Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment.

This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.

Radiation-Induced Molecular Processes in DNA: A Perspective on Gas-Phase Interaction Studies.

Studying the direct effects of DNA irradiation is essential for understanding the impact of radiation on biological systems. Gas-phase interactions are especially well suited to uncover the molecular mechanisms underlying these direct effects. Only relatively recently, isolated DNA oligonucleotides were irradiated by ionizing particles such as VUV or X-ray photons or ion beams, and ionic products were analyzed by mass spectrometry. This article provides a comprehensive review of primarily experimental investigations in this field over the past decade, emphasizing the description of processes such as ionization, fragmentation, charge and hydrogen transfer triggered by photoabsorption or ion collision, and the recent progress made thanks to specific atomic photoabsorption. Then, we outline ongoing experimental developments notably involving ion-mobility spectrometry, crossed beams or time-resolved measurements. The discussion extends to potential research directions for the future.

Soft X-ray absorption and fragmentation of tin-oxo cage photoresists.

"Tin-oxo cage" organometallic compounds are considered as photoresists for extreme ultraviolet (EUV) photolithography. To gain insight into their electronic structure and reactivity to ionizing radiation, we trapped bare gas-phase n-butyltin-oxo cage dications [(BuSn)12O14(OH)6]2+ in an ion trap and investigated their fragmentation upon soft X-ray photoabsorption by means of mass spectrometry. In complementary experiments, the tin-oxo cages with hydroxide and trifluoroacetate counter-anions were cast in thin films and studied using X-ray transmission spectroscopy. Quantum-chemical calculations were used to interpret the observed spectra. At the carbon K-edge, a distinct pre-edge absorption band can be attributed to transitions in which electrons are promoted from C1s orbitals to the lowest unoccupied molecular orbitals, which are delocalized orbitals with strong antibonding (Sn-C σ*) character. At higher energies, the most prominent resonant transitions involve C-C and C-H σ* valence states and Rydberg (3s and 3p) states. In the solid state, the onset of continuum ionization is shifted by ∼5 eV to lower energy with respect to the gas phase, due to the electrostatic effect of the counterions. The O K-edge also shows a pre-edge absorption, but it is devoid of any specific features, because there are many transitions from the different O1s orbitals to a large number of vacant orbitals. In the gas phase, formation of the parent [(BuSn)12O14(OH)6]3+ radical ion is not observed at the C K-edge nor at the O K-edge, because the loss of a butyl group from this species is very efficient. We do observe a number of triply charged photofragment ions, some of which have lost up to 5 butyl groups. Structures of these species are proposed based on quantum-chemical calculations, and pathways of formation are discussed. Our results provide insight into the electronic structure of alkyltin-oxo cages, which is a prerequisite for understanding their response to EUV photons and their performance as EUV photoresists.

Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems.

In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy. In the condensed phase, it is usually very difficult to distinguish direct effects from indirect effects. A straightforward solution for this problem is the use of gas-phase techniques, for instance from the field of mass spectrometry. In this review, we survey mainly experimental but also theoretical work, focusing on radiation-induced intra- and inter-molecular transfer of charge, atoms, and energy within biomolecular systems in the gas phase. Building blocks of DNA, proteins, and saccharides, but also antibiotics are considered. The emergence of general processes as well as their timescales and mechanisms are highlighted.

Direct Observation of Charge, Energy, and Hydrogen Transfer between the Backbone and Nucleobases in Isolated DNA Oligonucleotides.

Understanding how charge and energy, as well as protons and hydrogen atoms, are transferred in molecular systems as a result of an electronic excitation is fundamental for understanding the interaction between ionizing radiation and biological matter on the molecular level. To localize the excitation at the atomic scale, it was chosen to target phosphorus atoms in the backbone of gas-phase oligonucleotide anions and cations, by means of resonant photoabsorption at the L- and K-edges. The ionic photoproducts of the excitation process were studied by a combination of mass spectrometry and X-ray spectroscopy. The combination of absorption site selectivity and photoproduct sensitivity allowed the identification of X-ray spectral signatures of specific processes. Moreover, charge and/or energy as well as H transfer from the backbone to nucleobases has been directly observed. Although the probability of one versus two H transfer following valence ionization depends on the nucleobase, ionization of sugar or phosphate groups at the carbon K-edge or the phosphorus L-edge mainly leads to single H transfer to protonated adenine. Moreover, our results indicate a surprising proton-transfer process to specifically form protonated guanine after excitation or ionization of P 2p electrons.

Ionizing radiation induces cross-linking of two noncovalently bound collagen mimetic peptide triple helices in the absence of a molecular environment.

Cross-linking is a fundamental molecular process that is highly important for many applications, in particular, to tune the properties of collagen-based biomaterials. Chemical reagents, the action of enzymes or physical factors such as heat or radiation can facilitate collagen cross-linking. Ionizing radiation has the advantages of being fast, efficient and free from potentially toxic reagents. Collagen cross-linking by ionizing radiation is thought to occur via a water-mediated pathway. In the past, synthesized collagen mimetic peptides have proven to be of great value for understanding the influence of the amino acid sequence on the stability of tertiary (fibrous) as well as secondary (triple helical) structures of collagen. Cross-linking of synthetic collagen mimetic peptides is often used for modifying the properties of biomaterials. In this work, for the first time, we apply radiation-induced cross-linking to synthetic collagen mimetic peptides and present an experimental and theoretical study of peptide hexamers consisting of two noncovalently bound triple helices in the absence of a molecular environment, i.e. in the gas phase. Our results show that X-ray photoabsorption of the hydroxylated hexamer leads to ionization and cross-linking of the two triple helices: thus, we found evidence that cross-linking can be achieved by ionizing radiation, without the presence of any reagent or water. We propose a cross-linking mechanism involving the creation of two radicals on hydroxyproline side-chains and their recombination, ultimately leading to covalent bond formation between the triple helices.

Mn12 -Acetate Complexes Studied as Single Molecules.

The phenomenon of single molecule magnet (SMM) behavior of mixed valent Mn12 coordination clusters of general formula [MnIII 8 MnIV 4 O12 (RCOO)16 (H2 O)4 ] had been exemplified by bulk samples of the archetypal [MnIII 8 MnIV 4 O12 (CH3 COO)16 (H2 O)4 ] (4) molecule, and the molecular origin of the observed magnetic behavior has found support from extensive studies on the Mn12 system within crystalline material or on molecules attached to a variety of surfaces. Here we report the magnetic signature of the isolated cationic species [Mn12 O12 (CH3 COO)15 (CH3 CN)]+ (1) by gas phase X-ray Magnetic Circular Dichroism (XMCD) spectroscopy, and we find it closely resembling that of the corresponding bulk samples. Furthermore, we report broken symmetry DFT calculations of spin densities and single ion tensors of the isolated, optimized complexes [Mn12 O12 (CH3 COO)15 (CH3 CN)]+ (1), [Mn12 O12 (CH3 COO)16 ] (2), [Mn12 O12 (CH3 COO)16 (H2 O)4 ] (3), and the complex in bulk geometry [MnIII 8 MnIV 4 O12 (CH3 COO)16 (H2 O)4 ] (5). The found magnetic fingerprints - experiment and theory alike - are of a remarkable robustness: The MnIV 4 core bears almost no magnetic anisotropy while the surrounding MnIII 8 ring is highly anisotropic. These signatures are truly intrinsic properties of the Mn12 core scaffold within all of these complexes and largely void of the environment. This likely holds irrespective of bulk packing effects.

Intramolecular hydrogen transfer in DNA induced by site-selective resonant core excitation.

We present experimental evidence for soft X-ray induced intramolecular hydrogen transfer in the protonated synthetic tri-oligonucleotide d(FUAG) in the gas-phase (FU: fluorouracil). The trinucleotide cations were stored in a cryogenic ion trap and exposed to monochromatic synchrotron radiation. Photoionization and photofragmentation product ion yields were recorded as a function of photon energy. Predominanly glycosidic bond cleavage leading to formation of nucleobase-related fragments is observed. In most cases, glycosidic bond cleavage is accompanied by single or double hydrogen transfer. The combination of absorption-site-sensitive soft X-ray spectroscopy with fragment specific mass spectrometry allows to directly relate X-ray absorption site and fragmentation site. We observe pronounced resonant features in the competition between single and double hydrogen transfer towards nucleobases. A direct comparison of experimental data with time-dependent density functional theory calculations, using short range corrected hybrid functionals, reveal that these hydrogen transfer processes are universal and not limited to population of particular excited states localized at the nucleobases. Instead, hydrogen transfer can occur upon X-ray absorption in any nucleobase and in the DNA backbone. Resonances seem to occur because of site-selective suppression of hydrogen transfer channels. Furthermore, non-covalent interactions of the optimized ground state geometries were investigated to identify intramolecular hydrogen bonds along which hydrogen transfer is most likely.

Ionization and Photofragmentation of Isolated Metalloporphyrin Cations Investigated by VUV Action Spectroscopy*.

We investigated the photoionization and fragmentation of isolated metal protoporphyrin IX cations (MPPIX+ with M=Fe, Co, Zn) by means of vacuum-ultraviolet (VUV) action spectroscopy in the energy range of 8.5-35 eV. Experiments were carried out in the gas phase by interfacing an electrospray ionization tandem mass spectrometer with a synchrotron beamline. The mass spectra and partial ion yields show that photoexcitation of the precursor ions predominantly leads to . CH2 COOH radical side-chain losses of the macrocycle with additional methyl radical (. CH3 ) side-chain losses. Ionization, in contrast, leads to the formation of the intact ionized precursor and various doubly charged fragments which are mostly due to side-chain cleavages. Although statistical fragmentation dominates, we found evidence for non-statistical processes such as new fragments involving for example single and double H2 O losses, indicating that different relaxation mechanisms are at play upon photoionization compared to photoexcitation. The measured ionization energies were 9.6±0.2 eV, 9.4±0.2 eV and 9.6±0.2 eV for FePPIX+ , CoPPIX+ and ZnPPIX+ , respectively.

Site-selective soft X-ray absorption as a tool to study protonation and electronic structure of gas-phase DNA.

The conformation and the electronic structure of gas-phase oligonucleotides depends strongly on the protonation site. 5'-d(FUAG) can either be protonated at the A-N1 or at the G-N7 position. We have stored protonated 5'-d(FUAG) cations in a cryogenic ion trap held at about 20 K. To identify the protonation site and the corresponding electronic structure, we have employed soft X-ray absorption spectroscopy at the nitrogen K-edge. The obtained spectra were interpreted by comparison to time-dependent density functional theory calculations using a short-range exchange correlation functional. Despite the fact that guanine has a significantly higher proton affinity than adenine, the agreement between experiment and theory is better for the A-N1 protonated system. Furthermore, an inverse site sensitivity is observed in which the yield of the nucleobase fragments that contain the absorption site appears substantially reduced, which could be explained by non-statistical fragmentation processes, localized on the photoabsorbing nucleobase.

Photoinduced Processes within Noncovalent Complexes Involved in Molecular Recognition.

Investigating the intrinsic properties of molecular complexes is crucial for understanding the influence of noncovalent interactions on fundamental chemical reactions. Moreover, specific molecular recognition between a ligand and its receptor is a highly important biological process, but little is known about the effects of ionizing radiation on ligand-receptor complexes. The processes triggered by VUV photoabsorption on isolated noncovalent complexes between the glycopeptide antibiotic vancomycin and a mimic of its receptor have been probed by means of mass spectrometry and synchrotron radiation. In the case of protonated species, the glycosidic bond of vancomycin was cleaved with low activation energy, regardless of the molecular environment. In sharp contrast, for deprotonated species, electron photodetachment from carboxylate groups only triggered CO2 loss, whereas the glycosidic bond remained intact. Importantly, the noncovalent complex was also found to survive VUV photoabsorption only when the native structure is conserved in the gas phase.

Direct Radiation Effects on the Structure and Stability of Collagen and Other Proteins.

In this review, recent progress in understanding the direct effects of radiation on the structure and stability of collagen, the most abundant protein in the human body, and other proteins is surveyed. Special emphasis is placed on the triple-helical structure of collagen, as studied by means of collagen mimetic peptides. The emerging patterns are the dose dependence of radiation processes and their abundance, the crucial role of radicals in covalent-bond formation (crosslinking) or cleavage, and the influence of the radiation energy and nature. Future research should allow fundamental questions, such as charge transfer and fragmentation dynamics triggered by ionization, to be answered, as well as developing applications such as protein-based biomaterials, notably with properties controlled by irradiation.

Hole Migration in Telomere-Based Oligonucleotide Anions and G-Quadruplexes.

Vacuum ultraviolet photoionization of a gas-phase oligonucleotide anion leads to the formation of a valence hole. This hole migrates towards an energetically favorable site where it can weaken bonds and ultimately lead to bond cleavage. We have studied Vacuum UV photoionization of deprotonated oligonucleotides containing the human telomere sequence dTTAGGG and G-quadruplex structures consisting of four dTGGGGT single strands, stabilized by NH4 + counter ions. The oligonucleotide and G-quadruplex anions were confined in a radiofrequency ion trap, interfaced with a synchrotron beamline and the photofragmentation was studied using time-of-flight mass spectrometry. Oligonucleotide 12-mers containing the 5'-TTAGGG sequence were found to predominantly break in the GGG region, whereas no selective bond cleavage region was observed for the reversed 5'-GGGATT sequence. For G-quadruplex structures, fragmentation was quenched and mostly non-dissociative single and double electron removal was observed.

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

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 protein's 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 1 s-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.

Atomic hydrogen interactions with gas-phase coronene cations: hydrogenation versus fragmentation.

Sequential hydrogenation of polycyclic aromatic hydrocarbon (PAH) cations drives a gradual transition from a planar to a puckered geometry and from an aromatic to an aliphatic electronic structure. The resulting H-induced weakening of the molecular structure together with the exothermic nature of the consecutive H-attachment processes can lead to substantial molecular fragmentation. We have studied H attachment to gas-phase coronene cations in a radiofrequency ion trap using tandem mass spectrometry. With increasing hydrogenation, C2Hi loss and multifragmentation are identified as main de-excitation channels. To understand the dependence of both channels on H-exposure time, we have simulated the molecular stability and fragmentation channels of hydrogenated PAHs using a molecular dynamics approach employing potential energies determined by a density functional based tight binding method. As the coronene fragmentation patterns depend on the balance between energy deposition by H-attachment and the extent of cooling in between subsequent attachment processes, we investigate several scenarios for the energy distribution of hydrogenated PAHs. Good agreement between experiment and simulation is reached, when realistic energy distributions are considered.

Radical-driven processes within a peptidic sequence of type I collagen upon single-photon ionisation in the gas phase.

We report on an experimental single-photon absorption study on gas-phase protonated collagen peptides employing a combination of mass spectrometry and synchrotron radiation. Partial ion yields for the main photoabsorption products vary steadily with photon energy over the range from 14 to 545 eV. At low energy, non-dissociative photoionisation competes with neutral molecule loss from the precursor ion, whereas fragmentation of the peptide backbone dominates at soft X-ray energies. Neutral molecule losses from the ionised peptide are found to have low energy barriers and most likely involve amino-acid residue side-chains with radical character, in particular aspartic acid. A particularly interesting finding is photoinduced loss of proline hydroxylation. The loss of this typical collagen post-translational modification might play a destabilizing role in the collagen structure.

Single-photon absorption of isolated collagen mimetic peptides and triple-helix models in the VUV-X energy range.

Cartilage and tendons owe their special mechanical properties to the fibrous collagen structure. These strong fibrils are aggregates of a sub-unit consisting of three collagen proteins wound around each other in a triple helix. Even though collagen is the most abundant protein in the human body, the response of this protein complex to ionizing radiation has never been studied. In this work, we probe the direct effects of VUV and soft X-ray photons on isolated models of the collagen triple helix, by coupling a tandem mass spectrometer to a synchrotron beamline. Single-photon absorption is found to induce electronic excitation, ionization and conversion into internal energy leading to inter- and intra-molecular fragmentation, mainly due to Gly-Pro peptide bond cleavages. Our results indicate that increasing the photon energy from 14 to 22 eV reduces fragmentation. We explain this surprising behavior by a smooth transition from excitation to ionization occurring with increasing photon energy. Moreover, our data support the assumption of a stabilization of the triple helix models by proline hydroxylation via intra-complex stereoelectronic effects, instead of the influence of solvent.

Multiple Ionization of Free Ubiquitin Molecular Ions in Extreme Ultraviolet Free-Electron Laser Pulses.

The fragmentation of free tenfold protonated ubiquitin in intense 70 femtosecond pulses of 90 eV photons from the FLASH facility was investigated. Mass spectrometric investigation of the fragment cations produced after removal of many electrons revealed fragmentation predominantly into immonium ions and related ions, with yields increasing linearly with intensity. Ionization clearly triggers a localized molecular response that occurs before the excitation energy equilibrates. Consistent with this interpretation, the effect is almost unaffected by the charge state, as fragmentation of sixfold deprotonated ubiquitin leads to a very similar fragmentation pattern. Ubiquitin responds to EUV multiphoton ionization as an ensemble of small peptides.

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.

Probing Structural Information of Gas-Phase Peptides by Near-Edge X-ray Absorption Mass Spectrometry.

Near-edge X-ray absorption mass spectrometry (NEXAMS) is an action-spectroscopy technique of growing interest for investigations into the spatial and electronic structure of biomolecules. It has been used successfully to give insights into different aspects of the photodissociation of peptides and to probe the conformation of proteins. It is a current question whether the fragmentation pathways are sensitive toward effects of conformational isomerism, tautomerism, and intramolecular interactions in gas-phase peptides. To address this issue, we studied the cationic fragments of cryogenically cooled gas-phase leucine enkephalin ([LeuEnk+H]+) and methionine enkephalin ([MetEnk+H]+) produced upon soft X-ray photon absorption at the carbon, nitrogen, and oxygen K-edges. The interpretation of the experimental ion yield spectra was supported by density-functional theory and restricted-open-shell configuration interaction with singles (DFT/ROCIS) calculations. The analysis revealed several effects that could not be rationalized based on the peptide's amino acid sequences alone. Clear differences between the partial ion yields measured for both peptides upon C 1s → π*(C═C) excitations in the aromatic amino acid side chains give evidence for a sulfur-aromatic interaction between the methionine and phenylalanine side chain of [MetEnk+H]+. Furthermore, a peak associated with N 1s → π*(C═N) transitions, linked to a tautomeric keto-to-enol conversion of peptide bonds, was only present in the photon energy resolved ion yield spectra of [MetEnk+H]+.