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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] [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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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] [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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Mishra PM, Avaldi L, Bolognesi P, Prince KC, Richter R, Kadhane UR. Valence Shell Photoelectron Spectroscopy of Pyrene and Fluorene: Photon Energy Dependence in the Far-Ultraviolet Region. J Phys Chem A 2014; 118:3128-35. [DOI: 10.1021/jp502445d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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54
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Mazza T, Ilchen M, Rafipoor AJ, Callegari C, Finetti P, Plekan O, Prince KC, Richter R, Danailov MB, Demidovich A, De Ninno G, Grazioli C, Ivanov R, Mahne N, Raimondi L, Svetina C, Avaldi L, Bolognesi P, Coreno M, O'Keeffe P, Di Fraia M, Devetta M, Ovcharenko Y, Möller T, Lyamayev V, Stienkemeier F, Düsterer S, Ueda K, Costello JT, Kazansky AK, Kabachnik NM, Meyer M. Determining the polarization state of an extreme ultraviolet free-electron laser beam using atomic circular dichroism. Nat Commun 2014; 5:3648. [DOI: 10.1038/ncomms4648] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 03/14/2014] [Indexed: 11/09/2022] Open
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55
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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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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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57
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O'Keeffe P, Ripani E, Bolognesi P, Coreno M, Devetta M, Callegari C, Di Fraia M, Prince KC, Richter R, Alagia M, Kivimäki A, Avaldi L. The Role of the Partner Atom and Resonant Excitation Energy in Interatomic Coulombic Decay in Rare Gas Dimers. J Phys Chem Lett 2013; 4:1797-1801. [PMID: 26283111 DOI: 10.1021/jz400671h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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58
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Sokell E, Bolognesi P, Kheifets A, Bray I, Safgren S, Avaldi L. Signature of two-electron interference in angular resolved double photoionization of Mg. PHYSICAL REVIEW LETTERS 2013; 110:083001. [PMID: 23473139 DOI: 10.1103/physrevlett.110.083001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 10/25/2012] [Indexed: 06/01/2023]
Abstract
The double photoionization of Mg has been studied experimentally and theoretically in a kinematic where the two photoelectrons equally share the excess energy. The observation of a symmetrized gerade amplitude, which strongly deviates from the Gaussian ansatz, is explained by a two-electron interference predicted theoretically, but never before observed experimentally. Similar to the Cooper minima in the single photoionization cross section, the effect finds its origin in the radial extent and oscillation of the target wave function.
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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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60
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O'Keeffe P, Bolognesi P, Moise A, Richter R, Ovcharenko Y, Avaldi L. Vibrationally resolved photoionization of N2 near threshold. J Chem Phys 2012; 136:104307. [PMID: 22423838 DOI: 10.1063/1.3692687] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A recently developed velocity map imaging spectrometer has been used to study the photoionization of molecular nitrogen near threshold. The potentialities of the spectrometer have been exploited to measure simultaneously the energy and angular distribution of the photoelectrons corresponding to the residual N(2)(+) X(2)Σ(g) v = 0-3 ion states. In a single experiment all the experimental observables, i.e., the total and partial cross sections, their branching ratios and the asymmetry parameter of the angular distributions have been determined.
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61
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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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Stener M, Bolognesi P, Coreno M, O’Keeffe P, Feyer V, Fronzoni G, Decleva P, Avaldi L, Kivimäki A. Photoabsorption and S 2p photoionization of the SF6 molecule: Resonances in the excitation energy range of 200–280 eV. J Chem Phys 2011; 134:174311. [DOI: 10.1063/1.3583815] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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63
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Bolognesi P, Kivimäki A, O'Keeffe P, Feyer V, Tarantelli F, Storchi L, Avaldi L. Radiationless decay in the region of the 2t2g and 4eg resonances in SF6. J Chem Phys 2011; 134:094308. [PMID: 21384970 DOI: 10.1063/1.3559455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The S 2p Auger spectrum of SF(6) has been studied in the region of the 2t(2g) and 4e(g) resonances. The partial Auger spectra due to the ionization of the 2p spin-orbit components and of a shake-up satellite state have been measured selectively by tuning the photon energy and using the Auger electron-photoelectron coincidence technique. A detailed analysis of the Auger spectrum has also been performed using the Green's function-based second-order algebraic diagrammatic construction method.
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64
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O'Keeffe P, Bolognesi P, Coreno M, Moise A, Richter R, Cautero G, Stebel L, Sergo R, Pravica L, Ovcharenko Y, Avaldi L. A photoelectron velocity map imaging spectrometer for experiments combining synchrotron and laser radiations. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:033109. [PMID: 21456720 DOI: 10.1063/1.3563723] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A velocity map imaging/ion time-of-flight spectrometer designed specifically for pump-probe experiments combining synchrotron and laser radiations is described. The in-house built delay line detector can be used in two modes: the high spatial resolution mode and the coincidence mode. In the high spatial resolution mode a kinetic energy resolution of 6% has been achieved. The coincidence mode can be used to improve signal-to-noise ratio for the pump-probe experiments either by using a gate to count electrons only when the laser is present or by recording coincidences with the ion formed in the ionization process.
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Bolognesi P, O'Keeffe P, Ovcharenko Y, Coreno M, Avaldi L, Feyer V, Plekan O, Prince KC, Zhang W, Carravetta V. Pyrimidine and halogenated pyrimidines near edge x-ray absorption fine structure spectra at C and N K-edges: experiment and theory. J Chem Phys 2010; 133:034302. [PMID: 20649325 DOI: 10.1063/1.3442489] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The inner shell excitation of pyrimidine and some halogenated pyrimidines near the C and N K-edges has been investigated experimentally by near edge x-ray absorption fine structure spectroscopy and theoretically by density functional theory calculations. The selected targets, 5-Br-pyrimidine, 2-Br-pyrimidine, 2-Cl-pyrimidine, and 5-Br-2-Cl-pyrimidine, allow the effects of the functionalization of the pyrimidine ring to be studied either as a function of different halogen atoms bound to the same molecular site or as a function of the same halogen atom bound to different molecular sites. The results show that the individual characteristics of the different spectra of the substituted pyrimidines can be rationalized in terms of variations in electronic and geometrical structures of the molecule depending on the localization and the electronegativity of the substituent.
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66
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Bolognesi P, O'Keeffe P, Feyer V, Plekan O, Prince K, Coreno M, Mattioli G, Bonapasta AA, Zhang W, Carravetta V, Ovcharenko Y, Avaldi L. Inner shell excitation, ionization and fragmentation of pyrimidine. ACTA ACUST UNITED AC 2010. [DOI: 10.1088/1742-6596/212/1/012002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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67
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Bolognesi P, Mattioli G, O'Keeffe P, Feyer V, Plekan O, Ovcharenko Y, Prince KC, Coreno M, Amore Bonapasta A, Avaldi L. Investigation of halogenated pyrimidines by X-ray photoemission spectroscopy and theoretical DFT methods. J Phys Chem A 2010; 113:13593-600. [PMID: 19929014 DOI: 10.1021/jp908512v] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The inner shell ionization of pyrimidine and some halogenated pyrimidines has been investigated experimentally by X-ray photoemission spectroscopy (XPS) and theoretically by density functional theory (DFT) methods. The selected targets-5-Br-pyrimidine, 2-Br-pyrimidine, 2-Cl-pyrimidine, and 5-Br-2-Cl-pyrimidine-allowed the study of the effect of the functionalization of the pyrimidine ring by different halogen atoms bound to the same molecular site, or by the same halogen atom bound to different molecular sites. The theoretical investigation of the inductive and resonance effects in the C(1s) ionization confirms the soundness of the resonance model for a qualitative description of the properties of an aromatic system. Moreover, the combination of the experimental results and the theoretical analysis provides a detailed description of the effects of the halogen atom on the screening of a C(1s) hole in the aromatic pyrimidine ring.
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Bolognesi P, O'Keeffe P, Avaldi L. The OCS S L3MM auger spectrum and angular distributions studied by photoelectron-auger electron coincidence experiments. J Phys Chem A 2009; 113:15136-41. [PMID: 20028181 DOI: 10.1021/jp9053007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The selectivity of the photoelectron-Auger electron coincidence technique has been used to isolate the S L(3)MM contribution to the L(2,3)MM Auger spectrum in OCS. In this way, a direct comparison of the energies, widths, and relative intensities of the final OCS(2+) states with theoretical calculations has been achieved. Moreover, the angular distributions of some selected Auger electrons have been measured in coincidence with the photoelectron at two different photon energies. In contrast with the results of noncoincidence measurements, the coincidence angular distributions show a significant asymmetry and a dependence on the photon energy and OCS(2+) final state.
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69
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O'Keeffe P, Bolognesi P, Casavola AR, Catone D, Zema N, Turchini S, Avaldi L. An experimental and computational study of the valence photoelectron spectra of halogenated pyrimidines. Mol Phys 2009. [DOI: 10.1080/00268970903120328] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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70
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Truong S, Yencha A, Juarez A, Cavanagh S, Bolognesi P, King G. Photo-double ionization of water studied by threshold photoelectrons coincidence spectroscopy. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.04.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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71
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Storchi L, Tarantelli F, Veronesi S, Bolognesi P, Fainelli E, Avaldi L. The Auger spectroscopy of pyrimidine and halogen-substituted pyrimidines. J Chem Phys 2009; 129:154309. [PMID: 19045195 DOI: 10.1063/1.2993317] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The C 1s and N 1s Auger spectra of pyrimidine, 2-chloropyrimidine, and 5-bromopyrimidine have been measured in an electron impact experiment at 1000 eV. In the case of the halogen-substituted pyrimidines, also the Cl 2p and Br 3d Auger spectra have been recorded. We have thoroughly analyzed and interpreted all the Auger spectra recorded here with the aid of accurate Green's function calculations with a large basis set. The spectra are extremely complex with thousands of states contributing and almost no single-state feature even near the double ionization threshold. Besides reproducing and explaining with great detail nearly all the main spectral features observed, the calculations have successfully unraveled the interplay among the different C 1s core hole chemical shifts in each molecule and how this affects some fingerprinting details in the composite C 1s Auger spectra.
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72
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Truong S, Yencha A, Juarez A, Cavanagh S, Bolognesi P, King G. Threshold photoelectron spectroscopy of H2O and D2O over the photon energy range 12–40eV. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.12.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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73
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Reddish TJ, Colgan J, Bolognesi P, Avaldi L, Gisselbrecht M, Lavollée M, Pindzola MS, Huetz A. Physical interpretation of the "kinetic energy release" effect in the double photoionization of H(2). PHYSICAL REVIEW LETTERS 2008; 100:193001. [PMID: 18518448 DOI: 10.1103/physrevlett.100.193001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Indexed: 05/26/2023]
Abstract
A physical interpretation is given for the variation with internuclear separation of the fully differential cross section for double photoionization of H2. This effect is analyzed in a geometry where the fourbody interaction is completely probed. Excellent agreement is found between experiment and time-dependent close-coupling theory after convoluting the latter over the relevant solid angles. We show the observed variations are purely due to the epsilon(Sigma) component of the polarization vector epsilon along the molecular axis, a conclusion which is supported through calculations of the photoionization of H2(+).
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Gisselbrecht M, Lavollée M, Huetz A, Bolognesi P, Avaldi L, Seccombe DP, Reddish TJ. Photo-double ionization of H2. ACTA ACUST UNITED AC 2007. [DOI: 10.1088/1742-6596/88/1/012006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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75
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Contini G, Zema N, Turchini S, Catone D, Prosperi T, Carravetta V, Bolognesi P, Avaldi L, Feyer V. Vibrational state dependence of β and D asymmetry parameters: The case of the highest occupied molecular orbital photoelectron spectrum of methyl-oxirane. J Chem Phys 2007; 127:124310. [PMID: 17902906 DOI: 10.1063/1.2779324] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The beta angular asymmetry and D dichroic asymmetry parameters of the methyl-oxirane highest occupied molecular orbital (HOMO) band have been experimentally investigated with vibrational resolution using synchrotron radiation. A theoretical calculation of the Franck-Condon factors between vibrational ground state and different ionic vibrational states, in the Born-Oppenheimer harmonic approximation, has been performed in order to gain information on the vibrational states mainly involved in the HOMO photoelectron band. The general good agreement between theoretical and experimental results allows a reliable assignment of the major features. The experimental determination of beta and D shows their dependence on the different final vibrational states. This paper reports, for the first time, experimental evidence of the dependence of the dichroic D parameter on the vibrational excitation of the ion.
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