F. Ferreira da Silva

Dissociative Electron Attachment to DNA Bases Near Absolute Zero Temperature: Freezing Dissociation Intermediates

Solvation and temperature are two important variables for controlling chemical change. The rates and products of chemical reactions can alter dramatically in response to large changes in temperature or in moving from the gas to the condensed phase. Understanding such changes provides insight into fundamental aspects of chemistry. Herein, we explore a transition in chemistry brought about by a concomitant change in phase and temperature. We measure the dissociative attachment of electrons to biological molecules—a process important in the radiation damage of DNA—both as free molecules in the gas phase at 400 K and when embedded in superfluid helium at a temperature near absolute zero. The goal is to explore the extent to which the dissociation of the intermediate negative ion that is responsible for the initial attachment of the electrons can be frozen in the extreme environment of ultra-cold and superfluid helium in which molecular vibrations and rotations are in their lowest energy states. The pioneering work of Boudaiffa et al. has demonstrated that low-energy electrons have the potential effectively to induce strand breaks in plasmid DNA and this has motivated a wealth of electron attachment studies with building blocks of DNA in the gas phase 3] and when deposited on thin films , both experimental and theoretical. The unique capability of low-energy electrons to break specific bonds selectively has also been shown previously in gas-phase studies in our own laboratory with the isolated nucleobases (NBs) thymine (T), adenine (A) and uracil. The attachment of a free electron to an isolated nucleobase initially forms an unstable transient negative ion, [NBC ]*, with the same geometry as the neutral precursor (a vertical transition). The attached electron may occupy an antibonding orbital or the vertical transition may end up in the repulsive part of a potential energy curve that begins to separate parts of the transient negative ion. As long as the potential energy of [NBC ]* is higher than that of NB + e, the electron can be detached retaining its initial kinetic energy (elastic scattering) or a reduced kinetic energy (inelastic scattering). Moreover, autodetachment competes with dissociative electron attachment (DEA) until the internuclear separation between the charged and neutral fragments exceeds the intersection of the corresponding potential energy curves of the anionic and neutral system. The time to reach this point of no return towards DEA depends strongly on the mass of the lightest fragment and is shortest if one of the fragments is a hydrogen atom. This may be one reason for the high probability of DEA in NBs and other biomolecules to form a closed-shell anion [NB H] upon electron attachment. 9, 10] In the gas phase, the maximum cross section for hydrogen loss, illustrated in channel 1 a [Reaction (1 a)] , is at around 1 eV for all DNA bases . The H formation, channel 1 b [Reaction (1 b)] , is observed at higher electron energies and has a much lower cross section than neutral hydrogen loss. Furthermore, pronounced site selectivity as a function of the electron energy was discovered for H formation upon free electron attachment to NBs and other organic molecules, as shown in Reaction (1):

Ion–Molecule Reactions in Helium Nanodroplets Doped with C60 and Water Clusters†

Helium nanodroplets, which contain some 10 to 10 atoms, provide an avenue for important new experiments. In a lowpressure environment, the droplets cool within microseconds to 0.37 K by evaporation of weakly bound helium atoms. Molecules captured in collisions with a superfluid droplet will quickly aggregate in the droplet s interior into novel, often metastable structures. These “personal nanocryostats” may be used to explore chemical reactions. For example, M ller et al. reported that ionization initiates complete hydrolysis of cesium–water complexes within the droplets. Herein we report ion–molecule reactions between C60 and small water clusters. Water is an integral part of biomolecular organization; its bioactivity can be further understood by characterization of its function at the C60–H2O interface. [4] C60 is hydrophobic; its hard-core radius of 0.5 nm is close to the crossover point beyond which the breakage of hydrogen bonds becomes unavoidable. Molecular dynamics simulations show that fullerenes strongly bind to single and doublestrand DNA; addition of hydrated C60 to drinking water has been found to mitigate damage of ethanol to brain cells of rats without causing any adverse biological effects. In the present work, helium droplets were doped with C60 and water, and subsequently ionized by electron impact ionization. The interpretation of experimental results was aided by ab initio Hartree–Fock calculations. Two observations stand out: Firstly, the weak interaction between neutral C60 and water extends to the cationic system. Desorption of entire water clusters rather than evaporative loss of water molecules occurs for certain water cluster sizes. Secondly, C60OH + is a major product ion. We postulate that this ion results from doubly charged [C60(H2O)] 2+ intermediates that form by charge transfer from a primary He ion. The existence of doubly charged intermediates in doped helium droplets and their role in subsequent ion–molecule reactions has so far been ignored; these intermediates provide a compelling rationale for previous observations of hydrogen loss from clusters of organic molecules and biomolecules. We first summarize results obtained by ionization of helium droplets doped with water (either H2O or D2O) but no C60 . In agreement with a previous report, [11] electron impact ionization results in a prominent series of protonated water cluster ions. Unprotonated water cluster ions are observed with a 10 % abundance relative to the protonated cluster ions. Unprotonated ions are not observable upon electron impact or multiphoton ionization of bare water clusters, but they occur if water clusters are complexed with heavy rare-gas atoms. These trends are well understood—the ground state of (H2O)2 + corresponds to the proton-transferred isomer OH–H3O , and its dissociation to OH + H3O + is energetically much more facile than dissociation to H2O + H2O . Direct ab initio dynamics studies of water clusters show that vertical ionization is followed by one or more barrierless proton transfer reactions within 100 fs; solvent reorganization leads to a highly excited cluster ion and ejection of the OH radical within sub-picoseconds; enough energy remains for the evaporation of several more water molecules. The composition of cluster ions changes drastically when helium droplets are co-doped with C60 . The most prominent ion series in Figure 1 arises from C60(D2O)n , n = 0, 1, 2. Dehydrogenated ions, that is, ions with the stoichiometry C60(D2O)n 1OD + are also observed, while the abundance of protonated ions is weak. For a quantitative analysis, we fitted the distribution of C60 isotopologues by sets of four Gaussians with fixed ratios of amplitudes computed from the 1.11 % natural abundance of [*] Prof. Dr. O. Echt Department of Physics, University of New Hampshire Durham, NH 03824 (USA) Fax: (+ 1)603-862-2998 E-mail: olof.echt@unh.edu Homepage: http://www.physics.unh.edu/

NCO – , a Key Fragment Upon Dissociative Electron Attachment and Electron Transfer to Pyrimidine Bases: Site Selectivity for a Slow Decay Process

AbstractWe report gas phase studies on NCO– fragment formation from the nucleobases thymine and uracil and their N-site methylated derivatives upon dissociative electron attachment (DEA) and through electron transfer in potassium collisions. For comparison, the NCO– production in metastable decay of the nucleobases after deprotonation in matrix assisted laser desorption/ionization (MALDI) is also reported. We show that the delayed fragmentation of the dehydrogenated closed-shell anion into NCO– upon DEA proceeds few microseconds after the electron attachment process, indicating a rather slow unimolecular decomposition. Utilizing partially methylated thymine, we demonstrate that the remarkable site selectivity of the initial hydrogen loss as a function of the electron energy is preserved in the prompt as well as the metastable NCO– formation in DEA. Site selectivity in the NCO– yield is also pronounced after deprotonation in MALDI, though distinctly different from that observed in DEA. This is discussed in terms of the different electronic states subjected to metastable decay in these experiments. In potassium collisions with 1- and 3-methylthymine and 1- and 3-methyluracil, the dominant fragment is the NCO– ion and the branching ratios as a function of the collision energy show evidence of extraordinary site-selectivity in the reactions yielding its formation. Graphical abstractᅟ

The electronic states of pyrimidine studied by VUV photoabsorption and electron energy-loss spectroscopy

The electronic state spectroscopy of pyrimidine C(4)H(4)N(2) has been investigated using both high resolution VUV photoabsorption in the energy range 3.7 to 10.8 eV (335 to 115 nm) and lower resolution electron energy loss in the range 2 to 15 eV. The low energy absorption band, assigned to the (pi*) <-- 7b(2)(n(N)) (1(1)B(1)<-- 1(1)A(1)) transition, at 3.85(4) eV and the vibrational progressions superimposed upon it have been observed for the first time, due to the availability of a high-resolution photon beam (0.075 nm), corresponding to 3 meV at the midpoint of the energy range studied. Vibronic coupling has been shown to play an important role dictating the nature of the observed excited states, especially for the lowest (1)B(1) state. The 2(1)B(1) state is proposed to have its origin at 7.026 eV according to the vibrational excitation reported in this energy region (7.8-8.4 eV). New experimental evidence of 4(1)A(1) state with a maximum cross section at 8.800 eV is supported by previous ab initio quantum chemical calculations. Rydberg series have been assigned converging to the three lowest ionisation energy limits, 9.32 eV ((2)B(2)), 10.41 eV ((2)B(1)) and 11.1 eV ((2)A(1) + (2)A(2)) with new members reported for the first time and classified according to the magnitude of the quantum defects (delta). Additionally, the absolute differential cross section for inelastic electron scattering has been measured for the most intense band from 6.9 to 7.8 eV assigned to (1)pipi* (3(1)A(1) + 2(1)B(2)).

Electron attachment to amino acid clusters in helium nanodroplets: Glycine, alanine, and serine

The first detailed study of electron attachment to amino acid clusters is reported. The amino acids chosen for investigation were glycine, alanine, and serine. Clusters of these amino acids were formed inside helium nanodroplets, which provide a convenient low temperature (0.37 K) environment for growing noncovalent clusters. When subjected to low energy (2 eV) electron impact the chemistry for glycine and alanine clusters was found to be similar. In both cases, parent cluster anions were the major products, which contrasts with the corresponding monomers in the gas phase, where the dehydrogenated products ([AA(n)-H](-), where AA = amino acid monomer) dominate. Serine clusters are different, with the major product being the parent anion minus an OH group, an outcome presumably conferred by the facile loss of an OH group from the beta carbon of serine. In addition to the bare parent anions and various fragment anions, helium atoms are also observed attached to both the parent anion clusters and the dehydrogenated parent anion clusters. Finally, we present the first anion yield spectra of amino acid clusters from doped helium nanodroplets as a function of incident electron energy.

On the Size of Ions Solvated in Helium Clusters

Helium nanodroplets are doped with SF(6), C(4)F(8), CCl(4), C(6)H(5)Br, CH(3)I, and I(2). Upon interaction with free electrons a variety of positively and negatively charged cluster ions X(+/-)He(n) are observed where X(+/-) = F(+/-), Cl(+/-), Br(+/-), I(+), I(2) (+), or CH(3)I(+). The yield of these ions versus cluster size n drops at characteristic sizes n(s) that range from n(s) = 10.2+/-0.6 for F(+) to n(s) = 22.2+/-0.2 for Br(-). n(s) values for halide anions are about 70% larger than for the corresponding cations. The steps in the ion yield suggest closure of the first solvation shell. We propose a simple classical model to estimate ionic radii from n(s). Assuming the helium density in the first solvation shell equals the helium bulk density one finds that radii of halide anions in helium are nearly twice as large as in alkali halide crystals, indicating the formation of an anion bubble due to the repulsive forces that derive from the exchange interaction. In spite of the simplicity of our model, anion radii derived from it agree within approximately 10% with values derived from the mobility of halide anions in superfluid bulk helium, and with values computed by quantum Monte Carlo methods for X(-)He(n) cluster anions.

The Effect of Solvation on Electron Attachment to Pure and Hydrated Pyrimidine Clusters

Abstract The interaction of low‐energy electrons with biomolecules plays an important role in the radiation‐induced alteration of biological tissue at the molecular level. At electron energies below 15 eV, dissociative electron attachment is one of the most important processes in terms of the chemical transformation of molecules. So far, a common approach to study processes at the molecular level has been to carry out investigations with single biomolecular building blocks like pyrimidine as model molecules. Electron attachment to single pyrimidine, as well as to pure clusters and hydrated clusters, was investigated in this study. In striking contrast to the situation with isolated molecules and hydrated clusters, where no anionic monomer is detectable, we were able to observe the molecular anion for the pure clusters. Furthermore, there is evidence that solvation effectively prevents the ring fragmentation of pyrimidine after electron capture.

Electron attachment to trinitrotoluene (TNT) embedded in He droplets: complete freezing of dissociation intermediates in an extended range of electron energies

Electron attachment to the explosive trinitrotoluene (TNT) embedded in Helium droplets (TNT@He) generates the non-decomposed complexes (TNT)(n)(-), but no fragment ions in the entire energy range 0-12 eV. This strongly contrasts the behavior of single TNT molecules in the gas phase at ambient temperatures, where electron capture leads to a variety of different fragmentation products via different dissociative electron attachment (DEA) reactions. Single TNT molecules decompose by attachment of an electron at virtually no extra energy reflecting the explosive nature of the compound. The complete freezing of dissociation intermediates in TNT embedded in the droplet is explained by the particular mechanisms of DEA in nitrobenzenes, which is characterized by complex rearrangement processes in the transient negative ion (TNI) prior to decomposition. These mechanisms provide the condition for effective energy withdrawal from the TNI into the dissipative environment thereby completely suppressing its decomposition.

Electron transfer-induced fragmentation of thymine and uracil in atom-molecule collisions

Ion-pair formation has been studied in hyperthermal (30-100 eV) neutral potassium collisions with gas phase thymine (C(5)H(6)N(2)O(2)) and uracil (C(4)H(4)N(2)O(2)). Negative ions formed by electron transfer from the alkali atom to the target molecule were analysed by time-of-flight (TOF) mass spectrometry. The most abundant product anions are assigned to CNO(-) and (U-H)(-)/(T-H)(-) and the associated electron transfer mechanisms are discussed. Special emphasis is given to the enhancement of ring breaking pathways in the present experiments, notably CNO(-) formation, compared with free electron attachment measurements.

An investigation into electron scattering from pyrazine at intermediate and high energies

Total electron scattering cross sections for pyrazine in the energy range 10-500 eV have been measured with a new magnetically confined electron transmission-beam apparatus. Theoretical differential and integral elastic, as well as integral inelastic, cross sections have been calculated by means of a screening-corrected form of the independent-atom representation (IAM-SCAR) from 10 to 1000 eV incident electron energies. The present experimental and theoretical total cross sections show a good level of agreement, to within 10%, in the overlapping energy range. Consistency of these results with previous calculations (i.e., the R-matrix and Schwinger Multichannel methods) and elastic scattering measurements at lower energies, below 10 eV, is also discussed.