Total dissociative electron attachment cross sections for molecular constituents of DNA

Interaction of low-energy electrons with the pyrimidine bases and nucleosides of DNA

We report computed cross sections for the elastic scattering of slow electrons by the pyrimidine bases of DNA, thymine and cytosine, and by the associated nucleosides, deoxythymidine and deoxycytidine. For the isolated bases, we carried out calculations both with and without the inclusion of polarization effects. For the nucleosides, we neglect polarization effects but estimate their influence on resonance positions by comparison with the results for the corresponding bases. Where possible, we compare our results with experiment and previous calculations.

Total dissociative electron attachment cross sections of selected amino acids

Total dissociative electron attachment cross sections are presented for the amino acids, glycine, alanine, proline, phenylalanine, and tryptophan, at energies below the first ionization energy. Cross section magnitudes were determined by observation of positive ion production and normalization to ionization cross sections calculated using the binary-encounter-Bethe method. The prominent 1.2 eV feature in the cross sections of the amino acids and the closely related HCOOH molecule is widely attributed to the attachment into the -COOH pi* orbital. The authors discuss evidence that direct attachment to the lowest sigma* orbital may instead be responsible. A close correlation between the energies of the core-excited anion states of glycine, alanine, and proline and the ionization energies of the neutral molecules is found. A prominent feature in the total dissociative electron attachment cross section of these compounds is absent in previous studies using mass analysis, suggesting that the missing fragment is energetic H-.

Low-energy electron attachment to 5'-thymidine monophosphate: modeling single strand breaks through dissociative electron attachment

Mechanisms of low-energy electron (LEE) attachment and subsequent single-strand break (SSB) formation are investigated by density functional theory treatment of a simple model for DNA, i.e., the nucleotide, 5'-thymidine monophosphate (5'-dTMPH). In the present study, the C5'-O5' bond dissociation due to LEE attachment has been followed along the adiabatic as well as on the vertical (electron attached to the optimized geometry of the neutral molecule) anionic surfaces using B3LYP functional and 6-31G* and 6-31++G** basis sets. Surprisingly, it is found that the PES of C5'-O5' bond dissociation in the anion radicals have approximately the same barrier for both adiabatic and vertical pathways. These results provide support for the hypothesis that transiently bound electrons (shape resonances) to the virtual molecular orbitals of the neutral molecule likely play a key role in the cleavage of the sugar-phosphate C5'-O5' bond in DNA resulting in the direct formation of single strand breaks without significant molecular relaxation. To take into account the solvation effects, we considered the neutral and anion radical of 5'-dTMP surrounded by 5 or 11 water molecules with Na+ as a counterion. These structures were optimized using the B3LYP/6-31G** level of theory. We find the barrier height for adiabatic C5'-O5' bond dissociation of 5'-dTMP anion radical in aqueous environment is so substantially higher than in the gas phase that the adiabatic route will not contribute to DNA strand cleavage in aqueous systems. This result is in agreement with experiment.

On the mechanism of anion desorption from DNA induced by low energy electrons

Our knowledge of the mechanisms of radiation damage to DNA induced by secondary electrons is still very limited, mainly due to the large sizes of the system involved and the complexity of the interactions. To reduce the problem to its simplest form, we investigated specific electron interactions with one of the most simple model system of DNA, an oligonucleotide tetrameter compound of the four bases. We report anion desorption yields from a thin solid film of the oligonucleotide GCAT induced by the impact of 3-15 eV electrons. All observed anions (H-, O-, OH-, CN-, and OCN-) are produced by dissociative electron attachment to the molecule, which results in desorption peaks between 6 and 12 eV. Above 14 eV nonresonant dipolar dissociation dominates the desorption yields. By comparing the shapes and relative intensities of the anion yield functions from GCAT physisorbed on a tantalum substrate with those obtained from isolated DNA basic subunits (i.e., bases, deoxyribose, and phosphate groups) from either the gas phase or condensed phase experiments, it is possible to obtain more details on the mechanisms involved in low energy electron damage to DNA, particularly on those producing single strand breaks.

Interaction of low-energy electrons with the purine bases, nucleosides, and nucleotides of DNA

The authors report results from computational studies of the interaction of low-energy electrons with the purine bases of DNA, adenine and guanine, as well as with the associated nucleosides, deoxyadenosine and deoxyguanosine, and the nucleotide deoxyadenosine monophosphate. Their calculations focus on the characterization of the pi* shape resonances associated with the bases and also provide general information on the scattering of slow electrons by these targets. Results are obtained for adenine and guanine both with and without inclusion of polarization effects, and the resonance energy shifts observed due to polarization are used to predict pi* resonance energies in associated nucleosides and nucleotides, for which static-exchange calculations were carried out. They observe slight shifts between the resonance energies in the isolated bases and those in the nucleosides.

Low energy electron-induced reactions in gas phase 1,2,3,5-tetra-O-acetyl-β-D-ribofuranose: A model system for the behavior of sugar in DNA

Dissociative electron attachment to 1,2,3,5-tetra-O-acetyl-beta-D-ribofuranose (TAR) is studied in a crossed electron-molecular beam experiment with mass spectrometric detection of the observed fragment ions. Since in TAR acetyl groups are coupled at the relevant positions to the five membered ribose ring, it may serve as an appropriate model compound to study the response of the sugar unit in DNA towards low energy electrons. Intense resonances close to 0 eV are observed similar to the pure gas phase sugars (2-deoxyribose, ribose, and fructose). Further strong resonances appear in the range of 1.6-1.8 eV (not present in the pure sugars). Based on calculations on transient anions adopting the stabilization method, this feature is assigned to a series of closely spaced shape resonances of pi* character with the extra electron localized on the acetyl groups outside the ribose ring system. Further but weaker resonant contributions are observed in the range of 7-11 eV, representing core excited resonances and/or sigma* shape resonances. The decomposition processes involve single bond ruptures but also more complex reactions associated with substantial rearrangement. The authors hence propose that the sugar unit in DNA plays an active role in the molecular mechanism towards single strand breaks induced by low energy electrons.

Cross sections for electron trapping by DNA and its component subunits I: Condensed tetrahydrofuran deposited on Kr

We report cross sections for electron capture processes occurring in condensed tetrahydrofuran (THF) for incident electron energies in the range of 0-9 eV. The charge trapping cross section for 6-9 eV electrons is very small, and an upper limit of 4 x 10(-19) cm2 is estimated from our results. This latter is thus also an upper bound for the cross section for dissociative electron attachment process that is known to occur at these energies for condensed THF. At energies close to zero eV electron trapping proceeds via intermolecular stabilization. The cross section for this process is strongly dependent on the quantity of deposited THF. Since THF may model the furyl ring found in deoxyribose, these measurements indicate that this ring likely plays little role in either initiating or enhancing strand break damage via the attachment of the low energy secondary electrons produced when DNA is exposed to ionizing radiation.

Electron-induced chemistry of alcohols

We studied dissociative electron attachment to a series of compounds with one or two hydroxyl groups. For the monoalcohols we found, apart from the known fragmentations in the 6-12 eV range proceeding via Feshbach resonances, also new weaker processes at lower energies, around 3 eV. They have a steep onset at the dissociation threshold and show a dramatic D/H isotope effect. We assigned them as proceeding via shape resonances with temporary occupation of sigma orbitals. These low energy fragmentations become much stronger in the larger molecules and the strongest DEA process in the compounds with two hydroxyl groups, which thus represent an intermediate case between the behavior of small alcohols and the sugar ribose which was discovered to have strong DEA fragmentations near zero electron energy [S. Ptasińska, S. Denifl, P. Scheier and T. D. Märk, J. Chem. Phys., 2004, 120, 8505]. Above 6 eV, in the Feshbach resonance regime, the dominant process is a fast loss of a hydrogen atom from the hydroxyl group. In some cases the resulting (M- 1)(-) anion (loss of hydrogen atom) is sufficiently energy-rich to further dissociate by loss of stable, closed shell molecules like H(2) or ethene. The fast primary process is state- and site selective in several cases, the negative ion states with a hole in the n(O) orbital losing the OH hydrogen, those with a hole in the sigma(C-H) orbitals the alkyl hydrogen.

Cross sections for low-energy electron scattering from adenine in the condensed phase

Measurements of the vibrational and electronic excitation of a sub-monolayer up to a monolayer film of adenine were performed with a high resolution electron energy-loss (HREEL) spectrometer. The integral cross sections (over the half-space angle) for excitation of the normal vibrational modes of the ground electronic state and electronically excited states are calculated from the measured reflectivity EEL spectra. Most cross sections for vibrational excitation are of the order of 10(-17) cm(2), the largest being the out-of-plane wagging of the amino-group and the six-member ring deformations. A wide resonance feature appears in the incident energy dependence of the vibrational cross sections at 3-5 eV, while a weak shoulder is present in this dependence for combined ring deformations and bending of hydrogen atoms. For the five excited electronic states, at 4.7, 5.0, 5.5, 6.1 and 6.6 eV, the cross sections are of the order of 10(-18) cm(2), except in the case of the state at the energy of 6.1 eV, for which it is two to three times higher.

Radiation damage to DNA: Electron scattering from the backbone subunits

In the context of damage to DNA by low energy electrons, we carry out calculations of electron scattering from tetrahydrofuran and phosphoric acid, models of the subunits in the DNA backbone, as a first step in simulating the electron capture process that occurs in the cell. In the case of tetrahydrofuran, we also compare with previous theoretical and experimental data. A comparison of the shape of the resonant structures to virtual orbitals is also performed to gain insight into the systematic connections with electron scattering from similar molecules and dissociative electron attachment experiments.

High resolution dissociative electron attachment to gas phase adenine

The dissociative electron attachment to the gas phase nucleobase adenine is studied using two different experiments. A double focusing sector field mass spectrometer is utilized for measurements requiring high mass resolution, high sensitivity, and relative ion yields for all the fragment anions and a hemispherical electron monochromator instrument for high electron energy resolution. The negative ion mass spectra are discussed at two different electron energies of 2 and 6 eV. In contrast to previous gas phase studies a number of new negative ions are discovered in the mass spectra. The ion efficiency curves for the negative ions of adenine are measured for the electron energy range from about 0 to 15 eV with an electron energy resolution of about 100 meV. The total anion yield derived via the summation of all measured fragment anions is compared with the total cross section for negative ion formation measured recently without mass spectrometry. For adenine the shape of the two cross section curves agrees well, taking into account the different electron energy resolutions; however, for thymine some peculiar differences are observed.