Valence Anions of 9-Methylguanine−1-Methylcytosine Complexes. Computational and Photoelectron Spectroscopy Studies

Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials

Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.

Electron Attachment to Wobble Base Pairs

We have analyzed the low-energy electron attachment to wobble base pairs using the equation of motion coupled cluster method and extended basis sets. A doorway mechanism exists for the attachment of the additional electron to the base pairs, where the initially formed dipole-bound anion captures the incoming electron. The doorway dipole-bound anionic state subsequently leads to the formation of a valence-bound state, and the transfer of extra electron occurs by mixing of electronic and nuclear degrees of freedom. The formation of the valence-bound anion is associated with proton transfer in hypoxanthine-cytosine and hypoxanthine-adenine base pairs, which happens through a concerted electron-proton transfer process. The calculated rate constant for the dipole-bound to valence-bound transition in wobble base pairs is slower than that observed in the Watson-Crick guanine-cytosine base pair.

Flying DNA Cation Radicals in the Gas Phase: Generation and Action Spectroscopy of Canonical and Noncanonical Nucleobase Forms

Gas-phase chemistry of cation radicals related to ionized nucleic acids has enjoyed significant recent progress thanks to the development of new methods for cation radical generation, ion spectroscopy, and reactivity studies. Oxidative methods based on intramolecular electron transfer in transition-metal complexes have been used to generate nucleobase and nucleoside cation radicals. Reductive methods relying on intermolecular electron transfer in gas-phase ion-ion reactions have been utilized to generate a number of di- and tetranucleotide cation radicals, as well as charge-tagged nucleoside radicals. The generated cation radicals have been studied by infrared and UV-visible action spectroscopy and ab initio and density functional theory calculations, providing optimized structures, harmonic frequencies, and excited-state analysis. This has led to the discovery of stable noncanonical nucleobase cation radicals of unusual electronic properties and extremely low ion-electron recombination energies. Intramolecular proton-transfer reactions in cation radical oligonucleotides and Watson-Crick nucleoside pairs have been studied experimentally, and their mechanisms have been elucidated by theory. Whereas the range of applications of the oxidative methods is currently limited to nucleobases and readily oxidizable guanosine, the reductive methods can be scaled up to generate large oligonucleotide cation radicals including double-strand DNA. Challenges in the experimental and computational approach to DNA cation radicals are discussed.

Tackling a Curious Case: Generation of Charge-Tagged Guanosine Radicals by Gas-Phase Electron Transfer and Their Characterization by UV-vis Photodissociation Action Spectroscopy and Theory

We report the generation of gas-phase riboguanosine radicals that were tagged at ribose with a fixed-charge 6-(trimethylammonium)hexane-1-aminocarbonyl group. The radical generation relied on electron transfer from fluoranthene anion to noncovalent dibenzocrown-ether dication complexes which formed nucleoside cation radicals upon one-electron reduction and crown-ether ligand loss. The cation radicals were characterized by collision-induced dissociation (CID), photodissociation (UVPD), and UV-vis action spectroscopy. Identification of charge-tagged guanosine radicals was challenging because of spontaneous dissociations by loss of a hydrogen atom and guanine that occurred upon storing the ions in the ion trap without further excitation. The loss of H proceeded from an exchangeable position on N-7 in guanine that was established by deuterium labeling and was the lowest energy dissociation of the guanosine radicals according to transition-state energy calculations. Rate constant measurements revealed an inverse isotope effect on the loss of either hydrogen or deuterium with rate constants k_H = 0.25-0.26 s^-1 and k_D = 0.39-0.54 s^-1. We used time-dependent density functional theory calculations, including thermal vibronic effects, to predict the absorption spectra of several protomeric radical isomers. The calculated spectra of low-energy N-7-H guanine-radical tautomers closely matched the action spectra. Transition-state-theory calculations of the rate constants for the loss of H-7 and guanine agreed with the experimental rate constants for a narrow range of ion effective temperatures. Our calculations suggest that the observed inverse isotope effect does not arise from the isotope-dependent differences in the transition-state energies. Instead, it may be caused by the dynamics of post-transition-state complexes preceding the product separation.

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

Intramolecular proton-transfers (prototropic conversions) have been studied for the guanine building block isocytosine (iC), and effects of positive ionization, called one-electron oxidation (iC - e → iC^+•), and negative ionization, called one-electron reduction (iC + e → iC^-•), on tautomeric conversions when proceeding from neutral to ionized isocytosine have been discussed. Although radical cations and radical anions are very short-lived species, the ionization effects could be investigated by quantum-chemical methods. Such kind of studies gives some information about the labile protons and the most basic positions in the neutral and radical forms of the tautomeric system. For investigations, the complete isomeric mixture of isocytosine has been considered and calculations performed in two extreme environments, apolar {DFT(B3LYP)/6-311+G(d,p)} and polar {PCM(water)//DFT(B3LYP)/6-311+G(d,p)}. For selected isomers, the G4 theory has also been applied. There are no good relations for energetic parameters of neutral and ionized forms. Ionization energies depend on localization of labile protons. Tautomeric equilibria for neutral and ionized isocytosine, favored sites of protonation and deprotonation, and favored structures of protonated and deprotonated forms strongly depend on environment. Acidity of iC^+• is close to that of the iC conjugate acid, and basicity of iC^-• is close to that of the iC conjugate base. This increase of acid-base properties of charged radicals explains the proton-transfer in ionized pairs of nucleobases. When compared to other pyrimidine bases such as uracil (U) and cytosine (C), which exhibit analogous tautomeric equilibria between nine prototropic tautomers as isocytosine, the tautomeric preferences for iC, iC^+•, iC^-•, U, U^+•, U^-•, C, C^+•, and C^-• are completely different. The differences suggest that acid-base properties of functional groups, their stabilities, and ionization energies play a principal role in proton-transfers for pyrimidine bases and influence compositions of tautomeric mixtures.

Negative ion photoelectron spectra of ISO3-, IS2O3-, and IS2O4- intermediates formed in interfacial reactions of ozone and iodide/sulfite aqueous microdroplets

Three short-lived, anionic intermediates, ISO₃^-, IS₂O₃^-, and IS₂O₄^-, are detected during reactions between ozone and aqueous iodine/sulfur oxide microdroplets. These species may play an important role in ozone-driven inorganic aerosol formation; however their chemical properties remain largely unknown. This is the issue addressed in this work using negative ion photoelectron spectroscopy (NIPES) and ab initio modeling. The NIPE spectra reveal that all of the three anionic species are characterized by high adiabatic detachment energies (ADEs) - 4.62 ± 0.10, 4.52 ± 0.10, and 4.60 ± 0.10 eV for ISO₃^-, IS₂O₃^-, and IS₂O₄^-, respectively. Vibrational progressions with frequencies assigned to the S-O symmetric stretching modes are discernable in the ground state transition features. Density functional theory calculations show the presence of several low-lying isomers involving different bonding scenarios. Further analysis based on high level CCSD(T) calculations reveal that the lowest energy structures are characterized by the formation of I-S and S-S bonds and can be structurally viewed as SO₃ linked with I, IS, and ISO for ISO₃^-, IS₂O₃^-, and IS₂O₄^-, respectively. The calculated ADEs and vertical detachment energies are in excellent agreement with the experimental results, further supporting the identified minimum energy structures. The obtained intrinsic molecular properties of these anionic intermediates and neutral radicals should be useful to help understand their photochemical reactions in the atmosphere.

Effects of ionization on stability of 1-methylcytosine - DFT and PCM studies

Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (MC)—a model of the nucleobase cytosine (C) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of exo heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized MC. Its contribution in neutral and negatively ionized MC is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral MC. Gas-phase acidity of radical cations is close to that of the conjugate acid of MC, and gas-phase basicity of radical anions is close to that of the conjugate base of MC. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in MC is close to that in the parent system—formamidine.

The onset of electron-induced proton-transfer in hydrated azabenzene cluster anions

The prospect that protons from water may be transferred to N-heterocyclic molecules due to the presence of an excess electron is studied in hydrated azabenzene cluster anions using spectroscopy and computational chemistry.

DFT reinvestigation of DNA strand breaks induced by electron attachment

The benchmark study of DFT methods on the activation energies of phosphodiester C3'-O and C5'-O bond ruptures and glycosidic C1'-N bond ruptures induced by electron attachment was performed. While conventional pure and hybrid functionals provide a relatively reasonable description for the C1'-N bond rupture, they significantly underestimate the energy barriers of the C-O bond ruptures. This is because the transition states of the later reactions, which are characterized by an electron distribution delocalized from the nucleobase to sugar-phosphate backbone, suffer from a severe self-interaction error in common DFT methods. CAM-B3LYP, M06-2X, and ωB97XD are the top three methods that emerged from the benchmark study; the mean absolute errors relative to the CCSD(T) values are 1.7, 1.9, and 2.2 kcal/mol, respectively. The C-O bond cleavages of 3'- and 5'-dXMP(•-), where X represents four nucleobases, were then recalculated at the M06-2X/6-31++G**//M06-2X/6-31+G* level, and it turned out that the C-O bond cleavages do not proceed as easily as previously predicted by the B3LYP calculations. Our calculations revealed that the C-O bonds of purine nucleotides are more susceptible than pyrimidine nucleotides to the electron attachment. The energies of electron attachment to nucleotides were calculated and discussed as well.

Electron attachment to the guanine-cytosine nucleic acid base pair and the effects of monohydration and proton transfer

The guanine-cytosine (GC) radical anion and its interaction with a single water molecule is studied using ab initio and density functional methods. Z-averaged second-order perturbation theory (ZAPT2) was applied to GC radical anion for the first time. Predicted spin densities show that the radical character is localized on cytosine. The Watson-Crick monohydrated GC anion is compared to neutral GC·H2O, as well as to the proton-transferred analogue on the basis of structural and energetic properties. In all three systems, local minima are identified that correspond to water positioned in the major and minor grooves of macromolecular DNA. On the anionic surface, two novel structures have water positioned above or below the GC plane. On the neutral and anionic surfaces, the global minimum can be described as water interacting with the minor groove. These structures are predicted to have hydration energies of 9.7 and 11.8 kcal mol(-1), respectively. Upon interbase proton-transfer (PT), the anionic global minimum has water positioned in the major groove, and the hydration energy increases to 13.4 kcal mol(-1). PT GC·H2O(•-) has distonic character; the radical character resides on cytosine, while the negative charge is localized on guanine. The effects of proton transfer are further investigated through the computed adiabatic electron affinities (AEA) of GC and monohydrated GC, and the vertical detachment energies (VDE) of the corresponding anions. Monohydration increases the AEAs and VDEs by only 0.1 eV, while proton-transfer increases the VDEs substantially (0.8 eV). The molecular charge distribution of monohydrated guanine-cytosine radical anion depends heavily on interbase proton transfer.

Valence anions of N-acetylproline in the gas phase: computational and anion photoelectron spectroscopic studies

We report the photoelectron spectrum of anionic N-acetylproline, (N-AcPro)(-), measured with 3.49 eV photons. This spectrum, which consists of a band centered at an electron binding energy of 1.4 eV and a higher energy spectral tail, confirms that N-acetylproline forms a valence anion in the gas phase. The neutrals and anions of N-AcPro were also studied computationally at the B3LYP∕6-31++G(d,p) level. Based on the calculations, we conclude that the photoelectron spectrum is due to anions which originated from proton transfer induced by electron attachment to the π* orbital localized at the acetyl group of N-AcPro. We also characterized the energetics of reaction paths leading to pyrrolidine ring opening in the anionic N-AcPro. These data suggest that electron induced decomposition of peptides/proteins comprising proline strongly depends on the presence of proton donors in the close vicinity to the proline residue.

Stability of the valence anion of cytosine is governed by nucleobases sequence in the double stranded DNA pi-stack: A computational study

The stabilities of the valence anion of cytosine (C(-)) in model trimers of complementary base pairs that possess the B-DNA geometry but differ in base sequence are reported. In order to estimate the energetics of electron attachment to the middle cytosine incorporated in the trimer, a thermodynamic cycle employing all possible two-body interaction energies in the neutral and anionic duplex as well as the adiabatic electron affinity of isolated cytosine were developed. All calculations were carried out at the MP2 level of theory with the aug-cc-pVDZ basis set. We have demonstrated that contrary to the literature reports, concerning single stranded DNA, the sequence of nucleic bases has a profound effect on the stability of the cytosine valence anion. The anionic 3(')-CCC-5(') complex is the most stable configuration (EA=0.399 eV) and the 3(')-GCG-5(') trimer anion is the most unstable species (EA=-0.193 eV). Moreover, with the energetic correction for the presence of sugar-phosphate backbone all possible double stranded DNA sequences lead to the stable C(-). The predicted electron affinities of the cytosine anion have been compared to the results of analogous studies on the thymine anion published recently [M. Kobyłecka et al., J. Am. Chem. Soc. 130, 15683 (2008)]. The consequences of low-energy barrier proton transfer in the GC anion have been discussed in the context of induced by electrons DNA single strand breaks. The DNA sequences that should dramatically differ in their vulnerability to be damaged by low energy electrons have been proposed.