DNA as a training platform for photodynamic processes in soft materials

Deliverables

Open-source code for the simulation of pump-probe and 2D electron spectra from quantum-dynamics.
Introduction Week: DNA fundamentals

Introduction Week: DNA fundamentals.

First Annual LightDyNAmics Week

3 annual LightDyNAmics Weeks. Due Dates M14, M26 and M38All beneficiaries are responsible

Day of Light and Matter
Technology Training Camps

Technology Training Camps, due in M18 and M22. Lead Beneficiaries UNIVIE and POLIMI

15 PhD theses (full drafts)

15 PhD theses (full drafts)All host insitutions are the main responsibles for this deliverable.

LightDyNAmics Lab Experience
Website

Outreach Plan
Progress report 2
Supervisory and External Advisory Boards established
Min. 30 manuscripts submitted to peer-reviewed journals

Min 30 manuscripts submitted to peerreviewed journals

Progress report 1

Progress Report 1

Publications

Parameterization of a linear vibronic coupling model with multiconfigurational electronic structure methods to study the quantum dynamics of photoexcited pyrene.

Author(s): Flavia Aleotti; Daniel Aranda; Martha Yaghoubi Jouybari; Marco Garavelli; Artur Nenov; Fabrizio Santoro
Published in: The Journal of Chemical Physics, Issue Issue 154. art. 104106, 2021, ISSN 1551-7616
Publisher: AIP Publishing
DOI: 10.1063/5.0044693

Deprotonation Dynamics of Guanine Radical Cations

Author(s): Evangelos Balanikas, Akos Banyasz, Gérard Baldacchino, Dimitra Markovitsi
Published in: Photochemistry and Photobiology, Issue Volume 98/ issue 3, 2021, Page(s) 523-531, ISSN 1467-6281
Publisher: Wiley Online Library
DOI: 10.1111/php.13540

Analysis of an Active Deformylation Mechanism of 5-Formyl-deoxycytidine (fdC) in Stem Cells

Author(s): M. Sc. Alexander Schön, Ewelina Kaminska, M. Sc. Florian Schelter, M. Sc. Eveliina Ponkkonen, M. Sc. Eva Korytiaková, Dr. Sarah Schiffers, Prof. Dr. Thomas Carell
Published in: Angewandte Chemie - International Edition, Issue Volume 59/ issue 14, 2020, Page(s) 5591-5594, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202100271

Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States.

Author(s): Haritha Asha; James A. Green; Lara Martínez-Fernández; Luciana Esposito; Roberto Improta
Published in: Molecules Volume 26/ Issue 16, Issue 13, 2021, ISSN 2078-2489
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26164789

Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives

Author(s): Fabrizio Santoro; James A. Green; Lara Martínez-Fernández; Javier Cerezo; Roberto Improta
Published in: Physical Chemistry Chemical Physics, Issue Volume 23, 2021, Page(s) 8181-8199, ISSN 1463-9084
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0cp05907b

Unified Description of Ultrafast Excited State Decay Processes in Epigenetic Deoxycytidine Derivatives

Author(s): Piotr Kabacinski; Marco Romanelli; Eveliina Ponkkonen; Vishal K. Jaiswal; Thomas Carell; Marco Garavelli; Giulio Cerullo; Irene Conti
Published in: The Journal of Physical Chemistry Letters, Issue 12/45, 2021, Page(s) 11070–11077, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.1c02909

Ultrafast Dynamics of the Two Lowest Bright Excited States of Cytosine and 1-Methylcytosine: A Quantum Dynamical Study.

Author(s): Martha Yaghoubi Jouybari; Yanli Liu; Roberto Improta; Fabrizio Santoro
Published in: Journal of chemical theory and computation, Issue 6, 2020, Page(s) 3646–3652, ISSN 1520-5215
Publisher: ASC Publications
DOI: 10.1021/acs.jctc.0c00455

Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments

Author(s): Zhengyue Zhang, Jennifer Vögele, Klaudia Mráziková, Holger Kruse, Xiaohui Cang, Jens Wöhnert, Miroslav Krepl, Jiří Šponer
Published in: The Journal of Physical Chemistry B, Issue Volume 125 / issue 3, 2021, Page(s) 825–840, ISSN 1520-5207
Publisher: ACS Publications
DOI: 10.1021/acs.jpcb.0c10192

Electron Holes in G-Quadruplexes: The Role of Adenine Ending Groups

Author(s): Evangelos Balanikas; Lara Martinez-Fernandez; Gérard Baldacchino; Dimitra Markovitsi
Published in: International Journal of Molecular Sciences, Issue 4, 2021, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222413436

Ultrafast Dynamics of the Isolated Adenosine-5'-triphosphate Dianion Probed by Time-Resolved Photoelectron Imaging.

Author(s): Maria Elena Castellani; Davide Avagliano; Jan R. R. Verlet
Published in: The Journal of Physical Chemistry A, Issue Volu8me 125/ issue 17, 2021, Page(s) 3646–3652, ISSN 1520-5215
Publisher: ACS Publications
DOI: 10.1021/acs.jpca.1c01646

Site-Specific Photo-oxidation of the Isolated Adenosine-5'-triphosphate Dianion Determined by Photoelectron Imaging.

Author(s): Maria Elena Castellani; Davide Avagliano; Leticia González; Jan R. R. Verlet
Published in: The journal of physical chemistry letters, Issue 25, 2020, Page(s) 8195-8201, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.0c02089

QM/MM Nonadiabatic Dynamics: the SHARC/COBRAMM Approach.

Author(s): Davide Avagliano; Matteo Bonfanti; Marco Garavelli; Leticia González
Published in: Journal of Chemical Theory and Computation, Issue Volume 17 / issue 8, 2021, Page(s) 4639–4647, ISSN 1549-9626
Publisher: ACS Publications
DOI: 10.1021/acs.jctc.1c00318

The Structural Duality of Nucleobases in Guanine Quadruplexes Controls Their Low-Energy Photoionization.

Author(s): Evangelos Balanikas; Lara Martínez-Fernández; Roberto Improta; Peter Podbevšek; Gérard Baldacchino; Dimitra Markovitsi
Published in: Journal of Physical Chemistry Letters, Issue 12/34, 2021, Page(s) 8309-8313, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.1c01846

Excitonic Model for Strongly Coupled Multichromophoric Systems: The Electronic Circular Dichroism Spectra of Guanine Quadruplexes as Test Cases.

Author(s): James A. Green; Haritha Asha; Fabrizio Santoro; Roberto Improta
Published in: Journal of Chemical Theory and Computation, Issue 17/1, 2020, Page(s) 405–415, ISSN 1549-9626
Publisher: ASC Publications
DOI: 10.1021/acs.jctc.0c01100

Direct and Base Excision Repair-Mediated Regulation of a GC-Rich cis-Element in Response to 5-Formylcytosine and 5-Carboxycytosine

Author(s): Nadine Müller, Eveliina Ponkkonen, Thomas Carell, Andriy Khobta
Published in: International Journal of Molecular Sciences, Issue 22, 2021, Page(s) 11025, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222011025

Enhanced Rigidity Changes Ultraviolet Absorption: Effect of a Merocyanine Binder on G-Quadruplex Photophysics.

Author(s): Davide Avagliano; Sara Tkaczyk; Pedro A. Sánchez-Murcia; Leticia González
Published in: The Journal of Physical Chemistry Letters, Issue Volume 11 / issue 23, 2020, Page(s) 10212–10218, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.0c03070

Tracking excited state decay mechanisms of pyrimidine nucleosides in real time

Author(s): Rocío Borrego-Varillas; Artur Nenov; Piotr Kabaciński; Irene Conti; Lucia Ganzer; Aurelio Oriana; Vishal Kumar Jaiswal; Ines Delfino; Oliver Weingart; Cristian Manzoni; Ivan Rivalta; Marco Garavelli; Giulio Cerullo
Published in: Nature Communications, Issue 12, 2021, Page(s) 7285 (2021), ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27535-7

The Ultrafast Quantum Dynamics of Photoexcited Adenine–Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling Model

Author(s): Martha Yaghoubi Jouybari, James A. Green, Roberto Improta, and Fabrizio Santoro
Published in: The Journal of Physical Chemistry A, Issue Volume 125/ issue 40, 2021, Page(s) 8912–8924, ISSN 1520-5215
Publisher: ASC Publications
DOI: 10.1021/acs.jpca.1c08132

Guanine Radicals Induced in DNA by Low-Energy Photoionization

Author(s): Evangelos Balanikas; Akos Banyasz; Thierry Douki; Gérard Baldacchino; Dimitra Markovitsi
Published in: "Accounts of Chemical Research, American Chemical Society, In press, 11 (8), pp.1305 - 1309. ⟨10.1021/acs.accounts.0c00245⟩", Issue Volume 53/ issue 8, 2020, Page(s) 1305 - 1309, ISSN 1520-4898
Publisher: ACS Publications
DOI: 10.1021/acs.accounts.0c00245

Fluorescence of bimolecular guanine quadruplexes: from femtoseconds to nanoseconds

Author(s): Evangelos Balanikas, Thomas Gustavsson, Dimitra Markovitsi
Published in: The Journal of Physical Chemistry B, 2022, ISSN 1520-5207
Publisher: ACS Publications
DOI: 10.1021/acs.jpcb.2c07647

Revealing Ultrafast Population Transfer between Nearly Degenerate Electronic States

Author(s): Pascal Heim, Sebastian Mai, Bernhard Thaler, Stefan Cesnik, Davide Avagliano, Dimitra Bella-Velidou, Wolfgang E. Ernst, Leticia González, Markus Koch
Published in: The Journal of Physical Chemistry Letters, Issue Volume 11/ issue 4, 2020, Page(s) 1443–1449, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.9b03462

Excited-State Absorption of Uracil in the Gas Phase: Mapping the Main Decay Paths by Different Electronic Structure Methods.

Author(s): Daniil A. Fedotov; Alexander C. Paul; Paolo Posocco; Fabrizio Santoro; Marco Garavelli; Henrik Koch; Sonia Coriani; Sonia Coriani; Roberto Improta
Published in: Journal of Chemical Theory and Computation, Issue Volume 7 / issue 3, 2021, Page(s) 1638–1652, ISSN 1549-9626
Publisher: ACS Publishing
DOI: 10.1021/acs.jctc.0c01150

The Absorption Spectrum of Guanine Based Radicals: a Comparative Computational Analysis

Author(s): Lara Martínez Fernández, Javier Cerezo, Haritha Asha, Fabrizio Santoro, Sonia Coriani, Roberto Improta
Published in: ChemPhotoChem, Issue 3/9, 2019, Page(s) 846-855, ISSN 2367-0932
Publisher: European Chemical Societies Publishing
DOI: 10.1002/cptc.201900107

Radicals Generated in Tetramolecular Guanine Quadruplexes by Photoionization: Spectral and Dynamical Features

Author(s): Akos Banyasz, Evangelos Balanikas, Lara Martinez-Fernandez, Gérard Baldacchino, Thierry Douki, Roberto Improta, Dimitra Markovitsi
Published in: The Journal of Physical Chemistry B, Issue 123/23, 2019, Page(s) 4950-4957, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.9b02637

Potassium Ions Enhance Guanine Radical Generation upon Absorption of Low-Energy Photons by G-Quadruplexes and Modify Their Reactivity

Author(s): Behnaz Behmand, Evangelos Balanikas, Lara Martinez-Fernandez, Roberto Improta, Akos Banyasz, Gérard Baldacchino, Dimitra Markovitsi
Published in: The Journal of Physical Chemistry Letters, Issue 11/4, 2020, Page(s) 1305-1309, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.9b03667

Populations and Dynamics of Guanine Radicals in DNA strands—Direct versus Indirect Generation

Author(s): Evangelos Balanikas, Akos Banyasz, Gérard Baldacchino, Dimitra Markovitsi
Published in: Molecules, Issue 24/13, 2019, Page(s) 2347, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules24132347

Directional and regioselective hole injection of spiropyran photoswitches intercalated into A/T-duplex DNA

Author(s): Davide Avagliano, Pedro A. Sánchez-Murcia, Leticia González
Published in: Physical Chemistry Chemical Physics, Issue 21/32, 2019, Page(s) 17971-17977, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9cp03398j

A Click‐Chemistry‐Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry

Author(s): Michael Stadlmeier, Leander Simon Runtsch, Filipp Streshnev, Martin Wühr, Thomas Carell
Published in: ChemBioChem, Issue 21/1-2, 2019, Page(s) 103-107, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.201900611

On the stability of a dipole-bound state in the presence of a molecule

Author(s): Maria Elena Castellani, Cate S. Anstöter, Jan R. R. Verlet
Published in: Physical Chemistry Chemical Physics, Issue 21/44, 2019, Page(s) 24286-24290, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9cp04942h

DNA-binding mechanism of spiropyran photoswitches: the role of electrostatics

Author(s): Davide Avagliano, Pedro A. Sánchez-Murcia, Leticia González
Published in: Physical Chemistry Chemical Physics, Issue 21/17, 2019, Page(s) 8614-8618, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c8cp07508e

A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding

Author(s): Irene Ponzo, Friederike M. Möller, Herwin Daub, Nena Matscheko
Published in: Molecules, Issue 24/16, 2019, Page(s) 2877, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules24162877

Guanine Radicals Generated in Telomeric G-Quadruplexes by Direct Absorption of Low-Energy UV Photons: Effect of Potassium Ions

Author(s): Evangelos Balanikas, Akos Banyasz, Gérard Baldacchino, Dimitra Markovitsi
Published in: Molecules, Issue 25/9, 2020, Page(s) 2094, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules25092094

Analysis of an Active Deformylation Mechanism of 5‐Formyl‐deoxycytidine (fdC) in Stem Cells

Author(s): Alexander Schön, Ewelina Kaminska, Florian Schelter, Eveliina Ponkkonen, Eva Korytiaková, Sarah Schiffers, Thomas Carell
Published in: Angewandte Chemie International Edition, Issue 59/14, 2020, Page(s) 5591-5594, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202000414

Spiropyran meets guanine quadruplexes: Isomerization mechanism and DNA binding modes of quinolizidine‐substituted spiropyran probes

Author(s): Davide Avagliano, Pedro A. Sánchez-Murcia, Leticia González
Published in: Chemistry – A European Journal, 2020, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.202001586

Linear absorption spectra of solvated thiouracils resolved at the hybrid RASPT2/MM level

Author(s): Artur Nenov, Irene Conti, Rocio Borrego-Varillas, Giulio Cerullo, Marco Garavelli
Published in: Chemical Physics, Issue 515, 2018, Page(s) 643-653, ISSN 0301-0104
Publisher: Elsevier BV
DOI: 10.1016/j.chemphys.2018.07.025

Observation of the Sub-100 Femtosecond Population of a Dark State in a Thiobase Mediating Intersystem Crossing

Author(s): Rocío Borrego-Varillas, Danielle C. Teles-Ferreira, Artur Nenov, Irene Conti, Lucia Ganzer, Cristian Manzoni, Marco Garavelli, Ana Maria de Paula, Giulio Cerullo
Published in: Journal of the American Chemical Society, Issue 140/47, 2018, Page(s) 16087-16093, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.8b07057

Vibrations of the guanine–cytosine pair in chloroform: an anharmonic computational study

Author(s): James A. Green, Roberto Improta
Published in: Physical Chemistry Chemical Physics, Issue 22/10, 2020, Page(s) 5509-5522, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9cp06373k

Exciton Trapping Dynamics in DNA Multimers

Author(s): Rocio Borrego-Varillas, Giulio Cerullo, Dimitra Markovitsi
Published in: The Journal of Physical Chemistry Letters, Issue 10/7, 2019, Page(s) 1639-1643, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.9b00450

Triplet‐Induced Lesion Formation at CpT and TpC Sites in DNA

Author(s): Julia Gontcharov, Lizhe Liu, Bert M. Pilles, Thomas Carell, Wolfgang J. Schreier, Wolfgang Zinth
Published in: Chemistry – A European Journal, Issue 25/66, 2019, Page(s) 15164-15172, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201903573

Ultrafast Carotenoid to Retinal Energy Transfer in Xanthorhodopsin Revealed by the Combination of Transient Absorption and Two‐Dimensional Electronic Spectroscopy

Author(s): Francesco Segatta, Itay Gdor, Julien Réhault, Simone Taioli, Noga Friedman, Mordechai Sheves, Ivan Rivalta, Sanford Ruhman, Giulio Cerullo, Marco Garavelli
Published in: Chemistry – A European Journal, Issue 24/46, 2018, Page(s) 12084-12092, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201803525

Two-dimensional UV spectroscopy: a new insight into the structure and dynamics of biomolecules

Author(s): R. Borrego-Varillas, A. Nenov, L. Ganzer, A. Oriana, C. Manzoni, A. Tolomelli, I. Rivalta, S. Mukamel, M. Garavelli, G. Cerullo
Published in: Chemical Science, Issue 10/43, 2019, Page(s) 9907-9921, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sc03871j

Synthesis of galactosyl‐queuosine and distribution of hypermodified Q‐nucleosides in mouse tissues

Author(s): Peter Thumbs; Timm T. Ensfelder; Markus Hillmeier; Mirko Wagner; Matthias Heiss; Constanze Scheel; Alexander Schön; Markus Müller; Stylianos Michalakis; Stefanie Kellner; Thomas Carell
Published in: Angewandte Chemie (International Ed. in English), Issue Volume 59 / Issue 30, 2020, Page(s) 12352-12356, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202002295

Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

Author(s): James A. Green; Martha Yaghoubi Jouybari; Daniel Aranda; Roberto Improta; Fabrizio Santoro
Published in: Molecules, Issue Volume 12/ Issue 6, 2021, ISSN 2078-2489
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26061743

Cas12a target search and cleavage on force-stretched DNA

Author(s): Marialucrezia Losito; Marialucrezia Losito; Quentin M Smith; Matthew D. Newton; Maria Emanuela Cuomo; David Rueda
Published in: Physical Chemistry Chemical Physics, Issue Volume 23, 2021, Page(s) 26640-26644, ISSN 1463-9084
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1cp03408a

Photophysical Properties and DNA Binding of Two Intercalating Osmium Polypyridyl Complexes Showing Light-Switch Effects

Author(s): Mark Stitch; Rayhaan Z. Boota; Alannah S. Chalkley; Tony D. Keene; Jeremy C. Simpson; Paul A. Scattergood; Paul I. P. Elliott; Susan J Quinn
Published in: Inorganic Chemistry, Issue Volume 61/ issue 38, 2022, Page(s) 14947–14961, ISSN 1520-510X
Publisher: ACS Publications
DOI: 10.1021/acs.inorgchem.2c01231

Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine

Author(s): Haritha Asha, Petr Stadlbauer, Lara Martínez-Fernández, Pavel Banáš, Jiří Šponer, Roberto Improta, Luciana Esposito
Published in: International Journal of Biological Macromolecules, Issue Volume 194 / issue 1, 2022, Page(s) 882-894, ISSN 0141-8130
Publisher: Elsevier BV
DOI: 10.1016/j.ijbiomac.2021.11.143

Environment-Driven Coherent Population Transfer Governs the Ultrafast Photophysics of Tryptophan

Author(s): Vishal Kumar Jaiswal; Piotr Kabaciński; Barbara E. Nogueira de Faria; Marziogiuseppe Gentile; Ana Maria de Paula; Rocio Borrego-Varillas; Artur Nenov; Irene Conti; Giulio Cerullo; Marco Garavelli
Published in: Journal of the American Chemical Society, Issue Volume 144/ issue 28, 2022, Page(s) 12884–12892, ISSN 1520-5126
Publisher: ACS Publications
DOI: 10.1021/jacs.2c04565

Quantum dynamics of the ππ*/nπ* decay of the epigenetic nucleobase 1,5-dimethyl-cytosine in the gas phase.

Author(s): Martha Yaghoubi Jouybari; Yanli Liu; Roberto Improta; Fabrizio Santoro
Published in: Physical Chemistry Chemical Physics, Issue 45, 2020, Page(s) 26525-26535, ISSN 1463-9084
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0cp04123h

Intramolecular Photo-Oxidation as a Potential Source to Probe Biological Electron Damage: A Carboxylated Adenosine Analogue as Case Study.

Author(s): Maria Elena Castellani; Jan R. R. Verlet
Published in: Molecules, Issue Volume 26/ issue 10, 2021, Page(s) 2877, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26102877

Adenine Radical Cation Formation by a Ligand-Centered Excited State of an Intercalated Chromium Polypyridyl Complex Leads to Enhanced DNA Photo-oxidation.

Author(s): Frederico A Baptista; Dorottya Krizsan; Mark Stitch; Igor V. Sazanovich; Ian P. Clark; Michael Towrie; Conor Long; Lara Martínez-Fernández; Roberto Improta; Noel A. P. Kane-Maguire; John M. Kelly; Susan J. Quinn
Published in: Journal of the American Chemical Society, Issue 143/36, 2021, Page(s) 14766–14779, ISSN 1520-5126
Publisher: ASC Publications
DOI: 10.1021/jacs.1c06658

Fragment Diabatization Linear Vibronic Coupling Model for Quantum Dynamics of Multichromophoric Systems: Population of the Charge-Transfer State in the Photoexcited Guanine-Cytosine Pair.

Author(s): James A. Green; Martha Yaghoubi Jouybari; Haritha Asha; Fabrizio Santoro; Roberto Improta
Published in: Journal of chemical theory and computation, Issue 17/8, 2021, Page(s) 4660–4674, ISSN 1549-9626
Publisher: ASC Publications
DOI: 10.1021/acs.jctc.1c00416

c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry

Author(s): Kateřina Peterková; Kateřina Peterková; Ivo Durník; Ivo Durník; Radek Marek; Radek Marek; Janez Plavec; Peter Podbevšek
Published in: Nucleic Acids Research, Issue Volume 49/ Issue 15, 2021, Page(s) 8947–8960, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab659

Sampling effects in quantum mechanical/molecular mechanics trajectory surface hopping non-adiabatic dynamics

Author(s): Davide Avagliano; Emilio Lorini; Leticia González
Published in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Issue Volume 380/ issue 2223, 2022, ISSN 1364-503X
Publisher: Royal Society of London
DOI: 10.1098/rsta.2020.0381

Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study

Author(s): Daniil A. Fedotov; Fabrizio Santoro; Henrik Koch; Alexander Paul; Sonia Coriani; Roberto Improta
Published in: Physical Chemistry Chemical physics, Issue Volume 24, 2022, Page(s) 4987-5000, ISSN 1463-9084
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1cp04340d

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