| 1. |
- Barreiro-Lage, Darío, et al.
(författare)
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Photofragmentation specificity of photoionized cyclic amino acids (diketopiperazines) as precursors of peptide building blocks
- 2023
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - 1463-9076 .- 1463-9084. ; 25:23, s. 15635-15646
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Tidskriftsartikel (refereegranskat)abstract
- The photoionisation and photofragmentation of the two cyclic dipetides cyclo(alanyl-glycine) cGA and cyclo(glycyl-glycine) cGG, have been studied combining experiments and simulations. State selected fragments from the ionized molecules are detected using photo-electron photo-ion coincidence (PEPICO) measurements and specific fragmentation paths are identified and characterized via the use of ion-neutral coincidence maps. The simulations, performed using Quantum Chemistry methods, allow us to infer the fragmentation mechanisms of the ionized and excited molecules. We show that ring opening is followed by emission of the neutral fragments CO and HNCO. In the case of cGG the emission of neutral CO leads to a metastable structure that breaks producing small cationic fragments. The studied cyclic dipeptides evolve under ionizing radiation generating different small aziridin moieties and oxazolidinones. These two species are key reactants to elongate producing peptide chains. The corresponding mechanisms have been computed and show that the reaction requires very low energy and may occur in the presence of ionizing radiation.
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| 2. |
- Barreiro-Lage, Darío, et al.
(författare)
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"Smart Decomposition" of Cyclic Alanine-Alanine Dipeptide by VUV Radiation : A Seed for the Synthesis of Biologically Relevant Species
- 2021
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 12:30, s. 7379-7386
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Tidskriftsartikel (refereegranskat)abstract
- A combined experimental and theoretical study shows how the interaction of VUV radiation with cyclo-(alanine-alanine), one of the 2,5-diketopiperazines (DKPs), produces reactive oxazolidinone intermediates. The theoretical simulations reveal that the interaction of these intermediates with other neutral and charged fragments, released in the molecular decomposition, leads either to the reconstruction of the cyclic dipeptide or to the formation of longer linear peptide chains. These results may explain how DKPs could have, on one hand, survived hostile chemical environments and, on the other, provided the seed for amino acid polymerization. Shedding light on the mechanisms of production of such prebiotic building blocks is of paramount importance to understanding the abiotic synthesis of relevant biologically active compounds.
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| 3. |
- Chiarinelli, Jacopo, et al.
(författare)
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Electron and ion spectroscopy of the cyclo-alanine–alanine dipeptide
- 2022
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 24:10, s. 5855-5867
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Tidskriftsartikel (refereegranskat)abstract
- The VUV photoionisation and photofragmentation of cyclo-alanine–alanine (cAA) has been studied in a joint experimental and theoretical work. The photoelectron spectrum and the photoelectron–photoion coincidence (PEPICO) measurements, which enable control of the energy being deposited, combined with quantum chemistry calculations, provide direct insight into the cAA molecular stability after photoionisation. The analysis of the ion-neutral coincidence experiments with the molecular dynamics simulations and the exploration of the potential energy surface allows a complete identification of the fragmentation pathways. It has been found that the fragmentation always starts with the ring opening through the C–C bond cleavage, followed by release of neutral CO or HNCO moieties.
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| 4. |
- da Silva, Humberto, Jr., et al.
(författare)
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Multiple electron capture, excitation, and fragmentation in C6+-C-60 collisions
- 2014
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Ingår i: Physical Review A. Atomic, Molecular, and Optical Physics. - 1050-2947 .- 1094-1622. ; 90:3, s. 032701-
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Tidskriftsartikel (refereegranskat)abstract
- We present experimental and theoretical results on single- and multiple-electron capture, and fragmentation, in C6+ + C-60 collisions at velocities in the v(col) = 0.05 - 0.4 a.u. range. We use time-of-flight mass spectrometry and coincidence detection of charged fragments to separate pure target ionization from processes in which the C-60 target is both ionized and fragmented. The coincidence technique allows us to identify different types of fragmentation processes such as C-60(q+) -> C-58(q+) + C-2 and C-60(q+) -> C-58((q-1)+) + C-2(+). A quasimolecular approach is employed to calculate charge transfer and target excitation cross sections. First-order time-dependent perturbation and statistical methods are used to treat the postcollisional processes: the calculated rate constants for C-2 and C-2(+) emission from the excited and charged fullerene are then used to evaluate the fragmentation dynamics. We show that the target ionization cross section decreases with the induced target charge state and the impact energy. C-2 emission from C-60(q+) is found to dominate when q <= 2 while C-2(+) emission dominates when q >= 5, in agreement with the present and previous experimental results.
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| 5. |
- Díaz-Tendero, Sergio, et al.
(författare)
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Theoretical study of electron confinement in Cu corrals on a Cu(111) surface
- 2008
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Ingår i: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 77:20
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Tidskriftsartikel (refereegranskat)abstract
- We present a theoretical study of the energies, lifetimes, wave functions, and decay paths of the excited electronic states in corral structures formed by Cu adatoms on the Cu(111) surface. Three different corrals with 35, 48, and 70 Cu adatoms have been studied within a joint approach including the density functional theory and wave packet propagation. Confinement of the electronic surface state inside the corral structure leads to the formation of well-defined resonances in the density of electronic states. Particular emphasis is given in the present work to the role of excited electronic states localized on the ring of Cu adatoms forming the corral. While never discussed in the past for corral structures, these states are equivalent to the one-dimensional sp band of Cu atomic chains assembled on the Cu(111) surface that has been recently studied thoroughly. The coupling between the confined surface state resonances and the sp state localized on the Cu ring have been studied in detail. It is shown that the sp state localized on the corral wall appears as a strong perturbation in the spectrum of confined states. © 2008 The American Physical Society.
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| 6. |
- Ganguly, Smita, et al.
(författare)
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Coincidence study of core-ionized adamantane: Site-sensitivity within a carbon cage?
- 2022
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Ingår i: Physical chemistry chemical physics : PCCP. - 1463-9084. ; 24:47, s. 28994-29003
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the fragmentation dynamics of adamantane dications produced after core-ionization at the carbon edge followed by Auger decay. The combination of high-resolution electron spectroscopy, energy-resolved electron-ion multi-coincidence spectroscopy and different theoretical models allows us to give a complete characterization of the processes involved after ionization. We show that energy- and site-sensitivity is observed even for a highly-symmetric molecule that lacks any unique atomic site.
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| 7. |
- Ganguly, Smita, et al.
(författare)
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The origin of enhanced O2+ production from photoionized CO2 clusters
- 2022
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Ingår i: Communications Chemistry. - 2399-3669.
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Tidskriftsartikel (refereegranskat)abstract
- CO2-rich planetary atmospheres are continuously exposed to ionising radiation driving major photochemical processes. In the Martian atmosphere, CO2 clusters are predicted to exist at high altitudes motivating a deeper understanding of their photochemistry. In this joint experimental-theoretical study, we investigate the photoreactions of CO2 clusters (≤2 nm) induced by soft X-ray ionisation. We observe dramatically enhanced production of O2- from photoionized CO2 clusters compared to the case of the isolated molecule and identify two relevant reactions. Using quantum chemistry calculations and multi-coincidence mass spectrometry, we pinpoint the origin of this enhancement: A size-dependent structural transition of the clusters from a covalently bonded arrangement to a weakly bonded polyhedral geometry that activates an exothermic reaction producing O+2. Our results unambiguously demonstrate that the photochemistry of small clusters/particles will likely have a strong influence on the ion balance in atmospheres.
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| 8. |
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| 9. |
- Oostenrijk, Bart, et al.
(författare)
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Fission of charged nano-hydrated ammonia clusters - microscopic insights into the nucleation processes
- 2019
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 21:46, s. 25749-25762
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Tidskriftsartikel (refereegranskat)abstract
- While largely studied on the macroscopic scale, the dynamics leading to nucleation and fission processes in atmospheric aerosols are still poorly understood at the molecular level. Here, we present a joint experimental-theoretical study of a model system consisting of hydrogen-bonded ammonia and water molecules. Experimentally, the clusters were produced via adiabatic co-expansion. Double ionization ionic products were prepared using synchrotron radiation and analyzed with coincidence mass- and 3D momentum spectroscopy. Calculations were carried out using ab initio molecular dynamics to understand the fragmentation within the first similar to 500 fs. Further exploration of the potential energy surfaces was performed at a DFT level of theory to gain information on the energetics of the processes. Water was identified as an efficient nano-droplet stabilizer, and is found to have a significant effect even at low water content. On the molecular level, the stabilizing role of water can be related to an increase in the dissociation energy between ammonia molecules and the water enriched environment at the cluster surface. Furthermore, our results support the role of ammonium as a charge carrier in the solution, preferentially bound to surrounding ammonia molecules, which can influence the atmospheric nucleation process.
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