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Chem. Sci., 2019, 10, 7200
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Impact of electronic polarizability on protein-functional group interactions

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Phys. Chem. Chem. Phys., 2020, 22, 6848
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Efficient and accurate density-based prediction of macromolecular polarizabilities

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Phys. Chem. Chem. Phys., 2023, 25, 2131
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Investigation of the stability of D5SIC-DNAM-incorporated DNA duplex in Taq polymerase binary system: a systematic classical MD approach

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Phys. Chem. Chem. Phys., 2024, 26, 7287
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Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

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Phys. Chem. Chem. Phys., 2020, 22, 14433
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Solvation effects drive the selectivity in Diels–Alder reaction under hyperbaric conditions

Daniele Loco, Riccardo Spezia, François Cartier, Isabelle Chataigner and Jean-Philip Piquemal

Chem. Commun., 2020, 56, 6632
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Simulating the binding of key organic functional groups to aqueous calcium carbonate species

Alicia Schuitemaker, Julie Aufort, Katarzyna B. Koziara, Raffaella Demichelis, Paolo Raiteri and Julian D. Gale

Phys. Chem. Chem. Phys., 2021, 23, 27253
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Non-covalent interactions between sertraline stereoisomers and 2-hydroxypropyl-β-cyclodextrin: a quantum chemistry analysis

Joanatan-Michael Bautista-Renedo, Erick Cuevas-Yañez, Horacio Reyes-Pérez, Rubicelia Vargas, Jorge Garza and Nelly González-Rivas

RSC Adv., 2020, 10, 20202
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Investigation of dynamical flexibility of D5SIC-DNAM inside DNA duplex in aqueous solution: a systematic classical MD approach

Tanay Debnath and G. Andrés Cisneros

Phys. Chem. Chem. Phys., 2024, 26, 7435
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Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects

Théo Jaffrelot Inizan, Thomas Plé, Olivier Adjoua, Pengyu Ren, Hatice Gökcan, Olexandr Isayev, Louis Lagardère and Jean-Philip Piquemal

Chem. Sci., 2023, 14, 5438
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DP4-AI automated NMR data analysis: straight from spectrometer to structure

Alexander Howarth, Kristaps Ermanis and Jonathan M. Goodman

Chem. Sci., 2020, 11, 4351
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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
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Computationally driven discovery of SARS-CoV-2 Mproinhibitors: from design to experimental validation

Léa El Khoury, Zhifeng Jing, Alberto Cuzzolin, Alessandro Deplano, Daniele Loco, Boris Sattarov, Florent Hédin, Sebastian Wendeborn, Chris Ho, Dina El Ahdab, Theo Jaffrelot Inizan, Mattia Sturlese, Alice Sosic, Martina Volpiana, Angela Lugato, Marco Barone, Barbara Gatto, Maria Ludovica Macchia, Massimo Bellanda, Roberto Battistutta, Cristiano Salata, Ivan Kondratov, Rustam Iminov, Andrii Khairulin, Yaroslav Mykhalonok, Anton Pochepko, Volodymyr Chashka-Ratushnyi, Iaroslava Kos, Stefano Moro, Matthieu Montes, Pengyu Ren, Jay W. Ponder, Louis Lagardère, Jean-Philip Piquemal and Davide Sabbadin

Chem. Sci., 2022, 13, 3674
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Creating water-in-salt-like environment using coordinating anions in non-concentrated aqueous electrolytes for efficient Zn batteries

Dario Gomez Vazquez, Travis P. Pollard, Julian Mars, Ji Mun Yoo, Hans-Georg Steinrück, Sharon E. Bone, Olga V. Safonova, Michael F. Toney, Oleg Borodin and Maria R. Lukatskaya

Energy Environ. Sci., 2023, 16, 1982
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Improved modeling of battery electrolytes: betting on model fitting or quantum effects?

Defne Saraç, Diego Moreno Martinez, Marie-Liesse Doublet and Christophe Raynaud

Phys. Chem. Chem. Phys., 2025, 27, 20084
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Force-field-enhanced neural network interactions: from local equivariant embedding to atom-in-molecule properties and long-range effects

Thomas Plé, Louis Lagardère and Jean-Philip Piquemal

Chem. Sci., 2023, 14, 12554
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Rational design of perylene diimide macrocycles with diverse electron transfer properties in complexes with fullerene

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An extensive assessment of the performance of pairwise and many-body interaction potentials in reproducing ab initio benchmark binding energies for water clusters n = 2–25

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Phys. Chem. Chem. Phys., 2023, 25, 7120
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Vibrational exciton delocalization precludes the use of infrared intensities as proxies for surfactant accumulation on aqueous surfaces

Kimberly A. Carter-Fenk, Kevin Carter-Fenk, Michelle E. Fiamingo, Heather C. Allen and John M. Herbert

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Design of a fluorescent and clickable Ag38(SRN3)24 nanocluster platform: synthesis, modeling and self-assembling

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Water–glycan interactions drive the SARS-CoV-2 spike dynamics: insights into glycan-gate control and camouflage mechanisms

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High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

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Electrostatic embedding machine learning for ground and excited state molecular dynamics of solvated molecules

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Digital Discovery, 2024, 3, 2560
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Investigating the properties of fatty acid-based ionic liquids: advancement in AMOEBA force field

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

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Phys. Chem. Chem. Phys., 2020, 22, 19532
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Photoinduced electron transfer in [10]CPP⊃C60 oligomers with stable and well-defined supramolecular structures

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Accurate Biomolecular Simulations Account for Electronic Polarization

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Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

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Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

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AENET–LAMMPS and AENET–TINKER: Interfaces for accurate and efficient molecular dynamics simulations with machine learning potentials

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The Journal of Chemical Physics, 2021, 155
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Velocity jump processes: An alternative to multi-timestep methods for faster and accurate molecular dynamics simulations

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The Journal of Chemical Physics, 2020, 153
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Enabling large-scale quantum path integral molecular dynamics simulations through the integration of Dcdftbmd and i-PI codes

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The Journal of Chemical Physics, 2023, 158
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Simulation of Nuclear Quantum Effects in Condensed Matter Systems via Quantum Baths

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Molecular Dynamics Using Nonvariational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation, and Application to the Bond Capacity Model

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Extended Lagrangian Born–Oppenheimer molecular dynamics: from density functional theory to charge relaxation models

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Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples

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Variational formulation of the bond capacity charge polarization model

Pier Paolo Poier

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Synergistic Integration of Physical Embedding and Machine Learning Enabling Precise and Reliable Force Field

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CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

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Molecular dynamics simulations of liquid–liquid interfaces in an electric field: The water–1,2-dichloroethane interface

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The Journal of Chemical Physics, 2020, 153
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Accurate Deep Learning-Aided Density-Free Strategy for Many-Body Dispersion-Corrected Density Functional Theory

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Improvement of the Gaussian Electrostatic Model by separate fitting of Coulomb and exchange-repulsion densities and implementation of a new dispersion term

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The Journal of Chemical Physics, 2021, 155
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Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor

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

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O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

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Quantum-Chemistry Based Design of Halobenzene Derivatives With Augmented Affinities for the HIV-1 Viral G4/C16 Base-Pair

Perla El Darazi, Léa El Khoury, Krystel El Hage, Richard G. Maroun, Zeina Hobaika, Jean-Philip Piquemal and Nohad Gresh

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Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations

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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

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Fast Conversion of Molecular Diagrams into Plausible Crystal Structures Using Graph-Based Force Fields

Didier Mathieu

AI Chemistry, 2025, 1, 2
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Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions

Shanlin Rao, Gianni Klesse, Charlotte I. Lynch, Stephen J. Tucker and Mark S. P. Sansom

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Phenol Molecular Sheets Woven by Water Cavities in Hydrophobic Slit Nanospaces

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Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications

Zhifeng Jing, Chengwen Liu, Sara Y. Cheng, Rui Qi, Brandon D. Walker, Jean-Philip Piquemal and Pengyu Ren

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Generalized Many-Body Dispersion Correction through Random-Phase Approximation for Chemically Accurate Density Functional Theory

Pier Paolo Poier, Olivier Adjoua, Louis Lagardère and Jean-Philip Piquemal

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A coherent derivation of the Ewald summation for arbitrary orders of multipoles: The self-terms

Benjamin Stamm, Louis Lagardère, Étienne Polack, Yvon Maday and Jean-Philip Piquemal

The Journal of Chemical Physics, 2018, 149
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QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential

Hatice Gökcan, Eric Kratz, Thomas A. Darden, Jean-Philip Piquemal and G. Andrés Cisneros

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Dielectric continuum methods for quantum chemistry

John M. Herbert

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Correction to “Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Nonpolarizable Simulations of Realistic Systems”

Frédéric Célerse, Louis Lagardère, Etienne Derat and Jean-Philip Piquemal

J. Chem. Theory Comput., 2021, 17, 3235
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Polarizable charges in a generalized Born reaction potential

Pier Paolo Poier and Frank Jensen

The Journal of Chemical Physics, 2020, 153
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Temperature dependent network stability in simple alcohols and pure water: The evolution of Laplace spectra

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Secondary structure analysis of peptides with relevance to iron–sulfur cluster nesting

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J Comput Chem, 2019, 40, 515
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Dividing the Periodic Box into Subdivisions with Their Surroundings to Accelerate Molecular Dynamics Simulation with High Accuracy

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Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules—Preliminary validations of a polarizable potential by ab initio quantum chemistry

Nohad Gresh and David Perahia

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Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

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Probing Interfacial Effects on Ionization Energies: The Surprising Banality of Anion–Water Hydrogen Bonding at the Air/Water Interface

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A Polarizable Forcefields for Glyoxal Acetals as Electrolyte Components for Lithium‐Ion Batteries

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Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential

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Water Nanodroplet on a Hydrocarbon “Carpet”—The Mechanism of Water Contact Angle Stabilization by Airborne Contaminations on Graphene, Au, and PTFE Surfaces

Artur P. Terzyk, Paweł Bryk, Emil Korczeniewski, Piotr Kowalczyk, Anna Zawadzka, Przemysław Płóciennik, Marek Wiśniewski and Radosław P. Wesołowski

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Overcoming Sampling Issues and Improving Computational Efficiency in Collective-Variable-Based Enhanced-Sampling Simulations: A Tutorial

Haohao Fu, Mengchen Zhou, Christophe Chipot and Wensheng Cai

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Improvements to the AMOEBA Force Field by Introducing Anisotropic Atomic Polarizability of the Water Molecule

Akshaya K. Das, Omar N. Demerdash and Teresa Head-Gordon

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

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Terahertz and dielectric spectral calculations of aqueous CaCl2 solutions using polarizable models: Intra- and inter-species contributions involving permanent and induced dipoles and ion current

Himanshu Kumar Vishwakarma, Ravi Malik and Amalendu Chandra

The Journal of Chemical Physics, 2025, 163
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations

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How Do Molecular Dynamics Data Complement Static Structural Data of GPCRs

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IJMS, 2020, 21, 5933
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Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics

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J. Phys. Chem. B, 2021, 125, 10282
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AMOEBA+ Classical Potential for Modeling Molecular Interactions

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J. Chem. Theory Comput., 2019, 15, 4122
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Modelling Lithium‐Ion Transport Properties in Sulfoxides and Sulfones with Polarizable Molecular Dynamics and NMR Spectroscopy

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Sharing Data from Molecular Simulations

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Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes

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A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

Gerhard König, Frank Pickard, Jing Huang, Walter Thiel, Alexander MacKerell, Bernard Brooks and Darrin York

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A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization

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Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials

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γ-graphynes with extended polyyne chains for efficient photoinduced electron transfer in complexes with fullerenes

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Carbon, 2023, 215, 118460
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AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms

Xiaojing Wu, Carine Clavaguera, Louis Lagardère, Jean-Philip Piquemal and Aurélien de la Lande

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Lithium‐Ion Transport Properties in DMSO and TEGDME: Exploring the Influence of Solvation through Molecular Dynamics and Experiments

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Polarizability of Pyruvate Anion in Small Water Clusters

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86 PFLOPS Deep Potential Molecular Dynamics simulation of 100 million atoms with ab initio accuracy

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Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review

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Uncovering Membrane-Bound Models of Coagulation Factors by Combined Experimental and Computational Approaches

Y. Zenmei Ohkubo and Jesper J. Madsen

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All-temperature zinc batteries with high-entropy aqueous electrolyte

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Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems

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Challenges in RNA Regulation in Huntington's Disease: Insights from Computational Studies

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Selectivity of parvalbumin B protein binding to Ca2+ and Mg2+ at anab initioQM/MM level using the reference-potential method

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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?

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How to make continuum solvation incredibly fast in a few simple steps: A practical guide to the domain decomposition paradigm for the conductor‐like screening model

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FeNNol: An efficient and flexible library for building force-field-enhanced neural network potentials

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Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators

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Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities

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

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Implicit Electronic Polarization via Charge Scaling in Amber OLx Nucleic Acid Force Fields Improves Ion Pairing without Backbone Reparametrization

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An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations

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

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Simulations of γ-Valerolactone Solvents and Electrolytes for Lithium Batteries Using Polarizable Molecular Dynamics

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Testing the self-cleaning properties of a coordination polymer surface

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Histidine 73 methylation coordinates β-actin plasticity in response to key environmental factors

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Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics

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On the convergence of multi-scale free energy simulations

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Vaccine design and development: Exploring the interface with computational biology and AI

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Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

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Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields

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Calibration of the dianionic phosphate group: Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase

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Contributions and Limitations of Biophysical Approaches to Study of the Interactions between Amphiphilic Molecules and the Plant Plasma Membrane

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Terahertz and Dielectric Spectroscopy of Aqueous MgCl2 Solutions: Self- and Cross-Correlation Contributions of Permanent and Induced Dipoles Using Polarizable Models

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Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems

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Unveiling the Full Dynamical and Reactivity Profiles of Acetylcholinesterase: A Comprehensive All-Atom Investigation

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Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins

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High‐Resolution Molecular‐Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2)

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Velocity Jumps for Molecular Dynamics

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The Q-AMOEBA (CF) Polarizable Potential

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Intermolecular interactions of the extended recognition site of VIM‐2 metallo‐β‐lactamase with 1,2,4‐triazole‐3‐thione inhibitors. Validations of a polarizable molecular mechanics potential by ab initio QC

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Current status of deMon2k for the investigation of the early stages of matter irradiation by time-dependent DFT approaches

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