Light-Induced Function: from Excitation to Signal through Time and Space

Project Information

LIFETimeS

Grant agreement ID: 786714

DOI

10.3030/786714

Project closed

EC signature date 17 April 2018

Start date 1 September 2018

End date 29 February 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 400 000,00

EU contribution

€ 2 400 000,00

Coordinated by

UNIVERSITA DI PISA
Italy

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (52)

Ultrafast Excited-State Dynamics of Carotenoids and the Role of the SX State

Author(s): Davide Accomasso, Serra Arslancan, Lorenzo Cupellini, Giovanni Granucci, Benedetta Mennucci
Published in: The Journal of Physical Chemistry Letters, 2022, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.2c01555

How orange carotenoid protein controls the excited state dynamics of canthaxanthin

Author(s): Amanda Arcidiacono; Davide Accomasso; Lorenzo Cupellini; Benedetta Mennucci
Published in: Chemical Science, 2023, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d3sc02662k

Excited state Born–Oppenheimer molecular dynamics through coupling between time dependent DFT and AMOEBA

Author(s): Michele Nottoli, Benedetta Mennucci, Filippo Lipparini
Published in: Physical Chemistry Chemical Physics, Issue 22/35, 2020, Page(s) 19532-19541, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0cp03688a

Molecular Mechanisms of Activation in the Orange Carotenoid Protein Revealed by Molecular Dynamics

Author(s): Mattia Bondanza, Lorenzo Cupellini, Pietro Faccioli, Benedetta Mennucci
Published in: Journal of the American Chemical Society, Issue 142/52, 2020, Page(s) 21829-21841, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.0c10461

The nature of carotenoid S* state and its role in the nonphotochemical quenching of plants

Author(s): Davide Accomasso, Giacomo Londi, Lorenzo Cupellini, Benedetta Mennucci
Published in: Nature Communications, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-45090-9

Excited States of Xanthophylls Revisited: Toward the Simulation of Biologically Relevant Systems

Author(s): Mattia Bondanza, Denis Jacquemin, Benedetta Mennucci
Published in: The Journal of Physical Chemistry Letters, Issue 12/28, 2021, Page(s) 6604-6612, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.1c01929

Trajectory Surface Hopping for a Polarizable Embedding QM/MM Formulation

Author(s): Mattia Bondanza; Baptiste Demoulin; Filippo Lipparini; Mario Barbatti; Benedetta Mennucci
Published in: The Journal of Physical Chemistry A, Issue 23, 2022, ISSN 1089-5639
Publisher: American Chemical Society
DOI: 10.1021/acs.jpca.2c04756

Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation

Author(s): Michele Nottoli, Riccardo Nifosì, Benedetta Mennucci, Filippo Lipparini
Published in: Journal of Chemical Theory and Computation, Issue 17/9, 2021, Page(s) 5661-5672, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.1c00555

Integrated Computational Study of the Light-Activated Structure of the AppA BLUF Domain and Its Spectral Signatures

Author(s): Hashem, Shaima; Alteri, Giovanni Battista; Cupellini, Lorenzo; Mennucci, Benedetta
Published in: The Journal of Physical Chemistry A, 2023, ISSN 1089-5639
Publisher: American Chemical Society
DOI: 10.1021/acs.jpca.3c02385

Electronic couplings for photo-induced processes from subsystem time-dependent density-functional theory: The role of the diabatization

Author(s): Johannes Tölle, Lorenzo Cupellini, Benedetta Mennucci, Johannes Neugebauer
Published in: The Journal of Chemical Physics, Issue 153/18, 2020, Page(s) 184113, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0022677

Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor

Author(s): Patrizia Mazzeo, Shaima Hashem, Filippo Lipparini, Lorenzo Cupellini, and Benedetta Mennucci
Published in: The Journal of Physical Chemistry Letters, 2023, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.2c03797

Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes

Author(s): Edoardo Cignoni, Lorenzo Cupellini, and Benedetta Mennucci
Published in: Journal of Chemical Theory and Computation, 2023, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.2c01044

Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

Author(s): Mattia Bondanza, Michele Nottoli, Lorenzo Cupellini, Filippo Lipparini, Benedetta Mennucci
Published in: Physical Chemistry Chemical Physics, Issue 22/26, 2020, Page(s) 14433-14448, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0cp02119a

A different perspective for nonphotochemical quenching in plant antenna complexes

Author(s): Edoardo Cignoni, Margherita Lapillo, Lorenzo Cupellini, Silvia Acosta-Gutiérrez, Francesco Luigi Gervasio, Benedetta Mennucci
Published in: Nature Communications, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27526-8

Newton-X Platform: New Software Developments for Surface Hopping and Nuclear Ensembles

Author(s): Mario Barbatti; Mattia Bondanza; Rachel Crespo-Otero; Baptiste Demoulin; Pavlo O. Dral; Giovanni Granucci; Fábris Kossoski; Hans Lischka; Benedetta Mennucci; Saikat Mukherjee; Marek Pederzoli; Maurizio Persico; Max Pinheiro Jr; Jiří Pittner; Felix Plasser; Eduarda Sangiogo Gil; Ljiljana Stojanovic
Published in: Journal of Chemical Theory and Computation, Issue 21, 2022, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.2c00804

Computational Investigation of Structural and Spectroscopic Properties of LOV-Based Proteins with Improved Fluorescence

Author(s): Felipe Cardoso Ramos, Lorenzo Cupellini, Benedetta Mennucci
Published in: The Journal of Physical Chemistry B, Issue 125/7, 2021, Page(s) 1768-1777, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.0c10834

Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response

Author(s): Giacomo Salvadori, Patrizia Mazzeo, Davide Accomasso, Lorenzo Cupellini, Benedetta Mennucci
Published in: Journal of Molecular Biology, 2024, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2023.168358

Electronic Excited States from Physically Constrained Machine Learning

Author(s): Edoardo Cignoni; Divya Suman; Jigyasa Nigam; Lorenzo Cupellini; Benedetta Mennucci; Michele Ceriotti
Published in: ACS Central Science, 2024, ISSN 2470-1343
Publisher: American Chemical Society
DOI: 10.1021/acscentsci.3c01480

Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex

Author(s): Lorenzo Cupellini, Pu Qian, Tu C Nguyen-Phan, Alastair T Gardiner, Richard J Cogdell
Published in: Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex, 2022, ISSN 0166-8595
Publisher: Kluwer Academic Publishers
DOI: 10.1101/2022.04.09.487728

Exciton properties and optical spectra of light harvesting complex II from a fully atomistic description

Author(s): Vladislav Sláma, Lorenzo Cupellini, Benedetta Mennucci
Published in: Physical Chemistry Chemical Physics, Issue 22/29, 2020, Page(s) 16783-16795, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0cp02492a

Structure of the stress-related LHCSR1 complex determined by an integrated computational strategy

Author(s): Ingrid Guarnetti Prandi; Vladislav Sláma; Cristina Pecorilla; Lorenzo Cupellini; Benedetta Mennucci
Published in: Communications Biology, Issue 2, 2022, ISSN 2399-3642
Publisher: Nature Publishing Group
DOI: 10.1038/s42003-022-03083-8

Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes

Author(s): Paul V. Sauer, Lorenzo Cupellini, Markus Sutter, Mattia Bondanza, María Agustina Domínguez Martin, Henning Kirst, David Bína, Adrian Fujiet Koh, Abhay Kotecha, Basil J. Greber, Eva Nogales, Tomáš Polívka, Benedetta Mennucci, Cheryl A. Kerfeld
Published in: Science Advances, 2024, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.adk7535

From crystallographic data to the solution structure of photoreceptors: the case of the AppA BLUF domain

Author(s): Shaima Hashem; Veronica Macaluso; Michele Nottoli; Filippo Lipparini; Lorenzo Cupellini; Benedetta Mennucci
Published in: Chemical Science, Issue 2, 2021, ISSN 2041-6539
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1sc03000k

How the pH Controls Photoprotection in the Light-Harvesting Complex of Mosses

Author(s): Laura Pedraza-González, Edoardo Cignoni, Jacopo D’Ascenzi, Lorenzo Cupellini, Benedetta Mennucci
Published in: Journal of the American Chemical Society, 2023, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.3c00377

Dye Stabilization and Wavelength Tunability in Lasing Fibers Based on DNA

Author(s): Luana Persano, Adam Szukalski, Michele Gaio, Maria Moffa, Giacomo Salvadori, Lech Sznitko, Andrea Camposeo, Jaroslaw Mysliwiec, Riccardo Sapienza, Benedetta Mennucci, Dario Pisignano
Published in: Advanced Optical Materials, Issue 8/22, 2020, Page(s) 2001039, ISSN 2195-1071
Publisher: Wiley
DOI: 10.1002/adom.202001039

A fast method for electronic couplings in embedded multichromophoric systems

Author(s): Edoardo Cignoni, Lorenzo Cupellini, Benedetta Mennucci
Published in: Journal of Physics: Condensed Matter, 2022, ISSN 0953-8984
Publisher: Institute of Physics Publishing
DOI: 10.1088/1361-648x/ac6f3c

QM/AMOEBA description of properties and dynamics of embedded molecules

Author(s): Michele Nottoli, Mattia Bondanza, Patrizia Mazzeo, Lorenzo Cupellini, Carles Curutchet, Daniele Loco, Louis Lagardère, Jean-Philip Piquemal, Benedetta Mennucci, Filippo Lipparini
Published in: WIREs Comput Mol Sci., 2023, ISSN 1759-0876
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1674

Protein control of photochemistry and transient intermediates in phytochromes

Author(s): Giacomo Salvadori, Veronica Macaluso, Giulia Pellicci, Lorenzo Cupellini, Giovanni Granucci, Benedetta Mennucci
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-34640-8

Absorption and Circular Dichroism Spectra of Molecular Aggregates With the Full Cumulant Expansion

Author(s): Lorenzo Cupellini, Filippo Lipparini, Jianshu Cao
Published in: The Journal of Physical Chemistry B, Issue 124/39, 2020, Page(s) 8610-8617, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.0c05180

The molecular mechanisms of light adaption in light-harvesting complexes of purple bacteria revealed by a multiscale modeling

Author(s): Felipe Cardoso Ramos, Michele Nottoli, Lorenzo Cupellini, Benedetta Mennucci
Published in: Chemical Science, Issue 10/42, 2019, Page(s) 9650-9662, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/C9SC02886B

Multiscale modelling of photoinduced processes in composite systems

Author(s): Benedetta Mennucci, Stefano Corni
Published in: Nature Reviews Chemistry, Issue 3/5, 2019, Page(s) 315-330, ISSN 2397-3358
Publisher: Springer Nature
DOI: 10.1038/s41570-019-0092-4

The Multiple Roles of the Protein in the Photoactivation of Orange Carotenoid Protein

Author(s): Mattia Bondanza, Lorenzo Cupellini, Filippo Lipparini, Benedetta Mennucci
Published in: Chem, Issue 6/1, 2020, Page(s) 187-203, ISSN 2451-9294
Publisher: Cell Press
DOI: 10.1016/j.chempr.2019.10.014

Quantum Chemical Modeling of the Photoinduced Activity of Multichromophoric Biosystems

Author(s): Francesco Segatta, Lorenzo Cupellini, Marco Garavelli, Benedetta Mennucci
Published in: Chemical Reviews, Issue 119/16, 2019, Page(s) 9361-9380, ISSN 0009-2665
Publisher: American Chemical Society
DOI: 10.1021/acs.chemrev.9b00135

Successes & challenges in the atomistic modeling of light-harvesting and its photoregulation

Author(s): Lorenzo Cupellini, Mattia Bondanza, Michele Nottoli, Benedetta Mennucci
Published in: Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2019, Page(s) 148049, ISSN 0005-2728
Publisher: Elsevier BV
DOI: 10.1016/j.bbabio.2019.07.004

The key to the yellow-to-cyan tuning in the green fluorescent protein family is polarisation

Author(s): Riccardo Nifosì, Benedetta Mennucci, Claudia Filippi
Published in: Physical Chemistry Chemical Physics, Issue 21/35, 2019, Page(s) 18988-18998, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9cp03722e

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

Author(s): Daniele Loco, Louis Lagardère, Gérardo A. Cisneros, Giovanni Scalmani, Michael Frisch, Filippo Lipparini, Benedetta Mennucci, Jean-Philip Piquemal
Published in: Chemical Science, Issue 10/30, 2019, Page(s) 7200-7211, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sc01745c

Charge transfer from the carotenoid can quench chlorophyll excitation in antenna complexes of plants

Author(s): Lorenzo Cupellini, Dario Calvani, Denis Jacquemin, Benedetta Mennucci
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-14488-6

Elucidating the role of structural fluctuations, intermolecular & vibronic interactions in the spectroscopic response of a bacteriophytochrome

Author(s): Veronica Macaluso, Lorenzo Cupellini, Giacomo Salvadori, Filippo Lipparini, Benedetta Mennucci
Published in: Physical Chemistry Chemical Physics, 2020, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/D0CP00372G

The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol

Author(s): Benedetta Mennucci; Lorenzo Cupellini; Edoardo Cignoni; Vladislav Slama
Published in: The Journal of Chemical Physics, Issue 3, 2022, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0086275

A polarisable QM/MM description of NMR chemical shifts of a photoreceptor protein

Author(s): Shaima Hashem, Lorenzo Cupellini, Filippo Lipparini, Benedetta Mennucci
Published in: Molecular Physics, Issue 118/19-20, 2020, Page(s) e1771449, ISSN 0026-8976
Publisher: Taylor & Francis
DOI: 10.1080/00268976.2020.1771449

The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation

Author(s): Veronica Macaluso, Giacomo Salvadori, Lorenzo Cupellini, Benedetta Mennucci
Published in: Chemical Science, 2021, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1sc00186h

First-principles simulation of excitation energy transfer and transient absorption spectroscopy in the CP29 light-harvesting complex

Author(s): Piermarco Saraceno, Vladislav Slama, Lorenzo Cupellini
Published in: The Journal of Chemical Physics, 2023, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0170295

Origin of Low-Lying Red States in the Lhca4 Light-Harvesting Complex of Photosystem I

Author(s): Vladislav Sláma; Lorenzo Cupellini; Vincenzo Mascoli; Nicoletta Liguori; Roberta Croce; Benedetta Mennucci
Published in: The Journal of Physical chemistry Letters, 2023, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.3c02091

Ultrafast excited-state dynamics of Luteins in the major light-harvesting complex LHCII

Author(s): Laura Pedraza-González, Davide Accomasso, Lorenzo Cupellini, Giovanni Granucci, Benedetta Mennucci
Published in: Photochemical & Photobiological Sciences, 2024, ISSN 1474-905X
Publisher: Royal Society of Chemistry
DOI: 10.1007/s43630-023-00518-x

Excitonic Nature of Carotenoid–Phthalocyanine Dyads and Its Role in Transient Absorption Spectra

Author(s): Vladislav Sláma; Lorenzo Cupellini; Benedetta Mennucci
Published in: ACS Physical Chemistry Au, Issue 9, 2022, ISSN 2694-2445
Publisher: American Chemical Society
DOI: 10.1021/acsphyschemau.1c00049

Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics

Author(s): Veronica Macaluso, Shaima Hashem, Michele Nottoli, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Published in: The Journal of Physical Chemistry B, Issue 125/36, 2021, Page(s) 10282-10292, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.1c05753

Uncovering the interactions driving carotenoid binding in light-harvesting complexes

Author(s): Vincenzo Mascoli, Nicoletta Liguori, Lorenzo Cupellini, Eduard Elias, Benedetta Mennucci, Roberta Croce
Published in: Chemical Science, Issue 12/14, 2021, Page(s) 5113-5122, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1sc00071c

The energy transfer model of nonphotochemical quenching: Lessons from the minor CP29 antenna complex of plants

Author(s): Margherita Lapillo, Edoardo Cignoni, Lorenzo Cupellini, Benedetta Mennucci
Published in: Biochimica et Biophysica Acta (BBA) - Bioenergetics, Issue 1861/11, 2020, Page(s) 148282, ISSN 0005-2728
Publisher: Elsevier BV
DOI: 10.1016/j.bbabio.2020.148282

Hybrid QM/classical models: Methodological advances and new applications

Author(s): Filippo Lipparini; Benedetta Mennucci
Published in: Chemical Physics Review, Issue 4, 2021, ISSN 2688-4070
Publisher: AIP Publishing
DOI: 10.1063/5.0064075

Multiscale Models for Light-Driven Processes

Author(s): Michele Nottoli, Lorenzo Cupellini, Filippo Lipparini, Giovanni Granucci, Benedetta Mennucci
Published in: Annual Review of Physical Chemistry, Issue 72/1, 2021, Page(s) 489-513, ISSN 0066-426X
Publisher: Annual Reviews, Inc.
DOI: 10.1146/annurev-physchem-090419-104031

Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy

Author(s): Manoop Chenchiliyan, Joachim Kübel, Saik Ann Ooi, Giacomo Salvadori, Benedetta Mennucci, Sebastian Westenhoff, Michał Maj
Published in: Journal of Chemical Physics, 2023, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0135268

An enhanced sampling QM/AMOEBA approach: The case of the excited state intramolecular proton transfer in solvated 3-hydroxyflavone

Author(s): Michele Nottoli, Mattia Bondanza, Filippo Lipparini, Benedetta Mennucci
Published in: The Journal of Chemical Physics, Issue 154/18, 2021, Page(s) 184107, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0046844