| 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. |
- Bonassi, Stefano, et al.
(författare)
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An increased micronucleus frequency in peripheral blood lymphocytes predicts the risk of cancer in humans
- 2007
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Ingår i: Carcinogenesis. - : Oxford University Press (OUP). - 0143-3334 .- 1460-2180. ; 28:3, s. 625-631
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Tidskriftsartikel (refereegranskat)abstract
- The frequency of micronuclei (MN) in peripheral blood lymphocytes (PBL) is extensively used as a biomarker of chromosomal damage and genome stability in human populations. Much theoretical evidence has been accumulated supporting the causal role of MN induction in cancer development, although prospective cohort studies are needed to validate MN as a cancer risk biomarker. A total of 6718 subjects from of 10 countries, screened in 20 laboratories for MN frequency between 1980 and 2002 in ad hoc studies or routine cytogenetic surveillance, were selected from the database of the HUman MicroNucleus (HUMN) international collaborative project and followed up for cancer incidence or mortality. To standardize for the inter-laboratory variability subjects were classified according to the percentiles of MN distribution within each laboratory as low, medium or high frequency. A significant increase of all cancers incidence was found for subjects in the groups with medium (RR = 1.84; 95% CI: 1.28-2.66) and high MN frequency (RR = 1.53; 1.04-2.25). The same groups also showed a decreased cancer-free survival, i.e. P = 0.001 and P = 0.025, respectively. This association was present in all national cohorts and for all major cancer sites, especially urogenital (RR = 2.80; 1.17-6.73) and gastro-intestinal cancers (RR = 1.74; 1.01-4.71). The results from the present study provide preliminary evidence that MN frequency in PBL is a predictive biomarker of cancer risk within a population of healthy subjects. The current wide-spread use of the MN assay provides a valuable opportunity to apply this assay in the planning and validation of cancer surveillance and prevention programs.
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| 4. |
- Bull, James N., et al.
(författare)
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Autoionization from the plasmon resonance in isolated 1-cyanonaphthalene
- 2023
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Ingår i: Journal of Chemical Physics. - 0021-9606 .- 1089-7690. ; 158:24
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Tidskriftsartikel (refereegranskat)abstract
- Polycyclic aromatic hydrocarbons have widely been conjectured to be ubiquitous in space, as supported by the recent discovery of two isomers of cyanonaphthalene, indene, and 2-cyanoindene in the Taurus molecular cloud-1 using radioastronomy. Here, the photoionization dynamics of 1-cyanonaphthalene (1-CNN) are investigated using synchrotron radiation over the hν = 9.0–19.5 eV range, revealing that prompt autoionization from the plasmon resonance dominates the photophysics for hν = 11.5–16.0 eV. Minimal photo-induced dissociation, whether originating from an excited state impulsive bond rupture or through internal conversion followed by a statistical bond cleavage process, occurs over the microsecond timescale (as limited by the experimental setup). The direct photoionization cross section and photoelectron angular distributions are simulated using an ezDyson model combining Dyson orbitals with Coulomb wave photoejection. When considering these data in conjunction with recent radiative cooling measurements on 1-CNN+, which showed that cations formed with up to 5 eV of internal energy efficiently stabilize through recurrent fluorescence, we conclude that the organic backbone of 1-CNN is resilient to photodestruction by VUV and soft XUV radiation. These dynamics may prove to be a common feature for the survival of small polycyclic aromatic hydrocarbons in space, provided that the cations have a suitable electronic structure to support recurrent fluorescence.
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| 5. |
- 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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| 6. |
- Mattioli, Giuseppe, et al.
(författare)
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Unravelling molecular interactions in uracil clusters by XPS measurements assisted by ab initio and tight-binding simulations
- 2020
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The C, N and O 1s XPS spectra of uracil clusters in the gas phase have been measured. A new bottom-up approach, which relies on computational simulations starting from the crystallographic structure of uracil, has been adopted to interpret the measured spectra. This approach sheds light on the different molecular interactions (H-bond, pi -stacking, dispersion interactions) at work in the cluster and provides a good understanding of the observed XPS chemical shifts with respect to the isolated molecule in terms of intramolecular and intermolecular screening occurring after the core-hole ionization. The proposed bottom-up approach, reasonably expensive in terms of computational resources, has been validated by finite-temperature molecular dynamics simulations of clusters composed of up to fifty molecules.
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| 7. |
- Ueda, Kiyoshi, et al.
(författare)
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Roadmap on photonic, electronic and atomic collision physics : I. Light-matter interaction
- 2019
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Ingår i: Journal of Physics B. - : IOP PUBLISHING LTD. - 0953-4075 .- 1361-6455. ; 52:17
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Tidskriftsartikel (refereegranskat)abstract
- We publish three Roadmaps on photonic, electronic and atomic collision physics in order to celebrate the 60th anniversary of the ICPEAC conference. In Roadmap I, we focus on the light-matter interaction. In this area, studies of ultrafast electronic and molecular dynamics have been rapidly growing, with the advent of new light sources such as attosecond lasers and x-ray free electron lasers. In parallel, experiments with established synchrotron radiation sources and femtosecond lasers using cutting-edge detection schemes are revealing new scientific insights that have never been exploited. Relevant theories are also being rapidly developed. Target samples for photon-impact experiments are expanding from atoms and small molecules to complex systems such as biomolecules, fullerene, clusters and solids. This Roadmap aims to look back along the road, explaining the development of these fields, and look forward, collecting contributions from twenty leading groups from the field.
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