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

Publikacje

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

Autorzy: Michele Nottoli, Benedetta Mennucci, Filippo Lipparini
Opublikowane w: Physical Chemistry Chemical Physics, Numer 22/35, 2020, Strona(/y) 19532-19541, ISSN 1463-9076
Wydawca: Royal Society of Chemistry
DOI: 10.1039/d0cp03688a

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

Autorzy: Mattia Bondanza, Lorenzo Cupellini, Pietro Faccioli, Benedetta Mennucci
Opublikowane w: Journal of the American Chemical Society, Numer 142/52, 2020, Strona(/y) 21829-21841, ISSN 0002-7863
Wydawca: American Chemical Society
DOI: 10.1021/jacs.0c10461

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

Autorzy: Mattia Bondanza, Denis Jacquemin, Benedetta Mennucci
Opublikowane w: The Journal of Physical Chemistry Letters, Numer 12/28, 2021, Strona(/y) 6604-6612, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.1c01929

Trajectory Surface Hopping for a Polarizable Embedding QM/MM Formulation

Autorzy: Mattia Bondanza; Baptiste Demoulin; Filippo Lipparini; Mario Barbatti; Benedetta Mennucci
Opublikowane w: The Journal of Physical Chemistry A, Numer 23, 2022, ISSN 1089-5639
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpca.2c04756

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

Autorzy: Michele Nottoli, Riccardo Nifosì, Benedetta Mennucci, Filippo Lipparini
Opublikowane w: Journal of Chemical Theory and Computation, Numer 17/9, 2021, Strona(/y) 5661-5672, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.1c00555

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

Autorzy: Johannes Tölle, Lorenzo Cupellini, Benedetta Mennucci, Johannes Neugebauer
Opublikowane w: The Journal of Chemical Physics, Numer 153/18, 2020, Strona(/y) 184113, ISSN 0021-9606
Wydawca: 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

Autorzy: Patrizia Mazzeo, Shaima Hashem, Filippo Lipparini, Lorenzo Cupellini, and Benedetta Mennucci
Opublikowane w: The Journal of Physical Chemistry Letters, 2023, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.2c03797

Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes

Autorzy: Edoardo Cignoni, Lorenzo Cupellini, and Benedetta Mennucci
Opublikowane w: Journal of Chemical Theory and Computation, 2023, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.2c01044

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

Autorzy: Mattia Bondanza, Michele Nottoli, Lorenzo Cupellini, Filippo Lipparini, Benedetta Mennucci
Opublikowane w: Physical Chemistry Chemical Physics, Numer 22/26, 2020, Strona(/y) 14433-14448, ISSN 1463-9076
Wydawca: Royal Society of Chemistry
DOI: 10.1039/d0cp02119a

A different perspective for nonphotochemical quenching in plant antenna complexes

Autorzy: Edoardo Cignoni, Margherita Lapillo, Lorenzo Cupellini, Silvia Acosta-Gutiérrez, Francesco Luigi Gervasio, Benedetta Mennucci
Opublikowane w: Nature Communications, 2021, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-021-27526-8

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

Autorzy: 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
Opublikowane w: Journal of Chemical Theory and Computation, Numer 21, 2022, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.2c00804

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

Autorzy: Felipe Cardoso Ramos, Lorenzo Cupellini, Benedetta Mennucci
Opublikowane w: The Journal of Physical Chemistry B, Numer 125/7, 2021, Strona(/y) 1768-1777, ISSN 1520-6106
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpcb.0c10834

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

Autorzy: Vladislav Sláma, Lorenzo Cupellini, Benedetta Mennucci
Opublikowane w: Physical Chemistry Chemical Physics, Numer 22/29, 2020, Strona(/y) 16783-16795, ISSN 1463-9076
Wydawca: Royal Society of Chemistry
DOI: 10.1039/d0cp02492a

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

Autorzy: Ingrid Guarnetti Prandi; Vladislav Sláma; Cristina Pecorilla; Lorenzo Cupellini; Benedetta Mennucci
Opublikowane w: Communications Biology, Numer 2, 2022, ISSN 2399-3642
Wydawca: Nature Publishing Group
DOI: 10.1038/s42003-022-03083-8

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

Autorzy: Shaima Hashem; Veronica Macaluso; Michele Nottoli; Filippo Lipparini; Lorenzo Cupellini; Benedetta Mennucci
Opublikowane w: Chemical Science, Numer 2, 2021, ISSN 2041-6539
Wydawca: Royal Society of Chemistry
DOI: 10.1039/d1sc03000k

Dye Stabilization and Wavelength Tunability in Lasing Fibers Based on DNA

Autorzy: Luana Persano, Adam Szukalski, Michele Gaio, Maria Moffa, Giacomo Salvadori, Lech Sznitko, Andrea Camposeo, Jaroslaw Mysliwiec, Riccardo Sapienza, Benedetta Mennucci, Dario Pisignano
Opublikowane w: Advanced Optical Materials, Numer 8/22, 2020, Strona(/y) 2001039, ISSN 2195-1071
Wydawca: Wiley
DOI: 10.1002/adom.202001039

Protein control of photochemistry and transient intermediates in phytochromes

Autorzy: Giacomo Salvadori, Veronica Macaluso, Giulia Pellicci, Lorenzo Cupellini, Giovanni Granucci, Benedetta Mennucci
Opublikowane w: Nature Communications, 2022, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-34640-8

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

Autorzy: Lorenzo Cupellini, Filippo Lipparini, Jianshu Cao
Opublikowane w: The Journal of Physical Chemistry B, Numer 124/39, 2020, Strona(/y) 8610-8617, ISSN 1520-6106
Wydawca: 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

Autorzy: Felipe Cardoso Ramos, Michele Nottoli, Lorenzo Cupellini, Benedetta Mennucci
Opublikowane w: Chemical Science, Numer 10/42, 2019, Strona(/y) 9650-9662, ISSN 2041-6520
Wydawca: Royal Society of Chemistry
DOI: 10.1039/C9SC02886B

Multiscale modelling of photoinduced processes in composite systems

Autorzy: Benedetta Mennucci, Stefano Corni
Opublikowane w: Nature Reviews Chemistry, Numer 3/5, 2019, Strona(/y) 315-330, ISSN 2397-3358
Wydawca: Springer Nature
DOI: 10.1038/s41570-019-0092-4

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

Autorzy: Mattia Bondanza, Lorenzo Cupellini, Filippo Lipparini, Benedetta Mennucci
Opublikowane w: Chem, Numer 6/1, 2020, Strona(/y) 187-203, ISSN 2451-9294
Wydawca: Cell Press
DOI: 10.1016/j.chempr.2019.10.014

Quantum Chemical Modeling of the Photoinduced Activity of Multichromophoric Biosystems

Autorzy: Francesco Segatta, Lorenzo Cupellini, Marco Garavelli, Benedetta Mennucci
Opublikowane w: Chemical Reviews, Numer 119/16, 2019, Strona(/y) 9361-9380, ISSN 0009-2665
Wydawca: American Chemical Society
DOI: 10.1021/acs.chemrev.9b00135

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

Autorzy: Lorenzo Cupellini, Mattia Bondanza, Michele Nottoli, Benedetta Mennucci
Opublikowane w: Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2019, Strona(/y) 148049, ISSN 0005-2728
Wydawca: 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

Autorzy: Riccardo Nifosì, Benedetta Mennucci, Claudia Filippi
Opublikowane w: Physical Chemistry Chemical Physics, Numer 21/35, 2019, Strona(/y) 18988-18998, ISSN 1463-9076
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c9cp03722e

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

Autorzy: Daniele Loco, Louis Lagardère, Gérardo A. Cisneros, Giovanni Scalmani, Michael Frisch, Filippo Lipparini, Benedetta Mennucci, Jean-Philip Piquemal
Opublikowane w: Chemical Science, Numer 10/30, 2019, Strona(/y) 7200-7211, ISSN 2041-6520
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c9sc01745c

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

Autorzy: Lorenzo Cupellini, Dario Calvani, Denis Jacquemin, Benedetta Mennucci
Opublikowane w: Nature Communications, Numer 11/1, 2020, ISSN 2041-1723
Wydawca: 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

Autorzy: Veronica Macaluso, Lorenzo Cupellini, Giacomo Salvadori, Filippo Lipparini, Benedetta Mennucci
Opublikowane w: Physical Chemistry Chemical Physics, 2020, ISSN 1463-9076
Wydawca: Royal Society of Chemistry
DOI: 10.1039/D0CP00372G

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

Autorzy: Benedetta Mennucci; Lorenzo Cupellini; Edoardo Cignoni; Vladislav Slama
Opublikowane w: The Journal of Chemical Physics, Numer 3, 2022, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/5.0086275

Ultrafast Excited-State Dynamics of Carotenoids and the Role of the S<sub><i>X</i></sub> State

Autorzy: Davide Accomasso; Serra Arslancan; Lorenzo Cupellini; Giovanni Granucci; Benedetta Mennucci
Opublikowane w: The Journal of Physical Chemistry Letters, Numer 11, 2021, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.2c01555

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

Autorzy: Shaima Hashem, Lorenzo Cupellini, Filippo Lipparini, Benedetta Mennucci
Opublikowane w: Molecular Physics, Numer 118/19-20, 2020, Strona(/y) e1771449, ISSN 0026-8976
Wydawca: 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

Autorzy: Veronica Macaluso, Giacomo Salvadori, Lorenzo Cupellini, Benedetta Mennucci
Opublikowane w: Chemical Science, 2021, ISSN 2041-6520
Wydawca: Royal Society of Chemistry
DOI: 10.1039/d1sc00186h

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

Autorzy: Vladislav Sláma; Lorenzo Cupellini; Benedetta Mennucci
Opublikowane w: ACS Physical Chemistry Au, Numer 9, 2022, ISSN 2694-2445
Wydawca: American Chemical Society
DOI: 10.1021/acsphyschemau.1c00049

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

Autorzy: Veronica Macaluso, Shaima Hashem, Michele Nottoli, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Opublikowane w: The Journal of Physical Chemistry B, Numer 125/36, 2021, Strona(/y) 10282-10292, ISSN 1520-6106
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpcb.1c05753

Uncovering the interactions driving carotenoid binding in light-harvesting complexes

Autorzy: Vincenzo Mascoli, Nicoletta Liguori, Lorenzo Cupellini, Eduard Elias, Benedetta Mennucci, Roberta Croce
Opublikowane w: Chemical Science, Numer 12/14, 2021, Strona(/y) 5113-5122, ISSN 2041-6520
Wydawca: Royal Society of Chemistry
DOI: 10.1039/d1sc00071c

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

Autorzy: Margherita Lapillo, Edoardo Cignoni, Lorenzo Cupellini, Benedetta Mennucci
Opublikowane w: Biochimica et Biophysica Acta (BBA) - Bioenergetics, Numer 1861/11, 2020, Strona(/y) 148282, ISSN 0005-2728
Wydawca: Elsevier BV
DOI: 10.1016/j.bbabio.2020.148282

Hybrid QM/classical models: Methodological advances and new applications

Autorzy: Filippo Lipparini; Benedetta Mennucci
Opublikowane w: Chemical Physics Review, Numer 4, 2021, ISSN 2688-4070
Wydawca: AIP Publishing
DOI: 10.1063/5.0064075

Multiscale Models for Light-Driven Processes

Autorzy: Michele Nottoli, Lorenzo Cupellini, Filippo Lipparini, Giovanni Granucci, Benedetta Mennucci
Opublikowane w: Annual Review of Physical Chemistry, Numer 72/1, 2021, Strona(/y) 489-513, ISSN 0066-426X
Wydawca: 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

Autorzy: Manoop Chenchiliyan, Joachim Kübel, Saik Ann Ooi, Giacomo Salvadori, Benedetta Mennucci, Sebastian Westenhoff, Michał Maj
Opublikowane w: Journal of Chemical Physics, 2023, ISSN 0021-9606
Wydawca: 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

Autorzy: Michele Nottoli, Mattia Bondanza, Filippo Lipparini, Benedetta Mennucci
Opublikowane w: The Journal of Chemical Physics, Numer 154/18, 2021, Strona(/y) 184107, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/5.0046844

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