Fragmentation dynamics of ionised amino acids and neutral clusters of amino acids in the gas phase: a theoretical study

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Química. Fecha de lectura: 11-07-2017Esta tesis tiene embargado el acceso al texto completo hasta el 11-01-201

Dynamics of excited clusters of β-alanine in the gas phase

We present a theoretical study of excited clusters of β-alanine molecules in the gas phase: (β-ala)n, n=2-5. Classical molecular dynamics simulations performed for different internal excitation energies showed a thermal decomposition dependence with the cluster size. We also present an assessment study performed with different families of density functionals using the dimer, (β-ala)2 as a benchmark system. M06-2X provides the best agreement for the relative energies of 20 isomers in comparison with the reference values computed with the MP2 method. The stability and reactivity of several cluster sizes have been investigated with this functional in combination with the 6-311++G(d,p) basis se

X-ray induced fragmentation dynamics of doubly charged L-alanine in gas phase

The molecular fragmentation of doubly charged L-alanine in gas phase was studied in radiation synchrotron experiments. In this presentation, we summarize our theoretical study on the dynamics of this fragmentation, using various computational methods. We show that in practice the ground state MD simulations are able to statistically reproduce the experimental results of the photo-fragmentation initiated at the excited stat

Unusual hydrogen and hydroxyl migration in the fragmentation of excited doubly-positively-charged amino acids in the gas phase

We present a combined experimental and theoretical study of the fragmentation of doubly-positively- charged amino acids in the gas phase. The combination of ab initio molecular dynamics simulations with ion- molecule collisions followed by multiple-coincidence mass spectrometric techniques, allows us to obtain a complete picture of the fragmentation dynamics. In addition to the expected Coulomb explosion, we have found evidence of hydrogen and hydroxyl-group migration processes, which leads to unusual fragmentation product

Internal energy dependence in x-ray-induced molecular fragmentation: An experimental and theoretical study of thiophene

A detailed experimental and theoretical investigation of the dynamics leading to fragmentation of doubly ionized molecular thiophene is presented. Dissociation of double-ionized molecules was induced by S 2p core photoionization and the ionic fragments were detected in coincidence with Auger electrons from the core-hole decay. Rich molecular dynamics was observed in electron-ion-ion coincidence maps exhibiting ring breaks accompanied by hydrogen losses and/or migration. The probabilities of various dissociation channels were seen to be very sensitive to the internal energy of the molecule. Theoretical simulations were performed by using the semiempirical self-consistent charge-density-functional tight-binding method. By running thousands of these simulations, the initial conditions encountered in the experiment were properly taken into account, including the systematic dependencies on the internal (thermal) energy. This systematic approach, not affordable with first-principle methods, provides a good overall description of the complex molecular dynamics observed in the experiment and shows good promise for applicability to larger molecules or clusters, thus opening the door to systematic investigations of complex dynamical processes occurring in radiation damageThis work was supported by a grant of the Academy of Finland, Finnish Cultural Foundation, MICINN Project No. FIS2010-15127 and ERA-Chemistry Project No. PIM2010EEC-00751, the MINECO Projects No. FIS2013- 42002-R and No. CTQ2013-43698-P, the European COST Action No. CM1204 XLIC, an Advanced Grant of the European Research Council XCHEM No. 290853, the CAM Project NANOFRONTMAG, and the European Grant MCITN CORIN

Molecular dynamics of photodissociation: towards more complex systems

We present a combined experimental and theoretical study of the photodissociation of thiophene mole-cule using energy-resolved electron-ion-ion coincidence technique and self-consistent charge density functional tight-binding theory combined with a statistical approach. The observed complex molecular dynamics with many internal-energy-dependent fragmentation pathways is successfully described by the theoretical simulation

Slow ion interaction with N-methylglycine and N-acetylglycine

N-acetyl glycine and N-methyl glycine molecules in the gas phase are ionized by electron exchange with slow O6+ ions at an energy of 48 keV. After ionization, the methyl and acetyl substituted glycines dissociate into fragments analogous to that resulting from ionization and fragmentation of amino acids and peptides, respectively. N-acetylglycine which contains a peptide bond also effectively tautomerizes to the diol form. Such tautomerization is typical for amino acids, however, we show that the tautomerization mechanism of the N-acetylglycine is differen

Charge and energy flows in ionised thymidine

We present a combined experimental and theoretical study of the ionisation and fragmentation of the nucleoside thymidine in the gas phase. Two sources of ionisation/excitation are used, namely UV photons and low-energy multiply charged ions, associated with coincidences measurements, respectively photoelec- tron/photofragment (PEPICO) and fragment/fragment. Coupling these experiments with quantum chemistry calculations, we obtain a complete picture of the fragmentation dynamics, in particular the charge and energy transfers within the molecular edific

Polypeptide formation in clusters of β-alanine amino acids by single ion impact

International audienceThe formation of peptide bonds by energetic processing of amino acids is an important step towards the formation of biologically relevant molecules. As amino acids are present in space, scenarios have been developed to identify the roots of life on Earth, either by processes occurring in outer space or on Earth itself. We study the formation of peptide bonds in single collisions of low-energy He 2+ ions (α-particles) with loosely bound clusters of β-alanine molecules at impact energies typical for solar wind. Experimental fragmentation mass spectra produced by collisions are compared with results of molecular dynamics simulations and an exhaustive exploration of potential energy surfaces. We show that peptide bonds are efficiently formed by water molecule emission, leading to the formation of up to tetrapeptide. The present results show that a plausible route to polypeptides formation in space is the collision of energetic ions with small clusters of amino acids