ESR publications

  1. Piotr Kabaciński (ESR1), Marco Romanelli, Eveliina Ponkkonen (ESR11),
    Vishal Kumar Jaiswal (ESR2), Thomas Carell, Marco Garavelli, Giulio Cerullo, Irene Conti (2021). Unified Description of Ultrafast Excited State
    Decay Processes in Epigenetic Deoxycytidine Derivatives.     The Journal of Physical Chemistry Letters
  2. Rocío Borrego-Varillas, Artur Nenov, Piotr Kabaciński (ESR1), Irene Conti, Lucia
    Ganzer, Aurelio Oriana, Vishal Kumar Jaiswal (ESR2), Ines Delfino, Oliver Weingart, Cristian
    Manzoni, Ivan Rivalta, Marco Garavelli, Giulio Cerullo (2021). Tracking excited state decay mechanisms of pyrimidine nucleosides in real time. Nature
    communications
  3. Martha Yaghoubi Jouybari (ESR3), Yanli Liu, Roberto Improta, Fabrizio Santoro (2020). Ultrafast Dynamics of the Two Lowest Bright
    Excited States of Cytosine and 1-Methylcytosine: A Quantum Dynamical Study    . Journal of Chemical Theory and
    Computation
  4. Martha Yaghoubi Jouybari (ESR3), Yanli Liu, Roberto Improta, Fabrizio Santoro (2020). Quantum dynamics of the ππ*/nπ* decay of the
    epigenetic nucleobase 1,5-dimethyl-cytosine in the gas phase    . Physical Chemistry Chemical Physics
  5. Flavia Aleotti, Daniel Aranda, Martha Yaghoubi Jouybari (ESR3), Marco Garavelli, Artur Nenov,
    Fabrizio Santoro (2021). Parameterization of a linear
    vibronic coupling model with multiconfigurational electronic structure methods to study the quantum dynamics of
    photoexcited pyrene.     The Journal of Chemical Physics
  6. James A. Green, Martha Yaghoubi Jouybari (ESR3), Daniel Aranda, Roberto Improta, Fabrizio Santoro
    (2021). Nonadiabatic Absorption Spectra and
    Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases.     Molecules
  7. James A. Green, Martha Yaghoubi Jouybari (ESR3), Haritha Asha (ESR4), Fabrizio
    Santoro, Roberto Improta (2021). Fragment
    Diabatization Linear Vibronic Coupling Model for Quantum Dynamics of Multichromophoric Systems: Population of the
    Charge-Transfer State in the Photoexcited Guanine–Cytosine Pair.     Journal of Chemical Theory and
    Computation.
  8. Martha Yaghoubi Jouybari (ESR3), James A. Green, Roberto Improta, Fabrizio Santoro (2021). The Ultrafast Quantum Dynamics of Photoexcited
    Adenine–Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling
    Model.     The Journal of Physical Chemistry A.
  9. Lara Martínez Fernández, Javier Cerezo, Haritha Asha (ESR4), Fabrizio
    Santoro, Sonia Coriani, Roberto Improta (2019). The
    Absorption Spectrum of Guanine Based Radicals: a Comparative Computational Analysis.     ChemPhotoChem.
  10. James A. Green, Haritha Asha (ESR4), Fabrizio Santoro, Roberto Improta (2020). Excitonic Model for Strongly Coupled
    Multichromophoric Systems: The Electronic Circular Dichroism Spectra of Guanine Quadruplexes as Test Cases.
    Journal of Chemical Theory and Computation.
  11. Haritha Asha (ESR4), James A. Green, Lara Martinez-Fernandez, Luciana Esposito, Roberto Improta
    (2021). Electronic Circular Dichroism Spectra of
    DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge
    Transfer States.     Molecules.
  12. Haritha Asha (ESR4), Petr Stadlbauer, Lara Martínez-Fernández, Pavel
    Banáš, Jiří Šponer, Roberto Improta, Luciana Esposito (2022). Early steps of oxidative damage in DNA
    quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric
    sequence containing ionized guanine    . International Journal of Biological Macromolecules.
  13. Zhengyue Zhang (ESR5), Jennifer Vögele, Klaudia Mráziková, Holger Kruse,
    Xiaohui Cang, Jens Wöhnert, Miroslav Krepl, Jiří Šponer (2021). Phosphorothioate Substitutions in RNA Structure
    Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments    . The Journal of Physical
    Chemistry B.
  14. Kateřina Peterková (ESR6), Ivo Durník, Radek Marek, Janez Plavec, Peter
    Podbevšek (2021). c-kit2 G-quadruplex
    stabilized via a covalent probe: exploring G-quartet asymmetry    . Nucleic Acids Research.
  15. Akos Banyasz, Evangelos Balanikas (ESR7), Lara Martinez-Fernandez, Gérard Baldacchino,
    Thierry Douki, Roberto Improta, Dimitra Markovitsi (2019). Radicals Generated in Tetramolecular Guanine Quadruplexes by Photoionization: Spectral and
    Dynamical Features    . The Journal of Physical Chemistry B.
  16. Evangelos Balanikas (ESR7), Akos Banyasz, Gérard Baldacchino, Dimitra Markovitsi (2019).
    Populations and Dynamics of Guanine Radicals in
    DNA strands—Direct versus Indirect Generation    . Molecules.
  17. Behnaz Behmand, Evangelos Balanikas (ESR7), Lara Martinez-Fernandez, Roberto Improta, Akos
    Banyasz, Gérard Baldacchino, Dimitra Markovitsi (2020). Potassium Ions Enhance Guanine Radical Generation upon Absorption of Low-Energy Photons by
    G-Quadruplexes and Modify Their Reactivity    . The Journal of Physical Chemistry Letters.
  18. Evangelos Balanikas (ESR7), Akos Banyasz, Gérard Baldacchino, Dimitra Markovitsi (2020).
    Guanine Radicals Generated in Telomeric
    G-Quadruplexes by Direct Absorption of Low-Energy UV Photons: Effect of Potassium Ions    . Molecules.
  19. Evangelos Balanikas (ESR7), Akos Banyasz, Thierry Douki, Gérard Baldacchino, Dimitra
    Markovitsi (2020). Guanine Radicals Induced
    in DNA by Low-Energy Photoionization    . Accounts of Chemical Research.
  20. Evangelos Balanikas (ESR7), Lara Martinez-Fernandez, Roberto Improta, Peter Podbevšek,
    Gérard Baldacchino, Dimitra Markovitsi (2021). The Structural Duality of Nucleobases in Guanine Quadruplexes Controls Their Low-Energy
    Photoionization    . The Journal of Physical Chemistry Letters.
  21. Evangelos Balanikas (ESR7), Lara Martinez-Fernandez, Gérard Baldacchino, Dimitra
    Markovitsi (2021). Electron Holes in G-Quadruplexes:
    The Role of Adenine Ending Groups    . International Journal of Molecular Sciences.
  22. Evangelos Balanikas (ESR7), Akos Banyasz, Gérard Baldacchino, Dimitra Markovitsi (2021).
    Deprotonation Dynamics of Guanine Radical Cations.
    Photochemistry and Photobiology.
  23. Frederico A. Baptista, Dorottya Krizsan, Mark Stitch (ESR8), Igor V. Sazanovich, Ian P. Clark,
    Michael Towrie, Conor Long, Lara Martinez-Fernandez, Roberto Improta, Noel A. P. Kane-Maguire, John M. Kelly, Susan
    J. Quinn (2021). Adenine Radical Cation Formation by
    a Ligand-Centered Excited State of an Intercalated Chromium Polypyridyl Complex Leads to Enhanced DNA
    Photo-oxidation    . Journal of the American Chemical Society.
  24. Maria Elena Castellani (ESR9), Cate S. Anstöter, Jan R. R. Verlet (2019). On the stability of a dipole-bound state in the presence
    of a molecule    . Physical Chemistry Chemical Physics.
  25. Maria Elena Castellani (ESR9), Davide Avagliano (ESR10), Leticia González, Jan R. R.
    Verlet (2020). Site-Specific Photo-oxidation
    of the Isolated Adenosine-5′-triphosphate Dianion Determined by Photoelectron Imaging.     The Journal of
    Physical Chemistry Letters.
  26. Maria Elena Castellani (ESR9), Davide Avagliano (ESR10),  Leticia González, Jan R. R.
    Verlet (2021). Ultrafast Dynamics of the Isolated
    Adenosine-5′-triphosphate Dianion Probed by Time-Resolved Photoelectron Imaging    . The Journal of Physical
    Chemistry A.
  27. Maria Elena Castellani (ESR9), Jan R. R. Verlet (2021). Intramolecular Photo-Oxidation as a Potential
    Source to Probe Biological Electron Damage: A Carboxylated Adenosine Analogue as Case Study.     Molecules.
  28. Davide Avagliano (ESR10), Pedro A. Sánchez-Murcia,  Leticia González (2019).
    DNA-binding mechanism of spiropyran photoswitches: the
    role of electrostatics    . Physical Chemistry Chemical Physics.
  29. Davide Avagliano (ESR10), Pedro A. Sánchez-Murcia, Leticia González (2019). Directional and regioselective hole injection of
    spiropyran photoswitches intercalated into A/T-duplex DNA.     Physical Chemistry Chemical Physics.
  30. Davide Avagliano (ESR10), Pedro A. Sánchez-Murcia, Leticia González (2020). Spiropyran Meets Guanine Quadruplexes: Isomerization
    Mechanism and DNA Binding Modes of Quinolizidine-Substituted Spiropyran Probes.     Chemistry a European Journal.
  31. Davide Avagliano (ESR10), Sara Tkaczyk, Pedro A. Sánchez-Murcia, Leticia González
    (2020). Enhanced Rigidity Changes Ultraviolet
    Absorption: Effect of a Merocyanine Binder on G-Quadruplex Photophysics    . The Journal of Physical Chemistry
    Letters
  32. Davide Avagliano (ESR10), Matteo Bonfanti, Marco Garavelli, Leticia González (2021). QM/MM Nonadiabatic Dynamics: the SHARC/COBRAMM
    Approach    . Journal of Chemical Theory and Computation.
  33. Pascal Heim, Sebastian Mai, Bernhard Thaler, Stefan Cesnik, Davide Avagliano (ESR10), Dimitra
    Bella-Velidou, Wolfgang E. Ernst, Leticia González, Markus Koch (2020). Revealing Ultrafast Population Transfer between
    Nearly Degenerate Electronic States    . The Journal of Physical Chemistry Letters.
  34. Alexander Schön, Ewelina Kaminska, Florian Schelter, Eveliina Ponkkonen (ESR11), Eva
    Korytiaková, Sarah Schiffers, Thomas Carell (2020). Analysis of an Active Deformylation Mechanism of 5-Formyl-deoxycytidine (fdC) in Stem Cells.
    Angewandte Chemie International Edition.
  35. Nadine Müller, Eveliina Ponkkonen (ESR11), Thomas Carell, Andriy Khobta (2021). Direct and Base Excision Repair-Mediated Regulation
    of a GC-Rich cis-Element in Response to 5-Formylcytosine and 5-Carboxycytosine    . International Journal of
    Molecular Sciences.
  36. Michael Stadlmeier, Leander Simon Runtsch, Filipp Streshnev (ESR12), Martin Wühr, Thomas
    Carell (2019). A Click-Chemistry-Based Enrichable
    Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry.     ChemBioChem.
  37. Irene Ponzo (ESR14), Friederike M. Möller, Herwin Daub, Nena Matscheko (2019). A DNA-Based Biosensor Assay for the Kinetic
    Characterization of Ion-Dependent Aptamer Folding and Protein Binding.     Molecules.
  38. Marialucrezia Losito (ESR15), Quentin M. Smith, Matthew D. Newton, Maria Emanuela Cuomo, David S.
    Rueda (2021). Cas12a target search and cleavage on
    force-stretched DNA    . Physical Chemistry Chemical Physics

PI publications

  1. Rocío Borrego-Varillas, Danielle C. Teles-Ferreira, Artur Nenov, Irene Conti, Lucia Ganzer, Cristian
    Manzoni, Marco Garavelli, Ana Maria de Paula and Giulio Cerullo (2018). Observation of the Sub-100 Femtosecond
    Population of a Dark State in a Thiobase Mediating Intersystem Crossing    . J. Am. Chem. Soc., 140, 47,
    16087-16093
  2. Nenov A.; Conti I.; Borrego-Varillas R.; Cerullo G.; Garavelli M., (2018) Linear absorption
    spectra of solvated thiouracils resolved at the hybrid RASPT2/MM level    , Chem. Phys., 515, 643-653. DOI
    (repository):10.1016/j.chemphys.2018.07.025
  3. Irene Conti and Marco Garavelli (2018). Evolution of the Excitonic State of
    DNA Stacked Thymines: Intrabase ππ* → S0 Decay Paths Account for Ultrafast (Subpicosecond) and Longer
    (>100 ps) Deactivations.     Journal Physical Chemistry Letters, 9, 9.
  4. Francesco Segatta, Itay Gdor, Julien Réhault, Simone Taioli, Noga Friedman, Mordechai Sheves, Ivan
    Rivalta, Giulio Cerullo and Marco Garavelli (2018). Ultrafast Carotenoid to
    Retinal Energy Transfer in Xanthorhodopsin Revealed by the Combination of Transient Absorption and
    Two-Dimensional Electronic Spectroscopy    . Chemistry, 24, 46, 12084-12092.
  5. Borrego-Varillas R.; Ganzer L.; Cerullo G.; Manzoni C., Ultraviolet Transient Absorption Spectrometer with Sub-20-fs
    Time Resolution    , Appl. Sci., (2018), 8, 989. DOI: 10.3390/app8060989
  6. El-Tahawy M. M. T.; Nenov A.; Weingart O.; Olivucci M.; Garavelli M., (2018) Relationship between Excited State Lifetime and
    Isomerization Quantum Yield in Animal Rhodopsins: Beyond the One-Dimensional Landau–Zener Model    , J.
    Phys. Chem. Lett., 9, 3315-3322. DOI (repository): 10.1021/acs.jpclett.8b01062
  7. Rocio Borrego-Varillas, Giulio Cerullo and Dimitra Markovitsi (2019). Exciton Trapping Dynamics in DNA
    Multimers    . J. Phys. Chem. Lett.2019, 10, 7 DOI: 10.1021/acs.jpclett.9b00450
  8. Rocío Borrego-Varillas, Artur Nenov, Lucia Ganzer, Aurelio Oriana, Cristian Manzoni, Alessandra
    Tolomelli, Ivan Rivalta, Shaul Mukamel, Marco Garavelli, Giulio Cerullo
    (2019). Two-dimensional UV
    spectroscopy: a new insight into the structure and dynamics of biomolecules    .      10,
    9907-9921
  9. Francesco Segatta, Lorenzo Cupellini, Marco Garavelli, Benedetta Mennucci (2019) Quantum Chemical Modeling of the
    Photoinduced Activity of Multichromophoric Biosystems    . Chemical Reviews 119, 16,
    9361-9380.
  10. Okamura H.; Crisp A.; Hübner S.; Becker S.; Rovó P.; Carell T.,(2019) Proto‐Urea‐RNA (Wöhler
    RNA) Containing Unusually Stable Urea Nucleosides    , Angew. Chem. Int., 58, 18691-18696. DOI:
    10.1002/anie.201911746
  11. Gontcharov J.; Liu L.; Pilles B. M.; Carell T.; Schreier W. J.; Zinth W., (2019) Triplet‐Induced
    Lesion Formation at CpT and TpC Sites in DNA    , Chem. Eur., 25, 15164-15172, DOI: 10.1002/chem.201903573
  12. Thumbs P.; Ensfelder T. T.; Hillmeier M.; Wagner M.; Heiss M.; Scheel C.;  Schön A.; Müller M.;
    Michalakis S.; Kellner S.; Carell T., (2020) Synthesis of Galactosyl‐Queuosine
    and Distribution of Hypermodified Q‐Nucleosides in Mouse Tissues    , Angew. Chem. Int., DOI:
    10.1002/anie.202002295
  13. Raddaoui N.; Croce S.; Geiger F.; Borodavka A.; Möckl L.; Stazzoni S.;  Viverge B.; Bräuchle C.;
    Frischmuth T.; Engelke H.; Carell T., (2020) Supersensitive
    Multifluorophore RNA‐FISH for Early Virus Detection and Flow‐FISH by Using Click Chemistry    ,
    ChemBioChem, DOI: 10.1002/cbic.202000081
  14. Martinez-Fernandez, L.; Gustavsson T.; Diederichsen U.; Improta R., Excited State Dynamics of 8-Vinyldeoxyguanosine in Aqueous
    Solution Studied by Time-Resolved Fluorescence Spectroscopy and Quantum Mechanical Calculations    , Molecules,
    (2020), 25, 824. DOI: 10.3390/molecules25040824
  15. Green J. A.; Improta R., (2020) Vibrations of the
    guanine–cytosine pair in chloroform: an anharmonic computational study    , Phys. Chem. Chem. Phys., 
    22, 5509-5522. DOI: 10.1039/C9CP06373K
  16. Cerezo J.; Aranda D.; Avila Ferrer F. J.; Prampolini G.; Santoro F., (2020) Adiabatic-Molecular Dynamics Generalized Vertical
    Hessian Approach: A Mixed Quantum Classical Method To Compute Electronic Spectra of Flexible Molecules in the
    Condensed Phase    , J. Chem. Theory Comput., 16, 1215-1231. DOI (repository): 10.1021/acs.jctc.9b0100

This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie grant agreement No 765266.

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