Adenine radicals in the gas phase: an experimental and computational study of hydrogen atom adducts to adenine

Structural Characterization of the Metalized Radical Cations of Adenosine ([Ade+Li-H]•+ and [Ade+Na-H]•+) by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Studies

Nucleoside radicals are key intermediates in the process of DNA damage, and alkali metal ions are a common group of ions in living organisms. However, so far, there has been a significant lack of research on the structural effects of alkali metal ions on nucleoside free radicals. In this study, we report a new method for generating metalized nucleoside radical cations in the gas phase. The radical cations [Ade+M-H]•+ (M = Li, Na) are generated by the 280 nm ultraviolet photodissociation (UVPD) of the precursor ions of lithiated and sodiated ions of 2-iodoadenine in a Fourier transform ion cyclotron resonance (FT ICR) cell. Further infrared multiphoton dissociation (IRMPD) spectra of both radical cations were recorded in the region of 2750-3750 cm-1. By combining these results with theoretical calculations, the most stable isomers of both radicals can be identified, which share the common characteristics of triple coordination patterns of the metal ions. For both radical species, the lowest-energy isomers undergo hydrogen transfer. Although the sugar ring in the most stable isomer of [Ade+Li-H]•+ is in a (South, syn) conformation similar to that of [Ado+Na]+, [Ade+Na-H]•+ is distinguished by the unexpected opening of the sugar ring. Their theoretical spectra are in good agreement with experimental spectra. However, due to the flexibility of the structures and the complexity of their potential energy surfaces, the hydrogen transfer pathways still need to be further studied. Considering that the free radicals formed directly after C-I cleavage have some similar spectral characteristics, the existence of these corresponding isomers cannot be ruled out. The findings imply that the structures of nucleoside radicals may be significantly influenced by the attached alkali metal ions. More detailed experiments and theoretical calculations are still crucial.

Capturing Hydrogen Radicals by Neutral Metal Hydroxides

Capturing the hydrogen radical is of central importance in various systems ranging from catalysis to biology to astronomy, but it has been proven to be challenging experimentally because of its high reactivity and short lifetime. Here, neutral MO₃H₄ (M = Sc, Y, La) complexes were characterized by size-specific infrared-vacuum ultraviolet spectroscopy. All these products were determined to be the hydrogen radical adducts in the form of H•M(OH)₃. The results indicate that the addition of the hydrogen radical to the M(OH)₃ complex is both thermodynamically exothermic and kinetically facile in the gas phase. Moreover, the soft collisions in the cluster growth channel with the helium expansion were found to be demanded for the formation of H•M(OH)₃. This work highlights the pivotal roles played by the soft collisions in the formation of hydrogen radical adducts and also opens new avenues toward the design and chemical control of compounds.

The DNA Radical Code. Resolution of Identity in Dissociations of Trinucleotide Codon Cation Radicals in the Gas Phase

Sixty DNA trinucleotide cation radicals covering a large part of the genetic code alphabet were generated by electron transfer in the gas phase, and their chemistry was studied by collision-induced dissociation tandem mass spectrometry and theoretical calculations. The major dissociations involved loss of nucleobase molecules and radicals, backbone cleavage, and cross-ring fragmentations that depended on the nature and position of the nucleobases. Mass identity in dissociations of symmetrical trinucleotide cation radicals of the (XXX+2H)^+• and (XYX+2H)^+• type was resolved by specific ¹⁵N labeling. The specific features of trinucleotide cation radical dissociations involved the dominant formation of d₂⁺ ions, hydrogen atom migrations accompanying the formation of (w₂+H)^+•, (w₂+2H)⁺, and (d₂+2H)⁺ sequence ions, and cross-ring cleavages in the 3'- and 5'-deoxyribose moieties that depended on the nucleobase type and its position in the ion. Born-Oppenheimer molecular dynamics (BOMD) and density functional theory calculations were used to obtain structures and energies of several cation-radical protomers and conformers for (AAA+2H)^+•, (CCC+2H)^+•, (GGG+2H)^+•, (ACA+2H)^+•, and (CAA+2H)^+• that were representative of the different types of backbone dissociations. The ion electronic structure, protonation and radical sites, and hydrogen bonding were used to propose reaction mechanisms for the dissociations.

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.

Hydrogen-Atom Addition to Nucleobases in the Solid State: Characterization of the Corresponding Muoniated Radicals Using μSR

The radicals formed by muonium (Mu) addition to four nucleobases (adenine, guanine, cytosine, and thymine) have been characterized by avoided level-crossing muon spin resonance (ALC-μSR). Mu is considered to be a light isotope of the hydrogen atom, and the muoniated radicals observed by ALC-μSR are isotopomers of the radicals initially produced by H addition to the nucleobases. The observed radicals have been assigned by considering the relative energies of the possible radicals reported in the literature and comparing the experimental muon and proton hyperfine coupling constants with values from previously reported electron paramagnetic resonance and ab initio calculations that have been scaled to account for the larger magnetic moment of the muon and its lighter mass compared with the proton. Mu addition is observed to occur only at secondary carbons of the purine rings in adenine and guanine. Mu adds to C8 and C2 of adenine with the relative amount being ∼70:30%, and Mu adds exclusively to C8 of guanine. Mu addition is predominantly to the secondary carbons of the pyrimidine ring in cytosine (C5 and C6 with relative yields ∼80:20%) with a small amount of addition at N3. Mu adds to both the secondary C6 and tertiary C5 in thymine with approximately equal yields as well as the O4 adduct being a minor product.

UV-Vis Action Spectroscopy Reveals a Conformational Collapse in Hydrogen-Rich Dinucleotide Cation Radicals

We report the generation of deoxyriboadenosine dinucleotide cation radicals by gas-phase electron transfer to dinucleotide dications and their noncovalent complexes with crown ether ligands. Stable dinucleotide cation radicals of a novel hydrogen-rich type were generated and characterized by tandem mass spectrometry and UV-vis photodissociation (UVPD) action spectroscopy. Electron structure theory analysis indicated that upon electron attachment the dinucleotide dications underwent a conformational collapse followed by intramolecular proton migrations between the nucleobases to give species whose calculated UV-vis absorption spectra matched the UVPD action spectra. Hydrogen-rich cation radicals generated from chimeric riboadenosine 5'-diesters gave UVPD action spectra that pointed to novel zwitterionic structures consisting of aromatic π-electron anion radicals intercalated between stacked positively charged adenine rings. Analogies with DNA ionization are discussed.

The protonated guanine-cytosine base pair

Protonated base pairs were recently implicated in the context of DNA proton transfer and charge migration. The effects of protonating different sites of the guanine-cytosine (GC) base pair are studied here by using the DZP++ B3LYP density functional method. Optimized structures for the protonated GC base pair are compared with those of parent GC and the neutral hydrogenated GC radical (GCH). Proton and hydrogen-atom additions significantly disturb the structure of the GC base pair. However, the structural perturbations arising from protonation are often less than those arising from hydrogenation of GC. Protonation of the GC base pair causes significant strengthening of the interstrand hydrogen bonds and a concomitant increase in the base dissociation energies. The adiabatic ionization potentials (AIPs), vertical ionization potentials (VIPs), and proton affinities (PAs) for the different protonation sites of the GC base pair are predicted. The N7 site of guanine is the preferred site for protonation of the GC base pair.

The ion funnel: theory, implementations, and applications

The electrodynamic ion funnel has enabled the manipulation and focusing of ions in a pressure regime (0.1-30 Torr) that has challenged traditional approaches, and provided the basis for much greater mass spectrometer ion transmission efficiencies. The initial ion funnel implementations aimed to efficiently capture ions in the expanding gas jet of an electrospray ionization interface and radially focus them for efficient transfer through a conductance limiting orifice. We review the improvements in fundamental understanding of ion motion in ion funnels, the evolution in its implementations that have brought the ion funnel to its current state of refinement, as well as applications of the ion funnel for purposes such as ion trapping, ion cooling, low pressure electrospray, and ion mobility spectrometry.

On the hydrogen loss from protonated nucleobases after electronic excitation or collisional electron capture

In this work, we have subjected protonated nucleobases MH(+) (M = guanine, adenine, thymine, uracil and cytosine) to a range of experiments that involve high-energy (50 keV) collision induced dissociation and electron capture induced dissociation. In the latter case, both neutralisation reionisation and charge reversal were done. For the collision induced dissociation experiments, the ions interacted with O(2). In neutral reionisation, caesium atoms were used as the target gas and the protonated nucleobases captured electrons to give neutrals. These were reionised to cations a microsecond later in collisions with O(2). In choosing Cs as the target gas, we have assured that the first electron transfer process is favourable (by about 0.1-0.8 eV depending on the base). In the case of protonated adenine, charge reversal experiments (two Cs collisions) were also carried out, with the results corroborating those from the neutralisation reionisation experiments. We find that while collisional excitation of protonated nucleobases in O(2) may lead to hydrogen loss with limited probabilities, this channel becomes dominant for electron capture events. Indeed, when sampling reionised neutrals on a microsecond timescale, we see that the ratio between MH(+) and M(+) is 0.2-0.4 when one electron is captured from Cs. There are differences in these ratios between the bases but no obvious correlation with recombination energies was found.

Electron attachment to the hydrogenated Watson-Crick guanine cytosine base pair (GC+H): conventional and proton-transferred structures

The anionic species resulting from hydride addition to the Watson-Crick guanine-cytosine (GC) DNA base pair are investigated theoretically. Proton-transferred structures of GC hydride, in which proton H1 of guanine or proton H4 of cytosine migrates to the complementary base-pair side, have been studied also. All optimized geometrical structures are confirmed to be minima via vibrational frequency analyses. The lowest energy structure places the additional hydride on the C6 position of cytosine coupled with proton transfer, resulting in the closed-shell anion designated 1T (G(-)C(C6)). Energetically, the major groove side of the GC pair has a greater propensity toward hydride/hydrogen addition than does the minor grove side. The pairing (dissociation) energy and electron-attracting ability of each anionic structure are predicted and compared with those of the neutral GC and the hydrogenated GC base pairs. Anion 8T (G(O6)C(-)) is a water-extracting complex and has the largest dissociation energy. Anion 2 (GC(C4)(-)) and the corresponding open-shell radical GC(C4) have the largest vertical electron detachment energy and adiabatic electron affinity, respectively. From the difference between the dissociation energy and electron-removal ability of the normal GC anion and the most favorable structure of GC hydride, it is clear that one may dissociate the GC anion and maintain the integrity of the GC hydride.

Electron capture in spin-trap capped peptides. An experimental example of ergodic dissociation in peptide cation-radicals

Electron capture dissociation was studied with tetradecapeptides and pentadecapeptides that were capped at N-termini with a 2-(4'-carboxypyrid-2'-yl)-4-carboxamide group (pepy), e.g., pepy-AEQLLQEEQLLQEL-NH(2), pepy-AQEFGEQGQKALKQL-NH(2), and pepy-AQEGSEQAQKFFKQL-NH(2). Doubly and triply protonated peptide cations underwent efficient electron capture in the ion-cyclotron resonance cell to yield charge-reduced species. However, the electron capture was not accompanied by backbone dissociations. When the peptide ions were preheated by absorption of infrared photons close to the dissociation threshold, subsequent electron capture triggered ion dissociations near the remote C-terminus forming mainly (b(11-14) + 1)(+)* fragment ions that were analogous to those produced by infrared multiphoton dissociation alone. Ab initio calculations indicated that the N-1 and N-1' positions in the pepy moiety had topical gas-phase basicities (GB = 923 kJ mol(-1)) that were greater than those of backbone amide groups. Hence, pepy was a likely protonation site in the doubly and triply charged ions. Electron capture in the protonated pepy moiety produced the ground electronic state of the charge-reduced cation-radical with a topical recombination energy, RE = 5.43-5.46 eV, which was greater than that of protonated peptide residues. The hydrogen atom in the charge-reduced pepy moiety was bound by >160 kJ mol(-1), which exceeded the hydrogen atom affinity of the backbone amide groups (21-41 kJ mol(-1)). Thus, the pepy moiety functioned as a stable electron and hydrogen atom trap that did not trigger radical-type dissociations in the peptide backbone that are typical of ECD. Instead, the internal energy gained by electron capture was redistributed over the peptide moiety, and when combined with additional IR excitation, induced proton-driven ion dissociations which occurred at sites that were remote from the site of electron capture. This example of a spin-remote fragmentation provided the first clear-cut experimental example of an ergodic dissociation upon ECD.

Modeling deoxyribonucleic acid and ribonucleic acid damage in the gas phase

This short review outlines the tandem mass spectrometric methods for the generation and analysis of transient nucleobase radicals relevant to deoxyribonucleic acid and ribonucleic acid damage. Radical hydrogen atom adducts to uracil, adenine, cytosine and N-methylcytosine were generated by femtosecond electron transfer to the corresponding gas-phase cations in fast beams at 8 keV kinetic energy. Radical unimolecular dissociations were monitored by product analysis following collisional ionization to cations or anions using neutralization-reionization mass spectrometry. The radical energetics and dissociation kinetics were further analyzed by mapping the potential energy surfaces by high-level ab initio calculations in combination with Rice-Remsberger-Kassel-Marcus calculations of unimolecular rate constants. This first- principles-based approach allows one to model radical dissociations occurring from doublet ground electronic states of radical intermediates, assign reaction mechanisms and derive quantitative branching ratios for dissociation channels that are in agreement with experiments. Theoretical analysis also provides distinction between radical dissociations occurring on the ground and excited electronic state potential energy surfaces. Specific characterization of excited state dissociations of nucleobase and other polyatomic radicals remains a challenging topic for both experimentalists and computational chemists.

Use of DFT-based reactivity descriptors for rationalizing radical addition reactions: applicability and difficulties

The use of density functional theory-based reactivity descriptors, including global (hardness, electronegativity) and local (Fukui function, local softness) indices in rationalizing the reactivity and regioselectivity of radical addition reactions has been critically analyzed. We demonstrate that there is a severe inherent deficiency in the current way of defining the Fukui functions and local softness for radical attack parameters (f(0) and s(0)), and propose a (preliminary) alternative.

Hydrogen Atom and Hydride Anion Addition to Adenine: Structures and Energetics

The radicals and anions derived from the 9H tautomer of adenine by adding a hydrogen atom to one of the four double bonds of the adenine framework have been studied. Computations were carried out using a carefully calibrated density functional (B3LYP) method and basis set (DZP++). Optimized geometries, energies, and vibrational frequencies are predicted for eight radicals and anions. The radicals are found to lie in a range of 22 kcal mol(-1), with the radical derived by addition to the C(8) carbon atom being the lowest lying energetically. The anions are predicted to be bound species in the gas phase with an energetic range of 43 kcal mol(-1). Anions produced by addition of a hydride ion to adenine carbon atoms are found to be the most favorable. Six of the anions are predicted to be stable species with respect to electron detachment. The adiabatic electron affinities, vertical electron affinities, and vertical detachment energies are computed for the first time. Electron affinities for these radicals range from 0.0 to 2.0 eV. Radicals produced by addition to a nitrogen atom have near-zero adiabatic electron affinities, while radicals produced by addition at carbon atoms have considerably higher electron affinities.