Sadia Bari

Photodissociation of protonated leucine-enkephalin in the VUV range of 8–40 eV

Until now, photodissociation studies on free complex protonated peptides were limited to the UV wavelength range accessible by intense lasers. We have studied photodissociation of gas-phase protonated leucine-enkephalin cations for vacuum ultraviolet (VUV) photons energies ranging from 8 to 40 eV. We report time-of-flight mass spectra of the photofragments and various photofragment-yields as a function of photon energy. For sub-ionization energies our results are in line with existing studies on UV photodissociation of leucine-enkephalin. For photon energies exceeding 10 eV we could identify a new dissociation scheme in which photoabsorption leads to a fast loss of the tyrosine side chain. This loss process leads to the formation of a residual peptide that is remarkably cold internally.

Quantification of ion-induced molecular fragmentation of isolated 2-deoxy-D-ribose molecules.

Recent experiments on low energy ion-induced damage to DNA building blocks indicate that ion induced DNA damage is dominated by deoxyribose disintegration (Phys. Rev. Lett., 2005, 95, 153201). We have studied interactions of keV H+ and He(q+) with isolated deoxyribose molecules by means of high resolution time-of-flight spectrometry. Extensive statistical fragmentation of the molecules is observed. The fragment distribution is found to follow a power law dependence. The exponent can be used to characterize and quantify the molecular damage.

IONIZATION AND FRAGMENTATION OF ANTHRACENE UPON INTERACTION WITH keV PROTONS AND α PARTICLES

The interaction of keV ions with polyaromatic hydrocarbons is dominated by charge exchange and electronic stopping. We have studied the response of the polyaromatic hydrocarbon anthracene (C14H10) upon keV H+ and He2+ impact using high-resolution time-of-flight mass spectrometry. Extensive fragmentation into small C n H q+ m as well as formation of up to triply charged parent ions is observed. Ab initio electron densities are used to calculate the molecular excitation due to electronic stopping. Fragment yields increase with the increase of electronic stopping as a function of projectile velocity. For equal electronic stopping, He2+ is found to induce more fragmentation than H+. The difference in fragmentation is concluded to be due to two electron processes, which are relevant channels only for He2+.

Interactions of neutral and singly charged keV atomic particles with gas-phase adenine molecules

KeV atomic particles traversing biological matter are subject to charge exchange and screening effects which dynamically change this particles effective charge. The understanding of the collision cascade along the track thus requires a detailed knowledge of the interaction dynamics of radiobiologically relevant molecules, such as DNA building blocks or water, not only with ionic but also with neutral species. We have studied collisions of keV H(+), He(+), and C(+) ions and H(0), He(0), and C(0) atoms with the DNA base adenine by means of high resolution time-of-flight spectrometry. For H(0) and H(+) we find qualitatively very similar fragmentation patterns, while for carbon, strong differences are observed when comparing C(0) and C(+) impact. For collisions with He(0) and He(+) projectiles, a pronounced delayed fragmentation channel is observed, which has not been reported before.

Ion-Induced Fragmentation of Amino Acids: Effect of the Environment

In general, radiation-induced fragmentation of small amino acids is governed by the cleavage of the C-C(α) bond. We present results obtained with 300 keV Xe(20+) ions that allow molecules (glycine and valine) to be ionised at large distances without appreciable energy transfer. Also in the present case, the C-C(α) bond turns out to be the weakest link and hence its scission is the dominant fragmentation channel. Intact ionised molecules are observed with very low intensities. When the molecules are embedded in a cluster of amino acids, a protective effect of the environment is observed. The fragmentation pattern changes: the C-C(α) bond becomes more protected and stable amino acid cations are observed as fragments of the molecular clusters. Evidently, the molecular cluster acts as a buffer for the excess energy, capable of rapidly redistributing excess energy and charge.

Fragmentation of α - and β-alanine molecules by ions at Bragg-peak energies

The interaction of keV He(+), He(2+), and O(5+) ions with isolated alpha and beta isomers of the amino acid alanine was studied by means of high resolution coincidence time-of-flight mass spectrometry. We observed a strong isomer dependence of characteristic fragmentation channels which manifests in strongly altered branching ratios. Despite the ultrashort initial perturbation by the incoming ion, evidence for molecular rearrangement leading to the formation of H(3)(+) was found. The measured kinetic energies of ionic alanine fragments can be sufficient to induce secondary damage to DNA in a biological environment.

Ion-induced ionization and fragmentation of DNA building blocks

The interaction of singly and multiply charged ions with DNA can play a crucial role in biological radiation damage processes. In proton or heavy-ion therapy, high-energy ion beams are already employed for tumour treatment. The most relevant bio-molecular processes occur in the Bragg-peak region and involve primary as well as secondary ions of much lower kinetic energies. Bio-molecular mechanisms relevant in this regime are largely unexplored. First steps towards a better understanding of the relevant processes are ion-induced ionization and fragmentation studies on DNA building blocks, either isolated or in clusters or deposited on surfaces. In this paper, we will briefly summarize the current state of knowledge regarding low-energy ion interactions with DNA building blocks and try to identify important open questions.

Coulomb-explosion imaging of concurrent CH2BrI photodissociation dynamics.

The dynamics following laser-induced molecular photodissociation of gas-phase CH2BrI at 271.6 nm were investigated by time-resolved Coulomb-explosion imaging using intense near-IR femtosecond laser pulses. The observed delay-dependent photofragment momenta reveal that CH2BrI undergoes C-I cleavage, depositing 65.6% of the available energy into internal product states, and that absorption of a second UV photon breaks the C-Br bond of CH2Br. Simulations confirm that this mechanism is consistent with previous data recorded at 248 nm, demonstrating the sensitivity of Coulomb-explosion imaging as a real-time probe of chemical dynamics.

Time-resolved inner-shell photoelectron spectroscopy : From a bound molecule to an isolated atom

Due to its element and site specificity, inner-shell photoelectron spectroscopy is a widely used technique to probe the chemical structure of matter. Here, we show that time-resolved inner-shell photoelectron spectroscopy can be employed to observe ultrafast chemical reactions and the electronic response to the nuclear motion with high sensitivity. The ultraviolet dissociation of iodomethane (CH3I) is investigated by ionization above the iodine 4d edge, using time-resolved inner-shell photoelectron and photoion spectroscopy. The dynamics observed in the photoelectron spectra appear earlier and are faster than those seen in the iodine fragments. The experimental results are interpreted using crystal-field and spin-orbit configuration interaction calculations, and demonstrate that time-resolved inner-shell photoelectron spectroscopy is a powerful tool to directly track ultrafast structural and electronic transformations in gas-phase molecules.

Soft X-ray Spectroscopy as a Probe for Gas-Phase Protein Structure : Electron Impact Ionization from Within

Abstract Preservation of protein conformation upon transfer into the gas phase is key for structure determination of free single molecules, for example using X‐ray free‐electron lasers. In the gas phase, the helicity of melittin decreases strongly as the proteins protonation state increases. We demonstrate the sensitivity of soft X‐ray spectroscopy to the gas‐phase structure of melittin cations ([melittin+qH]q+, q=2–4) in a cryogenic linear radiofrequency ion trap. With increasing helicity, we observe a decrease of the dominating carbon 1u2009s–π* transition in the amide C=O bonds for non‐dissociative single ionization and an increase for non‐dissociative double ionization. As the underlying mechanism we identify inelastic electron scattering. Using an independent atom model, we show that the more compact nature of the helical protein conformation substantially increases the probability for off‐site intramolecular ionization by inelastic Auger electron scattering.