Temporary anion states of three herbicide families.

Electron scattering studies are used to locate the energies of temporary negative ion states of three chloro-substituted molecular families of herbicidal importance: salicylic and phenoxyacetic acids and acetamides. The correlation between these energies and the computed virtual orbital energies of the compounds is examined and used to put the latter on an absolute energy scale. Such scaling of orbital energies permits the anion states of other members of these families, for which experimental data may not be available, to be estimated from the calculated orbital energies. Studies of electron reduction rates often rely on calculated LUMO energies as molecular descriptors. The use of measured anion energies as well as appropriately scaled orbital energies should serve to improve such studies in these and in related herbicides.

On the treatment of LUMO energies for their use as descriptors.

Calculated energies of lowest unoccupied molecular orbitals (LUMOs) are frequently employed as descriptors in studies of quantitative structure-activity relationships and linear free energy relationships involving electron transfer. However, the quantum chemical programs with which these are carried out, whether Hartree-Fock or density functional theory, do not treat orbitals of different character, for example, C=C π(∗) and C-Cl σ(∗), consistently, nor is there consistency among different families of compounds. These problems can be ameliorated with the use of the experimental equivalent of the LUMO energy, the vertical attachment energy (VAE), or by shifting and scaling LUMO energies to a training set of available VAEs in similar compounds. Examples from the literature are used to illustrate these points.

Dissociative electron attachment in nonplanar chlorocarbons with pi*/sigma*-coupled molecular orbitals.

Total absolute cross sections for the dissociative electron attachment (DEA) process are reported for a series of nonplanar ethylenic and phenylic compounds monosubstituted with (CH(2))(n)Cl groups, where n=1-4. Coupling between the local pi* molecular orbitals provided by the unsaturated moieties and the sigma* (C-Cl) orbital is thus examined as a function of the separation of these groups. In particular, the coupling is viewed from the perspective of the interacting temporary negative ions formed by short lived occupation of these orbitals and their decay into the DEA channel. A theoretical treatment of "remote" bond breaking, presented elsewhere, satisfactorily accounts for DEA in the chloroethylenic compounds presented here and emphasizes not only the delocalization of the coupled anionic wave functions but the importance of their relative phases. The dependence of the cross sections on the vertical attachment energies, measured by electron transmission spectroscopy, is also explored and compared to that found previously in chlorinated alkanes.

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-.

Remote bond breaking by interacting temporary anion states.

The cross section for bond breaking at the site of a dissociative temporary negative ion state through the dissociative electron attachment process can be considerably enhanced by the presence of a second longer-lived temporary negative ion state elsewhere in the molecule, even one quite remote from the first. In a series of chloroalkenes possessing both C-Cl and C==C bonds separated by various distances, we show that the cross sections are determined by the lifetime of the lower anion state created by the mixing of the anion states of these two moieties, with the wave function's coefficients giving the probability that the electron is located at the dissociative site. Furthermore, the lifetime of the composite anion state can be expressed in terms of these same coefficients and the lifetimes of the unmixed resonances. We also discuss how these results may give insight into the means by which strand breaks are induced in DNA by the attachment of slow electrons.

Total dissociative electron attachment cross sections for molecular constituents of DNA.

Total cross sections for the dissociative electron attachment process are presented for the DNA bases thymine, cytosine, and adenine and for three compounds used as surrogates for the ribose and phosphate groups, tetrahydrofuran, 3-hydroxytetrahydrofuran, and trimethylphosphate, respectively. Cross section magnitudes are obtained by observation of positive ion production and normalization to ionization cross sections calculated elsewhere using the binary-encounter-Bethe method. The average cross section of the three bases is 3-10 times smaller than the effective cross section per nucleotide reported for single strand breaks in surface-bound supercoiled DNA. Consequently, damage to the bases alone does not appear to account for the major portion of the strand breaks. The presence of an OH group on the ribose surrogate considerably enhances its cross section. Model compounds in which protonation or OH groups are used to terminate bonds may therefore display larger cross sections than in DNA itself.

Vibrational Feshbach resonances in uracil and thymine.

Sharp peaks in the dissociative electron attachment (DEA) cross sections of uracil and thymine at energies below 3 eV are assigned to vibrational Feshbach resonances (VFRs) arising from coupling between the dipole bound state and the temporary anion state associated with occupation of the lowest sigma* orbital. Three distinct vibrational modes are identified, and their presence as VFRs is consistent with the amplitudes and bonding characteristics of the sigma* orbital wave function. A deconvolution method is also employed to yield higher effective energy resolution in the DEA spectra. The site dependence of DEA cross sections is evaluated using methyl substituted uracil and thymine to block H atom loss selectively. Implications for the broader issue of DNA damage are briefly discussed.

Comment on "Radiation damage of biosystems mediated by secondary electrons: Resonant precursors for uracil molecules" [J. Chem. Phys. 120, 7446 (2004)].

Resonances computed by Gianturco and Lucchese are incorrectly correlated with those observed experimentally. A shift of their pi* resonances by 2 eV gives satisfactory agreement. Arguments for determining whether a resonance is a suitable precursor for the fragmentation products are too simplistic, and in one example, incorrect.

Bond breaking and temporary anion states in uracil and halouracils: implications for the DNA bases.

Low energy electrons are capable of breaking bonds in gas phase DNA bases by means of the dissociative electron attachment process. With the aid of new total scattering data in the halouracils and input from quantum chemical calculations, we describe the dipole bound and valence anion states in these compounds and present assignments for the two types of structure appearing in the cross sections. A clear distinction between the two mechanisms for bond breaking is necessary for an understanding of electron induced damage to DNA.