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Tikhonov DS, Lee JWL, Schnell M. On the thermodynamic stability of polycations. J Chem Phys 2024; 160:244110. [PMID: 38934634 DOI: 10.1063/5.0207526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
We present a simple approximation to estimate the largest charge that a given molecule can hold until fragmentation into smaller charged species becomes more energetically favorable. This approximation solely relies on the ionization potentials, electron affinities of the parent and fragment species, and also on the neutral parent's dissociation energy. By parameterizing these quantities, it is possible to obtain analytical phase diagrams of polycationic stability. We demonstrate the applicability of this approach by discussing the maximal charge dependence on the size of the molecular system. A numerical demonstration for linear polyenes, monocyclic annulenes, and helium clusters is provided.
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Affiliation(s)
- Denis S Tikhonov
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jason W L Lee
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118 Kiel, Germany
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2
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Aguilar-Galindo F, Nguyen VTT, Singh R, Domaracka A, Huber BA, Díaz-Tendero S, Rousseau P, Maclot S. Unexpected and delayed fragmentation dynamics of the organometallic ferrocene induced by ion-collision. Phys Chem Chem Phys 2024; 26:7638-7646. [PMID: 38363201 DOI: 10.1039/d3cp05430f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
We have investigated the fragmentation dynamics of the organometallic ferrocene molecule after interaction with multiply charged ions using multicoincidence mass spectrometry and quantum chemistry calculations. We observed unexpected fragmentation dynamics of the two-body breakup channels from ferrocene dications revealing a charge screening effect from the iron atom and delayed fragmentation dynamics. These observations are rationalized through the population of a specific long-lived excited state, where one positive charge is located on each cyclopentadienyl ring.
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Affiliation(s)
- F Aguilar-Galindo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - V T T Nguyen
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000, Caen, France
| | - R Singh
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000, Caen, France
| | - A Domaracka
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000, Caen, France
| | - B A Huber
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000, Caen, France
| | - S 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
| | - P Rousseau
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000, Caen, France
| | - S Maclot
- Institut Lumière Matière UMR 5306, Université Claude Bernard Lyon 1, CNRS, Univ Lyon, 69100 Villeurbanne, France.
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3
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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] [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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4
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Tiefenthaler L, Scheier P, Erdmann E, Aguirre NF, Díaz-Tendero S, Luxford TFM, Kočišek J. Non-ergodic fragmentation upon collision-induced activation of cysteine-water cluster cations. Phys Chem Chem Phys 2023; 25:5361-5371. [PMID: 36647750 PMCID: PMC9930733 DOI: 10.1039/d2cp04172c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cysteine-water cluster cations Cys(H2O)3,6+ and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collision-induced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies from DFT calculations showing that clusters do not only fragment exclusively by sequential emission of single water molecules but also by the release of small water clusters. Release of clustered water is observed also in the ADMP (atom centered density matrix propagation) molecular dynamics model of small Cys(H2O)3+ and Cys(H2O)3H+ clusters. For large clusters Cys(H2O)6+ and Cys(H2O)6H+ the less computationally demanding statistical Microcanonical Metropolis Monte-Carlo method (M3C) is used to model the experimental fragmentation patterns. We are able to detail the energy redistribution in clusters upon collision activation. In the present case, about two thirds of the collision energy redistribute via an ergodic process, while the remaining one third is transferred into a non-ergodic channel leading to ejection of a single water molecule from the cluster. In contrast to molecular fragmentation, which can be well described by statistical models, modelling of collision-induced activation of weakly bound clusters requires inclusion of non-ergodic processes.
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Affiliation(s)
- Lukas Tiefenthaler
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Austria.
| | - Paul Scheier
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Austria.
| | - Ewa Erdmann
- Faculty of Applied Physics and Mathematics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.,Departamento de Química, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | | | - 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 ChemicalSciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Thomas F. M. Luxford
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of SciencesDolejškova 318223 PragueCzechia
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czechia.
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5
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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] [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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6
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Prieto Zamudio E, Cisneros Gudiño C, Hallado Abaunza LX, Álvarez Torres I, Guerrero Tapia AE. Effect of radiation intensity on the fragmentation of furan through multiphoton ionization at 532 and 355 nm. Radiat Phys Chem Oxf Engl 1993 2022. [DOI: 10.1016/j.radphyschem.2022.110261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Sen S, Mandal S, Sen A, Gopal R, Ben Ltaief L, Turchini S, Catone D, Zema N, Coreno M, Richter R, Mudrich M, Krishnan SR, Sharma V. Fragmentation dynamics of doubly charged camphor molecule following C 1s Auger decay. Phys Chem Chem Phys 2022; 24:2944-2957. [PMID: 35076648 DOI: 10.1039/d1cp05176h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fragmentation dynamics of the gas-phase, doubly charged camphor molecule, formed by Auger decay following carbon 1s ionisation, using soft X-ray synchrotron radiation, is presented in this work. The technique of velocity map imaging combined with a photoelectron-photoion-photoion coincidence (VMI-PEPIPICO) is used for both electron energy and ion momentum (in-sequence) measurements. The experimental study is complemented by molecular dynamics simulation, performed with an NVT (moles, volume, and temperature) ensemble. Velocity Verlet algorithms were used for time integration at various internal energies. These simulations validate observed dissociation pathways. From these, we successfully deduce that the internal energy of the doubly charged molecular ion has a significant contribution to the fragmentation mechanism. Notably, a prominent signature of the internal energy was observed in the experimentally determined energies of the neutral fragment in these deferred charge separation pathways, entailing a more detailed theoretical study to uncover the exact dissociation dynamics.
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Affiliation(s)
- Sanket Sen
- Indian Institute of Technology Hyderabad, Kandi 502285, India.
| | - S Mandal
- Indian Institute of Science Education and Research, Pune 411008, India
| | - Arnab Sen
- Indian Institute of Science Education and Research, Pune 411008, India
| | - R Gopal
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | | | - S Turchini
- Istituto di Struttura della Materia - CNR (ISM-CNR), Area di Ricerca di Tor Vergata via del Fosso del Cavaliere, 100, Rome 00133, Italy
| | - D Catone
- Istituto di Struttura della Materia - CNR (ISM-CNR), Area di Ricerca di Tor Vergata via del Fosso del Cavaliere, 100, Rome 00133, Italy
| | - N Zema
- Istituto di Struttura della Materia - CNR (ISM-CNR), Area di Ricerca di Tor Vergata via del Fosso del Cavaliere, 100, Rome 00133, Italy
| | - M Coreno
- Elettra-Sincrotrone Trieste, Basovizza 34149, Italy.,Consiglio Nazionale delle Ricerche - Istituto di Struttura della Materia, Trieste 34149, Italy
| | - R Richter
- Elettra-Sincrotrone Trieste, Basovizza 34149, Italy
| | - M Mudrich
- Aarhus University, 8000 Aarhus C, Denmark.,QuCenDiEM - group and Department of Physics, Indian Institute of Technology - Madras, Chennai 600036, India.
| | - S R Krishnan
- QuCenDiEM - group and Department of Physics, Indian Institute of Technology - Madras, Chennai 600036, India.
| | - V Sharma
- Indian Institute of Technology Hyderabad, Kandi 502285, India.
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8
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Barreiro-Lage D, Nicolafrancesco C, Kočišek J, Luna A, Kopyra J, Alcamí M, Huber BA, Martín F, Domaracka A, Rousseau P, Díaz-Tendero S. Controlling the diversity of ion-induced fragmentation pathways by N-methylation of amino acids. Phys Chem Chem Phys 2022; 24:941-954. [PMID: 34913940 DOI: 10.1039/d1cp04097a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We present a combined experimental and theoretical study of the fragmentation of singly and doubly N-methylated glycine (sarcosine and N,N-dimethyl glycine, respectively) induced by low-energy (keV) O6+ ions. Multicoincidence mass spectrometry techniques and quantum chemistry simulations (ab initio molecular dynamics and density functional theory) allow us to characterise different fragmentation pathways as well as the associated mechanisms. We focus on the fragmentation of doubly ionised species, for which coincidence measurements provide unambiguous information on the origin of the various charged fragments. We have found that single N-methylation leads to a larger variety of fragmentation channels than in no methylation of glycine, while double N-methylation effectively closes many of these fragmentation channels, including some of those appearing in pristine glycine. Importantly, the closure of fragmentation channels in the latter case does not imply a protective effect by the methyl group.
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Affiliation(s)
- Darío Barreiro-Lage
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Madrid 28049, Spain.
| | - Chiara Nicolafrancesco
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, Caen 14000, France. .,Synchrotron SOLEIL, LOrme des Merisiers, St Aubin, BP 48, Gif sur Yvette Cedex 91192, France
| | - Jaroslav Kočišek
- J. Heyrovsky Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejskova 3, Prague 18223, Czech Republic
| | - Alberto Luna
- Centro de Computación Científica, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Janina Kopyra
- Faculty of Exact and Natural Sciences, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, Siedlce 08-110, Poland
| | - Manuel Alcamí
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Madrid 28049, Spain. .,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nano), Campus de Cantoblanco, Madrid 28049, Spain.,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Bernd A Huber
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, Caen 14000, France.
| | - Fernando Martín
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Madrid 28049, Spain. .,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nano), Campus de Cantoblanco, Madrid 28049, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Alicja Domaracka
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, Caen 14000, France.
| | - Patrick Rousseau
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, Caen 14000, France.
| | - Sergio Díaz-Tendero
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Madrid 28049, Spain. .,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid 28049, Spain
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