the depiction of basic building blocks of DNA at the molecular level.

Guanosine Dianions Hydrated by One to Four Water Molecules

“… The 20 K NIPE spectra of [dGMP – 2H] 2– · n H 2 O ( n = 1–4) (red) and [dGMP – 2H] 2– (blue, ref ( 14 )) at 157 nm (7.866 eV) (left panel) and the most stable conformations of particular clusters having VDE and ADE characteristics that reproduce the measured values (right panel). The dashed line serves as an eye-guide for the increasing trend of the VDEs as the number of water molecules increases from 0 to 4.…”

“… 6 − 14 As such, a broad range of knowledge on isolated nucleotides in various charge states, that is, neutral, [dNMP], deprotonated or radical anions, [dNMP – H] − /[dNMP] •– , and double-deprotonated dianions [dNMP – 2H] 2– (N = A, G, C, or T), including their geometric and electronic structures, as well as the mechanisms of indirect and direct electron detachments, has been established. 6 , 7 , 14 …”

“…Moreover, doubly deprotonated 2′-deoxynucleoside 5′-monophosphate dianions, which possesses two charged sites to bind to the H 2 O molecule, were recently found to be stable in the gas phase and bring further challenges toward the analysis of binding with H 2 O molecules. 14 …”

“…Figure 1 exhibits the 20 K negative ion photoelectron (NIPE) spectra of [dGMP – 2H] 2– · n H 2 O ( n = 1–4) (red) recorded at 157 nm (7.866 eV) and the comparison to previously recorded [dGMP – 2H] 2– (blue 14 ) spectrum (for experimental details see section 1.1 of the Supporting Information ). The spectra of microsolvated clusters possess similar patterns to that of the [dGMP – 2H] 2– anion, 14 which are composed of a distinct low-intensity band followed by a series of more intense highly congested bands.…”

“…According to our previous studies, guanosine phosphate deprotonates at the guanine amine and phosphate group, producing dianionic [dGMP – 2H] 2– system, where negative charges are maximally separated, that is, they are localized on the phosphate group and on the purine moiety (see Scheme 1 ). 14 Therefore, it could be expected that polar water molecules attach to [dGMP – 2H] 2– , either close to the deprotonated phosphate group or close to the purine ring, interacting with the deprotonated N10 nitrogen. Indeed, we can observe such localization of water molecules in all the optimized [dGMP – 2H] 2– ·H 2 O geometries (see Figure 2 ).…”