Geethanjali Gopakumar, Eva Muchová, Isaak Unger, Sebastian Malerz, Florian Trinter, Gunnar Öhrwall, Filippo Lipparini, Benedetta Mennucci, Denis Céolin, Carl Caleman, Iain Wilkinson, Bernd Winter, Petr Slavíček, Uwe Hergenhahn and Olle Björneholm

Phys. Chem. Chem. Phys., 2022, 24, 8661
DOI: 10.1039/D2CP00227B

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

Shaima Hashem, Veronica Macaluso, Michele Nottoli, Filippo Lipparini, Lorenzo Cupellini and Benedetta Mennucci

Chem. Sci., 2021, 12, 13331
DOI: 10.1039/D1SC03000K

New relativistic quantum chemical methods for understanding light-induced therapeutics

Erik Donovan Hedegård and Joel Creutzberg

Dalton Trans., 2022, 51, 16055
DOI: 10.1039/D2DT02233H

Intermolecular resonance energy transfer between two lutein pigments in light-harvesting complex II studied by frenkel exciton models

Jiarui Li, Tao Zeng, Yu Zhai, Zexing Qu and Hui Li

Phys. Chem. Chem. Phys., 2023, 25, 24636
DOI: 10.1039/D3CP03092J

Continuum vs. atomistic approaches to computational spectroscopy of solvated systems

Tommaso Giovannini and Chiara Cappelli

Chem. Commun., 2023, 59, 5644
DOI: 10.1039/D2CC07079K

Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines

T. Kubař, M. Elstner and Q. Cui

Annu. Rev. Biophys., 2023, 52, 525
DOI: 10.1146/annurev-biophys-111622-091140

Grassmann Extrapolation of Density Matrices for Born–Oppenheimer Molecular Dynamics

Étienne Polack, Geneviève Dusson, Benjamin Stamm and Filippo Lipparini

J. Chem. Theory Comput., 2021, 17, 6965
DOI: 10.1021/acs.jctc.1c00751

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

Shaima Hashem, Giovanni Battista Alteri, Lorenzo Cupellini and Benedetta Mennucci

J. Phys. Chem. A, 2023, 127, 5065
DOI: 10.1021/acs.jpca.3c02385

Effects of Conformational Sampling on Computing Redox Properties Using Linear Response Approach

Suman Maity, Ronit Sarangi and Atanu Acharya

J. Phys. Chem. B, 2025, 129, 7465
DOI: 10.1021/acs.jpcb.5c01121

Computer-aided drug design, quantum-mechanical methods for biological problems

Madushanka Manathunga, Andreas W. Götz and Kenneth M. Merz

Current Opinion in Structural Biology, 2022, 75, 102417
DOI: 10.1016/j.sbi.2022.102417

QM/MM optimization with quantum coupling: Host–guest interactions in a pentacene-doped p-terphenyl crystal

Andrés I. Bertoni, Richard M. Fogarty, Cristián G. Sánchez and Andrew P. Horsfield

The Journal of Chemical Physics, 2022, 156
DOI: 10.1063/5.0079788

Polarizable Embedding Complex Polarization Propagator in Four- and Two-Component Frameworks

Joel Creutzberg and Erik. D. Hedegård

J. Chem. Theory Comput., 2022, 18, 3671
DOI: 10.1021/acs.jctc.1c01249

Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees

Maximilian Scheurer, Peter Reinholdt, Jógvan Magnus Haugaard Olsen, Andreas Dreuw and Jacob Kongsted

J. Chem. Theory Comput., 2021, 17, 3445
DOI: 10.1021/acs.jctc.1c00225

Bringing Quantum Mechanics to Coarse-Grained Soft Materials Modeling

Chun-I Wang and Nicholas E. Jackson

Chem. Mater., 2023, 35, 1470
DOI: 10.1021/acs.chemmater.2c03712

Biomolecular QM/MM Simulations: What Are Some of the “Burning Issues”?

Qiang Cui, Tanmoy Pal and Luke Xie

J. Phys. Chem. B, 2021, 125, 689
DOI: 10.1021/acs.jpcb.0c09898

State averaged CASSCF in AMOEBA polarizable water model for simulating nonadiabatic molecular dynamics with nonequilibrium solvation effects

Chenchen Song

The Journal of Chemical Physics, 2023, 158
DOI: 10.1063/5.0131689

Polarizable Embedding without Artificial Boundary Polarization

Sonata Kvedaravičiūtė, David Carrasco-Busturia, Klaus B. Møller and Jógvan Magnus Haugaard Olsen

J. Chem. Theory Comput., 2023, 19, 5122
DOI: 10.1021/acs.jctc.3c00434

General formulation of polarizable embedding models and of their coupling

Michele Nottoli and Filippo Lipparini

The Journal of Chemical Physics, 2020, 153
DOI: 10.1063/5.0035165

Explicit environmental and vibronic effects in simulations of linear and nonlinear optical spectroscopy

Sapana V. Shedge, Tim J. Zuehlsdorff, Ajay Khanna, Stacey Conley and Christine M. Isborn

The Journal of Chemical Physics, 2021, 154
DOI: 10.1063/5.0038196

Theoretical and Numerical Comparison of Quantum- and Classical Embedding Models for Optical Spectra

Marina Jansen, Peter Reinholdt, Erik D. Hedegård and Carolin König

J. Phys. Chem. A, 2023, 127, 5689
DOI: 10.1021/acs.jpca.3c02540

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

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 and Ljiljana Stojanovic

J. Chem. Theory Comput., 2022, 18, 6851
DOI: 10.1021/acs.jctc.2c00804

Accuracy of One- and Two-Photon Intensities with the Extended Polarizable Density Embedding Model

Ernst Dennis Larsson, Peter Reinholdt, Erik Donovan Hedegård and Jacob Kongsted

J. Phys. Chem. B, 2023, 127, 9905
DOI: 10.1021/acs.jpcb.3c05029

Progress and challenges in understanding of photoluminescence properties of carbon dots based on theoretical computations

Michal Langer, Markéta Paloncýová, Miroslav Medveď, Martin Pykal, Dana Nachtigallová, Baimei Shi, Adélia J.A. Aquino, Hans Lischka and Michal Otyepka

Applied Materials Today, 2021, 22, 100924
DOI: 10.1016/j.apmt.2020.100924

PhysNet meets CHARMM: A framework for routine machine learning/molecular mechanics simulations

Kaisheng Song, Silvan Käser, Kai Töpfer, Luis Itza Vazquez-Salazar and Markus Meuwly

The Journal of Chemical Physics, 2023, 159
DOI: 10.1063/5.0155992

Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment

Arpan Choudhury, Supriyo Santra and Debashree Ghosh

J. Chem. Theory Comput., 2024, 20, 4951
DOI: 10.1021/acs.jctc.4c00027

An algorithm for very high pressure molecular dynamics simulations

Marina Tesi, Roberto Cammi, Giovanni Granucci and Maurizio Persico

J Comput Chem, 2024, 45, 2848
DOI: 10.1002/jcc.27461

Induction effects on the absorption maxima of photoreceptor proteins

Jonathan R. Church, Jógvan Magnus Haugaard Olsen and Igor Schapiro

BIOPHYSICS, 2023, 20, n/a
DOI: 10.2142/biophysico.bppb-v20.s007

Excitation Energies of Embedded Chromophores from Frozen-Density Embedding Theory Using State-Specific Electron Densities of the Environment

Mingxue Fu and Tomasz A. Wesolowski

J. Phys. Chem. A, 2023, 127, 535
DOI: 10.1021/acs.jpca.2c07747

Fast Approximate but Accurate QM/MM Interactions for Polarizable Embedding

Peter Reinholdt, Jacob Kongsted and Filippo Lipparini

J. Chem. Theory Comput., 2022, 18, 344
DOI: 10.1021/acs.jctc.1c01037

Importance of Polarizable Embedding for Computing Optical Rotation: The Case of Camphor in Ethanol

Michele Nottoli, Edoardo Vanich, Lorenzo Cupellini, Giovanni Scalmani, Chiara Pelosi and Filippo Lipparini

J. Phys. Chem. Lett., 2024, 15, 7992
DOI: 10.1021/acs.jpclett.4c01550

Accounting for Vibronic Features through a Mixed Quantum-Classical Scheme: Structure, Dynamics, and Absorption Spectra of a Perylene Diimide Dye in Solution

Alekos Segalina, Javier Cerezo, Giacomo Prampolini, Fabrizio Santoro and Mariachiara Pastore

J. Chem. Theory Comput., 2020, 16, 7061
DOI: 10.1021/acs.jctc.0c00919

UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA

Sara Gómez, Piero Lafiosca, Franco Egidi, Tommaso Giovannini and Chiara Cappelli

J. Chem. Inf. Model., 2023, 63, 1208
DOI: 10.1021/acs.jcim.2c01495

LVC/MM: A Hybrid Linear Vibronic Coupling/Molecular Mechanics Model with Distributed Multipole-Based Electrostatic Embedding for Highly Efficient Surface Hopping Dynamics in Solution

Severin Polonius, Oleksandra Zhuravel, Brigitta Bachmair and Sebastian Mai

J. Chem. Theory Comput., 2023, 19, 7171
DOI: 10.1021/acs.jctc.3c00805

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

Piermarco Saraceno, Vladislav Sláma and Lorenzo Cupellini

The Journal of Chemical Physics, 2023, 159
DOI: 10.1063/5.0170295

A Subsystem Perspective on Vibrational Coupled Cluster Response Theory

Lars Henrik Olsen, Carolin König and Ove Christiansen

J. Phys. Chem. A, 2025, 129, 8699
DOI: 10.1021/acs.jpca.5c03752

A Polarizable CASSCF/MM Approach Using the Interface Between OpenMMPol Library and Cfour

Tommaso Nottoli, Mattia Bondanza, Filippo Lipparini and Benedetta Mennucci

J Comput Chem, 2025, 46
DOI: 10.1002/jcc.27550

Exact Two-Component Relativistic Polarizable Density Embedding

Ernst Dennis Larsson, Peter Reinholdt, Jacob Kongsted and Erik Donovan Hedegård

J. Chem. Theory Comput., 2025, 21, 4447
DOI: 10.1021/acs.jctc.5c00014

Insight into the isomerization mechanism of retinal proteins from hybrid quantum mechanics/molecular mechanics simulations

Saumik Sen, Rajiv K. Kar, Veniamin A. Borin and Igor Schapiro

WIREs Comput Mol Sci, 2022, 12
DOI: 10.1002/wcms.1562

Fluorescent Rhodopsins: A Challenging Test for Cost-Effective QM/MM Approaches

Duccio Di Prima, Laura Pedraza-González, Peter Reinholdt, Jacob Kongsted and Benedetta Mennucci

J. Phys. Chem. A, 2025, 129, 1769
DOI: 10.1021/acs.jpca.4c07733

Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP

Jorge Nochebuena, Andrew C. Simmonett and G. Andrés Cisneros

The Journal of Chemical Physics, 2024, 160
DOI: 10.1063/5.0200722

Hybrid QM/classical models: Methodological advances and new applications

Filippo Lipparini and Benedetta Mennucci

Chemical Physics Reviews, 2021, 2
DOI: 10.1063/5.0064075

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

Michele Nottoli, Mattia Bondanza, Filippo Lipparini and Benedetta Mennucci

The Journal of Chemical Physics, 2021, 154
DOI: 10.1063/5.0046844

A Many-Body, Fully Polarizable Approach to QM/MM Simulations

Eleftherios Lambros, Filippo Lipparini, Gerardo Andrés Cisneros and Francesco Paesani

J. Chem. Theory Comput., 2020, 16, 7462
DOI: 10.1021/acs.jctc.0c00932

UniversalQM/MMapproaches for general nanoscale applications

Katja‐Sophia Csizi and Markus Reiher

WIREs Comput Mol Sci, 2023, 13
DOI: 10.1002/wcms.1656

First-Principles Calculations of Excited-State Decay Rate Constants in Organic Fluorophores

Mariana T. do Casal, Koen Veys, Manon H. E. Bousquet, Daniel Escudero and Denis Jacquemin

J. Phys. Chem. A, 2023, 127, 10033
DOI: 10.1021/acs.jpca.3c06191

Decoherence and vibrational energy relaxation of the electronically excited PtPOP complex in solution

Benedikt O. Birgisson, Asmus Ougaard Dohn, Hannes Jónsson and Gianluca Levi

The Journal of Chemical Physics, 2025, 162
DOI: 10.1063/5.0241573

Improving the Efficiency of Electrostatic Embedding Using the Fast Multipole Method

Pauline Colinet, Frank Neese and Benjamin Helmich‐Paris

J Comput Chem, 2025, 46
DOI: 10.1002/jcc.27532

A quantum chemical perspective of photoactivated biological functions

Benedetta Mennucci

Pure and Applied Chemistry, 2025
DOI: 10.1515/pac-2025-0517

Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins

Vyshnavi Vennelakanti, Azadeh Nazemi, Rimsha Mehmood, Adam H. Steeves and Heather J. Kulik

Current Opinion in Structural Biology, 2022, 72, 9
DOI: 10.1016/j.sbi.2021.07.004

Vibronic and Environmental Effects in Simulations of Optical Spectroscopy

Tim J. Zuehlsdorff, Sapana V. Shedge, Shao-Yu Lu, Hanbo Hong, Vincent P. Aguirre, Liang Shi and Christine M. Isborn

Annu. Rev. Phys. Chem., 2021, 72, 165
DOI: 10.1146/annurev-physchem-090419-051350

MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations

Gustavo Cárdenas, Jesús Lucia‐Tamudo, Henar Mateo‐delaFuente, Vito F. Palmisano, Nuria Anguita‐Ortiz, Lorena Ruano, Álvaro Pérez‐Barcia, Sergio Díaz‐Tendero, Marcos Mandado and Juan J. Nogueira

J Comput Chem, 2023, 44, 516
DOI: 10.1002/jcc.27018

Unraveling Water Solvation Effects with Quantum Mechanics/Molecular Mechanics Semiclassical Vibrational Spectroscopy: The Case of Thymidine

Davide Moscato, Giacomo Mandelli, Mattia Bondanza, Filippo Lipparini, Riccardo Conte, Benedetta Mennucci and Michele Ceotto

J. Am. Chem. Soc., 2024, 146, 8179
DOI: 10.1021/jacs.3c12700

Multistate, Polarizable QM/MM Embedding Scheme Based on the Direct Reaction Field Method: Solvatochromic Shifts, Analytical Gradients and Optimizations of Conical Intersections in Solution

Alexander Humeniuk and William J. Glover

J. Chem. Theory Comput., 2024, 20, 2111
DOI: 10.1021/acs.jctc.3c01018

Alchemical Free-Energy Calculations at Quantum-Chemical Precision

Radek Crha, Peter Poliak, Michael Gillhofer and Chris Oostenbrink

J. Phys. Chem. Lett., 2025, 16, 863
DOI: 10.1021/acs.jpclett.4c03213

Δ-Machine Learning of Polarizability Tensors Using a Dipole Interaction Model

Imran Chaudhry, Mark J. Bronson and Lasse Jensen

J. Chem. Theory Comput., 2025, 21, 7040
DOI: 10.1021/acs.jctc.5c00752

Evaluation of molecular photophysical and photochemical properties using linear response time-dependent density functional theory with classical embedding: Successes and challenges

WanZhen Liang, Zheng Pei, Yuezhi Mao and Yihan Shao

The Journal of Chemical Physics, 2022, 156
DOI: 10.1063/5.0088271

SparcleQC: Automated Input File Creation for QM/MM Studies of Protein:Ligand Complexes

Caroline S. Glick, Isabel P. Berry and C. David Sherrill

J. Chem. Inf. Model., 2025, 65, 6433
DOI: 10.1021/acs.jcim.5c00617

BuRNN: Buffer Region Neural Network Approach for Polarizable-Embedding Neural Network/Molecular Mechanics Simulations

Bettina Lier, Peter Poliak, Philipp Marquetand, Julia Westermayr and Chris Oostenbrink

J. Phys. Chem. Lett., 2022, 13, 3812
DOI: 10.1021/acs.jpclett.2c00654

Modeling UV/Vis Absorption Spectra of Food Colorants in Solution: Anthocyanins and Curcumin as Case Studies

Sara Gómez, Piero Lafiosca and Tommaso Giovannini

Molecules, 2024, 29, 4378
DOI: 10.3390/molecules29184378

Structural determinants for red‐shifted absorption in higher‐plants Photosystem I

Stefano Capaldi, Zeno Guardini, Daniele Montepietra, Vittorio Flavio Pagliuca, Antonello Amelii, Elena Betti, Chris John, Laura Pedraza‐González, Lorenzo Cupellini, Benedetta Mennucci, Diane Marie Valerie Bonnet, Antonio Chaves‐Sanjuan, Luca Dall'Osto and Roberto Bassi

New Phytologist, 2025
DOI: 10.1111/nph.70562

Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms

Alexander Zlobin, Julia Belyaeva and Andrey Golovin

J. Chem. Inf. Model., 2023, 63, 546
DOI: 10.1021/acs.jcim.2c01071

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

Andrey V. Solov’yov, Alexey V. Verkhovtsev, Nigel J. Mason, Richard A. Amos, Ilko Bald, Gérard Baldacchino, Brendan Dromey, Martin Falk, Juraj Fedor, Luca Gerhards, Michael Hausmann, Georg Hildenbrand, Miloš Hrabovský, Stanislav Kadlec, Jaroslav Kočišek, Franck Lépine, Siyi Ming, Andrew Nisbet, Kate Ricketts, Leo Sala, Thomas Schlathölter, Andrew E. H. Wheatley and Ilia A. Solov’yov

Chem. Rev., 2024, 124, 8014
DOI: 10.1021/acs.chemrev.3c00902

Quantum dynamics of dissipative polarizable media

Frank Ernesto Quintela Rodriguez, Piero Lafiosca, Tommaso Giovannini and Chiara Cappelli

Phys. Rev. B, 2025, 111
DOI: 10.1103/nxs1-rhqx

Quantifying the Long‐Range Coupling of Electronic Properties in Proteins with ab initio Molecular Dynamics**

Zhongyue Yang, Natalia Hajlasz, Adam H. Steeves and Heather J. Kulik

Chemistry Methods, 2021, 1, 362
DOI: 10.1002/cmtd.202100012

Spectral Signatures of Canthaxanthin Translocation in the Orange Carotenoid Protein

Natalia B. Pigni, Kevin L. Clark, Warren F. Beck and José A. Gascón

J. Phys. Chem. B, 2020, 124, 11387
DOI: 10.1021/acs.jpcb.0c08756

How Accurate Are QM/MM Models?

Junming Ho, Haibo Yu, Yihan Shao, Mackenzie Taylor and Junbo Chen

J. Phys. Chem. A, 2025, 129, 1517
DOI: 10.1021/acs.jpca.4c06521

Protein-Driven Electron-Transfer Process in a Fatty Acid Photodecarboxylase

Giacomo Londi, Giacomo Salvadori, Patrizia Mazzeo, Lorenzo Cupellini and Benedetta Mennucci

JACS Au, 2025, 5, 158
DOI: 10.1021/jacsau.4c00853

Predicting Solvatochromism of Chromophores in Proteins through QM/MM and Machine Learning

Amanda Arcidiacono, Edoardo Cignoni, Patrizia Mazzeo, Lorenzo Cupellini and Benedetta Mennucci

J. Phys. Chem. A, 2024, 128, 3646
DOI: 10.1021/acs.jpca.4c00249

The ΔSCF method for non-adiabatic dynamics of systems in the liquid phase

Eva Vandaele, Momir Mališ and Sandra Luber

The Journal of Chemical Physics, 2022, 156
DOI: 10.1063/5.0083340

Designing drugs when there is low data availability: one-shot learning and other approaches to face the issues of a long-term concern

Gabriel C. Veríssimo, Mateus Sá M. Serafim, Thales Kronenberger, Rafaela S. Ferreira, Kathia M. Honorio and Vinícius G. Maltarollo

Expert Opinion on Drug Discovery, 2022, 17, 929
DOI: 10.1080/17460441.2022.2114451

Static versus dynamically polarizable environments within the many-body GW formalism

David Amblard, Xavier Blase and Ivan Duchemin

The Journal of Chemical Physics, 2024, 160
DOI: 10.1063/5.0203637

Multiple Facets of Modeling Electronic Absorption Spectra of Systems in Solution

Sara Gómez, Tommaso Giovannini and Chiara Cappelli

ACS Phys. Chem Au, 2023, 3, 1
DOI: 10.1021/acsphyschemau.2c00050

Polarizable Continuum Models and Green’s Function GW Formalism: On the Dynamics of the Solvent Electrons

Ivan Duchemin, David Amblard and Xavier Blase

J. Chem. Theory Comput., 2024, 20, 9072
DOI: 10.1021/acs.jctc.4c00745

Automatic Rhodopsin Modeling with Multiple Protonation Microstates

Gustavo Cárdenas, Vincent Ledentu, Miquel Huix-Rotllant, Massimo Olivucci and Nicolas Ferré

J. Phys. Chem. A, 2023, 127, 9365
DOI: 10.1021/acs.jpca.3c05413

Local-Field Effects in Linear Response Properties within a Polarizable Frozen Density Embedding Method

Aparna K. Harshan, Mark J. Bronson and Lasse Jensen

J. Chem. Theory Comput., 2022, 18, 380
DOI: 10.1021/acs.jctc.1c00816

Quantum Mechanics/Fluctuating Charge Protocol to Compute Solvatochromic Shifts

Matteo Ambrosetti, Sulejman Skoko, Tommaso Giovannini and Chiara Cappelli

J. Chem. Theory Comput., 2021, 17, 7146
DOI: 10.1021/acs.jctc.1c00763

Polarizable MD and QM/MM investigation of acrylamide-based leads to target the main protease of SARS-CoV-2

Jorge Nochebuena and G. Andrés Cisneros

The Journal of Chemical Physics, 2022, 157
DOI: 10.1063/5.0123698

Reproducibility of QM/MM Calculations for the SARS-CoV-2 Main Protease

Xiaoli Sun and Ulf Ryde

J. Chem. Theory Comput., 2025, 21, 7711
DOI: 10.1021/acs.jctc.5c00841

Embedding Beyond Electrostatics: The Extended Polarizable Density Embedding Model

Willem Van den Heuvel, Peter Reinholdt and Jacob Kongsted

J. Phys. Chem. B, 2023, 127, 3248
DOI: 10.1021/acs.jpcb.2c08721

Electrostatically embedded symmetry-adapted perturbation theory

Caroline S. Glick, Asem Alenaizan, Daniel L. Cheney, Chapin E. Cavender and C. David Sherrill

The Journal of Chemical Physics, 2024, 161
DOI: 10.1063/5.0221974

Massively parallel fragment-based quantum chemistry for large molecular systems: the serestipy software

Patrick Eschenbach, Niklas Niemeyer and Johannes Neugebauer

Can. J. Chem., 2023, 101, 641
DOI: 10.1139/cjc-2022-0243

The OpenMMPol library for polarizable QM/MM calculations of properties and dynamics

Mattia Bondanza, Tommaso Nottoli, Michele Nottoli, Lorenzo Cupellini, Filippo Lipparini and Benedetta Mennucci

The Journal of Chemical Physics, 2024, 160
DOI: 10.1063/5.0198251

How Can We Predict Accurate Electrochromic Shifts for Biochromophores? A Case Study on the Photosynthetic Reaction Center

Abhishek Sirohiwal, Frank Neese and Dimitrios A. Pantazis

J. Chem. Theory Comput., 2021, 17, 1858
DOI: 10.1021/acs.jctc.0c01152

Assessing the quality of QM/MM approaches to describe vacuo-to-water solvatochromic shifts

Luca Nicoli, Tommaso Giovannini and Chiara Cappelli

The Journal of Chemical Physics, 2022, 157
DOI: 10.1063/5.0118664

Solvent Effects on Nonadiabatic Dynamics: Ab Initio Multiple Spawning Propagated on CASPT2/xTB Potentials

Davide Avagliano

J. Chem. Theory Comput., 2025, 21, 1905
DOI: 10.1021/acs.jctc.4c01715

Understanding the complete bioluminescence cycle from a multiscale computational perspective: A review

Ya-Jun Liu

Journal of Photochemistry and Photobiology C: Photochemistry Reviews, 2022, 52, 100537
DOI: 10.1016/j.jphotochemrev.2022.100537

Simulating Ionized States in Realistic Chemical Environments with Algebraic Diagrammatic Construction Theory and Polarizable Embedding

James D. Serna and Alexander Yu. Sokolov

J. Phys. Chem. A, 2025, 129, 1156
DOI: 10.1021/acs.jpca.4c07742

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

Michele Nottoli, Riccardo Nifosì, Benedetta Mennucci and Filippo Lipparini

J. Chem. Theory Comput., 2021, 17, 5661
DOI: 10.1021/acs.jctc.1c00555

A Vision for the Future of Multiscale Modeling

Matteo Capone, Marco Romanelli, Davide Castaldo, Giovanni Parolin, Alessandro Bello, Gabriel Gil and Mirko Vanzan

ACS Phys. Chem Au, 2024, 4, 202
DOI: 10.1021/acsphyschemau.3c00080

Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex

Lorenzo Cupellini, Pu Qian, Tu C. Nguyen-Phan, Alastair T. Gardiner and Richard J. Cogdell

Photosynth Res, 2023, 156, 75
DOI: 10.1007/s11120-022-00925-8

Explicit Modelling of Spectral Bandshapes by a Mixed Quantum‐Classical Approach: Solvent Order and Temperature Effects in the Optical Spectra of Distyrylbenzene

Javier Cerezo, Johannes Gierschner, Fabrizio Santoro and Giacomo Prampolini

ChemPhysChem, 2024, 25
DOI: 10.1002/cphc.202400307

Recent progress in atomistic modeling of light-harvesting complexes: a mini review

Sayan Maity and Ulrich Kleinekathöfer

Photosynth Res, 2023, 156, 147
DOI: 10.1007/s11120-022-00969-w

Importance of Polarizable Embedding for Absorption Spectrum Calculations of Arabidopsis thaliana Cryptochrome 1

Anders Frederiksen, Luca Gerhards, Peter Reinholdt, Jacob Kongsted and Ilia A. Solov’yov

J. Phys. Chem. B, 2024, 128, 6283
DOI: 10.1021/acs.jpcb.4c02168

Contribution of the Molecular Fluorophore IPCA to Excitation-Independent Photoluminescence of Carbon Dots

Michal Langer, Tomáš Hrivnák, Miroslav Medved’ and Michal Otyepka

J. Phys. Chem. C, 2021, 125, 12140
DOI: 10.1021/acs.jpcc.1c02243

The Influence of Electronic Polarization on Nonlinear Optical Spectroscopy

Shao-Yu Lu, Tim J. Zuehlsdorff, Hanbo Hong, Vincent P. Aguirre, Christine M. Isborn and Liang Shi

J. Phys. Chem. B, 2021, 125, 12214
DOI: 10.1021/acs.jpcb.1c05914

QM/AMOEBA description of properties and dynamics of embedded molecules

Michele Nottoli, Mattia Bondanza, Patrizia Mazzeo, Lorenzo Cupellini, Carles Curutchet, Daniele Loco, Louis Lagardère, Jean‐Philip Piquemal, Benedetta Mennucci and Filippo Lipparini

WIREs Comput Mol Sci, 2023, 13
DOI: 10.1002/wcms.1674

Towards a cost-effective modeling of fluorescence in the condensed phase

Sulejman Skoko, Cosimo Micheletti, Emanuele Grifoni, Franco Egidi, Tommaso Giovannini, Andrea Pucci and Chiara Cappelli

Dyes and Pigments, 2023, 215, 111227
DOI: 10.1016/j.dyepig.2023.111227

Reconciling TD‐DFT and CASPT2 electronic structure methods for describing the photophysics of DNA

Vishal Kumar Jaiswal, Mario Taddei, Daniel R. Nascimento, Marco Garavelli, Irene Conti and Artur Nenov

Photochem & Photobiology, 2024, 100, 443
DOI: 10.1111/php.13922

Trajectory Surface Hopping for a Polarizable Embedding QM/MM Formulation

Mattia Bondanza, Baptiste Demoulin, Filippo Lipparini, Mario Barbatti and Benedetta Mennucci

J. Phys. Chem. A, 2022, 126, 6780
DOI: 10.1021/acs.jpca.2c04756

Nuclear Magnetic Shielding Constants with the Polarizable Density Embedding Model

Frederik Kamper Jørgensen, Peter Reinholdt, Erik Donovan Hedegård and Jacob Kongsted

J. Chem. Theory Comput., 2022, 18, 7384
DOI: 10.1021/acs.jctc.2c00829

Multiscale Models for Light-Driven Processes

Michele Nottoli, Lorenzo Cupellini, Filippo Lipparini, Giovanni Granucci and Benedetta Mennucci

Annu. Rev. Phys. Chem., 2021, 72, 489
DOI: 10.1146/annurev-physchem-090419-104031

Insights into the stability of engineered mini-proteins from their dynamic electronic properties

Adam H Steeves and Heather J Kulik

Electron. Struct., 2022, 4, 034005
DOI: 10.1088/2516-1075/ac8c73

Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach

Juan S. Grassano, Ignacio Pickering, Adrian E. Roitberg, Mariano C. González Lebrero, Dario A. Estrin and Jonathan A. Semelak

J. Chem. Inf. Model., 2024, 64, 4047
DOI: 10.1021/acs.jcim.4c00478

A fast method for electronic couplings in embedded multichromophoric systems

Edoardo Cignoni, Lorenzo Cupellini and Benedetta Mennucci

J. Phys.: Condens. Matter, 2022, 34, 304004
DOI: 10.1088/1361-648X/ac6f3c

Towards Quantum-Chemical Modeling of the Activity of Anesthetic Compounds

Janusz Cukras and Joanna Sadlej

IJMS, 2021, 22, 9272
DOI: 10.3390/ijms22179272

Color Tuning in Bovine Rhodopsin through Polarizable Embedding

Duccio Di Prima, Peter Reinholdt and Jacob Kongsted

J. Phys. Chem. B, 2024, 128, 2864
DOI: 10.1021/acs.jpcb.3c07891

Modeling Raman Spectra in Complex Environments: From Solutions to Surface-Enhanced Raman Scattering

Tommaso Giovannini, Sara Gómez and Chiara Cappelli

J. Phys. Chem. Lett., 2025, 16, 3106
DOI: 10.1021/acs.jpclett.4c03591

Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes

Edoardo Cignoni, Lorenzo Cupellini and Benedetta Mennucci

J. Chem. Theory Comput., 2023, 19, 965
DOI: 10.1021/acs.jctc.2c01044

MiMiC: A high-performance framework for multiscale molecular dynamics simulations

Andrej Antalík, Andrea Levy, Sonata Kvedaravičiūtė, Sophia K. Johnson, David Carrasco-Busturia, Bharath Raghavan, François Mouvet, Angela Acocella, Sambit Das, Vikram Gavini, Davide Mandelli, Emiliano Ippoliti, Simone Meloni, Paolo Carloni, Ursula Rothlisberger and Jógvan Magnus Haugaard Olsen

The Journal of Chemical Physics, 2024, 161
DOI: 10.1063/5.0211053

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

Edoardo Cignoni, Vladislav Slama, Lorenzo Cupellini and Benedetta Mennucci

The Journal of Chemical Physics, 2022, 156
DOI: 10.1063/5.0086275

A Polarizable QM/MM Model That Combines the State-Averaged CASSCF and AMOEBA Force Field for Photoreactions in Proteins

Chenchen Song and Lee-Ping Wang

J. Chem. Theory Comput., 2024, 20, 6632
DOI: 10.1021/acs.jctc.4c00623

Machine learning accelerated photodynamics simulations

Jingbai Li and Steven A. Lopez

Chemical Physics Reviews, 2023, 4
DOI: 10.1063/5.0159247

OpenMM–MiMiC Interface for Efficient and Flexible Multiscale Simulations

Andrea Levy, Andrej Antalík, Jógvan Magnus Haugaard Olsen and Ursula Rothlisberger

J. Chem. Inf. Model., 2025, 65, 6874
DOI: 10.1021/acs.jcim.5c00415

Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials

Jorge Nochebuena, Sehr Naseem‐Khan and G. Andrés Cisneros

WIREs Comput Mol Sci, 2021, 11
DOI: 10.1002/wcms.1515

The Seamless Connection of Local and Collective Excited States in Subsystem Time-Dependent Density Functional Theory

Johannes Tölle and Johannes Neugebauer

J. Phys. Chem. Lett., 2022, 13, 1003
DOI: 10.1021/acs.jpclett.1c04023

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

Patrizia Mazzeo, Shaima Hashem, Filippo Lipparini, Lorenzo Cupellini and Benedetta Mennucci

J. Phys. Chem. Lett., 2023, 14, 1222
DOI: 10.1021/acs.jpclett.2c03797

Insights into Energy Transfer in Light-Harvesting Complex II Through Machine-Learning Assisted Simulations

Elena Betti, Piermarco Saraceno, Edoardo Cignoni, Lorenzo Cupellini and Benedetta Mennucci

J. Phys. Chem. B, 2024, 128, 5188
DOI: 10.1021/acs.jpcb.4c01494

Combined Multireference–Multiscale Approach to the Description of Photosynthetic Reaction Centers

Maria Drosou, Sinjini Bhattacharjee and Dimitrios A. Pantazis

J. Chem. Theory Comput., 2024
DOI: 10.1021/acs.jctc.4c00578

Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine‐Cytosine in Chloroform

James A. Green, Sandra Gómez, Graham Worth, Fabrizio Santoro and Roberto Improta

Chemistry A European J, 2022, 28
DOI: 10.1002/chem.202201731

Impact of Fluctuations in the Peridinin-Chlorophyll a-Protein on the Energy Transfer: Insights from Classical and QM/MM Molecular Dynamics Simulations

Monja Sokolov and Qiang Cui

Biochemistry, 2025, 64, 879
DOI: 10.1021/acs.biochem.4c00568

The quantum revolution in enzymatic chemistry: combining quantum and classical mechanics to understand biochemical processes

Kirill Zinovjev, J. Javier Ruiz-Pernía and Iñaki Tuñón

Pure and Applied Chemistry, 2025
DOI: 10.1515/pac-2025-0500

Importance of Lattice Constants in QM/MM Calculations on Metal–Organic Frameworks

Bo Yang, Xin-Ping Wu, Laura Gagliardi and Donald G. Truhlar

J. Phys. Chem. B, 2021, 125, 5786
DOI: 10.1021/acs.jpcb.1c02328

Taming the third order cumulant approximation to linear optical spectroscopy

Lucas Allan and Tim J. Zuehlsdorff

The Journal of Chemical Physics, 2024, 160
DOI: 10.1063/5.0182745

Raman, surface‐enhanced Raman and density functional theory analyses of poorly soluble pharmaceuticals in water

Giacomo D'Arcangelo, Stefano Legnaioli, Filippo Lipparini and Beatrice Campanella

Microchemical Journal, 2024, 202, 110767
DOI: 10.1016/j.microc.2024.110767

Deciphering the Luminescence Spectral Shape of an Oxyluciferin Analogue through a Mixed Quantum-Classical Approach

Houda Moumene, Giacomo Prampolini, Cristina García-Iriepa, Javier Cerezo, Isabelle Navizet and Fabrizio Santoro

J. Phys. Chem. B, 2025, 129, 2829
DOI: 10.1021/acs.jpcb.4c06683

Computational Spectroscopy of Aqueous Solutions: The Underlying Role of Conformational Sampling

Chiara Sepali, Sara Gómez, Emanuele Grifoni, Tommaso Giovannini and Chiara Cappelli

J. Phys. Chem. B, 2024, 128, 5083
DOI: 10.1021/acs.jpcb.4c01443

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

Vladislav Sláma, Lorenzo Cupellini, Vincenzo Mascoli, Nicoletta Liguori, Roberta Croce and Benedetta Mennucci

J. Phys. Chem. Lett., 2023, 14, 8345
DOI: 10.1021/acs.jpclett.3c02091

Automated Molecular Cluster Growing for Explicit Solvation by Efficient Force Field and Tight Binding Methods

Sebastian Spicher, Christoph Plett, Philipp Pracht, Andreas Hansen and Stefan Grimme

J. Chem. Theory Comput., 2022, 18, 3174
DOI: 10.1021/acs.jctc.2c00239

Conical Intersections in Solution with Polarizable Embedding: Integral-Exact Direct Reaction Field

Xiao Liu, Alexander Humeniuk and William J. Glover

J. Chem. Theory Comput., 2022, 18, 6826
DOI: 10.1021/acs.jctc.2c00662

State-averaged CASSCF with polarizable continuum model for studying photoreactions in solvents: Energies, analytical nuclear gradients, and non-adiabatic couplings

Chenchen Song

The Journal of Chemical Physics, 2022, 156
DOI: 10.1063/5.0085855

Efficient Polarizable QM/MM Using the Direct Reaction Field Hamiltonian with Electrostatic Potential Fitted Multipole Operators

Thomas P. Fay, Nicolas Ferré and Miquel Huix-Rotllant

J. Chem. Theory Comput., 2025, 21, 183
DOI: 10.1021/acs.jctc.4c01219

Analytic Gradients and Periodic Boundary Conditions for Direct Reaction Field Polarizable QM/MM with Electrostatic Potential Fitting

Thomas P. Fay, Miquel Huix-Rotllant and Nicolas Ferré

J. Chem. Theory Comput., 2025
DOI: 10.1021/acs.jctc.5c00863

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

Veronica Macaluso, Shaima Hashem, Michele Nottoli, Filippo Lipparini, Lorenzo Cupellini and Benedetta Mennucci

J. Phys. Chem. B, 2021, 125, 10282
DOI: 10.1021/acs.jpcb.1c05753

The development of the QM/MM interface and its application for the on-the-fly QM/MM nonadiabatic dynamics in JADE package: Theory, implementation, and applications

Haiyi Huang, Jiawei Peng, Yulin Zhang, Feng Long Gu, Zhenggang Lan and Chao Xu

The Journal of Chemical Physics, 2024, 160
DOI: 10.1063/5.0215036

A ΔSCF model for excited states within a polarisable embedding

Michele Nottoli, Patrizia Mazzeo, Filippo Lipparini, Lorenzo Cupellini and Benedetta Mennucci

Molecular Physics, 2023, 121
DOI: 10.1080/00268976.2022.2089605

Improved Description of Environment and Vibronic Effects with Electrostatically Embedded ML Potentials

Kirill Zinovjev and Carles Curutchet

J. Phys. Chem. Lett., 2025, 16, 774
DOI: 10.1021/acs.jpclett.4c02949

Exciton transport in molecular organic semiconductors boosted by transient quantum delocalization

Samuele Giannini, Wei-Tao Peng, Lorenzo Cupellini, Daniele Padula, Antoine Carof and Jochen Blumberger

Nat Commun, 2022, 13
DOI: 10.1038/s41467-022-30308-5

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

Felipe Cardoso Ramos, Lorenzo Cupellini and Benedetta Mennucci

J. Phys. Chem. B, 2021, 125, 1768
DOI: 10.1021/acs.jpcb.0c10834

Quantum mechanical/molecular mechanical studies of photophysical properties of fluorescent proteins

Maria Rossano‐Tapia and Alex Brown

WIREs Comput Mol Sci, 2022, 12
DOI: 10.1002/wcms.1557

Structural dynamics and computational design of synthetic enzymes

Valerie Vaissier Welborn

Chem Catalysis, 2022, 2, 19
DOI: 10.1016/j.checat.2021.10.009