Revealing the Role of N Heteroatoms in Noncovalent Aromatic Interactions by Ultrafast Intermolecular Coulombic Decay.

Despite the widely recognized importance of noncovalent interactions involving aromatic rings in many fields, our understanding of the underlying forces and structural patterns, especially the impact of heteroaromaticity, is still incomplete. Here, we investigate the relaxation processes that follow inner-valence ionization in a range of molecular dimers involving various combinations of benzene, pyridine, and pyrimidine, which initiate an ultrafast intermolecular Coulombic decay process. Multiparticle coincidence momentum spectroscopy, combined with ab initio calculations, enables us to explore the principal orientations of these fundamental dimers and, thus, to elucidate the influence of N heteroatoms on the relative preference of the aromatic π-stacking, H-bonding, and CH-π interactions and their dependence on the number of nitrogen atoms in the rings. Our studies reveal a sensitive tool for the structural imaging of molecular complexes and provide a more complete understanding of the effects of N heteroatoms on the noncovalent aromatic interactions at the molecular level.

Electron Scattering from 1-Methyl-5-Nitroimidazole: Cross-Sections for Modeling Electron Transport through Potential Radiosensitizers.

In this study, we present a complete set of electron scattering cross-sections from 1-Methyl-5-Nitroimidazole (1M5NI) molecules for impact energies ranging from 0.1 to 1000 eV. This information is relevant to evaluate the potential role of 1M5NI as a molecular radiosensitizers. The total electron scattering cross-sections (TCS) that we previously measured with a magnetically confined electron transmission apparatus were considered as the reference values for the present analysis. Elastic scattering cross-sections were calculated by means of two different schemes: The Schwinger multichannel (SMC) method for the lower energies (below 15 eV) and the independent atom model-based screening-corrected additivity rule with interferences (IAM-SCARI) for higher energies (above 15 eV). The latter was also applied to calculate the total ionization cross-sections, which were complemented with experimental values of the induced cationic fragmentation by electron impact. Double differential ionization cross-sections were measured with a reaction microscope multi-particle coincidence spectrometer. Using a momentum imaging spectrometer, direct measurements of the anion fragment yields and kinetic energies by the dissociative electron attachment are also presented. Cross-sections for the other inelastic channels were derived with a self-consistent procedure by sampling their values at a given energy to ensure that the sum of the cross-sections of all the scattering processes available at that energy coincides with the corresponding TCS. This cross-section data set is ready to be used for modelling electron-induced radiation damage at the molecular level to biologically relevant media containing 1M5NI as a potential radiosensitizer. Nonetheless, a proper evaluation of its radiosensitizing effects would require further radiobiological experiments.

TRAX-CHEMxt: Towards the Homogeneous Chemical Stage of Radiation Damage.

The indirect effect of radiation plays an important role in radio-induced biological damages. Monte Carlo codes have been widely used in recent years to study the chemical evolution of particle tracks. However, due to the large computational efforts required, their applicability is typically limited to simulations in pure water targets and to temporal scales up to the µs. In this work, a new extension of TRAX-CHEM is presented, namely TRAX-CHEMxt, able to predict the chemical yields at longer times, with the capability of exploring the homogeneous biochemical stage. Based on the species coordinates produced around one track, the set of reaction-diffusion equations is solved numerically with a computationally light approach based on concentration distributions. In the overlapping time scale (500 ns-1 µs), a very good agreement to standard TRAX-CHEM is found, with deviations below 6% for different beam qualities and oxygenations. Moreover, an improvement in the computational speed by more than three orders of magnitude is achieved. The results of this work are also compared with those from another Monte Carlo-based algorithm and a fully homogeneous code (Kinetiscope). TRAX-CHEMxt will allow for studying the variation in chemical endpoints at longer timescales with the introduction, as the next step, of biomolecules, for more realistic assessments of biological response under different radiation and environmental conditions.

Intermolecular Charge Transfer Induced Fragmentation of Formic Acid Dimers.

We investigate the intermolecular nonradiative charge transfer process in a double hydrogen-bonded formic acid (FA) dimer, initiated by electron-collision induced double ionization of one FA molecule. Through fragment ions and electron coincident momentum measurements and ab initio calculations, we obtain direct evidence that electron transfer from the neighboring FA molecule to fill one of the two vacancies occurs by a potential energy curve crossing of FA^{++}+FA with FA^{+}+FA^{+*} curves, forming an electronic excited state of dicationic dimers. This process causes the breaking of two hydrogen bonds and subsequently the cleavage of C─H and C─O covalent bonds in the dimers, which is expected to be a general phenomenon occurring in molecular complexes and can have important implications for radiation damage to biological matter.

Concerted Double Hydrogen-Bond Breaking by Intermolecular Coulombic Decay in the Formic Acid Dimer.

Hydrogen bonds are ubiquitous in nature and of fundamental importance to the chemical and physical properties of molecular systems in the condensed phase. Nevertheless, our understanding of the structural and dynamical properties of hydrogen-bonded complexes in particular in electronic excited states remains very incomplete. Here, by using formic acid (FA) dimer as a prototype of DNA base pair, we investigate the ultrafast decay process initiated by removal of an electron from the inner-valence shell of the molecule upon electron-beam irradiation. Through fragment-ion and electron coincident momentum measurements and ab initio calculations, we find that de-excitation of an outer-valence electron at the same site can initiate ultrafast energy transfer to the neighboring molecule, which is in turn ionized through the emission of low-energy electrons. Our study reveals a concerted breaking of double hydrogen-bond in the dimer initiated by the ultrafast molecular rotations of two FA+ cations following this nonlocal decay mechanism.

What is the spatial-temporal behavior of a low, medium and high adsorptive compound in two contrasting natural sediments in OECD 218/219 test systems?

Artificial sediment used in studies according to OECD 218/219 (Sediment Water Chironomid Toxicity Test Using Spiked Sediment/Water) does not necessarily mirror the characteristics of natural sediments. To investigate the influence of sediment characteristics on the spatial-temporal behaviors of bixafen (KfOM = 2244 mL/g), fluopyram (KfOM = 162 mL/g) and N,N-dimethylsulfamide (KfOM ≈ 0 mL/g), experiments according to OECD 218/219 with two contrasting natural sediments were conducted. The silt loam sediment provided a high content of organic matter (OM) (13.1%), while the OM (0.45%) of the sandy sediment was low. Diffusion into (OECD 219) or out (OECD 218) of the sediment was dependent on the extent of adsorption, which is linked to the model compounds ́ adsorption affinities and the sediments ́ OM. Consequently, N,N-dimethylsulfamide showed unhindered mobility in each experimental set up, while the high adsorption affinities of fluopyram and bixafen limited the diffusion in the respective sediments. Therefore, in experiments with the silt loam sediment, both compounds revealed a limited mobility and either accumulated in the top 5 mm of the sediment (OECD 219) or remained homogenously distributed over the sediment depth (OECD 218). A greater mobility was observed within the sandy sediment.The influence of OM as found in a study using artificial sediment could be confirmed. Moreover, the applicability of a TOXSWA model was reassured to predict the measured concentrations at different sediment depths. TOXSWA is used in the regulatory exposure assessment to simulate the behavior of pesticides in surface waters. Calibration of three driving input parameters by inverse modelling (diffusion-, adsorption coefficient and OM) revealed no potential for improvement. The core sampling technique used and the model may contribute to a more realistic determination of concentration to which the Chironomid larvae are exposed to. This applies to water sediment test systems where the test organisms do not evenly inhabit the sediment.

Ultrafast energy transfer between π-stacked aromatic rings upon inner-valence ionization.

Non-covalently bound aromatic systems are ubiquitous and govern the physicochemical properties of various organic materials. They are important to many phenomena of biological and technological relevance, such as protein folding, base-pair stacking in nucleic acids, molecular recognition and self-assembly, DNA-drug interactions, crystal engineering and organic electronics. Nevertheless, their molecular dynamics and chemical reactivity, particularly in electronic excited states, are not fully understood. Here, we observe intermolecular Coulombic decay in benzene dimers, (C6H6)2-the simplest prototypes of noncovalent π-π interactions between aromatic systems. Intermolecular Coulombic decay is initiated by a carbon 2s vacancy state produced by electron-impact ionization and proceeds through ultrafast energy transfer between the benzene molecules. As a result, the dimer relaxes with the emission of a further low-energy electron (<10 eV) and a pair of C6H6+ cations undergoing Coulomb explosion. Coincident fragment-ion and electron momentum spectroscopy, accompanied by ab initio calculations, enables us to elucidate the dynamical details of this ultrafast relaxation process.

Formation of covalently bound C4H4 + upon electron-impact ionization of acetylene dimer.

We investigate the formation mechanisms of covalently bound C4H4 + cations from direct ionization of hydrogen bonded dimers of acetylene molecules through fragment ion and electron coincident momentum spectroscopy and quantum chemistry calculations. The measurements of momenta and energies of two outgoing electrons and one ion in triple-coincidence allow us to assign the ionization channels associated with different ionic fragments. The measured binding energy spectra show that the formation of C4H4 + can be attributed to the ionization of the outermost 1πu orbital of acetylene. The kinetic energy distributions of the ionic fragments indicate that the C4H4 + ions originate from direct ionization of acetylene dimers while ions resulting from the fragmentation of larger clusters would obtain significantly larger momenta. The formation of C4H4 + through the evaporation mechanism in larger clusters is not identified in the present experiments. The calculated potential energy curves show a potential well for the electronic ground state of (C2H2)2+, supporting that the ionization of (C2H2)2 dimers can form stable C2H2⋅C2H2 +(1πu -1) cations. Further transition state analysis and ab initio molecular dynamics simulations reveal a detailed picture of the formation dynamics. After ionization of (C2H2)2, the system undergoes a significant rearrangement of the structure involving, in particular, C-C bond formation and hydrogen migrations, leading to different C44+ isomers.

Double and Triple Differential Cross Sections for Single Ionization of Benzene by Electron Impact.

Experimental results for the electron impact ionization of benzene, providing double (DDCS) and triple differential cross sections (TDCS) at the incident energy of 90 eV, measured with a multi-particle momentum spectrometer, are reported in this paper. The most intense ionization channel is assigned to the parent ion (C6H6+) formation. The DDCS values are presented for three different transferred energies, namely 30, 40 and 50 eV. The present TDCS are given for two fixed values of the ejected electron energy (E2), at 5 and 10 eV, and an electron scattering angle (θ1) of 10°. Different features related to the molecular orbitals of benzene from where the electron is extracted are observed. In addition, a semi-empirical formula to be used as the inelastic angular distribution function in electron transport simulations has been derived from the present DDCS result and compared with other expressions available in the literature.

What is the actual exposure of organic compounds on Chironomus riparius? - A novel methodology enabling the depth-related analysis in sediment microcosms.

A novel active sampling method enabled determination of sediment depth profiles revealing the spatial distribution of model compounds N,N-dimethylsulfamide, fluopyram and bixafen (low, medium, high adsorption affinity) in sediment microcosms according to OECD Test 218/219 (Sediment-Water Chironomid Toxicity Test Using Spiked Sediment/Spiked Water). After the overlying water was removed, plastic tubes were inserted into the sediment and the microcosms were frozen. For depth-related analysis, each "sediment core" was mounted in a cutting device and sawed into three 5-mm-slices, respectively (top, middle, bottom). Each slice was centrifuged for sediment and pore water separation. By various sampling dates within 28 days, we could follow the behavior of model compounds depending on sorption affinities and display specific distribution patterns within the sediment. N,N-dimethylsulfamide showing no sediment adsorption, migrated unhindered in (OECD 219) and out (OECD 218) of the sediment via pore water, resulting in homogenous distributions in both test designs. Fluopyram with moderate adsorption affinity revealed a concentration gradient with declining amounts from top to bottom layer (OECD 219) and higher amounts in the middle and bottom layer as compared to the top layer (OECD 218). Bixafen providing a strong adsorption affinity accumulated in the top layer in OECD 219, while no concentration gradients became visible in OECD 218. For establishing a Toxic Substances in Surface Waters (TOXSWA) model, we compared our measurements with simulated results revealing good agreements. The presented methodology is a useful tool to determine more realistic sediment and pore water concentrations, which the Chironomid larvae are exposed to.

Role of the Environment in Quenching the Production of H_{3}

Ionization and subsequent isomerization of organic molecules has been suggested as an important source of trihydrogen H_{3}^{+} cations in outer space. The high interest in such reactions has initiated many experimental and theoretical studies for various molecules. Here, we report measurements as well as ab initio molecular dynamics simulations on the fragmentation of dicationic methanol monomers and clusters ionized by low-energy (90 eV) electrons. Experimentally, for dicationic monomers, a fragmentation channel for the formation of H_{3}^{+} in coincidence with a COH^{+} cation is observed. The simulations show that an intermediate neutral H_{2} is formed in the first step, and its roaming around the dication ends in the formation of H_{3}^{+}. The entire reaction takes about 100-500 fs. The calculated kinetic energy release for the H_{3}^{+}+COH^{+} ion pair is in excellent agreement with the experimental result. In contrast, for the dicationic clusters, due to the possibility of distributing the two charges onto different molecules, several fast dissociation channels occur and suppress the roaming of H_{2} and formation of H_{3}^{+}. The present Letter suggests that the quenching of H_{3}^{+} formation by the chemical environment is a general phenomenon in dicationic clusters of organic molecules.

A Complete Cross Section Data Set for Electron Scattering by Pyridine: Modelling Electron Transport in the Energy Range 0-100 eV.

Electron scattering cross sections for pyridine in the energy range 0-100 eV, which we previously measured or calculated, have been critically compiled and complemented here with new measurements of electron energy loss spectra and double differential ionization cross sections. Experimental techniques employed in this study include a linear transmission apparatus and a reaction microscope system. To fulfill the transport model requirements, theoretical data have been recalculated within our independent atom model with screening corrected additivity rule and interference effects (IAM-SCAR) method for energies above 10 eV. In addition, results from the R-matrix and Schwinger multichannel with pseudopotential methods, for energies below 15 eV and 20 eV, respectively, are presented here. The reliability of this complete data set has been evaluated by comparing the simulated energy distribution of electrons transmitted through pyridine, with that observed in an electron-gas transmission experiment under magnetic confinement conditions. In addition, our representation of the angular distribution of the inelastically scattered electrons is discussed on the basis of the present double differential cross section experimental results.

Water acting as a catalyst for electron-driven molecular break-up of tetrahydrofuran.

Low-energy electron-induced reactions in hydrated molecular complexes are important in various fields ranging from the Earth's environment to radiobiological processes including radiation therapy. Nevertheless, our understanding of the reaction mechanisms in particular in the condensed phase and the role of water in aqueous environments is incomplete. Here we use small hydrogen-bonded pure and mixed dimers of the heterocyclic molecule tetrahydrofuran (THF) and water as models for biochemically relevant systems. For electron-impact-induced ionization of these dimers, a molecular ring-break mechanism is observed, which is absent for the THF monomer. Employing coincident fragment ion mass and electron momentum spectroscopy, and theoretical calculations, we find that ionization of the outermost THF orbital initiates significant rearrangement of the dimer structure increasing the internal energy and leading to THF ring-break. These results demonstrate that the local environment in form of hydrogen-bonded molecules can considerably affect the stability of molecular covalent bonds.

Ultrafast Proton Transfer Dynamics on the Repulsive Potential of the Ethanol Dication: Roaming-Mediated Isomerization versus Coulomb Explosion.

If a molecular dication is produced on a repulsive potential energy surface (PES), it normally dissociates. Before that, however, ultrafast nuclear dynamics can change the PES and significantly influence the fragmentation pathway. Here, we investigate the electron-impact-induced double ionization and subsequent fragmentation processes of the ethanol molecule using multiparticle coincident momentum spectroscopy and ab initio dynamical simulations. For the electronic ground state of the ethanol dication, we observe several fragmentation channels that cannot be reached by direct Coulomb explosion (CE) but require preceding isomerization. Our simulations show that ultrafast hydrogen or proton transfer (PT) can stabilize the repulsive PES of the dication before the direct CE and form intermediate H2 or H2O. These neutrals stay in the vicinity of the precursor, and roaming mechanisms lead to isomerization and finally PT resulting in emission of H3+ or H3O+. The present findings can help to understand the complex fragmentation dynamics of molecular cations.

Fragmentation dynamics of CS2 in collisions with 1.0 keV electrons.

The dissociation dynamics of CS2 molecules in collisions with 1.0 keV electrons is studied. We observe a series of two- and three-body fragmentation channels which are identified from the correlation map between fragment ions. For all of the channels, the kinetic energy release (KER) distributions are obtained. The Dalitz plot and Newton diagram are adopted to analyze the fragmentation dynamics of the three-body dissociation channels. For C S 2 3 + and C S 2 4 + , both the concerted and sequential fragmentation mechanisms are observed where the concerted mechanism dominates. For C S 2 5 + , only the concerted mechanism is observed. Two types of Coulomb explosion models considering the molecular vibration are adopted to simulate the experimental KER distributions of the three-body channels. While obvious deviations are observed considering each ion during the whole dissociation process with an integer charge, good agreement can be achieved within deviation less than 5% if the charge state of the ions are adopted from ab initio calculations.

Damaging Intermolecular Energy and Proton Transfer Processes in Alpha-Particle-Irradiated Hydrogen-Bonded Systems.

Although the biological hazard of alpha-particle radiation is well-recognized, the molecular mechanisms of biodamage are still far from being understood. Irreparable lesions in biomolecules may not only have mechanical origin but also appear due to various electronic and nuclear relaxation processes of ionized states produced by an alpha-particle impact. Two such processes were identified in the present study by considering an acetylene dimer, a biologically relevant system possessing an intermolecular hydrogen bond. The first process is the already well-established intermolecular Coulombic decay of inner-valence-ionized states. The other is a novel relaxation mechanism of dicationic states involving intermolecular proton transfer. Both processes are very fast and trigger Coulomb explosion of the dimer due to creation of charge-separated states. These processes are general and predicted to occur also in alpha-particle-irradiated nucleobase pairs in DNA molecules.

Direct evidence of two interatomic relaxation mechanisms in argon dimers ionized by electron impact.

In weakly bound systems like liquids and clusters electronically excited states can relax in inter-particle reactions via the interplay of electronic and nuclear dynamics. Here we report on the identification of two prominent examples, interatomic Coulombic decay (ICD) and radiative charge transfer (RCT), which are induced in argon dimers by electron collisions. After initial ionization of one dimer constituent ICD and RCT lead to the ionization of its neighbour either by energy transfer to or by electron transfer from the neighbour, respectively. By full quintuple-coincidence measurements, we unambiguously identify ICD and RCT, and trace the relaxation dynamics as function of the collisional excited state energies. Such interatomic processes multiply the number of electrons and shift their energies down to the critical 1-10 eV range, which can efficiently cause chemical degradation of biomolecules. Therefore, the observed relaxation channels might contribute to cause efficient radiation damage in biological systems.

High-resolution (e, 2e + ion) study of electron-impact ionization and fragmentation of methane.

The ionization and fragmentation of methane induced by low-energy (E0 = 66 eV) electron-impact is investigated using a reaction microscope. The momentum vectors of all three charged final state particles, two outgoing electrons, and one fragment ion, are detected in coincidence. Compared to the earlier study [Xu et al., J. Chem. Phys. 138, 134307 (2013)], considerable improvements to the instrumental mass and energy resolutions have been achieved. The fragment products CH4 (+), CH3 (+), CH2 (+), CH(+), and C(+) are clearly resolved. The binding energy resolution of ΔE = 2.0 eV is a factor of three better than in the earlier measurements. The fragmentation channels are investigated by measuring the ion kinetic energy distributions and the binding energy spectra. While being mostly in consistence with existing photoionization studies the results show differences including missing fragmentation channels and previously unseen channels.

The strange case of East African annual fishes: aridification correlates with diversification for a savannah aquatic group?

BACKGROUND: Annual Nothobranchius fishes are distributed in East and Southern Africa and inhabit ephemeral pools filled during the monsoon season. Nothobranchius show extreme life-history adaptations: embryos survive by entering diapause and they are the vertebrates with the fastest maturation and the shortest lifespan. The distribution of Nothobranchius overlaps with the East Africa Rift System. The geological and paleoclimatic history of this region is known in detail: in particular, aridification of East Africa and expansion of grassland habitats started 8 Mya and three humid periods between 3 and 1 Mya are superimposed on the longer-term aridification. These climatic oscillations are thought to have shaped evolution of savannah African mammals. We reconstructed the phylogeny of Nothobranchius and dated the different stages of diversification in relation to these paleoclimatic events. RESULTS: We sequenced one mitochondrial locus and five nuclear loci in 63 specimens and obtained a robust phylogeny. Nothobranchius can be divided in four geographically separated clades whose boundaries largely correspond to the East Africa Rift system. Statistical analysis of dispersal and vicariance identifies a Nilo-Sudan origin with southwards dispersion and confirmed that these four clades are the result of vicariance events In the absence of fossil Nothobranchius, molecular clock was calibrated using more distant outgroups (secondary calibration). This method estimates the age of the Nothobranchius genus to be 8.3 (6.0 - 10.7) My and the separation of the four clades 4.8 (2.7-7.0) Mya. Diversification within the clades was estimated to have started ~3 Mya and most species pairs were estimated to have an age of 0.5-1 My. CONCLUSIONS: The mechanism of Nothobranchius diversification was allopatric and driven by geographic isolation. We propose a scenario where diversification of Nothobranchius started in rough coincidence with aridification of East Africa, establishment of grassland habitats and the appearance of the typical African bovid fauna of the savannah. Although confidence intervals for the estimated ages of the four Nothobranchius clades are quite large, this scenario is compatible with the biology of extant Nothobranchius that are critically dependent on savannah habitats. Therefore, Nothobranchius diversification might have been shaped by the same paleoclimatic events that shaped African ungulate evolution.

An (e, 2e + ion) study of low-energy electron-impact ionization and fragmentation of tetrahydrofuran with high mass and energy resolutions.

We study the low-energy (E0 = 26 eV) electron-impact induced ionization and fragmentation of tetrahydrofuran using a reaction microscope. All three final-state charged particles, i.e., two outgoing electrons and one fragment ion, are detected in triple coincidence such that the momentum vectors and, consequently, the kinetic energies for charged reaction products are determined. The ionic fragments are clearly identified in the experiment with a mass resolution of 1 amu. The fragmentation pathways of tetrahydrofuran are investigated by measuring the ion kinetic energy spectra and the binding energy spectra where an energy resolution of 1.5 eV has been achieved using the recently developed photoemission electron source. Here, we will discuss the fragmentation reactions for the cations C4H8O(+), C4H7O(+), C2H3O(+), C3H6(+), C3H5(+), C3H3(+), CH3O(+), CHO(+), and C2H3(+).