| 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. |
- 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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| 4. |
- Castrovilli, Mattea Carmen, et al.
(författare)
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Improved reuse and storage performances at room temperature of a new environmental-friendly lactate oxidase biosensor made by ambient electrospray immobilization
- 2023
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Ingår i: Green Chemistry. - : Royal Society of Chemistry. - 1463-9262 .- 1463-9270. ; :13, s. 5257-5266
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Tidskriftsartikel (refereegranskat)abstract
- A new, environmentally friendly lactate oxidase (LOX) based biosensor for lactate detection, with unprecedented reuse and storage capabilities at room temperature, has been manufactured using the ambient electrospray deposition (ESD) technique. This technology allows for an efficient, green and easy ambient soft-landing immobilization of the LOX enzyme on a cheap commercial screen-printed Prussian blue/carbon electrode (PB/C-SPE), employing sustainable chemistry. This study shows how ESD can confer the biosensor the ability to be stored at ambient pressure and temperature for long periods without compromising the enzymatic activity. The fabricated biosensor shows a storage capability for up to 90 days, without any particular care under storage conditions, and a reuse performance for up to 24 measurements on both the electrode just prepared and on a three-months-old electrode. The LOX-based biosensor has been tested for lactate detection in the linear range of 0.1–1 mM with a limit of detection of 0.07 ± 0.02 mM and does not show any memory effects. The absence of an entrapment matrix as well as any additional hazardous chemicals during the immobilization phase makes the process competitive in terms of environmental sustainability and toxicity. Moreover, the application of a new electrospray deposition cycle on the used biosensors makes the biosensors work again with performances comparable to those of freshly made ones. This demonstrates that the technique is excellent for recycling and eliminates the waste of disposable devices.
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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. |
- Liu, Ji-Cai, et al.
(författare)
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Multimode Resonant Auger Scattering from the Ethene Molecule
- 2011
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 115:18, s. 5103-5112
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Tidskriftsartikel (refereegranskat)abstract
- Resonant Auger spectra of ethene molecule have been measured with vibrational resolution at several excitation energies in the region of the C1s(-1)1b(2g)(π*) resonance. The main features observed in the experiment have been assigned and are accurately interpreted on the basis of ab initio multimode calculations. Theory explains the extended vibrational distribution of the resonant Auger spectra and its evolution as a function of the excitation energy by multimode excitation during the scattering process. As a result, the resonant Auger spectra display two qualitatively different spectral features following the Raman and non-Raman dispersion laws, respectively. Calculations show that two observed thresholds of formation of non-Raman spectral bands are related to the "double-edge" structure of the X-ray absorption spectrum.
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| 7. |
- 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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| 8. |
- Söderström, Johan, 1978-
(författare)
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Soft X-ray Scattering Dynamics Close to Core Ionization Thresholds in Atoms and Molecules
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this Thesis studies of highly excited states in gas-phase atoms and molecules (He, Ne, N2, O2, N2O and CO2) using a variety of synchrotron-radiation based techniques are presented. The three techniques used most frequently are X-ray-emission-threshold-electron coincidence (XETECO), X-ray emission spectroscopy (XES) and X-ray photoelectron spectroscopy (XPS) and they are all given a brief introduction. The fluorescence yield (FY) from doubly excited states in helium near the N=2 threshold(s) has been investigated in weak static external magnetic and electric fields, but also in a field free environment. The FY spectra in weak static magnetic fields show the importance of including the diamagnetic interaction in the theoretical models. The presence of weak static electric fields shows that even weak fields (as low as 44 V/cm) has a great impact on the observed FY spectra. Resonant XES spectra from some of the first doubly excited states in helium has been recorded in a field free environment, and compared to theory. The XETECO technique is presented and the first XETECO results from Ne, N2, O2, CO2 and N2O are shown, together with interpretations of possible threshold dynamics. I show that XETECO can be interpreted as threshold photoelectron spectra free from post collision interaction, and can hence be compared to above threshold XPS measurements. The observed below-threshold structures in the XETECO spectra are discussed and given a tentative explanation. The results from the analysis of the N2O XETECO spectrum lead to further investigations using XPS. Results showing the vibrational parameters and vibrationally resolved cross-sections and asymmetry parameters for N2O are presented together with theoretical predictions.
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| 9. |
- 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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