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Wong NL, Howard J, Delaney B, Sokell E, Bolognesi P, Avaldi L. Coincidence measurements of photodouble ionization of benzene and thiophene. Phys Chem Chem Phys 2024; 26:10784-10795. [PMID: 38516916 DOI: 10.1039/d3cp05908a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Photodouble ionization (PDI) triple-differential cross sections (TDCSs) of benzene and thiophene have been measured in electron-electron coincidence experiments under 10-10 eV and 20-20 eV equal energy sharing conditions. A multi-Gaussian fit method has been employed to characterize the TDCSs. The trends and features observed for benzene and thiophene do highlight differences with helium most likely from molecular PDI contributions to the TDCS. A comparison with the well-known helium PDI TDCS for equal energy sharing conditions [Avaldi and Huetz J. Phys. B: At. Mol. Opt. Phys., 2005, 38, S861-S891] supported the validity of the multi-Gaussian fitting method and contextualized the benzene and thiophene fits. The molecular targets and energy sharing conditions were chosen to provide insight into the unexpected resonances observed in aromatic hydrocarbons but not aromatic heterocyclic molecules [Wehlitz et al., Phys. Rev. Lett., 2012, 109, 193001]. Contrary to the work of [Wehlitz et al., Phys. Rev. Lett., 2012, 109, 193001], no significant differences between benzene and thiophene were found.
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Affiliation(s)
- Nicholas L Wong
- School of Physics, Science Centre North, University College Dublin, Belfield Dublin 4, Ireland.
| | - Jason Howard
- School of Physics, Science Centre North, University College Dublin, Belfield Dublin 4, Ireland.
| | - Ben Delaney
- School of Physics, Science Centre North, University College Dublin, Belfield Dublin 4, Ireland.
| | - Emma Sokell
- School of Physics, Science Centre North, University College Dublin, Belfield Dublin 4, Ireland.
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, 00015 Monterontondo Scalo, Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, 00015 Monterontondo Scalo, Italy
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2
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Ascenzi D, Erdmann E, Bolognesi P, Avaldi L, Castrovilli MC, Thissen R, Romanzin C, Alcaraz C, Rabadan I, Mendez L, Díaz-Tendero S, Cartoni A. H 2O˙ + and OH + reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage. Phys Chem Chem Phys 2023; 25:24643-24656. [PMID: 37665608 DOI: 10.1039/d3cp02772d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Radiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This work reports the first experimental study of the ion-molecule reactions of the H2O˙+ and OH+ ions, produced by photoionization with synchrotron radiation, with a furan (c-C4H4O) molecule, a template for deoxyribose sugar in DNA. The present experiments, performed as a function of the collision energy of the ions and the tunable photoionization energy, provide key parameters for the theoretical modelling of the effect of radiation dose, like the absolute cross sections for producing protonated furan (furanH+) and a radical cation (furan˙+), the most abundant products, which can amount up to 200 Å2 at very low collision energies (<1.0 eV). The experimental results show that furanH+ is more fragile, indicating how the protonation of the sugar component of the DNA may favor its dissociation with possible major radiosensitizing effects. Moreover, the ring opening of furanH+ isomers and the potential energy surface of the most important fragmentation channels have been explored by molecular dynamics simulations and quantum chemistry calculations. The results show that, in the most stable isomer of furanH+, the ring opening occurs via a low energy pathway with carbon-oxygen bond cleavage, followed by the loss of neutral carbon monoxide and the formation of the allyl cation CH2CHCH2+, which instead is not observed in the fragmentation of furan˙+. At higher energies the ring opening through the carbon-carbon bond is accompanied by the loss of formaldehyde, producing HCCCH2+, the most intense fragment ion detected in the experiments. This work highlights the importance of the secondary processes, like the ion-molecule reactions at low energies in the radiation damage due to their very large cross sections, and it aims to provide benchmark data for the development of suitable models to approach this low collision energy range.
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Affiliation(s)
- Daniela Ascenzi
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Trento, Italy
| | - Ewa Erdmann
- Faculty of Applied Physics and Mathematics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Paola Bolognesi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015, Monterotondo, Italy
| | - Lorenzo Avaldi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015, Monterotondo, Italy
| | - Mattea Carmen Castrovilli
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015, Monterotondo, Italy
| | - Roland Thissen
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Saint Aubin, Gif-sur-Yvette, France
| | - Claire Romanzin
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Saint Aubin, Gif-sur-Yvette, France
| | - Christian Alcaraz
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Saint Aubin, Gif-sur-Yvette, France
| | - Ismanuel Rabadan
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Luis Mendez
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Antonella Cartoni
- Department of Chemistry, Sapienza University of Rome, P. le Aldo Moro 5, Rome, 00185, Italy.
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015, Monterotondo, Italy
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3
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S A, Ramanathan K, Selvaraj M, Cautero M, Richter R, Pal N, Chiarinelli J, Bolognesi P, Avaldi L, Vinitha MV, Jureddy CS, Kadhane UR. In search of universalities in the dissociative photoionization of PANHs via isomerizations. J Chem Phys 2023; 159:104308. [PMID: 37702355 DOI: 10.1063/5.0158189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
In search of the cause behind the similarities often seen in the fragmentation of PANHs, vacuum ultraviolet (VUV) photodissociation of two pairs of isomers quinoline-isoquinoline and 2-naphthylamine-3-methyl-quinoline are studied using the velocity map imaging technique. The internal energy dependence of all primary fragmentation channels is obtained for all four target molecules. The decay dynamics of the four molecules is studied by comparing their various experimental signatures. The dominant channel for the first pair of isomers is found to be hydrogen cyanide (HCN) neutral loss, while the second pair of isomers lose HCNH neutral as its dominant channel. Despite this difference in their primary decay products and the differences in the structures of the four targets, various similarities in their experimental signatures are found, which could be explained by isomerization mechanisms to common structures. The fundamental role of these isomerization in controlling different dissociative channels is explored via a detailed analysis of the experimental photoelectron-photoion coincidences and the investigation of the theoretical potential energy surface. These results add to the notion of a universal PANH fragmentation mechanism and suggests the seven member isomerization as a key candidate for this universal mechanism. The balance between isomerization, dissociation, and other key mechanistic processes in the reaction pathways, such as hydrogen migrations, is also highlighted for the four molecules.
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Affiliation(s)
- Arun S
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Karthick Ramanathan
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | | | - Marco Cautero
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163, 5 in AREA Science Park, Basovizza, TS 34149, Italy
| | - Robert Richter
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163, 5 in AREA Science Park, Basovizza, TS 34149, Italy
| | - Nitish Pal
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163, 5 in AREA Science Park, Basovizza, TS 34149, Italy
| | - Jacopo Chiarinelli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo, Roma 00015, Italy
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo, Roma 00015, Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo, Roma 00015, Italy
| | - M V Vinitha
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Chinmai Sai Jureddy
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Umesh R Kadhane
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
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4
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Bull JN, Bolognesi P, Anstöter CS, Ashworth EK, Navarro Navarrete JE, Zhu B, Richter R, Pal N, Chiarinelli J, Avaldi L, Zettergren H, Stockett MH. Autoionization from the plasmon resonance in isolated 1-cyanonaphthalene. J Chem Phys 2023; 158:241101. [PMID: 37347125 DOI: 10.1063/5.0153058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
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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Affiliation(s)
- James N Bull
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, United Kingdom
- Centre for Photonics and Quantum Science, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Rome, Italy
| | - Cate S Anstöter
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Eleanor K Ashworth
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | | | - Boxing Zhu
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden
| | | | - Nitish Pal
- Elettra Sincrotrone Trieste, Trieste, Italy
| | - Jacopo Chiarinelli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Rome, Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Rome, Italy
| | | | - Mark H Stockett
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden
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5
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Barreiro-Lage D, Chiarinelli J, Bolognesi P, Richter R, Zettergren H, Stockett MH, Díaz-Tendero S, Avaldi L. Photofragmentation specificity of photoionized cyclic amino acids (diketopiperazines) as precursors of peptide building blocks. Phys Chem Chem Phys 2023. [PMID: 37166113 DOI: 10.1039/d3cp00608e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
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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Affiliation(s)
- Darío Barreiro-Lage
- Departamento de Química, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Jacopo Chiarinelli
- Institute of Structure of Matter-CNR (ISM-CNR), 00015 Monterotondo, Italy.
| | - Paola Bolognesi
- Institute of Structure of Matter-CNR (ISM-CNR), 00015 Monterotondo, Italy.
| | - Robert Richter
- Elettra Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | | | - Mark H Stockett
- Department of Physics, Stockholm University, Se-10691 Stockholm, Sweden
| | - Sergio Díaz-Tendero
- Departamento de Química, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Science (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lorenzo Avaldi
- Institute of Structure of Matter-CNR (ISM-CNR), 00015 Monterotondo, Italy.
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6
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Mattioli G, Avaldi L, Bolognesi P, Casavola A, Morini F, Van Caekenberghe T, Bozek JD, Castrovilli MC, Chiarinelli J, Domaracka A, Indrajith S, Maclot S, Milosavljević AR, Nicolafrancesco C, Nicolas C, Rousseau P. A study of the valence photoelectron spectrum of uracil and mixed water-uracil clusters. J Chem Phys 2023; 158:114301. [PMID: 36948841 DOI: 10.1063/5.0135574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The valence ionization of uracil and mixed water-uracil clusters has been studied experimentally and by ab initio calculations. In both measurements, the spectrum onset shows a red shift with respect to the uracil molecule, with the mixed cluster characterized by peculiar features unexplained by the sum of independent contributions of the water or uracil aggregation. To interpret and assign all the contributions, we performed a series of multi-level calculations, starting from an exploration of several cluster structures using automated conformer-search algorithms based on a tight-binding approach. Ionization energies have been assessed on smaller clusters via a comparison between accurate wavefunction-based approaches and cost-effective DFT-based simulations, the latter of which were applied to clusters up to 12 uracil and 36 water molecules. The results confirm that (i) the bottom-up approach based on a multilevel method [Mattioli et al. Phys. Chem. Chem. Phys. 23, 1859 (2021)] to the structure of neutral clusters of unknown experimental composition converges to precise structure-property relationships and (ii) the coexistence of pure and mixed clusters in the water-uracil samples. A natural bond orbital (NBO) analysis performed on a subset of clusters highlighted the special role of H-bonds in the formation of the aggregates. The NBO analysis yields second-order perturbative energy between the H-bond donor and acceptor orbitals correlated with the calculated ionization energies. This sheds light on the role of the oxygen lone-pairs of the uracil CO group in the formation of strong H-bonds, with a stronger directionality in mixed clusters, giving a quantitative explanation for the formation of core-shell structures.
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Affiliation(s)
- Giuseppe Mattioli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy
| | - Annarita Casavola
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy
| | - Filippo Morini
- X-lab, Faculty of Sciences, University of Hasselt, Campus Diepenbeek, BE 3590 Diepenbeek, Belgium
| | - Thomas Van Caekenberghe
- X-lab, Faculty of Sciences, University of Hasselt, Campus Diepenbeek, BE 3590 Diepenbeek, Belgium
| | - John D Bozek
- Synchrotron SOLEIL, L'Orme de Merisiers, 91192, Saint Aubin, BP48, 1192 Gif-sur-Yvette Cedex, France
| | - Mattea C Castrovilli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy
| | - Jacopo Chiarinelli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy
| | - Alicja Domaracka
- Normandie University, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | | | - Sylvain Maclot
- Institut Lumière Matière, UMR5306 CNRS, Université Claude Bernard Lyon 1, 69622 Villeurbanne CEDEX, France
| | | | - Chiara Nicolafrancesco
- Synchrotron SOLEIL, L'Orme de Merisiers, 91192, Saint Aubin, BP48, 1192 Gif-sur-Yvette Cedex, France
| | - Christophe Nicolas
- Synchrotron SOLEIL, L'Orme de Merisiers, 91192, Saint Aubin, BP48, 1192 Gif-sur-Yvette Cedex, France
| | - Patrick Rousseau
- Normandie University, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
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7
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Carlini L, Montorsi F, Wu Y, Bolognesi P, Borrego-Varillas R, Casavola AR, Castrovilli MC, Chiarinelli J, Mocci D, Vismarra F, Lucchini M, Nisoli M, Mukamel S, Garavelli M, Richter R, Nenov A, Avaldi L. Electron and ion spectroscopy of azobenzene in the valence and core shells. J Chem Phys 2023; 158:054201. [PMID: 36754795 DOI: 10.1063/5.0133824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Azobenzene is a prototype and a building block of a class of molecules of extreme technological interest as molecular photo-switches. We present a joint experimental and theoretical study of its response to irradiation with light across the UV to x-ray spectrum. The study of valence and inner shell photo-ionization and excitation processes combined with measurement of valence photoelectron-photoion coincidence and mass spectra across the core thresholds provides a detailed insight into the site- and state-selected photo-induced processes. Photo-ionization and excitation measurements are interpreted via the multi-configurational restricted active space self-consistent field method corrected by second order perturbation theory. Using static modeling, we demonstrate that the carbon and nitrogen K edges of azobenzene are suitable candidates for exploring its photoinduced dynamics thanks to the transient signals appearing in background-free regions of the NEXAFS and XPS.
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Affiliation(s)
- L Carlini
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - F Montorsi
- Dipartimento di Chimica Industriale, Università Degli Studi di Bologna, Bologna, Italy
| | - Y Wu
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - P Bolognesi
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - R Borrego-Varillas
- CNR-Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, Milano, Italy
| | - A R Casavola
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - M C Castrovilli
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - J Chiarinelli
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - D Mocci
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - F Vismarra
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - M Lucchini
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - M Nisoli
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - S Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
| | - M Garavelli
- Dipartimento di Chimica Industriale, Università Degli Studi di Bologna, Bologna, Italy
| | - R Richter
- Elettra Sincrotrone Trieste, Area Science Park, Basovizza, Italy
| | - A Nenov
- Dipartimento di Chimica Industriale, Università Degli Studi di Bologna, Bologna, Italy
| | - L Avaldi
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
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8
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Bolognesi P, Avaldi L. Photoelectron-photoion(s) coincidence studies of molecules of biological interest. Phys Chem Chem Phys 2022; 24:22356-22370. [PMID: 36124990 DOI: 10.1039/d2cp03079a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoelectron-photoion(s) coincidence, PEPICO, experiments with synchrotron radiation have become one of the most powerful tools to investigate dissociative photoionization thanks to their selectivity. In this paper their application to the study of molecular species of biological interest in the gas phase is reviewed. Some applications of PEPICO to the study of potential radiosensitizers, amino acids and small peptides and opportunities offered by the advent of novel methods for the production of beams of these molecules are discussed.
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Affiliation(s)
- P Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 00015 Monterotondo Scalo, Italy.
| | - L Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 00015 Monterotondo Scalo, Italy.
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9
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Ramanathan K, S. A, Bouwman J, Avaldi L, Vinitha MV, Bolognesi P, Richter R, Kadhane U. Photodissociation of Quinoline Cation: Mapping the Potential Energy Surface. J Chem Phys 2022; 157:064303. [DOI: 10.1063/5.0092161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A detailed exploration of the potential energy surface of quinoline cation (C9H7N ·+) is carried out to extend the present understanding of its fragmentation mechanisms. DFT calculations have been performed to explore new fragmentation mechanisms giving special attention to previously unexplored pathways such as isomerisation and elimination of HNC. The isomerization mechanisms producing 5-7 membered ring intermediates have been described and are found to be a dominant channel both energetically and kinetically. Energetically competing pathways have been established for the astrochemically important HNC-loss channel, which has hitherto never been considered in the context of the loss of a 27 amu fragment from the parent ions. Elimination of acetylene was also studied in great detail. Overall computational results are found to complement the experimental observations from the concurrently conducted PEPICO investigation. These could potentially open the doors for rich and interesting VUV radiation driven chemistry on the planetary atomospheres, meteorites and comets.
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Affiliation(s)
| | - Arun S.
- Physics, Indian Institute of Space Science and Technology, India
| | - Jordy Bouwman
- University of Colorado Boulder Laboratory for Atmospheric and Space Physics, United States of America
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche Area della Ricerca di Roma 1, Italy
| | - M. V. Vinitha
- Indian Institute of Space Science and Technology, India
| | - Paola Bolognesi
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche Area della Ricerca di Roma 1, Italy
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10
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Kadhane UR, Vinitha MV, Ramanathan K, S. A, Bouwman J, Avaldi L, Bolognesi P, Richter R. Comprehensive survey of dissociative photoionization of quinoline by PEPICO experiments. J Chem Phys 2022; 156:244304. [DOI: 10.1063/5.0092158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dissociative photoionization of quinoline induced by vacuum ultraviolet radiation is investigated using photoelectron–photoion coincidence spectroscopy. Branching ratios of all the detectable fragment ions are measured as a function of internal energy ranging from 2 to 30 eV. A specific generation hierarchy is observed in the breakdown curves of a set of dissociation channels. Moreover, a careful comparison of the breakdown curves of fragments among the successive generations allowed to establish a decay sequence in the fragmentation of quinoline cation. This enabled us to revisit and refine the understanding of the first generation decay and reassign the origin of a few of the higher generation decay products of quinoline cation. With the help of the accompanying computational work (reported concurrently), we have demonstrated the dominance of two different HCN elimination pathways over previously interpreted mechanisms. For the first time, a specific pathway for acetylene elimination is identified in quinoline+ and the role of isomerization in both acetylene as well as hydrogen cyanide loss is also demonstrated. The experiment also established that the acetylene elimination exclusively occurs from the non-nitrogen containing rings of quinoline cation. The formation of a few astronomically important species is also discussed.
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Affiliation(s)
- Umesh R. Kadhane
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - M. V. Vinitha
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Karthick Ramanathan
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Arun S.
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Jordy Bouwman
- Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, Colorado 80303, USA
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo, Roma 00015, Italy
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo, Roma 00015, Italy
| | - Robert Richter
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163, 5 in AREA Science Park, Basovizza TS 34149, Italy
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11
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Satta M, Catone D, Castrovilli MC, Bolognesi P, Avaldi L, Zema N, Cartoni A. Ion Chemistry of Carbon Dioxide in Nonthermal Reaction with Molecular Hydrogen. J Phys Chem A 2022; 126:3463-3471. [PMID: 35638704 PMCID: PMC9189832 DOI: 10.1021/acs.jpca.2c01695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The exothermic hydrogen transfer from H2 to CO2·+ leading to H and HCO2+ is investigated in a combined experimental and theoretical work. The experimental mass/charge ratios of the ionic product (HCO2+) and the ionic reactant (CO2·+) are recorded as a function of the photoionization energy of the synchrotron radiation. Theoretical density functional calculations and variational transition state theory are employed and adapted to analyze the energetic and the kinetics of the reaction, which turns out to be barrierless and with nonthermal rate coefficients controlled by nonstatistical processes. This study aims to understand the mechanisms and energetics that drive the reactivity of the elementary reaction of CO2·+ with H2 in different processes.
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Affiliation(s)
- Mauro Satta
- Department of Chemistry, Institute of the Study of Nanostructured Materials-CNR (ISMN-CNR), Sapienza University of Rome, P. le Aldo Moro 5, Rome 00185, Italy
| | - Daniele Catone
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Tor Vergata, Via del Fosso del Cavaliere, Rome 00133, Italy
| | - Mattea Carmen Castrovilli
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, Monterotondo 00015, Italy
| | - Paola Bolognesi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, Monterotondo 00015, Italy
| | - Lorenzo Avaldi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, Monterotondo 00015, Italy
| | - Nicola Zema
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Tor Vergata, Via del Fosso del Cavaliere, Rome 00133, Italy
| | - Antonella Cartoni
- Department of Chemistry, Sapienza University of Rome, P. le Aldo Moro 5, Rome 00185, Italy
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12
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Carlini L, Chiarinelli J, Mattioli G, Castrovilli MC, Valentini V, De Stefanis A, Bauer EM, Bolognesi P, Avaldi L. Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide. J Phys Chem B 2022; 126:2968-2978. [PMID: 35438499 PMCID: PMC9059117 DOI: 10.1021/acs.jpcb.1c10736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Dipeptides, the prototype
peptides, exist in both linear (l-) and cyclo (c-) structures. Since the
first mass spectrometry experiments, it has been observed that some l-structures may turn into the cyclo ones, likely via a
temperature-induced process. In this work, combining several different
experimental techniques (mass spectrometry, infrared and Raman spectroscopy,
and thermogravimetric analysis) with tight-binding and ab initio simulations,
we provide evidence that, in the case of l-phenylalanyl-l-alanine, an irreversible cyclization mechanism, catalyzed
by water and driven by temperature, occurs in the condensed phase.
This process can be considered as a very efficient strategy to improve
dipeptide stability by turning the comparatively fragile linear structure
into the robust and more stable cyclic one. This mechanism may have
played a role in prebiotic chemistry and can be further exploited
in the preparation of nanomaterials and drugs.
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Affiliation(s)
- Laura Carlini
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Jacopo Chiarinelli
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Giuseppe Mattioli
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Mattea Carmen Castrovilli
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Veronica Valentini
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Adriana De Stefanis
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Elvira Maria Bauer
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
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13
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Castrovilli MC, Tempesta E, Cartoni A, Plescia P, Bolognesi P, Chiarinelli J, Calandra P, Cicco N, Verrastro MF, Centonze D, Gullo L, Del Giudice A, Galantini L, Avaldi L. Fabrication of a New, Low-Cost, and Environment-Friendly Laccase-Based Biosensor by Electrospray Immobilization with Unprecedented Reuse and Storage Performances. ACS Sustain Chem Eng 2022; 10:1888-1898. [PMID: 35154910 PMCID: PMC8830555 DOI: 10.1021/acssuschemeng.1c07604] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/10/2022] [Indexed: 05/06/2023]
Abstract
The fabrication of enzyme-based biosensors has received much attention for their selectivity and sensitivity. In particular, laccase-based biosensors have attracted a lot of interest for their capacity to detect highly toxic molecules in the environment, becoming essential tools in the fields of white biotechnology and green chemistry. The manufacturing of a new, metal-free, laccase-based biosensor with unprecedented reuse and storage capabilities has been achieved in this work through the application of the electrospray deposition (ESD) methodology as the enzyme immobilization technique. Electrospray ionization (ESI) has been used for ambient soft-landing of laccase enzymes on a carbon substrate, employing sustainable chemistry. This study shows how the ESD technique can be successfully exploited for the fabrication of a new promising environment-friendly electrochemical amperometric laccase-based biosensor, with storage capability up to two months without any particular care and reuse performance up to 63 measurements on the same electrode just prepared and 20 measurements on the one-year-old electrode subjected to redeposition. The laccase-based biosensor has been tested for catechol detection in the linear range 2-100 μM, with a limit of detection of 1.7 μM, without interference from chrome, cadmium, arsenic, and zinc and without any memory effects.
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Affiliation(s)
- Mattea Carmen Castrovilli
- Istituto
di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, 00015 Monterotondo, Italy
| | - Emanuela Tempesta
- CNR-Institute
of Environmental Geology and Geoengineering (CNR-IGAG), Area della Ricerca Roma1, Via Salaria
km 29.300, 00015 Monterotondo, Italy
| | - Antonella Cartoni
- Department
of Chemistry, Sapienza University, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Paolo Plescia
- CNR-Institute
of Environmental Geology and Geoengineering (CNR-IGAG), Area della Ricerca Roma1, Via Salaria
km 29.300, 00015 Monterotondo, Italy
| | - Paola Bolognesi
- Istituto
di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, 00015 Monterotondo, Italy
| | - Jacopo Chiarinelli
- Istituto
di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, 00015 Monterotondo, Italy
| | - Pietro Calandra
- CNR-Institute
for the Study of Nanostructured Materials (CNR-ISMN), Area della Ricerca Roma1, Via Salaria
km 29.300, 00015 Monterotondo, Italy
| | - Nunzia Cicco
- CNR-Institute
of Methodologies for Environmental Analysis (CNR-IMAA), Contrada Santa Loja, Tito Scalo, 85050 Potenza, Italy
| | - Maria Filomena Verrastro
- Istituto
di Struttura della Materia-CNR (ISM-CNR), Contrada Santa Loja, Tito
Scalo 85050, Potenza, Italy
| | - Diego Centonze
- Dipartimento
di Scienze Agrarie, degli Alimenti e dell’Ambiente, Università degli Studi di Foggia, via Napoli, 25, 71122 Foggia, Italy
| | - Ludovica Gullo
- Department
of Chemistry, Sapienza University, P.le Aldo Moro 5, 00185 Roma, Italy
| | | | - Luciano Galantini
- Department
of Chemistry, Sapienza University, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Lorenzo Avaldi
- Istituto
di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, 00015 Monterotondo, Italy
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14
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Chiarinelli J, Barreiro-Lage D, Bolognesi P, RICHTER R, Zettergren H, Stockett MH, Díaz-Tendero S, Avaldi L. Electron and ion spectroscopy of the cyclo-alanine-alanine dipeptide. Phys Chem Chem Phys 2022; 24:5855-5867. [DOI: 10.1039/d1cp05811h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The VUV photoionisation and photofragmentation of cyclo-alanine-alanine (cAA) has been studiedin a joint experimental and theoretical work. The photoelectron spectrum and the photoelectron-photoion coincidence (PEPICO) measurements, which enable a control...
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15
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Molteni E, Mattioli G, Alippi P, Avaldi L, Bolognesi P, Carlini L, Vismarra F, Wu Y, Varillas RB, Nisoli M, Singh M, Valadan M, Altucci C, Richter R, Sangalli D. A systematic study of the valence electronic structure of cyclo(Gly-Phe), cyclo(Trp-Tyr) and cyclo(Trp-Trp) dipeptides in the gas phase. Phys Chem Chem Phys 2021; 23:26793-26805. [PMID: 34816853 DOI: 10.1039/d1cp04050b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The electronic energy levels of cyclo(glycine-phenylalanine), cyclo(tryptophan-tyrosine) and cyclo(tryptophan-tryptophan) dipeptides are investigated with a joint experimental and theoretical approach. Experimentally, valence photoelectron spectra in the gas phase are measured using VUV radiation. Theoretically, we first obtain low-energy conformers through an automated conformer-rotamer ensemble sampling scheme based on tight-binding simulations. Then, different first principles computational schemes are considered to simulate the spectra: Hartree-Fock (HF), density functional theory (DFT) within the B3LYP approximation, the quasi-particle GW correction, and the quantum-chemistry CCSD method. Theory allows assignment of the main features of the spectra. A discussion on the role of electronic correlation is provided, by comparing computationally cheaper DFT scheme (and GW) results with the accurate CCSD method.
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Affiliation(s)
- Elena Molteni
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy. .,Dipartimento di Fisica, Universita' degli Studi di Milano, via Celoria 16, I-20133 Milano, Italy
| | - Giuseppe Mattioli
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Paola Alippi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Paola Bolognesi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Laura Carlini
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Federico Vismarra
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | - Yingxuan Wu
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | | | - Mauro Nisoli
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | - Manjot Singh
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy
| | - Mohammadhassan Valadan
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy.,Istituto Nazionale Fisica Nucleare (INFN), Sezione di Napoli, Napoli, Italy
| | - Carlo Altucci
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy.,Istituto Nazionale Fisica Nucleare (INFN), Sezione di Napoli, Napoli, Italy
| | - Robert Richter
- Sincrotrone Trieste, Area Science Park, Basovizza, Trieste, Italy
| | - Davide Sangalli
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy. .,Dipartimento di Fisica, Universita' degli Studi di Milano, via Celoria 16, I-20133 Milano, Italy
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16
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Satta M, Casavola AR, Cartoni A, Castrovilli MC, Catone D, Chiarinelli J, Borocci S, Avaldi L, Bolognesi P. Ionization of 2- and 4(5)-Nitroimidazoles Radiosensitizers: A "Kinetic Competition" Between NO 2 and NO Losses. Chemphyschem 2021; 22:2387-2391. [PMID: 34597457 PMCID: PMC9293481 DOI: 10.1002/cphc.202100629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Nitroimidazoles are a class of chemicals with a remarkable broad spectrum of applications from the production of explosives to the use as radiosensitizers in radiotherapy. The understanding of thedynamics of their fragmentation induced by ionizing sources is of fundamental interest. The goal of this work is to theoretically investigate the kinetic competition between the two most important decomposition channels of 2, 4 and 5‐Nitroimidazole cations: the NO and NO2 losses. The calculated rate constants of the two processes are in very good agreement with the experimental Photoelectron‐Photoion Coincidence (PEPICO) branching ratio. This study solves the intriguing and theoretically unexplained experimental observation that 2‐Nitroimidazole, at variance with the other two regio‐isomers is a source for only NO at low energies (<12.76 eV). This is a key point for biomedical application of the nitroimidazoles, because NO is the vasodilator that favors the reoxigenation of hypoxic tumor tissues.
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Affiliation(s)
- Mauro Satta
- Istituto per lo Studio dei Materiali Nanostrutturati (ISMN-CNR), Dipartimento di Chimica, Università degli studi di Roma La Sapienza, P.le Aldo Moro 5, 00185, Roma, Italy
| | - Anna Rita Casavola
- Istituto di Struttura della Materia (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria Km 29,300, 00016, Monterotondo Scalo (RM), Italy
| | - Antonella Cartoni
- Dipartimento di Chimica, Università degli studi di Roma La Sapienza, Pl.e Aldo Moro 5, 00185, Roma, Italy
| | - Mattea Carmen Castrovilli
- Istituto di Struttura della Materia (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria Km 29,300, 00016, Monterotondo Scalo (RM), Italy
| | - Daniele Catone
- Istituto di Struttura della Materia (ISM-CNR), Area della Ricerca di Roma 2, Via del Fosso del Cavaliere 10, 00133, Roma, Italy
| | - Jacopo Chiarinelli
- Istituto di Struttura della Materia (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria Km 29,300, 00016, Monterotondo Scalo (RM), Italy
| | - Stefano Borocci
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università della Tuscia, Viterbo, Italy
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria Km 29,300, 00016, Monterotondo Scalo (RM), Italy
| | - Paola Bolognesi
- Istituto di Struttura della Materia (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria Km 29,300, 00016, Monterotondo Scalo (RM), Italy
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17
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Barreiro-Lage D, Bolognesi P, Chiarinelli J, Richter R, Zettergren H, Stockett MH, Carlini L, Diaz-Tendero S, Avaldi L. "Smart Decomposition" of Cyclic Alanine-Alanine Dipeptide by VUV Radiation: A Seed for the Synthesis of Biologically Relevant Species. J Phys Chem Lett 2021; 12:7379-7386. [PMID: 34324354 DOI: 10.1021/acs.jpclett.1c01788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
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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Affiliation(s)
- Darío Barreiro-Lage
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Paola Bolognesi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
| | - Jacopo Chiarinelli
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
| | - Robert Richter
- Elettra Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | | | - Mark H Stockett
- Department of Physics, Stockholm University, Se-10691 Stockholm, Sweden
| | - Laura Carlini
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
| | - Sergio Diaz-Tendero
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Science (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lorenzo Avaldi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
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18
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Mattioli G, Avaldi L, Bolognesi P, Bozek JD, Castrovilli MC, Chiarinelli J, Domaracka A, Indrajith S, Maclot S, Milosavljević AR, Nicolafrancesco C, Rousseau P. Water-biomolecule clusters studied by photoemission spectroscopy and multilevel atomistic simulations: hydration or solvation? Phys Chem Chem Phys 2021; 23:15049-15058. [PMID: 34231588 DOI: 10.1039/d1cp02031e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The properties of mixed water-uracil nanoaggregates have been probed by core electron-photoemission measurements to investigate supramolecular assembly in the gas phase driven by weak interactions. The interpretation of the measurements has been assisted by multilevel atomistic simulations, based on semi-empirical tight-binding and DFT-based methods. Our protocol established a positive-feedback loop between experimental and computational techniques, which has enabled a sound and detailed atomistic description of such complex heterogeneous molecular aggregates. Among biomolecules, uracil offers interesting and generalized skeletal features; its structure encompasses an alternation of hydrophilic H-bond donor and acceptor sites and hydrophobic moieties, typical in biomolecular systems, that induces a supramolecular core-shell-like organization of the mixed clusters with a water core and an uracil shell. This structure is far from typical models of both solid-state hydration, with water molecules in defined positions, or liquid solvation, where disconnected uracil molecules are completely surrounded by water.
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Affiliation(s)
- Giuseppe Mattioli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10, Monterotondo Scalo, Italy.
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10, Monterotondo Scalo, Italy.
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10, Monterotondo Scalo, Italy.
| | - John D Bozek
- Synchrotron SOLEIL, L'Orme de Merisiers, 91192, Saint Aubin, BP48, 1192, Gif-sur-Yvette Cedex, France
| | - Mattea C Castrovilli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10, Monterotondo Scalo, Italy.
| | - Jacopo Chiarinelli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10, Monterotondo Scalo, Italy.
| | - Alicja Domaracka
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | | | - Sylvain Maclot
- Physics Department, University of Gothenburg, Origovägen 6B, 41296 Göteborg, Sweden
| | | | - Chiara Nicolafrancesco
- Synchrotron SOLEIL, L'Orme de Merisiers, 91192, Saint Aubin, BP48, 1192, Gif-sur-Yvette Cedex, France and Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - Patrick Rousseau
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
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19
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Ponzi A, Bernes E, Toffoli D, Fronzoni G, Callegari C, Ciavardini A, Di Fraia M, Richter R, Prince KC, Sa'adeh H, Devetta M, Faccialà D, Vozzi C, Avaldi L, Bolognesi P, Castrovilli MC, Catone D, Coreno M, Plekan O. Carbon and Nitrogen K-Edge NEXAFS Spectra of Indole, 2,3-Dihydro-7-azaindole, and 3-Formylindole. J Phys Chem A 2021; 125:4160-4172. [PMID: 33961434 DOI: 10.1021/acs.jpca.1c02570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The near-edge X-ray absorption fine structure (NEXAFS) spectra of indole, 2,3-dihydro-7-azaindole, and 3-formylindole in the gas phase have been measured at the carbon and nitrogen K-edges. The spectral features have been interpreted based on density functional theory (DFT) calculations within the transition potential (TP) scheme, which is accurate enough for a general description of the measured C 1s NEXAFS spectra as well as for the assignment of the most relevant features. For the nitrogen K-edge, the agreement between experimental data and theoretical spectra calculated with TP-DFT was not quite satisfactory. This discrepancy was mainly attributed to the many-body effects associated with the excitation of the core electron, which are better described using the time-dependent density functional theory (TDDFT) with the range-separated hybrid functional CAM-B3LYP. An assignment of the measured N 1s NEXAFS spectral features has been proposed together with a complete description of the observed resonances. Intense transitions from core levels to unoccupied antibonding π* states as well as several transitions with mixed-valence/Rydberg or pure Rydberg character have been observed in the C and N K-edge spectra of all investigated indoles.
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Affiliation(s)
| | - Elisa Bernes
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, via L. Giorgieri 1, I-34127 Trieste, Italy
| | - Daniele Toffoli
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, via L. Giorgieri 1, I-34127 Trieste, Italy
| | - Giovanna Fronzoni
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, via L. Giorgieri 1, I-34127 Trieste, Italy
| | | | | | | | - Robert Richter
- Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
| | - Kevin C Prince
- Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
| | - Hanan Sa'adeh
- Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy.,Department of Physics, The University of Jordan, Amman 11942, Jordan
| | - Michele Devetta
- CNR-Istituto di Fotonica e Nanotecnologie (CNR-IFN), 20133 Milano, Italy
| | - Davide Faccialà
- CNR-Istituto di Fotonica e Nanotecnologie (CNR-IFN), 20133 Milano, Italy
| | - Caterina Vozzi
- CNR-Istituto di Fotonica e Nanotecnologie (CNR-IFN), 20133 Milano, Italy
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia-CNR (ISM-CNR), 00133 Rome, Italy
| | - Paola Bolognesi
- Istituto di Struttura della Materia-CNR (ISM-CNR), 00133 Rome, Italy
| | | | - Daniele Catone
- Istituto di Struttura della Materia-CNR (ISM-CNR), 00133 Rome, Italy
| | - Marcello Coreno
- Istituto di Struttura della Materia-CNR (ISM-CNR), 00133 Rome, Italy
| | - Oksana Plekan
- Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
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20
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Catone D, Satta M, Castrovilli MC, Bolognesi P, Avaldi L, Cartoni A. Photoionization of methanol: a molecular source for the prebiotic chemistry. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Erdmann E, Aguirre NF, Indrajith S, Chiarinelli J, Domaracka A, Rousseau P, Huber BA, Bolognesi P, Richter R, Avaldi L, Díaz-Tendero S, Alcamí M, Łabuda M. A general approach to study molecular fragmentation and energy redistribution after an ionizing event. Phys Chem Chem Phys 2021; 23:1859-1867. [PMID: 33439170 DOI: 10.1039/d0cp04890a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We propose to combine quantum chemical calculations, statistical mechanical methods, and photoionization and particle collision experiments to unravel the redistribution of internal energy of the furan cation and its dissociation pathways. This approach successfully reproduces the relative intensity of the different fragments as a function of the internal energy of the system in photoelectron-photoion coincidence experiments and the different mass spectra obtained when ions ranging from Ar+ to Xe25+ or electrons are used in collision experiments. It provides deep insights into the redistribution of the internal energy in the ionized molecule and its influence on the dissociation pathways and resulting charged fragments. The present pilot study demonstrates the efficiency of a statistical exchange of excitation energy among various degrees of freedom of the molecule and proves that the proposed approach is mature to be extended to more complex systems.
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Affiliation(s)
- Ewa Erdmann
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.
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22
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Casavola AR, Cartoni A, Castrovilli MC, Borocci S, Bolognesi P, Chiarinelli J, Catone D, Avaldi L. VUV Photofragmentation of Chloroiodomethane: The Iso-CH 2I-Cl and Iso-CH 2Cl-I Radical Cation Formation. J Phys Chem A 2020; 124:7491-7499. [PMID: 32786965 PMCID: PMC8010789 DOI: 10.1021/acs.jpca.0c05754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Dihalomethanes
XCH2Y (X and Y = F, Cl, Br, and I) are a class of compounds
involved in several processes leading to the release of halogen atoms,
ozone consumption, and aerosol particle formation. Neutral dihalomethanes
have been largely studied, but chemical physics properties and processes
involving their radical ions, like the pathways of their decomposition,
have not been completely investigated. In this work the photodissociation
dynamics of the ClCH2I molecule has been explored in the
photon energy range 9–21 eV using both VUV rare gas discharge
lamps and synchrotron radiation. The experiments show that, among
the different fragment ions, CH2I+ and CH2Cl+, which correspond to the Cl- and I-losses,
respectively, play a dominant role. The experimental ionization energy
of ClCH2I and the appearance energies of the CH2I+ and CH2Cl+ ions are in agreement
with the theoretical results obtained at the MP2/CCSD(T) level of
theory. Computational investigations have been also performed to study
the isomerization of geminal [ClCH2I]•+ into the iso-chloroiodomethane isomers: [CH2I–Cl]•+ and [CH2Cl–I]•+.
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Affiliation(s)
- Anna Rita Casavola
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
| | - Antonella Cartoni
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy.,Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Mattea Carmen Castrovilli
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
| | - Stefano Borocci
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo 01100, Italy.,Institute for Biological Systems-CNR (ISB-CNR), Area della Ricerca di Roma 1, Via Salaria, Km 29.500,, 00015 Monterotondo, Italy
| | - Paola Bolognesi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
| | - Jacopo Chiarinelli
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
| | - Daniele Catone
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Tor Vergata, Via del Fosso del Cavaliere, 00133 Rome, Italy
| | - Lorenzo Avaldi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
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23
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Chiarinelli J, Bolognesi P, Avaldi L. Ion optics simulation of an ion beam setup coupled to an electrospray ionization source, strengths, and limitations. Rev Sci Instrum 2020; 91:073203. [PMID: 32752820 DOI: 10.1063/5.0006641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
A unified approach to achieve a start-to-end ion optics simulation of an ion beam apparatus coupled to an electrospray ionization source is presented. We demonstrate that simulations enable reliable information on the behavior and operation of the apparatus to be obtained, but due to the collisions with the buffer gas in the initial stages of the setup, the results concerning the kinetic energy of the ion beam must be treated with care.
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Affiliation(s)
- J Chiarinelli
- CNR-ISM, Area della Ricerca Roma 1, Monterotondo Scalo, Roma 00015, Italy
| | - P Bolognesi
- CNR-ISM, Area della Ricerca Roma 1, Monterotondo Scalo, Roma 00015, Italy
| | - L Avaldi
- CNR-ISM, Area della Ricerca Roma 1, Monterotondo Scalo, Roma 00015, Italy
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24
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Satta M, Cartoni A, Catone D, Castrovilli MC, Bolognesi P, Zema N, Avaldi L. The Reaction of Sulfur Dioxide Radical Cation with Hydrogen and its Relevance in Solar Geoengineering Models. Chemphyschem 2020; 21:1146-1156. [PMID: 32203633 DOI: 10.1002/cphc.202000194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/23/2020] [Indexed: 11/06/2022]
Abstract
SO2 has been proposed in solar geoengineering as a precursor of H2 SO4 aerosol, a cooling agent active in the stratosphere to contrast climate change. Atmospheric ionization sources can ionize SO2 into excited states of S O 2 · + , which quickly reacts with trace gases in the stratosphere. In this work we explore the reaction of H 2 D 2 with S O 2 · + excited by tunable synchrotron radiation, leading to H S O 2 + + H ( D S O 2 + + D ), where H contributes to O3 depletion and OH formation. Density Functional Theory and Variational Transition State Theory have been used to investigate the dynamics of the title barrierless and exothermic reaction. The present results suggest that solar geoengineering models should test the reactivity of S O 2 · + with major trace gases in the stratosphere, such as H2 since this is a relevant channel for the OH formation during the nighttime when there is not OH production by sunlight. OH oxides SO2 , triggering the chemical reactions leading to H2 SO4 aerosol.
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Affiliation(s)
- Mauro Satta
- ISMN (CNR) c/o Dipartimento di Chimica Sapienza Universita' di Roma, Pl.e Aldo Moro 5, Roma, Italy
| | - Antonella Cartoni
- Dipartimento di Chimica, Sapienza Universitá di Roma, Pl.e Aldo Moro 5, Roma, Italy
| | - Daniele Catone
- CNR-ISM, Area della Ricerca di Tor Vergata, Via del Fosso del Cavaliere, Roma, Italy
| | | | - Paola Bolognesi
- CNR-ISM, Area della Ricerca di Roma 1, Via Salaria Km 29,300, Monterotondo Scalo (RM), Italy
| | - Nicola Zema
- CNR-ISM, Area della Ricerca di Tor Vergata, Via del Fosso del Cavaliere, Roma, Italy
| | - Lorenzo Avaldi
- CNR-ISM, Area della Ricerca di Roma 1, Via Salaria Km 29,300, Monterotondo Scalo (RM), Italy
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25
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Castrovilli MC, Bolognesi P, Chiarinelli J, Avaldi L, Cartoni A, Calandra P, Tempesta E, Giardi MT, Antonacci A, Arduini F, Scognamiglio V. Electrospray deposition as a smart technique for laccase immobilisation on carbon black-nanomodified screen-printed electrodes. Biosens Bioelectron 2020; 163:112299. [PMID: 32568697 DOI: 10.1016/j.bios.2020.112299] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 01/11/2023]
Abstract
Enzymes immobilisation represents a critical issue in the design of biosensors to achieve standardization as well as suitable analytical performances in terms of sensitivity, selectivity, and stability. In this work electrospray deposition (ESD) has been exploited as a novel technique for the immobilisation of laccase enzyme on carbon black modified screen-printed electrodes. The aim is to fabricate an amperometric biosensor for phenolic compound detection. The electrodes produced by ESD have been analysed by scanning electron microscopy and characterised electrochemically to prove that this immobilisation technique is suited to manufacture high performance biosensors. The results show that the laccase enzyme maintains its activity after undergoing the electrospray ionisation process and deposition and the fabricated biosensor has improved performances in terms of storage (up to 3 months at room temperature) and working (up to 25 measurements on the same electrode) stability. The laccase-based biosensor has been tested for phenolic compound detection, with catechol as target analyte, in the linear range 2.5-50 μM, with 2.0 μM limit of detection, without interference from lead, cadmium, atrazine, and paraoxon, and without matrix effect in drinking, surface, and wastewater.
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Affiliation(s)
- Mattea Carmen Castrovilli
- Institute of Structure of Matter, National Research Council, Area Della Ricerca di Roma 1, Via Salaria Km 29.300, 00015, Monterotondo, Italy
| | - Paola Bolognesi
- Institute of Structure of Matter, National Research Council, Area Della Ricerca di Roma 1, Via Salaria Km 29.300, 00015, Monterotondo, Italy
| | - Jacopo Chiarinelli
- Institute of Structure of Matter, National Research Council, Area Della Ricerca di Roma 1, Via Salaria Km 29.300, 00015, Monterotondo, Italy
| | - Lorenzo Avaldi
- Institute of Structure of Matter, National Research Council, Area Della Ricerca di Roma 1, Via Salaria Km 29.300, 00015, Monterotondo, Italy
| | | | - Pietro Calandra
- Institute of Nanostructured Materials, National Research Council, Area Della Ricerca di Roma 1, Via Salaria Km 29.300, 00015, Monterotondo, Italy
| | - Emanuela Tempesta
- Institute of Environmental Geology and Geoengineering, National Research Council, Via Salaria Km 29.300, 00015, Monterotondo, Italy
| | - Maria Teresa Giardi
- Institute of Crystallography, National Research Council, Area Della Ricerca di Roma 1, Via Salaria Km 29.300, 00015, Monterotondo, Italy; Biosensor Srl, Via Degli Olmetti 4, 00060, Formello, Rome, Italy
| | - Amina Antonacci
- Institute of Crystallography, National Research Council, Area Della Ricerca di Roma 1, Via Salaria Km 29.300, 00015, Monterotondo, Italy
| | - Fabiana Arduini
- Department of Chemical Science and Technologies, University of Rome "Tor Vergata", Via Della Ricerca Scientifica, 00133, Rome, Italy; SENSE4MED, Via Renato Rascel 30, 00128, Rome, Italy
| | - Viviana Scognamiglio
- Institute of Crystallography, National Research Council, Area Della Ricerca di Roma 1, Via Salaria Km 29.300, 00015, Monterotondo, Italy.
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26
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Plekan O, Sa'adeh H, Ciavardini A, Callegari C, Cautero G, Dri C, Di Fraia M, Prince KC, Richter R, Sergo R, Stebel L, Devetta M, Faccialà D, Vozzi C, Avaldi L, Bolognesi P, Castrovilli MC, Catone D, Coreno M, Zuccaro F, Bernes E, Fronzoni G, Toffoli D, Ponzi A. Experimental and Theoretical Photoemission Study of Indole and Its Derivatives in the Gas Phase. J Phys Chem A 2020; 124:4115-4127. [PMID: 32329341 DOI: 10.1021/acs.jpca.0c02719] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The valence and core-level photoelectron spectra of gaseous indole, 2,3-dihydro-7-azaindole, and 3-formylindole have been investigated using VUV and soft X-ray radiation supported by both an ab initio electron propagator and density functional theory calculations. Three methods were used to calculate the outer valence band photoemission spectra: outer valence Green function, partial third order, and renormalized partial third order. While all gave an acceptable description of the valence spectra, the last method yielded very accurate agreement, especially for indole and 3-formylindole. The carbon, nitrogen, and oxygen 1s core-level spectra of these heterocycles were measured and assigned. The double ionization appearance potential for indole has been determined to be 21.8 ± 0.2 eV by C 1s and N 1s Auger photoelectron spectroscopy. Theoretical analysis identifies the doubly ionized states as a band consisting of two overlapping singlet states and one triplet state with dominant configurations corresponding to holes in the two uppermost molecular orbitals. One of the singlet states and the triplet state can be described as consisting largely of a single configuration, but other doubly ionized states are heavily mixed by configuration interactions. This work provides full assignment of the relative binding energies of the core level features and an analysis of the electronic structure of substituted indoles in comparison with the parent indole.
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Affiliation(s)
- Oksana Plekan
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Hanan Sa'adeh
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy.,Department of Physics, The University of Jordan, Amman 11942, Jordan
| | | | - Carlo Callegari
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Giuseppe Cautero
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Carlo Dri
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy.,IOM-CNR Laboratorio TASC, Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Michele Di Fraia
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Kevin C Prince
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy.,Centre for Translational Atomaterials, Swinburne University of Technology, Melbourne 3122, Australia
| | - Robert Richter
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Rudi Sergo
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Luigi Stebel
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Michele Devetta
- Istituto di Fotonica e Nanotecnologie, CNR, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Davide Faccialà
- Istituto di Fotonica e Nanotecnologie, CNR, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Caterina Vozzi
- Istituto di Fotonica e Nanotecnologie, CNR, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Lorenzo Avaldi
- CNR - Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, 00133 Rome, Italy
| | - Paola Bolognesi
- CNR - Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, 00133 Rome, Italy
| | - Mattea Carmen Castrovilli
- CNR - Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, 00133 Rome, Italy
| | - Daniele Catone
- CNR - Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Tor Vergata, 00133 Rome, Italy
| | - Marcello Coreno
- CNR - Istituto di Struttura Della Materia (CNR-ISM), Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Fabio Zuccaro
- CNR - Istituto di Struttura Della Materia (CNR-ISM), Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Elisa Bernes
- Dipartimento di Scienze Chimiche, Università degli Studi di Trieste, 34127 Trieste, Italy
| | - Giovanna Fronzoni
- Dipartimento di Scienze Chimiche, Università degli Studi di Trieste, 34127 Trieste, Italy
| | - Daniele Toffoli
- Dipartimento di Scienze Chimiche, Università degli Studi di Trieste, 34127 Trieste, Italy
| | - Aurora Ponzi
- Institut Ruđer Bošković, Bijenička cesta 54, 10000 Zagreb, Croatia
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27
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Castrovilli MC, Bolognesi P, Chiarinelli J, Avaldi L, Calandra P, Antonacci A, Scognamiglio V. The convergence of forefront technologies in the design of laccase-based biosensors – An update. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.07.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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Chiarinelli J, Casavola AR, Castrovilli MC, Bolognesi P, Cartoni A, Wang F, Richter R, Catone D, Tosic S, Marinkovic BP, Avaldi L. Radiation Damage Mechanisms of Chemotherapeutically Active Nitroimidazole Derived Compounds. Front Chem 2019; 7:329. [PMID: 31157205 PMCID: PMC6528692 DOI: 10.3389/fchem.2019.00329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/24/2019] [Indexed: 11/15/2022] Open
Abstract
Photoionization mass spectrometry, photoelectron-photoion coincidence spectroscopic technique, and computational methods have been combined to investigate the fragmentation of two nitroimidazole derived compounds: the metronidazole and misonidazole. These molecules are used in radiotherapy thanks to their capability to sensitize hypoxic tumor cells to radiation by "mimicking" the effects of the presence of oxygen as a damaging agent. Previous investigations of the fragmentation patterns of the nitroimidazole isomers (Bolognesi et al., 2016; Cartoni et al., 2018) have shown their capacity to produce reactive molecular species such as nitric oxide, carbon monoxide or hydrogen cyanide, and their potential impact on the biological system. The results of the present work suggest that different mechanisms are active for the more complex metronidazole and misonidazole molecules. The release of nitric oxide is hampered by the efficient formation of nitrous acid or nitrogen dioxide. Although both metronidazole and misonidazole contain imidazole ring in the backbone, the side branches of these molecules lead to very different bonding mechanisms and properties.
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Affiliation(s)
- Jacopo Chiarinelli
- CNR-Istituto di Struttura Della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, Italy
- Dipartimento di Scienze, Università di Roma Tre, Rome, Italy
| | - Anna Rita Casavola
- CNR-Istituto di Struttura Della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, Italy
| | - Mattea Carmen Castrovilli
- CNR-Istituto di Struttura Della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, Italy
| | - Paola Bolognesi
- CNR-Istituto di Struttura Della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, Italy
| | - Antonella Cartoni
- CNR-Istituto di Struttura Della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, Italy
- Dipartimento di Chimica, Sapienza Università di Roma, Rome, Italy
| | - Feng Wang
- Molecular Modelling Discovery Laboratory, Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, VIC, Australia
| | - R. Richter
- Elettra-Sincrotrone Trieste, Trieste, Italy
| | - Daniele Catone
- CNR-Istituto di Struttura Della Materia, Area della Ricerca di Tor Vergata, Rome, Italy
| | - Sanja Tosic
- Institute of Physics, Laboratory for Atomic Collision Processes, University of Belgrade, Belgrade, Serbia
| | - Bratislav P. Marinkovic
- Institute of Physics, Laboratory for Atomic Collision Processes, University of Belgrade, Belgrade, Serbia
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura Della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, Italy
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29
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Bolognesi P, Carravetta V, Sementa L, Barcaro G, Monti S, Manjari Mishra P, Cartoni A, Castrovilli MC, Chiarinelli J, Tosic S, Marinkovic BP, Richter R, Avaldi L. Core Shell Investigation of 2-nitroimidazole. Front Chem 2019; 7:151. [PMID: 31001511 PMCID: PMC6454003 DOI: 10.3389/fchem.2019.00151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/28/2019] [Indexed: 02/01/2023] Open
Abstract
Tunability and selectivity of synchrotron radiation have been used to study the excitation and ionization of 2-nitroimidazole at the C, N, and O K-edges. The combination of a set of different measurements (X-ray photoelectron spectroscopy, near-edge photoabsorption spectroscopy, Resonant Auger electron spectroscopy, and mass spectrometry) and computational modeling have successfully disclosed local effects due to the chemical environment on both excitation/ionization and fragmentation of the molecule.
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Affiliation(s)
- Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Montelibretti, Italy
| | | | - Luca Sementa
- CNR-Istituto per i Processi Chimico Fisici, Pisa, Italy
| | | | - Susanna Monti
- CNR-Istituto di Chimica dei Composti Organo Metallici, Pisa, Italy
| | - Preeti Manjari Mishra
- Stored and Cooled Ions Division, Max Planck Institute for Nuclear Physics, Heidelberg, Germany
| | - Antonella Cartoni
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Montelibretti, Italy.,Dipartimento di Chimica, Sapienza Università di Roma, Rome, Italy
| | - Mattea C Castrovilli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Montelibretti, Italy
| | - Jacopo Chiarinelli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Montelibretti, Italy.,Dipartimento di Scienze, Università degli Studi di Roma 3, Rome, Italy
| | - Sanja Tosic
- Institute of Physics, University of Belgrade, Belgrade, Serbia
| | | | - Robert Richter
- Elettra Sincrotrone Trieste, Area Science Park, Trieste, Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Montelibretti, Italy
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30
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Catone D, Satta M, Cartoni A, Castrovilli MC, Bolognesi P, Turchini S, Avaldi L. Gas Phase Oxidation of Carbon Monoxide by Sulfur Dioxide Radical Cation: Reaction Dynamics and Kinetic Trend With the Temperature. Front Chem 2019; 7:140. [PMID: 30972318 PMCID: PMC6443698 DOI: 10.3389/fchem.2019.00140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/25/2019] [Indexed: 01/16/2023] Open
Abstract
Gas phase ion chemistry has fundamental and applicative purposes since it allows the study of the chemical processes in a solvent free environment and represents models for reactions occurring in the space at low and high temperatures. In this work the ion-molecule reaction of sulfur dioxide ion SO 2 . + with carbon monoxide CO is investigated in a joint experimental and theoretical study. The reaction is a fast and exothermic chemical oxidation of CO into more stable CO2 by a metal free species, as SO 2 . + , excited into ro-vibrational levels of the electronic ground state by synchrotron radiation. The results show that the reaction is hampered by the enhancement of internal energy of sulfur dioxide ion and the only ionic product is SO.+. The theoretical approach of variational transition state theory (VTST) based on density functional electronic structure calculations, shows an interesting and peculiar reaction dynamics of the interacting system along the reaction path. Two energy minima corresponding to [SO2-CO].+ and [OS-OCO].+ complexes are identified. These minima are separated by an intersystem crossing barrier which couples the bent 3B2 state of CO2 with C2v symmetry and the 1A1 state with linear D∞h symmetry. The spin and charge reorganization along the minimum energy path (MEP) are analyzed and eventually the charge and spin remain allocated to the SO.+ moiety and the stable CO2 molecule is easily produced. There is no bottleneck that slows down the reaction and the values of the rate coefficient k at different temperatures are calculated with capture theory. A value of 2.95 × 10-10 cm3s-1molecule-1 is obtained at 300 K in agreement with the literature experimental measurement of 3.00 × 10-10 ± 20% cm3s-1molecule-1, and a negative trend with temperature is predicted consistently with the experimental observations.
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Affiliation(s)
- Daniele Catone
- Istituto di Struttura della Materia, Consiglio Nazionale Delle Ricerche (CNR-ISM), Area della Ricerca di Roma Tor Vergata, Rome, Italy
| | - Mauro Satta
- Istituto per lo Studio dei Materiali Nanostrutturati (CNR-ISMN), Dipartimento di Chimica, Sapienza Università di Roma, Rome, Italy
| | - Antonella Cartoni
- Dipartimento di Chimica, Sapienza Università di Roma, Rome, Italy.,Istituto di Struttura della Materia, Consiglio Nazionale Delle Ricerche (CNR-ISM), Area della Ricerca di Roma 1, Rome, Italy
| | - Mattea C Castrovilli
- Istituto di Struttura della Materia, Consiglio Nazionale Delle Ricerche (CNR-ISM), Area della Ricerca di Roma 1, Rome, Italy
| | - Paola Bolognesi
- Istituto di Struttura della Materia, Consiglio Nazionale Delle Ricerche (CNR-ISM), Area della Ricerca di Roma 1, Rome, Italy
| | - Stefano Turchini
- Istituto di Struttura della Materia, Consiglio Nazionale Delle Ricerche (CNR-ISM), Area della Ricerca di Roma Tor Vergata, Rome, Italy
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia, Consiglio Nazionale Delle Ricerche (CNR-ISM), Area della Ricerca di Roma 1, Rome, Italy
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31
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Castrovilli MC, Trabattoni A, Bolognesi P, O'Keeffe P, Avaldi L, Nisoli M, Calegari F, Cireasa R. Ultrafast Hydrogen Migration in Photoionized Glycine. J Phys Chem Lett 2018; 9:6012-6016. [PMID: 30253105 DOI: 10.1021/acs.jpclett.8b02089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hydrogen migration in the glycine cation has been investigated using a combination of a short train of attosecond extreme ultraviolet pulses with few-optical-cycle near-infrared pulses. The yield of the photofragments produced has been measured as a function of pump-probe delay. These time-dependent measurements reveal the presence of a hydrogen migration process occurring in 48 fs. Previous mass spectrometric experiments and theoretical calculations have allowed us to identify the conformations and cation states involved in the process induced by the broad band extreme ultraviolet radiation.
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Affiliation(s)
- M C Castrovilli
- Istituto Struttura della Materia, ISM-CNR , 00016 Monterotondo Scalo, Roma , Italy
- Institute for Photonics and Nanotechnologies, IFN-CNR , 20133 Milano , Italy
| | - A Trabattoni
- Department of Physics , Politecnico di Milano , 20133 Milano , Italy
- CFEL-DESY , Notkerstrasse 85 , 22607 Hamburg , Germany
| | - P Bolognesi
- Istituto Struttura della Materia, ISM-CNR , 00016 Monterotondo Scalo, Roma , Italy
| | - P O'Keeffe
- Istituto Struttura della Materia, ISM-CNR , 00016 Monterotondo Scalo, Roma , Italy
| | - L Avaldi
- Istituto Struttura della Materia, ISM-CNR , 00016 Monterotondo Scalo, Roma , Italy
| | - M Nisoli
- Institute for Photonics and Nanotechnologies, IFN-CNR , 20133 Milano , Italy
- Department of Physics , Politecnico di Milano , 20133 Milano , Italy
| | - F Calegari
- Institute for Photonics and Nanotechnologies, IFN-CNR , 20133 Milano , Italy
- CFEL-DESY , Notkerstrasse 85 , 22607 Hamburg , Germany
- Department of Physics , University of Hamburg , 20355 Hamburg , Germany
| | - R Cireasa
- Institut des Sciences Moléculaires d'Orsay, CNRS , Université Paris Sud , 91400 Orsay, France
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32
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Chiarinelli J, Markus P, Bolognesi P, Avaldi L, Turco Liveri V, Calandra P. Photo-fragmentation of alkyl phosphates in the gas-phase. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Cartoni A, Casavola AR, Bolognesi P, Castrovilli MC, Catone D, Chiarinelli J, Richter R, Avaldi L. Insights into 2- and 4(5)-Nitroimidazole Decomposition into Relevant Ions and Molecules Induced by VUV Ionization. J Phys Chem A 2018; 122:4031-4041. [DOI: 10.1021/acs.jpca.8b01144] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. Cartoni
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
- Dipartimento di Chimica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Roma, Italy
| | - A. R. Casavola
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
| | - P. Bolognesi
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
| | - M. C. Castrovilli
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
| | - D. Catone
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 2, via del Fosso del Cavaliere 10, 00133, Roma, Italy
| | - J. Chiarinelli
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
| | - R. Richter
- Elettra Sincrotrone Trieste, Area Science
Park, 34149, Basovizza, Trieste, Italy
| | - L. Avaldi
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
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34
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Castrovilli MC, Bolognesi P, Bodo E, Mattioli G, Cartoni A, Avaldi L. An experimental and theoretical investigation of XPS and NEXAFS of 5-halouracils. Phys Chem Chem Phys 2018; 20:6657-6667. [PMID: 29457179 DOI: 10.1039/c8cp00026c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C, N and O 1s excitation and ionization processes of 5X-uracil (X = F, Cl, Br, and I) were investigated using near edge X-ray absorption fine structure (NEXAFS) and X-ray photoemission (XPS) spectroscopies. This study aims at the fine assessment of the effects of the functionalization of uracil molecules by halogen atoms having different electronegativity and bound to the same molecular site. Two DFT-based approaches, which rely on different paradigms, have been used to simulate the experimental spectra and to assign the corresponding features. The analysis of the screening of the core holes of the different atoms via electronic charge density plots has turned out to be a useful tool to illustrate the competition between the partially aromatic and partially conjugate properties of this class of molecules.
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Affiliation(s)
- M C Castrovilli
- Istituto di Struttura della Materia-CNR, ISM-CNR, Area della Ricerca di Roma 1, CP10, 00015 Monterotondo Scalo, Italy.
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35
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Bolognesi P, Bañares L, Alcamí M. XUV/X-ray light and fast ions for ultrafast chemistry. Phys Chem Chem Phys 2018; 19:19533-19535. [PMID: 28744548 DOI: 10.1039/c7cp90137b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The deposition of large amounts of energy in a molecule by XUV/X-ray photon absorption or fast-ion collision, triggers a set of complex ultrafast electronic and nuclear dynamics that allow a deep understanding and control of chemical reactivity. This themed issue showcases the research performed in the understanding, monitoring and control of these processes.
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Affiliation(s)
- P Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo Scalo, Italy.
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36
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Chiarinelli J, Bolognesi P, Domaracka A, Rousseau P, Castrovilli MC, Richter R, Chatterjee S, Wang F, Avaldi L. Insights into the dissociative ionization of glycine by PEPICO experiments. Phys Chem Chem Phys 2018; 20:22841-22848. [PMID: 30151535 DOI: 10.1039/c8cp03473g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fragmentation of glycine (NH2CH2COOH) has been studied by photoelectron–photoion coincidence, PEPICO, experiments at 60 eV photon energy.
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Affiliation(s)
- Jacopo Chiarinelli
- Dipartimento di Scienze, Università di Roma Tre
- Roma
- Italy
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1
- Monterotondo Scalo
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1
- Monterotondo Scalo
- Italy
| | - Alicja Domaracka
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP
- 14000 Caen
- France
| | - Patrick Rousseau
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP
- 14000 Caen
- France
| | | | - Robert Richter
- Molecular Modelling Discovery Laboratory, Department of Chemistry and Biotechnology
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne
- Vic 3122
- Australia
| | | | - Feng Wang
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5
- Basovizza
- Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1
- Monterotondo Scalo
- Italy
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37
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Cartoni A, Catone D, Bolognesi P, Satta M, Markus P, Avaldi L. Frontispiece: HSO 2
+
Formation from Ion-Molecule Reactions of SO 2
⋅+
with Water and Methane: Two Fast Reactions with Reverse Temperature-Dependent Kinetic Trend. Chemistry 2017. [DOI: 10.1002/chem.201782863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Antonella Cartoni
- Dipartimento di Chimica; Sapienza Università di Roma; Pl.e Aldo Moro 5 00185 Roma Italy
- Istituto di Struttura della Materia (ISM); Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1; via Salaria Km 29,300 Monterotondo Scalo (RM) 00016 Italy
| | - Daniele Catone
- Istituto di Struttura della Materia (ISM); Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 2; via del Fosso del Cavaliere 10 00133 Roma Italy
| | - Paola Bolognesi
- Istituto di Struttura della Materia (ISM); Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1; via Salaria Km 29,300 Monterotondo Scalo (RM) 00016 Italy
| | - Mauro Satta
- Istituto per lo Studio dei Materiali Nanostrutturati (ISMN); Dipartimento di Chimica; Sapienza Università di Roma; P.le Aldo Moro 5 00185 Roma Italy
| | - Pal Markus
- Istituto di Struttura della Materia (ISM); Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1; via Salaria Km 29,300 Monterotondo Scalo (RM) 00016 Italy
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia (ISM); Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1; via Salaria Km 29,300 Monterotondo Scalo (RM) 00016 Italy
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38
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Cartoni A, Catone D, Bolognesi P, Satta M, Markus P, Avaldi L. HSO2
+
Formation from Ion-Molecule Reactions of SO2
⋅+
with Water and Methane: Two Fast Reactions with Reverse Temperature-Dependent Kinetic Trend. Chemistry 2017; 23:6772-6780. [DOI: 10.1002/chem.201700028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Antonella Cartoni
- Dipartimento di Chimica; Sapienza Università di Roma; Pl.e Aldo Moro 5 00185 Roma Italy
- Istituto di Struttura della Materia (ISM); Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1; via Salaria Km 29,300 Monterotondo Scalo (RM) 00016 Italy
| | - Daniele Catone
- Istituto di Struttura della Materia (ISM); Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 2; via del Fosso del Cavaliere 10 00133 Roma Italy
| | - Paola Bolognesi
- Istituto di Struttura della Materia (ISM); Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1; via Salaria Km 29,300 Monterotondo Scalo (RM) 00016 Italy
| | - Mauro Satta
- Istituto per lo Studio dei Materiali Nanostrutturati (ISMN); Dipartimento di Chimica; Sapienza Università di Roma; P.le Aldo Moro 5 00185 Roma Italy
| | - Pal Markus
- Istituto di Struttura della Materia (ISM); Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1; via Salaria Km 29,300 Monterotondo Scalo (RM) 00016 Italy
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia (ISM); Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1; via Salaria Km 29,300 Monterotondo Scalo (RM) 00016 Italy
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39
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Ilchen M, Douguet N, Mazza T, Rafipoor AJ, Callegari C, Finetti P, Plekan O, Prince KC, Demidovich A, Grazioli C, Avaldi L, Bolognesi P, Coreno M, Di Fraia M, Devetta M, Ovcharenko Y, Düsterer S, Ueda K, Bartschat K, Grum-Grzhimailo AN, Bozhevolnov AV, Kazansky AK, Kabachnik NM, Meyer M. Circular Dichroism in Multiphoton Ionization of Resonantly Excited He^{+} Ions. Phys Rev Lett 2017; 118:013002. [PMID: 28106422 DOI: 10.1103/physrevlett.118.013002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Indexed: 06/06/2023]
Abstract
Intense, circularly polarized extreme-ultraviolet and near-infrared (NIR) laser pulses are combined to double ionize atomic helium via the oriented intermediate He^{+}(3p) resonance state. Applying angle-resolved electron spectroscopy, we find a large photon helicity dependence of the spectrum and the angular distribution of the electrons ejected from the resonance by NIR multiphoton absorption. The measured circular dichroism is unexpectedly found to vary strongly as a function of the NIR intensity. The experimental data are well described by theoretical modeling and possible mechanisms are discussed.
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Affiliation(s)
- M Ilchen
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld Hamburg, Germany
- PULSE at Stanford, 2575 Sand Hill Road, Menlo Park, 94025 California, USA
| | - N Douguet
- Department of Physics and Astronomy, Drake University, Des Moines, Iowa 50311, USA
| | - T Mazza
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld Hamburg, Germany
| | - A J Rafipoor
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld Hamburg, Germany
| | - C Callegari
- Elettra-Sincrotrone Trieste, I-34149 Basovizza, Italy
| | - P Finetti
- Elettra-Sincrotrone Trieste, I-34149 Basovizza, Italy
| | - O Plekan
- Elettra-Sincrotrone Trieste, I-34149 Basovizza, Italy
| | - K C Prince
- Elettra-Sincrotrone Trieste, I-34149 Basovizza, Italy
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, Area Science Park, I-34149 Trieste, Italy
- Molecular Model Discovery Laboratory, Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - A Demidovich
- Elettra-Sincrotrone Trieste, I-34149 Basovizza, Italy
| | - C Grazioli
- Elettra-Sincrotrone Trieste, I-34149 Basovizza, Italy
| | - L Avaldi
- CNR Istituto Struttura della Materia, Via del Fosso del Cavaliere, 100-00133 Roma, Italy
| | - P Bolognesi
- CNR Istituto Struttura della Materia, Via del Fosso del Cavaliere, 100-00133 Roma, Italy
| | - M Coreno
- CNR Istituto Struttura della Materia, Via del Fosso del Cavaliere, 100-00133 Roma, Italy
| | - M Di Fraia
- Department of Physics, University of Trieste, I-34128 Trieste, Italy
| | - M Devetta
- Istituto di fotonica e nanotecnologie CNR-IFN, 20133 Milano, Italy
| | - Y Ovcharenko
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld Hamburg, Germany
| | - S Düsterer
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, D-22603 Hamburg, Germany
| | - K Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - K Bartschat
- Department of Physics and Astronomy, Drake University, Des Moines, Iowa 50311, USA
| | - A N Grum-Grzhimailo
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld Hamburg, Germany
- Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - A V Bozhevolnov
- Sankt Petersburg State University, Universitetskaya nab. 7/9, Sankt Petersburg 199164, Russia
| | - A K Kazansky
- Departamento de Fisica de Materiales, UPV/EHU, E-20018 San Sebastian/Donostia, Spain
- IKERBASQUE, Basque Foundation for Science, E-48011 Bilbao, Spain
- Donostia International Physics Center (DIPC), E-20018 San Sebastian/Donostia, Spain
| | - N M Kabachnik
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld Hamburg, Germany
- Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, Moscow 119991, Russia
- Donostia International Physics Center (DIPC), E-20018 San Sebastian/Donostia, Spain
| | - M Meyer
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld Hamburg, Germany
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40
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Castrovilli MC, Markush P, Bolognesi P, Rousseau P, Maclot S, Cartoni A, Delaunay R, Domaracka A, Kočišek J, Huber BA, Avaldi L. Fragmentation of pure and hydrated clusters of 5Br-uracil by low energy carbon ions: observation of hydrated fragments. Phys Chem Chem Phys 2017; 19:19807-19814. [DOI: 10.1039/c7cp02233f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The fragmentation of the isolated 5-bromouracil (5BrU) molecule and pure and nano-hydrated 5BrU clusters induced by low energy 12C4+ ions has been studied.
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Affiliation(s)
| | | | | | | | - S. Maclot
- Normandie Université
- ENSICAEN
- UNICAEN
- CEA
- CNRS
| | - A. Cartoni
- CNR-ISM
- Monterotondo Scalo
- Italy
- Dipartimento di Chimica
- Sapienza Università di Roma
| | | | | | - J. Kočišek
- Normandie Université
- ENSICAEN
- UNICAEN
- CEA
- CNRS
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41
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Bolognesi P, Casavola AR, Cartoni A, Richter R, Markus P, Borocci S, Chiarinelli J, Tošić S, Sa’adeh H, Masič M, Marinković B, Prince K, Avaldi L. Communication: “Position” does matter: The photofragmentation of the nitroimidazole isomers. J Chem Phys 2016; 145:191102. [DOI: 10.1063/1.4967770] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- P. Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma1, Monterotondo, Italy
| | - A. R. Casavola
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma1, Monterotondo, Italy
| | - A. Cartoni
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma1, Monterotondo, Italy
- Dipartimento di Chimica, Sapienza Università di Roma, Roma, Italy
| | - R. Richter
- Elettra-Sincrotrone Trieste, Basovizza, Italy
| | - P. Markus
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma1, Monterotondo, Italy
| | - S. Borocci
- Dipartimento per l’Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università della Tuscia, Viterbo, Italy
| | - J. Chiarinelli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma1, Monterotondo, Italy
| | - S. Tošić
- Institute of Physics Belgrade, University of Belgrade, Belgrade, Serbia
| | - H. Sa’adeh
- Department of Physics, The University of Jordan, Amman, Jordan
| | - M. Masič
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - B.P. Marinković
- Institute of Physics Belgrade, University of Belgrade, Belgrade, Serbia
| | - K.C. Prince
- Elettra-Sincrotrone Trieste, Basovizza, Italy
| | - L. Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma1, Monterotondo, Italy
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42
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Maclot S, Delaunay R, Piekarski DG, Domaracka A, Huber BA, Adoui L, Martín F, Alcamí M, Avaldi L, Bolognesi P, Díaz-Tendero S, Rousseau P. Determination of Energy-Transfer Distributions in Ionizing Ion-Molecule Collisions. Phys Rev Lett 2016; 117:073201. [PMID: 27563959 DOI: 10.1103/physrevlett.117.073201] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 06/06/2023]
Abstract
The ionization and fragmentation of the nucleoside thymidine in the gas phase has been investigated by combining ion collision with state-selected photoionization experiments and quantum chemistry calculations. The comparison between the mass spectra measured in both types of experiments allows us to accurately determine the distribution of the energy deposited in the ionized molecule as a result of the collision. The relation of two experimental techniques and theory shows a strong correlation between the excited states of the ionized molecule with the computed dissociation pathways, as well as with charge localization or delocalization.
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Affiliation(s)
- S Maclot
- Normandie Université-CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/UNICAEN, Boulevard Henri Becquerel, BP 5133-14070 Caen cedex 5, France
| | - R Delaunay
- Normandie Université-CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/UNICAEN, Boulevard Henri Becquerel, BP 5133-14070 Caen cedex 5, France
| | - D G Piekarski
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - A Domaracka
- Normandie Université-CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/UNICAEN, Boulevard Henri Becquerel, BP 5133-14070 Caen cedex 5, France
| | - B A Huber
- Normandie Université-CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/UNICAEN, Boulevard Henri Becquerel, BP 5133-14070 Caen cedex 5, France
| | - L Adoui
- Normandie Université-CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/UNICAEN, Boulevard Henri Becquerel, BP 5133-14070 Caen cedex 5, France
| | - F Martín
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencias (IMDEANanociencia), Cantoblanco 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - M Alcamí
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencias (IMDEANanociencia), Cantoblanco 28049 Madrid, Spain
| | - L Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo Scalo, Italy
| | - P Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo Scalo, Italy
| | - S Díaz-Tendero
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - P Rousseau
- Normandie Université-CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/UNICAEN, Boulevard Henri Becquerel, BP 5133-14070 Caen cedex 5, France
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43
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Markush P, Bolognesi P, Cartoni A, Rousseau P, Maclot S, Delaunay R, Domaracka A, Kocisek J, Castrovilli MC, Huber BA, Avaldi L. The role of the environment in the ion induced fragmentation of uracil. Phys Chem Chem Phys 2016; 18:16721-9. [DOI: 10.1039/c6cp01940d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fragmentation of uracil molecules and pure and nano-hydrated uracil clusters by 12C4+ ion impact is investigated.
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Affiliation(s)
| | | | - Antonella Cartoni
- CNR-ISM
- Monterotondo Scalo
- Italy
- Dipartimento di Chimica
- Sapienza Università di Roma
| | - Patrick Rousseau
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Sylvain Maclot
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Rudy Delaunay
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Alicja Domaracka
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Jaroslav Kocisek
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
- J. Heyrovský Institute of Physical Chemistry
| | | | - Bernd A. Huber
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
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44
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Satta M, Bolognesi P, Cartoni A, Casavola AR, Catone D, Markus P, Avaldi L. A joint theoretical and experimental study on diiodomethane: Ions and neutrals in the gas phase. J Chem Phys 2015; 143:244312. [DOI: 10.1063/1.4937425] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mauro Satta
- Dipartimento di Chimica, CNR-ISMN, Sapienza Università di Roma, Roma 00185, Italy
| | - Paola Bolognesi
- CNR-ISM, Area della Ricerca di Roma 1, Monterotondo Scalo, RM 00015, Italy
| | - Antonella Cartoni
- Dipartimento di Chimica, Sapienza Università di Roma, Roma 00185, Italy
| | - Anna Rita Casavola
- CNR-ISM, Area della Ricerca di Roma 1, Monterotondo Scalo, RM 00015, Italy
| | - Daniele Catone
- CNR-ISM, Area della Ricerca di Roma 2, Roma 00133, Italy
| | - Pal Markus
- CNR-ISM, Area della Ricerca di Roma 1, Monterotondo Scalo, RM 00015, Italy
| | - Lorenzo Avaldi
- CNR-ISM, Area della Ricerca di Roma 1, Monterotondo Scalo, RM 00015, Italy
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45
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Bolognesi P, Kettunen JA, Cartoni A, Richter R, Tosic S, Maclot S, Rousseau P, Delaunay R, Avaldi L. Site- and state-selected photofragmentation of 2Br-pyrimidine. Phys Chem Chem Phys 2015; 17:24063-9. [PMID: 26314495 DOI: 10.1039/c5cp02601f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The fragmentation of the 2Br-pyrimidine molecule following direct valence photoionization or inner shell excitation has been studied by electron-ion coincidence experiments. 2Br-pyrimidine has been chosen as a model for the class of pyrimidinic building blocks of three nucleic acids and several radiosensitizers. It is known that the site- and state-localization of energy deposition, typical of inner shell excitation, results in the enhancement of the total ion yield as well as in changes in the relative intensity of the different fragmentation channels. Here we address the question of the origin of this selective fragmentation by using electron-ion coincidence techniques. The results show that the fragmentation is strongly selective in the final singly charged ion state, independently of the process that leads to the population of that state, and the dominant fragmentation patterns correlate with the nearest appearance potential.
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Affiliation(s)
- P Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma1, Monterotondo Scalo, Italy.
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46
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Cartoni A, Casavola AR, Bolognesi P, Borocci S, Avaldi L. VUV Photofragmentation of CH2I2: The [CH2I–I]•+ Iso-diiodomethane Intermediate in the I-Loss Channel from [CH2I2]•+. J Phys Chem A 2015; 119:3704-9. [DOI: 10.1021/jp511067d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Antonella Cartoni
- Dipartimento
di Chimica, Sapienza Università di Roma, P. le Aldo Moro
5, Rome 00185, Italy
| | - Anna Rita Casavola
- CNR-ISM, Area della Ricerca di Roma 1, Monterotondo
Scalo (RM) 00015, Italy
| | - Paola Bolognesi
- CNR-ISM, Area della Ricerca di Roma 1, Monterotondo
Scalo (RM) 00015, Italy
| | - Stefano Borocci
- Dipartimento
per l’ Innovazione nei sistemi Biologici, Agroalimentari e
Forestali (DIBAF), Università della Tuscia, L.go dell’Università, s.n.c., 01100 Viterbo, Italy
| | - Lorenzo Avaldi
- CNR-ISM, Area della Ricerca di Roma 1, Monterotondo
Scalo (RM) 00015, Italy
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47
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Jabbari G, Miteva T, Stumpf V, Gokhberg K, O'Keeffe P, Ciavardini A, Bolognesi P, Coreno M, Avaldi L, Keshavarz E, Ghandehari M, Tozihi M, Callegari C, Alagia M, Prince KC, Kivimäki A, Richter R. Soft X-ray absorption spectroscopy of Ar2 and ArNe dimers and small Ar clusters. Phys Chem Chem Phys 2015; 17:22160-9. [DOI: 10.1039/c5cp03276h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The X-ray absorption spectra of rare gas dimers and clusters have been studied experimentally and theoretically.
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Affiliation(s)
- Ghazal Jabbari
- Theoretische Chemie
- Physikalisch-Chemisches Institut
- Universität Heidelberg
- 69120 Heidelberg
- Germany
| | - Tsveta Miteva
- Theoretische Chemie
- Physikalisch-Chemisches Institut
- Universität Heidelberg
- 69120 Heidelberg
- Germany
| | - Vasili Stumpf
- Theoretische Chemie
- Physikalisch-Chemisches Institut
- Universität Heidelberg
- 69120 Heidelberg
- Germany
| | - Kirill Gokhberg
- Theoretische Chemie
- Physikalisch-Chemisches Institut
- Universität Heidelberg
- 69120 Heidelberg
- Germany
| | | | | | | | | | - Lorenzo Avaldi
- CNR-ISM
- Area della Ricerca di Roma 1
- Monterotondo Scalo
- Italy
| | | | | | - Manijeh Tozihi
- Department of Chemistry
- University of Zanjan
- Zanjan 45371-38791
- Iran
| | | | - Michele Alagia
- Molecular Model Discovery Laboratory
- Department of Chemistry and Biotechnology
- Faculty of Sciences, Engineering and Technology
- Swinburne University of Technology
- Melbourne
| | - Kevin Charles Prince
- Elettra-Sincrotrone Trieste
- Basovizza 34149
- Italy
- Molecular Model Discovery Laboratory
- Department of Chemistry and Biotechnology
| | - Antti Kivimäki
- Molecular Model Discovery Laboratory
- Department of Chemistry and Biotechnology
- Faculty of Sciences, Engineering and Technology
- Swinburne University of Technology
- Melbourne
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48
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Cartoni A, Bolognesi P, Fainelli E, Avaldi L. Publisher's Note: “Photofragmentation spectra of halogenated methanes in the VUV photon energy range” [J. Chem. Phys. 140, 184307 (2014)]. J Chem Phys 2014. [DOI: 10.1063/1.4884128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Murphy BF, Osipov T, Jurek Z, Fang L, Son SK, Mucke M, Eland JHD, Zhaunerchyk V, Feifel R, Avaldi L, Bolognesi P, Bostedt C, Bozek JD, Grilj J, Guehr M, Frasinski LJ, Glownia J, Ha DT, Hoffmann K, Kukk E, McFarland BK, Miron C, Sistrunk E, Squibb RJ, Ueda K, Santra R, Berrah N. Femtosecond X-ray-induced explosion of C60 at extreme intensity. Nat Commun 2014; 5:4281. [PMID: 24969734 DOI: 10.1038/ncomms5281] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 06/02/2014] [Indexed: 11/09/2022] Open
Abstract
Understanding molecular femtosecond dynamics under intense X-ray exposure is critical to progress in biomolecular imaging and matter under extreme conditions. Imaging viruses and proteins at an atomic spatial scale and on the time scale of atomic motion requires rigorous, quantitative understanding of dynamical effects of intense X-ray exposure. Here we present an experimental and theoretical study of C60 molecules interacting with intense X-ray pulses from a free-electron laser, revealing the influence of processes not previously reported. Our work illustrates the successful use of classical mechanics to describe all moving particles in C60, an approach that scales well to larger systems, for example, biomolecules. Comparisons of the model with experimental data on C60 ion fragmentation show excellent agreement under a variety of laser conditions. The results indicate that this modelling is applicable for X-ray interactions with any extended system, even at higher X-ray dose rates expected with future light sources.
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Affiliation(s)
- B F Murphy
- 1] Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008, USA [2]
| | - T Osipov
- 1] Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008, USA [2]
| | - Z Jurek
- 1] Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany [2] The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany [3]
| | - L Fang
- Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - S-K Son
- 1] Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany [2] The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
| | - M Mucke
- Gothenburg University, Department of Physics Origovägen 6, SE-412 96 Gothenburg, Sweden
| | - J H D Eland
- 1] Gothenburg University, Department of Physics Origovägen 6, SE-412 96 Gothenburg, Sweden [2] Department of Chemistry, Oxford University, Oxford OX1 3QZ, UK
| | - V Zhaunerchyk
- Gothenburg University, Department of Physics Origovägen 6, SE-412 96 Gothenburg, Sweden
| | - R Feifel
- Gothenburg University, Department of Physics Origovägen 6, SE-412 96 Gothenburg, Sweden
| | - L Avaldi
- Instituto di Metodologie Inorganiche e dei Plasmi, C.N.R., Rome 00133, Italy
| | - P Bolognesi
- Instituto di Metodologie Inorganiche e dei Plasmi, C.N.R., Rome 00133, Italy
| | - C Bostedt
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - J D Bozek
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - J Grilj
- PULSE, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - M Guehr
- PULSE, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - L J Frasinski
- Blackett Laboratory, Imperial College London, London SW7 2AZ, UK
| | - J Glownia
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - D T Ha
- Department of Physics, University of Turku, FIN-20014 Turku, Finland
| | - K Hoffmann
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, USA
| | - E Kukk
- Department of Physics, University of Turku, FIN-20014 Turku, Finland
| | - B K McFarland
- PULSE, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - C Miron
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - E Sistrunk
- PULSE, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - R J Squibb
- 1] Gothenburg University, Department of Physics Origovägen 6, SE-412 96 Gothenburg, Sweden [2] Blackett Laboratory, Imperial College London, London SW7 2AZ, UK
| | - K Ueda
- Department of Physics, Tohoku University, Sendai 980-8577, Japan
| | - R Santra
- 1] Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany [2] The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany [3] Department of Physics, University of Hamburg, 20355 Hamburg, Germany
| | - N Berrah
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, USA
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50
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Cartoni A, Bolognesi P, Fainelli E, Avaldi L. Photofragmentation spectra of halogenated methanes in the VUV photon energy range. J Chem Phys 2014; 140:184307. [PMID: 24832270 DOI: 10.1063/1.4874114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this paper an investigation of the photofragmentation of dihalomethanes CH2X2 (X = F, Cl, Br, I) and chlorinated methanes (CH(n)Cl(4-n) with n = 0-3) with VUV helium, neon, and argon discharge lamps is reported and the role played by the different halogen atoms is discussed. Halogenated methanes are a class of molecules used in several fields of chemistry and the study of their physical and chemical proprieties is of fundamental interest. In particular their photodissociation and photoionization are of great importance since the decomposition of these compounds in the atmosphere strongly affects the environment. The results of the present work show that the halogen-loss is the predominant fragmentation channel for these molecules in the VUV photon energy range and confirm their role as reservoir of chlorine, bromine, and iodine atoms in the atmosphere. Moreover, the results highlight the peculiar feature of CH2F2 as a source of both fluorine and hydrogen atoms and the characteristic formation of I2(+) and CH2(+) ions from the photofragmentation of the CH2I2 molecule.
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Affiliation(s)
- Antonella Cartoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, P.le Aldo Moro 5, Roma 00185, Italy
| | - Paola Bolognesi
- CNR-IMIP, Area della Ricerca di Roma 1, Monterotondo Scalo (Rm) 00015, Italy
| | - Ettore Fainelli
- CNR-IMIP, Area della Ricerca di Roma 1, Monterotondo Scalo (Rm) 00015, Italy
| | - Lorenzo Avaldi
- CNR-IMIP, Area della Ricerca di Roma 1, Monterotondo Scalo (Rm) 00015, Italy
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