Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions.

Resonance effects in elastic cross sections for electron scattering on pyrimidine: Experiment and theory.

We measured differential cross sections for elastic (rotationally integrated) electron scattering on pyrimidine, both as a function of angle up to 180(∘) at electron energies of 1, 5, 10, and 20 eV and as a function of electron energy in the range 0.1-14 eV. The experimental results are compared to the results of the fixed-nuclei Schwinger variational and R-matrix theoretical methods, which reproduce satisfactorily the magnitudes and shapes of the experimental cross sections.

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.

Absolute electron scattering cross sections for the CF2 radical.

Using a crossed electron-molecular beam experiment, featuring a skimmed nozzle beam with pyrolytic radical production, absolute elastic cross sections for electron scattering from the CF2 molecule have been measured. A new technique for placing measured cross sections on an absolute scale is used for molecular beams produced as skimmed supersonic jets. Absolute differential cross sections for CF2 are reported for incident electron energies of 30-50 eV and over an angular range of 20-135 deg.

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.

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.

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.

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.

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 C(2v) 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.