Posts Tagged ‘WG2’
Electronic properties of Flavin Adenine Dinucleotide anions
The purpose of this Short Term Scientific Mission (STSM) was to investigate the photo-induced dissociation of flavin adenine dinucleotide (FAD) anions in vacuo. These experiments utilized the Sep1 accelerator mass spectrometer complex at Aarhus University, Department of Physics and Astronomy. Our scientific aim was to assess the plausibility of the proposed role if FAD in the perception of magnetic fields by migratory birds. Using a combination of optical spectroscopy and mass spectrometry techniques known as action spectroscopy, we investigated the excited state photophysics and relaxation dynamics of isolated FAD anions.
At Sep1, FAD anions were transferred into vacuum by electrospray ionizaton and accelerated to 50 keV. The photo-induced dissociation (PID) mass spectrum was recorded by irradiating mass-selected FAD anions with a high-intensity pulsed OPO laser at a fixed wavelength and separating the daughter anions with an electrostatic energy analyzer. For the most abundant daughter ions, excitation energy (wavelength) dependence measurements, so-called action spectra, and pulse energy dependence measurements were performed. A surprising result was the observation of dissociation channels activated by the absorption of a single photon, and which were much less prominent in collision induced dissociation (CID) experiments. This suggests that ultrafast excited state processes may lead to non-statistical fragmentation of these ions.
This highly productive STSM resulted in a wealth of new data on the photo-physics FAD anions. After further analyzing these results, including computational modeling of the dissociation processes, we will prepare a manuscript for publication. We expect follow-up measurements and experiments on similar systems to lead to a long a fruitful collaboration between Stockholm and Aarhus Universities.
A new method to determine of energy-transfer distributions in ionizing ion-molecule collisions via photoelectron-photoion coincidence experiments in furan molecule
A detailed knowledge of the response of complex molecular systems to ionization or excitation and its influence on chemical reactivity is required to fully understand processes in astrophysical environments, planetary atmospheres as well as mechanisms associated with radiation damage. The study of such systems requires the support of theoretical investigations. However, a meaningful comparison between experimental and theoretical results requires the knowledge of the energy transferred in the radiation interaction. This is straightforward in photon absorption processes, but in case of ion interaction very difficult as collisions occur at different impact parameters, thus associated with a wide distribution of energy transfer. Recently, the joint effort of the CIMAP group (France), the CNR-ISM group (Italy) and the UAM group (Spain) has proposed a new method to determine of energy-transfer distributions in ionizing ion-molecule collisions via photoelectron-photoion coincidence experiments in the case of thymidine molecule (S. Maclot et al, Phys. Rev. Lett. 117, 07321 (2016)).
The objective of the present mission to the Elettra Synchrotron (Trieste, Italy) was to investigate the state-selected fragmentation of furan (a prototype of planar five membered hetero-aromatic compounds) and glycine (the simplest amino acid) molecules in the valence and inner valence ionization region. Figure 1a) shows obtained photoelectron spectra (PES) at 60 eV for glycine molecule. Based on obtained PES we selected binding energy values in vide range from the ionization threshold up to 30-40 eV to perform Photoelectron-Photoion Coincidence spectra (PEPICO), see Figure 1b).
The obtained results will be implemented in the proposed method to determine energy transfer ion –molecule collisions. Our aim is to fully validate the proposed method and to estimate the energy transfer in ion collisions with different impact parameters. The CIMAP group, from the French ion beam facility (GANIL), has already measured mass spectra for different ions (He2+, O3+, O6+, Ar11+ and Xe25+) at for glycine molecule and the experiments with furan molecule are planned in this year.
Figure 1 a) Photoelectron spectra obtained at 60 eV for glycine (83°C) molecule. The lines indicate selected binding energy values for PEPICO investigations. b) PEPICO spectra for glycine molecules for six selected binding energy between 8.5 eV and 32 eV.
Photochemistry of small acetamide and acetic acid clusters
Experimental studies of biological bulk systems (proteins, DNA) tend to obscure the details of photoinduced reaction mechanisms due to the influence of the environment. Therefore, experiments with clusters of small molecules of biological interest offer an elegant solution to the problem mentioned above.
We combined the synchrotron radiation with the ion mass spectroscopy to study gas-phase clusters of acetamide, (CH3CONH2)n, and acetic acid molecules, (CH3COOH)n, produced by the supersonic expansion source. Clusters of studied compounds are capable of contributing to C–H…O=C, O–H…O=C and N–H…O=C types of intermolecular hydrogen bond interactions that play an important role in biology, being responsible, for example, for the structural organization of proteins. We explored photodissociation pathways of the clusters using mass spectroscopy as well as their electronic properties as a function of their size using partial ion yield (PIY) technique, where an array of time-of-flight mass spectra was measured at increasing photon energies (see PIY map of acetamide clusters and extracted PIY curves in Fig.1).
Our study showed that almost identical structures of the studied compounds that differ only by one functional group result in different photodissociation behavior under vacuum ultraviolet ionization. They both readily undergo dissociation by proton transfer; in acetamide clusters, proton transfer mainly occurs from the amino group, while in acetic acid clusters from the hydroxyl group. The second fragmentation channel for acetamide clusters is multistep ammonia ion transfer that was detected for clusters up to tetramers, while in acetic acid clusters, only dimer fragments by the methyl group loss (not a transfer). The structures of the ionized dimers were optimized, and the proton transfer and ammonia transfer processes probed using ab initio calculations.
As an outcome of the visit, the initial draft for the publication with reported experimental ionization and appearance energies of the clusters and their fragments was prepared.
Fig. 1. Partial ion yield (PIY) map of acetamide clusters plotted as ion flight time versus photon energy. Below that are extracted PIY curves of acetamide monomer and protonated monomer. Blue lines represent the fit to the curves. The intersection point of the lines (marked with vertical black line) is assigned to the ion appearance energy (AE).
Dynamical, energetic and entropic aspects of the fragmentation of excited neutral and cationic furan molecules in the gas phase
The aim of this Short Term Scientific Mission within the COST XLIC Action was to continue our collaborative study on the fragmentation of small ring molecule: furan (C4H4O). Furan belongs to the family of ring structures that are analogous to the deoxyribose building block of the DNA helix; hence it can serve as model system for track simulations in biological medium. The fragmentation mechanism of going through various intermediates is still unclear, so in this work our goal is to extend and complement previous studies.
Firstly, we investigated possible isomerization and dehydrogenation of furan by exploration of the appropriate regions in the potential energy surface with Density Functional Theory. In order to improve the description of the process, we applied a statistical approach that allows to describe the unimolecular decomposition of excited systems: M3C (Microcanonical Metropolis Monte Carlo). With the new 2.0 version of the M3C program we performed multiple simulations. In Figure 1 we present the probability of the most populated species as a function of the internal energy. In accordance with the results of previous pyrolysis experiments, the major observed products were the following species: CO, H3C4, H2C2 and H2C2O. Additionally, we note the constantly high probability of CO production for higher energies (purple line in Figure 1). This result is consistent with our previous calculations using ADMP molecular dynamics method. In conclusion, the improved M3C code has the capacity to become a convenient tool for the description of fragmentation processes.
We are currently working on a manuscript describing the obtained results that we plan to submit to the special issue of the PCCP journal devoted to the XLIC-COST Action. We also intend to continue the collaboration between the groups in Gdańsk and Madrid by extending the applied methodology to charged furan. These results will be useful to help in the interpretation of recent experimental measurements carried out by other groups in the XLIC network.
Figure 1 M3C results: Species probabilities as a function of the internal energy
Ion-molecule reactivity monitoring with synchrotron radiation: reactions of CH2CN+ isomers with hydrocarbons
The atmosphere of Titan, Saturn’s largest satellite, hosts one of the most complex organic chemistry in the Solar system, initiated by N2 and CH4 and leading to the synthesis of complex hydrocarbons, nitriles and prebiotic molecules. Titan’s atmosphere is very similar to the Earth’s primordial atmosphere, thus understanding Titan atmospheric chemistry is extremely relevant for the chemical evolution of our planet.
Titan has a significant ionosphere and results from the Cassini-Huygens mission have demonstrated a strong implication of ionospheric chemistry in the synthesis of complex N-containing molecules, that maybe the precursors of stratospheric tholins.
Among N-containing ions, C2H2N+ have been detected on Titan, and during the STSM we have studied the reactivity of C2H2N+ isomers with CH4, C2H2 and C2H6. Using dissociative photoionization of appropriate neutral precursors, we have successfully demonstrated the possibility to generate different C2H2N+ isomers, namely the cyclic one (from the CH3CN precursor) and the cyanomethyl CH2CN+ cation (from the ICH2CN precursor). The experiments have been performed using the CERISES set-up, a guided ion beam mass spectrometer that permits the measurement of absolute reactive cross sections and branching ratios as a function of photon and collision energies.
Among the most relevant results we mention:
a) in the case of CH4, the CH2CN+ cation is the only reactive isomer, and one of the three most abundant product is C3H4N+ (plus H2) in which a new C-C bond has been formed
b) in the case of C2H2, both c-C2H2N+ and CH2CN+ are responsible for the synthesis of the most abundant C3H3+ product, while minor channels CH3+ (plus HC3N) and C4H2N+ (plus H2) derive exclusively from the linear isomer, as shown in the Figure.
The experiments have been carried out in a joint collaboration among the Host Institution in Orsay/SOLEIL Synchrotron (C. Alcaraz, C. Romanzin, R. Thissen), the Trento group (D. Ascenzi), the Stockholm group (W. Geppert) and the Prague team (M. Polasek) and we are confident that they will results in at least one scientific publication.
Formation of neutral high-Rydberg fragments in heterocyclic molecules after VUV excitation with pulsed field ionization
Our recent studies on the production of neutral high-Rydberg (HR) fragments at the K edges of different molecules (see e.g. A. Kivimäki, et al., J. Phys. Chem. A 120 (2016) 4360–4367) have revealed to the presence of ultrafast photoelectron recapture processes, where the photoelectron is pushed back to HR orbital of the molecular ion. This occurs via the population of val-2 HR1 states, whose dissociation can then yield neutral fragments in HR states. Those fragments may also be produced following resonant Auger decay after core–excitation.
In the present Short-Term Scientific Mission we extended the above research to observation of the high-Rydberg (HR) fragments formed in the dissociative photoionization of the heterocyclic molecules (isoxazole, pyridine) triggered by the VUV and soft x-ray excitation. To identify the neutral fragments being in the high-Rydberg orbitals and elucidate the processes underlying their production we have performed the measurements of the total ion yields, the yields of neutral HR fragments without mass resolution, the TOF spectra of the HR fragments as well as the PEPICO coincidence maps utilizing the TOF mass spectrometer that was modified for pulsed field ionization measurements. An example of our results on the dissociative photoionization of the isoxazole after the VUV excitation is shown in figure below. Because recapture processes to Rydberg states cannot be observed at valence ionization region since there is no Auger electron emission, our preliminary results suggest that in the valence region the fragmentation into the HR fragments may occur via the 2p-2 virt1 states (where virt1 may also be the HR orbitals). These val-2 HR1 states may be populated either as shake-up photoionization or as correlation satellites of inner-valence states.
We plan to publish the results in high-profile journal as soon as possible. This STSM was successfully accomplished and I am grateful to the COST Action CM1204 XLIC for the opportunity to cooperate with the Elettra GasPhase and CiPo beamlines teams.
The stability of interstellar fullerenes
Fullerenes C60 and C70 are the largest molecules detected in space so far. Because of their highly symmetric structures, they are two of the most resistant molecules known on Earth. However, their actual stability under the harsh conditions of the interstellar medium has not been investigated yet. Retrieving such information is important to establish the role of fullerenes in the evolutionary scheme of cosmic dust, in terms of possible building blocks of larger grains and also in terms of possible implications for astrobiology.
The goal of this STSM has been to start investigating the interactions between C60 and a gas of H, He and C ions for collision energies below few tens of keV, typically arising from supernova shocks. The shocks propagate into the interstellar medium, heating and accelerating the gas. We have determined the energy ranges of our projectiles and evaluated the collision rate expected under astrophysical conditions. This information is necessary to properly model the fragmentation of C60 molecules via classical Molecular Dynamics (MD) simulations.
The theoretical work started during this STSM will result in at least two separate publications and will be complemented by experiments at the DESIREE facility, which we planned during my stay. The aim is to measure the absolute destruction cross sections and threshold energies for C60 following ionic bombardment in the sub-keV energy regime. This project also represents the beginning of a long-term collaboration to investigate
the stability of more carbonaceous structures of astrophysical relevance, like e. g. hydrocarbon nanoparticles.
Figure: Kinetic energy distribution of the considered ionic projectiles for the minimum and maximum gas temperature relevant for this study. The specific energy ranges resulting from non-thermal acceleration are reported in the top panel.
Study of pesticides degradation by solar radiation
The main objective of the activities performed during this short-term STSM scientific mission in the group of Dr. Paola Bolognesi was to study the photo induced fragmentation of three long life pesticides of common use, under exposition to VUV radiation, at the fixed wavelengths of rare gas discharge lamps, in controlled experimental conditions. Pendimethalin, 4,4’-DDT and lindane were the pesticides selected to perform the studies, while the rare gas discharge lamps were those of He, Ne, Ar and Kr.
The work was performed in a home-made apparatus developed at the ISM-CNR. In the set-up, the rare gas discharge lamps coupled to a time of flight (TOF) spectrometer allowed to fully address the next three issues: (i) To study the fragmentation spectra of the pesticides, together with their main dissociation channels, at the discrete photon energies provided by the rare gas discharge lamps; (ii) To compare the fragmentation spectra of these molecules at the different radiation wavelengths. This provided a rough estimation of the appearance energy of each fragment; (iii) To analyse the effect of chlorine atoms and nitro functional groups in the photofragmentation and in the possible formation of degradation products.
Photolysis could govern pesticides life-time in the atmosphere and the kind of degradation products formed. The behaviour and distribution of these pesticides and their degradation products in the environment, taking into account distant locations from their use following long-range environmental transportation, are of particular concern in the risk assessment that should overcome to achieve their commercialization in Europe. Therefore, results obtained in this study might be a first step to develop a methodology to determine pesticides impact into the environments, in order to fulfil the requirements and conditions established by Article 4 of the Regulation 1107/2009 for their approval and authorization at EU level.
Taking into account the novelty of the study, the most promising results will be disclosed in SCI journals and proceedings from international conferences related to the research subjects. The dissemination of results among companies within the agrochemical sector will be another outlet for results. The experimental results obtained in the CNR-ISM will also be compared with those obtained via molecular dynamics simulations performed in the CCC-UAM (Scientific Computing Center – Autonomous University of Madrid) under the supervision of Prof. Manuel Alcamí (Department of Chemistry – UAM). This will allow to assessing the potential of both home-made apparatus at the ISM-CNR together with the UAM theoretical tools to be implemented in the risk assessment of pesticides within the European legislative framework.
Homochiral and heterochiral clusters of amino acids: What makes the difference?
Amino acids build peptides and proteins which are major building blocks of cells. Most of them exist in two structural motifs namely L-chirality and D-chirality. In this collaboration which was initiated within the COST XLIC network, we studied clusters of a single or two different amino acids with a focus on the influence of chirality on the clustering behavior. Intrigued by the fact that homochiral samples can form particularly stable clusters, we studied their collision activated fragmentation and also started with combinations that have not yet been reported and that will give us more hints on the structure of theses hydrogen-bonded clusters.
A homochiral mass-selected Serine octamer cluster has been activated by collisions with argon. With increasing collision energy, the clusters sequentially lose single Serine molecules. The mass distributions do not point to a particularly stable substructure such as a dimer or trimer unit. With further increase of the collision energy, the Serine monomer starts to fragment by loss of water or formic acid. Furthermore, spectra for mixed Serine-Valine and mixed Proline-AA clusters have been obtained for several amino acids (AA) and different chirality.
We plan to write a publication on our results and to extend our studies within a new collaborative research project.
XUV attosecond ionisation of ferrocene: fragmentation and charge dynamics
How charge and energy redistribute in a complex molecular system? What are timescales of subsequent electronic and nuclear dynamics? These questions are the main topics of the present STSM.
In the Lund Laser Centre, in collaboration with the group of Per Johnsson, we have investigated the ionisation of ferrocene by XUV attosecond pulse trains (APTs). This organometallic molecule [Fe(C5H5)2] is formed by an iron atom in sandwich between two aromatic rings. During this one week STSM, we successfully obtained results on the ionisation/fragmentation of the ferrocene which paved the way for a next experimental campaign on time-resolved measurements.
We have measured the fragmentation mass spectra following the ionisation by XUV APT. The molecular fragmentation is reduced as shown by the intense peak of intact molecule. Moreover due to the photon energy a good signal of the intact molecular dication is also observed. Covariance measurements have been also obtained and their analysis is under progress. Together with fragmentation patterns, the obtained results during this STSM will allow to select some decay channels to be specifically studied using XUV pump-XUV probe time resolved technique.