Water mediated electron attachment to nucleobases: Surface-bound vs bulk solvated electrons

Interaction of low-energy electrons with radiosensitizers

We provide an experimentalist's perspective on the present state-of-the-art in the studies of low-energy electron interactions with common radiosensitizers, including compounds used in combined chemo-radiation therapy and their model systems. Low-energy electrons are important secondary species formed during the interaction of ionizing radiation with matter. Their role in the radiation chemistry of living organisms has become an important topic for more than 20 years. With the increasing number of works and reviews in the field, we would like to focus here on a very narrow area of compounds that have been shown to have radio-sensitizing properties on the one hand, and high reactivity towards low-energy electrons on the other hand. Gas phase experiments studying electron attachment to isolated molecules and environmental effects on reaction dynamics are reviewed for modified DNA components, nitroimidazoles, and organometallics. In the end, we provide a perspective on the future directions that may be important for transferring the fundamental knowledge about the processes induced by low-energy electrons into practice in the field of rational design of agents for concomitant chemo-radiation therapy.

Shape resonance induced electron attachment to cytosine: The effect of aqueous media

We have investigated the impact of microsolvation on shape-type resonance states of nucleobases, taking cytosine as a case study. To characterize the resonance position and decay width of the metastable states, we employed the newly developed DLPNO-based EA-EOM-CCSD method in conjunction with the resonance via Padé (RVP) method. Our calculations show that the presence of water molecules causes a redshift in the resonance position and an increase in the lifetime for the three lowest-lying resonance states of cytosine. Furthermore, there are some indications that the lowest resonance state in isolated cytosine may get converted to a bound state in the presence of an aqueous environment. The obtained results are extremely sensitive to the basis set used for the calculations.

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 DNA: The Protective Role of Amino Acids

We have studied the effect of amino acids on the electron attachment properties of a DNA nucleobase, with cytosine as a model system. The equation of motion coupled cluster theory with an extended basis set has been used to simulate the electron-attached state of the DNA model system. Arginine, alanine, lysine, and glycine are the four amino acids considered to investigate their role in electron attachment to a DNA nucleobase. The electron attachment to cytosine in all the four cytosine-amino acid gas-phase dimer complexes follows a doorway mechanism, where the electron gets transferred from the initial dipole-bound doorway state to the final nucleobase-bound state through the mixing of electronic and nuclear degrees of freedom. When cytosine is bulk-solvated with glycine, the glycine-bound state acts as the doorway state, where the initial electron density is localized on the bulk amino acid and away from the nucleobase, thus leading to the physical shielding of the nucleobase from the incoming electron. At the same time, the presence of amino acids can increase the stability of the nucleobase-bound anionic state, which can suppress the sugar-phosphate bond rupture caused by dissociative electron attachment to DNA.

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.

State-Specific Chemical Dynamics of the Nonvalence Bound State of the Molecular Anions

Nonvalence bound states (NBS) are anionic states where the excess electron is extremely loosely bound to the neutral core through long-range potentials. In contrast to the valence orbitals of which the electron occupancy determines the molecular structure, as well as the chemical reactivity, the nonvalence orbital is quite diffuse and located far from the neutral core. The NBS can be classified into the dipole-bound state (DBS), quadruple-bound state (QBS), or correlation-bound state (CBS) according to the nature of the electron-neutral interaction, although their interaction potentials may cooperatively contribute. The NBS is ubiquitous in nature and has the strong implications in atmospheric, interstellar, or biological chemistry. Accordingly, NBS has long been conceived to play the role of the doorway into the formation of a stable anion or dissociative electron attachment (DEA). Despite intensive and extensive studies, however, the quantum-mechanical nature of NBS is still far from being thorough understanding. Herein, we describe a new aspect of state-specific NBS-mediated chemical dynamics, which has been revealed through a series of recent studies by our group. We have employed picosecond time-resolved pump-probe spectroscopy combined with cryogenically cooled ion trap and velocity-map imaging techniques to study closed-shell anions generated by electrospray ionization. DBS vibrational Feshbach resonances are prepared by the optical excitation of phenoxide, for instance, and their individual lifetimes have been precisely measured in a state-specific manner to reveal the strong mode-dependency of the autodetachment rate. Fermi's golden rule turns out to be extremely useful for a rational explanation of the experiment, although the more sophisticated theoretical model is desirable for the more quantitative analysis. For the DBS of para-chlorophenoxide or para-bromophenoxide where the polarizability of neutral core is substantial, the Fermi's golden rule based on the charge-dipole potential needs to be significantly modified to include the correlation effects to explain the exceptionally slow autodetachment rates. For the QBS of 4-cyanophenoxide, the mode-specific behavior of the quadrupole ellipsoid tensor explains the strong mode-dependent autodetachment rate. Meanwhile, the nonadiabatic transition of the excess electron into the valence orbital can result in stable anion formation or immediate chemical bond rupture. In the DBS of ortho-, meta-, or para-iodophenoxide, the transformation of the loosely bound excess electron into the πσ* antibonding orbital occurs to give I^- as a final fragment. The fragmentation mediated by DBS occurs competitively with the concomitant autodetachment, paving a new way of the reaction control by tuning the quantum-mechanical nature of the DBS Feshbach resonance. This experimental observation provides the foremost evidence for the dynamic role of the DBS as a doorway into anion chemistry, such as DEA. The ponderomotive force on the electron in the nonvalence orbital has been demonstrated for the first time in a strong optical field, giving great promise for the manipulation of polyatomic molecules in terms of the spatial location, as well as the AC-Stark control of the chemical reaction.

Experimental Observation of the Resonant Doorways to Anion Chemistry: Dynamic Role of Dipole-Bound Feshbach Resonances in Dissociative Electron Attachment

Anion chemical dynamics of autodetachment and fragmentation mediated by the dipole-bound state (DBS) have been thoroughly investigated in a state-specific way by employing the picosecond time-resolved or the nanosecond frequency-resolved spectroscopy combined with the cryogenically cooled ion trap and velocity-map imaging techniques. For the ortho-, meta-, or para-iodophenoxide anion (o-, m-, or p-IPhO^-), the C-I bond rupture occurs via the nonadiabatic transition from the DBS to the nearby valence-bound states (VBS) of the anion where the vibronic coupling into the S₁ (πσ*) state (repulsive along the C-I bond extension coordinate) should be largely responsible. Dynamic details are governed by the isomer-specific nature of the potential energy surfaces in the vicinity of the DBS-VBS curve crossings, as manifested in the huge different chemical reactivity of o-, m-, or p-IPhO^-. It is confirmed here that the C-I bond dissociation is mediated by DBS resonances, providing the foremost evidence that the metastable DBS plays the critical role as the doorway into the anion chemistry especially of the dissociative electron attachment (DEA). The fragmentation channel is dominant when it is mediated by the DBS resonances located below the electron-affinity (EA) threshold, whereas it is kinetically adjusted by the competitive autodetachment when the DBS resonances above EA convey the electron to the valence orbitals. The product yield of the C-I bond cleavage is strongly mode-dependent as the rate of the concomitant autodetachment is much influenced by the characteristics of the individual vibrational modes, paving a new way of the reaction control of the anion chemistry.

Doorway Mechanism for Electron Attachment Induced DNA Strand Breaks

We report a new doorway mechanism for the dissociative electron attachment to genetic materials. The dipole-bound state of the nucleotide anion acts as the doorway for electron capture in the genetic material. The electron gets subsequently transferred to a dissociative σ*-type anionic state localized on a sugar-phosphate or a sugar-nucleobase bond, leading to their cleavage. The electron transfer is mediated by the mixing of electronic and nuclear degrees of freedom. The cleavage rate of the sugar-phosphate bond predicted by this new mechanism is higher than that of the sugar-nucleobase bond breaking, and both processes are considerably slower than the formation of a stable valence-bound anion. The new mechanism can explain the relative rates of electron attachment induced bond cleavages in genetic materials.

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.

Intermediate state representation approach to physical properties of molecular electron-attached states: Theory, implementation, and benchmarking

Computational schemes for comprehensive studies of molecular electron-attached states and the calculation of electron affinities (EAs) are formulated and implemented employing the intermediate state representation (ISR) formalism and the algebraic-diagrammatic construction approximation for the electron propagator (EA-ADC). These EA-ADC(n)/ISR(m) schemes allow for a consistent treatment of not only electron affinities and pole strengths up to third-order of perturbation theory (n = 3) but also one-electron properties of electron-attached states up to second order (m = 2). The EA-ADC/ISR equations were implemented in the Q-Chem program for Ŝ_z-adapted intermediate states, allowing also open-shell systems to be studied using unrestricted Hartree-Fock references. For benchmarking of the EA-(U)ADC/ISR schemes, EAs and dipole moments of various electron-attached states of small closed- and open-shell molecules were computed and compared to full configuration interaction data. As an illustrative example, EA-ADC(3)/ISR(2) has been applied to the thymine-thymine (6-4) DNA photolesion.

Electron Attachment to Cytosine: The Role of Water

We present an EOM-CCSD-based quantum mechanical/molecular mechanical (QM/MM) study on the electron attachment process to solvated cytosine. The electron attachment in the bulk solvated cytosine occurs through a doorway mechanism, where the initial electron is localized on water. The electron is subsequently transferred to cytosine by the mixing of electronic and nuclear degrees of freedom, which occurs on an ultrafast time scale. The bulk water environment stabilizes the cytosine-bound anion by an extensive hydrogen-bond network and drastically enhances the electron transfer rate from that observed in the gas phase. Microhydration studies cannot reproduce the effect of the bulk water environment on the electron attachment process, and one needs to include a large number of water molecules in the calculation to obtain converged results. The predicted adiabatic electron affinity and electron transfer rate obtained from our QM/MM calculations are consistent with the available experimental results.