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Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: from Force Fields to Machine Learning Potentials
Thomas Plé
,
Nastasia Mauger
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Olivier Adjoua
,
Théo Jaffrelot Inizan
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Louis Lagardère
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Journal articles
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ANKH: A Generalized O(N) Interpolated Ewald Strategy for Molecular Dynamics Simulations
Igor Chollet
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Louis Lagardère
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Jean-Philip Piquemal
Journal articles
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Generalized Many-Body Dispersion Correction through Random-phase Approximation for Chemically Accurate Density Functional Theory
Pier Paolo Poier
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Olivier Adjoua
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Louis Lagardère
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Jean-Philip Piquemal
Journal articles
hal-03819436v1
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Scalable Hybrid Deep Neural Networks/Polarizable Potentials Biomolecular Simulations including Long-range Effects
Théo Jaffrelot-Inizan
,
Thomas Plé
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Olivier Adjoua
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Pengyu Ren
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Hatice Gökcan
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Journal articles
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Extension of the Trotterized Unitary Coupled Cluster to Triple Excitations
Mohammad Haidar
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Marko Rančić
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Yvon Maday
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Jean-Philip Piquemal
Journal articles
hal-03912869v1
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Open Source Variational Quantum Eigensolver Extension of the Quantum Learning Machine (QLM) for Quantum Chemistry
Mohammad Haidar
,
Marko J. Rančić
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Thomas Ayral
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Yvon Maday
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Jean-Philip Piquemal
et al.
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2023, pp.e1664. ⟨10.1002/wcms.1664⟩
Journal articles
hal-03698549v1
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QM / AMOEBA description of properties and dynamics of embedded molecules
Michele Nottoli
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Mattia Bondanza
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Patrizia Mazzeo
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Lorenzo Cupellini
,
Carles Curutchet
et al.
Journal articles
hal-04122813v1
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Calculating the ground state energy of benzene under spatial deformations with noisy quantum computing
Wassil Sennane
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Jean-Philip Piquemal
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Marko J. Rančić
Journal articles
hal-03608627v1
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Accurate Deep Learning-aided Density-free Strategy for Many-Body Dispersion-corrected Density Functional Theory
Pier Paolo Poier
,
Théo Jaffrelot Inizan
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Olivier Adjoua
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Louis Lagardère
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Jean-Philip Piquemal
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Journal articles
hal-03624156v1
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Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators
Krystel El Hage
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Giovanni Ribaudo
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Louis Lagardère
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Alberto Ongaro
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Philippe H. Kahn
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Journal articles
hal-03624169v1
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An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems.
F. Célerse
,
T. Jaffrelot Inizan
,
L. Lagardère
,
O. Adjoua
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P. Monmarché
et al.
Journal articles
hal-03360596v1
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On the Quantum Chemical Nature of Lead(II) "Lone Pair"
Christophe Gourlaouen
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Jean-Philip Piquemal
Journal articles
hal-03232340v1
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Improving Condensed Phase Water Dynamics with Explicit Nuclear Quantum Effects: the Polarizable Q-AMOEBA Force Field
Nastasia Mauger
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Thomas Plé
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Louis Lagardère
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Simon Huppert
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Jean-Philip Piquemal
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Journal articles
hal-03706599v1
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Computationally driven discovery of targeting SARS-CoV-2 Mpro inhibitors: from design to experimental validation
Léa El Khoury
,
Zhifeng Jing
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Daniele Loco
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Alberto Cuzzolin
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Alessandro Deplano
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Journal articles
hal-03361062v1
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Development of the Quantum Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed Phase Molecular Dynamics Simulations.
S. Naseem Kahn
,
L. Lagardère
,
C. Narth
,
G. A. Cisneros
,
P. Ren
et al.
Journal articles
hal-03508892v1
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Efficient and Accurate Description of Diels‐Alder Reactions Using Density Functional Theory
Daniele Loco
,
Isabelle Chataigner
,
Jean-Philip Piquemal
,
Riccardo Spezia
Journal articles
hal-03806627v1
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O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems
Pier Paolo Poier
,
Louis Lagardère
,
Jean-Philip Piquemal
Journal articles
hal-03501135v1
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Nuclear Quantum Effects in liquid water at near classical computational cost using the adaptive Quantum Thermal Bath
Nastasia Mauger
,
Thomas Plé
,
Louis Lagardère
,
Sara Bonella
,
Etienne Mangaud
et al.
Journal articles
hal-03132347v1
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Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface
Dina El Ahdab
,
Louis Lagardère
,
Theo Jaffrelot Inizan
,
Frédéric Célerse
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Chengwen Liu
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Journal articles
hal-03220156v1
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Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field
Rae Corrigan
,
Guowei Qi
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Andrew Thiel
,
Jack Lynn
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Brandon D Walker
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Journal articles
hal-03183306v1
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NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient
Rubén Laplaza
,
Francesca Peccati
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Roberto A. Boto
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Chaoyu Quan
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Alessandra Carbone
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Journal articles
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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
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Louis Lagardère
,
Etienne Derat
,
Jean-Philip Piquemal
Journal articles
hal-03210774v1
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Assessment of SAPT and Supermolecular EDAs Approaches for the Development of Separable and Polarizable force fields
Sehr Naseem-Khan
,
Nohad Gresh
,
Alston J. Misquitta
,
Jean-Philip Piquemal
Journal articles
hal-02912013v1
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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
Olivier Adjoua
,
Louis Lagardère
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Luc-Henri Jolly
,
Arnaud Durocher
,
Thibaut Véry
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Journal articles
hal-03179730v1
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High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling
Théo Jaffrelot Inizan
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Frederic Célerse
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Olivier Adjoua
,
Dina El Ahdab
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Luc-Henri Jolly
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Journal articles
hal-02943694v1
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Atomistic Polarizable embeddings: energy, dynamics, spectroscopy and reactivity.
Daniele Loco
,
Louis Lagardère
,
Olivier Adjoua
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Jean-Philip Piquemal
Journal articles
hal-03210111v1
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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
Sehr Naseem-Khan
,
Jean-Philip Piquemal
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G. Andrés Cisneros
Journal articles
hal-03353343v1
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Velocity jump processes : an alternative to multi-time-step methods for faster and accurate molecular dynamics simulations
Pierre Monmarché
,
Jeremy Weisman
,
Louis Lagardère
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Jean-Philip Piquemal
Journal articles
hal-02314428v1
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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
et al.
Journal articles
hal-02377718v1
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Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations
Léa El-Khoury
,
Frederic Célerse
,
Louis Lagardère
,
Luc-Henri Jolly
,
Etienne Derat
et al.
Journal articles
hal-03046841v1
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Calibration of the dianionic phosphate group. Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase.
M. Devillers
,
Jean-Philip Piquemal
,
L. Salmon
,
N. Gresh
Journal articles
hal-02377726v1
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Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential
Chengwen Liu
,
Jean-Philip Piquemal
,
Pengyu Ren
Journal articles
hal-02410854v1
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A New Way for Probing Bond Strength
J. Klein
,
H. Khartabil
,
J.C. Boisson
,
J. Contreras-Garcia
,
Jean-Philip Piquemal
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Journal articles
hal-02377737v1
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Solvation Effects Drive the Selectivity in Diels-Alder Reaction Under Hyperbaric Conditions
Daniele Loco
,
Riccardo Spezia
,
François Cartier
,
Isabelle Chataigner
,
Jean-Philip Piquemal
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Journal articles
hal-02504716v1
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NCIPLOT4: fast, robust and quantitative analysis of noncovalent interactions
Roberto A Boto
,
Francesca Peccati
,
Rubén Laplaza
,
Chaoyu Quan
,
Alessandra Carbone
et al.
Journal articles
hal-02377999v1
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Pushing the limits of Multiple-Timestep Strategies for Polarizable Point Dipole Molecular Dynamics
Louis Lagardère
,
Félix Aviat
,
Jean-Philip Piquemal
Journal articles
hal-02119888v1
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Polarizable force fields for biomolecular simulations: Recent advances and applications
Zhifeng F Jing
,
Chengwen Liu
,
Sara y Cheng
,
Rui Qi
,
Brandon D Walker
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Journal articles
hal-01821899v1
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Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities
Léa El-Khoury
,
Krystel El Hage
,
Jean-Philip Piquemal
,
Serge Fermandjian
,
Richard G. Maroun
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Journal articles
hal-02372493v1
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Massively parallel implementation of Steered Molecular Dynamics in Tinker-HP: comparisons of polarizable and non-polarizable simulations of realistic systems
Frederic Célerse
,
Louis Lagardère
,
Etienne Derat
,
Jean-Philip Piquemal
Journal articles
hal-02122209v1
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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 Continuum Solvation, Linear Scaling, Domain Decomposition
Benjamin Stamm
,
Louis Lagardère
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Giovanni Scalmani
,
Paolo Gatto
,
Eric Cancès
et al.
Journal articles
hal-01793770v1
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Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields
Dmitry Bedrov
,
Jean-Philip Piquemal
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Oleg V. Borodin
,
Alexander Mackerell
,
Benoît Roux
et al.
Journal articles
hal-02144165v1
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Towards Large Scale Hybrid QM/MM Dynamics of Complex Systems with Advanced Point Dipole Polarizable Embeddings
Daniele Loco
,
Louis Lagardère
,
G. Andrés Cisneros
,
Giovanni Scalmani
,
Michael Frisch
et al.
Journal articles
hal-02152908v1
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Accurate biomolecular simulations account for electronic polarization
Josef Melcr
,
Jean-Philip Piquemal
Journal articles
hal-02283625v1
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Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0]
Luc-Henri Jolly
,
Alejandro Duran
,
Louis Lagardère
,
Jay W. Ponder
,
Pengyu Ren
et al.
Journal articles
hal-02147771v2
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AMOEBA+ Classical Potential for Modeling Molecular Interactions
Chengwen Liu
,
Jean-Philip Piquemal
,
Pengyu Ren
Journal articles
hal-02142886v1
|
|
Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model
Poier Pier Paolo
,
Louis Lagardère
,
Jean-Philip Piquemal
,
Frank Jensen
Journal articles
hal-02299827v1
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A coherent derivation of the Ewald summation for arbitrary orders of multipoles: The self-terms
Benjamin Stamm
,
Louis Lagardere
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Etienne Polack
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Yvon Maday
,
Jean-Philip Piquemal
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Journal articles
hal-01897263v1
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The Independent Gradient Model: a new approach for probing strong and weak interactions in molecules from wave function calculations
Corentin Lefebvre
,
Hassan Khartabil
,
Jean-Charles Boisson
,
Julia Contreras-García
,
Jean-Philip Piquemal
et al.
Journal articles
hal-03377532v1
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Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution
Rui R. Qi
,
Zhifeng F Jing
,
Chengwen Liu
,
Jean-Philip Piquemal
,
Kevin Dalby
et al.
Journal articles
hal-02126853v1
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Tinker 8: Software Tools for Molecular Design
Joshua A Rackers
,
Zhi Wang
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Chao Lu
,
Marie L Laury
,
Louis Lagardere
et al.
Journal articles
hal-01820747v1
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Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields
Louis Lagardère
,
Luc-Henri Jolly
,
Filippo Lipparini
,
Félix Aviat
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Benjamin Stamm
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Journal articles
hal-01648245v3
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AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms
Xiaojing Wu
,
Carine Clavaguera
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Louis Lagardère
,
Jean-Philip Piquemal
,
Aurelien de La Lande
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Journal articles
hal-02126731v1
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QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential
Hatice Gökcan
,
Eric Kratz
,
Thomas Darden
,
Jean-Philip Piquemal
,
G. Andrés Cisneros
et al.
Journal articles
hal-02126841v1
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AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids
Changsheng Zhang
,
Chao Lu
,
Zhifeng F Jing
,
Chuanjie Wu
,
Jean-Philip Piquemal
et al.
Journal articles
hal-02126772v1
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Capturing Many-Body Interactions with Classical Dipole Induction Models
Chengwen Liu
,
Rui R. Qi
,
Qiantao Qi
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J.-P. Piquemal
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Pengyu Ren
et al.
Journal articles
hal-02126842v1
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The inhibition process of HIV-1 integrase by diketoacids molecules: Understanding the factors governing the better efficiency of dolutegravir
Léa El Khoury
,
Jean-Philip Piquemal
,
Serge Fermandjian
,
Richard G. Maroun
,
Nohad Gresh
et al.
Journal articles
hal-01520237v1
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Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs
Matthew Harger
,
Daniel Li
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Zhi Wang
,
Kevin Dalby
,
Louis Lagardère
et al.
Journal articles
hal-01571313v1
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Towards scalable and accurate molecular dynamics using the SIBFA polarizable force field
Louis Lagardère
,
Léa El-Khoury
,
Sehr Naseem-Khan
,
Félix Aviat
,
Nohad Gresh
et al.
AIP Conference Proceedings, 2017
Journal articles
hal-01521838v1
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Channeling Through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li + , Na + , K + and Rb + Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential
Nohad Gresh
,
Sehr Naseem-Khan
,
Louis Lagardère
,
Jean-Philip Piquemal
,
Judit E. Sponer
et al.
Journal articles
hal-01502376v1
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Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions
Léa El Khoury
,
Sehr Naseem-Khan
,
Karolina Kwapien
,
Zeina El Hobaika
,
Richard El Maroun
et al.
Journal articles
hal-01571959v1
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The Truncated Conjugate Gradient (TCG), a Non-iterative/Fixed-cost Strategy for Computing Polarization in Molecular Dynamics: Fast Evaluation of Analytical Forces
Félix Aviat
,
Louis Lagardère
,
Jean-Philip Piquemal
Journal articles
hal-01571663v2
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An Optimized Charge Penetration Model for Use with the AMOEBA Force Field
Joshua A. Rackers
,
Qiantao Wang
,
Chengwen Liu
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Jean-Philip Piquemal
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Pengyu Ren
et al.
Journal articles
hal-01405847v1
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Preface: Special Topic: From Quantum Mechanics to Force Fields
Jean-Philip Piquemal
,
Kenneth Jordan
Journal articles
hal-02127251v1
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Truncated Conjugate Gradient (TCG): an optimal strategy for the analytical evaluation of the many-body polarization energy and forces in molecular simulations
Félix Aviat
,
Antoine Levitt
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Benjamin Stamm
,
Yvon Maday
,
Pengyu Ren
et al.
Journal articles
hal-01395833v4
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Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding
Daniele Loco
,
Louis Lagardère
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Stefano Caprasecca
,
Filippo Lipparini
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Benedetta Mennucci
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Journal articles
hal-01571619v2
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A Simple Isomerization of the Purine Scaffold of a Kinase Inhibitor, Roscovitine, Affords a Four- to Seven-Fold Enhancement of Its Affinity for Four CDKs. Could This Be Traced Back to Conjugation-Induced Stiffenings/Loosenings of Rotational Barriers?
Krystel El Hage
,
Jean-Philip Piquemal
,
Nassima Oumata
,
Laurent Meijer
,
Hervé Galons
et al.
Journal articles
hal-02126840v1
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Revealing strong interactions with the reduced density gradient: a benchmark for covalent, ionic and charge-shift bonds
Roberto A Boto
,
Jean-Philip Piquemal
,
Julia Contreras-García
Theoretical Chemistry Accounts: Theory, Computation, and Modeling, 2017, 136, pp.139
Journal articles
hal-01636270v1
|
|
Calibration of 1,2,4-Triazole-3-Thione, an Original Zn-Binding Group of Metallo-β-Lactamase Inhibitors. Validation of a Polarizable MM/MD Potential by Quantum Chemistry
Karolina Kwapien
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Mirna Damergi
,
Serge Nader
,
Léa El Khoury
,
Zeina Hobaika
et al.
Journal articles
hal-02126854v1
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|
Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown
Nohad Gresh
,
David Perahia
,
Benoit de Courcy
,
Johanna Foret
,
Céline Roux
et al.
Journal articles
hal-02126855v1
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Butanethiol adsorption and dissociation on Ag (111): A periodic DFT study
Aixiao Li
,
Jean-Philip Piquemal
,
Johannes Richardi
,
Monica Calatayud
Journal articles
hal-01171804v1
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LICHEM: A QM/MM Program for Simulations with Multipolar and Polarizable Force Fields
E. G. Kratz
,
L. Lagardere
,
F. Lipparini
,
J.-P. Piquemal
,
G. A. Cisneros
et al.
Journal articles
hal-01287204v1
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A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations
Daniele Loco
,
Etienne Polack
,
Stefano Caprasecca
,
Louis Lagardère
,
Filippo Lipparini
et al.
Journal articles
hal-02126716v1
|
|
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles
Christophe Narth
,
Louis Lagardère
,
Etienne Polack
,
Nohad Gresh
,
Qiantao Wang
et al.
Journal articles
hal-01223008v1
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Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe
Krystel El Hage
,
Jean-Philip Piquemal
,
Zeina Hobaika
,
Richard G. Maroun
,
Nohad Gresh
et al.
Journal articles
hal-02126856v1
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Polarizable Molecular Dynamics in a Polarizable Continuum Solvent
Filippo Lipparini
,
Louis Lagardère
,
Christophe Raynaud
,
Benjamin Stamm
,
Eric Cancès
et al.
Journal articles
hal-01114784v1
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|
Quantum-chemistry based calibration of the alkali metal cation series (Li + Cs + ) for large-scale polarizable molecular mechanics/dynamics simulations
Todor Dudev
,
Mike Devereux
,
Markus Meuwly
,
Carmay Lim
,
Jean-Philip Piquemal
et al.
Journal articles
hal-02126857v1
|
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Could the “Janus-like” properties of the halobenzene CX bond (XCl, Br) be leveraged to enhance molecular recognition?
Krystel El Hage
,
Jean-Philip Piquemal
,
Zeina Hobaika
,
Richard G. Maroun
,
Nohad Gresh
et al.
Journal articles
hal-02126858v1
|
|
A General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field
Qiantao Wang
,
Joshua A. Rackers
,
Chenfeng He
,
Rui Qi
,
Christophe Narth
et al.
Journal articles
hal-01287207v1
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Stacked and H-bonded cytosine dimers. Analysis of the intermolecular interaction energies by parallel quantum chemistry and polarizable molecular mechanics.
N. Gresh
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J. E. Sponer
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M. Devereux
,
B. De Courcy
,
Jean-Philip Piquemal
et al.
Journal articles
hal-01287484v1
|
|
Interpretation of the reduced density gradient
Roberto A. Boto
,
Julia Contreras-García
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Julien Tierny
,
Jean-Philip Piquemal
Journal articles
hal-01253888v1
|
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Bridging Organometallics and Quantum Chemical Topology: Understanding Electronic Relocalisation During Palladium-Catalyzed Reductive Elimination
Benoit De Courcy
,
Etienne Derat
,
Jean-Philip Piquemal
Journal articles
hal-01397958v1
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Entasis Through Hook-and-Loop Fastening in a Glycoligand with Cumulative Weak Forces Stabilizing Cu(I).
Ludivine Garcia
,
Federico Cisnetti
,
Natacha Gillet
,
Régis Guillot
,
Magali Aumont-Nicaise
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Journal articles
hal-01101575v1
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Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Towards Massively Parallel Computations using Smooth Particle Mesh Ewald
Louis Lagardere
,
Filippo Lipparini
,
Etienne Polack
,
Benjamin Stamm
,
Eric Cancès
et al.
Journal articles
hal-01223161v1
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|
S/G-1: An Ab Initio Force-field Blending Frozen Hermite Gaussian Densities and Distributed Multipoles. Proof of Concept and First Applications to Metal Cations
R. Chaudret
,
N. Gresh
,
C. Narth
,
L. Lagardere
,
T. A. Darden
et al.
Journal articles
hal-01287208v1
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Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field
Xiaojiao Mu
,
Qiantao Wang
,
Lee-Ping Wang
,
Stephen Fried
,
Jean-Philip Piquemal
et al.
Journal articles
hal-02126799v1
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|
Characterizing Molecular Interactions in Chemical Systems
David Guenther
,
Roberto Alvarez-Boto
,
Julia Contreras-Garcia
,
Jean-Philip Piquemal
,
Julien Tierny
et al.
Journal articles
hal-01146475v1
|
|
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations
Filippo Lipparini
,
Louis Lagardère
,
Benjamin Stamm
,
Eric Cancès
,
Michael Schnieders
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Journal articles
hal-01090942v1
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Substituent-Modulated Affinities of Halobenzene Derivatives to the HIV-1 Integrase Recognition Site. Analyses of the Interaction Energies by Parallel Quantum Chemical and Polarizable Molecular Mechanics
Krystel El Hage
,
Jean-Philip Piquemal
,
Zeina Hobaika
,
Richard G. Maroun
,
Nohad Gresh
et al.
Journal articles
hal-02126859v1
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Quantum, classical, and hybrid QM/MM calculations in solution: General implementation of the ddCOSMO linear scaling strategy
Filippo Lipparini
,
Giovanni Scalmani
,
Louis Lagardère
,
Benjamin Stamm
,
Eric Cancès
et al.
Journal articles
hal-01090954v1
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Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy
R. Chaudret
,
B. De Courcy
,
J. Contreras-García
,
Eric Gloaguen
,
A. Zehnacker-Rentien
et al.
Journal articles
hal-01131254v1
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Conformational analysis of a polyconjugated protein-binding ligand by joint quantum chemistry and polarizable molecular mechanics. Addressing the issues of anisotropy, conjugation, polarization, and multipole transferability
Elodie Goldwaser
,
Benoit de Courcy
,
Luc Demange
,
Christiane Garbay
,
Françoise Raynaud
et al.
Journal articles
hal-02126794v1
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DFT-steric-based energy decomposition analysis of intermolecular interactions
Dong Fang
,
Jean-Philip Piquemal
,
Shubin Liu
,
G. Andrés Cisneros
Journal articles
hal-02126797v1
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Polarizable Molecular Mechanics Studies of Cu(I)/Zn(II) Superoxide Dismutase: Bimetallic Binding Site and Structured Waters
Nohad Gresh
,
Krystel El Hage
,
David Perahia
,
Jean-Philip Piquemal
,
C. Berthomieu
et al.
Journal articles
hal-01081843v1
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A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field
Mike Devereux
,
Nohad Gresh
,
Jean-Philip Piquemal
,
Markus Meuwly
Journal articles
hal-02126862v1
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Revisiting H2O Nucleation around Au + and Hg 2+ : The Peculiar “Pseudo-Soft” Character of the Gold Cation
Robin Chaudret
,
Julia Contreras-García
,
Mickaël Delcey
,
Olivier Parisel
,
Weitao Yang
et al.
Journal articles
hal-02126798v1
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Quantum Calculations in Solution for Large to Very Large Molecules: A New Linear Scaling QM/Continuum Approach
Filippo Lipparini
,
Louis Lagardère
,
Giovanni Scalmani
,
Benjamin Stamm
,
Eric Cancès
et al.
Journal articles
hal-00956401v1
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Synthesis and structure–activity relationship of non-peptidic antagonists of neuropilin-1 receptor
Wang-Qing Liu
,
Valentino Megale
,
Lucia Borriello
,
Bertrand Leforban
,
Matthieu Montes
et al.
Journal articles
hal-02126861v1
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GEM*: A Molecular Electronic Density--Based Force Field for Classical Molecular Dynamics Simulations
R. Duke
,
O. Starovoytov
,
J.-P. Piquemal
,
G. A. Cisneros
Journal articles
hal-01287209v1
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Hydration gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics
Aude Marjolin
,
Christophe Gourlaouen
,
Carine Clavaguéra
,
Pengyu Y. Ren
,
Jean-Philip Piquemal
et al.
Journal articles
hal-01157657v1
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La surface d'énergie potentielle vue par les champs de forces
Isabelle Demachy
,
Jean-Philip Piquemal
L'Actualité Chimique, 2014, 388-389, pp.37-42
Journal articles
hal-00960389v1
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Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins
Marie-Céline van Severen
,
Ulf Ryde
,
Olivier Parisel
,
Jean-Philip Piquemal
Journal articles
hal-02126839v1
|
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Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes
Dong Fang
,
Robin Chaudret
,
Jean-Philip Piquemal
,
G. Andrés Cisneros
Journal articles
hal-02126800v1
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Towards energy decomposition analysis for open and closed shell f-elements mono aqua complexes
A. Marjolin
,
C. Gourlaouen
,
Carine Clavaguéra
,
J. -P. Dognon
,
J. -P. Piquemal
et al.
Journal articles
hal-00880177v1
|
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Further refinements of next-generation force fields -- Nonempirical localization of off-centered points in molecules
Robin Chaudret
,
Nohad Gresh
,
Andrés Cisneros
,
Anthony Scemama
,
Jean-Philip Piquemal
et al.
Journal articles
hal-00875425v1
|
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Are Bond Critical Points Really Critical for Hydrogen Bonding?
Joseph Lane
,
Julia Contreras-García
,
Jean-Philip Piquemal
,
Benjamin Miller
,
Henrik Kjaergaard
et al.
Journal articles
hal-02126863v1
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Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds?
Krystel El Hage
,
Jean-Philip Piquemal
,
Zeina Hobaika
,
Richard G. Maroun
,
Nohad Gresh
et al.
Journal articles
hal-02126864v1
|
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Understanding the structure and electronic properties of Th4+-water complexes
Christophe Gourlaouen
,
Carine Clavaguéra
,
Aude Marjolin
,
Jean-Philip Piquemal
,
Jean-Pierre Dognon
et al.
Journal articles
hal-00926680v1
|
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Ionic interactions: Comparative topological approach
Julia Contreras-García
,
Monica Calatayud
,
Jean-Philip Piquemal
,
J.M. Recio
Journal articles
hal-02126866v1
|
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Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential
Jiajing Zhang
,
Wei Yang
,
Jean-Philip Piquemal
,
Pengyu Ren
Journal articles
hal-02126837v1
|
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From quantum mechanics to force fields: new methodologies for the classical simulation of complex systems
Jean-Philip Piquemal
,
Kenneth Jordan
Journal articles
hal-02127244v1
|
|
Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: From gas-phase energetics to hydration free energies
A. Marjolin
,
C. Gourlaouen
,
Carine Clavaguéra
,
P.Y. Ren
,
J.C. Wu
et al.
Journal articles
hal-00904389v1
|
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Toward a ligand specific of Pb2+ with respect to the Zn2+ and Ca2+ cations: A track from quantum chemistry
Marie-Céline van Severen
,
Robin Chaudret
,
Olivier Parisel
,
Jean-Philip Piquemal
Journal articles
hal-02126868v1
|
|
Coupling Quantum Interpretative Techniques: Another Look at Chemical Mechanisms in Organic Reactions
Natacha Gillet
,
Robin Chaudret
,
Julia Contreras-García
,
Weitao Yang
,
Bernard Silvi
et al.
Journal articles
hal-02126838v1
|
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Electron Pair Localization Function (EPLF) for Density Functional Theory and ab Initio Wave Function-Based Methods: A New Tool for Chemical Interpretation
Anthony Scemama
,
Michel Caffarel
,
Robin Chaudret
,
Jean-Philip Piquemal
Journal articles
hal-00874618v1
|
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Competitive ligand/chelate binding in [Cu(TMPA)]+ and [Cu(tren)]+ based complexes
Lauréline Bonniard
,
Aurelien de La Lande
,
Simon Ulmer
,
Jean-Philip Piquemal
,
Olivier Parisel
et al.
Journal articles
hal-02126870v1
|
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Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations
Robin Chaudret
,
Jean-Philip Piquemal
,
G. Andrés Cisneros
Journal articles
hal-02126836v1
|
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NCIPLOT: A Program for Plotting Noncovalent Interaction Regions
Julia Contreras-García
,
Erin Johnson
,
Shahar Keinan
,
Robin Chaudret
,
Jean-Philip Piquemal
et al.
Journal articles
hal-02126834v1
|
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Spin-driven activation of dioxygen in various metalloenzymes and their inspired models.
Aurelien de La Lande
,
Dennis R Salahub
,
Jacques Maddaluno
,
Anthony Scemama
,
Julien Pilme
et al.
Journal articles
hal-00992047v1
|
|
The reaction mechanism of type I phosphomannose isomerases: New information from inhibition and polarizable molecular mechanics studies
Céline Roux
,
Forum Bhatt
,
Johanna Foret
,
Benoit de Courcy
,
Nohad Gresh
et al.
Journal articles
hal-02126875v1
|
|
Unraveling Low-Barrier Hydrogen Bonds in Complex Systems with a Simple Quantum Topological Criterion
Robin Chaudret
,
G. Andrés Cisneros
,
Olivier Parisel
,
Jean-Philip Piquemal
Journal articles
hal-02126873v1
|
|
Many-body exchange-repulsion in polarizable molecular mechanics. I. orbital-based approximations and applications to hydrated metal cation complexes
Robin Chaudret
,
Nohad Gresh
,
Olivier Parisel
,
Jean-Philip Piquemal
Journal articles
hal-02126872v1
|
|
Polarizable Water Networks in Ligand–Metalloprotein Recognition. Impact on the Relative Complexation Energies of Zn-Dependent Phosphomannose Isomerase with d -Mannose 6-Phosphate Surrogates
Nohad Gresh
,
Benoit de Courcy
,
Jean-Philip Piquemal
,
Johanna Foret
,
Stéphanie Courtiol-Legourd
et al.
Journal articles
hal-02126871v1
|
|
Enforcing hemidirectionality in Pb(II) complexes: The importance of anionic ligands
M.-C. van Severen
,
J.-P. Piquemal
,
O. Parisel
Journal articles
hal-02126869v1
|
|
Interactions within the alcohol dehydrogenase Zn(II)-metalloenzyme active site: Interplay between subvalence, electron correlation/dispersion, and charge transfer/induction effects
Benoit de Courcy
,
Jean-Pierre Dognon
,
Carine Clavaguéra
,
Nohad Gresh
,
Jean-Philip Piquemal
et al.
Journal articles
hal-00926669v1
|
|
Polarizable water molecules in ligand-macromolecule recognition. Impact on the relative affinities of competing pyrrolopyrimidine inhibitors for FAK kinase.
B. de Courcy
,
J. P. Piquemal
,
C. Garbay
,
N. Gresh
Journal of the American Chemical Society, 2010, 132, pp.3312
Journal articles
hal-00494585v1
|
|
Analysis of the interactions taking place in the recognition site of a bimetallic Mg(II)-Zn(II) enzyme, isopentenyl diphosphate isomerase. A parallel quantum-chemical and polarizable molecular mechanics study.
Nohad Gresh
,
N. Audiffren
,
J.-P. Piquemal
,
J. de Ruyck
,
M. Ledecq
et al.
Journal articles
hal-00494595v1
|
|
Editorial: Special issue on quantum mechanical modeling of biological systems
Jean-Philip Piquemal
,
Dennis R. Salahub
Journal articles
hal-02127241v1
|
|
Understanding selectivity of hard and soft metal cations within biological systems using the subvalence concept. I. Application to blood coagulation: direct cation-protein electronic effects vs. indirect interactions through water networks.
B. de Courcy
,
L. G. Pedersen
,
O. Parisel
,
N. Gresh
,
B. Silvi
et al.
Journal articles
hal-00996393v1
|
|
Study of the docking of competitive inhibitors at a model of tyrosinase active site: Insights from joint broken-symmetry/spin-flip DFT computations and ELF topological analysis
A. de La Lande
,
J. Maddaluno
,
O. Parisel
,
A. Darden
,
J. Piquemal
et al.
Journal articles
hal-02126831v1
|
|
Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field
Johnny Wu
,
Jean-Philip Piquemal
,
Robin Chaudret
,
Peter Reinhardt
,
Pengyu Ren
et al.
Journal articles
hal-02126833v1
|
|
Importance of backdonation in [M–(CO)]p+ complexes isoelectronic to [Au–(CO)]+
C. Gourlaouen
,
O. Parisel
,
J.-P. Piquemal
Journal articles
hal-02126876v1
|
|
Gas-phase folding of a two-residue model peptide chain: on the importance of an interplay between experiment and theory.
Eric Gloaguen
,
B. de Courcy
,
J.-P. Piquemal
,
J. Pilmé
,
O. Parisel
et al.
Journal articles
hal-00915204v1
|
|
Role of Cation Polarization in holo- and hemi- Directed [Pb(H 2 O) n ] 2+ Complexes and Development of a Pb 2+ Polarizable Force Field
Mike Devereux
,
Marie-Céline van Severen
,
Olivier Parisel
,
Jean-Philip Piquemal
,
Nohad Gresh
et al.
Journal articles
hal-02126874v1
|
|
Lead Substitution in Synaptotagmin: A Case Study
M.-C. van Severen
,
J.-P. Piquemal
,
O. Parisel
Journal articles
hal-02126877v1
|
|
Importance of lone pair interactions/redistribution in hard and soft ligands within the active site of alcohol dehydrogenase Zn-metalloenzyme: Insights from electron localization function
B. de Courcy
,
N. Gresh
,
J.-P. Piquemal
Journal articles
hal-02126823v1
|
|
Gaussian Multipole Model (GMM)
Dennis Elking
,
G. Andrés Cisneros
,
Jean-Philip Piquemal
,
Thomas Darden
,
Lee Pedersen
et al.
Journal articles
hal-02126830v1
|
|
Dioxygen Activation by Mononuclear Copper Enzymes: Insights from a Tripodal Ligand Mimicking Their Cu M Coordination Sphere
Aurélien de La Lande
,
Dennis R. Salahub
,
Vicent Moliner
,
Hélène Gérard
,
Jean-Philip Piquemal
et al.
Journal articles
hal-02126825v1
|
|
Synthesis and evaluation of non-hydrolyzable d-mannose 6-phosphate surrogates reveal 6-deoxy-6-dicarboxymethyl-d-mannose as a new strong inhibitor of phosphomannose isomerases
Johanna Foret
,
Benoit de Courcy
,
Nohad Gresh
,
Jean-Philip Piquemal
,
Laurent Salmon
et al.
Journal articles
hal-02126828v1
|
|
New intermolecular benchmark calculations on the water dimer: SAPT and supermolecular post-Hartree-Fock approaches
P. Reinhardt
,
J-P. Piquemal
Journal articles
hal-02126824v1
|
|
Progress Towards Accurate Molecular Modeling of Metal Complexes Using Polarizable Force Fields
R. Chaudret
,
S. Ulmer
,
M.-C. van Severen
,
N. Gresh
,
O. Parisel
et al.
Journal articles
hal-02126821v1
|
|
Beyond holo/hemidirectionality in Pb(II) complexes: Can the valence lone pair be bisdirected?
M. van Severen
,
J.-P. Piquemal
,
O. Parisel
Journal articles
hal-02126826v1
|
|
Trends in ns2np0 [M(CO)]q+ complexes: From germanium to element 114 (Uuq)
C. Gourlaouen
,
O. Parisel
,
J.-P. Piquemal
Journal articles
hal-02126822v1
|
|
What can be learnt on biologically relevant systems from the topological analysis of the electron localization function?
J.-P. Piquemal
,
J. Pilmé
,
O. Parisel
,
H. Gerard
,
I. Fourré
et al.
Journal articles
hal-02126817v1
|
|
Understanding Lead Chemistry from Topological Insights: The Transition between Holo- and Hemidirected Structures within the [Pb(CO)n]2+ Model Series
Christophe Gourlaouen
,
Hélène Gérard
,
Jean-Philip Piquemal
,
Olivier Parisel
Journal articles
hal-02126879v1
|
|
Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments
Julien Pilmé
,
Jean-Philip Piquemal
Journal articles
hal-02126878v1
|
|
Energy Analysis of Zn Polycoordination in a Metalloprotein Environment and of the Role of a Neighboring Aromatic Residue. What Is the Impact of Polarization?
Benoit de Courcy
,
Jean-Philip Piquemal
,
Nohad Gresh
Journal articles
hal-02126819v1
|
|
Simple formulas for improved point-charge electrostatics in classical force fields and hybrid quantum mechanical/molecular mechanical embedding
G. Cisneros
,
S. Na-Im Tholander
,
O. Parisel
,
T. Darden
,
D. Elking
et al.
Journal articles
hal-02126814v1
|
|
Fragment-Localized Kohn−Sham Orbitals via a Singles Configuration-Interaction Procedure and Application to Local Properties and Intermolecular Energy Decomposition Analysis
Peter Reinhardt
,
Jean-Philip Piquemal
,
Andreas Savin
Journal articles
hal-02126818v1
|
|
The specificity of acyl transfer from 2-mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein. ]
L. M Miller Jenkins
,
T. Hara
,
S. R Durell
,
R. Hayashi
,
J. K Inman
et al.
Journal of the American Chemical Society, 2007, 131, pp.11067
Journal articles
hal-00494580v1
|
|
Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase fromCandida albicans studied by polarizable molecular mechanics and quantum mechanics
Céline Roux
,
Nohad Gresh
,
Lalith Perera
,
Jean-Philip Piquemal
,
Laurent Salmon
et al.
Journal articles
hal-02126881v1
|
|
Anisotropic, polarizable molecular mechanics studies of inter-, intramolecular interactions, and ligand-macromolecule complexes.A bottom-up strategy
Nohad Gresh
,
G. Andres Cisneros
,
T.A. Darden
,
J.-P. Piquemal
Journal of Chemical Theory and Computation, 2007, 3, pp.1960
Journal articles
hal-00494588v1
|
|
Binding of 5-Phospho-D-Arabinonohydoxamate and 5-Phospho-D-Arabinonate Inhibitors to Zinc Phosphomannoisomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics.
Nohad Gresh
,
Clément Roux
,
N. Gresh
,
L. E. Perera
,
J.-P. Piquemal
et al.
Journal of Computational Chemistry, 2007, 28, pp.938
Journal articles
hal-00494629v1
|
|
Numerical Fitting of Molecular Properties to Hermite Gaussians
G. Andrés Cisneros
,
Dennis Elking
,
Jean-Philip Piquemal
,
Thomas Darden
Journal articles
hal-02126812v1
|
|
Key Role of the Polarization Anisotropy of Water in Modeling Classical Polarizable Force Fields
Jean-Philip Piquemal |