1
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Kawsar SMA, Munia NS, Saha S, Ozeki Y. In Silico Pharmacokinetics, Molecular Docking and Molecular Dynamics Simulation Studies of Nucleoside Analogs for Drug Discovery- A Mini Review. Mini Rev Med Chem 2024; 24:1070-1088. [PMID: 37957918 DOI: 10.2174/0113895575258033231024073521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/26/2023] [Accepted: 09/22/2023] [Indexed: 11/15/2023]
Abstract
Nucleoside analogs have been widely used as antiviral, antitumor, and antiparasitic agents due to their ability to inhibit nucleic acid synthesis. Adenosine, cytidine, guanosine, thymidine and uridine analogs such as didanosine, vidarabine, remdesivir, gemcitabine, lamivudine, acyclovir, abacavir, zidovusine, stavudine, and idoxuridine showed remarkable anticancer and antiviral activities. In our previously published articles, our main intention was to develop newer generation nucleoside analogs with acylation-induced modification of the hydroxyl group and showcase their biological potencies. In the process of developing nucleoside analogs, in silico studies play an important role and provide a scientific background for biological data. Molecular interactions between drugs and receptors followed by assessment of their stability in physiological environments, help to optimize the drug development process and minimize the burden of unwanted synthesis. Computational approaches, such as DFT, FMO, MEP, ADMET prediction, PASS prediction, POM analysis, molecular docking, and molecular dynamics simulation, are the most popular tools to culminate all preclinical study data and deliver a molecule with maximum bioactivity and minimum toxicity. Although clinical drug trials are crucial for providing dosage recommendations, they can only indirectly provide mechanistic information through researchers for pathological, physiological, and pharmacological determinants. As a result, in silico approaches are increasingly used in drug discovery and development to provide mechanistic information of clinical value. This article portrays the current status of these methods and highlights some remarkable contributions to the development of nucleoside analogs with optimized bioactivity.
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Affiliation(s)
- Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Nasrin S Munia
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Premnagar, 248007, Dehradun, Uttarakhand, 248007, India
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Kanazawa-ku, Yokohama, 236-0027, Japan
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2
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Chevalier F, Schlathölter T, Poully JC. Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems. Chembiochem 2023; 24:e202300543. [PMID: 37712497 DOI: 10.1002/cbic.202300543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy. In the condensed phase, it is usually very difficult to distinguish direct effects from indirect effects. A straightforward solution for this problem is the use of gas-phase techniques, for instance from the field of mass spectrometry. In this review, we survey mainly experimental but also theoretical work, focusing on radiation-induced intra- and inter-molecular transfer of charge, atoms, and energy within biomolecular systems in the gas phase. Building blocks of DNA, proteins, and saccharides, but also antibiotics are considered. The emergence of general processes as well as their timescales and mechanisms are highlighted.
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Affiliation(s)
- François Chevalier
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Groningen (The, Netherlands
- University College Groningen, University of Groningen, Groningen (The, Netherlands
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
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3
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Liu M, O'Reilly D, Schwob L, Wang X, Zamudio-Bayer V, Lau JT, Bari S, Schlathölter T, Poully JC. Direct Observation of Charge, Energy, and Hydrogen Transfer between the Backbone and Nucleobases in Isolated DNA Oligonucleotides. Chemistry 2023; 29:e202203481. [PMID: 36478608 DOI: 10.1002/chem.202203481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Understanding how charge and energy, as well as protons and hydrogen atoms, are transferred in molecular systems as a result of an electronic excitation is fundamental for understanding the interaction between ionizing radiation and biological matter on the molecular level. To localize the excitation at the atomic scale, it was chosen to target phosphorus atoms in the backbone of gas-phase oligonucleotide anions and cations, by means of resonant photoabsorption at the L- and K-edges. The ionic photoproducts of the excitation process were studied by a combination of mass spectrometry and X-ray spectroscopy. The combination of absorption site selectivity and photoproduct sensitivity allowed the identification of X-ray spectral signatures of specific processes. Moreover, charge and/or energy as well as H transfer from the backbone to nucleobases has been directly observed. Although the probability of one versus two H transfer following valence ionization depends on the nucleobase, ionization of sugar or phosphate groups at the carbon K-edge or the phosphorus L-edge mainly leads to single H transfer to protonated adenine. Moreover, our results indicate a surprising proton-transfer process to specifically form protonated guanine after excitation or ionization of P 2p electrons.
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Affiliation(s)
- Min Liu
- CIMAP UMR 6252, CEA/, CNRS/, ENSICAEN/, Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - David O'Reilly
- CIMAP UMR 6252, CEA/, CNRS/, ENSICAEN/, Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | | | - Xin Wang
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | | | - J Tobias Lau
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Germany
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.,University College Groningen, University of Groningen, Groningen, The Netherlands
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA/, CNRS/, ENSICAEN/, Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
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4
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Chordiya K, Despré V, Nagyillés B, Zeller F, Diveki Z, Kuleff AI, Kahaly MU. Photo-ionization initiated differential ultrafast charge migration: impacts of molecular symmetries and tautomeric forms. Phys Chem Chem Phys 2023; 25:4472-4480. [PMID: 36317562 DOI: 10.1039/d2cp02681c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Photo-ionization induced ultrafast electron dynamics is considered as a precursor for the slower nuclear dynamics associated with molecular dissociation. Here, using the ab initio multielectron wave-packet propagation method, we study the overall many-electron dynamics, triggered by ionizing the outer-valence orbitals of different tautomers for a prototype molecule with more than one symmetry element. From the time evolution of the initially created averaged hole density of each system, we identify distinctly different charge dynamics responses in the tautomers. We observe that the keto form shows a charge migration direction away from the nitrogen bonded with hydrogen, while in enol-U - away from oxygen bonded to hydrogen. Additionally, the dynamics following the ionization of molecular orbitals with different symmetries reveals that a' orbitals show a fast and highly delocalized charge density in comparison to a'' symmetry. These observations indicate why different tautomers respond differently to an XUV ionization, and might explain the subsequent different fragmentation pathways. An experimental schematics allowing the detection and reconstruction of such charge dynamics is also proposed. Although the present study uses a simple, prototypical bio-relevant molecule, it reveals the explicit role of molecular symmetry and tautomerism in the ionization-triggered charge migration that controls many ultrafast physical, chemical, and biological processes, making tautomeric forms a promising tool of molecular design for desired charge migration.
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Affiliation(s)
- Kalyani Chordiya
- ELI-ALPS, ELI-HU Non-Profit Ltd., Wolfgang Sandner utca 3., Szeged, H-6728, Hungary. .,Institute of Physics, University of Szeged, Dóm tér 9, H-6720, Szeged, Hungary
| | - Victor Despré
- Theoretische Chemie, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120, Heidelberg, Germany.
| | - Balázs Nagyillés
- ELI-ALPS, ELI-HU Non-Profit Ltd., Wolfgang Sandner utca 3., Szeged, H-6728, Hungary. .,Institute of Physics, University of Szeged, Dóm tér 9, H-6720, Szeged, Hungary
| | - Felix Zeller
- Theoretische Chemie, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120, Heidelberg, Germany.
| | - Zsolt Diveki
- ELI-ALPS, ELI-HU Non-Profit Ltd., Wolfgang Sandner utca 3., Szeged, H-6728, Hungary.
| | - Alexander I Kuleff
- ELI-ALPS, ELI-HU Non-Profit Ltd., Wolfgang Sandner utca 3., Szeged, H-6728, Hungary. .,Theoretische Chemie, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120, Heidelberg, Germany.
| | - Mousumi Upadhyay Kahaly
- ELI-ALPS, ELI-HU Non-Profit Ltd., Wolfgang Sandner utca 3., Szeged, H-6728, Hungary. .,Institute of Physics, University of Szeged, Dóm tér 9, H-6720, Szeged, Hungary
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5
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Salen P, Schio L, Richter R, Alagia M, Stranges S, Falcinelli S, Zhaunerchyk V. Electronic state influence on selective bond breaking of core-excited nitrosyl chloride (ClNO). J Chem Phys 2022; 157:124306. [DOI: 10.1063/5.0106642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The potential for selective bond breaking of a small molecule was investigated with electron-spectroscopy and electron-ion coincidence experiments on ClNO. The electron spectra were measured upon direct valence photo-ionization and upon resonant core-excitation at the N 1s- and O 1s-edges followed by emission of resonant Auger (RA) electrons. The RA spectra were analyzed with particular emphasis on the assignment of the participator and spectator states. The latter are of special relevance for investigations of how distinct electronic configurations influence selective bond breaking. The electron-ion coincidence measurements provided branching fractions of the produced ion-fragments as a function of electron binding energy. It explicitly demonstrates the influence of the final electronic states created after the photo-ionization and RA decay, on the fragmentation. In particular, we observe a significantly different branching fraction for spectator states compared with participator states. The bonds broken for the spectator states are also found to correlate with the anti-bonding character of the spectator-electron orbital.
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Affiliation(s)
- Peter Salen
- Physics and Astronomy, Uppsala Universitet, Sweden
| | - Luca Schio
- IOM CNR Laboratorio TASC, 34012 Trieste, Italy
| | | | | | - Stefano Stranges
- Chemistry and Technologies of Drugs, University of Rome La Sapienza, Italy
| | - Stefano Falcinelli
- Department of Civil and Environmental Engineering, University of Perugia, Italy
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg Department of Physics, Sweden
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6
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Perspectives of Gas Phase Ion Chemistry: Spectroscopy and Modeling. CONDENSED MATTER 2022. [DOI: 10.3390/condmat7030046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The study of ions in the gas phase has a long history and has involved both chemists and physicists. The interplay of their competences with the use of very sophisticated commercial and/or homemade instrumentations and theoretical models has improved the knowledge of thermodynamics and kinetics of many chemical reactions, even if still many stages of these processes need to be fully understood. The new technologies and the novel free-electron laser facilities based on plasma acceleration open new opportunities to investigate the chemical reactions in some unrevealed fundamental aspects. The synchrotron light source can be put beside the FELs, and by mass spectrometric techniques and spectroscopies coupled with versatile ion sources it is possible to really change the state of the art of the ion chemistry in different areas such as atmospheric and astro chemistry, plasma chemistry, biophysics, and interstellar medium (ISM). In this manuscript we review the works performed by a joint combination of the experimental studies of ion–molecule reactions with synchrotron radiation and theoretical models adapted and developed to the experimental evidence. The review concludes with the perspectives of ion–molecule reactions by using FEL instrumentations as well as pump probe measurements and the initial attempt in the development of more realistic theoretical models for the prospective improvement of our predictive capability.
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7
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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] [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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8
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Borrego-Varillas R, Lucchini M, Nisoli M. Attosecond spectroscopy for the investigation of ultrafast dynamics in atomic, molecular and solid-state physics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:066401. [PMID: 35294930 DOI: 10.1088/1361-6633/ac5e7f] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Since the first demonstration of the generation of attosecond pulses (1 as = 10-18s) in the extreme-ultraviolet spectral region, several measurement techniques have been introduced, at the beginning for the temporal characterization of the pulses, and immediately after for the investigation of electronic and nuclear ultrafast dynamics in atoms, molecules and solids with unprecedented temporal resolution. The attosecond spectroscopic tools established in the last two decades, together with the development of sophisticated theoretical methods for the interpretation of the experimental outcomes, allowed to unravel and investigate physical processes never observed before, such as the delay in photoemission from atoms and solids, the motion of electrons in molecules after prompt ionization which precede any notable nuclear motion, the temporal evolution of the tunneling process in dielectrics, and many others. This review focused on applications of attosecond techniques to the investigation of ultrafast processes in atoms, molecules and solids. Thanks to the introduction and ongoing developments of new spectroscopic techniques, the attosecond science is rapidly moving towards the investigation, understanding and control of coupled electron-nuclear dynamics in increasingly complex systems, with ever more accurate and complete investigation techniques. Here we will review the most common techniques presenting the latest results in atoms, molecules and solids.
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Affiliation(s)
- Rocío Borrego-Varillas
- Institute for Photonics and Nanotechnologies (IFN), Consiglio Nazionale delle Ricerche (CNR), Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Matteo Lucchini
- Institute for Photonics and Nanotechnologies (IFN), Consiglio Nazionale delle Ricerche (CNR), Piazza Leonardo da Vinci 32, 20133 Milano, Italy
- Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Mauro Nisoli
- Institute for Photonics and Nanotechnologies (IFN), Consiglio Nazionale delle Ricerche (CNR), Piazza Leonardo da Vinci 32, 20133 Milano, Italy
- Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
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9
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Bocková J, Rebelo A, Ryszka M, Pandey R, Mészáros D, Limão-Vieira P, Papp P, Mason NJ, Townsend D, Nixon KL, Vizcaino V, Poully JC, Eden S. Thermal desorption effects on fragment ion production from multi-photon ionized uridine and selected analogues. RSC Adv 2021; 11:20612-20621. [PMID: 35479354 PMCID: PMC9033967 DOI: 10.1039/d1ra01873f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/09/2021] [Indexed: 12/22/2022] Open
Abstract
Experiments on neutral gas-phase nucleosides are often complicated by thermal lability. Previous mass spectrometry studies of nucleosides have identified enhanced relative production of nucleobase ions (e.g. uracil+ from uridine) as a function of desorption temperature to be the critical indicator of thermal decomposition. On this basis, the present multi-photon ionization (MPI) experiments demonstrate that laser-based thermal desorption is effective for producing uridine, 5-methyluridine, and 2′-deoxyuridine targets without thermal decomposition. Our experiments also revealed one notable thermal dependence: the relative production of the sugar ion C5H9O4+ from intact uridine increased substantially with the desorption laser power and this only occurred at MPI wavelengths below 250 nm (full range studied 222–265 nm). We argue that this effect can only be rationalized plausibly in terms of changing populations of different isomers, tautomers, or conformers in the target as a function of the thermal desorption conditions. Furthermore, the wavelength threshold behavior of this thermally-sensitive MPI channel indicates a critical dependence on neutral excited state dynamics between the absorption of the first and second photons. The experimental results are complemented by density functional theory (DFT) optimizations of the lowest-energy structure of uridine and two further conformers distinguished by different orientations of the hydroxymethyl group on the sugar part of the molecule. The energies of the transitions states between these three conformers are low compared with the energy required for decomposition. This work reveals the first experimental evidence supporting isomer-dependence in the radiation response of a nucleoside.![]()
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Affiliation(s)
- J Bocková
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK
| | - A Rebelo
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK .,Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, FCT - Universidade NOVA de Lisboa P-2829-516 Caparica Portugal
| | - M Ryszka
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK
| | - R Pandey
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK
| | - D Mészáros
- Department of Experimental Physics, Comenius University in Bratislava Mlynská dolina F2 84248 Bratislava Slovakia
| | - P Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, FCT - Universidade NOVA de Lisboa P-2829-516 Caparica Portugal
| | - P Papp
- Department of Experimental Physics, Comenius University in Bratislava Mlynská dolina F2 84248 Bratislava Slovakia
| | - N J Mason
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK .,School of Physical Sciences, Ingram Building, University of Kent Canterbury CT2 7NH UK
| | - D Townsend
- Institute of Photonics and Quantum Sciences, Heriot-Watt University Edinburgh EH14 4AS UK.,Institute of Chemical Sciences, Heriot-Watt University Edinburgh EH14 4AS UK
| | - K L Nixon
- School of Life, Health, and Chemical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK.,School of Sciences, University of Wolverhampton Wulfruna Street Wolverhampton WV1 1LY UK
| | - V Vizcaino
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, GANIL Bd Becquerel BP 5133 14070 Caen France
| | - J-C Poully
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, GANIL Bd Becquerel BP 5133 14070 Caen France
| | - S Eden
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK
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10
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Wang X, Rathnachalam S, Bijlsma K, Li W, Hoekstra R, Kubin M, Timm M, von Issendorff B, Zamudio-Bayer V, Lau JT, Faraji S, Schlathölter T. Site-selective soft X-ray absorption as a tool to study protonation and electronic structure of gas-phase DNA. Phys Chem Chem Phys 2021; 23:11900-11906. [PMID: 33997879 DOI: 10.1039/d1cp01014j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The conformation and the electronic structure of gas-phase oligonucleotides depends strongly on the protonation site. 5'-d(FUAG) can either be protonated at the A-N1 or at the G-N7 position. We have stored protonated 5'-d(FUAG) cations in a cryogenic ion trap held at about 20 K. To identify the protonation site and the corresponding electronic structure, we have employed soft X-ray absorption spectroscopy at the nitrogen K-edge. The obtained spectra were interpreted by comparison to time-dependent density functional theory calculations using a short-range exchange correlation functional. Despite the fact that guanine has a significantly higher proton affinity than adenine, the agreement between experiment and theory is better for the A-N1 protonated system. Furthermore, an inverse site sensitivity is observed in which the yield of the nucleobase fragments that contain the absorption site appears substantially reduced, which could be explained by non-statistical fragmentation processes, localized on the photoabsorbing nucleobase.
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Affiliation(s)
- Xin Wang
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Sivasudhan Rathnachalam
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Klaas Bijlsma
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Wen Li
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Ronnie Hoekstra
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Markus Kubin
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
| | - Martin Timm
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
| | | | - Vicente Zamudio-Bayer
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
| | - J Tobias Lau
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany and Physikalisches Institut, Universität Freiburg, Freiburg, Germany
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
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11
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Yang L, Reimers JR, Kobayashi R, Hush NS. Competition between charge migration and charge transfer induced by nuclear motion following core ionization: Model systems and application to Li 2. J Chem Phys 2019; 151:124108. [PMID: 31575213 DOI: 10.1063/1.5117246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Attosecond and femtosecond spectroscopies present opportunities for the control of chemical reaction dynamics and products, as well as for quantum information processing; we address the somewhat unique situation of core-ionization spectroscopy which, for dimeric chromophores, leads to strong valence charge localization and hence tightly paired potential-energy surfaces of very similar shape. Application is made to the quantum dynamics of core-ionized Li2 +. This system is chosen as Li2 is the simplest stable molecule facilitating both core ionization and valence ionization. First, the quantum dynamics of some model surfaces are considered, with the surprising result that subtle differences in shape between core-ionization paired surfaces can lead to dramatic differences in the interplay between electronic charge migration and charge transfer induced by nuclear motion. Then, equation-of-motion coupled-cluster calculations are applied to determine potential-energy surfaces for 8 core-excited state pairs, calculations believed to be the first of their type for other than the lowest-energy core-ionized molecular pair. While known results for the lowest-energy pair suggest that Li2 + is unsuitable for studying charge migration, higher-energy pairs are predicted to yield results showing competition between charge migration and charge transfer. Central is a focus on the application of Hush's 1975 theory for core-ionized X-ray photoelectron spectroscopy to understand the shapes of the potential-energy surfaces and hence predict key features of charge migration.
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Affiliation(s)
- Likun Yang
- International Centre for Quantum and Molecular Structures and Department of Physics, Shanghai University, Shanghai 200444, China
| | - Jeffrey R Reimers
- School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Rika Kobayashi
- International Centre for Quantum and Molecular Structures and Department of Physics, Shanghai University, Shanghai 200444, China
| | - Noel S Hush
- School of Molecular Biosciences, The University of Sydney, Sydney, NSW 2006, Australia
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12
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Lalande M, Schwob L, Vizcaino V, Chirot F, Dugourd P, Schlathölter T, Poully J. Direct Radiation Effects on the Structure and Stability of Collagen and Other Proteins. Chembiochem 2019; 20:2972-2980. [DOI: 10.1002/cbic.201900202] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/28/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Mathieu Lalande
- CIMAP LaboratoryUMR 6252CEA/CNRS/ENSICAEN/Université de Caen Normandie) Boulevard Becquerel 14070 Caen France
| | - Lucas Schwob
- Helmholtz AssociationDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
| | - Violaine Vizcaino
- CIMAP LaboratoryUMR 6252CEA/CNRS/ENSICAEN/Université de Caen Normandie) Boulevard Becquerel 14070 Caen France
| | - Fabien Chirot
- Université Claude Bernard Lyon 1ENS de LyonUMR 5280 Institut des Sciences Analytiques 5, rue de la Doua 69100 Villeurbanne France
| | - Philippe Dugourd
- Université Claude Bernard Lyon 1CNRSUMR 5306 Institut Lumière Matière 10 rue Ada Byron 69622 Villeurbanne Cedex France
| | - Thomas Schlathölter
- Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Jean‐Christophe Poully
- CIMAP LaboratoryUMR 6252CEA/CNRS/ENSICAEN/Université de Caen Normandie) Boulevard Becquerel 14070 Caen France
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Månsson EP, Wanie V, Galli M, Castrovilli MC, Frassetto F, Poletto L, Nisoli M, Calegari F. High-resolution mass spectrometry and velocity map imaging for ultrafast electron dynamics in complex biomolecules. EPJ WEB OF CONFERENCES 2019. [DOI: 10.1051/epjconf/201920503007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a design combining a velocity map imaging electron spectrometer with a reflectron mass spectrometer. Since the two spectrometer sides have different intrinsic requirements for the electric field in the central region, a large number of electrodes and a reflectron-geometry of the mass spectrometer were employed to achieve simultaneous high resolutions. Together with femtosecond and attosecond pump-probe methods it will enable studies of ultrafast dynamics in large molecular systems.
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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] [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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