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.     

The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase

Near edge x-ray absorption fine structure spectra have been measured and interpreted by means of density functional theory for five different azabenzenes (pyridine, pyridazine, pyrimidine, pyrazine, and s-triazine) in the gas phase. The experimental and theoretical spectra at the N 1s and C 1s edges show a strong resonance assigned to the transition of the 1s electron in the respective N or C atoms to the lowest unoccupied molecular orbital with pi(*) symmetry. As opposed to the N 1s edge, at the C 1s edge this resonance is split due to the different environments of the core hole atom in the molecule. The shift in atomic core-level energy due to a specific chemical environment is explained with the higher electronegativity of the N atom compared to the C atom. The remaining resonances below the ionization potential (IP) are assigned to sigma or pi [corrected] orbitals with mixed valence/Rydberg [corrected] character. Upon N addition, a reduction of intensity is observed in the Rydberg region at both edges as compared to the intensity in the continuum. Above the IP one or more resonances are seen and ascribed here to transitions to sigma(*) orbitals. Calculating the experimental and theoretical Delta(pi) term values at both edges, we observe that they are almost the same within +/-1 eV as expected for isoelectronic bonded pairs. The term values of the pi(*) and sigma(*) resonances are discussed in terms of the total Z number of the atoms participating in the bond.     

Dissociative electron attachment to Pt(PF3)4--a precursor for focused electron beam induced processing (FEBIP)

Experimental absolute cross sections for dissociative electron attachment (DEA) to Pt(PF(3))(4) are presented. Fragment anions resulting from the loss of one, two, three and four PF(3) ligands as well as the Pt(PF(3))F(-) and the F(-) ions were observed. The parent anion Pt(PF(3)) is too short-lived to be detected. The dominant process is loss of one ligand, with a very large cross section of 20?000 pm(2); the other processes are about 200× weaker, with cross sections around 100 pm(2), the naked Pt(-) anion is formed with a cross section of only 1.8 pm(2). The resonances responsible for the DEA bands were assigned based on comparison with electron energy-loss spectra and spectra of vibrational excitation by electron impact. Bands around 0.5 eV and 2 eV were assigned to shape resonances with single occupation of virtual orbitals. A DEA band at 5.9 eV was assigned to a core-excited resonance corresponding to an electron very weakly bound to the lowest excited state. An F(-) band at 12.1 eV is assigned to a core excited resonance with a vacancy in an orbital corresponding to the 2nd ionization energy of the PF(3) ligand. Implications of these findings for FEBIP are discussed.     

High resolution electron attachment to CO₂ clusters

Electron attachment to CO? clusters performed at high energy resolution (0.1 eV) is studied for the first time in the extended electron energy range from threshold (0 eV) to about 10 eV. Dissociative electron attachment (DEA) to single molecules yields O(-) as the only fragment ion arising from the well known (2)Π(u) shape resonance (ion yield centered at 4.4 eV) and a core excited resonance (at 8.2 eV). On proceeding to CO? clusters, non-dissociated complexes of the form (CO?)(n)(-) including the monomer CO?(-) are generated as well as solvated fragment ions of the form (CO?)(n)O(-). The non-decomposed complexes appear already within a resonant feature near threshold (0 eV) and also within a broad contribution between 1 and 4 eV which is composed of two resonances observed for example for (CO?)(4)(-) at 2.2 eV and 3.1 eV (peak maxima). While the complexes observed around 3.1 eV are generated via the (2)Π(u) resonance as precursor with subsequent intracluster relaxation, the contribution around 2.2 eV can be associated with a resonant scattering feature, recently discovered in single CO? in the selective excitation of the higher energy member of the well known Fermi dyad [M. Allan, Phys. Rev. Lett., 2001, 87, 0332012]. Formation of (CO?)(n)(-) in the threshold region involves vibrational Feshbach resonances (VFRs) as previously discovered via an ultrahigh resolution (1 meV) laser photoelectron attachment method [E. Leber, S. Barsotti, I. I. Fabrikant, J. M. Weber, M.-W. Ruf and H. Hotop, Eur. Phys. J. D, 2000, 12, 125]. The complexes (CO?)(n)O(-) clearly arise from DEA at an individual molecule within the cluster involving both the (2)Π(u) and the core excited resonance.     

Mechanism of negative ion formation from phenol and para-chlorophenol by interaction with free electrons

Dissociative electron attachment (DEA) to phenol and para-chlorophenol in the energy range 0-12 eV is studied. Analogies in formation of the resonance states in an ionic benzene and its derivatives are found to arise from the similarity of the aromatic base of the molecules. Differences in DEA processes are defined mainly by the influence of the functional OH-group and, to a lesser degree, by the presence of a chlorine atom. A correlation between the energies of the resonance states and ionization energies of p-chlorophenol and phenol, analogous to that found previously for phenol, is proved. On this basis it is established that the dominating mechanism for formation of molecular negative ions at energies above 5 eV is Feshbach resonance.Copyright 2000 John Wiley & Sons, Ltd.     

Reactions in Nitroimidazole Triggered by Low‐Energy (0–2 eV) Electrons: Methylation at N1‐H Completely Blocks Reactivity

Low‐energy electrons (LEEs) at energies of less than 2 eV effectively decompose 4‐nitroimidazole (4NI) by dissociative electron attachment (DEA). The reactions include simple bond cleavages but also complex reactions involving multiple bond cleavages and formation of new molecules. Both simple and complex reactions are associated with pronounced sharp features in the anionic yields, which are interpreted as vibrational Feshbach resonances acting as effective doorways for DEA. The remarkably rich chemistry of 4NI is completely blocked in 1‐methyl‐4‐nitroimidazole (Me4NI), that is, upon methylation of 4NI at the N1 site. These remarkable results have also implications for the development of nitroimidazole based radiosensitizers in tumor radiation therapy.     

Isomerization and fragmentation reactions of gaseous phenylarsane radical cations and phenylarsanyl cations. A study by tandem mass spectrometry and theoretical calculations

The unimolecular reactions of radical cations and cations derived from phenylarsane, C6H5AsH2 (1) and dideutero phenylarsane, C6H5AsD2 (1-d2), were investigated by methods of tandem mass spectrometry and theoretical calculations. The mass spectrometric experiments reveal that the molecular ion of phenylarsane, 1*+, exhibits different reactivity at low and high internal excess energy. Only at low internal energy the observed fragmentations are as expected, that is the molecular ion 1*+ decomposes almost exclusively by loss of an H atom. The deuterated derivative 1-d2 with an AsD2 group eliminates selectively a D atom under these conditions. The resulting phenylarsenium ion [C6H5AsH]+, 2+, decomposes rather easily by loss of the As atom to give the benzene radical cation [C6H6]*+ and is therefore of low abundance in the 70 eV EI mass spectrum. At high internal excess energy, the ion 1*+ decomposes very differently either by elimination of an H2 molecule, or by release of the As atom, or by loss of an AsH fragment. Final products of these reactions are either the benzoarsenium ion 4*+, or the benzonium ion [C6H7]+, or the benzene radical cation, [C6H6]*+. As key-steps, these fragmentations contain reductive eliminations from the central As atom under H-H or C-H bond formation. Labeling experiments show that H/D exchange reactions precede these fragmentations and, specifically, that complete positional exchange of the H atoms in 1*+ occurs. Computations at the UMP2/6-311+G(d)//UHF/6-311+G(d) level agree best with the experimental results and suggest: (i) 1*+ rearranges (activation enthalpy of 93 kJ mol(-1)) to a distinctly more stable (DeltaH(r)(298) = -64 kJ mol(-1)) isomer 1 sigma*+ with a structure best represented as a distonic radical cation sigma complex between AsH and benzene. (ii) The six H atoms of the benzene moiety of 1 sigma*+ become equivalent by a fast ring walk of the AsH group. (iii) A reversible isomerization 1+<==>1 sigma*+ scrambles eventually all H atoms over all positions in 1*+. The distonic radical cation 1*+ is predisposed for the elimination of an As atom or an AsH fragment. The calculations are in accordance with the experimentally preferred reactions when the As atom and the AsH fragment are generated in the quartet and triplet state, respectively. Alternatively, 1*(+) undergoes a reductive elimination of H2 from the AsH2 group via a remarkably stable complex of the phenylarsandiyl radical cation, [C6H5As]*+ and an H2 molecule.     

Origins of dihydrogen binding to metal-inserted porphyrins: electric polarization and Kubas interaction

Using density functional theory calculations, we have investigated the interactions between hydrogen molecules and metalloporphyrins. A metal atom, such as Ca or Ti, is introduced for incorporation in the central N(4) cavity. Within local density approximation (generalized gradient approximation), we find that the average binding energy of H(2) to the Ca atom is about 0.25 (0.1) eV/H(2) up to four H(2) molecules, whereas that to the Ti atom is about 0.6 (0.3) eV per H(2) up to two H(2) molecules. Our analysis of orbital hybridization between the inserted metal atom and molecular hydrogen shows that H(2) binds weakly to Ca-porphyrin through a weak electric polarization in dihydrogen, but is strongly hybridized with Ti-porphyrin through the Kubas interaction. The presence of d orbitals in Ti may explain the difference in the interaction types.     

Spectroscopy of excited states of carbon anions above the photodetachment threshold

Electronic transitions of C3- and C5- to states lying above the electron affinity of the neutral (EA) have been recorded in the gas phase by laser photodetachment spectroscopy. The excited states are identified by comparison with absorption spectra for the mass-selected ions deposited in neon matrices and with ab initio calculations. The C 2 sigma u (+)-X 2 pi g transition and two higher energy band systems are observed for C3-, corresponding to excitation energies more than 1.5 eV above the EA. In the case of C5- the strongest features, at about 0.6 eV above the EA, are attributed to close lying 2 delta g-X 2 pi u and 2 sigma g(-)-X 2 pi u transitions. The dominant configurations in these states identify them as long-lived Feshbach resonances. Lifetimes for these resonances in C3- are estimated to be between 200 fs and 3 ps from the band widths.     

Functional group dependent dissociative electron attachment to simple organic molecules

Dissociative electron attachment (DEA) cross sections for simple organic molecules, namely, acetic acid, propanoic acid, methanol, ethanol, and n-propyl amine are measured in a crossed beam experiment. We find that the H(-) ion formation is the dominant channel of DEA for these molecules and takes place at relatively higher energies (>4 eV) through the core excited resonances. Comparison of the cross sections of the H(-) channel from these molecules with those from NH(3), H(2)O, and CH(4) shows the presence of functional group dependence in the DEA process. We analyze this new phenomenon in the context of the results reported on other organic molecules. This discovery of functional group dependence has important implications such as control in electron induced chemistry and understanding radiation induced damage in biological systems.     

Angle-resolved photoelectron spectroscopy of the chloro-substituted methanes

The angular distribution parameter, β, was determined for the valence orbitals (IP ′ 21.2 eV) of CCl₄, CHCl₃, CH₂Cl₂, and CH₃Cl in the 10–30 eV photon energy range using dispersed polarized synchrotron radiation. The energy dependence of β in the photoelectron energy range of 2 to 10 eV for the non-bonding chlorine n(Cl) orbitals of these molecules was found to be similar for all n(Cl) orbitals investigated. The energy dependence of β for the σ orbitals in these molecules was similar to that observed previously for other σ orbitals. The experimental CCl₄ results were compared with theoretical CCl₄ results obtained using the Xα multiple scattering formalism. Theory predicts the existence of two strong shape resonances in each of the valence orbitals of CCl₄. The overall agreement between experiment and theory is evaluated along with the experimental evidence concerning the verification of the predicted shape resonances.     

Electron super-rich radicals in the gas phase. A neutralization-reionization mass spectrometric and ab initio/RRKM study of diaminohydroxymethyl and triaminomethyl radicals

Diaminohydroxymethyl (1) and triaminomethyl (2) radicals were generated by femtosecond collisional electron transfer to their corresponding cations (1+ and 2+, respectively) and characterized by neutralization-reionization mass spectrometry and ab initio/RRKM calculations at correlated levels of theory up to CCSD(T)/aug-cc-pVTZ. Ion 1+ was generated by gas-phase protonation of urea which was predicted to occur preferentially at the carbonyl oxygen with the 298 K proton affinity that was calculated as PA = 875 kJ mol-1. Upon formation, radical 1 gains vibrational excitation through Franck-Condon effects and rapidly dissociates by loss of a hydrogen atom, so that no survivor ions are observed after reionization. Two conformers of 1, syn-1 and anti-1, were found computationally as local energy minima that interconverted rapidly by inversion at one of the amine groups with a <7 kJ mol-1 barrier. The lowest energy dissociation of radical 1 was loss of the hydroxyl hydrogen atom from anti-1 with ETS = 65 kJ mol-1. The other dissociation pathways of 1 were a hydroxyl hydrogen migration to an amine group followed by dissociation to H2N-C=O* and NH3. Ion 2+ was generated by protonation of gas-phase guanidine with a PA = 985 kJ mol-1. Electron transfer to 2+ was accompanied by large Franck-Condon effects that caused complete dissociation of radical 2 by loss of an H atom on the experimental time scale of 4 mus. Radicals 1 and 2 were calculated to have extremely low ionization energies, 4.75 and 4.29 eV, respectively, which belong to the lowest among organic molecules and bracket the ionization energy of atomic potassium (4.34 eV). The stabilities of amino group containing methyl radicals, *CH2NH2, *CH(NH2)2, and 2, were calculated from isodesmic hydrogen atom exchange with methane. The pi-donating NH2 groups were found to increase the stability of the substituted methyl radicals, but the stabilities did not correlate with the radical ionization energies.     

Electron attachment to dye-sensitized solar cell components: cyanoacetic acid

The energies of electron attachment associated with temporary occupation of the lower-lying virtual orbitals of cyanoacetic acid (CAA), proposed as a possible component of dye-sensitized solar cells, and its derivative methyl cyanoacetate (MCA) are measured in the gas phase with electron transmission spectroscopy (ETS). The corresponding orbital energies of the neutral molecule, supplied by B3LYP/6-31G(d) calculations and scaled using an empirically calibrated linear equation, are compared with the experimental vertical attachment energies (VAEs). The vertical and adiabatic electron affinities are also evaluated at the B3LYP/6-31+G(d) level as the anion/neutral total energy difference. Dissociative electron attachment spectroscopy (DEAS) is used to measure the total anion current as a function of the incident electron energy in the 0-4 eV energy range, and the negative fragments generated through the dissociative decay channels of the molecular anion are detected with a mass filter. In both compounds only two intense fragment anion currents are observed, that due to loss of a hydrogen atom from the molecular anion ([M - H](-)) and that due to formation of CN(-). In CAA the former signal displays a very sharp feature at 0.68 eV, assigned to a vibrational Feshbach resonance arising from coupling between a dipole bound anion state and a temporary σ* anion state.     

A dramatic difference between the electron-driven dissociation of alcohols and ethers and its relation to Rydberg states

A difference was observed in the reactivity of alcohols and ethers toward free electrons. Whereas the lowest core-excited state of the negative ion-a (2)(n,3s(2)) Feshbach resonance-of the alcohols readily dissociates by losing a hydrogen atom, ethers show no observable signal from this resonance. This difference in reactivity has a parallel in the anomalous shapes and energies of the parent states of the Feshbach resonances, the (1)(n,3s) Rydberg states of the neutral alcohols. We explained this anomaly using potential surfaces of the alcohols and ethers calculated using the TD-DFT method as a function of the dissociation coordinate. The lowest excited state of alcohols was found to be repulsive, whereas a barrier to dissociation was found in the ethers. Rydberg-valence mixing and avoided crossings are decisive in determining the shapes of the potential surfaces. It is concluded that the reactivities of alcohols and ethers toward free electrons are rationalized by assuming that the potential surfaces of the daughter Feshbach resonances closely follow those of the parent Rydberg states, i.e., the lowest Feshbach resonance is repulsive, but a barrier occurs in ethers. The potential surfaces of both the Rydberg states and the Feshbach resonances thus differ dramatically from the non-dissociative surface of the grandparent (2)(n(-1)) positive ions, despite the nominally non-bonding character of the Rydberg electrons.     

The mass spectrum of 2-cyclohexenol: Loss of CH3⋅ and H⋅ from the molecular ion

Methyl radical and hydrogen atom losses from the molecular ion of 2-cyclohexenol and deuterium labelled analogues have been studied. For fragmentations occurring in the first field free region, H? loss is a random process, whereas CH₃? loss is highly specific involving the C-1 hydrogen atom and the C-5 methylene group. A mechanism consistent with these results is proposed.     

Fragmentations des Hydroxyesters a Longue Chaine: Effet Sterique Provoque par un Noyau Benzenique Intercale Entre les Deux Fonctions

The introduction of a benzene ring between the hydroxyl and carbomethoxyl groups of long chain aliphatic hydroxy esters results in a steric hindrance which restrains the interactions between the functional groups and the resulting fragmentations. The study of a series of methyl p-(hydroxyalky) benzoates shows that the importance of these interactions decreases considerably state with (9 + ?)links, or less to the benefit of those fragmentations which do not require such interactions. It is further shown that the specific transfer of a benzylic hydrogen atom to the carbomethoxyl group involves transfer via the hydroxyl group.     

Anomalously long‐lived molecular negative ions of duroquinone

The problem under investigation here is establishment of mechanisms of the resonant electron capture by molecules, using the example of duroquinone (2,3,5,6‐tetramethyl‐1,4‐benzoquinone). A solution is important because it will provide new insights into the fundamental physical laws and widespread applications in various fields like molecular nanoelectronics, touched upon herein too. Resonant electron capture (REC) in duroquinone was studied with negative ion mass spectrometry of the REC as the main method, and UV absorption and the photoelectron spectroscopy as the auxiliary ones. The latter were used to study the electronic structures of the various neutral molecular states that are the parent ones for the negative molecular ions formed by electron attachment to the molecules. B3LYP/6‐311 + G(d,p) calculations were widely used throughout the study. As a result, an intensive peak of the negative molecular ions with anomalously high lifetime (200 microseconds) was registered at the attached electron energy of 1.8 eV. The ions were determined to be quartets delaying the electron autodetachment because of spin prohibition and appearing via inter‐system crossing from the negative molecular ion doublets produced in the core‐excited Feshbach resonances. Finally, the pattern of the REC in duroquinone was obtained for the energy region of 1–4 eV which is presented by shape resonances, core‐excited Feshbach resonances and by mechanisms little‐known for molecules of inter‐shell resonances and the formation of ion quartets. The latter were proposed to be related to the negative differential resistance in molecular nanoelectronics. Copyright © 2012 John Wiley & Sons, Ltd.     

Sigma stellation: a design strategy for electron boxes

The carbon-fluorine antibonding (sigma*) orbitals in a fluorocarbon cage are directed toward a central, common point. If the cage is not too large or too small, then the sigma* orbitals will overlap at that point. An added electron can occupy the resulting molecular orbital, suggesting that cage perfluorocarbons will have large electron affinities. This prediction is supported by electronic structure calculations of all of the fluorinated derivatives of tetrahedrane, cyclopropane, and cubane and of some other fluorinated cage and ring compounds. Perfluorododecahedrane (C20F20) is predicted to have an electron affinity of about 3.4 eV, which is equal to that of the fluorine atom. A few speculative extensions and applications are suggested.     

Elimination sous Impact Electronique de HCN et H· a partir de l'Indole. Comparaison avec l'Indolizine

The two primary electron impact induced fragmentations of indole, loss of HCN and loss of H?, are investigated by the examination of eleven deuterated indoles. All the hydrogen atoms are involved in HCN loss, but predominantly the 5-membered ring hydrogens. This is more pronounced in the 70 eV mass spectrum than in the metastable ions energy range, where the three positions of the 5-membered ring are equivalent. The qualitative results achieved for H? loss give clear indication of the occurrence of an isotope effect and are also consistent with the predominant loss of the 5-membered ring hydrogens, especially of the hydrogen bonded to the nitrogen atom. This behaviour is compared with the behaviour of indolizine, and the energy requirements for HCN loss from the two isomers are discussed.     

Resonant Formation of Strand Breaks in Sensitized Oligonucleotides Induced by Low‐Energy Electrons (0.5–9 eV)

Halogenated nucleobases are used as radiosensitizers in cancer radiation therapy, enhancing the reactivity of DNA to secondary low‐energy electrons (LEEs). LEEs induce DNA strand breaks at specific energies (resonances) by dissociative electron attachment (DEA). Although halogenated nucleobases show intense DEA resonances at various electron energies in the gas phase, it is inherently difficult to investigate the influence of halogenated nucleobases on the actual DNA strand breakage over the broad range of electron energies at which DEA can take place (<12 eV). By using DNA origami nanostructures, we determined the energy dependence of the strand break cross‐section for oligonucleotides modified with 8‐bromoadenine (^8BrA). These results were evaluated against DEA measurements with isolated ^8BrA in the gas phase. Contrary to expectations, the major contribution to strand breaks is from resonances at around 7 eV while resonances at very low energy (<2 eV) have little influence on strand breaks.