Dipole-Supported Electronic Resonances Mediate Electron-Induced Amide Bond Cleavage.

Dissociative electron attachment (DEA) plays a key role in radiation damage of biomolecules under high-energy radiation conditions. The initial step in DEA is often rationalized in terms of resonant electron capture into one of the metastable valence states of a molecule followed by its fragmentation. Our combined theoretical and experimental investigations indicate that the manifold of states responsible for electron capture in the DEA process can be dominated by core-excited (shake-up) dipole-supported resonances. Specifically, we present the results of experimental and computational studies of the gas-phase DEA to three prototypical peptide molecules, formamide, N-methylformamide (NMF), and N,N-dimethyl-formamide (DMF). In contrast to the case of electron capture by positively charged peptides in which amide bond rupture is rare compared to N─C_{α} bond cleavage, fragmentation of the amide bond was observed in each of these three molecules. The ion yield curves for ions resulting from this amide bond cleavage, such as NH_{2}^{-} for formamide, NHCH_{3}^{-} for NMF, and N(CH_{3})_{2}^{-} for DMF, showed a double-peak structure in the region between 5 and 8 eV. The peaks are assigned to Feshbach resonances including core-excited dipole-supported resonances populated upon electron attachment based on high-level electronic structure calculations. Moreover, the lower energy peak is attributed to formation of the core-excited resonance that correlates with the triplet state of the neutral molecule. The latter process highlights the role of optically spin-forbidden transitions promoted by electron impact in the DEA process.

Dissociative electron attachment to the gas-phase nucleobase hypoxanthine.

We present high-resolution measurements of the dissociative electron attachment (DEA) to isolated gas-phase hypoxanthine (C5H4N4O, Hyp), a tRNA purine base. The anion mass spectra and individual ion efficiency curves from Hyp were measured as a function of electron energy below 9 eV. The mass spectra at 1 and 6 eV exhibit the highest anion yields, indicating possible common precursor ions that decay into the detectable anionic fragments. The (Hyp - H) anion (C5H3N4O(-)) exhibits a sharp resonant peak at 1 eV, which we tentatively assign to a dipole-bound state of the keto-N1H,N9H tautomer in which dehydrogenation occurs at either the N1 or N9 position based upon our quantum chemical computations (B3LYP/6-311+G(d,p) and U(MP2-aug-cc-pVDZ+)) and prior studies with adenine. This closed-shell dehydrogenated anion is the dominant fragment formed upon electron attachment, as with other nucleobases. Seven other anions were also observed including (Hyp - NH)(-), C4H3N4 (-)/C4HN3O(-), C4H2N3 (-), C3NO(-)/HC(HCN)CN(-), OCN(-), CN(-), and O(-). Most of these anions exhibit broad but weak resonances between 4 and 8 eV similar to many analogous anions from adenine. The DEA to Hyp involves significant fragmentation, which is relevant to understanding radiation damage of biomolecules.

Electron ionization of the nucleobases adenine and hypoxanthine near the threshold: a combined experimental and theoretical study.

Electron ionization of the DNA nucleobase, adenine, and the tRNA nucleobase, hypoxanthine, was investigated near the threshold region (∼5-20 eV) using a high-resolution hemispherical electron monochromator and a quadrupole mass spectrometer. Ion efficiency curves of the threshold regions and the corresponding appearance energies (AEs) are presented for the parent cations and the five most abundant fragment cations of each molecule. The experimental ionization energies (IEs) of adenine and hypoxanthine were determined to be 8.70 ± 0.3 eV and 8.88 ± 0.5 eV, respectively. Quantum chemical calculations (B3LYP/6-311+G(2d,p)) yielded a vertical IE of 8.08 eV and an adiabatic IE of 8.07 eV for adenine and a vertical IE of 8.51 eV and an adiabatic IE of 8.36 eV for hypoxanthine, and the lowest energy optimized structures of the fragment cations and their respective neutral species were calculated. The enthalpies of the possible reactions from the adenine and hypoxanthine cations were also obtained computationally, which assisted in determining the most likely electron ionization pathways leading to the major fragment cations. Our results suggest that the imidazole ring is more stable than the pyrimidine ring in several of the fragmentation reactions from both adenine and hypoxanthine. This electron ionization study contributes to the understanding of the biological effects of electrons on nucleobases and to the database of the electronic properties of biomolecules, which is necessary for modeling the damage of DNA in living cells that is induced by ionizing radiation.

Thermal processing of formamide ices on silicate grain analogue.

Fourier transform-infrared spectroscopy (FT-IR) and temperature programmed desorption (TPD) have been used to examine the thermal processing of three isotopes of pure formamide ice (HCONH2, DCONH2, and HCOND2) adsorbed on a SiO2 interstellar grain analogue. Pure formamide ice on SiO2 nanoparticles displays at least three different phases that we interpret as a porous phase from ∼70-145 K, a compacted polycrystalline phase from ∼145-210 K, and a third slow diffusion and sublimation phase from ∼210-380 K. Possible dimerization is also discussed. Formamide desorption from the SiO2 grain surface is characterized by TPD of pure HCONH2 and mixed H2O:HCONH2 ices. Water desorbs at 160 K, and formamide has a TPD peak maximum at ∼228 K. A mean Eact of ∼14.7 kcal/mol (0.64 eV) was obtained using Redhead analysis, indicating strong intermolecular forces within formamide ice. The mixed H2O:HCONH2 ice TPD data suggests possible formamide accumulation if the grains are exposed to temperature cycles <180 K.

Radiation processing of formamide and formamide:water ices on silicate grain analogue.

Lyman-α (121.6 nm) photon and 1 keV electron-beam irradiation of pure HCONH2 (FA) ice and H2O:HCONH2 ice mixtures on high-surface-area SiO2 nanoparticles have been investigated with FT-IR spectroscopy and temperature programmed desorption (TPD). Lyman-α photolysis of pure amorphous FA ice grown at 70 K and crystalline FA ice produced by annealing to 165 K gives spectral signatures between 2120 and 2195 cm(-1) that we assign primarily to OCN(-) and CO. The OCN(-) and CO yields are ∼25% less abundant for crystalline FA ice. Photon and electron processing also produces H2 that is released from the ice between ∼90 and 140 K. A decrease in the H2 TPD peak is seen for irradiated crystalline HCONH2 ice. Lyman-α photolysis of H2O:HCONH2 mixed ices increases OCN(-) and CO production, suggesting a catalytic role of H2O. Also, for pure FA, 1 keV electron irradiation slightly increases the yield of OCN(-), while CO decarboxylation is selectively prevented. CO is also not produced in H2O:HCONH2 ices upon electron irradiation. Dissociative ionization, direct dissociative excitation, and dissociative electron attachment (DEA) channels are accessible in the Lyman-α (121.6 nm) photon and 1 keV electron-beam energy range. DEA energetically favors OCN(-) and H(-) formation, with the latter leading to H2 formation. The FA fragment product identities, yields, and branching ratios are considerably different relative to the gas phase and depend upon the radiation type, ice structure, and the presence of SiO2 nanoparticles. The latter may increase ion-electron recombination and radical recombination rates. The main products observed suggest very different condensed-phase dissociation channels from those reported for gas-phase dissociation. Formation of ions/products from FA is not negligible upon Lyman-α photolysis or electron irradiation, both of which could process ices in interstellar regions as well as in Titan's atmosphere.

Theoretical study of formamide decomposition pathways.

The chemical transformations of formamide (NH(2)CHO), a molecule of prebiotic interest as a precursor for biomolecules, are investigated using methods of electronic structure computations and Rice-Rampserger-Kassel-Marcus (RRKM) theory. Specifically, quantum chemical calculations applying the coupled-cluster theory CCSD(T), whose energies are extrapolated to the complete basis set limit (CBS), are carried out to construct the [CH(3)NO] potential energy surface. RRKM theory is then used to systematically examine decomposition channels leading to the formation of small molecules including CO, NH(3), H(2)O, HCN, HNC, H(2), HNCO, and HOCN. The energy barriers for the decarboxylation, dehydrogenation, and dehydration processes are found to be in the range of 73-78 kcal/mol. H(2) loss is predicted to be a one-step process although a two-step process is competitive. CO elimination is found to prefer a two-step pathway involving the carbene isomer NH(2)CHO (aminohydroxymethylene) as an intermediate. This CO-elimination channel is also favored over the one-step H(2) loss, in agreement with experiment. The H(2)O loss is a multistep process passing through a formimic acid conformer, which subsequently undergoes a rate-limiting dehydration. The dehydration appears to be particularly favored in the low-temperature regime. The new feature identifies aminohydroxymethylene as a transient but crucial intermediate in the decarboxylation of formamide.