2024
Mazzeo, P.; Cignoni, E.; Arcidiacono, A.; Cupellini, L. & Mennucci, B.
Electrostatic embedding machine learning for ground and excited state molecular dynamics of solvated molecules
Digital Discovery (2024)
<Abstract> <Article>
Salvadori, G. & Mennucci, B.
Analogies and Differences in the Photoactivation Mechanism of Bathy and Canonical Bacteriophytochromes Revealed by Multiscale Modeling
The Journal of Physical Chemistry Letters, 15, 31 (2024)
<Abstract> <Article>
Saraceno, P.; Sardar, S.; Caferri, R.; Camargo, F.V.A.; Dall’Osto, L.; D’Andrea, C.; Bassi, R.; Cupellini, L.; Cerullo, G. & Mennucci, B.
Probing the Effect of Mutations on Light Harvesting in CP29 by Transient Absorption and First-Principles Simulations
J. Phys. Chem. Lett. 6398–6408 (2024)
<Abstract> <Article>
Greiner, J.; Gianni, I.; Nottoli, T.; Lipparini, F.; Eriksen, J.J. & Gauss, J.
MBE-CASSCF Approach for the Accurate Treatment of Large Active Spaces
J. Chem. Theory Comput. (2024)
<Abstract> <Article>
Betti, E.; Saraceno, P.; Cignoni, E.; Cupellini, L. & Mennucci, B.
Insights into Energy Transfer in Light-Harvesting Complex II Through Machine-Learning Assisted Simulations
J. Phys. Chem. B, 128, 21, 5188–5200 (2024)
<Abstract> <Article>
Arcidiacono, A.; Cignoni, E.; Mazzeo, P.; Cupellini, L. & Mennucci, B.
Predicting Solvatochromism of Chromophores in Proteins through QM/MM and Machine Learning
J. Phys. Chem. A, 128, 18, 3646–3658 (2024)
<Abstract> <Article>
Bondanza, M.; Nottoli, T.; Michele Nottoli, M.; Cupellini, L.; Lipparini, F. & Mennucci, B.
The OpenMMPol library for polarizable QM/MM calculations of properties and dynamics
J. Chem. Phys. 160 134106 (2024)
<Article>
Sauer, P.V.; Cupellini, L.; Sutter, M.; Bondanza, M.; Domínguez Martin, M.A.; Kirst, H.; Bína, D.; Fujiet Koh, A.; Kotecha, A.; Greber, B.J.; Nogales, E.; Polívka, T.; Mennucci, B. & Kerfeld, C.A.
Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes
Sci. Adv. 10, eadk7535 (2024)
<Article>
Moscato, D.; Mandelli, G.; Bondanza, M.; Lipparini, F.; Conte, R.; Mennucci, M. & Ceotto, M.
Unraveling Water Solvation Effects with Quantum Mechanics/Molecular Mechanics Semiclassical Vibrational Spectroscopy: The Case of Thymidine
J. Am. Chem. Soc. 146, 8179–8188 (2024)
<Article>
Salvadori, G.; Mazzeo, P.; Accomasso, D.; Cupellini, L. & Mennucci, B.
Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response
Journal of Molecular Biology, 436, 168358 (2024)
<Abstract> <Article>
Cignoni, E.; Suman, D.; Nigam, J.; Cupellini, L.; Mennucci, B. & Ceriotti, M.
Electronic Excited States from Physically Constrained Machine Learning
ACS Cent. Sci. (2024)
<Abstract> <Article>
Accomasso, D.; Londi, G.; Cupellini, L. & Mennucci, B.
The nature of carotenoid S* state and its role in the nonphotochemical quenching of plants.
Nat Commun 15, 847 (2024)
<Abstract> <Article>
Pedraza-González, L.; Accomasso, D.; Cupellini, L.; Granucci, G. & Mennucci, B.
Ultrafast excited-state dynamics of Luteins in the major light-harvesting complex LHCII
Photochem Photobiol Sci, 23, 303-314 (2024)
<Abstract> <Article>
2023
Nottoli, T.; Gauss, J. & Lipparini, F.
A novel coupled-cluster singles and doubles implementation that combines the exploitation of point-group symmetry and Cholesky decomposition of the two-electron integrals
J. Chem. Phys. 159, 231101 (2023)
<Abstract> <Article>
Alessandro, R.; Giannì, I.; Pes, F.; Nottoli, T. & Lipparini, F.
Linear Response Equations Revisited: A Simple and Efficient Iterative Algorithm
J. Chem. Theory Comput. (2023)
<Abstract> <Article>
Saraceno, P.; Sláma, V. & Cupellini, L.
First-principles simulation of excitation energy transfer and transient absorption spectroscopy in the CP29 light-harvesting complex
J. Chem. Phys. 159, 184112 (2023)
<Abstract> <Article>
Lambros, E.; Link, B.; Chow, M.; Lipparini, F.; Hammes-Schiffer, S. & Li, X.
Assessing Implicit and Explicit Polarizable Solvation Models for Nuclear–Electronic Orbital Systems: Quantum Proton Polarization and Solvation Energetics
J. Phys. Chem. A, 127, 44, 9322–9333 (2023)
<Abstract> <Article>
Pes, F.; Polack, E.; Mazzeo, P.; Dusson, G.; Stamm, B. & Lipparini, F.
A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born–Oppenheimer Molecular Dynamics
J. Phys. Chem. Lett., 14, 43, 9720–9726 (2023)
<Abstract> <Article>
Arcidiacono, A.; Accomasso, D.; Cupellini, L. & Mennucci, B.
How orange carotenoid protein controls the excited state dynamics of canthaxanthin
Chem. Sci. 14, 11158-11169 (2023)
<Abstract> <Article>
Sláma, V.; Cupellini, L.; Mascoli, V.; Liguori, N.; Croce, R. & Mennucci, B.
Origin of Low-Lying Red States in the Lhca4 Light-Harvesting Complex of Photosystem I
J. Phys. Chem. Lett. 14, 37, 8345–8352 (2023)
<Abstract> <Article>
Dr. Preda, G.; Dr. Jung, S.; Prof. Pescitelli, G.; Prof. Cupellini, L.; Prof. Armspach, D. & Prof. Pasini, D.
Enabling Stereochemical Communication and Stimuli-Responsive Chiroptical Properties in Biphenyl-Capped Cyclodextrins
Chem. Eur. J. 29, e202302376 (2023)
<Abstract> <Article>
Nottoli, T., Giannì, I., Levitt, A. & Lipparini, F.
A robust, open-source implementation of the locally optimal block preconditioned conjugate gradient for large eigenvalue problems in quantum chemistry
Theor Chem Acc 142, 69 (2023)
<Abstract> <Article>
Michaelis, M.; Cupellini, L.; Mensch, C.; Perry, C. C.; Delle Piane, M. & Ciacchi, L. C.
Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints
Chem. Sci., 14, 8483-8496 (2023)
<Abstract> <Article>
Hashem, S.; Battista Alteri, G.; Cupellini, L. & Mennucci,B.
Integrated Computational Study of the Light-Activated Structure of the AppA BLUF Domain and Its Spectral Signatures
J. Phys. Chem. A 127, 23, 5065–5074 (2023)
<Abstract> <Article>
Nottoli, M.; Bondanza, M.; Mazzeo, P.; Cupellini, L.; Curutchet, C.; Loco, D.; Lagardère, L.; Piquemal, J-P.; Mennucci, B. & Filippo Lipparini
QM/AMOEBA description of properties and dynamics of embedded molecules
WIREs Computational Molecular Science, 13(6) (2023)
<Abstract> <Article>
Gauss, J.; Blaschke, S.; Burger, S.; Nottoli, T.; Lipparini, F. & Stopkowicz, S.
Cholesky decomposition of two-electron integrals in quantum-chemical calculations with perturbative or finite magnetic fields using gauge-including atomic orbitals
Molecular Physics, 121:11-12 (2023)
<Abstract> <Article>
Pedraza-González, L.; Cignoni, E.; D'Ascenzi, J.; Cupellini, L. & Mennucci, B.
How the pH Controls Photoprotection in the Light-Harvesting Complex of Mosses
J. Am. Chem. Soc. 145, 13, 7482–7494 (2023)
<Abstract> <Article>
Chenchiliyan, M.; Kübel, J.; Ooi, S. A.; Salvadori, G.; Mennucci, B.; Westenhoff, S. & Maj, M.
Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy
J. Chem. Phys. 158, 085103 (2023)
<Abstract> <Article>
Mazzeo, P.; Hashem, S.; Lipparini, F.; Cupellini, L. & Mennucci, B.
Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor
J. Phys. Chem. Lett. 14, 1222–1229 (2023)
<Abstract> <Article>
Cignoni, E.; Cupellini, L. & Mennucci, B.
Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes
J. Chem. Theory Comput. 19, 3, 965–977 (2023)
<Abstract> <Article>