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 scattering by deoxyribose and related molecules

We apply first-principles computational methods to study elastic scattering of low-energy electrons by 2-deoxyribose and 2-deoxyribose monophosphate, which are of interest as components of the DNA backbone, and to tetrahydrofuran (THF), which has been studied as a deoxyribose analog. To investigate the dependence of the scattering process on the molecular conformation, we examine Cs and C2 conformers of THF as well as the planar C2v geometry imposed in earlier calculations. There is little difference between the elastic cross sections determined at the nonplanar geometries, but there are noticeable differences between those results and the cross sections computed using the planar ring. By comparing results for tetrahydrofuran obtained with and without inclusion of polarization effects, we obtain energy shifts that are applied to the computed resonance positions for deoxyribose and deoxyribose monophosphate

Low-energy electron collisions with gas-phase uracil

We have studied gas-phase collisions between slow electrons and uracil molecules with a view to understanding the resonance structure of the scattering cross section. Our symmetry-resolved results for elastic scattering, computed in the fixed-nuclei, static-exchange and static-exchange-plus-polarization approximations, provide locations for the expected pi* shape resonances and indicate the possible presence of a low-energy sigma* resonance as well. Electron-impact excitation calculations were carried out for low-lying triplet and singlet excitation channels and yield a very large singlet cross section. We discuss the connection between the resonances found in our elastic cross section and features observed in dissociative attachment

Developing Cross Section Sets for Fluorocarbon Etchants

Successful modeling of plasmas used in materials processing depends on knowledge of a variety of collision cross sections and reaction rates, both within the plasma and at the surface. Electron-molecule collision cross sections are especially important, affecting both electron transport and the generation of reactive fragments by dissociation and ionization. Because the supply of cross section data is small and measurements are difficult, computational approaches may make a valuable contribution, provided they can cope with the significant challenges posed. In particular, a computational method must deal with the full complexity of low-energy electron-molecule interactions, must treat polyatomic molecules, and must be capable of computing cross sections for electronic excitation. These requirements imply that the method will be numerically intensive and thus must exploit high-performance computers to be practical. We have developed an ab initio computational method, the Schwinger multichannel (SMC) method, that possesses the characteristics just described, and we have applied it to compute cross sections for a variety of molecules, with particular emphasis on fluorocarbon and hydrofluorocarbon etchants used in the semiconductor industry. A key aspect of this work has been an awareness that cross section sets, validated when possible against swarm data, are more useful than individual cross sections. To develop such sets, cross section calculations must be integrated within a focused collaborative effort. Here we describe electron cross section calculations carried out within the context of such a focused effort, with emphasis on fluorinated hydrocarbons including CHF3 (trifluoromethane), c-C_(4)F_(8) (octafluorocyclobutane), and C_(2)F_(4) (tetrafluoroethene)

Resonant Channel Coupling in Electron Scattering by Pyrazine

Detailed investigation of the three low-energy resonances seen in electron scattering by the diazabenzene molecule pyrazine reveals that the first two are nearly pure single-channel shape resonances, but the third is, as long suspected, heavily mixed with core-excited resonances built on low-lying triplet states. Such resonant channel coupling is likely to be widespread in pi-ring molecules, including the nucleobases of DNA and RNA, where it may form a pathway for radiation damage

Low-energy electron scattering by pyrazine

We report cross sections for low-energy elastic electron collisions with the diazabenzene molecule pyrazine, obtained from first-principles calculations. The integral elastic cross section exhibits three sharp peaks that are nominally shape resonances associated with trapping in the vacant pi* molecular orbitals. Although the two lowest-energy resonances do in fact prove to be nearly pure single-channel shape resonances, the third contains a considerable admixture of core-excited character, and accounting for this channel coupling effect is essential to obtaining an accurate resonance energy. Such resonant channel coupling has implications for electron interactions with the DNA bases, especially the pyrimidine bases for which pyrazine is a close analog. In the absence of data on pyrazine itself, we compare our elastic differential cross section to measurements on benzene and find close agreement

Interactions of slow electrons with biomolecules

We report on results of computational studies of the interaction of slow electrons with the purine and pyrimidine bases of DNA, as well as with their associated nucleosides and nucleotides. The calculations focus on characterisation of the π* resonances associated with the bases and also provide general information on the scattering of slow electrons by these targets. High-level studies of the π* resonances in pyrazine, a close analogue of the pyrimidine bases, indicate that the higher-energy π* resonances in these bases may in fact contain large admixtures of core-excited character built on low-lying triplet states. Decay into such triplet states may provide a mechanism for damage to DNA

Electron collisions with biomolecules

We report on results of recent studies of collisions of low-energy electrons with nucleobases and other DNA constituents. A particular focus of these studies has been the identification and characterization of resonances that play a role in electron attachment leading to strand breaks in DNA. Comparison of the calculated resonance positions with results of electron transmission measurements is quite encouraging. However, the higher-lying π* resonances of the nucleobases appear to be of mixed elastic and core-excited character. Such resonant channel coupling raises the interesting possibility that the higher π*resonances in the nucleobases may promote dissociation of DNA by providing doorway states to triplet excited states

Comment on “Ring-breaking electron attachment to uracil: Following bond dissociations via evolving resonances” [J. Chem. Phys. 128, 174302 (2008)]

We point out that the assignment of pi* resonances to calculated features in a recent paper by Gianturco et al. [J. Chem. Phys.128, 174302 (2008)] cannot be correct

Parallel computing and the generation of basic plasma data

Comprehensive simulations of the processing plasmas used in semiconductor fabrication will depend on the availability of basic data for many microscopic processes that occur in the plasma and at the surface. Cross sections for electron collisions, a principal mechanism for producing reactive species in these plasmas, are among the most important such data; however, electron-collision cross sections are difficult to measure, and the available data are, at best, sketchy for the polyatomic feed gases of interest. While computational approaches to obtaining such data are thus potentially of significant value, studies of electron collisions with polyatomic gases at relevant energies are numerically intensive. In this article, we report on the progress we have made in exploiting large-scale distributed-memory parallel computers, consisting of hundreds of interconnected microprocessors, to generate electron-collision cross sections for gases of interest in plasma simulations