Posts Tagged ‘fragmentation dynamics’
STSM by Nestor Aguirre, Universidad Autónoma de Madrid (ES) with Paul-Antoine Hervieux, Institut de Physique et Chimie des Materiaux de Strasbourg, IPCMS (FR)
On May 19th, 2014 (12 days)
From SPAIN to FRANCE
Fragmentation of (multi)charged carbon-based molecules by using statistical methods
The propose of this short term scientific mission hosted by Prof. Paul-Antoine Hervieux was to extend and improve the available options of our recently developed software code (M3C). This program allows to study the fragmentation of any kind of molecules by providing structural quantities from standard electronic-structure methods, e.g. electronic energies, vibrational frequencies and equilibrium geometries.
Angular momentum couplings play an important role in fragmentation processes of molecules, where the most important contribution comes from the coupling between the rotational and orbital angular momenta. A good description of this kind of effect is necessary for any fragmentation processes and it is crucial in the description of weakly bound systems, where its contribution reaches the maximum value. During this stay, we worked on the improvement of the fundamental aspects of the theory, paying particular attention to the combinatorial probability term and the rotational coupling scheme. By other hand, we also have taken advantage to discuss with Dr. Marin Chabot and Dr. Karine Béroff from Institut des Sciences moléculaires d’Orsay, consequently allowed us to adapt the program in order to compare with their most recent experimental results, e.g. calculation of breaking curves ( probability of the number of fragments as a function of excitation energy) and kinetic energy releases also as a function of excitation energy.
X-ray induced fragmentation of nucleic acids building blocks and their halogenated analogues
The purpose of this short term scientific mission hosted by Dr Paola Bolognesi was to study the ionisation/fragmentation of nucleic acids building blocks. Particularly, using photoelectron/photoion coincidence technique (PEPICO) and tunable synchrotron light, we can obtain site/state selective mass spectrum giving insights into the fragmentation dynamics following the ionisation. The systems under study were halogenated analogues of the pyrimidine molecule, namely the 2-Cl-pyrimidine, the 2-Br-pyrimidine, and the 5-Br-pyrimidine (see the molecular structures in Figure).
We perform several PEPICO measurements where, at a fixed photon energy, the photoion mass spectrum is recorded in coincidence with an electron of a given kinetic energy. As an example, the direct photoionisation of 2-Cl-pyrimidine at 100 eV photon energy is given in Figure where the mass spectrum associated to electronic states of increasing binding energies are shown. A marked selectivity in the fragmentation of these different ionic states is clearly visible. In the case of the X-ray photoabsorption, the PEPICO technique is applied by setting the photon energy for the resonant excitation of the 1s ® p* transition of a specific atomic site in the molecule and recording the mass spectrum in coincidence with the resonant Auger electron emitted.
The analysis of the different sets of results is in progress. Their presentation in international conferences as well as the publication in peer-reviewed journal is foreseen. In the near future, we expect to further the collaboration between our two groups in order to apply coincidence techniques (PEPICO, ion-ion coincidence after ionisation by ion-impact  or X-ray) to study the fragmentation dynamics of complex molecular systems.
Fragmentation dynamics of N-methyl substituted glycine
The purpose of the STSM was to study the fragmentation dynamics of methyl derivatives of amino acid, namely N,N,N-trimethylglycine (glycine-betaine) and its fully deuterated analogue, with respect to low-energy ion collisions. The molecule exists in the zwitterionic form thus carry two opposite formal charges located at the clearly separated molecular sites. Since in a real biological environment amino acids exist as zwitterionic (twin-ion molecules) therefore the investigation of the glycine-betaine is of particular interest in order to understand the physico-chemical stage of radiation damage.
The experiments were performed by using COLIMACON set-up within ARIBE facility. Briefly, we obtain molecules in the gas phase by evaporation of powders in the ovens. The collimated molecular beam interacts with a pulsed ion beam of O6+. The cationic products are analysed by linear TOF mass spectrometer.
We have performed the experiments with isolated molecules of glycine-betaine and its labelled analogue, which allow us to precisely determine from which side of the molecule a projectile captures the electrons.
The most abundant ionic fragment is observed at m/z 44 and can unambiguously be assigned to COO+. This type of fragmentation has been previously reported from canonical amino acids, however, the fragment has been attributed to N-containing cationic species. Further prominent fragments appear at m/z 58 and 59 from non-labelled molecule and at m/z 66 and 68 from its deuterated analogue. These observations indicate that the fragments are generated from the cleavage of the Ca-Cb bond with the charge localised at the N-terminal group. In addition we observe that for zwitterionic amino acid the probability of nondissociative ionization is negligible (see Figure). The future experiments are planned as a continuation of this project, which will concern the different projectiles and different charge states.
Figure: Mass spectrum of product ions from 48 keV O6+ collisions with fully deuterated N,N,N-trimethylglycine.
STSM by Ana Martín Sómer, Universidad Autonoma de Madrid with Marie-Pierre Gaigeot, Laboratoire Analyse et Modelisation pour la Biologie et l`environnement, LAMBE, Evry
On November 17th, 2013 (14 days)
From SPAIN to FRANCE
Statistical approaches and chemical dynamics simulations to study CID experiments
This STSM allowed the Early Stage Researcher (Ana Martín Sómer) to learn how to perform the kinetic analysis of the unimolecular fragmentation dynamics of formamide-M^(2+) (M=Ca, Sr). Now, the researcher will be able to acomplish the kinetic analysis of the whole surface following the learned procedure.
The ESR also learn to use VENUS-MOPAC program, design the set-up for the AlaGlnAla protonated tripeptide system CID modelization and do some preliminary trajectories on the system. Some preliminary trajectories firsts to set-up the right parameters for running the dynamics simulations were submitted to have an idea of the computational time required to compute one trajectory.