Theoretical Study on the Mechanism of Low-Energy Dissociative Electron Attachment for Uracil

Impact of solvation on the electronic resonances in uracil

Interactions of low-energy electrons with the DNA and RNA nucleobases are known to form metastable states, known as electronic resonances. In this work, we study electron attachment to solvated uracil, an RNA nucleobase, using the orbital stabilization method at the Equation of Motion-Coupled Cluster for Electron Affinities with Singles and Doubles (EOM-EA-CCSD) level of theory with the Effective Fragment Potential (EFP) solvation method. We benchmarked the approach using multireference methods, as well as by comparing EFP and full quantum calculations. The impact of solvation on the first one particle (1p) shape resonance, formed by electron attachment to the π* LUMO orbital, as well as the first two particle one hole (2p1h) resonance, formed by electron attachment to neutral uracil's π-π* excited state, was investigated. We used molecular dynamics simulations for solvent configurations and applied charge stabilization technique-based biased sampling to procure configurations adequate to cover the entire range of the electron attachment energy distribution. The electron attachment energy in solution is found to be distributed over a wide range of energies, between 4.6 eV to 6.8 eV for the 2p1h resonance, and between -0.1 eV to 2 eV for the 1p resonance. The solvent effects were similar for the two resonances, indicating that the exact electron density of the state is not as important as the solvent configurations. Multireference calculations extended the findings showing that solvation effects are similar for the lowest four resonances, further indicating that the specific solute electron density is not as important, but rather the water configurations play the most important role in solvation effects. Finally, by comparing bulk solvation to clusters of uracil with a few water molecules around it, we find that the impact of microsolvation is very different from that of bulk solvation.

Electron-Binding Dynamics of the Dipole-Bound State: Correlation Effect on the Autodetachment Dynamics

The nature of the electron-binding forces in the dipole-bound states (DBS) of anions is interrogated through experimental and theoretical means by investigating the autodetachment dynamics from DBS Feshbach resonances of ortho-, meta-, and para-bromophenoxide (BrPhO-). Though the charge-dipole electrostatic potential has been widely regarded to be mainly responsible for the electron binding in DBS, the effect of nonclassical electron correlation has been conceived to be quite significant in terms of its static and/or dynamic contributions toward the binding of the excess electron to the neutral core. State-specific real-time autodetachment dynamics observed by picosecond time-resolved photoelectron velocity-map imaging spectroscopy reveal that the autodetachment processes from the DBS Feshbach resonances of BrPhO- anions cannot indeed be rationalized by the conventional charge-dipole potential. Specifically, the autodetachment lifetime is drastically lengthened depending on differently positioned Br-substitution, and this rate change cannot be explained within the framework of Fermi's golden rule based on the charge-dipole assumption. High-level ab initio quantum chemical calculations with EOM-EA-CCSD, which intrinsically takes into account electron correlations, generate more reasonable predictions on the binding energies than density functional theory (DFT) calculations, and semiclassical quantum dynamics simulations based on the EOM-EA-CCSD data excellently predict the trend in the autodetachment rates. These findings illustrate that static and dynamic properties of the excess electron in the DBS are strongly influenced by correlation interactions among electrons in the nonvalence orbital of the dipole-bound electron and highly polarizable valence orbitals of the bromine atom, which, in turn, dictate the interesting chemical fate of exotic anion species.

Modeling the Ultrafast Electron Attachment Dynamics of Solvated Uracil

Electron attachment to DNA by low energy electrons can lead to DNA damage, so a fundamental understanding of how electrons interact with the components of nucleic acids in solution is an open challenge. In solution, low energy electrons can generate presolvated electrons, e_pre^-, which are efficiently scavanged by pyrimidine nucleobases to form transient negative ions, able to relax to either stable valence bound anions or undergo dissociative electron detachment or transfer to other parts of DNA/RNA leading to strand breakages. In order to understand the initial electron attachment dynamics, this paper presents a joint molecular dynamics and high-level electronic structure study into the behavior of the electronic states of the solvated uracil anion. Both the valence π* and nonvalence e_pre^- states of the solvated uracil system are studied, and the effect of the solvent environment and the geometric structure of the uracil core are uncoupled to gain insight into the physical origin of the stabilization of the solvated uracil anion. Solvent reorganization is found to play a dominant role followed by relaxation of the uracil core.

Time-resolved dynamics in iodide-uracil-water clusters upon excitation of the nucleobase

The dynamics of iodide-uracil-water (I^-·U·H₂O) clusters following π-π^* excitation of the nucleobase are probed using time-resolved photoelectron spectroscopy. Photoexcitation of this cluster at 4.77 eV results in electron transfer from the iodide moiety to the uracil, creating a valence-bound anion within the cross correlation of the pump and probe laser pulses. This species can decay by a number of channels, including autodetachment and dissociation to I^- or larger anion fragments. Comparison of the energetics of the photoexcited cluster and its decay dynamics with those of the bare iodide-uracil (I^-·U) complex provides a sensitive probe of the effects of microhydration on these species.

Time-resolved radiation chemistry: femtosecond photoelectron spectroscopy of electron attachment and photodissociation dynamics in iodide-nucleobase clusters

Iodide-nucleobase (I-·N) clusters studied by time-resolved photoelectron spectroscopy (TRPES) are an opportune model system for examining radiative damage of DNA induced by low-energy electrons. By initiating charge transfer from iodide to the nucleobase and following the dynamics of the resulting transient negative ions (TNIs) with femtosecond time resolution, TRPES provides a novel window into the chemistry triggered by the attachment of low-energy electrons to nucleobases. In this Perspective, we examine and compare the dynamics of electron attachment, autodetachment, and photodissociation in a variety of I-·N clusters, including iodide-uracil (I-·U), iodide-thymine (I-·T), iodide-uracil-water (I-·U·H2O), and iodide-adenine (I-·A), to develop a more unified representation of our understanding of nucleobase TNIs. The experiments probe whether dipole-bound or valence-bound TNIs are formed initially and the subsequent time evolution of these species. We also provide an outlook for forthcoming applications of TRPES to larger iodide-containing complexes to enable the further investigation of microhydration dynamics in nucleobases, as well as electron attachment and photodissociation in more complex nucleic acid constituents.

Photodissociation dynamics of the iodide-uracil (I(-)U) complex

Photofragment action spectroscopy and femtosecond time-resolved photoelectron imaging are utilized to probe the dissociation channels in iodide-uracil (I(-) ⋅ U) binary clusters upon photoexcitation. The photofragment action spectra show strong I(-) and weak [U-H](-) ion signal upon photoexcitation. The action spectra show two bands for I(-) and [U-H](-) production peaking around 4.0 and 4.8 eV. Time-resolved experiments measured the rate of I(-) production resulting from excitation of the two bands. At 4.03 eV and 4.72 eV, the photoelectron signal from I(-) exhibits rise times of 86 ± 7 ps and 36 ± 3 ps, respectively. Electronic structure calculations indicate that the lower energy band, which encompasses the vertical detachment energy (4.11 eV) of I(-)U, corresponds to excitation of a dipole-bound state of the complex, while the higher energy band is primarily a π-π(∗) excitation on the uracil moiety. Although the nature of the two excited states is very different, the long lifetimes for I(-) production suggest that this channel results from internal conversion to the I(-) ⋅ U ground state followed by evaporation of I(-). This hypothesis was tested by comparing the dissociation rates to Rice-Ramsperger-Kassel-Marcus calculations.

Complete-active-space second-order perturbation theory (CASPT2//CASSCF) study of the dissociative electron attachment in canonical DNA nucleobases caused by low-energy electrons (0-3 eV)

Low-energy (0-3 eV) ballistic electrons originated during the irradiation of biological material can interact with DNA/RNA nucleobases yielding transient-anion species which undergo decompositions. Since the discovery that these reactions can eventually lead to strand breaking of the DNA chains, great efforts have been dedicated to their study. The main fragmentation at the 0-3 eV energy range is the ejection of a hydrogen atom from the specific nitrogen positions. In the present study, the methodological approach introduced in a previous work on uracil [I. González-Ramírez et al., J. Chem. Theory Comput. 8, 2769-2776 (2012)] is employed to study the DNA canonical nucleobases fragmentations of N-H bonds induced by low-energy electrons. The approach is based on minimum energy path and linear interpolation of internal coordinates computations along the N-H dissociation channels carried out at the complete-active-space self-consistent field//complete-active-space second-order perturbation theory level. On the basis of the calculated theoretical quantities, new assignations for the adenine and cytosine anion yield curves are provided. In addition, the π1 (-) and π2 (-) states of the pyrimidine nucleobases are expected to produce the temporary anions at electron energies close to 1 and 2 eV, respectively. Finally, the present theoretical results do not allow to discard neither the dipole-bound nor the valence-bound mechanisms in the range of energies explored, suggesting that both possibilities may coexist in the experiments carried out with the isolated nucleobases.

Bifurcate localization modes of excess electron in aqueous Ca(2+)amide solution revealed by ab initio molecular dynamics simulation: towards hydrated electron versus hydrated amide anion

In this work, we conduct ab initio molecular dynamics simulations on the localization dynamics of an excess electron (EE) in acetamide/Ca(2+) aqueous solutions with three different interaction modes of Ca(2+) with acetamide: tight contact, solvent-shared state, and separated interaction. The simulated results reveal that an EE could exhibit two different localization behaviors in these acetamide/Ca(2+) aqueous solutions depending on different amideCa(2+) interactions featuring different contact distances. For the tight contact and solvent-shared state of amideCa(2+) solutions, vertically injected diffuse EEs follow different mechanisms with different dynamics, forming a cavity-shaped hydrated electron or a hydrated amide anion, respectively. Meanwhile, for the separated state, only one localization pattern of a vertically injected diffuse EE towards the formation of hydrated amide anion is observed. The hindrance of hydrated Ca(2+) and the attraction of the hydrated amide group originating from its polarity and low energy π* orbital are the main driving forces. Additionally, different EE localization modes have different effects on the interaction between the amide group and Ca(2+) in turn. This work provides an important basis for further understanding the mechanisms and dynamics of localizations/transfers of radiation-produced EEs and associated EE-induced lesions and damage to biological species in real biological environments or other aqueous solutions.

Dynamics of dipole- and valence bound anions in iodide-adenine binary complexes: A time-resolved photoelectron imaging and quantum mechanical investigation

Dipole bound (DB) and valence bound (VB) anions of binary iodide-adenine complexes have been studied using one-color and time-resolved photoelectron imaging at excitation energies near the vertical detachment energy. The experiments are complemented by quantum chemical calculations. One-color spectra show evidence for two adenine tautomers, the canonical, biologically relevant A9 tautomer and the A3 tautomer. In the UV-pump/IR-probe time-resolved experiments, transient adenine anions can be formed by electron transfer from the iodide. These experiments show signals from both DB and VB states of adenine anions formed on femto- and picosecond time scales, respectively. Analysis of the spectra and comparison with calculations suggest that while both the A9 and A3 tautomers contribute to the DB signal, only the DB state of the A3 tautomer undergoes a transition to the VB anion. The VB anion of A9 is higher in energy than both the DB anion and the neutral, and the VB anion is therefore not accessible through the DB state. Experimental evidence of the metastable A9 VB anion is instead observed as a shape resonance in the one-color photoelectron spectra, as a result of UV absorption by A9 and subsequent electron transfer from iodide into the empty π-orbital. In contrast, the iodide-A3 complex constitutes an excellent example of how DB states can act as doorway state for VB anion formation when the VB state is energetically available.

Ultrafast dynamics of formation and autodetachment of a dipole-bound state in an open-shell π-stacked dimer anion

Isolated π-stacked dimer radical anions present the simplest model of an excess electron in a π-stacked environment. Here, frequency-, angle-, and time-resolved photoelectron imaging together with electronic structure calculations have been used to characterise the π-stacked coenzyme Q₀ dimer radical anion and its exited state dynamics. In the ground electronic state, the excess electron is localised on one monomer with a planar para-quinone ring, which is solvated by the second monomer in which carbonyl groups are bent out of the para-quinone ring plane. Through the π-stacking interaction, the dimer anion exhibits a number of charge-transfer (intermolecular) valence-localised resonances situated in the detachment continuum that undergo efficient internal conversion to a cluster dipole-bound state (DBS) on a ∼60 fs timescale. In turn, the DBS undergoes vibration-mediated autodetachment on a 2.0 ± 0.2 ps timescale. Experimental vibrational structure and supporting calculations assign the intermolecular dynamics to be facilitated by vibrational wagging modes of the carbonyl groups on the non-planar monomer. At photon energies ∼0.6-1.0 eV above the detachment threshold, a competition between photoexcitation of an intermolecular resonance leading to the DBS, and photoexcitation of an intramolecular resonance leading to monomer-like dynamics further illustrates the π-stacking specific dynamics. Overall, this study provides the first direct observation of both internal conversion of resonances into a DBS, and characterisation of a vibration-mediated autodetachment in real-time.

Time-resolved radiation chemistry: dynamics of electron attachment to uracil following UV excitation of iodide-uracil complexes

Electron attachment to uracil was investigated by applying time-resolved photoelectron imaging to iodide-uracil (I(-)U) complexes. In these studies, an ultraviolet pump pulse initiated charge transfer from the iodide to the uracil, and the resulting dynamics of the uracil temporary negative ion were probed. Five different excitation energies were used, 4.00 eV, 4.07 eV, 4.14 eV, 4.21 eV, and 4.66 eV. At the four lowest excitation energies, which lie near the vertical detachment energy of the I(-)U complex (4.11 eV), signatures of both the dipole bound (DB) as well as the valence bound (VB) anion of uracil were observed. In contrast, only the VB anion was observed at 4.66 eV, in agreement with previous experiments in this higher energy range. The early-time dynamics of both states were highly excitation energy dependent. The rise time of the DB anion signal was ∼250 fs at 4.00 eV and 4.07 eV, ∼120 fs at 4.14 eV and cross-correlation limited at 4.21 eV. The VB anion rise time also changed with excitation energy, ranging from 200 to 300 fs for excitation energies 4.00-4.21 eV, to a cross-correlation limited time at 4.66 eV. The results suggest that the DB state acts as a "doorway" state to the VB anion at 4.00-4.21 eV, while direct attachment to the VB anion occurs at 4.66 eV.

Excess electron interaction with radiosensitive 5-bromopyrimidine in aqueous solution: a combined ab initio molecular dynamics and time-dependent wave-packet study

Radiation-generated secondary electrons can induce resonance processes in a target molecule and fragment it via different pathways.

Shape resonance spectra of uracil, 5-fluorouracil, and 5-chlorouracil

We report on the shape resonance spectra of uracil, 5-fluorouracil, and 5-chlorouracil, as obtained from fixed-nuclei elastic scattering calculations performed with the Schwinger multichannel method with pseudopotentials. Our results are in good agreement with the available electron transmission spectroscopy data, and support the existence of three π∗ resonances in uracil and 5-fluorouracil. As expected, the anion states are more stable in the substituted molecules than in uracil. Since the stabilization is stronger in 5-chlorouracil, the lowest π∗ resonance in this system becomes a bound anion state. The present results also support the existence of a low-lying σCCl (*) shape resonance in 5-chlorouracil. Exploratory calculations performed at selected C-Cl bond lengths suggest that the σCCl (*) resonance could couple to the two lowest π∗ states, giving rise to a very rich dissociation dynamics. These facts would be compatible with the complex branching of the dissociative electron attachment cross sections, even though we cannot discuss any details of the vibration dynamics based only on the present fixed-nuclei results.

NCO(-), a key fragment upon dissociative electron attachment and electron transfer to pyrimidine bases: site selectivity for a slow decay process

We report gas phase studies on NCO(-) fragment formation from the nucleobases thymine and uracil and their N-site methylated derivatives upon dissociative electron attachment (DEA) and through electron transfer in potassium collisions. For comparison, the NCO(-) production in metastable decay of the nucleobases after deprotonation in matrix assisted laser desorption/ionization (MALDI) is also reported. We show that the delayed fragmentation of the dehydrogenated closed-shell anion into NCO(-) upon DEA proceeds few microseconds after the electron attachment process, indicating a rather slow unimolecular decomposition. Utilizing partially methylated thymine, we demonstrate that the remarkable site selectivity of the initial hydrogen loss as a function of the electron energy is preserved in the prompt as well as the metastable NCO(-) formation in DEA. Site selectivity in the NCO(-) yield is also pronounced after deprotonation in MALDI, though distinctly different from that observed in DEA. This is discussed in terms of the different electronic states subjected to metastable decay in these experiments. In potassium collisions with 1- and 3-methylthymine and 1- and 3-methyluracil, the dominant fragment is the NCO(-) ion and the branching ratios as a function of the collision energy show evidence of extraordinary site-selectivity in the reactions yielding its formation.