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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] [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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2
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A new palladium-based antiproliferative agent: synthesis, characterization, computational calculations, cytotoxicity, and DNA binding properties. Biometals 2021; 34:1173-1189. [PMID: 34363565 DOI: 10.1007/s10534-021-00335-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
A new palladium(II) complex entitled [Pd(phendione)(8Q)]NO3, (PdPQ), where phendione is N,N-donor heterocyclic 1,10-phenanthroline-5,6-dion and 8Q is 8-hydroxyquinolinate, has been synthesized and then characterized by molar conductivity, CHN analysis and spectral data (UV-Vis, FT-IR, NMR). DFT/ TDDFT procedures were also performed to determine the electronic structure and the nature of the electronic transitions of PdPQ. Moreover, the affinity and binding properties of DNA to the desired complex have been studied in details using electronic absorption, fluorescence, circular dichroism spectroscopies, and viscosity measurement in combination with molecular docking technique. The obtained results exhibit relatively high DNA binding values with a static quenching mechanism, which suggest that an intercalative mode plays a peridominate role in interaction process concluded by experimental/theoretical measurements. As a result of drug exposure, in vitro cytotoxicity assay demonstrated the antiproliferative activity of the PdPQ against leukemia cancer cell line, K562.
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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] [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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4
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Mendes M, Kossoski F, Lozano AI, Pereira-da-Silva J, Rodrigues R, Ameixa J, Jones NC, Hoffmann SV, Ferreira da Silva F. Excited States of Bromopyrimidines Probed by VUV Photoabsorption Spectroscopy and Theoretical Calculations. Int J Mol Sci 2021; 22:6460. [PMID: 34208711 PMCID: PMC8235550 DOI: 10.3390/ijms22126460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/10/2021] [Accepted: 06/12/2021] [Indexed: 11/16/2022] Open
Abstract
We report absolute photoabsorption cross sections for gas-phase 2- and 5-bromopyrimidine in the 3.7-10.8 eV energy range, in a joint theoretical and experimental study. The measurements were carried out using high-resolution vacuum ultraviolet synchrotron radiation, with quantum chemical calculations performed through the nuclear ensemble approach in combination with time-dependent density functional theory, along with additional Franck-Condon Herzberg-Teller calculations for the first absorption band (3.7-4.6 eV). The cross sections of both bromopyrimidines are very similar below 7.3 eV, deviating more substantially from each other at higher energies. In the 7.3-9.0 eV range where the maximum cross-section is found, a single and broad band is observed for 5-bromopyrimidine, while more discernible features appear in the case of 2-bromopyrimidine. Several π* ← π transitions account for the most intense bands, while weaker ones are assigned to transitions involving the nitrogen and bromine lone pairs, the antibonding σ*Br orbital, and the lower-lying Rydberg states. A detailed comparison with the available photo-absorption data of bromobenzene is also reported. We have found significant differences regarding the main absorption band, which is more peaked in bromobenzene, becoming broader and shifting to higher energies in both bromopyrimidines. In addition, there is a significant suppression of vibrational structures and of Rydberg states in the pair of isomers, most noticeably for 2-bromopyrimidine.
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Affiliation(s)
- Mónica Mendes
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
| | - Fábris Kossoski
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, CEDEX 09, 31062 Toulouse, France
| | - Ana I. Lozano
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
| | - João Pereira-da-Silva
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
| | - Rodrigo Rodrigues
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
| | - João Ameixa
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
| | - Nykola C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Søren V. Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Filipe Ferreira da Silva
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
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5
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Unravelling molecular interactions in uracil clusters by XPS measurements assisted by ab initio and tight-binding simulations. Sci Rep 2020; 10:13081. [PMID: 32753713 PMCID: PMC7403593 DOI: 10.1038/s41598-020-69947-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/21/2020] [Indexed: 12/13/2022] Open
Abstract
The C, N and O 1s XPS spectra of uracil clusters in the gas phase have been measured. A new bottom-up approach, which relies on computational simulations starting from the crystallographic structure of uracil, has been adopted to interpret the measured spectra. This approach sheds light on the different molecular interactions (H-bond, π-stacking, dispersion interactions) at work in the cluster and provides a good understanding of the observed XPS chemical shifts with respect to the isolated molecule in terms of intramolecular and intermolecular screening occurring after the core–hole ionization. The proposed bottom-up approach, reasonably expensive in terms of computational resources, has been validated by finite-temperature molecular dynamics simulations of clusters composed of up to fifty molecules.
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6
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Abstract
The molecular structures of 12 azabenzenes have been optimized with the Gaussian09 package at the level of coupled cluster singles and doubles with the basis set cc-pVTZ. The optimized geometry of each is used in the ADF13 program for the calculation of the vertical ionization energies of all the electrons. For both outer-shell and inner-shell valence electrons, the 2009 method of ΔPBE0(SAOP) is used, whereas the 1999 method of ΔPW86PW91 + Crel is employed for the core electrons. For degenerate orbitals, the alternative method chosen is to use localized orbitals, keeping the integer number of electrons, while giving up proper symmetry, rather than to keep symmetry with fractional electrons. The success of the computed results of valence ionization potentials of pyridine and the diazabenzenes gives confidence for the predicted values for the higher azabenzenes. The calculated results for core-electron binding energies provide incentive to experimentalists to measure them with X-ray photoelectron spectrometers and (or) synchrotron facilities.
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Affiliation(s)
- Delano P. Chong
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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7
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Jin Y, Bartlett RJ. Accurate computation of X-ray absorption spectra with ionization potential optimized global hybrid functional. J Chem Phys 2018; 149:064111. [DOI: 10.1063/1.5038434] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yifan Jin
- Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, USA
| | - Rodney J. Bartlett
- Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, USA
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8
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Is there substituent cross-interaction effect in all the conjugated systems containing C N polar bond? The substituent effects on the NMR chemical shifts of 2,5-disubstituted pyrimidines. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.10.111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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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: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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10
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Zanotti G, Angelini N, Mattioli G, Paoletti AM, Pennesi G, Rossi G, Caschera D, de Marco L, Gigli G. Metal–organic green dye: chemical and physical insight into a modified Zn-benzoporphyrin for dye-sensitized solar cells. RSC Adv 2016. [DOI: 10.1039/c5ra20945e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A novel green benzoporphyrin has been synthesized, characterized, studied by theoretical methods and tested in DSSC devices. Ab initio simulations predict the actual charge displacement during S0 → S1 excitation.
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Affiliation(s)
| | | | | | | | | | | | | | - Luisa de Marco
- IIT – Center for Biomolecular Nanotechnologies
- Arnesano
- 73010-Italy
| | - Giuseppe Gigli
- CNR-NANOTEC
- Bari 70126
- Italy
- Dip. di Matematica e Fisica
- Università del Salento
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11
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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] [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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12
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Derricotte WD, Evangelista FA. Simulation of X-ray absorption spectra with orthogonality constrained density functional theory. Phys Chem Chem Phys 2015; 17:14360-74. [PMID: 25690350 PMCID: PMC4449318 DOI: 10.1039/c4cp05509h] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Orthogonality constrained density functional theory (OCDFT) [F. A. Evangelista, P. Shushkov and J. C. Tully, J. Phys. Chem. A, 2013, 117, 7378] is a variational time-independent approach for the computation of electronic excited states. In this work we extend OCDFT to compute core-excited states and generalize the original formalism to determine multiple excited states. Benchmark computations on a set of 13 small molecules and 40 excited states show that unshifted OCDFT/B3LYP excitation energies have a mean absolute error of 1.0 eV. Contrary to time-dependent DFT, OCDFT excitation energies for first- and second-row elements are computed with near-uniform accuracy. OCDFT core excitation energies are insensitive to the choice of the functional and the amount of Hartree-Fock exchange. We show that OCDFT is a powerful tool for the assignment of X-ray absorption spectra of large molecules by simulating the gas-phase near-edge spectrum of adenine and thymine.
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Affiliation(s)
- Wallace D Derricotte
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA.
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13
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Ahmed M, Wang F, Acres RG, Prince KC. Structures of cycloserine and 2-oxazolidinone probed by X-ray photoelectron spectroscopy: theory and experiment. J Phys Chem A 2014; 118:3645-54. [PMID: 24821292 DOI: 10.1021/jp500308j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The electronic structures and properties of 2-oxazolidinone and the related compound cycloserine (CS) have been investigated using theoretical calculations and core and valence photoelectron spectroscopy. Isomerization of the central oxazolidine heterocycle and the addition of an amino group yield cycloserine. Theory correctly predicts the C, N, and O 1s core spectra, and additionally, we report theoretical natural bond orbital (NBO) charges. The valence ionization energies are also in agreement with theory and previous measurements. Although the lowest binding energy part of the spectra of the two compounds shows superficial similarities, further analysis of the charge densities of the frontier orbitals indicates substantial reorganization of the wave functions as a result of isomerization. The highest occupied molecular orbital (HOMO) of CS shows leading carbonyl π character with contributions from other heavy (non-H) atoms in the molecule, while the HOMO of 2-oxazolidinone (OX2) has leading nitrogen, carbon, and oxygen pπ characters. The present study further theoretically predicts bond resonance effects of the compounds, evidence for which is provided by our experimental measurements and published crystallographic data.
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Affiliation(s)
- Marawan Ahmed
- eChemistry Laboratory, Department of Chemistry and Biotechnology, School of Science, Faculty of Science, Engineering and Technology, Swinburne University of Technology , Melbourne, Victoria 3122, Australia
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14
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Castrovilli MC, Bolognesi P, Cartoni A, Catone D, O'Keeffe P, Casavola AR, Turchini S, Zema N, Avaldi L. Photofragmentation of halogenated pyrimidine molecules in the VUV range. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:351-367. [PMID: 24385396 DOI: 10.1007/s13361-013-0783-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 11/11/2013] [Accepted: 11/17/2013] [Indexed: 06/03/2023]
Abstract
In the present work, we studied the photoinduced ion chemistry of the halogenated pyrimidines, a class of prototype radiosensitizing molecules, in the energy region 9-15 eV. The work was stimulated by previous studies on inner shell site-selective fragmentation of the pyrimidine molecule, which have shown that the fragmentation is governed by the population/formation of specific ionic states with a hole in valence orbitals, which in turn correlate to accessible dissociation limits. The combined experimental and theoretical study of the appearance energies of the main fragments provides information on the geometric structure of the products and on the role played by the specific halogen atom and the site of halogenation in the dissociation process. This information can be used to gain new insights on the elementary mechanisms that could possibly explain the enhanced radiation damage to the DNA bases or to the medium in which the bases are embedded, thereby contributing to their radiosensitizing effect.
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15
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Rondino F, Catone D, Mattioli G, Bonapasta AA, Bolognesi P, Casavola AR, Coreno M, O'Keeffe P, Avaldi L. Competition between electron-donor and electron-acceptor substituents in nitrotoluene isomers: a photoelectron spectroscopy and ab initio investigation. RSC Adv 2014. [DOI: 10.1039/c3ra45705b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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16
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Plekan O, Feyer V, Richter R, Moise A, Coreno M, Prince KC, Zaytseva IL, Moskovskaya TE, Soshnikov DY, Trofimov AB. X-ray spectroscopy of heterocyclic biochemicals: xanthine, hypoxanthine, and caffeine. J Phys Chem A 2012; 116:5653-64. [PMID: 22620864 DOI: 10.1021/jp300459p] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The electronic structures of the purine derivatives xanthine, hypoxanthine and caffeine have been investigated in the gas phase using C, N, and O 1s X-ray photoemission (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The results have been interpreted by means of ab initio calculations using the third-order algebraic-diagrammatic construction (ADC(3)) method for the one-particle Green's function and the second-order ADC method (ADC(2)) for the polarization propagator. The carbon, nitrogen and oxygen K-edge NEXAFS spectra of xanthine and caffeine are very similar, since the molecules differ only by substitution of three hydrogen atoms by methyl groups. For hypoxanthine, the electronic structure and spectra differ considerably from xanthine as the purine ring is more highly conjugated, and there is one less oxo group. Effects due to oxo-hydroxy tautomerism were not observed. However, the two oxo tautomeric forms of hypoxanthine oxo-N(9)-H and oxo-N(7)-H are populated in the gas phase, and the C 1s spectra can be simulated only by taking account of these two tautomers, with appropriate Boltzmann population ratios which we have also calculated. For xanthine and caffeine, single tautomeric forms were observed.
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Affiliation(s)
- Oksana Plekan
- Sincrotrone Trieste, Area Science Park, I-34149 Basovizza (Trieste), Italy
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17
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Bolognesi P, O'Keeffe P, Ovcharenko Y, Avaldi L, Carravetta V. Resonant Auger spectroscopy at the carbon and nitrogen K-edges of pyrimidine. J Chem Phys 2012; 136:154308. [DOI: 10.1063/1.4704893] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Takahashi O, Tashiro M, Ehara M, Yamasaki K, Ueda K. Theoretical Molecular Double-Core-Hole Spectroscopy of Nucleobases. J Phys Chem A 2011; 115:12070-82. [PMID: 21942319 DOI: 10.1021/jp205923m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Motomichi Tashiro
- Institute for Molecular Science, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
- Research Center for Computational Science, Okazaki 444-8585, Japan
| | - Masahiro Ehara
- Institute for Molecular Science, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
- Research Center for Computational Science, Okazaki 444-8585, Japan
- JST, CREST, Sanboncho-5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Katsuyoshi Yamasaki
- Department of Chemistry, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
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19
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Modelli A, Bolognesi P, Avaldi L. Temporary anion states of pyrimidine and halopyrimidines. J Phys Chem A 2011; 115:10775-82. [PMID: 21875136 DOI: 10.1021/jp206559d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The empty-level electronic structures of pyrimidine and its 2-chloro, 2-bromo, and 5-bromo derivatives have been studied with electron transmission spectroscopy (ETS) and dissociative electron attachment spectroscopy (DEAS) in the 0-5 eV energy range. The spectral features were assigned to the corresponding anion states with the support of theoretical calculations at the ab initio and density functional theory levels. The empty orbital energies obtained by simple Koopmans' theorem calculations, scaled with empirical equations, quantitatively reproduced the energies of vertical electron attachment to π* and σ* empty orbitals measured in the ET spectra and predicted vertical electron affinities close to zero for the three halo derivatives. The total anion currents of the halo derivatives, measured at the walls of the collision chamber as a function of the impact electron energy, presented intense maxima below 0.5 eV. The mass-selected spectra showed that, in this energy, range the total anion current is essentially due to halide fragment anions. The DEA cross sections of the bromo derivatives were found to be about six times larger than that of the chloro derivative. The absolute cross sections at incident electron energies close to zero were evaluated to be 10(-16)-10(-15) cm(2).
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Affiliation(s)
- Alberto Modelli
- Dipartimento di Chimica G. Ciamician, Università di Bologna, via Selmi 2, 40126 Bologna, Italy.
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20
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Feyer V, Plekan O, Kivimäki A, Prince KC, Moskovskaya TE, Zaytseva IL, Soshnikov DY, Trofimov AB. Comprehensive Core-Level Study of the Effects of Isomerism, Halogenation, and Methylation on the Tautomeric Equilibrium of Cytosine. J Phys Chem A 2011; 115:7722-33. [DOI: 10.1021/jp2017506] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vitaliy Feyer
- Sincrotrone Trieste, in Area Science Park, Basovizza (Trieste) I-34149, Italy
| | - Oksana Plekan
- Sincrotrone Trieste, in Area Science Park, Basovizza (Trieste) I-34149, Italy
| | - Antti Kivimäki
- Laboratorio TASC, CNR-IOM, Basovizza (Trieste) I-34149, Italy
| | - Kevin C. Prince
- Sincrotrone Trieste, in Area Science Park, Basovizza (Trieste) I-34149, Italy
- Laboratorio TASC, CNR-IOM, Basovizza (Trieste) I-34149, Italy
| | | | - Irina L. Zaytseva
- Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia
| | | | - Alexander B. Trofimov
- Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia
- Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia
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21
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Zanotti G, Angelini N, Paoletti AM, Pennesi G, Rossi G, Bonapasta AA, Mattioli G, Di Carlo A, Brown TM, Lembo A, Reale A. Synthesis of a novel unsymmetrical Zn(II) phthalocyanine bearing a phenyl ethynyl moiety as sensitizer for dye-sensitized solar cells. Dalton Trans 2010; 40:38-40. [PMID: 21076741 DOI: 10.1039/c0dt01292k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new unsymmetrical zinc phthalocyanine sensitizer has been synthesised. The anchoring of the molecule to nanocrystalline TiO(2) films is realised by a carboxylic group connected to a phenyl ethynyl moiety. Density Functional Theory (DFT) calculations show significant and positive effects of such a functionalization. Electron injection into the semiconductor and photocurrent generation in DSSC are also presented.
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Affiliation(s)
- Gloria Zanotti
- Center for Hybrid and Organic Solar Energy, Università di Tor Vergata, Via G. Peroni 400/402, 00131, Roma, Italy
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