DNA as a training platform for photodynamic processes in soft materials

Deliverables

Other (4)

Open-source code for the simulation of pump-probe and 2D electron spectra from quantum-dynamics.

Introduction Week: DNA fundamentals

Introduction Week: DNA fundamentals.

Technology Training Camps

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

Website

Documents, reports (5)

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

Peer reviewed articles (54)

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 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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⟩", 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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), 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, Volume 24, 2022, Page(s) 4987-5000, ISSN 1463-9084
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1cp04340d